WorldWideScience

Sample records for putative nanobacteria represent

  1. Putative nanobacteria represent physiological remnants and culture by-products of normal calcium homeostasis.

    Directory of Open Access Journals (Sweden)

    John D Young

    Full Text Available Putative living entities called nanobacteria (NB are unusual for their small sizes (50-500 nm, pleomorphic nature, and accumulation of hydroxyapatite (HAP, and have been implicated in numerous diseases involving extraskeletal calcification. By adding precipitating ions to cell culture medium containing serum, mineral nanoparticles are generated that are morphologically and chemically identical to the so-called NB. These nanoparticles are shown here to be formed of amorphous mineral complexes containing calcium as well as other ions like carbonate, which then rapidly acquire phosphate, forming HAP. The main constituent proteins of serum-derived NB are albumin, fetuin-A, and apolipoprotein A1, but their involvement appears circumstantial since so-called NB from different body fluids harbor other proteins. Accordingly, by passage through various culture media, the protein composition of these particles can be modulated. Immunoblotting experiments reveal that antibodies deemed specific for NB react in fact with either albumin, fetuin-A, or both, indicating that previous studies using these reagents may have detected these serum proteins from the same as well as different species, with human tissue nanoparticles presumably absorbing bovine serum antigens from the culture medium. Both fetal bovine serum and human serum, used earlier by other investigators as sources of NB, paradoxically inhibit the formation of these entities, and this inhibition is trypsin-sensitive, indicating a role for proteins in this inhibitory process. Fetuin-A, and to a lesser degree albumin, inhibit nanoparticle formation, an inhibition that is overcome with time, ending with formation of the so-called NB. Together, these data demonstrate that NB are most likely formed by calcium or apatite crystallization inhibitors that are somehow overwhelmed by excess calcium or calcium phosphate found in culture medium or in body fluids, thereby becoming seeds for calcification. The

  2. Putative nanobacteria represent physiological remnants and culture by-products of normal calcium homeostasis.

    Science.gov (United States)

    Young, John D; Martel, Jan; Young, Lena; Wu, Cheng-Yeu; Young, Andrew; Young, David

    2009-01-01

    Putative living entities called nanobacteria (NB) are unusual for their small sizes (50-500 nm), pleomorphic nature, and accumulation of hydroxyapatite (HAP), and have been implicated in numerous diseases involving extraskeletal calcification. By adding precipitating ions to cell culture medium containing serum, mineral nanoparticles are generated that are morphologically and chemically identical to the so-called NB. These nanoparticles are shown here to be formed of amorphous mineral complexes containing calcium as well as other ions like carbonate, which then rapidly acquire phosphate, forming HAP. The main constituent proteins of serum-derived NB are albumin, fetuin-A, and apolipoprotein A1, but their involvement appears circumstantial since so-called NB from different body fluids harbor other proteins. Accordingly, by passage through various culture media, the protein composition of these particles can be modulated. Immunoblotting experiments reveal that antibodies deemed specific for NB react in fact with either albumin, fetuin-A, or both, indicating that previous studies using these reagents may have detected these serum proteins from the same as well as different species, with human tissue nanoparticles presumably absorbing bovine serum antigens from the culture medium. Both fetal bovine serum and human serum, used earlier by other investigators as sources of NB, paradoxically inhibit the formation of these entities, and this inhibition is trypsin-sensitive, indicating a role for proteins in this inhibitory process. Fetuin-A, and to a lesser degree albumin, inhibit nanoparticle formation, an inhibition that is overcome with time, ending with formation of the so-called NB. Together, these data demonstrate that NB are most likely formed by calcium or apatite crystallization inhibitors that are somehow overwhelmed by excess calcium or calcium phosphate found in culture medium or in body fluids, thereby becoming seeds for calcification. The structures described

  3. Critical evaluation of gamma-irradiated serum used as feeder in the culture and demonstration of putative nanobacteria and calcifying nanoparticles.

    Directory of Open Access Journals (Sweden)

    Jan Martel

    Full Text Available The culture and demonstration of putative nanobacteria (NB and calcifying nanoparticles (CNP from human and animal tissues has relied primarily on the use of a culture supplement consisting of FBS that had been gamma-irradiated at a dose of 30 kGy (gamma-FBS. The use of gamma-FBS is based on the assumption that this sterilized fluid has been rid entirely of any residual NB/CNP, while it continues to promote the slow growth in culture of NB/CNP from human/animal tissues. We show here that gamma-irradiation (5-50 kGy produces extensive dose-dependent serum protein breakdown as demonstrated through UV and visible light spectrophotometry, fluorometry, Fourier-transformed infrared spectroscopy, and gel electrophoresis. Yet, both gamma-FBS and gamma-irradiated human serum (gamma-HS produce NB/CNP in cell culture conditions that are morphologically and chemically indistinguishable from their normal serum counterparts. Contrary to earlier claims, gamma-FBS does not enhance the formation of NB/CNP from several human body fluids (saliva, urine, ascites, and synovial fluid tested. In the presence of additional precipitating ions, both gamma-irradiated serum (FBS and HS and gamma-irradiated proteins (albumin and fetuin-A retain the inherent dual NB inhibitory and seeding capabilities seen also with their untreated counterparts. By gel electrophoresis, the particles formed from both gamma-FBS and gamma-HS are seen to have assimilated into their scaffold the same smeared protein profiles found in the gamma-irradiated sera. However, their protein compositions as identified by proteomics are virtually identical to those seen with particles formed from untreated serum. Moreover, particles derived from human fluids and cultured in the presence of gamma-FBS contain proteins derived from both gamma-FBS and the human fluid under investigation-a confusing and unprecedented scenario indicating that these particles harbor proteins from both the host tissue and the FBS

  4. Characterization of granulations of calcium and apatite in serum as pleomorphic mineralo-protein complexes and as precursors of putative nanobacteria.

    Directory of Open Access Journals (Sweden)

    John D Young

    Full Text Available Calcium and apatite granulations are demonstrated here to form in both human and fetal bovine serum in response to the simple addition of either calcium or phosphate, or a combination of both. These granulations are shown to represent precipitating complexes of protein and hydroxyapatite (HAP that display marked pleomorphism, appearing as round, laminated particles, spindles, and films. These same complexes can be found in normal untreated serum, albeit at much lower amounts, and appear to result from the progressive binding of serum proteins with apatite until reaching saturation, upon which the mineralo-protein complexes precipitate. Chemically and morphologically, these complexes are virtually identical to the so-called nanobacteria (NB implicated in numerous diseases and considered unusual for their small size, pleomorphism, and the presence of HAP. Like NB, serum granulations can seed particles upon transfer to serum-free medium, and their main protein constituents include albumin, complement components 3 and 4A, fetuin-A, and apolipoproteins A1 and B100, as well as other calcium and apatite binding proteins found in the serum. However, these serum mineralo-protein complexes are formed from the direct chemical binding of inorganic and organic phases, bypassing the need for any biological processes, including the long cultivation in cell culture conditions deemed necessary for the demonstration of NB. Thus, these serum granulations may result from physiologically inherent processes that become amplified with calcium phosphate loading or when subjected to culturing in medium. They may be viewed as simple mineralo-protein complexes formed from the deployment of calcification-inhibitory pathways used by the body to cope with excess calcium phosphate so as to prevent unwarranted calcification. Rather than representing novel pathophysiological mechanisms or exotic lifeforms, these results indicate that the entities described earlier as NB most

  5. Mineralization by nanobacteria

    Science.gov (United States)

    Kajander, E. Olavi; Bjorklund, Michael; Ciftcioglu, Neva

    1998-07-01

    Nanobacteria are the smallest cell-walled bacteria, only recently discovered in human and cow blood and in commercial cell culture serum. In this study, we identified with energy-dispersive x-ray microanalysis and chemical analysis that all growth phases of nanobacteria produce biogenic apatite on their cell envelope. Fourier transform IR spectroscopy revealed the mineral as carbonate apatite. Previous models for stone formation have lead to a hypothesis that an elevated pH due to urease and/or alkaline phosphatase activity are important lithogenic factors. Our results indicate that carbonate apatite can be formed without these factors at pH 7.4 at physiological phosphate and calcium concentrations. Due to their specific macromolecules, nanobacteria can produce apatite very efficiency in media mimicking tissue fluids and glomerular filtrate and rapidly mineralizing most of available calcium and phosphate. This can be also monitored by (superscript 85)Sr incorporation and provides a unique model for in vitro studies on calcification. Recently, bacteria have been implicated in the formation of carbonate (hydroxy)fluorapatite in marine sediments. Apatite grains are found so commonly in sedimentary rocks that apatite is omitted in naming the stone. To prove that apatite and other minerals are formed by bacteria would implicate that the bacteria could be observed and their actions followed in stones. We have started to approach this in two ways. Firstly, by the use of sensitive methods for detecting specific bacterial components, like antigens, muramic acid and nucleic acids, that allow for detecting the presence of bacteria and, secondly, by follow-up of volatile bacterial metabolites observed by continuous monitoring with ion mobility spectrometry, IMCELL, working like an artificial, educatable smelling nose. The latter method might allow for remote real time detection of bacterial metabolism, a signature of life, in rocks via fractures of drillholes with or without

  6. Extraordinary survival of nanobacteria under extreme conditions

    Science.gov (United States)

    Bjorklund, Michael; Ciftcioglu, Neva; Kajander, E. Olavi

    1998-07-01

    Nanobacteria show high resistance to gamma irradiation. To further examine their survival in extreme conditions several disinfecting and sterilizing chemicals as well as autoclaving, UV light, microwaves, heating and drying treatments were carried out. The effect of antibiotics used in cell culture were also evaluated. Two forms of nanobacteria were used in the tests: nanobacteria cultured in serum containing medium, and nanobacteria cultured in serum-free medium, the latter being more mineralized. Nanobacteria, having various amounts of apatite on their surfaces, were used to analyze the degree of protection given by the mineral. The chemicals tested included ethanol, glutaraldehyde, formalin, hypochlorite, hydrogen peroxide, hydrochloric acid, sodium hydroxide, detergents, and commercial disinfectants at concentrations generally used for disinfection. After chemical and physical treatments for various times, the nanobacteria were subcultered to detect their survival. The results show unique and wide resistance of nanobacteria to common agents used in disinfection. It can also be seen that the mineralization of the nanobacterial surface furthermore increases the resistance. Survival of nanobacteria is unique among living bacteria, but it can be compared with that observed in spores. Interestingly, nanobacteria have metabolic rate as slow as bacterial spores. A slow metabolic rate and protective structures, like mineral, biofilm and impermeable cell wall, can thus explain the observations made.

  7. Microbes produce nanobacteria-like structures, avoiding cell entombment

    Science.gov (United States)

    Bontognali, Tomaso R. R.; Vasconcelos, Crisógono; Warthmann, Rolf J.; Dupraz, Christophe; Bernasconi, Stefano M.; McKenzie, Judith A.

    2008-08-01

    Microsedimentary structures referred to as nanobacteria-likeparticles were described from modern carbonate environments,where they form in close spatial association with sulfate-reducingbacteria (SRB). However, the exact mechanism of their formation,as well as their paleontological significance, remains controversial.Here we report on an investigation of microbe-mineral interactionsin experimentally produced carbonate globules. The experimentswere carried out under anoxic conditions at 30 °C with Desulfovibriobrasiliensis, a SRB known to mediate dolomite formation. Weobserved that extracellular polymeric substances (EPS) secretedby the microbial community play a key role in the mineralizationprocess. Nanobacteria-like particles represent the early stageof carbonate nucleation within the EPS, which progressivelyevolve to larger globules displaying a grainy texture. We excludedthe possibilities that these structures are fossils of nanobacteria,dissolution surfaces, or artifacts created during sample preparation.D. brasiliensis cells are predominantly located outside of theEPS aggregates where mineral growth takes place. As a result,they remain mobile and are rarely entombed within the mineral.This self-preservation behavior may not be limited to D. brasiliensis.Other microbes may produce, or may have produced during thegeological past, biogenic minerals through a similar process.Mineralization within EPS explains why microbial relics arenot necessarily present in biogenic carbonates.

  8. CO 2 lasers to destroy defiance of nanobacteria

    Directory of Open Access Journals (Sweden)

    Jafar Kolahi

    2015-01-01

    Full Text Available Introduction: Nanobacteria are mysterious particles that have spurred one of the biggest controversies in modern microbiology. The apatite mineral around the nanobacteria serves as a primary defense shield against various chemicals and extremely harsh condition. It is combined with a very slow metabolism of nanobacteria. These two items would be the likely explanation for the sever resistance of nanobacteria. The Hypothesis: The CO 2 laser is a continuous wave gas laser and emits infrared light at 9,600-10,600 nm in an easily manipulated focused beam that is well absorbed by water and hydroxyapatite. Hence, it seems logical to postulate that CO 2 laser can be used successfully to destroy defensive external hydroxyapatite layer of nanobacteria. Evaluation of the Hypothesis: Main criticism with this hypothesis is differential radiation of nanobacteria. It is well known that CO 2 laser has high water absorption and consequently can cause unwanted damage to human host tissues.

  9. An overview on clinical implications of nanobacteria

    Directory of Open Access Journals (Sweden)

    C Anand Kumar

    2011-01-01

    Full Text Available Pathological calcification is becoming recognized as an important feature in the dynamics of a variety of diseases, such as renal stone, atherosclerosis, pulp stones, scleroderma and arthritis. etc. from which millions of human beings suffer in all ages. Nanobacterium sanguineum is the first calcium phosphate mineral containing nanoorganism isolated from human blood that causes pathological disease calcification in humans. Nanobacteria are the smallest cell-walled bacteria, recently discovered in human and cow blood and commercial cell culture serum. Herein the article controversy and critical role of calcifying nanoparticles as nidi and triggering factor inhuman pathologic calcifications are discussed.

  10. Activity in neurons of a putative protocerebral circuit representing information about a ten component plant odour blend in Heliothis virescens.

    Directory of Open Access Journals (Sweden)

    Bjarte Bye Løfaldli

    2012-09-01

    Full Text Available The olfactory pathway in the insect brain is anatomically well described from the antennal lobe to the mushroom bodies and the lateral protocerebrum in several species. Less is known about the further connections of the olfactory network in protocerebrum and how information about relevant plant odorants and mixtures are represented in this network, resulting in output information mediated by descending neurons. In the present study we have recorded intracellularly followed by dye injections from neurons in the lateral- and superior protocerebrum of the moth, Heliothis virescens. As relevant stimuli, we have used selected primary plant odorants and mixtures of them. The results provide the morphology and physiological responses of neurons involved in a putative circuit connecting the mushroom body lobes, the superior and the lateral protocerebrum, as well as input to superior and lateral protocerebrum by one multiglomerular antennal lobe neuron and output from the lateral protocerebrum by one descending neuron. All neurons responded to one particular mixture of ten primary plant odorants, some of them also to single odorants of the mixture. Altogether, the physiological data indicate integration in protocerebral neurons of information from several of the receptor neuron types functionally described in this species.

  11. Nanobacteria in clouds can spread oral pathologic calcifications around the world

    Directory of Open Access Journals (Sweden)

    Jafar Kolahi

    2012-01-01

    Full Text Available Introduction: Nanobacteria (calcifying nanoparticles, nanobes are one of the most controversial issues in contemporary biology. Studies show accumulating evidence on association of nanobacteria with oral pathologic calcifications such as calculus, pulp stone, and salivary gland stones. The Hypothesis: Experiments have shown that nanobacteria are excreted from the body in urine and saliva, lifted from the ground by winds into the cloud, and transit between the high humidity region of the clouds and the relatively dry inter-cloud regions. Remnants of a sticky protein coating that nanobacteria make it act as an extremely efficient cloud condensation nuclei. Following condensation of cloud, nanobacteria return to the earth via rain and snow. Evaluation of the Hypothesis: Transmission of nanobacteria via clouds is not surprising when compared with cosmic transmission of nanobacteria. The apatite mineral layer around the organism serves as a primary defence shield against various seriously life-threatening conditions. A double defence with the apatite layer and an impermeable membrane combined with a very slow metabolism is a likely explanation for the resistance of nanobacteria.

  12. Cosmic Transmission of Periodontal, Cardiovascular and Kidney Disease via Nanobacteria

    Directory of Open Access Journals (Sweden)

    Jafar Kolahi

    2011-04-01

    Full Text Available Introduction: Nanobacteria (NB are mysterious particles that have spurred one of the biggest controversies in modern micro-biology. NB has been reported to be present in animal and human blood, tissue culture cell lines, wastewater and etc. NB appear to cause or contribute to common diseases of the mankind e.g. periodontitis, formation of kidney stone, heart calcifications, coronary artery calcification, atherosclerotic plaque. Recent data on the far-ultraviolet extinction of starlight in our galaxy and in external galaxies is interpreted in terms of the widespread occurrence of organic particles of optical refractive index 1.4 and radii less than or equal to 20 nm. Such particles are candidates for NB such as recently been found in abundance on the Earth. Unbelievably nanobacteria-like rods observed at the surface of the Tataouine meteorite and Martian rock.The hypothesis: It seems logic to hypothesize that aliens from inner space, nanobacteria, can bring us new disease such as periodontal, cardiovascular and kidney diseases via space travels or meteorites or interstellar dusts.Evaluation of the hypothesis: The main criticism with this idea is how NB can keep alive during transfer among seriously life threatening condition in interstellar space. NB are generally thought to be very difficult to deactivation, exceptionally resistant to heat, are not deactivated by physical or chemical treatments including autoclaving, UV treatment, and various biocides. Health care providers, health policy makers and space agencies e.g. NASA and European Space Agency should make a concentrated effort to prevent transmission of NB especially following space travels.

  13. Detection of nanobacteria in serum, bile and gallbladder mucosa of patients with cholecystolithiasis

    Institute of Scientific and Technical Information of China (English)

    WEN Yu; YANG Jing; E. Olavi Kajander; Neva Ciftcioglu; LI Yong-guo; YANG Zhu-lin; WANG Xue-jun; WEI Hong; LIU Wei; MIAO Xiong-ying; WANG Qun-wei; HUANG Sheng-fu

    2005-01-01

    @@ In 1990, nanobacterium was found and named by Kajander.1 With distinct mineralizing ability, nanobacteria are thought to play a role in extraskeletal calcifying diseases. It have been found in many human tissues, but whether they exist in the bile or gallbladder mucosa remains unclear. The present study was undertaken to investigate by ELISA, bacterial culturing, immunohistochemical staining and transmission electron microscopy (TEM), whether nanobacteria exist in serum, bile or gallbladder mucosa of healthy people and patients with cholecystolithiasis.

  14. Study on nanobacteria%纳米细菌研究

    Institute of Scientific and Technical Information of China (English)

    王利民; 沈文律; 张士莲

    2005-01-01

    纳米细菌(nanobacteria,Nb)是近年来才被发现的超微细菌.纳米细菌体积极其微小,其最小直径仅50 nm,大大低于理论上细菌体积的下限.因此纳米细菌在被发现的初期,其存在的真实性就受到许多学者的质疑,并且由此引发了一场关于微生物最小体积的争论.随着研究的不断深入,纳米细菌的生物学特性不断地被揭示,纳米细菌已经成为当前研究的一个热点问题.在医学界,纳米细菌被认为与肾结石、胆囊结石、动脉粥样硬化等病理性钙化疾病的发生有关系.本文在复习大量文献的基础上,针对纳米细菌的生物学特性以及纳米细菌与人类疾病等方面作一简单的回顾与总结.

  15. Role of nanobacteria in the pathogenesis of kidney stone formation

    Science.gov (United States)

    Hong, Xin; Wang, Xiaofeng; Wang, Tian; Yu, Chengfan; Li, Hui

    2016-01-01

    Objective: This study aimed to investigate the nanobacteria (NB) induced damage to human tubular epithelial HK-2 cells and the potential role of NB in the kidney stone formation. Methods: Serum sample from 15 patients with kidney stone was collected. Four groups were included: control, NB group, nanograde hydroxyapatite (nHAP) and calcium oxalate monohydrate (COM) group. Catalase (CAT), malonaldehyde (MDA) and Na+/K+ ATPase activity was detected in the supernatant at 12 and 24 h. At 12 and 24 h, COM was added. Results: At 12 h and 24 h, the CAT in NB group was significantly higher than in control group and nHAP group (P<0.01). CAT at 24 h was significantly higher than in COM group (P<0.01). At 12 h and 24 h, the MDA in NB group was significantly higher than in control group and nHAP group (P<0.01) and significantly lower than in COM group (P<0.01). At 12 h, the Na+/K+ ATPase activity in NB group and nHAP group was significantly lower than in control group, but dramatically increased as compared to COM group (P<0.01). At 24 h, the Na+/K+ ATPase activity in NB group and nHAP group was significantly lower than in control group (P<0.01). Conclusion: NB may induce lipid peroxidation in HK-2 cells and cause adhesion of HK-2 cells to COM in a time-dependent manner, resulting in damage to HK-2 cells. This injury-causing capability of NB is more potent than nHAP and might be involved in the pathogenesis of kidney stone formation. PMID:27508044

  16. Nanobacteria-like calcite single crystals at the surface of the Tataouine meteorite.

    Science.gov (United States)

    Benzerara, Karim; Menguy, Nicolas; Guyot, Francois; Dominici, Christian; Gillet, Philippe

    2003-06-24

    Nanobacteria-like objects evidenced at the surface of the orthopyroxenes of the Tataouine meteorite in South Tunisia have been studied by scanning and transmission electron microscopies. A method of micromanipulation has been developed to ensure that exactly the same objects were studied by both methods. We have shown that the nanobacteria-like objects are spatially correlated with filaments of microorganisms that colonized the surface of the meteoritic pyroxene during its 70 years of residence in the aridic Tataouine soil. Depressions of a few micrometers in depth are observed in the pyroxene below the carbonates, indicating preferential dissolution of the pyroxene and calcite precipitation at these locations. The nanobacteria-like small rods that constitute calcium carbonate rosettes are well crystallized calcite single crystals surrounded by a thin amorphous layer of carbonate composition that smoothes the crystal edges and induces rounded shapes. Those morphologies are unusual for calcite single crystals observed in natural samples. A survey of recent literature suggests that the intervention of organic compounds derived from biological activity is likely in their formation.

  17. The molecular dimension of microbial species: 2. Synechococcus strains representative of putative ecotypes inhabiting different depths in the Mushroom Spring microbial mat exhibit different adaptive and acclimative responses to light

    Directory of Open Access Journals (Sweden)

    Shane eNowack

    2015-06-01

    Full Text Available Closely related strains of thermophilic Synechococcus were cultivated from the microbial mats found in the effluent channels of Mushroom Spring, Yellowstone National Park (YNP. These strains have identical or nearly identical 16S rRNA sequences but are representative of separate, predicted putative ecotype populations, which were identified by using the more highly resolving psaA locus and which predominate at different vertical positions within the 1-mm-thick upper-green layer of the mat. Pyrosequencing confirmed that each strain contained a single, predominant psaA genotype. Strains differed in growth rate as a function of irradiance. A strain with a psaA genotype corresponding to a predicted putative ecotype that predominates near the mat surface grew fastest at high irradiances, whereas strains with psaA genotypes representative of predominant subsurface populations grew faster at low irradiance and exhibited greater sensitivity to abrupt shifts to high light. The high-light-adapted and low-light-adapted strains also exhibited differences in pigment content and the composition of the photosynthetic apparatus (photosystem ratio when grown under different light intensities. Cells representative of the different strains had similar morphologies under low-light conditions, but under high-light conditions, cells of low-light-adapted strains became elongated and formed short chains of cells. Collectively, the results presented here are consistent with the hypothesis that closely related, but distinct, ecological species of Synechococcus occupy different light niches in the Mushroom Spring microbial mat and acclimate differently to changing light environments.

  18. A potential cause for kidney stone formation during space flights: enhanced growth of nanobacteria in microgravity

    Science.gov (United States)

    Ciftcioglu, Neva; Haddad, Ruwaida S.; Golden, D. C.; Morrison, Dennis R.; McKay, David S.

    2005-01-01

    BACKGROUND: Although some information is available regarding the cellular/molecular changes in immune system exposed to microgravity, little is known about the reasons of the increase in the kidney stone formation in astronauts during and/or after long duration missions at zero gravity (0 g). In our earlier studies, we have assessed a unique agent, nanobacteria (NB), in kidney stones and hypothesized that NB have an active role in calcium phosphate-carbonate deposition in kidney. In this research we studied effect of microgravity on multiplication and calcification of NB in vitro. METHODS: We examined NB cultures in High Aspect Rotating Vessels (HARVs) designed at the NASA's Johnson Space Center, which are designed to stimulate some aspects of microgravity. Multiplication rate and calcium phosphate composition of those NB were compared with NB cultured on stationary and shaker flasks. Collected aliquots of the cultures from different incubation periods were analyzed using spectrophotometer, SEM, TEM, EDX, and x-ray diffraction techniques. RESULTS: The results showed that NB multiplied 4.6x faster in HARVs compared to stationary cultures, and 3.2x faster than shaker flask conditions. X-ray diffraction and EDX analysis showed that the degree of apatite crystal formation and the properties of the apatite depend on the specific culture conditions used. CONCLUSION: We now report an increased multiplication rate of NB in microgravity-simulated conditions. Thus, NB infection may have a potential role in kidney stone formation in crew members during space flights. For further proof to this hypothesis, screening of the NB antigen and antibody level in flight crew before and after flight would be necessary.

  19. 纳米细菌的分离培养和保存方法探讨%Method for isolation, culture and conservation of nanobacteria

    Institute of Scientific and Technical Information of China (English)

    郭亚楠; 张德纯; 陆合; 李金玲; 沈学成; 刘明方

    2011-01-01

    目的 以钙化的胎盘组织为例,寻求在钙化组织中分离纳米细菌的最佳方法,以便更多疑似与纳米细菌感染有关的疾病得以准确分离出纳米细菌菌株,并探讨培养和保存纳米细菌的最适宜的条件.方法 (Ⅰ)胎盘钙化组织标本分别用盐酸脱矿与超声振荡脱矿的方法分离纳米细菌,计算其分离阳性率.(2)分离出的纳米细菌分别用细胞培养箱与细菌培养箱培养1个月,利用分光光度计记录两种条件下纳米细菌浓度的变化,并描绘生长曲线.(3)分别用4、- 20与- 80℃冰箱保存钙化组织和纳米细菌,记录纳米细菌分离和复苏的生长状况并绘制生长曲线.结果 (1)钙化组织用盐酸脱矿更易分离得到纳米细菌.(2)细胞与细菌培养环境下纳米细菌的生长速度并无明显差别.(3)4℃保存钙化组织和纳米细菌对于其分离和复苏都要优于- 20℃和- 80℃.结论 对钙化组织进行盐酸脱矿可以更好的分离出纳米细菌,并且可以在细菌培养箱内培养纳米细菌,新鲜钙化组织标本和纳米细菌可以短时间保存在4℃.%Objective To find an optimal method for isolating nanobacteria in calcified tissues and the most suitable condition to culture and observe nanobacteria. Method Calcified placental tissue were used in this research in a hope that the method could be used to other calcified tissues as well. (1) Calcified placental tissues were demineralized separately with hydrochloric acid and ultrasonic vibration to isolate nanobacteria from the samples; the positive rates of isolation were calculated and compared. (2) Nanobacteria were cultured separately in cells and bacteria culture conditions and concentration was recorded with spectophoto fluorometer. (3) Fresh calcified tissues and cultured nanobacteria were preserved in different low temperature conditions, recovery and concentration was recorded. Result (1) Nanobacteria were obtained more easily in HC1

  20. 乳腺肿瘤微钙化与纳米细菌的关系%Relationship between Nanobacteria and Microcalcification in Breast Cancer

    Institute of Scientific and Technical Information of China (English)

    李涛; 潘晓燕; 陈海鸣; 张伟

    2014-01-01

    目的:探讨纳米细菌在伴钙化和不伴钙化的乳腺恶性肿瘤与良性肿瘤患者血清与组织中的分布情况。方法将110例乳腺肿瘤患者根据良恶性及是否伴钙化分组。 A组30例恶性伴钙化,B组30例恶性无钙化,C组20例良性伴钙化,D组30例良性无钙化。 ELASA法测定各组患者血清中纳米细菌的感染情况,免疫组化法检测各组患者组织中纳米细菌的感染情况。结果 A、B、C、D各组血清中纳米细菌的感染率分别为73.3%,10.0%,5.0%,6.7%。 A、B、C、D各组组织中纳米细菌的感染率分别为93.3%,13.3%,5.0%,0.0%。 A组血清与组织中纳米细菌感染率与其他组相比,差异均有统计学意义(P<0.01)。结论伴微钙化的乳腺癌患者血清和组织中纳米细菌感染率明显增高,提示纳米细菌可能和乳腺癌微钙化的形成相关。%Objective To explore the distribution of nanobacteria in serum and tissues of calcified and non calcified breast malignant tumors and breast benign tumors .Methods 110 patients with breast tumors were divided into 4 groups based on microcalcification and tumor types .Group A (n=30):cancer with microcalcification:Group B(n=30):cancer without microcal-cification:Group C ( n=30 ):benign tumor with microcalcification:Group D ( n=20 ):benign tumor without microcalcification . Nanobacteria in serum samples were detected by ELASA .Nanobacteria in tissue samples were detected by SABC immunohisto-chemistry (IHC).Results The nanobacterial infection rates in serum samples in Group A ,B,C and D were 73.3%,10.0%, 5.0%and 6.7%respectively.The nanobacterial infection rates in tissue samples in Group A ,B,C and D were 93.3%,13.3%, 5.0%and 0%respectively.Nanobacterial infection rates in serum and tissue samples in Group A and the rest groups had statisti -cal difference (P<0.01).Conclusion Breast cancer patients with microcalcification have a significantly

  1. Isolation, cultivation and initial identification of Nanobacteria from dental pulp stone%髓石中Nanobacteria细菌的分离、培养与鉴定

    Institute of Scientific and Technical Information of China (English)

    曾劲峰; 张伟; 蒋宏伟; 凌均棨

    2006-01-01

    目的 从髓石中分离Nanobacteria,并进行培养和鉴定.方法 收集新鲜的27颗髓石分为9个样本,每个样本含3颗髓石,进行Nanobacteria的分离、培养,观察该菌形态学及生长特性,采用von Kossa染色、Nanobacteria单克隆抗体8D10和G1B8免疫组化和间接免疫荧光染色、Hoechst染色和von Kossa染色双重染色法联合进行Nanobacteria鉴定.结果 本次实验7个样本中所分离、培养出的细菌形态学特征与生长特性与Nanobacteria相似,von Kossa染色呈阳性反应,单克隆抗体免疫组化染色和间接免疫荧光染色阳性.双重染色实验中,样本Hoechst染色呈阴性反应,von Kossa染色呈阳性反应,而牙髓细胞的Hoechst染色可见胞核呈明显阳性反应,有2个样本中未见细菌生长.结论 髓石中可分离得到Nanobacteria,该菌的生物学特性可能在髓石的形成中起重要作用.

  2. 纳米细菌在口腔疾病和其他全身性疾病中的作用%Role of nanobacteria in oral disease and other systemic disease

    Institute of Scientific and Technical Information of China (English)

    莫莉基

    2011-01-01

    纳米细菌是已知的最小细菌,它所产生的坚硬的矿化外壳,与病理性钙化有关.有关纳米细菌的生物性,业界争论激烈.在人类的唾液、牙齿表面、牙菌斑、牙石和牙髓石中存在着大量的纳米细菌.本文就纳米细菌、纳米细菌在口腔疾病和其他全身性疾病中的作用等作一综述.%Nanobacteria are the smallest known bacteria, and the adamant shells they form have relations with pathologic calcification. About its “living organism”, a great deal of controversy has raised within the scientific community in recent years. There have been evidences that abundance of nanobacteria in the oral cavity such as saliva, the surface of the teeth, dental plaque, calculus dentalis, pulp stone and so on. This article reviews nanobacteria and its role in oral disease and other systemic disease.

  3. Representing dispositions

    Directory of Open Access Journals (Sweden)

    Röhl Johannes

    2011-08-01

    Full Text Available Abstract Dispositions and tendencies feature significantly in the biomedical domain and therefore in representations of knowledge of that domain. They are not only important for specific applications like an infectious disease ontology, but also as part of a general strategy for modelling knowledge about molecular interactions. But the task of representing dispositions in some formal ontological systems is fraught with several problems, which are partly due to the fact that Description Logics can only deal well with binary relations. The paper will discuss some of the results of the philosophical debate about dispositions, in order to see whether the formal relations needed to represent dispositions can be broken down to binary relations. Finally, we will discuss problems arising from the possibility of the absence of realizations, of multi-track or multi-trigger dispositions and offer suggestions on how to deal with them.

  4. The culture and detection of nanobacteria in abdominal aorta atherosclerotic plaque%腹主动脉粥样硬化斑块中纳米细菌的培养与鉴定

    Institute of Scientific and Technical Information of China (English)

    耿文茂; 张倩; 吴亚光; 秦成坤; 苏忠学

    2012-01-01

    目的 观察腹主动脉粥样硬化斑块中是否存在纳米细菌,并对其进行鉴定.方法 12例腹主动脉粥样硬化斑块及12例正常动脉血管组织研磨,取上清液培养.8周后收集培养瓶底白色粉末,用纳米细菌单克隆抗体间接免疫荧光法对其进行检测,并利用电镜进一步观察.结果 12例动脉粥样硬化斑块中10例纳米细菌检测阳性,2例阴性,12例正常动脉血管组织中1例纳米细菌检测阳性,11例阴性,差异有统计学意义(P<0.05).纳米细菌单克隆抗体间接免疫荧光检测时可发出绿色荧光,电镜下测量纳米细菌直径约为100 ~ 300 nm.结论 腹主动脉粥样硬化斑块中存在纳米细菌,它可能导致粥样硬化斑块不稳定.%Objective To investigate whether the nanobacteria exists in abdominal aorta atherosclerotic plaque or not and detect it.Methods 12 case of abdominal aorta atherosclerotic plaques and 12 case of normal artery were grinded,the supematant fluid was cultured for eight weeks.Subsequently,the white extract from the culture flask was detected by nanobacteria monoclonal antibody immunofluorescence and electron microscope.Results Nanobacteria was positive in 10 case of atherosclerotic plaques but only in 1 case of normal artery,the difference was statistically significant (P < 0.05).Green fluorescence could be present during indirect immunofluorescence detection.The size of nanobacreria was measured ranging from 100nm to 300nm by electron microscope analysis.Conclusion Nanobacteria was detected in abdominal aorta atherosclerotic plaques and might led to atherosclerotic plaques instability.

  5. Putative archaeal viruses from the mesopelagic ocean.

    Science.gov (United States)

    Vik, Dean R; Roux, Simon; Brum, Jennifer R; Bolduc, Ben; Emerson, Joanne B; Padilla, Cory C; Stewart, Frank J; Sullivan, Matthew B

    2017-01-01

    Oceanic viruses that infect bacteria, or phages, are known to modulate host diversity, metabolisms, and biogeochemical cycling, while the viruses that infect marine Archaea remain understudied despite the critical ecosystem roles played by their hosts. Here we introduce "MArVD", for Metagenomic Archaeal Virus Detector, an annotation tool designed to identify putative archaeal virus contigs in metagenomic datasets. MArVD is made publicly available through the online iVirus analytical platform. Benchmarking analysis of MArVD showed it to be >99% accurate and 100% sensitive in identifying the 127 known archaeal viruses among the 12,499 viruses in the VirSorter curated dataset. Application of MArVD to 10 viral metagenomes from two depth profiles in the Eastern Tropical North Pacific (ETNP) oxygen minimum zone revealed 43 new putative archaeal virus genomes and large genome fragments ranging in size from 10 to 31 kb. Network-based classifications, which were consistent with marker gene phylogenies where available, suggested that these putative archaeal virus contigs represented six novel candidate genera. Ecological analyses, via fragment recruitment and ordination, revealed that the diversity and relative abundances of these putative archaeal viruses were correlated with oxygen concentration and temperature along two OMZ-spanning depth profiles, presumably due to structuring of the host Archaea community. Peak viral diversity and abundances were found in surface waters, where Thermoplasmata 16S rRNA genes are prevalent, suggesting these archaea as hosts in the surface habitats. Together these findings provide a baseline for identifying archaeal viruses in sequence datasets, and an initial picture of the ecology of such viruses in non-extreme environments.

  6. Representing Development

    DEFF Research Database (Denmark)

    Representing Development presents the different social representations that have formed the idea of development in Western thinking over the past three centuries. Offering an acute perspective on the current state of developmental science and providing constructive insights into future pathways...... and development, addressing their contemporary enactments and reflecting on future theoretical and empirical directions. The first section of the book provides an historical account of early representations of development that, having come from life science, has shaped the way in which developmental science has...... approached development. Section two focuses upon the contemporary issues of developmental psychology, neuroscience and developmental science at large. The final section offers a series of commentaries pointing to the questions opened by the previous chapters, looking to outline the future lines...

  7. The present status and prospect of studies on relationship between nanobacteria and congenital rickets%先天性佝偻病与纳米细菌关系研究的现状与展望

    Institute of Scientific and Technical Information of China (English)

    刘英; 张德纯; 陆合; 郭亚楠

    2011-01-01

    Congenital rickets is a special period of rickets after fetal born. It is etiology undetermined and would affect children skeletal development and immunity if deferment. Nanobacteria induced placental calcification has a relationship with children rickets, and is speculated to be linked with congenital rickets. Diagnosis and prevention of nanobacteria infection may have a clinical significance for the prevention of congenital rickets.%先天性佝偻病是胎儿出生后就发生的特殊阶段的佝偻病,病因并不十分清楚,迁延不愈会影响小儿骨骼发育和免疫功能.纳米细菌导致的胎盘钙化与小儿佝偻病有关,推测纳米细菌与先天性佝偻病有关.因此诊断和防治纳米细菌感染可能对于先天性佝偻病的预防有一定临床意义.

  8. 纳米细菌在前列腺结石形成中的作用%Role of nanobacteria in the formation of the prostate stone

    Institute of Scientific and Technical Information of China (English)

    沈学成; 熊朝晖; 陈军; 詹绍洋; 李丹洋; 周占松

    2014-01-01

    Objective To study the role of nanobacteria (NB) in prostatic calculi formation,investigate anti-NB treatment of benign prostatic calculi is valid.Methods In prostate stones isolated,cultured and identified NB,NB established rat model induced prostate stones,and anti-NB-line therapy in patients with prostate stones.Results From the prostate stones isolated NB,and successfully build NB-induced rat model of prostatic calculi.Patients with prostatic calculi anti-NB treatment,ultrasonography showed stone diameter gradually reduced,significantly improved chronic pelvic pain syndrome.Conclusions NB are related with prostate stones formation,anti-NB treatment of prostate stones is effective.%目的 探讨纳米细菌(NB)在前列腺结石形成中的作用,观察抗NB治疗前列腺结石是否有效.方法 本组50例,从2例手术治疗取出的前列腺结石中分离、培养、鉴定NB,建立NB致大鼠前列腺结石模型,并对28例保守治疗的前列腺结石患者行抗NB治疗.结果 从前列腺结石中分离出NB,并成功建立NB致大鼠前列腺结石模型.前列腺结石患者行抗NB治疗后,彩超显示结石直径逐渐缩小,慢性骨盆疼痛综合征(C PPS)症状显著改善.结论 NB与前列腺结石形成有关,抗NB治疗前列腺结石有效.

  9. Research of nanobacteria leading to rabbit gallstone produce%纳米细菌致兔胆囊结石的研究

    Institute of Scientific and Technical Information of China (English)

    刘亚楠; 张国彬; 马立人

    2011-01-01

    ①目的 通过对胆汁培养的纳米细菌(Nanobacteria Nb)感染日本大耳白兔致胆结石形成,探讨纳米细菌感染与胆石症发生的相关性.②方法 用从胆汁中培养出的纳米细菌感染日本大耳白兔,3周后处死日本大耳白兔,记录成石情况.③结果 胆石症患者胆汁纳米细菌感染性实验中纳米细菌感染组胆结石发生率81.25%与DMEM对照组6.25%和羟基磷灰石(Hap)对照组18.75%比较,差异有统计学意义(P<0.05).日本大耳白兔胆汁纳米细菌感染性实验中Nb感染组胆结石发生率56.25%与含各种氨基酸和葡萄糖的培养基(DMEM)对照组6.25%和灭活纳米细菌对照组12.50%比较,差异有统计学意义P<0.05.④结论 实验动物感染纳米细菌后能在短期内产生胆囊结石;由被感染的实验日本大耳白兔胆汁培养出的纳米细菌能再次感染日本大耳白兔并致胆结石形成.

  10. Nanobacteria induces Type Ⅲ prostatitis in rats%纳米细菌致Ⅲ型前列腺炎的实验研究

    Institute of Scientific and Technical Information of China (English)

    明爱民; 沈学成; 周占松; 宋波

    2009-01-01

    目的 研究纳米细菌(nanobacteria,NB)对大鼠前列腺的慢性致炎作用.方法 成年雄性SD大鼠40只,分为3组:对照组、模型组、四环素治疗组,分别为16、16、8只.模型组和四环素治疗组由尿道逆行注入NB建立大鼠动物模型.4周后,对照组、模型组各处死8只动物,观察前列腺组织中白细胞、卵磷脂小体及病理变化.治疗组用四环素灌胃治疗,其余动物用蒸馏水灌胃,连续4周,处死剩余动物,进行同样的观察.并将所有动物前列腺组织进行NB再分离、培养和鉴定.结果 同对照组比较,4周后所有模型组动物前列腺组织呈慢性炎症改变,白细胞数明显升高,卵磷脂小体数明显下降(P<0.05).8周后同模型组比较,治疗组动物炎症明显减轻,白细胞数明显下降,卵磷脂小体数明显升高(P<0.05).模型组16只动物NB培养均阳性,对照组均阴性.结论 NB能引起大鼠前列腺慢性炎症,NB可能是Ⅲ型前列腺炎的病因.四环素抗NB治疗有效.

  11. Chronic Inflaming Effect of Nanobacteria on Prostates of Rats%纳米细菌对大鼠前列腺的慢性致炎作用

    Institute of Scientific and Technical Information of China (English)

    明爱民; 沈学成; 周占松; 宋波

    2009-01-01

    目的 研究纳米细菌(nanobacteria, NB)对大鼠前列腺的慢性致炎作用,为Ⅲ型前列腺炎病因学研究提供实验依据. 方法 成年雄性SD大鼠50只,随机分为3组:对照组20只,模型组20只,四环素治疗组10只.模型组和四环素治疗组由尿道逆行注入NB建立大鼠动物模型.4周后, 对照组、模型组各处死10只动物,观察前列腺组织中白细胞、卵磷脂小体及病理变化.治疗组用四环素灌胃治疗,其余动物用蒸馏水灌胃,连续4周,处死剩余动物,进行同样的观察.并将所有动物前列腺组织进行NB再分 离、培养和鉴定.结果 同对照组比较,4周后模型组动物前列腺组织呈慢性炎症改变,白细胞数明显升高,卵磷脂小体数明显下降,有明显差异(P<0.05);8周后同模型组比较,治疗组动物炎症明显减轻,白细胞数明显下降,卵磷脂小体数升高;模型组与对照组和治疗组比较有差异(P<0.05).对照组和治疗组无差异.模型组有19只动物NB培养阳性,对照组均阴性.结论 NB能引起大鼠前列腺慢性炎症,四环素抗NB治疗有效.NB可能是Ⅲ型前列腺炎的病因.

  12. Morphological observation of nanobacteria in calcified placenta and umbilical cord blood%钙化胎盘及脐带血中纳米细菌的形态学观察

    Institute of Scientific and Technical Information of China (English)

    刘胜男; 张德纯; 张名均; 郭亚楠; 杨晓容; 杨顺杰

    2013-01-01

    目的 研究纳米细菌(nanobacteria,NB)的分布,寻求检测胎盘钙化NB感染的更好组织来源.方法 收集孕妇胎盘钙化组织和脐带血20例,并以20例正常胎盘组织作对照,分离培养NB;用革兰染色和茜素红染色法、扫描电镜和透射电镜进行形态学鉴定.结果 培养沉淀物符合NB的特性.脐带血NB分离率为80%(16/20),钙化胎盘组织为65%(13/20),均明显高于正常胎盘组织的10%(2/20),X2分别为12.07、9.09,P均<0.01;脐带血与钙化胎盘组织比较,差异无统计学意义(x2=1.33,P>0.05).油镜下脐带血和钙化胎盘组织分离的NB为球状或球杆状,形态相似;茜素红染色脐带血中NB较多且聚集成簇;透射电镜和扫描电镜下NB呈球形,大小为80 ~ 500 nm,并可见毛刺结构.结论 胎盘钙化与NB感染有关,脐带血适用于检测钙化胎盘的NB感染.%Objective To study the distribution of nanobacteria (NB) and explore an appropriate tissue as the source for detection of placental calcification infected with nanobacteria. Methods The calcified placental tissues and umbilical cord blood from 20 pregnant women for isolation and culture of NB, and normal placental tissues were used as controls. The morphological identification of NB was performed with Gram and alizarin red staining and scanning electron microscope (SEM) , transmission electron microscope (TEM). Results The precipitates were corresponding to the characteristics of NB. The isolation rate of NB was 65% (13/20) in the specimens of calcified placental tissues and 80% (16/20) in the cord blood, and both of them were higher than that in normal placental tissues (10% ) with a significantly statistical difference ( chi-square values were 12. 07 and 9. 09 respectively, P 0. 05). The shape of NB isolated from calcified placental tissue and umbilical cord blood under oil lens was spherical or rhabdoid with burr edge, and was globoid with size of 80-500 nm and staining of Gram

  13. 上尿路结石患者血清、尿液、结石中纳米细菌的检测%Detection of nanobacteria in serum,urine and calculus of patients with upper urinary calculi

    Institute of Scientific and Technical Information of China (English)

    粟宏伟; 朱永生; 邓清富; 陈同良

    2013-01-01

    Objective To investigate the infection status of nanobacteria on patients with upper urinary calculi and healthy sub-jects ,and analyze the role of nanobacteria in the formation of upper urinary calculi .Methods The serum ,urine and calculus of 42 patients with upper urinary calculi were investigated by polymerase chain reaction (PCR) and by bacteria cultivation with 10% γ-FBS and PMBI 1640 .The resulting PCR products were sequenced for further comparison with the reported sequence in gene bank . The serum and urine from 30 healthy adults were used as controls .Results After 4 to 6 weeks′culture ,the white or yellow precipi-tate was visible at the bottom of the tube .The positive rate of PCR was 90 .4% in calculous patients urine and 6 .7% in healthy a-dults urine ,as the positive was 92 .8% and 6 .7% in serum .which there is significant difference (P<0 .01) .The positive rate of the nanabactria in urinary calculi was 95 .2% .The coincidence rate was 98 .72% between the PCR products and the reported sequence in gene bank .Conclusion Nanobacteria are widely existed in the serum ,urine and calculus of the patients with upper urinary calcu-li ,this indicate that the nanobacteria might be have the most important influence on the formation process of urinary calculi .%目的:检测上尿路结石患者与健康者的血清、尿液里纳米细菌和尿路结石标本里的纳米细菌感染情况,分析纳米细菌在尿路结石形成中的作用。方法对30例健康者和42例上尿路结石患者的血清、尿液标本以及后者的结石标本处理后用含10%热灭活γ-胎牛血清(γ-FBS)的 PMBI 1640培养基行纳米细菌培养,观察其生长情况,并对培养后的标本行聚合酶链反应(PCR)检测,PCR产物通过测序与原序列比对进一步分析。结果培养4~6周后,部分培养管底出现肉眼可见的白色(或黄色)絮状物或沉淀物。PCR检测结石患者与健康者的血清纳

  14. Ⅲ型前列腺炎纳米细菌快速检测方法研究及临床评价%Rapid detection and clinical evaluation of nanobacteria infection in type Ⅲ prostatitis

    Institute of Scientific and Technical Information of China (English)

    唐金元; 周占松; 沈学成; 袁宇峰

    2011-01-01

    目的 通过对几种Ⅲ型前列腺炎纳米细菌感染检测方法评价比较,找出一种最快速、可靠的纳米细菌检测方法.方法 以培养后间接免疫荧光鉴定结果为基准对照,分别采用间接免疫荧光法、茜素红钙染色法及PCR法对西南医院泌尿外科门诊150例Ⅲ型前列腺炎患者前列腺液标本进行纳米细菌检测,比较其阳性检出率、灵敏度和特异度差异.结果 评价阳性检出率、灵敏度、特异度:间接免疫荧光法依次为23.3%、42.2%、100.0%;茜素红钙染色法依次为21.3%、34.9%、95.5%;PCR法依次为57.3%、95.2%、89.6%.间接免疫荧光法、茜素红钙染色法检出率与培养后间接免疫荧光法比较,均有统计学差异(P0.05).结论 PCR法检出率优于间接免疫荧光法及茜素红钙染色法,灵敏度及特异度均较高,可广泛应用于Ⅲ型前列腺炎患者纳米细菌感染快速检测.%Objective To discover the rapidest and most reliable method for detecting nanobacteria infection in type Ⅲ prostatitis by comparing several available methods. Methods Expressed prostatic secretion (EPS) specimens were obtained from 150 outpatients suffering from type Ⅲ prostatitis from the Department of Urology, Southwest Hospital, Chongqing, China. Nanobacteria infection in the EPS specimens was detected by indirect immunofluorescence staining (IIFS), alizarin red staining of calcium, and polymerase chain reaction (PCR). With the result of indirect immunofluorescence staining after culture (IIFSC) as a benchmark, the differences of the concerning the positive detection rate, sensitivity and specificity were compared. Results The positive detection rate, sensitivity and specificity of IIFS were 23.3%, 42.2% and 100%, respectively.Those of alizarin red staining of calcium were 21.3%, 34.9% and 95.5%, and those of PCR were 57.3%,95.2% and 89.6%, respectively. The positive detection rate of IIFS or alizarin red calcium staining had a

  15. Overview of Biomineralization and Nanobacteria

    Science.gov (United States)

    Ciftcioglu, N.; McKay, D. S.

    2005-01-01

    Biomineralization is a frequently used term in nanotechnology, astrobiology, geology, and medicine. In the process of biomineralization, a living organism provides a chemical environment that controls the nucleation and growth of unique mineral phases. Often these materials exhibit hierarchical structural order, leading to superior physical properties, not found either in their inorganic counterparts or in synthetic materials. Biomineralization is widespread in the biosphere and hundreds of different minerals are produced or assisted by a variety of organisms from bacteria to humans. Teeth, bones, kidney stones, and skeletons of algae, mussels, and magnetotactic bacteria are all examples of biomineralization. We do not fully understand the control mechanism of biomineralization either in primitive or in developed organisms. The presence of organic molecules, among other characteristics, can influence the coherence length for X-ray scattering in biogenic crystals. Control over biomineral properties can be accomplished at a myriad of levels, including the regulation of particle size, shape, crystal orientation, polymorphic structure, defect texture, and particle assembly. In the latter case, cellular processes enable control in both the spatial and temporal domain in such a way that hierarchical composite structures can be built which increase the toughness and durability of the material, which is invaluable for load-bearing materials such as bones, teeth, mollusk shells, etc. Durability of biominerals produces remarkably preserved bacterial and cyanobacterial microfossils from billions of years-old samples. The differentiation between microfossils and nonbiogenic artifacts has been a lively discussion subject in astrobiology especially in the last decade. Clearly, more detailed information on the mechanism of biomineralization, and the effect of organic matter on crystal formation/fossilization would help focus such discussions.

  16. 纳米细菌感染致SD大鼠前列腺结石的实验研究%Prostatic calculus caused by nanobacteria infection in SD rats

    Institute of Scientific and Technical Information of China (English)

    明爱民; 张新际; 郭君毅; 吴永吉; 王海飞; 沈学成; 宋波

    2011-01-01

    目的 建立前列腺纳米细菌(NB)感染的SD大鼠模型,探讨NB在前列腺炎以及前列腺结石形成中的致病作用.方法 40只成年雄性SD大鼠随机分为对照组和模型组,每组20只.分别经尿道注入生理盐水0.2 ml和NB混悬液0.2 ml(浓度为1个麦氏单位).将2组动物分别在4周、8周后处死(每次每组10只).HE染色观察2组大鼠前列腺组织的病理改变,透射电镜和扫描电镜观察有无结石形成.取前列腺组织做NB细菌的再培养和鉴定.结果 4周后模型组大鼠前列腺组织出现慢性炎症,并持续到8周后.8周后模型组7只大鼠前列腺组织中发现小结石.前列腺组织NB再培养均有NB生长.对照组动物前列腺组织未见炎症及结石,NB细菌的再培养未见NB生长.结论 NB感染大鼠前列腺能造成前列腺慢性炎症,并形成结石,NB感染可能是前列腺结石形成的重要病因.%Objective To reproduce an SD rat model of prostatic calculus by using nanobacteria (NB), and explore the role of NB in contributing to prostatitis and prostatic calculus. Methods Twenty adult male SD rats were randomized to the control group and 20 to the model group. Rat prostate infection models were reproduced by infusing 0. 2 ml (Concentration, 1 Mai unit) NB suspension transurethrally. 0.2 ml physiological saline was infused transurethrally in the rat control group. The rats were sacrificed 4 and 8 weeks later and prostatic pathology were viewed by hematoxylin and eosin (HE) staining. Lithogenesis was observed by scanning electron microscope (SEM) or Transmission electron microscopy (TEM). Re-isolation, culture and identification of nanobacteria were also done in rat prostatic tissues. Results Chronic inflammatory changes of prostates were shown in the model group at both 4 weeks and 8 weeks after infusing NB suspension. Prostatic calculi were detected by SEM and TEM at 8 weeks in the prostates of the rat model group (7/10). Neither chronic inflammatory

  17. Nanobacteria infection caused Type Ⅲ prostatitis:clinical treatment study%纳米细菌感染致Ⅲ型前列腺炎的临床治疗研究

    Institute of Scientific and Technical Information of China (English)

    李军; 吕宏迪; 明爱民; 李文俊; 李重先; 杨玉荣; 张新际; 张正臣

    2014-01-01

    目的:观察四环素治疗纳米细菌感染的Ⅲ型前列腺炎的临床效果。方法360例纳米细菌感染的Ⅲ型前列腺炎患者分为治疗组和对照组,每组180例。观察组患者给予四环素治疗,对照组患者给予左氧氟沙星治疗,连续用药1个月后,观察2组患者前列腺炎症状指数(NIH-CPSI)评分、前列腺液卵磷脂小体及纳米细菌再培养情况。结果观察组患者NIH-CPSI评分及疼痛、排尿症状和生活质量评分显著低于对照组(P<0.01),观察组卵磷脂小体级别评分显著高于对照组(P<0.05)。观察组患者治疗后前列腺液再培养后纳米细菌阳性率为22.2%显著低于对照组的100.0%(P<0.05)。结论四环素治疗“纳米细菌”感染的Ⅲ型前列腺炎有更显著效果。%Objective To observe the clinical effect of nanobacteria infection caused Type Ⅲ prostatitis with tetracycline. Methods The 360 cases of nanobacteria infection caused Type Ⅲ prostatitis were divided into treatment group and control group,180 cases for each. The patients in the treatment group were given tetracycline while the control group were given levofloxacin. 1 month after continously using drugs ,the patient's symptom index (NIH-CPSI) score,prostate fluid lecithin corpuscle and nanobacterial reculture were observed and compared. Results The NIH-CPSI score and pain,urinary symptoms and score on life quality of the treatment group patients was significantly lower than that of control group (P<0.01),also in treatment group lecithin corpuscle scale score was significantly higher than in control group (P<0.05). In treatment group and control group after prostate fluid and cultured the positive cases of nanobacterial numbers were 40 (22.2%) and 180 cases(100%) respectively,the positive rate of treatment group was significantly lower than that of control group (P<0.05). Conclusion Using tetracycline to treat nanobacterial infection caused

  18. Identification of nanobacteria from blood and stool of rats suffering severe infection of abdominal cavity%SD大鼠严重腹腔感染前后血、粪纳米细菌的检测

    Institute of Scientific and Technical Information of China (English)

    郑永波; 吴承堂

    2004-01-01

    目的检测SD大鼠腹腔感染前后血、粪纳米细菌(nanobacteria,NB),探讨NB与严重腹腔感染的相关性.方法40只SD大鼠,通过盲肠结扎加穿孔法制作SD大鼠严重腹腔感染模型,分别于感染前后取血、粪标本进行电镜下观察;NB培养;NB 16S rRNA基因聚合酶链反应(polymerase chain reaction,pCR)扩增,电泳分析.结果电镜下观察NB,感染前、后血阳性率分别为17.5%和35.0%,P=0.118;感染前、后粪阳性率分别为40.0%和32.5%,P=0.250.经28 d培养,结果均未见有NB特异性白色沉淀物形成.PCR法检测NB 16SrRNA基因,感染前、后血阳性率分别为52.5%和90.0%,P=0.000;感染前、后粪阳性率均为95.0%.结论PCR法检测NB 16S rRNA基因,SD大鼠粪普遍阳性,腹腔感染前、后血阳性率差异有显著意义,其作用尚待进一步研究.%Objective: To detect nanobacteria (NB) from blood and stool of rats suffering severe infection of abdominal cavity. Methods: 40 SD rats were involved in the study. The severe infection models of abdominal cavity were made by cecal ligation plus puncture (CLP). The test samples of blood and stool were obtained before or after infected respectively and filtered through 0.22 μm filters to eradicate the general germs and cells. The samples were stained with phosphoric tungstic acid and observed with transmission electron microscopy (TEM). RPMI1640 culture with 10.0% fetal bovine serum (FBS) was added into the filtered samples for culturing NB. Polymerase chain reaction (PCR) was made with the primers that designed from the sequences of NB 16S rRNA gene recorded in the genebank (GenBank accession No. X98419) [1]. PCR products were analyzed by agarose gel electrophoresis. Results: NB was detected with TEM from some samples. The positive rates before and after CLP respectively were 17.5% and 35.0%in the blood samples (P=0.118), 40.0% and 32.5% in the stool samples (P=0.250). We failed to find any white precipitate in any culture bottle in 28 d

  19. Cultivation and identification of nanobacteria in aqueous humor of patients with age-related cataract%年龄相关性白内障患者房水中纳米细菌的培养和检测

    Institute of Scientific and Technical Information of China (English)

    郑幼平; 蓝兴锐; 郭少琼; 刘洁梅; 王桂芳

    2012-01-01

    目的:分离、培养与检测年龄相关性白内障房水中的纳米细菌(nanobacteria,NB),为进一步探讨NB致白内障的机制奠定基础.方法:白内障超声乳化联合人工晶状体植入手术术前收集30份房水标本,通过脱矿、过滤、离心处理,用细胞培养的方法进行NB培养,观察其生长情况.采用免疫组织化学、透射电镜方法观察培养物形态.结果:培养6wk后,对培养标本进行观察,发现12瓶(40%)培养液中存在絮状漂浮成团的NB,并且其中8瓶培养液瓶底亦可见贴壁生长的成团的或散在分布的颗粒沉淀状NB;对照组一看见1例絮状漂浮,并可见管底颗粒沉淀;对照组二未见絮状漂浮和颗粒沉淀.透射电镜可见NB为针状物的聚集体,大小不一.结论:从年龄相关性白内障患者房水中分离培养鉴定出NB,表明其感染与白内障发病可能有关,需进一步研究其致病机制.

  20. 前列腺结石患者结石中纳米细菌的培养和形态学鉴定%Culture and morphological identification of nanobacteria from prostatic calculus

    Institute of Scientific and Technical Information of China (English)

    沈学成; 杨杰; 饶贤才; 宋波; 周占松

    2008-01-01

    目的 分离、培养、鉴定纳米细菌(nanobacteria, NB),探索其在前列腺结石中的分布情况,分析其在前列腺结石发病中的作用.方法 手术中无菌收集前列腺结石患者的结石标本,经过稀释、过滤、离心处理后,用细胞培养的方法进行细菌培养,观察其生长情况.运用透射电镜、钙染色和革兰染色等手段观察其形态特征,采用单克隆抗体间接免疫荧光染色进行细菌鉴定.结果 ①培养3~4周后,对前列腺结石标本进行观察,发现部分培养管底部出现紧贴管壁生长的白色沉淀物.②钙染色和革兰染色观察可发现NB成簇分布.③单克隆抗体间接免疫荧光染色鉴定发现26例标本中存在着NB,阳性率为65.0%.④免疫荧光阳性标本透射电镜下观察,NB呈球状或球杆状,大小100~500 nm.结论 前列腺结石患者的结石中存在着NB的感染,表明NB与前列腺结石发病的关系密切.

  1. Putative cryptoendolithic life in Devonian pillow basalt, Rheinisches Schiefergebirge, Germany.

    Science.gov (United States)

    Peckmann, J; Bach, W; Behrens, K; Reitner, J

    2008-03-01

    Middle Devonian (Givetian) pillow basalt and inter-pillow breccia from the Rheinisches Schiefergebirge in Germany were found to contain putative biogenic filaments that indicate that life once proliferated within these volcanic rocks. Mineralized filaments are found in carbonate amygdules (vesicles filled by carbonate cement) in the volcanic rock, where they started to form on the internal surface of the once water-filled vesicles. Biogenicity of the filaments is indicated by (1) their size and shape resembling modern microorganisms including a constant diameter along the length of curved filaments, (2) their independence of crystal faces or cleavage planes, (3) branching patterns reminiscent of modern microorganisms, and (4) their spatial clustering and preferential occurrence close to the margin of pillows and in the inter-pillow breccias. A time lag between the deposition of pillow basalt and the activity of endoliths is revealed by the sequence of carbonate cements filling the amygdules. The putative filamentous microorganisms thrived after the formation of early fibrous rim cement, but before later equant calcite spar filled most of the remaining porosity. Microbial clay authigenesis analogous to the encrustation of prokaryotes in modern iron-rich environments led to the preservation of filaments. The filaments predominantly consist of the clay minerals chamosite and illite. Having dwelled in water-filled vesicles, the Devonian basalt-hosted filaments apparently represent cryptoendoliths. This finding suggests that a previously unrecognized niche for life exists within volcanic rock.

  2. List of Accredited Representatives

    Data.gov (United States)

    Department of Veterans Affairs — VA accreditation is for the sole purpose of providing representation services to claimants before VA and does not imply that a representative is qualified to provide...

  3. The representative animal

    OpenAIRE

    Harrison, J M

    1994-01-01

    The anthropocentric approach to the study of animal behavior uses representative nonhuman animals to understand human behavior. This approach raises problems concerning the comparison of the behavior of two different species. The datum of behavior analysis is the behavior of humans and representative animal phenotypes. The behavioral phenotype is the product of the ontogeny and phylogeny of each species, and this requires that contributions of genotype as well as behavioral history to experim...

  4. [Advance directives. Representatives' opinions].

    Science.gov (United States)

    Busquets I Font, J M; Hernando Robles, P; Font I Canals, R; Diestre Ortin, G; Quintana, S

    The use and usefulness of Advance Directives has led to a lot of controversy about their validity and effectiveness. Those areas are unexplored in our country from the perspective of representatives. To determine the opinion of the representatives appointed in a registered Statement of Advance Directives (SAD) on the use of this document. Telephone survey of representatives of 146 already dead people and who, since February 2012, had registered a SAD document. More the two-thirds (98) of respondents recalled that the SAD was consulted, with 86 (58.9%) saying that their opinion as representative was consulted, and 120 (82.1%) believe that the patient's will was respected. Of those interviewed, 102 (69.9%) believe that patients who had previously planned their care using a SAD had a good death, with 33 (22.4%) saying it could have been better, and 10 (6.9%) believe they suffered greatly. The SAD were mostly respected and consulted, and possibly this is related to the fact that most of the representatives declare that the death of those they represented was perceived as comfortable. It would be desirable to conduct further studies addressed at health personnel in order to know their perceptions regarding the use of Advance Directives in the process of dying. Copyright © 2016 SECA. Publicado por Elsevier España, S.L.U. All rights reserved.

  5. Basal ganglia calcification as a putative cause for cognitive decline

    Directory of Open Access Journals (Sweden)

    João Ricardo Mendes de Oliveira

    Full Text Available ABSTRACT Basal ganglia calcifications (BGC may be present in various medical conditions, such as infections, metabolic, psychiatric and neurological diseases, associated with different etiologies and clinical outcomes, including parkinsonism, psychosis, mood swings and dementia. A literature review was performed highlighting the main neuropsychological findings of BGC, with particular attention to clinical reports of cognitive decline. Neuroimaging studies combined with neuropsychological analysis show that some patients have shown progressive disturbances of selective attention, declarative memory and verbal perseveration. Therefore, the calcification process might represent a putative cause for dementia syndromes, suggesting a probable link among calcinosis, the aging process and eventually with neuronal death. The increasing number of reports available will foster a necessary discussion about cerebral calcinosis and its role in determining symptomatology in dementia patients

  6. Detection of putative new mutacins by bioinformatic analysis using available web tools

    Directory of Open Access Journals (Sweden)

    Nicolas Guillaume G

    2011-07-01

    Full Text Available Abstract In order to characterise new bacteriocins produced by Streptococcus mutans we perform a complete bioinformatic analyses by scanning the genome sequence of strains UA159 and NN2025. By searching in the adjacent genomic context of the two-component signal transduction system we predicted the existence of many putative new bacteriocins' maturation pathways and some of them were only exclusive to a group of Streptococcus. Computational genomic and proteomic analysis combined to predictive functionnal analysis represent an alternative way for rapid identification of new putative bacteriocins as well as new potential antimicrobial drugs compared to the more traditional methods of drugs discovery using antagonism tests.

  7. Representing properties locally.

    Science.gov (United States)

    Solomon, K O; Barsalou, L W

    2001-09-01

    Theories of knowledge such as feature lists, semantic networks, and localist neural nets typically use a single global symbol to represent a property that occurs in multiple concepts. Thus, a global symbol represents mane across HORSE, PONY, and LION. Alternatively, perceptual theories of knowledge, as well as distributed representational systems, assume that properties take different local forms in different concepts. Thus, different local forms of mane exist for HORSE, PONY, and LION, each capturing the specific form that mane takes in its respective concept. Three experiments used the property verification task to assess whether properties are represented globally or locally (e.g., Does a PONY have mane?). If a single global form represents a property, then verifying it in any concept should increase its accessibility and speed its verification later in any other concept. Verifying mane for PONY should benefit as much from having verified mane for LION earlier as from verifying mane for HORSE. If properties are represented locally, however, verifying a property should only benefit from verifying a similar form earlier. Verifying mane for PONY should only benefit from verifying mane for HORSE, not from verifying mane for LION. Findings from three experiments strongly supported local property representation and ruled out the interpretation that object similarity was responsible (e.g., the greater overall similarity between HORSE and PONY than between LION and PONY). The findings further suggest that property representation and verification are complicated phenomena, grounded in sensory-motor simulations.

  8. Representing and Performing Businesses

    DEFF Research Database (Denmark)

    Boll, Karen

    2014-01-01

    and MacKenzie’s idea of performativity. Based on these two approaches, the article demonstrates that the segmentation model represents and performs the businesses as it makes up certain new ways to be a business and as the businesses can be seen as moving targets. Inspired by MacKenzie the argument......This article investigates a segmentation model used by the Danish Tax and Customs Administration to classify businesses’ motivational postures. The article uses two different conceptualisations of performativity to analyse what the model’s segmentations do: Hacking’s notion of making up people...... is that the segmentation model embodies cleverness in that it simultaneously alters what it represents and then represents this altered reality to confirm the accuracy of its own model of the businesses’ postures. Despite the cleverness of the model, it also has a blind spot. The model assumes a world wherein everything...

  9. Ten Putative Contributors to the Obesity Epidemic

    Science.gov (United States)

    McAllister, Emily J.; Dhurandhar, Nikhil V.; Keith, Scott W.; Aronne, Louis J.; Barger, Jamie; Baskin, Monica; Benca, Ruth M.; Biggio, Joseph; Boggiano, Mary M.; Eisenmann, Joe C.; Elobeid, Mai; Fontaine, Kevin R.; Gluckman, Peter; Hanlon, Erin C.; Katzmarzyk, Peter; Pietrobelli, Angelo; Redden, David T.; Ruden, Douglas M.; Wang, Chenxi; Waterland, Robert A.; Wright, Suzanne M.; Allison, David B.

    2010-01-01

    The obesity epidemic is a global issue and shows no signs of abating, while the cause of this epidemic remains unclear. Marketing practices of energy-dense foods and institutionally-driven declines in physical activity are the alleged perpetrators for the epidemic, despite a lack of solid evidence to demonstrate their causal role. While both may contribute to obesity, we call attention to their unquestioned dominance in program funding and public efforts to reduce obesity, and propose several alternative putative contributors that would benefit from equal consideration and attention. Evidence for microorganisms, epigenetics, increasing maternal age, greater fecundity among people with higher adiposity, assortative mating, sleep debt, endocrine disruptors, pharmaceutical iatrogenesis, reduction in variability of ambient temperatures, and intrauterine and intergenerational effects, as contributing factors to the obesity epidemic are reviewed herein. While the evidence is strong for some contributors such as pharmaceutical-induced weight gain, it is still emerging for other reviewed factors. Considering the role of such putative etiological factors of obesity may lead to comprehensive, cause specific, and effective strategies for prevention and treatment of this global epidemic. PMID:19960394

  10. Diversity of secondary endosymbionts among different putative species of the whitefly Bemisia tabaci.

    Science.gov (United States)

    Bing, Xiao-Li; Ruan, Yong-Ming; Rao, Qiong; Wang, Xiao-Wei; Liu, Shu-Sheng

    2013-04-01

    Endosymbionts are important components of arthropod biology. The whitefly Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is a cryptic species complex composed of ≥ 28 putative species. In addition to the primary endosymbiont Portiera aleyrodidarum, six secondary endosymbionts (S-endosymbionts), Hamiltonella, Rickettsia, Wolbachia, Cardinium, Arsenophonus and Fritschea, have been identified in B. tabaci thus far. Here, we tested five of the six S-endosymbiont lineages (excluding Fritschea) from 340 whitely individuals representing six putative species from China. Hamiltonella was detected only in the two exotic invaders, Middle East-Asia Minor 1 (MEAM1) and Mediterranean (MED). Rickettsia was absent in Asia II 1 and MED, scarce in Asia II 3 (13%), but abundant in Asia II 7 (63.2%), China 1 (84.7%) and MEAM1 (100%). Wolbachia, Cardinium and Arsenophonus were absent in the invasive MEAM1 and MED but mostly abundant in the native putative species. Furthermore, phylogenetic analyses revealed that some S-endosymbionts have several clades and different B. tabaci putative species can harbor different clades of a given S-endosymbiont, demonstrating further the complexity of S-endosymbionts in B. tabaci. All together, our results demonstrate the variation and diversity of S-endosymbionts in different putative species of B. tabaci, especially between invasive and native whiteflies.

  11. Diversity of secondary endosymbionts among different putative species of the whitefly Bemisia tabaci

    Institute of Scientific and Technical Information of China (English)

    Xiao-Li Bing; Yong-Ming Ruan; Qiong Rao; Xiao-Wei Wang; Shu-Sheng Liu

    2013-01-01

    Endosymbionts are important components of arthropod biology.The whitefly Bemisia tabaci (Gennadius) (Hemiptera:Aleyrodidae) is a cryptic species complex composed of≥28 putative species.In addition to the primary endosymbiont Portiera aleyrodidarum,six secondary endosymbionts (S-endosymbionts),Hamiltonella,Rickettsia,Wolbachia,Cardinium,Arsenophonus and Fritschea,have been identified in B.tabaci thus far.Here,we tested five of the six S-endosymbiont lineages (excluding Fritschea) from 340 whitely individuals representing six putative species from China.Hamiltonella was detected only in the two exotic invaders,Middle East-Asia Minor 1 (MEAM 1) and Mediterranean (MED).Rickettsia was absent in Asia Ⅱ 1 and MED,scarce in Asia Ⅱ 3 (13%),but abundant in Asia Ⅱ 7 (63.2%),China 1 (84.7%) and MEAM1 (100%).Wolbachia,Cardinium and Arsenophonus were absent in the invasive MEAM 1 and MED but mostly abundant in the native putative species.Furthermore,phylogenetic analyses revealed that some S-endosymbionts have several clades and different B.tabaci putative species can harbor different clades of a given S-endosymbiont,demonstrating further the complexity of S-endosymbionts in B.tabaci.All together,our results demonstrate the variation and diversity of S-endosymbionts in different putative species ofB.tabaci,especially between invasive and native whiteflies.

  12. Relationship of nanobacteria and hs-CRP in serum in patients with coronary heart disease%冠心病患者血清中纳米细菌与高敏C反应蛋白的关系

    Institute of Scientific and Technical Information of China (English)

    高劲松; 李豫皖; 彭忠; 陈晓泉; 游浩; 李佳森; 杨康; 颜海燕; 王夜明

    2012-01-01

    目的:检测冠心病患者血清中纳米细菌感染率与高敏C反应蛋白(hs-CRP)的浓度,并探讨其临床意义.方法:采用酶联免疫吸附试验(ELISA)检测冠心病组与对照组血清中的纳米细菌抗原,同时用免疫比浊法测定其血清中的hs-CRP,并进行相关性分析.结果:冠心病组血清纳米细菌感染率为27.08%(13/48),与对照组6.25%(3/48)比较,差异有统计学意义(P<0.05).冠心病组hs-CRP浓度(4.81±7.12)mg/L显著高于对照组(0.73±0.80)mg/L,差异有统计学意义(P<0.05).冠心病组血清hs-CRP与纳米细菌血清检测结果呈正相关(r=0.489,P<0.05).结论:冠心病患者血清中的纳米细菌感染率与hs-CRP浓度均升高,二者具有正相关关系.%The infection rate of nanobacterial in the control group was significantly lower than the CHD group ( 6 . 2 5 % vs 27. 08% , P<0. 05). In control group the concentration of hs-CRP was (0. 73 ± 0. 80)mg/L, significantly lower than (4. 81 ±7. 12)mg/L in CHD group (P<0. 05). Correlation analysis showed a positive relationship between nanobacterial infection and serum hs-CRP (r=0. 489, P<0. 05). Conclusion:Both serum nanobacteria and hs-CRP increase in patients with CHD, which show a positive correlation between them.

  13. Establishment nephrolithiasis rat model induced by nanobacteria and analysis of stone formation%纳米细菌大鼠肾结石模型初步建立及成石因素分析

    Institute of Scientific and Technical Information of China (English)

    胡卫国; 王晓峰; 徐涛; 李建兴; 陈亮; 于澄钒; 黄晓波

    2010-01-01

    目的:初步建立纳米细菌(nanobacteria,NB)大鼠肾结石模型,探讨NB与肾结石形成的相关性和成石机制.方法:应用人肾结石患者血清培养NB.SD雄性大鼠30只随机分成NB诱石组(A组,鼠尾静脉注射NB)、NB+四环素组(B组,鼠尾静脉注射NB和胃饲四环素)、空白对照组(C组,鼠尾静脉注射生理盐水),每组各10只.8周后处死大鼠,镜下观察肾组织晶体分布并计数.检测各组大鼠24h尿N-乙酰-β-D-氨基葡萄糖苷酶(Nacetyl-B-D-glucosaminidase,NAG)、乳酸脱氢酶(lactate dehydrogenase,LDH)浓度.结果:A组和B组大鼠肾脏肾小管内产生含钙结晶,Von kossa染色阳性,主要分布于远曲小管和近曲小管,C组大鼠肾组织未见晶体,3组间差异有统计学意义(P=0.033).B组晶体少于A组,有减少趋势.24h尿NAG和LDH浓度在3组间差异有统计学意义(P<0.001).结论:NB通过肾小管上皮细胞损伤机制诱导大鼠肾脏肾小管内产生含钙结晶,参与肾结石形成.四环素通过抗NB机制,可能有抑制结晶形成和肾结石形成作用.

