Abundance of adiponectin system and G-protein coupled receptor GPR109A mRNA in adipose tissue and liver of F2 offspring cows of Charolais × German Holstein crosses that differ in body fat accumulation.

Science.gov (United States)

Mielenz, M; Kuhla, B; Hammon, H M

2013-01-01

In addition to its role in energy storage, adipose tissue (AT) is an important endocrine organ and it secretes adipokines. The adipokine adiponectin improves insulin sensitivity by activation of its receptors AdipoR1 and AdipoR2. Lipolysis in AT is downregulated by the G-protein coupled receptor (GPR109A), which binds the endogenous ligand β-hydroxybutyrate (BHBA). Insulin sensitivity is reduced during the transition from late pregnancy to early lactation in dairy cattle and BHBA is increased postpartum, implying the involvement of the adiponectin system and GPR109A in this process. The aim of the current investigation was to study the effect of the genetic background of cows on the mRNA abundance of the adiponectin system, as well as GPR109A, in an F(2) population of 2 Charolais × German Holstein families. These families were deduced from full- and half-sibs sharing identical but reciprocal paternal and maternal Charolais grandfathers. The animals of the 2 families showed significant differences in fat accretion and milk secretion and were designated fat-type (high fat accretion but low milk production) and lean-type (low fat accretion but high milk production). The mRNA of the adiponectin system and GPR109A were quantified by real-time PCR in different fat depots (subcutaneous from back, mesenteric, kidney) and liver. The mRNA data were correlated with AT masses (intermuscular topside border fat, kidney, mesenteric, omental, total inner fat mass, total subcutaneous fat mass, and total fat mass) and blood parameters (glucose, nonesterified fatty acids, BHBA, urea, insulin, and glucagon). The abundance of adiponectin system mRNA was higher in discrete AT depots of fat-type cows [adiponectin mRNA in mesenteric fat (trend), AdipoR1 in kidney and mesenteric AT, and AdipoR2 in subcutaneous fat (trend)] than in lean-type cows. More GPR109A mRNA was found in kidney fat of the lean-type family than in that of the fat-type family. In liver, the abundance of AdipoR2 and

Characterization of DNA polymerase. beta. mRNA: cell-cycle growth response in cultured human cells

Energy Technology Data Exchange (ETDEWEB)

Zmudzka, B Z; Fornace, A; Collins, J; Wilson, S H

1988-10-25

DNA polymerase ..beta.. (..beta..-polymerase) is a housekeeping enzyme involved in DNA repair in vertebrate cells. The authors used a cDNA probe to study abundance of ..beta..-polymerase mRNA in cultured human cells. The mRNA level in synchronized HeLa cells, representing different stages of the cell-cycle, varied only slightly. Contact inhibited fibroblasts AG-1522 contained the same level of mRNA as growing cells. The steady-state level of mRNA in fibroblasts is equivalent to 6 molecules per cell. The results indicate that the ..beta..-polymerase transcript is low abundance and is neither cell-cycles nor growth phase responsive.

Relative Abundance of Adult Mosquitoes in University of Abuja Main ...

African Journals Online (AJOL)

Relative Abundance of Adult Mosquitoes in University of Abuja Main ... relative abundance of adult mosquitoes in four selected sites in University of Abuja ... These results indicated that vectors of mosquito-borne diseases are breeding in the ...

The Effect of Lysophosphatidic Acid during In Vitro Maturation of Bovine Oocytes: Embryonic Development and mRNA Abundances of Genes Involved in Apoptosis and Oocyte Competence

Directory of Open Access Journals (Sweden)

Dorota Boruszewska

2014-01-01

Full Text Available In the present study we examined whether LPA can be synthesized and act during in vitro maturation of bovine cumulus oocyte complexes (COCs. We found transcription of genes coding for enzymes of LPA synthesis pathway (ATX and PLA2 and of LPA receptors (LPAR 1–4 in bovine oocytes and cumulus cells, following in vitro maturation. COCs were matured in vitro in presence or absence of LPA (10−5 M for 24 h. Supplementation of maturation medium with LPA increased mRNA abundance of FST and GDF9 in oocytes and decreased mRNA abundance of CTSs in cumulus cells. Additionally, oocytes stimulated with LPA had higher transcription levels of BCL2 and lower transcription levels of BAX resulting in the significantly lower BAX/BCL2 ratio. Blastocyst rates on day 7 were similar in the control and the LPA-stimulated COCs. Our study demonstrates for the first time that bovine COCs are a potential source and target of LPA action. We postulate that LPA exerts an autocrine and/or paracrine signaling, through several LPARs, between the oocyte and cumulus cells. LPA supplementation of maturation medium improves COC quality, and although this was not translated into an enhanced in vitro development until the blastocyst stage, improved oocyte competence may be relevant for subsequent in vivo survival.

Interleukin (IL)-1 in rat parturition: IL-1 receptors 1 and 2 and accessory proteins abundance in pregnant rat uterus at term - regulation by progesterone.

Science.gov (United States)

Ishiguro, Tomohito; Takeda, Jun; Fang, Xin; Bronson, Heather; Olson, David M

2016-07-01

The role of interleukin-1 (IL-1), a pro-inflammatory cytokine, in parturition is typically noted by changes in its concentrations. Studying the expression of its receptor family, IL-1 receptor (IL-1R) 1, IL-1R2, IL-1R accessory protein (IL-1RAcP), and its predominantly brain isoform, IL-1RAcPb, during late gestation in the uterus in the Long-Evans rat is another. We assessed changes in their mRNA and protein relative abundance in the uterus and compared IL-1RAcP and IL-1RAcPb mRNA abundance in uterus, cervix, ovaries, placenta, and whole blood of Long-Evans rats during late gestation or in RU486 and progesterone-treated dams using quantitative real-time PCR and western immunoblotting. IL-1R1, IL-1RAcP, and IL-1RAcPb mRNA abundance significantly increased in the uterus at delivery whereas IL-1R2 mRNA abundance significantly decreased. IL-1R1 protein increased at term and IL-1R2 protein decreased at term compared to nonpregnant uteri. IL1-RAcPb mRNA abundance was less than IL-1RAcP, but in the lower uterine segment it was the highest of all tissues examined. RU486 stimulated preterm delivery and an increase in IL-1R1 mRNA abundance whereas progesterone administration extended pregnancy and suppressed the increase in IL-1R1. These data suggest that changes in uterine sensitivity to IL-1 occur during late gestation and suggest another level of regulation for the control of delivery. The roles for IL-1RAcP and IL-1RAcPb need to be determined, but may relate to different intracellular signaling pathways. © 2016 The Authors. Physiological Reports published by Wiley Periodicals, Inc. on behalf of the American Physiological Society and The Physiological Society.

Extracellular tumor-related mRNA in plasma of lymphoma patients and survival implications.

Directory of Open Access Journals (Sweden)

Vanesa Garcia

Full Text Available BACKGROUND: We studied anomalous extracellular mRNAs in plasma from patients with diffuse large B-cell lymphoma (DLBCL and their survival implications. mRNAs studied have been reported in the literature as markers of poor (BCL2, CCND2, MYC and favorable outcome (LMO2, BCL6, FN1 in tumors. These markers were also analyzed in lymphoma tissues to test possible associations with their presence in plasma. METHODOLOGY/PRINCIPAL FINDINGS: mRNA from 42 plasma samples and 12 tumors from patients with DLBCL was analyzed by real-time PCR. Samples post-treatment were studied. The immunohistochemistry of BCL2 and BCL6 was defined. Presence of circulating tumor cells was determined by analyzing the clonality of the immunoglobulin heavy-chain genes by PCR. In DLBCL, MYC mRNA was associated with short overall survival. mRNA targets with unfavorable outcome in tumors were associated with characteristics indicative of poor prognosis, with partial treatment response and with short progression-free survival in patients with complete response. In patients with low IPI score, unfavorable mRNA targets were related to shorter overall survival, partial response, high LDH levels and death. mRNA disappeared in post-treatment samples of patients with complete response, and persisted in those with partial response or death. No associations were found between circulating tumor cells and plasma mRNA. Absence of BCL6 protein in tumors was associated with presence of unfavorable plasma mRNA. CONCLUSIONS/SIGNIFICANCE: Through a non-invasive procedure, tumor-derived mRNAs can be obtained in plasma. mRNA detected in plasma did not proceed from circulating tumor cells. In our study, unfavorable targets in plasma were associated with poor prognosis in B-cell lymphomas, mainly MYC mRNA. Moreover, the unfavorable targets in plasma could help us to classify patients with poor outcome within the good prognosis group according to IPI.

Relative abundance of desert tortoises on the Nevada Test Site

International Nuclear Information System (INIS)

Rautenstrauch, K.R.; O'Farrell, T.P.

1993-01-01

Seven hundred fifty-nine transects having a total length of 1,191 km were walked during 1981--1986 to determine the distribution and relative abundance of desert tortoises (Gopherus agassizii) on the Nevada Test Site (NTS). The abundance of tortoises on NTS was low to very low relative to other populations in the Mojave Desert. Sign of tortoises was found from 880 to 1,570 m elevation and was more abundant above 1,200 m than has been reported previously for Nevada. Tortoises were more abundant on NTS on the upper alluvial fans and slopes of mountains than in valley bottoms. They also were more common on or near limestone and dolomite mountains than on mountains of volcanic origin

The RDE-10/RDE-11 complex triggers RNAi-induced mRNA degradation by association with target mRNA in C. elegans.

Science.gov (United States)

Yang, Huan; Zhang, Ying; Vallandingham, Jim; Li, Hua; Li, Hau; Florens, Laurence; Mak, Ho Yi

2012-04-15

The molecular mechanisms for target mRNA degradation in Caenorhabditis elegans undergoing RNAi are not fully understood. Using a combination of genetic, proteomic, and biochemical approaches, we report a divergent RDE-10/RDE-11 complex that is required for RNAi in C. elegans. Genetic analysis indicates that the RDE-10/RDE-11 complex acts in parallel to nuclear RNAi. Association of the complex with target mRNA is dependent on RDE-1 but not RRF-1, suggesting that target mRNA recognition depends on primary but not secondary siRNA. Furthermore, RDE-11 is required for mRNA degradation subsequent to target engagement. Deep sequencing reveals a fivefold decrease in secondary siRNA abundance in rde-10 and rde-11 mutant animals, while primary siRNA and microRNA biogenesis is normal. Therefore, the RDE-10/RDE-11 complex is critical for amplifying the exogenous RNAi response. Our work uncovers an essential output of the RNAi pathway in C. elegans.

Dietary Selenium Deficiency or Excess Reduces Sperm Quality and Testicular mRNA Abundance of Nuclear Glutathione Peroxidase 4 in Rats.

Science.gov (United States)

Zhou, Ji-Chang; Zheng, Shijie; Mo, Junluan; Liang, Xiongshun; Xu, Yuanfei; Zhang, Huimin; Gong, Chunmei; Liu, Xiao-Li; Lei, Xin Gen

2017-10-01

Background: Glutathione peroxidase (GPX) 4 and selenoprotein P (SELENOP) are abundant, and several variants are expressed in the testis. Objective: We determined the effects of dietary selenium deficiency or excess on sperm quality and expressions of GPX4 and SELENOP variants in rat testis and liver. Methods: After weaning, male Sprague-Dawley rats were fed a Se-deficient basal diet (BD) for 5 wk until they were 9 wk old [mean ± SEM body weight (BW) = 256 ± 5 g]. They were then fed the BD diet alone (deficient) or with 0.25 (adequate), 3 (excess), or 5 (excess) mg Se/kg for 4 wk. Testis, liver, blood, and semen were collected to assay for selenoprotein mRNA and protein abundances, selenium concentration, GPX activity, 8-hydroxy-deoxyguanosine concentration, and sperm quality. Results: Dietary selenium supplementations elevated ( P selenium concentrations and GPX activities. Compared with those fed BD + 0.25 mg Se/kg, rats fed BD showed lower ( P selenium-adequate group. Compared with the selenium-adequate group, dietary selenium deficiency (BD) or excess (BD + 3 or 5 mg Se/kg) resulted in 45-77% lower ( P selenium concentrations in similar ways to sperm parameters and may be used as a sensitive marker to assess appropriate Se status for male function. © 2017 American Society for Nutrition.

Clinical significance of LUNX mRNA, CK19 mRNA, CEA mRNA expression in detecting micrometastasis from lung cancer

International Nuclear Information System (INIS)

Zhu Guangying; Liu Delin; Chen Jie

2003-01-01

Objective: To evaluate the sensitivity, specificity and clinical significance of CK19 mRNA, CEA mRNA and LUNX mRNA for detecting micrometastasis by sampling the peripheral blood and regional lymph nodes of lung cancer patients. Methods: Reverse transcriptase chain reaction (RT-PCR) was used to detect LUNX mRNA, CK19 mRNA, CEA mRNA for micrometastasis by sampling the peripheral blood of 48 lung cancer patients and 44 regional lymph nodes of such patients treated by curative resection. Peripheral blood of 30 patients with pulmonary benign lesions and 10 normal healthy volunteers and lymph nodes of 6 patients with benign pulmonary diseases served as control. Results: 1) LUNX mRNA, CK19 mRNA, CEA mRNA were expressed in all (35/35) lung cancer tissues. 2) In the peripheral blood from 48 lung cancer patients, 30 (62.5%) were positive for LUNX mRNA, 24 (50.0%) positive for CK19 mRNA and 32(66.7%) positive for CEA mRNA. The positive detection rates of micrometastasis in 44 lymph nodes from lung cancer patients were 36.4% (16 out of 44) for LUNX mRNA, 27.3% (12 out of 44) for CK19 mRNA and 40.9% (18 out of 44) for CEA mRNA. 3) In the 30 blood samples from patients with pulmonary benign diseases, 2 (6.7%) expressed CK19 mRNA, but none expressed LUNX mRNA or CEA mRNA. All the 3 molecular markers were negative in the 10 blood samples from healthy volunteers. In 11 lymph nodes from patients with pulmonary benign lesions, none was positive for any of the three markers. 4) In 44 regional lymph nodes from lung cancer patients, 6 (13.6%) were positive for metastasis by histopathological examination, with a positive rate significantly lower than that of the RT-PCR (P<0.05). 5) The micrometastatic positive rate in the peripheral blood of 40 non-small cell lung cancer (NSCLC) patients was significantly related to TNM stage (P=0.01). Conclusions: LUNX mRNA, CK19 MRNA, CEA mRNA are all appropriate target genes for the detection of micrometastasis from lung cancer. LUNX mRNA and CEA mRNA

Profiles of mRNA expression of genes related to sex differentiation of the gonads in the chicken embryo.

Science.gov (United States)

Yamamoto, I; Tsukada, A; Saito, N; Shimada, K

2003-09-01

Sex is determined genetically in birds. The homogametic sex is male (ZZ), whereas the heterogametic sex is female (ZW). According to the genetic sex, gonads develop into testes or ovary. In this study, we performed experiments to reveal mRNA expression patterns in the gonad between d 5.5 and 8.5 of incubation and examined a possible role of Dss-Ahc critical region on the X chromosome 1 (Dax1), Steroidogenic factor 1 (Sf1), P450aromatase (P450arom), Estrogen receptor alpha (ER alpha), doublesex and mab3 related transcription factor 1 (Dmrt1), Sry-related HMG box gene 9 (Sox9), Gata binding protein 4 (Gata4), and anti-müllerian hormone (Amh) in sex differentiation in chicken embryonic gonads using RNase protection assay. In embryonic chicken gonads, Dax1 mRNA was expressed in both sexes but was higher in females than in males at d 6.5 and 7.5 of incubation. The Sf1 mRNA was expressed in both sexes, but it was expressed more in males at d 5.5 than in females but more in females than in males at d 7.5 and 8.5 of incubation. The P450arom mRNA was expressed only in female gonads from d 5.5 of incubation. The ER alpha mRNA was expressed in both sexes, but it did not show a sex difference. On the other hand, the Dmrt1 mRNA was expressed in both sexes, but it showed a male-specific expression pattern. The male-specific expression pattern was observed in Sox9 mRNA, but it was not expressed in female gonads. The Gata4 mRNA was expressed in both sexes, and sex differences were not revealed throughout the observational period. Amh mRNA was expressed in both sexes, but it had male-specific mRNA expression pattern at d 6.5 to 8.5 of incubation. These results indicate that Dax1, Sf1, and P450arom have possible roles in ovary formation, whereas Dmrt1, Sox9, and Amh are related to testis formation in differentiating chicken gonads at d 5.5 to 8.5 of incubation.

Cloning and tissue distribution of rat hear fatty acid binding protein mRNA: identical forms in heart and skeletal muscle

International Nuclear Information System (INIS)

Claffey, K.P.; Herrera, V.L.; Brecher, P.; Ruiz-Opazo, N.

1987-01-01

A fatty acid binding protein (FABP) as been identified and characterized in rat heart, but the function and regulation of this protein are unclear. In this study the cDNA for rat heart FABP was cloned from a λ gt11 library. Sequencing of the cDNA showed an open reading frame coding for a protein with 133 amino acids and a calculated size of 14,776 daltons. Several differences were found between the sequence determined from the cDNA and that reported previously by protein sequencing techniques. Northern blot analysis using rat heart FABP cDNA as a probe established the presence of an abundant mRNA in rat heart about 0.85 kilobases in length. This mRNA was detected, but was not abundant, in fetal heart tissue. Tissue distribution studies showed a similar mRNA species in red, but not white, skeletal muscle. In general, the mRNA tissue distribution was similar to that of the protein detected by Western immunoblot analysis, suggesting that heart FABP expression may be regulated at the transcriptional level. S1 nuclease mapping studies confirmed that the mRNA hybridized to rat heart FABP cDNA was identical in heart and red skeletal muscle throughout the entire open reading frame. The structural differences between heart FABP and other members of this multigene family may be related to the functional requirements of oxidative muscle for fatty acids as a fuel source

Cloning and tissue distribution of rat hear fatty acid binding protein mRNA: identical forms in heart and skeletal muscle

Energy Technology Data Exchange (ETDEWEB)

Claffey, K.P.; Herrera, V.L.; Brecher, P.; Ruiz-Opazo, N.

1987-12-01

A fatty acid binding protein (FABP) as been identified and characterized in rat heart, but the function and regulation of this protein are unclear. In this study the cDNA for rat heart FABP was cloned from a lambda gt11 library. Sequencing of the cDNA showed an open reading frame coding for a protein with 133 amino acids and a calculated size of 14,776 daltons. Several differences were found between the sequence determined from the cDNA and that reported previously by protein sequencing techniques. Northern blot analysis using rat heart FABP cDNA as a probe established the presence of an abundant mRNA in rat heart about 0.85 kilobases in length. This mRNA was detected, but was not abundant, in fetal heart tissue. Tissue distribution studies showed a similar mRNA species in red, but not white, skeletal muscle. In general, the mRNA tissue distribution was similar to that of the protein detected by Western immunoblot analysis, suggesting that heart FABP expression may be regulated at the transcriptional level. S1 nuclease mapping studies confirmed that the mRNA hybridized to rat heart FABP cDNA was identical in heart and red skeletal muscle throughout the entire open reading frame. The structural differences between heart FABP and other members of this multigene family may be related to the functional requirements of oxidative muscle for fatty acids as a fuel source.

Localization of insulin receptor mRNA in rat brain by in situ hybridization

International Nuclear Information System (INIS)

Marks, J.L.; Porte, D. Jr.; Stahl, W.L.; Baskin, D.G.

1990-01-01

Insulin receptor mRNA was demonstrated in rat brain slices by in situ hybridization with three 35 S-oligonucleotide probes and contact film autoradiography. Specificity was confirmed by showing that (a) excess unlabeled probe abolished the signal, (b) an oligonucleotide probe for rat neuropeptide Y mRNA showed a different distribution of hybridization signal, and (c) the distribution of insulin receptor binding was consistent with the distribution of insulin receptor mRNA. Insulin receptor mRNA was most abundant in the granule cell layers of the olfactory bulb, cerebellum and dentate gyrus, in the pyramidal cell body layers of the pyriform cortex and hippocampus, in the choroid plexus and in the arcuate nucleus of the hypothalamus

[Mammals' camera-trapping in Sierra Nanchititla, Mexico: relative abundance and activity patterns].

Science.gov (United States)

Monroy-Vilchis, Octavio; Zarco-González, Martha M; Rodríguez-Soto, Clarita; Soria-Díaz, Leroy; Urios, Vicente

2011-03-01

Species conservation and their management depend on the availability of their population behavior and changes in time. This way, population studies include aspects such as species abundance and activity pattern, among others, with the advantage that nowadays new technologies can be applied, in addition to common methods. In this study, we used camera-traps to obtain the index of relative abundance and to establish activity pattern of medium and large mammals in Sierra Nanchititla, Mexico. The study was conducted from December 2003 to May 2006, with a total sampling effort of 4 305 trap-days. We obtained 897 photographs of 19 different species. Nasua narica, Sylvilagus floridanus and Urocyon cinereoargenteus were the most abundant, in agreement with the relative abundance index (RAI, number of independent records/100 trap-days), and according to previous studies with indirect methods in the area. The activity patterns of the species showed that 67% of them are nocturnal, except Odocoileus virginianus, Nasua narica and others. Some species showed differences with previously reported patterns, which are related with seasonality, resources availability, organism sex, principally. The applied method contributed with reliable data about relative abundance and activity patterns.

Species Composition, Relative Abundance and Distribution of the ...

African Journals Online (AJOL)

Species Composition, Relative Abundance and Distribution of the Avian Fauna of Entoto Natural Park and Escarpment, Addis Ababa. ... Eucalyptus plantation, soil erosion, deforestation, habitat fragmentation, settlement and land degradation were the main threats for the distribution of birds in the present study area.

Relative abundance of mosquito species in Katsina Metropolis ...

African Journals Online (AJOL)

A study was conducted on the relative abundance of mosquito species, around selected areas of Katsina metropolis, Katsina State, Nigeria during the months of January, February, April and June 2010. Mosquitoes were collected from five sampling sites: Kofar Durbi, Kofar Kaura, Kofar Marusa, GRA and Layout. These were ...

Molecular Characterization of Aquaporin 1 and Aquaporin 3 from the Gills of the African Lungfish, Protopterus annectens, and Changes in Their Branchial mRNA Expression Levels and Protein Abundance during Three Phases of Aestivation.

Science.gov (United States)

Chng, You R; Ong, Jasmine L Y; Ching, Biyun; Chen, Xiu L; Hiong, Kum C; Wong, Wai P; Chew, Shit F; Lam, Siew H; Ip, Yuen K

2016-01-01

African lungfishes can undergo long periods of aestivation on land during drought. During aestivation, lungfishes are confronted with desiccation and dehydration, and their gills become non-functional and covered with a thick layer of dried mucus. Aquaporins (Aqps) are a superfamily of integral membrane proteins which generally facilitate the permeation of water through plasma membranes. This study aimed to obtain the complete cDNA coding sequences of aqp1 and aqp3 from the gills of Protopterus annectens , and to determine their branchial mRNA and protein expression levels during the induction, maintenance and arousal phases of aestivation. Dendrogramic analyses of the deduced Aqp1 and Aqp3 amino acid sequences of P. annectens revealed their close relationships with those of Latimeria chalumnae and tetrapods. During the induction phase, there were significant decreases in the transcript levels of aqp1 and aqp3 in the gills of P. annectens , but the branchial Aqp1 and Aqp3 protein abundance remained unchanged. As changes in transcription might precede changes in translation, this could be regarded as an adaptive response to decrease the protein abundance of Aqp1 and Aqp3 in the subsequent maintenance phase of aestivation. As expected, the branchial transcript levels and protein abundance of aqp1 /Aqp1 and aqp3 /Aqp3 were significantly down-regulated during the maintenance phase, probably attributable to the shutdown of branchial functions and the cessation of volume regulation of branchial epithelial cells. Additionally, these changes could reduce the loss of water through branchial epithelial surfaces, supplementing the anti-desiccating property of the dried mucus. Upon arousal, it was essential for the lungfish to restore branchial functions. Indeed, the protein abundance of Aqp1 recovered partially, with complete recovery of mRNA expression level and protein abundance of Aqp3, in the gills of P. annectens after 3 days of arousal. These results provide insights

DDAH2 mRNA expression is inversely associated with some cardiovascular risk-related features in healthy young adults.

Science.gov (United States)

Puchau, Blanca; Hermsdorff, Helen Hermana M; Zulet, M Angeles; Martínez, J Alfredo

2009-01-01

The purpose of this study was to evaluate whether the mRNA expression profiles of three genes (PRMT1, DDAH2 and NOS3) are related to ADMA metabolism and signalling, and the potential relationships with anthropometrical, biochemical, lifestyle and inflammatory indicators in healthy young adults. An emphasis on the putative effect of different mRNA expression on cardiovascular risk-related features was paid. Anthropometrical measurements as well as lifestyle features were analyzed in 120 healthy young adults. Fasting blood samples were collected for the measurement of glucose and lipid profiles as well as the concentrations of selected inflammatory markers. Profiles of mRNA expression were assessed for PRMT1, DDAH2 and NOS3 genes from peripheral blood mononuclear cells. Regarding inflammatory biomarkers, DDAH2 was inversely associated with IL-6 and TNF-alpha. Moreover, subjects in the highest quintile of DDAH2 mRNA expression showed a reduced risk to have higher values of waist circumference, and to be more prone to show higher values of HDL-c. Interestingly, DDAH2 gene expression seemed to be related with some anthropometrical, biochemical, lifestyle and inflammatory indicators linked to cardiovascular risk in apparently healthy young adults, emerging as a potential disease marker.

DDAH2 mRNA Expression Is Inversely Associated with Some Cardiovascular Risk-Related Features in Healthy Young Adults

Directory of Open Access Journals (Sweden)

Blanca Puchau

2009-01-01

Full Text Available The purpose of this study was to evaluate whether the mRNA expression profiles of three genes (PRMT1, DDAH2 and NOS3 are related to ADMA metabolism and signalling, and the potential relationships with anthropometrical, biochemical, lifestyle and inflammatory indicators in healthy young adults. An emphasis on the putative effect of different mRNA expression on cardiovascular risk-related features was paid. Anthropometrical measurements as well as lifestyle features were analyzed in 120 healthy young adults. Fasting blood samples were collected for the measurement of glucose and lipid profiles as well as the concentrations of selected inflammatory markers. Profiles of mRNA expression were assessed for PRMT1, DDAH2 and NOS3 genes from peripheral blood mononuclear cells. Regarding inflammatory biomarkers, DDAH2 was inversely associated with IL-6 and TNF-α. Moreover, subjects in the highest quintile of DDAH2 mRNA expression showed a reduced risk to have higher values of waist circumference, and to be more prone to show higher values of HDL-c. Interestingly, DDAH2 gene expression seemed to be related with some anthropometrical, biochemical, lifestyle and inflammatory indicators linked to cardiovascular risk in apparently healthy young adults, emerging as a potential disease marker.

Oestradiol reduces Liver Receptor Homolog-1 mRNA transcript stability in breast cancer cell lines

International Nuclear Information System (INIS)

Lazarus, Kyren A.; Zhao, Zhe; Knower, Kevin C.; To, Sarah Q.; Chand, Ashwini L.; Clyne, Colin D.

2013-01-01

Highlights: •LRH-1 is an orphan nuclear receptor that regulates tumor proliferation. •In breast cancer, high mRNA expression is associated with ER+ status. •In ER−ve cells, despite very low mRNA, we found abundant LRH-1 protein. •Our data show distinctly different LRH-1 protein isoforms in ER− and ER+ breast cancer cells. •This is due to differences in LRH-1 mRNA and protein stability rates. -- Abstract: The expression of orphan nuclear receptor Liver Receptor Homolog-1 (LRH-1) is elevated in breast cancer and promotes proliferation, migration and invasion in vitro. LRH-1 expression is regulated by oestrogen (E 2 ), with LRH-1 mRNA transcript levels higher in oestrogen receptor α (ERα) positive (ER+) breast cancer cells compared to ER− cells. However, the presence of LRH-1 protein in ER− cells suggests discordance between mRNA transcript levels and protein expression. To understand this, we investigated the impact of mRNA and protein stability in determining LRH-1 protein levels in breast cancer cells. LRH-1 transcript levels were significantly higher in ER+ versus ER− breast cancer cells lines; however LRH-1 protein was expressed at similar levels. We found LRH-1 mRNA and protein was more stable in ER− compared to ER+ cell lines. The tumor-specific LRH-1 variant isoform, LRH-1v4, which is highly responsive to E 2 , showed increased mRNA stability in ER− versus ER+ cells. In addition, in MCF-7 and T47-D cell lines, LRH-1 total mRNA stability was reduced with E 2 treatment, this effect mediated by ERα. Our data demonstrates that in ER− cells, increased mRNA and protein stability contribute to the abundant protein expression levels. Expression and immunolocalisation of LRH-1 in ER− cells as well as ER− tumors suggests a possible role in the development of ER− tumors. The modulation of LRH-1 bioactivity may therefore be beneficial as a treatment option in both ER− and ER+ breast cancer

Oestradiol reduces Liver Receptor Homolog-1 mRNA transcript stability in breast cancer cell lines

Energy Technology Data Exchange (ETDEWEB)

Lazarus, Kyren A. [Cancer Drug Discovery Laboratory, Prince Henry’s Institute of Medical Research, Clayton, Victoria 3168 (Australia); Environmental and Biotechnology Centre, Swinburne University, Hawthorn, Victoria 3122 (Australia); Zhao, Zhe; Knower, Kevin C. [Cancer Drug Discovery Laboratory, Prince Henry’s Institute of Medical Research, Clayton, Victoria 3168 (Australia); To, Sarah Q. [Cancer Drug Discovery Laboratory, Prince Henry’s Institute of Medical Research, Clayton, Victoria 3168 (Australia); Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3168 (Australia); Chand, Ashwini L. [Cancer Drug Discovery Laboratory, Prince Henry’s Institute of Medical Research, Clayton, Victoria 3168 (Australia); Clyne, Colin D., E-mail: Colin.clyne@princehenrys.org [Cancer Drug Discovery Laboratory, Prince Henry’s Institute of Medical Research, Clayton, Victoria 3168 (Australia); Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3168 (Australia)

2013-08-30

Highlights: •LRH-1 is an orphan nuclear receptor that regulates tumor proliferation. •In breast cancer, high mRNA expression is associated with ER+ status. •In ER−ve cells, despite very low mRNA, we found abundant LRH-1 protein. •Our data show distinctly different LRH-1 protein isoforms in ER− and ER+ breast cancer cells. •This is due to differences in LRH-1 mRNA and protein stability rates. -- Abstract: The expression of orphan nuclear receptor Liver Receptor Homolog-1 (LRH-1) is elevated in breast cancer and promotes proliferation, migration and invasion in vitro. LRH-1 expression is regulated by oestrogen (E{sub 2}), with LRH-1 mRNA transcript levels higher in oestrogen receptor α (ERα) positive (ER+) breast cancer cells compared to ER− cells. However, the presence of LRH-1 protein in ER− cells suggests discordance between mRNA transcript levels and protein expression. To understand this, we investigated the impact of mRNA and protein stability in determining LRH-1 protein levels in breast cancer cells. LRH-1 transcript levels were significantly higher in ER+ versus ER− breast cancer cells lines; however LRH-1 protein was expressed at similar levels. We found LRH-1 mRNA and protein was more stable in ER− compared to ER+ cell lines. The tumor-specific LRH-1 variant isoform, LRH-1v4, which is highly responsive to E{sub 2}, showed increased mRNA stability in ER− versus ER+ cells. In addition, in MCF-7 and T47-D cell lines, LRH-1 total mRNA stability was reduced with E{sub 2} treatment, this effect mediated by ERα. Our data demonstrates that in ER− cells, increased mRNA and protein stability contribute to the abundant protein expression levels. Expression and immunolocalisation of LRH-1 in ER− cells as well as ER− tumors suggests a possible role in the development of ER− tumors. The modulation of LRH-1 bioactivity may therefore be beneficial as a treatment option in both ER− and ER+ breast cancer.

Highly abundant and stage-specific mRNAs in the obligate pathogen Bremia lactucae.

Science.gov (United States)

Judelson, H S; Michelmore, R W

1990-01-01

Germinating spores of the obligate pathogen Bremia lactucae (lettuce downy mildew) contain several unusually abundant species of mRNA. Thirty-nine cDNA clones corresponding to prevalent transcripts were isolated from a library synthesized using poly(A)+ RNA from germinating spores; these clones represented only five distinct classes. Each corresponding mRNA accounted for from 0.4 to 9 percent by mass of poly(A)+ RNA from germinating spores and together represented greater than 20 percent of the mRNA. The expression of the corresponding genes, and a gene encoding Hsp70, was analyzed in spores during germination and during growth in planta. The Hsp70 mRNA and mRNA from one abundant cDNA clone (ham34) were expressed constitutively. Two clones (ham9 and ham12) hybridized only to mRNA from spores and germinating spores. Two clones (ham37 and ham27) showed hybridization specific to germinating spores. Quantification of the number of genes homologous to each cDNA clone indicated that four clones corresponded to one or two copies per haploid genome, and one hybridized to an approximately 11-member family of genes. A sequence of the gene corresponding to ham34 was obtained to investigate its function and to identify sequences conferring high levels of gene expression for use in constructing vectors for the transformation of B. lactucae.

Short interfering RNAs targeting a vampire-bat related rabies virus phosphoprotein mRNA.

Science.gov (United States)

Ono, Ekaterina Alexandrovna Durymanova; Taniwaki, Sueli Akemi; Brandão, Paulo

The aim of this study was to assess the in vitro and in vivo effects of short-interfering RNAs (siRNAs) against rabies virus phosphoprotein (P) mRNA in a post-infection treatment for rabies as an extension of a previous report (Braz J Microbiol. 2013 Nov 15;44(3):879-82). To this end, rabies virus strain RABV-4005 (related to the Desmodus rotundus vampire bat) were used to inoculate BHK-21 cells and mice, and the transfection with each of the siRNAs was made with Lipofectamine-2000™. In vitro results showed that siRNA 360 was able to inhibit the replication of strain RABV-4005 with a 1log decrease in virus titter and 5.16-fold reduction in P mRNA, 24h post-inoculation when compared to non-treated cells. In vivo, siRNA 360 was able to induce partial protection, but with no significant difference when compared to non-treated mice. These results indicate that, despite the need for improvement for in vivo applications, P mRNA might be a target for an RNAi-based treatment for rabies. Copyright © 2017 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Natural selection and algorithmic design of mRNA.

Science.gov (United States)

Cohen, Barry; Skiena, Steven

2003-01-01

Messenger RNA (mRNA) sequences serve as templates for proteins according to the triplet code, in which each of the 4(3) = 64 different codons (sequences of three consecutive nucleotide bases) in RNA either terminate transcription or map to one of the 20 different amino acids (or residues) which build up proteins. Because there are more codons than residues, there is inherent redundancy in the coding. Certain residues (e.g., tryptophan) have only a single corresponding codon, while other residues (e.g., arginine) have as many as six corresponding codons. This freedom implies that the number of possible RNA sequences coding for a given protein grows exponentially in the length of the protein. Thus nature has wide latitude to select among mRNA sequences which are informationally equivalent, but structurally and energetically divergent. In this paper, we explore how nature takes advantage of this freedom and how to algorithmically design structures more energetically favorable than have been built through natural selection. In particular: (1) Natural Selection--we perform the first large-scale computational experiment comparing the stability of mRNA sequences from a variety of organisms to random synonymous sequences which respect the codon preferences of the organism. This experiment was conducted on over 27,000 sequences from 34 microbial species with 36 genomic structures. We provide evidence that in all genomic structures highly stable sequences are disproportionately abundant, and in 19 of 36 cases highly unstable sequences are disproportionately abundant. This suggests that the stability of mRNA sequences is subject to natural selection. (2) Artificial Selection--motivated by these biological results, we examine the algorithmic problem of designing the most stable and unstable mRNA sequences which code for a target protein. We give a polynomial-time dynamic programming solution to the most stable sequence problem (MSSP), which is asymptotically no more complex

Transcript Abundance of Photorhabdus Insect-Related (Pir Toxin in Manduca sexta and Galleria mellonella Infections

Directory of Open Access Journals (Sweden)

Anaïs Castagnola

2016-09-01

Full Text Available In this study, we assessed pirAB toxin transcription in Photorhabdus luminescens laumondii (strain TT01 (Enterobacteriaceae by comparing mRNA abundance under in vivo and in vitro conditions. In vivo assays considered both natural and forced infections with two lepidopteran hosts: Galleria mellonella and Manduca sexta. Three portals of entry were utilized for the forced infection assays: (a integument; (b the digestive route (via mouth and anus; and (c the tracheal route (via spiracles. We also assessed plu4093-2 transcription during the course of a natural infection; this is when the bacteria are delivered by Heterorhabditis bacteriophora nematodes. Transcript abundance in G. mellonella was higher than in M. sexta at two of the observed time points: 15 and 18 h. Expression of pirAB plu4093-2 reached above endogenous control levels at 22 h in G. mellonella but not in M. sexta. Overall, pirAB plu4093-2 transcripts were not as highly expressed in M. sexta as in G. mellonella, from 15 to 22 h. This is the first study to directly compare pirAB plu4093-2 toxin transcript production considering different portals of entry.

Proteoglycans in Leiomyoma and Normal Myometrium: Abundance, Steroid Hormone Control, and Implications for Pathophysiology.

Science.gov (United States)

Barker, Nichole M; Carrino, David A; Caplan, Arnold I; Hurd, William W; Liu, James H; Tan, Huiqing; Mesiano, Sam

2016-03-01

Uterine leiomyoma are a common benign pelvic tumors composed of modified smooth muscle cells and a large amount of extracellular matrix (ECM). The proteoglycan composition of the leiomyoma ECM is thought to affect pathophysiology of the disease. To test this hypothesis, we examined the abundance (by immunoblotting) and expression (by quantitative real-time polymerase chain reaction) of the proteoglycans biglycan, decorin, and versican in leiomyoma and normal myometrium and determined whether expression is affected by steroid hormones and menstrual phase. Leiomyoma and normal myometrium were collected from women (n = 17) undergoing hysterectomy or myomectomy. In vitro studies were performed on immortalized leiomyoma (UtLM) and normal myometrial (hTERT-HM) cells with and without exposure to estradiol and progesterone. In leiomyoma tissue, abundance of decorin messenger RNA (mRNA) and protein were 2.6-fold and 1.4-fold lower, respectively, compared with normal myometrium. Abundance of versican mRNA was not different between matched samples, whereas versican protein was increased 1.8-fold in leiomyoma compared with myometrium. Decorin mRNA was 2.4-fold lower in secretory phase leiomyoma compared with proliferative phase tissue. In UtLM cells, progesterone decreased the abundance of decorin mRNA by 1.3-fold. Lower decorin expression in leiomyoma compared with myometrium may contribute to disease growth and progression. As decorin inhibits the activity of specific growth factors, its reduced level in the leiomyoma cell microenvironment may promote cell proliferation and ECM deposition. Our data suggest that decorin expression in leiomyoma is inhibited by progesterone, which may be a mechanism by which the ovarian steroids affect leiomyoma growth and disease progression. © The Author(s) 2015.

CCS mRNA transcripts and serum CCS protein as copper marker in adults suffering inflammatory processes.

Science.gov (United States)

Araya, Magdalena; Gutiérrez, Ricardo; Arredondo, Miguel

2014-08-01

The chaperone to Zn-Cu superoxide dismutase (CCS) has been postulated as a candidate copper indicator, changing in a consistent manner in induced and recovered copper deficiency, in experimental cell and animal models. In real life people have various conditions that may modify molecules acting as acute phase proteins, such as serum ceruloplasmin and copper concentration and could alter CCS responses. With the hypothesis that CCS mRNA transcripts and protein would be different in individuals suffering inflammatory processes in comparison to healthy individuals, we assessed adult individuals who, although not ill had conditions known to induce variable degrees of inflammation. Screening of 600 adults resulted in two study groups, formed on the basis of their clinical history and levels of serum C reactive protein (CRP): Group 1 (n = 61, mean (range) CRP = 0.9 (0.3-2.0 mg/dL) and Group 2 (n = 150, mean (range) CRP = 6.1 (4.3-8.7 mg/dL). Results showed that mRNA transcripts relative abundance was not different for CCS, MTIIA, TNF-alpha and Cu-Zn-SOD by group (p > 0.05, one way Anova), nor between sexes (p > 0.05, one way Anova). Distribution of CCS mRNA transcripts and CCS protein in serum did not show any differences or trends. Results disproved our hypothesis that CCS abundance of transcripts and CCS protein would be different in individuals suffering inflammatory processes, adding further support to the idea that CCS may be a copper marker.

types and abundance of arthropod fauna in relation to physico ...