  14. Cultivation and morphology of nanobacteria in sera of patients with kidney calculi%肾结石患者血清中纳米细菌的培养和形态学研究

    Institute of Scientific and Technical Information of China (English)

    陈亮; 黄晓波; 许清泉; 李建兴; 贾晓军; 王晓峰

    2010-01-01

    目的:探讨纳米细菌(nanobacteria,NB)在结石患者血清的感染情况,并对其进行形态学观察和特征描述.方法:采集北京大学人民医院泌尿外科24例行经皮肾镜碎石术治疗的肾结石患者和3例健康志愿者的血清进行NB的培养,应用免疫组织化学、von kossa染色、扫描电镜、透射电镜等方法对培养的NB予以观察和鉴定.结果:经鉴定,24位结石患者中有22例感染NB,而健康志愿者组未见NB感染,结石患者组NB的感染率高于健康对照组.培养4周后,NB在光镜下成球形,直径约100~500nm,能够被免疫组织化学和von kossa染色特异的识别.NB在透射电镜(负染法)下具有"毛刺"状磷灰石外壳、内部为着色较浅的菌体结构,并能够进行出芽繁殖.结论:绝大多数结石患者的血清中可以培养出NB,且阳性率高于健康对照组,这说明它可能与肾结石形成密切相关.免疫组织化学、von kossa染色、扫描电镜、透射电镜都是在不同方面对NB进行检测和鉴定的特异方法.NB的特异形态与特征是它区别于其他纳米颗粒的重要依据.

  15. 108例纳米细菌感染致Ⅲ型前列腺炎的诊断和治疗%Diagnosis and treatment of type Ⅲ prostatitis induced by inflammation of nanobacteria in 108 cases

    Institute of Scientific and Technical Information of China (English)

    袁宇峰; 唐吉元; 沈学成; 周占松

    2011-01-01

    目的 研究纳米细菌所致的Ⅲ型前列腺炎的综合治疗方案并探讨其作用机制.方法 对108例纳米细菌所致的Ⅲ型前列腺炎患者进行抗纳米细菌治疗(主要由四环素加EDTA等药物组成).动态观察治疗前后的前列腺液纳米细菌鉴定、前列腺液常规及NIH-CPSI评分.结果 经过为期3个月的治疗,患者的纳米细菌阳性率、前列腺液卵磷脂小体及NIH-CPSI评分均较治疗前有明显改善.结论 四环素加EDTA等药物对于纳米细菌感染的Ⅲ型前列腺炎安全有效.其机制可能与EDTA先溶解纳米细菌的钙化壳,再发挥四环素的穿透杀菌作用有关.%Objective To research into the diagnosis and treatment of type Ⅲ prostatitis induced by inflammation of nanobacteria ( NB)in 108 cases. Methods A total of 108 patients with type Ⅲ prostatitis induced by NB were treated with anti-nanobacterial therapy which consists of tetracycline and EDTA( ethylene diamine tetraacetic acid) . The identification of NB from prostatic fluid,indexes of expressed prostatic secretions ( EPS) and NIH-CPSI ( national institutes of health-chronic prostatitis symptom index) scores were observed at the beginning and ending of the therapy. Results The positive rate of NB from prostatic fluid,NIH-CPSI scores and lecithine of prostates were improved significantly after the treatment for three months. Conclusion Anti-nanobacterial therapy has desirable effect on type Ⅲ prostatitis induced by NB. Its mechanism may be related with the dissolution effect of EDTA on calcified shells of NB and bactericidal action of tetracycline.

  16. Putative Nitrogen Sensing Systems in Higher Plants

    Institute of Scientific and Technical Information of China (English)

    Hon-Ming Lam; Ying Ann Chiao; Man-Wah Li; Yuk-Kwong Yung; Sang Ji

    2006-01-01

    Nitrogen (N) metabolism is essential for the biosynthesis of vital biomolecules. N status thus exerts profound effects on plant growth and development, and must be closely monitored. In bacteria and fungi, a few sophisticated N sensing systems have been extensively studied. In animals, the ability to receive amino acid signals has evolved to become an integral part of the nervous coordination system. In this review, we will summarize recent developments in the search for putative N sensing systems in higher plants based on homologous systems in bacteria, fungi, and animals. Apparently, although plants have separated and diversified from other organisms during the evolution process, striking similarities can be found in their N sensing systems compared with those of their counterparts; however, our understanding of these systems is still incomplete. Significant modifications of the N sensing systems (including cross-talk with other signal transduction pathways) in higher plants may be a strategy of adaptation to their unique mode of life.

  17. Putative respiratory chain of Porphyromonas gingivalis.

    Science.gov (United States)

    Meuric, Vincent; Rouillon, Astrid; Chandad, Fatiha; Bonnaure-Mallet, Martine

    2010-05-01

    The electron transfer chain in Porphyromonas gingivalis, or periodontopathogens, has not yet been characterized. P. gingivalis, a strict anaerobic bacteria and the second colonizer of the oral cavity, is considered to be a major causal agent involved in periodontal diseases. Primary colonizers create a favorable environment for P. gingivalis growth by decreasing oxygen pressure. Oxygen does not appear to be the final electron acceptor of the respiratory chain. Fumarate and cytochrome b have been implicated as major components of the respiratory activity. However, the P. gingivalis genome shows many other enzymes that could be implicated in aerobic or nitrite respiration. Using bioinformatic tools and literature studies of respiratory pathways, the ATP synthesis mechanism from the sodium cycle and nutrients metabolism, the putative respirasome of P. gingivalis has been proposed.

  18. Putative regulatory factors associated with intramuscular fat content.

    Directory of Open Access Journals (Sweden)

    Aline S M Cesar

    Full Text Available Intramuscular fat (IMF content is related to insulin resistance, which is an important prediction factor for disorders, such as cardiovascular disease, obesity and type 2 diabetes in human. At the same time, it is an economically important trait, which influences the sensorial and nutritional value of meat. The deposition of IMF is influenced by many factors such as sex, age, nutrition, and genetics. In this study Nellore steers (Bos taurus indicus subspecies were used to better understand the molecular mechanisms involved in IMF content. This was accomplished by identifying differentially expressed genes (DEG, biological pathways and putative regulatory factors. Animals included in this study had extreme genomic estimated breeding value (GEBV for IMF. RNA-seq analysis, gene set enrichment analysis (GSEA and co-expression network methods, such as partial correlation coefficient with information theory (PCIT, regulatory impact factor (RIF and phenotypic impact factor (PIF were utilized to better understand intramuscular adipogenesis. A total of 16,101 genes were analyzed in both groups (high (H and low (L GEBV and 77 DEG (FDR 10% were identified between the two groups. Pathway Studio software identified 13 significantly over-represented pathways, functional classes and small molecule signaling pathways within the DEG list. PCIT analyses identified genes with a difference in the number of gene-gene correlations between H and L group and detected putative regulatory factors involved in IMF content. Candidate genes identified by PCIT include: ANKRD26, HOXC5 and PPAPDC2. RIF and PIF analyses identified several candidate genes: GLI2 and IGF2 (RIF1, MPC1 and UBL5 (RIF2 and a host of small RNAs, including miR-1281 (PIF. These findings contribute to a better understanding of the molecular mechanisms that underlie fat content and energy balance in muscle and provide important information for the production of healthier beef for human consumption.

  19. Representing distance, consuming distance

    DEFF Research Database (Denmark)

    Larsen, Gunvor Riber

    to mobility and its social context. Such an understanding can be approached through representations, as distance is being represented in various ways, most noticeably in maps and through the notions of space and Otherness. The question this talk subsequently asks is whether these representations of distance...... are being consumed in the contemporary society, in the same way as places, media, cultures and status are being consumed (Urry 1995, Featherstone 2007). An exploration of distance and its representations through contemporary consumption theory could expose what role distance plays in forming...... are present in theoretical and empirical elaborations on mobility, but these remain largely implicit and unchallenged (Bauman 1998). This talk will endeavour to unmask distance as a theoretical entity by exploring ways in which distance can be understood and by discussing distance through its representations...

  20. CLONING, SEQUENCE ANALYSIS, AND CHARACTERIZATION OF PUTATIVE BETA-LACTAMASE OF STENOTROPHOMONAS MALTOPHILIA

    Directory of Open Access Journals (Sweden)

    Chong Seng Shueh

    2012-10-01

    Full Text Available The main objective of current study was to explore the function of chromosomal putative beta-lactamase gene (smlt 0115 in clinical Stenotrophomonas maltophilia. Antibiotic susceptibility test (AST screening for current antimicrobial drugs was done and Minimum Inhibitory Concentration (MIC level towards beta-lactams was determined by E-test. Putative beta-lactamase gene of S. maltophilia was amplified via PCR, with specific primers, then cloned into pET-15 expression plasmid and transformed into Escherichia coli BL21. The gene was sequenced and analyzed. The expressed protein was purified by affinity chromatography and the kinetic assay was performed. S. maltophilia ATCC 13637 was included in this experiment. Besides, a hospital strain which exhibited resistant to a series of beta-lactams including cefepime was identified via AST and MIC, hence it was named as S2 strain and was considered in this study. Sequencing result showed that putative beta-lactamase gene obtained from ATCC 13637 and S2 strains were predicted to have cephalosporinase activity by National Center for Biotechnology Information (NCBI blast program. Differences in the sequences of both ATCC 13637 and S2 strains were found via ClustalW alignment software. Kinetic assay proved a cephalosporinase characteristic produced by E. coli BL21 clone that overexpressed the putative beta-lactamase gene cloned under the control of an external promoter. Yet, expressed protein purified from S2 strain had high catalytic activity against beta-lactam antibiotics which was 14-fold higher than expressed protein purified from ATCC 13637 strain. This study represents the characterization analysis of putative beta-lactamase gene (smlt 0115 of S. maltophilia. The presence of the respective gene in the chromosome of S. maltophilia suggested that putative beta-lactamase gene (smlt 0115 of S. maltophilia plays a role in beta-lactamase resistance.

  1. Representativity of TMA studies.

    Science.gov (United States)

    Sauter, Guido

    2010-01-01

    The smaller the portion of a tumor sample that is analyzed becomes, the higher is the risk of missing important histological or molecular features that might be present only in a subset of tumor cells. Many researchers have, therefore, suggested using larger tissue cores or multiple cores from the same donor tissue to enhance the representativity of TMA studies. However, numerous studies comparing the results of TMA studies with the findings from conventional large sections have shown that all well-established associations between molecular markers and tumor phenotype or patient prognosis can be reproduced with TMAs even if only one single 0.6 mm tissue spot is analyzed. Moreover, the TMA technology has proven to be superior to large section analysis in finding new clinically relevant associations. The high number of samples that are typically included in TMA studies, and the unprecedented degree of standardization during TMA experiments and analysis often give TMA studies an edge over traditional large-section studies.

  2. Putative bronchopulmonary flagellated protozoa in immunosuppressed patients.

    Science.gov (United States)

    Kilimcioglu, Ali Ahmet; Havlucu, Yavuz; Girginkardesler, Nogay; Celik, Pınar; Yereli, Kor; Özbilgin, Ahmet

    2014-01-01

    Flagellated protozoa that cause bronchopulmonary symptoms in humans are commonly neglected. These protozoal forms which were presumed to be "flagellated protozoa" have been previously identified in immunosuppressed patients in a number of studies, but have not been certainly classified so far. Since no human cases of bronchopulmonary flagellated protozoa were reported from Turkey, we aimed to investigate these putative protozoa in immunosuppressed patients who are particularly at risk of infectious diseases. Bronchoalveolar lavage fluid samples of 110 immunosuppressed adult patients who were admitted to the Department of Chest Diseases, Hafsa Sultan Hospital of Celal Bayar University, Manisa, Turkey, were examined in terms of parasites by light microscopy. Flagellated protozoal forms were detected in nine (8.2%) of 110 cases. Metronidazole (500 mg b.i.d. for 30 days) was given to all positive cases and a second bronchoscopy was performed at the end of the treatment, which revealed no parasites. In conclusion, immunosuppressed patients with bronchopulmonary symptoms should attentively be examined with regard to flagellated protozoa which can easily be misidentified as epithelial cells.

  3. The Biogeography of Putative Microbial Antibiotic Production.

    Directory of Open Access Journals (Sweden)

    Hélène Morlon

    Full Text Available Understanding patterns in the distribution and abundance of functional traits across a landscape is of fundamental importance to ecology. Mapping these distributions is particularly challenging for species-rich groups with sparse trait measurement coverage, such as flowering plants, insects, and microorganisms. Here, we use likelihood-based character reconstruction to infer and analyze the spatial distribution of unmeasured traits. We apply this framework to a microbial dataset comprised of 11,732 ketosynthase alpha gene sequences extracted from 144 soil samples from three continents to document the spatial distribution of putative microbial polyketide antibiotic production. Antibiotic production is a key competitive strategy for soil microbial survival and performance. Additionally, novel antibiotic discovery is highly relevant to human health, making natural antibiotic production by soil microorganisms a major target for bioprospecting. Our comparison of trait-based biogeographical patterns to patterns based on taxonomy and phylogeny is relevant to our basic understanding of microbial biogeography as well as the pressing need for new antibiotics.

  4. Mechanosensory neurons, cutaneous mechanoreceptors, and putative mechanoproteins.

    Science.gov (United States)

    Del Valle, M E; Cobo, T; Cobo, J L; Vega, J A

    2012-08-01

    The mammalian skin has developed sensory structures (mechanoreceptors) that are responsible for different modalities of mechanosensitivity like touch, vibration, and pressure sensation. These specialized sensory organs are anatomically and functionally connected to a special subset of sensory neurons called mechanosensory neurons, which electrophysiologically correspond with Aβ fibers. Although mechanosensory neurons and cutaneous mechanoreceptors are rather well known, the biology of the sense of touch still remains poorly understood. Basically, the process of mechanosensitivity requires the conversion of a mechanical stimulus into an electrical signal through the activation of ion channels that gate in response to mechanical stimuli. These ion channels belong primarily to the family of the degenerin/epithelium sodium channels, especially the subfamily acid-sensing ion channels, and to the family of transient receptor potential channels. This review compiles the current knowledge on the occurrence of putative mechanoproteins in mechanosensory neurons and mechanoreceptors, as well as the involvement of these proteins on the biology of touch. Furthermore, we include a section about what the knock-out mice for mechanoproteins are teaching us. Finally, the possibilities for mechanotransduction in mechanoreceptors, and the common involvement of the ion channels, extracellular membrane, and cytoskeleton, are revisited.

  5. A new putative alphapartitivirus recovered from the powdery mildew fungus Erysiphe palczewskii.

    Science.gov (United States)

    Xiong, Guihong; Qiu, Ping; Li, Cong; Chen, Zhuo; Islam, Saif Ul; Fang, Shouguo; Wu, Zujian; Zhang, Songbai; Du, Zhenguo

    2017-02-27

    Two double-stranded RNAs (dsRNA) likely representing the genome of a novel alphapartitivirus which we provisionally named Erysiphe palczewskii alphapartitivirus 1 (EpV1) were recovered from the powdery mildew fungus E. palczewskii infecting Sophora japonica in Jingzhou, Hubei province of China. The two dsRNAs, 1955 (dsRNA1) and 1917 (dsRNA2) bp in size, respectively, each contains a single open reading frame (ORF) encoding a 585- and 528-aa protein, respectively. The 585-aa protein contains a conserved RNA-dependent RNA polymerase (RdRp) domain and shows significant homology to RdRps of approved or putative partitiviruses, particularly those belonging to the genus Alphapartitivirus. However, it shares an aa sequence identity lower than 80% with its closest relative, the RdRp of the putative alphapartitivirus Grapevine partitivirus, and lower than 60% with the RdRps of other partitiviruses. In a phylogenetic tree constructed with RdRp aa sequences of selected partitiviruses, the putative virus EpV1 clustered with Grapevine partitivirus and formed a well-supported monophyletic clade with known or putative alphapartitiviruses.

  6. Phosphoglycerate Dehydrogenase: Potential Therapeutic Target and Putative Metabolic Oncogene

    Directory of Open Access Journals (Sweden)

    Cheryl K. Zogg

    2014-01-01

    Full Text Available Exemplified by cancer cells’ preference for glycolysis, for example, the Warburg effect, altered metabolism in tumorigenesis has emerged as an important aspect of cancer in the past 10–20 years. Whether due to changes in regulatory tumor suppressors/oncogenes or by acting as metabolic oncogenes themselves, enzymes involved in the complex network of metabolic pathways are being studied to understand their role and assess their utility as therapeutic targets. Conversion of glycolytic intermediate 3-phosphoglycerate into phosphohydroxypyruvate by the enzyme phosphoglycerate dehydrogenase (PHGDH—a rate-limiting step in the conversion of 3-phosphoglycerate to serine—represents one such mechanism. Forgotten since classic animal studies in the 1980s, the role of PHGDH as a potential therapeutic target and putative metabolic oncogene has recently reemerged following publication of two prominent papers near-simultaneously in 2011. Since that time, numerous studies and a host of metabolic explanations have been put forward in an attempt to understand the results observed. In this paper, I review the historic progression of our understanding of the role of PHGDH in cancer from the early work by Snell through its reemergence and rise to prominence, culminating in an assessment of subsequent work and what it means for the future of PHGDH.

  7. Ⅲ型前列腺炎患者前列腺液中纳米细菌的培养和形态学鉴定%Identification of the nanobacteria in prostatic fluid of CPPS

    Institute of Scientific and Technical Information of China (English)

    沈学成; 洪理; 饶贤才; 宋波; 周占松

    2008-01-01

    Objective To identify the nanobaeteria in prostate fluid of patients with CPPS.Methods Expressed prostatic secretion(EPS)and urine specimens were collected by Meares-Stamey way from CPPS patients(n=100)and normal controls(n=100).The specimens were cultured and nanobacteria was identified by indirect immunofluoreseenee staining with rnonoelonal antibody.The morphological features were observed by using transmission electron microscopy(TEM). Results The positive rate of nanobaeteria in the EPS cdture of CPPS patients and controls were 43% and 5% respectively,with significant statistical difference(X2=39.58,P<0.01).By TEM,the sizes of NB ranged from 100 to 500 nm and appeared eoccoid-ccccobacillary shape. Conclusion Nanobaeteria infection may exist in EPS of CPPS patients.%目的 探索纳米细菌在Ⅲ型前列腺炎(CPPS)患者前列腺液中的分布情况和微生物学特性及其在Ⅲ型前列腺炎发病中的意义. 方法门诊根据病史、尿常规细菌培养、前列腺液常规镜检结果筛选出CPPS患者100例作为试验对象,年龄26~48岁,平均36岁;选择100例健康成年男性作为正常对照组,年龄21~46岁,平均32岁.按照Mearea-Stamey法收集前列腺液,细胞培养方法进行纳米细菌培养,观察其生长情况;单克隆抗体间接免疫荧光染色进行纳米细菌鉴定,并在透射电镜下观察其形态特征.结果 CPPS患者前列腺液标本中发现纳米细菌生长43例,正常对照组仅5例,2组纳米细菌阳性率比较差异有统计学意义(X2=39.58,P<0.01);透射电镜下观察,纳米细菌呈球状或球棒状,大小100~500 nm,绝大多数聚集成簇,菌体周围有一层黑色物质包绕,并有羟基磷灰石分布.结论 纳米细菌与Ⅲ型前列腺炎发病密切相关.

  8. 纳米细菌促进乳腺癌细胞MDA-MB-231凋亡%Nanobacteria promotes apoptosis in breast cancer cell line MDA-MB-231

    Institute of Scientific and Technical Information of China (English)

    刘胜男; 张德纯; 张名均; 郭亚楠; 杨晓容; 许舸

    2013-01-01

    目的 观察纳米细菌(nanobacteria,NB)与纳米羟基磷灰石颗粒(nano hydroxyapatite,nHAP)对乳腺癌MDA-MB-231细胞的影响.方法 实验分为NB组、nHAP组和正常对照组,其中NB组和nHAP组悬液的浓度均为2麦氏浊度(M),正常对照组仅加培养基,与乳腺癌MDA-MB-231细胞共同培养24、48、72 h,通过CCK-8检测其对细胞的毒性作用;培养12、24、48、72 h,取上清,经全自动生化分析仪测定LDH活性;作用72 h,经流式细胞仪(flow cytometry,FCM)测定其凋亡率,透射电镜观察其超微结构的变化情况.结果 CCK-8显示,NB组24、48、72 h对细胞的抑制作用均强于nHAP组和正常对照组,差异有统计学意义(P<0.01);NB组LDH含量在24、48、72 h时均高于正常对照组,差异均有统计学意义(P <0.05);24、48、72 h均高于nHA组,但仅24、48 h有统计学差异(P<0.05).nHAP组LDH活性仅在72 h与正常对照组比较有统计学差异(P <0.01);72 h后NB组细胞凋亡率高于nHAP组,差异有统计学意义(P<0.01);透射电镜下观察,NB组可以看到胞质空泡样变,核固缩以及明显的凋亡小体,nHAP组未见明显异常.结论 NB可以抑制乳腺癌细胞的生长,促进其发生凋亡,其导致细胞凋亡的成分不仅仅是NB羟基磷灰石的外壳,也可能与NB的其他组分或代谢产物有关.

  9. The cytotoxic effect of nanobacteria on human osteoblast cells%纳米细菌对人成骨细胞C3H10的细胞毒作用

    Institute of Scientific and Technical Information of China (English)

    张名均; 傅长虹; 张德纯

    2015-01-01

    目的 比较纳米细菌(nanobacteria,NB)与羟基磷灰石(hydroxyapatite,HA)对成骨细胞的细胞毒作用,进一步探讨引起细胞毒作用的机制.方法 实验分为正常对照组、HA组、NB组,其中HA组和NB组悬液浓度均为2麦氏浊度(M),对照组只加培养基,分别作用成骨细胞,通过CCK-8试剂盒检测其对细胞的增殖抑制作用;采用Hoechest33258荧光染色和Annexin V-FITC/PC双标法流式细胞仪(flow cotymetry)检测细胞凋亡率;倒置显微镜和透射电镜观察细胞形态的变化;Western blot法检测钙化相关蛋白BMP-2、凋亡相关蛋白Bax的表达.结果 CCK-8结果显示:NB对人成骨细胞C3H10有细胞增殖抑制作用,而HA则没有.Hoechst33258荧光染色和双标法流式细胞仪结果显示:NB对人成骨细胞C3H10主要通过促进细胞凋亡发挥细胞毒作用,而HA对人成骨细胞C3H10无细胞毒性作用.在倒置显微镜下观察,作用48 h后的人成骨细胞C3H10形态无明显变化.透射电镜结果显示:NB可引起人成骨细胞C3H10发生凋亡,出现凋亡小体;而HA组和对照组无明显变化.Western blot结果显示:NB组的钙化相关蛋白BMP-2和凋亡相关蛋白Bax均高于对照组;而HA组和对照组比较,HA组钙化相关蛋白BMP-2高于对照组,而凋亡相关蛋白Bax无明显变化.结论 与对照组比较,纳米细菌能引起人成骨细胞C3H10细胞毒性作用,主要是通过促进细胞凋亡发挥细胞毒作用,能促进钙化相关蛋白BMP-2的表达,凋亡相关蛋白Bax的表达升高也预示着纳米细菌可促进细胞发生凋亡;而羟基磷灰石对人成骨细胞C3H10无细胞毒性作用,可促进钙化相关蛋白BMP-2的表达,但不能促进人成骨细胞C3H10发生凋亡.

  10. Effect of nanobacteria on cell damage and crystal retention in renal tubular epithelial cells%纳米细菌对肾小管上皮细胞的损伤及晶体滞留的影响

    Institute of Scientific and Technical Information of China (English)

    于澄钒; 黄晓波; 陈亮; 许清泉; 胡卫国; 王晓峰

    2010-01-01

    目的:研究纳米细菌(nanobacteria,NB)对HK-2细胞的损伤作用及机制,并探讨损伤后细胞与一水草酸钙(calcium oxalate monohydrate,COM)晶体粘附性的变化.方法:应用肾结石患者血清培养NB,免疫组化法对NB进行鉴定.实验分为4组:空白对照组、NB组、纳米级羟基磷灰石(nanograde hydroxuapatite,nHAP)组和COM组.HK-2细胞与各组作用物共同培养12、24h后进行形态学观察;培养6、12、24h后取培养液进行过氧化氢(H2O2)、LDH、MDA含量测定,消化细胞并超声粉碎后进行Na+/K+及Ca2+/Mg2+ATP酶活性的测定;培养6、12、24h后各组分别加入COM晶体,利用异硫氰酸荧光素-鬼笔环肽进行细胞荧光染色,于激光共聚焦显微镜下观察细胞与COM晶体的粘附情况.结果:NB组、nHAP组12h后出现细胞形态改变,刷状缘排列紊乱,胞浆、胞核松散,空泡形成;24h后线粒体肿胀,部分细胞核膜溶解、核仁消失,NB组核膜溶解细胞数量多于nHAP组.NB组12、24h H2O2含量高于空白对照组、nHAP组,6、24h MDA含量高于空白对照组、nHAP组,但NB组各时间点LDH含量与空白对照组、nHAP组无明显差异.Na+/K+ATP酶活性在12h后,NB组、nHAP组低于空白对照组,24h后,仅NB组低于空白对照组;Ca2+/Mg2+ATP酶活性在12h后,NB组、nHAP组低于空白对照组,24h后仅NB组低于空白对照组.12h后,NB组粘附COM晶体数量较前增多,而COM组还可见到部分晶体已进入细胞内;24h后,NB组与COM组晶体粘附情况与12h相近.空白对照组与nHAP组未观察到细胞与显著数量的COM晶体粘附.结论:NB对共同培养的HK-2细胞造成损伤,损伤程度随作用时间加长而加重,并强于nHAP,损伤过程中有脂质过氧化反应参与.NB损伤细胞后,细胞的晶体粘附性明显增强,随损伤作用时间的延长,细胞与一水草酸钙晶体的粘附量也会相应地增加;nHAP损伤细胞后未对细胞的晶体粘附性产生显著影响.

  11. Nanobacteria-like particles: a threat to cell cultures Partículas semelhantes à nanobactérias: uma ameaça às culturas de células

    Directory of Open Access Journals (Sweden)

    Amauri Braga Simonetti

    2007-03-01

    Full Text Available The main goal of this study is to alert researchers who work with cell cultures for the risk of contamination by structures called nanobacteria (NB. NB are tiny structures with size varying from 80 to 500 nm, commonly occurring in clusters and producing a biofilm which contains carbonate or hydroxyl apatite. The most likely source of cell culture contamination by such organisms is serum used as supplement in culture media. The presence of NB leads to a progressive culture deterioration with accumulation of granules (probably phagocytized NB in cytoplasmic vacuoles, an increasing number of dead cells in the supernatant and degeneration of cells that remained attached to the bottom of the vessel. NB can also be found in culture supernatants where they are found in clusters with variable size and displaying brownian movement. In this study, 19 cell lineages, 8 batches of sera and 1 batch of growth supplement from different sources were analyzed. Samples from sera were cultured in Eagle's Minimum Essential Medium (E-MEM or incubated directly at 37ºC. Tests carried out to detect the presence of extracellular bacteria, Mycoplasma sp and viruses were all negative. Analysis by scanning electron microscopy (SEM revealed tiny oval structures less than 500 nm in size, isolated or in small groups, in all material analyzed except in one fetal bovine serum batch.O principal objetivo deste estudo é alertar aos pesquisadores que trabalham com cultivos celulares sobre o risco de contaminação por estruturas denominadas nanobactérias (NB. NB são estruturas muito pequenas cujo tamanho varia de 80 a 500 nm e que comumente ocorrem em agrupamentos, produzindo biofilme de carbonato ou hidroxiapatita. A fonte mais provável de contaminação dos cultivos celulares por tais organismos é o soro utilizado como suplemento nos meios de cultura. A presença de NB leva a uma progressiva deterioração do cultivo com acúmulo de grânulos (provavelmente NB fagocitadas em

  12. Comprehensive Phenotyping in Multiple Sclerosis: Discovery Based Proteomics and the Current Understanding of Putative Biomarkers

    Directory of Open Access Journals (Sweden)

    Kevin C. O’Connor

    2006-01-01

    Full Text Available Currently, there is no single test for multiple sclerosis (MS. Diagnosis is confirmed through clinical evaluation, abnormalities revealed by magnetic resonance imaging (MRI, and analysis of cerebrospinal fluid (CSF chemistry. The early and accurate diagnosis of the disease, monitoring of progression, and gauging of therapeutic intervention are important but elusive elements of patient care. Moreover, a deeper understanding of the disease pathology is needed, including discovery of accurate biomarkers for MS. Herein we review putative biomarkers of MS relating to neurodegeneration and contributions to neuropathology, with particular focus on autoimmunity. In addition, novel assessments of biomarkers not driven by hypotheses are discussed, featuring our application of advanced proteomics and metabolomics for comprehensive phenotyping of CSF and blood. This strategy allows comparison of component expression levels in CSF and serum between MS and control groups. Examination of these preliminary data suggests that several CSF proteins in MS are differentially expressed, and thus, represent putative biomarkers deserving of further evaluation.

  13. Putative Corneal Neuralgia Responding to Vitamin D Supplementation

    Directory of Open Access Journals (Sweden)

    Eric L. Singman

    2013-09-01

    Full Text Available A patient with putative corneal neuralgia was incidentally discovered to have hypovitaminosis D. Supplementation of vitamin D appears to have led to a resolution of the patient's pain, whereas other efforts to treat the patient were unsuccessful.

  14. Genomic identification of a putative circadian system in the cladoceran crustacean Daphnia pulex

    Science.gov (United States)

    Tilden, Andrea R.; McCoole, Matthew D.; Harmon, Sarah M.; Baer, Kevin N.; Christie, Andrew E.

    2011-01-01

    Essentially nothing is known about the molecular underpinnings of crustacean circadian clocks. The genome of Daphnia pulex, the only crustacean genome available for public use, provides a unique resource for identifying putative circadian proteins in this species. Here, the Daphnia genome was mined for putative circadian protein genes using Drosophila melanogaster queries. The sequences of core clock (e.g. CLOCK, CYCLE, PERIOD, TIMELESS and CRYPTOCHROME 2), clock input (CRYPTOCHROME 1) and clock output (PIGMENT DISPERSING HORMONE RECEPTOR) proteins were deduced. Structural analyses and alignment of the Daphnia proteins with their Drosophila counterparts revealed extensive sequence conservation, particularly in functional domains. Comparisons of the Daphnia proteins with other sequences showed that they are, in most cases, more similar to homologs from other species, including vertebrates, than they are to those of Drosophila. The presence of both CRYPTOCHROME 1 and 2 in Daphnia suggests the organization of its clock may be more similar to that of the butterfly Danaus plexippus than to that of Drosophila (which possesses CRYPTOCHROME 1 but not CRYPTOCHROME 2). These data represent the first description of a putative circadian system from any crustacean, and provide a foundation for future molecular, anatomical and physiological investigations of circadian signaling in Daphnia. PMID:21798832

  15. Genetic diversity of bovine papillomavirus types, including two putative new types, in teat warts from dairy cattle herds.

    Science.gov (United States)

    Lunardi, Michele; de Camargo Tozato, Claudia; Alfieri, Alice Fernandes; de Alcântara, Brígida Kussumoto; Vilas-Boas, Laurival Antonio; Otonel, Rodrigo Alejandro Arellano; Headley, Selwyn Arlington; Alfieri, Amauri Alcindo

    2016-06-01

    Teat papillomatosis affects dairy cows worldwide. Milking can become difficult due to teat warts, and maintaining affected cows in the herds may diminish economic profit in the dairy industry. Currently, 13 bovine papillomavirus (BPV) types have been fully characterized, and numerous putative BPV types have been identified through partial L1 gene PCR. In order to identify the viral types present in warts on the udders of dairy cows, 40 teat lesions from 24 cows from 13 cattle farms in three States of Brazil were evaluated by PV L1 gene PCR. The warts that were evaluated contained sequences from BPVs 6-10, the putative BPV types BAPV9 and BAPV4, and two unreported putative papillomavirus (PV) types, named BPV/BR-UEL6 and BPV/BR-UEL7. In addition, mixed infections and coinfections were identified, since more than one lesion was observed on the udders of 13 cows. Phylogenetic analysis showed that BPV/BR-UEL6 is closely related to BPVs belonging to the genus Xipapillomavirus, while BPV/BR-UEL7 clustered with the previously reported strains Cervus timorensis and Pudu puda PVs, which represent a putative new PV type, and it was only distantly related to xi-, epsilon-, delta- and dyoxi-PVs. These results provide information that will assist in the understanding of the association of BPVs 6, 7, 8, 9, and 10, as well as putative BPV types BAPV4 and BAPV9, with mammary papillomatosis. This is the first characterization of putative novel PV types BPV/BR-UEL6 and BPV/BR-UEL7 in teat warts of dairy cows, highlighting the high genetic diversity of BPVs associated with teat papillomatosis.

  16. Small-fragment genomic libraries for the display of putative epitopes from clinically significant pathogens.

    Science.gov (United States)

    Henics, T; Winkler, B; Pfeifer, U; Gill, S R; Buschle, M; von Gabain, A; Meinke, A L

    2003-07-01

    Taking advantage of whole genome sequences of bacterial pathogens in many thriving diseases with global impact, we developed a comprehensive screening procedure for the identification of putative vaccine candidate antigens. Importantly, this procedure relies on highly representative small-fragment genomic libraries that are expressed to display frame-selected epitope-size peptides on a bacterial cell surface and to interact directly with carefully selected disease-relevant high-titer sera. Here we describe the generation of small-fragment genomic libraries of Gram-positive and Gram-negative clinically significant pathogens, including Staphylococcus aureus and Staphylococcus epidermidis, Streptococcus pyogenes, Streptococcus agalactiae, and Streptococcus pneumoniae, Enterococcus faecalis, Helicobacter pylori, Chlamydia pneumoniae, the enterotoxigenic Escherichia coli, and Campylobacter jejuni. Large-scale sequencing revealed that the libraries, which provide an average of 20-fold coverage, were random and, as demonstrated with two S. aureus libraries, highly representative. Consistent with the comprehensive nature of this approach is the identification of epitopes that reside in both annotated and putatively novel open reading frames. The use of these libraries therefore allows for the rapid and direct identification of immunogenic epitopes with no apparent bias or difficulty that often associate with conventional expression methods.

  17. A putative viral defence mechanism in archaeal cells

    DEFF Research Database (Denmark)

    Lillestøl, Reidun K; Redder, Peter; Garrett, Roger Antony

    2006-01-01

    in cells, and that both the mode of inhibition of viral propagation and the mechanism of adding spacer-repeat units to clusters, are dependent on RNAs transcribed from the clusters. Moreover, the putative inhibitory apparatus (piRNA-based) may be evolutionarily related to the interference RNA systems (si...

  18. Putative Lineage of Novel African Usutu Virus, Central Europe

    Centers for Disease Control (CDC) Podcasts

    2015-10-15

    Sarah Gregory reads an abridged version of "Putative Lineage of Novel African Usutu Virus, Central Europe.".  Created: 10/15/2015 by National Center for Emerging and Zoonotic Infectious Diseases (NCEZID).   Date Released: 10/15/2015.

  19. Putative golden proportions as predictors of facial esthetics in adolescents.

    NARCIS (Netherlands)

    Kiekens, R.M.A.; Kuijpers-Jagtman, A.M.; Hof, M.A. van 't; Hof, BE van 't; Maltha, J.C.

    2008-01-01

    INTRODUCTION: In orthodontics, facial esthetics is assumed to be related to golden proportions apparent in the ideal human face. The aim of the study was to analyze the putative relationship between facial esthetics and golden proportions in white adolescents. METHODS: Seventy-six adult laypeople

  20. Marc Treib: Representing Landscape Architecture

    DEFF Research Database (Denmark)

    Braae, Ellen Marie

    2008-01-01

    The editor of Representing Landscape Architecture, Marc Treib, argues that there is good reason to evaluate the standard practices of representation that landscape architects have been using for so long. In the rush to the promised land of computer design these practices are now in danger of being...... left by the wayside. The 14 often both fitting and well crafted contributions of this publication offer an approach to how landscape architecture has been and is currently represented; in the design study, in presentation, in criticism, and in the creation of landscape architecture....

  1. Representative process sampling - in practice

    DEFF Research Database (Denmark)

    Esbensen, Kim; Friis-Pedersen, Hans Henrik; Julius, Lars Petersen

    2007-01-01

    Didactic data sets representing a range of real-world processes are used to illustrate "how to do" representative process sampling and process characterisation. The selected process data lead to diverse variogram expressions with different systematics (no range vs. important ranges; trends and....../or periodicity; different nugget effects and process variations ranging from less than one lag to full variogram lag). Variogram data analysis leads to a fundamental decomposition into 0-D sampling vs. 1-D process variances, based on the three principal variogram parameters: range, sill and nugget effect...

  2. Further insight into reproductive incompatibility between putative cryptic species of the Bemisia tabaci whitefly complex.

    Science.gov (United States)

    Qin, Li; Pan, Li-Long; Liu, Shu-Sheng

    2016-04-01

    The whitefly Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae), with its global distribution and extensive genetic diversity, is now known to be a complex of over 35 cryptic species. However, a satisfactory resolution of the systematics of this species complex is yet to be achieved. Here, we designed experiments to examine reproductive compatibility among species with different levels of mitochondrial cytochrome oxidase I (mtCOI) divergence. The data show that putative species with mtCOI divergence of >8% between them consistently exhibited complete reproductive isolation. However, two of the putative species, Asia II 9 and Asia II 3, with mtCOI divergence of 4.47% between them, exhibited near complete reproductive compatibility in one direction of their cross, and partial reproductive compatibility in the other direction. Together with some recent reports on this topic from the literature, our data indicates that, while divergence in the mtCOI sequences provides a valid molecular marker for species delimitation in most clades, more genetic markers and more sophisticated molecular phylogeny will be required to achieve adequate delimitation of all species in this whitefly complex. While many attempts have been made to examine the reproductive compatibility among genetic groups of the B. tabaci complex, our study represents the first effort to conduct crossing experiments with putative species that were chosen with considerations of their genetic divergence. In light of the new data, we discuss the best strategy and protocols to conduct further molecular phylogenetic analysis and crossing trials, in order to reveal the overall pattern of reproductive incompatibility among species of this whitefly complex.

  3. Putative melatonin receptors in a human biological clock

    Energy Technology Data Exchange (ETDEWEB)

    Reppert, S.M.; Weaver, D.R.; Rivkees, S.A.; Stopa, E.G.

    1988-10-07

    In vitro autoradiography with /sup 125/I-labeled melatonin was used to examine melatonin binding sites in human hypothalamus. Specific /sup 125/I-labeled melatonin binding was localized to the suprachiasmatic nuclei, the site of a putative biological clock, and was not apparent in other hypothalamic regions. Specific /sup 125/I-labeled melatonin binding was consistently found in the suprachiasmatic nuclei of hypothalami from adults and fetuses. Densitometric analysis of competition experiments with varying concentrations of melatonin showed monophasic competition curves, with comparable half-maximal inhibition values for the suprachiasmatic nuclei of adults (150 picomolar) and fetuses (110 picomolar). Micromolar concentrations of the melatonin agonist 6-chloromelatonin completely inhibited specific /sup 125/I-labeled melatonin binding, whereas the same concentrations of serotonin and norepinephrine caused only a partial reduction in specific binding. The results suggest that putative melatonin receptors are located in a human biological clock.

  4. Trypanosoma brucei: a putative RNA polymerase II promoter.

    Science.gov (United States)

    Bayele, Henry K

    2009-12-01

    RNA polymerase II (pol II) promoters are rare in the African trypanosome Trypanosoma brucei because gene regulation in the parasite is complex and polycistronic. Here, we describe a putative pol II promoter and its structure-function relationship. The promoter has features of an archetypal eukaryotic pol II promoter including putative canonical CCAAT and TATA boxes, and an initiator element. However, the spatial arrangement of these elements is only similar to yeast pol II promoters. Deletion mapping and transcription assays enabled delineation of a minimal promoter that could drive orientation-independent reporter gene expression suggesting that it may be a bidirectional promoter. In vitro transcription in a heterologous nuclear extract revealed that the promoter can be recognized by the basal eukaryotic transcription complex. This suggests that the transcription machinery in the parasite may be very similar to those of other eukaryotes.

  5. Chromosomal Abnormalities and Putative Susceptibility Genes in Autism Spectrum Disorders

    DEFF Research Database (Denmark)

    Nielsen, Mette Gilling

    Autism spectrum disorders (ASDs) is a heterogeneous group of neurodevelopmental disorders with a significant genetic component as shown by family and twin studies. However, only a few genes have repeatedly been shown to be involved in the development of ASDs. The aim of this study has been...... to identify possible ASD susceptibility genes. Genome screens in ASD patients suggest possible susceptibility gene regions on almost every chromosome. We identified four ASD patients with chromosomal rearrangements, two of which were familial rearrangements involving one of these putative susceptibility gene......) was performed for all four patients. By combination of these methods we identified several putative susceptibility genes for ASDs. Expression patterns were established for several of these genes by Quantitative PCR (Q-PCR) or in situ hybridization and one gene was sequenced in 157 ASD patients. Our results...

  6. Cloning of partial putative gonadotropin hormone receptor sequence from fish

    Indian Academy of Sciences (India)

    G Kumaresan; T Venugopal; A Vikas; T J Pandian; S M Athavan

    2000-03-01

    A search for the presence of mariner-like elements in the Labeo rohita genome by polymerase chain reaction led to the amplification of a partial DNA sequence coding for a putative transmembrane domain of gonadotropin hormone receptor. The amplified DNA sequence shows a high degree of homology to the available turkey and human luteinizing and follicle stimulating hormone receptor coding sequences. This is the first report on cloning such sequences of piscine origin.

  7. A putative role for apelin in the etiology of obesity.

    Science.gov (United States)

    Rayalam, Srujana; Della-Fera, Mary Anne; Krieg, Paul A; Cox, Christopher M; Robins, Allan; Baile, Clifton A

    2008-04-11

    Apelin, the endogenous ligand of the G protein-coupled APJ receptor has been shown to promote tumor angiogenesis. However, the effect of apelin on inducing angiogenesis in adipose tissue has not been investigated. In this review, we propose a putative role for apelin in promoting angiogenesis in adipose tissue. We further propose that targeting adipose tissue vasculature by blocking apelin signaling with anti-apelin antibodies will lead not only to inhibition of angiogenesis in adipose tissue but also to decreased adiposity.

  8. Representative process sampling - in practice

    DEFF Research Database (Denmark)

    Esbensen, Kim; Friis-Pedersen, Hans Henrik; Julius, Lars Petersen

    2007-01-01

    /or periodicity; different nugget effects and process variations ranging from less than one lag to full variogram lag). Variogram data analysis leads to a fundamental decomposition into 0-D sampling vs. 1-D process variances, based on the three principal variogram parameters: range, sill and nugget effect......Didactic data sets representing a range of real-world processes are used to illustrate "how to do" representative process sampling and process characterisation. The selected process data lead to diverse variogram expressions with different systematics (no range vs. important ranges; trends and...... presented cases of variography either solved the initial problems or served to understand the reasons and causes behind the specific process structures revealed in the variograms. Process Analytical Technologies (PAT) are not complete without process TOS....

  9. Judgments of and by Representativeness

    Science.gov (United States)

    1981-05-15

    probably agree that John Updike is a more representative American writer than Norman Mailer. rlearly, such a judgment does not have a frequentistic...example, in an early study we presented people with the following description, " John is 27 years old, with an outgoing personality. At college he was an...outstanding athlete but did not show much ability or interest in in- tellectual matters". We found that John was judged to be more likely to be "a gym

  10. Characterization of putative multidrug resistance transporters of the major facilitator-superfamily expressed in Salmonella Typhi.

    Science.gov (United States)

    Shaheen, Aqsa; Ismat, Fouzia; Iqbal, Mazhar; Haque, Abdul; De Zorzi, Rita; Mirza, Osman; Walz, Thomas; Rahman, Moazur

    2015-05-01

    Multidrug resistance mediated by efflux pumps is a well-known phenomenon in infectious bacteria. Although much work has been carried out to characterize multidrug efflux pumps in Gram-negative and Gram-positive bacteria, such information is still lacking for many deadly pathogens. The aim of this study was to gain insight into the substrate specificity of previously uncharacterized transporters of Salmonella Typhi to identify their role in the development of multidrug resistance. S. Typhi genes encoding putative members of the major facilitator superfamily were cloned and expressed in the drug-hypersensitive Escherichia coli strain KAM42, and tested for transport of 25 antibacterial compounds, including representative antibiotics of various classes, antiseptics, dyes and detergents. Of the 15 tested putative transporters, STY0901, STY2458 and STY4874 exhibited a drug-resistance phenotype. Among these, STY4874 conferred resistance to at least ten of the tested antimicrobials: ciprofloxacin, norfloxacin, levofloxacin, kanamycin, streptomycin, gentamycin, nalidixic acid, chloramphenicol, ethidium bromide, and acriflavine, including fluoroquinolone antibiotics, which were drugs of choice to treat S. Typhi infections. Cell-based functional studies using ethidium bromide and acriflavine showed that STY4874 functions as a H(+)-dependent exporter. These results suggest that STY4874 may be an important drug target, which can now be tested by studying the susceptibility of a STY4874-deficient S. Typhi strain to antimicrobials.

  11. Identification and functional analysis of Penicillium digitatum genes putatively involved in virulence towards citrus fruit.

    Science.gov (United States)

    López-Pérez, Mario; Ballester, Ana-Rosa; González-Candelas, Luis

    2015-04-01

    The fungus Penicillium digitatum, the causal agent of green mould rot, is the most destructive post-harvest pathogen of citrus fruit in Mediterranean regions. In order to identify P. digitatum genes up-regulated during the infection of oranges that may constitute putative virulence factors, we followed a polymerase chain reaction (PCR)-based suppression subtractive hybridization and cDNA macroarray hybridization approach. The origin of expressed sequence tags (ESTs) was determined by comparison against the available genome sequences of both organisms. Genes coding for fungal proteases and plant cell wall-degrading enzymes represent the largest categories in the subtracted cDNA library. Northern blot analysis of a selection of P. digitatum genes, including those coding for proteases, cell wall-related enzymes, redox homoeostasis and detoxification processes, confirmed their up-regulation at varying time points during the infection process. Agrobacterium tumefaciens-mediated transformation was used to generate knockout mutants for two genes encoding a pectin lyase (Pnl1) and a naphthalene dioxygenase (Ndo1). Two independent P. digitatum Δndo1 mutants were as virulent as the wild-type. However, the two Δpnl1 mutants analysed were less virulent than the parental strain or an ectopic transformant. Together, these results provide a significant advance in our understanding of the putative determinants of the virulence mechanisms of P. digitatum.

  12. Isolation and Identification of Putative Oral Cancer Stem Cells

    Institute of Scientific and Technical Information of China (English)

    ZHANG Min; ZHAO Yan-Hua; TANG Xiao-Fei

    2011-01-01

    Objective: To isolate and characterize putative cancer stem cells in Tea8113 oral squmous cell carcinoma cell line. Methods: Putative cancer stem cells were isolated by limited dilution assay in Tea8113 cell line. Biological features of putative cancer stem cells were detected by MTT assay, flow cytometry, immunofluorescence, Colony Forming Efficiency assays, cell motility assay and in vivo tumor formation experiment. Results: Compared with untreated Tea8113 cells, the putative cancer stem cells proliferated more quickly and showed heteroploid cell cycle,higher G0/G1-arrested cells, higher CFE and higher expression levels of ABCG2 belonged to tumor stem cell phenotypes. The putative cancer stem cells had stronger capacity to generate tumors in vivo. Conclusion: The holoclone cells have higher proliferation and self-renewal abilities, which may be cancer stem cells existed in Tea8113 oral squmous cell carcinoma cell line.%目的:分离鉴定口腔鳞癌细胞系Tca8113中的肿瘤干细胞.方法:利用有限稀释的方法分离Tca8113细胞系中的肿瘤干细胞.通过MTT法、流式细胞技术、细胞免疫荧光、克隆形成率分析、细胞迁移能力检测和裸鼠皮下成瘤实验确定分离得到的肿瘤干细胞的生物学特点.结果:分离得到的紧密型克隆肿瘤细胞表现为异倍体样细胞周期,大部分细胞处于G0/G1期,增殖能力、克隆形成率和体外迁移能力都明显高于未分离的肿瘤细胞.紧密型克隆肿瘤细胞肿瘤干细胞标记物ABCG2表达也高于未分离的肿瘤细胞,并且具有更强的裸鼠皮下成瘤能力.结论:我们分离得到的紧密型克隆细胞具有较强的细胞增殖和自我更新能力,可能就是口腔鳞癌细胞系Tca8113中的肿瘤干细胞.

  13. Representing culture in interstellar messages

    Science.gov (United States)

    Vakoch, Douglas A.

    2008-09-01

    As scholars involved with the Search for Extraterrestrial Intelligence (SETI) have contemplated how we might portray humankind in any messages sent to civilizations beyond Earth, one of the challenges they face is adequately representing the diversity of human cultures. For example, in a 2003 workshop in Paris sponsored by the SETI Institute, the International Academy of Astronautics (IAA) SETI Permanent Study Group, the International Society for the Arts, Sciences and Technology (ISAST), and the John Templeton Foundation, a varied group of artists, scientists, and scholars from the humanities considered how to encode notions of altruism in interstellar messages art_science/2003>. Though the group represented 10 countries, most were from Europe and North America, leading to the group's recommendation that subsequent discussions on the topic should include more globally representative perspectives. As a result, the IAA Study Group on Interstellar Message Construction and the SETI Institute sponsored a follow-up workshop in Santa Fe, New Mexico, USA in February 2005. The Santa Fe workshop brought together scholars from a range of disciplines including anthropology, archaeology, chemistry, communication science, philosophy, and psychology. Participants included scholars familiar with interstellar message design as well as specialists in cross-cultural research who had participated in the Symposium on Altruism in Cross-cultural Perspective, held just prior to the workshop during the annual conference of the Society for Cross-cultural Research . The workshop included discussion of how cultural understandings of altruism can complement and critique the more biologically based models of altruism proposed for interstellar messages at the 2003 Paris workshop. This paper, written by the chair of both the Paris and Santa Fe workshops, will explore the challenges of communicating concepts of altruism that draw on both biological and cultural models.

  14. Semantic Representatives of the Concept

    Directory of Open Access Journals (Sweden)

    Elena N. Tsay

    2013-01-01

    Full Text Available In the article concept as one of the principle notions of cognitive linguistics is investigated. Considering concept as culture phenomenon, having language realization and ethnocultural peculiarities, the description of the concept “happiness” is presented. Lexical and semantic paradigm of the concept of happiness correlates with a great number of lexical and semantic variants. In the work semantic representatives of the concept of happiness, covering supreme spiritual values are revealed and semantic interpretation of their functioning in the Biblical discourse is given.

  15. Representative mass reduction in sampling

    DEFF Research Database (Denmark)

    Petersen, Lars; Esbensen, Harry Kim; Dahl, Casper Kierulf

    2004-01-01

    We here present a comprehensive survey of current mass reduction principles and hardware available in the current market. We conduct a rigorous comparison study of the performance of 17 field and/or laboratory instruments or methods which are quantitatively characterized (and ranked) for accuracy...... always be representative in the full Theory of Sampling (TOS) sense. This survey also allows empirical verification of the merits of the famous ??Gy?s formula?? for order-of-magnitude estimation of the Fundamental Sampling Error (FSE).......We here present a comprehensive survey of current mass reduction principles and hardware available in the current market. We conduct a rigorous comparison study of the performance of 17 field and/or laboratory instruments or methods which are quantitatively characterized (and ranked) for accuracy...... dividers, the Boerner Divider, the ??spoon method??, alternate/fractional shoveling and grab sampling. Only devices based on riffle splitting principles (static or rotational) passes the ultimate representativity test (with minor, but significant relative differences). Grab sampling, the overwhelmingly...

  16. Revision of the stereochemistry of elisabethatriene, a putative biosynthetic intermediate of pseudopterosins.

    Science.gov (United States)

    Nasuda, Masayuki; Ohmori, Miho; Ohyama, Kiyoshi; Fujimoto, Yoshinori

    2012-01-01

    In the past, we have questioned the accuracy of the stereochemistry of elisabethatriene, a putative biosynthetic intermediate of pseudopterosins, in light of the configuration of elisabethatrienol isolated from Pseudopterogorgia elisabethae, which was represented as 1S,4R,9S,11S. We have reinvestigated the stereochemistry of elisabethatriene. Elisabethatriene with the reported 1S,4R,9R,11S configuration was synthesized starting from (-)-isopulegol in its enantiomeric form. The (1)H- and (13)C-NMR data of the synthesized compound differed from those reported for elisabethatriene. In addition to the fact that elisabethatriene is converted into pseudopterosins, this finding has allowed us to propose that elisabethatriene should have the 1S,4R,9S,11S stereochemistry, which is identical to that of elisabethatrienol.

  17. Representing Conversations for Scalable Overhearing

    CERN Document Server

    Gutnik, G; 10.1613/jair.1829

    2011-01-01

    Open distributed multi-agent systems are gaining interest in the academic community and in industry. In such open settings, agents are often coordinated using standardized agent conversation protocols. The representation of such protocols (for analysis, validation, monitoring, etc) is an important aspect of multi-agent applications. Recently, Petri nets have been shown to be an interesting approach to such representation, and radically different approaches using Petri nets have been proposed. However, their relative strengths and weaknesses have not been examined. Moreover, their scalability and suitability for different tasks have not been addressed. This paper addresses both these challenges. First, we analyze existing Petri net representations in terms of their scalability and appropriateness for overhearing, an important task in monitoring open multi-agent systems. Then, building on the insights gained, we introduce a novel representation using Colored Petri nets that explicitly represent legal joint conv...

  18. Molecular genetics: DNA analysis of a putative dog clone.

    Science.gov (United States)

    Parker, Heidi G; Kruglyak, Leonid; Ostrander, Elaine A

    2006-03-09

    In August 2005, Lee et al. reported the first cloning of a domestic dog from adult somatic cells. This putative dog clone was the result of somatic-cell nuclear transfer from a fibroblast cell of a three-year-old male Afghan hound into a donor oocyte provided by a dog of mixed breed. In light of recent concerns regarding the creation of cloned human cell lines from the same institution, we have undertaken an independent test to determine the validity of the claims made by Lee et al..

  19. Putative golden proportions as predictors of facial esthetics in adolescents.

    Science.gov (United States)

    Kiekens, Rosemie M A; Kuijpers-Jagtman, Anne Marie; van 't Hof, Martin A; van 't Hof, Bep E; Maltha, Jaap C

    2008-10-01

    In orthodontics, facial esthetics is assumed to be related to golden proportions apparent in the ideal human face. The aim of the study was to analyze the putative relationship between facial esthetics and golden proportions in white adolescents. Seventy-six adult laypeople evaluated sets of photographs of 64 adolescents on a visual analog scale (VAS) from 0 to 100. The facial esthetic value of each subject was calculated as a mean VAS score. Three observers recorded the position of 13 facial landmarks included in 19 putative golden proportions, based on the golden proportions as defined by Ricketts. The proportions and each proportion's deviation from the golden target (1.618) were calculated. This deviation was then related to the VAS scores. Only 4 of the 19 proportions had a significant negative correlation with the VAS scores, indicating that beautiful faces showed less deviation from the golden standard than less beautiful faces. Together, these variables explained only 16% of the variance. Few golden proportions have a significant relationship with facial esthetics in adolescents. The explained variance of these variables is too small to be of clinical importance.

  20. CRYSTAL STRUCTURE ANALYSIS OF A PUTATIVE OXIDOREDUCTASE FROM KLEBSIELLA PNEUMONIAE

    Energy Technology Data Exchange (ETDEWEB)

    Baig, M.; Brown, A.; Eswaramoorthy, S.; Swaminathan, S.

    2009-01-01

    Klebsiella pneumoniae, a gram-negative enteric bacterium, is found in nosocomial infections which are acquired during hospital stays for about 10% of hospital patients in the United States. The crystal structure of a putative oxidoreductase from K. pneumoniae has been determined. The structural information of this K. pneumoniae protein was used to understand its function. Crystals of the putative oxidoreductase enzyme were obtained by the sitting drop vapor diffusion method using Polyethylene glycol (PEG) 3350, Bis-Tris buffer, pH 5.5 as precipitant. These crystals were used to collect X-ray data at beam line X12C of the National Synchrotron Light Source (NSLS) at Brookhaven National Laboratory (BNL). The crystal structure was determined using the SHELX program and refi ned with CNS 1.1. This protein, which is involved in the catalysis of an oxidation-reduction (redox) reaction, has an alpha/beta structure. It utilizes nicotinamide adenine dinucleotide phosphate (NADP) or nicotine adenine dinucleotide (NAD) to perform its function. This structure could be used to determine the active and co-factor binding sites of the protein, information that could help pharmaceutical companies in drug design and in determining the protein’s relationship to disease treatment such as that for pneumonia and other related pathologies.

  1. Whole-genome survey of the putative ATP-binding cassette transporter family genes in Vitis vinifera.

    Directory of Open Access Journals (Sweden)

    Birsen Çakır

    Full Text Available The ATP-binding cassette (ABC protein superfamily constitutes one of the largest protein families known in plants. In this report, we performed a complete inventory of ABC protein genes in Vitis vinifera, the whole genome of which has been sequenced. By comparison with ABC protein members of Arabidopsis thaliana, we identified 135 putative ABC proteins with 1 or 2 NBDs in V. vinifera. Of these, 120 encode intrinsic membrane proteins, and 15 encode proteins missing TMDs. V. vinifera ABC proteins can be divided into 13 subfamilies with 79 "full-size," 41 "half-size," and 15 "soluble" putative ABC proteins. The main feature of the Vitis ABC superfamily is the presence of 2 large subfamilies, ABCG (pleiotropic drug resistance and white-brown complex homolog and ABCC (multidrug resistance-associated protein. We identified orthologs of V. vinifera putative ABC transporters in different species. This work represents the first complete inventory of ABC transporters in V. vinifera. The identification of Vitis ABC transporters and their comparative analysis with the Arabidopsis counterparts revealed a strong conservation between the 2 species. This inventory could help elucidate the biological and physiological functions of these transporters in V. vinifera.

  2. Whole-genome survey of the putative ATP-binding cassette transporter family genes in Vitis vinifera.

    Science.gov (United States)

    Çakır, Birsen; Kılıçkaya, Ozan

    2013-01-01

    The ATP-binding cassette (ABC) protein superfamily constitutes one of the largest protein families known in plants. In this report, we performed a complete inventory of ABC protein genes in Vitis vinifera, the whole genome of which has been sequenced. By comparison with ABC protein members of Arabidopsis thaliana, we identified 135 putative ABC proteins with 1 or 2 NBDs in V. vinifera. Of these, 120 encode intrinsic membrane proteins, and 15 encode proteins missing TMDs. V. vinifera ABC proteins can be divided into 13 subfamilies with 79 "full-size," 41 "half-size," and 15 "soluble" putative ABC proteins. The main feature of the Vitis ABC superfamily is the presence of 2 large subfamilies, ABCG (pleiotropic drug resistance and white-brown complex homolog) and ABCC (multidrug resistance-associated protein). We identified orthologs of V. vinifera putative ABC transporters in different species. This work represents the first complete inventory of ABC transporters in V. vinifera. The identification of Vitis ABC transporters and their comparative analysis with the Arabidopsis counterparts revealed a strong conservation between the 2 species. This inventory could help elucidate the biological and physiological functions of these transporters in V. vinifera.

  3. A novel putative enterococcal pathogenicity island linked to the esp virulence gene of Enterococcus faecium and associated with epidemicity.

    Science.gov (United States)

    Leavis, Helen; Top, Janetta; Shankar, Nathan; Borgen, Katrine; Bonten, Marc; van Embden, Jan; Willems, Rob J L

    2004-02-01

    Enterococcus faecalis harbors a virulence-associated surface protein encoded by the esp gene. This gene has been shown to be part of a 150-kb putative pathogenicity island. A gene similar to esp has recently been found in Enterococcus faecium isolates recovered from hospitalized patients. In the present study we analyzed the polymorphism in the esp gene of E. faecium, and we investigated the association of esp with neighboring chromosomal genes. The esp gene showed considerable sequence heterogeneity in the regions encoding the nonrepeat N- and C-terminal domains of the Esp protein as well as differences in the number of repeats. DNA sequencing of chromosomal regions flanking the esp gene of E. faecium revealed seven open reading frames, representing putative genes implicated in virulence, regulation of transcription, and antibiotic resistance. These flanking regions were invariably associated with the presence or absence of the esp gene in E. faecium, indicating that esp in E. faecium is part of a distinct genetic element. Because of the presence of virulence genes in this gene cluster, the lower G+C content relative to that of the genome, and the presence of esp in E. faecium isolates associated with nosocomial outbreaks and clinically documented infections, we conclude that this genetic element constitutes a putative pathogenicity island, the first one described in E. faecium. Except for the presence of esp and araC, this pathogenicity island is completely different from the esp-containing pathogenicity island previously disclosed in E. faecalis.

  4. Exceptional error minimization in putative primordial genetic codes

    Directory of Open Access Journals (Sweden)

    Koonin Eugene V

    2009-11-01

    Full Text Available Abstract Background The standard genetic code is redundant and has a highly non-random structure. Codons for the same amino acids typically differ only by the nucleotide in the third position, whereas similar amino acids are encoded, mostly, by codon series that differ by a single base substitution in the third or the first position. As a result, the code is highly albeit not optimally robust to errors of translation, a property that has been interpreted either as a product of selection directed at the minimization of errors or as a non-adaptive by-product of evolution of the code driven by other forces. Results We investigated the error-minimization properties of putative primordial codes that consisted of 16 supercodons, with the third base being completely redundant, using a previously derived cost function and the error minimization percentage as the measure of a code's robustness to mistranslation. It is shown that, when the 16-supercodon table is populated with 10 putative primordial amino acids, inferred from the results of abiotic synthesis experiments and other evidence independent of the code's evolution, and with minimal assumptions used to assign the remaining supercodons, the resulting 2-letter codes are nearly optimal in terms of the error minimization level. Conclusion The results of the computational experiments with putative primordial genetic codes that contained only two meaningful letters in all codons and encoded 10 to 16 amino acids indicate that such codes are likely to have been nearly optimal with respect to the minimization of translation errors. This near-optimality could be the outcome of extensive early selection during the co-evolution of the code with the primordial, error-prone translation system, or a result of a unique, accidental event. Under this hypothesis, the subsequent expansion of the code resulted in a decrease of the error minimization level that became sustainable owing to the evolution of a high

  5. Endometrial Glandular Dysplasia (EmGD): morphologically and biologically distinctive putative precursor lesions of Type II endometrial cancers.

    Science.gov (United States)

    Fadare, Oluwole; Zheng, Wenxin

    2008-02-08

    In this article, the authors briefly review the historical evolution of the various putative precursor lesions for Type II endometrial cancers, with an emphasis on the newly defined "Endometrial Glandular Dysplasia (EmGD)". The evidentiary basis for delineating serous EmGD as the most probable precursor lesions to endometrial serous carcinoma is reviewed in detail. An argument is advanced for the discontinuation of the term serous "endometrial intraepithelial carcinoma (EIC)" as a descriptor for a supposedly intraepithelial, precancerous lesion. Preliminary evidence is also presented that suggests that there is a morphologically recognizable "clear cell EmGD" that probably represents a precancerous lesion to endometrial clear cell carcinomas.

  6. Identification of putative drug targets of Listeria monocytogenes F2365 by subtractive genomics approach

    Directory of Open Access Journals (Sweden)

    Md. Musharaf Hossain

    2013-01-01

    Full Text Available The prolonged and uncontrolled use of antibiotics in treatment against many pathogens causes the multiple drug resistance. The drug resistance of Listeria monocytogenes F2365 has been evolved, which cause a major disease listeriosis. The drug dose limit against that pathogen was also increased for currently prescribed antibiotics and more often combinational therapy was preferred. Therefore, identification of an extensive novel drug target, unique and essential to the microorganism and subjected to its validation and drug development is imperative. Availability of the total proteome of L. monocytogenes F2365 enabled in silico identification of putative common drug targets and their subcellular localization by subtractive genomics approach. In the present work subtractive genomics approach is used to identify vaccine and drug targets of L. monocytogenes F2365 to speed up the rational drug and vaccine design. It has revealed that out of 2821 reference sequences of the pathogen, 744 represent essential proteins and among them 274 are human non-homolog proteins. Besides, all predicted human non-homologs were then analyzed by subcellular localization servers, in which 46 proteins were identified as surface exposed proteins and can be considered as potential drug and vaccine targets for the pathogen. The 3D structure of two human non-homolog putative drug targets, pantothenate kinase (LmPK and holliday junction resolvase-like protein (LmHJR of L. monocytogenes F2365 were generated by homology modeling program Easymodeller 4.0; a GUI version of modeller. Generated structures were also validated by several online servers. The overall stereochemical quality of the model was assessed by Ramachandran plot analysis that was provided by PROCHECK. ProQ, ERRAT, Pro-SA web and VERIFY 3D of SAVES programs were also used to compute several validation parameters during the evaluation of the model. This protein structure information is important in structure

  7. Probing the putative active site of YjdL

    DEFF Research Database (Denmark)

    Jensen, Johanne Mørch; Ismat, Fouzia; Szakonyi, Gerda;

    2012-01-01

    YjdL from E. coli is an unusual proton-coupled oligopeptide transporter (POT). Unlike prototypical POTs, dipeptides are preferred over tripeptides, in particular dipeptides with a positively charged C-terminal residue. To further understand this difference in peptide specificity, the sequences...... of YjdL and YdgR, a prototypical E. coli POT, were compared in light of the crystal structure of a POT from Shewanella oneidensis. Several residues found in the putative active site were mutated and the activities of the mutated variants were assessed in terms of substrate uptake assays, and changes...... pocket that opens towards the extracellular space. The C-terminal side chain faces in the opposite direction into a sub pocket that faces the cytoplasm. These data indicated a stabilizing effect on a bulky N-terminal residue by an Ala281Phe variant and on the dipeptide backbone by Trp278...

  8. Novel putative mechanisms to link circadian clocks to healthy aging.

    Science.gov (United States)

    Popa-Wagner, Aurel; Catalin, Bogdan; Buga, Ana-Maria

    2015-08-01

    The circadian clock coordinates the internal physiology to increase the homeostatic capacity thereby providing both a survival advantage to the system and an optimization of energy budgeting. Multiple-oscillator circadian mechanisms are likely to play a role in regulating human health and may contribute to the aging process. Our aim is to give an overview of how the central clock in the hypothalamus and peripheral clocks relate to aging and metabolic disorders, including hyperlipidemia and hyperglycemia. In particular, we unravel novel putative mechanisms to link circadian clocks to healthy aging. This review may lead to the design of large-scale interventions to help people stay healthy as they age by adjusting daily activities, such as feeding behavior, and or adaptation to age-related changes in individual circadian rhythms.

  9. Ballistic gelatin as a putative substrate for EEG phantom devices

    CERN Document Server

    Hairston, W David; Yu, Alfred B

    2016-01-01

    Phantom devices allow the human variable to be controlled for in order to allow clear comparison and validation of biomedical imaging hardware and software. There is currently no standard phantom for electroencephalography (EEG). To be useful, such a device would need to: (a) accurately recreate the real and imaginary components of scalp electrical impedance, (b) contain internal emitters to create electrical dipoles, and (c) be easily replicable across various labs and research groups. Cost-effective materials, which are conductive, repeatable, and easily formed are a missing key enabler for EEG phantoms. Here, we explore the use of ballistics gelatin, an inexpensive, easily-formable and repeatable material, as a putative substrate by examining its electrical properties and physical stability over time. We show that varied concentrations of NaCl salt relative to gelatin powder shifts the phase/frequency response profile, allowing for selective tuning of the material electrical properties.

  10. Putative benefits of microalgal astaxanthin on exercise and human health

    Directory of Open Access Journals (Sweden)

    Marcelo P. Barros

    2011-04-01

    Full Text Available Astaxanthin (ASTA is a pinkish-orange carotenoid produced by microalgae, but also commonly found in shrimp, lobster and salmon, which accumulate ASTA from the aquatic food chain. Numerous studies have addressed the benefits of ASTA for human health, including the inhibition of LDL oxidation, UV-photoprotection and prophylaxis of bacterial stomach ulcers. ASTA is recognized as a powerful scavenger of reactive oxygen species (ROS, especially those involved in lipid peroxidation. Both aerobic and anaerobic exercise are closely related to overproduction of ROS in muscle tissue. Post-exercise inflammatory processes can even exacerbate the oxidative stress imposed by exercise. Thus, ASTA is suggested here as a putative nutritional alternative/coadjutant for antioxidant therapy to afford additional protection to muscle tissues against oxidative damage induced by exercise, as well as for an (overall integrative redox re-balance and general human health.

  11. Cryptic species in putative ancient asexual darwinulids (Crustacea, Ostracoda.

    Directory of Open Access Journals (Sweden)

    Isa Schön

    Full Text Available BACKGROUND: Fully asexually reproducing taxa lack outcrossing. Hence, the classic Biological Species Concept cannot be applied. METHODOLOGY/PRINCIPAL FINDINGS: We used DNA sequences from the mitochondrial COI gene and the nuclear ITS2 region to check species boundaries according to the evolutionary genetic (EG species concept in five morphospecies in the putative ancient asexual ostracod genera, Penthesilenula and Darwinula, from different continents. We applied two methods for detecting cryptic species, namely the K/θ method and the General Mixed Yule Coalescent model (GMYC. We could confirm the existence of species in all five darwinulid morphospecies and additional cryptic diversity in three morphospecies, namely in Penthesilenula brasiliensis, Darwinula stevensoni and in P. aotearoa. The number of cryptic species within one morphospecies varied between seven (P. brasiliensis, five to six (D. stevensoni and two (P. aotearoa, respectively, depending on the method used. Cryptic species mainly followed continental distributions. We also found evidence for coexistence at the local scale for Brazilian cryptic species of P. brasiliensis and P. aotearoa. Our ITS2 data confirmed that species exist in darwinulids but detected far less EG species, namely two to three cryptic species in P. brasiliensis and no cryptic species at all in the other darwinulid morphospecies. CONCLUSIONS/SIGNIFICANCE: Our results clearly demonstrate that both species and cryptic diversity can be recognized in putative ancient asexual ostracods using the EG species concept, and that COI data are more suitable than ITS2 for this purpose. The discovery of up to eight cryptic species within a single morphospecies will significantly increase estimates of biodiversity in this asexual ostracod group. Which factors, other than long-term geographic isolation, are important for speciation processes in these ancient asexuals remains to be investigated.

  12. Expression of putative immune response genes during early ontogeny in the coral Acropora millepora.

    Directory of Open Access Journals (Sweden)

    Eneour Puill-Stephan

    Full Text Available BACKGROUND: Corals, like many other marine invertebrates, lack a mature allorecognition system in early life history stages. Indeed, in early ontogeny, when corals acquire and establish associations with various surface microbiota and dinoflagellate endosymbionts, they do not efficiently distinguish between closely and distantly related individuals from the same population. However, very little is known about the molecular components that underpin allorecognition and immunity responses or how they change through early ontogeny in corals. METHODOLOGY/PRINCIPAL FINDINGS: Patterns in the expression of four putative immune response genes (apextrin, complement C3, and two CELIII type lectin genes were examined in juvenile colonies of Acropora millepora throughout a six-month post-settlement period using quantitative real-time PCR (qPCR. Expression of a CELIII type lectin gene peaked in the fourth month for most of the coral juveniles sampled and was significantly higher at this time than at any other sampling time during the six months following settlement. The timing of this increase in expression levels of putative immune response genes may be linked to allorecognition maturation which occurs around this time in A. millepora. Alternatively, the increase may represent a response to immune challenges, such as would be involved in the recognition of symbionts (such as Symbiodinium spp. or bacteria during winnowing processes as symbioses are fine-tuned. CONCLUSIONS/SIGNIFICANCE: Our data, although preliminary, are consistent with the hypothesis that lectins may play an important role in the maturation of allorecognition responses in corals. The co-expression of lectins with apextrin during development of coral juveniles also raises the possibility that these proteins, which are components of innate immunity in other invertebrates, may influence the innate immune systems of corals through a common pathway or system. However, further studies

  13. Putative Cross-Contamination Routes of Listeria monocytogenes in a Meat Processing Facility in Romania.

    Science.gov (United States)

    Bolocan, Andrei Sorin; Oniciuc, Elena Alexandra; Alvarez-Ordóñez, Avelino; Wagner, Martin; Rychli, Kathrin; Jordan, Kieran; Nicolau, Anca Ioana

    2015-09-01

    Putative routes of Listeria monocytogenes contamination, based on the workflow of the employees, were studied in a meat processing facility by investigating 226 samples collected from food contact surfaces, non-food contact surfaces, raw materials, and ready-to-eat meat products on four occasions over a 1-year period. In total, 19.7% of non-food contact surfaces, 22.9% of food contact surfaces, 45% of raw materials, and 20% of ready-to-eat meat products were positive for L. monocytogenes (analyzed by the International Organization for Standardization standard method ISO 11290). Pulsed-field gel electrophoresis (PFGE) profiles were determined for a representative subset of these isolates, and 11 distinct pulsotypes were identified, two of which were frequently isolated (T4 and T8) and considered persistent. Strains from the various pulsotypes were screened for the presence of bcrABC and qacH, the genes responsible for tolerance responses to quaternary ammonium compounds. Two strains harbored bcrABC, and these strains had a higher benzalkonium chloride tolerance; however, they were not considered persistent strains. The frequently isolated PFGE pulsotype T8 strains were highly adhesive to abiotic surfaces at 10 and 20°C; however, the pulsotype T6 strain, which was isolated only at the last sampling time, had the highest adhesion ability, and the pulsotype T4 strain (the second most persistent pulsotype) had only modest adhesion. Four putative cross-contamination routes were confirmed by mapping the persistent and other isolates. This information could allow a food safety manager to adjust the work flow to improve the hygienic conditions in a meat processing facility. This study revealed the prevalence and persistence of L. monocytogenes strains in a meat processing facility and established the importance of developing strategies to avoid cross-contamination, recalls, and outbreaks of listeriosis.

  14. Putative cross-kingdom horizontal gene transfer in sponge (Porifera mitochondria

    Directory of Open Access Journals (Sweden)

    Ilan Micha

    2006-09-01

    Full Text Available Abstract Background The mitochondrial genome of Metazoa is usually a compact molecule without introns. Exceptions to this rule have been reported only in corals and sea anemones (Cnidaria, in which group I introns have been discovered in the cox1 and nad5 genes. Here we show several lines of evidence demonstrating that introns can also be found in the mitochondria of sponges (Porifera. Results A 2,349 bp fragment of the mitochondrial cox1 gene was sequenced from the sponge Tetilla sp. (Spirophorida. This fragment suggests the presence of a 1143 bp intron. Similar to all the cnidarian mitochondrial introns, the putative intron has group I intron characteristics. The intron is present in the cox1 gene and encodes a putative homing endonuclease. In order to establish the distribution of this intron in sponges, the cox1 gene was sequenced from several representatives of the demosponge diversity. The intron was found only in the sponge order Spirophorida. A phylogenetic analysis of the COI protein sequence and of the intron open reading frame suggests that the intron may have been transmitted horizontally from a fungus donor. Conclusion Little is known about sponge-associated fungi, although in the last few years the latter have been frequently isolated from sponges. We suggest that the horizontal gene transfer of a mitochondrial intron was facilitated by a symbiotic relationship between fungus and sponge. Ecological relationships are known to have implications at the genomic level. Here, an ecological relationship between sponge and fungus is suggested based on the genomic analysis.

  15. Putative cross-kingdom horizontal gene transfer in sponge (Porifera) mitochondria

    Science.gov (United States)

    Rot, Chagai; Goldfarb, Itay; Ilan, Micha; Huchon, Dorothée

    2006-01-01

    Background The mitochondrial genome of Metazoa is usually a compact molecule without introns. Exceptions to this rule have been reported only in corals and sea anemones (Cnidaria), in which group I introns have been discovered in the cox1 and nad5 genes. Here we show several lines of evidence demonstrating that introns can also be found in the mitochondria of sponges (Porifera). Results A 2,349 bp fragment of the mitochondrial cox1 gene was sequenced from the sponge Tetilla sp. (Spirophorida). This fragment suggests the presence of a 1143 bp intron. Similar to all the cnidarian mitochondrial introns, the putative intron has group I intron characteristics. The intron is present in the cox1 gene and encodes a putative homing endonuclease. In order to establish the distribution of this intron in sponges, the cox1 gene was sequenced from several representatives of the demosponge diversity. The intron was found only in the sponge order Spirophorida. A phylogenetic analysis of the COI protein sequence and of the intron open reading frame suggests that the intron may have been transmitted horizontally from a fungus donor. Conclusion Little is known about sponge-associated fungi, although in the last few years the latter have been frequently isolated from sponges. We suggest that the horizontal gene transfer of a mitochondrial intron was facilitated by a symbiotic relationship between fungus and sponge. Ecological relationships are known to have implications at the genomic level. Here, an ecological relationship between sponge and fungus is suggested based on the genomic analysis. PMID:16972986

  16. Coleopteran-specific and putative novel cry genes in Iranian native Bacillus thuringiensis collection.

    Science.gov (United States)

    Nazarian, Amin; Jahangiri, Rosa; Jouzani, Gholamreza Salehi; Seifinejad, Ali; Soheilivand, Saeed; Bagheri, Omolbanin; Keshavarzi, Mansoureh; Alamisaeid, Khalil

    2009-10-01

    The characterization of the strains containing Coleopteran-specific and also putative novel cry genes in Iranian native Bacillus thuringiensis collection is presented. Characterization was based on PCR analysis using 31 general and specific primers for cry1B, cry1I, cry3A, cry3B, cry3C, cry7A, cry8A, cry8B, cry8C, cry14, cry18, cry26, cry28, cry34 and cry35 genes, protein band patterns as well as their insecticidal activity on Xanthogaleruca luteola Mull. larvae. Forty six isolates (65.7%) contained minimum one Coleopteran-active cry gene. Based on universal primers, strains containing cry18 and cry26 genes were the most abundant and represent 27.1% and 24% of the isolates, respectively, whereas cry14, cry3, cry28, cry34, cry35, cry7, cry8 genes were less abundant, found in 14.2, 12.5, 10, 7, 7 and 5.6% of the strains, respectively. Based on specific primers, isolates containing cry1I were the most abundant (48.5%). Two strains containing Coleopteran-active cry genes showed higher activity against X. luteola larvae than B. thuringiensis subsp. morrisoni pathovar tenebrionis. Thirty isolates, when assayed for cry1C, cry5, cry6, cry8b, cry9, cry10, cry11, cry18, cry24 and cry35 genes, showed unexpected size bands. Cloning and sequencing of the amplicons allowed both the identification of known cry genes and the detection of putative novel cry1C sequences.

  17. 10 CFR 63.332 - Representative volume.

    Science.gov (United States)

    2010-01-01

    ... 10 Energy 2 2010-01-01 2010-01-01 false Representative volume. 63.332 Section 63.332 Energy... Protection Standards § 63.332 Representative volume. (a) The representative volume is the volume of ground... radionuclides released from the Yucca Mountain disposal system that will be in the representative volume....

  18. Experimental studies on the relationship between nanobacteria translocation and SIRS of rats which suffering critical infection of abdominal cavity%严重腹腔感染时血、粪纳米细菌的检测及其与SIRS关系的实验研究

    Institute of Scientific and Technical Information of China (English)

    黄美泰; 伍颖君; 郑永波; 钟俊新; 段雪飞; 李晶晶; 吴承堂

    2013-01-01

    Objective To explore the relationship between nanobacteria(NB) translocation from blood and stool and SIRS of rats suffering critical infection of abdominal cavity. Methods Forty SD rats were involved in the study. The models of critical abdominal cavity infection were made by cecal ligation plus puncture (CLP). The test samples of blood and stool were obtained before and two days after infected, respectively. The samples were cultured with NB culture medium and identified by transmission electron microscopy (TEM). The morphological change of the pathologic lesion in the ileum tissue of the rats were observed. Results Two days after infected, it showed epithelia abscission and tight junction loosening in some area of intestinal mucosa of the rats. Compared with preoperative, the average rectal temperature (℃) of the experimental group rats was higher significantly (39.98±0.43 vs 38.37±0.34,t=18.538,P<0.01), and the average numer of leukocyte (×109/L) was higher significantly(21.13±3.27 vs 10.43±2.23, t= 15.909, P<0.01) at postoperative 2 d. The positive rates of NB were 17.5%and 42.5%(χ2=5.952, P=0.015) in the blood samples before and after CLP 2 d respectively by TEM, and that were 90.0%and 92.5%(χ2=0.156, P=0.692) in the stool. Conclusion The positive rates of NB increases in the blood samples, which may be associated with SIRS induced by critical abdominal cavity infection.%目的探讨严重腹腔感染时血、粪中纳米细菌(nanobacteria, NB)的检测情况及其与全身炎症反应综合征(SIRS)的关系。方法40只SD大鼠采用盲肠结扎加穿孔手术(CLP)制作严重腹腔感染模型,分别于术前、术后2 d取血、粪标本进行NB培养,电镜下观察NB并加以鉴定。另取回肠组织作病理观察。结果造模后的大鼠符合SIRS标准,病理观察肠黏膜层部分区域有黏膜上皮脱落,肠上皮细胞间紧密连接出现异常,结构松弛。与CLP手术前比较,术后2 d

  19. Putative cis-regulatory elements associated with heat shock genes activated during excystation of Cryptosporidium parvum.

    Directory of Open Access Journals (Sweden)

    Benjamin Cohn

    Full Text Available BACKGROUND: Cryptosporidiosis is a ubiquitous infectious disease, caused by the protozoan parasites Cryptosporidium hominis and C. parvum, leading to acute, persistent and chronic diarrhea worldwide. Although the complications of this disease can be serious, even fatal, in immunocompromised patients of any age, they have also been found to lead to long term effects, including growth inhibition and impaired cognitive development, in infected immunocompetent children. The Cryptosporidium life cycle alternates between a dormant stage, the oocyst, and a highly replicative phase that includes both asexual vegetative stages as well as sexual stages, implying fine genetic regulatory mechanisms. The parasite is extremely difficult to study because it cannot be cultured in vitro and animal models are equally challenging. The recent publication of the genome sequence of C. hominis and C. parvum has, however, significantly advanced our understanding of the biology and pathogenesis of this parasite. METHODOLOGY/PRINCIPAL FINDINGS: Herein, our goal was to identify cis-regulatory elements associated with heat shock response in Cryptosporidium using a combination of in silico and real time RT-PCR strategies. Analysis with Gibbs-Sampling algorithms of upstream non-translated regions of twelve genes annotated as heat shock proteins in the Cryptosporidium genome identified a highly conserved over-represented sequence motif in eleven of them. RT-PCR analyses, described herein and also by others, show that these eleven genes bearing the putative element are induced concurrent with excystation of parasite oocysts via heat shock. CONCLUSIONS/SIGNIFICANCE: Our analyses suggest that occurrences of a motif identified in the upstream regions of the Cryptosporidium heat shock genes represent parts of the transcriptional apparatus and function as stress response elements that activate expression of these genes during excystation, and possibly at other stages in the life

  20. Putative uremic encephalopathy in horses: five cases (1978-1998).

    Science.gov (United States)

    Frye, M A; Johnson, J S; Traub-Dargatz, J L; Savage, C J; Fettman, M J; Gould, D H

    2001-02-15

    To determine historical, physical examination, clinicopathologic, and postmortem findings in horses with putative uremic encephalopathy. Design-Retrospective study. Animals-5 horses with renal failure and neurologic disease not attributable to abnormalities in any other organ system. Medical records from 1978 to 1998 were examined for horses with renal disease and neurologic signs not attributable to primary neurologic, hepatic, or other diseases. Signalment, history, physical examination findings, clinicopathologic data, renal ultrasonographic findings, and postmortem data were reviewed. Of 332 horses with renal disease, 5 met selection criteria. Historical findings, physical examination findings, clinicopathologic data, ultrasonographic data, and postmortem findings were consistent with chronic renal failure. Swollen astrocytes were detected in all 4 horses examined at necropsy. A single criterion was not determined to be pathognomonic for uremic encephalopathy in horses. Uremic encephalopathy should be considered as a differential diagnosis in horses with evidence of chronic renal failure and encephalopathic neurologic sign not attributable to other causes. Astrocyte swelling, which was common to all 4 horses examined at necropsy, may serve as a microscopic indicator of uremic encephalopathy in horses.

  1. Phytophthora infestans specific phosphorylation patterns and new putative control targets.

    Science.gov (United States)

    Frades, Itziar; Andreasson, Erik

    2016-04-01

    In this study we applied biomathematical searches of gene regulatory mechanisms to learn more about oomycete biology and to identify new putative targets for pesticides or biological control against Phytophthora infestans. First, oomycete phylum-specific phosphorylation motifs were found by discriminative n-gram analysis. We found 11.600 P. infestans specific n-grams, mapping 642 phosphoproteins. The most abundant group among these related to phosphatidylinositol metabolism. Due to the large number of possible targets found and our hypothesis that multi-level control is a sign of usefulness as targets for intervention, we identified overlapping targets with a second screen. This was performed to identify proteins dually regulated by small RNA and phosphorylation. We found 164 proteins to be regulated by both sRNA and phosphorylation and the dominating functions where phosphatidylinositol signalling/metabolism, endocytosis, and autophagy. Furthermore we performed a similar regulatory study and discriminative n-gram analysis of proteins with no clear orthologs in other species and proteins that are known to be unique to P. infestans such as the RxLR effectors, Crinkler (CRN) proteins and elicitins. We identified CRN proteins with specific phospho-motifs present in all life stages. PITG_12626, PITG_14042 and PITG_23175 are CRN proteins that have species-specific phosphorylation motifs and are subject to dual regulation.

  2. Rapid Discrimination Among Putative Mechanistic Models of Biochemical Systems.

    Science.gov (United States)

    Lomnitz, Jason G; Savageau, Michael A

    2016-08-31

    An overarching goal in molecular biology is to gain an understanding of the mechanistic basis underlying biochemical systems. Success is critical if we are to predict effectively the outcome of drug treatments and the development of abnormal phenotypes. However, data from most experimental studies is typically noisy and sparse. This allows multiple potential mechanisms to account for experimental observations, and often devising experiments to test each is not feasible. Here, we introduce a novel strategy that discriminates among putative models based on their repertoire of qualitatively distinct phenotypes, without relying on knowledge of specific values for rate constants and binding constants. As an illustration, we apply this strategy to two synthetic gene circuits exhibiting anomalous behaviors. Our results show that the conventional models, based on their well-characterized components, cannot account for the experimental observations. We examine a total of 40 alternative hypotheses and show that only 5 have the potential to reproduce the experimental data, and one can do so with biologically relevant parameter values.

  3. Putative role of Tat-Env interaction in HIV infection.

    Science.gov (United States)

    Poon, Selina; Moscoso, Carlos G; Xing, Li; Kan, Elaine; Sun, Yide; Kolatkar, Prasanna R; Vahlne, Anders G; Srivastava, Indresh K; Barnett, Susan W; Cheng, R Holland

    2013-09-24

    To study the complex formed between Tat protein and Env soluble trimeric immunogen, and compare with previously determined structures of Env native trimers and Env-CD4m complexes. The soluble Env trimer was used to mimic the spike glycoprotein on the virus surface for the study. To overcome limitations of other structural determination methods, cryoelectron microscopy was employed to image the complex, and single particle reconstruction was utilized to reconstruct the structure of the complex from collected micrographs. Molecular modeling of gp120-Tat was performed to provide atomic coordinates for docking. Images were preprocessed by multivariate statistical analysis to identify principal components of variation then submitted for reconstruction. Reconstructed structures were docked with modeled gp120-Tat atomic coordinates to study the positions of crucial epitopes. Analysis of the Env-Tat complex demonstrated an intermediate structure between Env native trimers and Env-CD4m structures. Docking results indicate that the CD4-binding site and the V3 loop are exposed in the Env-Tat complex. The integrin-binding sequence in Tat was also exposed in Env-Tat docking. The intermediate structure induced by Tat-interaction with Env could potentially provide an explanation for increased virus infection in the presence of Tat protein. Consequently, exposure of CD4-binding sites and a putative integrin-binding sequence on Tat in the complex may provide a new avenue for rational design of an effective HIV vaccine. © 2013 Wolters Kluwer Health | Lippincott Williams & Wilkins

  4. Small intestinal mucosa expression of putative chaperone fls485

    Directory of Open Access Journals (Sweden)

    Raupach Kerstin

    2010-03-01

    Full Text Available Abstract Background Maturation of enterocytes along the small intestinal crypt-villus axis is associated with significant changes in gene expression profiles. fls485 coding a putative chaperone protein has been recently suggested as a gene involved in this process. The aim of the present study was to analyze fls485 expression in human small intestinal mucosa. Methods fls485 expression in purified normal or intestinal mucosa affected with celiac disease was investigated with a molecular approach including qRT-PCR, Western blotting, and expression strategies. Molecular data were corroborated with several in situ techniques and usage of newly synthesized mouse monoclonal antibodies. Results fls485 mRNA expression was preferentially found in enterocytes and chromaffine cells of human intestinal mucosa as well as in several cell lines including Rko, Lovo, and CaCo2 cells. Western blot analysis with our new anti-fls485 antibodies revealed at least two fls485 proteins. In a functional CaCo2 model, an increase in fls485 expression was paralleled by cellular maturation stage. Immunohistochemistry demonstrated fls485 as a cytosolic protein with a slightly increasing expression gradient along the crypt-villus axis which was impaired in celiac disease Marsh IIIa-c. Conclusions Expression and synthesis of fls485 are found in surface lining epithelia of normal human intestinal mucosa and deriving epithelial cell lines. An interdependence of enterocyte differentiation along the crypt-villus axis and fls485 chaperone activity might be possible.

  5. Small intestinal mucosa expression of putative chaperone fls485.

    Science.gov (United States)

    Reinartz, Andrea; Ehling, Josef; Franz, Susanne; Simon, Verena; Bravo, Ignacio G; Tessmer, Claudia; Zentgraf, Hanswalter; Lyer, Stefan; Schneider, Ursula; Köster, Jan; Raupach, Kerstin; Kämmerer, Elke; Klaus, Christina; Tischendorf, Jens J W; Kopitz, Jürgen; Alonso, Angel; Gassler, Nikolaus

    2010-03-07

    Maturation of enterocytes along the small intestinal crypt-villus axis is associated with significant changes in gene expression profiles. fls485 coding a putative chaperone protein has been recently suggested as a gene involved in this process. The aim of the present study was to analyze fls485 expression in human small intestinal mucosa. fls485 expression in purified normal or intestinal mucosa affected with celiac disease was investigated with a molecular approach including qRT-PCR, Western blotting, and expression strategies. Molecular data were corroborated with several in situ techniques and usage of newly synthesized mouse monoclonal antibodies. fls485 mRNA expression was preferentially found in enterocytes and chromaffine cells of human intestinal mucosa as well as in several cell lines including Rko, Lovo, and CaCo2 cells. Western blot analysis with our new anti-fls485 antibodies revealed at least two fls485 proteins. In a functional CaCo2 model, an increase in fls485 expression was paralleled by cellular maturation stage. Immunohistochemistry demonstrated fls485 as a cytosolic protein with a slightly increasing expression gradient along the crypt-villus axis which was impaired in celiac disease Marsh IIIa-c. Expression and synthesis of fls485 are found in surface lining epithelia of normal human intestinal mucosa and deriving epithelial cell lines. An interdependence of enterocyte differentiation along the crypt-villus axis and fls485 chaperone activity might be possible.

  6. Putative impact of RNA editing on drug discovery.

    Science.gov (United States)

    Decher, Niels; Netter, Michael F; Streit, Anne K

    2013-01-01

    Virtually all organisms use RNA editing as a powerful post-transcriptional mechanism to recode genomic information and to increase functional protein diversity. The enzymatic editing of pre-mRNA by ADARs and CDARs is known to change the functional properties of neuronal receptors and ion channels regulating cellular excitability. However, RNA editing is also an important mechanism for genes expressed outside the brain. The fact that RNA editing breaks the 'one gene encodes one protein' hypothesis is daunting for scientists and a probable drawback for drug development, as scientists might search for drugs targeting the 'wrong' protein. This possible difficulty for drug discovery and development became more evident from recent publications, describing that RNA editing events have profound impact on the pharmacology of some common drug targets. These recent studies highlight that RNA editing can cause massive discrepancies between the in vitro and in vivo pharmacology. Here, we review the putative impact of RNA editing on drug discovery, as RNA editing has to be considered before using high-throughput screens, rational drug design or choosing the right model organism for target validation.

  7. Epigenetic regulation of putative tumor suppressor TGFBI in human leukemias

    Institute of Scientific and Technical Information of China (English)

    Fang Hongbo; Liu Jing; Guo Dan; Liu Peixiang; Zhao Yongliang

    2014-01-01

    Background Both in vitro and in vivo data have demonstrated the TGFBI gene functions as a putative tumor suppressor and is frequently downregulated in human tumors of different histological types.The hypermethylation of the TGFBI promoter,as one of the main regulatory mechanisms,is associated with TGFBI silencing.In this study,we used a methylation-specific PCR (MSP) method to evaluate the methylation status of the TGFBI promoter in human leukemias.Methods Real-time RT-PCR and methylation-specific PCR approaches were performed to define the TGFBI expression and promoter methylation in human leukemia call lines and clinical samples.Genomic DNA was isolated from peripheral blood mononuclear cells from leukemia patients,bisulfite-converted,and analyzed by the MSP method.Results Hypermethylation of the TGFBI promoter occurred in leukemia cell lines and demethylation treatment reexpressed TGFBI at a substantially increased level in most of leukemia cell lines tested.Furthermore,a much higher level of CpG island methylation and a significantly lower TGFBI expression were also identified in clinical leukemia samples.Conclusion The results suggest an important role of promoter methylation in regulating TGFBI expression in leukemia,which provides a useful diagnostic marker for clinical management of human leukemias.

  8. Expression and characterization of rice putative PAUSED gene

    Institute of Scientific and Technical Information of China (English)

    Chengguo Yao; Liangfa Ge; Wei Li; Botao Zhao; Chaoqun Li; Kangcheng Ruan; Hongxuan Lin; Youxin Jin

    2008-01-01

    In Arab idopsis, PA USED ( PSD ) encodes the ortholog of loslp/ exportin-t, which mediates the nuclear export of transfer RNA (tRNA) in yeast and mammals. However, in monocot plants such as rice, knowledge of the corresponding ortholog is limited, and its effects on growth development and productivity remain unknown. In this study, we verified a rice transfer-DNA insertional mutantpsd line and analyzed its phenotypes;the mutant displayed severe morphological defects including retarded development and low fertility compared with wild-type rice. Examining intronless tRNA-Tyr and intron-containing pre-tRNA-Ala expression levels in cytoplasmic and nuclear fraction with Northern blot analysis between wild -type and mutant leaf tissue suggested that rice PSD might be involved in tRNA export from the nucleus to the cytoplasm.Additionally, reverse transcription-polymerase chain reaction analysis revealed that PSD transcript was expressed throughout normal rice plant development, and subcellular localization assays showed that rice PSD protein was present in both the nucleus and cytoplasm. In summary, our data implied that the putative PSD gene might be indispensable for normal rice development and its function might be the same as that ofArabidopsis PSD.

  9. Conformational study of a putative HLTV-1 retroviral protease inhibitor.

    Science.gov (United States)

    Llido, S; d'Estaintot, B L; Dautant, A; Geoffre, S; Picard, P; Precigoux, G

    1993-05-01

    The crystal structure of prolyl-glutaminyl-valyl-statyl-alanyl-leucine (Pro-Gln-Val-Sta-Ala-Leu, C(32)H(57)N(7)0(9).5H(2)0, M(r) = 683.9 + 90.1), a putative HTLV-1 protease inhibitor based on one of the consensus retroviral protease cleavage sequences, and containing the statine residue [(4S,3S)-4-amino-3-hydroxy-6-methylheptanoic acid], has been determined by X-ray diffraction. The same molecule has been modelled in the active site of the HTLV-1 protease and both conformations have been compared. The peptide crystallizes as a pentahydrate in space group P2(1) with a = 10.874(2), b = 9.501(2), c = 21.062(5) A, beta = 103.68 (1) degrees, Z = 2, V= 2114.3 A(3), D(x) = 1.21 g cm(-3), micro = 8.02 cm(-1), T= 293 K, lambda(Cu Kalpha) = 1.5418 A. The structure has been refined to an R value of 0.070 for 2152 observed reflections. The peptide main chain can be described as extended and adopts the usual zigzag conformation from the prolyl to the statyl residue. The main difference in conformation between the individual observed and modelled molecules is located on the Sta, Ala and Leu residues with the main chain of the modelled molecule rotated by about 180 degrees as compared to the observed conformation in the crystal state.

  10. A new putative sigma factor of Myxococcus xanthus.

    Science.gov (United States)

    Apelian, D; Inouye, S

    1993-06-01

    A third putative sigma factor gene, sigC, has been isolated from Myxococcus xanthus by using the sigA gene (formerly rpoD of M. xanthus) as a probe. The nucleotide sequence of sigC has been determined, and an open reading frame of 295 residues (M(r) = 33,430) has been identified. The deduced amino acid sequence of sigC exhibits the features which are characteristic of other bacterial sigma factors. The characterization of a sigC-lacZ strain has demonstrated that sigC expression is induced immediately after cells enter into the developmental cycle and is dramatically reduced at the onset of sporulation. A deletion mutant of sigC grows normally in vegetative culture and is able to develop normally. However, in contrast to the wild-type cells, the sigC deletion mutant cells became capable of forming fruiting bodies and myxospores on semirich agar plates. This suggests that sigC may play a role in expression of genes involved in negatively regulating the initiation of fruiting body formation.

  11. VT Biodiversity Project - Representative Landscapes boundary lines

    Data.gov (United States)

    Vermont Center for Geographic Information — (Link to Metadata) This coverage represents the results of an analysis of landscape diversity in Vermont. Polygons in the dataset represent as much as possible (in a...

  12. Representing Uncertainty by Probability and Possibility

    DEFF Research Database (Denmark)

    Uncertain parameters in modeling are usually represented by probability distributions reflecting either the objective uncertainty of the parameters or the subjective belief held by the model builder. This approach is particularly suited for representing the statistical nature or variance of uncer......Uncertain parameters in modeling are usually represented by probability distributions reflecting either the objective uncertainty of the parameters or the subjective belief held by the model builder. This approach is particularly suited for representing the statistical nature or variance...

  13. Representing Uncertainty by Probability and Possibility

    DEFF Research Database (Denmark)

    Uncertain parameters in modeling are usually represented by probability distributions reflecting either the objective uncertainty of the parameters or the subjective belief held by the model builder. This approach is particularly suited for representing the statistical nature or variance of uncer......Uncertain parameters in modeling are usually represented by probability distributions reflecting either the objective uncertainty of the parameters or the subjective belief held by the model builder. This approach is particularly suited for representing the statistical nature or variance...

  14. 7 CFR 1280.611 - Representative period.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 10 2010-01-01 2010-01-01 false Representative period. 1280.611 Section 1280.611... INFORMATION ORDER Procedures To Request a Referendum Definitions § 1280.611 Representative period. Representative period means the period designated by the Secretary pursuant to § 518 of the Act. ...

  15. 29 CFR 548.405 - Representative period.

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 3 2010-07-01 2010-07-01 false Representative period. 548.405 Section 548.405 Labor... Application § 548.405 Representative period. (a) The application must set forth the facts relied upon to show... employee exclusive of overtime premiums over a representative period of time. 21 The basic rate will be...

  16. 7 CFR 1230.618 - Representative period.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 10 2010-01-01 2010-01-01 false Representative period. 1230.618 Section 1230.618... CONSUMER INFORMATION Procedures for the Conduct of Referendum Definitions § 1230.618 Representative period. The term Representative period means the 12-consecutive months prior to the first day of absentee and...

  17. 7 CFR 1220.612 - Representative period.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 10 2010-01-01 2010-01-01 false Representative period. 1220.612 Section 1220.612... CONSUMER INFORMATION Procedures To Request a Referendum Definitions § 1220.612 Representative period. Representative period means the period designated by the Secretary pursuant to section 1970 of the Act. ...

  18. The aerosols' fate in a putative ammonia ocean on Titan

    Science.gov (United States)

    Ramírez, S. I.; Coll, P.; Buch, A.; Brassé, C.; Poch, O.; Raulin, F.

    2010-04-01

    A laboratory study on the chemical transformation of Titan's aerosol analogues placed under putative surface conditions of the satellite was performed. The surface of Titan was one of the targets of the Cassini-Huygens mission and of several of the Cassini orbiter instruments, especially ISS, VIMS and Radar. The first images revealed an interesting solid surface with features that suggest aeolian, tectonic, fluvial processes and even an impact structure[1]. Since then, more detailed descriptions of dunes, channels, lakes, impact craters and cryovolcanic structures have been documented[2]. The existence of an internal liquid water ocean, containing a few percent ammonia has been proposed[2, 3]. It has also been proposed that ammonia-water mixtures can erupt from the putative subsurface ocean leading to cryovolcanism[4]. The Cassini Titan Radar Mapper obtained Synthetic Aperture Radar (SAR) images during 2004 and 2005 that revealed a highly complex geology occurring at Titan's surface[5], among which cryovolcanic features play a central role. The composition of the cryomagma is mainly proposed to be a mixture of water ice and ammonia[6, 7, 8], although ammonia has not been directly detected on Titan, but suggested by recent Cassini-VIMS observations[9]. In order to understand the role that ammonia may play on the chemical transformation of atmospheric aerosols once they reach the surface, we designed the following protocol: laboratory analogues of Titan's aerosols were synthesized from a N2:CH4 (98:2) mixture irradiated under a continuous flow regime of 845 sccm inside which, a cold plasma of 180 W was established. The synthesized analogues were recovered and partitioned in several 10.0 mg samples that were placed in 4.0 mL-volume of aqueous ammonia solutions (25.00, 12.50, 6.25 and 3.125%) at different temperatures (298, 277, 253 and 93 K) for 10 weeks. After a derivatization process performed to the aerosols' refractory phase with N

  19. Molecular diagnosis of putative Stargardt disease probands by exome sequencing

    Directory of Open Access Journals (Sweden)

    Strom Samuel P

    2012-08-01

    Full Text Available Abstract Background The commonest genetic form of juvenile or early adult onset macular degeneration is Stargardt Disease (STGD caused by recessive mutations in the gene ABCA4. However, high phenotypic and allelic heterogeneity and a small but non-trivial amount of locus heterogeneity currently impede conclusive molecular diagnosis in a significant proportion of cases. Methods We performed whole exome sequencing (WES of nine putative Stargardt Disease probands and searched for potentially disease-causing genetic variants in previously identified retinal or macular dystrophy genes. Follow-up dideoxy sequencing was performed for confirmation and to screen for mutations in an additional set of affected individuals lacking a definitive molecular diagnosis. Results Whole exome sequencing revealed seven likely disease-causing variants across four genes, providing a confident genetic diagnosis in six previously uncharacterized participants. We identified four previously missed mutations in ABCA4 across three individuals. Likely disease-causing mutations in RDS/PRPH2, ELOVL, and CRB1 were also identified. Conclusions Our findings highlight the enormous potential of whole exome sequencing in Stargardt Disease molecular diagnosis and research. WES adequately assayed all coding sequences and canonical splice sites of ABCA4 in this study. Additionally, WES enables the identification of disease-related alleles in other genes. This work highlights the importance of collecting parental genetic material for WES testing as the current knowledge of human genome variation limits the determination of causality between identified variants and disease. While larger sample sizes are required to establish the precision and accuracy of this type of testing, this study supports WES for inherited early onset macular degeneration disorders as an alternative to standard mutation screening techniques.

  20. A putatively novel form of spontaneous coordination in neural activity.

    Science.gov (United States)

    Hermer-Vazquez, Raymond; Hermer-Vazquez, Linda; Srinivasan, Sridhar

    2009-04-06

    We simultaneously recorded local field potentials from three sites along the olfactory-entorhinal axis in rats lightly anesthetized with isoflurane, as part of another experiment. While analyzing the initial data from that experiment with spectrograms, we discovered a potentially novel form of correlated neural activity, with near-simultaneous occurrence across the three widely separated brain sites. After validating their existence further, we named these events Synchronous Frequency Bursts (SFBs). Here we report our initial investigations into their properties and their potential functional significance. In Experiment 1, we found that SFBs have highly regular properties, consisting of brief (approximately 250 ms), high amplitude bursts of LFP energy spanning frequency ranges from the delta band (1-4 Hz) to at least the low gamma band (30-50 Hz). SFBs occurred almost simultaneously across recording sites, usually with onsets sites. While the SFBs had fairly typical, exponentially decaying power spectral density plots, their coherence structure was unusual, with high peaks in several narrow frequency ranges and little coherence in other bands. In Experiment 2, we found that SFBs occurred far more often under light anesthesia than deeper anesthetic states, and were especially prevalent as the animals regained consciousness. Finally, in Experiment 3 we showed that SFBs occur simultaneously at a significant rate across brain sites from putatively different functional subsystems--olfactory versus motor pathways. We suggest that SFBs do not carry information per se, but rather, play a role in coordinating activity in different frequency bands, potentially brain-wide, as animals progress from sleep or anesthesia toward full consciousness.

  1. Tissue factor residues that putatively interact with membrane phospholipids.

    Directory of Open Access Journals (Sweden)

    Ke Ke

    Full Text Available Blood clotting is initiated by the two-subunit enzyme consisting of the plasma protease, factor VIIa (the catalytic subunit, bound to the integral membrane protein, tissue factor (the regulatory subunit. Molecular dynamics simulations have predicted that certain residues in the tissue factor ectodomain interact with phosphatidylserine headgroups to ensure optimal positioning of the tissue factor/factor VIIa complex relative to its membrane-bound protein substrates, factors IX and X. In this study, we individually mutated to alanine all the putative phosphatidylserine-interactive residues in the tissue factor ectodomain and measured their effects on tissue factor cofactor function (activation of factors IX and X by tissue factor/factor VIIa, and clotting of plasma. Some tissue factor mutants exhibited decreased activity in all three assays, with the most profound defects observed from mutations in or near the flexible loop from Lys159 to Gly164. The decreased activity of all of these tissue factor mutants could be partially or completely overcome by increasing the phosphatidylserine content of tissue factor-liposomes. Additionally, yeast surface display was used to screen a random library of tissue factor mutants for enhanced factor VIIa binding. Surprisingly, mutations at a single amino acid (Lys165 predominated, with the Lys165→Glu mutant exhibiting a 3-fold enhancement in factor VIIa binding affinity. Our studies reveal the functional contributions of residues in the C-terminal half of the tissue factor ectodomain that are implicated in interacting with phosphatidylserine headgroups to enhance tissue factor cofactor activity, possibly by allosterically modulating the conformation of the adjacent substrate-binding exosite region of tissue factor.

  2. A putative viral defence mechanism in archaeal cells

    Directory of Open Access Journals (Sweden)

    Reidun Lillestøl

    2006-01-01

    Full Text Available Clusters of regularly spaced direct repeats, separated by unconserved spacer sequences, are ubiquitous in archaeal chromosomes and occur in some plasmids. Some clusters constitute around 1% of chromosomal DNA. Similarly structured clusters, generally smaller, also occur in some bacterial chromosomes. Although early studies implicated these clusters in segregation/partition functions, recent evidence suggests that the spacer sequences derive from extrachromosomal elements, and, primarily, viruses. This has led to the proposal that the clusters provide a defence against viral propagation in cells, and that both the mode of inhibition of viral propagation and the mechanism of adding spacer-repeat units to clusters, are dependent on RNAs transcribed from the clusters. Moreover, the putative inhibitory apparatus (piRNA-based may be evolutionarily related to the interference RNA systems (siRNA and miRNA, which are common in eukarya. Here, we analyze all the current data on archaeal repeat clusters and provide some new insights into their diverse structures, transcriptional properties and mode of structural development. The results are consistent with larger cluster transcripts being processed at the centers of the repeat sequences and being further trimmed by exonucleases to yield a dominant, intracellular RNA species, which corresponds approximately to the size of a spacer. Furthermore, analysis of the extensive clusters of Sulfolobus solfataricus strains P1 and P2B provides support for the presence of a flanking sequence adjoining a cluster being a prerequisite for the incorporation of new spacer-repeat units, which occurs between the flanking sequence and the cluster. An archaeal database summarizing the data will be maintained at http://dac.molbio.ku.dk/dbs/SRSR/.

  3. Putative Risk Factors in Developmental Dyslexia: A Case-Control Study of Italian Children

    Science.gov (United States)

    Mascheretti, Sara; Marino, Cecilia; Simone, Daniela; Quadrelli, Ermanno; Riva, Valentina; Cellino, Maria Rosaria; Maziade, Michel; Brombin, Chiara; Battaglia, Marco

    2015-01-01

    Although dyslexia runs in families, several putative risk factors that cannot be immediately identified as genetic predict reading disability. Published studies analyzed one or a few risk factors at a time, with relatively inconsistent results. To assess the contribution of several putative risk factors to the development of dyslexia, we conducted…

  4. Putative Risk Factors in Developmental Dyslexia: A Case-Control Study of Italian Children

    Science.gov (United States)

    Mascheretti, Sara; Marino, Cecilia; Simone, Daniela; Quadrelli, Ermanno; Riva, Valentina; Cellino, Maria Rosaria; Maziade, Michel; Brombin, Chiara; Battaglia, Marco

    2015-01-01

    Although dyslexia runs in families, several putative risk factors that cannot be immediately identified as genetic predict reading disability. Published studies analyzed one or a few risk factors at a time, with relatively inconsistent results. To assess the contribution of several putative risk factors to the development of dyslexia, we conducted…

  5. Antagonistic activity expressed by Shigella sonnei: identification of a putative new bacteriocin

    Directory of Open Access Journals (Sweden)

    Mireille Angela Bernardes Sousa

    2013-09-01

    Full Text Available Bacteriocins are antibacterial, proteinaceous substances that mediate microbial dynamics. Bacteriocin production is a highly disseminated property among all major lineages of bacteria, including Shigella. In this paper, we addressed the purification and characterisation of a bacteriocin produced by a Shigella sonnei strain (SS9 isolated from a child with acute diarrhoea. The substance was purified through ammonium-sulphate precipitation and sequential steps of chromatography. The intracellular fraction obtained at 75% ammonium sulphate maintained activity following exposure to pH values from 1-11 and storage at -80ºC for more than two years and was inactivated by high temperatures and proteases. The molecular mass of the purified bacteriocin was determined by mass spectrometry to be 18.56 kDa. The N-terminal sequence of the bacteriocin did not match any other antibacterial proteins described. A putative new bacteriocin produced by S. sonnei has been detected. This bacteriocin may represent a newly described protein or a previously described protein with a newly detected function. Considering that SS9 expresses antagonism against other diarrhoeagenic bacteria, the bacteriocin may contribute to S. sonnei virulence and is potentially applicable to either preventing or controlling diarrhoeal disease.

  6. Malignant transformation of a putative eyelid papilloma to squamous cell carcinoma in a dog.

    Science.gov (United States)

    Wiggans, K Tomo; Hoover, Clare E; Ehrhart, E J; Wobeser, Bruce K; Cohen, Loren B; Gionfriddo, Juliet R

    2013-07-01

    A 6-year-old female spayed Chihuahua was presented for the evaluation of generalized pigmented cutaneous masses, one of which was present on the lower right eyelid. The dog was not on immunosuppressive medications and did not have historical or laboratory evidence of underlying endocrine disease, including hypothyroidism and hyperadrenocorticism. Histopathology, immunohistochemistry, and polymerase chain reaction of a cutaneous biopsy from the left antebrachium containing representative lesions confirmed viral papillomatosis. Additionally, histopathology of the antebrachial mass revealed regions of epithelial dysplasia suggestive of possible early transformation to malignancy. Over the course of 5 months, the mass on the right lower eyelid progressed to encompass and efface the majority of the eyelid margin. Additionally, the eyelid tumor had changed from an ovoid, brown pigmented mass to an irregular, flesh-colored mass. At the dog's last recheck examination, a corneal ulcer had developed beneath the irregular dorsal margin of the tumor. Histopathology of the eyelid mass was consistent with squamous cell carcinoma (SCC) and was positive for the presence of papillomavirus using polymerase chain reaction. This report describes the transformation of a putative viral eyelid papilloma into a malignant SCC in an adult dog.

  7. "SP-G", a putative new surfactant protein--tissue localization and 3D structure.

    Directory of Open Access Journals (Sweden)

    Felix Rausch

    Full Text Available Surfactant proteins (SP are well known from human lung. These proteins assist the formation of a monolayer of surface-active phospholipids at the liquid-air interface of the alveolar lining, play a major role in lowering the surface tension of interfaces, and have functions in innate and adaptive immune defense. During recent years it became obvious that SPs are also part of other tissues and fluids such as tear fluid, gingiva, saliva, the nasolacrimal system, and kidney. Recently, a putative new surfactant protein (SFTA2 or SP-G was identified, which has no sequence or structural identity to the already know surfactant proteins. In this work, computational chemistry and molecular-biological methods were combined to localize and characterize SP-G. With the help of a protein structure model, specific antibodies were obtained which allowed the detection of SP-G not only on mRNA but also on protein level. The localization of this protein in different human tissues, sequence based prediction tools for posttranslational modifications and molecular dynamic simulations reveal that SP-G has physicochemical properties similar to the already known surfactant proteins B and C. This includes also the possibility of interactions with lipid systems and with that, a potential surface-regulatory feature of SP-G. In conclusion, the results indicate SP-G as a new surfactant protein which represents an until now unknown surfactant protein class.

  8. KLIKK proteases of Tannerella forsythia: putative virulence factors with a unique domain structure

    Science.gov (United States)

    Ksiazek, Miroslaw; Mizgalska, Danuta; Eick, Sigrum; Thøgersen, Ida B.; Enghild, Jan J.; Potempa, Jan

    2015-01-01

    Comparative genomics of virulent Tannerella forsythia ATCC 43037 and a close health-associated relative, Tannerella BU063, revealed, in the latter, the absence of an entire array of genes encoding putative secretory proteases that possess a nearly identical C-terminal domain (CTD) that ends with a -Lys-Leu-Ile-Lys-Lys motif. This observation suggests that these proteins, referred to as KLIKK proteases, may function as virulence factors. Re-sequencing of the loci of the KLIKK proteases found only six genes grouped in two clusters. All six genes were expressed by T. forsythia in routine culture conditions, although at different levels. More importantly, a transcript of each gene was detected in gingival crevicular fluid (GCF) from periodontitis sites infected with T. forsythia indicating that the proteases are expressed in vivo. In each protein, a protease domain was flanked by a unique N-terminal profragment and a C-terminal extension ending with the CTD. Partially purified recombinant proteases showed variable levels of proteolytic activity in zymography gels and toward protein substrates, including collagen, gelatin, elastin, and casein. Taken together, these results indicate that the pathogenic strain of T. forsythia secretes active proteases capable of degrading an array of host proteins, which likely represents an important pathogenic feature of this bacterium. PMID:25954253

  9. Season of conception in rural gambia affects DNA methylation at putative human metastable epialleles.

    Directory of Open Access Journals (Sweden)

    Robert A Waterland

    Full Text Available Throughout most of the mammalian genome, genetically regulated developmental programming establishes diverse yet predictable epigenetic states across differentiated cells and tissues. At metastable epialleles (MEs, conversely, epigenotype is established stochastically in the early embryo then maintained in differentiated lineages, resulting in dramatic and systemic interindividual variation in epigenetic regulation. In the mouse, maternal nutrition affects this process, with permanent phenotypic consequences for the offspring. MEs have not previously been identified in humans. Here, using an innovative 2-tissue parallel epigenomic screen, we identified putative MEs in the human genome. In autopsy samples, we showed that DNA methylation at these loci is highly correlated across tissues representing all 3 embryonic germ layer lineages. Monozygotic twin pairs exhibited substantial discordance in DNA methylation at these loci, suggesting that their epigenetic state is established stochastically. We then tested for persistent epigenetic effects of periconceptional nutrition in rural Gambians, who experience dramatic seasonal fluctuations in nutritional status. DNA methylation at MEs was elevated in individuals conceived during the nutritionally challenged rainy season, providing the first evidence of a permanent, systemic effect of periconceptional environment on human epigenotype. At MEs, epigenetic regulation in internal organs and tissues varies among individuals and can be deduced from peripheral blood DNA. MEs should therefore facilitate an improved understanding of the role of interindividual epigenetic variation in human disease.

  10. Lectin chromatography/mass spectrometry discovery workflow identifies putative biomarkers of aggressive breast cancers.

    Science.gov (United States)

    Drake, Penelope M; Schilling, Birgit; Niles, Richard K; Prakobphol, Akraporn; Li, Bensheng; Jung, Kwanyoung; Cho, Wonryeon; Braten, Miles; Inerowicz, Halina D; Williams, Katherine; Albertolle, Matthew; Held, Jason M; Iacovides, Demetris; Sorensen, Dylan J; Griffith, Obi L; Johansen, Eric; Zawadzka, Anna M; Cusack, Michael P; Allen, Simon; Gormley, Matthew; Hall, Steven C; Witkowska, H Ewa; Gray, Joe W; Regnier, Fred; Gibson, Bradford W; Fisher, Susan J

    2012-04-06

    We used a lectin chromatography/MS-based approach to screen conditioned medium from a panel of luminal (less aggressive) and triple negative (more aggressive) breast cancer cell lines (n=5/subtype). The samples were fractionated using the lectins Aleuria aurantia (AAL) and Sambucus nigra agglutinin (SNA), which recognize fucose and sialic acid, respectively. The bound fractions were enzymatically N-deglycosylated and analyzed by LC-MS/MS. In total, we identified 533 glycoproteins, ∼90% of which were components of the cell surface or extracellular matrix. We observed 1011 glycosites, 100 of which were solely detected in ≥3 triple negative lines. Statistical analyses suggested that a number of these glycosites were triple negative-specific and thus potential biomarkers for this tumor subtype. An analysis of RNaseq data revealed that approximately half of the mRNAs encoding the protein scaffolds that carried potential biomarker glycosites were up-regulated in triple negative vs luminal cell lines, and that a number of genes encoding fucosyl- or sialyltransferases were differentially expressed between the two subtypes, suggesting that alterations in glycosylation may also drive candidate identification. Notably, the glycoproteins from which these putative biomarker candidates were derived are involved in cancer-related processes. Thus, they may represent novel therapeutic targets for this aggressive tumor subtype.

  11. Markiana nigripinnis (Perugia, 1891 as a putative member of the subfamily Stevardiinae (Characiformes: Characidae: spermatic evidence

    Directory of Open Access Journals (Sweden)

    Clarianna Martins Baicere-Silva

    Full Text Available The genus Markiana was until recently recognized as incertae sedis in the family Characidae, even though alternative placements for this genus have been advanced since its original description. More recently, it was hypothesized that Markiana nigripinnis is part of a clade informally named the Astyanax clade, indicating the putative close relationship of Markiana with the genus Astyanax. Examination of sperm ultrastructure of representatives of Astyanax and M. nigripinnis shows no evidence for this hypothesized close relationship. Rather, the spermatozoa of M. nigripinnis share characters found in spermatozoa of the non-inseminating members of the subfamily Stevardiinae, such as an angle of nuclear rotation equal to 85º resulting in a lateral position of the double nuclear fossa and flagellum. As with the non-inseminating Stevardiinae, sperm nuclei are also slightly elongate toward the flagellum, the proximal centriole is partially inside the nuclear fossa and anterior and oblique to the distal centriole, and the midpiece is short and strongly asymmetric. Additionally, M. nigripinnis shares with the other members of the Stevardiinae the presence of only four teeth in the inner row of the premaxillary and a short triangular ectopterygoid, which is never more than twice the length of the palatine.

  12. Antagonistic activity expressed by Shigella sonnei: identification of a putative new bacteriocin.

    Science.gov (United States)

    Sousa, Mireille Ângela Bernardes; Farias, Luiz de Macêdo; Oliveira, Patrícia Luciana de; Moreira, Jaqueline Silvana; Apolônio, Ana Carolina Morais; Oliveira, Jamil Silvano; Santoro, Marcelo Matos; Mendes, Edilberto Nogueira; Magalhães, Paula Prazeres

    2013-09-01

    Bacteriocins are antibacterial, proteinaceous substances that mediate microbial dynamics. Bacteriocin production is a highly disseminated property among all major lineages of bacteria, including Shigella. In this paper, we addressed the purification and characterisation of a bacteriocin produced by a Shigella sonnei strain (SS9) isolated from a child with acute diarrhoea. The substance was purified through ammonium-sulphate precipitation and sequential steps of chromatography. The intracellular fraction obtained at 75% ammonium sulphate maintained activity following exposure to pH values from 1-11 and storage at -80ºC for more than two years and was inactivated by high temperatures and proteases. The molecular mass of the purified bacteriocin was determined by mass spectrometry to be 18.56 kDa. The N-terminal sequence of the bacteriocin did not match any other antibacterial proteins described. A putative new bacteriocin produced by S. sonnei has been detected. This bacteriocin may represent a newly described protein or a previously described protein with a newly detected function. Considering that SS9 expresses antagonism against other diarrhoeagenic bacteria, the bacteriocin may contribute to S. sonnei virulence and is potentially applicable to either preventing or controlling diarrhoeal disease.

  13. A Putative Blood-Based Biomarker for Autism Spectrum Disorder-Associated Ileocolitis

    Science.gov (United States)

    Walker, Stephen J.; Beavers, Daniel P.; Fortunato, John; Krigsman, Arthur

    2016-01-01

    Gastrointestinal symptoms are common in children with autism spectrum disorder (ASD). A significant proportion of children with ASD and gastrointestinal symptoms have histologic evidence of ileocolitis (inflammation of the terminal ileum and/or colon). We previously reported the molecular characterization of gastrointestinal biopsy tissue from ASD children with ileocolitis (ASDIC+) compared to anatomically similar inflamed tissue from typically developing children with inflammatory bowel disease (IBD; i.e. Crohn’s disease or ulcerative colitis) and typically developing children with gastrointestinal symptoms but no evidence of gastrointestinal mucosal inflammation (TDIC−). ASDIC+ children had a gene expression profile that, while primarily overlapping with known IBD, had distinctive differences. The present study confirms these findings and replicates this molecular characterization in a second cohort of cases (ASDIC+) and controls (TDIC−). In these two separate case/control mucosal-based cohorts, we have demonstrated overlap of 59 differentially expressed transcripts (DETs) unique to inflamed ileocolonic tissue from symptomatic ASDIC+ children. We now report that 9 of these 59 transcripts are also differentially expressed in the peripheral blood of the second cohort of ASDIC+ children. This set of transcripts represents a putative blood-based biomarker for ASD-associated ileocolonic inflammation. PMID:27767057

  14. Detoxification of polycyclic aromatic hydrocarbons (PAHs) in Arabidopsis thaliana involves a putative flavonol synthase.

    Science.gov (United States)

    Hernández-Vega, Juan C; Cady, Brian; Kayanja, Gilbert; Mauriello, Anthony; Cervantes, Natalie; Gillespie, Andrea; Lavia, Lisa; Trujillo, Joshua; Alkio, Merianne; Colón-Carmona, Adán

    2017-01-05

    Polycyclic aromatic hydrocarbons (PAHs) are environmental contaminants with cytotoxic, teratogenic and carcinogenic properties. Bioremediation studies with bacteria have led to the identification of dioxygenases (DOXs) in the first step to degrade these recalcitrant compounds. In this study, we characterized the role of the Arabidopsis thaliana AT5G05600, a putative DOX of the flavonol synthase family, in the transformation of PAHs. Phenotypic analysis of loss-of-function mutant lines showed that these plant lines were less sensitive to the toxic effects of phenanthrene, suggesting possible roles of this gene in PAH degradation in vivo. Interestingly, these mutant lines showed less accumulation of H2O2 after PAH exposure. Transgenic lines over-expressing At5g05600 showed a hypersensitive response and more oxidative stress after phenanthrene treatments. Moreover, fluorescence spectra results of biochemical assays with the recombinant His-tagged protein AT5G05600 detected chemical modifications of phenanthrene. Taken together, these results support the hypothesis that AT5G05600 is involved in the catabolism of PAHs and the accumulation of toxic intermediates during PAH biotransformation in plants. This research represents the first step in the design of transgenic plants with the potential to degrade PAHs, leading to the development of vigorous plant varieties that can reduce the levels of these pollutants in the environment. Copyright © 2016 Elsevier B.V. All rights reserved.

  15. KLIKK proteases of Tannerella forsythia: putative virulence factors with a unique domain structure

    Directory of Open Access Journals (Sweden)

    Miroslaw eKsiazek

    2015-04-01

    Full Text Available Comparative genomics of virulent Tannerella forsythia ATCC 43037 and a close health-associated relative, Tannerella BU063, revealed, in the latter, the absence of an entire array of genes encoding putative secretory proteases that possess a nearly identical C-terminal domain (CTD that ends with a -Lys-Leu-Ile-Lys-Lys motif. This observation suggests that these proteins, referred to as KLIKK proteases, may function as virulence factors. Re-sequencing of the loci of the KLIKK proteases found only six genes grouped in two clusters. All six genes were expressed by T. forsythia in routine culture conditions, although at different levels. More importantly, a transcript of each gene was detected in gingival crevicular fluid (GCF from periodontitis sites infected with T. forsythia indicating that the proteases are expressed in vivo. In each protein, a protease domain was flanked by a unique N-terminal profragment and a C-terminal extension ending with the CTD. Partially purified recombinant proteases showed variable levels of proteolytic activity in zymography gels and toward protein substrates, including collagen, gelatin, elastin, and casein. Taken together, these results indicate that the pathogenic strain of T. forsythia secretes active proteases capable of degrading an array of host proteins, which likely represents an important pathogenic feature of this bacterium.

  16. KLIKK proteases of Tannerella forsythia: putative virulence factors with a unique domain structure.

    Science.gov (United States)

    Ksiazek, Miroslaw; Mizgalska, Danuta; Eick, Sigrum; Thøgersen, Ida B; Enghild, Jan J; Potempa, Jan

    2015-01-01

    Comparative genomics of virulent Tannerella forsythia ATCC 43037 and a close health-associated relative, Tannerella BU063, revealed, in the latter, the absence of an entire array of genes encoding putative secretory proteases that possess a nearly identical C-terminal domain (CTD) that ends with a -Lys-Leu-Ile-Lys-Lys motif. This observation suggests that these proteins, referred to as KLIKK proteases, may function as virulence factors. Re-sequencing of the loci of the KLIKK proteases found only six genes grouped in two clusters. All six genes were expressed by T. forsythia in routine culture conditions, although at different levels. More importantly, a transcript of each gene was detected in gingival crevicular fluid (GCF) from periodontitis sites infected with T. forsythia indicating that the proteases are expressed in vivo. In each protein, a protease domain was flanked by a unique N-terminal profragment and a C-terminal extension ending with the CTD. Partially purified recombinant proteases showed variable levels of proteolytic activity in zymography gels and toward protein substrates, including collagen, gelatin, elastin, and casein. Taken together, these results indicate that the pathogenic strain of T. forsythia secretes active proteases capable of degrading an array of host proteins, which likely represents an important pathogenic feature of this bacterium.

  17. Mining Representative Subset Based on Fuzzy Clustering

    Institute of Scientific and Technical Information of China (English)

    ZHOU Hongfang; FENG Boqin; L(U) Lintao

    2007-01-01

    Two new concepts-fuzzy mutuality and average fuzzy entropy are presented. Then based on these concepts, a new algorithm-RSMA (representative subset mining algorithm) is proposed, which can abstract representative subset from massive data.To accelerate the speed of producing representative subset, an improved algorithm-ARSMA(accelerated representative subset mining algorithm) is advanced, which adopt combining putting forward with backward strategies. In this way, the performance of the algorithm is improved. Finally we make experiments on real datasets and evaluate the representative subset. The experiment shows that ARSMA algorithm is more excellent than RandomPick algorithm either on effectiveness or efficiency.

  18. Identification and expression profiling of putative odorant-binding proteins in the malaria mosquitoes, Anopheles gambiae and A.arabiensis

    Institute of Scientific and Technical Information of China (English)

    LI; Zhengxi; Jing-Jiang; ZHOU; SHEN; Zuorui; Lin; FIELD

    2004-01-01

    Olfaction plays a major role in host-seeking behaviour of mosquitoes. An informatics-based genome-wide analysis of odorant-binding protein (OBP) homologues is undertaken,and 32 putative OBP genes in total in the whole genome sequences of Anopheles gambiae are identified. Tissue-specific expression patterns of all A. gambiae OBP candidates are determined by semi-quantitative Reverse Transcription (RT)-PCR using mosquito actin gene as internal expression control standard. The results showed that 20 OBP candidates had strong expression in mosquito olfactory tissues (female antennae), which indicate that OBPs may play an important role in regulating mosquito olfactory behaviours. Species-specific expression patterns of all putative anopheline OBPs are also studied in two of the most important malaria vectors in A. gambiae complex, i.e.A. gambiae and A. arabiensis, which found 12 of the putative OBP genes examined displayed species-differential expression patterns. The cumulative relative expression intensity of the OBPs in A. arabiensis antennae was higher than that in A. gambiae (the ratio is 1441.45:1314.12), which might be due to their different host preference behaviour. While A.gambiae is a highly anthropophilic mosquito, A. arabiensis is more opportunistic (varying from anthropophilic to zoophilic). So the latter should need more OBPs to support its host selection preference. Identification of mosquito OBPs and verification of their tissue- and species-specific expression patterns represent the first step towards further molecular analysis of mosquito olfactory mechanism, such as recombinant expression and ligand identification.

  19. Pyrosequencing of the Camptotheca acuminata transcriptome reveals putative genes involved in camptothecin biosynthesis and transport

    Directory of Open Access Journals (Sweden)

    Sun Yongzhen

    2011-10-01

    Full Text Available Abstract Background Camptotheca acuminata is a Nyssaceae plant, often called the "happy tree", which is indigenous in Southern China. C. acuminata produces the terpenoid indole alkaloid, camptothecin (CPT, which exhibits clinical effects in various cancer treatments. Despite its importance, little is known about the transcriptome of C. acuminata and the mechanism of CPT biosynthesis, as only few nucleotide sequences are included in the GenBank database. Results From a constructed cDNA library of young C. acuminata leaves, a total of 30,358 unigenes, with an average length of 403 bp, were obtained after assembly of 74,858 high quality reads using GS De Novo assembler software. Through functional annotation, a total of 21,213 unigenes were annotated at least once against the NCBI nucleotide (Nt, non-redundant protein (Nr, Uniprot/SwissProt, Kyoto Encyclopedia of Genes and Genomes (KEGG, and Arabidopsis thaliana proteome (TAIR databases. Further analysis identified 521 ESTs representing 20 enzyme genes that are involved in the backbone of the CPT biosynthetic pathway in the library. Three putative genes in the upstream pathway, including genes for geraniol-10-hydroxylase (CaPG10H, secologanin synthase (CaPSCS, and strictosidine synthase (CaPSTR were cloned and analyzed. The expression level of the three genes was also detected using qRT-PCR in C. acuminata. With respect to the branch pathway of CPT synthesis, six cytochrome P450s transcripts were selected as candidate transcripts by detection of transcript expression in different tissues using qRT-PCR. In addition, one glucosidase gene was identified that might participate in CPT biosynthesis. For CPT transport, three of 21 transcripts for multidrug resistance protein (MDR transporters were also screened from the dataset by their annotation result and gene expression analysis. Conclusion This study produced a large amount of transcriptome data from C. acuminata by 454 pyrosequencing. According to

  20. Putative functions of extracellular matrix glycoproteins in secondary palate morphogenesis

    Science.gov (United States)

    d'Amaro, Rocca; Scheidegger, Rolf; Blumer, Susan; Pazera, Pawel; Katsaros, Christos; Graf, Daniel; Chiquet, Matthias

    2012-01-01

    Cleft palate is a common birth defect in humans. Elevation and fusion of paired palatal shelves are coordinated by growth and transcription factors, and mutations in these can cause malformations. Among the effector genes for growth factor signaling are extracellular matrix (ECM) glycoproteins. These provide substrates for cell adhesion (e.g., fibronectin, tenascins), but also regulate growth factor availability (e.g., fibrillins). Cleft palate in Bmp7 null mouse embryos is caused by a delay in palatal shelf elevation. In contrast, palatal shelves of Tgf-β3 knockout mice elevate normally, but a cleft develops due to their failure to fuse. However, nothing is known about a possible functional interaction between specific ECM proteins and Tgf-β/Bmp family members in palatogenesis. To start addressing this question, we studied the mRNA and protein distribution of relevant ECM components during secondary palate development, and compared it to growth factor expression in wildtypewild type and mutant mice. We found that fibrillin-2 (but not fibrillin-1) mRNA appeared in the mesenchyme of elevated palatal shelves adjacent to the midline epithelial cells, which were positive for Tgf-β3 mRNA. Moreover, midline epithelial cells started expressing fibronectin upon contact of the two palatal shelves. These findings support the hypothesis that fibrillin-2 and fibronectin are involved in regulating the activity of Tgf-β3 at the fusing midline. In addition, we observed that tenascin-W (but not tenascin-C) was misexpressed in palatal shelves of Bmp7-deficient mouse embryos. In contrast to tenascin-C, tenascin-W secretion was strongly induced by Bmp7 in embryonic cranial fibroblasts in vitro. These results are consistent with a putative function for tenascin-W as a target of Bmp7 signaling during palate elevation. Our results indicate that distinct ECM proteins are important for morphogenesis of the secondary palate, both as downstream effectors and as regulators of Tgf

  1. Representing Others in a Public Good Game

    Directory of Open Access Journals (Sweden)

    Karen Evelyn Hauge

    2015-09-01

    Full Text Available In many important public good situations the decision-making power and authority is delegated to representatives who make binding decisions on behalf of a larger group. The purpose of this study is to compare contribution decisions made by individuals with contribution decisions made by group representatives. We present the results from a laboratory experiment that compares decisions made by individuals in inter-individual public good games with decisions made by representatives on behalf of their group in inter-group public good games. Our main finding is that contribution behavior differs between individuals and group representatives, but only for women. While men’s choices are equally self-interested as individuals and group representatives, women make less self-interested choices as group representatives.

  2. Represented Speech in Qualitative Health Research

    DEFF Research Database (Denmark)

    Musaeus, Peter

    2017-01-01

    Represented speech refers to speech where we reference somebody. Represented speech is an important phenomenon in everyday conversation, health care communication, and qualitative research. This case will draw first from a case study on physicians’ workplace learning and second from a case study...... on nurses’ apprenticeship learning. The aim of the case is to guide the qualitative researcher to use own and others’ voices in the interview and to be sensitive to represented speech in everyday conversation. Moreover, reported speech matters to health professionals who aim to represent the voice...... of their patients. Qualitative researchers and students might learn to encourage interviewees to elaborate different voices or perspectives. Qualitative researchers working with natural speech might pay attention to how people talk and use represented speech. Finally, represented speech might be relevant...

  3. Representing Quadric Surfaces Using NURBS Surfaces

    Institute of Scientific and Technical Information of China (English)

    秦开怀

    1997-01-01

    A method for representing quadrc surfaces using NURBS is presented.By means of the necessary and sufficient conditons for NURBS curves to precisely represent circular arcs and other conics,quadric surfaces can be represented by NURBS surfaces with fewer control vertices.The method can be used not only for NURBS surface representation of quadric surfaces,but also for rounding polyhedrons.Many examples are given in the paper.

  4. Evidence that the Malaria Parasite Plasmodium falciparum Putative Rhoptry Protein 2 Localizes to the Golgi Apparatus throughout the Erythrocytic Cycle.

    Science.gov (United States)

    Hallée, Stéphanie; Richard, Dave

    2015-01-01

    Invasion of a red blood cell by Plasmodium falciparum merozoites is an essential step in the malaria lifecycle. Several of the proteins involved in this process are stored in the apical complex of the merozoite, a structure containing secretory organelles that are released at specific times during invasion. The molecular players involved in erythrocyte invasion thus represent potential key targets for both therapeutic and vaccine-based strategies to block parasite development. In our quest to identify and characterize new effectors of invasion, we investigated the P. falciparum homologue of a P. berghei protein putatively localized to the rhoptries, the Putative rhoptry protein 2 (PbPRP2). We show that in P. falciparum, the protein colocalizes extensively with the Golgi apparatus across the asexual erythrocytic cycle. Furthermore, imaging of merozoites caught at different times during invasion show that PfPRP2 is not secreted during the process instead staying associated with the Golgi apparatus. Our evidence therefore suggests that PfPRP2 is a Golgi protein and that it is likely not a direct effector in the process of merozoite invasion.

  5. The putative Leishmania telomerase RNA (LeishTER undergoes trans-splicing and contains a conserved template sequence.

    Directory of Open Access Journals (Sweden)

    Elton J R Vasconcelos

    Full Text Available Telomerase RNAs (TERs are highly divergent between species, varying in size and sequence composition. Here, we identify a candidate for the telomerase RNA component of Leishmania genus, which includes species that cause leishmaniasis, a neglected tropical disease. Merging a thorough computational screening combined with RNA-seq evidence, we mapped a non-coding RNA gene localized in a syntenic locus on chromosome 25 of five Leishmania species that shares partial synteny with both Trypanosoma brucei TER locus and a putative TER candidate-containing locus of Crithidia fasciculata. Using target-driven molecular biology approaches, we detected a ∼2,100 nt transcript (LeishTER that contains a 5' spliced leader (SL cap, a putative 3' polyA tail and a predicted C/D box snoRNA domain. LeishTER is expressed at similar levels in the logarithmic and stationary growth phases of promastigote forms. A 5'SL capped LeishTER co-immunoprecipitated and co-localized with the telomerase protein component (TERT in a cell cycle-dependent manner. Prediction of its secondary structure strongly suggests the existence of a bona fide single-stranded template sequence and a conserved C[U/C]GUCA motif-containing helix II, representing the template boundary element. This study paves the way for further investigations on the biogenesis of parasite TERT ribonucleoproteins (RNPs and its role in parasite telomere biology.

  6. Prioritization of putative metabolite identifications in LC-MS/MS experiments using a computational pipeline.

    Science.gov (United States)

    Zhou, Bin; Xiao, Jun Feng; Ressom, Habtom W

    2013-01-01

    One of the major bottle-necks in current LC-MS-based metabolomic investigations is metabolite identification. An often-used approach is to first look up metabolites from databases through peak mass, followed by verification of the obtained putative identifications using MS/MS data. However, the mass-based search may provide inappropriate putative identifications when the observed peak is from isotopes, fragments, or adducts. In addition, a large fraction of peaks is often left with multiple putative identifications. To differentiate these putative identifications, manual verification of metabolites through comparison between biological samples and authentic compounds is necessary. However, such experiments are laborious, especially when multiple putative identifications are encountered. It is desirable to use computational approaches to obtain more reliable putative identifications and prioritize them before performing experimental verification of the metabolites. In this article, a computational pipeline is proposed to assist metabolite identification with improved metabolome coverage and prioritization capability. Multiple publicly available software tools and databases, along with in-house developed algorithms, are utilized to fully exploit the information acquired from LC-MS/MS experiments. The pipeline is successfully applied to identify metabolites on the basis of LC-MS as well as MS/MS data. Using accurate masses, retention time values, MS/MS spectra, and metabolic pathways/networks, more appropriate putative identifications are retrieved and prioritized to guide subsequent metabolite verification experiments.

  7. Representing Object Colour in Language Comprehension

    Science.gov (United States)

    Connell, Louise

    2007-01-01

    Embodied theories of cognition hold that mentally representing something "red" engages the neural subsystems that respond to environmental perception of that colour. This paper examines whether implicit perceptual information on object colour is represented during sentence comprehension even though doing so does not necessarily facilitate task…

  8. DNA and RNA from Uninfected Vertebrate Cells Contain Nucleotide Sequences Related to the Putative Transforming Gene of Avian Myelocytomatosis Virus

    Science.gov (United States)

    Sheiness, Diana; Bishop, J. Michael

    1979-01-01

    The avian carcinoma virus MC29 (MC29V) contains a sequence of approximately 1,500 nucleotides which may represent a gene responsible for tumorigenesis by MC29V. We present evidence that MC29V has acquired this nucleotide sequence from the DNA of its host. The host sequence which has been incorporated by MC29V is transcribed into RNA in uninfected chicken cells and thus probably encodes a cellular gene. We have prepared radioactive DNA complementary to the putative MC29V transforming gene (cDNAmc29) and have found that sequences homologous to cDNAmc29 are present in the genomes of several uninfected vertebrate species. The DNA of chicken, the natural host for MC29V, contains at least 90% of the sequences represented by cDNAmc29. DNAs from other animals show significant but decreasing amounts of complementarity to cDNAmc29 in accordance with their evolutionary divergence from chickens; the thermal stabilities of duplexes formed between cDNAmc29 and avian DNAs also reflect phylogenetic divergence. Sequences complementary to cDNAmc29 are transcribed into approximately 10 copies per cell of polyadenylated RNA in uninfected chicken fibroblasts. Thus, the vertebrate homolog of cDNAmc29 may be a gene which has been conserved throughout vertebrate evolution and which served as a progenitor for the putative transforming gene of MC29V. Recent experiments suggest that the putative transforming gene of avian erythroblastosis virus, like that of MC29V, may have arisen by incorporation of a host gene (Stehelin et al., personal communication). These findings for avian erythroblastosis virus and MC29V closely parallel previous results, suggesting a host origin for src (D. H. Spector, B. Baker, H. E. Varmus, and J. M. Bishop, Cell 13:381-386, 1978; D. H. Spector, K. Smith, T. Padgett, P. McCombe, D. Roulland-Dussoix, C. Moscovici, H. E. Varmus, and J. M. Bishop, Cell 13:371-379, 1978; D. H. Spector, H. E. Varmus, and J. M. Bishop, Proc. Natl. Acad. Sci. U.S.A. 75:4102-4106, 1978; D

  9. Tropomyosin-1, A Putative Tumor-Suppressor and a Biomarker of Human Breast Cancer

    Science.gov (United States)

    2004-10-01

    cDNA. Lobular carcinoma - 2 A polyclonal pan-TM antibody that recognizes multiple TM Phyllodes tumor - 1 Not determined from the initial pathology...AD Award Number: DAMD17-98-1-8162 TITLE: Tropomyosin-1, A Putative Tumor -Suppressor and a Biomarker of Human Breast Cancer PRINCIPAL INVESTIGATOR...4. TITLE AND SUBTITLE 5. FUNDING NUMBERS Tropomyosin-l, A Putative Tumor -Suppressor and a Biomarker DAMD17-98-1-8162 of Human Breast Cancer 6. A UTHOR

  10. Fluoroquinolone-Resistant Haemophilus parasuis Isolates Exhibit More Putative Virulence Factors than Their Susceptible Counterparts

    OpenAIRE

    Zhang, Qiang; Liu, Jiantao; Yan, Shuxian; Yang, Yujie; Zhang, Anding; Jin, Meilin

    2013-01-01

    The prevalence of 23 putative virulence factors among fluoroquinolone-susceptible and -resistant Haemophilus parasuis isolates was analyzed. Putative hemolysin precursor, fimbrial assembly chaperone, and type I site-specific restriction modification system R subunit genes were more prevalent among fluoroquinolone-resistant H. parasuis isolates than among fluoroquinolone-susceptible H. parasuis isolates. Fluoroquinolone resistance may be associated with an increase in the presence of some viru...

  11. Genetic diversity of donkey populations from the putative centers of domestication.

    Science.gov (United States)

    Rosenbom, S; Costa, V; Al-Araimi, N; Kefena, E; Abdel-Moneim, A S; Abdalla, M A; Bakhiet, A; Beja-Pereira, A

    2015-02-01

    Donkey domestication drastically changed ancient transport systems in Africa and Asia, enabling overland circulation of people and goods and influencing the organization of early cities and pastoral societies. Genetic studies based on mtDNA have pointed to the African wild ass as the most probable ancestor of the domestic donkey, but questions regarding its center of origin remain unanswered. Endeavoring to pinpoint the geographical origin of domestic donkey, we assessed levels and patterns of genetic diversity at 15 microsatellite loci from eight populations, representing its three hypothesized centers of origin: northeast Africa, the Near East and the Arabian Peninsula. Additionally, we compared the donkey genotypes with those from their wild relative, the African wild ass (Equus africanus somaliensis) to visualize patterns of differentiation among wild and domestic individuals. Obtained results revealed limited variation in levels of unbiased expected heterozygosity across populations in studied geographic regions (ranging from 0.637 in northeast Africa to 0.679 in the Near East). Both allelic richness (Ar) and private allelic richness presented considerably higher values in northeast Africa and in the Arabian Peninsula. By looking at variation at the country level, for each region, we were able to identify Sudan and Yemen as the countries possessing higher allelic richness and, cumulatively, Yemen also presented higher values for private allelic richness. Our results support previously proposed northeast Africa as a putative center of origin, but the high levels of unique diversity in Yemen opens the possibility of considering this region as yet another center of origin for this species.

  12. Epidermal growth factor receptor in the prawn Macrobrachium rosenbergii: function and putative signaling cascade.

    Science.gov (United States)

    Sharabi, Omri; Ventura, Tomer; Manor, Rivka; Aflalo, Eliahu D; Sagi, Amir

    2013-09-01

    Epidermal growth factor receptors (EGFRs) are highly conserved members of the tyrosine kinase receptor superfamily found in metazoans and plants. In arthropods, EGFRs are vital for the proper development of embryos and of adult limbs, gonads, and eyes as well as affecting body size. In searching for genes involved in the growth and development of our model organism, the decapod crustacean (Macrobrachium rosenbergii), a comprehensive transcript library was established using next-generation sequencing. Using this library, the expression of several genes assigned to the signal transduction pathways mediated by EGFRs was observed, including a transcript encoding M. rosenbergii EGFR (Mr-EGFR), several potential ligands upstream to the receptor, and most of the putative downstream signal transducer genes. The deduced protein encoded by Mr-EGFR, representing the first such receptor reported thus far in crustaceans, shows sequence similarity to other arthropod EGFRs. The M. rosenbergii gene is expressed in most tested tissues. The role of Mr-EGFR was revealed by temporarily silencing the transcript through weekly injections of double-stranded Mr-EGFR RNA. Such treatment resulted in a significant reduction in growth and a delay in the appearance of a male secondary sexual characteristic, namely the appendix masculina. An additional function of Mr-EGFR was revealed with respect to eye development. Although the optic ganglion appeared to have retained its normal morphology, Mr-EGFR-silenced individuals developed abnormal eyes that presented irregular organization of the ommatidia, reflected by unorganized receptor cells occupying large areas of the dioptric portion and by a shortened crystalline tract layer.

  13. Implications of Galaxy Buildup for Putative IMF Variations in Massive Galaxies

    Science.gov (United States)

    Blancato, Kirsten; Genel, Shy; Bryan, Greg

    2017-08-01

    Recent observational evidence for initial mass function (IMF) variations in massive quiescent galaxies at z = 0 challenges the long-established paradigm of a universal IMF. While a few theoretical models relate the IMF to birth cloud conditions, the physical driver underlying these putative IMF variations is still largely unclear. Here we use post-processing analysis of the Illustris cosmological hydrodynamical simulation to investigate possible physical origins of IMF variability with galactic properties. We do so by tagging stellar particles in the simulation (each representing a stellar population of ≈ {10}6 {M}⊙ ) with individual IMFs that depend on various physical conditions, such as velocity dispersion, metallicity, or star formation rate, at the time and place in which the stars are formed. We then follow the assembly of these populations throughout cosmic time and reconstruct the overall IMF of each z = 0 galaxy from the many distinct IMFs it is composed of. Our main result is that applying the observed relations between IMF and galactic properties to the conditions at the star formation sites does not result in strong enough IMF variations between z = 0 galaxies. Steeper physical IMF relations are required for reproducing the observed IMF trends, and some stellar populations must form with more extreme IMFs than those observed. The origin of this result is the hierarchical nature of massive galaxy assembly, and it has implications for the reliability of the strong observed trends, for the ability of cosmological simulations to capture certain physical conditions in galaxies, and for theories of star formation aiming to explain the physical origin of a variable IMF.

  14. Putative cognitive enhancers in preclinical models related to schizophrenia: the search for an elusive target.

    Science.gov (United States)

    Barak, Segev; Weiner, Ina

    2011-08-01

    Several developments have converged to drive what may be called "the cognitive revolution" in drug discovery in schizophrenia (SCZ), including the emphasis on cognitive deficits as a core disabling aspect of SCZ, the increasing consensus that cognitive deficits are not treated satisfactorily by the available antipsychotic drugs (APDs), and the failure of animal models to predict drug efficacy for cognitive deficits in clinical trials. Consequently, in recent years, a paradigm shift has been encouraged in animal modeling, triggered by the NIMH sponsored Measurement and Treatment Research to Improve Cognition in Schizophrenia (MATRICS) initiative, and intended to promote the development and use of behavioral measures in animals that can generate valid (clinically relevant) measures of cognition and thus promote the identification of cognition enhancers for SCZ. Here, we provide a non-exhaustive survey of the effects of putative cognition enhancers (PCEs) representing 10 pharmacological targets as well as antipsychotic drugs (APDs), on SCZ-mimetic drugs (NMDA antagonists, muscarinic antagonist scopolamine and dopaminergic agonist amphetamine), in several tasks considered to measure cognitive processes/domains that are disrupted in SCZ (the five choice serial reaction time task, sustain attention task, working and/or recognition memory (delayed (non)matching to sample, delayed alternation task, radial arm maze, novel object recognition), reversal learning, attentional set shifting, latent inhibition and spatial learning and memory). We conclude that most of the available models have no capacity to distinguish between PCEs and APDs and that there is a need to establish models based on tasks whose perturbations lead to performance impairments that are resistant to APDs, and/or to accept APDs as a "weak gold standard". Several directions derived from the surveyed data are suggested.

  15. Identification of putative cis-regulatory elements in Cryptosporidium parvum by de novo pattern finding

    Directory of Open Access Journals (Sweden)

    Kissinger Jessica C

    2007-01-01

    Full Text Available Abstract Background Cryptosporidium parvum is a unicellular eukaryote in the phylum Apicomplexa. It is an obligate intracellular parasite that causes diarrhea and is a significant AIDS-related pathogen. Cryptosporidium parvum is not amenable to long-term laboratory cultivation or classical molecular genetic analysis. The parasite exhibits a complex life cycle, a broad host range, and fundamental mechanisms of gene regulation remain unknown. We have used data from the recently sequenced genome of this organism to uncover clues about gene regulation in C. parvum. We have applied two pattern finding algorithms MEME and AlignACE to identify conserved, over-represented motifs in the 5' upstream regions of genes in C. parvum. To support our findings, we have established comparative real-time -PCR expression profiles for the groups of genes examined computationally. Results We find that groups of genes that share a function or belong to a common pathway share upstream motifs. Different motifs are conserved upstream of different groups of genes. Comparative real-time PCR studies show co-expression of genes within each group (in sub-sets during the life cycle of the parasite, suggesting co-regulation of these genes may be driven by the use of conserved upstream motifs. Conclusion This is one of the first attempts to characterize cis-regulatory elements in the absence of any previously characterized elements and with very limited expression data (seven genes only. Using de novo pattern finding algorithms, we have identified specific DNA motifs that are conserved upstream of genes belonging to the same metabolic pathway or gene family. We have demonstrated the co-expression of these genes (often in subsets using comparative real-time-PCR experiments thus establishing evidence for these conserved motifs as putative cis-regulatory elements. Given the lack of prior information concerning expression patterns and organization of promoters in C. parvum we

  16. 7 CFR 1205.20 - Representative period.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 10 2010-01-01 2010-01-01 false Representative period. 1205.20 Section 1205.20 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (MARKETING... period means the 2006 calendar year....

  17. Enhancing policy innovation by redesigning representative democracy

    DEFF Research Database (Denmark)

    Sørensen, Eva

    2016-01-01

    . Two Danish case studies indicate that collaboration between politicians and relevant and affected stakeholders can promote policy innovation, but also that a redesign of representative democracy is needed in order to establish a productive combination of political leadership, competition...

  18. REFractions: The Representing Equivalent Fractions Game

    Science.gov (United States)

    Tucker, Stephen I.

    2014-01-01

    Stephen Tucker presents a fractions game that addresses a range of fraction concepts including equivalence and computation. The REFractions game also improves students' fluency with representing, comparing and adding fractions.