African Journals Online (AJOL)

DJFLEX

TYPES AND ABUNDANCE OF ARTHROPOD FAUNA IN RELATION ... The occurrence of arthropods associated with the bottom sediment of Warri River was investigated, and samples were collected ..... to analysis of the vegetation on Danish.

The abundance properties of nearby late-type galaxies. II. The relation between abundance distributions and surface brightness profiles

International Nuclear Information System (INIS)

Pilyugin, L. S.; Grebel, E. K.; Zinchenko, I. A.; Kniazev, A. Y.

2014-01-01

The relations between oxygen abundance and disk surface brightness (OH–SB relation) in the infrared W1 band are examined for nearby late-type galaxies. The oxygen abundances were presented in Paper I. The photometric characteristics of the disks are inferred here using photometric maps from the literature through bulge-disk decomposition. We find evidence that the OH–SB relation is not unique but depends on the galactocentric distance r (taken as a fraction of the optical radius R 25 ) and on the properties of a galaxy: the disk scale length h and the morphological T-type. We suggest a general, four-dimensional OH–SB relation with the values r, h, and T as parameters. The parametric OH–SB relation reproduces the observed data better than a simple, one-parameter relation; the deviations resulting when using our parametric relation are smaller by a factor of ∼1.4 than that of the simple relation. The influence of the parameters on the OH–SB relation varies with galactocentric distance. The influence of the T-type on the OH–SB relation is negligible at the centers of galaxies and increases with galactocentric distance. In contrast, the influence of the disk scale length on the OH–SB relation is at a maximum at the centers of galaxies and decreases with galactocentric distance, disappearing at the optical edges of galaxies. Two-dimensional relations can be used to reproduce the observed data at the optical edges of the disks and at the centers of the disks. The disk scale length should be used as a second parameter in the OH–SB relation at the center of the disk while the morphological T-type should be used as a second parameter in the relation at optical edge of the disk. The relations between oxygen abundance and disk surface brightness in the optical B and infrared K bands at the center of the disk and at optical edge of the disk are also considered. The general properties of the abundance–surface brightness relations are similar for the three

The decapping activator Edc3 and the Q/N-rich domain of Lsm4 function together to enhance mRNA stability and alter mRNA decay pathway dependence in Saccharomyces cerevisiae

Directory of Open Access Journals (Sweden)

Susanne Huch

2016-10-01

Full Text Available The rate and regulation of mRNA decay are major elements in the proper control of gene expression. Edc3 and Lsm4 are two decapping activator proteins that have previously been shown to function in the assembly of RNA granules termed P bodies. Here, we show that deletion of edc3, when combined with a removal of the glutamine/asparagine rich region of Lsm4 (edc3Δ lsm4ΔC reduces mRNA stability and alters pathways of mRNA degradation. Multiple tested mRNAs exhibited reduced stability in the edc3Δ lsm4ΔC mutant. The destabilization was linked to an increased dependence on Ccr4-mediated deadenylation and mRNA decapping. Unlike characterized mutations in decapping factors that either are neutral or are able to stabilize mRNA, the combined edc3Δ lsm4ΔC mutant reduced mRNA stability. We characterized the growth and activity of the major mRNA decay systems and translation in double mutant and wild-type yeast. In the edc3Δ lsm4ΔC mutant, we observed alterations in the levels of specific mRNA decay factors as well as nuclear accumulation of the catalytic subunit of the decapping enzyme Dcp2. Hence, we suggest that the effects on mRNA stability in the edc3Δ lsm4ΔC mutant may originate from mRNA decay protein abundance or changes in mRNPs, or alternatively may imply a role for P bodies in mRNA stabilization.

Abundance of specific mRNA transcripts impacts hatching success in European eel, Anguilla anguilla L

DEFF Research Database (Denmark)

Rozenfeld, Christoffer; Butts, Ian A.E.; Tomkiewicz, Jonna

2016-01-01

-tubulin, insulin-like growth factor 2 (igf2), nucleoplasmin (npm2), prohibitin 2 (phb2), phosphatidylinositol glycan biosynthesis class F protein 5 (pigf5), and carnitine O-palmitoyltransferase liver isoform-like 1 (cpt1) are associated with embryonic developmental competence in other teleosts. Here, the relations...... and no hatching groups for any of the selected genes at 0, 2.5, and 5 HPF. However, at 30 HPF the hatch group showed significantly higher abundance of cpt1a, cpt1b, β-tubulin, phb2, and pigf5 transcripts than the no hatch group. Therefore, these results indicate that up-regulation of the transcription...

Relative abundance of mesopredators and size of oak patches in the cross-timbers ecoregion

Science.gov (United States)

Disney, M.R.; Hellgren, E.C.; Davis, C.A.; Leslie, David M.; Engle, David M.

2008-01-01

Mesopredators (e.g., raccoon Procyon lotor, Virginia opossum Didelphis virginiana, striped skunk Mephitis mephitis) have received considerable attention because of links to population declines in birds via increased nest predation, especially in landscapes fragmented by anthropogenic forces. Relationships of abundance of mesopredators to size of habitat patches have received less attention than relationships to other metrics of fragmentation, particularly edge characteristics. We tested the hypothesis that relative abundance of mesopredators (e.g., raccoons and Virginia opossums) was related negatively to size of forest patch. We delineated 15 patches of oak (Quercus) forest ranging from 0.2 to 55.3 ha within a grassland-woodland mosaic in the cross-timbers ecoregion of Oklahoma. Scent stations and live traps within these patches were used to index relative abundance of mesopredators in summers 2003 and 2004. Both indices of relative abundance were related weakly and negatively to area of forest patch. However, rate of capture and visitation to scent station were not correlated consistently throughout the study. Our results suggested that the two methods to index abundance provided separate information on functional and numerical responses to size of patch. Our evidence that mesopredators within the cross timbers were more likely to be in smaller patches of oak forest may have implications to success of avian nesting in these patches.

Rhythmic expression of Nocturnin mRNA in multiple tissues of the mouse

Directory of Open Access Journals (Sweden)

Green Carla B

2001-05-01

Full Text Available Abstract Background Nocturnin was originally identified by differential display as a circadian clock regulated gene with high expression at night in photoreceptors of the African clawed frog, Xenopus laevis. Although encoding a novel protein, the nocturnin cDNA had strong sequence similarity with a C-terminal domain of the yeast transcription factor CCR4, and with mouse and human ESTs. Since its original identification others have cloned mouse and human homologues of nocturnin/CCR4, and we have cloned a full-length cDNA from mouse retina, along with partial cDNAs from human, cow and chicken. The goal of this study was to determine the temporal pattern of nocturnin mRNA expression in multiple tissues of the mouse. Results cDNA sequence analysis revealed a high degree of conservation among vertebrate nocturnin/CCR4 homologues along with a possible homologue in Drosophila. Northern analysis of mRNA in C3H/He and C57/Bl6 mice revealed that the mNoc gene is expressed in a broad range of tissues, with greatest abundance in liver, kidney and testis. mNoc is also expressed in multiple brain regions including suprachiasmatic nucleus and pineal gland. Furthermore, mNoc exhibits circadian rhythmicity of mRNA abundance with peak levels at the time of light offset in the retina, spleen, heart, kidney and liver. Conclusion The widespread expression and rhythmicity of mNoc mRNA parallels the widespread expression of other circadian clock genes in mammalian tissues, and suggests that nocturnin plays an important role in clock function or as a circadian clock effector.

Recruitment of Staufen2 Enhances Dendritic Localization of an Intron-Containing CaMKIIα mRNA

Directory of Open Access Journals (Sweden)

Raúl Ortiz

2017-07-01

Full Text Available Regulation of mRNA localization is a conserved cellular process observed in many types of cells and organisms. Asymmetrical mRNA distribution plays a particularly important role in the nervous system, where local translation of localized mRNA represents a key mechanism in synaptic plasticity. CaMKIIα is a very abundant mRNA detected in neurites, consistent with its crucial role at glutamatergic synapses. Here, we report the presence of CaMKIIα mRNA isoforms that contain intron i16 in dendrites, RNA granules, and synaptoneurosomes from primary neurons and brain. This subpopulation of unspliced mRNA preferentially localizes to distal dendrites in a synaptic-activity-dependent manner. Staufen2, a well-established marker of RNA transport in dendrites, interacts with intron i16 sequences and enhances its distal dendritic localization, pointing to the existence of intron-mediated mechanisms in the molecular pathways that modulate dendritic transport and localization of synaptic mRNAs.

The relative abundance of desert tortoises on the Nevada Test Site within ecological landform units

International Nuclear Information System (INIS)

Woodward, R.; Rautenstrauch, K.R.; Hall, D.B.; Ostler, W.K.

1998-09-01

Sign-survey transects were sampled in 1996 to better determine the relative abundance of desert tortoises on the Nevada Test Site (NTS). These transects were sampled within ecological land-form units (ELUs), which are small, ecologically homogeneous units of land. Two-hundred and six ELUs were sampled by walking 332 transects totaling 889 kilometers (km). These ELUs covered 528 km 2 . Two-hundred and eight-one sign were counted. An average of 0.32 sign was found per km walked. Seventy percent of the area sampled had a very low abundance of tortoises, 29% had a low abundance, and 1% had a moderate abundance. A revised map of the relative abundance of desert tortoise on the NTS is presented. Within the 1,330 km 2 of desert tortoise habitat on the NTS, 49% is classified as having no tortoises or a very low abundance, 18% has a low or moderate abundance, 12% is unclassified land being used by the Yucca Mountain Site Characterization Project, and the remaining 21% still has an unknown abundance of desert tortoises. Based on the results of this work, the amount of tortoise habitat previously classified as having an unknown or low-moderate abundance, and on which clearance surveys and on-site monitoring was required, has been reduced by 20%

Relative abundance estimations of Chengal trees in a tropical rainforest by using modified canopy fractional cover (mCFC)

International Nuclear Information System (INIS)

Hassan, N

2014-01-01

Tree species composition estimations are important to sustain forest management. This study estimates relative abundance of useful timber tree species (chengal) using Hyperion EO-1 satellite data. For the estimation, modified Canopy Fractional Cover (mCFC) was developed using Canopy Fractional Cover (CFC). mCFC was more sensitive to estimate relative abundance of chengal trees rather than Mixture Tuned Matched Filtering (MTMF). Meanwhile, MTMF was more sensitive to estimate the relative abundance of undisturbed forest. Accuracy suggests that the mCFC model is better to explain relative abundance of chengal trees than MTMF. Therefore, it can be concluded that relative abundance of tree species extracted from Hyperion EO-1 satellite data using modified Canopy Fractional Cover is an obtrusive approach used for identifying tree species composition

Peptide inhibitors of botulinum neurotoxin by mRNA display

International Nuclear Information System (INIS)

Yiadom, Kwabena P.A.B.; Muhie, Seid; Yang, David C.H.

2005-01-01

Botulinum neurotoxins (BoNTs) are extremely toxic. The metalloproteases associated with the toxins cleave proteins essential for neurotransmitter secretion. Inhibitors of the metalloprotease are currently sought to control the toxicity of BoNTs. Toward that goal, we produced a synthetic cDNA for the expression and purification of the metalloprotease of BoNT/A in Escherichia coli as a biotin-ubiquitin fusion protein, and constructed a combinatorial peptide library to screen for BoNT/A light chain inhibitors using mRNA display. A protease assay was developed using immobilized intact SNAP-25 as the substrate. The new peptide inhibitors showed a 10-fold increase in affinity to BoNT/A light chain than the parent peptide. Interestingly, the sequences of the new peptide inhibitors showed abundant hydrophobic residues but few hydrophilic residues. The results suggest that mRNA display may provide a general approach in developing peptide inhibitors of BoNTs

Application of hierarchical oligonucleotide primer extension (HOPE) to assess relative abundances of ammonia- and nitrite-oxidizing bacteria

KAUST Repository

Scarascia, Giantommaso

2017-04-04

Background: Establishing an optimal proportion of nitrifying microbial populations, including ammonia-oxidizing bacteria (AOB), nitrite-oxidizing bacteria (NOB), complete nitrite oxidizers (comammox) and ammonia-oxidizing archaea (AOA), is important for ensuring the efficiency of nitrification in water treatment systems. Hierarchical oligonucleotide primer extension (HOPE), previously developed to rapidly quantify relative abundances of specific microbial groups of interest, was applied in this study to track the abundances of the important nitrifying bacterial populations. Results: The method was tested against biomass obtained from a laboratory-scale biofilm-based trickling reactor, and the findings were validated against those obtained by 16S rRNA gene-based amplicon sequencing. Our findings indicated a good correlation between the relative abundance of nitrifying bacterial populations obtained using both HOPE and amplicon sequencing. HOPE showed a significant increase in the relative abundance of AOB, specifically Nitrosomonas, with increasing ammonium content and shock loading (p < 0.001). In contrast, Nitrosospira remained stable in its relative abundance against the total community throughout the operational phases. There was a corresponding significant decrease in the relative abundance of NOB, specifically Nitrospira and those affiliated to comammox, during the shock loading. Based on the relative abundance of AOB and NOB (including commamox) obtained from HOPE, it was determined that the optimal ratio of AOB against NOB ranged from 0.2 to 2.5 during stable reactor performance. Conclusions: Overall, the HOPE method was developed and validated against 16S rRNA gene-based amplicon sequencing for the purpose of performing simultaneous monitoring of relative abundance of nitrifying populations. Quantitative measurements of these nitrifying populations obtained via HOPE would be indicative of reactor performance and nitrification functionality.

The hypoxic proteome is influenced by gene-specific changes in mRNA translation

International Nuclear Information System (INIS)

Koritzinsky, Marianne; Seigneuric, Renaud; Magagnin, Michael G.; Beucken, Twan van den; Lambin, Philippe; Wouters, Bradly G.

2005-01-01

Background and purpose: Hypoxia causes a rapid reduction in mRNA translation efficiency. This inhibition does not affect all mRNA species to the same extent and can therefore contribute significantly to hypoxia-induced differential protein expression. Our aim in this study was to characterize changes in gene expression during acute hypoxia and evaluate the contribution of regulation via mRNA translation on these changes. For each gene, the contribution of changes in mRNA abundance versus mRNA translation was determined. Materials and methods: DU145 prostate carcinoma cells were exposed to 4 h of hypoxia ( 2 ). Efficiently translated mRNAs were isolated by sedimentation through a sucrose gradient. Affymetrix microarray technology was used to evaluate both the transcriptional and translational contribution to gene expression. Results were validated by quantitative PCR. Results: One hundred and twenty genes were more than 4-fold upregulated by hypoxia in the efficiently translated fraction of mRNA, in comparison to only 76 genes at the level of transcription. Of the 50 genes demonstrating the largest changes in translation, 11 were found to be more than 2-fold over represented in the translated fraction in comparison to their overall transcriptional level. The gene with the highest translational contribution to its induction was CITED-2, which is a negative regulator of HIF-1 transcriptional activity. Conclusions: Gene-specific regulation of mRNA translation contributes significantly to differential gene expression during hypoxia

Comparison of codon usage bias across Leishmania and Trypanosomatids to understand mRNA secondary structure, relative protein abundance and pathway functions.

Science.gov (United States)

Subramanian, Abhishek; Sarkar, Ram Rup

2015-10-01

Understanding the variations in gene organization and its effect on the phenotype across different Leishmania species, and to study differential clinical manifestations of parasite within the host, we performed large scale analysis of codon usage patterns between Leishmania and other known Trypanosomatid species. We present the causes and consequences of codon usage bias in Leishmania genomes with respect to mutational pressure, translational selection and amino acid composition bias. We establish GC bias at wobble position that governs codon usage bias across Leishmania species, rather than amino acid composition bias. We found that, within Leishmania, homogenous codon context coding for less frequent amino acid pairs and codons avoiding formation of folding structures in mRNA are essentially chosen. We predicted putative differences in global expression between genes belonging to specific pathways across Leishmania. This explains the role of evolution in shaping the otherwise conserved genome to demonstrate species-specific function-level differences for efficient survival. Copyright © 2015 Elsevier Inc. All rights reserved.

A pilot trial assessing urinary gene expression profiling with an mRNA array for diabetic nephropathy.

Directory of Open Access Journals (Sweden)

Min Zheng

Full Text Available BACKGROUND: The initiation and progression of diabetic nephropathy (DN is complex. Quantification of mRNA expression in urinary sediment has emerged as a novel strategy for studying renal diseases. Considering the numerous molecules involved in DN development, a high-throughput platform with parallel detection of multiple mRNAs is needed. In this study, we constructed a self-assembling mRNA array to analyze urinary mRNAs in DN patients with aims to reveal its potential in searching novel biomarkers. METHODS: mRNA array containing 88 genes were fabricated and its performance was evaluated. A pilot study with 9 subjects including 6 DN patients and 3 normal controls were studied with the array. DN patients were assigned into two groups according to their estimate glomerular rate (eGFR: DNI group (eGFR>60 ml/min/1.73 m(2, n = 3 and DNII group (eGFR<60 ml/min/1.73 m(2, n = 3. Urinary cell pellet was collected from each study participant. Relative abundance of these target mRNAs from urinary pellet was quantified with the array. RESULTS: The array we fabricated displayed high sensitivity and specificity. Moreover, the Cts of Positive PCR Controls in our experiments were 24±0.5 which indicated high repeatability of the array. A total of 29 mRNAs were significantly increased in DN patients compared with controls (p<0.05. Among these genes, α-actinin4, CDH2, ACE, FAT1, synaptopodin, COL4α, twist, NOTCH3 mRNA expression were 15-fold higher than those in normal controls. In contrast, urinary TIMP-1 mRNA was significantly decreased in DN patients (p<0.05. It was shown that CTGF, MCP-1, PAI-1, ACE, CDH1, CDH2 mRNA varied significantly among the 3 study groups, and their mRNA levels increased with DN progression (p<0.05. CONCLUSION: Our pilot study demonstrated that mRNA array might serve as a high-throughput and sensitive tool for detecting mRNA expression in urinary sediment. Thus, this primary study indicated that mRNA array probably could be a

Analysis of mRNA expression of genes related to fatty acids synthesis in goose fatty liver

Directory of Open Access Journals (Sweden)

Shuxia Xiang

2010-11-01

Full Text Available The aim of our study was to evaluate the effect of overfeeding on mRNA expression levels of genes involved in lipogenesis, in order to understand the mechanism of hepatic stea - tosis in the goose. Using Landes geese (Anser anser and Sichuan White geese (Anser cygnoides as experimental animals, we quantified the mRNA expression of lipogenic genes, acetyl-CoA carboxylase-α (ACCα and fatty acid synthase (FAS, and of two transcription factors, sterol regulatory element-binding proteins- 1 (SREBP-1 and carbohydrate responsive element-binding protein (ChREBP by real-time polymerase chain reaction (RTPCR, and measured the lipid and triglyceride (TG content in the liver and the plasma level of glucose, insulin and TG. Our results indicated that compared to the control group, the overfeeding induced an increase of the lipid and TG content in the liver and also of the plasma insulin and TG concentration in both breeds. However, the plasma glucose level decreased after overfeeding in the Sichuan White goose, and there was no evident change in the Landes goose. Lastly, the mRNA expression of ACCα, FAS, SREBP-1 and ChREBP in the overfed group was lower than in the control group in both breeds. We concluded that the lipogenesis pathway plays a role in overfeeding- induced hepatic steatosis and that the decreased mRNA level of related genes may be the indicator of hepatic steatosis.

Relative abundance estimations of chengal tree in a tropical rainforest by using modified Canopy Fractional Cover (mCFC)

International Nuclear Information System (INIS)

Hassan, N

2014-01-01

Tree species composition estimations are important to sustain forest management. This study challenged estimates of relative abundance of useful timber tree species (chengal) using Hyperion EO-1 satellite data. For the estimation, modified Canopy Fractional Cover (mCFC) was developed using Canopy Fractional Cover (CFC). mCFC was more sensitive to estimate relative abundance of chengal trees rather than Mixture Tuned Matched Filtering (MTMF). Meanwhile, MTMF was more sensitive to estimate the relative abundance of undisturbed forest. Accuracy suggests that the mCFC model is better to explain relative abundance of chengal trees than MTMF. Therefore, it can be concluded that relative abundance of trees species extracted from Hyperion EO-1 satellite data using modified Canopy Fractional Cover is an obtrusive approach used for identifying trees species composition

Effects of temperature and melatonin on day-night expression patterns of arginine vasotocin and isotocin mRNA in the diencephalon of a temperate wrasse Halichoeres tenuispinis.

Science.gov (United States)

Bouchekioua, Selma; Hur, Sung-Pyo; Takeuchi, Yuki; Lee, Young-Don; Takemura, Akihiro

2018-06-01

Most wrasses are protogynous species that swim to feed, reproduce during the daytime, and bury themselves under the sandy bottom at night. In temperate and subtropical wrasses, low temperature influences emergence from the sandy bottom in the morning, and induces a hibernation-like state in winter. We cloned and characterized the prohormone complementary DNAs (cDNAs) of arginine vasotocin (AVT) and isotocin (IT) in a temperate wrasse (Halichoeres tenuispinis) and examined the effects of day/night and temperature on their expression in the diencephalon, because these neurohypophysial peptides are related to the sex behavior of wrasses. The full-length cDNAs of pro-AVT and pro-IT were 938 base pairs (154 amino acids) and 759 base pairs (156 amino acids) in length, respectively. Both pro-peptides contained a signal sequence followed by the respective hormones and neurophysin connected by a Gly-Lys-Arg bridge. Reverse-transcription polymerase chain reaction (RT-PCR) revealed that pro-AVT mRNA expression was specifically observed in the diencephalon, whereas pro-IT mRNA expression was seen in the whole brain. Quantitative RT-PCR revealed that the mRNA abundance of pro-AVT and pro-IT was higher at midday (zeitgeber time 6; ZT6) than at midnight (ZT18) under 12 h light and 12 h darkness (LD 12:12) conditions, but not under constant light. Intraperitoneal injection of melatonin decreased the mRNA abundance of pro-AVT, but not of pro-IT. When fish were reared under LD 12:12 conditions at 25, 20, and 15 °C, day high and night low mRNA expressions of pro-AVT and pro-IT were maintained. A field survey revealed seasonal variation in the number of swimming fish at observatory sites; many fish emerged from the sandy bottom in summer, but not in winter, suggesting a hibernation-like state under the sandy bottom under low temperature conditions. We conclude that the day-night fluctuation of pro-AVT and pro-IT mRNA abundance in the brain is not affected by temperature and

GABAergic Neurons in the Rat Medial Septal Complex Express Relaxin-3 Receptor (RXFP3 mRNA

Directory of Open Access Journals (Sweden)

Hector Albert-Gascó

2018-01-01

Full Text Available The medial septum (MS complex modulates hippocampal function and related behaviors. Septohippocampal projections promote and control different forms of hippocampal synchronization. Specifically, GABAergic and cholinergic projections targeting the hippocampal formation from the MS provide bursting discharges to promote theta rhythm, or tonic activity to promote gamma oscillations. In turn, the MS is targeted by ascending projections from the hypothalamus and brainstem. One of these projections arises from the nucleus incertus in the pontine tegmentum, which contains GABA neurons that co-express the neuropeptide relaxin-3 (Rln3. Both stimulation of the nucleus incertus and septal infusion of Rln3 receptor agonist peptides promotes hippocampal theta rhythm. The Gi/o-protein-coupled receptor, relaxin-family peptide receptor 3 (RXFP3, is the cognate receptor for Rln3 and identification of the transmitter phenotype of neurons expressing RXFP3 in the septohippocampal system can provide further insights into the role of Rln3 transmission in the promotion of septohippocampal theta rhythm. Therefore, we used RNAscope multiplex in situ hybridization to characterize the septal neurons expressing Rxfp3 mRNA in the rat. Our results demonstrate that Rxfp3 mRNA is abundantly expressed in vesicular GABA transporter (vGAT mRNA- and parvalbumin (PV mRNA-positive GABA neurons in MS, whereas ChAT mRNA-positive acetylcholine neurons lack Rxfp3 mRNA. Approximately 75% of Rxfp3 mRNA-positive neurons expressed vGAT mRNA (and 22% were PV mRNA-positive, while the remaining 25% expressed Rxfp3 mRNA only, consistent with a potential glutamatergic phenotype. Similar proportions were observed in the posterior septum. The occurrence of RXFP3 in PV-positive GABAergic neurons gives support to a role for the Rln3-RXFP3 system in septohippocampal theta rhythm.

Skeletal muscle myostatin mRNA expression is fiber-type specific and increases during hindlimb unloading

Science.gov (United States)

Carlson, C. J.; Booth, F. W.; Gordon, S. E.

1999-01-01

Transgenic mice lacking a functional myostatin (MSTN) gene demonstrate greater skeletal muscle mass resulting from muscle fiber hypertrophy and hyperplasia (McPherron, A. C., A. M. Lawler, and S. -J. Lee. Nature 387: 83-90, 1997). Therefore, we hypothesized that, in normal mice, MSTN may act as a negative regulator of muscle mass. Specifically, we hypothesized that the predominately slow (type I) soleus muscle, which demonstrates greater atrophy than the fast (type II) gastrocnemius-plantaris complex (Gast/PLT), would show more elevation in MSTN mRNA abundance during hindlimb unloading (HU). Surprisingly, MSTN mRNA was not detectable in weight-bearing or HU soleus muscle, which atrophied 42% by the 7th day of HU in female ICR mice. In contrast, MSTN mRNA was present in weight-bearing Gast/PLT muscle and was significantly elevated (67%) at 1 day but not at 3 or 7 days of HU. However, the Gast/PLT muscle had only atrophied 17% by the 7th day of HU. Because the soleus is composed only of type I and IIa fibers, whereas the Gast/PLT expresses type IId/x and IIb in addition to type I and IIa, it was necessary to perform a more careful analysis of the relationship between MSTN mRNA levels and myosin heavy-chain (MHC) isoform expression (as a marker of fiber type). A significant correlation (r = 0.725, P < 0. 0005) was noted between the percentage of MHC isoform IIb expression and MSTN mRNA abundance in several muscles of the mouse hindlimb. These results indicate that MSTN expression is not strongly associated with muscle atrophy induced by HU; however, it is strongly associated with MHC isoform IIb expression in normal muscle.

Green tea increases anti-inflammatory tristetraprolin and decreases pro-inflammatory tumor necrosis factor mRNA levels in rats

Directory of Open Access Journals (Sweden)

Roussel Anne M

2007-01-01

Full Text Available Abstract Background Tristetraprolin (TTP/ZFP36 family proteins have anti-inflammatory activity by binding to and destabilizing pro-inflammatory mRNAs such as Tnf mRNA, and represent a potential therapeutic target for inflammation-related diseases. Tea has anti-inflammatory properties but the molecular mechanisms have not been completely elucidated. We hypothesized that TTP and/or its homologues might contribute to the beneficial effects of tea as an anti-inflammatory product. Methods Quantitative real-time PCR was used to investigate the effects of green tea (0, 1, and 2 g solid extract/kg diet on the expression of Ttp family genes (Ttp/Tis11/Zfp36, Zfp36l1/Tis11b, Zfp36l2/Tis11d, Zfp36l3, pro-inflammatory genes (Tnf, Csf2/Gm-csf, Ptgs2/Cox2, and Elavl1/Hua/Hur and Vegf genes in liver and muscle of rats fed a high-fructose diet known to induce insulin resistance, oxidative stress, inflammation, and TNF-alpha levels. Results Ttp and Zfp36l1 mRNAs were the major forms in both liver and skeletal muscle. Ttp, Zfp36l1, and Zfp36l2 mRNA levels were more abundant in the liver than those in the muscle. Csf2/Gm-csf and Zfp36l3 mRNAs were undetectable in both tissues. Tea (1 g solid extract/kg diet increased Ttp mRNA levels by 50–140% but Tnf mRNA levels decreased by 30% in both tissues, and Ptgs2/Cox2 mRNA levels decreased by 40% in the muscle. Tea (2 g solid extract/kg diet increased Elavl1/Hua/Hur mRNA levels by 40% in the liver but did not affect any of the other mRNA levels in liver or muscle. Conclusion These results show that tea can modulate Ttp mRNA levels in animals and suggest that a post-transcriptional mechanism through TTP could partially account for tea's anti-inflammatory properties. The results also suggest that drinking adequate amounts of green tea may play a role in the prevention of inflammation-related diseases.

Archaeal and bacterial H-GDGTs are abundant in peat and their relative abundance is positively correlated with temperature

Science.gov (United States)

Naafs, B. D. A.; McCormick, D.; Inglis, G. N.; Pancost, R. D.; T-GRES Peat Database Collaborators

2018-04-01

Glycerol monoalkyl glycerol tetraether lipids (GMGTs; also called 'H-GDGTs') differ from the more commonly studied glycerol dialkyl glycerol tetraether (GDGTs) in that they have an additional covalent bond that links the two alkyl chains. Six different archaeal isoprenoidal H-GDGTs (H-isoGDGTs) and one branched H-GDGT (H-brGDGT), presumably produced by bacteria, have previously been found. However, the function of H-GDGTs in both domains of life is unknown. It is thought that the formation of this additional covalent bond results in enhanced membrane stability, accounting for the high abundance of H-GDGTs in extreme environments such as geothermal settings, but so far there has been little evidence to support this hypothesis. Here we report the distribution of H-GDGTs in a global peat database (n = 471) with a broad range in mean annual air temperature (MAAT) and pH. This is the first finding of H-GDGTs in soils (specifically, peat), highlighting that H-GDGTs are widespread in mesophilic settings. In addition, we report the presence of two new H-brGDGTs with one (H-1034) and two (H-1048) additional methyl groups, respectively. Our results suggest that the relative abundance of both bacterial and archaeal H-GDGTs compared to regular GDGTs is related to temperature with the highest relative abundance of H-GDGTs in tropical peats. Although other factors besides temperature likely also play a role, these results do support the hypothesis that H-GDGTs are an adaptation to temperature to maintain membrane stability. The observation that both bacterial and archaeal membrane lipids respond to temperature indicates the same adaption across the lipid divide between these two domains of life, suggesting parallel or convergent evolution (potentially facilitated by lateral gene transfer).

The NO signaling pathway differentially regulates KCC3a and KCC3b mRNA expression.

Science.gov (United States)

Di Fulvio, Mauricio; Lauf, Peter K; Adragna, Norma C

2003-11-01

Nitric oxide (NO) donors and protein kinase G (PKG) acutely up-regulate K-Cl cotransporter-1 and -3 (KCC1 and KCC3) mRNA expression in vascular smooth muscle cells (VSMCs). Here, we report the presence, relative abundance, and regulation by sodium nitroprusside (SNP) of the novel KCC3a and KCC3b mRNAs, in primary cultures of rat VSMCs. KCC3a and KCC3b mRNAs were expressed in an approximate 3:1 ratio, as determined by semiquantitative RT-PCR analysis. SNP as well as YC-1 and 8-Br-cGMP, a NO-independent stimulator of soluble guanylyl cyclase (sGC) and PKG, respectively, increased KCC3a and KCC3b mRNA expression by 2.5-fold and 8.1-fold in a time-dependent manner, following a differential kinetics. Stimulation of the NO/sGC/PKG signaling pathway with either SNP, YC-1, or 8-Br-cGMP decreased the KCC3a/KCC3b ratio from 3.0+/-0.4 to 0.9+/-0.1. This is the first report on a differential regulation by the NO/sGC/PKG signaling pathway of a cotransporter and of KCC3a and KCC3b mRNA expression.

Contraction-induced increases in Na+-K+-ATPase mRNA levels in human skeletal muscle are not amplified by activation of additional muscle mass

DEFF Research Database (Denmark)

Nordsborg, Nikolai; Thomassen, Martin; Lundby, Carsten

2005-01-01

The present study tested the hypothesis that exercise with a large compared with a small active muscle mass results in a higher contraction-induced increase in Na+-K+-ATPase mRNA expression due to greater hormonal responses. Furthermore, the relative abundance of Na+-K+-ATPase subunit a1, a2, a3, a......% of the a2 expression, and no reliable detection of a3 and a4 was possible. In conclusion, activation of additional muscle mass does not result in a higher exercise-induced increase in Na+-K+-ATPase subunit-specific mRNA.......4, ß1, ß2, and ß3 mRNA in human skeletal muscle was investigated. On two occasions, eight subjects performed one-legged knee extension exercise (L) or combined one-legged knee extension and bilateral arm cranking (AL) for 5.00, 4.25, 3.50, 2.75, and 2.00 min separated by 3 min of rest. Leg exercise...

Relation between grade and abundance of manganese nodules

Digital Repository Service at National Institute of Oceanography (India)

Sudhakar, M.

Data from more than 1000 locations in the Central Indian Ocean Basin (CIOB) where both bulk nodule chemistry and abundance were determined and utilized to study the relationship between grade and abundance of manganese nodule deposits. Grade...

Housing system influences abundance of Pax3 and Pax7 in postnatal chicken skeletal muscles.

Science.gov (United States)

Yin, H D; Li, D Y; Zhang, L; Yang, M Y; Zhao, X L; Wang, Y; Liu, Y P; Zhu, Q

2014-06-01

Paired box (Pax) proteins 3 and 7 are associated with activation of muscle satellite cells and play a major role in hyperplastic and hypertrophic growth in postnatal skeletal muscle fibers. The objective of this study was to evaluate the effect of housing system on abundance of Pax3 and Pax7 in postnatal chicken skeletal muscles. At 42 d, 1,200 chickens with similar BW were randomly assigned to cage, pen, and free-range group. The mRNA abundance was measured in pectoralis major and thigh muscle at d 56, 70, and 84, and the protein expression was quantified at d 84. Increases in mRNA abundance of PAX3 and PAX7 with age were less pronounced in caged system chickens than in pen and free-range chickens from d 56 to 84, and free-range chickens showed a more pronounced increase in gene expression with age compared with penned chickens. At d 84, quantities of PAX3 and PAX7 mRNA and protein were highest in both pectoralis major and thigh muscle of chickens raised in the free-range group, lowest in penned chickens, and intermediate in caged chickens (P system may influence muscle fiber muscle accretion by coordinating the expression of Pax3 and Pax7 in adult chicken skeletal muscles. Poultry Science Association Inc.

[Effects of lipopolysaccharides extracted from Porphyromonas endodontalis on the expression of IL-1beta mRNA and IL-6 mRNA in osteoblasts].

Science.gov (United States)

Yang, Di; Li, Ren; Qiu, Li-Hong; Li, Chen

2009-04-01

To quantify the IL-1 beta mRNA and IL-6 mRNA expression induced by lipopolysaccharides (LPS)extracted from Porphyromonas endodontalis(P.e) in osteoblasts, and to relate P.e-LPS to bone absorption pathogenesis in lesions of chronical apical periodontitis. MG63 was treated with different concentrations of P.e-LPS(0-50 microg/mL) for different hours(0-24h). The expression of IL-1 beta mRNA and IL-6 mRNA was detected by reverse transcription polymerase chain reaction (RT-PCR).Statistical analysis was performed using one- way ANOVA and Dunnett t test with SPSS11.0 software package. The level of IL-1 beta mRNA and IL-6 mRNA increased significantly after treatment with P.e-LPS at more than 5 microg/mL (P<0.01)and for more than 1 hour (P<0.01), which indicated that P.e-LPS induced osteoblasts to express IL-1 beta mRNA and IL-6 mRNA in dose and time dependent manners. P.e-LPS may promote bone resorption in lesions of chronical apical periodontitis by inducing IL-1 beta mRNA and IL-6 mRNA expression in osteoblasts.

Parametric scaling from species relative abundances to absolute abundances in the computation of biological diversity: a first proposal using Shannon's entropy.

Science.gov (United States)

Ricotta, Carlo

2003-01-01

Traditional diversity measures such as the Shannon entropy are generally computed from the species' relative abundance vector of a given community to the exclusion of species' absolute abundances. In this paper, I first mention some examples where the total information content associated with a given community may be more adequate than Shannon's average information content for a better understanding of ecosystem functioning. Next, I propose a parametric measure of statistical information that contains both Shannon's entropy and total information content as special cases of this more general function.

CCS and SOD1 mRNA are reduced after copper supplementation in peripheral mononuclear cells of individuals with high serum ceruloplasmin concentration.

Science.gov (United States)

Suazo, Miriam; Olivares, Felipe; Mendez, Marco A; Pulgar, Rodrigo; Prohaska, Joseph R; Arredondo, Miguel; Pizarro, Fernando; Olivares, Manuel; Araya, Magdalena; González, Mauricio

2008-04-01

The limits of copper homeostatic regulation in humans are not known, making it difficult to define the milder effects of early copper excess. Furthermore, a robust assay to facilitate the detection of early stages of copper excess is needed. To address these issues, we assessed changes in relative mRNA abundance of methallothionein 2A (MT2A), prion (PrP), amyloid precursor-like protein 2 (APLP2), Cu/Zn superoxide dismutase (SOD1) and its copper chaperone (CCS) in peripheral mononuclear cells (PMNCs) from healthy adults representing the 5% highest and lowest extremes in the distribution curve of serum ceruloplasmin (Cp) concentrations of 800 individuals. The intracellular Cu content was also determined. PMNCs were isolated from individuals before and after exposure to a single daily dose of 10 mg Cu (as CuSO(4)) for 2 months. Results showed that although there were fluctuations in serum Cp values of the samples assessed before copper exposure, no significant differences were observed in cell copper content or in the relative abundance of MT2A, PrP and APLP2 transcripts in PMNCs. Also, these values were not modified after copper supplementation. However, CCS and SOD1 mRNA levels were reduced in PMNCs after copper supplementation in the individuals with the high Cp values, suggesting that they should be further explored as biomarkers of moderate copper overload in humans.

Endogenous ribosomal frameshift signals operate as mRNA destabilizing elements through at least two molecular pathways in yeast.

Science.gov (United States)

Belew, Ashton T; Advani, Vivek M; Dinman, Jonathan D

2011-04-01

Although first discovered in viruses, previous studies have identified operational -1 ribosomal frameshifting (-1 RF) signals in eukaryotic genomic sequences, and suggested a role in mRNA stability. Here, four yeast -1 RF signals are shown to promote significant mRNA destabilization through the nonsense mediated mRNA decay pathway (NMD), and genetic evidence is presented suggesting that they may also operate through the no-go decay pathway (NGD) as well. Yeast EST2 mRNA is highly unstable and contains up to five -1 RF signals. Ablation of the -1 RF signals or of NMD stabilizes this mRNA, and changes in -1 RF efficiency have opposing effects on the steady-state abundance of the EST2 mRNA. These results demonstrate that endogenous -1 RF signals function as mRNA destabilizing elements through at least two molecular pathways in yeast. Consistent with current evolutionary theory, phylogenetic analyses suggest that -1 RF signals are rapidly evolving cis-acting regulatory elements. Identification of high confidence -1 RF signals in ∼10% of genes in all eukaryotic genomes surveyed suggests that -1 RF is a broadly used post-transcriptional regulator of gene expression.

Long-term changes in species composition and relative abundances of sharks at a provisioning site.