  19. Prevalence and characteristics of Streptococcus pneumoniae "putative serotype 6E" isolates from Asian countries.

    Science.gov (United States)

    Baek, Jin Yang; Park, In Ho; So, Thomas Man-kit; Lalitha, M K; Shimono, Nobuyuki; Yasin, Rohani Md; Carlos, Celia C; Perera, Jennifer; Thamlikitkul, Visanu; Hsueh, Po-Ren; Van, Pham Hung; Shibl, Atef M; Song, Jae-Hoon; Ko, Kwan Soo

    2014-12-01

    The prevalence, antimicrobial susceptibility, and genotypes of Streptococcus pneumoniae “putative serotype 6E” isolates from Asian countries were investigated. A total of 244 S. pneumoniae serogroup 6 isolates obtained from 11 Asian countries were included in this study. Of the 244 serogroup 6 isolates, 101 (41.4%) were typed as "putative serotype 6E," followed by serotypes 6A, 6B, 6C, and 6D (27.0, 20.1, 5.7, and 5.7%, respectively). Multilocus sequence typing revealed that clonal complex (CC) 90, including ST90 and its variants, was the most prevalent clonal group of "putative serotype 6E" isolates (n = 63; 62.4%). CC146 and CC315 were also found frequently in some of the countries. Most of the "putative serotype 6E" isolates showed very high resistance rates against cefuroxime, erythromycin, azithromycin, clarithromycin, clindamycin, and trimethoprim/sulfamethoxazole, probably due to their highly resistant to antimicrobials clone, CC90. Our results indicate that “putative serotype 6E” is prevalent in Asian countries. The clonal dissemination of "putative serotype 6E" isolates was also identified.

  20. Characterization of putative effectors from the cereal cyst nematode Heterodera avenae.

    Science.gov (United States)

    Cui, Jiangkuan; Peng, Huan; Qiao, Fen; Wang, Gaofeng; Huang, Wenkun; Wu, Duqign; Peng, Deliang

    2017-09-20

    Few molecular details of effectors of Heterodera avenae parasitism are known. We performed a high-throughput sequencing analysis of the H. avenae transcriptome at five developmental stages. A total of 82,549 unigenes were ultimately obtained, and 747 transcripts showed best hits to genes putatively encoding carbohydrate-active enzymes in plant parasitic nematodes that play an important role in the invasion process. A total of 1480 unigenes were homologous to known phytonematode effectors, and 63 putative novel effectors were identified in the H. avenae transcriptomes. Twenty-three unigenes were analyzed by qRT-PCR and confirmed to be highly expressed during at least one developmental stage. For in situ hybridization, 17 of the 22 tested putative effectors were specifically expressed and located in the subventral gland cells, and five putative novel effectors were specifically expressed in the dorsal gland. Furthermore, 115 transcripts were found to have putative lethal RNA interference (RNAi) phenotypes. Three target genes with lethal RNAi phenotypes and two of the four tested putative effectors were associated with a decrease in the number of cysts through in vitro RNAi technology. These transcriptomic data lay a foundation for further studies of interactions of H. avenae with cereal and H. avenae parasitic control.

  1. Caspar Wessel on representing complex numbers (1799)

    DEFF Research Database (Denmark)

    Branner, Bodil

    1999-01-01

    In celebration of the bicentenary of the publication of Wessel's paper on the geometric interpretation of complex numbers it is decsribed how Wessel used complex numbers to represent directions in surveying, at least as early as 1787.......In celebration of the bicentenary of the publication of Wessel's paper on the geometric interpretation of complex numbers it is decsribed how Wessel used complex numbers to represent directions in surveying, at least as early as 1787....

  2. Quadratic forms representing all odd positive integers

    CERN Document Server

    Rouse, Jeremy

    2011-01-01

    We consider the problem of classifying all positive-definite integer-valued quadratic forms that represent all positive odd integers. Kaplansky considered this problem for ternary forms, giving a list of 23 candidates, and proving that 19 of those represent all positive odds. (Jagy later dealt with a 20th candidate.) Assuming that the remaining three forms represent all positive odds, we prove that an arbitrary, positive-definite quadratic form represents all positive odds if and only if it represents the odd numbers from 1 up to 451. This result is analogous to Bhargava and Hanke's celebrated 290-theorem. In addition, we prove that these three remaining ternaries represent all positive odd integers, assuming the generalized Riemann hypothesis. This result is made possible by a new analytic method for bounding the cusp constants of integer-valued quaternary quadratic forms $Q$ with fundamental discriminant. This method is based on the analytic properties of Rankin-Selberg $L$-functions, and we use it to prove...

  3. Do regional climate models represent regional climate?

    Science.gov (United States)

    Maraun, Douglas; Widmann, Martin

    2014-05-01

    When using climate change scenarios - either from global climate models or further downscaled - to assess localised real world impacts, one has to ensure that the local simulation indeed correctly represents the real world local climate. Representativeness has so far mainly been discussed as a scale issue: simulated meteorological variables in general represent grid box averages, whereas real weather is often expressed by means of point values. As a result, in particular simulated extreme values are not directly comparable with observed local extreme values. Here we argue that the issue of representativeness is more general. To illustrate this point, assume the following situations: first, the (GCM or RCM) simulated large scale weather, e.g., the mid-latitude storm track, might be systematically distorted compared to observed weather. If such a distortion at the synoptic scale is strong, the simulated local climate might be completely different from the observed. Second, the orography even of high resolution RCMs is only a coarse model of true orography. In particular in mountain ranges the simulated mesoscale flow might therefore considerably deviate from the observed flow, leading to systematically displaced local weather. In both cases, the simulated local climate does not represent observed local climate. Thus, representativeness also encompasses representing a particular location. We propose to measure this aspect of representativeness for RCMs driven with perfect boundary conditions as the correlation between observations and simulations at the inter-annual scale. In doing so, random variability generated by the RCMs is largely averaged out. As an example, we assess how well KNMIs RACMO2 RCM at 25km horizontal resolution represents winter precipitation in the gridded E-OBS data set over the European domain. At a chosen grid box, RCM precipitation might not be representative of observed precipitation, in particular in the rain shadow of major moutain ranges

  4. Comparative Investigation of Copper Tolerance and Identification of Putative Tolerance Related Genes in Tardigrades

    Science.gov (United States)

    Hygum, Thomas L.; Fobian, Dannie; Kamilari, Maria; Jørgensen, Aslak; Schiøtt, Morten; Grosell, Martin; Møbjerg, Nadja

    2017-01-01

    Tardigrades are microscopic aquatic animals renowned for their tolerance toward extreme environmental conditions. The current study is the first to investigate their tolerance toward heavy metals and we present a novel tardigrade toxicant tolerance assay based on activity assessments as a measure of survival. Specifically, we compare tolerance toward copper in four species representing different evolutionary lineages, habitats and adaptation strategies, i.e., a marine heterotardigrade, Echiniscoides sigismundi, a limno-terrestrial heterotardigrade, Echiniscus testudo, a limno-terrestrial eutardigrade, Ramazzottius oberhaeuseri, and a marine eutardigrade, Halobiotus crispae. The latter was sampled at a time of year, when the population is predominantly represented by aberrant P1 cysts, while the other species were in normal active states prior to exposure. Based on volume measurements and a general relation between body mass and copper tolerance, expected tardigrade EC50 values were estimated at 0.5–2 μg l−1. Following 24 h of exposure, tolerance was high with no apparent link to lineage or habitat. EC50s (95% CI), 24 h after exposure, were estimated at 178 (168–186) and 310 (295–328) μg l−1, respectively, for E. sigismundi and R. oberhaeuseri, whereas E. testudo and H. crispae were less affected. Highest tolerance was observed in H. crispae with a mean ± s.e.m. activity of 77 ± 2% (n = 3) 24 h after removal from ~3 mg l−1 copper, suggesting that tardigrade cysts have increased tolerance toward toxicants. In order to identify putative tolerance related genes, an E. sigismundi transcriptome was searched for key enzymes involved in osmoregulation, antioxidant defense and copper metabolism. We found high expression of Na/K ATPase and carbonic anhydrase, known targets for copper. Our transcriptome, furthermore, revealed high expression of antioxidant enzymes, copper transporters, ATOX1, and a Cu-ATPase. In summary, our results indicate that tardigrades

  5. Identification of putative candidate genes for juvenile wood density in Pinus radiata.

    Science.gov (United States)

    Li, Xinguo; Wu, Harry X; Southerton, Simon G

    2012-08-01

    Wood formation is a complex developmental process driven by the annual activity of the vascular cambium. Conifers usually produce juvenile wood at young ages followed by mature wood for the rest of their lifetime. Juvenile wood exhibits poorer wood quality (i.e., lower density) compared with mature wood and can account for up to 50% of short-rotation harvested logs, thus representing a major challenge for commercial forestry globally. Wood density is an important quality trait for many timber-related products. Understanding the molecular mechanisms involved in the regulation of juvenile wood density is critical for the improvement of juvenile wood quality via marker-aided selection. A previous study has identified several candidate genes affecting mature wood density in Picea sitchensis (Bong.) Carr.; however, genes associated with juvenile wood density in conifers remain poorly characterized. Here, cDNA microarrays containing 3320 xylem unigenes were used to investigate genes differentially transcribed in juvenile wood with high (HD) and low density (LD) in Pinus radiata D.Don. In total, 814 xylem unigenes with differential transcription were identified in at least one of two microarray experiments and 73 genes (45 for HD, 28 for LD) were identified in both experiments, thus representing putative candidate genes for juvenile wood density. Interestingly, cellulose synthases (PrCesA3, PrCesA11) and sucrose synthase (SuSy), which are involved in secondary cell wall formation, had stronger transcription in juvenile wood with HD, while genes functioning in primary wall formation (pectin synthesis, cell expansion and other modifications) were more transcribed in LD wood. Cell wall genes encoding monolignol biosynthesis enzymes, arabinogalactan proteins, actins and tubulins were differentially transcribed in either HD or LD juvenile wood; however, the latter had exclusively greater transcription of genes involved in monolignol polymerization (laccase and peroxidase). The

  6. Effect of specific amino acid substitutions in the putative fusion peptide of structural glycoprotein E2 on Classical Swine Fever Virus replication

    Energy Technology Data Exchange (ETDEWEB)

    Fernández-Sainz, I.J. [Plum Island Animal Disease Center, ARS, USDA (United States); Largo, E. [Biophysics Unit (CSIC-UPV/EHU), Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), P.O. Box 644, 48080 Bilbao (Spain); Gladue, D.P.; Fletcher, P. [Plum Island Animal Disease Center, ARS, USDA (United States); O’Donnell, V. [Plum Island Animal Disease Center, ARS, USDA (United States); Plum Island Animal Disease Center, DHS, Greenport, NY 11944 (United States); Holinka, L.G. [Plum Island Animal Disease Center, ARS, USDA (United States); Carey, L.B. [Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), E-08003 Barcelona (Spain); Lu, X. [Plum Island Animal Disease Center, DHS, Greenport, NY 11944 (United States); Nieva, J.L. [Biophysics Unit (CSIC-UPV/EHU), Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), P.O. Box 644, 48080 Bilbao (Spain); Borca, M.V., E-mail: manuel.borca@ars.usda.gov [Plum Island Animal Disease Center, ARS, USDA (United States)

    2014-05-15

    E2, along with E{sup rns} and E1, is an envelope glycoprotein of Classical Swine Fever Virus (CSFV). E2 is involved in several virus functions: cell attachment, host range susceptibility and virulence in natural hosts. Here we evaluate the role of a specific E2 region, {sup 818}CPIGWTGVIEC{sup 828}, containing a putative fusion peptide (FP) sequence. Reverse genetics utilizing a full-length infectious clone of the highly virulent CSFV strain Brescia (BICv) was used to evaluate how individual amino acid substitutions within this region of E2 may affect replication of BICv. A synthetic peptide representing the complete E2 FP amino acid sequence adopted a β-type extended conformation in membrane mimetics, penetrated into model membranes, and perturbed lipid bilayer integrity in vitro. Similar peptides harboring amino acid substitutions adopted comparable conformations but exhibited different membrane activities. Therefore, a preliminary characterization of the putative FP {sup 818}CPIGWTGVIEC{sup 828} indicates a membrane fusion activity and a critical role in virus replication. - Highlights: • A putative fusion peptide (FP) region in CSFV E2 protein was shown to be critical for virus growth. • Synthetic FPs were shown to efficiently penetrate into lipid membranes using an in vitro model. • Individual residues in the FP affecting virus replication were identified by reverse genetics. • The same FP residues are also responsible for mediating membrane fusion.

  7. Representative Democracy in Australian Local Government

    Directory of Open Access Journals (Sweden)

    Colin Hearfield

    2009-01-01

    Full Text Available In an assessment of representative democracy in Australian local government, this paper considers long-run changes in forms of political representation, methods of vote counting, franchise arrangements, numbers of local government bodies and elected representatives, as well as the thorny question of constitutional recognition. This discussion is set against the background of ongoing tensions between the drive for economic efficiency and the maintenance of political legitimacy, along with more deep-seated divisions emerging from the legal relationship between local and state governments and the resultant problems inherent in local government autonomy versus state intervention.

  8. Representative Sampling for reliable data analysis

    DEFF Research Database (Denmark)

    Petersen, Lars; Esbensen, Kim Harry

    2005-01-01

    The Theory of Sampling (TOS) provides a description of all errors involved in sampling of heterogeneous materials as well as all necessary tools for their evaluation, elimination and/or minimization. This tutorial elaborates on—and illustrates—selected central aspects of TOS. The theoretical...... regime in order to secure the necessary reliability of: samples (which must be representative, from the primary sampling onwards), analysis (which will not mean anything outside the miniscule analytical volume without representativity ruling all mass reductions involved, also in the laboratory) and data...

  9. Representing Context in Hypermedia Data Models

    DEFF Research Database (Denmark)

    Hansen, Frank Allan

    2005-01-01

    As computers and software systems move beyond the desktopand into the physical environments we live and workin, the systems are required to adapt to these environmentsand the activities taking place within them. Making applicationscontext-aware and representing context informationalong side...... application data can be a challenging task. Thispaper describes how digital context traditionally has beenrepresented in hypermedia data models and how this representationcan scale to also represent physical context. TheHyCon framework and data model, designed for the developmentof mobile context...

  10. Representing uncertainty on model analysis plots

    Science.gov (United States)

    Smith, Trevor I.

    2016-12-01

    Model analysis provides a mechanism for representing student learning as measured by standard multiple-choice surveys. The model plot contains information regarding both how likely students in a particular class are to choose the correct answer and how likely they are to choose an answer consistent with a well-documented conceptual model. Unfortunately, Bao's original presentation of the model plot did not include a way to represent uncertainty in these measurements. I present details of a method to add error bars to model plots by expanding the work of Sommer and Lindell. I also provide a template for generating model plots with error bars.

  11. Representative Sampling for reliable data analysis

    DEFF Research Database (Denmark)

    Petersen, Lars; Esbensen, Kim Harry

    2005-01-01

    regime in order to secure the necessary reliability of: samples (which must be representative, from the primary sampling onwards), analysis (which will not mean anything outside the miniscule analytical volume without representativity ruling all mass reductions involved, also in the laboratory) and data...... analysis (“data” do not exist in isolation of their provenance). The Total Sampling Error (TSE) is by far the dominating contribution to all analytical endeavours, often 100+ times larger than the Total Analytical Error (TAE).We present a summarizing set of only seven Sampling Unit Operations (SUOs...

  12. Attributes Heeded When Representing an Osmosis Problem.

    Science.gov (United States)

    Zuckerman, June Trop

    Eighteen high school science students were involved in a study to determine what attributes in the problem statement they need when representing a typical osmosis problem. In order to realize this goal students were asked to solve problems aloud and to explain their answers. Included as a part of the results are the attributes that the students…

  13. A Framework for Representing Moving Objects

    DEFF Research Database (Denmark)

    Becker, Ludger; Blunck, Henrik; Hinrichs, Klaus

    2004-01-01

    We present a framework for representing the trajectories of moving objects and the time-varying results of operations on moving objects. This framework supports the realization of discrete data models of moving objects databases, which incorporate representations of moving objects based on non-li...

  14. 26 CFR 601.502 - Recognized representative.

    Science.gov (United States)

    2010-04-01

    .... 230; (4) Enrolled actuary. Any individual who is enrolled as an actuary by and is in active status with the Joint Board for the Enrollment of Actuaries pursuant to 29 U.S.C. 1242. (5) Other individuals... actuaries, and others); (3) I am authorized to represent the taxpayer(s) identified in the power of...

  15. Developing Creativity and Abstraction in Representing Data

    Science.gov (United States)

    South, Andy

    2012-01-01

    Creating charts and graphs is all about visual abstraction: the process of representing aspects of data with imagery that can be interpreted by the reader. Children may need help making the link between the "real" and the image. This abstraction can be achieved using symbols, size, colour and position. Where the representation is close to what…

  16. Identification of putative regulatory motifs in the upstream regions of co-expressed functional groups of genes in Plasmodium falciparum

    Directory of Open Access Journals (Sweden)

    Joshi NV

    2009-01-01

    Full Text Available Abstract Background Regulation of gene expression in Plasmodium falciparum (Pf remains poorly understood. While over half the genes are estimated to be regulated at the transcriptional level, few regulatory motifs and transcription regulators have been found. Results The study seeks to identify putative regulatory motifs in the upstream regions of 13 functional groups of genes expressed in the intraerythrocytic developmental cycle of Pf. Three motif-discovery programs were used for the purpose, and motifs were searched for only on the gene coding strand. Four motifs – the 'G-rich', the 'C-rich', the 'TGTG' and the 'CACA' motifs – were identified, and zero to all four of these occur in the 13 sets of upstream regions. The 'CACA motif' was absent in functional groups expressed during the ring to early trophozoite transition. For functional groups expressed in each transition, the motifs tended to be similar. Upstream motifs in some functional groups showed 'positional conservation' by occurring at similar positions relative to the translational start site (TLS; this increases their significance as regulatory motifs. In the ribonucleotide synthesis, mitochondrial, proteasome and organellar translation machinery genes, G-rich, C-rich, CACA and TGTG motifs, respectively, occur with striking positional conservation. In the organellar translation machinery group, G-rich motifs occur close to the TLS. The same motifs were sometimes identified for multiple functional groups; differences in location and abundance of the motifs appear to ensure different modes of action. Conclusion The identification of positionally conserved over-represented upstream motifs throws light on putative regulatory elements for transcription in Pf.

  17. Rice-Infecting Pseudomonas Genomes Are Highly Accessorized and Harbor Multiple Putative Virulence Mechanisms to Cause Sheath Brown Rot.

    Science.gov (United States)

    Quibod, Ian Lorenzo; Grande, Genelou; Oreiro, Eula Gems; Borja, Frances Nikki; Dossa, Gerbert Sylvestre; Mauleon, Ramil; Cruz, Casiana Vera; Oliva, Ricardo

    2015-01-01

    Sheath rot complex and seed discoloration in rice involve a number of pathogenic bacteria that cannot be associated with distinctive symptoms. These pathogens can easily travel on asymptomatic seeds and therefore represent a threat to rice cropping systems. Among the rice-infecting Pseudomonas, P. fuscovaginae has been associated with sheath brown rot disease in several rice growing areas around the world. The appearance of a similar Pseudomonas population, which here we named P. fuscovaginae-like, represents a perfect opportunity to understand common genomic features that can explain the infection mechanism in rice. We showed that the novel population is indeed closely related to P. fuscovaginae. A comparative genomics approach on eight rice-infecting Pseudomonas revealed heterogeneous genomes and a high number of strain-specific genes. The genomes of P. fuscovaginae-like harbor four secretion systems (Type I, II, III, and VI) and other important pathogenicity machinery that could probably facilitate rice colonization. We identified 123 core secreted proteins, most of which have strong signatures of positive selection suggesting functional adaptation. Transcript accumulation of putative pathogenicity-related genes during rice colonization revealed a concerted virulence mechanism. The study suggests that rice-infecting Pseudomonas causing sheath brown rot are intrinsically diverse and maintain a variable set of metabolic capabilities as a potential strategy to occupy a range of environments.

  18. Eliciting maltreated and nonmaltreated children's transgression disclosures: narrative practice rapport building and a putative confession.

    Science.gov (United States)

    Lyon, Thomas D; Wandrey, Lindsay; Ahern, Elizabeth; Licht, Robyn; Sim, Megan P Y; Quas, Jodi A

    2014-01-01

    This study tested the effects of narrative practice rapport building (asking open-ended questions about a neutral event) and a putative confession (telling the child an adult "told me everything that happened and he wants you to tell the truth") on 4- to 9-year-old maltreated and nonmaltreated children's reports of an interaction with a stranger who asked them to keep toy breakage a secret (n = 264). Only one third of children who received no interview manipulations disclosed breakage; in response to a putative confession, one half disclosed. Narrative practice rapport building did not affect the likelihood of disclosure. Maltreated children and nonmaltreated children responded similarly to the manipulations. Neither narrative practice rapport building nor a putative confession increased false reports.

  19. Molecular diagnosis of putative Stargardt disease by capture next generation sequencing.

    Science.gov (United States)

    Zhang, Xiao; Ge, Xianglian; Shi, Wei; Huang, Ping; Min, Qingjie; Li, Minghan; Yu, Xinping; Wu, Yaming; Zhao, Guangyu; Tong, Yi; Jin, Zi-Bing; Qu, Jia; Gu, Feng

    2014-01-01

    Stargardt Disease (STGD) is the commonest genetic form of juvenile or early adult onset macular degeneration, which is a genetically heterogeneous disease. Molecular diagnosis of STGD remains a challenge in a significant proportion of cases. To address this, seven patients from five putative STGD families were recruited. We performed capture next generation sequencing (CNGS) of the probands and searched for potentially disease-causing genetic variants in previously identified retinal or macular dystrophy genes. Seven disease-causing mutations in ABCA4 and two in PROM1 were identified by CNGS, which provides a confident genetic diagnosis in these five families. We also provided a genetic basis to explain the differences among putative STGD due to various mutations in different genes. Meanwhile, we show for the first time that compound heterozygous mutations in PROM1 gene could cause cone-rod dystrophy. Our findings support the enormous potential of CNGS in putative STGD molecular diagnosis.

  20. Climate Change and the Representative Agent

    Energy Technology Data Exchange (ETDEWEB)

    Howarth, R.B. [Environmental Studies Program, Dartmouth College, Hanover, New Hampshire 03755 (United States)

    2000-02-01

    The artifice of an infinitely-lived representative agent is commonly invoked to balance the present costs and future benefits of climate stabilization policies. Since actual economies are populated by overlapping generations of finite-lived persons, this approach begs important questions of welfare aggregation. This paper compares the results of representative agent and overlapping generations models that are numerically calibrated based on standard assumptions regarding climate economy interactions. Under two social choice rules - Pareto efficiency and classical utilitarianism - the models generate closely similar simulation results. In the absence of policies to redistribute income between present and future generations, efficient rates of carbon dioxide emissions abatement rise from 15 to 20% between the years 2000 and 2105. Under classical utilitarianism, in contrast, optimal control rates rise from 48 to 79% this same period. 23 refs.

  1. Representing Boolean Functions by Decision Trees

    KAUST Repository

    Chikalov, Igor

    2011-01-01

    A Boolean or discrete function can be represented by a decision tree. A compact form of decision tree named binary decision diagram or branching program is widely known in logic design [2, 40]. This representation is equivalent to other forms, and in some cases it is more compact than values table or even the formula [44]. Representing a function in the form of decision tree allows applying graph algorithms for various transformations [10]. Decision trees and branching programs are used for effective hardware [15] and software [5] implementation of functions. For the implementation to be effective, the function representation should have minimal time and space complexity. The average depth of decision tree characterizes the expected computing time, and the number of nodes in branching program characterizes the number of functional elements required for implementation. Often these two criteria are incompatible, i.e. there is no solution that is optimal on both time and space complexity. © Springer-Verlag Berlin Heidelberg 2011.

  2. Data structures and apparatuses for representing knowledge

    Science.gov (United States)

    Hohimer, Ryan E; Thomson, Judi R; Harvey, William J; Paulson, Patrick R; Whiting, Mark A; Tratz, Stephen C; Chappell, Alan R; Butner, Robert S

    2014-02-18

    Data structures and apparatuses to represent knowledge are disclosed. The processes can comprise labeling elements in a knowledge signature according to concepts in an ontology and populating the elements with confidence values. The data structures can comprise knowledge signatures stored on computer-readable media. The knowledge signatures comprise a matrix structure having elements labeled according to concepts in an ontology, wherein the value of the element represents a confidence that the concept is present in an information space. The apparatus can comprise a knowledge representation unit having at least one ontology stored on a computer-readable medium, at least one data-receiving device, and a processor configured to generate knowledge signatures by comparing datasets obtained by the data-receiving devices to the ontologies.

  3. Representing a public that does not exist

    DEFF Research Database (Denmark)

    Korsgaard, Morten Timmermann

    and function of the teacher. Confronted by this teachers and educationalists in Denmark have chosen different paths. One current returns to nationalistic and traditional educational ideals and another accepts the global agenda and attempts to find a new form of legitimacy within the ‘what works’ framework......In her seminal essay ‘The Crisis in Education’ Hannah Arendt presents teachers with the challenge of having to represent a world that is becoming out of joint. This means that the teacher stands as a representative of a world that is becoming increasingly inexplicable and incomprehensible......, and the only way of retaining any form of authority (and legitimacy as a teacher) is to remain loyal to the task of presenting this world to the child. This challenge presents itself acutely in the form of a global reform agenda that legitimizes standardisation and accountability while eroding the authority...

  4. Can Monkeys (Macaca mulatta) Represent Invisible Displacement?

    Science.gov (United States)

    Filion, Christine M.; Washburn, David A.; Gulledge, Jonathan P.

    1996-01-01

    Four experiments were conducted to assess whether or not rhesus macaques (Macaca mulatta) could represent the unperceived movements of a stimulus. Subjects were tested on 2 computerized tasks, HOLE (monkeys) and LASER (humans and monkeys), in which subjects needed to chase or shoot at, respectively, a moving target that either remained visible or became invisible for a portion of its path of movement. Response patterns were analyzed and compared between target-visible and target-invisible conditions. Results of Experiments 1, 2, and 3 demonstrated that the monkeys are capable of extrapolating movement. That this extrapolation involved internal representation of the target's invisible movement was suggested but not confirmed. Experiment 4, however, demonstrated that the monkeys are capable of representing the invisible displacements of a stimulus.

  5. Representing exact number visually using mental abacus.

    Science.gov (United States)

    Frank, Michael C; Barner, David

    2012-02-01

    Mental abacus (MA) is a system for performing rapid and precise arithmetic by manipulating a mental representation of an abacus, a physical calculation device. Previous work has speculated that MA is based on visual imagery, suggesting that it might be a method of representing exact number nonlinguistically, but given the limitations on visual working memory, it is unknown how MA structures could be stored. We investigated the structure of the representations underlying MA in a group of children in India. Our results suggest that MA is represented in visual working memory by splitting the abacus into a series of columns, each of which is independently stored as a unit with its own detailed substructure. In addition, we show that the computations of practiced MA users (but not those of control participants) are relatively insensitive to verbal interference, consistent with the hypothesis that MA is a nonlinguistic format for exact numerical computation.

  6. Representativeness and significance factors in ESP texts

    Directory of Open Access Journals (Sweden)

    Alejandro Curado Fuentes

    2000-04-01

    Full Text Available The development of communicative approaches and strategies in specialized discourse has led to revising notions of representative and significant language . Particularly in the work with academic genres, in science and technology (EST settings such as our own institution, the need for determining these factors is ever growing. The application of empirical resources such as specific language corpora, in fact, becomes convenient. In this paper, the aim is to specify the type of corpus linguistic representativeness and significance sought in the case of teaching English to our groups of Computer Science students. In that scope, we present data and samples on which to base our suggestions and claims regarding the exploitation of textual material.

  7. Meeting staff representatives of the European Agencies

    CERN Multimedia

    Staff Association

    2014-01-01

      The AASC (Assembly of Agency Staff Committee) held its 27th Meeting of the specialized European Agencies on 26 and 27 May on the premises of the OHIM (Office for Harmonization in the Internal Market) in Alicante, Spain. Two representatives of the CERN Staff Association, in charge of External Relations, attended as observers. This participation is a useful complement to regular contacts we have with FICSA (Federation of International Civil Servants' Associations), which groups staff associations of the UN Agencies, and the annual CSAIO conferences (Conference of Staff Associations of International Organizations), where each Autumn representatives of international organizations based in Europe meet to discuss themes of common interest to better promote and defend the rights of the international civil servants. All these meetings allow us to remain informed on items that are directly or indirectly related to employment and social conditions of our colleagues in other international and Europ...

  8. Putative epidermal stem cell convert into corneal epithelium-like cell under corneal tissue in vitro

    Institute of Scientific and Technical Information of China (English)

    GAO Nan; CUI GuangHui; WANG ZhiChong; HUANG Bing; GE Jian; LU Rong; ZHANG KeFei; FAN ZhiGang; LU Li; PENG Zhan

    2007-01-01

    Rhesus putative epidermal stem cells are being investigated for their potential use in regenerative corneal epithelium-like cells, which may provide a practical source of autologous seed cells for the construction of bioengineered corneas. The goal of this study was to investigate the potential of epidermal stem cells for trans-differentiation into corneal epithelium-like cells. Rhesus putative epidermal stem cells were isolated by type IV collagen attachment method. Flow cytometry analysis, immunohistology and RT-PCR were conducted to identify the expression of specific markers (β1, α6 integrin, K15, K1/K10, K3/K12 and CD71) on the isolated rapid attaching cells. The isolated cells were cocultured with human corneal limbal stroma and corneal epithelial cells. After coculture, the expression of the same specific markers was evaluated in order to identify expression difference caused by the coculture conditions. K3/K12 expression was analyzed in coculture cells on day 2, 4, 6, 8 and 10. Putative epidermal stem cells in conditioned culture media were used as control. Putative epidermal stem cells were predominant in rapid attaching cells by type IV collagen attachment isolation. Before being cocultured, the rhesus putative epidermal stem cells expressed K15, α6 and β1 integrin, but no CD71, K1/K10 and K3/K12. After coculture, these cells expressed K3/K12 (a marker of corneal epithelial cells), K15 and β 1 integrin, but no K1/K10. Cells being not coculture converted into terminally differentiated cells expressing K1/K10. These results indicate that rhesus putative epidermal stem cells can trans-differentiate into corneal epithelium-like cells and, therefore, may have potential therapeutic application as autologous seed cells for the construction of bioengineered corneas.

  9. Putative epidermal stem cell convert into corneal epithelium-like cell under corneal tissue in vitro

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Rhesus putative epidermal stem cells are being investigated for their potential use in regenerative corneal epithelium-like cells, which may provide a practical source of autologous seed cells for the construction of bioengineered corneas. The goal of this study was to investigate the potential of epi-dermal stem cells for trans-differentiation into corneal epithelium-like cells. Rhesus putative epidermal stem cells were isolated by type IV collagen attachment method. Flow cytometry analysis, immuno-histology and RT-PCR were conducted to identify the expression of specific markers (β1, α6 integrin, K15, K1/K10, K3/K12 and CD71) on the isolated rapid attaching cells. The isolated cells were cocultured with human corneal limbal stroma and corneal epithelial cells. After coculture, the expression of the same specific markers was evaluated in order to identify expression difference caused by the coculture conditions. K3/K12 expression was analyzed in coculture cells on day 2, 4, 6, 8 and 10. Putative epi-dermal stem cells in conditioned culture media were used as control. Putative epidermal stem cells were predominant in rapid attaching cells by type IV collagen attachment isolation. Before being co-cultured, the rhesus putative epidermal stem cells expressed K15, α6 and β1 integrin, but no CD71, K1/K10 and K3/K12. After coculture, these cells expressed K3/K12 (a marker of corneal epithelial cells), K15 and β 1 integrin, but no K1/K10. Cells being not coculture converted into terminally differentiated cells expressing K1/K10. These results indicate that rhesus putative epidermal stem cells can trans-differentiate into corneal epithelium-like cells and, therefore, may have potential therapeutic application as autologous seed cells for the construction of bioengineered corneas.

  10. Yucca Mountain Climate Technical Support Representative

    Energy Technology Data Exchange (ETDEWEB)

    Sharpe, Saxon E

    2007-10-23

    The primary objective of Project Activity ORD-FY04-012, “Yucca Mountain Climate Technical Support Representative,” was to provide the Office of Civilian Radioactive Waste Management (OCRWM) with expertise on past, present, and future climate scenarios and to support the technical elements of the Yucca Mountain Project (YMP) climate program. The Climate Technical Support Representative was to explain, defend, and interpret the YMP climate program to the various audiences during Site Recommendation and License Application. This technical support representative was to support DOE management in the preparation and review of documents, and to participate in comment response for the Final Environmental Impact Statement, the Site Recommendation Hearings, the NRC Sufficiency Comments, and other forums as designated by DOE management. Because the activity was terminated 12 months early and experience a 27% reduction in budget, it was not possible to complete all components of the tasks as originally envisioned. Activities not completed include the qualification of climate datasets and the production of a qualified technical report. The following final report is an unqualified summary of the activities that were completed given the reduced time and funding.

  11. Latency represents sound frequency in mouse IC

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Frequency is one of the fundamental parameters of sound.The frequency of an acoustic stimulus can be represented by a neural response such as spike rate,and/or first spike latency(FSL)of a given neuron.The spike rates/frequency function of most neurons changes with different acoustic ampli-tudes,whereas FSL/frequency function is highly stable.This implies that FSL might represent the fre-quency of a sound stimulus more efficiently than spike rate.This study involved representations of acoustic frequency by spike rate and FSL of central inferior colliculus(IC)neurons responding to free-field pure-tone stimuli.We found that the FSLs of neurons responding to characteristic frequency(CF)of sound stimulus were usually the shortest,regardless of sound intensity,and that spike rates of most neurons showed a variety of function according to sound frequency,especially at high intensities.These results strongly suggest that FSL of auditory IC neurons can represent sound frequency more precisely than spike rate.

  12. Latency represents sound frequency in mouse IC

    Institute of Scientific and Technical Information of China (English)

    QIU Qiang; TANG Jie; YU ZuLin; ZHANG Juan; ZHOU YingJie; XIAO ZhongJu; SHEN JunXian

    2007-01-01

    Frequency is one of the fundamental parameters of sound. The frequency of an acoustic stimulus can be represented by a neural response such as spike rate, and/or first spike latency (FSL) of a given neuron. The spike rates/frequency function of most neurons changes with different acoustic amplitudes, whereas FSL/frequency function is highly stable. This implies that FSL might represent the frequency of a sound stimulus more efficiently than spike rate. This study involved representations of acoustic frequency by spike rate and FSL of central inferior colliculus (IC) neurons responding to free-field pure-tone stimuli. We found that the FSLs of neurons responding to characteristic frequency (CF) of sound stimulus were usually the shortest, regardless of sound intensity, and that spike rates of most neurons showed a variety of function according to sound frequency, especially at high intensities.These results strongly suggest that FSL of auditory IC neurons can represent sound frequency more precisely than spike rate.

  13. Diversity and representativeness: two key factors

    CERN Multimedia

    Staff Association

    2013-01-01

    In the past few weeks many of you have filled out the questionnaire for preparing the upcoming Five-yearly review. Similarly, Staff Association members have elected their delegates to the Staff Council for the coming two years. Once again we would like to thank all those who have taken the time and effort to make their voice heard on these two occasions. Elections to the Staff Council Below we publish the new Staff Council with its forty delegates who will represent in 2014 and 2015 all CERN staff in the discussions with Management and Member States in the various bodies and committees. Therefore it is important that the Staff Council represents as far as possible the diversity of the CERN population. By construction, the election process with its electoral colleges and two-step voting procedure guarantees that all Departments, even the small ones, and the various staff categories are correctly represented. Figure 1 shows the participation rate in the elections. The average rate is just above 52 %, with ...

  14. 40 CFR 72.26 - Delegation by designated representative and alternate designated representative.

    Science.gov (United States)

    2010-07-01

    ... designated representative may delegate, to one or more natural persons, his or her authority to make an... representative may delegate, to one or more natural persons, his or her authority to make an electronic... this part and parts 73 through 77 of this chapter. (c) In order to delegate authority to make an...

  15. Recommendations for representative ballast water sampling

    Science.gov (United States)

    Gollasch, Stephan; David, Matej

    2017-05-01

    Until now, the purpose of ballast water sampling studies was predominantly limited to general scientific interest to determine the variety of species arriving in ballast water in a recipient port. Knowing the variety of species arriving in ballast water also contributes to the assessment of relative species introduction vector importance. Further, some sampling campaigns addressed awareness raising or the determination of organism numbers per water volume to evaluate the species introduction risk by analysing the propagule pressure of species. A new aspect of ballast water sampling, which this contribution addresses, is compliance monitoring and enforcement of ballast water management standards as set by, e.g., the IMO Ballast Water Management Convention. To achieve this, sampling methods which result in representative ballast water samples are essential. We recommend such methods based on practical tests conducted on two commercial vessels also considering results from our previous studies. The results show that different sampling approaches influence the results regarding viable organism concentrations in ballast water samples. It was observed that the sampling duration (i.e., length of the sampling process), timing (i.e., in which point in time of the discharge the sample is taken), the number of samples and the sampled water quantity are the main factors influencing the concentrations of viable organisms in a ballast water sample. Based on our findings we provide recommendations for representative ballast water sampling.

  16. [Sensitivity of four representative angular cephalometric measures].

    Science.gov (United States)

    Xü, T; Ahn, J; Baumrind, S

    2000-05-01

    Examined the sensitivity of four representative cephalometric angles to the detection of different vectors of craniofacial growth. Landmark coordinate data from a stratified random sample of 48 adolescent subjects were used to calculate conventional values for changes between the pretreatment and end-of-treatment lateral cephalograms. By modifying the end-of-treatment coordinate values appropriately, the angular changes could be recalculated reflecting three hypothetical situations: Case 1. What if there were no downward landmark displacement between timepoints? Case 2. What if there were no forward landmark displacement between timepoints? Case 3. What if there were no Nasion change? These questions were asked for four representative cephalometric angles: SNA, ANB, NAPg and UI-SN. For Case 1, the associations (r) between the baseline and the modified measure for the three angles were very highly significant (P < 0.001) with r2 values no lower than 0.94! For Case 2, however, the associations were much weaker and no r value reached significance. These angular measurements are less sensitive for measuring downward landmark displacement than they are for measuring forward landmark displacement.

  17. How Are Feedbacks Represented in Land Models?

    Directory of Open Access Journals (Sweden)

    Yang Chen

    2016-09-01

    Full Text Available Land systems are characterised by many feedbacks that can result in complex system behaviour. We defined feedbacks as the two-way influences between the land use system and a related system (e.g., climate, soils and markets, both of which are encompassed by the land system. Land models that include feedbacks thus probably more accurately mimic how land systems respond to, e.g., policy or climate change. However, representing feedbacks in land models is a challenge. We reviewed articles incorporating feedbacks into land models and analysed each with predefined indicators. We found that (1 most modelled feedbacks couple land use systems with transport, soil and market systems, while only a few include feedbacks between land use and social systems or climate systems; (2 equation-based land use models that follow a top-down approach prevail; and (3 feedbacks’ effects on system behaviour remain relatively unexplored. We recommend that land system modellers (1 consider feedbacks between land use systems and social systems; (2 adopt (bottom-up approaches suited to incorporating spatial heterogeneity and better representing land use decision-making; and (3 pay more attention to nonlinear system behaviour and its implications for land system management and policy.

  18. Occurrence of Putative Pathogenicity Islands in Enterococci from Distinct Species and of Differing Origins▿ †

    OpenAIRE

    Semedo-Lemsaddek, Teresa; Barreto-Crespo, Maria Teresa; Tenreiro, Rogério

    2009-01-01

    Enterococci isolated from ewe's milk and cheese, clinical isolates of human and veterinary origins, and reference strains obtained from culture collections were screened for the occurrence of putative pathogenicity island (PAIs). Results obtained after PCR amplification and hybridization point toward PAI dissemination among enterococci of diverse origins (food/clinical) and species (Enterococcus faecalis/non-E. faecalis).

  19. Cloning and characterization of prunus serotina AGAMOUS, a putative flower homeotic gene

    Science.gov (United States)

    Xiaomei Liu; Joseph Anderson; Paula Pijut

    2010-01-01

    Members of the AGAMOUS subfamily of MADS-box transcription factors play an important role in regulating the development of reproductive organs in flowering plants. To help understand the mechanism of floral development in black cherry (Prunus serotina), PsAG (a putative flower homeotic identity gene) was isolated...

  20. A rapid approach to evaluate putative nursery sites for penaeid prawns

    Science.gov (United States)

    Taylor, Matthew D.; Smith, James A.; Boys, Craig A.; Whitney, Hannah

    2016-08-01

    Identifying nursery habitats for an aquatic species generally requires tracing adult individuals back through time and space to the area or habitat in which they developed as juveniles. We develop and trial a study design and analytical approach to evaluate the suitability of using stable isotopes to trace emigrating prawns to putative nursery sites, and evaluate assumptions inherent in the application of the approach using two penaeid species with Type-II life cycles: Penaeus (Melicertus) plebejus and Metapenaeus macleayi. Prawns were collected in putative nursery sites within the Hunter River, Australia, and analysed as composite samples of 6 individuals to provide habitat-specific isotopic signatures. Prawns emigrating from the mouth of the river were used as a proxy for individuals recruiting to the adult population, and assigned to putative nursery sites using a probabilistic mixing model and a simple, distance-based approach. Bivariate (δ15N and δ13C) isotopic data was sufficient to distinguish prawns from different putative nursery sites, and isotopic composition correlated closely with salinity. Approximately 90% of emigrating prawns collected could be assigned to these sites using bivariate isotopic data, and both analytical approaches gave similar results. The design developed here is broadly applicable to a suite of penaeid species, but its application will be most powerful when sampling is also aimed at understanding nursery function by simultaneous monitoring of size structure/growth, density, and trophic relationships within nursery habitats.

  1. Mapping the flow of information within the putative mirror neuron system during gesture observation

    NARCIS (Netherlands)

    Schippers, Marleen B.; Keysers, Christian

    2011-01-01

    The putative mirror neuron system may either function as a strict feed-forward system or as a dynamic control system. A strict feed-forward system would predict that action observation leads to a predominantly temporal -> parietal -> premotor flow of information in which a visual representation is t

  2. Complete Genome Sequence of a Putative Densovirus of the Asian Citrus Psyllid, Diaphorina citri.

    Science.gov (United States)

    Nigg, Jared C; Nouri, Shahideh; Falk, Bryce W

    2016-07-28

    Here, we report the complete genome sequence of a putative densovirus of the Asian citrus psyllid, Diaphorina citri Diaphorina citri densovirus (DcDNV) was originally identified through metagenomics, and here, we obtained the complete nucleotide sequence using PCR-based approaches. Phylogenetic analysis places DcDNV between viruses of the Ambidensovirus and Iteradensovirus genera.

  3. Expression of putative expansin genes in phylloxera (Daktulosphaira vitifoliae Fitch) induced root galls of Vitis spp.

    Science.gov (United States)

    Lawo, N C; Griesser, M; Forneck, A

    Grape phylloxera (Daktulosphaira vitifoliae Fitch) is a serious global pest in viticulture. The insects are sedentary feeders and require a gall to feed and reproduce. The insects induce their feeding site within the meristematic zone of the root tip, where they stay attached, feeding both intra- and intercellularly, and causing damage by reducing plant vigour. Several changes in cell structure and composition, including increased cell division and tissue swelling close to the feeding site, cause an organoid gall called a nodosity to develop. Because alpha expansin genes are involved in cell enlargement and cell wall loosening in many plant tissues it may be anticipated that they are also involved in nodosity formation. To identify expansin genes in Vitis vinifera cv. Pinot noir, we mined for orthologues genes in a comparative analysis. Eleven putative expansin genes were identified and shown to be present in the rootstock Teleki 5C (V. berlandieri Planch. x V. riparia Michx.) using specific PCR followed by DNA sequencing. Expression analysis of young and mature nodosities and uninfested root tips were conducted via quantitative real time PCR (qRT-PCR). Up-regulation was measured for three putative expansin genes (VvEXPA15, -A17 and partly -A20) or down-regulation for three other putative genes (VvEXPA7, -A12, -A20) in nodosities. The present study clearly shows the involvement of putative expansin genes in the phylloxera-root interaction.

  4. A review on the putative association between beta-blockers and depression

    NARCIS (Netherlands)

    Verbeek, D.E.; van Riezen, J.; de Boer, R.A.; van Melle, J.P.; de Jonge, P.

    Several kinds of systematic studies have been conducted verifying the putative association between beta-blockers and depressive symptoms. However, many of these studies had important limitations in their design. In most of the studies, no effect of beta-blockers on depressive symptoms was seen.

  5. A review on the putative association between beta-blockers and depression

    NARCIS (Netherlands)

    Verbeek, D.E.; van Riezen, J.; de Boer, R.A.; van Melle, J.P.; de Jonge, P.

    2011-01-01

    Several kinds of systematic studies have been conducted verifying the putative association between beta-blockers and depressive symptoms. However, many of these studies had important limitations in their design. In most of the studies, no effect of beta-blockers on depressive symptoms was seen. Beca

  6. DETERMINATION OF ROCURONIUM AND ITS PUTATIVE METABOLITES IN BODY-FLUIDS AND TISSUE-HOMOGENATES

    NARCIS (Netherlands)

    KLEEF, UW; PROOST, JH; ROGGEVELD, J

    1993-01-01

    A sensitive and selective HPLC method was developed for the quantification of the neuromuscular blocking agent rocuronium and its putative metabolites (the 17-desacetyl derivative and the N-desallyl derivative of rocuronium) in plasma, urine, bile, tissue homogenates and stoma fluid. Samples were pr

  7. Search strings for the study of putative occupational determinants of disease

    NARCIS (Netherlands)

    S. Mattioli; F. Zanardi; A. Baldasseroni; F. Schaafsma; R.M.T. Cooke; G. Mancini; M. Fierro; C. Santangelo; A. Farioli; S. Fucksia; S. Curti; F.S. Violante; J. Verbeek

    2010-01-01

    Objective To identify efficient PubMed search strategies to retrieve articles regarding putative occupational determinants of conditions not generally considered to be work related. Methods Based on MeSH definitions and expert knowledge, we selected as candidate search terms the four MeSH terms desc

  8. Search strings for the study of putative occupational determinants of disease

    NARCIS (Netherlands)

    Mattioli, S.; Zanardi, F.; Baldasseroni, A.; Schaafsma, F.; Cooke, R.M.T.; Mancini, G.; Fierro, M.; Santangelo, C.; Farioli, A.; Fucksia, S.; Curti, S.; Violante, F.S.; Verbeek, J.

    2010-01-01

    Objective To identify efficient PubMed search strategies to retrieve articles regarding putative occupational determinants of conditions not generally considered to be work related. Methods Based on MeSH definitions and expert knowledge, we selected as candidate search terms the four MeSH terms

  9. Isolation of Bartonella quintana from a Woman and a Cat following Putative Bite Transmission▿

    OpenAIRE

    Breitschwerdt, Edward B; Maggi, Ricardo G; Sigmon, Betsy; Nicholson, William L.

    2006-01-01

    We report here the detection of Bartonella quintana, after putative bite transmission, in pre-enrichment blood cultures from a woman and from two feral barn cats. Prospective molecular epidemiological studies are necessary to characterize the risk of human Bartonella quintana infection following cat bites.

  10. Isolation and characterization of 17 different genes encoding putative endopolygalacturonase genes from Rhizopus oryzae

    Science.gov (United States)

    Polygalacturonase enzymes are a valuable aid in the retting of flax for production of linens and, more recently, production of biofuels from citrus wastes. In a search of the recently sequenced Rhizopus oryzae strain 99-880 genome database, 18 putative endopolygalacturonase genes were identified, w...

  11. Quantifying Heuristic Bias: Anchoring, Availability, and Representativeness.

    Science.gov (United States)

    Richie, Megan; Josephson, S Andrew

    2017-07-28

    Construct: Authors examined whether a new vignette-based instrument could isolate and quantify heuristic bias. Heuristics are cognitive shortcuts that may introduce bias and contribute to error. There is no standardized instrument available to quantify heuristic bias in clinical decision making, limiting future study of educational interventions designed to improve calibration of medical decisions. This study presents validity data to support a vignette-based instrument quantifying bias due to the anchoring, availability, and representativeness heuristics. Participants completed questionnaires requiring assignment of probabilities to potential outcomes of medical and nonmedical scenarios. The instrument randomly presented scenarios in one of two versions: Version A, encouraging heuristic bias, and Version B, worded neutrally. The primary outcome was the difference in probability judgments for Version A versus Version B scenario options. Of 167 participants recruited, 139 enrolled. Participants assigned significantly higher mean probability values to Version A scenario options (M = 9.56, SD = 3.75) than Version B (M = 8.98, SD = 3.76), t(1801) = 3.27, p = .001. This result remained significant analyzing medical scenarios alone (Version A, M = 9.41, SD = 3.92; Version B, M = 8.86, SD = 4.09), t(1204) = 2.36, p = .02. Analyzing medical scenarios by heuristic revealed a significant difference between Version A and B for availability (Version A, M = 6.52, SD = 3.32; Version B, M = 5.52, SD = 3.05), t(404) = 3.04, p = .003, and representativeness (Version A, M = 11.45, SD = 3.12; Version B, M = 10.67, SD = 3.71), t(396) = 2.28, p = .02, but not anchoring. Stratifying by training level, students maintained a significant difference between Version A and B medical scenarios (Version A, M = 9.83, SD = 3.75; Version B, M = 9.00, SD = 3.98), t(465) = 2.29, p = .02, but not residents or attendings. Stratifying by heuristic and training level, availability maintained

  12. Representing the vacuum polarization on de Sitter

    Energy Technology Data Exchange (ETDEWEB)

    Leonard, Katie E.; Woodard, Richard P. [Department of Physics, University of Florida, Gainesville, Florida 32611 (United States); Prokopec, Tomislav [Institute of Theoretical Physics (ITP) and Spinoza Institute, Utrecht University, Postbus 80195, 3508 TD Utrecht (Netherlands)

    2013-03-15

    Previous studies of the vacuum polarization on de Sitter have demonstrated that there is a simple, noncovariant representation of it in which the physics is transparent. There is also a cumbersome, covariant representation in which the physics is obscure. Despite being unwieldy, the latter form has a powerful appeal for those who are concerned about de Sitter invariance. We show that nothing is lost by employing the simple, noncovariant representation because there is a closed form procedure for converting its structure functions to those of the covariant representation. We also present a vastly improved technique for reading off the noncovariant structure functions from the primitive diagrams. And we discuss the issue of representing the vacuum polarization for a general metric background.

  13. Towards a representative periphytic diatom sample

    Directory of Open Access Journals (Sweden)

    2007-01-01

    Full Text Available The need to acquire a representative periphytic diatom sample for river water quality monitoring has been recognised in the development of existing diatom indices, important in the development and employment of diatom monitoring tools for the Water Framework Directive. In this study, a nested design with replication is employed to investigate the magnitude of variation in diatom biomass, composition and Trophic Diatom Index at varying scales within a small chalk river. The study shows that the use of artificial substrates may not result in diatom communities that are typical of the surrounding natural substrates. Periphytic diatom biomass and composition varies between artificial and natural substrates, riffles and glides and between two stretches of the river channel. The study also highlights the existence of high variation in diatom frustule frequency and biovolume at the individual replicate scale which may have implications for the use of diatoms in routine monitoring.

  14. STATISTICAL MODELS OF REPRESENTING INTELLECTUAL CAPITAL

    Directory of Open Access Journals (Sweden)

    Andreea Feraru

    2016-07-01

    Full Text Available This article entitled Statistical Models of Representing Intellectual Capital approaches and analyses the concept of intellectual capital, as well as the main models which can support enterprisers/managers in evaluating and quantifying the advantages of intellectual capital. Most authors examine intellectual capital from a static perspective and focus on the development of its various evaluation models. In this chapter we surveyed the classical static models: Sveiby, Edvisson, Balanced Scorecard, as well as the canonical model of intellectual capital. Among the group of static models for evaluating organisational intellectual capital the canonical model stands out. This model enables the structuring of organisational intellectual capital in: human capital, structural capital and relational capital. Although the model is widely spread, it is a static one and can thus create a series of errors in the process of evaluation, because all the three entities mentioned above are not independent from the viewpoint of their contents, as any logic of structuring complex entities requires.

  15. Recent activities of the Seismology Division Early Career Representative(s)

    Science.gov (United States)

    Agius, Matthew; Van Noten, Koen; Ermert, Laura; Mai, P. Martin; Krawczyk, CharLotte

    2016-04-01

    The European Geosciences Union is a bottom-up-organisation, in which its members are represented by their respective scientific divisions, committees and council. In recent years, EGU has embarked on a mission to reach out for its numerous 'younger' members by giving awards to outstanding young scientists and the setting up of Early Career Scientists (ECS) representatives. The division representative's role is to engage in discussions that concern students and early career scientists. Several meetings between all the division representatives are held throughout the year to discuss ideas and Union-wide issues. One important impact ECS representatives have had on EGU is the increased number of short courses and workshops run by ECS during the annual General Assembly. Another important contribution of ECS representatives was redefining 'Young Scientist' to 'Early Career Scientist', which avoids discrimination due to age. Since 2014, the Seismology Division has its own ECS representative. In an effort to more effectively reach out for young seismologists, a blog and a social media page dedicated to seismology have been set up online. With this dedicated blog, we'd like to give more depth to the average browsing experience by enabling young researchers to explore various seismology topics in one place while making the field more exciting and accessible to the broader community. These pages are used to promote the latest research especially of young seismologists and to share interesting seismo-news. Over the months the pages proved to be popular, with hundreds of views every week and an increased number of followers. An online survey was conducted to learn more about the activities and needs of early career seismologists. We present the results from this survey, and the work that has been carried out over the last two years, including detail of what has been achieved so far, and what we would like the ECS representation for Seismology to achieve. Young seismologists are

  16. Putative and unique gene sequence utilization for the design of species specific probes as modeled by Lactobacillus plantarum

    Science.gov (United States)

    The concept of utilizing putative and unique gene sequences for the design of species specific probes was tested. The abundance profile of assigned functions within the Lactobacillus plantarum genome was used for the identification of the putative and unique gene sequence, csh. The targeted gene (cs...

  17. Quantitative Trait Locus and Genetical Genomics Analysis Identifies Putatively Causal Genes for Fecundity and Brooding in the Chicken

    Directory of Open Access Journals (Sweden)

    Martin Johnsson

    2016-02-01

    Full Text Available Life history traits such as fecundity are important to evolution because they make up components of lifetime fitness. Due to their polygenic architectures, such traits are difficult to investigate with genetic mapping. Therefore, little is known about their molecular basis. One possible way toward finding the underlying genes is to map intermediary molecular phenotypes, such as gene expression traits. We set out to map candidate quantitative trait genes for egg fecundity in the chicken by combining quantitative trait locus mapping in an advanced intercross of wild by domestic chickens with expression quantitative trait locus mapping in the same birds. We measured individual egg fecundity in 232 intercross chickens in two consecutive trials, the second one aimed at measuring brooding. We found 12 loci for different aspects of egg fecundity. We then combined the genomic confidence intervals of these loci with expression quantitative trait loci from bone and hypothalamus in the same intercross. Overlaps between egg loci and expression loci, and trait–gene expression correlations identify 29 candidates from bone and five from hypothalamus. The candidate quantitative trait genes include fibroblast growth factor 1, and mitochondrial ribosomal proteins L42 and L32. In summary, we found putative quantitative trait genes for egg traits in the chicken that may have been affected by regulatory variants under chicken domestication. These represent, to the best of our knowledge, some of the first candidate genes identified by genome-wide mapping for life history traits in an avian species.

  18. Quantitative Trait Locus and Genetical Genomics Analysis Identifies Putatively Causal Genes for Fecundity and Brooding in the Chicken.

    Science.gov (United States)

    Johnsson, Martin; Jonsson, Kenneth B; Andersson, Leif; Jensen, Per; Wright, Dominic

    2015-12-04

    Life history traits such as fecundity are important to evolution because they make up components of lifetime fitness. Due to their polygenic architectures, such traits are difficult to investigate with genetic mapping. Therefore, little is known about their molecular basis. One possible way toward finding the underlying genes is to map intermediary molecular phenotypes, such as gene expression traits. We set out to map candidate quantitative trait genes for egg fecundity in the chicken by combining quantitative trait locus mapping in an advanced intercross of wild by domestic chickens with expression quantitative trait locus mapping in the same birds. We measured individual egg fecundity in 232 intercross chickens in two consecutive trials, the second one aimed at measuring brooding. We found 12 loci for different aspects of egg fecundity. We then combined the genomic confidence intervals of these loci with expression quantitative trait loci from bone and hypothalamus in the same intercross. Overlaps between egg loci and expression loci, and trait-gene expression correlations identify 29 candidates from bone and five from hypothalamus. The candidate quantitative trait genes include fibroblast growth factor 1, and mitochondrial ribosomal proteins L42 and L32. In summary, we found putative quantitative trait genes for egg traits in the chicken that may have been affected by regulatory variants under chicken domestication. These represent, to the best of our knowledge, some of the first candidate genes identified by genome-wide mapping for life history traits in an avian species.

  19. Structure of the HIV-1 gp41 Membrane-Proximal Ectodomain Region in a Putative Prefusion Conformation

    Energy Technology Data Exchange (ETDEWEB)

    Liu, J.; Deng, Y; Dey, A; Moore, J; Lu, M

    2009-01-01

    The conserved membrane-proximal external region (MPER) of the HIV-1 gp41 envelope protein is the established target for very rare but broadly neutralizing monoclonal antibodies (NAbs) elicited during natural human infection. Nevertheless, attempts to generate an HIV-1 neutralizing antibody response with immunogens bearing MPER epitopes have met with limited success. Here we show that the MPER peptide (residues 662-683) forms a labile ?-helical trimer in aqueous solution and report the crystal structure of this autonomous folding subdomain stabilized by addition of a C-terminal isoleucine zipper motif. The structure reveals a parallel triple-stranded coiled coil in which the neutralization epitope residues are buried within the interface between the associating MPER helices. Accordingly, both the 2F5 and 4E10 NAbs recognize the isolated MPER peptide but fail to bind the trimeric MPER subdomain. We propose that the trimeric MPER structure represents the prefusion conformation of gp41, preceding the putative prehairpin intermediate and the postfusion trimer-of-hairpins structure. As such, the MPER trimer should inform the design of new HIV-1 immunogens to elicit broadly neutralizing antibodies.

  20. Identification of genes coding for putative wax ester synthase/diacylglycerol acyltransferase enzymes in terrestrial and marine environments.

    Science.gov (United States)

    Lanfranconi, Mariana P; Alvarez, Adrián F; Alvarez, Héctor M

    2015-12-01

    Synthesis of neutral lipids such as triacylglycerols (TAG) and wax esters (WE) is catalyzed in bacteria by wax ester synthase/diacylglycerol acyltransferase enzymes (WS/DGAT). We investigated the diversity of genes encoding this enzyme in contrasting natural environments from Patagonia (Argentina). The content of petroleum hydrocarbons in samples collected from oil-producing areas was measured. PCR-based analysis covered WS/DGAT occurrence in marine sediments and soil. No product was obtained in seawater samples. All clones retrieved from marine sediments affiliated with gammaproteobacterial sequences and within them, most phylotypes formed a unique cluster related to putative WS/DGAT belonging to marine OM60 clade. In contrast, soils samples contained phylotypes only related to actinomycetes. Among them, phylotypes affiliated with representatives largely or recently reported as oleaginous bacteria, as well as with others considered as possible lipid-accumulating bacteria based on the analysis of their annotated genomes. Our study shows for the first time that the environment could contain a higher variety of ws/dgat than that reported from bacterial isolates. The results of this study highlight the relevance of the environment in a natural process such as the synthesis and accumulation of neutral lipids. Particularly, both marine sediments and soil may serve as a useful source for novel WS/DGAT with biotechnological interest.

  1. Validation of candidate genes putatively associated with resistance to SCMV and MDMV in maize (Zea mays L.) by expression profiling.

    Science.gov (United States)

    Uzarowska, Anna; Dionisio, Giuseppe; Sarholz, Barbara; Piepho, Hans-Peter; Xu, Mingliang; Ingvardsen, Christina Rønn; Wenzel, Gerhard; Lübberstedt, Thomas

    2009-02-02

    The potyviruses sugarcane mosaic virus (SCMV) and maize dwarf mosaic virus (MDMV) are major pathogens of maize worldwide. Two loci, Scmv1 and Scmv2, have ealier been shown to confer complete resistance to SCMV. Custom-made microarrays containing previously identified SCMV resistance candidate genes and resistance gene analogs were utilised to investigate and validate gene expression and expression patterns of isogenic lines under pathogen infection in order to obtain information about the molecular mechanisms involved in maize-potyvirus interactions. By employing time course microarray experiments we identified 68 significantly differentially expressed sequences within the different time points. The majority of differentially expressed genes differed between the near-isogenic line carrying Scmv1 resistance locus at chromosome 6 and the other isogenic lines. Most differentially expressed genes in the SCMV experiment (75%) were identified one hour after virus inoculation, and about one quarter at multiple time points. Furthermore, most of the identified mapped genes were localised outside the Scmv QTL regions. Annotation revealed differential expression of promising pathogenesis-related candidate genes, validated by qRT-PCR, coding for metallothionein-like protein, S-adenosylmethionine synthetase, germin-like protein or 26S ribosomal RNA. Our study identified putative candidate genes and gene expression patterns related to resistance to SCMV. Moreover, our findings support the effectiveness and reliability of the combination of different expression profiling approaches for the identification and validation of candidate genes. Genes identified in this study represent possible future targets for manipulation of SCMV resistance in maize.

  2. The Two Sides of the Representative Coin

    Directory of Open Access Journals (Sweden)

    Keith Sutherland

    2011-12-01

    Full Text Available In Federalist 10 James Madison drew a functional distinction between “parties” (advocates for factional interests and “judgment” (decision-making for the public good and warned of the corrupting effect of combining both functions in a “single body of men.” This paper argues that one way of overcoming “Madisonian corruption” would be by restricting political parties to an advocacy role, reserving the judgment function to an allotted (randomly-selected microcosm of the whole citizenry, who would determine the outcome of parliamentary debates by secret ballot—a division of labour suggested by James Fishkin’s experiments in deliberative polling. The paper then defends this radical constitutional proposal against Bernard Manin’s (1997 claim that an allotted microcosm could not possibly fulfil the “consent” requirement of Natural Right theory. Not only does the proposal challenge Manin’s thesis, but a 28th Amendment implementing it would finally reconcile the competing visions that have bedevilled representative democracy since the Constitutional Convention of 1787.

  3. The Two Sides of the Representative Coin

    Directory of Open Access Journals (Sweden)

    Keith Sutherland

    2011-12-01

    Full Text Available In Federalist 10 James Madison drew a functional distinction between “parties” (advocates for factional interests and “judgment” (decision-making for the public good and warned of the corrupting effect of combining both functions in a “single body of men.” This paper argues that one way of overcoming “Madisonian corruption” would be by restricting political parties to an advocacy role, reserving the judgment function to an allotted (randomly-selected microcosm of the whole citizenry, who would determine the outcome of parliamentary debates by secret ballot—a division of labour suggested by James Fishkin’s experiments in deliberative polling. The paper then defends this radical constitutional proposal against Bernard Manin’s (1997 claim that an allotted microcosm could not possibly fulfil the “consent” requirement of Natural Right theory. Not only does the proposal challenge Manin’s thesis, but a 28th Amendment implementing it would finally reconcile the competing visions that have bedevilled representative democracy since the Constitutional Convention of 1787.

  4. Structure, regulation, and putative function of the arginine deiminase system of Streptococcus suis.

    Science.gov (United States)

    Gruening, Petra; Fulde, Marcus; Valentin-Weigand, Peter; Goethe, Ralph

    2006-01-01

    Streptococcus suis is an important cause of infectious diseases in young pigs. Little is known about the virulence factors or protective antigens of S. suis. Recently, we have identified two proteins of the arginine deiminase system (ADS) of S. suis, which were temperature induced and expressed on the streptococcal surface (N. Winterhoff, R. Goethe, P. Gruening, M. Rohde, H. Kalisz, H. E. Smith, and P. Valentin-Weigand, J. Bacteriol. 184:6768-6776, 2002). In the present study, we analyzed the complete ADS of S. suis. Due to their homologies to the recently published S. gordonii ADS genes, the genes for arginine deiminase, ornithine carbamoyl-transferase, and carbamate kinase, which were previously designated adiS, octS, and ckS, respectively, were renamed arcA, arcB, and arcC, respectively. Our data revealed that arcA, arcB, and arcC of the S. suis ADS are transcribed from an operon (arcABC operon). Additionally, putative ADS-associated genes were cloned and sequenced which, however, did not belong to the arcABC operon. These were the flpS gene upstream of the arcABC operon with homology to the flp transcription regulator of S. gordonii and the arcD, arcT, arcH, and argR genes downstream of the arcABC operon with high homologies to a putative arginine-ornithine antiporter, a putative dipeptidase of S. gordonii, a putative beta-N-acetylhexosaminidase of S. pneumoniae, and a putative arginine repressor of S. gordonii, respectively. The transcriptional start point of the arcABC operon was determined, and promoter analysis provided evidence that multiple factors contribute to the regulation of the ADS. Thus, a putative binding site for a transcription regulator of the Crp/Fnr family, an ArgR-binding site, and two cis-acting catabolite response elements were identified in the promoter-operator region of the operon. Consistent with this, we could demonstrate that the ADS of S. suis is inducible by arginine and reduced O2 tension and subject to carbon catabolite

  5. Comparison of 454-ESTs from Huperzia serrata and Phlegmariurus carinatus reveals putative genes involved in lycopodium alkaloid biosynthesis and developmental regulation

    Directory of Open Access Journals (Sweden)

    Steinmetz André

    2010-09-01

    Full Text Available Abstract Background Plants of the Huperziaceae family, which comprise the two genera Huperzia and Phlegmariurus, produce various types of lycopodium alkaloids that are used to treat a number of human ailments, such as contusions, swellings and strains. Huperzine A, which belongs to the lycodine type of lycopodium alkaloids, has been used as an anti-Alzheimer's disease drug candidate. Despite their medical importance, little genomic or transcriptomic data are available for the members of this family. We used massive parallel pyrosequencing on the Roche 454-GS FLX Titanium platform to generate a substantial EST dataset for Huperzia serrata (H. serrata and Phlegmariurus carinatus (P. carinatus as representative members of the Huperzia and Phlegmariurus genera, respectively. H. serrata and P. carinatus are important plants for research on the biosynthesis of lycopodium alkaloids. We focused on gene discovery in the areas of bioactive compound biosynthesis and transcriptional regulation as well as genetic marker detection in these species. Results For H. serrata, 36,763 unique putative transcripts were generated from 140,930 reads totaling over 57,028,559 base pairs; for P. carinatus, 31,812 unique putative transcripts were generated from 79,920 reads totaling over 30,498,684 base pairs. Using BLASTX searches of public databases, 16,274 (44.3% unique putative transcripts from H. serrata and 14,070 (44.2% from P. carinatus were assigned to at least one protein. Gene Ontology (GO and Kyoto Encyclopedia of Genes and Genomes (KEGG orthology annotations revealed that the functions of the unique putative transcripts from these two species cover a similarly broad set of molecular functions, biological processes and biochemical pathways. In particular, a total of 20 H. serrata candidate cytochrome P450 genes, which are more abundant in leaves than in roots and might be involved in lycopodium alkaloid biosynthesis, were found based on the comparison of H

  6. A putative morphological substrate of the catecholamine-influenced neuropeptide Y (NPY) release in the human hypothalamus.

    Science.gov (United States)

    Ko, Laam; Rotoli, Giorgio; Grignol, George; Hu, Walter; Merchenthaler, Istvan; Dudas, Bertalan

    2011-06-01

    Neuropeptide Y (NPY) is a 36 amino acid peptide, which among others, plays a pivotal role in stress response. Although previous studies confirmed that NPY release is increased by stress in several species, the exact mechanism of the stress-induced NPY release has not been elucidated yet. In the present study, we examined, with morphological means, the possibility that catecholamines directly influence NPY release in the human hypothalamus. Since the use of electron microscopic techniques is virtually impossible in immunostained human samples due to the long post mortem time, double-label immunohistochemistry was utilised in order to reveal the putative catecholaminergic-NPY associations. The present study is the first to demonstrate juxtapositions between the catecholaminergic, tyrosine hydroxylase (TH)/dopamine-beta hydroxylase (DBH)-immunoreactive (IR) and NPY-IR neural elements in the human hypothalamus. These en passant type associations are most numerous in the infundibular and periventricular areas of the human diencephalon. Here, NPY-IR neurons often form several contacts with catecholaminergic fibre varicosities, without any observable gaps between the contacting elements, suggesting that these juxtapositions may represent functional synapses. The lack of phenylethanolamine N-methyltransferase (PNMT)-NPY juxtapositions and the relatively few observed DBH-NPY associations suggest that the vast majority of the observed TH-NPY juxtapositions represent dopaminergic synapses. Since catecholamines are known to be the crucial components of the stress response, the presence of direct, catecholaminergic (primarily dopaminergic)-NPY-IR synapses may explain the increased NPY release during stress. The released NPY in turn is believed to play an active role in the responses that are directed to maintain the homeostasis during stressful conditions.

  7. Branched-chain fatty acids produced by mutants of Streptomyces fradiae, putative precursors of the lactone ring of tylosin.

    Science.gov (United States)

    Huber, M L; Paschal, J W; Leeds, J P; Kirst, H A; Wind, J A; Miller, F D; Turner, J R

    1990-01-01

    Three branched-chain fatty acids (7-hydroxy-4,6-dimethylnona-2,4-dienoic acid [compound 1], its 7-epimer [compound 2], and 7-keto-4,6-dimethylnona-2,4-dienoic acid [compound 3]) and a ketone (9-hydroxy-6,8-dimethylundeca-4,6-dien-3-one [compound 4]) were isolated from the culture broth of mutants of Streptomyces fradiae which were blocked in the biosynthesis of the macrolide antibiotic tylosin. Two phenotypic classes of mutants of this organism which were blocked in the addition of mycaminose to tylactone (compound 6) accumulated these compounds. These compounds were not produced by mutants which were blocked in lactone synthesis, in steps beyond mycaminose addition, or by the wild-type strain. Synthesis of these compounds, like synthesis of tylosin, was inhibited by the addition of cerulenin. Compounds 1, 2, and 3 were partially interconvertible by these mutants; but they were not produced from the degradation of tylactone and they were not directly incorporated into tylosin by intact cells. The structures of compounds 1 and 2 were equivalent to that of a predicted intermediate (S. Yue, J. S. Duncan, Y. Yamamoto, and C. R. Hutchinson, J. Am. Chem. Soc. 109:1253-1255, 1987) in the biosynthesis of tylactone. The ketone (compound 4) reported previously (N. D. Jones, M. O. Chaney, H. A. Kirst, G. M. Wild, R. H. Baltz, R. L. Hamill, and J. W. Paschal, J. Antibiot. 35:420-425, 1982) appears to be the decarboxylation product of the intermediate following that represented by compound 1. This represents the first report of the isolation of putative precursors of tylactone from tylosin-producing organisms. PMID:2221862

  8. Do Female Representatives Adhere More Closely to Citizens’ Preferences Than Male Representatives?

    OpenAIRE

    2012-01-01

    We analyze whether female or male members of parliament adhere more closely to citizens’ revealed preferences with quasi-experimental data. By matching individual representatives’ voting behavior on legislative proposals with real referenda outcomes on the same issues, we identify the effect of gender on representatives’ responsiveness to revealed preferences of the majority of voters. Overall, female members of parliament tend to adhere less to citizens’ preferences than male parliam...

  9. Hippocampal and thalamic neuronal metabolism in a putative rat model of schizophrenia○

    Institute of Scientific and Technical Information of China (English)

    Guolin Ma; Tianbin Song; Min Chen; Yuan Fu; Yong Xu; Ensen Ma; Wu Wang; Jiang Du; Mingxiong Huang

    2013-01-01

    The transcription factor early growth response protein 3 (EGR3) is involved in schizophrenia. We developed a putative rat model of schizophrenia by transfecting lentiviral particles carrying the Egr3 gene into bilateral hippocampal dentate gyrus. We assessed spatial working memory using the Morris water maze test, and neuronal metabolite levels in bilateral hippocampus and thalamus were determined by 3.0 T proton magnetic resonance spectroscopy. Choline content was significantly greater in the hippocampus after transfection, while N-acetylaspartate and the ratio of N-acetylaspartate to creatine/phosphocreatine in the thalamus were lower than in controls. This study is the first to report evaluation of brain metabolites using 3.0 T proton magnetic resonance spectroscopy in rats transfected with Egr3, and reveals metabolic abnormalities in the hippocampus and thalamus in this putative model of schizophrenia.

  10. Functional characterization of a putative β-lactamase gene in the genome of Zymomonas mobilis.

    Science.gov (United States)

    Rajnish, K Narayanan; Asraf, Sheik Abdul Kader Sheik; Manju, Nagarajan; Gunasekaran, Paramasamy

    2011-12-01

    Zymomonas mobilis ZM4 is resistant to β-lactam antibiotics but there are no reports of a β-lactam resistance gene and its regulation. A putative β-lactamase gene sequence (ZMO0103) in the genome of Z. mobilis showed a 55% amino acid sequence identity with class C β-lactamase genes. qPCR analysis of the β-lactamase transcript indicated a higher level expression of the β-lactamase compared to the relative transcript quantities in antibiotic-susceptible bacteria. The putative β-lactamase gene was cloned, expressed in Escherichia coli BL21 and the product, AmpC, was purified to homogeneity. Its optimal activity was at pH 6 and 30 °C. Further, the β-lactamase had a higher affinity towards penicillins than cephalosporin antibiotics. © Springer Science+Business Media B.V. 2011

  11. Putative Biomarkers and Targets of Estrogen Receptor Negative Human Breast Cancer

    Directory of Open Access Journals (Sweden)

    Stephen W. Byers

    2011-07-01

    Full Text Available Breast cancer is a progressive and potentially fatal disease that affects women of all ages. Like all progressive diseases, early and reliable diagnosis is the key for successful treatment and annihilation. Biomarkers serve as indicators of pathological, physiological, or pharmacological processes. Her2/neu, CA15.3, estrogen receptor (ER, progesterone receptor (PR, and cytokeratins are biomarkers that have been approved by the Food and Drug Administration for disease diagnosis, prognosis, and therapy selection. The structural and functional complexity of protein biomarkers and the heterogeneity of the breast cancer pathology present challenges to the scientific community. Here we review estrogen receptor-related putative breast cancer biomarkers, including those of putative breast cancer stem cells, a minor population of estrogen receptor negative tumor cells that retain the stem cell property of self renewal. We also review a few promising cytoskeleton targets for ER alpha negative breast cancer.

  12. A putative ABC transporter is involved in negative regulation of biofilm formation by Listeria monocytogenes

    DEFF Research Database (Denmark)

    Zhu, Xinna; Long, Fei; Chen, Yonghui

    2008-01-01

    Listeria monocytogenes may persist for long periods in food processing environments. In some instances, this may be due to aggregation or biofilm formation. To investigate the mechanism controlling biofilm formation in the food-borne pathogen L. monocytogenes, we characterized LM-49, a mutant...... with enhanced ability of biofilm-formation generated via transposon Tn917 mutagenesis of L. monocytogenes 4b G. In this mutant, a Tn917 insertion has disrupted the coding region of the gene encoding a putative ATP binding cassette (ABC) transporter permease identical to Lmof2365_1771 (a putative ABC......-transporter permease) presented in the sequenced strain L. monocytogenes str. 4b F2365. This disrupted gene, denoted lm.G_1771, encoded a protein with 10 transmembrane helixes. The revertant, LM-49RE, was obtained by replacing lm.G_1771::Tn917 with lm.G_1771 via homologous recombination. We found that LM-49RE formed...

  13. The solution structure of ChaB, a putative membrane ion antiporter regulator from Escherichia coli

    Directory of Open Access Journals (Sweden)

    Iannuzzi Pietro

    2004-08-01

    Full Text Available Abstract Background ChaB is a putative regulator of ChaA, a Na+/H+ antiporter that also has Ca+/H+ activity in E. coli. ChaB contains a conserved 60-residue region of unknown function found in other bacteria, archaeabacteria and a series of baculoviral proteins. As part of a structural genomics project, the structure of ChaB was elucidated by NMR spectroscopy. Results The structure of ChaB is composed of 3 α-helices and a small sheet that pack tightly to form a fold that is found in the cyclin-box family of proteins. Conclusion ChaB is distinguished from its putative DNA binding sequence homologues by a highly charged flexible loop region that has weak affinity to Mg2+ and Ca2+ divalent metal ions.