Directory of Open Access Journals (Sweden)

Juerg M Brunnschweiler

Full Text Available Diving with sharks, often in combination with food baiting/provisioning, has become an important product of today's recreational dive industry. Whereas the effects baiting/provisioning has on the behaviour and abundance of individual shark species are starting to become known, there is an almost complete lack of equivalent data from multi-species shark diving sites. In this study, changes in species composition and relative abundances were determined at the Shark Reef Marine Reserve, a multi-species shark feeding site in Fiji. Using direct observation sampling methods, eight species of sharks (bull shark Carcharhinus leucas, grey reef shark Carcharhinus amblyrhynchos, whitetip reef shark Triaenodon obesus, blacktip reef shark Carcharhinus melanopterus, tawny nurse shark Nebrius ferrugineus, silvertip shark Carcharhinus albimarginatus, sicklefin lemon shark Negaprion acutidens, and tiger shark Galeocerdo cuvier displayed inter-annual site fidelity between 2003 and 2012. Encounter rates and/or relative abundances of some species changed over time, overall resulting in more individuals (mostly C. leucas of fewer species being encountered on average on shark feeding dives at the end of the study period. Differences in shark community composition between the years 2004-2006 and 2007-2012 were evident, mostly because N. ferrugineus, C. albimarginatus and N. acutidens were much more abundant in 2004-2006 and very rare in the period of 2007-2012. Two explanations are offered for the observed changes in relative abundances over time, namely inter-specific interactions and operator-specific feeding protocols. Both, possibly in combination, are suggested to be important determinants of species composition and encounter rates, and relative abundances at this shark provisioning site in Fiji. This study, which includes the most species from a spatially confined shark provisioning site to date, suggests that long-term provisioning may result in competitive

Long-term changes in species composition and relative abundances of sharks at a provisioning site.

Science.gov (United States)

Brunnschweiler, Juerg M; Abrantes, Kátya G; Barnett, Adam

2014-01-01

Diving with sharks, often in combination with food baiting/provisioning, has become an important product of today's recreational dive industry. Whereas the effects baiting/provisioning has on the behaviour and abundance of individual shark species are starting to become known, there is an almost complete lack of equivalent data from multi-species shark diving sites. In this study, changes in species composition and relative abundances were determined at the Shark Reef Marine Reserve, a multi-species shark feeding site in Fiji. Using direct observation sampling methods, eight species of sharks (bull shark Carcharhinus leucas, grey reef shark Carcharhinus amblyrhynchos, whitetip reef shark Triaenodon obesus, blacktip reef shark Carcharhinus melanopterus, tawny nurse shark Nebrius ferrugineus, silvertip shark Carcharhinus albimarginatus, sicklefin lemon shark Negaprion acutidens, and tiger shark Galeocerdo cuvier) displayed inter-annual site fidelity between 2003 and 2012. Encounter rates and/or relative abundances of some species changed over time, overall resulting in more individuals (mostly C. leucas) of fewer species being encountered on average on shark feeding dives at the end of the study period. Differences in shark community composition between the years 2004-2006 and 2007-2012 were evident, mostly because N. ferrugineus, C. albimarginatus and N. acutidens were much more abundant in 2004-2006 and very rare in the period of 2007-2012. Two explanations are offered for the observed changes in relative abundances over time, namely inter-specific interactions and operator-specific feeding protocols. Both, possibly in combination, are suggested to be important determinants of species composition and encounter rates, and relative abundances at this shark provisioning site in Fiji. This study, which includes the most species from a spatially confined shark provisioning site to date, suggests that long-term provisioning may result in competitive exclusion among shark

Snipper, an Eri1 homologue, affects histone mRNA abundance and is crucial for normal Drosophila melanogaster development.

Science.gov (United States)

Alexiadis, Anastasios; Delidakis, Christos; Kalantidis, Kriton

2017-07-01

The conserved 3'-5' RNA exonuclease ERI1 is implicated in RNA interference inhibition, 5.8S rRNA maturation and histone mRNA maturation and turnover. The single ERI1 homologue in Drosophila melanogaster Snipper (Snp) is a 3'-5' exonuclease, but its in vivo function remains elusive. Here, we report Snp requirement for normal Drosophila development, since its perturbation leads to larval arrest and tissue-specific downregulation results in abnormal tissue development. Additionally, Snp directly interacts with histone mRNA, and its depletion results in drastic reduction in histone transcript levels. We propose that Snp protects the 3'-ends of histone mRNAs and upon its absence, histone transcripts are readily degraded. This in turn may lead to cell cycle delay or arrest, causing growth arrest and developmental perturbations. © 2017 Federation of European Biochemical Societies.

Heritability in the efficiency of nonsense-mediated mRNA decay in humans.

LENUS (Irish Health Repository)

Seoighe, Cathal

2010-01-01

BACKGROUND: In eukaryotes mRNA transcripts of protein-coding genes in which an intron has been retained in the coding region normally result in premature stop codons and are therefore degraded through the nonsense-mediated mRNA decay (NMD) pathway. There is evidence in the form of selective pressure for in-frame stop codons in introns and a depletion of length three introns that this is an important and conserved quality-control mechanism. Yet recent reports have revealed that the efficiency of NMD varies across tissues and between individuals, with important clinical consequences. PRINCIPAL FINDINGS: Using previously published Affymetrix exon microarray data from cell lines genotyped as part of the International HapMap project, we investigated whether there are heritable, inter-individual differences in the abundance of intron-containing transcripts, potentially reflecting differences in the efficiency of NMD. We identified intronic probesets using EST data and report evidence of heritability in the extent of intron expression in 56 HapMap trios. We also used a genome-wide association approach to identify genetic markers associated with intron expression. Among the top candidates was a SNP in the DCP1A gene, which forms part of the decapping complex, involved in NMD. CONCLUSIONS: While we caution that some of the apparent inter-individual difference in intron expression may be attributable to different handling or treatments of cell lines, we hypothesize that there is significant polymorphism in the process of NMD, resulting in heritable differences in the abundance of intronic mRNA. Part of this phenotype is likely to be due to a polymorphism in a decapping enzyme on human chromosome 3.

Heritability in the efficiency of nonsense-mediated mRNA decay in humans

KAUST Repository

Seoighe, Cathal

2010-07-21

Background: In eukaryotes mRNA transcripts of protein-coding genes in which an intron has been retained in the coding region normally result in premature stop codons and are therefore degraded through the nonsense-mediated mRNA decay (NMD) pathway. There is evidence in the form of selective pressure for in-frame stop codons in introns and a depletion of length three introns that this is an important and conserved quality-control mechanism. Yet recent reports have revealed that the efficiency of NMD varies across tissues and between individuals, with important clinical consequences. Principal Findings: Using previously published Affymetrix exon microarray data from cell lines genotyped as part of the International HapMap project, we investigated whether there are heritable, inter-individual differences in the abundance of intron-containing transcripts, potentially reflecting differences in the efficiency of NMD. We identified intronic probesets using EST data and report evidence of heritability in the extent of intron expression in 56 HapMap trios. We also used a genome-wide association approach to identify genetic markers associated with intron expression. Among the top candidates was a SNP in the DCP1A gene, which forms part of the decapping complex, involved in NMD. Conclusions: While we caution that some of the apparent inter-individual difference in intron expression may be attributable to different handling or treatments of cell lines, we hypothesize that there is significant polymorphism in the process of NMD, resulting in heritable differences in the abundance of intronic mRNA. Part of this phenotype is likely to be due to a polymorphism in a decapping enzyme on human chromosome 3. © 2010 Seoighe, Gehring.

Impacts of different exposure scenarios on transcript abundances in Danio rerio embryos when investigating the toxicological burden of riverine sediments.

Directory of Open Access Journals (Sweden)

Kerstin Bluhm

Full Text Available PURPOSE: Recently, a proof-of-concept study revealed the suitability of transcriptome analyses to obtain and assess changes in the abundance of transcripts in zebrafish (Danio rerio embryos after exposure to organic sediment extracts. The present study investigated changes in the transcript abundance in zebrafish embryos exposed to whole sediment samples and corresponding organic extracts in order to identify the impact of different exposure pathways on sediment toxicity. MATERIALS AND METHODS: Danio rerio embryos were exposed to sublethal concentrations of three sediment samples from the Danube River, Germany. The sediment samples were investigated both as freeze-dried samples and as organic extracts. Silica dust and a process control of the extraction procedure were used as references. After exposure, mRNA was isolated and changes in profiles of gene expression levels were examined by an oligonucleotide microarray. The microarray results were compared with bioassays, chemical analysis of the sediments and profiles of gene expression levels induced by several single substances. RESULTS AND DISCUSSION: The microarray approach elucidated significant changes in the abundance of transcripts in exposed zebrafish embryos compared to the references. Generally, results could be related to Ah-receptor-mediated effects as confirmed by bioassays and chemical analysis of dioxin-like contaminants, as well as to exposure to stress-inducing compounds. Furthermore, the results indicated that mixtures of chemicals, as present in sediment and extract samples, result in complex changes of gene expression level profiles difficult to compare with profiles induced by single chemical substances. Specifically, patterns of transcript abundances were less influenced by the chemical composition at the sampling site compared t the method of exposure (sediment/extract. This effect might be related to different bioavailability of chemicals. CONCLUSIONS: The apparent

Fear or food - abundance of red fox in relation to occurrence of lynx and wolf.

Science.gov (United States)

Wikenros, Camilla; Aronsson, Malin; Liberg, Olof; Jarnemo, Anders; Hansson, Jessica; Wallgren, Märtha; Sand, Håkan; Bergström, Roger

2017-08-22

Apex predators may affect mesopredators through intraguild predation and/or supply of carrion from their prey, causing a trade-off between avoidance and attractiveness. We used wildlife triangle snow-tracking data to investigate the abundance of red fox (Vulpes vulpes) in relation to lynx (Lynx lynx) and wolf (Canis lupus) occurrence as well as land composition and vole (Microtus spp.) density. Data from the Swedish wolf-monitoring system and VHF/GPS-collared wolves were used to study the effect of wolf pack size and time since wolf territory establishment on fox abundance. Bottom-up processes were more influential than top-down effects as the proportion of arable land was the key indicator of fox abundance at the landscape level. At this spatial scale, there was no effect of wolf abundance on fox abundance, whereas lynx abundance had a positive effect. In contrast, at the wolf territory level there was a negative effect of wolves on fox abundance when including detailed information of pack size and time since territory establishment, whereas there was no effect of lynx abundance. This study shows that different apex predator species may affect mesopredator abundance in different ways and that the results may be dependent on the spatiotemporal scale and resolution of the data.

Longitudinal profiling of the tissue-specific expression of genes related with insulin sensitivity in dairy cows during lactation focusing on different fat depots.

Directory of Open Access Journals (Sweden)

Behnam Saremi

Full Text Available In dairy cows the milk associated energy output in early lactation exceeds the input via voluntary feed intake. To spare glucose for mammary lactose synthesis, peripheral insulin sensitivity (IS is reduced and fat mobilization is stimulated. For these processes a link between IS and the endocrine functions of adipose tissue (AT is likely; we thus aimed to characterise the mRNA expression from bovine AT derived proteins and receptors that are related to IS according to the literature in metabolically active tissues plus systemic IS throughout lactation. Conjugated linoleic acids (CLA reduce milk fat thus decreasing the milk drain of energy and potentially dampening lipolysis, but may also affect IS. Subcutaneous (s.c. AT and liver from pluriparous cows receiving either control fat or CLA supplement (100 g/day from 1 to 182 days in milk each were biopsied covering week -3 to 36 relative to parturition. In an additional trial with primiparous cows treated analogously and slaughtered on days in milk 1, 42 or 105, samples from liver, udder, skeletal muscle and 3 visceral and 3 s.c. AT were obtained and assayed for mRNA abundance of adiponectin, its receptors, leptin, leptin receptor, PPARγ, PPARγ2, IL-6, and TNF-α. In pluriparous animals, the mRNA abundance of most of the target genes decreased after parturition in s.c. AT but increased in liver. In primiparous cows, AT depot specific differences were mostly related to retroperitoneal AT; adiponectin receptor 1 and TNF-α were affected predominantly. CLA effects in primiparous cows were largely limited to decreased PPARγ2 mRNA abundance in udder tissue. In pluriparous cows, insulin secretion was increased by CLA resulting in decreased systemic IS but without consistent changes in tissue target mRNA abundance. The temporal gene expression profiles from the adipokines and related receptors support their coactive function in adapting to the needs of lactation.

Longitudinal Profiling of the Tissue-Specific Expression of Genes Related with Insulin Sensitivity in Dairy Cows during Lactation Focusing on Different Fat Depots

Science.gov (United States)

Saremi, Behnam; Winand, Sarah; Friedrichs, Paula; Kinoshita, Asako; Rehage, Jürgen; Dänicke, Sven; Häussler, Susanne; Breves, Gerhard; Mielenz, Manfred; Sauerwein, Helga

2014-01-01

In dairy cows the milk associated energy output in early lactation exceeds the input via voluntary feed intake. To spare glucose for mammary lactose synthesis, peripheral insulin sensitivity (IS) is reduced and fat mobilization is stimulated. For these processes a link between IS and the endocrine functions of adipose tissue (AT) is likely; we thus aimed to characterise the mRNA expression from bovine AT derived proteins and receptors that are related to IS according to the literature in metabolically active tissues plus systemic IS throughout lactation. Conjugated linoleic acids (CLA) reduce milk fat thus decreasing the milk drain of energy and potentially dampening lipolysis, but may also affect IS. Subcutaneous (s.c.) AT and liver from pluriparous cows receiving either control fat or CLA supplement (100 g/day from 1 to 182 days in milk each) were biopsied covering week −3 to 36 relative to parturition. In an additional trial with primiparous cows treated analogously and slaughtered on days in milk 1, 42 or 105, samples from liver, udder, skeletal muscle and 3 visceral and 3 s.c. AT were obtained and assayed for mRNA abundance of adiponectin, its receptors, leptin, leptin receptor, PPARγ, PPARγ2, IL-6, and TNF-α. In pluriparous animals, the mRNA abundance of most of the target genes decreased after parturition in s.c. AT but increased in liver. In primiparous cows, AT depot specific differences were mostly related to retroperitoneal AT; adiponectin receptor 1 and TNF-α were affected predominantly. CLA effects in primiparous cows were largely limited to decreased PPARγ2 mRNA abundance in udder tissue. In pluriparous cows, insulin secretion was increased by CLA resulting in decreased systemic IS but without consistent changes in tissue target mRNA abundance. The temporal gene expression profiles from the adipokines and related receptors support their coactive function in adapting to the needs of lactation. PMID:24465964

The relative contribution of climate to changes in lesser prairie-chicken abundance

Science.gov (United States)

Ross, Beth E.; Haukos, David A.; Hagen, Christian A.; Pitman, James

2016-01-01

Managing for species using current weather patterns fails to incorporate the uncertainty associated with future climatic conditions; without incorporating potential changes in climate into conservation strategies, management and conservation efforts may fall short or waste valuable resources. Understanding the effects of climate change on species in the Great Plains of North America is especially important, as this region is projected to experience an increased magnitude of climate change. Of particular ecological and conservation interest is the lesser prairie-chicken (Tympanuchus pallidicinctus), which was listed as “threatened” under the U.S. Endangered Species Act in May 2014. We used Bayesian hierarchical models to quantify the effects of extreme climatic events (extreme values of the Palmer Drought Severity Index [PDSI]) relative to intermediate (changes in El Niño Southern Oscillation) and long-term climate variability (changes in the Pacific Decadal Oscillation) on trends in lesser prairie-chicken abundance from 1981 to 2014. Our results indicate that lesser prairie-chicken abundance on leks responded to environmental conditions of the year previous by positively responding to wet springs (high PDSI) and negatively to years with hot, dry summers (low PDSI), but had little response to variation in the El Niño Southern Oscillation and the Pacific Decadal Oscillation. Additionally, greater variation in abundance on leks was explained by variation in site relative to broad-scale climatic indices. Consequently, lesser prairie-chicken abundance on leks in Kansas is more strongly influenced by extreme drought events during summer than other climatic conditions, which may have negative consequences for the population as drought conditions intensify throughout the Great Plains.

Molecular evolution of adiponectin in Carnivora and its mRNA expression in relation to hepatic lipidosis.

Science.gov (United States)

Nieminen, Petteri; Rouvinen-Watt, Kirsti; Kapiainen, Suvi; Harris, Lora; Mustonen, Anne-Mari

2010-09-15

Adiponectin is a novel adipocyte-derived hormone with low circulating concentrations and/or mRNA expression in obesity and non-alcoholic fatty liver disease (NAFLD). The adiponectin mRNA of several Carnivora species was sequenced to enable further gene expression studies in this clade with potential experimental species to examine the connections of hypoadiponectinemia to hepatic lipidosis. In addition, adiponectin mRNA expression was studied in the retroperitoneal fat of the American mink (Neovison vison), as hepatic lipidosis with close similarities to NAFLD can be rapidly induced to the species by fasting. The mRNA expression was determined after overnight-7d of food deprivation and 28d of re-feeding and correlated to the liver fat %. The homologies between the determined carnivoran mRNA sequences and that of the domestic dog were 92.2-99.1%. As the mRNA expression was not affected by short-term fasting and did not correlate with the liver fat %, there seems to be no clear connection between adiponectin and the development of lipidosis in the American mink. In the future, the obtained sequences can be utilized in further studies of adiponectin expression in comparative endocrinology. Copyright (c) 2010 Elsevier Inc. All rights reserved.

Multidirectional abundance shifts among North American birds and the relative influence of multifaceted climate factors.

Science.gov (United States)

Huang, Qiongyu; Sauer, John R; Dubayah, Ralph O

2017-09-01

Shifts in species distributions are major fingerprint of climate change. Examining changes in species abundance structures at a continental scale enables robust evaluation of climate change influences, but few studies have conducted these evaluations due to limited data and methodological constraints. In this study, we estimate temporal changes in abundance from North American Breeding Bird Survey data at the scale of physiographic strata to examine the relative influence of different components of climatic factors and evaluate the hypothesis that shifting species distributions are multidirectional in resident bird species in North America. We quantify the direction and velocity of the abundance shifts of 57 permanent resident birds over 44 years using a centroid analysis. For species with significant abundance shifts in the centroid analysis, we conduct a more intensive correlative analysis to identify climate components most strongly associated with composite change of abundance within strata. Our analysis focus on two contrasts: the relative importance of climate extremes vs. averages, and of temperature vs. precipitation in strength of association with abundance change. Our study shows that 36 species had significant abundance shifts over the study period. The average velocity of the centroid is 5.89 km·yr -1 . The shifted distance on average covers 259 km, 9% of range extent. Our results strongly suggest that the climate change fingerprint in studied avian distributions is multidirectional. Among 6 directions with significant abundance shifts, the northwestward shift was observed in the largest number of species (n = 13). The temperature/average climate model consistently has greater predictive ability than the precipitation/extreme climate model in explaining strata-level abundance change. Our study shows heterogeneous avian responses to recent environmental changes. It highlights needs for more species-specific approaches to examine contributing

Penguin tissue as a proxy for relative krill abundance in East Antarctica during the Holocene.

Science.gov (United States)

Huang, Tao; Sun, Liguang; Long, Nanye; Wang, Yuhong; Huang, Wen

2013-09-30

Antarctic krill (Euphausia superba) is a key component of the Southern Ocean food web. It supports a large number of upper trophic-level predators, and is also a major fishery resource. Understanding changes in krill abundance has long been a priority for research and conservation in the Southern Ocean. In this study, we performed stable isotope analyses on ancient Adélie penguin tissues and inferred relative krill abundance during the Holocene epoch from paleodiets of Adélie penguin (Pygoscelis adeliae), using inverse of δ¹⁵N (ratio of ¹⁵N/¹⁴N) value as a proxy. We find that variations in krill abundance during the Holocene are in accord with episodes of regional climate changes, showing greater krill abundance in cold periods. Moreover, the low δ¹⁵N values found in modern Adélie penguins indicate relatively high krill availability, which supports the hypothesis of krill surplus in modern ages due to recent hunt for krill-eating seals and whales by humans.

Interactions between the HIV-1 Unspliced mRNA and Host mRNA Decay Machineries

Directory of Open Access Journals (Sweden)

Daniela Toro-Ascuy

2016-11-01

Full Text Available The human immunodeficiency virus type-1 (HIV-1 unspliced transcript is used both as mRNA for the synthesis of structural proteins and as the packaged genome. Given the presence of retained introns and instability AU-rich sequences, this viral transcript is normally retained and degraded in the nucleus of host cells unless the viral protein REV is present. As such, the stability of the HIV-1 unspliced mRNA must be particularly controlled in the nucleus and the cytoplasm in order to ensure proper levels of this viral mRNA for translation and viral particle formation. During its journey, the HIV-1 unspliced mRNA assembles into highly specific messenger ribonucleoproteins (mRNPs containing many different host proteins, amongst which are well-known regulators of cytoplasmic mRNA decay pathways such as up-frameshift suppressor 1 homolog (UPF1, Staufen double-stranded RNA binding protein 1/2 (STAU1/2, or components of miRNA-induced silencing complex (miRISC and processing bodies (PBs. More recently, the HIV-1 unspliced mRNA was shown to contain N6-methyladenosine (m6A, allowing the recruitment of YTH N6-methyladenosine RNA binding protein 2 (YTHDF2, an m6A reader host protein involved in mRNA decay. Interestingly, these host proteins involved in mRNA decay were shown to play positive roles in viral gene expression and viral particle assembly, suggesting that HIV-1 interacts with mRNA decay components to successfully accomplish viral replication. This review summarizes the state of the art in terms of the interactions between HIV-1 unspliced mRNA and components of different host mRNA decay machineries.

Weed management practices affect the diversity and relative abundance of physic nut mites.

Science.gov (United States)

Saraiva, Althiéris de Sousa; Sarmento, Renato A; Erasmo, Eduardo A L; Pedro-Neto, Marçal; de Souza, Danival José; Teodoro, Adenir V; Silva, Daniella G

2015-03-01

Crop management practices determine weed community, which in turn may influence patterns of diversity and abundance of associated arthropods. This study aimed to evaluate whether local weed management practices influence the diversity and relative abundance of phytophagous and predatory mites, as well as mites with undefined feeding habits--of the families Oribatidae and Acaridae--in a physic nut (Jatropha curcas L.) plantation subjected to (1) within-row herbicide spraying and between-row mowing; (2) within-row herbicide spraying and no between-row mowing; (3) within-row weeding and between-row mowing; (4) within-row weeding and no between-row mowing; and (5) unmanaged (control). The herbicide used was glyphosate. Herbicide treatments resulted in higher diversity and relative abundance of predatory mites and mites with undefined feeding habit on physic nut shrubs. This was probably due to the toxic effects of the herbicide on mites or to removal of weeds. Within-row herbicide spraying combined with between-row mowing was the treatment that most contributed to this effect. Our results show that within-row weeds harbor important species of predatory mites and mites with undefined feeding habit. However, the dynamics of such mites in the system can be changed according to the weed management practice applied. Among the predatory mites of the family Phytoseiidae Amblydromalus sp. was the most abundant, whereas Brevipalpus phoenicis was the most frequent phytophagous mite and an unidentified oribatid species was the most frequent mite with undefined feeding habit.

Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances

Science.gov (United States)

Chen, Wei-Hua; van Noort, Vera; Lluch-Senar, Maria; Hennrich, Marco L.; H. Wodke, Judith A.; Yus, Eva; Alibés, Andreu; Roma, Guglielmo; Mende, Daniel R.; Pesavento, Christina; Typas, Athanasios; Gavin, Anne-Claude; Serrano, Luis; Bork, Peer

2016-01-01

We developed a comprehensive resource for the genome-reduced bacterium Mycoplasma pneumoniae comprising 1748 consistently generated ‘-omics’ data sets, and used it to quantify the power of antisense non-coding RNAs (ncRNAs), lysine acetylation, and protein phosphorylation in predicting protein abundance (11%, 24% and 8%, respectively). These factors taken together are four times more predictive of the proteome abundance than of mRNA abundance. In bacteria, post-translational modifications (PTMs) and ncRNA transcription were both found to increase with decreasing genomic GC-content and genome size. Thus, the evolutionary forces constraining genome size and GC-content modify the relative contributions of the different regulatory layers to proteome homeostasis, and impact more genomic and genetic features than previously appreciated. Indeed, these scaling principles will enable us to develop more informed approaches when engineering minimal synthetic genomes. PMID:26773059

Defense Response in Slash Pine: Chitosan Treatment Alters the Abundance of Specific mRNAs

Science.gov (United States)

Mary E. Mason; John M. Davis

1997-01-01

We used differential display to identify chitosan responsive cDNAs in slashpine cell cultures. Two clones that showed increased mRNA abundance had sequence similarity to genes with roles in major plant defense responses, clone 18 to cinnamic acid 4-hydroxylase, and clone 30 to chitinase.

Effect of physical training on glucose transporter protein and mRNA levels in rat adipocytes

DEFF Research Database (Denmark)

Stallknecht, B; Andersen, P H; Vinten, J

1993-01-01

Physical training increases insulin-stimulated glucose transport and the number of glucose transporters in adipocytes measured by cytochalasin B binding. In the present study we used immunoblotting to measure the abundance of two glucose transporters (GLUT-4, GLUT-1) in white adipocytes from....../or intrinsic activity). GLUT-1 protein and mRNA levels/adipocyte volume did not change with age or training....

Quantitative analyses of postmortem heat shock protein mRNA profiles in the occipital lobes of human cerebral cortices: implications in cause of death.

Science.gov (United States)

Chung, Ukhee; Seo, Joong-Seok; Kim, Yu-Hoon; Son, Gi Hoon; Hwang, Juck-Joon

2012-11-01

Quantitative RNA analyses of autopsy materials to diagnose the cause and mechanism of death are challenging tasks in the field of forensic molecular pathology. Alterations in mRNA profiles can be induced by cellular stress responses during supravital reactions as well as by lethal insults at the time of death. Here, we demonstrate that several gene transcripts encoding heat shock proteins (HSPs), a gene family primarily responsible for cellular stress responses, can be differentially expressed in the occipital region of postmortem human cerebral cortices with regard to the cause of death. HSPA2 mRNA levels were higher in subjects who died due to mechanical asphyxiation (ASP), compared with those who died by traumatic injury (TI). By contrast, HSPA7 and A13 gene transcripts were much higher in the TI group than in the ASP and sudden cardiac death (SCD) groups. More importantly, relative abundances between such HSP mRNA species exhibit a stronger correlation to, and thus provide more discriminative information on, the death process than does routine normalization to a housekeeping gene. Therefore, the present study proposes alterations in HSP mRNA composition in the occipital lobe as potential forensic biological markers, which may implicate the cause and process of death.

SR proteins are NXF1 adaptors that link alternative RNA processing to mRNA export.

Science.gov (United States)

Müller-McNicoll, Michaela; Botti, Valentina; de Jesus Domingues, Antonio M; Brandl, Holger; Schwich, Oliver D; Steiner, Michaela C; Curk, Tomaz; Poser, Ina; Zarnack, Kathi; Neugebauer, Karla M

2016-03-01

Nuclear export factor 1 (NXF1) exports mRNA to the cytoplasm after recruitment to mRNA by specific adaptor proteins. How and why cells use numerous different export adaptors is poorly understood. Here we critically evaluate members of the SR protein family (SRSF1-7) for their potential to act as NXF1 adaptors that couple pre-mRNA processing to mRNA export. Consistent with this proposal, >1000 endogenous mRNAs required individual SR proteins for nuclear export in vivo. To address the mechanism, transcriptome-wide RNA-binding profiles of NXF1 and SRSF1-7 were determined in parallel by individual-nucleotide-resolution UV cross-linking and immunoprecipitation (iCLIP). Quantitative comparisons of RNA-binding sites showed that NXF1 and SR proteins bind mRNA targets at adjacent sites, indicative of cobinding. SRSF3 emerged as the most potent NXF1 adaptor, conferring sequence specificity to RNA binding by NXF1 in last exons. Interestingly, SRSF3 and SRSF7 were shown to bind different sites in last exons and regulate 3' untranslated region length in an opposing manner. Both SRSF3 and SRSF7 promoted NXF1 recruitment to mRNA. Thus, SRSF3 and SRSF7 couple alternative splicing and polyadenylation to NXF1-mediated mRNA export, thereby controlling the cytoplasmic abundance of transcripts with alternative 3' ends. © 2016 Müller-McNicoll et al.; Published by Cold Spring Harbor Laboratory Press.

A mRNA and cognate microRNAs localize in the nucleolus.

Science.gov (United States)

Reyes-Gutierrez, Pablo; Ritland Politz, Joan C; Pederson, Thoru

2014-01-01

We previously discovered that a set of 5 microRNAs are concentrated in the nucleolus of rat myoblasts. We now report that several mRNAs are also localized in the nucleoli of these cells as determined by microarray analysis of RNA from purified nucleoli. Among the most abundant of these nucleolus-localized mRNAs is that encoding insulin-like growth factor 2 (IGF2), a regulator of myoblast proliferation and differentiation. The presence of IGF2 mRNA in nucleoli was confirmed by fluorescence in situ hybridization, and RT-PCR experiments demonstrated that these nucleolar transcripts are spliced, thus arriving from the nucleoplasm. Bioinformatics analysis predicted canonically structured, highly thermodynamically stable interactions between IGF2 mRNA and all 5 of the nucleolus-localized microRNAs. These results raise the possibility that the nucleolus is a staging site for setting up particular mRNA-microRNA interactions prior to export to the cytoplasm.

Differential regulation of amyloid-β-protein mRNA expression within hippocampal neuronal subpopulations in Alzheimer disease

International Nuclear Information System (INIS)

Higgins, G.A.; Lewis, D.A.; Bahmanyar, S.; Goldgaber, D.; Gajdusek, D.C.; Young, W.G.; Morrison, J.H.; Wilson, M.C.

1988-01-01

The authors have mapped the neuroanatomical distribution of amyloid-β-protein mRNA within neuronal subpopulations of the hippocampal formation in the cynomolgus monkey (Macaca fascicularis), normal aged human, and patients with Alzheimer disease. Amyloid-β-protein mRNA appears to be expressed in all hippocampal neurons, but at different levels of abundance. In the central nervous system of monkey and normal aged human, image analysis shows that neurons of the dentate gyrus and cornu Ammonis fields contain a 2.5-times-greater hybridization signal than is present in neurons of the subiculum and entorhinal cortex. In contrast, in the Alzheimer disease hippocampal formation, the levels of amyloid-β-protein mRNA in the cornu Ammonis field 3 and parasubiculum are equivalent. These findings suggest that within certain neuronal subpopulations cell type-specific regulation of amyloid-β-protein gene expression may be altered in Alzheimer disease

Distribution and relative abundance of the marine catfish (Siluriformes, Ariidae) in Sepetiba Bay, Rio de Janeiro

OpenAIRE

Azevedo, Márcia Cristina Costa de; Araújo, Francisco Gerson; Cruz Filho, Antônio Gomes da; Santos, Alexandre Clístenes de Alcântara

1998-01-01

Marine catfish (Ariidae) are abundant resources in otter trawl fisheries carried out at Sepetiba Bay, Rio de Janeiro (Lat. 22º54, 23º04'S; Long. 43º34 44º10'W). Relative abundance and distribution were assessed, based in 158 fishing sampling at seven sites in the Bay, between July-1993 e June-1996. Five species were recorded in the following abundance rank order: Genidens genidens (Valenciennes, 1839), Caihorops spixii (Agassiz,1829), Sciadeichthys lunisculis (Valenciennes, 1840), Nelunia bar...

Effects of dietary nitrogen concentration on messenger RNA expression and protein abundance of urea transporter-B and aquaporins in ruminal papillae from lactating Holstein cows

DEFF Research Database (Denmark)

Røjen, Betina Amdisen; Poulsen, Søren Brandt; Theil, Peter Kappel

2011-01-01

To test the hypothesis that dietary N concentrations affect gut epithelial urea transport by modifying the expression of urea transporter B (UT-B) and aquaporins (AQP), the mRNA expression and protein abundance of UT-B and AQP3, AQP7, AQP8, and AQP10 were investigated in ruminal papillae from 9...... lactating dairy cows. Ruminal papillae were harvested from cows fed low N (12.9% crude protein) and high N (17.1% crude protein) diets in a crossover design with 21-d periods. The mRNA expression was determined by real-time reverse transcription-PCR and protein abundance by immunoblotting. The m......RNA expression of UT-B was not affected by dietary treatment, whereas mRNA expression of AQP3, 7, and 10 were greater in the high N compared with the low N fed cows. Using peptide-derived rabbit antibodies to cow AQP3, 7, and 8, immunoblotting revealed bands of approximately 27, 27, and 24 kDa in ruminal...

Relative abundance and diel variation of zooplankton from south west coast of India

Digital Repository Service at National Institute of Oceanography (India)

Santhakumari, V.; Peter, K.J.

abundant group, of which calanoids predominated. A swarm of the hydromedusan species, Aequorea conica, (181/m sup(-3)) was seen at night. Quantitative and qualitative variations of various zooplankton groups from six stations in relation to selected physico...

The relative importance of water temperature and residence time in predicting cyanobacteria abundance in regulated rivers.

Science.gov (United States)

Cha, YoonKyung; Cho, Kyung Hwa; Lee, Hyuk; Kang, Taegu; Kim, Joon Ha

2017-11-01

Despite a growing awareness of the problems associated with cyanobacterial blooms in rivers, and particularly in regulated rivers, the drivers of bloom formation and abundance in rivers are not well understood. We developed a Bayesian hierarchical model to assess the relative importance of predictors of summer cyanobacteria abundance, and to test whether the relative importance of each predictor varies by site, using monitoring data from 16 sites in the four major rivers of South Korea. The results suggested that temperature and residence time, but not nutrient levels, are important predictors of summer cyanobacteria abundance in rivers. Although the two predictors were of similar significance across the sites, the residence time was marginally better in accounting for the variation in cyanobacteria abundance. The model with spatial hierarchy demonstrated that temperature played a consistently significant role at all sites, and showed no effect from site-specific factors. In contrast, the importance of residence time varied significantly from site to site. This variation was shown to depend on the trophic state, indicated by the chlorophyll-a and total phosphorus levels. Our results also suggested that the magnitude of weir inflow is a key factor determining the cyanobacteria abundance under baseline conditions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Relative abundance and size of coastal sharks derived from commercial shark longline catch and effort data.

Science.gov (United States)

Carlson, J K; Hale, L F; Morgan, A; Burgess, G

2012-04-01

In the north-west Atlantic Ocean, stock assessments conducted for some commercially harvested coastal sharks indicate declines from 64 to 80% with respect to virgin population levels. While the status of commercially important species is available, abundance trend information for other coastal shark species in the north-west Atlantic Ocean are unavailable. Using a generalized linear modelling (GLM) approach, a relative abundance index was derived from 1994 to 2009 using observer data collected in a commercial bottom longline fishery. Trends in abundance and average size were estimated for bull shark Carcharhinus leucas, spinner shark Carcharhinus brevipinna, tiger shark Galeocerdo cuvier and lemon shark Negaprion brevirostris. Increases in relative abundance for all shark species ranged from 14% for C. brevipinna, 12% for C. leucas, 6% for N. brevirostris and 3% for G. cuvier. There was no significant change in the size at capture over the time period considered for all species. While the status of shark populations should not be based exclusively on abundance trend information, but ultimately on stock assessment models, results from this study provide some cause for optimism on the status of these coastal shark species. Published 2012. This article is a U.S. Government work and is in the public domain in the USA.

Xe isotopic abundances in enstatite meteorites and relations to other planetary reservoirs

International Nuclear Information System (INIS)

Lee, Jee-Yon; Marti, Kurt; Wacker, John F.

2009-01-01

This paper describes the interpretation of xenon that was measured in the Abee meteorite. Reported Xe isotopic abundances in enstatite chondrites (EC's) show some variability, and this makes comparisons to other solar system reservoirs rather difficult. In contrast, we find uniform Xe isotopic abundances in the EC chondrite Abee for a variety of clasts, except for 128 Xe and 129 Xe, the isotopes affected by neutron capture in I and by extinct 129 I. We report averages for the studied clasts which are consistent within error limits with OC-Xe and with the Q-Xe signature. On the other hand, the elemental abundance ratios Ar/Xe are variable between clasts. A strongly reducing environment which is indicated for enstatite meteorites was generally assumed to be consistent with conditions existing in the early inner solar system. Xe isotopic abundances in SNC meteorites from Mars and also those in some terrestrial wells show that distinct isotopic reservoirs coexisted on the same planets. In particular, the Xe isotopic signatures in terrestrial well gases show the presence of a minor distinct component in two of the reported four well gases. These authors suggested that the extra component represents solar Xe, but we show that also a meteoritic xenon reservoir of the Abee-Xe structure is an option. The reported Xe data in Ar-rich (subsolar) EC's show isotopic abundances slightly lighter than those in Abee-Xe, but the relative abundances of Ar, Kr, and Xe indicate only a minor component of elementally unfractionated solar Xe. The elemental ratios suggest rather a different origin for these gases: the loading of solar particles into grain surfaces during exposure at elevated temperatures during accretion of matter in the inner solar system. A model of this type was suggested for the accretion of gases now observed in the atmosphere on Venus. We note that disks of crystalline silicates (including enstatite and olivine) have been observed in T Tauri stars during their early

Two tandem RNase III cleavage sites determine betT mRNA stability in response to osmotic stress in Escherichia coli.

Directory of Open Access Journals (Sweden)

Minji Sim

Full Text Available While identifying genes regulated by ribonuclease III (RNase III in Escherichia coli, we observed that steady-state levels of betT mRNA, which encodes a transporter mediating the influx of choline, are dependent on cellular concentrations of RNase III. In the present study, we also observed that steady-state levels of betT mRNA are dependent on RNase III activity upon exposure to osmotic stress, indicating the presence of cis-acting elements controlled by RNase III in betT mRNA. Primer extension analyses of betT mRNA revealed two tandem RNase III cleavage sites in its stem-loop region, which were biochemically confirmed via in vitro cleavage assays. Analyses of cleavage sites suggested the stochastic selection of cleavage sites by RNase III, and mutational analyses indicated that RNase III cleavage at either site individually is insufficient for efficient betT mRNA degradation. In addition, both the half-life and abundance of betT mRNA were significantly increased in association with decreased RNase III activity under hyper-osmotic stress conditions. Our findings demonstrate that betT mRNA stability is controlled by RNase III at the post-transcriptional level under conditions of osmotic stress.

Cellular localization of transforming growth factor-alpha mRNA in rat forebrain.

Science.gov (United States)

Seroogy, K B; Lundgren, K H; Lee, D C; Guthrie, K M; Gall, C M

1993-05-01

The cellular localization of transforming growth factor-alpha (TGF alpha) mRNA in juvenile and adult rat forebrain was examined using in situ hybridization with a 35S-labeled cRNA probe. TGF alpha cRNA-labeled neuronal perikarya were distributed across many forebrain regions including the olfactory bulb, caudate-putamen, nucleus accumbens, olfactory tubercle, ventral pallidum, amygdala, hippocampal stratum granulosum and CA3 stratum pyramidale, and piriform, entorhinal, and retrosplenial cortices. TGF alpha cRNA-hybridizing cells were also localized to several thalamic nuclei and to the suprachiasmatic, dorsomedial, and ventromedial nuclei of the hypothalamus. In addition, labeled cells were present in regions of white matter including the corpus callosum, anterior commissure, internal and external capsules, optic tract, and lateral olfactory tract. Thus, both neurons and glia appear to synthesize TGF alpha in normal brain. Hybridization densities were greater in neuronal fields at 2 weeks of age compared with the adult, suggesting a role for TGF alpha in the development of several forebrain systems. Our results demonstrating the prominent and wide-spread expression of TGF alpha mRNA in forebrain, combined with the extremely low abundance of epidermal growth factor mRNA in brain, support the argument that TGF alpha is the principal endogenous ligand for the epidermal growth factor receptor in normal brain.

Long-Term Changes in Species Composition and Relative Abundances of Sharks at a Provisioning Site

OpenAIRE

Brunnschweiler, Juerg M.; Abrantes, Kátya G.; Barnett, Adam

2014-01-01

Diving with sharks, often in combination with food baiting/provisioning, has become an important product of today's recreational dive industry. Whereas the effects baiting/provisioning has on the behaviour and abundance of individual shark species are starting to become known, there is an almost complete lack of equivalent data from multi-species shark diving sites. In this study, changes in species composition and relative abundances were determined at the Shark Reef Marine Reserve, a multi-...

Variable liver fat concentration as a proxy for body fat mobilization postpartum has minor effects on insulin-induced changes in hepatic gene expression related to energy metabolism in dairy cows.

Science.gov (United States)

Weber, C; Schäff, C T; Kautzsch, U; Börner, S; Erdmann, S; Bruckmaier, R M; Röntgen, M; Kuhla, B; Hammon, H M

2017-02-01

The liver plays a central role in adaptation for energy requirements around calving, and changes in the effects of insulin on hepatic energy metabolism contribute to metabolic adaptation in dairy cows. Hepatic insulin effects may depend on body fat mobilization. The objective of this study was to investigate the effects of insulin on the hepatic gene expression of enzymes involved in energy metabolism and factors related to nutrition partitioning in cows with high and low total liver fat concentration (LFC) after calving. Holstein cows were retrospectively grouped according to their LFC after calving as a proxy for body fat mobilization. Cows were classified as low (LLFC; LFC 24.4% fat/dry matter; n = 10) fat-mobilizing after calving. Euglycemic-hyperinsulinemic clamps [6 mU/(kg × min) of insulin for 6 h] were performed in wk 5 antepartum (ap) and wk 3 postpartum (pp). Before and at the end of the euglycemic-hyperinsulinemic clamps, liver biopsies were taken to measure the mRNA abundance of enzymes involved in carbohydrate and lipid metabolism, expression related to the somatotropic axis, and adrenergic and glucocorticoid receptors. The mRNA abundance of pyruvate carboxylase, cytosolic phosphoenolpyruvate carboxykinase (PEPCK; PCK1), acyl-CoA-dehydrogenase very long chain (ACADVL), and hydroxyl-methyl-glutaryl-CoA-synthase 1 increased, but the mRNA abundance of solute carrier family 2 (SLC2A2 and SLC2A4), growth hormone receptor 1A (GHR1A), insulin-like growth factor 1 (IGF1), sterol regulatory element binding factor 1, adrenoceptor α 1A, and glucocorticoid receptor decreased from ap to pp. Insulin treatment was associated with decreased PCK1, mitochondrial PEPCK, glucose-6-phosphatase, propionyl-CoA-carboxylase α, carnitine-palmitoyl-transferase 1A, ACADVL, and insulin receptor mRNA, but increased IGF1 and SLC2A4 mRNA ap and pp and GHR1A mRNA pp. The mRNA abundance of SLC2A4 was greater, and the mRNA abundance of GHR1A and IGF1 tended to be lower in LLFC than

Seasonal abundance of soil arthropods in relation to meteorological and edaphic factors in the agroecosystems of Faisalabad, Punjab, Pakistan.

Science.gov (United States)

Shakir, Muhammad Mussadiq; Ahmed, Sohail

2015-05-01

Soil arthropods are an important component of agroecosystems, contributing significantly to their biodiversity and functioning. However, seasonal patterns, population dynamics, and significant roles of these soil arthropods in improvement of soil structures and functions are influenced by many factors. The objective of the current study was to investigate soil arthropod abundance in relation to a blend of meteorological and edaphic factors and to find out the difference in abundance among various crops (sugarcane, cotton, wheat, alfalfa fodder, and citrus orchards). The arthropod sampling was done by pitfall traps and Tullgren extractions on fortnightly intervals. Soil temperature and relative humidity were noted on the field sites while analysis for soil pH, organic matter, and soil moisture contents were done in the laboratory. The rainfall data was obtained from an observatory. Results showed that significant differences were found in soil arthropod abundance across different sampling months and crops. Out of total 13,673 soil arthropods sampled, 38 % belonged to Collembola, followed by 15 % Hymenoptera, 15 % Acarina, 11 % Myriapods, 6 % Coleoptera, 5 % Orthoptera, and 5 % Araneae. Mean abundance per sample was highest in summer months as compared to winter. Overall abundance per sample was significantly different between all crops (p arthropods according to abundance, i.e., highly abundant (Collembola, Acarina, Myripoda, Hymenoptera), moderately abundant (Orthoptera, Aranae, Coleoptera), least abundant (Dermaptera, Hemiptera, Diptera), and rare (Blattaria, Isoptera, Diplura, Lepidoptera). Soil temperature and soil organic matter showed significant positive correlation with abundance, while relative humidity was significantly negatively correlated. Soil moisture and soil pH showed no significant correlations while no correlation was found with total rainfall. PCA analysis revealed that soil surface arthropods were the major contributors of variation in overall

Stellar Oxygen Abundances

Science.gov (United States)

King, Jeremy

1994-04-01

This dissertation addresses several issues concerning stellar oxygen abundances. The 7774 {\\AA} O I triplet equivalent widths of Abia & Rebolo [1989, AJ, 347, 186] for metal-poor dwarfs are found to be systematically too high. I also argue that current effective temperatures used in halo star abundance studies may be ~150 K too low. New color-Teff relations are derived for metal-poor stars. Using the revised Teff values and improved equivalent widths for the 7774A O I triplet, the mean [O/Fe] ratio for a handful of halo stars is found to be +0.52 with no dependence on Teff or [Fe/H]. Possible cosmological implications of the hotter Teff scale are discussed along with additional evidence supporting the need for a higher temperature scale for metal-poor stars. Our Teff scale leads to a Spite Li plateau value of N(Li)=2.28 +/- 0.09. A conservative minimal primordial value of N(Li)=2.35 is inferred. If errors in the observations and models are considered, consistency with standard models of Big Bang nucleosynthesis is still achieved with this larger Li abundance. The revised Teff scale raises the observed B/Be ratio of HD 140283 from 10 to 12, making its value more comfortably consistent with the production of the observed B and Be by ordinary spallation. Our Teff values are found to be in good agreement with values predicted from both the Victoria and Yale isochrone color-Teff relations. Thus, it appears likely that no changes in globular cluster ages would result. Next, we examine the location of the break in the [O/Fe] versus [Fe/H] plane in a quantitative fashion. Analysis of a relatively homogeneous data set does not favor any unique break point in the range -1.7 /= -3), in agreement with the new results for halo dwarfs. We find that the gap in the observed [O/H] distribution, noted by Wheeler et al. [1989, ARAA, 27, 279], persists despite the addition of more O data and may betray the occurrence of a hiatus in star formation between the end of halo formation and

Single-cell mRNA transfection studies: delivery, kinetics and statistics by numbers.

Science.gov (United States)

Leonhardt, Carolin; Schwake, Gerlinde; Stögbauer, Tobias R; Rappl, Susanne; Kuhr, Jan-Timm; Ligon, Thomas S; Rädler, Joachim O

2014-05-01

In artificial gene delivery, messenger RNA (mRNA) is an attractive alternative to plasmid DNA (pDNA) since it does not require transfer into the cell nucleus. Here we show that, unlike for pDNA transfection, the delivery statistics and dynamics of mRNA-mediated expression are generic and predictable in terms of mathematical modeling. We measured the single-cell expression time-courses and levels of enhanced green fluorescent protein (eGFP) using time-lapse microscopy and flow cytometry (FC). The single-cell analysis provides direct access to the distribution of onset times, life times and expression rates of mRNA and eGFP. We introduce a two-step stochastic delivery model that reproduces the number distribution of successfully delivered and translated mRNA molecules and thereby the dose-response relation. Our results establish a statistical framework for mRNA transfection and as such should advance the development of RNA carriers and small interfering/micro RNA-based drugs. This team of authors established a statistical framework for mRNA transfection by using a two-step stochastic delivery model that reproduces the number distribution of successfully delivered and translated mRNA molecules and thereby their dose-response relation. This study establishes a nice connection between theory and experimental planning and will aid the cellular delivery of mRNA molecules. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Sex ratios, mating frequencies and relative abundance of sympatric millipedes in the genus Chersastus (Diplopoda: Pachybolidae

Directory of Open Access Journals (Sweden)

Mark Ian Cooper

2014-12-01

Full Text Available Three hypotheses exist for explaining climbing behavior in millipedes: 1 waterlogging, 2 detritus limiting, and 3 mate avoidance. Data of sex ratios, mating frequency and relative abundance are provided to suggest an alternative explanation for the pattern in sympatric forest millipedes. Sex ratio differences - from equality - were tested using a G-test comparing millipedes on and above ground. Mating frequencies were calculated based on the percentage of paired individuals. Relative abundance may correlate with male-biases in the sex ratios. All three factors suggest Chersastus inscriptus has a higher reproductive potential than C. anulatus. This is evidence for mating hotspots.

TP53 and ATM mRNA expression in skin and skeletal muscle after low-level laser exposure.

Science.gov (United States)

Guedes de Almeida, Luciana; Sergio, Luiz Philippe da Silva; de Paoli, Flavia; Mencalha, Andre Luiz; da Fonseca, Adenilson de Souza

2017-08-01

Low-level lasers are widespread in regenerative medicine, but the molecular mechanisms involved in their biological effects are not fully understood, particularly those on DNA stability. Therefore, this study aimed to investigate mRNA expression of genes related to DNA genomic stability in skin and skeletal muscle tissue from Wistar rats exposed to low-level red and infrared lasers. For this, TP53 (Tumor Protein 53) and ATM (Ataxia Telangiectasia Mutated gene) mRNA expressions were evaluated by real-time quantitative PCR (RT-qPCR) technique 24 hours after low-level red and infrared laser exposure. Our data showed that relative TP53 mRNA expression was not significantly altered in both tissues exposed to lasers. For ATM, relative mRNA expression in skin tissue was not significantly altered, but in muscle tissue, laser exposure increased relative ATM mRNA expression. Low-level red and infrared laser radiations alter ATM mRNA expression related to DNA stability in skeletal muscle tissue.

[Differential expression of IGF-I and its mRNA in mandibular condylar cartilage of rat--direct evidence for servosystem theory of facial growth].

Science.gov (United States)

Zhou, Z; Luo, S

1998-05-01

It was studied the expression of IGF-I and its mRNA in the condylar cartilage of 10 7-week-old SD male rats by using in situ hybridization and immunohisto-chemistry technique. The results showed both IGF-I and its gene expressed in growing rat condyle. IGF-I peptide was abundant in germinal zone, and positive reaction of its mRNA was strongest in transitional and maturational zones. These indicate that condylar cartilage has the capability of local production and secretion of IGF-I, mediating the command effect of STH, and differential expression of IGF-I and its mRNA might establish the local feedback loop, which supply a direct evidence for servosystem theory of facial growth.

Microbial abundance on the eggs of a passerine bird and related fitness consequences between urban and rural habitats.

Science.gov (United States)

Lee, Sang-Im; Lee, Hyunna; Jablonski, Piotr G; Choe, Jae Chun; Husby, Magne

2017-01-01

Urban environments present novel and challenging habitats to wildlife. In addition to well-known difference in abiotic factors between rural and urban environments, the biotic environment, including microbial fauna, may also differ significantly. In this study, we aimed to compare the change in microbial abundance on eggshells during incubation between urban and rural populations of a passerine bird, the Eurasian Magpie (Pica pica), and examine the consequences of any differences in microbial abundances in terms of hatching success and nestling survival. Using real-time PCR, we quantified the abundances of total bacteria, Escherichia coli/Shigella spp., surfactin-producing Bacillus spp. and Candida albicans on the eggshells of magpies. We found that urban magpie eggs harboured greater abundances of E. coli/Shigella spp. and C. albicans before incubation than rural magpie eggs. During incubation, there was an increase in the total bacterial load, but a decrease in C. albicans on urban eggs relative to rural eggs. Rural eggs showed a greater increase in E. coli/Shigella spp. relative to their urban counterpart. Hatching success of the brood was generally lower in urban than rural population. Nestling survival was differentially related with the eggshell microbial abundance between urban and rural populations, which was speculated to be the result of the difference in the strength of the interaction among the microbes. This is the first demonstration that avian clutches in urban and rural populations differ in eggshell microbial abundance, which can be further related to the difference in hatching success and nestling survival in these two types of environments. We suggest that future studies on the eggshell microbes should investigate the interaction among the microbes, because the incubation and/or environmental factors such as urbanization or climate condition can influence the dynamic interactions among the microbes on the eggshells which can further determine the

Fluorescent peptide biosensor for probing the relative abundance of cyclin-dependent kinases in living cells.

Directory of Open Access Journals (Sweden)

Laetitia Kurzawa

Full Text Available Cyclin-dependant kinases play a central role in coordinating cell growth and division, and in sustaining proliferation of cancer cells, thereby constituting attractive pharmacological targets. However, there are no direct means of assessing their relative abundance in living cells, current approaches being limited to antigenic and proteomic analysis of fixed cells. In order to probe the relative abundance of these kinases directly in living cells, we have developed a fluorescent peptide biosensor with biligand affinity for CDKs and cyclins in vitro, that retains endogenous CDK/cyclin complexes from cell extracts, and that bears an environmentally-sensitive probe, whose fluorescence increases in a sensitive fashion upon recognition of its targets. CDKSENS was introduced into living cells, through complexation with the cell-penetrating carrier CADY2 and applied to assess the relative abundance of CDK/Cyclins through fluorescence imaging and ratiometric quantification. This peptide biosensor technology affords direct and sensitive readout of CDK/cyclin complex levels, and reports on differences in complex formation when tampering with a single CDK or cyclin. CDKSENS further allows for detection of differences between different healthy and cancer cell lines, thereby enabling to distinguish cells that express high levels of these heterodimeric kinases, from cells that present decreased or defective assemblies. This fluorescent biosensor technology provides information on the overall status of CDK/Cyclin complexes which cannot be obtained through antigenic detection of individual subunits, in a non-invasive fashion which does not require cell fixation or extraction procedures. As such it provides promising perspectives for monitoring the response to therapeutics that affect CDK/Cyclin abundance, for cell-based drug discovery strategies and fluorescence-based cancer diagnostics.

Differences in correlation of mRNA gene expression in mice sensitive and resistant to radiation-induced pulmonary fibrosis

International Nuclear Information System (INIS)

Johnston, C.J.; Piedboeuf, B.; Finkelstein, J.N.; Baggs, R.; Rubin, P.

1995-01-01

Fibrosis, characterized by the accumulation of collagen, is a late result of thoracic irradiation. The purpose of this study was to determine if extracellular matrix protein and transforming growth factor β mRNA expression are altered late in the course of pulmonary fibrosis after irradiation, and then to determine if these changes differ between two strains of mice which vary in their sensitivity to radiation. Radiation-sensitive (C57BL/6) and radiation-resistant (C3H/HeJ) mice were irradiated with a single dose of 5 or 12.5 Gy to the thorax. Total lung RNA was prepared and immobilized by Northern and slot blotting and hybridized with radiolabeled cDNA probes for collagens I, III and IV, fibronectin, and transforming growth factor β 1 and β 3 . Autoradiographic data were quantified by video densitometry and results normalized to a control probe encoding for glyceralde-hyde-3-phosphate dehydrogenase. Alterations in mRNA abundance were observed in the sensitive mice at all times, while levels in the resistant mice were unaffected until 26 weeks after irradiation. The relationship between extracellular matrix protein per se and increased mRNA abundance suggests that late matrix protein accumulation may be a function of gene expression. Differences in levels of transforming growth factor βmRNA may lead to strain-dependent variation in fibrotic response and may also contribute to the radiation-induced component of pulmonary fibrosis. 32 refs., 5 figs

Full-length mRNA sequencing uncovers a widespread coupling between transcription initiation and mRNA processing.

Science.gov (United States)

Anvar, Seyed Yahya; Allard, Guy; Tseng, Elizabeth; Sheynkman, Gloria M; de Klerk, Eleonora; Vermaat, Martijn; Yin, Raymund H; Johansson, Hans E; Ariyurek, Yavuz; den Dunnen, Johan T; Turner, Stephen W; 't Hoen, Peter A C

2018-03-29

The multifaceted control of gene expression requires tight coordination of regulatory mechanisms at transcriptional and post-transcriptional level. Here, we studied the interdependence of transcription initiation, splicing and polyadenylation events on single mRNA molecules by full-length mRNA sequencing. In MCF-7 breast cancer cells, we find 2700 genes with interdependent alternative transcription initiation, splicing and polyadenylation events, both in proximal and distant parts of mRNA molecules, including examples of coupling between transcription start sites and polyadenylation sites. The analysis of three human primary tissues (brain, heart and liver) reveals similar patterns of interdependency between transcription initiation and mRNA processing events. We predict thousands of novel open reading frames from full-length mRNA sequences and obtained evidence for their translation by shotgun proteomics. The mapping database rescues 358 previously unassigned peptides and improves the assignment of others. By recognizing sample-specific amino-acid changes and novel splicing patterns, full-length mRNA sequencing improves proteogenomics analysis of MCF-7 cells. Our findings demonstrate that our understanding of transcriptome complexity is far from complete and provides a basis to reveal largely unresolved mechanisms that coordinate transcription initiation and mRNA processing.

mRNA Cancer Vaccines-Messages that Prevail.

Science.gov (United States)

Grunwitz, Christian; Kranz, Lena M

2017-01-01

During the last decade, mRNA became increasingly recognized as a versatile tool for the development of new innovative therapeutics. Especially for vaccine development, mRNA is of outstanding interest and numerous clinical trials have been initiated. Strikingly, all of these studies have proven that large-scale GMP production of mRNA is feasible and concordantly report a favorable safety profile of mRNA vaccines. Induction of T-cell immunity is a multi-faceted process comprising antigen acquisition, antigen processing and presentation, as well as immune stimulation. The effectiveness of mRNA vaccines is critically dependent on making the antigen(s) of interest available to professional antigen-presenting cells, especially DCs. Efficient delivery of mRNA into DCs in vivo remains a major challenge in the mRNA vaccine field. This review summarizes the principles of mRNA vaccines and highlights the importance of in vivo mRNA delivery and recent advances in harnessing their therapeutic potential.

Principles of mRNA transport in yeast.

Science.gov (United States)

Heym, Roland Gerhard; Niessing, Dierk

2012-06-01

mRNA localization and localized translation is a common mechanism by which cellular asymmetry is achieved. In higher eukaryotes the mRNA transport machinery is required for such diverse processes as stem cell division and neuronal plasticity. Because mRNA localization in metazoans is highly complex, studies at the molecular level have proven to be cumbersome. However, active mRNA transport has also been reported in fungi including Saccharomyces cerevisiae, Ustilago maydis and Candida albicans, in which these events are less difficult to study. Amongst them, budding yeast S. cerevisiae has yielded mechanistic insights that exceed our understanding of other mRNA localization events to date. In contrast to most reviews, we refrain here from summarizing mRNA localization events from different organisms. Instead we give an in-depth account of ASH1 mRNA localization in budding yeast. This approach is particularly suited to providing a more holistic view of the interconnection between the individual steps of mRNA localization, from transcriptional events to cytoplasmic mRNA transport and localized translation. Because of our advanced mechanistic understanding of mRNA localization in yeast, the present review may also be informative for scientists working, for example, on mRNA localization in embryogenesis or in neurons.

Weed-Species Abundance and Diversity Indices in Relation to Tillage Systems and Fertilization

Directory of Open Access Journals (Sweden)

Ilias S. Travlos

2018-04-01

Full Text Available Weeds pose a major threat to world agriculture by reducing detrimentally crop yield and quality. However, at the same time, weeds are major interacting components of the agroecosystems. Abundance and diversity of weeds vary significantly among the several communities. In order to evaluate each community's structure and the interactions among them, several population indices are used as key tools. In parallel, various cultivation and land management strategies, such as tillage and fertilization, are commonly used in terms of integrated weed management. Estimating the response of weed species on those practices is crucial for both biodiversity maintenance and alternative weed control methods. Many experiments have confirmed the fundamental role of tillage intensity and nutrition supply in weed species' abundance and diversity. For instance, in some studies, the abundance of perennial weeds was doubled under reduced tillage intensity. In addition, higher values of Shannon-Weiner and Pielou indices were reported in the PK fertilization treatment compared to the control and NK fertilization treatments. The objective of this paper is to provide a brief overview of the key results of these experiments and summarize the part of the literature related to the effect of tillage systems and fertilization on weed species abundance and diversity. Such knowledge could contribute to the sound design and implementation of integrated weed management programs which in turn may lead to a decrease in the density of serious and noxious weeds and an increase in the overall balance of agroecosystems.

Increased IL-10 mRNA and IL-23 mRNA expression in multiple sclerosis: interferon-beta treatment increases IL-10 mRNA expression while reducing IL-23 mRNA expression

DEFF Research Database (Denmark)

Krakauer, M.; Sorensen, P.; Khademi, M.

2008-01-01

volunteers served to confirm initial findings. mRNA was analyzed by real-time reverse transcriptase polymerase chain reaction (PCR). RESULTS: We found elevated expression of interleukin (IL)-23 and IL-10 in untreated MS patients. IFN-beta therapy increased IL-10 and decreased IL-23 expression independently...... of the regulatory cytokine IL-10. The elevated IL-23 mRNA levels in MS patients are noteworthy in view of the newly discovered IL-23-driven Th17 T-cell subset, which is crucial in animal models of MS. Since IFN-beta therapy resulted in decreased IL-23 mRNA levels, the Th17 axis could be another target of IFN...

Nucleolin Mediates MicroRNA-directed CSF-1 mRNA Deadenylation but Increases Translation of CSF-1 mRNA*

Science.gov (United States)

Woo, Ho-Hyung; Baker, Terri; Laszlo, Csaba; Chambers, Setsuko K.

2013-01-01

CSF-1 mRNA 3′UTR contains multiple unique motifs, including a common microRNA (miRNA) target in close proximity to a noncanonical G-quadruplex and AU-rich elements (AREs). Using a luciferase reporter system fused to CSF-1 mRNA 3′UTR, disruption of the miRNA target region, G-quadruplex, and AREs together dramatically increased reporter RNA levels, suggesting important roles for these cis-acting regulatory elements in the down-regulation of CSF-1 mRNA. We find that nucleolin, which binds both G-quadruplex and AREs, enhances deadenylation of CSF-1 mRNA, promoting CSF-1 mRNA decay, while having the capacity to increase translation of CSF-1 mRNA. Through interaction with the CSF-1 3′UTR miRNA common target, we find that miR-130a and miR-301a inhibit CSF-1 expression by enhancing mRNA decay. Silencing of nucleolin prevents the miRNA-directed mRNA decay, indicating a requirement for nucleolin in miRNA activity on CSF-1 mRNA. Downstream effects followed by miR-130a and miR-301a inhibition of directed cellular motility of ovarian cancer cells were found to be dependent on nucleolin. The paradoxical effects of nucleolin on miRNA-directed CSF-1 mRNA deadenylation and on translational activation were explored further. The nucleolin protein contains four acidic stretches, four RNA recognition motifs (RRMs), and nine RGG repeats. All three domains in nucleolin regulate CSF-1 mRNA and protein levels. RRMs increase CSF-1 mRNA, whereas the acidic and RGG domains decrease CSF-1 protein levels. This suggests that nucleolin has the capacity to differentially regulate both CSF-1 RNA and protein levels. Our finding that nucleolin interacts with Ago2 indirectly via RNA and with poly(A)-binding protein C (PABPC) directly suggests a nucleolin-Ago2-PABPC complex formation on mRNA. This complex is in keeping with our suggestion that nucleolin may work with PABPC as a double-edged sword on both mRNA deadenylation and translational activation. Our findings underscore the complexity of

Identification of prophages in bacterial genomes by dinucleotide relative abundance difference.

Directory of Open Access Journals (Sweden)

K V Srividhya

Full Text Available BACKGROUND: Prophages are integrated viral forms in bacterial genomes that have been found to contribute to interstrain genetic variability. Many virulence-associated genes are reported to be prophage encoded. Present computational methods to detect prophages are either by identifying possible essential proteins such as integrases or by an extension of this technique, which involves identifying a region containing proteins similar to those occurring in prophages. These methods suffer due to the problem of low sequence similarity at the protein level, which suggests that a nucleotide based approach could be useful. METHODOLOGY: Earlier dinucleotide relative abundance (DRA have been used to identify regions, which deviate from the neighborhood areas, in genomes. We have used the difference in the dinucleotide relative abundance (DRAD between the bacterial and prophage DNA to aid location of DNA stretches that could be of prophage origin in bacterial genomes. Prophage sequences which deviate from bacterial regions in their dinucleotide frequencies are detected by scanning bacterial genome sequences. The method was validated using a subset of genomes with prophage data from literature reports. A web interface for prophage scan based on this method is available at http://bicmku.in:8082/prophagedb/dra.html. Two hundred bacterial genomes which do not have annotated prophages have been scanned for prophage regions using this method. CONCLUSIONS: The relative dinucleotide distribution difference helps detect prophage regions in genome sequences. The usefulness of this method is seen in the identification of 461 highly probable loci pertaining to prophages which have not been annotated so earlier. This work emphasizes the need to extend the efforts to detect and annotate prophage elements in genome sequences.

A Metastable Equilibrium Model for the Relative Abundances of Microbial Phyla in a Hot Spring

Science.gov (United States)

Dick, Jeffrey M.; Shock, Everett L.

2013-01-01

Many studies link the compositions of microbial communities to their environments, but the energetics of organism-specific biomass synthesis as a function of geochemical variables have rarely been assessed. We describe a thermodynamic model that integrates geochemical and metagenomic data for biofilms sampled at five sites along a thermal and chemical gradient in the outflow channel of the hot spring known as “Bison Pool” in Yellowstone National Park. The relative abundances of major phyla in individual communities sampled along the outflow channel are modeled by computing metastable equilibrium among model proteins with amino acid compositions derived from metagenomic sequences. Geochemical conditions are represented by temperature and activities of basis species, including pH and oxidation-reduction potential quantified as the activity of dissolved hydrogen. By adjusting the activity of hydrogen, the model can be tuned to closely approximate the relative abundances of the phyla observed in the community profiles generated from BLAST assignments. The findings reveal an inverse relationship between the energy demand to form the proteins at equal thermodynamic activities and the abundance of phyla in the community. The distance from metastable equilibrium of the communities, assessed using an equation derived from energetic considerations that is also consistent with the information-theoretic entropy change, decreases along the outflow channel. Specific divergences from metastable equilibrium, such as an underprediction of the relative abundances of phototrophic organisms at lower temperatures, can be explained by considering additional sources of energy and/or differences in growth efficiency. Although the metabolisms used by many members of these communities are driven by chemical disequilibria, the results support the possibility that higher-level patterns of chemotrophic microbial ecosystems are shaped by metastable equilibrium states that depend on both the

Differential abundance of egg white proteins in laying hens treated with corticosterone.

Science.gov (United States)

Kim, Jimin; Choi, Yang-Ho

2014-12-24

Stressful environments can affect not only egg production and quality but also gene and protein abundance in the ovary and oviduct in laying hens. The oviductal magnum of laying hens is the organ responsible for the synthesis and secretion of egg white proteins. The objective of this study was to investigate the effects of dietary corticosterone as a stress model on the abundance of proteins in the egg white and of mRNA and proteins in the magnum in laying hens. After a 14-day acclimation, 40 laying hens were divided into two groups which were provided for the next 14 days with either control (Control) or corticosterone (Stress) diet containing at 30 mg/kg. Corticosterone treatment resulted in increased feed intake (P ≤ 0.05) and decreased egg production. Two-dimensional electrophoresis (2DE) with MALDI-TOF/TOF MS/MS using eggs obtained on days 0 and 5 revealed differential abundance of egg white proteins by Stress: transiently expressed in neural precursors (TENP), hemopexin (HPX), IgY-Fcυ3-4, and extracellular fatty acid-binding protein (Ex-FABP) were decreased while ovoinhibitor and ovalbumin-related protein X (OVAX) were increased on days 5 vs 0 (P ≤ 0.05). Expression of mRNAs and proteins was also significantly modulated in the magnum of hens in Stress on day 14 (P ≤ 0.05). In conclusion, the current study provides the first evidence showing that dietary corticosterone modulates protein abundance in the egg white in laying hens, and it suggests that environmental stress can differentially modify expression of egg white proteins in laying hens.

Increased FXYD1 and PGC-1α mRNA after blood flow-restricted running is related to fibre type-specific AMPK signalling and oxidative stress in human muscle

DEFF Research Database (Denmark)

Christiansen, Danny; Murphy, Robyn M; Bangsbo, Jens

2018-01-01

AIM: This study explored the effects of blood flow restriction (BFR) on mRNA responses of PGC-1α (total, 1α1, and 1α4) and Na+ ,K+ -ATPase isoforms (NKA; α1-3 , β1-3 , and FXYD1) to an interval running session, and determined if these effects were related to increased oxidative stress, hypoxia......). A muscle sample was collected before (Pre) and after exercise (+0h, +3h) to quantify mRNA, indicators of oxidative stress (HSP27 protein in type I and II fibres, and catalase and HSP70 mRNA), metabolites, and α-AMPK Thr172 /α-AMPK, ACC Ser221 /ACC, CaMKII Thr287 /CaMKII, and PLBSer16 /PLB ratios in type I...... of oxidative stress and type-I fibre ACC Ser221 /ACC ratio, but dissociated from muscle hypoxia, lactate, and CaMKII signalling. CONCLUSION: Blood flow restriction augmented exercise-induced increases in muscle FXYD1 and PGC-1α mRNA in men. This effect was related to increased oxidative stress and fibre type...

Relative quantification of mRNA: comparison of methods currently used for real-time PCR data analysis

Directory of Open Access Journals (Sweden)

Koppel Juraj

2007-12-01

Full Text Available Abstract Background Fluorescent data obtained from real-time PCR must be processed by some method of data analysis to obtain the relative quantity of target mRNA. The method chosen for data analysis can strongly influence results of the quantification. Results To compare the performance of six techniques which are currently used for analysing fluorescent data in real-time PCR relative quantification, we quantified four cytokine transcripts (IL-1β, IL-6 TNF-α, and GM-CSF in an in vivo model of colonic inflammation. Accuracy of the methods was tested by quantification on samples with known relative amounts of target mRNAs. Reproducibility of the methods was estimated by the determination of the intra-assay and inter-assay variability. Cytokine expression normalized to the expression of three reference genes (ACTB, HPRT, SDHA was then determined using the six methods for data analysis. The best results were obtained with the relative standard curve method, comparative Ct method and with DART-PCR, LinRegPCR and Liu & Saint exponential methods when average amplification efficiency was used. The use of individual amplification efficiencies in DART-PCR, LinRegPCR and Liu & Saint exponential methods significantly impaired the results. The sigmoid curve-fitting (SCF method produced medium performance; the results indicate that the use of appropriate type of fluorescence data and in some instances manual selection of the number of amplification cycles included in the analysis is necessary when the SCF method is applied. We also compared amplification efficiencies (E and found that although the E values determined by different methods of analysis were not identical, all the methods were capable to identify two genes whose E values significantly differed from other genes. Conclusion Our results show that all the tested methods can provide quantitative values reflecting the amounts of measured mRNA in samples, but they differ in their accuracy and

Nonparametric testing for DNA copy number induced differential mRNA gene expression

NARCIS (Netherlands)

van Wieringen, W.N.; van de Wiel, M.A.

2009-01-01

The central dogma of molecular biology relates DNA with mRNA. Array CGH measures DNA copy number and gene expression microarrays measure the amount of mRNA. Methods that integrate data from these two platforms may uncover meaningful biological relationships that further our understanding of cancer.

Size matters: abundance matching, galaxy sizes, and the Tully-Fisher relation in EAGLE

Science.gov (United States)

Ferrero, Ismael; Navarro, Julio F.; Abadi, Mario G.; Sales, Laura V.; Bower, Richard G.; Crain, Robert A.; Frenk, Carlos S.; Schaller, Matthieu; Schaye, Joop; Theuns, Tom

2017-02-01

The Tully-Fisher relation (TFR) links the stellar mass of a disc galaxy, Mstr, to its rotation speed: it is well approximated by a power law, shows little scatter, and evolves weakly with redshift. The relation has been interpreted as reflecting the mass-velocity scaling (M ∝ V3) of dark matter haloes, but this interpretation has been called into question by abundance-matching (AM) models, which predict the galaxy-halo mass relation to deviate substantially from a single power law and to evolve rapidly with redshift. We study the TFR of luminous spirals and its relation to AM using the EAGLE set of Λ cold dark matter (ΛCDM) cosmological simulations. Matching both relations requires disc sizes to satisfy constraints given by the concentration of haloes and their response to galaxy assembly. EAGLE galaxies approximately match these constraints and show a tight mass-velocity scaling that compares favourably with the observed TFR. The TFR is degenerate to changes in galaxy formation efficiency and the mass-size relation; simulations that fail to match the galaxy stellar mass function may fit the observed TFR if galaxies follow a different mass-size relation. The small scatter in the simulated TFR results because, at fixed halo mass, galaxy mass and rotation speed correlate strongly, scattering galaxies along the main relation. EAGLE galaxies evolve with lookback time following approximately the prescriptions of AM models and the observed mass-size relation of bright spirals, leading to a weak TFR evolution consistent with observation out to z = 1. ΛCDM models that match both the abundance and size of galaxies as a function of stellar mass have no difficulty reproducing the observed TFR and its evolution.

Expression proteomics of UPF1 knockdown in HeLa cells reveals autoregulation of hnRNP A2/B1 mediated by alternative splicing resulting in nonsense-mediated mRNA decay

Directory of Open Access Journals (Sweden)

Zavolan Mihaela

2010-10-01

Full Text Available Abstract Background In addition to acting as an RNA quality control pathway, nonsense-mediated mRNA decay (NMD plays roles in regulating normal gene expression. In particular, the extent to which alternative splicing is coupled to NMD and the roles of NMD in regulating uORF containing transcripts have been a matter of debate. Results In order to achieve a greater understanding of NMD regulated gene expression we used 2D-DiGE proteomics technology to examine the changes in protein expression induced in HeLa cells by UPF1 knockdown. QPCR based validation of the corresponding mRNAs, in response to both UPF1 knockdown and cycloheximide treatment, identified 17 bona fide NMD targets. Most of these were associated with bioinformatically predicted NMD activating features, predominantly upstream open reading frames (uORFs. Strikingly, however, the majority of transcripts up-regulated by UPF1 knockdown were either insensitive to, or even down-regulated by, cycloheximide treatment. Furthermore, the mRNA abundance of several down-regulated proteins failed to change upon UPF1 knockdown, indicating that UPF1's role in regulating mRNA and protein abundance is more complex than previously appreciated. Among the bona fide NMD targets, we identified a highly conserved AS-NMD event within the 3' UTR of the HNRNPA2B1 gene. Overexpression of GFP tagged hnRNP A2 resulted in a decrease in endogenous hnRNP A2 and B1 mRNA with a concurrent increase in the NMD sensitive isoforms. Conclusions Despite the large number of changes in protein expression upon UPF1 knockdown, a relatively small fraction of them can be directly attributed to the action of NMD on the corresponding mRNA. From amongst these we have identified a conserved AS-NMD event within HNRNPA2B1 that appears to mediate autoregulation of HNRNPA2B1 expression levels.

Cytochrome P450-2C11 mRNA is not expressed in endothelial cells dissected from rat renal arterioles.

Science.gov (United States)

Heil, Sandra G; De Vriese, An S; Kluijtmans, Leo A J; Dijkman, Henry; van Strien, Denise; Akkers, Robert; Blom, Henk J

2005-01-01

Cytochrome P450 (CYP) isoenzymes (CYP2C and CYP2J) are involved in the production of epoxyeicosatrienoic acids, which are postulated as endothelium-derived hyperpolarizing factors (EDHFs). We hypothesized that if CYP2C11 is involved in the EDHF-mediated responses, its mRNA should be expressed in endothelial cells. We, therefore, examined the mRNA expression of CYP2C11 in endothelial cells of renal arterioles. Laser microdissection was applied to isolate endothelial cells from the renal arterioles of 4 male and 4 female Wistar rats. As a positive control of CYP2C11 expression, hepatocytes were also dissected from these rats. RNA was isolated and real-time quantitative polymerase chain reaction (Q-PCR) analysis was applied. Q-PCR analysis showed that CYP2C11 mRNA was not expressed in laser microdissected endothelial cells of renal arterioles of male and female rats. CYP2C11 mRNA expression was highly abundant in hepatocytes dissected from male livers, but in female livers hardly any CYP2C11 mRNA was detected. We have shown that endothelial cells can be dissected from small renal arterioles by laser microdissection to study the mRNA expression of specific genes by Q-PCR. Using this novel tool, we demonstrated that the CYP2C11 mRNA was not expressed in the endothelial cells of renal arterioles. Therefore, we speculate that CYP2C11 does not contribute to the EDHF-mediated responses in renal arterioles. Copyright (c) 2005 S. Karger AG, Basel.

Regulation of mRNA translation during mitosis.

Science.gov (United States)

Tanenbaum, Marvin E; Stern-Ginossar, Noam; Weissman, Jonathan S; Vale, Ronald D

2015-08-25

Passage through mitosis is driven by precisely-timed changes in transcriptional regulation and protein degradation. However, the importance of translational regulation during mitosis remains poorly understood. Here, using ribosome profiling, we find both a global translational repression and identified ~200 mRNAs that undergo specific translational regulation at mitotic entry. In contrast, few changes in mRNA abundance are observed, indicating that regulation of translation is the primary mechanism of modulating protein expression during mitosis. Interestingly, 91% of the mRNAs that undergo gene-specific regulation in mitosis are translationally repressed, rather than activated. One of the most pronounced translationally-repressed genes is Emi1, an inhibitor of the anaphase promoting complex (APC) which is degraded during mitosis. We show that full APC activation requires translational repression of Emi1 in addition to its degradation. These results identify gene-specific translational repression as a means of controlling the mitotic proteome, which may complement post-translational mechanisms for inactivating protein function.

Species richness and relative abundance of birds in natural and anthropogenic fragments of Brazilian Atlantic forest

Directory of Open Access Journals (Sweden)

Luiz dos Anjos

2004-06-01

Full Text Available Bird communities were studied in two types of fragmented habitat of Atlantic forest in the State of Paraná, southern Brazil; one consisted of forest fragments that were created as a result of human activities (forest remnants, the other consisted of a set of naturally occurring forest fragments (forest patches. Using quantitative data obtained by the point counts method in 3 forest patches and 3 forest remnants during one year, species richness and relative abundance were compared in those habitats, considering species groups according to their general feeding habits. Insectivores, omnivores, and frugivores presented similar general tendencies in both habitats (decrease of species number with decreasing size and increasing isolation of forest fragment. However, these tendencies were different, when considering the relative abundance data: the trunk insectivores presented the highest value in the smallest patch while the lowest relative abundance was in the smallest remnant. In the naturally fragmented landscape, time permitted that the loss of some species of trunk insectivores be compensated for the increase in abundance of other species. In contrast, the remnants essentially represented newly formed islands that are not yet at equilibrium and where future species losses would make them similar to the patches.Comunidades de aves foram estudadas em duas regiões fragmentadas de floresta Atlântica no Estado do Paraná, sul do Brasil; uma região é constituída de fragmentos florestais que foram criados como resultado de atividades humanas (remanescentes florestais e a outra de um conjunto de fragmentos florestais naturais (manchas de floresta. Usando dados quantitativos (o método de contagens pontuais previamente obtidos em 3 manchas de floresta e em 3 remanescentes florestais durante um ano, a riqueza e a abundância relativa de aves foram comparadas naqueles habitats considerando as espécies pelos seus hábitos alimentares. Inset

Studies on the role of NonA in mRNA biogenesis

International Nuclear Information System (INIS)

Kozlova, Natalia; Braga, Jose; Lundgren, Josefin; Rino, Jose; Young, Patrick; Carmo-Fonseca, Maria; Visa, Neus

2006-01-01

The NonA protein of Drosophila melanogaster is an abundant nuclear protein that belongs to the DBHS (Drosophila behavior, human splicing) protein family. The DBHS proteins bind both DNA and RNA in vitro and have been involved in different aspects of gene expression, including pre-mRNA splicing, transcription regulation and nuclear retention of mRNA. We have used double-stranded RNA interference in Drosophila S2 cells to silence the expression of NonA and to investigate its role in mRNA biogenesis. We show that knockdown of NonA does not affect transcription nor splicing. We demonstrate that NonA forms a complex with the essential nuclear export factor NXF1 in an RNA-dependent manner. We have constructed stable S2 cell lines that express full-length and truncated NXF1 fused to GFP in order to perform fluorescence recovery after photobleaching experiments. We show that knockdown of NonA reduces the intranuclear mobility of NXF1-GFP associated with poly(A) + RNA in vivo, while the mobility of the truncated NXF1-GFP that does not bind RNA is not affected. Our data suggest that NonA facilitates the intranuclear mobility of mRNP particles

Relative abundance of total subgingival plaque-specific bacteria in salivary microbiota reflects the overall periodontal condition in patients with periodontitis.