  14. Exploring Universal Partnerships and Putative Marriages as Tools for Awarding Partnership Property in Contemporary Family Law

    Directory of Open Access Journals (Sweden)

    Elsje Bonthuys

    2016-12-01

    Full Text Available Following upon the Supreme Court of Appeal's judgment in Butters v Mncora 2012 4 SA 1 (SCA, which broadened the criteria and consequences of universal partnerships in cohabitation relationships, this article investigates the potential of universal partnerships and putative marriages to allocate rights to share in partnership property in other intimate relationships. It traverses several instances in which marriages are not recognised - bigamous marriages, Muslim and Hindu religious marriages and invalid customary marriages – examining whether the wives in these marriages could use universal partnerships and putative marriages to claim a share in property. It then considers the use of universal partnerships to obtain a share of property in civil marriages out of community of property. It concludes by pointing out several issues which are in need of clarification and where the common law should be developed to give effect to fundamental constitutional rights.

  15. Enrichment of putative stem cells from adipose tissue using dielectrophoretic field-flow fractionation

    Science.gov (United States)

    Vykoukal, Jody; Vykoukal, Daynene M.; Freyberg, Susanne; Alt, Eckhard U.; Gascoyne, Peter R. C.

    2009-01-01

    We have applied the microfluidic cell separation method of dielectrophoretic field-flow fractionation (DEP-FFF) to the enrichment of a putative stem cell population from an enzyme-digested adipose tissue derived cell suspension. A DEP-FFF separator device was constructed using a novel microfluidic-microelectronic hybrid flex-circuit fabrication approach that is scaleable and anticipates future low-cost volume manufacturing. We report the separation of a nucleated cell fraction from cell debris and the bulk of the erythrocyte population, with the relatively rare (<2% starting concentration) NG2-positive cell population (pericytes and/or putative progenitor cells) being enriched up to 14-fold. This work demonstrates a potential clinical application for DEP-FFF and further establishes the utility of the method for achieving label-free fractionation of cell subpopulations. PMID:18651083

  16. Composition of the Putative Prepore Complex of Bacillus thuringiensis Cry1Ab Toxin

    Science.gov (United States)

    Nair, Manoj S.; Dean, Donald H.

    2015-01-01

    Prepore formation is hypothesized to be an obligate step in the insertion of Cry1Ab toxin into insect brush border membrane vesicles. We examined the architecture of the putative prepore when isolated using the published protocols [1] [2]. Our results demonstrate that the putative prepore form of Cry1Ab is a combination of receptor proteins attached to the toxin, when purified. The results also suggest that this prepore form as prepared by the methods published is different from other membrane-extracted oligomeric forms of Cry toxins and prepore of other toxins in general. While most other known prepores are composed of multimers of a single protein, the Cry1Ab prepore, as generated, is a protein-receptor complex oligomer and monomers of Cry toxins. PMID:26702367

  17. Analysis of the transcriptome of Panax notoginseng root uncovers putative triterpene saponin-biosynthetic genes and genetic markers

    Directory of Open Access Journals (Sweden)

    Luo Hongmei

    2011-12-01

    Full Text Available Abstract Background Panax notoginseng (Burk F.H. Chen is important medicinal plant of the Araliacease family. Triterpene saponins are the bioactive constituents in P. notoginseng. However, available genomic information regarding this plant is limited. Moreover, details of triterpene saponin biosynthesis in the Panax species are largely unknown. Results Using the 454 pyrosequencing technology, a one-quarter GS FLX titanium run resulted in 188,185 reads with an average length of 410 bases for P. notoginseng root. These reads were processed and assembled by 454 GS De Novo Assembler software into 30,852 unique sequences. A total of 70.2% of unique sequences were annotated by Basic Local Alignment Search Tool (BLAST similarity searches against public sequence databases. The Kyoto Encyclopedia of Genes and Genomes (KEGG assignment discovered 41 unique sequences representing 11 genes involved in triterpene saponin backbone biosynthesis in the 454-EST dataset. In particular, the transcript encoding dammarenediol synthase (DS, which is the first committed enzyme in the biosynthetic pathway of major triterpene saponins, is highly expressed in the root of four-year-old P. notoginseng. It is worth emphasizing that the candidate cytochrome P450 (Pn02132 and Pn00158 and UDP-glycosyltransferase (Pn00082 gene most likely to be involved in hydroxylation or glycosylation of aglycones for triterpene saponin biosynthesis were discovered from 174 cytochrome P450s and 242 glycosyltransferases by phylogenetic analysis, respectively. Putative transcription factors were detected in 906 unique sequences, including Myb, homeobox, WRKY, basic helix-loop-helix (bHLH, and other family proteins. Additionally, a total of 2,772 simple sequence repeat (SSR were identified from 2,361 unique sequences, of which, di-nucleotide motifs were the most abundant motif. Conclusion This study is the first to present a large-scale EST dataset for P. notoginseng root acquired by next

  18. Identification of putative effector genes and their transcripts in three strains related to 'Candidatus Phytoplasma aurantifolia'.

    Science.gov (United States)

    Anabestani, Ameneh; Izadpanah, Keramat; Abbà, Simona; Galetto, Luciana; Ghorbani, Abozar; Palmano, Sabrina; Siampour, Majid; Veratti, Flavio; Marzachì, Cristina

    2017-06-01

    Molecular mechanisms underlying phytoplasma interactions with host plants are largely unknown. In this study attempts were made to identify effectors of three phytoplasma strains related to 'Ca. P. aurantifolia', crotalaria phyllody (CrP), faba bean phyllody (FBP), and witches' broom disease of lime (WBDL), using information from draft genome of peanut witches' broom phytoplasma. Seven putative effectors were identified in WBDL genome (SAP11, SAP21, Eff64, Eff115, Eff197, Eff211 and EffSAP67), five (SAP11, SAP21, Eff64, Eff99 and Eff197) in CrP and two (SAP11, Eff64) in FBP. No homologs to Eff64, Eff197 and Eff211 in phytoplasmas of other phylogenetic groups were found. SAP11 and Eff64 homologs of 'Ca. P. aurantifolia' strains shared at least 95.9% identity and were detected in the three phytoplasmas, supporting their role within the group. Five of the putative effectors (SAP11, SAP21, Eff64, Eff115, and Eff99) were transcribed from total RNA extracts of periwinkle plants infected with these phytoplasmas. Transcription profiles of selected putative effectors of CrP, FBP and WBDL indicated that SAP11 transcripts were the most abundant in the three phytoplasmas. SAP21 transcript levels were comparable to those of SAP11 for CrP and not measurable for the other phytoplasmas. Eff64 had the lowest transcription level irrespective of sampling date and phytoplasma isolate. Eff115 transcript levels were the highest in WBDL infected plants. This work reports the first sequence information for 14 putative effectors in three strains related to 'Ca. P. aurantifolia', and offers novel insight into the transcription profile of five of them during infection of periwinkle. Copyright © 2017 Elsevier GmbH. All rights reserved.

  19. A novel putative auxin carrier family regulates intracellular auxin homeostasis in plants

    OpenAIRE

    2012-01-01

    The phytohormone auxin acts as a prominent signal, providing, by its local accumulation or depletion in selected cells, a spatial and temporal reference for changes in the developmental program. The distribution of auxin depends on both auxin metabolism (biosynthesis, conjugation and degradation) and cellular auxin transport. We identified in silico a novel putative auxin transport facilitator family, called PIN-LIKES (PILS). Here we illustrate that PILS proteins are required for auxin-depend...

  20. ANTIBIOTICS RESISTANCE AND PUTATIVE VIRULENCE FACTORS OF AEROMONAS HYDROPHILA ISOLATED FROM ESTUARY

    OpenAIRE

    Olumide Adedokun Odeyemi; Ahmad Asmat; Gires Usup

    2012-01-01

    This study aim to investigate antibiotics resistance profile and putative virulence factors of Aeromonas hydrophila isolated from estuary. Bacteria used for this study were isolated from water and sediment samples obtained from Sungai Melayu, Johor, Malaysia. Serially diluted 100 µL water and 1g sediment were inoculated on modified Rimler - Shott (mRS) agar. Colonies with distinct cultural characteristics were picked for further studies. Isolates were tested for biofilm productions, protease ...

  1. Bioinformatic Analysis of Putative Gene Products Encoded in SARS-HCoV Genome

    Institute of Scientific and Technical Information of China (English)

    赵心刚; 韩敬东; 宁元亨; 孟安明; 陈晔光

    2003-01-01

    The cause of severe acute respiratory syndrome (SARS) has been identified as a new coronavirus named as SARS-HCoV.Using bioinformatic methods, we have performed a detailed domain search.In addition to the viral structure proteins, we have found that several putative polypeptides share sequence similarity to known domains or proteins.This study may provide a basis for future studies on the infection and replication process of this notorious virus.

  2. Detection of putative periodontopathic bacteria in type 1 diabetic and healthy children: A comparative study

    OpenAIRE

    2013-01-01

    Aim: The aim of this study was to compare and assess the risk of periodontitis due to the presence of four putative periodontopathic bacteria (Porphyromonas gingivalis, Treponema denticola, Tannerella forsythia, and Aggregatibacter actinomycetemcomitans) in type 1 diabetic and healthy children. Materials and Methods: Fifty type 1 diabetic and 50 healthy children in the age group of 7-14 years were recruited for the study. Subgingival plaque samples collected from permanent first molars w...

  3. Representing Identity and Equivalence for Scientific Data

    Science.gov (United States)

    Wickett, K. M.; Sacchi, S.; Dubin, D.; Renear, A. H.

    2012-12-01

    Matters of equivalence and identity are central to the stewardship of scientific data. In order to properly prepare for and manage the curation, preservation and sharing of digitally-encoded data, data stewards must be able to characterize and assess the relationships holding between data-carrying digital resources. However, identity-related questions about resources and their information content may not be straightforward to answer: for example, what exactly does it mean to say that two files contain the same data, but in different formats? Information content is frequently distinguished from particular representations, but there is no adequately developed shared understanding of what this really means and how the relationship between content and its representations hold. The Data Concepts group at the Center for Informatics Research in Science and Scholarship (CIRSS), University of Illinois at Urbana Champaign, is developing a logic-based framework of fundamental concepts related to scientific data to support curation and integration. One project goal is to develop precise accounts of information resources carrying the same data. We present two complementary conceptual models for information representation: the Basic Representation Model (BRM) and the Systematic Assertion Model (SAM). We show how these models provide an analytical account of digitally-encoded scientific data and a precise understanding of identity and equivalence. The Basic Representation Model identifies the core entities and relationships involved in representing information carried by digital objects. In BRM, digital objects are symbol structures that express propositional content, and stand in layered encoding relationships. For example, an RDF description may be serialized as either XML or N3, and those expressions in turn may be encoded as either UTF-8 or UTF-16 sequences. Defining this encoding stack reveals distinctions necessary for a precise account of identity and equivalence

  4. HOW TO REPRESENT THE GENETIC CODE?

    Directory of Open Access Journals (Sweden)

    N.S. Santos-Magalhães

    2004-05-01

    Full Text Available The advent of molecular genetic comprises a true revolution of far-reaching consequences for human-kind, which evolved into a specialized branch of the modern-day Biochemistry. The analysis of specicgenomic information are gaining wide-ranging interest because of their signicance to the early diag-nosis of disease, and the discovery of modern drugs. In order to take advantage of a wide assortmentof signal processing (SP algorithms, the primary step of modern genomic SP involves convertingsymbolic-DNA sequences into complex-valued signals. How to represent the genetic code? Despitebeing extensively known, the DNA mapping into proteins is one of the relevant discoveries of genetics.The genetic code (GC is revisited in this work, addressing other descriptions for it, which can beworthy for genomic SP. Three original representations are discussed. The inner-to-outer map buildson the unbalanced role of nucleotides of a codon. A two-dimensional-Gray genetic representationis oered as a structured map that can help interpreting DNA spectrograms or scalograms. Theseare among the powerful visual tools for genome analysis, which depends on the choice of the geneticmapping. Finally, the world-chart for the GC is investigated. Evoking the cyclic structure of thegenetic mapping, it can be folded joining the left-right borders, and the top-bottom frontiers. As aresult, the GC can be drawn on the surface of a sphere resembling a world-map. Eight parallels oflatitude are required (four in each hemisphere as well as four meridians of longitude associated tofour corresponding anti-meridians. The tropic circles have 11.25o, 33.75o, 56.25o, and 78.5o (Northand South. Starting from an arbitrary Greenwich meridian, the meridians of longitude can be plottedat 22.5o, 67.5o, 112.5o, and 157.5o (East and West. Each triplet is assigned to a single point on thesurface that we named Nirenberg-Kohamas Earth. Despite being valuable, usual representations forthe GC can be

  5. Immunodiagnosis of episomal Banana streak MY virus using polyclonal antibodies to an expressed putative coat protein.

    Science.gov (United States)

    Sharma, Susheel Kumar; Kumar, P Vignesh; Baranwal, Virendra Kumar

    2014-10-01

    A cryptic Badnavirus species complex, known as banana streak viruses (BSV) poses a serious threat to banana production and genetic improvement worldwide. Due to the presence of integrated BSV sequences in the banana genome, routine detection is largely based on serological and nucleo-serological diagnostic methods which require high titre specific polyclonal antiserum. Viral structural proteins like coat protein (CP) are the best target for in vitro expression, to be used as antigen for antiserum production. However, in badnaviruses precise CP sequences are not known. In this study, two putative CP coding regions (p48 and p37) of Banana streak MY virus (BSMYV) were identified in silico by comparison with caulimoviruses, retroviruses and Rice tungro bacilliform virus. The putative CP coding region (p37) was in vitro expressed in pMAL system and affinity purified. The purified fusion protein was used as antigen for raising polyclonal antiserum in rabbit. The specificity of antiserum was confirmed in Western blots, immunosorbent electron microscopy (ISEM) and antigen coated plate-enzyme linked immunosorbent assay (ACP-ELISA). The antiserum (1:2000) was successfully used in ACP-ELISA for specific detection of BSMYV infection in field and tissue culture raised banana plants. The antiserum was also utilized in immuno-capture PCR (IC-PCR) based indexing of episomal BSMYV infection. This is the first report of in silico identification of putative CP region of BSMYV, production of polyclonal antiserum against recombinant p37 and its successful use in immunodetection.

  6. Identification of Putative Coffee Rust Mycoparasites via Single-Molecule DNA Sequencing of Infected Pustules.

    Science.gov (United States)

    James, Timothy Y; Marino, John A; Perfecto, Ivette; Vandermeer, John

    2015-11-13

    The interaction of crop pests with their natural enemies is a fundament to their control. Natural enemies of fungal pathogens of crops are poorly known relative to those of insect pests, despite the diversity of fungal pathogens and their economic importance. Currently, many regions across Latin America are experiencing unprecedented epidemics of coffee rust (Hemileia vastatrix). Identification of natural enemies of coffee rust could aid in developing management strategies or in pinpointing species that could be used for biocontrol. In the present study, we characterized fungal communities associated with coffee rust lesions by single-molecule DNA sequencing of fungal rRNA gene bar codes from leaf discs (≈28 mm(2)) containing rust lesions and control discs with no rust lesions. The leaf disc communities were hyperdiverse in terms of fungi, with up to 69 operational taxonomic units (putative species) per control disc, and the diversity was only slightly reduced in rust-infected discs, with up to 63 putative species. However, geography had a greater influence on the fungal community than whether the disc was infected by coffee rust. Through comparisons between control and rust-infected leaf discs, as well as taxonomic criteria, we identified 15 putative mycoparasitic fungi. These fungi are concentrated in the fungal family Cordycipitaceae and the order Tremellales. These data emphasize the complexity of diverse fungi of unknown ecological function within a leaf that might influence plant disease epidemics or lead to the development of species for biocontrol of fungal disease.

  7. Emissions of putative isoprene oxidation products from mango branches under abiotic stress

    Science.gov (United States)

    Jardine, Kolby J.; Meyers, Kimberly; Abrell, Leif; Alves, Eliane G.; Yanez Serrano, Ana Maria; Kesselmeier, Jürgen; Karl, Thomas; Guenther, Alex; Vickers, Claudia; Chambers, Jeffrey Q.

    2013-01-01

    Although several per cent of net carbon assimilation can be re-released as isoprene emissions to the atmosphere by many tropical plants, much uncertainty remains regarding its biological significance. In a previous study, we detected emissions of isoprene and its oxidation products methyl vinyl ketone (MVK) and methacrolein (MACR) from tropical plants under high temperature/light stress, suggesting that isoprene is oxidized not only in the atmosphere but also within plants. However, a comprehensive analysis of the suite of isoprene oxidation products in plants has not been performed and production relationships with environmental stress have not been described. In this study, putative isoprene oxidation products from mango (Mangifera indica) branches under abiotic stress were first identified. High temperature/light and freeze–thaw treatments verified direct emissions of the isoprene oxidation products MVK and MACR together with the first observations of 3-methyl furan (3-MF) and 2-methyl-3-buten-2-ol (MBO) as putative novel isoprene oxidation products. Mechanical wounding also stimulated emissions of MVK and MACR. Photosynthesis under 13CO2 resulted in rapid (<30min) labelling of up to five carbon atoms of isoprene, with a similar labelling pattern observed in the putative oxidation products. These observations highlight the need to investigate further the mechanisms of isoprene oxidation within plants under stress and its biological and atmospheric significance. PMID:23881400

  8. Cloning and molecular characterization of a putative voltage-gated sodium channel gene in the crayfish.

    Science.gov (United States)

    Coskun, Cagil; Purali, Nuhan

    2016-06-01

    Voltage-gated sodium channel genes and associated proteins have been cloned and studied in many mammalian and invertebrate species. However, there is no data available about the sodium channel gene(s) in the crayfish, although the animal has frequently been used as a model to investigate various aspects of neural cellular and circuit function. In the present work, by using RNA extracts from crayfish abdominal ganglia samples, the complete open reading frame of a putative sodium channel gene has firstly been cloned and molecular properties of the associated peptide have been analyzed. The open reading frame of the gene has a length of 5793 bp that encodes for the synthesis of a peptide, with 1930 amino acids, that is 82% similar to the α-peptide of a sodium channel in a neighboring species, Cancer borealis. The transmembrane topology analysis of the crayfish peptide indicated a pattern of four folding domains with several transmembrane segments, as observed in other known voltage-gated sodium channels. Upon analysis of the obtained sequence, functional regions of the putative sodium channel responsible for the selectivity filter, inactivation gate, voltage sensor, and phosphorylation have been predicted. The expression level of the putative sodium channel gene, as defined by a qPCR method, was measured and found to be the highest in nervous tissue.

  9. Putative periodontopathic bacteria and herpesviruses in pregnant women: a case-control study

    Science.gov (United States)

    Lu, Haixia; Zhu, Ce; Li, Fei; Xu, Wei; Tao, Danying; Feng, Xiping

    2016-01-01

    Little is known about herpesvirus and putative periodontopathic bacteria in maternal chronic periodontitis. The present case-control study aimed to explore the potential relationship between putative periodontopathic bacteria and herpesviruses in maternal chronic periodontitis.Saliva samples were collected from 36 pregnant women with chronic periodontitis (cases) and 36 pregnant women with healthy periodontal status (controls). Six putative periodontopathic bacteria (Porphyromonas gingivalis [Pg], Aggregatibacer actinomycetemcomitans [Aa], Fusobacterium nucleatum [Fn], Prevotella intermedia [Pi], Tannerella forsythia [Tf], and Treponema denticola [Td]) and three herpesviruses (Epstein-Barr virus [EBV], human cytomegalovirus [HCMV], and herpes simplex virus [HSV]) were detected. Socio-demographic data and oral health related behaviors, and salivary estradiol and progesterone levels were also collected. The results showed no significant differences in socio-demographic background, oral health related behaviors, and salivary estradiol and progesterone levels between the two groups (all P > 0.05). The detection rates of included periodontopathic microorganisms were not significantly different between the two groups (all P > 0.05), but the coinfection rate of EBV and Pg was significantly higher in the case group than in the control group (P = 0.028). EBV and Pg coinfection may promote the development of chronic periodontitis among pregnant women. PMID:27301874

  10. Phylogeny of algal sequences encoding carbohydrate sulfotransferases, formylglycine-dependent sulfatases and putative sulfatase modifying factors

    Directory of Open Access Journals (Sweden)

    Chai-Ling eHo

    2015-11-01

    Full Text Available Many algae are rich sources of sulfated polysaccharides with biological activities. The physicochemical/rheological properties and biological activities of sulfated polysaccharides are affected by the pattern and number of sulfate moieties. Sulfation of carbohydrates is catalyzed by carbohydrate sulfotransferases (CHSTs while modification of sulfate moieties on sulfated polysaccharides was presumably catalyzed by sulfatases including formylglycine-dependent sulfatases (FGly-SULFs. Post-translationally modification of Cys to FGly in FGly-SULFs by sulfatase modifiying factors (SUMFs is necessary for the activity of this enzyme. The aims of this study are to mine for sequences encoding algal CHSTs, FGly-SULFs and putative SUMFs from the fully sequenced algal genomes and to infer their phylogenetic relationships to their well characterized counterparts from other organisms. Algal sequences encoding CHSTs, FGly-SULFs, SUMFs and SUMF-like proteins were successfully identified from green and brown algae. However, red algal FGly-SULFs and SUMFs were not identified. In addition, a group of SUMF-like sequences with different gene structure and possibly different functions were identified for green, brown and red algae. The phylogeny of these putative genes contributes to the corpus of knowledge of an unexplored area. The analyses of these putative genes contribute towards future production of existing and new sulfated carbohydrate polymers through enzymatic synthesis and metabolic engineering.

  11. Overexpression, crystallization and preliminary X-ray crystallographic analysis of a putative transposase from Thermoplasma acidophilum encoded by the Ta0474 gene

    Energy Technology Data Exchange (ETDEWEB)

    Kang, Ji Yong; Lee, Hyung Ho; Kim, Do Jin; Han, Sang Hee; Kim, Olesya; Kim, Hyoun Sook; Lee, Sang Jae; Suh, Se Won, E-mail: sewonsuh@snu.ac.kr [Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742 (Korea, Republic of)

    2006-11-01

    A putative transposase from T. acidophilum encoded by the Ta0474 gene was crystallized and X-ray diffraction data were collected to 1.78 Å. IS200 transposases, originally identified in Salmonella typhimurium LT2, are present in many bacteria and archaea and are distinct from other groups of transposases. To facilitate further structural comparisons among IS200-like transposases, structural analysis has been initiated of a putative transposase from Thermoplasma acidophilum encoded by the Ta0474 gene. Its 137-residue polypeptide shows high levels of sequence similarity to other members of the IS200 transposase family. The protein was overexpressed in intact form in Escherichia coli and crystallized at 297 K using a reservoir solution consisting of 100 mM Na HEPES pH 7.5 and 20%(v/v) ethanol. X-ray diffraction data were collected to 1.78 Å. The crystals belong to the monoclinic space group P2{sub 1}, with unit-cell parameters a = 65.00, b = 34.07, c = 121.58 Å, α = 90, β = 100.20, γ = 90°. Four monomers, representing two copies of a dimeric molecule, are present in the asymmetric unit, giving a crystal volume per protein weight (V{sub M}) of 2.02 Å{sup 3} Da{sup −1} and a solvent content of 39.2%.

  12. Molecular cloning, immunochemical localization to the vacuole, and expression in transgenic yeast and tobacco of a putative sugar transporter from sugar beet.

    Science.gov (United States)

    Chiou, T J; Bush, D R

    1996-02-01

    Several plant genes have been cloned that encode members of the sugar transporter subgroup of the major facilitator superfamily of transporters. Here we report the cloning, expression, and membrane localization of one of these porters found in sugar beet (Beta vulgaris L.). This clone, cDNA-1, codes for a protein with 490 amino acids and an estimated molecular mass of 54 kD. The predicted membrane topology and sequence homology suggest that cDNA-1 is a member of the sugar transporter family. RNA gel blot analysis revealed that this putative sugar transporter is expressed in all vegetative tissues and expression increases with development in leaves. DNA gel blot analysis indicated that multiple gene copies exist for this putative sugar transporter in the sugar beet genome. Antibodies directed against small peptides representing the N- and C-terminal domains of the cDNA1 protein identified a 40-kD polypeptide in microsomes isolated from cDNA-1-transformed yeast (Saccharomyces cerevisiae). Moreover, the same protein was identified in sugar beet and transgenic tobacco (Nicotaina tobacum L.) membrane fractions. Detailed analysis of the transporter's distribution across linear sucrose gradients and flotation centrifugations showed that it co-migrates with tonoplast membrane markers. We conclude that this carrier is located on the tonoplast membrane and that it may mediate sugar partitioning between the vacuole and cytoplasmic compartments.

  13. Localization of putative carbonic anhydrases in two marine diatoms, Phaeodactylum tricornutum and Thalassiosira pseudonana.

    Science.gov (United States)

    Tachibana, Masaaki; Allen, Andrew E; Kikutani, Sae; Endo, Yuri; Bowler, Chris; Matsuda, Yusuke

    2011-09-01

    It is believed that intracellular carbonic anhydrases (CAs) are essential components of carbon concentrating mechanisms in microalgae. In this study, putative CA-encoding genes were identified in the genome sequences of the marine diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana. Subsequently, the subcellular localizations of the encoded proteins were determined. Nine and thirteen CA sequences were found in the genomes of P. tricornutum and T. pseudonana, respectively. Two of the β-CA genes in P. tricornutum corresponded to ptca1 and ptca2 identified previously. Immunostaining transmission electron microscopy of a PtCA1:YFP fusion expressed in the cells of P. tricornutum clearly showed the localization of PtCA1 within the central part of the pyrenoid structure in the chloroplast. Besides these two β-CA genes, P. tricornutum likely contains five α- and two γ-CA genes, whereas T. pseudonana has three α-, five γ-, four δ-, and one ζ-CA genes. Semi-quantitative reverse transcription PCR performed on mRNA from the two diatoms grown in changing light and CO(2) conditions revealed that levels of six putative α- and γ-CA mRNAs in P. tricornutum did not change between cells grown in air-level CO(2) and 5% CO(2). However, mRNA levels of one putative α-CA gene, CA-VII in P. tricornutum, were reduced in the dark compared to that in the light. In T. pseudonana, mRNA accumulation levels of putative α-CA (CA-1), ζ-CA (CA-3) and δ-CA (CA-7) were analyzed and all levels found to be significantly reduced when cells were grown in 0.16% CO(2). Intercellular localizations of eight putative CAs were analyzed by expressing GFP fusion in P. tricornutum and T. pseudonana. In P. tricornutum, CA-I and II localized in the periplastidial compartment, CA-III, VI, VII were found in the chloroplast endoplasmic reticulum, and CA-VIII was localized in the mitochondria. On the other hand, T. pseudonana CA-1 localized in the stroma and CA-3 was found in the periplasm

  14. Registration Appointment and Services for Representatives Management Information

    Data.gov (United States)

    Social Security Administration — A new internet/intranet application that collects all representative information and establishes the relationship between the claimant and the representative. Allow...

  15. Tomato Cutin Deficient 1 (CD1) and putative orthologs comprise an ancient family of cutin synthase‐like (CUS) proteins that are conserved among land plants

    DEFF Research Database (Denmark)

    Yeats, Trevor H.; Huang, Wenlin; Chatterjee, Subhasish;

    2014-01-01

    The aerial epidermis of all land plants is covered with a hydrophobic cuticle that provides essential protection from desiccation, and so its evolution is believed to have been prerequisite for terrestrial colonization. A major structural component of apparently all plant cuticles is cutin......, a polyester of hydroxy fatty acids; however, despite its ubiquity, the details of cutin polymeric structure and the mechanisms of its formation and remodeling are not well understood. We recently reported that cutin polymerization in tomato (Solanum lycopersicum) fruit occurs via transesterification...... of hydroxyacylglycerol precursors, catalyzed by the GDSL‐motif lipase/hydrolase family protein (GDSL) Cutin Deficient 1 (CD1). Here, we present additional biochemical characterization of CD1 and putative orthologs from Arabidopsis thaliana and the moss Physcomitrella patens, which represent a distinct clade of cutin...

  16. A subset of the diverse COG0523 family of putative metal chaperones is linked to zinc homeostasis in all kingdoms of life

    Directory of Open Access Journals (Sweden)

    Merchant Sabeeha S

    2009-10-01

    Full Text Available Abstract Background COG0523 proteins are, like the nickel chaperones of the UreG family, part of the G3E family of GTPases linking them to metallocenter biosynthesis. Even though the first COG0523-encoding gene, cobW, was identified almost 20 years ago, little is known concerning the function of other members belonging to this ubiquitous family. Results Based on a combination of comparative genomics, literature and phylogenetic analyses and experimental validations, the COG0523 family can be separated into at least fifteen subgroups. The CobW subgroup involved in cobalamin synthesis represents only one small sub-fraction of the family. Another, larger subgroup, is suggested to play a predominant role in the response to zinc limitation based on the presence of the corresponding COG0523-encoding genes downstream from putative Zur binding sites in many bacterial genomes. Zur binding sites in these genomes are also associated with candidate zinc-independent paralogs of zinc-dependent enzymes. Finally, the potential role of COG0523 in zinc homeostasis is not limited to Bacteria. We have predicted a link between COG0523 and regulation by zinc in Archaea and show that two COG0523 genes are induced upon zinc depletion in a eukaryotic reference organism, Chlamydomonas reinhardtii. Conclusion This work lays the foundation for the pursuit by experimental methods of the specific role of COG0523 members in metal trafficking. Based on phylogeny and comparative genomics, both the metal specificity and the protein target(s might vary from one COG0523 subgroup to another. Additionally, Zur-dependent expression of COG0523 and putative paralogs of zinc-dependent proteins may represent a mechanism for hierarchal zinc distribution and zinc sparing in the face of inadequate zinc nutrition.

  17. 29 CFR 417.19 - Assistant Secretary's representative.

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 2 2010-07-01 2010-07-01 false Assistant Secretary's representative. 417.19 Section 417.19... Union To Take Appropriate Remedial Action Following Subpart A Procedures § 417.19 Assistant Secretary's representative. The Assistant Secretary shall appoint a representative or representatives whose functions shall...

  18. 48 CFR 1830.7002-3 - Representative investment calculations.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 6 2010-10-01 2010-10-01 true Representative investment... Representative investment calculations. (a) The calculation of the representative investment requires... accounting period, the contractor shall either: (1) Determine a representative investment for the...

  19. A Hypothesis for the Abiotic and Non-Martian Origins of Putative Signs of Ancient Martian Life in ALH84001

    Science.gov (United States)

    Treiman, Allan H.

    2001-01-01

    Putative evidence of martian life in ALH84001 can be explained by abiotic and non-martian processes consistent with the meteorite's geological history. Additional information is contained in the original extended abstract.

  20. Haemolytic and cytotoxic activities of the Tween 80-extracted putative haemolysin of Pasteurella multocida B:2.

    Science.gov (United States)

    Chachra, D; Coote, J G; Parton, R; Jand, S K

    2011-06-02

    The objective of this study was to investigate the haemolytic and cytotoxic activity of Pasteurella multocida B:2 strains, originally from cases of haemorrhagic septicaemia in cattle. All six P. multocida B:2 strains were non-haemolytic on sheep blood agar (SBA) and horse blood agar (HBA) when grown aerobically and on SBA anaerobically but they were haemolytic on HBA when grown anaerobically. No haemolytic activity against horse red blood cells was detected in culture supernates from aerobically or anaerobically grown cultures and only very weak haemolytic activity was obtained in supernates or pellet fractions from sonicated cells. However, after repeated extraction of sonicated cells with Tween 80, haemolytic activity was found in various cell fractions, both Tween-soluble and -insoluble. The Tween-extracted putative haemolysin and other bacterial fractions were also cytotoxic for mouse macrophage-like J774.2 cells. Further characterisation of the putative haemolysin revealed it to be a heat-labile, non-pore-forming protein of molecular weight >10 kDa whose activity was completely destroyed by trypsin and greatly reduced with protease and proteinase K treatment. Congo red also reduced the haemolytic activity. Non-denaturing gel-electrophoresis and RBC agar overlay revealed clear haemolytic zones but suggested that Tween was bound to some component of the P. multocida B:2 fractions and was responsible, to some extent, for the haemolytic activity observed. However, the effect of heat and other reagents on the Tween-extracted fractions and the lack of haemolytic activity in different Tween-extracted cell fractions of organisms other than P. multocida suggested that some proteinaceous component of the organism could indeed act as a haemolysin. This putative haemolysin may be one of the virulence attributes of P. multocida, but its characterisation and role in pathogenesis require further study.

  1. Isolation and characterization of two mitoviruses and a putative alphapartitivirus from Fusarium spp.

    Science.gov (United States)

    Osaki, Hideki; Sasaki, Atsuko; Nomiyama, Koji; Sekiguchi, Hiroyuki; Tomioka, Keisuke; Takehara, Toshiaki

    2015-06-01

    The filamentous fungus Fusarium spp. includes several important plant pathogens. We attempted to reveal presence of double-stranded (ds) RNAs in the genus. Thirty-seven Fusarium spp. at the MAFF collection were analyzed. In the strains of Fusarium coeruleum, Fusarium globosum and Fusarium solani f. sp. pisi, single dsRNA bands were detected. The strains of F. coeruleum and F. solani f. sp. pisi cause potato dry rot and mulberry twig blight, respectively. Sequence analyses revealed that dsRNAs in F. coeruleum and F. globosum consisted of 2423 and 2414 bp, respectively. Using the fungal mitochondrial translation table, the positive strands of these cDNAs were found to contain single open reading frames with the potential to encode a protein of putative 757 and 717 amino acids (molecular mass 88.5 and 84.0 kDa, respectively), similar to RNA-dependent RNA polymerases of members of the genus Mitovirus. These dsRNAs in F. coeruleum and F. globosum were assigned to the genus Mitovirus (family Narnaviridae), and these two mitoviruses were designated as Fusarium coeruleum mitovirus 1 and Fusarium globosum mitovirus 1. On the other hand, a positive strand of cDNA (1950 bp) from dsRNA in F. solani f. sp. pisi contained an ORF potentially encoding a putative RdRp of 608 amino acids (72.0 kDa). The putative RdRp was shown to be related to those of members of the genus of Alphapartitivirus (family Partitiviridae). We coined the name Fusarium solani partitivirus 2 for dsRNA in F. solani f. sp. pisi.

  2. The intracellular mobility of NPY and a putative mitochondrial form of NPY in neuronal cells.

    Science.gov (United States)

    Kaipio, Katja; Pesonen, Ullamari

    2009-01-30

    Preproneuropeptide Y is a precursor peptide to mature neuropeptide Y (NPY), which is a universally expressed peptide in the central and peripheral nervous system. NPY is normally routed to endoplasmic reticulum and secretory vesicles in cells, which secrete NPY. In our previous studies, we found a functional Leucine7 to Proline7 (L7P) polymorphism in the signal peptide sequence of preproNPY. This polymorphism affects the secretion of NPY and causes multiple physiological effects in humans. The sequence of NPY mRNA contains two in frame kozak sequences that allow translation initiation to shift, and translation of two proteins. In addition to mature NPY(1-36) also a putative truncated NPY(17-36) with mitochondrial targeting signal is produced. The purpose of this study was to investigate the protein mobility of the putative mitochondrial fragment and the effect of the L7P polymorphism on the cellular level using GFP tagged constructs. The mobility was studied with fluorescence recovery after photobleaching technique in a neuronal cell line. We found that the mobility of the secretory vesicles with NPY(1-36) in cells with L7P genotype was increased in comparison to vesicle mobility in cells with the more abundant L7L genotype. The mobility in the cells with the putative mitochondrial construct was found to be very low. According to the results of the present study, the mitochondrial truncated peptide stays in the mitochondrion. It can be hypothesized that this could be one of the factors affecting energy balance of the membranes of the mitochondrion.

  3. Identification and characterization of a gene encoding a putative lysophosphatidyl acyltransferase from Arachis hypogaea

    Indian Academy of Sciences (India)

    Si-Long Chen; Jia-Quan Huang; Lei Yong; Yue-Ting Zhang; Xiao-Ping Ren; Yu-Ning Chen; Hui-Fang Jiang; Li-Ying Yan; Yu-Rong Li; Bo-Shou Liao

    2012-12-01

    Lysophosphatidyl acyltransferase (LPAT) is the important enzyme responsible for the acylation of lysophosphatidic acid (LPA), leading to the generation of phosphatidic acid (PA) in plant. Its encoding gene is an essential candidate for oil crops to improve oil composition and increase seed oil content through genetic engineering. In this study, a full-length AhLPAT4 gene was isolated via cDNA library screening and rapid amplification of cDNA ends (RACE); our data demonstrated that AhLPAT4 had 1631 nucleotides, encoding a putative 43.8 kDa protein with 383 amino acid residues. The deduced protein included a conserved acyltransferase domain and four motifs (I–IV) with putative LPA and acyl-CoA catalytic and binding sites. Bioinformatic analysis indicated that AhLPAT4 contained four transmembrane domains (TMDs), localized to the endoplasmic reticulum (ER) membrane; detailed analysis indicated that motif I and motifs II–III in AhLPAT4 were separated by the third TMD, which located on cytosolic and ER luminal side respectively, and hydrophobic residues on the surface of AhLPAT4 protein fold to form a hydrophobic tunnel to accommodate the acyl chain. Subcellular localization analysis confirmed that AhLPAT4 was a cytoplasm protein. Phylogenetic analysis revealed that AhLPAT4 had a high homology (63.7–78.3%) with putative LPAT4 proteins from Glycine max, Arabidopsis thaliana and Ricinus communis. AhLPAT4 was ubiquitously expressed in diverse tissues except in flower, which is almost undetectable. The expression analysis in different developmental stages in peanut seeds indicated that AhLPAT4 did not coincide with oil accumulation.

  4. Identification of putative rhamnogalacturonan-II specific glycosyltransferases in Arabidopsis using a combination of bioinformatics approaches.

    Science.gov (United States)

    Voxeur, Aline; André, Aurélie; Breton, Christelle; Lerouge, Patrice

    2012-01-01

    Rhamnogalacturonan-II (RG-II) is a complex plant cell wall polysaccharide that is composed of an α(1,4)-linked homogalacturonan backbone substituted with four side chains. It exists in the cell wall in the form of a dimer that is cross-linked by a borate di-ester. Despite its highly complex structure, RG-II is evolutionarily conserved in the plant kingdom suggesting that this polymer has fundamental functions in the primary wall organisation. In this study, we have set up a bioinformatics strategy aimed at identifying putative glycosyltransferases (GTs) involved in RG-II biosynthesis. This strategy is based on the selection of candidate genes encoding type II membrane proteins that are tightly coexpressed in both rice and Arabidopsis with previously characterised genes encoding enzymes involved in the synthesis of RG-II and exhibiting an up-regulation upon isoxaben treatment. This study results in the final selection of 26 putative Arabidopsis GTs, including 10 sequences already classified in the CAZy database. Among these CAZy sequences, the screening protocol allowed the selection of α-galacturonosyltransferases involved in the synthesis of α4-GalA oligogalacturonides present in both homogalacturonans and RG-II, and two sialyltransferase-like sequences previously proposed to be involved in the transfer of Kdo and/or Dha on the pectic backbone of RG-II. In addition, 16 non-CAZy GT sequences were retrieved in the present study. Four of them exhibited a GT-A fold. The remaining sequences harbored a GT-B like fold and a fucosyltransferase signature. Based on homologies with glycosyltransferases of known functions, putative roles in the RG-II biosynthesis are proposed for some GT candidates.

  5. Novel mutations in the GH gene (GH1) uncover putative splicing regulatory elements.

    Science.gov (United States)

    Babu, Deepak; Mellone, Simona; Fusco, Ileana; Petri, Antonella; Walker, Gillian E; Bellone, Simonetta; Prodam, Flavia; Momigliano-Richiardi, Patricia; Bona, Gianni; Giordano, Mara

    2014-05-01

    Mutations affecting exon 3 splicing are the main cause of autosomal dominant Isolated GH Deficiency II (IGHDII) by increasing the level of exon 3-skipped mRNA encoding the functionally inactive dominant-negative 17.5-kDa isoform. The exons and introns of the gene encoding GH (GH1) were screened for the presence of mutations in 103 sporadic isolated GH deficiency cases. Four different variations within exon 3 were identified in 3 patients. One carried c.261C>T (p.Pro87Pro) and c.272A>T (p.Glu91Val), the second c.255G>A (p.Pro85Pro) and c.261 C>T, and the third c.246G>C (p.Glu82Asp). All the variants were likely generated by gene conversion from an homologous gene in the GH1 cluster. In silico analysis predicted that positions c.255 and c.272 were included within 2 putative novel exon splicing enhancers (ESEs). Their effect on splicing was confirmed in vitro. Constructs bearing these 2 variants induced consistently higher levels both of transcript and protein corresponding to the 17.5-kDa isoform. When c.255 and c.272 were combined in cis with the c.261 variant, as in our patients, their effect was weaker. In conclusion, we identified 2 variations, c.255G>A and c.272A>T, located in 2 novel putative exon splicing enhancers and affecting GH1 splicing in vitro by increasing the production of alternatively spliced isoforms. The amount of aberrant isoforms is further regulated by the presence in cis of the c.261 variant. Thus, our results evidenced novel putative splicing regulatory elements within exon 3, confirming the crucial role of this exon in mRNA processing.

  6. A Proteomics Approach to Identify New Putative Cardiac Intercalated Disk Proteins.

    Directory of Open Access Journals (Sweden)

    Siddarth Soni

    Full Text Available Synchronous beating of the heart is dependent on the efficient functioning of the cardiac intercalated disk (ID. The ID is composed of a complex protein network enabling electrical continuity and chemical communication between individual cardiomyocytes. Recently, several different studies have shed light on increasingly prevalent cardiac diseases involving the ID. Insufficient knowledge of its composition makes it difficult to study these disease mechanisms in more detail and therefore here we aim expand the ID proteome. Here, using a combination of general membrane enrichment, in-depth quantitative proteomics and an intracellular location driven bioinformatics approach, we aim to discover new putative ID proteins in rat ventricular tissue.General membrane isolation, enriched amongst others also with ID proteins as based on presence of the established markers connexin-43 and n-cadherin, was performed using centrifugation. By mass spectrometry, we quantitatively evaluated the level of 3455 proteins in the enriched membrane fraction (EMF and its counterpart, the soluble cytoplasmic fraction. These data were stringently filtered to generate a final set of 97 enriched, putative ID proteins. These included Cx43 and n-cadherin, but also many interesting novel candidates. We selected 4 candidates (Flotillin-2 (FLOT2, Nexilin (NEXN, Popeye-domain-containg-protein 2 (POPDC2 and thioredoxin-related-transmembrane-protein 2 (TMX2 and confirmed their co-localization with n-cadherin in the ID of human and rat heart cryo-sections, and isolated dog cardiomyocytes.The presented proteomics dataset of putative new ID proteins is a valuable resource for future research into this important molecular intersection of the heart.

  7. Two putative-aquaporin genes are differentially expressed during arbuscular mycorrhizal symbiosis in Lotus japonicus

    Science.gov (United States)

    2012-01-01

    Background Arbuscular mycorrhizas (AM) are widespread symbioses that provide great advantages to the plant, improving its nutritional status and allowing the fungus to complete its life cycle. Nevertheless, molecular mechanisms that lead to the development of AM symbiosis are not yet fully deciphered. Here, we have focused on two putative aquaporin genes, LjNIP1 and LjXIP1, which resulted to be upregulated in a transcriptomic analysis performed on mycorrhizal roots of Lotus japonicus. Results A phylogenetic analysis has shown that the two putative aquaporins belong to different functional families: NIPs and XIPs. Transcriptomic experiments have shown the independence of their expression from their nutritional status but also a close correlation with mycorrhizal and rhizobial interaction. Further transcript quantification has revealed a good correlation between the expression of one of them, LjNIP1, and LjPT4, the phosphate transporter which is considered a marker gene for mycorrhizal functionality. By using laser microdissection, we have demonstrated that one of the two genes, LjNIP1, is expressed exclusively in arbuscule-containing cells. LjNIP1, in agreement with its putative role as an aquaporin, is capable of transferring water when expressed in yeast protoplasts. Confocal analysis have demonstrated that eGFP-LjNIP1, under its endogenous promoter, accumulates in the inner membrane system of arbusculated cells. Conclusions Overall, the results have shown different functionality and expression specificity of two mycorrhiza-inducible aquaporins in L. japonicus. One of them, LjNIP1 can be considered a novel molecular marker of mycorrhizal status at different developmental stages of the arbuscule. At the same time, LjXIP1 results to be the first XIP family aquaporin to be transcriptionally regulated during symbiosis. PMID:23046713

  8. Enrichment of putative human epidermal stem cells based on cell size and collagen type IV adhesiveness

    Institute of Scientific and Technical Information of China (English)

    Juxue Li; Enkui Duan; Chenglin Miao; Weixiang Guo; Liwei Jia; Jiaxi Zhou; Baohua Ma; Sha Peng; Shuang Liu; Yujing Cao

    2008-01-01

    The enrichment and identification of human epidermal stem cells (EpSCs) are of paramount importance for both basic research and clinical application. Although several approaches for the enrichment of EpSCs have been established, enriching a pure population of viable EpSCs is still a challenging task. An improved approach is worth developing to enhance the purity and viability of EpSCs. Here we report that cell size combined with collagen type IV adhesiveness can be used in an improved approach to enrich pure and viable human EpSCs. We separated the rapidly adherent keratinocytes into three populations that range in size from 5-7 μm (population A), to 7-9 μm (population B), to >9 μm (population C) in diameter, and found that human putative EpSCs could be further enriched in population A with the smallest size. Among the three populations, population A displayed the highest density of βl-integrin receptor, contained the highest percentage of cells in G0/G1 phase, showed the highest nucleus to cytoplasm ratio, and possessed the highest colony formation efficiency (CFE). When injected into murine blastocysts, these cells participated in multi-tissue formation. More significantly, compared with a previous approach that sorted putative EpSCs according to pl-integrin antibody staining, the viability of the EpSCs enriched by the improved approach was significantly enhanced. Our results provide a putative strategy for the enrichment of human EpSCs, and encourage further study into the role of cell size in stem cell biology.

  9. Two putative-aquaporin genes are differentially expressed during arbuscular mycorrhizal symbiosis in Lotus japonicus

    Directory of Open Access Journals (Sweden)

    Giovannetti Marco

    2012-10-01

    Full Text Available Abstract Background Arbuscular mycorrhizas (AM are widespread symbioses that provide great advantages to the plant, improving its nutritional status and allowing the fungus to complete its life cycle. Nevertheless, molecular mechanisms that lead to the development of AM symbiosis are not yet fully deciphered. Here, we have focused on two putative aquaporin genes, LjNIP1 and LjXIP1, which resulted to be upregulated in a transcriptomic analysis performed on mycorrhizal roots of Lotus japonicus. Results A phylogenetic analysis has shown that the two putative aquaporins belong to different functional families: NIPs and XIPs. Transcriptomic experiments have shown the independence of their expression from their nutritional status but also a close correlation with mycorrhizal and rhizobial interaction. Further transcript quantification has revealed a good correlation between the expression of one of them, LjNIP1, and LjPT4, the phosphate transporter which is considered a marker gene for mycorrhizal functionality. By using laser microdissection, we have demonstrated that one of the two genes, LjNIP1, is expressed exclusively in arbuscule-containing cells. LjNIP1, in agreement with its putative role as an aquaporin, is capable of transferring water when expressed in yeast protoplasts. Confocal analysis have demonstrated that eGFP-LjNIP1, under its endogenous promoter, accumulates in the inner membrane system of arbusculated cells. Conclusions Overall, the results have shown different functionality and expression specificity of two mycorrhiza-inducible aquaporins in L. japonicus. One of them, LjNIP1 can be considered a novel molecular marker of mycorrhizal status at different developmental stages of the arbuscule. At the same time, LjXIP1 results to be the first XIP family aquaporin to be transcriptionally regulated during symbiosis.

  10. Temporal dynamics and decay of putatively allochthonous and autochthonous viral genotypes in contrasting freshwater lakes.

    Science.gov (United States)

    Hewson, Ian; Barbosa, Jorge G; Brown, Julia M; Donelan, Ryan P; Eaglesham, James B; Eggleston, Erin M; LaBarre, Brenna A

    2012-09-01

    Aquatic viruses play important roles in the biogeochemistry and ecology of lacustrine ecosystems; however, their composition, dynamics, and interactions with viruses of terrestrial origin are less extensively studied. We used a viral shotgun metagenomic approach to elucidate candidate autochthonous (i.e., produced within the lake) and allochthonous (i.e., washed in from other habitats) viral genotypes for a comparative study of their dynamics in lake waters. Based on shotgun metagenomes prepared from catchment soil and freshwater samples from two contrasting lakes (Cayuga Lake and Fayetteville Green Lake), we selected two putatively autochthonous viral genotypes (phycodnaviruses likely infecting algae and cyanomyoviruses likely infecting picocyanobacteria) and two putatively allochthonous viral genotypes (geminiviruses likely infecting terrestrial plants and circoviruses infecting unknown hosts but common in soil libraries) for analysis by genotype-specific quantitative PCR (TaqMan) applied to DNAs from viruses in the viral size fraction of lake plankton, i.e., 0.2 μm > virus > 0.02 μm. The abundance of autochthonous genotypes largely reflected expected host abundance, while the abundance of allochthonous genotypes corresponded with rainfall and storm events in the respective catchments, suggesting that viruses with these genotypes may have been transported to the lake in runoff. The decay rates of allochthonous and autochthonous genotypes, assessed in incubations where all potential hosts were killed, were generally lower (0.13 to 1.50% h(-1)) than those reported for marine virioplankton but similar to those for freshwater virioplankton. Both allochthonous and autochthonous viral genotypes were detected at higher concentrations in subsurface sediments than at the water-sediment interface. Our data indicate that putatively allochthonous viruses are present in lake plankton and sediments, where their temporal dynamics reflect active transport to the lake during

  11. Evaluation of two putative susceptibility loci for oral clefts in the Danish population

    DEFF Research Database (Denmark)

    Mitchell, L E; Murray, J C; O'Brien, S;

    2001-01-01

    Previous studies suggest that the risk of nonsyndromic cleft lip with or without cleft palate (CL+/-P) and isolated cleft palate (CP) is influenced by genetic variation at several loci and that the relation between specific genetic variants and disease risk may be modified by environmental factors....... The present study evaluated potential associations between CL+/-P and CP and two putative clefting susceptibility loci, MSX1 and TGFB3, using data from a nationwide case-control study conducted in Denmark from 1991 to 1994. The potential effects of interactions between these genes and two common environmental...

  12. Role of putative neurotransmitters in the central gastric antisecretory effect of prostaglandin E2 in rats.

    OpenAIRE

    Puurunen, J.

    1985-01-01

    The role of putative neurotransmitters of the central nervous system in the central gastric antisecretory effect of prostaglandin E2 (PGE2) was investigated in pylorus-ligated rats. Pretreatment of the rats with an intracerebroventricular (i.c.v.) injection of 6-hydroxydopamine (6-OHDA) prevented the antisecretory effect of the i.c.v. administration of PGE2, whereas pretreatment with 5,6-dihydroxytryptamine (5,6-DHT) plus p-chlorophenylalanine (PCPA) had no effect. I.c.v.-administered phentol...

  13. A putative, novel coli surface antigen 8B (CS8B) of enterotoxigenic Escherichia coli.

    Science.gov (United States)

    Njoroge, Samuel M; Boinett, Christine J; Madé, Laure F; Ouko, Tom T; Fèvre, Eric M; Thomson, Nicholas R; Kariuki, Samuel

    2015-10-01

    Enterotoxigenic Escherichia coli (ETEC) strains harbor multiple fimbriae and pili to mediate host colonization, including the type IVb pilus, colonization factor antigen III (CFA/III). Not all colonization factors are well characterized or known in toxin positive ETEC isolates, which may have an impact identifying ETEC isolates based on molecular screening of these biomarkers. We describe a novel coli surface antigen (CS) 8 subtype B (CS8B), a family of CFA/III pilus, in a toxin producing ETEC isolate from a Kenyan collection. In highlighting the existence of this putative CS, we provide the sequence and specific primers, which can be used alongside other ETEC primers previously described.

  14. A specimen of Rhamphorhynchus with soft tissue preservation, stomach contents and a putative coprolite

    Directory of Open Access Journals (Sweden)

    David Hone

    2015-08-01

    Full Text Available Despite being known for nearly two centuries, new specimens of the derived non-pterodactyloid pterosaur Rhamphorhynchus continue to be discovered and reveal new information about their anatomy and palaeobiology. Here we describe a specimen held in the collections of the Royal Tyrrell Museum of Palaeontology, Alberta, Canada that shows both preservation and impressions of soft tissues, and also preserves material interpreted as stomach contents of vertebrate remains and, uniquely, a putative coprolite. The specimen also preserves additional evidence for fibers in the uropatagium.

  15. A putative transglycosylase encoded by SCO4132 influences morphological differentiation and actinorhodin production in Streptomyces coelicolor

    Institute of Scientific and Technical Information of China (English)

    Pengfei Xie; Ana Zeng; Xiaoting Lv; Qiuxiang Cheng; Zhongjun Qin

    2013-01-01

    Here we report that tgdA,a novel gene encoding a putative transglycosylase,affects both the morphological differentiation and the yield of blue-pigmented compound actinorhodin in Streptomyces coelicolor.The tgdA null mutant displays sparse aerial hyphae and irregular spore chains frequently lacking chromosomal DNA.Elevated actinorhodin production coincides with the overexpression of actⅡ-orf4 in mutant.tgdA expression is temporally and developmentally regulated.The tgdA orthologs in Streptomyces avermilitis and Streptomyces lividans also affect differentiation.

  16. Prevalence of Clinical Periodontitis and Putative Periodontal Pathogens among South Indian Pregnant Women

    Directory of Open Access Journals (Sweden)

    Chaitanya Tellapragada

    2014-01-01

    Full Text Available In view of recent understanding of the association of periodontal infections and adverse pregnancy outcomes, the present investigation was undertaken to study the periodontal infections among 390 asymptomatic pregnant women and to find an association of bacterial etiologies with the disease. Prevalence of gingivitis was 38% and clinical periodontitis was 10% among the study population. Subgingival plaque specimens were subjected to multiplex PCR targeting ten putative periodontopathogenic bacteria. Among the periodontitis group, high detection rates of Porphyromonas gingivalis (56%, Prevotella nigrescens (44%, Treponema denticola (32%, and Prevotella intermedius (24% were noted along with significant association with the disease (P<0.05.

  17. A specimen of Rhamphorhynchus with soft tissue preservation, stomach contents and a putative coprolite.

    Science.gov (United States)

    Hone, David; Henderson, Donald M; Therrien, François; Habib, Michael B

    2015-01-01

    Despite being known for nearly two centuries, new specimens of the derived non-pterodactyloid pterosaur Rhamphorhynchus continue to be discovered and reveal new information about their anatomy and palaeobiology. Here we describe a specimen held in the collections of the Royal Tyrrell Museum of Palaeontology, Alberta, Canada that shows both preservation and impressions of soft tissues, and also preserves material interpreted as stomach contents of vertebrate remains and, uniquely, a putative coprolite. The specimen also preserves additional evidence for fibers in the uropatagium.

  18. A comparison of the effects of two putative 5-hydroxytryptamine renal prodrugs in normal man.

    OpenAIRE

    LI KAM WA, T. C.; Freestone, S.; Samson, R. R.; JOHNSTON, N. R.; Lee, M.R.

    1993-01-01

    1. The effects of 1 h intravenous infusions of equimolar amounts of two putative 5-hydroxytryptamine (5-HT) renal prodrugs, 5-hydroxy-L-tryptophan (5-HTP, 10 micrograms kg-1 min-1) and gamma-L-glutamyl-5-hydroxy-L-tryptophan (glu-5-HTP, 16.6 micrograms kg-1 min-1) were examined in five healthy male volunteers in a randomised, placebo-controlled, cross-over study. 2. Both compounds increased urinary excretion of 5-HT and there was greater extra-renal formation of 5-HT following 5-HTP administr...

  19. Identification and characterization of citrus yellow vein clearing virus, a putative new member of the genus Mandarivirus.

    Science.gov (United States)

    Loconsole, G; Onelge, N; Potere, O; Giampetruzzi, A; Bozan, O; Satar, S; De Stradis, A; Savino, V; Yokomi, R K; Saponari, M

    2012-12-01

    Molecular features and genomic organization were determined for Citrus yellow vein clearing virus (CYVCV), the putative viral causal agent of yellow vein clearing disease of lemon trees, reported in Pakistan, India, and more recently in Turkey and China. CYVCV isolate Y1 from Adana, Turkey, was used for deep sequencing analysis of the virus-induced small RNA fractions and for mechanical and graft inoculation of herbaceous and citrus indicator plants. A polyclonal antiserum was developed from CYVCV-Y1 purified from Phaseolus vulgaris and used in western blot assays to characterize the coat protein of CYVCV-Y1 and determine its serological relationship with related viruses. Contigs assembled from the Illumina sequenced short reads were used to construct the whole genome of Citrus yellow vein clearing virus (CYVCV), consisting in a positive-sense RNA of 7,529 nucleotides and containing six predicted open reading frames. The CYVCV genome organization and size resembled that of flexiviruses, and search for sequence homologies revealed that Indian citrus ringspot virus (ICRSV) (Mandarivirus, Alphaflexiviridae) is the most closely related virus. However, CYVCV had an overall nucleotide sequence identity of ≈74% with ICRSV. Although the two viruses were similar with regard to genome organization, viral particles, and herbaceous host range, CYVCV caused different symptoms in citrus and was serologically distinct from ICRSV. Primer pairs were designed and used to detect the virus by conventional and quantitative reverse transcription-polymerase chain reaction on yellow vein clearing symptomatic field trees as well as graft- and mechanically inoculated host plants. Collectively, these data suggest that CYVCV is the causal agent of yellow vein clearing disease and represents a new species in the genus Mandarivirus.

  20. Coexistence in Field Samples of Two Variants of the Infectious Salmon Anemia Virus: A Putative Shift to Pathogenicity

    Science.gov (United States)

    Cárdenas, Constanza; Carmona, Marisela; Gallardo, Alicia; Labra, Alvaro; Marshall, Sergio H.

    2014-01-01

    Genetic reassortment plays an important role in the evolution of several segmented RNA viruses and in the epidemiology of their associated diseases. In particular, orthomyxoviruses show rapid fluctuation in the proportion of viral variants coexisting in an infected individual, especially under strong selective pressure. This is particularly relevant in salmon production carried out under confined and stressful conditions where one of the most feared pathogenic agents is the Infectious Salmon Anemia Virus, an orthomyxovirus family member whose biological behavior is only recently beginning to be understood. Pathogenicity of the virus has been mainly associated with deletions of the HPR region in coding segment 6 and the presence or absence of a specific insertion in a key region in coding segment 5. In this study we report, for the first time in Chile, the coexistence of two variants in fully asymptomatic fish. Of five samples analyzed, two were identified as the non-pathogenic variant, HPR0, and two as the highly pathogenic HPR7b variant, though with no clinical signs detectable in the fish. Interestingly, one of the samples unequivocally carried both variants, again without any clinical signs. Considering that in none of the samples the typical insertion in coding segment 5 was detected, it is our impression that this may represent a shift from the non-pathogenic HPR0 variant towards the highly infective HPR7b variant. If this were the case, the transition may be triggered first by deleting the corresponding sequence of the HPR region of segment 6, followed by the putative insertion in segment 5 to generate a virulent strain. PMID:24498206

  1. Occurrence of putative virulence genes on Arcobacter butzleri isolated from three different environmental sites throughout the dairy chain.

    Science.gov (United States)

    Piva, S; Gariano, G R; Bonilauri, P; Giacometti, F; Decastelli, L; Florio, D; Massella, E; Serraino, A

    2017-04-01

    This comparative study investigated the occurrence of cadF, cj1349, ciaB, pldA, tlyA, hecA, hecB, mviN, irgA and IroE genes in 212 Arcobacter butzleri isolated from three different environmental sites linked to the dairy chain (farms, industrial and artisanal dairy plants) located in three Italian regions (Lombardy, Emilia-Romagna and Calabria). According to the presence of these genes, different pathotypes (P-types) were determined. The main genes detected were ciaB, mviN, tlyA, cj1349, pldA and cadF, while the least common genes were iroE, hecA, hecB and irgA. TlyA, irgA, hecA, hecB and iroE, which were significantly more frequent in isolates recovered in industrial dairy plants. Twelve P-types were detected. The occurrence of the most frequently detected P-types (P-types 1, 2, 3 and 5) differed significantly (P genes and virulence genotype variability depending on the environmental site and geographical origin of the isolates. The present study provides insights into the similar distribution of putative virulence genes in a dairy chain and other sources' isolates and also into a geographical distribution of some P-types. We have shown that industrial dairy plants may represent an environmental site favouring a selection of the isolates with a higher pathogenetic pattern. © 2017 The Society for Applied Microbiology.

  2. Identification of Putative Stage-Specific Grapevine Berry Biomarkers and Omics Data Integration into Networks1[C][W][OA

    Science.gov (United States)

    Zamboni, Anita; Di Carli, Mariasole; Guzzo, Flavia; Stocchero, Matteo; Zenoni, Sara; Ferrarini, Alberto; Tononi, Paola; Toffali, Ketti; Desiderio, Angiola; Lilley, Kathryn S.; Pè, M. Enrico; Benvenuto, Eugenio; Delledonne, Massimo; Pezzotti, Mario

    2010-01-01

    The analysis of grapevine (Vitis vinifera) berries at the transcriptomic, proteomic, and metabolomic levels can provide great insight into the molecular events underlying berry development and postharvest drying (withering). However, the large and very different data sets produced by such investigations are difficult to integrate. Here, we report the identification of putative stage-specific biomarkers for berry development and withering and, to our knowledge, the first integrated systems-level study of these processes. Transcriptomic, proteomic, and metabolomic data were integrated using two different strategies, one hypothesis free and the other hypothesis driven. A multistep hypothesis-free approach was applied to data from four developmental stages and three withering intervals, with integration achieved using a hierarchical clustering strategy based on the multivariate bidirectional orthogonal projections to latent structures technique. This identified stage-specific functional networks of linked transcripts, proteins, and metabolites, providing important insights into the key molecular processes that determine the quality characteristics of wine. The hypothesis-driven approach was used to integrate data from three withering intervals, starting with subdata sets of transcripts, proteins, and metabolites. We identified transcripts and proteins that were modulated during withering as well as specific classes of metabolites that accumulated at the same time and used these to select subdata sets of variables. The multivariate bidirectional orthogonal projections to latent structures technique was then used to integrate the subdata sets, identifying variables representing selected molecular processes that take place specifically during berry withering. The impact of this holistic approach on our knowledge of grapevine berry development and withering is discussed. PMID:20826702

  3. Validation of candidate genes putatively associated with resistance to SCMV and MDMV in maize (Zea mays L. by expression profiling

    Directory of Open Access Journals (Sweden)

    Wenzel Gerhard

    2009-02-01

    Full Text Available Abstract Background The potyviruses sugarcane mosaic virus (SCMV and maize dwarf mosaic virus (MDMV are major pathogens of maize worldwide. Two loci, Scmv1 and Scmv2, have ealier been shown to confer complete resistance to SCMV. Custom-made microarrays containing previously identified SCMV resistance candidate genes and resistance gene analogs were utilised to investigate and validate gene expression and expression patterns of isogenic lines under pathogen infection in order to obtain information about the molecular mechanisms involved in maize-potyvirus interactions. Results By employing time course microarray experiments we identified 68 significantly differentially expressed sequences within the different time points. The majority of differentially expressed genes differed between the near-isogenic line carrying Scmv1 resistance locus at chromosome 6 and the other isogenic lines. Most differentially expressed genes in the SCMV experiment (75% were identified one hour after virus inoculation, and about one quarter at multiple time points. Furthermore, most of the identified mapped genes were localised outside the Scmv QTL regions. Annotation revealed differential expression of promising pathogenesis-related candidate genes, validated by qRT-PCR, coding for metallothionein-like protein, S-adenosylmethionine synthetase, germin-like protein or 26S ribosomal RNA. Conclusion Our study identified putative candidate genes and gene expression patterns related to resistance to SCMV. Moreover, our findings support the effectiveness and reliability of the combination of different expression profiling approaches for the identification and validation of candidate genes. Genes identified in this study represent possible future targets for manipulation of SCMV resistance in maize.

  4. Marketing norm perception among medical representatives in Indian pharmaceutical industry.

    Science.gov (United States)

    Nagashekhara, Molugulu; Agil, Syed Omar Syed; Ramasamy, Ravindran

    2012-03-01

    Study of marketing norm perception among medical representatives is an under-portrayed component that deserves further perusal in the pharmaceutical industry. The purpose of this study is to find out the perception of marketing norms among medical representatives. The research design is quantitative and cross sectional study with medical representatives as unit of analysis. Data is collected from medical representatives (n=300) using a simple random and cluster sampling using a structured questionnaire. Results indicate that there is no difference in the perception of marketing norms among male and female medical representatives. But there is a difference in opinion among domestic and multinational company's medical representatives. Educational back ground of medical representatives also shows the difference in opinion among medical representatives. Degree holders and multinational company medical representatives have high perception of marketing norms compare to their counterparts. The researchers strongly believe that mandatory training on marketing norms is beneficial in decision making process during the dilemmas in the sales field.

  5. Putative cholesterol-binding sites in human immunodeficiency virus (HIV) coreceptors CXCR4 and CCR5.

    Science.gov (United States)

    Zhukovsky, Mikhail A; Lee, Po-Hsien; Ott, Albrecht; Helms, Volkhard

    2013-04-01

    Using molecular docking, we identified a cholesterol-binding site in the groove between transmembrane helices 1 and 7 near the inner membrane-water interface of the G protein-coupled receptor CXCR4, a coreceptor for HIV entry into cells. In this docking pose, the amino group of lysine K67 establishes a hydrogen bond with the hydroxyl group of cholesterol, whereas tyrosine Y302 stacks with cholesterol by its aromatic side chain, and a number of residues form hydrophobic contacts with cholesterol. Sequence alignment showed that a similar putative cholesterol-binding site is also present in CCR5, another HIV coreceptor. We suggest that the interaction of cholesterol with these putative cholesterol-binding sites in CXCR4 and CCR5 is responsible for the presence of these receptors in lipid rafts, for the effect of cholesterol on their conformational stability and function, and for the role that cell cholesterol plays in the cell entry of HIV strains that use these membrane proteins as coreceptors. We propose that mutations of residues that are involved in cholesterol binding will make CXCR4 and CCR5 insensitive to membrane cholesterol content. Cholesterol-binding sites in HIV coreceptors are potential targets for steroid drugs that bind to CXCR4 and CCR5 with higher binding affinity than cholesterol, but do not stabilize the native conformation of these proteins.

  6. On the Origin of the Supergiant HI Shell and Putative Companion in NGC 6822

    CERN Document Server

    Cannon, John M; Weisz, Daniel R; Skillman, Evan D; Dolphin, Andrew E; Bigiel, Frank; Cole, Andrew A; de Blok, W J G; Walter, Fabian

    2012-01-01

    We present new Hubble Space Telescope Advanced Camera for Surveys imaging of six positions spanning 5.8 kpc of the HI major axis of the Local Group dIrr NGC 6822, including both the putative companion galaxy and the large HI hole. The resulting deep color magnitude diagrams show that NGC 6822 has formed >50% of its stars in the last ~5 Gyr. The star formation histories of all six positions are similar over the most recent 500 Myr, including low-level star formation throughout this interval and a weak increase in star formation rate during the most recent 50 Myr. Stellar feedback can create the giant HI hole, assuming that the lifetime of the structure is longer than 500 Myr; such long-lived structures have now been observed in multiple systems and may be the norm in galaxies with solid-body rotation. The old stellar populations (red giants and red clump stars) of the putative companion are consistent with those of the extended halo of NGC 6822; this argues against the interpretation of this structure as a bon...

  7. ON THE ORIGIN OF THE SUPERGIANT H I SHELL AND PUTATIVE COMPANION IN NGC 6822

    Energy Technology Data Exchange (ETDEWEB)

    Cannon, John M.; O' Leary, Erin M. [Department of Physics and Astronomy, Macalester College, 1600 Grand Avenue, Saint Paul, MN 55105 (United States); Weisz, Daniel R. [Department of Astronomy, University of Washington, Seattle, WA 98195 (United States); Skillman, Evan D. [Minnesota Institute for Astrophysics, University of Minnesota, Minneapolis, MN 55455 (United States); Dolphin, Andrew E. [Raytheon Company, 1151 East Hermans Road, Tucson, AZ 85706 (United States); Bigiel, Frank [Institut fuer Theoretische Astrophysik, Universitaet Heidelberg, Albert-Ueberle-Str. 2, 69120 Heidelberg (Germany); Cole, Andrew A.; Walter, Fabian [School of Mathematics and Physics, University of Tasmania, Private Bag 37, Hobart 7001, Tasmania (Australia); De Blok, W.J.G., E-mail: jcannon@macalester.edu, E-mail: eoleary@macalester.edu, E-mail: dweisz@astro.washington.edu, E-mail: skillman@astro.umn.edu, E-mail: adolphin@raytheon.com, E-mail: bigiel@uni-heidelberg.de, E-mail: andrew.cole@utas.edu.au, E-mail: edeblok@ast.uct.ac.za, E-mail: walter@mpia.de [Department of Astronomy, University of Cape Town, Rondebosch 7700 (South Africa)

    2012-03-10

    We present new Hubble Space Telescope Advanced Camera for Surveys imaging of six positions spanning 5.8 kpc of the H I major axis of the Local Group dIrr NGC 6822, including both the putative companion galaxy and the large H I hole. The resulting deep color-magnitude diagrams show that NGC 6822 has formed >50% of its stars in the last {approx}5 Gyr. The star formation histories of all six positions are similar over the most recent 500 Myr, including low-level star formation throughout this interval and a weak increase in star formation rate during the most recent 50 Myr. Stellar feedback can create the giant H I hole, assuming that the lifetime of the structure is longer than 500 Myr; such long-lived structures have now been observed in multiple systems and may be the norm in galaxies with solid-body rotation. The old stellar populations (red giants and red clump stars) of the putative companion are consistent with those of the extended halo of NGC 6822; this argues against the interpretation of this structure as a bona fide interacting companion galaxy and against its being linked to the formation of the H I hole via an interaction. Since there is no evidence in the stellar population of a companion galaxy, the most likely explanation of the extended H I structure in NGC 6822 is a warped disk inclined to the line of sight.

  8. Transcriptome-Based Examination of Putative Pollen Allergens of Rice(Oryza sativa ssp.japonica)

    Institute of Scientific and Technical Information of China (English)

    Scott D.Russell; Prem L Bhalla; Mohan B.Singh

    2008-01-01

    Pollen allergens are among the most abundantly transcribed and translated products in the Iife history of plants,and particularly grasses.To identify different pollen allergens in rice,putative allergens were identified in the rice genome and their expression characterized using the Affymetrix 57K rice GeneChip microarray.Among the most abundant pollen-specific candidate transcripts were Ory s 1 beta-expansin.Ory s 2,Ory s 7 EFhand,Ory s 11,Ory s 12 profilin A,Ory s 23,glycosyl hydrolase family 28(polygalacturonase).and FAD binding proteins.Highly expressed pollen proteins are frequently present in multiple copy numbers,sometimes with mirror images Iocated on nearby regions of the opposite DNA strand.Many of these are intronless and inserted as copies that retain nearly exact copies of their regulatory elements.Ory s 23 reflects low variability and high copy number,suggesting recent gene amplification.Some copies contain pseudogenes,which may reflect their origin through activity of retrotransposition;some putative allergenic sequences bear fusion products with repeat sequences of transposable elements(LTRs).The abundance of nearby repetitive sequences,activation of transposable elements.and high production of mRNA transcripts appear to coincide in pollen and may contribute to a syndrome in which highly transcribed proteins may be copied and inserted with streamlined features for translation,including grouping and removaI of introns.

  9. Identification of putative DnaN-binding motifs in plasmid replication initiation proteins.

    Science.gov (United States)

    Dalrymple, Brian P; Kongsuwan, Kritaya; Wijffels, Gene

    2007-01-01

    Recently the plasmid RK2 replication initiation protein, TrfA, has been shown to bind to the beta subunit of DNA Polymerase III (DnaN) via a short pentapeptide with the consensus QL[S/D]LF. A second consensus peptide, the hexapeptide QLxLxL, has also been demonstrated to mediate binding to DnaN. Here we describe the results of a comprehensive survey of replication initiation proteins encoded by bacterial plasmids to identify putative DnaN-binding sites. Both pentapeptide and hexapeptide motifs have been identified in a number of families of replication initiation proteins. The distribution of sites is sporadic and closely related families of proteins may differ in the presence, location, or type of putative DnaN-binding motif. Neither motif has been identified in replication initiation proteins encoded by plasmids that replicate via rolling circles or strand displacement. The results suggest that the recruitment of DnaN to the origin of replication of a replisome by plasmid replication initiation proteins is not generally required for plasmid replication, but that in some cases it may be beneficial for efficiency of replication initiation.

  10. Uncovering the Putative B-Star Binary Companion of the SN 1993J Progenitor

    CERN Document Server

    Fox, Ori D; Van Dyk, Schuyler D; Filippenko, Alexei V; Fransson, Claes; Matheson, Thomas; Cenko, S Bradley; Chandra, Poonam; Dwarkadas, Vikram; Li, Weidong; Parker, Alex H; Smith, Nathan

    2014-01-01

    The Type IIb supernova (SN) 1993J is one of only a few stripped-envelope supernovae with a progenitor star identified in pre-explosion images. SN IIb models typically invoke H envelope stripping by mass transfer in a binary system. For the case of SN 1993J, the models suggest that the companion grew to 22 M_solar and became a source of ultraviolet (UV) excess. Located in M81, at a distance of only 3.6 Mpc, SN 1993J offers one of the best opportunities to detect the putative companion and test the progenitor model. Previously published near-UV spectra in 2004 showed evidence for absorption lines consistent with a hot (B2 Ia) star, but the field was crowded and dominated by flux from the SN. Here we present Hubble Space Telescope (HST) Cosmic Origins Spectrograph (COS) and Wide-Field Camera 3 (WFC3) observations of SN 1993J from 2012, at which point the flux from the SN had faded sufficiently to potentially measure the UV continuum properties from the putative companion. The resulting UV spectrum is consistent ...

  11. Evolution and structural diversification of PILS putative auxin carriers in plants

    Directory of Open Access Journals (Sweden)

    Elena eFeraru

    2012-10-01

    Full Text Available The phytohormone auxin contributes to virtually every aspect of the plant development. The spatiotemporal distribution of auxin depends on a complex interplay between auxin metabolism and intercellular auxin transport. Intracellular auxin compartmentalization provides another link between auxin transport processes and auxin metabolism. The PIN-LIKES (PILS putative auxin carriers localize to the endoplasmic reticulum (ER and contribute to cellular auxin homeostasis. PILS proteins regulate intracellular auxin accumulation, the rate of auxin conjugation and subsequently, affect nuclear auxin signalling. Here, we investigate sequence diversification of the PILS family in Arabidopsis thaliana and provide insights into the evolution of these novel putative auxin carriers in plants. Our data suggest that PILS proteins are conserved throughout the plant lineage and expanded during higher plant evolution. PILS proteins diversified early during plant evolution into three clades. Besides the ancient Clade I encompassing non-land plant species, PILS proteins evolved into two clades. The diversification of Clade II and Clade III occurred already at the level of non-vascular plant evolution and, hence, both clades contain vascular and non-vascular plant species. Nevertheless, Clade III contains fewer non- and increased numbers of vascular plants, indicating higher importance of Clade III for vascular plant evolution. Notably, PILS proteins are distinct and appear evolutionarily older than the prominent PIN-FORMED auxin carriers. Moreover, we revealed particular PILS sequence divergence in Arabidopsis and assume that these alterations could contribute to distinct gene regulations and protein functions.