Science.gov (United States)

Kageyama, Shinya; Takeshita, Toru; Asakawa, Mikari; Shibata, Yukie; Takeuchi, Kenji; Yamanaka, Wataru; Yamashita, Yoshihisa

2017-01-01

Increasing attention is being focused on evaluating the salivary microbiota as a promising method for monitoring oral health; however, its bacterial composition greatly differs from that of dental plaque microbiota, which is a dominant etiologic factor of oral diseases. This study evaluated the relative abundance of subgingival plaque-specific bacteria in the salivary microbiota and examined a relationship between the abundance and severity of periodontal condition in patients with periodontitis. Four samples (subgingival and supragingival plaques, saliva, and tongue coating) per each subject were collected from 14 patients with a broad range of severity of periodontitis before periodontal therapy. The bacterial composition was analyzed by 16S rRNA gene amplicon sequencing using Ion PGM. Of the 66 species-level operational taxonomic units (OTUs) representing the mean relative abundance of ≥ 1% in any of the four niches, 12 OTUs corresponding to known periodontal pathogens, including Porphyromonas gingivalis, were characteristically predominant in the subgingival plaque and constituted 37.3 ± 22.9% of the microbiota. The total relative abundance of these OTUs occupied only 1.6 ± 1.2% of the salivary microbiota, but significantly correlated with the percentage of diseased sites (periodontal pocket depth ≥ 4 mm; r = 0.78, P periodontal therapy, the total relative abundance of these 12 OTUs was evaluated as well as before periodontal therapy and reductions of the abundance through periodontal therapy were strongly correlated in saliva and subgingival plaque (r = 0.81, P bacteria representing the present condition of periodontal health.

Muscarinic receptor subtype mRNA expression in the human prostate: association with age, pathological diagnosis, prostate size, or potentially interfering medications?

NARCIS (Netherlands)

Witte, Lambertus P. W.; Teitsma, Christine A.; de La Rosette, Jean J. M. C. H.; Michel, Martin C.

2014-01-01

As the prostate abundantly expresses muscarinic receptors and antagonists for such receptors are increasingly used in the treatment of men with voiding function and large prostates, we have explored an association of the mRNA expression of human M1, M2, M3, M4, and M5 receptors in human prostate

Frequency of intron loss correlates with processed pseudogene abundance: a novel strategy to test the reverse transcriptase model of intron loss.

Science.gov (United States)

Zhu, Tao; Niu, Deng-Ke

2013-03-05

Although intron loss in evolution has been described, the mechanism involved is still unclear. Three models have been proposed, the reverse transcriptase (RT) model, genomic deletion model and double-strand-break repair model. The RT model, also termed mRNA-mediated intron loss, suggests that cDNA molecules reverse transcribed from spliced mRNA recombine with genomic DNA causing intron loss. Many studies have attempted to test this model based on its predictions, such as simultaneous loss of adjacent introns, 3'-side bias of intron loss, and germline expression of intron-lost genes. Evidence either supporting or opposing the model has been reported. The mechanism of intron loss proposed in the RT model shares the process of reverse transcription with the formation of processed pseudogenes. If the RT model is correct, genes that have produced more processed pseudogenes are more likely to undergo intron loss. In the present study, we observed that the frequency of intron loss is correlated with processed pseudogene abundance by analyzing a new dataset of intron loss obtained in mice and rats. Furthermore, we found that mRNA molecules of intron-lost genes are mostly translated on free cytoplasmic ribosomes, a feature shared by mRNA molecules of the parental genes of processed pseudogenes and long interspersed elements. This feature is likely convenient for intron-lost gene mRNA molecules to be reverse transcribed. Analyses of adjacent intron loss, 3'-side bias of intron loss, and germline expression of intron-lost genes also support the RT model. Compared with previous evidence, the correlation between the abundance of processed pseudogenes and intron loss frequency more directly supports the RT model of intron loss. Exploring such a correlation is a new strategy to test the RT model in organisms with abundant processed pseudogenes.

Seasonal abundance of soil arthropods in relation to meteorological and edaphic factors in the agroecosystems of Faisalabad, Punjab, Pakistan

Science.gov (United States)

Shakir, Muhammad Mussadiq; Ahmed, Sohail

2015-05-01

Soil arthropods are an important component of agroecosystems, contributing significantly to their biodiversity and functioning. However, seasonal patterns, population dynamics, and significant roles of these soil arthropods in improvement of soil structures and functions are influenced by many factors. The objective of the current study was to investigate soil arthropod abundance in relation to a blend of meteorological and edaphic factors and to find out the difference in abundance among various crops (sugarcane, cotton, wheat, alfalfa fodder, and citrus orchards). The arthropod sampling was done by pitfall traps and Tullgren extractions on fortnightly intervals. Soil temperature and relative humidity were noted on the field sites while analysis for soil pH, organic matter, and soil moisture contents were done in the laboratory. The rainfall data was obtained from an observatory. Results showed that significant differences were found in soil arthropod abundance across different sampling months and crops. Out of total 13,673 soil arthropods sampled, 38 % belonged to Collembola, followed by 15 % Hymenoptera, 15 % Acarina, 11 % Myriapods, 6 % Coleoptera, 5 % Orthoptera, and 5 % Araneae. Mean abundance per sample was highest in summer months as compared to winter. Overall abundance per sample was significantly different between all crops ( p Aranae, Coleoptera), least abundant (Dermaptera, Hemiptera, Diptera), and rare (Blattaria, Isoptera, Diplura, Lepidoptera). Soil temperature and soil organic matter showed significant positive correlation with abundance, while relative humidity was significantly negatively correlated. Soil moisture and soil pH showed no significant correlations while no correlation was found with total rainfall. PCA analysis revealed that soil surface arthropods were the major contributors of variation in overall abundance in extreme temperature months while microarthropods in low-temperature months. CCA analysis revealed the occurrence of

Modeled distribution and abundance of a pelagic seabird reveal trends in relation to fisheries

Science.gov (United States)

Renner, Martin; Parrish, Julia K.; Piatt, John F.; Kuletz, Kathy J.; Edwards, Ann E.; Hunt, George L.

2013-01-01

The northern fulmar Fulmarus glacialis is one of the most visible and widespread seabirds in the eastern Bering Sea and Aleutian Islands. However, relatively little is known about its abundance, trends, or the factors that shape its distribution. We used a long-term pelagic dataset to model changes in fulmar at-sea distribution and abundance since the mid-1970s. We used an ensemble model, based on a weighted average of generalized additive model (GAM), multivariate adaptive regression splines (MARS), and random forest models to estimate the pelagic distribution and density of fulmars in the waters of the Aleutian Archipelago and Bering Sea. The most important predictor variables were colony effect, sea surface temperature, distribution of fisheries, location, and primary productivity. We calculated a time series from the ratio of observed to predicted values and found that fulmar at-sea abundance declined from the 1970s to the 2000s at a rate of 0.83% (± 0.39% SE) per annum. Interpolating fulmar densities on a spatial grid through time, we found that the center of fulmar distribution in the Bering Sea has shifted north, coinciding with a northward shift in fish catches and a warming ocean. Our study shows that fisheries are an important, but not the only factor, shaping fulmar distribution and abundance trends in the eastern Bering Sea and Aleutian Islands.

Introduction of enteral food increases plasma GLP-2 and decreases GLP-2 receptor mRNA abundance during pig development

DEFF Research Database (Denmark)

Petersen, Y. M.; Hartmann, B.; Holst, Jens Juul

2003-01-01

increased before birth, peaked in suckling 1-d-old pigs (87 +/- 14 pmol/L, P anorexia (34 +/- 5 pmol/L, P ... in these pigs. We conclude that the introduction of enteral feeding transiently increases plasma GLP-2 concentrations and decreases small intestinal GLP-2R mRNA levels during pig development. GLP-2 may play a role in the growth of the small intestine around birth and weaning via a response to enteral nutrition....

Presence of albumin mRNA precursors in nuclei of analbuminemic rat liver lacking cytoplasmic albumin mRNA.

OpenAIRE

Esumi, H; Takahashi, Y; Sekiya, T; Sato, S; Nagase, S; Sugimura, T

1982-01-01

Analbuminemic rats, which lack serum albumin, were previously found to have no albumin mRNA in the cytoplasm of the liver. In the present study, the existence of nuclear albumin mRNA precursors in the liver of analbuminemic rats was examined by RNA X cDNA hybridization kinetics. Albumin mRNA precursors were present in the nuclei of analbuminemic rat liver at almost normal levels, despite the absence of albumin mRNA from the cytoplasm. Nuclear RNA of analbuminemic rat liver was subjected to el...

Relative foraminiferan abundance as an indicator of seagrass sediment health:

Science.gov (United States)

Cajandig, P.; Quiros, A.; Nolan, H.; Tallman, R.; Cooper, N.; Ayala, J.; Courtier, C.

2013-12-01

Authors: Patrick Cajandig*, Jose Ayala**, Nathaniel Cooper**, Catherine Courtier**, Hannah Nolan**, Rachelle Tallman**, T.E. Angela L. Quiros** * Davis High-School CA, **University of California Santa Cruz, Ecology and Evolutionary Biology Department Seagrasses are a key component in coastal ecosystems. Found in shallow marine environments, they make a large contribution to coastal ecosystem health by sustaining water quality, stabilizing the sea bottom, and providing habitat as well as food for other organisms. Seagrasses accumulate tiny grains of sediment, increasing water clarity. Just like barren hills are prone to erosion compared to vegetated, rooted down hills, we find a similar situation in the ocean. Seagrasses have broad roots that extend vertically and horizontally to help stabilize the seabed. Seagrasses support a whole ecosystem, because some organisms feed off of the seagrass alone, while others feed off the inhabitants of the seagrass. The quality of sediment is a vital part of seagrass health, just like nutrient rich soils are important to land plants. But what in seagrass sediment is a good indication of health? We hypothesize that seagrass health measures such as percent cover and seagrass species diversity are related to the abundance of foraminiferans relative to other seagrass sediment components. My mentor, T. E. Angela L. Quiros, from the University of California, Santa Cruz (UCSC), collected the sediment samples from seagrass beds in the Philippines. Samples were dried and brought to UCSC for sediment sieving. We used different sized sieves to sort the sediment. These sieves ranged from coarse to very fine sieves (Phi -2.0 (coarse) through +3.0 (fine) going in 0.5 intervals on a log scale). We weighed the sediment that was caught in each tray and separated them into bags of different size classes. To analyze each sample, we subsampled four size classes (Phi's -2.0, -1.5,-1.0, 0.0), and used a dissecting scope to identify and then weigh the

Abundances in field dwarf stars. II. Carbon and nitrogen abundances

Energy Technology Data Exchange (ETDEWEB)

Laird, J.B.

1985-02-15

Intermediate-dispersion spectra of 116 field dwarf stars, plus 10 faint field giants and 3 Hyades dwarfs, have been used to derive carbon and nitrogen abundances relative to iron. The program sample includes both disk and halo stars, spanning a range in (Fe/H) of +0.50 to -2.45. Synthetic spectra of CH and NH bands have been used to determine carbon and nitrogen abundances. The C/Fe ratio is solar over the range of metallicity studied, with an estimated intrinsic scatter of 0.10 dex. Down to (Fe/H)roughly-equal-1.8, below which the nitrogen abundance could not be measured, the N/Fe ratio is also constant for the majority of stars, indicating that nitrogen production is largely primary. Four halo stars are found to be enhanced in nitrogen relative to iron, by factors between 5 and 50, although their carbon abundances appear to be normal. These results are discussed in connection with the chemical evolution of the Galaxy and the sites of C, N, and Fe nucleosynthesis. The results require that C, N, and Fe be produced in stars of similar mass. Our current understanding of N production, then, implies that most Type I supernovae have intermediate-mass progenitors. The nitrogen in the N-enhanced halo stars is very probably primordial, indicating that the interstellar medium at early epochs contained substantial inhomogeneities.

Abundances in field dwarf stars. II. Carbon and nitrogen abundances

International Nuclear Information System (INIS)

Laird, J.B.

1985-01-01

Intermediate-dispersion spectra of 116 field dwarf stars, plus 10 faint field giants and 3 Hyades dwarfs, have been used to derive carbon and nitrogen abundances relative to iron. The program sample includes both disk and halo stars, spanning a range in [Fe/H] of +0.50 to -2.45. Synthetic spectra of CH and NH bands have been used to determine carbon and nitrogen abundances. The C/Fe ratio is solar over the range of metallicity studied, with an estimated intrinsic scatter of 0.10 dex. Down to [Fe/H]roughly-equal-1.8, below which the nitrogen abundance could not be measured, the N/Fe ratio is also constant for the majority of stars, indicating that nitrogen production is largely primary. Four halo stars are found to be enhanced in nitrogen relative to iron, by factors between 5 and 50, although their carbon abundances appear to be normal. These results are discussed in connection with the chemical evolution of the Galaxy and the sites of C, N, and Fe nucleosynthesis. The results require that C, N, and Fe be produced in stars of similar mass. Our current understanding of N production, then, implies that most Type I supernovae have intermediate-mass progenitors. The nitrogen in the N-enhanced halo stars is very probably primordial, indicating that the interstellar medium at early epochs contained substantial inhomogeneities

Protein functional features are reflected in the patterns of mRNA translation speed.

Science.gov (United States)

López, Daniel; Pazos, Florencio

2015-07-09

The degeneracy of the genetic code makes it possible for the same amino acid string to be coded by different messenger RNA (mRNA) sequences. These "synonymous mRNAs" may differ largely in a number of aspects related to their overall translational efficiency, such as secondary structure content and availability of the encoded transfer RNAs (tRNAs). Consequently, they may render different yields of the translated polypeptides. These mRNA features related to translation efficiency are also playing a role locally, resulting in a non-uniform translation speed along the mRNA, which has been previously related to some protein structural features and also used to explain some dramatic effects of "silent" single-nucleotide-polymorphisms (SNPs). In this work we perform the first large scale analysis of the relationship between three experimental proxies of mRNA local translation efficiency and the local features of the corresponding encoded proteins. We found that a number of protein functional and structural features are reflected in the patterns of ribosome occupancy, secondary structure and tRNA availability along the mRNA. One or more of these proxies of translation speed have distinctive patterns around the mRNA regions coding for certain protein local features. In some cases the three patterns follow a similar trend. We also show specific examples where these patterns of translation speed point to the protein's important structural and functional features. This support the idea that the genome not only codes the protein functional features as sequences of amino acids, but also as subtle patterns of mRNA properties which, probably through local effects on the translation speed, have some consequence on the final polypeptide. These results open the possibility of predicting a protein's functional regions based on a single genomic sequence, and have implications for heterologous protein expression and fine-tuning protein function.

Arc mRNA induction in striatal efferent neurons associated with response learning.

Science.gov (United States)

Daberkow, D P; Riedy, M D; Kesner, R P; Keefe, K A

2007-07-01

The dorsal striatum is involved in motor-response learning, but the extent to which distinct populations of striatal efferent neurons are differentially involved in such learning is unknown. Activity-regulated, cytoskeleton-associated (Arc) protein is an effector immediate-early gene implicated in synaptic plasticity. We examined arc mRNA expression in striatopallidal vs. striatonigral efferent neurons in dorsomedial and dorsolateral striatum of rats engaged in reversal learning on a T-maze motor-response task. Male Sprague-Dawley rats learned to turn right or left for 3 days. Half of the rats then underwent reversal training. The remaining rats were yoked to rats undergoing reversal training, such that they ran the same number of trials but ran them as continued-acquisition trials. Brains were removed and processed using double-label fluorescent in situ hybridization for arc and preproenkephalin (PPE) mRNA. In the reversal, but not the continued-acquisition, group there was a significant relation between the overall arc mRNA signal in dorsomedial striatum and the number of trials run, with rats reaching criterion in fewer trials having higher levels of arc mRNA expression. A similar relation was seen between the numbers of PPE(+) and PPE(-) neurons in dorsomedial striatum with cytoplasmic arc mRNA expression. Interestingly, in behaviourally activated animals significantly more PPE(-) neurons had cytoplasmic arc mRNA expression. These data suggest that Arc in both striatonigral and striatopallidal efferent neurons is involved in striatal synaptic plasticity mediating motor-response learning in the T-maze and that there is differential processing of arc mRNA in distinct subpopulations of striatal efferent neurons.

Stimulation of S14 mRNA and lipogenesis in brown fat by hypothyroidism, cold exposure, and cafeteria feeding: evidence supporting a general role for S14 in lipogenesis and lipogenesis in the maintenance of thermogenesis

Energy Technology Data Exchange (ETDEWEB)

Freake, H.C.; Oppenheimer, J.H.

1987-05-01

In liver, thyroid hormone rapidly induces S14 mRNA, which encodes a small acidic protein. This sequence is abundantly expressed only in lipogenic tissues and is thought to have some function in fat metabolism. In the euthyroid rat, we measured 20-fold higher levels of S14 mRNA in interscapular brown adipose tissue than liver. Furthermore, whereas in liver or epididymal fat, hypothyroidism resulted in an 80% fall in S14 mRNA, in brown fat the level of this sequence increased a further 3-fold. In all three tissues, the expression of S14 mRNA correlated well with lipogenesis, as assessed by /sup 3/H/sub 2/O incorporation. Physiological activation of brown fat by chronic cold exposure or cafeteria feeding increased the concentration of S14 mRNA in this tissue and again this was accompanied by a greater rate of fatty acid synthesis. Overall, in liver and white and brown adipose tissue, S14 mRNA and lipogenesis were well correlated and strongly suggest a function of the S14 protein related to fat synthesis. These studies suggest that the S14 protein and lipogenesis may be important for thyroid hormone-induced and brown adipose tissue thermogenesis and that stimulation of these functions in hypothyroid brown fat is a consequence of decreased thyroid hormone-induced thermogenesis elsewhere.

Stimulation of S14 mRNA and lipogenesis in brown fat by hypothyroidism, cold exposure, and cafeteria feeding: evidence supporting a general role for S14 in lipogenesis and lipogenesis in the maintenance of thermogenesis

International Nuclear Information System (INIS)

Freake, H.C.; Oppenheimer, J.H.

1987-01-01

In liver, thyroid hormone rapidly induces S14 mRNA, which encodes a small acidic protein. This sequence is abundantly expressed only in lipogenic tissues and is thought to have some function in fat metabolism. In the euthyroid rat, we measured 20-fold higher levels of S14 mRNA in interscapular brown adipose tissue than liver. Furthermore, whereas in liver or epididymal fat, hypothyroidism resulted in an 80% fall in S14 mRNA, in brown fat the level of this sequence increased a further 3-fold. In all three tissues, the expression of S14 mRNA correlated well with lipogenesis, as assessed by 3 H 2 O incorporation. Physiological activation of brown fat by chronic cold exposure or cafeteria feeding increased the concentration of S14 mRNA in this tissue and again this was accompanied by a greater rate of fatty acid synthesis. Overall, in liver and white and brown adipose tissue, S14 mRNA and lipogenesis were well correlated and strongly suggest a function of the S14 protein related to fat synthesis. These studies suggest that the S14 protein and lipogenesis may be important for thyroid hormone-induced and brown adipose tissue thermogenesis and that stimulation of these functions in hypothyroid brown fat is a consequence of decreased thyroid hormone-induced thermogenesis elsewhere

Relation of desert pupfish abundance to selected environmental variables in natural and manmade habitats in the Salton Sea basin

Science.gov (United States)

Martin, B.A.; Saiki, M.K.

2005-01-01

We assessed the relation between abundance of desert pupfish, Cyprinodon macularius, and selected biological and physicochemical variables in natural and manmade habitats within the Salton Sea Basin. Field sampling in a natural tributary, Salt Creek, and three agricultural drains captured eight species including pupfish (1.1% of the total catch), the only native species encountered. According to Bray-Curtis resemblance functions, fish species assemblages differed mostly between Salt Creek and the drains (i.e., the three drains had relatively similar species assemblages). Pupfish numbers and environmental variables varied among sites and sample periods. Canonical correlation showed that pupfish abundance was positively correlated with abundance of western mosquitofish, Gambusia affinis, and negatively correlated with abundance of porthole livebearers, Poeciliopsis gracilis, tilapias (Sarotherodon mossambica and Tilapia zillii), longjaw mudsuckers, Gillichthys mirabilis, and mollies (Poecilia latipinnaandPoecilia mexicana). In addition, pupfish abundance was positively correlated with cover, pH, and salinity, and negatively correlated with sediment factor (a measure of sediment grain size) and dissolved oxygen. Pupfish abundance was generally highest in habitats where water quality extremes (especially high pH and salinity, and low dissolved oxygen) seemingly limited the occurrence of nonnative fishes. This study also documented evidence of predation by mudsuckers on pupfish. These findings support the contention of many resource managers that pupfish populations are adversely influenced by ecological interactions with nonnative fishes. ?? Springer 2005.

Significance of the BRAF mRNA Expression Level in Papillary Thyroid Carcinoma: An Analysis of The Cancer Genome Atlas Data.

Directory of Open Access Journals (Sweden)

Young Jun Chai

Full Text Available BRAFV600E is the most common mutation in papillary thyroid carcinoma (PTC, and it is associated with high-risk prognostic factors. However, the significance of the BRAF mRNA level in PTC remains unknown. We evaluated the significance of BRAF mRNA expression level by analyzing PTC data from The Cancer Genome Atlas (TCGA database.Data from 499 patients were downloaded from the TCGA database. After excluding other PTC variants, we selected 353 cases of classic PTC, including 193 cases with BRAFV600E and 160 cases with the wild-type BRAF. mRNA abundances were measured using RNA-Seq with the Expectation Maximization algorithm.The mean BRAF mRNA level was significantly higher in BRAFV600E patients than in patients with wild-type BRAF (197.6 vs. 179.3, p = 0.031. In wild-type BRAF patients, the mean BRAF mRNA level was higher in cases with a tumor > 2 cm than those with a tumor ≤ 2.0 cm (189.4 vs. 163.8, p = 0.046, and was also higher in cases with lymph node metastasis than in those without lymph node metastasis (188.5 vs. 157.9, p = 0.040. Within BRAFV600E patients, higher BRAF mRNA expression was associated with extrathyroidal extension (186.4 vs. 216.4, p = 0.001 and higher T stage (188.1 vs. 210.2, p = 0.016.A higher BRAF mRNA expression level was associated with tumor aggressiveness in classic PTC regardless of BRAF mutational status. Evaluation of BRAF mRNA level may be helpful in prognostic risk stratification of PTC.

Longitudinal patterns in flathead catfish relative abundance and length at age within a large river: Effects of an urban gradient

Science.gov (United States)

Paukert, C.P.; Makinster, A.S.

2009-01-01

We investigated the spatial variation of flathead catfish (Pylodictis olivaris) relative abundance and growth in the 274 km long Kansas River to determine if population dynamics of catfish are related to urbanization. Electrofishing was conducted at 462 random sites throughout the river in summer, 2005-2006 to collect fish. Relative abundance of age 1 fish (???200mm), subadult (>200-400mm) and adult fish (>400 mm) ranged from 0.34 to 14.67 fish h-1, mean length at age 1 was 165 (range: 128-195) mm total length (TL) and mean length at age 3 was 376 mm TL (range: 293-419mm TL). The proportion of land use within 200 m of the river edge was between 0 and 0.54 urban. River reaches with high relative abundance of age 1 flathead catfish had high relative abundance of subadult and adult catfish. River reaches with fast flathead catfish growth to age 1 had fast growth to age 3. High urban land use and riprap in the riparian area were evident in river reaches near the heavily populated Kansas City and Topeka, Kansas, USA. Reaches with increased number of log jams and islands had decreased riparian agriculture. Areas of low urbanization had faster flathead catfish growth (r = 0.67, p = 0.005). Relative abundance of flathead catfish was higher in more agricultural areas (r = -0.57, p = 0.02). Changes in land use in riverine environments may alter population dynamics of a fish species within a river. Spatial differences in population dynamics need to be considered when evaluating riverine fish populations. Published in 2008 by John Wiley & Sons Ltd.

Diversity and relative abundance of the bacterial pathogen, Flavobacterium spp., infecting reproductive ecotypes of kokanee salmon.

Science.gov (United States)

Lemay, Matthew A; Russello, Michael A

2014-11-04

Understanding the distribution and abundance of pathogens can provide insight into the evolution and ecology of their host species. Previous research in kokanee, the freshwater form of sockeye salmon (Oncorhynchus nerka), found evidence that populations spawning in streams may experience a greater pathogen load compared with populations that spawn on beaches. In this study we tested for differences in the abundance and diversity of the gram-negative bacteria, Flavobacterium spp., infecting tissues of kokanee in both of these spawning habitats (streams and beaches). Molecular assays were carried out using primers designed to amplify a ~200 nucleotide region of the gene encoding the ATP synthase alpha subunit (AtpA) within the genus Flavobacterium. Using a combination of DNA sequencing and quantitative PCR (qPCR) we compared the diversity and relative abundance of Flavobacterium AtpA amplicons present in DNA extracted from tissue samples of kokanee collected from each spawning habitat. We identified 10 Flavobacterium AtpA haplotypes among the tissues of stream-spawning kokanee and seven haplotypes among the tissues of beach-spawning kokanee, with only two haplotypes shared between spawning habitats. Haplotypes occurring in the same clade as F. psychrophilum were the most prevalent (92% of all reads, 60% of all haplotypes), and occurred in kokanee from both spawning habitats (streams and beaches). Subsequent qPCR assays did not find any significant difference in the relative abundance of Flavobacterium AtpA amplicons between samples from the different spawning habitats. We confirmed the presence of Flavobacterium spp. in both spawning habitats and found weak evidence for increased Flavobacterium diversity in kokanee sampled from stream-spawning sites. However, the quantity of Flavobacterium DNA did not differ between spawning habitats. We recommend further study aimed at quantifying pathogen diversity and abundance in population-level samples of kokanee combined with

Protein degradation rate is the dominant mechanism accounting for the differences in protein abundance of basal p53 in a human breast and colorectal cancer cell line.

Directory of Open Access Journals (Sweden)

Eszter Lakatos

Full Text Available We determine p53 protein abundances and cell to cell variation in two human cancer cell lines with single cell resolution, and show that the fractional width of the distributions is the same in both cases despite a large difference in average protein copy number. We developed a computational framework to identify dominant mechanisms controlling the variation of protein abundance in a simple model of gene expression from the summary statistics of single cell steady state protein expression distributions. Our results, based on single cell data analysed in a Bayesian framework, lends strong support to a model in which variation in the basal p53 protein abundance may be best explained by variations in the rate of p53 protein degradation. This is supported by measurements of the relative average levels of mRNA which are very similar despite large variation in the level of protein.

Protein degradation rate is the dominant mechanism accounting for the differences in protein abundance of basal p53 in a human breast and colorectal cancer cell line.

Science.gov (United States)

Lakatos, Eszter; Salehi-Reyhani, Ali; Barclay, Michael; Stumpf, Michael P H; Klug, David R

2017-01-01

We determine p53 protein abundances and cell to cell variation in two human cancer cell lines with single cell resolution, and show that the fractional width of the distributions is the same in both cases despite a large difference in average protein copy number. We developed a computational framework to identify dominant mechanisms controlling the variation of protein abundance in a simple model of gene expression from the summary statistics of single cell steady state protein expression distributions. Our results, based on single cell data analysed in a Bayesian framework, lends strong support to a model in which variation in the basal p53 protein abundance may be best explained by variations in the rate of p53 protein degradation. This is supported by measurements of the relative average levels of mRNA which are very similar despite large variation in the level of protein.

Correlation between Heart-type Fatty Acid-binding Protein Gene Polymorphism and mRNA Expression with Intramuscular Fat in Baicheng-oil Chicken

Directory of Open Access Journals (Sweden)

Yong Wang

2015-10-01

Full Text Available This study aims to determine the polymorphism and mRNA expression pattern of the heart-type fatty acid-binding protein (H-FABP gene and their association with intramuscular fat (IMF content in the breast and leg muscles of Baicheng oil chicken (BOC. A total of 720 chickens, including 240 black Baicheng oil chicken (BBOC, 240 silky Baicheng oil chicken (SBOC, and 240 white Baicheng oil chicken (WBOC were raised. Three genotypes of H-FABP gene second extron following AA, AB, and BB were detected by polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP strategy. The G939A site created AA genotype and G956A site created BB genotype. The content of IMF in AA genotype in breast muscle of BBOC was significantly higher than that of AB (p = 0.0176 and the genotype in leg muscle of WBOC was significantly higher than that of AB (p = 0.0145. The G939A site could be taken as genetic marker for higher IMF content selecting for breast muscle of BBOC and leg muscle of WBOC. The relative mRNA expression of H-FABP was measured by real-time PCR at 30, 60, 90, and 120 d. The IMF content significantly increased with age in both muscles. The mRNA expression level of H-FABP significantly decreased with age in both muscles of the three types of chickens. Moreover, a significant negative correlation between H-FABP abundance and IMF content in the leg muscles of WBOC (p = 0.035 was observed. The mRNA expression of H-FABP negatively correlated with the IMF content in both breast and leg muscles of BOC sat slaughter time.

FTO, m6 Am , and the hypothesis of reversible epitranscriptomic mRNA modifications.

Science.gov (United States)

Mauer, Jan; Jaffrey, Samie R

2018-05-12

The fate of mRNA is regulated by epitranscriptomic nucleotide modifications, the most abundant of which is N 6 -methyladenosine (m 6 A). Although the pattern and distribution of m 6 A in mRNA is mediated by specific methyltransferases, a recent hypothesis is that specific demethylases or 'erasers' allow m 6 A to be dynamically reversed by signaling pathways. In this Review, we discuss the data in support and against this model. New insights into the function of fat mass and obesity-associated protein (FTO), the original enzyme thought to be an m 6 A eraser, reveal that its physiologic target is not m 6 A, but instead is N 6 ,2'-O-dimethyladenosine (m 6 A m ). Another m 6 A demethylase, ALKBH5, appears to have functions limited to sperm development in normal mice. Overall, the majority of the data suggest that m 6 A is generally not reversible, although m 6 A may be susceptible to demethylation in pathophysiological states such as cancer. © 2018 Federation of European Biochemical Societies.

Allergen relative abundance in several wheat varieties as revealed via a targeted quantitative approach using MS.

Science.gov (United States)

Rogniaux, Hélène; Pavlovic, Marija; Lupi, Roberta; Lollier, Virginie; Joint, Mathilde; Mameri, Hamza; Denery, Sandra; Larré, Colette

2015-05-01

Food allergy has become a major health issue in developed countries, therefore there is an urgent need to develop analytical methods able to detect and quantify with a good sensitivity and reliability some specific allergens in complex food matrices. In this paper, we present a targeted MS/MS approach to compare the relative abundance of the major recognized wheat allergens in the salt-soluble (albumin/globulin) fraction of wheat grains. Twelve allergens were quantified in seven wheat varieties, selected from three Triticum species: T. aestivum (bread wheat), T. durum (durum wheat), and T. monococcum. The allergens were monitored from one or two proteotypic peptides and their relative abundance was deduced from the intensity of one fragment measured in MS/MS. Whereas the abundance of some of the targeted allergens was quite stable across the genotypes, others like alpha-amylase inhibitors showed clear differences according to the wheat species, in accordance with the results of earlier functional studies. This study enriches the scarce knowledge available on allergens content in wheat genotypes, and brings new perspectives for food safety and plant breeding. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Nature's starships. I. Observed abundances and relative frequencies of amino acids in meteorites

International Nuclear Information System (INIS)

Cobb, Alyssa K.; Pudritz, Ralph E.

2014-01-01

The class of meteorites called carbonaceous chondrites are examples of material from the solar system which have been relatively unchanged from the time of their initial formation. These meteorites have been classified according to the temperatures and physical conditions of their parent planetesimals. We collate available data on amino acid abundance in these meteorites and plot the concentrations of different amino acids for each meteorite within various meteorite subclasses. We plot average concentrations for various amino acids across meteorites separated by subclass and petrologic type. We see a predominance in the abundance and variety of amino acids in CM2 and CR2 meteorites. The range in temperature corresponding to these subclasses indicates high degrees of aqueous alteration, suggesting aqueous synthesis of amino acids. Within the CM2 and CR2 subclasses, we identify trends in relative frequencies of amino acids to investigate how common amino acids are as a function of their chemical complexity. These two trends (total abundance and relative frequencies) can be used to constrain formation parameters of amino acids within planetesimals. Our organization of the data supports an onion shell model for the temperature structure of planetesimals. The least altered meteorites (type 3) and their amino acids originated near cooler surface regions. The most active amino acid synthesis likely took place at intermediate depths (type 2). The most altered materials (type 1) originated furthest toward parent body cores. This region is likely too hot to either favor amino acid synthesis or for amino acids to be retained after synthesis.

Expression of LDL receptor-related proteins (LRPs in common solid malignancies correlates with patient survival.

Directory of Open Access Journals (Sweden)

Steven L Gonias

Full Text Available LDL receptor-related proteins (LRPs are transmembrane receptors involved in endocytosis, cell-signaling, and trafficking of other cellular proteins. Considerable work has focused on LRPs in the fields of vascular biology and neurobiology. How these receptors affect cancer progression in humans remains largely unknown. Herein, we mined provisional databases in The Cancer Genome Atlas (TCGA to compare expression of thirteen LRPs in ten common solid malignancies in patients. Our first goal was to determine the abundance of LRP mRNAs in each type of cancer. Our second goal was to determine whether expression of LRPs is associated with improved or worsened patient survival. In total, data from 4,629 patients were mined. In nine of ten cancers studied, the most abundantly expressed LRP was LRP1; however, a correlation between LRP1 mRNA expression and patient survival was observed only in bladder urothelial carcinoma. In this malignancy, high levels of LRP1 mRNA were associated with worsened patient survival. High levels of LDL receptor (LDLR mRNA were associated with decreased patient survival in pancreatic adenocarcinoma. High levels of LRP10 mRNA were associated with decreased patient survival in hepatocellular carcinoma, lung adenocarcinoma, and pancreatic adenocarcinoma. LRP2 was the only LRP for which high levels of mRNA expression correlated with improved patient survival. This correlation was observed in renal clear cell carcinoma. Insights into LRP gene expression in human cancers and their effects on patient survival should guide future research.

Oxygen abundances in halo stars

Science.gov (United States)

Bessell, Michael S.; Sutherland, Ralph S.; Ruan, Kui

1991-12-01

The present study determines the oxygen abundance for a sample of metal-poor G dwarfs by analysis of OH lines between 3080 and 3200 A and the permitted high-excitation far-red O I triple. The oxygen abundances determined from the low-excitation OH lines are up to 0.55 dex lower than those measured from the high-excitation O I lines. The abundances for the far-red O I triplet lines agree with those rederived from Abia and Rebolo (1989), and the abundances from the OH lines in dwarfs and giants are in agreement with the rederived O abundances of Barbuy (1988) and others from the forbidden resonance O I line. Because the chi = 0.1.7 eV OH lines are formed in the same layers as the majority of Fe, Ti, and other neutral metal lines used for abundance analyses, it is argued that the OH lines and the forbidden O I line yield the true oxygen abundances relative to the metals.

Self-amplifying mRNA vaccines.

Science.gov (United States)

Brito, Luis A; Kommareddy, Sushma; Maione, Domenico; Uematsu, Yasushi; Giovani, Cinzia; Berlanda Scorza, Francesco; Otten, Gillis R; Yu, Dong; Mandl, Christian W; Mason, Peter W; Dormitzer, Philip R; Ulmer, Jeffrey B; Geall, Andrew J

2015-01-01

This chapter provides a brief introduction to nucleic acid-based vaccines and recent research in developing self-amplifying mRNA vaccines. These vaccines promise the flexibility of plasmid DNA vaccines with enhanced immunogenicity and safety. The key to realizing the full potential of these vaccines is efficient delivery of nucleic acid to the cytoplasm of a cell, where it can amplify and express the encoded antigenic protein. The hydrophilicity and strong net negative charge of RNA impedes cellular uptake. To overcome this limitation, electrostatic complexation with cationic lipids or polymers and physical delivery using electroporation or ballistic particles to improve cellular uptake has been evaluated. This chapter highlights the rapid progress made in using nonviral delivery systems for RNA-based vaccines. Initial preclinical testing of self-amplifying mRNA vaccines has shown nonviral delivery to be capable of producing potent and robust innate and adaptive immune responses in small animals and nonhuman primates. Historically, the prospect of developing mRNA vaccines was uncertain due to concerns of mRNA instability and the feasibility of large-scale manufacturing. Today, these issues are no longer perceived as barriers in the widespread implementation of the technology. Currently, nonamplifying mRNA vaccines are under investigation in human clinical trials and can be produced at a sufficient quantity and quality to meet regulatory requirements. If the encouraging preclinical data with self-amplifying mRNA vaccines are matched by equivalently positive immunogenicity, potency, and tolerability in human trials, this platform could establish nucleic acid vaccines as a versatile new tool for human immunization. Copyright © 2015 Elsevier Inc. All rights reserved.

Abundance variations in solar active regions

Science.gov (United States)

Strong, K. T.; Lemen, J. R.; Linford, G. A.

1991-01-01

The diversity in the published values of coronal abundances is unsettling, especially as the range of results seems to be beyond the quoted uncertainties. Measurements of the relative abundance of iron and neon derived from soft X-ray spectra of active regions are presented. From a data base of over 200 spectra taken by the Solar Maximum Mission Flat Crystal Spectrometer, it is found that the relative abundance can vary by as much as a factor of about 7 and can change on timescales of less than 1 h.

The upstream open reading frame of cyclin-dependent kinase inhibitor 1A mRNA negatively regulates translation of the downstream main open reading frame

Energy Technology Data Exchange (ETDEWEB)

Kim, Kyoung Mi; Cho, Hana [School of Life Sciences and Biotechnology, Korea University, Seoul 136-701 (Korea, Republic of); Kim, Yoon Ki, E-mail: yk-kim@korea.ac.kr [School of Life Sciences and Biotechnology, Korea University, Seoul 136-701 (Korea, Republic of)

2012-08-03

Highlights: Black-Right-Pointing-Pointer CDKN1A mRNA is a bona fide NMD substrate. Black-Right-Pointing-Pointer The uORF of CDKN1A mRNA is efficiently translated. Black-Right-Pointing-Pointer Translation of downstream main ORF is negatively regulated by translation of uORF in CDKN1A mRNA. -- Abstract: The first round of translation occurs on mRNAs bound by nuclear cap-binding complex (CBC), which is composed of nuclear cap-binding protein 80 and 20 (CBP80/20). During this round of translation, aberrant mRNAs are recognized and downregulated in abundance by nonsense-mediated mRNA decay (NMD), which is one of the mRNA quality control mechanisms. Here, our microarray analysis reveals that the level of cyclin-dependent kinase inhibitor 1A (CDKN1A; also known as Waf1/p21) mRNAs increases in cells depleted of cellular NMD factors. Intriguingly, CDKN1A mRNA contains an upstream open reading frame (uORF), which is a NMD-inducing feature. Using chimeric reporter constructs, we find that the uORF of CDKN1A mRNA negatively modulates translation of the main downstream ORF. These findings provide biological insights into the possible role of NMD in diverse biological pathways mediated by CDKN1A.

Subdwarf ultraviolet excesses and metal abundances

International Nuclear Information System (INIS)

Carney, B.W.

1979-01-01

The relation between stellar ultraviolet excesses and abundances is reexamined with the aid of new data, and an investigation is made of the accuracy of previous abundance analyses. A high-resolution echellogram of the subdwarf HD 201891 is analyzed to illustrate some of the problems. Generally, the earliest and latest analytical techniques yield consistent results for dwarfs. New UBV data yield normalized ultraviolet excesses, delta (U-B)/sub 0.6/, which are compared to abundances to produce a graphical relation that may be used to estimate [Fe/H] to +- 0.2 dex, given UBV colors accurate to +- 0.01 mag. The relation suggests a possible discontinuity between the halo and old-disk stars

Iron Abundance in the Prototype PG 1159 Star, GW Vir Pulsator PG 1159-035, and Related Objects

Science.gov (United States)

Werner, K.; Rauch, T.; Kruk, J. W.; Kurucz, R. L.