  12. Mutation analysis of novel human liver-related putative tumor suppressor gene in hepatocellular carcinoma

    Institute of Scientific and Technical Information of China (English)

    Cheng Liao; Tsai-Ping Li; Mu-Jun Zhao; Jing Zhao; Hai Song; Pascal Pineau; Agnès Marchio; Anne Dejean; Pierre Tiollais; Hong-Yang Wang

    2003-01-01

    AIM: To find the point mutations meaningful for inactivationof liver-related putative tumor suppressor gene (LPTS) gene,a human novel liver-related putative tumor suppressor geneand telomerase inhibitor in hepatocellular carcinoma.METHODS: The entire coding sequence of LPTS genewas examined for mutations by single strand conformationpolymorphism (SSCP) assay and PCR products directsequencing in 56 liver cancer cell lines, 7 ovarian cancerand 7 head & neck tumor cell lines and 70 pairs of HCCtissues samples. The cDNA fragment coding for the mostfrequent mutant protein was subcloned into GST fusionexpression vector. The product was expressed in E. coliand purified by glutathione-agarose column. Telomericrepeat amplification protocol (TRAP) assays wereperformed to study the effect of point mutation totelomerase inhibitory activity.RESULTS: SSCP gels showed the abnormal shifting bandsand DNA sequencing found that there were 5 differentmutations and/or polymorphisms in 12 tumor cell lineslocated at exon2, exon5 and exon7. The main alterationswere A(778)A/G and A(880)T in exon7. The change in siteof 778 could not be found in HCC tissue samples, while themutation in position 880 was seen in 7 (10 %) cases. Themutation in the site of 880 had no effect on telomeraseinhibitory activity.CONCLUSION: Alterations identified in this study arepolymorphisms of LPTS gene. LPTS mutations occur in HCCbut are infrequent and of little effect on the telomeraseinhibitory function of the protein. Epigenetics, such asmethylation, acetylation, may play the key role in inactivationof LPTS.

  13. Expression of putative virulence factors in the potato pathogen Clavibacter michiganensis subsp. sepedonicus during infection.

    Science.gov (United States)

    Holtsmark, Ingrid; Takle, Gunnhild W; Brurberg, May Bente

    2008-02-01

    The Gram-positive bacterium Clavibacter michiganensis subsp. sepedonicus is the causal agent of bacterial wilt and ring rot of potato. So far, only two proteins have been shown to be essential for virulence, namely a plasmid-encoded cellulase CelA and a hypersensitive response-inducing protein. We have examined the relative expression of CelA and eight putative virulence factors during infection of potato and in liquid culture, using quantitative real-time PCR. The examined putative virulence genes were celB, a cellulase-encoding gene and genes encoding a pectate lyase, a xylanase and five homologues of the Clavibacter michiganensis subsp. michiganensis pathogenicity factor Pat-1 thought to encode a serine protease. Six of the nine assayed genes were up-regulated during infection of potato, including celA, celB, the xylanase gene, and two of the pat genes. The pectate lyase gene showed only slightly elevated expression, whereas three of the five examined pat genes were down-regulated during infection in potato. Interestingly, the two up-regulated pat genes showed a noticeable sequence difference compared to the three down-regulated pat genes. These results reveal several new proteins that are likely to be involved in Clavibacter michiganensis subsp. sepedonicus pathogenicity.

  14. Transcriptome of Aphanomyces euteiches: new oomycete putative pathogenicity factors and metabolic pathways.

    Directory of Open Access Journals (Sweden)

    Elodie Gaulin

    Full Text Available Aphanomyces euteiches is an oomycete pathogen that causes seedling blight and root rot of legumes, such as alfalfa and pea. The genus Aphanomyces is phylogenically distinct from well-studied oomycetes such as Phytophthora sp., and contains species pathogenic on plants and aquatic animals. To provide the first foray into gene diversity of A. euteiches, two cDNA libraries were constructed using mRNA extracted from mycelium grown in an artificial liquid medium or in contact to plant roots. A unigene set of 7,977 sequences was obtained from 18,864 high-quality expressed sequenced tags (ESTs and characterized for potential functions. Comparisons with oomycete proteomes revealed major differences between the gene content of A. euteiches and those of Phytophthora species, leading to the identification of biosynthetic pathways absent in Phytophthora, of new putative pathogenicity genes and of expansion of gene families encoding extracellular proteins, notably different classes of proteases. Among the genes specific of A. euteiches are members of a new family of extracellular proteins putatively involved in adhesion, containing up to four protein domains similar to fungal cellulose binding domains. Comparison of A. euteiches sequences with proteomes of fully sequenced eukaryotic pathogens, including fungi, apicomplexa and trypanosomatids, allowed the identification of A. euteiches genes with close orthologs in these microorganisms but absent in other oomycetes sequenced so far, notably transporters and non-ribosomal peptide synthetases, and suggests the presence of a defense mechanism against oxidative stress which was initially characterized in the pathogenic trypanosomatids.

  15. Regulation of Arabidopsis Early Anther Development by Putative Cell-Cell Signaling Molecules and Transcriptional Regulators

    Institute of Scientific and Technical Information of China (English)

    Yu-Jin Sun; Carey LH Hord; Chang-Bin Chen; Hong Ma

    2007-01-01

    Anther development in flowering plants involves the formation of several cell types, including the tapetal and pollen mother cells. The use of genetic and molecular tools has led to the identification and characterization of genes that are critical for normal cell division and differentiation in Arabidopsis early anther development. We review here several recent studies on these genes, including the demonstration that the putative receptor protein kinases BAM1 and BAM2 together play essential roles in the control of early cell division and differentiation. In addition, we discuss the hypothesis that BAM1/2 may form a positive-negative feedback regulatory loop with a previously identified key regulator, SPOROCYTELESS (also called NOZZLE),to control the balance between sporogenous and somatic cell types in the anther. Furthermore, we summarize the isolation and functional analysis of the DYSFUNCTIONAL TAPETUM1 (DYT1) gene in promoting proper tapetal cell differentiation. Our finding that DYT1 encodes a putative transcription factor of the bHLH family, as well as relevant expression analyses, strongly supports a model that DYT1 serves as a critical link between upstream factors and downstream target genes that are critical for normal tapetum development and function. These studies, together with other recently published works, indicate that cell-cell communication and transcriptional control are key processes essential for cell fate specification in anther development.

  16. Characterization of Putative cis-Regulatory Elements in Genes Preferentially Expressed in Arabidopsis Male Meiocytes

    Directory of Open Access Journals (Sweden)

    Junhua Li

    2014-01-01

    Full Text Available Meiosis is essential for plant reproduction because it is the process during which homologous chromosome pairing, synapsis, and meiotic recombination occur. The meiotic transcriptome is difficult to investigate because of the size of meiocytes and the confines of anther lobes. The recent development of isolation techniques has enabled the characterization of transcriptional profiles in male meiocytes of Arabidopsis. Gene expression in male meiocytes shows unique features. The direct interaction of transcription factors (TFs with DNA regulatory sequences forms the basis for the specificity of transcriptional regulation. Here, we identified putative cis-regulatory elements (CREs associated with male meiocyte-expressed genes using in silico tools. The upstream regions (1 kb of the top 50 genes preferentially expressed in Arabidopsis meiocytes possessed conserved motifs. These motifs are putative binding sites of TFs, some of which share common functions, such as roles in cell division. In combination with cell-type-specific analysis, our findings could be a substantial aid for the identification and experimental verification of the protein-DNA interactions for the specific TFs that drive gene expression in meiocytes.

  17. Identification and site of action of the remaining four putative pseudouridine synthases in Escherichia coli.

    Science.gov (United States)

    Del Campo, M; Kaya, Y; Ofengand, J

    2001-11-01

    There are 10 known putative pseudouridine synthase genes in Escherichia coli. The products of six have been previously assigned, one to formation of the single pseudouridine in 16S RNA, three to the formation of seven pseudouridines in 23S RNA, and three to the formation of three pseudouridines in tRNA (one synthase makes pseudouridine in 23S RNA and tRNA). Here we show that the remaining four putative synthase genes make bona fide pseudouridine synthases and identify which pseudouridines they make. RluB (formerly YciL) and RluE (formerly YmfC) make pseudouridine2605 and pseudouridine2457, respectively, in 23S RNA. RluF (formerly YjbC) makes the newly discovered pseudouridine2604 in 23S RNA, and TruC (formerly YqcB) makes pseudouridine65 in tRNA(Ile1) and tRNA(Asp). Deletion of each of these synthase genes individually had no effect on exponential growth in rich media at 25 degrees C, 37 degrees C, or 42 degrees C. A strain lacking RluB and RluF also showed no growth defect under these conditions. Mutation of a conserved aspartate in a common sequence motif, previously shown to be essential for the other six E. coli pseudouridine synthases and several yeast pseudouridine synthases, also caused a loss of in vivo activity in all four of the synthases studied in this work.

  18. Transcriptome Analysis Reveals Putative Genes Involved in Iridoid Biosynthesis in Rehmannia glutinosa

    Directory of Open Access Journals (Sweden)

    Xianen Li

    2012-10-01

    Full Text Available Rehmannia glutinosa, one of the most widely used herbal medicines in the Orient, is rich in biologically active iridoids. Despite their medicinal importance, no molecular information about the iridoid biosynthesis in this plant is presently available. To explore the transcriptome of R. glutinosa and investigate genes involved in iridoid biosynthesis, we used massively parallel pyrosequencing on the 454 GS FLX Titanium platform to generate a substantial EST dataset. Based on sequence similarity searches against the public sequence databases, the sequences were first annotated and then subjected to Gene Ontology (GO and Kyoto Encyclopedia of Genes and Genomes (KEGG based analysis. Bioinformatic analysis indicated that the 454 assembly contained a set of genes putatively involved in iridoid biosynthesis. Significantly, homologues of the secoiridoid pathway genes that were only identified in terpenoid indole alkaloid producing plants were also identified, whose presence implied that route II iridoids and route I iridoids share common enzyme steps in the early stage of biosynthesis. The gene expression patterns of four prenyltransferase transcripts were analyzed using qRT-PCR, which shed light on their putative functions in tissues of R. glutinosa. The data explored in this study will provide valuable information for further studies concerning iridoid biosynthesis.

  19. Mapping the flow of information within the putative mirror neuron system during gesture observation.

    Science.gov (United States)

    Schippers, Marleen B; Keysers, Christian

    2011-07-01

    The putative mirror neuron system may either function as a strict feed-forward system or as a dynamic control system. A strict feed-forward system would predict that action observation leads to a predominantly temporal→parietal→premotor flow of information in which a visual representation is transformed into motor-programs which contribute to action understanding. Instead, a dynamic feedback control system would predict that the reverse direction of information flow predominates because of a combination of inhibitory forward and excitatory inverse models. Here we test which of these conflicting predictions best matches the information flow within the putative mirror neuron system (pMNS) and between the pMNS and the rest of the brain during the observation of comparatively long naturalistic stretches of communicative gestures. We used Granger causality to test the dominant direction of influence. Our results fit the predictions of the dynamic feedback control system: we found predominantly an information flow within the pMNS from premotor to parietal and middle temporal cortices. This is more pronounced during an active guessing task than while passively reviewing the same gestures. In particular, the ventral premotor cortex sends significantly more information to other pMNS areas than it receives during active guessing than during passive observation.

  20. Unprecedented diversity of catalytic domains in the first four modules of the putative pederin polyketide synthase.

    Science.gov (United States)

    Piel, Jörn; Wen, Gaiping; Platzer, Matthias; Hui, Dequan

    2004-01-03

    Polyketides of the pederin group are highly potent antitumor compounds found in terrestrial beetles and marine sponges. Pederin is used by beetles of the genera Paederus and Paederidus as a chemical defense. We have recently identified a group of putative pederin biosynthesis genes and localized them to the genome of an as yet unculturable Pseudomonas sp. symbiont, the likely true pederin producer. However, this polyketide synthase cluster lacks several genes expected for pederin production. Here we report an additional polyketide synthase encoded on a separate region of the symbiont genome. It contains at least three novel catalytic domains that are predicted to be involved in pederin chain initiation and the formation of an unusual exomethylene bond. The region is bordered by mobility pseudogenes; this suggests that gene transposition led to the disjointed cluster organization. With this work, all putative pederin genes have been identified. Their heterologous expression in a culturable bacterium will provide important insights into how sustainable sources of invertebrate-derived drug candidates can be created.

  1. Biochemical Characterization of Putative Adenylate Dimethylallyltransferase and Cytokinin Dehydrogenase from Nostoc sp. PCC 7120.

    Science.gov (United States)

    Frébortová, Jitka; Greplová, Marta; Seidl, Michael F; Heyl, Alexander; Frébort, Ivo

    2015-01-01

    Cytokinins, a class of phytohormones, are adenine derivatives common to many different organisms. In plants, these play a crucial role as regulators of plant development and the reaction to abiotic and biotic stress. Key enzymes in the cytokinin synthesis and degradation in modern land plants are the isopentyl transferases and the cytokinin dehydrogenases, respectively. Their encoding genes have been probably introduced into the plant lineage during the primary endosymbiosis. To shed light on the evolution of these proteins, the genes homologous to plant adenylate isopentenyl transferase and cytokinin dehydrogenase were amplified from the genomic DNA of cyanobacterium Nostoc sp. PCC 7120 and expressed in Escherichia coli. The putative isopentenyl transferase was shown to be functional in a biochemical assay. In contrast, no enzymatic activity was detected for the putative cytokinin dehydrogenase, even though the principal domains necessary for its function are present. Several mutant variants, in which conserved amino acids in land plant cytokinin dehydrogenases had been restored, were inactive. A combination of experimental data with phylogenetic analysis indicates that adenylate-type isopentenyl transferases might have evolved several times independently. While the Nostoc genome contains a gene coding for protein with characteristics of cytokinin dehydrogenase, the organism is not able to break down cytokinins in the way shown for land plants.

  2. TiD: Standalone software for mining putative drug targets from bacterial proteome.

    Science.gov (United States)

    Gupta, Reena; Pradhan, Dibyabhaba; Jain, Arun Kumar; Rai, Chandra Shekhar

    2017-01-01

    TiD is a standalone application, which relies on basic assumption that a protein must be essential for pathogens survival and non-homologous with host to qualify as putative target. With an input bacterial proteome, TiD removes paralogous proteins, picks essential ones, and excludes proteins homologous with host organisms. The targets illustrate non-homology with at least 40 out of 84 gut microbes, considered safe for human. TiD classifies proposed targets as known, novel and virulent. Users can perform pathway analysis, choke point analysis, interactome analysis, subcellular localization and functional annotations through web servers cross-referenced with the application. Drug targets identified by TiD for Listeria monocytogenes, Bacillus anthracis and Pseudomonas aeruginosa have revealed significant overlaps with previous studies. TiD takes <2h to scan putative targets from a bacterial proteome with ~5000 proteins; hence, we propose it as a useful tool for rational drug design. TiD is available at http://bmicnip.in/TiD/. Copyright © 2016 Elsevier Inc. All rights reserved.

  3. VenomKB, a new knowledge base for facilitating the validation of putative venom therapies.

    Science.gov (United States)

    Romano, Joseph D; Tatonetti, Nicholas P

    2015-11-24

    Animal venoms have been used for therapeutic purposes since the dawn of recorded history. Only a small fraction, however, have been tested for pharmaceutical utility. Modern computational methods enable the systematic exploration of novel therapeutic uses for venom compounds. Unfortunately, there is currently no comprehensive resource describing the clinical effects of venoms to support this computational analysis. We present VenomKB, a new publicly accessible knowledge base and website that aims to act as a repository for emerging and putative venom therapies. Presently, it consists of three database tables: (1) Manually curated records of putative venom therapies supported by scientific literature, (2) automatically parsed MEDLINE articles describing compounds that may be venom derived, and their effects on the human body, and (3) automatically retrieved records from the new Semantic Medline resource that describe the effects of venom compounds on mammalian anatomy. Data from VenomKB may be selectively retrieved in a variety of popular data formats, are open-source, and will be continually updated as venom therapies become better understood.

  4. Five putative nucleoside triphosphate diphosphohydrolase genes are expressed in Trichomonas vaginalis.

    Science.gov (United States)

    Frasson, Amanda Piccoli; Dos Santos, Odelta; Meirelles, Lúcia Collares; Macedo, Alexandre José; Tasca, Tiana

    2016-01-01

    Trichomonas vaginalis is a protozoan that parasitizes the human urogenital tract causing trichomoniasis, the most common non-viral sexually transmitted disease. The parasite has unique genomic characteristics such as a large genome size and expanded gene families. Ectonucleoside triphosphate diphosphohydrolase (E-NTPDase) is an enzyme responsible for hydrolyzing nucleoside tri- and diphosphates and has already been biochemically characterized in T. vaginalis. Considering the important role of this enzyme in the production of extracellular adenosine for parasite uptake, we evaluated the gene expression of five putative NTPDases in T. vaginalis. We showed that all five putative TvNTPDase genes (TvNTPDase1-5) were expressed by both fresh clinical and long-term grown isolates. The amino acid alignment predicted the presence of the five crucial apyrase conserved regions, transmembrane domains, signal peptides, phosphorylation and catalytic sites. Moreover, a phylogenetic analysis showed that TvNTPDase sequences make up a clade with NTPDases intracellularly located. Biochemical NTPDase activity (ATP and ADP hydrolysis) is responsive to the serum-restrictive conditions and the gene expression of TvNTPDases was mostly increased, mainly TvNTPDase2 and TvNTPDase4, although there was not a clear pattern of expression among them. In summary, the present report demonstrates the gene expression patterns of predicted NTPDases in T. vaginalis.

  5. Functional characterization of PaLAX1, a putative auxin permease, in heterologous plant systems.

    Science.gov (United States)

    Hoyerová, Klára; Perry, Lucie; Hand, Paul; Lanková, Martina; Kocábek, Tomás; May, Sean; Kottová, Jana; Paces, Jan; Napier, Richard; Zazímalová, Eva

    2008-03-01

    We have isolated the cDNA of the gene PaLAX1 from a wild cherry tree (Prunus avium). The gene and its product are highly similar in sequences to both the cDNAs and the corresponding protein products of AUX/LAX-type genes, coding for putative auxin influx carriers. We have prepared and characterized transformed Nicotiana tabacum and Arabidopsis thaliana plants carrying the gene PaLAX1. We have proved that constitutive overexpression of PaLAX1 is accompanied by changes in the content and distribution of free indole-3-acetic acid, the major endogenous auxin. The increase in free indole-3-acetic acid content in transgenic plants resulted in various phenotype changes, typical for the auxin-overproducing plants. The uptake of synthetic auxin, 2,4-dichlorophenoxyacetic acid, was 3 times higher in transgenic lines compared to the wild-type lines and the treatment with the auxin uptake inhibitor 1-naphthoxyacetic acid reverted the changes caused by the expression of PaLAX1. Moreover, the agravitropic response could be restored by expression of PaLAX1 in the mutant aux1 plants, which are deficient in auxin influx carrier activity. Based on our data, we have concluded that the product of the gene PaLAX1 promotes the uptake of auxin into cells, and, as a putative auxin influx carrier, it affects the content and distribution of free endogenous auxin in transgenic plants.

  6. Sensitivity analysis of the relationship between disease occurrence and distance from a putative source of pollution

    Directory of Open Access Journals (Sweden)

    Emanuela Dreassi

    2008-05-01

    Full Text Available The relation between disease risk and a point source of pollution is usually investigated using distance from the source as a proxy of exposure. The analysis may be based on case-control data or on aggregated data. The definition of the function relating risk of disease and distance is critical, both in a classical and in a Bayesian framework, because the likelihood is usually very flat, even with large amounts of data. In this paper we investigate how the specification of the function relating risk of disease with distance from the source and of the prior distributions on the parameters of the function affects the results when case-control data and Bayesian methods are used. We consider different popular parametric models for the risk distance function in a Bayesian approach, comparing estimates with those derived by maximum likelihood. As an example we have analyzed the relationship between a putative source of environmental pollution (an asbestos cement plant and the occurrence of pleural malignant mesothelioma in the area of Casale Monferrato (Italy in 1987-1993. Risk of pleural malignant mesothelioma turns out to be strongly related to distance from the asbestos cement plant. However, as the models appeared to be sensitive to modeling choices, we suggest that any analysis of disease risk around a putative source should be integrated with a careful sensitivity analysis and possibly with prior knowledge. The choice of prior distribution is extremely important and should be based on epidemiological considerations.

  7. Putative monofunctional type I polyketide synthase units: a dinoflagellate-specific feature?

    Directory of Open Access Journals (Sweden)

    Karsten Eichholz

    Full Text Available Marine dinoflagellates (alveolata are microalgae of which some cause harmful algal blooms and produce a broad variety of most likely polyketide synthesis derived phycotoxins. Recently, novel polyketide synthesase (PKS transcripts have been described from the Florida red tide dinoflagellate Karenia brevis (gymnodiniales which are evolutionarily related to Type I PKS but were apparently expressed as monofunctional proteins, a feature typical of Type II PKS. Here, we investigated expression units of PKS I-like sequences in Alexandrium ostenfeldii (gonyaulacales and Heterocapsa triquetra (peridiniales at the transcript and protein level. The five full length transcripts we obtained were all characterized by polyadenylation, a 3' UTR and the dinoflagellate specific spliced leader sequence at the 5'end. Each of the five transcripts encoded a single ketoacylsynthase (KS domain showing high similarity to K. brevis KS sequences. The monofunctional structure was also confirmed using dinoflagellate specific KS antibodies in Western Blots. In a maximum likelihood phylogenetic analysis of KS domains from diverse PKSs, dinoflagellate KSs formed a clade placed well within the protist Type I PKS clade between apicomplexa, haptophytes and chlorophytes. These findings indicate that the atypical PKS I structure, i.e., expression as putative monofunctional units, might be a dinoflagellate specific feature. In addition, the sequenced transcripts harbored a previously unknown, apparently dinoflagellate specific conserved N-terminal domain. We discuss the implications of this novel region with regard to the putative monofunctional organization of Type I PKS in dinoflagellates.

  8. A CHASE domain containing protein kinase OsCRL4, represents a new AtCRE1-like gene family in rice

    Institute of Scientific and Technical Information of China (English)

    韩秋敏; 姜华武; 齐晓朋; 于洁; 吴平

    2004-01-01

    AtCRE1 is known to be a cytokinin receptor in Arabidopsis. The AtCRE1 protein contains CHASE domain at the N-terminal part, followed by a transmitter (histidine kinase) domain and two receiver domains. The N-terminal CHASE domain of AtCRE1 contains putative recognition sites for cytokinin. Five CHASE domains containing proteins were found in rice, OsCRL1a, OsCRL1b, OsCRL2, OsCRL3, and OsCRL4. OsCRL1a, OsCRL1b, OsCRL2 and OsCRL3 contain the four domains existing in CRE1, whereas OsCRL4 only contains the CHASE domain and a putative Ser/Thr protein kinase domain. The authors cloned the encoding gene OsCRL4 and found that it represents a new member of the cytokinin receptor protein in rice.

  9. A CHASE domain containing protein kinase OsCRL4, represents a new AtCRE1-like gene family in rice

    Institute of Scientific and Technical Information of China (English)

    韩秋敏; 姜华武; 齐晓朋; 丁洁; 吴平

    2004-01-01

    AtCRE1 is known to be a cytokinin receptor inArabidopsis. The AtCRE1 protein contains CHASE domain at the N-terminal part, followed by a transmitter (histidine kinase) domain and two receiver domains. The N-terminal CHASE domain of AtCRE1 contains putative recognition sites for cytokinin. Five CHASE domains containing proteins were found in rice, OsCRLla, OsCRLlb, OsCRL2, OsCRL3, and OsCRL4. OsCRL1a, OsCRL1b, OsCRL2 and OsCRL3 contain the four domains existing in CRE1, whereas OsCRL4 only contains the CHASE domain and a putative Ser/Thr protein kinase domain The authors cloned the encoding gene OsCRL4 and found that it represents a new member of the cytokinin receptor protein in rice.

  10. Statistics On Title II Direct Payments To Claimant Representatives

    Data.gov (United States)

    Social Security Administration — Every person has the right to be represented by an attorney or other representative while pursuing a claim or other rights. This dataset contains data around Title...

  11. VT Biodiversity Project - Representative Landscapes in Vermont polygons

    Data.gov (United States)

    Vermont Center for Geographic Information — (Link to Metadata) This coverage represents the results of an analysis of landscape diversity in Vermont. Polygons in the dataset represent as much as possible (in a...

  12. Metagenomic Classification and Characterization Marine Actinobacteria from the Gulf of Maine without Representative Genomes

    Science.gov (United States)

    Sachdeva, R.; Heidelberg, J.

    2012-12-01

    Actinobacteria represent one of the largest and most diverse bacterial phyla and unlike most marine prokaryotes are gram-positive. This phylum encompasses a broad range of physiologies, morphologies, and metabolic properties with a broad array of lifestyles. The marine actinobacterial assemblage is dominated by the orders Actinomycetales and Acidimicrobiales (also known as the marine Actinobacteria clade). The Acidimicrobiales bacteria typically outnumber the Actinomycetales bacteria and are mostly represented by the OCS155 group. Although bacteria of the order Acidimicrobiales make up ~7.6% of the 16S matches from the Global Ocean Survey shotgun metagenomic libraries; very little is known about their potential function and role in biogeochemical cycling. Samples were collected from surface seawater samples in the Gulf of Maine (GOM) from the summer and winter of 2006. Sanger sequences were generated from the 0.1-0.8 μm fractions using paired-end medium insert shotgun libraries. The resulting 2.2 Gb were assembled using the Celera Assembler package into 280 Mb of non-redundant scaffolds. Putative actinobacterial assemblies were identified using (1) ribosomal RNA genes (16S and 23S), (2) phylogenetically informative non-ribosomal core genes thought to be resistant to horizontal gene transfer (e.g. RecA and RpoB) and (3) compositional binning using oligonucleotide frequency pattern based hierarchical clustering. Binning resulted in 3.6 Mb (4.2X coverage) of actinobacterial scaffolds that were comprised of 15.1 Mb of unassembled reads. Putative actinobacterial assemblies included both summer and winter reads demonstrating that the Actinobacteria are abundant year round. Classification reveals that all of the sampled Actinobacteria are from the orders Acidimicrobiales and Actinomycetales and are similar to those found in the global ocean. The GOM Actinobacteria show a broad range of G+C % content (32-66%) indicating a high level of genomic diversity. Those assemblies

  13. 42 CFR 422.1010 - Authority of representatives.

    Science.gov (United States)

    2010-10-01

    ... 42 Public Health 3 2010-10-01 2010-10-01 false Authority of representatives. 422.1010 Section 422.1010 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES....1010 Authority of representatives. (a) A representative appointed and qualified in accordance with...

  14. 42 CFR 423.1010 - Authority of representatives.

    Science.gov (United States)

    2010-10-01

    ... 42 Public Health 3 2010-10-01 2010-10-01 false Authority of representatives. 423.1010 Section 423.1010 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES... Penalties § 423.1010 Authority of representatives. (a) A representative appointed and qualified...

  15. 40 CFR 197.31 - What is a representative volume?

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 24 2010-07-01 2010-07-01 false What is a representative volume? 197... a representative volume? (a) It is the volume of ground water that would be withdrawn annually from... Yucca Mountain disposal system that will be in the representative volume. The DOE must then use...

  16. 22 CFR 23.4 - Representative value in exchange.

    Science.gov (United States)

    2010-04-01

    ... 22 Foreign Relations 1 2010-04-01 2010-04-01 false Representative value in exchange. 23.4 Section 23.4 Foreign Relations DEPARTMENT OF STATE FEES AND FUNDS FINANCE AND ACCOUNTING § 23.4 Representative value in exchange. Representative value in exchange for the collection of a fee means...

  17. 20 CFR 266.7 - Accountability of a representative payee.

    Science.gov (United States)

    2010-04-01

    ... 20 Employees' Benefits 1 2010-04-01 2010-04-01 false Accountability of a representative payee. 266.7 Section 266.7 Employees' Benefits RAILROAD RETIREMENT BOARD REGULATIONS UNDER THE RAILROAD RETIREMENT ACT REPRESENTATIVE PAYMENT § 266.7 Accountability of a representative payee. (a) A...

  18. Dichotomous Distribution of Putative Cholinergic Interneurons in Mouse Accessory Olfactory Bulb

    Science.gov (United States)

    Marking, Sarah; Krosnowski, Kurt; Ogura, Tatsuya; Lin, Weihong

    2017-01-01

    Sensory information processing in the olfactory bulb (OB) relies on diverse populations of bulbar interneurons. In rodents, the accessory OB (AOB) is divided into two bulbar regions, the anterior (aAOB) and posterior (pAOB), which differ substantially in their circuitry connections and associated behaviors. We previously identified and characterized a large number of morphologically diverse cholinergic interneurons in the main OB (MOB) using transgenic mice to visualize the cell bodies of choline acetyltransferase (ChAT-expressing neurons and immunolabeling (Krosnowski et al., 2012)). However, whether there are cholinergic neurons in the AOB is controversial and there is no detailed characterization of such neurons. Using the same line of ChAT(bacterial artificial chromosome, BAC)-enhanced green fluorescent protein (eGFP) transgenic mice, we investigated cholinergic neurons in the AOB. We found significant differences in the number and location of GFP-expressing (GFP+), putative cholinergic interneurons between the aAOB and pAOB. The highest numbers of GFP+ interneurons were found in the aAOB glomerular layer (aGL) and pAOB mitral/tufted cell layer (pMCL). We also noted a high density of GFP+ interneurons encircling the border region of the pMCL. Interestingly, a small subset of glomeruli in the middle of the GL receives strong MCL GFP+ nerve processes. These local putative cholinergic-innervated glomeruli are situated just outside the aGL, setting the boundary between the pGL and aGL. Many but not all GFP+ neurons in the AOB were weakly labeled with antibodies against ChAT and vesicular acetylcholine transporter (VAChT). We further determined if these GFP+ interneurons differ from other previously characterized interneuron populations in the AOB and found that AOB GFP+ interneurons express neither GABAergic nor dopaminergic markers and most also do not express the glutamatergic marker. Similar to the cholinergic interneurons of the MOB, some AOB GFP+ interneurons

  19. Coral bleaching under thermal stress: putative involvement of host/symbiont recognition mechanisms

    Directory of Open Access Journals (Sweden)

    Tambutte Sylvie

    2009-08-01

    Full Text Available Abstract Background Coral bleaching can be defined as the loss of symbiotic zooxanthellae and/or their photosynthetic pigments from their cnidarian host. This major disturbance of reef ecosystems is principally induced by increases in water temperature. Since the beginning of the 1980s and the onset of global climate change, this phenomenon has been occurring at increasing rates and scales, and with increasing severity. Several studies have been undertaken in the last few years to better understand the cellular and molecular mechanisms of coral bleaching but the jigsaw puzzle is far from being complete, especially concerning the early events leading to symbiosis breakdown. The aim of the present study was to find molecular actors involved early in the mechanism leading to symbiosis collapse. Results In our experimental procedure, one set of Pocillopora damicornis nubbins was subjected to a gradual increase of water temperature from 28°C to 32°C over 15 days. A second control set kept at constant temperature (28°C. The differentially expressed mRNA between the stressed states (sampled just before the onset of bleaching and the non stressed states (control were isolated by Suppression Subtractive Hybridization. Transcription rates of the most interesting genes (considering their putative function were quantified by Q-RT-PCR, which revealed a significant decrease in transcription of two candidates six days before bleaching. RACE-PCR experiments showed that one of them (PdC-Lectin contained a C-Type-Lectin domain specific for mannose. Immunolocalisation demonstrated that this host gene mediates molecular interactions between the host and the symbionts suggesting a putative role in zooxanthellae acquisition and/or sequestration. The second gene corresponds to a gene putatively involved in calcification processes (Pdcyst-rich. Its down-regulation could reflect a trade-off mechanism leading to the arrest of the mineralization process under stress

  20. Genome-wide analysis of putative peroxiredoxin in unicellular and filamentous cyanobacteria

    Directory of Open Access Journals (Sweden)

    Cui Hongli

    2012-11-01

    Full Text Available Abstract Background Cyanobacteria are photoautotrophic prokaryotes with wide variations in genome sizes and ecological habitats. Peroxiredoxin (PRX is an important protein that plays essential roles in protecting own cells against reactive oxygen species (ROS. PRXs have been identified from mammals, fungi and higher plants. However, knowledge on cyanobacterial PRXs still remains obscure. With the availability of 37 sequenced cyanobacterial genomes, we performed a comprehensive comparative analysis of PRXs and explored their diversity, distribution, domain structure and evolution. Results Overall 244 putative prx genes were identified, which were abundant in filamentous diazotrophic cyanobacteria, Acaryochloris marina MBIC 11017, and unicellular cyanobacteria inhabiting freshwater and hot-springs, while poor in all Prochlorococcus and marine Synechococcus strains. Among these putative genes, 25 open reading frames (ORFs encoding hypothetical proteins were identified as prx gene family members and the others were already annotated as prx genes. All 244 putative PRXs were classified into five major subfamilies (1-Cys, 2-Cys, BCP, PRX5_like, and PRX-like according to their domain structures. The catalytic motifs of the cyanobacterial PRXs were similar to those of eukaryotic PRXs and highly conserved in all but the PRX-like subfamily. Classical motif (CXXC of thioredoxin was detected in protein sequences from the PRX-like subfamily. Phylogenetic tree constructed of catalytic domains coincided well with the domain structures of PRXs and the phylogenies based on 16s rRNA. Conclusions The distribution of genes encoding PRXs in different unicellular and filamentous cyanobacteria especially those sub-families like PRX-like or 1-Cys PRX correlate with the genome size, eco-physiology, and physiological properties of the organisms. Cyanobacterial and eukaryotic PRXs share similar conserved motifs, indicating that cyanobacteria adopt similar catalytic

  1. Identification of a putative protein profile associated with tamoxifen therapy resistance in breast cancer.

    Science.gov (United States)

    Umar, Arzu; Kang, Hyuk; Timmermans, Annemieke M; Look, Maxime P; Meijer-van Gelder, Marion E; den Bakker, Michael A; Jaitly, Navdeep; Martens, John W M; Luider, Theo M; Foekens, John A; Pasa-Tolić, Ljiljana

    2009-06-01

    Tamoxifen resistance is a major cause of death in patients with recurrent breast cancer. Current clinical factors can correctly predict therapy response in only half of the treated patients. Identification of proteins that are associated with tamoxifen resistance is a first step toward better response prediction and tailored treatment of patients. In the present study we intended to identify putative protein biomarkers indicative of tamoxifen therapy resistance in breast cancer using nano-LC coupled with FTICR MS. Comparative proteome analysis was performed on approximately 5,500 pooled tumor cells (corresponding to approximately 550 ng of protein lysate/analysis) obtained through laser capture microdissection (LCM) from two independently processed data sets (n = 24 and n = 27) containing both tamoxifen therapy-sensitive and therapy-resistant tumors. Peptides and proteins were identified by matching mass and elution time of newly acquired LC-MS features to information in previously generated accurate mass and time tag reference databases. A total of 17,263 unique peptides were identified that corresponded to 2,556 non-redundant proteins identified with > or = 2 peptides. 1,713 overlapping proteins between the two data sets were used for further analysis. Comparative proteome analysis revealed 100 putatively differentially abundant proteins between tamoxifen-sensitive and tamoxifen-resistant tumors. The presence and relative abundance for 47 differentially abundant proteins were verified by targeted nano-LC-MS/MS in a selection of unpooled, non-microdissected discovery set tumor tissue extracts. ENPP1, EIF3E, and GNB4 were significantly associated with progression-free survival upon tamoxifen treatment for recurrent disease. Differential abundance of our top discriminating protein, extracellular matrix metalloproteinase inducer, was validated by tissue microarray in an independent patient cohort (n = 156). Extracellular matrix metalloproteinase inducer levels were

  2. Genome-wide analysis of putative peroxiredoxin in unicellular and filamentous cyanobacteria

    Science.gov (United States)

    2012-01-01

    Background Cyanobacteria are photoautotrophic prokaryotes with wide variations in genome sizes and ecological habitats. Peroxiredoxin (PRX) is an important protein that plays essential roles in protecting own cells against reactive oxygen species (ROS). PRXs have been identified from mammals, fungi and higher plants. However, knowledge on cyanobacterial PRXs still remains obscure. With the availability of 37 sequenced cyanobacterial genomes, we performed a comprehensive comparative analysis of PRXs and explored their diversity, distribution, domain structure and evolution. Results Overall 244 putative prx genes were identified, which were abundant in filamentous diazotrophic cyanobacteria, Acaryochloris marina MBIC 11017, and unicellular cyanobacteria inhabiting freshwater and hot-springs, while poor in all Prochlorococcus and marine Synechococcus strains. Among these putative genes, 25 open reading frames (ORFs) encoding hypothetical proteins were identified as prx gene family members and the others were already annotated as prx genes. All 244 putative PRXs were classified into five major subfamilies (1-Cys, 2-Cys, BCP, PRX5_like, and PRX-like) according to their domain structures. The catalytic motifs of the cyanobacterial PRXs were similar to those of eukaryotic PRXs and highly conserved in all but the PRX-like subfamily. Classical motif (CXXC) of thioredoxin was detected in protein sequences from the PRX-like subfamily. Phylogenetic tree constructed of catalytic domains coincided well with the domain structures of PRXs and the phylogenies based on 16s rRNA. Conclusions The distribution of genes encoding PRXs in different unicellular and filamentous cyanobacteria especially those sub-families like PRX-like or 1-Cys PRX correlate with the genome size, eco-physiology, and physiological properties of the organisms. Cyanobacterial and eukaryotic PRXs share similar conserved motifs, indicating that cyanobacteria adopt similar catalytic mechanisms as eukaryotes. All

  3. Multi-mode entangled states represented as Grassmannian polynomials

    Science.gov (United States)

    Maleki, Y.

    2016-09-01

    We introduce generalized Grassmannian representatives of multi-mode state vectors. By implementing the fundamental properties of Grassmann coherent states, we map the Hilbert space of the finite-dimensional multi-mode states to the space of some Grassmannian polynomial functions. These Grassmannian polynomials form a well-defined space in the framework of Grassmann variables; namely Grassmannian representative space. Therefore, a quantum state can be uniquely defined and determined by an element of Grassmannian representative space. Furthermore, the Grassmannian representatives of some maximally entangled states are considered, and it is shown that there is a tight connection between the entanglement of the states and their Grassmannian representatives.

  4. Antiviral Activities and Putative Identification of Compounds in Microbial Extracts from the Hawaiian Coastal Waters

    Directory of Open Access Journals (Sweden)

    Yuanan Lu

    2012-02-01

    Full Text Available Marine environments are a rich source of significant bioactive compounds. The Hawaiian archipelago, located in the middle of the Pacific Ocean, hosts diverse microorganisms, including many endemic species. Thirty-eight microbial extracts from Hawaiian coastal waters were evaluated for their antiviral activity against four mammalian viruses including herpes simplex virus type one (HSV-1, vesicular stomatitis virus (VSV, vaccinia virus and poliovirus type one (poliovirus-1 using in vitro cell culture assay. Nine of the 38 microbial crude extracts showed antiviral potencies and three of these nine microbial extracts exhibited significant activity against the enveloped viruses. A secosteroid, 5α(H,17α(H,(20R-beta-acetoxyergost-8(14-ene was putatively identified and confirmed to be the active compound in these marine microbial extracts. These results warrant future in-depth tests on the isolation of these active elements in order to explore and validate their antiviral potential as important therapeutic remedies.

  5. Mycobacterium tuberculosis evolutionary pathogenesis and its putative impact on drug development.

    Science.gov (United States)

    Le Chevalier, Fabien; Cascioferro, Alessandro; Majlessi, Laleh; Herrmann, Jean Louis; Brosch, Roland

    2014-01-01

    Mycobacterium tuberculosis, the etiological agent of human TB, is the most important mycobacterial pathogen in terms of global patient numbers and gravity of disease. The molecular mechanisms by which M. tuberculosis causes disease are complex and the result of host-pathogen coevolution that might have started already in the time of its Mycobacterium canettii-like progenitors. Despite research progress, M. tuberculosis still holds many secrets of its successful strategy for circumventing host defences, persisting in the host and developing resistance, which makes anti-TB treatment regimens extremely long and often inefficient. Here, we discuss what we have learned from recent studies on the evolution of the pathogen and its putative new drug targets that are essential for mycobacterial growth under in vitro or in vivo conditions.

  6. Expression of putative markers of pluripotency in equine embryonic and adult tissues.

    Science.gov (United States)

    Esteves, Cristina L; Sharma, Ruchi; Dawson, Lucy; Taylor, Sarah E; Pearson, Gemma; Keen, John A; McDonald, Kieran; Aurich, Christine; Donadeu, F Xavier

    2014-12-01

    Expression of several putative markers of pluripotency (OCT4, SOX2, NANOG, LIN28A, REX1, DNMT3B and TERT) was examined in a range of equine tissues, including early embryos, induced pluripotent stem cells (iPSCs), testis, adipose- and bone marrow-derived mesenchymal stromal cells (MSCs), and keratinocytes. Transcript levels of all markers were highest in embryos and iPSCs and, except for SOX2, were very low or undetectable in keratinocytes. Mean expression levels of all markers were lower in testis than in embryos or iPSCs and, except for DNMT3B, were higher in testis than in MSCs. Expression of OCT4, NANOG and DNMT3B, but not the other markers, was detected in MSCs. Of all markers analysed, only LIN28A, REX1 and TERT were associated exclusively with pluripotent cells in the horse. Copyright © 2014 Elsevier Ltd. All rights reserved.

  7. Transcriptome outlier analysis implicates schizophrenia susceptibility genes and enriches putatively functional rare genetic variants.

    Science.gov (United States)

    Duan, Jubao; Sanders, Alan R; Moy, Winton; Drigalenko, Eugene I; Brown, Eric C; Freda, Jessica; Leites, Catherine; Göring, Harald H H; Gejman, Pablo V

    2015-08-15

    We searched a gene expression dataset comprised of 634 schizophrenia (SZ) cases and 713 controls for expression outliers (i.e., extreme tails of the distribution of transcript expression values) with SZ cases overrepresented compared with controls. These outlier genes were enriched for brain expression and for genes known to be associated with neurodevelopmental disorders. SZ cases showed higher outlier burden (i.e., total outlier events per subject) than controls for genes within copy number variants (CNVs) associated with SZ or neurodevelopmental disorders. Outlier genes were enriched for CNVs and for rare putative regulatory variants, but this only explained a small proportion of the outlier subjects, highlighting the underlying presence of additional genetic and potentially, epigenetic mechanisms.

  8. White Matter Abnormalities and Animal Models Examining a Putative Role of Altered White Matter in Schizophrenia

    Directory of Open Access Journals (Sweden)

    Haiyun Xu

    2011-01-01

    Full Text Available Schizophrenia is a severe mental disorder affecting about 1% of the population worldwide. Although the dopamine (DA hypothesis is still keeping a dominant position in schizophrenia research, new advances have been emerging in recent years, which suggest the implication of white matter abnormalities in schizophrenia. In this paper, we will briefly review some of recent human studies showing white matter abnormalities in schizophrenic brains and altered oligodendrocyte-(OL- and myelin-related genes in patients with schizophrenia and will consider abnormal behaviors reported in patients with white matter diseases. Following these, we will selectively introduce some animal models examining a putative role of white matter abnormalities in schizophrenia. The emphasis will be put on the cuprizone (CPZ model. CPZ-fed mice show demyelination and OLs loss, display schizophrenia-related behaviors, and have higher DA levels in the prefrontal cortex. These features suggest that the CPZ model is a novel animal model of schizophrenia.

  9. Identification of a putative tetrasporophyte-specific gene in Gracilaria lemaneiformis (Gracilariales, Rhodophyte)

    Science.gov (United States)

    Ren, Xueying; Zhang, Xuecheng

    2008-08-01

    A putative tetrasporophyte-specific gene, designated as SSH466 (GenBank accession No. DQ019223), was one of the genes identified in this work using suppression subtractive hybridization (SSH) method in Gracilaria lemaneiformis. The full length of the gene was obtained using SMART RACE strategy. Sequence analysis revealed that the gene had 1 019 nucleotides, including an open reading frame of 498 nucleotides encoding 166 amino acid residues, 158 nucleotides of 5' untranslated region and 363 nucleotides of 3' non-coding region. Protein motif and secondary structure prediction showed that there existed a transmembrane domain with a unique β-sheet. Thus, SSH466 protein might be a cross-membrane protein. Sequence homology search in the public GenBank databases did not reveal any significant match with SSH466. Virtual Northern blot analysis confirmed that it was a tetrasporophyte-specific gene.

  10. Comparative genomics study for identification of putative drug targets in Salmonella typhi Ty2.

    Science.gov (United States)

    Batool, Nisha; Waqar, Maleeha; Batool, Sidra

    2016-01-15

    Typhoid presents a major health concern in developing countries with an estimated annual infection rate of 21 million. The disease is caused by Salmonella typhi, a pathogenic bacterium acquiring multiple drug resistance. We aim to identify proteins that could prove to be putative drug targets in the genome of S. typhi str. Ty2. We employed comparative and subtractive genomics to identify targets that are absent in humans and are essential to S. typhi Ty2. We concluded that 46 proteins essential to pathogen are absent in the host genome. Filtration on the basis of drug target prioritization singled out 20 potentially therapeutic targets. Their absence in the host and specificity to S. typhi Ty2 makes them ideal targets for treating typhoid in Homo sapiens. 3D structures of two of the final target enzymes, MurA and MurB have been predicted via homology modeling which are then used for a docking study.

  11. Keratin 15 promoter targets putative epithelial stem cells in the hair follicle bulge.

    Science.gov (United States)

    Liu, Yaping; Lyle, Stephen; Yang, Zaixin; Cotsarelis, George

    2003-11-01

    Putative epithelial stem cells in the hair follicle bulge are thought to play pivotal roles in the homeostasis, aging, and carcinogenesis of the cutaneous epithelium. Elucidating the role of bulge cells in these processes has been hampered by the lack of gene promoters that target this area with specificity. Here we describe the isolation of the mouse keratin 15 (K15) promoter and demonstrate its utility for preferentially targeting hair follicle bulge cells in adult K15/lacZ transgenic mice. We found that patterns of K15 expression and promoter activity changed with age and correlated with levels of differentiation within the cutaneous epithelium; less differentiated keratinocytes in the epidermis of the neonatal mouse and in the bulge area of the adult mouse preferentially expressed K15. These findings demonstrate the utility of the K15 promoter for targeting epithelial stem cells in the hair follicle bulge and set the stage for elucidating the role of bulge cells in skin biology.

  12. Exploring the putative self-binding property of the human farnesyltransferase alpha-subunit.

    Science.gov (United States)

    Hagemann, Anna; Müller, Grit; Manthey, Iris; Bachmann, Hagen Sjard

    2017-09-26

    Farnesylation is an important post-translational protein modification in eukaryotes. Farnesylation is performed by protein farnesyltransferase, a heterodimer composed of an α- (FTα) and a β-subunit. Recently, homo-dimerization of truncated rat and yeast FTα has been detected, suggesting a new role for FTα homodimers in signal transduction. We investigated the putative dimerization behaviour of human and rat FTα. Different in vitro and in vivo approaches revealed no self-dimerization and a presumably artificial formation of homo-trimers and higher homo-oligomers in vitro. Our study contributes to the clarification of the physiological features of FTase in different species and may be important for the ongoing development of FTase inhibitors. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  13. Identification of calcium-transporting ATPases of Entamoeba histolytica and cellular localization of the putative SERCA.

    Science.gov (United States)

    Martinez-Higuera, Aarón; Salas-Casas, Andrés; Calixto-Gálvez, Mercedes; Chávez-Munguía, Bibiana; Pérez-Ishiwara, D Guillermo; Ximénez, Cecilia; Rodríguez, Mario A

    2013-09-01

    Calcium has an important role on signaling of different cellular processes in the protozoa parasite Entamoeba histolytica, including development and pathogenesis. However, the systems that control calcium responses in this parasite are incompletely understood. Calcium-ATPases (Ca(2+)-ATPases) are proteins that play an important role in calcium homeostasis by catalyzing the active efflux of this ion from cytoplasm and are essential to the correct functioning of the cell machinery. Here, we reported the identification of five E. histolytica genes encoding putative Ca(2+)-ATPases, three related to PMCA, and two related to organellar ATPases. RT-PCR assays showed that all those genes are expressed in trophozoites and specific antibodies against the SERCA-like member located this protein in a continuous cytoplasmic network, supporting the hypothesis that it corresponds to the Ca(2+)-ATPase responsible to sequester calcium in the endoplasmic reticulum of this parasite.

  14. PLCζ or PAWP: revisiting the putative mammalian sperm factor that triggers egg activation and embryogenesis.

    Science.gov (United States)

    Kashir, Junaid; Nomikos, Michail; Swann, Karl; Lai, F Anthony

    2015-05-01

    In mammals, egg activation is initiated by multiple cytosolic Ca(2+) transients (Ca(2+) oscillations) that are triggered following delivery of a putative sperm factor from the fertilizing sperm. The identity of this 'sperm factor' thus holds much significance, not only as a vital component in creating a new life, but also for its potential therapeutic and diagnostic value in human infertility. Recent data have emerged suggesting the sperm factor may be a post-acrosomal sheath WW domain-binding protein (PAWP). However, a significant body of research points to a testis-specific phospholipase C zeta (PLCζ) as the sperm factor. Herein, we examine the evidence presented in favour of PAWP in relation to PLCζ and the requisite physiological properties of the mammalian sperm factor.

  15. Identification of a Putative Tetrasporophyte-Specific Gene in Gracilaria lemaneiformis(Gracilariales, Rhodophyte)

    Institute of Scientific and Technical Information of China (English)

    REN Xueying; ZHANG Xuecheng

    2008-01-01

    A putative tetrasporophyte-specific gene, designated as SSH466 (GenBank accession No. DQ019223), was one of the genes identified in this work using suppression subtractive hybridization (SSH) method in Gracilaria lemaneiformis. The full length of the gene was obtained using SMART RACE strategy. Sequence analysis revealed that the gene had 1 019 nucleotides, including an open reading frame of 498 nucleotides encoding 166 amino acid residues, 158 nucleotides of 5' untranslated region and 363 nucleo- tides of 3' non-coding region. Protein motif and secondary structure prediction showed that there existed a transmembrane domain with a unique β-sheet. Thus, SSH466 protein might be a cross-membrane protein. Sequence homology search in the public GenBank databases did not reveal any significant match with SSH466. Virtual Northern blot analysis confirmed that it was a tetrasporo- phyte-specific gene.

  16. Excitatory amino acid b-N-methylamino-L-alanine is a putative environmental neurotoxin

    Directory of Open Access Journals (Sweden)

    VLADIMIR NEDELJKOV

    2011-04-01

    Full Text Available The amino acid b-N-methylamino-L-alanine (L-BMAA has been associated with the amyotrophic lateral sclerosis/parkinsonism-dementia complex in three distinct western Pacific populations. The putative neurotoxin is produced by cyanobacteria, which live symbiotically in the roots of cycad trees. L-BMAA was thought to be a threat only to those few populations whose diet and medicines rely heavily on cycad seeds. However, the recent discovery that cyanobacteria from diverse terrestrial, freshwater, and saltwater ecosystems around the world produce the toxin requires a reassessment of whether it poses a larger health threat. Therefore, it is proposed that monitoring L-BMAA levels in cyanobacteria-contaminated water supplies might be prudent.

  17. Molecular mapping of the putative gonadoblastoma locus on the Y chromosome.

    Science.gov (United States)

    Salo, P; Kääriäinen, H; Petrovic, V; Peltomäki, P; Page, D C; de la Chapelle, A

    1995-11-01

    Based on the high incidence of gonadoblastoma in females with XY gonadal dysgenesis or 45,X/46,XY mosaicism, the existence of a susceptibility locus on the Y chromosome (GBY) has been postulated. We attempted to map GBY by making use of a recently developed dense map of Y-chromosomal sequence-tagged sites (STSs). In two female patients with gonadoblastoma, small marker chromosomes contained portions of the Y chromosome, and a single region of overlap could be defined extending from probe pDP97 in interval 4B, which contains the centromere, to marker sY182 in interval 5E of the proximal long arm. This interval is contained in a YAC contig that comprises approximately 4 Mb of DNA. Our findings confirm the previous localization of GBY and greatly refine it. The localization of GBY overlaps with the region to which a putative growth determinant, GCY, was recently assigned.

  18. Identification of Pns6, a putative movement protein of RRSV, as a silencing suppressor

    Directory of Open Access Journals (Sweden)

    Lin Qiying

    2010-11-01

    Full Text Available Abstract RNA silencing is a potent antiviral response in plants. As a counterdefense, most plant and some animal viruses encode RNA silencing suppressors. In this study, we showed that Pns6, a putative movement protein of Rice ragged stunt virus (RRSV, exhibited silencing suppressor activity in coinfiltration assays with the reporter green fluorescent protein (GFP in transgenic Nicotiana benthamiana line 16c. Pns6 of RRSV suppressed local silencing induced by sense RNA but had no effect on that induced by dsRNA. Deletion of a region involved in RNA binding abolished the silencing suppressor activity of Pns6. Further, expression of Pns6 enhanced Potato virus × pathogenicity in N. benthamiana. Collectively, these results suggested that RRSV Pns6 functions as a virus suppressor of RNA silencing that targets an upstream step of the dsRNA formation in the RNA silencing pathway. This is the first silencing suppressor to be identified from the genus Oryzavirus.

  19. Analysis of the expression of putatively imprinted genes in bovine peri-implantation embryos

    DEFF Research Database (Denmark)

    Tveden-Nyborg, Pernille Yde; Alexopoulos, N.I.; Cooney, M.A.

    2008-01-01

    imprinted genes (Ata3, Dlk1, Gnas, Grb10, Magel2, Mest-1, Ndn and Sgce) in bovine peri-implantation embryos. Two embryonic developmental stages were examined, Day 14 and Day 21. The gene expression pattern of single embryos was recorded for in vivo, in vitro produced (IVP) and parthenogenetic embryos...... (LOS) in bovine embryos resulting in increased embryonic morbidity and mortality. In the bovine, limited numbers of imprinted genes have been studied and studies have primarily been restricted to pre-implantation stages. This study reports original data on the expression pattern of 8 putatively...... procedures, either by in vitro maturation, fertilization or culture. In conclusion, effects of genomic imprinting and of in vitro procedures for embryo production may influence the success of bovine embryo implantation....

  20. Identification of putative CLE peptide receptors involved in determinate nodulation on soybean.

    Science.gov (United States)

    Mortier, Virginie; Fenta, Berhanu Amsalu; Kunert, Karl; Holsters, Marcelle; Goormachtig, Sofie

    2011-07-01

    CLAVATA3/EMBRYO SURROUNDING REGION (CLE) peptides tightly control the balance between stem cell proliferation and differentiation in several plant developmental processes. Transmission of the CLE peptide signal has been shown to be rather complex. Despite their recent identification, little is known about the receptors by which nodulation-specific CLE peptides, which were identified in soybean, are perceived. Genetic analysis has indicated that the leucine-rich repeat receptor-like kinase NARK of soybean (Glycine max) and its orthologs in other legumes are possible candidates. However, more receptors need to be identified because CLE peptides are often detected by heteromultimeric complexes. Here, we identified two additional putative CLE peptide receptor pairs in the soybean genome with a nodulation-related expression pattern, GmRLK1-GmRLK2 and GmRLK3-GmRLK4, and discuss their role in CLE peptide perception during nodulation.

  1. Sequence Divergence of Microsatellites and Phylogeny Analysis in Tetraploid Cotton Species and Their Putative Diploid Ancestors

    Institute of Scientific and Technical Information of China (English)

    Wang-Zhen GUO; Dong FANG; Wen-Duo YU; Tian-Zhen ZHANG

    2005-01-01

    To determine the level of microsatellite sequence differences and to use the information to construct a phylogenetic relationship for cultivated tetraploid cotton (Gossypium spp.) species and their putative diploid ancestors, 10 genome-derived microsatellite primer pairs were used to amplify eight species,including two tetraploid and six diploid species, in Gossypium. A total of 92 unique amplicons were resolved using polyacrylamide gel electrophoresis. Each amplicon was cloned, sequenced, and analyzed using standard phylogenetic software. Allelic diversities were caused mostly by changes in the number of simple sequence repeat (SSR) motif repeats and only a small proportion resulted from interruption of the SSR motif within the locus for the same genome. The frequency of base substitutions was 0.5%-1.0% in different genomes, with only few indels found. Based on the combined 10 SSR flanking sequence data, the homology of A-genome diploid species averaged 98.9%, even though most of the amplicons were of the same size, and the sequence homology between G. gossypioides (Ulbr.) Standl. and three other D-genome species (G.raimondii Ulbr., G. davidsonii Kell., and G. thurberi Tod.) was 98.5%, 98.6%, and 98.5%, respectively.Phylogenetic trees of the two allotetraploid species and their putative diploid progenitors showed that homoelogous sequences from the A- and D-subgenome were still present in the polyploid subgenomes and they evolved independently. Meanwhile, homoelogous sequence interaction that duplicated loci in the polyploid subgenomes became phylogenetic sisters was also found in the evolutionary history of tetraploid cotton species. The results of the present study suggest that evaluation of SSR variation at the sequence level can be effective in exploring the evolutionary relationships among Gossypuim species.

  2. Chromosomal radiosensitivity in breast cancer patients with a known or putative genetic predisposition.

    LENUS (Irish Health Repository)

    Baeyens, A

    2002-12-02

    The chromosomal radiosensitivity of breast cancer patients with a known or putative genetic predisposition was investigated and compared to a group of healthy women. The chromosomal radiosensitivity was assessed with the G2 and the G0-micronucleus assay. For the G2 assay lymphocytes were irradiated in vitro with a dose of 0.4 Gy (60)Co gamma-rays after 71 h incubation, and chromatid breaks were scored in 50 metaphases. For the micronucleus assay lymphocytes were exposed in vitro to 3.5 Gy (60)Co gamma-rays at a high dose rate or low dose rate. 70 h post-irradiation cultures were arrested and micronuclei were scored in 1000 binucleate cells. The results demonstrated that the group of breast cancer patients with a known or putative genetic predisposition was on the average more radiosensitive than a population of healthy women, and this with the G2 as well as with the high dose rate and low dose rate micronucleus assay. With the G2 assay 43% of the patients were found to be radiosensitive. A higher proportion of the patients were radiosensitive with the micronucleus assay (45% with high dose rate and 61% with low dose rate). No correlation was found between the G2 and the G0-micronucleus chromosomal radiosensitivity. Out of the different subgroups considered, the group of the young breast cancer patients without family history showed the highest percentage of radiosensitive cases in the G2 (50%) as well as in the micronucleus assay (75-78%).

  3. Genetic analysis of BIRC4/XIAP as a putative modifier gene of Wilson disease.

    Science.gov (United States)

    Weiss, Karl Heinz; Runz, Heiko; Noe, Barbara; Gotthardt, Daniel Nils; Merle, Uta; Ferenci, Peter; Stremmel, Wolfgang; Füllekrug, Joachim

    2010-12-01

    Wilson disease (WD) is an autosomal-recessive copper overload disorder caused by mutations in the copper-transporting adenosine triphosphatase (ATPase) ATP7B. It presents with a highly variable clinical phenotype ranging from asymptomatic to fulminant hepatic failure or progressive neurological involvement. No clear genotype-phenotype correlation has been established. Thus, variants in modifier genes could have an impact on WD manifestation and severity. Recently, the antiapoptotic protein baculoviral IAP repeat-containing protein 4 BIRC4/XIAP has been suggested as a regulator of copper-induced cell death. With the aim of investigating a putative role of BIRC4/XIAP as modifier gene in individuals with copper overload, we analyzed a WD patient cohort (n = 98) for sequence variants at the BIRC4/XIAP locus. When compared with clinical data, the previously described coding single nucleotide polymorphisms (SNPs) at the BRIC4/XIAP locus (rs28382721, rs28382722, rs28382723, rs5956583, rs28382740, rs12838858, rs28382741) did not correlate with age of onset or clinical presentation in our collective. However, three previously unreported variants in the BIRC4/XIAP gene were identified (c.1-26 T > G; c.1408A > T; p.T470S; c.1019A > G; p.N340S). The two patients with variants leading to amino acid exchanges in the BIRC4/XIAP protein showed a remarkably early disease onset at the age of 5 years. Furthermore, one of these patients was only heterozygous for disease-causing mutations in the ATP7B gene. In summary, these data emphasize the need to further elucidate a role of BIRC4/XIAP variants as putative pathogenetic factors in copper overload disorders.

  4. Identification and Characterization of a Putative Manganese Export Protein in Vibrio cholerae.

    Science.gov (United States)

    Fisher, Carolyn R; Wyckoff, Elizabeth E; Peng, Eric D; Payne, Shelley M

    2016-10-15

    Manganese plays an important role in the cellular physiology and metabolism of bacterial species, including the human pathogen Vibrio cholerae The intracellular level of manganese ions is controlled through coordinated regulation of the import and export of this element. We have identified a putative manganese exporter (VC0022), named mneA (manganese exporter A), which is highly conserved among Vibrio spp. An mneA mutant exhibited sensitivity to manganese but not to other cations. Under high-manganese conditions, the mneA mutant showed an almost 50-fold increase in intracellular manganese levels and reduced intracellular iron relative to those of its wild-type parent, suggesting that the mutant's manganese sensitivity is due to the accumulation of toxic levels of manganese and reduced iron. Expression of mneA suppressed the manganese-sensitive phenotype of an Escherichia coli strain carrying a mutation in the nonhomologous manganese export gene, mntP, further supporting a manganese export function for V. cholerae MneA. The level of mneA mRNA was induced approximately 2.5-fold after addition of manganese to the medium, indicating regulation of this gene by manganese. This study offers the first insights into understanding manganese homeostasis in this important pathogen. Bacterial cells control intracellular metal concentrations by coordinating acquisition in metal-limited environments with export in metal-excess environments. We identified a putative manganese export protein, MneA, in Vibrio cholerae An mneA mutant was sensitive to manganese, and this effect was specific to manganese. The mneA mutant accumulated high levels of intracellular manganese with a concomitant decrease in intracellular iron levels when grown in manganese-supplemented medium. Expression of mneA in trans suppressed the manganese sensitivity of an E. coli mntP mutant. This study is the first to investigate manganese export in V. cholerae. Copyright © 2016, American Society for Microbiology

  5. High amino acid diversity and positive selection at a putative coral immunity gene (tachylectin-2

    Directory of Open Access Journals (Sweden)

    Hellberg Michael E

    2010-05-01

    Full Text Available Abstract Background Genes involved in immune functions, including pathogen recognition and the activation of innate defense pathways, are among the most genetically variable known, and the proteins that they encode are often characterized by high rates of amino acid substitutions, a hallmark of positive selection. The high levels of variation characteristic of immunity genes make them useful tools for conservation genetics. To date, highly variable immunity genes have yet to be found in corals, keystone organisms of the world's most diverse marine ecosystem, the coral reef. Here, we examine variation in and selection on a putative innate immunity gene from Oculina, a coral genus previously used as a model for studies of coral disease and bleaching. Results In a survey of 244 Oculina alleles, we find high nonsynonymous variation and a signature of positive selection, consistent with a putative role in immunity. Using computational protein structure prediction, we generate a structural model of the Oculina protein that closely matches the known structure of tachylectin-2 from the Japanese horseshoe crab (Tachypleus tridentatus, a protein with demonstrated function in microbial recognition and agglutination. We also demonstrate that at least three other genera of anthozoan cnidarians (Acropora, Montastrea and Nematostella possess proteins structurally similar to tachylectin-2. Conclusions Taken together, the evidence of high amino acid diversity, positive selection and structural correspondence to the horseshoe crab tachylectin-2 suggests that this protein is 1 part of Oculina's innate immunity repertoire, and 2 evolving adaptively, possibly under selective pressure from coral-associated microorganisms. Tachylectin-2 may serve as a candidate locus to screen coral populations for their capacity to respond adaptively to future environmental change.

  6. Characterization of ERAS, a putative novel human oncogene, in skin and breast

    Energy Technology Data Exchange (ETDEWEB)

    Peña Avalos, B.L. de la

    2014-07-01

    Most human tumors have mutations in genes of the RAS small GTPase protein family. RAS works as a molecular switch for signaling pathways that modulate many aspects of cell behavior, including proliferation, differentiation, motility and death. Oncogenic mutations in RAS prevent GTP hydrolysis, locking RAS in a permanently active state, being the most common mutations in HRAS, KRAS and NRAS. The human RAS family consists of at least 36 different genes, many of which have been scarcely studied. One of these relatively unknown genes is ERAS (ES cell-expressed RAS), which is a constitutively active RAS protein, localized in chromosome X and expressed only in embryonic cells, being undetectable in adult tissues. New high throughput technologies have made it possible to screen complete cancer genomes for identification of mutations associated to cancer. Using the Sleeping Beauty (SB) transposon system, ERAS was identified as a putative novel oncogene in non-melanoma skin and breast cancers. The major aim of this project is to determine the general characteristics of ERAS as a putative novel human oncogene in skin and breast cells. Forced expression of ERAS results in drastic changes in cell shape, proliferation and motility. When ERAS is overexpressed in skin and breast human cells it is mainly localized in the cytoplasmic membrane. ERAS activates the phosphatidylinositol-3-OH kinase (PI3K) pathway but not the mitogen-activated protein kinase (MAPK) pathway. ERAS-expressing cells suffer spontaneous morphologic and phenotypic EMT-like changes, including cytoskeleton reorganization, vimentin and N-cadherin up-regulation and down-regulation of E-cadherin, which can be associated with increased malignancy, and invasive and metastatic potential. Our results suggest that inappropriate expression of ERAS lead to transformation of human cells. (Author)

  7. Putative glycosyltransferases and other plant Golgi apparatus proteins are revealed by LOPIT proteomics.

    Science.gov (United States)

    Nikolovski, Nino; Rubtsov, Denis; Segura, Marcelo P; Miles, Godfrey P; Stevens, Tim J; Dunkley, Tom P J; Munro, Sean; Lilley, Kathryn S; Dupree, Paul

    2012-10-01

    The Golgi apparatus is the central organelle in the secretory pathway and plays key roles in glycosylation, protein sorting, and secretion in plants. Enzymes involved in the biosynthesis of complex polysaccharides, glycoproteins, and glycolipids are located in this organelle, but the majority of them remain uncharacterized. Here, we studied the Arabidopsis (Arabidopsis thaliana) membrane proteome with a focus on the Golgi apparatus using localization of organelle proteins by isotope tagging. By applying multivariate data analysis to a combined data set of two new and two previously published localization of organelle proteins by isotope tagging experiments, we identified the subcellular localization of 1,110 proteins with high confidence. These include 197 Golgi apparatus proteins, 79 of which have not been localized previously by a high-confidence method, as well as the localization of 304 endoplasmic reticulum and 208 plasma membrane proteins. Comparison of the hydrophobic domains of the localized proteins showed that the single-span transmembrane domains have unique properties in each organelle. Many of the novel Golgi-localized proteins belong to uncharacterized protein families. Structure-based homology analysis identified 12 putative Golgi glycosyltransferase (GT) families that have no functionally characterized members and, therefore, are not yet assigned to a Carbohydrate-Active Enzymes database GT family. The substantial numbers of these putative GTs lead us to estimate that the true number of plant Golgi GTs might be one-third above those currently annotated. Other newly identified proteins are likely to be involved in the transport and interconversion of nucleotide sugar substrates as well as polysaccharide and protein modification.

  8. The V-ATPase a2-subunit as a putative endosomal pH-sensor.

    Science.gov (United States)

    Marshansky, V

    2007-11-01

    V-ATPase (vesicular H(+)-ATPase)-driven intravesicular acidification is crucial for vesicular trafficking. Defects in vesicular acidification and trafficking have recently been recognized as essential determinants of various human diseases. An important role of endosomal acidification in receptor-ligand dissociation and in activation of lysosomal hydrolytic enzymes is well established. However, the molecular mechanisms by which luminal pH information is transmitted to the cytosolic small GTPases that control trafficking events such as budding, coat formation and fusion are unknown. Here, we discuss our recent discovery that endosomal V-ATPase is a pH-sensor regulating the degradative pathway. According to our model, V-ATPase is responsible for: (i) the generation of a pH gradient between vesicular membranes; (ii) sensing of intravesicular pH; and (iii) transmitting this information to the cytosolic side of the membrane. We also propose the hypothetical molecular mechanism involved in function of the V-ATPase a2-subunit as a putative pH-sensor. Based on extensive experimental evidence on the crucial role of histidine residues in the function of PSPs (pH-sensing proteins) in eukaryotic cells, we hypothesize that pH-sensitive histidine residues within the intra-endosomal loops and/or C-terminal luminal tail of the a2-subunit could also be involved in the pH-sensing function of V-ATPase. However, in order to identify putative pH-sensitive histidine residues and to test this hypothesis, it is absolutely essential that we increase our understanding of the folding and transmembrane topology of the a-subunit isoforms of V-ATPase. Thus the crucial role of intra-endosomal histidine residues in pH-dependent conformational changes of the V-ATPase a2-isoform, its interaction with cytosolic small GTPases and ultimately in its acidification-dependent regulation of the endosomal/lysosomal protein degradative pathway remain to be determined.

  9. Putative roles for a rhamnose binding lectin in Flavobacterium columnare pathogenesis in channel catfish Ictalurus punctatus.

    Science.gov (United States)

    Beck, Benjamin H; Farmer, Bradley D; Straus, David L; Li, Chao; Peatman, Eric

    2012-10-01

    Columnaris disease, caused by the bacterial pathogen Flavobacterium columnare, continues to be a major problem worldwide and commonly leads to tremendous losses of both wild and cultured freshwater fish, particularly in intensively farmed aquaculture species such as channel catfish. Despite its ecologic and economic impacts, the fundamental molecular mechanisms of the host immune response to this pathogen remain unclear. While F. columnare can induce marked pathologic changes in numerous ectopic tissues, the adhesion of F. columnare to the gill in particular is strongly associated with pathogen virulence and host susceptibility. Recently, in this regard, using RNA-seq expression profiling we found that a rhamnose-binding lectin (RBL) was dramatically upregulated in the gill of fish infected with F. columnare (as compared to naïve fish). Thus, in the present study we sought to further characterize and understand the RBL response in channel catfish (Ictalurus punctatus). We first identified two distinct catfish families with differential susceptibilities to columnaris disease; one family was found to be completely resistant while the other was susceptible (0% mortality versus 18.3% respectively, P catfish RBL that persisted for at least 24 h (P catfish to different doses of the putative RBL ligands l-rhamnose and d-galactose, and found that these sugars, protected channel catfish against columnaris disease, likely through competition with F. columnare binding of host RBL. Finally, we examined the role of nutritional status on RBL regulation and found that RBL expression was upregulated (>120-fold; P < 0.05) in fish fasted for 7 d (as compared to fish fed to satiation daily), yet expression levels returned to those of satiated fish within 4 h after re-feeding. Collectively, these findings highlight putative roles for RBL in the context of columnaris disease and reveal new aspects linking RBL regulation to feed availability.

  10. Bioinformatic selection of putative epigenetically regulated loci associated with obesity using gene expression data.

    Science.gov (United States)

    Turcot, Valérie; Groom, Alexandra; McConnell, James C; Pearce, Mark S; Potter, Catherine; Embleton, Nicholas D; Swan, Daniel C; Relton, Caroline L

    2012-05-10

    There is considerable interest in defining the relationship between epigenetic variation and the risk of common complex diseases. Strategies which assist in the prioritisation of target loci that have the potential to be epigenetically regulated might provide a useful approach in identifying concrete examples of epigenotype-phenotype associations. Focusing on the postulated role of epigenetic factors in the aetiopathogenesis of obesity this report outlines an approach utilising gene expression data and a suite of bioinformatic tools to prioritise a list of target candidate genes for more detailed experimental scrutiny. Gene expression microarrays were performed using peripheral blood RNA from children aged 11-13years selected from the Newcastle Preterm Birth Growth Study which were grouped by body mass index (BMI). Genes showing ≥2.0 fold differential expression between low and high BMI groups were selected for in silico analysis. Several bioinformatic tools were used for each following step; 1) a literature search was carried out to identify whether the differentially expressed genes were associated with adiposity phenotypes. Of those obesity-candidate genes, putative epigenetically regulated promoters were identified by 2) defining the promoter regions, 3) then by selecting promoters with a CpG island (CGI), 4) and then by identifying any transcription factor binding modules covering CpG sites within the CGI. This bioinformatic processing culminated in the identification of a short list of target obesity-candidate genes putatively regulated by DNA methylation which can be taken forward for experimental analysis. The proposed workflow provides a flexible, versatile and low cost methodology for target gene prioritisation that is applicable to multiple species and disease contexts. Copyright © 2012. Published by Elsevier B.V.

  11. Genetic profiling of putative breast cancer stem cells from malignant pleural effusions.

    Science.gov (United States)

    Tiran, Verena; Stanzer, Stefanie; Heitzer, Ellen; Meilinger, Michael; Rossmann, Christopher; Lax, Sigurd; Tsybrovskyy, Oleksiy; Dandachi, Nadia; Balic, Marija

    2017-01-01

    A common symptom during late stage breast cancer disease is pleural effusion, which is related to poor prognosis. Malignant cells can be detected in pleural effusions indicating metastatic spread from the primary tumor site. Pleural effusions have been shown to be a useful source for studying metastasis and for isolating cells with putative cancer stem cell (CSC) properties. For the present study, pleural effusion aspirates from 17 metastatic breast cancer patients were processed to propagate CSCs in vitro. Patient-derived aspirates were cultured under sphere forming conditions and isolated primary cultures were further sorted for cancer stem cell subpopulations ALDH1+ and CD44+CD24-/low. Additionally, sphere forming efficiency of CSC and non-CSC subpopulations was determined. In order to genetically characterize the different tumor subpopulations, DNA was isolated from pleural effusions before and after cell sorting, and compared with corresponding DNA copy number profiles from primary tumors or bone metastasis using low-coverage whole genome sequencing (SCNA-seq). In general, unsorted cells had a higher potential to form spheres when compared to CSC subpopulations. In most cases, cell sorting did not yield sufficient cells for copy number analysis. A total of five from nine analyzed unsorted pleura samples (55%) showed aberrant copy number profiles similar to the respective primary tumor. However, most sorted subpopulations showed a balanced profile indicating an insufficient amount of tumor cells and low sensitivity of the sequencing method. Finally, we were able to establish a long term cell culture from one pleural effusion sample, which was characterized in detail. In conclusion, we confirm that pleural effusions are a suitable source for enrichment of putative CSC. However, sequencing based molecular characterization is impeded due to insufficient sensitivity along with a high number of normal contaminating cells, which are masking genetic alterations of

  12. The Bacillus anthracis chromosome contains four conserved, excision-proficient, putative prophages

    Directory of Open Access Journals (Sweden)

    Sozhamannan Shanmuga

    2006-04-01

    Full Text Available Abstract Background Bacillus anthracis is considered to be a recently emerged clone within the Bacillus cereus sensu lato group. The B. anthracis genome sequence contains four putative lambdoid prophages. We undertook this study in order to understand whether the four prophages are unique to B. anthracis and whether they produce active phages. Results More than 300 geographically and temporally divergent isolates of B. anthracis and its near neighbors were screened by PCR for the presence of specific DNA sequences from each prophage region. Every isolate of B. anthracis screened by PCR was found to produce all four phage-specific amplicons whereas none of the non-B. anthracis isolates, produced more than one phage-specific amplicon. Excision of prophages could be detected by a PCR based assay for attP sites on extra-chromosomal phage circles and for attB sites on phage-excised chromosomes. SYBR-green real-time PCR assays indicated that prophage excision occurs at very low frequencies (2 × 10-5 - 8 × 10-8/cell. Induction with mitomycin C increased the frequency of excision of one of the prophages by approximately 250 fold. All four prophages appear to be defective since, mitomycin C induced culture did not release any viable phage particle or lyse the cells or reveal any phage particle under electron microscopic examination. Conclusion The retention of all four putative prophage regions across all tested strains of B. anthracis is further evidence of the very recent emergence of this lineage and the prophage regions may be useful for differentiating the B. anthracis chromosome from that of its neighbors. All four prophages can excise at low frequencies, but are apparently defective in phage production.

  13. The gene corresponding to the putative Goodpasture antigen is present in Alport's syndrome.

    Science.gov (United States)

    Savige, J A

    1991-08-01

    Alport's syndrome is a heterogeneous group of inherited abnormalities of basement membranes that may result in progressive renal failure, defective hearing and lens abnormalities. The glomerular basement membrane (GBM) characteristically has areas of reduplication, lamellation and attenuation on electron microscopic examination. In the majority of affected males and some females, there is reduced or variable binding of serum from patients with anti-GBM disease (Goodpasture's syndrome) to these basement membranes. These sera contain antibodies directed against the Goodpasture antigen which has been thought to be located in the non-collagenous domain of the alpha3 chain of type IV collagen and is presumed to be important in cross-linking of the collagen molecules. The reduced staining for the Goodpasture antigen suggests that this structure is either absent or masked in Alport's syndrome. We have tested DNA from six unrelated individuals with Alport's syndrome. All had been transplanted for renal failure. The diagnosis of Alport's syndrome was made on the characteristic electron microscopic appearance of the renal basement membranes (n = 4), the presence of sensori-neural deafness (n = 4), a family history of Alport's syndrome (n = 5) and the presence of circulating inhibitable anti-GBM antibody activity post-transplant (n = 2). Oligonucleotides (20mers) corresponding to the 5' and 3' ends of the known 25 amino acid sequence for the putative Goodpasture antigen were used as primers for amplification of genomic DNA. The products were then blotted and probed with an intermediate 19-mer DNA. All Alport's patients contained a 75-bp fragment corresponding to the published peptide sequence for the non-collagenous domain of the alpha 3 chain of type IV collagen, suggesting that a large deletion of this region, the putative Goodpasture antigen, is unlikely to account for the defect in Alport's syndrome.