2011-01-01

We performed an iron abundance determination of the hot, hydrogen deficient post-AGB star PG 1159-035. which is the prototype of the PG 1159 spectral class and the GW Vir pulsators, and of two related objects (PG 1520+525, PG 1144+005), based on the first detection of Fe VIII lines in stellar photospheres. In another PG 1159 star. PG 1424+535. we detect Fe VII lines. In all four stars, each within T(sub eff) = 110,000-150,000 K, we find a solar iron abundance. This result agrees with our recent abundance analysis of the hottest PG 1159 stars (T(sub eff) = 150,000-200,000 K) that exhibit Fe x lines. On the whole, we find that the PG 1159 stars are not significantly iron deficient, in contrast to previous notions.

Relative Abundance of Proteins in Blood Plasma Samples from Patients with Chronic Cerebral Ischemia.

Science.gov (United States)

Kaysheva, Anna L; Kopylov, Artur T; Ponomarenko, Elena A; Kiseleva, Olga I; Teryaeva, Nadezhda B; Potapov, Alexander A; Izotov, Alexander А; Morozov, Sergei G; Kudryavtseva, Valeria Yu; Archakov, Alexander I

2018-03-01

A comparative protein profile analysis of 17 blood plasma samples from patients with ischemia and 20 samples from healthy volunteers was carried out using ultra-high resolution mass spectrometry. The analysis of measurements was performed using the proteomics search engine OMSSA. Normalized spectrum abundance factor (NSAF) in the biological samples was assessed using SearchGUI. The findings of mass spectrometry analysis of the protein composition of blood plasma samples demonstrate that the depleted samples are quite similar in protein composition and relative abundance of proteins. By comparing them with the control samples, we have found a small group of 44 proteins characteristic of the blood plasma samples from patients with chronic cerebral ischemia. These proteins contribute to the processes of homeostasis maintenance, including innate immune response unfolding, the response of a body to stress, and contribution to the blood clotting cascade.

Analysis and prediction of translation rate based on sequence and functional features of the mRNA.

Directory of Open Access Journals (Sweden)

Tao Huang

Full Text Available Protein concentrations depend not only on the mRNA level, but also on the translation rate and the degradation rate. Prediction of mRNA's translation rate would provide valuable information for in-depth understanding of the translation mechanism and dynamic proteome. In this study, we developed a new computational model to predict the translation rate, featured by (1 integrating various sequence-derived and functional features, (2 applying the maximum relevance & minimum redundancy method and incremental feature selection to select features to optimize the prediction model, and (3 being able to predict the translation rate of RNA into high or low translation rate category. The prediction accuracies under rich and starvation condition were 68.8% and 70.0%, respectively, evaluated by jackknife cross-validation. It was found that the following features were correlated with translation rate: codon usage frequency, some gene ontology enrichment scores, number of RNA binding proteins known to bind its mRNA product, coding sequence length, protein abundance and 5'UTR free energy. These findings might provide useful information for understanding the mechanisms of translation and dynamic proteome. Our translation rate prediction model might become a high throughput tool for annotating the translation rate of mRNAs in large-scale.

Application of hierarchical oligonucleotide primer extension (HOPE) to assess relative abundances of ammonia- and nitrite-oxidizing bacteria

KAUST Repository

Scarascia, Giantommaso; Cheng, Hong; Harb, Moustapha; Hong, Pei-Ying

2017-01-01

for ensuring the efficiency of nitrification in water treatment systems. Hierarchical oligonucleotide primer extension (HOPE), previously developed to rapidly quantify relative abundances of specific microbial groups of interest, was applied in this study

Noise stress changes mRNA expressions of corticotropin-releasing hormone, its receptors in amygdala, and anxiety-related behaviors

Directory of Open Access Journals (Sweden)

Evren Eraslan

2015-01-01

Full Text Available Noise is a psychological, environmental stressor that activates limbic sites in the brain. Limbic sites such as the amygdala and the amygdaloid corticotropin-releasing hormone (CRH system play an important role in integrating stress response. We investigated the association between noise exposures, CRH-related molecules in the amygdala, and behavioral alterations. In total 54 Sprague-Dawley rats were divided into the following three groups: Control (CON, acute noise exposure (ANE, and chronic noise exposure (CNE. The ANE group was exposed to 100 dB white noise only once in 4 h and the CNE group was exposed to the same for 4 h per day for 30 days. Expression profiles of CRH and its receptors CRH-R1 and CRH-R2 were analyzed by quantitative real-time polymerase chain reaction (qPCR. The same stress procedure was applied to the ANE and CNE groups for behavior testing. The anxiety responses of the animals after acute and chronic stress exposure were measured in the defensive withdrawal test. CNE upregulated CRH and CRH-R1 mRNA levels but downregulated CRH-R2 mRNA levels. ANE led to a decrease in both CRH-R1 and CRH-R2 expression. In the defensive withdrawal test, while the ANE increased, CNE reduced anxiety-like behaviors. The present study shows that the exposure of rats to white noise (100 dB leads to behavioral alterations and molecule-specific changes in the CRH system. Behavioral alterations can be related to these molecular changes in the amygdala.

Noise stress changes mRNA expressions of corticotropin-releasing hormone, its receptors in amygdala, and anxiety-related behaviors.

Science.gov (United States)

Eraslan, Evren; Akyazi, Ibrahim; Erg L-Ekiz, Elif; Matur, Erdal

2015-01-01

Noise is a psychological, environmental stressor that activates limbic sites in the brain. Limbic sites such as the amygdala and the amygdaloid corticotropin-releasing hormone (CRH) system play an important role in integrating stress response. We investigated the association between noise exposures, CRH-related molecules in the amygdala, and behavioral alterations. In total 54 Sprague-Dawley rats were divided into the following three groups: Control (CON), acute noise exposure (ANE), and chronic noise exposure (CNE). The ANE group was exposed to 100 dB white noise only once in 4 h and the CNE group was exposed to the same for 4 h per day for 30 days. Expression profiles of CRH and its receptors CRH-R1 and CRH-R2 were analyzed by quantitative real-time polymerase chain reaction (qPCR). The same stress procedure was applied to the ANE and CNE groups for behavior testing. The anxiety responses of the animals after acute and chronic stress exposure were measured in the defensive withdrawal test. CNE upregulated CRH and CRH-R1 mRNA levels but downregulated CRH-R2 mRNA levels. ANE led to a decrease in both CRH-R1 and CRH-R2 expression. In the defensive withdrawal test, while the ANE increased, CNE reduced anxiety-like behaviors. The present study shows that the exposure of rats to white noise (100 dB) leads to behavioral alterations and molecule-specific changes in the CRH system. Behavioral alterations can be related to these molecular changes in the amygdala.

AthMethPre: a web server for the prediction and query of mRNA m6A sites in Arabidopsis thaliana.

Science.gov (United States)

Xiang, Shunian; Yan, Zhangming; Liu, Ke; Zhang, Yaou; Sun, Zhirong

2016-10-18

N 6 -Methyladenosine (m 6 A) is the most prevalent and abundant modification in mRNA that has been linked to many key biological processes. High-throughput experiments have generated m 6 A-peaks across the transcriptome of A. thaliana, but the specific methylated sites were not assigned, which impedes the understanding of m 6 A functions in plants. Therefore, computational prediction of mRNA m 6 A sites becomes emergently important. Here, we present a method to predict the m 6 A sites for A. thaliana mRNA sequence(s). To predict the m 6 A sites of an mRNA sequence, we employed the support vector machine to build a classifier using the features of the positional flanking nucleotide sequence and position-independent k-mer nucleotide spectrum. Our method achieved good performance and was applied to a web server to provide service for the prediction of A. thaliana m 6 A sites. The server also provides a comprehensive database of predicted transcriptome-wide m 6 A sites and curated m 6 A-seq peaks from the literature for query and visualization. The AthMethPre web server is the first web server that provides a user-friendly tool for the prediction and query of A. thaliana mRNA m 6 A sites, which is freely accessible for public use at .

Molecular characterization of three Rhesus glycoproteins from the gills of the African lungfish, Protopterus annectens, and effects of aestivation on their mRNA expression levels and protein abundance.

Directory of Open Access Journals (Sweden)

You R Chng

Full Text Available African lungfishes are ammonotelic in water. They can aestivate for long periods on land during drought. During aestivation, the gills are covered with dried mucus and ammonia excretion ceases. In fishes, ammonia excretion through the gills involves Rhesus glycoproteins (RhGP/Rhgp. This study aimed to obtain the complete cDNA coding sequences of rhgp from the gills of Protopterus annectens, and to determine their branchial mRNA and protein expression levels during the induction, maintenance and arousal phases of aestivation. Three isoforms of rhgp (rhag, rhbg and rhcg were obtained in the gills of P. annectens. Their complete cDNA coding sequences ranged between 1311 and 1398 bp, coding for 436 to 465 amino acids with estimated molecular masses between 46.8 and 50.9 kDa. Dendrogramic analyses indicated that Rhag was grouped closer to fishes, while Rhbg and Rhcg were grouped closer to tetrapods. During the induction phase, the protein abundance of Rhag, but not its transcript level, was down-regulated in the gills, suggesting that there could be a decrease in the release of ammonia from the erythrocytes to the plasma. Furthermore, the branchial transcript levels of rhbg and rhcg decreased significantly, in preparation for the subsequent shutdown of gill functions. During the maintenance phase, the branchial expression levels of rhag/Rhag, rhbg/Rhbg and rhcg/Rhcg decreased significantly, indicating that their transcription and translation were down-regulated. This could be part of an overall mechanism to shut down branchial functions and save metabolic energy used for transcription and translation. It could also be regarded as an adaptive response to stop ammonia excretion. During the arousal phase, it is essential for the lungfish to regain the ability to excrete ammonia. Indeed, the protein abundance of Rhag, Rhbg and Rhcg recovered to the corresponding control levels after 1 day or 3 days of recovery from 6 months of aestivation.

Relating species abundance distributions to species-area curves in two Mediterranean-type shrublands

Science.gov (United States)

Keeley, Jon E.

2003-01-01

Based on both theoretical and empirical studies there is evidence that different species abundance distributions underlie different species-area relationships. Here I show that Australian and Californian shrubland communities (at the scale from 1 to 1000 m2) exhibit different species-area relationships and different species abundance patterns. The species-area relationship in Australian heathlands best fits an exponential model and species abundance (based on both density and cover) follows a narrow log normal distribution. In contrast, the species-area relationship in Californian shrublands is best fit with the power model and, although species abundance appears to fit a log normal distribution, the distribution is much broader than in Australian heathlands. I hypothesize that the primary driver of these differences is the abundance of small-stature annual species in California and the lack of annuals in Australian heathlands. Species-area is best fit by an exponential model in Australian heathlands because the bulk of the species are common and thus the species-area curves initially rise rapidly between 1 and 100 m2. Annuals in Californian shrublands generate very broad species abundance distributions with many uncommon or rare species. The power function is a better model in these communities because richness increases slowly from 1 to 100 m2 but more rapidly between 100 and 1000 m2due to the abundance of rare or uncommon species that are more likely to be encountered at coarser spatial scales. The implications of this study are that both the exponential and power function models are legitimate representations of species-area relationships in different plant communities. Also, structural differences in community organization, arising from different species abundance distributions, may lead to different species-area curves, and this may be tied to patterns of life form distribution.

CYP3A5 mRNA degradation by nonsense-mediated mRNA decay.

Science.gov (United States)

Busi, Florent; Cresteil, Thierry

2005-09-01

The total CYP3A5 mRNA level is significantly greater in carriers of the CYP3A5*1 allele than in CYP3A5*3 homozygotes. Most of the CYP3A5*3 mRNA includes an intronic sequence (exon 3B) containing premature termination codons (PTCs) between exons 3 and 4. Two models were used to investigate the degradation of CYP3A5 mRNA: a CYP3A5 minigene consisting of CYP3A5 exons and introns 3 to 6 transfected into MCF7 cells, and the endogenous CYP3A5 gene expressed in HepG2 cells. The 3'-untranslated region g.31611C>T mutation has no effect on CYP3A5 mRNA decay. Splice variants containing exon 3B were more unstable than wild-type (wt) CYP3A5 mRNA. Cycloheximide prevents the recognition of PTCs by ribosomes: in transfected MCF7 and HepG2 cells, cycloheximide slowed down the degradation of exon 3B-containing splice variants, suggesting the participation of nonsense-mediated decay (NMD). When PTCs were removed from pseudoexon 3B or when UPF1 small interfering RNA was used to impair the NMD mechanism, the decay of the splice variant was reduced, confirming the involvement of NMD in the degradation of CYP3A5 splice variants. Induction could represent a source of variability for CYP3A5 expression and could modify the proportion of splice variants. The extent of CYP3A5 induction was investigated after exposure to barbiturates or steroids: CYP3A4 was markedly induced in a pediatric population compared with untreated neonates. However, no effect could be detected in either the total CYP3A5 RNA, the proportion of splice variant RNA, or the protein level. Therefore, in these carriers, induction is unlikely to switch on the phenotypic CYP3A5 expression in carriers of CYP3A5*3/*3.

Three-Dimensional Mapping of mRNA Export through the Nuclear Pore Complex

Directory of Open Access Journals (Sweden)

Steven J. Schnell

2014-11-01

Full Text Available The locations of transcription and translation of mRNA in eukaryotic cells are spatially separated by the nuclear envelope (NE. Plenty of nuclear pore complexes (NPCs embedded in the NE function as the major gateway for the export of transcribed mRNAs from the nucleus to the cytoplasm. Whereas the NPC, perhaps one of the largest protein complexes, provides a relatively large channel for macromolecules to selectively pass through it in inherently three-dimensional (3D movements, this channel is nonetheless below the diffraction limit of conventional light microscopy. A full understanding of the mRNA export mechanism urgently requires real-time mapping of the 3D dynamics of mRNA in the NPC of live cells with innovative imaging techniques breaking the diffraction limit of conventional light microscopy. Recently, super-resolution fluorescence microscopy and single-particle tracking (SPT techniques have been applied to the study of nuclear export of mRNA in live cells. In this review, we emphasize the necessity of 3D mapping techniques in the study of mRNA export, briefly summarize the feasibility of current 3D imaging approaches, and highlight the new features of mRNA nuclear export elucidated with a newly developed 3D imaging approach combining SPT-based super-resolution imaging and 2D-to-3D deconvolution algorithms.

An investigation into the population abundance distribution of mRNAs, proteins, and metabolites in biological systems.

Science.gov (United States)

Lu, Chuan; King, Ross D

2009-08-15

Distribution analysis is one of the most basic forms of statistical analysis. Thanks to improved analytical methods, accurate and extensive quantitative measurements can now be made of the mRNA, protein and metabolite from biological systems. Here, we report a large-scale analysis of the population abundance distributions of the transcriptomes, proteomes and metabolomes from varied biological systems. We compared the observed empirical distributions with a number of distributions: power law, lognormal, loglogistic, loggamma, right Pareto-lognormal (PLN) and double PLN (dPLN). The best-fit for mRNA, protein and metabolite population abundance distributions was found to be the dPLN. This distribution behaves like a lognormal distribution around the centre, and like a power law distribution in the tails. To better understand the cause of this observed distribution, we explored a simple stochastic model based on geometric Brownian motion. The distribution indicates that multiplicative effects are causally dominant in biological systems. We speculate that these effects arise from chemical reactions: the central-limit theorem then explains the central lognormal, and a number of possible mechanisms could explain the long tails: positive feedback, network topology, etc. Many of the components in the central lognormal parts of the empirical distributions are unidentified and/or have unknown function. This indicates that much more biology awaits discovery.

Temporal Patterns in the Abundance of a Critically Endangered Marsupial Relates to Disturbance by Roads and Agriculture.

Science.gov (United States)

Yeatman, Georgina J; Wayne, Adrian F; Mills, Harriet R; Prince, Jane

2016-01-01

The aim of this study was to investigate how landscape disturbance associated with roads, agriculture and forestry influenced temporal patterns in woylie (Bettongia penicillata) abundance before, during and after periods of rapid population change. Data were collected from an area of approximately 140,000 ha of forest within the Upper Warren region in south-western Australia. Woylie abundance was measured using cage trapping at 22 grid and five transect locations with varying degrees of landscape disturbance between 1994 and 2012. We found evidence that the distribution and abundance of woylies over time appears to be related to the degree of fragmentation by roads and proximity to agriculture. Sites furthest from agriculture supported a greater abundance of woylies and had slower rates of population decline. Sites with fewer roads had a greater abundance of woylies generally and a greater rate of increase in abundance after the implementation of invasive predator control. The results of this study suggest that landscape disturbance is less important at peak population densities, but during times of environmental and population change, sites less dissected by roads and agriculture better support woylie populations. This may be due to the role these factors play in increasing the vulnerability of woylies to introduced predators, population fragmentation, weed species invasion, mortality from road collisions or a reduction in available habitat. Strategies that reduce the impact of disturbance on woylie populations could include the rationalisation of forest tracks and consolidation of contiguous habitat through the acquisition of private property. Reducing the impact of disturbance in the Upper Warren region could improve the resilience of this critically important woylie population during future environmental change.

Sodium arsenite-induced inhibition of cell proliferation is related to inhibition of IL-2 mRNA expression in mouse activated T cells

Energy Technology Data Exchange (ETDEWEB)

Conde, Patricia; Acosta-Saavedra, Leonor C.; Calderon-Aranda, Emma S. [Centro de Investigacion y de Estudios Avanzados, CINVESTAV, Seccion Toxicologia, P.O. Box 14-740, Mexico, D.F. (Mexico); Goytia-Acevedo, Raquel C. [Universidad Juarez del Estado de Durango, Facultad de Medicina, Gomez Palacio, Durango (Mexico)

2007-04-15

A proposed mechanism for the As-induced inhibition of cell proliferation is the inhibition of IL-2 secretion. However, the effects of arsenite on IL-2 mRNA expression or on the ERK pathway in activated-T cells have not yet been described. We examined the effect of arsenite on IL-2 mRNA expression, cell activation and proliferation in PHA-stimulated murine lymphocytes. Arsenite (1 and 10 {mu}M) decreased IL-2 mRNA expression, IL-2 secretion and cell proliferation. Arsenite (10 {mu}M) strongly inhibited ERK-phosphorylation. However, the partial inhibition (50%) of IL-2 mRNA produced by 1 {mu}M, consistent with the effects on IL-2 secretion and cell proliferation, could not be explained by the inhibition of ERK-phosphorylation, which was not affected at this concentration. The inhibition of IL-2 mRNA expression caused by 1 {mu}M could be associated to effects on pathways located downstream or parallel to ERK. Arsenite also decreased early activation (surface CD69{sup +} expression) in both CD4{sup +} and CD8{sup +}, and decreased total CD8{sup +} count without significantly affecting CD4{sup +}, supporting that the cellular immune response mediated by cytotoxic T cells is an arsenic target. Thus, our results suggest that arsenite decreases IL-2 mRNA levels and T-cell activation and proliferation. However, further studies on the effects of arsenite on IL-2 gene transcription and IL-2 mRNA stability are needed. (orig.)

Abundances in the Galactic bulge

Energy Technology Data Exchange (ETDEWEB)

Barbuy, B; Alves-Brito, A [Universidade de Sao Paulo, IAG, Rua do Matao 1226, Sao Paulo 05508-900 (Brazil); Ortolani, S; Zoccali, M [Dipartimento di Astronomia, Universita di Padova, Vicolo dell' Osservatorio 2, I-35122 Padova (Italy); Hill, V; Gomez, A [Observatoire de Paris-Meudon, 92195 Meudon Cedex (France); Melendez, J [Centro de AstrofIsica da Universidade de Porto, Rua das Estrelas, 4150-762 Porto (Portugal); Asplund, M [Max Planck Institute for Astrophysics, Postfach 1317, 85741 Garching (Germany); Bica, E [Departamento de Astronomia, Universidade Federal do Rio Grande do Sul, CP 15051, Porto Alegre 91501-970 (Brazil); Renzini, A [Osservatorio Astronomico di Padova, Vicolo dell' Osservatorio 5, I-35122 Padova (Italy); Minniti, D [Department of Astronomy and Astrophysics, Universidad Catolica de Chile, Casilla 306, Santiago 22 (Chile)], E-mail: barbuy@astro.iag.usp.br

2008-12-15

The metallicity distribution and abundance ratios of the Galactic bulge are reviewed. Issues raised by recent work of different groups, in particular the high metallicity end, the overabundance of {alpha}-elements in the bulge relative to the thick disc and the measurement of giants versus dwarfs, are discussed. Abundances in the old moderately metal-poor bulge globular clusters are described.

Photobiomodulation effects on mRNA levels from genomic and chromosome stabilization genes in injured muscle.

Science.gov (United States)

da Silva Neto Trajano, Larissa Alexsandra; Trajano, Eduardo Tavares Lima; da Silva Sergio, Luiz Philippe; Teixeira, Adilson Fonseca; Mencalha, Andre Luiz; Stumbo, Ana Carolina; de Souza da Fonseca, Adenilson

2018-04-26

Muscle injuries are the most prevalent type of injury in sports. A great number of athletes have relapsed in muscle injuries not being treated properly. Photobiomodulation therapy is an inexpensive and safe technique with many benefits in muscle injury treatment. However, little has been explored about the infrared laser effects on DNA and telomeres in muscle injuries. Thus, the aim of this study was to evaluate photobiomodulation effects on mRNA relative levels from genes related to telomere and genomic stabilization in injured muscle. Wistar male rats were randomly divided into six groups: control, laser 25 mW, laser 75 mW, injury, injury laser 25 mW, and injury laser 75 mW. Photobiomodulation was performed with 904 nm, 3 J/cm 2 at 25 or 75 mW. Cryoinjury was induced by two applications of a metal probe cooled in liquid nitrogen directly on the tibialis anterior muscle. After euthanasia, skeletal muscle samples were withdrawn and total RNA extracted for evaluation of mRNA levels from genomic (ATM and p53) and chromosome stabilization (TRF1 and TRF2) genes by real-time quantitative polymerization chain reaction. Data show that photobiomodulation reduces the mRNA levels from ATM and p53, as well reduces mRNA levels from TRF1 and TRF2 at 25 and 75 mW in injured skeletal muscle. In conclusion, photobiomodulation alters mRNA relative levels from genes related to genomic and telomere stabilization in injured skeletal muscle.

Transcriptional profiling of immune-related genes in Pacific white shrimp (Litopenaeus vannamei) during ontogenesis.

Science.gov (United States)

Quispe, Ruth L; Justino, Emily B; Vieira, Felipe N; Jaramillo, Michael L; Rosa, Rafael D; Perazzolo, Luciane M

2016-11-01

We have performed here a gene expression analysis to determine the developmental stage at the main genes involved in crustacean immune response begin to be expressed and their changes in mRNA abundance during shrimp development. By using a quantitative PCR-based approach, we have measured the mRNA abundance of 24 immune-related genes from different functional categories in twelve developmental stages ranging from fertilized eggs to larval and postlarval stages and also in juveniles. We showed for the first time that the main genes from the RNAi-based post-transcriptional pathway involved in shrimp antiviral immunity are transcribed in all developmental stages, but exhibit a diverse pattern of gene expression during shrimp ontogenesis. On the other hand, hemocyte-expressed genes mainly involved in antimicrobial defenses appeared to be transcribed in larval stages, indicating that hematopoiesis initiates early in development. Moreover, transcript levels of some genes were early detected in fertilized eggs at 0-4 h post-spawning, suggesting a maternal contribution of immune-related transcripts to shrimp progeny. Altogether, our results provide important clues regarding the ontogenesis of hemocytes as well the establishment of antiviral and antimicrobial defenses in shrimp. Copyright © 2016 Elsevier Ltd. All rights reserved.

mRNA related to insulin family in human placenta

International Nuclear Information System (INIS)

Younes, M.A.; D'Agostino, J.B.; Frazier, M.L.; Besch, P.K.

1986-01-01

The authors have previously reported that human term placenta contains mRNA displaying sequence homology to a rat preproinsulin I cDNA clone (p119). When placental poly(A + ) RNA was analyzed for homology to p119 by RNA/DNA blot hybridization, prominent hybridization was observed which was found by densitometric analysis to be three-fold higher than control. To further characterize this insulin-like message, a cDNA library was generated (approx.7000 transformants) using normal term cesarean-sectioned tissue to prepare placental poly(A + ) RNA templates. Five hundred transformants were initially screened by colony hybridization using a 32 P-labeled rat preproinsulin I cDNA as probe. Of the ten initial positives obtained, three were found to be true positives based on Southern hybridization analyses of the recombinant plasmids. Using Taq I digested pBr322 as a size marker, the cDNAs were found to be approximately 300 bp in length. Preliminary DNA sequencing using the Sanger dideoxy chain termination method has revealed that one of these clones displays significant homology to the 5' region of human insulin-like growth factors I and II

mRNA related to insulin family in human placenta

Energy Technology Data Exchange (ETDEWEB)

Younes, M.A.; D' Agostino, J.B.; Frazier, M.L.; Besch, P.K.

1986-03-01

The authors have previously reported that human term placenta contains mRNA displaying sequence homology to a rat preproinsulin I cDNA clone (p119). When placental poly(A/sup +/) RNA was analyzed for homology to p119 by RNA/DNA blot hybridization, prominent hybridization was observed which was found by densitometric analysis to be three-fold higher than control. To further characterize this insulin-like message, a cDNA library was generated (approx.7000 transformants) using normal term cesarean-sectioned tissue to prepare placental poly(A/sup +/) RNA templates. Five hundred transformants were initially screened by colony hybridization using a /sup 32/P-labeled rat preproinsulin I cDNA as probe. Of the ten initial positives obtained, three were found to be true positives based on Southern hybridization analyses of the recombinant plasmids. Using Taq I digested pBr322 as a size marker, the cDNAs were found to be approximately 300 bp in length. Preliminary DNA sequencing using the Sanger dideoxy chain termination method has revealed that one of these clones displays significant homology to the 5' region of human insulin-like growth factors I and II.

ON THE RELATIVE ABUNDANCE OF LiH AND LiH+ MOLECULES IN THE EARLY UNIVERSE: NEW RESULTS FROM QUANTUM REACTIONS

International Nuclear Information System (INIS)

Bovino, Stefano; Tacconi, Mario; Gianturco, Franco A.; Galli, Daniele; Palla, Francesco

2011-01-01

The relative efficiencies of the chemical pathways that can lead to the destruction of LiH and LiH + molecules, conjectured to be present in the primordial gas and to control molecular cooling processes in the gravitational collapse of the post-recombination era, are revisited by using accurate quantum calculations for the several reactions involved. The new rates are employed to survey the behavior of the relative abundance of these molecules at redshifts of interest for early universe conditions. We find significant differences with respect to previous calculations, the present ones yielding LiH abundances higher than LiH + at all redshifts.

454 pyrosequencing to describe microbial eukaryotic community composition, diversity and relative abundance: a test for marine haptophytes.

Directory of Open Access Journals (Sweden)

Elianne Egge

Full Text Available Next generation sequencing of ribosomal DNA is increasingly used to assess the diversity and structure of microbial communities. Here we test the ability of 454 pyrosequencing to detect the number of species present, and assess the relative abundance in terms of cell numbers and biomass of protists in the phylum Haptophyta. We used a mock community consisting of equal number of cells of 11 haptophyte species and compared targeting DNA and RNA/cDNA, and two different V4 SSU rDNA haptophyte-biased primer pairs. Further, we tested four different bioinformatic filtering methods to reduce errors in the resulting sequence dataset. With sequencing depth of 11000-20000 reads and targeting cDNA with Haptophyta specific primers Hap454 we detected all 11 species. A rarefaction analysis of expected number of species recovered as a function of sampling depth suggested that minimum 1400 reads were required here to recover all species in the mock community. Relative read abundance did not correlate to relative cell numbers. Although the species represented with the largest biomass was also proportionally most abundant among the reads, there was generally a weak correlation between proportional read abundance and proportional biomass of the different species, both with DNA and cDNA as template. The 454 sequencing generated considerable spurious diversity, and more with cDNA than DNA as template. With initial filtering based only on match with barcode and primer we observed 100-fold more operational taxonomic units (OTUs at 99% similarity than the number of species present in the mock community. Filtering based on quality scores, or denoising with PyroNoise resulted in ten times more OTU99% than the number of species. Denoising with AmpliconNoise reduced the number of OTU99% to match the number of species present in the mock community. Based on our analyses, we propose a strategy to more accurately depict haptophyte diversity using 454 pyrosequencing.

Magellanic Clouds Cepheids: Thorium Abundances

Directory of Open Access Journals (Sweden)

Yeuncheol Jeong

2018-03-01

Full Text Available The analysis of the high-resolution spectra of 31 Magellanic Clouds Cepheid variables enabled the identification of thorium lines. The abundances of thorium were found with spectrum synthesis method. The calculated thorium abundances exhibit correlations with the abundances of other chemical elements and atmospheric parameters of the program stars. These correlations are similar for both Clouds. The correlations of iron abundances of thorium, europium, neodymium, and yttrium relative to the pulsational periods are different in the Large Magellanic Cloud (LMC and the Small Magellanic Cloud (SMC, namely the correlations are negative for LMC and positive or close to zero for SMC. One of the possible explanations can be the higher activity of nucleosynthesis in SMC with respect to LMC in the recent several hundred million years.

Coordinated Regulations of mRNA Synthesis and Decay during Cold Acclimation in Arabidopsis Cells.

KAUST Repository

Arae, Toshihiro

2017-04-18

Plants possess a cold acclimation system to acquire freezing tolerance through pre-exposure to non-freezing low temperatures. The transcriptional cascade of C-repeat binding factors (CBFs)/dehydration response element-binding factors (DREBs) is considered a major transcriptional regulatory pathway during cold acclimation. However, little is known regarding the functional significance of mRNA stability regulation in the response of gene expression to cold stress. The actual level of individual mRNAs is determined by a balance between mRNA synthesis and degradation. Therefore, it is important to assess the regulatory steps to increase our understanding of gene regulation. Here, we analyzed temporal changes in mRNA amounts and half-lives in response to cold stress in Arabidopsis cell cultures based on genome-wide analysis. In this mRNA decay array method, mRNA half-life measurements and microarray analyses were combined. In addition, temporal changes in the integrated value of transcription rates were estimated from the above two parameters using a mathematical approach. Our results showed that several cold-responsive genes, including Cold-regulated 15a, were relatively destabilized, whereas the mRNA amounts were increased during cold treatment by accelerating the transcription rate to overcome the destabilization. Considering the kinetics of mRNA synthesis and degradation, this apparently contradictory result supports that mRNA destabilization is advantageous for the swift increase in CBF-responsive genes in response to cold stress.

READSCAN: A fast and scalable pathogen discovery program with accurate genome relative abundance estimation

KAUST Repository

Naeem, Raeece

2012-11-28

Summary: READSCAN is a highly scalable parallel program to identify non-host sequences (of potential pathogen origin) and estimate their genome relative abundance in high-throughput sequence datasets. READSCAN accurately classified human and viral sequences on a 20.1 million reads simulated dataset in <27 min using a small Beowulf compute cluster with 16 nodes (Supplementary Material). Availability: http://cbrc.kaust.edu.sa/readscan Contact: or raeece.naeem@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online. 2012 The Author(s).

READSCAN: A fast and scalable pathogen discovery program with accurate genome relative abundance estimation

KAUST Repository

Naeem, Raeece; Rashid, Mamoon; Pain, Arnab

2012-01-01

Summary: READSCAN is a highly scalable parallel program to identify non-host sequences (of potential pathogen origin) and estimate their genome relative abundance in high-throughput sequence datasets. READSCAN accurately classified human and viral sequences on a 20.1 million reads simulated dataset in <27 min using a small Beowulf compute cluster with 16 nodes (Supplementary Material). Availability: http://cbrc.kaust.edu.sa/readscan Contact: or raeece.naeem@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online. 2012 The Author(s).

Financial development and oil resource abundance-growth relations: evidence from panel data.

Science.gov (United States)

Law, Siong Hook; Moradbeigi, Maryam

2017-10-01

This study investigates whether financial development dampens the negative impact of oil resource abundance on economic growth. Because of substantial cross-sectional dependence in our data, which contain a core sample of 63 oil-producing countries from 1980 through 2010, we use the common correlated effect mean group (CCEMG) estimator to account for the high degree of heterogeneity and drop the outlier countries. The empirical results reveal that oil resource abundance affects the growth rate in output contingent on the degree of development in financial markets. More developed financial markets can channel the revenues from oil into more productive activities and thus offset the negative effects of oil resource abundance on economic growth. Thus, better financial development can reverse resource curse or enhance resource blessing in oil-rich economies.

Diversity, composition and abundance of macroinvertebrates ...

African Journals Online (AJOL)

user

these genera were found at all sampling stations as shown in Table 2. Out of the orders sampled, Hemiptera, Pulmonata and. Coleoptera had the highest number of genera with 5, 4 and 4, respectively. In terms of relative abundance, dipterans and Pulmonata were the most abundant while. Hydracarina (water mites) were ...

Maternal diets deficient in folic acid and related methyl donors modify mechanisms associated with lipid metabolism in the fetal liver of the rat.

Science.gov (United States)

McNeil, Christopher J; Hay, Susan M; Rucklidge, Garry J; Reid, Martin D; Duncan, Gary J; Rees, William D

2009-11-01

Previously we have examined the effects of diets deficient in folic acid ( - F) or folate deficient with low methionine and choline ( - F LM LC) on the relative abundance of soluble proteins in the liver of the pregnant rat. In the present study we report the corresponding changes in the fetal liver at day 21 of gestation. The abundance of eighteen proteins increased when dams were fed the - F diet. When dams were fed the - F LM LC diet, thirty-three proteins increased and eight decreased. Many of the differentially abundant proteins in the fetal liver could be classified into the same functional groups as those previously identified in the maternal liver, namely protein synthesis, metabolism, lipid metabolism and proteins associated with the cytoskeleton and endoplasmic reticulum. The pattern was consistent with reduced cell proliferation in the - F LM LC group but not in the - F group. Metabolic enzymes associated with lipid metabolism changed in both the - F and - F LM LC groups. The mRNA for carnitine palmitoyl transferase were up-regulated and CD36 (fatty acid translocase) down-regulated in the - F group, suggesting increased mitochondrial oxidation of fatty acids as an indirect response to altered maternal lipid metabolism. In the - F LM LC group the mRNA for acetyl CoA carboxylase was down-regulated, suggesting reduced fatty acid synthesis. The mRNA for transcriptional regulators including PPARalpha and sterol response element-binding protein-1c were unchanged. These results suggest that an adequate supply of folic acid and the related methyl donors may benefit fetal development directly by improving lipid metabolism in fetal as well as maternal tissues.

Orion A helium abundance

International Nuclear Information System (INIS)

Tsivilev, A.P.; Ershov, A.A.; Smirnov, G.T.; Sorochenko, R.L.

1986-01-01

The 22.4-GHz (H,He)66-alpha and 36.5-GHz (H,He)56-alpha radio recombination lines have been observed at several Jaffe-Pankonin positions in the central part of the Orion A source. The measured relative abundance of ionized helium increases with distance, averaging 11.6 percent at peripheral points. The observed behavior is interpreted by a blister-type model nebula, which implies that Orion A has a true He abundance of 12 percent, is moving with a radial velocity of 5 km/sec, and is expanding. 18 references

Tumor protein D52 expression is post-transcriptionally regulated by T-cell intercellular antigen (TIA) 1 and TIA-related protein via mRNA stability.

Science.gov (United States)

Motohashi, Hiromi; Mukudai, Yoshiki; Ito, Chihiro; Kato, Kosuke; Shimane, Toshikazu; Kondo, Seiji; Shirota, Tatsuo

2017-05-04

Although tumor protein D52 (TPD52) family proteins were first identified nearly 20 years ago, their molecular regulatory mechanisms remain unclear. Therefore, we investigated the post-transcriptional regulation of TPD52 family genes. An RNA immunoprecipitation (RIP) assay showed the potential binding ability of TPD52 family mRNAs to several RNA-binding proteins, and an RNA degradation assay revealed that TPD52 is subject to more prominent post-transcriptional regulation than are TPD53 and TPD54. We subsequently focused on the 3'-untranslated region (3'-UTR) of TPD52 as a cis -acting element in post-transcriptional gene regulation. Several deletion mutants of the 3'-UTR of TPD52 mRNA were constructed and ligated to the 3'-end of a reporter green fluorescence protein gene. An RNA degradation assay revealed that a minimal cis -acting region, located in the 78-280 region of the 5'-proximal region of the 3'-UTR, stabilized the reporter mRNA. Biotin pull-down and RIP assays revealed specific binding of the region to T-cell intracellular antigen 1 (TIA-1) and TIA-1-related protein (TIAR). Knockdown of TIA-1/TIAR decreased not only the expression, but also the stability of TPD52 mRNA; it also decreased the expression and stability of the reporter gene ligated to the 3'-end of the 78-280 fragment. Stimulation of transforming growth factor-β and epidermal growth factor decreased the binding ability of these factors, resulting in decreased mRNA stability. These results indicate that the 78-280 fragment and TIA-1/TIAR concordantly contribute to mRNA stability as a cis -acting element and trans -acting factor(s), respectively. Thus, we here report the specific interactions between these elements in the post-transcriptional regulation of the TPD52 gene. © 2017 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society.

mRNA localization mechanisms in Trypanosoma cruzi.

Directory of Open Access Journals (Sweden)

Lysangela R Alves

Full Text Available Asymmetric mRNA localization is a sophisticated tool for regulating and optimizing protein synthesis and maintaining cell polarity. Molecular mechanisms involved in the regulated localization of transcripts are widespread in higher eukaryotes and fungi, but not in protozoa. Trypanosomes are ancient eukaryotes that branched off early in eukaryote evolution. We hypothesized that these organisms would have basic mechanisms of mRNA localization. FISH assays with probes against transcripts coding for proteins with restricted distributions showed a discrete localization of the mRNAs in the cytoplasm. Moreover, cruzipain mRNA was found inside reservosomes suggesting new unexpected functions for this vacuolar organelle. Individual mRNAs were also mobilized to RNA granules in response to nutritional stress. The cytoplasmic distribution of these transcripts changed with cell differentiation, suggesting that localization mechanisms might be involved in the regulation of stage-specific protein expression. Transfection assays with reporter genes showed that, as in higher eukaryotes, 3'UTRs were responsible for guiding mRNAs to their final location. Our results strongly suggest that Trypanosoma cruzi have a core, basic mechanism of mRNA localization. This kind of controlled mRNA transport is ancient, dating back to early eukaryote evolution.

Rapid Upregulation of Orai1 Abundance in the Plasma Membrane of Platelets Following Activation with Thrombin and Collagen Related Peptide

Directory of Open Access Journals (Sweden)

Guilai Liu

2015-11-01

Full Text Available Background: Blood platelets accomplish primary hemostasis following vascular injury and contribute to the orchestration of occlusive vascular disease. Platelets are activated by an increase of cytosolic Ca2+-activity ([Ca2+]i, which is accomplished by Ca2+-release from intracellular stores and subsequent store operated Ca2+ entry (SOCE through Ca2+ release activated Ca2+ channel moiety Orai1. Powerful activators of platelets include thrombin and collagen related peptide (CRP, which are in part effective by activation of small G- protein Rac1. The present study explored the influence of thrombin and CRP on Orai1 protein abundance and cytosolic Ca2+-activity ([Ca2+]i in platelets drawn from wild type mice. Methods: Orai1 protein surface abundance was quantified utilizing CF™488A conjugated antibodies, and [Ca2+]i was determined with Fluo3-fluorescence. Results: In resting platelets, Orai1 protein abundance and [Ca2+]i were low. Thrombin (0.02 U/ml and CRP (5ug/ml within 2 min increased [Ca2+]i and Orai1 protein abundance at the platelet surface. [Ca2+]i was further increased by Ca2+ ionophore ionomycin (1 µM and by store depletion with the sarcoendoplasmatic Ca2+ ATPase inhibitor thapsigargin (1 µM. However, Orai1 protein abundance at the platelet surface was not significantly affected by ionomycin and only slightly increased by thapsigargin. The effect of thrombin and CRP on Orai1 abundance and [Ca2+]i was significantly blunted by Rac1 inhibitor NSC23766 (50 µM. Conclusion: The increase of [Ca2+]i following stimulation of platelets with thrombin and collagen related peptide is potentiated by ultrarapid Rac1 sensitive translocation of Orai1 into the cell membrane.