  14. Identification of Putative Receptors for the Novel Adipokine CTRP3 Using Ligand-Receptor Capture Technology

    Science.gov (United States)

    Li, Ying; Ozment, Tammy; Wright, Gary L.

    2016-01-01

    C1q TNF Related Protein 3 (CTRP3) is a member of a family of secreted proteins that exert a multitude of biological effects. Our initial work identified CTRP3’s promise as an effective treatment for Nonalcoholic fatty liver disease (NAFLD). Specifically, we demonstrated that mice fed a high fat diet failed to develop NAFLD when treated with CTRP3. The purpose of this current project is to identify putative receptors which mediate the hepatic actions of CTRP3. Methods We used Ligand-receptor glycocapture technology with TriCEPS™-based ligand-receptor capture (LRC-TriCEPS; Dualsystems Biotech AG). The LRC-TriCEPS experiment with CTRP3-FLAG protein as ligand and insulin as a control ligand was performed on the H4IIE rat hepatoma cell line. Results Initial analysis demonstrated efficient coupling of TriCEPS to CTRP3. Further, flow cytometry analysis (FACS) demonstrated successful oxidation and crosslinking of CTRP3-TriCEPS and Insulin-TriCEPS complexes to cell surface glycans. Demonstrating the utility of TriCEPS under these conditions, the insulin receptor was identified in the control dataset. In the CTRP3 treated cells a total enrichment of 261 peptides was observed. From these experiments 5 putative receptors for CTRP3 were identified with two reaching statistically significance: Lysosomal-associated membrane protein 1 (LAMP-1) and Lysosome membrane protein 2 (LIMP II). Follow-up Co-immunoprecipitation analysis confirmed the association between LAMP1 and CTRP3 and further testing using a polyclonal antibody to block potential binding sites of LAMP1 prevented CTRP3 binding to the cells. Conclusion The LRC-TriCEPS methodology was successful in identifying potential novel receptors for CTRP3. Relevance The identification of the receptors for CTRP3 are important prerequisites for the development of small molecule drug candidates, of which none currently exist, for the treatment NAFLD. PMID:27727322

  15. UNC79 and UNC80, putative auxiliary subunits of the NARROW ABDOMEN ion channel, are indispensable for robust circadian locomotor rhythms in Drosophila.

    Directory of Open Access Journals (Sweden)

    Bridget C Lear

    Full Text Available In the fruit fly Drosophila melanogaster, a network of circadian pacemaker neurons drives daily rhythms in rest and activity. The ion channel NARROW ABDOMEN (NA, orthologous to the mammalian sodium leak channel NALCN, functions downstream of the molecular circadian clock in pacemaker neurons to promote behavioral rhythmicity. To better understand the function and regulation of the NA channel, we have characterized two putative auxiliary channel subunits in Drosophila, unc79 (aka dunc79 and unc80 (aka CG18437. We have generated novel unc79 and unc80 mutations that represent strong or complete loss-of-function alleles. These mutants display severe defects in circadian locomotor rhythmicity that are indistinguishable from na mutant phenotypes. Tissue-specific RNA interference and rescue analyses indicate that UNC79 and UNC80 likely function within pacemaker neurons, with similar anatomical requirements to NA. We observe an interdependent, post-transcriptional regulatory relationship among the three gene products, as loss of na, unc79, or unc80 gene function leads to decreased expression of all three proteins, with minimal effect on transcript levels. Yet despite this relationship, we find that the requirement for unc79 and unc80 in circadian rhythmicity cannot be bypassed by increasing NA protein expression, nor can these putative auxiliary subunits substitute for each other. These data indicate functional requirements for UNC79 and UNC80 beyond promoting channel subunit expression. Immunoprecipitation experiments also confirm that UNC79 and UNC80 form a complex with NA in the Drosophila brain. Taken together, these data suggest that Drosophila NA, UNC79, and UNC80 function together in circadian clock neurons to promote rhythmic behavior.

  16. A comparative study on efficiency of adult fibroblast, putative embryonic stem cell and lymphocyte as donor cells for production of handmade cloned embryos in goat and characterization of putative ntES cells obtained from these embryos.

    Science.gov (United States)

    Dutta, Rahul; Malakar, Dhruba; Khate, Keviletsu; Sahu, Shailendra; Akshey, Yogesh; Mukesh, Manishi

    2011-09-15

    The main purpose of the experiment was to compare the efficiency of three cell types, namely adult fibroblast, putative embryonic stem (ES) cell, and lymphocyte, as donor cells for somatic cell nuclear transfer by handmade cloning in goats. The outcome clearly shows that putative embryonic stem cells, with a cleavage and blastocyst production rate of 74.69% ± 3.92 and 39.75% ± 3.86, respectively, performs better in comparison to adult fibroblast cell and lymphocyte. Between adult fibroblast cell and lymphocyte no statistically significant difference exists at P II DRB genes of cloned embryos and three donor cells were performed to verify the cloned embryos. The amplified PCR products were subjected to SSCP to confirm their genetic identity. The karyotyping of the cloned embryos showed normal chromosomal status as expected in goat. Significantly, in the second stage of the experiment, the produced cloned embryos were successfully used to derive ntES-like cells. The rate of primary colony formation rate was 62.50% ± 4.62 for fibroblast donor cell derived embryos. The same was 60.60% ± 4.62 for putative ES donor cell derived embryos and 66.66% ± 4.62 for lymphocyte donor cell derived embryos, respectively. The putative ntES colonies were positively characterized for alkaline phosphatase, Oct-4, TRA-1-60, TRA-1-81, Sox-2, and Nanog by Immunocytochemistry and Reverse Transcription PCR. To further validate the stem ness, the produced putative ntES colonies were differentiated to embryoid bodies. Immunocytochemistry revealed that embryoid bodies expressed NESTIN specific for ectodermal lineage; GATA-4 for endodermal lineage and smooth muscle actin-I, and troponin-I specific for mesodermal lineage. The study has established an efficient protocol for putative ntES cell derivation from HMC embryos. It could be of substantial significance as patient specific ntES cells have proven therapeutic significance.

  17. Prolactin-induced prostate tumorigenesis links sustained Stat5 signaling with the amplification of basal/stem cells and emergence of putative luminal progenitors.

    Science.gov (United States)

    Sackmann-Sala, Lucila; Chiche, Aurélie; Mosquera-Garrote, Nerea; Boutillon, Florence; Cordier, Corinne; Pourmir, Ivan; Pascual-Mathey, Luz; Kessal, Karima; Pigat, Natascha; Camparo, Philippe; Goffin, Vincent

    2014-11-01

    Current androgen ablation therapies for prostate cancer are initially successful, but the frequent development of castration resistance urges the generation of alternative therapies and represents an important health concern. Prolactin/signal transducer and activator of transcription 5 (STAT5) signaling is emerging as a putative target for alternative treatment for prostate cancer. However, mechanistic data for its role in development or progression of prostate tumors are scarce. In vivo mouse studies found that local prolactin induced the amplification of prostate epithelial basal/stem cells. Because these cells are proposed cells of origin for prostate cancer and disease recurrence, we looked further into this amplification. Our results indicated that sustained Stat5 activation was associated with the occurrence of abnormal basal/stem cell clusters in prostate epithelium of prostate-specific prolactin-transgenic mice. Analysis of epithelial areas containing these clusters found high proliferation, Stat5 activation, and expression of stem cell antigen 1. Furthermore, enhanced prolactin signaling also led to amplification of a luminal cell population that was positive for stem cell antigen 1. These cells may originate from amplified basal/stem cells and might represent important progenitors for tumor development in prostate epithelium. These data provide a deeper understanding of the initial stages of prostate tumorigenesis induced by prolactin to help determine whether this hormone or its downstream messengers could be useful targets for prostate cancer treatment in the future.

  18. [Quantitative method of representative contaminants in groundwater pollution risk assessment].

    Science.gov (United States)

    Wang, Jun-Jie; He, Jiang-Tao; Lu, Yan; Liu, Li-Ya; Zhang, Xiao-Liang

    2012-03-01

    In the light of the problem that stress vulnerability assessment in groundwater pollution risk assessment is lack of an effective quantitative system, a new system was proposed based on representative contaminants and corresponding emission quantities through the analysis of groundwater pollution sources. And quantitative method of the representative contaminants in this system was established by analyzing the three properties of representative contaminants and determining the research emphasis using analytic hierarchy process. The method had been applied to the assessment of Beijing groundwater pollution risk. The results demonstrated that the representative contaminants hazards greatly depended on different research emphasizes. There were also differences between the sequence of three representative contaminants hazards and their corresponding properties. It suggested that subjective tendency of the research emphasis had a decisive impact on calculation results. In addition, by the means of sequence to normalize the three properties and to unify the quantified properties results would zoom in or out of the relative properties characteristic of different representative contaminants.

  19. Using stories to disseminate research: the attributes of representative stories.

    Science.gov (United States)

    Steiner, John F

    2007-11-01

    When researchers communicate their findings to patients, clinicians, policy-makers, or media, they may find it helpful to supplement quantitative data with stories about individuals who represent themes in their research. Whether such stories are gathered during the research itself or identified from other sources, researchers must develop strategies for assessing their representativeness. This paper proposes 5 attributes of representative stories: (1) expression of important themes in the research, (2) explicit location in the "distribution" of stories that exemplify the theme, (3) verifiability, (4) acknowledgment of uncertainty, and (5) compelling narration. This paper summarizes research on substance abuse among physicians, and uses these 5 attributes to assess the representativeness of a published case report and a fictional short story about addicted physicians. While neither story is fully representative of the research, the process of evaluating these stories illustrates an approach to identifying representative stories for use in disseminating research.

  20. High School Students' perception of University Students as STEM representatives

    DEFF Research Database (Denmark)

    Poulsen, Eva Lykkegaard

    2012-01-01

    . Some representatives transmit information and are thereby definers, whereas other representatives illustrates as personal examples and are thereby models. This study focuses on high school students’ views on STEM representatives and the impact these representatives have on the high school students......The Danish government has an ambition to recruit more high school students into STEM educations (science, technology, engineering and/or mathematics). The students’ choice of further education is based on the people and jobs they have knowledge of. Therefore, to recruit more students into STEM...... studies, it is important to introduce high school students to good STEM representatives to make possible the development of potential STEM identities. A potential identity within a specific subject area relies on at least a situation bound relationship to the subject area or the person representing it...

  1. High School Students' Perception of University Students as STEM Representatives

    DEFF Research Database (Denmark)

    Poulsen, Eva Lykkegaard

    . Some representatives transmit infor-mation and are thereby definers, whereas other representatives illustrates as personal examples and are thereby models. This study focuses on high school students’ views on STEM representatives and the impact these representatives have on the high school students......The Danish government has an ambition to recruit more high school students into STEM edu-cations (science, technology, engineering and/or mathematics). The students’ choice of further education is based on the people and jobs they have knowledge of. Therefore, to recruit more students into STEM...... studies, it is important to introduce high school students to good STEM representatives to make possible the development of potential STEM identities. A potential identity within a specific subject area relies on at least a situation bound relation-ship to the subject area or the person representing it...

  2. Characterization of three putative xylulose 5-phosphate/fructose 6-phosphate phosphoketolases in the cyanobacterium Anabaena sp. PCC 7120.

    Science.gov (United States)

    Moriyama, Takashi; Tajima, Naoyuki; Sekine, Kohsuke; Sato, Naoki

    2015-01-01

    Xylulose 5-phosphate/fructose 6-phosphate phosphoketolase (Xfp) is a key enzyme in the central carbohydrate metabolism in heterofermentative bacteria, in which enzymatic property of Xfps is well characterized. This is not the case in other microbes. The cyanobacterium Anabaena sp. PCC 7120 possesses three putative genes encoding Xfp, all1483, all2567, and alr1850. We purified three putative Xfps as recombinant proteins. The results of gel filtration indicated that these proteins form homomultimer complex. All1483 and All2567 showed phosphoketolase activity, whereas Alr1850 did not show the activity. Kinetic analyses demonstrated that substrates, fructose 6-phosphate and inorganic phosphate, are cooperatively bound to enzymes positively and negatively, respectively.

  3. Molecular and functional characterization of cDNAs putatively encoding carboxylesterases from the migratory locust, Locusta migratoria.

    Directory of Open Access Journals (Sweden)

    Jianqin Zhang

    Full Text Available Carboxylesterases (CarEs belong to a superfamily of metabolic enzymes encoded by a number of genes and are widely distributed in microbes, plants and animals including insects. These enzymes play important roles in detoxification of insecticides and other xenobiotics, degradation of pheromones, regulation of neurodevelopment, and control of animal development. In this study, we characterized a total of 39 full-length cDNAs putatively encoding different CarEs from the migratory locust, Locusta migratoria, one of the most severe insect pests in many regions of the world, and evaluated the role of four CarE genes in insecticide detoxification. Our phylogenetic analysis grouped the 39 CarEs into five different clades including 20 CarEs in clade A, 3 in D, 13 in E, 1 in F and 2 in I. Four CarE genes (LmCesA3, LmCesA20, LmCesD1, LmCesE1, representing three different clades (A, D and E, were selected for further analyses. The transcripts of the four genes were detectable in all the developmental stages and tissues examined. LmCesA3 and LmCesE1 were mainly expressed in the fat bodies and Malpighian tubules, whereas LmCesA20 and LmCesD1 were predominately expressed in the muscles and hemolymph, respectively. The injection of double-stranded RNA (dsRNA synthesized from each of the four CarE genes followed by the bioassay with each of four insecticides (chlorpyrifos, malathion, carbaryl and deltamethrin increased the nymphal mortalities by 37.2 and 28.4% in response to malathion after LmCesA20 and LmCesE1 were silenced, respectively. Thus, we proposed that both LmCesA20 and LmCesE1 played an important role in detoxification of malathion in the locust. These results are expected to help researchers reveal the characteristics of diverse CarEs and assess the risk of insecticide resistance conferred by CarEs in the locust and other insect species.

  4. Molecular and functional characterization of cDNAs putatively encoding carboxylesterases from the migratory locust, Locusta migratoria.

    Science.gov (United States)

    Zhang, Jianqin; Li, Daqi; Ge, Pingting; Guo, Yaping; Zhu, Kun Yan; Ma, Enbo; Zhang, Jianzhen

    2014-01-01

    Carboxylesterases (CarEs) belong to a superfamily of metabolic enzymes encoded by a number of genes and are widely distributed in microbes, plants and animals including insects. These enzymes play important roles in detoxification of insecticides and other xenobiotics, degradation of pheromones, regulation of neurodevelopment, and control of animal development. In this study, we characterized a total of 39 full-length cDNAs putatively encoding different CarEs from the migratory locust, Locusta migratoria, one of the most severe insect pests in many regions of the world, and evaluated the role of four CarE genes in insecticide detoxification. Our phylogenetic analysis grouped the 39 CarEs into five different clades including 20 CarEs in clade A, 3 in D, 13 in E, 1 in F and 2 in I. Four CarE genes (LmCesA3, LmCesA20, LmCesD1, LmCesE1), representing three different clades (A, D and E), were selected for further analyses. The transcripts of the four genes were detectable in all the developmental stages and tissues examined. LmCesA3 and LmCesE1 were mainly expressed in the fat bodies and Malpighian tubules, whereas LmCesA20 and LmCesD1 were predominately expressed in the muscles and hemolymph, respectively. The injection of double-stranded RNA (dsRNA) synthesized from each of the four CarE genes followed by the bioassay with each of four insecticides (chlorpyrifos, malathion, carbaryl and deltamethrin) increased the nymphal mortalities by 37.2 and 28.4% in response to malathion after LmCesA20 and LmCesE1 were silenced, respectively. Thus, we proposed that both LmCesA20 and LmCesE1 played an important role in detoxification of malathion in the locust. These results are expected to help researchers reveal the characteristics of diverse CarEs and assess the risk of insecticide resistance conferred by CarEs in the locust and other insect species.

  5. [Lactase deficiency among representatives of various nationalities of Siberia].

    Science.gov (United States)

    Zhvavyĭ, N F; Kozlov, A I; Kondik, V M

    1991-01-01

    Some features of lactase tolerance were investigated in representatives of varying groups of indigenous population in Siberia-Mansi, Khanty, Nenets, Buryats. The indirect method was used to evaluate lactase activity. A total of 92 subjects were investigated. It was found that 32% of the representatives of the Urals population group and 53% of Buryats were capable of lactase assimilating. The data obtained correspond to the cultural-genetic hypothesis on the nature of lactase tolerance in the representatives of different ethnic groups.

  6. Groups without cultured representatives dominate eukaryotic picophytoplankton in the oligotrophic South East Pacific Ocean.

    Directory of Open Access Journals (Sweden)

    Xiao Li Shi

    Full Text Available BACKGROUND: Photosynthetic picoeukaryotes (PPE with a cell size less than 3 microm play a critical role in oceanic primary production. In recent years, the composition of marine picoeukaryote communities has been intensively investigated by molecular approaches, but their photosynthetic fraction remains poorly characterized. This is largely because the classical approach that relies on constructing 18S rRNA gene clone libraries from filtered seawater samples using universal eukaryotic primers is heavily biased toward heterotrophs, especially alveolates and stramenopiles, despite the fact that autotrophic cells in general outnumber heterotrophic ones in the euphotic zone. METHODOLOGY/PRINCIPAL FINDINGS: In order to better assess the composition of the eukaryotic picophytoplankton in the South East Pacific Ocean, encompassing the most oligotrophic oceanic regions on earth, we used a novel approach based on flow cytometry sorting followed by construction of 18S rRNA gene clone libraries. This strategy dramatically increased the recovery of sequences from putative autotrophic groups. The composition of the PPE community appeared highly variable both vertically down the water column and horizontally across the South East Pacific Ocean. In the central gyre, uncultivated lineages dominated: a recently discovered clade of Prasinophyceae (IX, clades of marine Chrysophyceae and Haptophyta, the latter division containing a potentially new class besides Prymnesiophyceae and Pavlophyceae. In contrast, on the edge of the gyre and in the coastal Chilean upwelling, groups with cultivated representatives (Prasinophyceae clade VII and Mamiellales dominated. CONCLUSIONS/SIGNIFICANCE: Our data demonstrate that a very large fraction of the eukaryotic picophytoplankton still escapes cultivation. The use of flow cytometry sorting should prove very useful to better characterize specific plankton populations by molecular approaches such as gene cloning or metagenomics

  7. Isolation and characterization of a new chemokine receptor gene, the putative chicken CXCR1.

    Science.gov (United States)

    Li, Q J; Lu, S; Ye, R D; Martins-Green, M

    2000-10-31

    This study delineates the isolation and characterization of a novel chemokine receptor gene, the putative chicken CXC receptor 1 (cCXCR1). Using a human CXCR1 probe, we isolated several positive clones from a chicken genomic library. One of the clones contained a fragment of approximately 5000bp that hybridized strongly with the hCXCR1 probe. This fragment was sequenced and subjected to a variety of computer analyses. The open reading frame for this gene predicts a seven transmembrane domain protein with all the characteristics of a chemokine receptor and with 67% sequence homology to hCXCR1, 65% to hCXCR2 and also with considerable sequence homology to other human chemokine receptors such as hCXCR4 (50%), hCCR2 (49%) and hCCR1 (49%). However, the homology to a previously isolated potential G-protein-coupled receptor for chickens (AvCRL1) is only 47%. Using 5' RACE, two transcription initiation sites were identified suggesting the potential for the expression of two protein isoforms (I and II) in vivo. The promoter for the putative cCXCR1 contains a variety of consensus transcription factor binding elements that can potentially be involved in the expression of this chicken receptor upon stimulation by stress-inducing agents. RT-PCR analysis was used to determine the pattern of expression of the larger isoform (I) of this receptor in a variety of tissues. This form of the receptor is expressed primarily in the organs of the gastrointestinal tract, tissues that are frequently exposed to stress-inducing agents, but not in the central nervous system, tissues that are protected from insult by the blood barrier. Using the same RT-PCR approach we show that stress-inducing agents, such as 'first-hand' and 'second-hand' cigarette smoke components, tumor promoters and thrombin, differentially stimulate the expression of the isoform I in primary fibroblasts. Thrombin is an enzyme that plays many important roles in thrombosis, angiogenesis and wound healing and exposure to

  8. Multiple functions of mfa-1, a putative pheromone precursor gene of Neurospora crassa.

    Science.gov (United States)

    Kim, Hyojeong; Metzenberg, Robert L; Nelson, Mary Anne

    2002-12-01

    A putative pheromone precursor gene of Neurospora crassa, mfa-1 (which encodes mating factor a-1), was identified as the most abundant clone in starved mycelial and perithecial cDNA libraries. Northern analysis demonstrated high mfa-1 expression in all mating type a tissues and suggested low expression levels in mat A tissues. The mfa-1 gene was expressed as an approximately 1.2-kb transcript predicted to encode a 24-residue peptide, followed by a long 3' untranslated region (3' UTR). The predicted MFA1 sequence showed 100% sequence identity to PPG2 of Sordaria macrospora and structural similarity (a carboxy-terminal CAAX motif) to many hydrophobic fungal pheromone precursors. Mutants with a disrupted open reading frame (ORF) in which the critical cysteine residue had been changed to a nonprenylatable residue, tyrosine (YAAX mutants), were isolated, as were mfa-1 mutants with intact ORFs but multiple mutations in the 3' noncoding region (CAAX mutants). The 3' UTR is required for the full range of mfa-1 gene activity. Both classes of mutants showed delayed and reduced vegetative growth (which was suppressed by supplementation with a minute amount [30 micro M] of ornithine, citrulline, or arginine), as well as aberrant sexual development. When crossed as female parents to wild-type males, the CAAX and YAAX mutants showed greatly reduced ascospore production. No ascospores were produced in homozygous mfa-1 crosses. As males, YAAX mat a mutants were unable to attract wild-type mat A trichogynes (female-specific hyphae) or to initiate sexual development, while CAAX mat a mutants were able to mate and produce sexual progeny despite their inability to attract mat A trichogynes. In the mat A background, both CAAX and YAAX mutants showed normal male fertility but defective vegetative growth and aberrant female sexual development. Thus, the mfa-1 gene appears to have multiple roles in N. crassa development: (i) it encodes a hydrophobic pheromone with a putative farnesylated

  9. Contrasting phenotypes of putative proprioceptive and nociceptive trigeminal neurons innervating jaw muscle in rat

    Directory of Open Access Journals (Sweden)

    Connor Mark

    2005-10-01

    Full Text Available Abstract Background Despite the clinical significance of muscle pain, and the extensive investigation of the properties of muscle afferent fibers, there has been little study of the ion channels on sensory neurons that innervate muscle. In this study, we have fluorescently tagged sensory neurons that innervate the masseter muscle, which is unique because cell bodies for its muscle spindles are in a brainstem nucleus (mesencephalic nucleus of the 5th cranial nerve, MeV while all its other sensory afferents are in the trigeminal ganglion (TG. We examine the hypothesis that certain molecules proposed to be used selectively by nociceptors fail to express on muscle spindles afferents but appear on other afferents from the same muscle. Results MeV muscle afferents perfectly fit expectations of cells with a non-nociceptive sensory modality: Opiates failed to inhibit calcium channel currents (ICa in 90% of MeV neurons, although ICa were inhibited by GABAB receptor activation. All MeV afferents had brief (1 msec action potentials driven solely by tetrodotoxin (TTX-sensitive Na channels and no MeV afferent expressed either of three ion channels (TRPV1, P2X3, and ASIC3 thought to be transducers for nociceptive stimuli, although they did express other ATP and acid-sensing channels. Trigeminal masseter afferents were much more diverse. Virtually all of them expressed at least one, and often several, of the three putative nociceptive transducer channels, but the mix varied from cell to cell. Calcium currents in 80% of the neurons were measurably inhibited by μ-opioids, but the extent of inhibition varied greatly. Almost all TG masseter afferents expressed some TTX-insensitive sodium currents, but the amount compared to TTX sensitive sodium current varied, as did the duration of action potentials. Conclusion Most masseter muscle afferents that are not muscle spindle afferents express molecules that are considered characteristic of nociceptors, but these

  10. PRE AND POST TRAINING EVALUATION ON UNIVERSAL PRECAUTIONS (UP PRACTICES AT PUTAT JAYA HEALTH CENTER, SURABAYA

    Directory of Open Access Journals (Sweden)

    Cholis Bachroen

    2012-11-01

    Full Text Available Praktek untuk mematuhi 'universal precaution' (UP di institusi pelayanan kesehatan (termasuk puskesmas, klinik dsb dimaksudkan untuk melindungi pasien dan petugas kesehatan dari penularan penyakit yang dapat terjadi karena tindakan pelayanan kesehatan yang kurang atau tidak tepat (tidak mengikuti UP. Penyakit  yang mungkin dapat menular dengan tidak ditepatinya UP oleh petugas kesehatan antara lain adalah penyakit yang dapat menular lewat darah (blood bome diseases termasuk HIV/AIDS dan Hepatitis B dan C. Mengingat kepatuhan  terhadap UP di antara petugas kesehatan selama melayani pasien dinilai masih kurang, maka dilaksanakan Pelatihan UP di puskesmas. Study ini dilakukan di Puskesmas Putat Jays yang Juga mempunyai klinik yang khusus melayani Pekerja Seksual Komersial (PSK dalam rangka menekan terjadinya penularan penyakit kelamin dan HIV/AIDS. Puskesmas Putat Jays merupakan sasaran yang strategis karena mempunyat daerah binaan antara lain Lokalisasi (PSK Dolly dan Jarak. Studi evaluatif ini dimaksudkan untuk melihat tingkat kepatuhan petugas terhadap UP selama melayani pasien serta mengkaji adanya perubahan kepatuhan tersebut setelah mendapat pelatihan. Data kualitaltf dan kuantitatif dikumpulkan melalui observasi, in depth interview dan diskusi. Hasil studi menunjukkan bahwa setelah pelatihan, pengetahuan tentang UP secara umum serta kesadaran untuk melindungi pasien dari penularan penyakit meningkat. Penggunaan ulang jarum suntik sudah tidak dilakukan (selalu memakai jarum diposable, spuit dan jarum di-disinfeksi sebelum dibuang serta pelaksanaan disinfeksilsterilisasi telah sesuai dengan prosedur. Data kuantitatif menunjukkan bahwa dengan pelatihan terjadi peningkatan jumlah petugas kesehatan yang mempunyai kebiasaan mencuci tangan secara tepat pada waktu melayani pasien yaitu dari 10% menjadi 90%, mengganti sarung tangan dengan tepat dari 33,3% menjadi 66,67%, memakai 'one hand technique' waktu menutup jarum dari 0% menjadi 100%, dan

  11. Can Genetic Analysis of Putative Blood Alzheimer's Disease Biomarkers Lead to Identification of Susceptibility Loci?

    Directory of Open Access Journals (Sweden)

    Robert C Barber

    Full Text Available Although 24 Alzheimer's disease (AD risk loci have been reliably identified, a large portion of the predicted heritability for AD remains unexplained. It is expected that additional loci of small effect will be identified with an increased sample size. However, the cost of a significant increase in Case-Control sample size is prohibitive. The current study tests whether exploring the genetic basis of endophenotypes, in this case based on putative blood biomarkers for AD, can accelerate the identification of susceptibility loci using modest sample sizes. Each endophenotype was used as the outcome variable in an independent GWAS. Endophenotypes were based on circulating concentrations of proteins that contributed significantly to a published blood-based predictive algorithm for AD. Endophenotypes included Monocyte Chemoattractant Protein 1 (MCP1, Vascular Cell Adhesion Molecule 1 (VCAM1, Pancreatic Polypeptide (PP, Beta2 Microglobulin (B2M, Factor VII (F7, Adiponectin (ADN and Tenascin C (TN-C. Across the seven endophenotypes, 47 SNPs were associated with outcome with a p-value ≤1x10(-7. Each signal was further characterized with respect to known genetic loci associated with AD. Signals for several endophenotypes were observed in the vicinity of CR1, MS4A6A/MS4A4E, PICALM, CLU, and PTK2B. The strongest signal was observed in association with Factor VII levels and was located within the F7 gene. Additional signals were observed in MAP3K13, ZNF320, ATP9B and TREM1. Conditional regression analyses suggested that the SNPs contributed to variation in protein concentration independent of AD status. The identification of two putatively novel AD loci (in the Factor VII and ATP9B genes, which have not been located in previous studies despite massive sample sizes, highlights the benefits of an endophenotypic approach for resolving the genetic basis for complex diseases. The coincidence of several of the endophenotypic signals with known AD loci may point

  12. Discovery of Putative Herbicide Resistance Genes and Its Regulatory Network in Chickpea Using Transcriptome Sequencing

    Directory of Open Access Journals (Sweden)

    Mir A. Iquebal

    2017-06-01

    Full Text Available Background: Chickpea (Cicer arietinum L. contributes 75% of total pulse production. Being cheaper than animal protein, makes it important in dietary requirement of developing countries. Weed not only competes with chickpea resulting into drastic yield reduction but also creates problem of harboring fungi, bacterial diseases and insect pests. Chemical approach having new herbicide discovery has constraint of limited lead molecule options, statutory regulations and environmental clearance. Through genetic approach, transgenic herbicide tolerant crop has given successful result but led to serious concern over ecological safety thus non-transgenic approach like marker assisted selection is desirable. Since large variability in tolerance limit of herbicide already exists in chickpea varieties, thus the genes offering herbicide tolerance can be introgressed in variety improvement programme. Transcriptome studies can discover such associated key genes with herbicide tolerance in chickpea.Results: This is first transcriptomic studies of chickpea or even any legume crop using two herbicide susceptible and tolerant genotypes exposed to imidazoline (Imazethapyr. Approximately 90 million paired-end reads generated from four samples were processed and assembled into 30,803 contigs using reference based assembly. We report 6,310 differentially expressed genes (DEGs, of which 3,037 were regulated by 980 miRNAs, 1,528 transcription factors associated with 897 DEGs, 47 Hub proteins, 3,540 putative Simple Sequence Repeat-Functional Domain Marker (SSR-FDM, 13,778 genic Single Nucleotide Polymorphism (SNP putative markers and 1,174 Indels. Randomly selected 20 DEGs were validated using qPCR. Pathway analysis suggested that xenobiotic degradation related gene, glutathione S-transferase (GST were only up-regulated in presence of herbicide. Down-regulation of DNA replication genes and up-regulation of abscisic acid pathway genes were observed. Study further reveals

  13. Determination and Analysis of the Putative AcaCD-Responsive Promoters of Salmonella Genomic Island 1

    Science.gov (United States)

    Olasz, Ferenc; Kiss, János

    2016-01-01

    The integrative genomic island SGI1 and its variants confer multidrug resistance in numerous Salmonella enterica serovariants and several Proteus mirabilis and Acinetobacter strains. SGI1 is mobilized by the IncA/C family plasmids. The island exploits not only the conjugation apparatus of the plasmid, but also utilizes the plasmid-encoded master regulator AcaCD to induce the excision and formation of its transfer-competent form, which is a key step in the horizontal transfer of SGI1. Triggering of SGI1 excision occurs via the AcaCD-dependent activation of xis gene expression. AcaCD binds in Pxis to an unusually long recognition sequence. Beside the Pxis promoter, upstream regions of four additional SGI1 genes, S004, S005, S012 and S018, also contain putative AcaCD-binding sites. Furthermore, SGI1 also encodes an AcaCD-related activator, FlhDCSGI1, which has no known function. Here, we have analysed the functionality of the putative AcaCD-dependent promoter regions and proved their activation by either AcaCD or FlhDCSGI1. Moreover, we provide evidence that both activators act on the same binding site in Pxis and that FlhDCSGI1 is able to complement the acaCD deletion of the IncA/C family plasmid R16a. We determined the transcription start sites for the AcaCD-responsive promoters and showed that orf S004 is expressed probably from a different start codon than predicted earlier. Additionally, expression of S003 from promoter PS004 was ruled out. Pxis and the four SGI1 promoters examined here also lack obvious -35 promoter box and their promoter profile is consistent with the class II-type activation pathway. Although the role of the four additionally analysed AcaCD/FlhDCSGI1-controlled genes in transfer and/or maintenance of SGI1 is not yet clear, the conservation of the whole region suggests the existence of some selection for their functionality. PMID:27727307

  14. Putative molecular mechanism underlying sperm chromatin remodelling is regulated by reproductive hormones

    Directory of Open Access Journals (Sweden)

    Gill-Sharma Manjeet Kaur

    2012-12-01

    Full Text Available Abstract Background The putative regulatory role of the male reproductive hormones in the molecular mechanism underlying chromatin condensation remains poorly understood. In the past decade, we developed two adult male rat models wherein functional deficits of testosterone or FSH, produced after treatments with 20 mg/Kg/d of cyproterone acetate (CPA per os, for a period of 15 days or 3 mg/Kg/d of fluphenazine decanoate (FD subcutaneously, for a period of 60 days, respectively, affected the rate of sperm chromatin decondensation in vitro. These rat models have been used in the current study in order to delineate the putative roles of testosterone and FSH in the molecular mechanism underlying remodelling of sperm chromatin. Results We report that deficits of both testosterone and FSH affected the turnover of polyubiquitylated histones and led to their accumulation in the testis. Functional deficits of testosterone reduced expression of MIWI, the 5-methyl cap binding RNA-binding protein (PIWIlike murine homologue of the Drosophila protein PIWI/P-element induced wimpy testis containing a PAZ/Piwi-Argonaut-Zwille domain and levels of histone deacetylase1 (HDAC1, ubiquitin ligating enzyme (URE-B1/E3, 20S proteasome α1 concomitant with reduced expression of ubiquitin activating enzyme (ube1, conjugating enzyme (ube2d2, chromodomain Y like protein (cdyl, bromodomain testis specific protein (brdt, hdac6 (histone deacetylase6, androgen-dependent homeobox placentae embryonic protein (pem/RhoX5, histones h2b and th3 (testis-specific h3. Functional deficits of FSH reduced the expression of cdyl and brdt genes in the testis, affected turnover of ubiquitylated histones, stalled the physiological DNA repair mechanism and culminated in spermiation of DNA damaged sperm. Conclusions We aver that deficits of both testosterone and FSH differentially affected the process of sperm chromatin remodelling through subtle changes in the ‘chromatin condensation

  15. Localization and transcriptional responses of Chrysoporthe austroafricana in Eucalyptus grandis identify putative pathogenicity factors

    Directory of Open Access Journals (Sweden)

    Ronishree Mangwanda

    2016-12-01

    Full Text Available Chrysoporthe austroafricana is a fungal pathogen that causes the development of stem cankers on susceptible Eucalyptus grandis trees. Clones of E. grandis that are partially resistant and highly susceptible have been identified based on the extent of lesion formation on the stem upon inoculation with C. austroafricana. These interactions have been used as a model pathosystem to enhance our understanding of interactions between pathogenic fungi and woody hosts, which may be different to herbaceous hosts. In previous research, transcriptomics of host responses in these two clones to C. austroafricana suggested roles for salicylic acid and gibberellic acid phytohormone signalling in defense. However, it is unclear how the pathogen infiltrates host tissue and which pathogenicity factors facilitate its spread in the two host genotypes. The aim of this study was to investigate these two aspects of the E. grandis-C. austroafricana interaction and to test the hypothesis that the pathogen possesses mechanisms to modulate the tree phytohormone-mediated defenses. Light microscopy showed that the pathogen occurred in most cell types and structures within infected E. grandis stem tissue. Notably, the fungus appeared to spread through the stem by penetrating cell wall pits. In order to understand the molecular interaction between these organisms and predict putative pathogenicity mechanisms of C. austroafricana, fungal gene expression was studied in vitro and in planta. Fungal genes associated with cell wall degradation, carbohydrate metabolism and phytohormone manipulation were expressed in planta by C. austroafricana. These genes could be involved in fungal spread by facilitating cell wall pit degradation and manipulating phytohormone mediated defense in each host environment, respectively. Specifically, the in planta expression of an ent-kaurene oxidase and salicylate hydroxylase in C. austroafricana suggests putative mechanisms by which the pathogen can

  16. 42 CFR 102.44 - Representatives of requesters.

    Science.gov (United States)

    2010-10-01

    ... COMPENSATION PROGRAM Procedures for Filing Request Packages § 102.44 Representatives of requesters. (a) Persons other than a requester (e.g., a lawyer, guardian, friend) may file a Request Package on a requester's behalf as his or her representative. A requester need not use the services of a lawyer to secure benefits...

  17. A geometric language for representing structure in polyphonic music

    DEFF Research Database (Denmark)

    Meredith, David

    2012-01-01

    is represented as a set of multidimensional points, generated by performing transformations on component patterns. The language introduces the concept of a periodic mask, a generalisation of Deutsch and Feroe’s notion of a pitch alphabet, that can be applied to any dimension of a geometric representation......, allowing for both rhythms and pitch collections to be represented parsimoniously in a uniform way....

  18. 16 CFR 460.6 - “Representative thickness” testing.

    Science.gov (United States)

    2010-01-01

    ... 16 Commercial Practices 1 2010-01-01 2010-01-01 false âRepresentative thicknessâ testing. 460.6 Section 460.6 Commercial Practices FEDERAL TRADE COMMISSION TRADE REGULATION RULES LABELING AND ADVERTISING OF HOME INSULATION § 460.6 “Representative thickness” testing. All tests except aluminum...

  19. State Tax Capacity and the Representative Tax System.

    Science.gov (United States)

    Lucke, Robert B.

    1984-01-01

    Discusses the merit of using the Representative Tax System to measure state fiscal capacity instead of the traditional measure of per capita income. The conclusion is that the Representative Tax System can play a major role in determining the allocation of federal grants. (MJL)

  20. 20 CFR 725.363 - Qualification of representative.

    Science.gov (United States)

    2010-04-01

    ... 20 Employees' Benefits 3 2010-04-01 2010-04-01 false Qualification of representative. 725.363... MINE HEALTH AND SAFETY ACT OF 1969, AS AMENDED CLAIMS FOR BENEFITS UNDER PART C OF TITLE IV OF THE....363 Qualification of representative. (a) Attorney. Any attorney in good standing who is admitted...

  1. Calls to Teen Line: Representative Concerns of Adolescents.

    Science.gov (United States)

    Boehm, Kathryn E.; Schondel, Connie K.; Ivoska, William J.; Marlowe, Alison L.; Manke-Mitchell, Laurie

    1998-01-01

    Study examines whether the concerns of teenagers calling a peer listening service are representative of the concerns of teenagers in the area served. Results indicate that students' biggest concerns involve family problems, peer relationships, self-esteem, and school problems. Concludes that calls to the teen line are representative. (Author/GCP)

  2. 40 CFR Appendix I to Part 261 - Representative Sampling Methods

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 25 2010-07-01 2010-07-01 false Representative Sampling Methods I...—Representative Sampling Methods The methods and equipment used for sampling waste materials will vary with the form and consistency of the waste materials to be sampled. Samples collected using the...

  3. Dontion From CCPIT Overseas Representative Offices To Earthquake

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    @@After the strong earthquake centered in Wenchuan County in the Southwestern Chinese Sichuan Province took place,the CCPIT Overseas Representative Offices immediately responding to the call of the CPC Central Committee,the State Council and following the instruction of CCPIT concerning disaster relief work,vigororsly organized.Below are the statistics of donation from partial overseas representative offices by May 19.

  4. 20 CFR 211.5 - Employee representative compensation.

    Science.gov (United States)

    2010-04-01

    ... 20 Employees' Benefits 1 2010-04-01 2010-04-01 false Employee representative compensation. 211.5... CREDITABLE RAILROAD COMPENSATION § 211.5 Employee representative compensation. All payments made by a railway... office he occupies with such organization are creditable as compensation, including payments made...

  5. 37 CFR 10.84 - Representing a client zealously.

    Science.gov (United States)

    2010-07-01

    ... 37 Patents, Trademarks, and Copyrights 1 2010-07-01 2010-07-01 false Representing a client... Office Code of Professional Responsibility § 10.84 Representing a client zealously. (a) A practitioner shall not intentionally: (1) Fail to seek the lawful objectives of a client through reasonably available...

  6. 37 CFR 1.34 - Acting in a representative capacity.

    Science.gov (United States)

    2010-07-01

    ... capacity. 1.34 Section 1.34 Patents, Trademarks, and Copyrights UNITED STATES PATENT AND TRADEMARK OFFICE... of Application and Appointment of Attorney Or Agent § 1.34 Acting in a representative capacity. When a patent practitioner acting in a representative capacity appears in person or signs a paper...

  7. 14 CFR 183.31 - Designated manufacturing inspection representatives.

    Science.gov (United States)

    2010-01-01

    ... 14 Aeronautics and Space 3 2010-01-01 2010-01-01 false Designated manufacturing inspection representatives. 183.31 Section 183.31 Aeronautics and Space FEDERAL AVIATION ADMINISTRATION, DEPARTMENT OF...: Privileges § 183.31 Designated manufacturing inspection representatives. A designated...

  8. 22 CFR 41.25 - NATO representatives, officials, and employees.

    Science.gov (United States)

    2010-04-01

    ... 22 Foreign Relations 1 2010-04-01 2010-04-01 false NATO representatives, officials, and employees... UNDER THE IMMIGRATION AND NATIONALITY ACT, AS AMENDED Foreign Government Officials § 41.25 NATO representatives, officials, and employees. (a) Classification. An alien shall be classified under the symbol...

  9. Family representative payeeship and violence risk in severe mental illness.

    Science.gov (United States)

    Elbogen, Eric B; Swanson, Jeffrey W; Swartz, Marvin S; Van Dorn, Richard

    2005-10-01

    Although representative payeeship is prevalent among people with mental illness and shows promise to positively influence clinically relevant outcomes, research also suggests this legal mechanism could be implemented in ways that are problematic. The current study examined whether family representative payeeship was associated with elevated risk of family violence perpetrated by persons with severe mental illness (SMI). Data were collected every 4 months for 1 year in structured interviews with N = 245 persons with SMI who received disability benefits. Multivariate analyses showed that substance abuse, history of violence, frequency of family contact, and family representative payeeship were associated with elevated odds of family violence. Analyses also showed family contact and family representative payeeship had a cumulative effect on increasing the predicted probability of family violence (controlling for covariates such as violence history and substance abuse). The data shed light on the potential for family representative payeeship to be associated with increased risk of interpersonal conflict and violence in SMI.

  10. Genome sequencing and analysis of Salmonella enterica serovar Typhi strain CR0063 representing a carrier individual during an outbreak of typhoid fever in Kelantan, Malaysia

    Directory of Open Access Journals (Sweden)

    Baddam Ramani

    2012-12-01

    Full Text Available Abstract Salmonella Typhi is a human restricted pathogen with a significant number of individuals as asymptomatic carriers of the bacterium. Salmonella infection can be effectively controlled if a reliable method for identification of these carriers is developed. In this context, the availability of whole genomes of carrier strains through high- throughput sequencing and further downstream analysis by comparative genomics approaches is very promising. Herein we describe the genome sequence of a Salmonella Typhi isolate representing an asymptomatic carrier individual during a prolonged outbreak of typhoid fever in Kelantan, Malaysia. Putative genomic coordinates relevant in pathogenesis and persistence of this carrier strain are identified and discussed.

  11. Genome sequencing and analysis of Salmonella enterica serovar Typhi strain CR0063 representing a carrier individual during an outbreak of typhoid fever in Kelantan, Malaysia.

    Science.gov (United States)

    Baddam, Ramani; Kumar, Narender; Shaik, Sabiha; Suma, Tiruvayipati; Ngoi, Soo Tein; Thong, Kwai-Lin; Ahmed, Niyaz

    2012-12-13

    Salmonella Typhi is a human restricted pathogen with a significant number of individuals as asymptomatic carriers of the bacterium. Salmonella infection can be effectively controlled if a reliable method for identification of these carriers is developed. In this context, the availability of whole genomes of carrier strains through high- throughput sequencing and further downstream analysis by comparative genomics approaches is very promising. Herein we describe the genome sequence of a Salmonella Typhi isolate representing an asymptomatic carrier individual during a prolonged outbreak of typhoid fever in Kelantan, Malaysia. Putative genomic coordinates relevant in pathogenesis and persistence of this carrier strain are identified and discussed.

  12. Flucloxacillin, still the empirical choice for putative Staphylococcus aureus infections in intensive care units in the Netherlands.

    NARCIS (Netherlands)

    Rijnders, M.I.; Deurenberg, R.H.; Boumans, M.L.; Hoogkamp-Korstanje, J.A.A.; Beisser, P.S.; Stobberingh, E.E.

    2009-01-01

    OBJECTIVES: To determine the usefulness of flucloxacillin as empirical therapy for putative Staphylococcus aureus infections in intensive care unit (ICU) patients in the Netherlands, the antibiotic resistance of S. aureus isolates from ICUs over a 13 year period was investigated. METHODS: From 1996

  13. Potential role of transient receptor potential channel M5 in sensing putative pheromones in mouse olfactory sensory neurons.

    Science.gov (United States)

    Oshimoto, Arisa; Wakabayashi, Yoshihiro; Garske, Anna; Lopez, Roberto; Rolen, Shane; Flowers, Michael; Arevalo, Nicole; Restrepo, Diego

    2013-01-01

    Based on pharmacological studies of chemosensory transduction in transient receptor potential channel M5 (TRPM5) knockout mice it was hypothesized that this channel is involved in transduction for a subset of putative pheromones in mouse olfactory sensory neurons (OSNs). Yet, in the same study an electroolfactogram (EOG) in the mouse olfactory epithelium showed no significant difference in the responses to pheromones (and odors) between wild type and TRPM5 knockout mice. Here we show that the number of OSNs expressing TRPM5 is increased by unilateral naris occlusion. Importantly, EOG experiments show that mice lacking TRPM5 show a decreased response in the occluded epithelia to putative pheromones as opposed to wild type mice that show no change upon unilateral naris occlusion. This evidence indicates that under decreased olfactory sensory input TRPM5 plays a role in mediating putative pheromone transduction. Furthermore, we demonstrate that cyclic nucleotide gated channel A2 knockout (CNGA2-KO) mice that show substantially decreased or absent responses to odors and pheromones also have elevated levels of TRPM5 compared to wild type mice. Taken together, our evidence suggests that TRPM5 plays a role in mediating transduction for putative pheromones under conditions of reduced chemosensory input.

  14. A Synthetic Peptide with the Putative Iron Binding Motif of Amyloid Precursor Protein (APP) Does Not Catalytically Oxidize Iron

    NARCIS (Netherlands)

    Honarmand Ebrahimi, K.; Hagedoorn, P.L.; Hagen, W.R.

    2012-01-01

    The β-amyloid precursor protein (APP), which is a key player in Alzheimer's disease, was recently reported to possess an Fe(II) binding site within its E2 domain which exhibits ferroxidase activity [Duce et al. 2010, Cell 142: 857]. The putative ligands of this site were compared to those in the fer

  15. Enhancement of Cry19Aa Mosquitocidal Activity against Aedes aegypti by Mutations in the Putative Loop Regions of Domain II

    OpenAIRE

    Abdullah, Mohd Amir F.; Donald H Dean

    2004-01-01

    Improvements in the mosquitocidal activity of Bacillus thuringiensis Cry19Aa were achieved by protein engineering of putative surface loop residues in domain II through rational design. The improvement of Aedes toxicity in Cry19Aa was 42,000-fold and did not affect its toxicity against Anopheles or Culex.

  16. Evidence for Conformational Protection of Nitrogenase against Oxygen in Gluconacetobacter diazotrophicus by a Putative FeSII Protein

    OpenAIRE

    Ureta, Alejandro; Nordlund, Stefan

    2002-01-01

    The mechanisms protecting nitrogenase in Gluconacetobacter diazotrophicus from damage by oxygen were studied. Evidence is provided suggesting that in G. diazotrophicus these mechanisms include respiratory protection as well as conformational protection in which a putative FeSII Shethna protein is involved.

  17. Evidence for conformational protection of nitrogenase against oxygen in Gluconacetobacter diazotrophicus by a putative FeSII protein.

    Science.gov (United States)

    Ureta, Alejandro; Nordlund, Stefan

    2002-10-01

    The mechanisms protecting nitrogenase in Gluconacetobacter diazotrophicus from damage by oxygen were studied. Evidence is provided suggesting that in G. diazotrophicus these mechanisms include respiratory protection as well as conformational protection in which a putative FeSII Shethna protein is involved.

  18. Machine learning techniques to identify putative genes involved in nitrogen catabolite repression in the yeast Saccharomyces cerevisiae

    Science.gov (United States)

    Kontos, Kevin; Godard, Patrice; André, Bruno; van Helden, Jacques; Bontempi, Gianluca

    2008-01-01

    Background Nitrogen is an essential nutrient for all life forms. Like most unicellular organisms, the yeast Saccharomyces cerevisiae transports and catabolizes good nitrogen sources in preference to poor ones. Nitrogen catabolite repression (NCR) refers to this selection mechanism. All known nitrogen catabolite pathways are regulated by four regulators. The ultimate goal is to infer the complete nitrogen catabolite pathways. Bioinformatics approaches offer the possibility to identify putative NCR genes and to discard uninteresting genes. Results We present a machine learning approach where the identification of putative NCR genes in the yeast Saccharomyces cerevisiae is formulated as a supervised two-class classification problem. Classifiers predict whether genes are NCR-sensitive or not from a large number of variables related to the GATA motif in the upstream non-coding sequences of the genes. The positive and negative training sets are composed of annotated NCR genes and manually-selected genes known to be insensitive to NCR, respectively. Different classifiers and variable selection methods are compared. We show that all classifiers make significant and biologically valid predictions by comparing these predictions to annotated and putative NCR genes, and by performing several negative controls. In particular, the inferred NCR genes significantly overlap with putative NCR genes identified in three genome-wide experimental and bioinformatics studies. Conclusion These results suggest that our approach can successfully identify potential NCR genes. Hence, the dimensionality of the problem of identifying all genes involved in NCR is drastically reduced. PMID:19091052

  19. A systematic review of amyloid-beta peptides as putative mediators of the association between affective disorders and Alzheimer's disease

    DEFF Research Database (Denmark)

    Abbasowa, L.; Heegaard, N. H. H.

    2014-01-01

    Background: Affective disorders are associated with an increased occurrence of cognitive deficits and have been linked to cognitive impairment and Alzheimer's disease. The putative molecular mechanisms involved in these associations are however not clear. The aim of this systematic review was to ...

  20. PUTATIVE CREATINE KINASE M-ISOFORM IN HUMAN SPERM IS IDENTIFIED AS THE 70-KILODALTON HEAT SHOCK PROTEIN HSPA2

    Science.gov (United States)

    THE PUTATIVE CREATINE KINASE M-ISOFORM IN HUMAN SPERM IS IDENTIFIED AS THE 70 kDa HEAT SHOCK PROTEIN HSPA2* Gabor Huszar1, Kathryn Stone2, David Dix3 and Lynne Vigue11The Sperm Physiology Laboratory, Department of Obstetrics and Gynecology, 2 W.M. Keck Foundatio...

  1. Promoter activity of a putative pollen monosaccharide transporter in Petunia hybrida and characterisation of a transposon insertion mutant

    NARCIS (Netherlands)

    Garrido, D.; Busscher-Lange, J.; Tunen, van A.J.

    2006-01-01

    For the growth of the male reproductive cells of plants, the pollen, the presence of sufficient sucrose or monosaccharides is of vital importance. From Petunia hybrida a pollen-specific putative monosaccharide transporter designated PMT1 (for petunia monosaccharide transporter) has been identified p

  2. Complete Genome Sequence of the Filamentous Fungus Aspergillus westerdijkiae Reveals the Putative Biosynthetic Gene Cluster of Ochratoxin A

    Science.gov (United States)

    Chakrabortti, Alolika; Li, Jinming

    2016-01-01

    Ochratoxin A (OTA) is a common mycotoxin that contaminates food and agricultural products. Sequencing of the complete genome of Aspergillus westerdijkiae, a major producer of OTA, reveals more than 50 biosynthetic gene clusters, including a putative OTA biosynthetic gene cluster that encodes a dozen of enzymes, transporters, and regulatory proteins. PMID:27635003

  3. Identification of Putative Molecular Markers Associated with Root Traits in Coffea canephora Pierre ex Froehner

    Directory of Open Access Journals (Sweden)

    Devaraja Achar

    2015-01-01

    Full Text Available Coffea canephora exhibit poor root system and are very sensitive to drought stress that affects growth and production. Deeper root system has been largely empirical as better avoidance to soil water limitation in drought condition. The present study aimed to identify molecular markers linked to high root types in Coffea canephora using molecular markers. Contrasting parents, L1 valley with low root and S.3334 with high root type, were crossed, and 134 F1 individuals were phenotyped for root and associated physiological traits (29 traits and genotyped with 41 of the 320 RAPD and 9 of the 55 SSR polymorphic primers. Single marker analysis was deployed for detecting the association of markers linked to root associated traits by SAS software. There were 13 putative RAPD markers associated with root traits such as root length, secondary roots, root dry weight, and root to shoot ratio, in which root length associated marker OPS1850 showed high phenotypic variance of 6.86%. Two microsatellite markers linked to root length (CPCM13400 and root to shoot ratio (CM211300. Besides, 25 markers were associated with more than one trait and few of the markers were associated with positively related physiological traits and can be used in marker assisted trait selection.

  4. Telocytes and putative stem cells in the lungs: electron microscopy, electron tomography and laser scanning microscopy.

    Science.gov (United States)

    Popescu, Laurentiu M; Gherghiceanu, Mihaela; Suciu, Laura C; Manole, Catalin G; Hinescu, Mihail E

    2011-09-01

    This study describes a novel type of interstitial (stromal) cell - telocytes (TCs) - in the human and mouse respiratory tree (terminal and respiratory bronchioles, as well as alveolar ducts). TCs have recently been described in pleura, epicardium, myocardium, endocardium, intestine, uterus, pancreas, mammary gland, etc. (see www.telocytes.com ). TCs are cells with specific prolongations called telopodes (Tp), frequently two to three per cell. Tp are very long prolongations (tens up to hundreds of μm) built of alternating thin segments known as podomers (≤ 200 nm, below the resolving power of light microscope) and dilated segments called podoms, which accommodate mitochondria, rough endoplasmic reticulum and caveolae. Tp ramify dichotomously, making a 3-dimensional network with complex homo- and heterocellular junctions. Confocal microscopy reveals that TCs are c-kit- and CD34-positive. Tp release shed vesicles or exosomes, sending macromolecular signals to neighboring cells and eventually modifying their transcriptional activity. At bronchoalveolar junctions, TCs have been observed in close association with putative stem cells (SCs) in the subepithelial stroma. SCs are recognized by their ultrastructure and Sca-1 positivity. Tp surround SCs, forming complex TC-SC niches (TC-SCNs). Electron tomography allows the identification of bridging nanostructures, which connect Tp with SCs. In conclusion, this study shows the presence of TCs in lungs and identifies a TC-SC tandem in subepithelial niches of the bronchiolar tree. In TC-SCNs, the synergy of TCs and SCs may be based on nanocontacts and shed vesicles.

  5. Evidence for positive selection in putative virulence factors within the Paracoccidioides brasiliensis species complex.

    Directory of Open Access Journals (Sweden)

    Daniel R Matute

    Full Text Available Paracoccidioides brasiliensis is a dimorphic fungus that is the causative agent of paracoccidioidomycosis, the most important prevalent systemic mycosis in Latin America. Recently, the existence of three genetically isolated groups in P. brasiliensis was demonstrated, enabling comparative studies of molecular evolution among P. brasiliensis lineages. Thirty-two gene sequences coding for putative virulence factors were analyzed to determine whether they were under positive selection. Our maximum likelihood-based approach yielded evidence for selection in 12 genes that are involved in different cellular processes. An in-depth analysis of four of these genes showed them to be either antigenic or involved in pathogenesis. Here, we present evidence indicating that several replacement mutations in gp43 are under positive balancing selection. The other three genes (fks, cdc42 and p27 show very little variation among the P. brasiliensis lineages and appear to be under positive directional selection. Our results are consistent with the more general observations that selective constraints are variable across the genome, and that even in the genes under positive selection, only a few sites are altered. We present our results within an evolutionary framework that may be applicable for studying adaptation and pathogenesis in P. brasiliensis and other pathogenic fungi.

  6. Dengue Virus Infection of Aedes aegypti Requires a Putative Cysteine Rich Venom Protein.

    Directory of Open Access Journals (Sweden)

    Berlin Londono-Renteria

    2015-10-01

    Full Text Available Dengue virus (DENV is a mosquito-borne flavivirus that causes serious human disease and mortality worldwide. There is no specific antiviral therapy or vaccine for DENV infection. Alterations in gene expression during DENV infection of the mosquito and the impact of these changes on virus infection are important events to investigate in hopes of creating new treatments and vaccines. We previously identified 203 genes that were ≥5-fold differentially upregulated during flavivirus infection of the mosquito. Here, we examined the impact of silencing 100 of the most highly upregulated gene targets on DENV infection in its mosquito vector. We identified 20 genes that reduced DENV infection by at least 60% when silenced. We focused on one gene, a putative cysteine rich venom protein (SeqID AAEL000379; CRVP379, whose silencing significantly reduced DENV infection in Aedes aegypti cells. Here, we examine the requirement for CRVP379 during DENV infection of the mosquito and investigate the mechanisms surrounding this phenomenon. We also show that blocking CRVP379 protein with either RNAi or specific antisera inhibits DENV infection in Aedes aegypti. This work identifies a novel mosquito gene target for controlling DENV infection in mosquitoes that may also be used to develop broad preventative and therapeutic measures for multiple flaviviruses.

  7. Dengue Virus Infection of Aedes aegypti Requires a Putative Cysteine Rich Venom Protein.

    Science.gov (United States)

    Londono-Renteria, Berlin; Troupin, Andrea; Conway, Michael J; Vesely, Diana; Ledizet, Michael; Roundy, Christopher M; Cloherty, Erin; Jameson, Samuel; Vanlandingham, Dana; Higgs, Stephen; Fikrig, Erol; Colpitts, Tonya M

    2015-10-01

    Dengue virus (DENV) is a mosquito-borne flavivirus that causes serious human disease and mortality worldwide. There is no specific antiviral therapy or vaccine for DENV infection. Alterations in gene expression during DENV infection of the mosquito and the impact of these changes on virus infection are important events to investigate in hopes of creating new treatments and vaccines. We previously identified 203 genes that were ≥5-fold differentially upregulated during flavivirus infection of the mosquito. Here, we examined the impact of silencing 100 of the most highly upregulated gene targets on DENV infection in its mosquito vector. We identified 20 genes that reduced DENV infection by at least 60% when silenced. We focused on one gene, a putative cysteine rich venom protein (SeqID AAEL000379; CRVP379), whose silencing significantly reduced DENV infection in Aedes aegypti cells. Here, we examine the requirement for CRVP379 during DENV infection of the mosquito and investigate the mechanisms surrounding this phenomenon. We also show that blocking CRVP379 protein with either RNAi or specific antisera inhibits DENV infection in Aedes aegypti. This work identifies a novel mosquito gene target for controlling DENV infection in mosquitoes that may also be used to develop broad preventative and therapeutic measures for multiple flaviviruses.

  8. Exploring associations between gaze patterns and putative human mirror neuron system activity

    Directory of Open Access Journals (Sweden)

    Peter Hugh Donaldson

    2015-07-01

    Full Text Available The human mirror neuron system (MNS is hypothesised to be crucial to social cognition. Given that key MNS-input regions such as the superior temporal sulcus are involved in biological motion processing, and mirror neuron activity in monkeys has been shown to vary with visual attention, aberrant MNS function may be partly attributable to atypical visual input. To examine the relationship between gaze pattern and interpersonal motor resonance (IMR; an index of putative MNS activity, healthy right-handed participants aged 18-40 (n = 26 viewed videos of transitive grasping actions or static hands, whilst the left primary motor cortex received transcranial magnetic stimulation (TMS. Motor-evoked potentials (MEPs recorded in contralateral hand muscles were used to determine IMR. Participants also underwent eyetracking analysis to assess gaze patterns whilst viewing the same videos. No relationship was observed between predictive gaze (PG and IMR. However, IMR was positively associated with fixation counts in areas of biological motion in the videos, and negatively associated with object areas. These findings are discussed with reference to visual influences on the MNS, and the possibility that MNS atypicalities might be influenced by visual processes such as aberrant gaze pattern.

  9. Structure and Expression of Several Putative Cdc42-Interacting Proteins in Magnaporthe grisea

    Institute of Scientific and Technical Information of China (English)

    ZHENG Wu; CHEN Ji-sheng; ZHENG Shi-qin; LU Guo-dong; WANG Zong-hua

    2006-01-01

    MgCdc42 (Cdc42 in Magnaporthe grisea), with high homology to ScCdc42 (Cdc42 in Saccharomyces cerevisiae), has been demonstrated to involve in the morphogenesis and infection process. To further understand the signaling network,the putative MgCdc42-interacting proteins were analyzed. ScCdc42-interacting protein sequences were first used to BLAST against the M. grisea genome database to retrieve their corresponding analogs. Subsequently, conserved domains of these proteins were compared and expression patterns of their encoding genes in different MgCdc42 mutation states were analyzed by semiquantitative RT-PCR. All retrieved analogs of ScCdc42-interacting proteins from the M.grisea database have conserved domains as those in S. cerevisiae. Expression of their encoding genes increased in MgCdc42CA mutant and decreased in MgCdc42KO mutant. However, MgBem1, Chm1, and MgGic1 in MgCdc42DN mutant had the same expression level as that in the wild type, although MgBem4, MgBoi2, MgCdc24, MgGic2, MgRga1,and Mst20 had decreased expression level, as expected. Overall, it is concluded that there may exist a similar Cdc42 signal pathway in M. grisea as in S. cerevisiae and MgCdc42 plays a key role in the pathway.

  10. Identification of salt-inducible peptide with putative kinase activity in halophilic bacterium Virgibacillus halodenitrificans.

    Science.gov (United States)

    Rafiee, Mahmoud-Reza; Sokhansanj, Ashrafaddin; Yoosefi, Mitra; Naghizadeh, Mohammad-Ali

    2007-09-01

    Strain XII, a moderately halophilic bacterium, expressed a peptide in response to saline media. This peptide was designated as salt-inducible factor (Sif-A). The purpose of this study is to describe Sif-A, which might be involved in the osmoresistance mechanism of strain XII. The complete sequence of sif-A was determined using PCR. sif-A codes for a polypeptide of 20.518 kDa. The polypeptide has a putative signal peptide of 27 amino acids (2.667 kDa) preceding the mature protein (17.869 kDa). Motif analysis of the deduced amino acid sequence indicated that there is a p-loop NTPase domain on the C-terminal of the peptide, which might correlate with its function. The sequence of the 16S rRNA gene was analyzed phylogenetically to classify strain XII. This organism was found to have the closest association with Virgibacillus halodenitrificans, which was proven by its phenotypic characteristics.

  11. Structural Analysis of a Putative Aminoglycoside N-Acetyltransferase from Bacillus anthracis

    Energy Technology Data Exchange (ETDEWEB)

    Klimecka, Maria M.; Chruszcz, Maksymilian; Font, Jose; Skarina, Tatiana; Shumilin, Igor; Onopryienko, Olena; Porebski, Przemyslaw J.; Cymborowski, Marcin; Zimmerman, Matthew D.; Hasseman, Jeremy; Glomski, Ian J.; Lebioda, Lukasz; Savchenko, Alexei; Edwards, Aled; Minor, Wladek (SC); (Toronto); (UV)

    2012-02-15

    For the last decade, worldwide efforts for the treatment of anthrax infection have focused on developing effective vaccines. Patients that are already infected are still treated traditionally using different types of standard antimicrobial agents. The most popular are antibiotics such as tetracyclines and fluoroquinolones. While aminoglycosides appear to be less effective antimicrobial agents than other antibiotics, synthetic aminoglycosides have been shown to act as potent inhibitors of anthrax lethal factor and may have potential application as antitoxins. Here, we present a structural analysis of the BA2930 protein, a putative aminoglycoside acetyltransferase, which may be a component of the bacterium's aminoglycoside resistance mechanism. The determined structures revealed details of a fold characteristic only for one other protein structure in the Protein Data Bank, namely, YokD from Bacillus subtilis. Both BA2930 and YokD are members of the Antibiotic-NAT superfamily (PF02522). Sequential and structural analyses showed that residues conserved throughout the Antibiotic-NAT superfamily are responsible for the binding of the cofactor acetyl coenzyme A. The interaction of BA2930 with cofactors was characterized by both crystallographic and binding studies.

  12. Screening and identification of putative allergens in berry fruits of the Rosaceae family: technical challenges.

    Science.gov (United States)

    Marzban, Gorji; Maghuly, Fatemeh; Herndl, Anita; Katinger, Hermann; Laimer, Margit

    2008-01-01

    Cross-reactive proteins in small fruits of the Rosaceae family like strawberry, raspberry and blackberry revealed an unexpected complex IgE-reactivity pattern. Several copies of PR-10 and PR-14 proteins were detected by Southern blots in strawberry, raspberry and blackberry. In raspberry, the highest similarity at the DNA level for PR-10 and PR-14 (Rub i 1 and Rub i 3) was detected to strawberry sequences of Fra a 1 and Fra a 3. At the protein level, Rub i 1 and Rub i 3 showed more than 70% identity with homologous proteins of rosaceous fruits. Furthermore, raspberries contained additional putative allergens, e.g. class III acidic chitinases and cyclophilins. Blackberries were shown to share at least two well-known major fruit allergens with other rosaceous fruits, namely PR-10s and PR-14s homologous proteins. However the IgE-reactive proteins of small fruits are still not extensively investigated. The main challenges in studying small fruit allergens are the complexity of the fruit matrix, the diversity of physico-chemical properties of fruit proteins, the lack of appropriate protein extraction procedures and the missing information about the influence of processing treatments on food components.

  13. New approaches to visual rehabilitation for cortical blindness: outcomes and putative mechanisms.

    Science.gov (United States)

    Das, Anasuya; Huxlin, Krystel R

    2010-08-01

    Cortical blindness is a chronic loss of vision following damage to the primary visual cortex (V1) or its postchiasmal afferents. Such damage is followed by a brief period of spontaneous plasticity that rarely lasts beyond 6 months. Following this initial phase, the visual deficit is thought to be stable, intractable, and permanent. Cortically blind subjects demonstrate spontaneous oculomotor adaptations to their deficits that can be further improved by saccadic localization training. However, saccadic training does not improve visual sensitivity in the blind field. In contrast, recent studies by a number of independent groups suggest that localized, repetitive perceptual training can improve visual sensitivity in the blind field, although mechanisms underlying the observed recovery remain unclear. This review discusses the current literature on rehabilitative strategies used for cortical blindness with emphasis on the use of perceptual training methods. The putative mechanisms that underlie the resulting, training-induced visual improvements are then outlined, along with the special challenges posed to their elucidation by the great variability in the extent and sometimes nature of the V1 damage sustained in different individuals.

  14. Putative Structural and Functional Coupling of the Mitochondrial BKCa Channel to the Respiratory Chain.

    Directory of Open Access Journals (Sweden)

    Piotr Bednarczyk

    Full Text Available Potassium channels have been found in the inner mitochondrial membranes of various cells. These channels regulate the mitochondrial membrane potential, the matrix volume and respiration. The activation of these channels is cytoprotective. In our study, the single-channel activity of a large-conductance Ca(2+-regulated potassium channel (mitoBKCa channel was measured by patch-clamping mitoplasts isolated from the human astrocytoma (glioblastoma U-87 MG cell line. A potassium-selective current was recorded with a mean conductance of 290 pS in symmetrical 150 mM KCl solution. The channel was activated by Ca(2+ at micromolar concentrations and by the potassium channel opener NS1619. The channel was inhibited by paxilline and iberiotoxin, known inhibitors of BKCa channels. Western blot analysis, immuno-gold electron microscopy, high-resolution immunofluorescence assays and polymerase chain reaction demonstrated the presence of the BKCa channel β4 subunit in the inner mitochondrial membrane of the human astrocytoma cells. We showed that substrates of the respiratory chain, such as NADH, succinate, and glutamate/malate, decrease the activity of the channel at positive voltages. This effect was abolished by rotenone, antimycin and cyanide, inhibitors of the respiratory chain. The putative interaction of the β4 subunit of mitoBKCa with cytochrome c oxidase was demonstrated using blue native electrophoresis. Our findings indicate possible structural and functional coupling of the mitoBKCa channel with the mitochondrial respiratory chain in human astrocytoma U-87 MG cells.

  15. Pharmacodynamics of S-dimethylarsino-glutathione, a putative metabolic intermediate of inorganic arsenic, in mice.

    Science.gov (United States)

    Kato, Ayaka; Kobayashi, Yayoi; Udagawa, Osamu; Hirano, Seishiro

    2017-02-15

    Inorganic arsenicals are well-known carcinogens, whereas arsenite (iAs(III)) compounds are now recognized as potent therapeutic agents for several leukemias, and arsenic trioxide has been used for the treatment of recurrent acute promyelocytic leukemia (APL). However, recent clinical trials revealed that arsenite is not always effective for non-APL malignancies. Another arsenical, S-dimethylarsino-glutathione ([DMA(III)(GS)]), which is a putative metabolic intermediate in the hepatic metabolism of iAs(III), shows promise for treating several types of lymphoma. However, the metabolism of [DMA(III)(GS)] has not been well investigated, probably because [DMA(III)(GS)] is not stable in biological fluids where the concentration of glutathione is low. In the present study, we injected [DMA(III)(GS)] intravenously into mice and compared the tissue distribution and metabolic dynamics of [DMA(III)(GS)] with those of sodium arsenite (NaAsO2). We found a unique organ preference for the distribution of [DMA(III)(GS)] to the lung and brain in comparison to NaAsO2. Furthermore, [DMA(III)(GS)] appeared to bind to serum albumin by exchanging its glutathione moiety quickly after administration, providing novel insights into the longer retention of [DMA(III)(GS)] in plasma. Copyright © 2016 Elsevier Inc. All rights reserved.

  16. Insilico Analysis unveils Putative Metabolic Pathways and Essential Genes within Leishmania donovani ‘Orfeome’

    Directory of Open Access Journals (Sweden)

    Nithin eRavooru

    2014-08-01

    Full Text Available Leishmaniasis is a parasitic disease caused by the protozoan Leishmania, which is active in two broad forms namely, Visceral Leishmaniasis (VL or Kala Azar and Cutaneous Leishmaniasis (CL. The disease is most prevalent in the tropical regions and poses a threat to more than 70 countries across the globe. In the Indian subcontinent, about 200 million people are estimated to be at risk of developing VL and this area harbours an estimated 67% of the global VL disease burden. The state of Bihar alone has captured almost 50% of the total cases in the Indian region. While no vaccination exists, several pentavalent antimonials and drugs like Paromomycin, Amphotericin, Miltefosine etc., are used in the treatment of Leishmaniasis. However, due to low efficacy of these drugs and the resistance developed by the bug to these medications, there is an urgent need to look into species specific targets. The proteome information available suggests that among the 7960 proteins, a staggering 65% of it remains to be annotated with clarity.Hence, in the present study, we have demonstrated a protocol to integrate the seqeunce and functional information from various databases, such as GO, PFAM, KEGG, String DB, COG and DEG, to assign putative functions to many of the hypothetical seqeucences present in this proteome. These crucial information related to pathways and essential genes show promise for exploring the design strategies towards developing drugs, to tackle this notorious parasitic disease.

  17. Immunodiagnosis of Citrus leprosis virus C using a polyclonal antibody to an expressed putative coat protein.

    Science.gov (United States)

    Choudhary, Nandlal; Roy, Avijit; Guillermo, Leon M; Picton, D D; Wei, G; Nakhla, M K; Levy, L; Brlansky, R H

    2013-11-01

    Citrus leprosis virus C (CiLV-C), a causal agent for citrus leprosis disease, is present in South and Central America and is a threat for introduction into the U.S. citrus industry. A specific, inexpensive and reliable antibody based detection system is needed for the rapid identification of CiLV-C. The CiLV-C is very labile and has not been purified in sufficient amount for antibody production. The p29 gene of CiLV-C genome that codes for the putative coat protein (PCP) was codon optimized for expression in Escherichia coli and synthesized in vitro. The optimized gene was sub-cloned into the bacterial expression vector pDEST17 and transferred into E. coli BL21AI competent cells. The expression of PCP containing N-terminal His-tag was optimized by induction with l-arabinose. Induced cells were disrupted by sonication and expressed PCP was purified by affinity chromatography using Ni-NTA agarose. The purified expressed PCP was then used as an immunogen for injections into rabbits to produce polyclonal antibody (PAb). The PAb specific to the expressed PCP was identified using Western blotting. The antibody was successfully used to detect CiLV-C in the symptomatic CiLV-C infected tissues using double antibody sandwich-enzyme-linked-immunosorbent (DAS-ELISA), indirect ELISA and dot-blot immunoassay (DBIA) formats. Copyright © 2013 Elsevier B.V. All rights reserved.

  18. A putative transcription factor MYT1 is required for female fertility in the ascomycete Gibberella zeae.

    Directory of Open Access Journals (Sweden)

    Yang Lin

    Full Text Available Gibberella zeae is an important pathogen of major cereal crops. The fungus produces ascospores that forcibly discharge from mature fruiting bodies, which serve as the primary inocula for disease epidemics. In this study, we characterized an insertional mutant Z39P105 with a defect in sexual development and identified a gene encoding a putative transcription factor designated as MYT1. This gene contains a Myb DNA-binding domain and is conserved in the subphylum Pezizomycotina of Ascomycota. The MYT1 protein fused with green fluorescence protein localized in nuclei, which supports its role as a transcriptional regulator. The MYT1 deletion mutant showed similar phenotypes to the wild-type strain in vegetative growth, conidia production and germination, virulence, and mycotoxin production, but had defect in female fertility. A mutant overexpressing MYT1 showed earlier germination, faster mycelia growth, and reduced mycotoxin production compared to the wild-type strain, suggesting that improper MYT1 expression affects the expression of genes involved in the cell cycle and secondary metabolite production. This study is the first to characterize a transcription factor containing a Myb DNA-binding domain that is specific to sexual development in G. zeae.

  19. Mycobacterium tuberculosis Rv0198c, a putative matrix metalloprotease is involved in pathogenicity.

    Science.gov (United States)

    Muttucumaru, D G Niranjala; Smith, Debbie A; McMinn, Elizabeth J; Reese, Valerie; Coler, Rhea N; Parish, Tanya

    2011-03-01

    We are interested in the role of proteases in the biology of the global human pathogen, Mycobacterium tuberculosis. We have focused on a putative matrix metalloprotease, Rv0198c. In order to investigate its role we constructed an unmarked chromosomal deletion of the gene and analysed the phenotype of the resulting mutant. No differences in growth in axenic culture were seen and there was no measurable change in overall protease activity in cell-free extracts. Transcriptome analysis revealed a small number of changes in gene expression in aerobic growth, with Rv2488c and Rv1971 being over 40-fold up-regulated and qor (Rv1454c) being 20-fold down-regulated; in addition, changes were seen in members of the heat shock regulon. Virulence assays demonstrated that the mutant was able to replicate in human macrophage-like cells (THP-1 cell line) to a comparable degree with the wild-type. However, the mutant was hyper-virulent in the SCID and C57BL/6 mouse models. Our data suggest that Rv0198c plays a role during infection. Copyright © 2010 Elsevier Ltd. All rights reserved.

  20. Depletion of putative chemosensitive respiratory neurons in the ventral medullary surface in multiple system atrophy.