Evidence for convergent evolution of SINE-directed Staufen-mediated mRNA decay.

Science.gov (United States)

Lucas, Bronwyn A; Lavi, Eitan; Shiue, Lily; Cho, Hana; Katzman, Sol; Miyoshi, Keita; Siomi, Mikiko C; Carmel, Liran; Ares, Manuel; Maquat, Lynne E

2018-01-30

Primate-specific Alu short interspersed elements (SINEs) as well as rodent-specific B and ID (B/ID) SINEs can promote Staufen-mediated decay (SMD) when present in mRNA 3'-untranslated regions (3'-UTRs). The transposable nature of SINEs, their presence in long noncoding RNAs, their interactions with Staufen, and their rapid divergence in different evolutionary lineages suggest they could have generated substantial modification of posttranscriptional gene-control networks during mammalian evolution. Some of the variation in SMD regulation produced by SINE insertion might have had a similar regulatory effect in separate mammalian lineages, leading to parallel evolution of the Staufen network by independent expansion of lineage-specific SINEs. To explore this possibility, we searched for orthologous gene pairs, each carrying a species-specific 3'-UTR SINE and each regulated by SMD, by measuring changes in mRNA abundance after individual depletion of two SMD factors, Staufen1 (STAU1) and UPF1, in both human and mouse myoblasts. We identified and confirmed orthologous gene pairs with 3'-UTR SINEs that independently function in SMD control of myoblast metabolism. Expanding to other species, we demonstrated that SINE-directed SMD likely emerged in both primate and rodent lineages >20-25 million years ago. Our work reveals a mechanism for the convergent evolution of posttranscriptional gene regulatory networks in mammals by species-specific SINE transposition and SMD.

Region specific regulation of glutamic acid decarboxylase mRNA expression by dopamine neurons in rat brain.

Science.gov (United States)

Lindefors, N; Brene, S; Herrera-Marschitz, M; Persson, H

1989-01-01

In situ hybridization histochemistry and RNA blots were used to study the expression of glutamic acid decarboxylase (GAD) mRNA in rats with or without a unilateral lesion of midbrain dopamine neurons. Two populations of GAD mRNA positive neurons were found in the intact caudate-putamen, substantia nigra and fronto-parietal cortex. In caudate-putamen, only one out of ten of the GAD mRNA positive neurons expressed high levels, while in substantia nigra every second of the positive neurons expressed high levels of GAD mRNA. Relatively few, but intensively labelled neurons were found in the intact fronto-parietal cerebral cortex. In addition, one out of six of the GAD mRNA positive neurons in the fronto-parietal cortex showed a low labeling. On the ipsilateral side, the forebrain dopamine deafferentation induced an increase in the number of neurons expressing high levels of GAD mRNA in caudate-putamen, and a decrease in fronto-parietal cortex. A smaller decrease was also seen in substantia nigra. However, the total number of GAD mRNA positive neurons were not significantly changed in any of these brain regions. The changes in the levels of GAD mRNA after the dopamine lesion were confirmed by RNA blot analysis. Hence, midbrain dopamine neurons appear to control neuronal expression of GAD mRNA by a tonic down-regulation in a fraction of GAD mRNA positive neurons in caudate-putamen, and a tonic up-regulation in a fraction of GAD mRNA positive neurons in fronto-parietal cortex and substantia nigra.

Evidence for a Complex Class of Nonadenylated mRNA in Drosophila

Science.gov (United States)

Zimmerman, J. Lynn; Fouts, David L.; Manning, Jerry E.

1980-01-01

The amount, by mass, of poly(A+) mRNA present in the polyribosomes of third-instar larvae of Drosophila melanogaster, and the relative contribution of the poly(A+) mRNA to the sequence complexity of total polysomal RNA, has been determined. Selective removal of poly(A+) mRNA from total polysomal RNA by use of either oligo-dT-cellulose, or poly(U)-sepharose affinity chromatography, revealed that only 0.15% of the mass of the polysomal RNA was present as poly(A+) mRNA. The present study shows that this RNA hybridized at saturation with 3.3% of the single-copy DNA in the Drosophila genome. After correction for asymmetric transcription and reactability of the DNA, 7.4% of the single-copy DNA in the Drosophila genome is represented in larval poly(A+) mRNA. This corresponds to 6.73 x 106 nucleotides of mRNA coding sequences, or approximately 5,384 diverse RNA sequences of average size 1,250 nucleotides. However, total polysomal RNA hybridizes at saturation to 10.9% of the single-copy DNA sequences. After correcting this value for asymmetric transcription and tracer DNA reactability, 24% of the single-copy DNA in Drosophila is represented in total polysomal RNA. This corresponds to 2.18 x 107 nucleotides of RNA coding sequences or 17,440 diverse RNA molecules of size 1,250 nucleotides. This value is 3.2 times greater than that observed for poly(A+) mRNA, and indicates that ≃69% of the polysomal RNA sequence complexity is contributed by nonadenylated RNA. Furthermore, if the number of different structural genes represented in total polysomal RNA is ≃1.7 x 104, then the number of genes expressed in third-instar larvae exceeds the number of chromomeres in Drosophila by about a factor of three. This numerology indicates that the number of chromomeres observed in polytene chromosomes does not reflect the number of structural gene sequences in the Drosophila genome. PMID:6777246

Lower FOXO3 mRNA expression in granulosa cells is involved in unexplained infertility.

Science.gov (United States)

Yamamoto, Hikaru; Yamashita, Yoshiki; Saito, Natsuho; Hayashi, Atsushi; Hayashi, Masami; Terai, Yoshito; Ohmichi, Masahide

2017-06-01

The aim of this study was to investigate whether FOXO1 and FOXO3 mRNA expression in granulosa cells is the cause of unexplained infertility. Thirty-one patients aged infertility and 18 with male partner infertility as a control group) whose serum anti-Müllerian hormone level was >0.5 ng/μL were enrolled in the study. All patients underwent oocyte retrieval under a short protocol from June 2012 to October 2013. Real-time PCR was carried out using mRNA extracted from granulosa cells retrieved from mature follicles. We compared FOXO1 and FOXO3 mRNA expression ratios in granulosa cells between the unexplained infertility group and the male infertility group. The relation between FOXO1 and FOXO3 mRNA expression ratios in granulosa cells and assisted reproduction technology clinical outcome was also examined. FOXO3 mRNA expression ratio was significantly lower in the unexplained infertility group than in the male infertility group. Moreover, FOXO3 mRNA expression ratio showed a positive correlation with both the number of retrieved oocytes and serum anti-Müllerian hormone level. A positive correlation was also identified between FOXO1 mRNA expression and total dose of hMG. As well, the number of retrieved oocytes in the unexplained infertility group was statistically lower than that in the male infertility group. A lower FOXO3 mRNA expression in granulosa cells leads to poor oocyte development in patients with unexplained infertility undergoing controlled ovarian stimulation for in vitro fertilization-embryo transfer. © 2017 Japan Society of Obstetrics and Gynecology.

A retinoic acid-inducible mRNA from F9 teratocarcinoma cells encodes a novel protease inhibitor homologue.

Science.gov (United States)

Wang, S Y; Gudas, L J

1990-09-15

We have previously isolated several cDNA clones specific for mRNA species that increase in abundance during the retinoic acid-associated differentiation of F9 teratocarcinoma stem cells. One of these mRNAs, J6, encodes a approximately 40 kDa protein as assayed by hybrid selection and in vitro translation (Wang, S.-Y., LaRosa, G., and Gudas, L. J. (1985) Dev. Biol. 107, 75-86). The time course of J6 mRNA expression is similar to those of both laminin B1 and collagen IV (alpha 1) messages following retinoic acid addition. To address the functional role of this protein, we have isolated a full-length cDNA clone complementary to this approximately 40-kDa protein mRNA. Sequence analysis reveals an open reading frame of 406 amino acids (Mr 45,652). The carboxyl-terminal portion of this predicted protein contains a region that is homologous to the reactive sites found among members of the serpin (serine protease inhibitor) family. The predicted reactive site (P1-P1') of this J6 protein is Arg-Ser, which is the same as that of antithrombin III. Like ovalbumin and human monocyte-derived plasminogen activator inhibitor (mPAI-2), which are members of the serpin gene family, the J6 protein appears to have no typical amino-terminal signal sequence.

Hierarchical spatial models for predicting pygmy rabbit distribution and relative abundance

Science.gov (United States)

Wilson, T.L.; Odei, J.B.; Hooten, M.B.; Edwards, T.C.

2010-01-01

Conservationists routinely use species distribution models to plan conservation, restoration and development actions, while ecologists use them to infer process from pattern. These models tend to work well for common or easily observable species, but are of limited utility for rare and cryptic species. This may be because honest accounting of known observation bias and spatial autocorrelation are rarely included, thereby limiting statistical inference of resulting distribution maps. We specified and implemented a spatially explicit Bayesian hierarchical model for a cryptic mammal species (pygmy rabbit Brachylagus idahoensis). Our approach used two levels of indirect sign that are naturally hierarchical (burrows and faecal pellets) to build a model that allows for inference on regression coefficients as well as spatially explicit model parameters. We also produced maps of rabbit distribution (occupied burrows) and relative abundance (number of burrows expected to be occupied by pygmy rabbits). The model demonstrated statistically rigorous spatial prediction by including spatial autocorrelation and measurement uncertainty. We demonstrated flexibility of our modelling framework by depicting probabilistic distribution predictions using different assumptions of pygmy rabbit habitat requirements. Spatial representations of the variance of posterior predictive distributions were obtained to evaluate heterogeneity in model fit across the spatial domain. Leave-one-out cross-validation was conducted to evaluate the overall model fit. Synthesis and applications. Our method draws on the strengths of previous work, thereby bridging and extending two active areas of ecological research: species distribution models and multi-state occupancy modelling. Our framework can be extended to encompass both larger extents and other species for which direct estimation of abundance is difficult. ?? 2010 The Authors. Journal compilation ?? 2010 British Ecological Society.

Relative abundance and distribution of bacteria in the gut of ...

African Journals Online (AJOL)

Escherichia coli, Aeromonas hydrophila, Salmonella typhi and Pseudomonas aeruginosa were the most abundant species in the samples from Epe Lagoon while Escherichia coli, Aeromonas hydrophila, Proteus vulgaris and Pseudomonas aeruginosa were predominant in Badagry Creek. It was noteworthy that Citrobacter ...

Golden alga presence and abundance are inversely related to salinity in a high-salinity river ecosystem, Pecos River, USA

Science.gov (United States)

Israël, Natascha M.D.; VanLandeghem, Matthew M.; Denny, Shawn; Ingle, John; Patino, Reynaldo

2014-01-01

Prymnesium parvum (golden alga, GA) is a toxigenic harmful alga native to marine ecosystems that has also affected brackish inland waters. The first toxic bloom of GA in the western hemisphere occurred in the Pecos River, one of the saltiest rivers in North America. Environmental factors (water quality) associated with GA occurrence in this basin, however, have not been examined. Water quality and GA presence and abundance were determined at eight sites in the Pecos River basin with or without prior history of toxic blooms. Sampling was conducted monthly from January 2012 to July 2013. Specific conductance (salinity) varied spatiotemporally between 4408 and 73,786 mS/cm. Results of graphical, principal component (PCA), and zero-inflated Poisson (ZIP) regression analyses indicated that the incidence and abundance of GA are reduced as salinity increases spatiotemporally. LOWESS regression and correlation analyses of archived data for specific conductance and GA abundance at one of the study sites retrospectively confirmed the negative association between these variables. Results of PCA also suggested that at <15,000 mS/cm, GA was present at a relatively wide range of nutrient (nitrogen and phosphorus) concentrations whereas at higher salinity, GA was observed only at mid-to-high nutrient levels. Generally consistent with earlier studies, results of ZIP regression indicated that GA presence is positively associated with organic phosphorus and in samples where GA is present, GA abundance is positively associated with organic nitrogen and negatively associated with inorganic nitrogen. This is the first report of an inverse relation between salinity and GA presence and abundance in riverine waters and of interaction effects of salinity and nutrients in the field. These observations contribute to a more complete understanding of environmental conditions that influence GA distribution in inland waters.

Adipose tissue interleukin-18 mRNA and plasma interleukin-18: effect of obesity and exercise

DEFF Research Database (Denmark)

Leick, Lotte; Lindegaard, Birgitte; Stensvold, Dorthe

2007-01-01

resistance was tested. Furthermore, we speculated that acute exercise and exercise training would regulate AT IL-18 mRNA expression. RESEARCH METHODS AND PROCEDURES: Non-obese subjects with BMI women: n = 18; men; n = 11) and obese subjects with BMI >30 kg/m(2) (women: n = 6; men: n = 7...... of regular physical activity with improved insulin sensitivity.......OBJECTIVES: Obesity and a physically inactive lifestyle are associated with increased risk of developing insulin resistance. The hypothesis that obesity is associated with increased adipose tissue (AT) interleukin (IL)-18 mRNA expression and that AT IL-18 mRNA expression is related to insulin...

PAX5α and PAX5β mRNA expression in breast Cancer: Relation to ...

African Journals Online (AJOL)

Background: Many studies evaluated the role of paired box gene 5 (PAX5) in breast cancer. However, few investigated PAX5α and PAX5β isoforms individually. Objective: The aim of the present study is to evaluate mRNA expression of PAX5α and PAX5β in breast cancer and assessing their underlying pathological roles ...

Coyote abundance in relation to habitat characteristics in Sierra San Luis, Sonora, Mexico

Science.gov (United States)

Eduardo Ponce Guevara; Karla Pelz Serrano; Carlos A. Lopez Gonzalez

2005-01-01

Coyotes have expanded their historical distribution range because of anthropogenic activities and habitat transformation, where forests have been considered marginal habitat. We tested the relationship between vegetation structure and coyote abundance in different habitat types. We expected to find a higher abundance in open lands than in thicker areas. We used scent...

Impact of exogenous lipase supplementation on growth, intestinal function, mucosal immune and physical barrier, and related signaling molecules mRNA expression of young grass carp (Ctenopharyngodon idella).

Science.gov (United States)

Liu, Sen; Feng, Lin; Jiang, Wei-Dan; Liu, Yang; Jiang, Jun; Wu, Pei; Zeng, Yun-Yun; Xu, Shu-De; Kuang, Sheng-Yao; Tang, Ling; Tang, Wu-Neng; Zhang, Yong-An; Zhou, Xiao-Qiu

2016-08-01

This study investigated the effects of exogenous lipase supplementation on the growth performance, intestinal growth and function, immune response and physical barrier function, and related signaling molecules mRNA expression of young grass carp (Ctenopharyngodon idella). A total of 450 grass carp (255.02 ± 0.34 g) were fed five diets for 60 days. There were 5 dietary treatments that included a normal protein and lipid diet containing 30% crude protein (CP) with 5% ether extract (EE), and the low-protein and high-lipid diets (28% CP, 6% EE) supplemented with graded levels of exogenous lipase supplementation activity at 0, 1193, 2560 and 3730 U/kg diet. The results indicated that compared with a normal protein and lipid diet (30% CP, 5% EE), a low-protein and high-lipid diet (28% CP, 6% EE) (un-supplemented lipase) improved lysozyme activities and complement component 3 contents in the distal intestine (DI), interleukin 10 mRNA expression in the proximal intestine (PI), and glutathione S-transferases activity and glutathione content in the intestine of young grass carp. In addition, in low-protein and high-lipid diets, optimal exogenous lipase supplementation significantly increased acid phosphatase (ACP) activities and complement component 3 (C3) contents (P exogenous lipase supplementation significantly decreased reactive oxygen species (ROS), malondialdehyde (MDA) and protein carbonyl (PC) contents (P exogenous lipase supplementation significantly elevated the mRNA levels of tight junction proteins (Occludin, zonula occludens 1, Claudin b, Claudin c and Claudin 3) (P exogenous lipase supplementation improved growth, intestinal growth and function, intestinal immunity, physical barrier, and regulated the mRNA expression of related signal molecules of fish. The optimal level of exogenous lipase supplementation in young grass carp (255-771 g) was estimated to be 1193 U kg(-1) diet. Copyright © 2016. Published by Elsevier Ltd.

Correlation of mRNA and protein levels: Cell type-specific gene expression of cluster designation antigens in the prostate

Directory of Open Access Journals (Sweden)

Deutsch Eric W

2008-05-01

Full Text Available Abstract Background: Expression levels of mRNA and protein by cell types exhibit a range of correlations for different genes. In this study, we compared levels of mRNA abundance for several cluster designation (CD genes determined by gene arrays using magnetic sorted and laser-capture microdissected human prostate cells with levels of expression of the respective CD proteins determined by immunohistochemical staining in the major cell types of the prostate – basal epithelial, luminal epithelial, stromal fibromuscular, and endothelial – and for prostate precursor/stem cells and prostate carcinoma cells. Immunohistochemical stains of prostate tissues from more than 50 patients were scored for informative CD antigen expression and compared with cell-type specific transcriptomes. Results: Concordance between gene and protein expression findings based on 'present' vs. 'absent' calls ranged from 46 to 68%. Correlation of expression levels was poor to moderate (Pearson correlations ranged from 0 to 0.63. Divergence between the two data types was most frequently seen for genes whose array signals exceeded background (> 50 but lacked immunoreactivity by immunostaining. This could be due to multiple factors, e.g. low levels of protein expression, technological sensitivities, sample processing, probe set definition or anatomical origin of tissue and actual biological differences between transcript and protein abundance. Conclusion: Agreement between these two very different methodologies has great implications for their respective use in both molecular studies and clinical trials employing molecular biomarkers.

Mosquitoes of the rice agroecosystem of Malaysia: species composition and their abundance in relation to rice farming

International Nuclear Information System (INIS)

Abu Hassan Ahmad; Che Salmah Md Rawi

2002-01-01

Mosquito abundance in relation to rice farming was studied in the Muda and the Kerian Irrigation Schemes. Mosquito larvae were collected using dippers for several growing seasons. Adult mosquitoes were collected by using human bait and cow bait and net trap at nights. Culex, Mansonia and Anopheles were the three genera of mosquito found in the rice agroecosystem. Four species of Mansonia were found biting on human bait. Culex mosquitoes were caught biting on human and cow baits. Culex tritaeniorhynchus, C pseudovishnui, C vishnui, C gelidus and C bitaeniorhynchus were the most common Culex mosquitoes found. Anoheles sinensis and A. peditaeniatus were the most dominant panopheline mosquitoes. High abundance of larvae and adult mosquitoes were observed during ploughing, planting, and tillering stages of rice farming. (Author)

Composition and abundance of tree regeneration

Science.gov (United States)

Todd F. Hutchinson; Elaine Kennedy Sutherland; Charles T. Scott

2003-01-01

The composition and abundance of tree seedlings and saplings in the four study areas in southern Ohio were related to soil moisture via a GIS-derived integrated moisture index and to soil texture and fertility. For seedlings, the total abundance of small stems (less than 30 cm tall) was significantly greater on xeric plots (81,987/ha) than on intermediate (54,531/ha)...

Glucosensing capacity in rainbow trout liver displays day-night variations possibly related to melatonin action.

Science.gov (United States)

Conde-Sieira, Marta; Patiño, Marcos A López; Míguez, Jesús M; Soengas, José L

2012-09-01

To assess whether the glucosensing capacity in peripheral (liver and Brockmann bodies) and central (hypothalamus and hindbrain) locations of rainbow trout displays day-night variations in its response to changes in circulating glucose levels, we evaluated the response of parameters related to glucosensing [glucose, glycogen and glucose 6-phosphate levels, activities of glucokinase (GK), glycogen synthetase (GSase) and pyruvate kinase (PK), and mRNA abundance of GK, glucose transporter 2 (GLUT2), and K(ATP) channel subunits Kir6.x-like and sulfonylurea receptor (SUR)-like] in fish subjected to hyperglycemic treatment under night or day conditions. No day-night significant variations were noticed in the glucosensing capacity of the hypothalamus, hindbrain and Brockmann bodies. In contrast, a clear differential response was noticed in the liver, where glucose levels, GK activity (and mRNA levels) and GSase activity displayed increased values during the day in hyperglycemic fish compared with controls, and lower (GK mRNA levels) or non-existent (glucose, GK and GSase activities, and Kir6.x-like mRNA levels) values during the night. A similar decrease in parameters related to glucosensing in the liver was observed when fish under day conditions were treated with melatonin, suggesting a modulatory role of melatonin in day-night changes of the glucosensing response in the same tissue.

T-lymphocyte cytokine mRNA expression in cystic echinococcosis.

Science.gov (United States)

Fauser, S; Kern, P

1997-04-01

In the present study we investigated cytokine mRNA expression by peripheral blood mononuclear cells (PBMC) from patients with cystic echinococcosis (CE) after stimulation with different antigens. By using reverse transcriptase polymerase chain reaction (RT-PCR) we could demonstrate that restimulation with crude Echinococcus granulosus antigen (Eg-Ag) induced or enhanced Th2 cytokine mRNA expression, especially IL-5 (by using antigen from sheep cyst fluid) in 23 out of 26 investigated CE patients and IL-10 (by using antigen from camel cyst fluid) in 10 out of 10 investigated CE patients. In contrast, IL-5 mRNA expression was absent in PBMC of healthy controls after Eg-Ag stimulation. To determine the specificity of this reaction we stimulated PBMC from 11 CE patients with crude Echinococcus multilocularis antigen (Em-Ag) and PBMC from 8 CE patients with Toxocara canis antigen (Tc-Ag). We found that the PBMC of patients showed a similar mRNA cytokine pattern on stimulation with Em-Ag when compared with Eg-Ag stimulation. The cytokine mRNA pattern on stimulation with Tc-Ag, however, resembled the cytokine mRNA pattern of unstimulated PBMC. Furthermore, the stimulation of PBMC with crude Mycobacterium tuberculosis antigen (H37Ra) and purified protein derivative (PPD) of M. tuberculosis revealed distinct IL-5 mRNA expression in all investigated CE patients, whereas in healthy controls IL-5 mRNA expression was very weak or totally absent. Thus, our results indicate an induction of Th2 cytokine mRNA expression in CE patients, which is frequently observed in parasite infections. Interestingly, this response persists after stimulation with tuberculosis antigens, which normally induce Th1 response.

Fas ligand expression in human and mouse cancer cell lines; a caveat on over-reliance on mRNA data

Directory of Open Access Journals (Sweden)

Ryan Aideen E

2006-02-01

Full Text Available Abstract Background During carcinogenesis, tumors develop multiple mechanisms for evading the immune response, including upregulation of Fas ligand (FasL/CD95L expression. Expression of FasL may help to maintain tumor cells in a state of immune privilege by inducing apoptosis of anti-tumor immune effector cells. Recently this idea has been challenged by studies reporting that tumor cells of varying origin do not express FasL. In the present study, we aimed to comprehensively characterize FasL expression in tumors of both murine and human origin over a 72 hour time period. Methods RNA and protein was extracted from six human (SW620, HT29, SW480, KM12SM, HCT116, Jurkat and three mouse (CMT93, CT26, B16F10 cancer cell lines at regular time intervals over a 72 hour time period. FasL expression was detected at the mRNA level by RT-PCR, using intron spanning primers, and at the protein level by Western Blotting and immunofluorescence, using a polyclonal FasL- specific antibody. Results Expression of FasL mRNA and protein was observed in all cell lines analysed. However, expression of FasL mRNA varied dramatically over time, with cells negative for FasL mRNA at many time points. In contrast, 8 of the 9 cell lines constitutively expressed FasL protein. Thus, cells can abundantly express FasL protein at times when FasL mRNA is absent. Conclusion These findings demonstrate the importance of complete analysis of FasL expression by tumor cells in order to fully characterize its biological function and may help to resolve the discrepancies present in the literature regarding FasL expression and tumor immune privilege.

Letrozole, an aromatase inhibitor, reduces post-peak age-related regression of rooster reproductive performance.

Science.gov (United States)

Ali, Emad Abdulgabbar; Zhandi, Mahdi; Towhidi, Armin; Zaghari, Mojtaba; Ansari, Mahdi; Najafi, Mojtaba; Deldar, Hamid

2017-08-01

This study was designed to evaluate orally administrated Letrozole (Lz) on reproductive performance, plasma testosterone and estradiol concentrations and relative abundance of mRNA of GnRH, FSH and LH in roosters. Ross 308 roosters (n=32) that were 40-weeks of age were individually housed and received a basal standard diet supplemented different amounts of capsulated Lz [0 (Lz-0), 0.5 (Lz-0.5), 1 (Lz-1) or 1.5 (Lz-1.5), mg Lz/bird/day] for 12 weeks. Sperm quality variables and plasma testosterone and estradiol concentrations were assessed from the first to the tenth week of the treatment period. Semen samples from the 11th to 12th week were used for artificial insemination and eggs were collected and allotted to assess fertility and hatchability rates. Relative abundance of hypothalamic and pituitary GnRH, LH and FSH mRNA was evaluated at the end of 12th week. The results indicated that total and forward sperm motility as well as egg hatchability rate were greater in the Lz-0.5 group. Greater sperm concentrations, ejaculate volume, sperm plasma membrane integrity, testis index and fertility rates were recorded for both Lz-0.5 and Lz-1 groups compared with the Lz-0 group (Proosters. Copyright © 2017 Elsevier B.V. All rights reserved.

Abundance of birds in Fukushima as judged from Chernobyl

International Nuclear Information System (INIS)

Møller, Anders Pape; Hagiwara, Atsushi; Matsui, Shin; Kasahara, Satoe; Kawatsu, Kencho; Nishiumi, Isao; Suzuki, Hiroyuki; Ueda, Keisuke; Mousseau, Timothy A.

2012-01-01

The effects of radiation on abundance of common birds in Fukushima can be assessed from the effects of radiation in Chernobyl. Abundance of birds was negatively related to radiation, with a significant difference between Fukushima and Chernobyl. Analysis of 14 species common to the two areas revealed a negative effect of radiation on abundance, differing between areas and species. The relationship between abundance and radiation was more strongly negative in Fukushima than in Chernobyl for the same 14 species, demonstrating a negative consequence of radiation for birds immediately after the accident on 11 March 2011 during the main breeding season in March–July, when individuals work close to their maximum sustainable level. - Highlights: ► Abundance of birds was negatively related to radiation in Chernobyl and Fukushima. ► Effects of radiation on abundance differed between Chernobyl and Fukushima and among species. ► For 14 species common to the two areas the effects of radiation on abundance were stronger in Fukushima than in Chernobyl. - The negative effect of radiation on abundance of birds in Fukushima exceeded that for the same species in Chernobyl.

Fear or food ? abundance of red fox in relation to occurrence of lynx and wolf

OpenAIRE

Wikenros, Camilla; Aronsson, Malin; Liberg, Olof; Jarnemo, Anders; Hansson, Jessica; Wallgren, M?rtha; Sand, H?kan; Bergstr?m, Roger

2017-01-01

Apex predators may affect mesopredators through intraguild predation and/or supply of carrion from their prey, causing a trade-off between avoidance and attractiveness. We used wildlife triangle snow-tracking data to investigate the abundance of red fox (Vulpes vulpes) in relation to lynx (Lynx lynx) and wolf (Canis lupus) occurrence as well as land composition and vole (Microtus spp.)?density. Data from the Swedish wolf-monitoring system and VHF/GPS-collared wolves were used to study the eff...

Expression of calmodulin mRNA in rat olfactory neuroepithelium.

Science.gov (United States)

Biffo, S; Goren, T; Khew-Goodall, Y S; Miara, J; Margolis, F L

1991-04-01

A calmodulin (CaM) cDNA was isolated by differential hybridization screening of a lambda gt10 library prepared from rat olfactory mucosa. This cDNA fragment, containing most of the open reading frame of the rat CaMI gene, was subcloned and used to characterize steady-state expression of CaM mRNA in rat olfactory neuroepithelium and bulb. Within the bulb mitral cells are the primary neuronal population expressing CaM mRNA. The major CaM mRNA expressed in the olfactory mucosa is 1.7 kb with smaller contributions from mRNAs of 4.0 and 1.4 kb. CaM mRNA was primarily associated with the olfactory neurons and, despite the cellular complexity of the tissue and the known involvement of CaM in diverse cellular processes, was only minimally evident in sustentacular cells, gland cells or respiratory epithelium. Following bulbectomy CaM mRNA declines in the olfactory neuroepithelium as does olfactory marker protein (OMP) mRNA. In contrast to the latter, CaM mRNA makes a partial recovery by one month after surgery. These results, coupled with those from in situ hybridization, indicate that CaM mRNA is expressed in both mature and immature olfactory neurons. The program regulating CaM gene expression in olfactory neurons is distinct from those controlling expression of B50/GAP43 in immature, or OMP in mature, neurons respectively.

Complement mRNA in the mammalian brain: responses to Alzheimer's disease and experimental brain lesioning.

Science.gov (United States)

Johnson, S A; Lampert-Etchells, M; Pasinetti, G M; Rozovsky, I; Finch, C E

1992-01-01

This study describes evidence in the adult human and rat brain for mRNAs that encode two complement (C) proteins, C1qB and C4. C proteins are important effectors of humoral immunity and inflammation in peripheral tissues but have not been considered as normally present in brain. Previous immunocytochemical studies showed that C proteins are associated with plaques, tangles, and dystrophic neurites in Alzheimer's disease (AD), but their source is unknown. Combined immunocytochemistry and in situ hybridization techniques show C4 mRNA in pyramidal neurons and C1qB mRNA in microglia. Primary rat neuron cultures also show C1qB mRNA. In the cortex from AD brains, there were two- to threefold increases of C1qB mRNA and C4 mRNA, and increased C1qB mRNA prevalence was in part associated with microglia. As a model for AD, we examined entorhinal cortex perforant path transection in the rat brain, which caused rapid increases of C1qB mRNA in the ipsilateral, but not contralateral, hippocampus and entorhinal cortex. The role of brain-derived acute and chronic C induction during AD and experimental lesions can now be considered in relation to functions of C proteins that pertain to cell degeneration and/or cell preservation and synaptic plasticity.

Stellar pulsation and the abundance of helium

International Nuclear Information System (INIS)

Schmidt, E.G.

1978-01-01

It has been suggested that the appearance of nonvariable stars within the Cepheid strip could be explained by a range in the helium abundance of Population I stars. In order to study this possibility, spectra were obtained of the main-sequence B stars in the galactic cluster NGC 129, which contains a nonvariable Cepheid-strip star, and M25, which contains a relatively hot Cepheid. Unfortunately, several of the stars in these clusters turn out to be helium-weak stars. In NGC 129 two stars which appear normal give a normal abundance, while in M25 all of the observed stars have abnormally low abundances. The significance of the low abundance in M25 is not clear. The abundance in NGC 129 is not low enough to support the above suggestion. 4 figures, 2 tables

Cup regulates oskar mRNA stability during oogenesis.

Science.gov (United States)

Broyer, Risa M; Monfort, Elena; Wilhelm, James E

2017-01-01

The proper regulation of the localization, translation, and stability of maternally deposited transcripts is essential for embryonic development in many organisms. These different forms of regulation are mediated by the various protein subunits of the ribonucleoprotein (RNP) complexes that assemble on maternal mRNAs. However, while many of the subunits that regulate the localization and translation of maternal transcripts have been identified, relatively little is known about how maternal mRNAs are stockpiled and stored in a stable form to support early development. One of the best characterized regulators of maternal transcripts is Cup - a broadly conserved component of the maternal RNP complex that in Drosophila acts as a translational repressor of the localized message oskar. In this study, we have found that loss of cup disrupts the localization of both the oskar mRNA and its associated proteins to the posterior pole of the developing oocyte. This defect is not due to a failure to specify the oocyte or to disruption of RNP transport. Rather, the localization defects are due to a drop in oskar mRNA levels in cup mutant egg chambers. Thus, in addition to its role in regulating oskar mRNA translation, Cup also plays a critical role in controlling the stability of the oskar transcript. This suggests that Cup is ideally positioned to coordinate the translational control function of the maternal RNP complex with its role in storing maternal transcripts in a stable form. Published by Elsevier Inc.

Comparison of mRNA splicing assay protocols across multiple laboratories: recommendations for best practice in standardized clinical testing.

Science.gov (United States)

Whiley, Phillip J; de la Hoya, Miguel; Thomassen, Mads; Becker, Alexandra; Brandão, Rita; Pedersen, Inge Sokilde; Montagna, Marco; Menéndez, Mireia; Quiles, Francisco; Gutiérrez-Enríquez, Sara; De Leeneer, Kim; Tenés, Anna; Montalban, Gemma; Tserpelis, Demis; Yoshimatsu, Toshio; Tirapo, Carole; Raponi, Michela; Caldes, Trinidad; Blanco, Ana; Santamariña, Marta; Guidugli, Lucia; de Garibay, Gorka Ruiz; Wong, Ming; Tancredi, Mariella; Fachal, Laura; Ding, Yuan Chun; Kruse, Torben; Lattimore, Vanessa; Kwong, Ava; Chan, Tsun Leung; Colombo, Mara; De Vecchi, Giovanni; Caligo, Maria; Baralle, Diana; Lázaro, Conxi; Couch, Fergus; Radice, Paolo; Southey, Melissa C; Neuhausen, Susan; Houdayer, Claude; Fackenthal, Jim; Hansen, Thomas Van Overeem; Vega, Ana; Diez, Orland; Blok, Rien; Claes, Kathleen; Wappenschmidt, Barbara; Walker, Logan; Spurdle, Amanda B; Brown, Melissa A

2014-02-01

Accurate evaluation of unclassified sequence variants in cancer predisposition genes is essential for clinical management and depends on a multifactorial analysis of clinical, genetic, pathologic, and bioinformatic variables and assays of transcript length and abundance. The integrity of assay data in turn relies on appropriate assay design, interpretation, and reporting. We conducted a multicenter investigation to compare mRNA splicing assay protocols used by members of the ENIGMA (Evidence-Based Network for the Interpretation of Germline Mutant Alleles) consortium. We compared similarities and differences in results derived from analysis of a panel of breast cancer 1, early onset (BRCA1) and breast cancer 2, early onset (BRCA2) gene variants known to alter splicing (BRCA1: c.135-1G>T, c.591C>T, c.594-2A>C, c.671-2A>G, and c.5467+5G>C and BRCA2: c.426-12_8delGTTTT, c.7988A>T, c.8632+1G>A, and c.9501+3A>T). Differences in protocols were then assessed to determine which elements were critical in reliable assay design. PCR primer design strategies, PCR conditions, and product detection methods, combined with a prior knowledge of expected alternative transcripts, were the key factors for accurate splicing assay results. For example, because of the position of primers and PCR extension times, several isoforms associated with BRCA1, c.594-2A>C and c.671-2A>G, were not detected by many sites. Variation was most evident for the detection of low-abundance transcripts (e.g., BRCA2 c.8632+1G>A Δ19,20 and BRCA1 c.135-1G>T Δ5q and Δ3). Detection of low-abundance transcripts was sometimes addressed by using more analytically sensitive detection methods (e.g., BRCA2 c.426-12_8delGTTTT ins18bp). We provide recommendations for best practice and raise key issues to consider when designing mRNA assays for evaluation of unclassified sequence variants.

The mRNA expression profile of metabolic genes relative to MHC isoform pattern in human skeletal muscles

DEFF Research Database (Denmark)

Plomgaard, Peter; Penkowa, Milena; Leick, Lotte

2006-01-01

The metabolic profile of rodent muscle is generally reflected in the myosin heavy chain (MHC) fiber-type composition. The present study was conducted to test the hypothesis that metabolic gene expression is not tightly coupled with MHC fiber-type composition for all genes in human skeletal muscle....... Triceps brachii, vastus lateralis quadriceps, and soleus muscle biopsies were obtained from normally physically active, healthy, young male volunteers, because these muscles are characterized by different fiber-type compositions. As expected, citrate synthase and 3-hydroxyacyl dehydrogenase activity...... of a broad range of metabolic genes. The triceps muscle had two- to fivefold higher MHC IIa, phosphofructokinase, and LDH A mRNA content and two- to fourfold lower MHC I, lipoprotein lipase, CD36, hormone-sensitive lipase, and LDH B and hexokinase II mRNA than vastus lateralis or soleus. Interestingly...

Variation in local abundance and species richness of stream fishes in relation to dispersal barriers: Implications for management and conservation

Science.gov (United States)

Nislow, K.H.; Hudy, M.; Letcher, B.H.; Smith, E.P.

2011-01-01

1.Barriers to immigration, all else being equal, should in principle depress local abundance and reduce local species richness. These issues are particularly relevant to stream-dwelling species when improperly designed road crossings act as barriers to migration with potential impacts on the viability of upstream populations. However, because abundance and richness are highly spatially and temporally heterogeneous and the relative importance of immigration on demography is uncertain, population- and community-level effects can be difficult to detect. 2.In this study, we tested the effects of potential barriers to upstream movements on the local abundance and species richness of a diverse assemblage of resident stream fishes in the Monongahela National Forest, West Virginia, U.S.A. Fishes were sampled using simple standard techniques above- and below road crossings that were either likely or unlikely to be barriers to upstream fish movements (based on physical dimensions of the crossing). We predicted that abundance of resident fishes would be lower in the upstream sections of streams with predicted impassable barriers, that the strength of the effect would vary among species and that variable effects on abundance would translate into lower species richness. 3.Supporting these predictions, the statistical model that best accounted for variation in abundance and species richness included a significant interaction between location (upstream or downstream of crossing) and type (passable or impassable crossing). Stream sections located above predicated impassable culverts had fewer than half the number of species and less than half the total fish abundance, while stream sections above and below passable culverts had essentially equivalent richness and abundance. 4.Our results are consistent with the importance of immigration and population connectivity to local abundance and species richness of stream fishes. In turn, these results suggest that when measured at

Tau mRNA 3'UTR-to-CDS ratio is increased in Alzheimer disease.

Science.gov (United States)

García-Escudero, Vega; Gargini, Ricardo; Martín-Maestro, Patricia; García, Esther; García-Escudero, Ramón; Avila, Jesús

2017-08-10

Neurons frequently show an imbalance in expression of the 3' untranslated region (3'UTR) relative to the coding DNA sequence (CDS) region of mature messenger RNAs (mRNA). The ratio varies among different cells or parts of the brain. The Map2 protein levels per cell depend on the 3'UTR-to-CDS ratio rather than the total mRNA amount, which suggests powerful regulation of protein expression by 3'UTR sequences. Here we found that MAPT (the microtubule-associated protein tau gene) 3'UTR levels are particularly high with respect to other genes; indeed, the 3'UTR-to-CDS ratio of MAPT is balanced in healthy brain in mouse and human. The tau protein accumulates in Alzheimer diseased brain. We nonetheless observed that the levels of RNA encoding MAPT/tau were diminished in these patients' brains. To explain this apparently contradictory result, we studied MAPT mRNA stoichiometry in coding and non-coding regions, and found that the 3'UTR-to-CDS ratio was higher in the hippocampus of Alzheimer disease patients, with higher tau protein but lower total mRNA levels. Our data indicate that changes in the 3'UTR-to-CDS ratio have a regulatory role in the disease. Future research should thus consider not only mRNA levels, but also the ratios between coding and non-coding regions. Copyright © 2017 Elsevier B.V. All rights reserved.

Collagen mRNA levels changes during colorectal cancer carcinogenesis

DEFF Research Database (Denmark)

Skovbjerg, Hanne; Anthonsen, Dorit; Lothe, Inger M B

2009-01-01

BACKGROUND: Invasive growth of epithelial cancers is a complex multi-step process which involves dissolution of the basement membrane. Type IV collagen is a major component in most basement membranes. Type VII collagen is related to anchoring fibrils and is found primarily in the basement membrane...... zone of stratified epithelia. Immunohistochemical studies have previously reported changes in steady-state levels of different alpha(IV) chains in several epithelial cancer types. In the present study we aimed to quantitatively determine the mRNA levels of type IV collagen (alpha1/alpha 4/alpha 6......) and type VII collagen (alpha1) during colorectal cancer carcinogenesis. METHODS: Using quantitative RT-PCR, we have determined the mRNA levels for alpha1(IV), alpha 4(IV), alpha 6(IV), and alpha1(VII) in colorectal cancer tissue (n = 33), adenomas (n = 29) and in normal tissue from the same individuals...