    Science.gov (United States)

    Benarroch, Eduardo E; Schmeichel, Ann M; Low, Phillip A; Parisi, Joseph E

    2007-02-01

    Multiple system atrophy (MSA) is a disorder that may manifest with reduced respiratory chemosensitivity and central sleep apnoea. Chemosensitive glutamatergic and serotonergic neurons located just beneath the ventral medullary surface, corresponding to the human arcuate nucleus (ArcN), have recently been implicated in control of automatic breathing in response to hypercapnia and hypoxia. We sought to determine whether these neurons were affected in MSA. Medullae were obtained at post-mortem from 11 patients (8 men, 3 women, age 64 +/- 3 years) with neuropathologically confirmed MSA and 11 control subjects (6 men and 5 women, age 66 +/- 4 years). Fifty micrometre sections obtained throughout the medulla were processed for vesicular glutamate transporter-2 (VGLUT-2), tryptophan-hydroxylase (TrOH), glial fibrillary acid protein (GFAP) and alpha-synuclein immunoreactivity. Cell counts, GFAP immunoreactivity and presence of glial cytoplasmic inclusions (GCIs) were assessed in the ArcN. In MSA, compared with controls, there was a marked depletion of ArcN neurons immunoreactive for either VGLUT-2 (74 +/- 21 versus 342 +/- 84 cells/section, P section, P medullary surface in all cases. Our results indicate that there is severe loss of putative chemosensitive glutamatergic and serotonergic neurons as well as marked astrocytic gliosis in the ventral medullary surface in MSA. This may provide a possible morphological basis for impaired respiratory chemosensitivity and central sleep apnoea in this disorder.

  1. Isolation and annotation of 10828 putative full length cDNAs from indica rice

    Institute of Scientific and Technical Information of China (English)

    XIE; Kabin; ZHANG; Jianwei; XIANG; Yong; FENG; Qi; HAN; Bin

    2005-01-01

    We reported the isolation and identification of 10828 putative full-length cDNAs (FL-cDNA) from an indica rice cultivar, Minghui 63, with the long-term goal to isolate all full-length cDNAs from indica genome. Comparison with the databases showed that 780 of them are new rice cDNAs with no match in japonica cDNA database. Totally, 9078 of the FL-cDNAs contained predicted ORFs matching with japonica FL-cDNAs and 6543 could find homologous proteins with complete ORFs. 53% of the matched FL-cDNAs isolated in this study had longer 5′UTR than japonica FL-cDNAs. In silico mapping showed that 9776 (90.28%) of the FL-cDNAs had matched genomic sequences in the japonica genome and 10046 (92.78%) had matched genomic sequences in the indica genome. The average nucleotide sequence identity between the two subspecies is 99.2%. A majority of FL-cDNAs (90%) could be classified with GO (gene ontology) terms based on homology proteins. More than 60% of the new cDNAs isolated in this study had no homology to the known proteins. This set of FL-cDNAs should be useful for functional genomics and proteomics studies.

  2. Characterization of the putative cholesterol transport protein metastatic lymph node 64 in the brain.

    Science.gov (United States)

    King, S R; Smith, A G A; Alpy, F; Tomasetto, C; Ginsberg, S D; Lamb, D J

    2006-01-01

    Intracellular management of cholesterol is a critical process in the brain. Deficits with cholesterol transport and storage are linked to neurodegenerative disorders such as Neimann-Pick disease type C and Alzheimer's disease. One protein putatively involved in cholesterol transport is metastatic lymph node 64 (MLN64). MLN64 localizes to late endosomes which are part of the cholesterol internalization pathway. However, a detailed pattern of MLN64 expression in the brain is unclear. Using immunocytochemical and immunoblot analyses, we demonstrated the presence of MLN64 in several tissue types and various regions within the brain. MLN64 immunostaining in the CNS was heterogeneous, indicating selective expression in discrete specific cell populations and regions. MLN64 immunoreactivity was detected in glia and neurons, which displayed intracellular labeling consistent with an endosomal localization. Although previous studies suggested that MLN64 may promote steroid production in the brain, MLN64 immunoreactivity did not colocalize with steroidogenic cells in the CNS. These results demonstrate that MLN64 is produced in the mouse and human CNS in a restricted pattern of expression, suggesting that MLN64 serves a cell-specific function in cholesterol transport.

  3. Emotion processing fails to modulate putative mirror neuron response to trained visuomotor associations.

    Science.gov (United States)

    Fitzgibbon, Bernadette M; Kirkovski, Melissa; Fornito, Alex; Paton, Bryan; Fitzgerald, Paul B; Enticott, Peter G

    2016-04-01

    Recent neuroimaging studies have demonstrated that activation of the putative human mirror neuron system (MNS) can be elicited via visuomotor training. This is generally interpreted as supporting an associative learning account of the mirror neuron system (MNS) that argues against the ontogeny of the MNS to be an evolutionary adaptation for social cognition. The current study assessed whether a central component of social cognition, emotion processing, would influence the MNS activity to trained visuomotor associations, which could support a broader role of the MNS in social cognition. Using functional magnetic resonance imaging (fMRI), we assessed repetition suppression to the presentation of stimulus pairs involving a simple hand action and a geometric shape that was either congruent or incongruent with earlier association training. Each pair was preceded by an image of positive, negative, or neutral emotionality. In support of an associative learning account of the MNS, repetition suppression was greater for trained pairs compared with untrained pairs in several regions, primarily supplementary motor area (SMA) and right inferior frontal gyrus (rIFG). This response, however, was not modulated by the valence of the emotional images. These findings argue against a fundamental role of emotion processing in the mirror neuron response, and are inconsistent with theoretical accounts linking mirror neurons to social cognition. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. A putative plant organelle RNA recognition protein gene is essential for maize kernel development

    Institute of Scientific and Technical Information of China (English)

    Antony M Chettoor; Gibum Yi; Elisa Gomez; Gregorio Hueros; Robert B Meeley; Philip W Becraft

    2015-01-01

    Basal endosperm transfer layer (BETL) cel s are responsible for transferring apoplastic solutes from the maternal pedicel into the endosperm, supplying the grain with compounds required for embryo development and storage reserve accumulation. Here, we analyze the maize (Zea mays L.) empty pericarp6 (emp6) mutant, which causes early arrest in grain development. The Emp6þgene function is required independently in both the embryo and endo-sperm. The emp6 mutant causes a notable effect on the differentiation of BETL cel s; the extensive cel wal ingrowths that distinguish BETL cel s are diminished and BETL marker gene expression is compromised in mutant kernels. Transposon tagging identified the emp6 locus as encoding a putative plant organel e RNA recognition (PORR) protein, 1 of 15 PORR family members in maize. The emp6 transcript is widely detected in plant tissues with highest levels in embryos and developing kernels. EMP6‐green fluorescent protein (GFP) fusion proteins transiently expressed in Nicotiana benthamiana leaves were targeted specifical y to mitochondria. These results suggest that BETL cel differentia-tion might be particularly energy intensive, or alternatively, that mitochondria might confer a developmental function.

  5. Sleep architecture impairment in epileptic children and putative role of anti epileptic drugs.

    Science.gov (United States)

    Racaru, Valentina M; Cheliout-Heraut, Fawzia; Azabou, Eric; Essid, Nouha; Brami, Marc; Benga, Ileana; Pinard, Jean-Marc

    2013-01-01

    The comorbidity between epilepsy and sleep disorders is well documented. However, the mechanisms underlining this comorbidity are not fully understood. The putative role of anti epileptic drugs in sleep architecture disturbances in epileptic children needs to be explored. In this study, we analysed sleep architecture of 75 epileptic children (30 females and 45 males), aged from 4 to 15 years (mean-age: 8.3 years). They were divided in three groups according to their antiepileptic treatments: NT group: no antiepileptic treatment (n = 20), MT group: monotherapy (n = 29) and PT group: polytherapy (n = 26). All underwent video-polysomnographic recordings to assess main sleep parameters: stages of light sleep and slow waves sleep, REM sleep, total sleep time and awakenings. Percentages of paroxystic activity duration (PA) on TST were also calculated and classified in three subgroups: (20%). As result, significant decreases of REM sleep and of the sleep efficiency as well as significant increased awakenings were observed in PT group comparing to the NT group. No significative difference was found concerning the light sleep and slow waves sleep. A correlation was also observed between awakenings and PA. First, our data confirm that sleep disorders remain a hidden companion of childhood epilepsy. Second, we demonstrate that anti epileptic drugs may have some causal contribution. Diagnosing sleep disturbances should be part of the management of childhood epilepsy and should be taken into account in the choice of therapeutic strategy.

  6. Identification of CBX3 and ABCA5 as Putative Biomarkers for Tumor Stem Cells in Osteosarcoma

    Science.gov (United States)

    Saini, Vaibhav; Hose, Curtis D.; Monks, Anne; Nagashima, Kunio; Han, Bingnan; Newton, Dianne L.; Millione, Angelena; Shah, Jalpa; Hollingshead, Melinda G.; Hite, Karen M.; Burkett, Mark W.; Delosh, Rene M.; Silvers, Thomas E.; Scudiero, Dominic A.; Shoemaker, Robert H.

    2012-01-01

    Recently, there has been renewed interest in the role of tumor stem cells (TSCs) in tumorigenesis, chemoresistance, and relapse of malignant tumors including osteosarcoma. The potential exists to improve osteosarcoma treatment through characterization of TSCs and identification of therapeutic targets. Using transcriptome, proteome, immunophenotyping for cell-surface markers, and bioinformatic analyses, heterogeneous expression of previously reported TSC or osteosarcoma markers, such as CD133, nestin, POU5F1 (OCT3/4), NANOG, SOX2, and aldehyde dehydrogenase, among others, was observed in vitro. However, consistently significantly lower CD326, CD24, CD44, and higher ABCG2 expression in TSC-enriched as compared with un-enriched osteosarcoma cultures was observed. In addition, consistently higher CBX3 expression in TSC-enriched osteosarcoma cultures was identified. ABCA5 was identified as a putative biomarker of TSCs and/or osteosarcoma. Lastly, in a high-throughput screen we identified epigenetic (5-azacytidine), anti-microtubule (vincristine), and anti-telomerase (3,11-difluoro-6,8,13-trimethyl- 8H-quino [4,3,2-kl] acridinium methosulfate; RHPS4)-targeted therapeutic agents as candidates for TSC ablation in osteosarcoma. PMID:22870217

  7. Molecular cloning and properties of a full-length putative thyroid hormone receptor coactivator.

    Science.gov (United States)

    Takeshita, A; Yen, P M; Misiti, S; Cardona, G R; Liu, Y; Chin, W W

    1996-08-01

    Thyroid hormone receptors (TRs) are ligand-dependent transcription factors that regulate target gene transcription. The conserved carboxy-terminal region of the ligand-binding domain (AF-2) has been thought to play a critical role in mediating ligand-dependent transactivation by the interaction with coactivator(s). Using bacterially-expressed TR as a probe, far-Western-based expression cDNA library screening identified cDNAs that encode, in part, the recently reported partial steroid receptor coactivator-1 (SRC-1) sequence. Additional work, including 5' RACE, has characterized a full-length cDNA that encodes a approximately 160 kD protein as a putative thyroid hormone receptor coactivator (F-SRC-1). In vitro binding studies show that F-SRC-1 binds to a variety of nuclear hormone receptors in a ligand-dependent manner, along with TBP and TFIIB, suggesting that F-SRC-1 may play a role as a bridging molecule between nuclear hormone receptors and general transcription factors. Interestingly, AF-2 mutants also retain ligand-dependent interaction with F-SRC-1. Although F-SRC-1 recognizes the ligand-induced conformational changes of nuclear hormone receptors, our observations suggest that F-SRC-1 may bind directly with subregion(s) in nuclear hormone receptors other than the AF-2 region.

  8. Identification of putative orthologous genes for the phylogenetic reconstruction of temperate woody bamboos (Poaceae: Bambusoideae).

    Science.gov (United States)

    Zhang, Li-Na; Zhang, Xian-Zhi; Zhang, Yu-Xiao; Zeng, Chun-Xia; Ma, Peng-Fei; Zhao, Lei; Guo, Zhen-Hua; Li, De-Zhu

    2014-09-01

    The temperate woody bamboos (Arundinarieae) are highly diverse in morphology but lack a substantial amount of genetic variation. The taxonomy of this lineage is intractable, and the relationships within the tribe have not been well resolved. Recent studies indicated that this tribe could have a complex evolutionary history. Although phylogenetic studies of the tribe have been carried out, most of these phylogenetic reconstructions were based on plastid data, which provide lower phylogenetic resolution compared with nuclear data. In this study, we intended to identify a set of desirable nuclear genes for resolving the phylogeny of the temperate woody bamboos. Using two different methodologies, we identified 209 and 916 genes, respectively, as putative single copy orthologous genes. A total of 112 genes was successfully amplified and sequenced by next-generation sequencing technologies in five species sampled from the tribe. As most of the genes exhibited intra-individual allele heterozygotes, we investigated phylogenetic utility by reconstructing the phylogeny based on individual genes. Discordance among gene trees was observed and, to resolve the conflict, we performed a range of analyses using BUCKy and HybTree. While caution should be taken when inferring a phylogeny from multiple conflicting genes, our analysis indicated that 74 of the 112 investigated genes are potential markers for resolving the phylogeny of the temperate woody bamboos. © 2014 John Wiley & Sons Ltd.

  9. Creation of a putative third metal binding site in type II dihydroorotases significantly enhances enzyme activity.

    Science.gov (United States)

    Huang, Yen-Hua; Huang, Cheng-Yang

    2015-01-01

    Dihydroorotase (DHOase) is the third enzyme in the de novo biosynthesis pathway of pyrimidine nucleotides. DHOase is divided into two types (I and II). Type II DHOase generally contains a binuclear metal center in its active site. Recently, the crystal structure of DHOase domain in human CAD protein (huDHOase) has revealed three metal ions in the protein's active site. However, whether type II DHOase can have the critical third metal ion, as observed in huDHOase, remains unknown. In the present study, the putative third metal binding site in type II enzymes, such as the prokaryotic Salmonella enterica serovar Typhimurium LT2 DHOase (StDHOase) and the eukaryotic Saccharomyces cerevisiae DHOase (ScDHOase), was created and identified. StDHOase T198E and ScDHOase T208E mutants had higher activities compared with their wild-type enzymes. The need for a higher DHOase stability and activity may drive creation of the third metal ion binding site in huDHOase, which can be achieved by mutating a highly conserved position T in type II dihydroorotases to E, similar to that in huDHOase.

  10. The putative effects of D-Aspartic acid on blood testosterone levels: A systematic review

    Science.gov (United States)

    Roshanzamir, Farzad; Safavi, Seyyed Morteza

    2017-01-01

    Background: D-Aspartic acid (D-Asp) is in invertebrate and vertebrate neuroendocrine tissues, where it carries out important physiological functions. Recently, it has been reported that D-Asp is involved in the synthesis and release of testosterone and is assumed can be used as a testosterone booster for infertile men, and by athletes to increase muscle mass and strength. Objective: The aim of this review is to summarize available evidence related to the effects of D-Asp on serum testosterone levels. Materials and Methods: We conducted a systematic review of all type studies, which evaluated the effect of the D-Asp on blood testosterone including published papers until October 2015, using PubMed, ISI Web of Science, ProQuest and Scopus database. Results: With 396 retrieved records, 23 animal studies and 4 human studies were included. In vivo and in vitro animal studies revealed the effect of D-Asp depending on species, sex and organ-specific. Our results showed that exogenous D-Asp enhances testosterone levels in male animal’s studies, whereas studies in human yielded inconsistent results. The evidence for this association in man is still sparse, mostly because of limited number and poor quality studies. Conclusion: There is an urgent need for more and well-designed human clinical trials with larger sample sizes and longer duration to investigate putative effects of D-Asp on testosterone concentrations. PMID:28280794

  11. Lipooligosaccharide locus classes and putative virulence genes among chicken and human Campylobacter jejuni isolates.

    Science.gov (United States)

    Ellström, Patrik; Hansson, Ingrid; Nilsson, Anna; Rautelin, Hilpi; Olsson Engvall, Eva

    2016-11-21

    Campylobacter cause morbidity and considerable economic loss due to hospitalization and post infectious sequelae such as reactive arthritis, Guillain Barré- and Miller Fischer syndromes. Such sequelae have been linked to C. jejuni harboring sialic acid structures in their lipooligosaccharide (LOS) layer of the cell wall. Poultry is an important source of human Campylobacter infections but little is known about the prevalence of sialylated C. jejuni isolates and the extent of transmission of such isolates to humans. Genotypes of C. jejuni isolates from enteritis patients were compared with those of broiler chicken with pulsed-field gel electrophoresis (PFGE), to study the patterns of LOS biosynthesis genes and other virulence associated genes and to what extent these occur among Campylobacter genotypes found both in humans and chickens. Chicken and human isolates generally had similar distributions of the putative virulence genes and LOS locus classes studied. However, there were significant differences regarding LOS locus class of PFGE types that were overlapping between chicken and human isolates and those that were distinct to each source. The study highlights the prevalence of virulence associated genes among Campylobacter isolates from humans and chickens and suggests possible patterns of transmission between the two species.

  12. Transcriptome analysis of Solanum melongena L. (eggplant) fruit to identify putative allergens and their epitopes.

    Science.gov (United States)

    Ramesh, Kumar Ramagoni; Hemalatha, R; Vijayendra, Chary Anchoju; Arshi, Uz Zaman Syed; Dushyant, Singh Baghel; Dinesh, Kumar Bharadwaj

    2016-01-15

    Eggplant is the third most important Solanaceae crop after tomato and potato, particularly in India and China. A transcriptome analysis of eggplant's fruit was performed to study genes involved in medicinal importance and allergies. Illumina HiSeq 2000 system generated 89,763,638 raw reads (~18 Gb) from eggplant. High quality reads (59,039,694) obtained after trimming process, were assembled into a total of 149,224 non redundant set of transcripts. Out of 80,482 annotated sequences of eggplant fruit (BLASTx results against nr-green plant database), 40,752 transcripts showed significant similarity with predicted proteins of Solanum tuberosum (51%) followed by Solanum lycopersicum (34%) and other sequenced plant genomes. With BLASTx top hit analysis against existing allergens, a total of 1986 homologous allergen sequences were found, which had >37% similarity with 48 different allergens existing in the database. From the 48 putative allergens, 526 B-cell linear epitopes were identified using BepiPred linear epitope prediction tool. Transcript sequences generated from this study can be used to map epitopes of monoclonal antibodies and polyclonal sera from patients. With the support of this whole transcriptome catalogue of eggplant fruit, complete list of genes can be predicted based on which secondary structures of proteins may be modeled.

  13. The Pun1 gene for pungency in pepper encodes a putative acyltransferase.

    Science.gov (United States)

    Stewart, Charles; Kang, Byoung-Cheorl; Liu, Kede; Mazourek, Michael; Moore, Shanna L; Yoo, Eun Young; Kim, Byung-Dong; Paran, Ilan; Jahn, Molly M

    2005-06-01

    Pungency in Capsicum fruits is due to the accumulation of the alkaloid capsaicin and its analogs. The biosynthesis of capsaicin is restricted to the genus Capsicum and results from the acylation of an aromatic moiety, vanillylamine, by a branched-chain fatty acid. Many of the enzymes involved in capsaicin biosynthesis are not well characterized and the regulation of the pathway is not fully understood. Based on the current pathway model, candidate genes were identified in public databases and the literature, and genetically mapped. A published EST co-localized with the Pun1 locus which is required for the presence of capsaicinoids. This gene, AT3, has been isolated and its nucleotide sequence has been determined in an array of genotypes within the genus. AT3 showed significant similarity to acyltransferases in the BAHD superfamily. The recessive allele at this locus contains a deletion spanning the promoter and first exon of the predicted coding region in every non-pungent accession tested. Transcript and protein expression of AT3 was tissue-specific and developmentally regulated. Virus-induced gene silencing of AT3 resulted in a decrease in the accumulation of capsaicinoids, a phenotype consistent with pun1. In conclusion, gene mapping, allele sequence data, expression profile and silencing analysis collectively indicate that the Pun1 locus in pepper encodes a putative acyltransferase, and the pun1 allele, used in pepper breeding for nearly 50 000 years, results from a large deletion at this locus.

  14. The Leptospiral Antigen Lp49 is a Two-Domain Protein with Putative Protein Binding Function

    Energy Technology Data Exchange (ETDEWEB)

    Oliveira Giuseppe,P.; Oliveira Neves, F.; Nascimento, A.; Gomes Guimaraes, B.

    2008-01-01

    Pathogenic Leptospira is the etiological agent of leptospirosis, a life-threatening disease that affects populations worldwide. Currently available vaccines have limited effectiveness and therapeutic interventions are complicated by the difficulty in making an early diagnosis of leptospirosis. The genome of Leptospira interrogans was recently sequenced and comparative genomic analysis contributed to the identification of surface antigens, potential candidates for development of new vaccines and serodiagnosis. Lp49 is a membrane-associated protein recognized by antibodies present in sera from early and convalescent phases of leptospirosis patients. Its crystal structure was determined by single-wavelength anomalous diffraction using selenomethionine-labelled crystals and refined at 2.0 Angstroms resolution. Lp49 is composed of two domains and belongs to the all-beta-proteins class. The N-terminal domain folds in an immunoglobulin-like beta-sandwich structure, whereas the C-terminal domain presents a seven-bladed beta-propeller fold. Structural analysis of Lp49 indicates putative protein-protein binding sites, suggesting a role in Leptospira-host interaction. This is the first crystal structure of a leptospiral antigen described to date.

  15. Structural analysis of a putative SAM-dependent methyltransferase, YtqB, from Bacillus subtilis.

    Science.gov (United States)

    Park, Sun Cheol; Song, Wan Seok; Yoon, Sung-il

    2014-04-18

    S-adenosyl-L-methionine (SAM)-dependent methyltransferases (MTases) methylate diverse biological molecules using a SAM cofactor. The ytqB gene of Bacillus subtilis encodes a putative MTase and its biological function has never been characterized. To reveal the structural features and the cofactor binding mode of YtqB, we have determined the crystal structures of YtqB alone and in complex with its cofactor, SAM, at 1.9 Å and 2.2 Å resolutions, respectively. YtqB folds into a β-sheet sandwiched by two α-helical layers, and assembles into a dimeric form. Each YtqB monomer contains one SAM binding site, which shapes SAM into a slightly curved conformation and exposes the reactive methyl group of SAM potentially to a substrate. Our comparative structural analysis of YtqB and its homologues indicates that YtqB is a SAM-dependent class I MTase, and provides insights into the substrate binding site of YtqB.

  16. The putative U94 integrase is dispensable for human herpesvirus 6 (HHV-6) chromosomal integration.

    Science.gov (United States)

    Wallaschek, Nina; Gravel, Annie; Flamand, Louis; Kaufer, Benedikt B

    2016-08-01

    Human herpesvirus 6 (HHV-6) can integrate its genome into the telomeres of host chromosomes and is present in the germline of about 1 % of the human population. HHV-6 encodes a putative integrase U94 that possesses all molecular functions required for recombination including DNA-binding, ATPase, helicase and nuclease activity, and was hypothesized by many researchers to facilitate integration ever since the discovery of HHV-6 integration. However, analysis of U94 in the virus context has been hampered by the lack of reverse-genetic systems and efficient integration assays. Here, we addressed the role of U94 and the cellular recombinase Rad51 in HHV-6 integration. Surprisingly, we could demonstrate that HHV-6 efficiently integrated in the absence of U94 using a new quantitative integration assay. Additional inhibition of the cellular recombinase Rad51 had only a minor impact on virus integration. Our results shed light on this complex integration mechanism that includes factors beyond U94 and Rad51.

  17. Two Putative Polysaccharide Deacetylases Are Required for Osmotic Stability and Cell Shape Maintenance in Bacillus anthracis.

    Science.gov (United States)

    Arnaouteli, Sofia; Giastas, Petros; Andreou, Athina; Tzanodaskalaki, Mary; Aldridge, Christine; Tzartos, Socrates J; Vollmer, Waldemar; Eliopoulos, Elias; Bouriotis, Vassilis

    2015-05-22

    Membrane-anchored lipoproteins have a broad range of functions and play key roles in several cellular processes in Gram-positive bacteria. BA0330 and BA0331 are the only lipoproteins among the 11 known or putative polysaccharide deacetylases of Bacillus anthracis. We found that both lipoproteins exhibit unique characteristics. BA0330 and BA0331 interact with peptidoglycan, and BA0330 is important for the adaptation of the bacterium to grow in the presence of a high concentration of salt, whereas BA0331 contributes to the maintenance of a uniform cell shape. They appear not to alter the peptidoglycan structure and do not contribute to lysozyme resistance. The high resolution x-ray structure of BA0330 revealed a C-terminal domain with the typical fold of a carbohydrate esterase 4 and an N-terminal domain unique for this family, composed of a two-layered (4 + 3) β-sandwich with structural similarity to fibronectin type 3 domains. Our data suggest that BA0330 and BA0331 have a structural role in stabilizing the cell wall of B. anthracis.

  18. Identification and developmental expression profiling of putative alkaloid biosynthetic genes in Corydalis yanhusuo bulbs.

    Science.gov (United States)

    Liao, Dengqun; Wang, Pengfei; Jia, Chan; Sun, Peng; Qi, Jianjun; Zhou, Lili; Li, Xian'en

    2016-01-18

    Alkaloids in bulbs of Corydalis (C.) yanhusuo are the major pharmacologically active compounds in treatment of blood vessel diseases, tumors and various pains. However, due to the absence of gene sequences in C. yanhusuo, the genes involved in alkaloid biosynthesis and their expression during bulb development remain unknown. We therefore established the first transcriptome database of C. yanhusuo via Illumina mRNA-Sequencing of a RNA composite sample collected at Bulb initiation (Day 0), early enlargement (Day 10) and maturation (Day 30). 25,013,630 clean 90 bp paired-end reads were de novo assembled into 47,081 unigenes with an average length of 489 bp, among which 30,868 unigenes (65.56%) were annotated in four protein databases. Of 526 putative unigenes involved in biosynthesis o f various alkaloids, 187 were identified as the candidate genes involved in the biosynthesis of benzylisoquinoline alkaloids (BIAs), the only alkaloid type reported in C. yanhusuo untill now. BIAs biosynthetic genes were highly upregulated in the overall pathway during bulb development. Identification of alkaloid biosynthetic genes in C. yanhusuo provide insights on pathways and molecular regulation of alkaloid biosynthesis, to initiate metabolic engineering in order to improve the yield of interesting alkaloids and to identify potentially new alkaloids predicted from the transcriptomic information.

  19. Functional Characterization of a Putative Nitrate Transporter Gene Promoter from Rice

    Institute of Scientific and Technical Information of China (English)

    Ting-Zhang HU; Kai-Ming CAO; Mian XIA; Xi-Ping WANG

    2006-01-01

    Drought is one of the most significant abiotic stresses that influence plant growth and development. Expression analysis revealed that OsNRT1.3, a putative nitrate transporter gene in rice, was induced by drought. To confirm if the OsNRT1.3 promoter can respond to drought stress, a 2019 bp upstream sequence of OsNRT1.3 was cloned. Three OsNRT1.3 promoter fragments were generated by 5'-deletion, and fused to the β-glucuronidase (GUS) gene. The chimeric genes were introduced into rice plants. NRT2019::GUS, NRT1196: :GUS and NRT719::GUS showed similar expression patterns in seeds,roots, leaves and flowers in all transgenic rice, and GUS activity conferred by different OsNRT1.3 promoter fragments was significantly upregulated by drought stress, indicating that OsNRT1.3 promoter responds to drought stress and the 719 bp upstream sequence of OsNRT1.3 contains the drought response elements.

  20. Cardiac autonomic imbalance by social stress in rodents: understanding putative biomarkers

    Directory of Open Access Journals (Sweden)

    Susan K Wood, Phd

    2014-08-01

    Full Text Available Exposure to stress or traumatic events can lead to the development of depression and anxiety disorders. In addition to the debilitating consequences on mental health, patients with psychiatric disorders also suffer from autonomic imbalance, making them susceptible to a variety of medical disorders. Emerging evidence utilizing spectral analysis of heart rate variability (HRV, a reliable noninvasive measure of cardiovascular autonomic regulation, indicates that patients with depression and various anxiety disorders (i.e., panic, social, generalized anxiety disorders, and post traumatic stress disorder are characterized by decreased HRV. Social stressors in rodents are ethologically relevant experimental stressors that recapitulate many of the dysfunctional behavioral and physiological changes that occur in psychological disorders. In this review, evidence from clinical studies and preclinical stress models identify putative biomarkers capable of precipitating the comorbidity between disorders of the mind and autonomic dysfunction. Specifically, the role of corticotropin releasing factor, neuropeptide Y and inflammation are investigated. The impetus for this review is to highlight stress-related biomarkers that may prove critical in the development of autonomic imbalance in stress -related psychiatric disorders.

  1. Putative filariosis outbreak in white and black rhinoceros at Meru National Park in Kenya

    Directory of Open Access Journals (Sweden)

    Mutinda Matthew

    2012-09-01

    Full Text Available Abstract Background Habitat and food supply loss and disruption, together with man’s pursuit of the animal’s unique horn pose significant threats to the charismatic rhinoceros. Filarial worms have been thought to cause cutaneous lesions in black rhinoceros (Diceros bicornis in Kenya and South Africa, but never in white rhinoceros (Ceratotherium simum in the wild, despite the fact that the two species live often in close proximity. Stephanofilaria dinniki has been implicated in the past as the causal agents for such lesions. Findings In this paper we report a putative filariosis outbreak in both black and white rhinos at Meru National Park in Kenya. Four black and five white rhinos were affected by various degrees of filarioid-like lesions, while apparently all sympatric wild and domestic animals were filarial worm-free. Affected rhinos were captured and successfully treated. Comparison between the epidemiological aspects of white and black rhinoceros filariosis, and the possible relations between this outbreak and annual seasons, the presence of oxpeckers and other host species are discussed. Conclusions Our study highlights (i that filarial infection is not restricted to black rhinos, but it affects both rhinoceros species, and (ii the importance of the earlier detection and immediate treatment (capture-treat and release of filarioid infections, which is of pivotal interest for wildlife conservation, and especially the endangered and isolated white and black rhinoceros populations.

  2. Characterization of a Novel Putative S-Adenosylmethionine Decarboxylase-Like Protein from Leishmania donovani.

    Directory of Open Access Journals (Sweden)

    Saurabh Pratap Singh

    Full Text Available In addition to the S-adenosylmethionine decarboxylase (AD present in all organisms, trypanosomatids including Leishmania spp. possess an additional copy, annotated as the putative S-adenosylmethionine decarboxylase-like proenzyme (ADL. Phylogenetic analysis confirms that ADL is unique to trypanosomatids and has several unique features such as lack of autocatalytic cleavage and a distinct evolutionary lineage, even from trypanosomatid ADs. In Trypanosoma ADL was found to be enzymaticaly dead but plays an essential regulatory role by forming a heterodimer complex with AD. However, no structural or functional information is available about ADL from Leishmania spp. Here, in this study, we report the cloning, expression, purification, structural and functional characterization of Leishmania donovani (L. donovani ADL using biophysical, biochemical and computational techniques. Biophysical studies show that, L. donovani ADL binds S-adenosylmethionine (SAM and putrescine which are natural substrates of AD. Computational modeling and docking studies showed that in comparison to the ADs of other organisms including human, residues involved in putrescine binding are partially conserved while the SAM binding residues are significantly different. In silico protein-protein interaction study reveals that L. donovani ADL can interact with AD. These results indicate that L. donovani ADL posses a novel substrate binding property and may play an essential role in polyamine biosynthesis with a different mode of function from known proteins of the S-adenosylmethionine decarboxylase super family.

  3. Dynamics of putative raft-associated proteins at the cell surface.

    Science.gov (United States)

    Kenworthy, Anne K; Nichols, Benjamin J; Remmert, Catha L; Hendrix, Glenn M; Kumar, Mukesh; Zimmerberg, Joshua; Lippincott-Schwartz, Jennifer

    2004-06-07

    Lipid rafts are conceptualized as membrane microdomains enriched in cholesterol and glycosphingolipid that serve as platforms for protein segregation and signaling. The properties of these domains in vivo are unclear. Here, we use fluorescence recovery after photobleaching to test if raft association affects a protein's ability to laterally diffuse large distances across the cell surface. The diffusion coefficients (D) of several types of putative raft and nonraft proteins were systematically measured under steady-state conditions and in response to raft perturbations. Raft proteins diffused freely over large distances (> 4 microm), exhibiting Ds that varied 10-fold. This finding indicates that raft proteins do not undergo long-range diffusion as part of discrete, stable raft domains. Perturbations reported to affect lipid rafts in model membrane systems or by biochemical fractionation (cholesterol depletion, decreased temperature, and cholesterol loading) had similar effects on the diffusional mobility of raft and nonraft proteins. Thus, raft association is not the dominant factor in determining long-range protein mobility at the cell surface.

  4. The dJ/dS Ratio Test Reveals Hundreds of Novel Putative Cancer Drivers.

    Science.gov (United States)

    Chen, Han; Xing, Ke; He, Xionglei

    2015-08-01

    Computational tools with a balanced sensitivity and specificity in identification of candidate cancer drivers are highly desired. In this study, we propose a new statistical test, namely the dJ/dS ratio test, to compute the relative mutation rate of exon/intron junction sites (dJ) to synonymous sites (dS); observation of dJ/dS ratio larger than 1 in cancer indicates positive selection for splicing deregulation, a signature of cancer driver genes. Using this method, we analyzed the data from The Cancer Genome Atlas and identified hundreds of novel putative cancer drivers. Interestingly, these genes are highly enriched in biological processes related to the development and maintenance of multicellularity, paralleling a previous finding that cancer evolves back to be unicellular by knocking down the multicellularity-associated genetic network. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  5. Putative human and avian risk factors for avian influenza virus infections in backyard poultry in Egypt.

    Science.gov (United States)

    Sheta, Basma M; Fuller, Trevon L; Larison, Brenda; Njabo, Kevin Y; Ahmed, Ahmed Samy; Harrigan, Ryan; Chasar, Anthony; Abdel Aziz, Soad; Khidr, Abdel-Aziz A; Elbokl, Mohamed M; Habbak, Lotfy Z; Smith, Thomas B

    2014-01-10

    Highly pathogenic influenza A virus subtype H5N1 causes significant poultry mortality in the six countries where it is endemic and can also infect humans. Egypt has reported the third highest number of poultry outbreaks (n=1084) globally. The objective of this cross-sectional study was to identify putative risk factors for H5N1 infections in backyard poultry in 16 villages in Damietta, El Gharbia, Fayoum, and Menofia governorates from 2010-2012. Cloacal and tracheal swabs and serum samples from domestic (n=1242) and wild birds (n=807) were tested for H5N1 via RT-PCR and hemagglutination inhibition, respectively. We measured poultry rearing practices with questionnaires (n=306 households) and contact rates among domestic and wild bird species with scan sampling. Domestic birds (chickens, ducks, and geese, n=51) in three governorates tested positive for H5N1 by PCR or serology. A regression model identified a significant correlation between H5N1 in poultry and the practice of disposing of dead poultry and poultry feces in the garbage (F=15.7, p<0.0001). In addition, contact between domestic and wild birds was more frequent in villages where we detected H5N1 in backyard flocks (F=29.5, p<0.0001).

  6. Overexpression of INCREASED CAMBIAL ACTIVITY, a putative methyltransferase, increases cambial activity and plant growth

    Institute of Scientific and Technical Information of China (English)

    Hyunsook Kim; Mikiko Kojima; Daeseok Choi; Soyoung Park; Minami Matsui; Hitoshi Sakakibara; Ildoo Hwang

    2016-01-01

    Cambial activity is a prerequisite for secondary growth in plants; however, regulatory factors control ing the activity of the secondary meristem in radial growth remain elusive. Here, we identified INCREASED CAMBIAL ACTIVITY (ICA), a gene encoding a putative pectin methyltransferase, which could function as a modulator for the meristematic activity of fascicular and interfascicular cambium in Arabidopsis. An overexpressing transgenic line, 35S::ICA, showed accelerated stem elongation and radial thickening, resulting in increased accumulation of biomass, and increased levels of cytokinins (CKs) and gibberel ins (GAs). Expression of genes encoding pectin methylesterases involved in pectin modification together with pectin methyltransferases was highly induced in 35S::ICA, which might contribute to an increase of methanol emission as a byproduct in 35S::ICA. Methanol treatment induced the expression of GA-or CK-responsive genes and stimulated plant growth. Overal , we propose that ectopic expression of ICA increases cambial activity by regulating CK and GA homeostasis, and methanol emission, eventual y leading to stem elongation and radial growth in the inflorescence stem.

  7. Sequence evolution of putative cytotoxic T cell epitopes in NS3 region of hepatitis C virus

    Institute of Scientific and Technical Information of China (English)

    Hua-Zhang Guo; Ying Yin; Wen-Liang Wang; Chuan-Shan Zhang; Tao Wang; Zhe Wang; Jing Zhang; Hong Cheng; Hai-Tao Wang

    2004-01-01

    AIM: Quasispecies of hepatitis C virus (HCV) are the foundation for rapid sequence evolution of HCV to evade immune surveillance of hosts. The consensus sequence evolution of a segment of HCV NS3 region, which encompasses putative cytotoxic T cell epitopes, was evaluated. METHODS: Three male patients, infected with HCV through multiple transfusions, were identified from clinical symptoms and monitored by aminotransferase for 60 months. Blood samples taken at months 0, 32, and 60 were used for viral RNA extraction. A segment of HCV NS3 region was amplified from the RNA extraction by RT-PCR and subjected to subcloning and sequencing. HLA types of these three patients were determined using complement-dependent microlymphocytotoxic assay. CTL epitopes were predicted using MHC binding motifs.RESULTS: No patient had clinical symptoms or elevation of aspartate/alanine aminotransferase. Two patients showed positive HCV PCR results at all 3 time points. The other one showed a positive HCV PCR result only at month O. A reported HLA-A2-restricted CTL epitope had no alteration in the HLA-A2-negative carrier over 60 months. In the HLA-A2-positive individuals, all the sequences from O month Oshowed an amber mutation on the initial codon of the epitope. Most changes of consensus sequences in the samepatient occurred on predicted cytotoxic T cell epitopes. CONCLUSION: Amber mutation and changes of consensussequence in HCV NS3 region may be related to viral immune escape.

  8. The putative oncogene Pim-1 in the mouse: its linkage and variation among t haplotypes.

    Science.gov (United States)

    Nadeau, J H; Phillips, S J

    1987-11-01

    Pim-1, a putative oncogene involved in T-cell lymphomagenesis, was mapped between the pseudo-alpha globin gene Hba-4ps and the alpha-crystallin gene Crya-1 on mouse chromosome 17 and therefore within the t complex. Pim-1 restriction fragment variants were identified among t haplotypes. Analysis of restriction fragment sizes obtained with 12 endonucleases demonstrated that the Pim-1 genes in some t haplotypes were indistinguishable from the sizes for the Pim-1b allele in BALB/c inbred mice. There are now three genes, Pim-1, Crya-1 and H-2 I-E, that vary among independently derived t haplotypes and that have indistinguishable alleles in t haplotypes and inbred strains. These genes are closely linked within the distal inversion of the t complex. Because it is unlikely that these variants arose independently in t haplotypes and their wild-type homologues, we propose that an exchange of chromosomal segments, probably through double crossingover, was responsible for indistinguishable Pim-1 genes shared by certain t haplotypes and their wild-type homologues. There was, however, no apparent association between variant alleles of these three genes among t haplotypes as would be expected if a single exchange introduced these alleles into t haplotypes. If these variant alleles can be shown to be identical to the wild-type allele, then lack of association suggests that multiple exchanges have occurred during the evolution of the t complex.

  9. Putative DNA-dependent RNA polymerase in Mitochondrial Plasmid of Paramecium caudatum Stock GT704

    Directory of Open Access Journals (Sweden)

    Trina Ekawati Tallei

    2015-10-01

    Full Text Available Mitochondria of Paramecium caudatum stock GT704 has a set of four kinds of linear plasmids with sizes of 8.2, 4.1, 2.8 and 1.4 kb. The plasmids of 8.2 and 2.8 kb exist as dimers consisting of 4.1- and 1.4-kb monomers, respectively. The plasmid 2.8 kb, designated as pGT704-2.8, contains an open reading frame encodes for putative DNA-dependent RNA polymerase (RNAP. This study reveals that this RNAP belongs to superfamily of DNA/RNA polymerase and family of T7/T3 single chain RNA polymerase and those of mitochondrial plasmid of fungi belonging to Basidiomycota and Ascomycota. It is suggested that RNAP of pGT704-2.8 can perform transcription without transcription factor as promoter recognition. Given that only two motifs were found, it could not be ascertained whether this RNAP has a full function independently or integrated with mtDNA in carrying out its function.

  10. Structure and functional annotation of hypothetical proteins having putative Rubisco activase function from Vitis vinifera.

    Science.gov (United States)

    Kumar, Suresh

    2015-01-01

    Rubisco is a very large, complex and one of the most abundant proteins in the world and comprises up to 50% of all soluble protein in plants. The activity of Rubisco, the enzyme that catalyzes CO2 assimilation in photosynthesis, is regulated by Rubisco activase (Rca). In the present study, we searched for hypothetical protein of Vitis vinifera which has putative Rubisco activase function. The Arabidopsis and tobacco Rubisco activase protein sequences were used as seed sequences to search against Vitis vinifera in UniprotKB database. The selected hypothetical proteins of Vitis vinifera were subjected to sequence, structural and functional annotation. Subcellular localization predictions suggested it to be cytoplasmic protein. Homology modelling was used to define the three-dimensional (3D) structure of selected hypothetical proteins of Vitis vinifera. Template search revealed that all the hypothetical proteins share more than 80% sequence identity with structure of green-type Rubisco activase from tobacco, indicating proteins are evolutionary conserved. The homology modelling was generated using SWISS-MODEL. Several quality assessment and validation parameters computed indicated that homology models are reliable. Further, functional annotation through PFAM, CATH, SUPERFAMILY, CDART suggested that selected hypothetical proteins of Vitis vinifera contain ATPase family associated with various cellular activities (AAA) and belong to the AAA+ super family of ring-shaped P-loop containing nucleoside triphosphate hydrolases. This study will lead to research in the optimization of the functionality of Rubisco which has large implication in the improvement of plant productivity and resource use efficiency.

  11. Putative miRNAs for the diagnosis of dyslexia, dyspraxia, and specific language impairment.

    Science.gov (United States)

    Rudov, Alexander; Rocchi, Marco Bruno Luigi; Accorsi, Augusto; Spada, Giorgio; Procopio, Antonio Domenico; Olivieri, Fabiola; Rippo, Maria Rita; Albertini, Maria Cristina

    2013-10-01

    Disorders of human communication abilities can be classified into speech and language disorders. Speech disorders (e.g., dyspraxia) affect the sound generation and sequencing, while language disorders (e.g., dyslexia and specific language impairment, or SLI) are deficits in the encoding and decoding of language according to its rules (reading, spelling, grammar). The diagnosis of such disorders is often complicated, especially when a patient presents more than one disorder at the same time. The present review focuses on these challenges. We have combined data available from the literature with an in silico approach in an attempt to identify putative miRNAs that may have a key role in dyspraxia, dyslexia and SLI. We suggest the use of new miRNAs, which could have an important impact on the three diseases. Further, we relate those miRNAs to the axon guidance pathway and discuss possible interactions and the role of likely deregulated proteins. In addition, we describe potential differences in expressional deregulation and its role in the improvement of diagnosis. We encourage experimental investigations to test the data obtained in silico.

  12. Putative RopGAPs impact division plane selection and interact with kinesin-12 POK1.

    Science.gov (United States)

    Stöckle, Dorothee; Herrmann, Arvid; Lipka, Elisabeth; Lauster, Theresa; Gavidia, Richard; Zimmermann, Steffi; Müller, Sabine

    2016-08-08

    Cell shape is defined by the surrounding cell walls in plants. Thus, spatial control over cell division planes and cell expansion polarity are essential to maintain cell morphology. In eukaryotes, cell polarity and expansion are controlled by Rho GTPase signalling, regulating cytoskeletal reorganization and vesicle trafficking(1). However, until now, Rho signalling was not implicated in mitotic events in plants. Here, we report a pair of putative Rho GTPase activating proteins (RhoGAPs) that interact with the mitosis-specific kinesin-12 POK1, a core component of the cortical division zone/site (CDZ/CDS) that is required for division plane maintenance in Arabidopsis(2-4). The designated pleckstrin homology GAPs (PHGAPs) are cytoplasmic and plasma membrane associated in interphase, but during mitosis they additionally localize to the CDZ/CDS in a POK-dependent manner. In contrast to pok1 pok2 mutants, phgap1 phgap2 double mutants show moderate cell wall positioning defects as a consequence of inaccurate positioning of the cortical division zone marker POK1. We conclude that loss of PHGAP function interferes with division plane selection in proliferative cell divisions.

  13. Putative Human and Avian Risk Factors for Avian Influenza Virus Infections in Backyard Poultry in Egypt

    Science.gov (United States)

    Sheta, Basma M.; Fuller, Trevon L.; Larison, Brenda; Njabo, Kevin Y.; Ahmed, Ahmed Samy; Harrigan, Ryan; Chasar, Anthony; Aziz, Soad Abdel; Khidr, Abdel-Aziz A.; Elbokl, Mohamed M.; Habbak, Lotfy Z.; Smith, Thomas B.

    2014-01-01

    Highly pathogenic influenza A virus subtype H5N1 causes significant poultry mortality in the six countries where it is endemic and can also infect humans. Egypt has reported the third highest number of poultry outbreaks (n=1,084) globally. The objective of this cross-sectional study was to identify putative risk factors for H5N1 infections in backyard poultry in 16 villages in Damietta, El Gharbia, Fayoum, and Menofia governorates from 2010–2012. Cloacal and tracheal swabs and serum samples from domestic (n=1242)and wild birds (n=807) were tested for H5N1 via RT-PCR and hemagglutination inhibition, respectively. We measured poultry rearing practices with questionnaires (n=306 households) and contact rates among domestic and wild bird species with scan sampling. Domestic birds (chickens, ducks, and geese, n = 51) in three governorates tested positive for H5N1 by PCR or serology. A regression model identified a significant correlation between H5N1 in poultry and the practice of disposing of dead poultry and poultry feces in the garbage (F = 15.7, p< 0.0001). In addition, contact between domestic and wild birds was more frequent in villages where we detected H5N1 in backyard flocks (F= 29.5, p< 0.0001). PMID:24315038

  14. Original and regenerating lizard tail cartilage contain putative resident stem/progenitor cells.

    Science.gov (United States)

    Alibardi, Lorenzo

    2015-11-01

    Regeneration of cartilaginous tissues is limited in mammals but it occurs with variable extension in lizards (reptiles), including in their vertebrae. The ability of lizard vertebrae to regenerate cartilaginous tissue that is later replaced with bone has been analyzed using tritiated thymidine autoradiography and 5BrdU immunocytochemistry after single pulse or prolonged-pulse and chase experiments. The massive cartilage regeneration that can restore broad vertebral regions and gives rise to a long cartilaginous tube in the regenerating tail, depends from the permanence of some chondrogenic cells within adult vertebrae. Few cells that retain tritiated thymidine or 5-bromodeoxy-uridine for over 35 days are mainly localized in the inter-vertebral cartilage and in sparse chondrogenic regions of the neural arch of the vertebrae, suggesting that they are putative resident stem/progenitor cells. The study supports previous hypothesis indicating that the massive regeneration of the cartilaginous tissue in damaged vertebrae and in the regenerating tail of lizards derive from resident stem cells mainly present in the cartilaginous areas of the vertebrae including in the perichondrium that are retained in adult lizards as growing centers for most of their lifetime.

  15. Identification of CBX3 and ABCA5 as putative biomarkers for tumor stem cells in osteosarcoma.

    Science.gov (United States)

    Saini, Vaibhav; Hose, Curtis D; Monks, Anne; Nagashima, Kunio; Han, Bingnan; Newton, Dianne L; Millione, Angelena; Shah, Jalpa; Hollingshead, Melinda G; Hite, Karen M; Burkett, Mark W; Delosh, Rene M; Silvers, Thomas E; Scudiero, Dominic A; Shoemaker, Robert H

    2012-01-01

    Recently, there has been renewed interest in the role of tumor stem cells (TSCs) in tumorigenesis, chemoresistance, and relapse of malignant tumors including osteosarcoma. The potential exists to improve osteosarcoma treatment through characterization of TSCs and identification of therapeutic targets. Using transcriptome, proteome, immunophenotyping for cell-surface markers, and bioinformatic analyses, heterogeneous expression of previously reported TSC or osteosarcoma markers, such as CD133, nestin, POU5F1 (OCT3/4), NANOG, SOX2, and aldehyde dehydrogenase, among others, was observed in vitro. However, consistently significantly lower CD326, CD24, CD44, and higher ABCG2 expression in TSC-enriched as compared with un-enriched osteosarcoma cultures was observed. In addition, consistently higher CBX3 expression in TSC-enriched osteosarcoma cultures was identified. ABCA5 was identified as a putative biomarker of TSCs and/or osteosarcoma. Lastly, in a high-throughput screen we identified epigenetic (5-azacytidine), anti-microtubule (vincristine), and anti-telomerase (3,11-difluoro-6,8,13-trimethyl- 8H-quino [4,3,2-kl] acridinium methosulfate; RHPS4)-targeted therapeutic agents as candidates for TSC ablation in osteosarcoma.

  16. Identification of CBX3 and ABCA5 as putative biomarkers for tumor stem cells in osteosarcoma.

    Directory of Open Access Journals (Sweden)

    Vaibhav Saini

    Full Text Available Recently, there has been renewed interest in the role of tumor stem cells (TSCs in tumorigenesis, chemoresistance, and relapse of malignant tumors including osteosarcoma. The potential exists to improve osteosarcoma treatment through characterization of TSCs and identification of therapeutic targets. Using transcriptome, proteome, immunophenotyping for cell-surface markers, and bioinformatic analyses, heterogeneous expression of previously reported TSC or osteosarcoma markers, such as CD133, nestin, POU5F1 (OCT3/4, NANOG, SOX2, and aldehyde dehydrogenase, among others, was observed in vitro. However, consistently significantly lower CD326, CD24, CD44, and higher ABCG2 expression in TSC-enriched as compared with un-enriched osteosarcoma cultures was observed. In addition, consistently higher CBX3 expression in TSC-enriched osteosarcoma cultures was identified. ABCA5 was identified as a putative biomarker of TSCs and/or osteosarcoma. Lastly, in a high-throughput screen we identified epigenetic (5-azacytidine, anti-microtubule (vincristine, and anti-telomerase (3,11-difluoro-6,8,13-trimethyl- 8H-quino [4,3,2-kl] acridinium methosulfate; RHPS4-targeted therapeutic agents as candidates for TSC ablation in osteosarcoma.

  17. Characterization of the putative tryptophan synthase β-subunit from Mycobacterium tuberculosis

    Institute of Scientific and Technical Information of China (English)

    Hongbo Shen; Yanping Yang; Feifei Wang; Ying Zhang; Naihao Ye; Shengfeng Xu; Honghai Wang

    2009-01-01

    The increasing emergence of drug-resistant tuberculosis (TB)poses a serious threat to the control of this disease.It is in urgent need to develop new TB drugs.Tryptophan biosynthetic pathway plays an important role in the growth and replication of Mycobacterium tuberculosis(Mtb).The β-subunit of tryptophan synthase(TrpB)catalyzes the last step of the tryptophan biosynthetic pathway,and it might be a potential target for TB drug design.In this study,we overexpressed,purified,and characterized the putative TrpB-encoding gene Rv1612 in Mtb H37Rv.Results showed that Mtb His-TrpB optimal enzymatic activity is at pH 7.8 with 0.15 M Na+or 0.18 M Mg2+ at 37℃.Structure analysis indicated that Mtb TrpB exhibited a typical β/α barrel structure.The amino acid residues believed to interact with the enzyme cofactor pyridoxal-5'-phosphate were predicted by homology modeling and structure alignment.The role of these residues in catalytic activity of the Mtb His-TrpB was confirmed by site-directed mutagenesis.These results provided reassuring structural information for drug design based on TrpB.

  18. Cloning and characterization of two putative seven-transmembrane receptor genes from cotton

    Institute of Scientific and Technical Information of China (English)

    Peng Gao; Piming Zhao; Juan Wang; Haiyun Wang; Guiling Wang; Guixian Xia

    2008-01-01

    Using rapid amplification of cDNA ends (RACE)-PCR,two full-length cDNAs encoding putative seven-transmembrane receptors (designated Gh7TMpR1 and Gh7TMpR2) were cloned from cotton plants.Southern blot and an ApaLl restriction site polymorphism analyses revealed that GhTTMpR1 was derived from the ancestral A diploid genome,while Gh7TMpR2 was from the D subgenome.Northern blot hybridization indicated that both Gh7TMpR1 and Gh7TMpR2 were expressed preferentially in the elongation phase of fiber development.Majority of the Gh7TMpR1 proteins were located within the membrane structure and displayed a punctuate pattern of distribution.Overexpression of Gh7TMpR1 in fission yeast disrupted the polar growth and caused the formation of rounded cells.These results suggest that GhT7MpRI may play a critical role in cotton fiber development,perhaps as a signaling receptor that is involved in controlling fiber elongation.

  19. Exome sequence analysis of Kaposiform hemangioendothelioma: identification of putative driver mutations*

    Science.gov (United States)

    Egashira, Sho; Jinnin, Masatoshi; Harada, Miho; Masuguchi, Shinichi; Fukushima, Satoshi; Ihn, Hironobu

    2016-01-01

    BACKGROUND Kaposiform hemangioendothelioma is a rare, intermediate, malignant tumor. The tumor's etiology remains unknown and there are no specific treatments. OBJECTIVE In this study, we performed exome sequencing using DNA from a Kaposiform hemangioendothelioma patient, and found putative candidates for the responsible mutations. METHOD The genomic DNA for exome sequencing was obtained from the tumor tissue and matched normal tissue from the same individual. Exome sequencing was performed on HiSeq2000 sequencer platform. RESULTS Among oncogenes, germline missense single nucleotide variants were observed in the TP53 and APC genes in both the tumor and normal tissue. As tumor-specific somatic mutations, we identified 81 candidate genes, including 4 nonsense changes, 68 missense changes and 9 insertions/deletions. The mutations in ITGB2, IL-32 and DIDO1 were included in them. CONCLUSION This is a pilot study, and future analysis with more patients is needed to clarify: the detailed pathogenesis of this tumor, the novel diagnostic methods by detecting specific mutations, and the new therapeutic strategies targeting the mutation. PMID:28099595

  20. The putative effects of D-Aspartic acid on blood testosterone levels: A systematic review

    Directory of Open Access Journals (Sweden)

    Farzad Roshanzamir

    2017-08-01

    Full Text Available Background: D-Aspartic acid (D-Asp is in invertebrate and vertebrate neuroendocrine tissues, where it carries out important physiological functions. Recently, it has been reported that D-Asp is involved in the synthesis and release of testosterone and is assumed can be used as a testosterone booster for infertile men, and by athletes to increase muscle mass and strength. Objective: The aim of this review is to summarize available evidence related to the effects of D-Asp on serum testosterone levels. Materials and Methods: We conducted a systematic review of all type studies, which evaluated the effect of the D-Asp on blood testosterone including published papers until October 2015, using PubMed, ISI Web of Science, ProQuest and Scopus database. Results: With 396 retrieved records, 23 animal studies and 4 human studies were included. In vivo and in vitro animal studies revealed the effect of D-Asp depending on species, sex and organ-specific. Our results showed that exogenous D-Asp enhances testosterone levels in male animal’s studies, whereas studies in human yielded inconsistent results. The evidence for this association in man is still sparse, mostly because of limited number and poor quality studies. Conclusion: There is an urgent need for more and well-designed human clinical trials with larger sample sizes and longer duration to investigate putative effects of D-Asp on testosterone concentrations.

  1. Benzoxazinoids: Cereal phytochemicals with putative therapeutic and health-protecting properties.

    Science.gov (United States)

    Adhikari, Khem B; Tanwir, Fariha; Gregersen, Per L; Steffensen, Stine K; Jensen, Bettina M; Poulsen, Lars K; Nielsen, Claus H; Høyer, Søren; Borre, Michael; Fomsgaard, Inge S

    2015-07-01

    Benzoxazinoids (BXs) are a group of natural chemical compounds with putative pharmacological and health-protecting properties. BXs were formerly identified in and isolated from selected dicot medicinal plants and young cereal plants. Recently, BXs were found to be present in mature cereal grains and bakery products, such that knowledge about the pharmacological properties of BXs, which until now have unknowingly been consumed through the daily bread and breakfast cereals, has come into new focus. This review discusses published results from in vitro studies and a few human and animal model studies on the health effects and pharmacological responses of various BX compounds. Many of these studies have reported antimicrobial, anticancer, reproductive system stimulatory, central nervous system stimulatory, immunoregulatory, and appetite- and weight-reducing effects of BXs and/or BX derivatives. The health benefits of wholegrain intake may be associated with the solitary and/or overlapping biological effects of fibers, lignans, phenolic acids, alkylresorcinols, BXs, and other bioactive compounds. In the context of BXs as dietary ingredients, further comprehensive investigations are required to understand their biological functions, to elucidate the underlying mechanisms, to explore their potential contribution on the health effects associated with wholegrain consumption, and to examine their potential as functional food ingredients.

  2. High-Resolution Genomic and Expression Profiling Reveals 105 Putative Amplification Target Genes in Pancreatic Cancer

    Directory of Open Access Journals (Sweden)

    Eija H. Mahlamaki

    2004-09-01

    Full Text Available Comparative genomic hybridization (CGH studies have provided a wealth of information on common copy number aberrations in pancreatic cancer, but the genes affected by these aberrations are largely unknown. To identify putative amplification target genes in pancreatic cancer, we performed a parallel copy number and expression survey in 13 pancreatic cancer cell lines using a 12,232-clone cDNA microarray, providing an average resolution of 300 kb throughout the human genome. CGH on cDNA microarray allowed highly accurate mapping of copy number increases and resulted in identification of 24 independent amplicons, ranging in size from 130 kb to 11 Mb. Statistical evaluation of gene copy number and expression data across all 13 cell lines revealed a set of 105 genes whose elevated expression levels were directly attributable to increased copy number. These included genes previously reported to be amplified in cancer as well as several novel targets for copy number alterations, such as p21-activated kinase 4 (PAK4, which was previously shown to be involved in cell migration, cell adhesion, and anchorage-independent growth. In conclusion, our results implicate a set of 105 genes that is likely to be actively involved in the development and progression of pancreatic cancer.

  3. A genome-wide analysis of putative functional and exonic variation associated with extremely high intelligence.

    Science.gov (United States)

    Spain, S L; Pedroso, I; Kadeva, N; Miller, M B; Iacono, W G; McGue, M; Stergiakouli, E; Smith, G D; Putallaz, M; Lubinski, D; Meaburn, E L; Plomin, R; Simpson, M A

    2016-08-01

    Although individual differences in intelligence (general cognitive ability) are highly heritable, molecular genetic analyses to date have had limited success in identifying specific loci responsible for its heritability. This study is the first to investigate exome variation in individuals of extremely high intelligence. Under the quantitative genetic model, sampling from the high extreme of the distribution should provide increased power to detect associations. We therefore performed a case-control association analysis with 1409 individuals drawn from the top 0.0003 (IQ >170) of the population distribution of intelligence and 3253 unselected population-based controls. Our analysis focused on putative functional exonic variants assayed on the Illumina HumanExome BeadChip. We did not observe any individual protein-altering variants that are reproducibly associated with extremely high intelligence and within the entire distribution of intelligence. Moreover, no significant associations were found for multiple rare alleles within individual genes. However, analyses using genome-wide similarity between unrelated individuals (genome-wide complex trait analysis) indicate that the genotyped functional protein-altering variation yields a heritability estimate of 17.4% (s.e. 1.7%) based on a liability model. In addition, investigation of nominally significant associations revealed fewer rare alleles associated with extremely high intelligence than would be expected under the null hypothesis. This observation is consistent with the hypothesis that rare functional alleles are more frequently detrimental than beneficial to intelligence.

  4. A Putative Type II Secretion System Is Involved in Cellulose Utilization in Cytophaga hutchisonii

    Directory of Open Access Journals (Sweden)

    Xia Wang

    2017-08-01

    Full Text Available Cytophaga hutchinsonii is a gliding cellulolytic bacterium that degrades cellulose in a substrate contact-dependent manner. Specific proteins are speculated to be translocated to its extracellular milieu or outer membrane surface to participate in adhesion to cellulose and further digestion. In this study, we show that three orthologous genes encoding the major components (T2S-D, -F, and -G of type II secretion system (T2SS are involved in cellulose degradation but not in cell motility. The individual disruption of the three t2s genes results in a significantly retarded growth on cellobiose, regenerated amorphous cellulose, and Avicel cellulose. Enzymatic analyses demonstrate that, whereas the endoglucanase activity of the t2s mutant cells is increased, the β-glucosidase activity is remarkably reduced compared to that of WT cells. Further analyses reveal that the t2s mutant cells not only exhibit a different profile of cellulose-bound outer membrane proteins from that of wild-type cells, but also display a significant decrease in their capability to adhere to cellulose. These results indicate that a functional link exits between the putative T2SS and cellulose utilization in C. hutchinsonii, and thus provide a conceptual framework to understand the unique strategy deployed by C. hutchinsonii to assimilate cellulose.

  5. The putative RNA helicase HELZ promotes cell proliferation, translation initiation and ribosomal protein S6 phosphorylation.

    Directory of Open Access Journals (Sweden)

    Philippe A Hasgall

    Full Text Available The hypoxia-inducible transcription factor (HIF is a key component of the cellular adaptation mechanisms to hypoxic conditions. HIFα subunits are degraded by prolyl-4-hydroxylase domain (PHD enzyme-dependent prolyl-4-hydroxylation of LxxLAP motifs that confer oxygen-dependent proteolytic degradation. Interestingly, only three non-HIFα proteins contain two conserved LxxLAP motifs, including the putative RNA helicase with a zinc finger domain HELZ. However, HELZ proteolytic regulation was found to be oxygen-independent, supporting the notion that a LxxLAP sequence motif alone is not sufficient for oxygen-dependent protein destruction. Since biochemical pathways involving RNA often require RNA helicases to modulate RNA structure and activity, we used luciferase reporter gene constructs and metabolic labeling to demonstrate that HELZ overexpression activates global protein translation whereas RNA-interference mediated HELZ suppression had the opposite effect. Although HELZ interacted with the poly(A-binding protein (PABP via its PAM2 motif, PABP was dispensable for HELZ function in protein translation. Importantly, downregulation of HELZ reduced translational initiation, resulting in the disassembly of polysomes, in a reduction of cell proliferation and hypophosphorylation of ribosomal protein S6.

  6. Occurrence of putative virulence genes in arcobacter species isolated from humans and animals.

    Science.gov (United States)

    Douidah, Laid; de Zutter, Lieven; Baré, Julie; De Vos, Paul; Vandamme, Peter; Vandenberg, Olivier; Van den Abeele, Anne-Marie; Houf, Kurt

    2012-03-01

    Interest in arcobacters in veterinary and human public health has increased since the first report of the isolation of arcobacters from food of animal origin. Since then, studies worldwide have reported the occurrence of arcobacters on food and in food production animals and have highlighted possible transmission, especially of Arcobacter butzleri, to the human population. In humans, arcobacters are associated with enteritis and septicemia. To assess their clinical relevance for humans and animals, evaluation of potential virulence factors is required. However, up to now, little has been known about the mechanisms of pathogenicity. Because of their close phylogenetic affiliation to the food-borne pathogen Campylobacter and their similar clinical manifestations, the presence of nine putative Campylobacter virulence genes (cadF, ciaB, cj1349, hecA, hecB, irgA, mviN, pldA, and tlyA) previously identified in the recent Arcobacter butzleri ATCC 49616 genome sequence was determined in a large set of human and animal Arcobacter butzleri, Arcobacter cryaerophilus, and Arcobacter skirrowii strains after the development of rapid and accurate PCR assays and confirmed by sequencing and dot blot hybridization.

  7. Modeling putative therapeutic implications of exosome exchange between tumor and immune cells.

    Science.gov (United States)

    Lu, Mingyang; Huang, Bin; Hanash, Samir M; Onuchic, José N; Ben-Jacob, Eshel

    2014-10-07

    Development of effective strategies to mobilize the immune system as a therapeutic modality in cancer necessitates a better understanding of the contribution of the tumor microenvironment to the complex interplay between cancer cells and the immune response. Recently, effort has been directed at unraveling the functional role of exosomes and their cargo of messengers in this interplay. Exosomes are small vesicles (30-200 nm) that mediate local and long-range communication through the horizontal transfer of information, such as combinations of proteins, mRNAs and microRNAs. Here, we develop a tractable theoretical framework to study the putative role of exosome-mediated cell-cell communication in the cancer-immunity interplay. We reduce the complex interplay into a generic model whose three components are cancer cells, dendritic cells (consisting of precursor, immature, and mature types), and killer cells (consisting of cytotoxic T cells, helper T cells, effector B cells, and natural killer cells). The framework also incorporates the effects of exosome exchange on enhancement/reduction of cell maturation, proliferation, apoptosis, immune recognition, and activation/inhibition. We reveal tristability-possible existence of three cancer states: a low cancer load with intermediate immune level state, an intermediate cancer load with high immune level state, and a high cancer load with low immune-level state, and establish the corresponding effective landscape for the cancer-immunity network. We illustrate how the framework can contribute to the design and assessments of combination therapies.

  8. Peptidomic Analysis of Amniotic Fluid for Identification of Putative Bioactive Peptides in Ventricular Septal Defect

    Directory of Open Access Journals (Sweden)

    Xing Li

    2016-05-01

    Full Text Available Background: Ventricular septal defect (VSD is one of the most common congenital heart diseases and to date the role of peptides in human amniotic fluid in the pathogenesis of VSD have been rarely investigated. Methods: To gain insight into the mechanisms of protein and peptides in cardiovascular development, we constructed a comparative peptidomic profiling of human amniotic fluid between normal and VSD fetuses using a stable isobaric labeling strategy involving tandem mass tag reagents, followed by nano liquid chromatography tandem mass spectrometry. Results: We identified and quantified 692 non-redundant peptides, 183 of which were differentially expressed in the amniotic fluid of healthy and VSD fetuses; 69 peptides were up regulated and 114 peptides were down regulated. These peptides were imported into the Ingenuity Pathway Analysis (IPA and identified putative roles in cardiovascular system morphogenesis and cardiogenesis. Conclusion: We concluded that 35 peptides located within the functional domains of their precursor proteins could be candidate bioactive peptides for VSD. The identified peptide changes in amniotic fluid of VSD fetuses may advance our current understanding of congenital heart disease and these peptides may be involved in the etiology of VSD.

  9. MstX and a putative potassium channel facilitate biofilm formation in Bacillus subtilis.

    Directory of Open Access Journals (Sweden)

    Matthew E Lundberg

    Full Text Available Biofilms constitute the predominant form of microbial life and a potent reservoir for innate antibiotic resistance in systemic infections. In the spore-forming bacterium Bacillus subtilis, the transition from a planktonic to sessile state is mediated by mutually exclusive regulatory pathways controlling the expression of genes required for flagellum or biofilm formation. Here, we identify mstX and yugO as novel regulators of biofilm formation in B. subtilis. We show that expression of mstX and the downstream putative K+ efflux channel, yugO, is necessary for biofilm development in B. subtilis, and that overexpression of mstX induces biofilm assembly. Transcription of the mstX-yugO operon is under the negative regulation of SinR, a transcription factor that governs the switch between planktonic and sessile states. Furthermore, mstX regulates the activity of Spo0A through a positive autoregulatory loop involving KinC, a histidine kinase that is activated by potassium leakage. The addition of potassium abrogated mstX-mediated biofilm formation. Our findings expand the role of Spo0A and potassium homeostasis in the regulation of bacterial development.

  10. Detection of putative periodontopathic bacteria in type 1 diabetic and healthy children: A comparative study

    Directory of Open Access Journals (Sweden)

    Ponnudurai Arangannal

    2013-01-01

    Full Text Available Aim: The aim of this study was to compare and assess the risk of periodontitis due to the presence of four putative periodontopathic bacteria (Porphyromonas gingivalis, Treponema denticola, Tannerella forsythia, and Aggregatibacter actinomycetemcomitans in type 1 diabetic and healthy children. Materials and Methods: Fifty type 1 diabetic and 50 healthy children in the age group of 7-14 years were recruited for the study. Subgingival plaque samples collected from permanent first molars were subjected to polymerase chain reaction assay to detect 16S rRNA gene of P. gingivalis, T. forsythia, T. denticola and A. actinomycetemcomitans. The data were analyzed using Fisher exact test. The P < 0.05 was considered statistically significant. Results: The prevalence of subgingival periodontal pathogens in diabetic and healthy children was 2% and 4% for P. gingivalis, 34% and 34% for T. denticola, 20% and 18% for A. actinomycetemcomitans and for T. forsythia, 4% and 34%, respectively. Significant statistical difference was not observed with regard to the prevalence of P. gingivalis, T. denticola, and A. actinomycetemcomitans among type 1 diabetic and healthy children (P = 1.00. Conversely, T. forsythia was less prevalent in diabetic children compared to healthy children. Conclusion: Statistical significance was not observed for the prevalence of periodontopathic bacteria in type 1 diabetic subjects. The results of the present study thus reveal the absence of risk of periodontitis by these bacterial species in type 1 diabetic subjects.

  11. Holophytochrome-interacting proteins in Physcomitrella: putative actors in phytochrome cytoplasmic signaling

    Directory of Open Access Journals (Sweden)

    Anna Lena eErmert

    2016-05-01

    Full Text Available Phytochromes are the principle photoreceptors in light-regulated plant development, primarily acting via translocation of the light-activated photoreceptor into the nucleus and subsequent gene regulation. However, several independent lines of evidence indicate unambiguously that an additional cytoplasmic signaling mechanism must exist. Directional responses in filament tip cells of the moss Physcomitrella patens are steered by phy4 which has been shown to interact physically with the blue light receptor phototropin at the plasma membrane. This complex might perceive and transduce vectorial information leading to cytoskeleton reorganization and finally a directional growth response. We developed yeast two-hybrid procedures using photochemically-functional, full-length phy4 as bait in Physcomitrella cDNA library screens and growth assays under different light conditions, revealing Pfr-dependent interactions possibly associated with phytochrome cytoplasmic signaling. Candidate proteins were then expressed in planta with fluorescent protein tags to determine their intracellular localization in darkness and red light. Of 14 candidates, 12 were confirmed to interact with phy4 in planta using bimolecular fluorescence complementation. We discuss the roles these putative holophytochrome-interacting proteins (HIP's might have in signaling.

  12. Differential expression of speckled POZ protein, SPOP: Putative regulation by miR-145

    Indian Academy of Sciences (India)

    Chiu-Jung Huang; Hsing-Yu Chen; Wan-Yi Lin; Kongbung Choo

    2014-06-01

    The speckle POZ protein, SPOP, is an adaptor of the Cul3-based ubiquitination process, and has been implicated in the carcinogenesis process. Despite recent elucidation of biological functions, regulation of SPOP gene expression has not been reported. In this study, the mRNA levels of the mouse SPOP (mSPOP) gene were first shown to vary noticeably in different tissues. However, the SPOP protein was detected in high abundance only in Purkinje cells of the cerebellum and seminiferous tubule of the testis, echoing previous reports of involvement of ubiquitination in neuron cells and in spermatogenesis. In other mouse tissues and human cancer cell lines analysed, only low SPOP protein levels were detected. The 3′-untranslated regions of both the mSPOP and human SPOP transcripts harbor a conserved putative miR-145 binding site (BS). In some tissues and cell lines, miR-145 and SPOP protein levels were in an inverse relationship suggesting miR-145 regulation. Luciferase assays of deletion and point mutation constructs of the miR-145 BS, and miR-145 induction by serum starvation that resulted in reduced endogenous SPOP levels provided further evidence that miR-145 is likely involved in post-transcriptional regulation of SPOP expression in selected tissues, and possibly with the participation of other miRNA species.

  13. Amplification of tumor inducing putative cancer stem cells (CSCs) by vitamin A/retinol from mammary tumors

    Energy Technology Data Exchange (ETDEWEB)

    Sharma, Rohit B. [Department of Microbiology and Molecular Genetics, University of Pittsburgh, PA 15261 (United States); Wang, Qingde [Department of Surgery, University of Pittsburgh, PA 15261 (United States); Khillan, Jaspal S., E-mail: khillan@pitt.edu [Department of Microbiology and Molecular Genetics, University of Pittsburgh, PA 15261 (United States)

    2013-07-12

    Highlights: •Vitamin A supports self renewal of putative CSCs from mammary tumors. •These cells exhibit impaired retinol metabolism into retinoic acid. •CSCs from mammary tumors differentiate into mammary specific cell lineages. •The cells express mammary stem cell specific CD29 and CD49f markers. •Putative CSCs form highly metastatic tumors in NOD SCID mouse. -- Abstract: Solid tumors contain a rare population of cancer stem cells (CSCs) that are responsible for relapse and metastasis. The existence of CSC however, remains highly controversial issue. Here we present the evidence for putative CSCs from mammary tumors amplified by vitamin A/retinol signaling. The cells exhibit mammary stem cell specific CD29{sup hi}/CD49f{sup hi}/CD24{sup hi} markers, resistance to radiation and chemo therapeutic agents and form highly metastatic tumors in NOD/SCID mice. The cells exhibit indefinite self renewal as cell lines. Furthermore, the cells exhibit impaired retinol metabolism and do not express enzymes that metabolize retinol into retinoic acid. Vitamin A/retinol also amplified putative CSCs from breast cancer cell lines that form highly aggressive tumors in NOD SCID mice. The studies suggest that high purity putative CSCs can be isolated from solid tumors to establish patient specific cell lines for personalized therapeutics for pre-clinical translational applications. Characterization of CSCs will allow understanding of basic cellular and molecular pathways that are deregulated, mechanisms of tumor metastasis and evasion of therapies that has direct clinical relevance.

  14. 7 CFR 1.610 - Who may represent a party, and what requirements apply to a representative?

    Science.gov (United States)

    2010-01-01

    ... ADMINISTRATIVE REGULATIONS Conditions in FERC Hydropower Licenses Hearing Process § 1.610 Who may represent a... may either represent himself or herself in the hearing process under this subpart or authorize an... documents under § 1.611; (2) Include the name and address of the person on whose behalf the appearance is...

  15. Choosing a Group Representative : The Impact of Perceived Organizational Support on the Preferences for Deviant Representatives in Work Negotiations

    NARCIS (Netherlands)

    Demoulin, Stephanie; Teixeira, Catia Pinto; Gillis, Celine; Goldoni, Edwine; Stinglhamber, Florence

    2016-01-01

    Group representative selection in negotiation is a topic that has only recently attracted researchers' attention. This article focuses on workplace negotiations and examines how employees' selection of representatives depends on their level of perceived organizational support (POS). We predict and s

  16. Choosing a Group Representative : The Impact of Perceived Organizational Support on the Preferences for Deviant Representatives in Work Negotiations

    NARCIS (Netherlands)

    Demoulin, Stephanie; Teixeira, Catia Pinto; Gillis, Celine; Goldoni, Edwine; Stinglhamber, Florence

    2016-01-01

    Group representative selection in negotiation is a topic that has only recently attracted researchers' attention. This article focuses on workplace negotiations and examines how employees' selection of representatives depends on their level of perceived organizational support (POS). We predict and s

  17. Direct and Representative Democracy - Supplementing, not Excluding Each Other

    DEFF Research Database (Denmark)

    Svensson, Palle

    2007-01-01

      This paper presents and discuses four main arguments for and against direct democracy, popular initiatives and referendums: (1) higher responsiveness versus lesser quality; (2) higher popular responsibility versus weaker representatives; (3) higher popular participation versus deeper conflicts...

  18. Statement of Bureau representative [template] [Laguna Atascosa National Wildlife Refuge

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This document is a template used for the statement of the bureau representative and the public hearing for the Laguna Atascosa National Wildlife Refuge Wilderness...

  19. Allegheny County Pennsylvania House of Representatives District Boundaries

    Data.gov (United States)

    Allegheny County / City of Pittsburgh / Western PA Regional Data Center — This dataset demarcates the Pennsylvania House of Representatives district boundaries within Allegheny County. If viewing this description on the Western...

  20. [Technical Representative - Monthly PMC Issues Reports : Rocky Mountain Arsenal NWR

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This collection of documents contains the Monthly PMC Issues reports for the Rocky Mountain Arsenal compiled by the Technical Representative. Reports in this...