Relative abundance and species richness of cerambycid beetles in partial cut and uncut bottomland hardwood forests

Science.gov (United States)

Newell, P.; King, S.

2009-01-01

Partial cutting techniques are increasingly advocated and used to create habitat for priority wildlife. However, partial cutting may or may not benefit species dependent on deadwood; harvesting can supplement coarse woody debris in the form of logging slash, but standing dead trees may be targeted for removal. We sampled cerambycid beetles during the spring and summer of 2006 and 2007 with canopy malaise traps in 1- and 2-year-old partial cut and uncut bottomland hardwood forests of Louisiana. We captured a total of 4195 cerambycid beetles representing 65 species. Relative abundance was higher in recent partial cuts than in uncut controls and with more dead trees in a plot. Total species richness and species composition were not different between treatments. The results suggest partial cuts with logging slash left on site increase the abundance of cerambycid beetles in the first few years after partial cutting and that both partial cuts and uncut forest should be included in the bottomland hardwood forest landscape.

Metabolic activity and mRNA levels of human cardiac CYP450s involved in drug metabolism.

Directory of Open Access Journals (Sweden)

Veronique Michaud

2010-12-01

Full Text Available Tissue-specific expression of CYP450s can regulate the intracellular concentration of drugs and explain inter-subject variability in drug action. The overall objective of our study was to determine in a large cohort of samples, mRNA levels and CYP450 activity expressed in the human heart.CYP450 mRNA levels were determined by RTPCR in left ventricular samples (n = 68 of explanted hearts from patients with end-stage heart failure. Samples were obtained from ischemic and non-ischemic hearts. In some instances (n = 7, samples were available from both the left and right ventricles. A technique for the preparation of microsomes from human heart tissue was developed and CYP450-dependent activity was determined using verapamil enantiomers as probe-drug substrates.Our results show that CYP2J2 mRNA was the most abundant isoform in all human heart left ventricular samples tested. Other CYP450 mRNAs of importance were CYP4A11, CYP2E1, CYP1A1 and CYP2C8 mRNAs while CYP2B6 and CYP2C9 mRNAs were present at low levels in only some of the hearts analyzed. CYP450 mRNAs did not differ between ischemic and non-ischemic hearts and appeared to be present at similar levels in the left and right ventricles. Incubation of verapamil with heart microsomes led to the formation of nine CYP450-dependent metabolites: a major finding was the observation that stereoselectivity was reversed compared to human liver microsomes, in which the R-enantiomer is metabolized to a greater extent.This study determined cardiac mRNA levels of various CYP450 isozymes involved in drug metabolism and demonstrated the prevalent expression of CYP2J2 mRNA. It revealed that cardiomyocytes can efficiently metabolize drugs and that cardiac CYP450s are highly relevant with regard to clearance of drugs in the heart. Our results support the claim that drug metabolism in the vicinity of a drug effector site can modulate drug effects.

FLT3-ITD and MLL-PTD influence the expression of MDR-1, MRP-1, and BCRP mRNA but not LRP mRNA assessed with RQ-PCR method in adult acute myeloid leukemia.

Science.gov (United States)

Nasilowska-Adamska, Barbara; Solarska, Iwona; Paluszewska, Monika; Malinowska, Iwona; Jedrzejczak, Wieslaw W; Warzocha, Krzysztof

2014-04-01

Fms-like tyrosine kinase 3-internal tandem duplication (FLT3-ITD) and mixed-lineage leukemia gene-partial tandem duplication (MLL-PTD) are aberrations associated with leukemia which indicate unsatisfactory prognosis. Downstream regulatory targets of FLT3-ITD and MLL-PTD are not well defined. We have analyzed the expression of MDR-1, multidrug resistant protein-1 (MRP-1), breast cancer resistance protein (BCRP), and lung resistance protein (LRP) messenger RNA (mRNA) in relation to the mutational status of FLT3-ITD and MLL-PTD in 185 acute myeloid leukemia (AML) adult patients. The real-time quantitative polymerase chain reaction method was performed to assess the expression of the MDR-1, MRP-1, BCRP, and LRP mRNA, and the results were presented as coefficients calculated using an intermediate method according to Pfaffl's rule. Significantly higher expressions of MDR-1 mRNA were found in patients who did not harbor FLT3-ITD (0.20 vs. 0.05; p = 0.0001) and MRP-1 mRNA in patients with this mutation (0.96 vs. 0.70; p = 0.002) and of BCRP mRNA in patients with MLL-PTD (0.61 vs. 0.38; p = 0.03). In univariate analysis, the high expression of MDR-1 mRNA (≥0.1317) negatively influenced the outcome of induction therapy (p = 0.05), whereas the high expression of BCRP mRNA (≥1.1487) was associated with a high relapse rate (RR) (p = 0.013). We found that the high expression of MDR-1 (≥0.1317), MRP-1 (≥0.8409), and BCRP mRNA (≥1.1487) significantly influenced disease-free survival (DFS; p = 0.059, 0.032, and 0.009, respectively) and overall survival (0.048, 0.014, and 0.059, respectively). Moreover, a high expression of BCRP mRNA (≥1.1487) proved to be an independent prognostic factor for RR (p = 0.01) and DFS (p = 0.002) in multivariate analysis. The significant correlation between the expression of MDR-1, MRP-1, and BCRP mRNA and FLT3-ITD or MLL-PTD in AML patients requires further investigation.

[Impacts of the formula of Suoquanwan(SQW) on expression of AQP-2 mRNA and AVPR-V2 mRNA in the kidney of rat polyuria model of Yang-deficiency].

Science.gov (United States)

Cao, Hong-Ying; Wu, Qing-He; Huang, Ping; He, Jin-Yang

2009-06-01

To observe the impacts of the formula of Suoquanwan (SQW) on the expression of AQP-2 mRNA and AVPR-V2 mRNA in the kidney of rat polyuria model of Yang-deficiency. The model rats were induced by adenine (250 mg/kg) for 4 weeks, then treated respectively with SQW or dDAVP. The expression of AQP-2 mRNA and AVPR-V2 mRNA in kidney of Yang-deficiency model by realtime fluorescence quantitative PCR method were investigated. In model rats, the expression of AQP-2 mRNA and AVPR-V2 mRNA in the kidney decreased, dDAVP and SQW high dose could increased the expression of AQP-2 mRNA and AVPR-V2 mRNA in the kidney. The others had no influence on the expression of AQP-2 mRNA and AVPR-V2 mRNA in the kidney. SQW can increase the expression of AQP-2 mRNA and AVPR-V2 mRNA in the kidney of rat polyuria model of Yang-deficiency.

Conventional oil and natural gas infrastructure increases brown-headed cowbird (Molothrus ater) relative abundance and parasitism in mixed-grass prairie.

Science.gov (United States)

Bernath-Plaisted, Jacy; Nenninger, Heather; Koper, Nicola

2017-07-01

The rapid expansion of oil and natural gas development across the Northern Great Plains has contributed to habitat fragmentation, which may facilitate brood parasitism of ground-nesting grassland songbird nests by brown-headed cowbirds ( Molothrus ater ), an obligate brood parasite, through the introduction of perches and anthropogenic edges. We tested this hypothesis by measuring brown-headed cowbird relative abundance and brood parasitism rates of Savannah sparrow ( Passerculus sandwichensis ) nests in relation to the presence of infrastructure features and proximity to potential perches and edge habitat. The presence of oil and natural gas infrastructure increased brown-headed cowbird relative abundance by a magnitude of four times, which resulted in four times greater brood parasitism rates at infrastructure sites. While the presence of infrastructure and the proximity to roads were influential in predicting brood parasitism rates, the proximity of perch sites was not. This suggests that brood parasitism associated with oil and natural gas infrastructure may result in additional pressures that reduce productivity of this declining grassland songbird.

Staphylococcus aureus RNAIII binds to two distant regions of coa mRNA to arrest translation and promote mRNA degradation.

Directory of Open Access Journals (Sweden)

Clément Chevalier

2010-03-01

Full Text Available Staphylococcus aureus RNAIII is the intracellular effector of the quorum sensing system that temporally controls a large number of virulence factors including exoproteins and cell-wall-associated proteins. Staphylocoagulase is one major virulence factor, which promotes clotting of human plasma. Like the major cell surface protein A, the expression of staphylocoagulase is strongly repressed by the quorum sensing system at the post-exponential growth phase. Here we used a combination of approaches in vivo and in vitro to analyze the mechanism used by RNAIII to regulate the expression of staphylocoagulase. Our data show that RNAIII represses the synthesis of the protein through a direct binding with the mRNA. Structure mapping shows that two distant regions of RNAIII interact with coa mRNA and that the mRNA harbors a conserved signature as found in other RNAIII-target mRNAs. The resulting complex is composed of an imperfect duplex masking the Shine-Dalgarno sequence of coa mRNA and of a loop-loop interaction occurring downstream in the coding region. The imperfect duplex is sufficient to prevent the formation of the ribosomal initiation complex and to repress the expression of a reporter gene in vivo. In addition, the double-strand-specific endoribonuclease III cleaves the two regions of the mRNA bound to RNAIII that may contribute to the degradation of the repressed mRNA. This study validates another direct target of RNAIII that plays a role in virulence. It also illustrates the diversity of RNAIII-mRNA topologies and how these multiple RNAIII-mRNA interactions would mediate virulence regulation.

Utilizing individual fish biomass and relative abundance models to map environmental niche associations of adult and juvenile targeted fishes.

Science.gov (United States)

Galaiduk, Ronen; Radford, Ben T; Harvey, Euan S

2018-06-21

Many fishes undergo ontogenetic habitat shifts to meet their energy and resource needs as they grow. Habitat resource partitioning and patterns of habitat connectivity between conspecific fishes at different life-history stages is a significant knowledge gap. Species distribution models were used to examine patterns in the relative abundance, individual biomass estimates and environmental niche associations of different life stages of three iconic West Australian fishes. Continuous predictive maps describing the spatial distribution of abundance and individual biomass of the study species were created as well predictive hotspot maps that identify possible areas for aggregation of individuals of similar life stages of multiple species (i.e. spawning grounds, fisheries refugia or nursery areas). The models and maps indicate that processes driving the abundance patterns could be different from the body size associated demographic processes throughout an individual's life cycle. Incorporating life-history in the spatially explicit management plans can ensure that critical habitat of the vulnerable stages (e.g. juvenile fish, spawning stock) is included within proposed protected areas and can enhance connectivity between various functional areas (e.g. nursery areas and adult populations) which, in turn, can improve the abundance of targeted species as well as other fish species relying on healthy ecosystem functioning.

Reef Sharks Exhibit Site-Fidelity and Higher Relative Abundance in Marine Reserves on the Mesoamerican Barrier Reef

Science.gov (United States)

Bond, Mark E.; Babcock, Elizabeth A.; Pikitch, Ellen K.; Abercrombie, Debra L.; Lamb, Norlan F.; Chapman, Demian D.

2012-01-01

Carcharhinid sharks can make up a large fraction of the top predators inhabiting tropical marine ecosystems and have declined in many regions due to intense fishing pressure. There is some support for the hypothesis that carcharhinid species that complete their life-cycle within coral reef ecosystems, hereafter referred to as “reef sharks”, are more abundant inside no-take marine reserves due to a reduction in fishing pressure (i.e., they benefit from marine reserves). Key predictions of this hypothesis are that (a) individual reef sharks exhibit high site-fidelity to these protected areas and (b) their relative abundance will generally be higher in these areas compared to fished reefs. To test this hypothesis for the first time in Caribbean coral reef ecosystems we combined acoustic monitoring and baited remote underwater video (BRUV) surveys to measure reef shark site-fidelity and relative abundance, respectively. We focused on the Caribbean reef shark (Carcharhinus perezi), the most common reef shark in the Western Atlantic, at Glover's Reef Marine Reserve (GRMR), Belize. Acoustically tagged sharks (N = 34) were detected throughout the year at this location and exhibited strong site-fidelity. Shark presence or absence on 200 BRUVs deployed at GRMR and three other sites (another reserve site and two fished reefs) showed that the factor “marine reserve” had a significant positive effect on reef shark presence. We rejected environmental factors or site-environment interactions as predominant drivers of this pattern. These results are consistent with the hypothesis that marine reserves can benefit reef shark populations and we suggest new hypotheses to determine the underlying mechanism(s) involved: reduced fishing mortality or enhanced prey availability. PMID:22412965

The effect of tissue decalcification on mRNA retention within bone for in-situ hybridization studies.

Science.gov (United States)

Walsh, L; Freemont, A J; Hoyland, J A

1993-06-01

Tissue decalcification is a routine part of the preparation of bone tissue for histological studies. Although in-situ hybridization has been employed to localize mRNA of collagenous and non-collagenous bone related proteins in skeletal tissue, little is known regarding the effects of decalcifying agents on mRNA retention within tissue. In this study in-situ hybridization using an oligonucleotide probe (i.e. a poly d(T) probe) to detect total messenger RNA has been employed to investigate the effects of the decalcifying agents nitric acid, formic acid and EDTA on mRNA retention compared to undeacalcified tissue. The results show that formalin fixation and EDTA decalcification preserve substantial amounts of mRNA within the tissue. In particular, this study illustrates that it is possible to perform in-situ hybridization on formalin fixed decalcified paraffin embedded tissue.

The ubiquitin ligase SEVEN IN ABSENTIA (SINA) ubiquitinates a defense-related NAC transcription factor and is involved in defense signaling.

Science.gov (United States)

Miao, Min; Niu, Xiangli; Kud, Joanna; Du, Xinran; Avila, Julian; Devarenne, Timothy P; Kuhl, Joseph C; Liu, Yongsheng; Xiao, Fangming

2016-07-01

We recently identified a defense-related tomato (Solanum lycopersicum) NAC (NAM, ATAF1,2, CUC2) transcription factor, NAC1, that is subjected to ubiquitin-proteasome system-dependent degradation in plant cells. In this study, we identified a tomato ubiquitin ligase (termed SEVEN IN ABSENTIA3; SINA3) that ubiquitinates NAC1, promoting its degradation. We conducted coimmunoprecipitation and bimolecular fluorescence complementation to determine that SINA3 specifically interacts with the NAC1 transcription factor in the nucleus. Moreover, we found that SINA3 ubiquitinates NAC1 in vitro and promotes NAC1 degradation via polyubiquitination in vivo, indicating that SINA3 is a ubiquitin ligase that ubiquitinates NAC1, promoting its degradation. Our real-time PCR analysis indicated that, in contrast to our previous finding that NAC1 mRNA abundance increases upon Pseudomonas infection, the SINA3 mRNA abundance decreases in response to Pseudomonas infection. Moreover, using Agrobacterium-mediated transient expression, we found that overexpression of SINA3 interferes with the hypersensitive response cell death triggered by multiple plant resistance proteins. These results suggest that SINA3 ubiquitinates a defense-related NAC transcription factor for degradation and plays a negative role in defense signaling. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

PAX5О± and PAX5ОІ mRNA expression in breast Cancer: Relation ...

African Journals Online (AJOL)

Manal Basyouni Ahmed

mRNA expression of PAX5a and PAX5b in breast cancer and assessing their underlying pathological roles through ... the molecular alterations that contribute to disease initiation and ... ring growth and survival of cancer cells [3]. PAX5 is ..... and CA15-3 are prognostic parameters for different molecular subtypes of · breast ...

Measurements of periods, relative abundances and absolute yields of delayed neutrons from fast neutron induced fission of {sup 237}Np

Energy Technology Data Exchange (ETDEWEB)

Piksaikine, V. [Institute of Physics and Power Engineering, Obninsk (Russian Federation)

1997-03-01

The experimental method for measurements of the delayed neutron yields and period is presented. The preliminary results of the total yield, relative abundances and periods are shown comparing with the previously reported values. (J.P.N.)

BOND: A quantum of solace for nebular abundance determinations

Science.gov (United States)

Vale Asari, N.; Stasińska, G.; Morisset, C.; Cid Fernandes, R.

2017-11-01

The abundances of chemical elements other than hydrogen and helium in a galaxy are the fossil record of its star formation history. Empirical relations such as mass-metallicity relation are thus seen as guides for studies on the history and chemical evolution of galaxies. Those relations usually rely on nebular metallicities measured with strong-line methods, which assume that H II regions are a one- (or at most two-) parameter family where the oxygen abundance is the driving quantity. Nature is however much more complex than that, and metallicities from strong lines may be strongly biased. We have developed the method BOND (Bayesian Oxygen and Nitrogen abundance Determinations) to simultaneously derive oxygen and nitrogen abundances in giant H II regions by comparing strong and semi-strong observed emission lines to a carefully-defined, finely-meshed grid of photoionization models. Our code and results are public and available at http://bond.ufsc.br.

Effects of branched-chain volatile fatty acids on lactation performance and mRNA expression of genes related to fatty acid synthesis in mammary gland of dairy cows.

Science.gov (United States)

Liu, Q; Wang, C; Guo, G; Huo, W J; Zhang, S L; Pei, C X; Zhang, Y L; Wang, H

2018-02-12

Branched-chain volatile fatty acids (BCVFA) supplements could promote lactation performance and milk quality by improving ruminal fermentation and milk fatty acid synthesis. This study was conducted to evaluate the effects of BCVFA supplementation on milk performance, ruminal fermentation, nutrient digestibility and mRNA expression of genes related to fatty acid synthesis in mammary gland of dairy cows. A total of 36 multiparous Chinese Holstein cows averaging 606±4.7 kg of BW, 65±5.2 day in milk (DIM) with daily milk production of 30.6±0.72 kg were assigned to one of four groups blocked by lactation number, milk yield and DIM. The treatments were control, low-BCVFA (LBCVFA), medium-BCVFA (MBCVFA) and high-BCVFA (HBCVFA) with 0, 30, 60 and 90 g BCVFA per cow per day, respectively. Experimental periods were 105 days with 15 days of adaptation and 90 days of data collection. Dry matter (DM) intake tended to increase, but BW changes were similar among treatments. Yields of actual milk, 4% fat corrected milk, milk fat and true protein linearly increased, but feed conversion ratio (FCR) linearly decreased with increasing BCVFA supplementation. Milk fat content linearly increased, but true protein content tended to increase. Contents of C4:0, C6:0, C8:0, C10:0, C12:0, C14:0 and C15:0 fatty acids in milk fat linearly increased, whereas other fatty acids were not affected with increasing BCVFA supplementation. Ruminal pH, ammonia N concentration and propionate molar proportion linearly decreased, but total VFA production and molar proportions of acetate and butyrate linearly increased with increasing BCVFA supplementation. Consequently, acetate to propionate ratios linearly increased. Digestibilities of DM, organic matter, CP, NDF and ADF also linearly increased. In addition, mRNA expressions of peroxisome proliferator-activated receptor γ, sterol regulatory element-binding factor 1 and fatty acid-binding protein 3 linearly increased, mRNA expressions of acetyl

Pressure overload stimulated cardiac hypertrophy leads to a rapid decrease in the mRNA for creatine kinase

International Nuclear Information System (INIS)

Boheler, K.; Popovich, B.; Dillmann, W.H.

1987-01-01

Cardiac hypertrophy (CH) leads to a decrease in creatine kinase (CK) enzymatic activity. To determine if the mRNA for CK also decreases with CH, they performed the following studies. Cardiac RNA was isolated from rats subjected to either abdominal aortic stenosis (AS) or sham surgery. Through Northern blot analysis, total cardiac RNA was quantitated with a CK specific 32 P-labelled cDNA clone. At 3 and 8 days post-constriction, the mRNA for CK decreases by 54.6 +/- 7% and 65.3 +/- 18% respectively, whereas the heart weight increases by 19% and 37% relative to controls. Further studies indicate that CK mRNA also decreases by 41.8% in hypothyroid rats (Tx) but decreases by a total of 68.1% in Tx rats subjected to 8 days of AS. Pressure overload stimulated CH leads to a rapid decrease in CK mRNA in normal and Tx rats. This CK mRNA decrease may account for the decreased efficiency of contraction seen in CH

Direct method gas-phase oxygen abundances of four Lyman break analogs

Energy Technology Data Exchange (ETDEWEB)

Brown, Jonathan S.; Croxall, Kevin V.; Pogge, Richard W. [Department of Astronomy, The Ohio State University, Columbus, OH 43201 (United States)

2014-09-10

We measure the gas-phase oxygen abundances in four Lyman break analogs using auroral emission lines to derive direct abundances. The direct method oxygen abundances of these objects are generally consistent with the empirically derived strong-line method values, confirming that these objects are low oxygen abundance outliers from the mass-metallicity (MZ) relation defined by star forming Sloan Digital Sky Survey galaxies. We find slightly anomalous excitation conditions (Wolf-Rayet features) that could potentially bias the empirical estimates toward high values if caution is not exercised in the selection of the strong-line calibration. The high rate of star formation and low oxygen abundance of these objects is consistent with the predictions of the fundamental metallicity relation, in which the infall of relatively unenriched gas simultaneously triggers an episode of star formation and dilutes the interstellar medium of the host galaxy.

Visfatin mRNA expression in human subcutaneous adipose tissue is regulated by exercise

DEFF Research Database (Denmark)

Frydelund-Larsen, Lone; Åkerström, Thorbjörn; Nielsen, Søren

2006-01-01

in abdominal subcutaneous adipose tissue and skeletal muscle biopsies obtained from healthy young men at time points 0, 3, 4.5, 6, 9, and 24 h in relation to either 3 h of ergometer cycle exercise at 60% of Vo(2 max) or rest. Adipose tissue visfatin mRNA expression increased threefold at the time points 3, 4......Visfatin [pre-beta-cell colony-enhancing factor (PBEF)] is a novel adipokine that is produced by adipose tissue, skeletal muscle, and liver and has insulin-mimetic actions. Regular exercise enhances insulin sensitivity. In the present study, we therefore examined visfatin mRNA expression.......5, and 6 h in response to exercise (n = 8) compared with preexercise samples and compared with the resting control group (n = 7, P = 0.001). Visfatin mRNA expression in skeletal muscle was not influenced by exercise. The exercise-induced increase in adipose tissue visfatin was, however, not accompanied...

Abundance of thraustochytridsand bacteria in the equatorial Indian Ocean, in relation totransparent exopolymeric particles (TEPs)

Digital Repository Service at National Institute of Oceanography (India)

Damare, V.; Raghukumar, S.

Thraustochytrid protists are often abundant in coastal waters. However, their population dynamics and substrate preferences in the oceanic water column are poorly understood.We studied the abundance and distribution of thraustochytrids, bacteria...

Exercise training and work task induced metabolic and stress-related mRNA and protein responses in myalgic muscles

DEFF Research Database (Denmark)

Sjøgaard, Gisela; Zebis, Mette Kreutzfeldt; Kiilerich, Kristian

2013-01-01

healthy controls. Those with myalgia performed similar to 7 hrs repetitive stressful work and were subsequently randomized to 10 weeks of specific strength training, general fitness training, or reference intervention. Muscles biopsies were taken from the trapezius muscle at baseline, after work and after...... 10 weeks intervention. The main findings are that the capacity of carbohydrate oxidation was reduced in myalgic compared with healthy muscle. Repetitive stressful work increased mRNA content for heat shock proteins and decreased levels of key regulators for growth and oxidative metabolism......The aim was to assess mRNA and/or protein levels of heat shock proteins, cytokines, growth regulating, and metabolic proteins in myalgic muscle at rest and in response to work tasks and prolonged exercise training. A randomized controlled trial included 28 females with trapezius myalgia and 16...

Alternative splicing of human elastin mRNA indicated by sequence analysis of cloned genomic and complementary DNA

International Nuclear Information System (INIS)

Indik, Z.; Yeh, H.; Ornstein-goldstein, N.; Sheppard, P.; Anderson, N.; Rosenbloom, J.C.; Peltonen, L.; Rosenbloom, J.

1987-01-01

Poly(A) + RNA, isolated from a single 7-mo fetal human aorta, was used to synthesize cDNA by the RNase H method, and the cDNA was inserted into λgt10. Recombinant phage containing elastin sequences were identified by hybridization with cloned, exon-containing fragments of the human elastin gene. Three clones containing inserts of 3.3, 2.7, and 2.3 kilobases were selected for further analysis. Three overlapping clones containing 17.8 kilobases of the human elastin gene were also isolated from genomic libraries. Complete sequence analysis of the six clones demonstrated that: (i) the cDNA encompassed the entire translated portion of the mRNA encoding 786 amino acids, including several unusual hydrophilic amino acid sequences not previously identified in porcine tropoelastin, (ii) exons encoding either hydrophobic or crosslinking domains in the protein alternated in the gene, and (iii) a great abundance of Alu repetitive sequences occurred throughout the introns. The data also indicated substantial alternative splicing of the mRNA. These results suggest the potential for significant variation in the precise molecular structure of the elastic fiber in the human population

Expression of insulin-like growth factor I receptors at mRNA and protein levels during metamorphosis of Japanese flounder (Paralichthys olivaceus).

Science.gov (United States)

Zhang, Junling; Shi, Zhiyi; Cheng, Qi; Chen, Xiaowu

2011-08-01

Insulin-like growth factor I (IGF-I) is an important regulator of fish growth and development, and its biological actions are initiated by binding to IGF-I receptor (IGF-IR). Our previous study has revealed that IGF-I could play an important role during metamorphosis of Japanese flounder, Paralichthys olivaceus. The analysis of IGF-IR expression thus helps further elucidate the IGF-I regulation of metamorphic processes. In this study, the spatial-temporal expression of two distinct IGF-IR mRNAs was investigated by real-time RT-PCR. The spatial distribution of two IGF-IR mRNAs in adult tissues is largely overlapped, but they exhibit distinct temporal expression patterns during larval development. A remarkable decrease in IGF-IR-2 mRNA was detected during metamorphosis. In contrast, a significant increase in IGF-IR-1 mRNA was determined from pre-metamorphosis to metamorphic completion. These indicate that they may play different function roles during the flounder metamorphosis. The levels and localization of IGF-IR proteins during larval development were further studied by Western blotting and immunohistochemistry. Immunoreactive IGF-IRs were detected throughout larval development, and the IGF-IR proteins displayed a relatively abundant expression during metamorphosis. Moreover, the IGF-IR proteins appeared in key tissues, such as thickened skin beneath the migrating eye, developing intestine, gills and kidney during metamorphosis. These results further suggest that the IGF-I system may be involved in metamorphic development of Japanese flounder. Copyright © 2011 Elsevier Inc. All rights reserved.

Terrestrial salamander abundance on reclaimed mountaintop removal mines

Science.gov (United States)

Wood, Petra Bohall; Williams, Jennifer M.

2013-01-01

Mountaintop removal mining, a large-scale disturbance affecting vegetation, soil structure, and topography, converts landscapes from mature forests to extensive grassland and shrubland habitats. We sampled salamanders using drift-fence arrays and coverboard transects on and near mountaintop removal mines in southern West Virginia, USA, during 2000–2002. We compared terrestrial salamander relative abundance and species richness of un-mined, intact forest with habitats on reclaimed mountaintop removal mines (reclaimed grassland, reclaimed shrubland, and fragmented forest). Salamanders within forests increased in relative abundance with increasing distance from reclaimed mine edge. Reclaimed grassland and shrubland habitats had lower relative abundance and species richness than forests. Characteristics of reclaimed habitats that likely contributed to lower salamander abundance included poor soils (dry, compacted, little organic matter, high rock content), reduced vertical structure of vegetation and little tree cover, and low litter and woody debris cover. Past research has shown that salamander populations reduced by clearcutting may rebound in 15–24 years. Time since disturbance was 7–28 years in reclaimed habitats on our study areas and salamander populations had not reached levels found in adjacent mature forests.

Distribution and abundance of juvenile demersal fishes in relation to summer hypoxia and other environmental variables in coastal Oregon, USA

Science.gov (United States)

Sobocinski, Kathryn L.; Ciannelli, Lorenzo; Wakefield, W. Waldo; Yergey, Matthew E.; Johnson-Colegrove, Angela

2018-05-01

The juvenile demersal fish assemblage along the Pacific Northwest coast has received little attention relative to adult life history stages since pioneering work in the 1970s. Increasing severity of hypoxia along the Oregon coast in recent years has prompted investigations into the response of biota in this region. We used summer data (2008-2013) from a beam trawl survey targeting juvenile demersal fishes in soft-bottom habitats along the Oregon coast to describe patterns of distribution and abundance at fixed sampling stations (from 30 m to 100 m depth). We relate the assemblage and abundance of the common species to environmental variables and analyze condition of recently settled fish (improve our understanding of this community, especially in light of changing environmental drivers such as decreasing pH, warming water, and episodic periods of low dissolved oxygen coinciding with settlement for many species.

Long-term temporal and spatial changes in the richness and relative abundance of the inshore fish community of the British North Sea Coast

Science.gov (United States)

Henderson, Peter A.

2017-09-01

Changes in temporal and spatial composition of the British inshore North Sea fish community are reviewed. Sampling from the cooling water filter screens of power stations bordering the North Sea commenced in the early 1960s. To date, a total of 112 marine fish species have been recorded, a high proportion of the total inshore fish species complement of shallow North Sea British waters. The unrecorded top predators, such as large sharks, swordfish and tuna are not regularly observed in waters fish diversity and abundance in large industrialised estuaries such as the Thames and the Firth of Forth. Linked to spawning and nursery habitat gain, smelt, Osmerus eperlangus, and bass, Dicentrarchus labrax, have greatly increased in abundance. There is no evidence for a decline in species richness since the 1970s. However, elasmobranch species number has declined while two species Raja clavata and Scyliorhinus canicula have remained abundant and one, Mustelus asterias, has increased in abundance. It is argued that overexploitation and habitat destruction remain, as they have been for the last 300 years, the most serious threats to the health of North Sea inshore fish communities. There are no clear signs that climate change is causing species loss, although it may be influencing relative species abundance as species at the southern edge of their range such as the viviparous blenny, Zoarces viviparous, have declined in the southern British North Sea. Power station water temperature records do not show a warming trend, in some estuarine locations temperature has declined with reduced thermal pollution; the temperature record cannot explain the observed major changes in fish relative abundance observed since the 1970s.

NOAA ESRI Grid - predictions of relative seabird abundance in the New York offshore planning area made by the NOAA Biogeography Branch

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — This dataset represents relative seabird abundance predictions from spatial models developed for the New York offshore spatial planning area. This raster was derived...

Distribution and relative abundance of anchovies (Clupeiformes-engraulididae in the Sepetiba Bay, Rio de Janeiro, Brazil

Directory of Open Access Journals (Sweden)

Márcio de Araújo Silva

2000-01-01

Full Text Available Distribution and relative abundance of juvenile fish of the family Engraulididae in the Sepetiba Bay, Rio de Janeiro, Brazil was assessed to detect patterns of use of the shallows during their early life cycle. Two yearly cycle (March-1996 to February-1997 and March-1997 to February-1998 were studied by a total of 120 beach net samples at five sites, two of them located in the inner Bay and three in the outer Bay near to the sea limit. Six Engraulididae species were identified in two genera: Anchoa januaria, Anchoa marinii, Anchoa tricolor, Anchoa lyolepis, Anchoviella lepidentostole and Anchoviella brevirostris, mainly juveniles in their early life cycle. A. januaria, A. brevirostris, A. lepidentostole and A. tricolor, in decreasing order, were the top numerical abundant species, while A. tricolor and A. januaria showed the highest weight contribution, amounting approximately to 90% of the total number of fish. Spatially, A. tricolor, A. lyolepis and A. marinii distributed mainly in the outer Bay. A. januaria show higher abundance in the inner Bay, while the species of genera Anchoviella show an ample distribution, without a particular zone of higher occurrence. Seasonally, only A. januaria, A. lepidentostole and A. brevirostris presented a clear pattern of occurrence, peaking in the Autumn.A abundância relativa e distribuição espacial de juvenis de peixes da familia Engraulididae ocorrentes na Baía de Sepetiba, Rio de Janeiro, Brasil, foram estudadas visando determinar os padrões de uso da margem continental durante a fase inicial de vida. Dois ciclos anuais (Março-1996 a Fevereiro-1997 e Março-1997 a Fevereiro-1998 foram investigados através de um total de 120 amostragens de arrastos de praia, distribuídas em 5 locais de coleta na margem continental da Baía, duas delas situadas na zona mais interna e três na zona mais externa e próxima do limite com o mar. Foram identificados 6 espécies de Engraulididae, compreendendo dois g

LARP6 Meets Collagen mRNA: Specific Regulation of Type I Collagen Expression

Directory of Open Access Journals (Sweden)

Yujie Zhang

2016-03-01

Full Text Available Type I collagen is the most abundant structural protein in all vertebrates, but its constitutive rate of synthesis is low due to long half-life of the protein (60–70 days. However, several hundred fold increased production of type I collagen is often seen in reparative or reactive fibrosis. The mechanism which is responsible for this dramatic upregulation is complex, including multiple levels of regulation. However, posttranscriptional regulation evidently plays a predominant role. Posttranscriptional regulation comprises processing, transport, stabilization and translation of mRNAs and is executed by RNA binding proteins. There are about 800 RNA binding proteins, but only one, La ribonucleoprotein domain family member 6 (LARP6, is specifically involved in type I collagen regulation. In the 5′untranslated region (5’UTR of mRNAs encoding for type I and type III collagens there is an evolutionally conserved stem-loop (SL structure; this structure is not found in any other mRNA, including any other collagen mRNA. LARP6 binds to the 5′SL in sequence specific manner to regulate stability of collagen mRNAs and their translatability. Here, we will review current understanding of how is LARP6 involved in posttranscriptional regulation of collagen mRNAs. We will also discuss how other proteins recruited by LARP6, including nonmuscle myosin, vimentin, serine threonine kinase receptor associated protein (STRAP, 25 kD FK506 binding protein (FKBP25 and RNA helicase A (RHA, contribute to this process.

Elevation of D4 dopamine receptor mRNA in postmortem schizophrenic brain.

Science.gov (United States)

Stefanis, N C; Bresnick, J N; Kerwin, R W; Schofield, W N; McAllister, G

1998-01-01

The D4 dopamine (DA) receptor has been proposed to be a target for the development of a novel antipsychotic drug based on its pharmacological and distribution profile. There is much interest in whether D4 DA receptor levels are altered in schizophrenia, but the lack of an available receptor subtype-specific radioligand made this difficult to quantitate. In this study, we examined whether D4 mRNA levels are altered in different brain regions of schizophrenics compared to controls. Ribonuclease protection assays were carried out on total RNA samples isolated postmortem from frontal cortex and caudate brain regions of schizophrenics and matched controls. 32P-labelled RNA probes to the D4 DA receptor and to the housekeeping gene, glyceraldehyde-3-phosphate dehydrogenase (G3PDH), were hybridised with the RNA samples, digested with ribonucleases to remove unhybridised probe, and separated on 6% sequencing gels. Densitometer analysis on the subsequent autoradiogams was used to calculate the relative optical density of D4 mRNA compared to G3PDH mRNA. Statistical analysis of the data revealed a 3-fold higher level (P<0.011) of D4 mRNA in the frontal cortex of schizophrenics compared to controls. No increase was seen in caudate. D4 receptors could play a role in mediating dopaminergic activity in frontal cortex, an activity which may be malfunctioning in schizophrenia.

Abundance of introduced species at home predicts abundance away in herbaceous communities

Science.gov (United States)

Firn, Jennifer; Moore, Joslin L.; MacDougall, Andrew S.; Borer, Elizabeth T.; Seabloom, Eric W.; HilleRisLambers, Janneke; Harpole, W. Stanley; Cleland, Elsa E.; Brown, Cynthia S.; Knops, Johannes M.H.; Prober, Suzanne M.; Pyke, David A.; Farrell, Kelly A.; Bakker, John D.; O'Halloran, Lydia R.; Adler, Peter B.; Collins, Scott L.; D'Antonio, Carla M.; Crawley, Michael J.; Wolkovich, Elizabeth M.; La Pierre, Kimberly J.; Melbourne, Brett A.; Hautier, Yann; Morgan, John W.; Leakey, Andrew D.B.; Kay, Adam; McCulley, Rebecca; Davies, Kendi F.; Stevens, Carly J.; Chu, Cheng-Jin; Holl, Karen D.; Klein, Julia A.; Fay, Phillip A.; Hagenah, Nicole; Kirkman, Kevin P.; Buckley, Yvonne M.

2011-01-01

Many ecosystems worldwide are dominated by introduced plant species, leading to loss of biodiversity and ecosystem function. A common but rarely tested assumption is that these plants are more abundant in introduced vs. native communities, because ecological or evolutionary-based shifts in populations underlie invasion success. Here, data for 26 herbaceous species at 39 sites, within eight countries, revealed that species abundances were similar at native (home) and introduced (away) sites - grass species were generally abundant home and away, while forbs were low in abundance, but more abundant at home. Sites with six or more of these species had similar community abundance hierarchies, suggesting that suites of introduced species are assembling similarly on different continents. Overall, we found that substantial changes to populations are not necessarily a pre-condition for invasion success and that increases in species abundance are unusual. Instead, abundance at home predicts abundance away, a potentially useful additional criterion for biosecurity programmes.

Normalization and microbial differential abundance strategies depend upon data characteristics.

Science.gov (United States)

Weiss, Sophie; Xu, Zhenjiang Zech; Peddada, Shyamal; Amir, Amnon; Bittinger, Kyle; Gonzalez, Antonio; Lozupone, Catherine; Zaneveld, Jesse R; Vázquez-Baeza, Yoshiki; Birmingham, Amanda; Hyde, Embriette R; Knight, Rob

2017-03-03

Data from 16S ribosomal RNA (rRNA) amplicon sequencing present challenges to ecological and statistical interpretation. In particular, library sizes often vary over several ranges of magnitude, and the data contains many zeros. Although we are typically interested in comparing relative abundance of taxa in the ecosystem of two or more groups, we can only measure the taxon relative abundance in specimens obtained from the ecosystems. Because the comparison of taxon relative abundance in the specimen is not equivalent to the comparison of taxon relative abundance in the ecosystems, this presents a special challenge. Second, because the relative abundance of taxa in the specimen (as well as in the ecosystem) sum to 1, these are compositional data. Because the compositional data are constrained by the simplex (sum to 1) and are not unconstrained in the Euclidean space, many standard methods of analysis are not applicable. Here, we evaluate how these challenges impact the performance of existing normalization methods and differential abundance analyses. Effects on normalization: Most normalization methods enable successful clustering of samples according to biological origin when the groups differ substantially in their overall microbial composition. Rarefying more clearly clusters samples according to biological origin than other normalization techniques do for ordination metrics based on presence or absence. Alternate normalization measures are potentially vulnerable to artifacts due to library size. Effects on differential abundance testing: We build on a previous work to evaluate seven proposed statistical methods using rarefied as well as raw data. Our simulation studies suggest that the false discovery rates of many differential abundance-testing methods are not increased by rarefying itself, although of course rarefying results in a loss of sensitivity due to elimination of a portion of available data. For groups with large (~10×) differences in the average

mRNA expression of 5-hydroxytryptamine 1B, 1D, and 1F receptors and their role in controlling the release of calcitonin gene-related peptide in the rat trigeminovascular system

DEFF Research Database (Denmark)

Amrutkar, Dipak V; Ploug, Kenneth B; Hay-Schmidt, Anders

2012-01-01

Triptans, a family of 5-hydroxytryptamine (5-HT) 1B, 1D, and 1F receptor agonists, are used in the acute treatment of migraine attacks. The site of action and subtypes of the 5-HT(1) receptor that mediate the antimigraine effect have still to be identified. This study investigated the mRNA expres......Triptans, a family of 5-hydroxytryptamine (5-HT) 1B, 1D, and 1F receptor agonists, are used in the acute treatment of migraine attacks. The site of action and subtypes of the 5-HT(1) receptor that mediate the antimigraine effect have still to be identified. This study investigated the m......RNA expression of these receptors and the role of 5-HT(1) receptor subtypes in controlling the release of calcitonin gene-related peptide (CGRP) in rat dura mater, trigeminal ganglion (TG), and trigeminal nucleus caudalis (TNC). The mRNA for each receptor subtype was quantified by quantitative real...

Comparing relative abundance, lengths, and habitat of temperate reef fishes using simultaneous underwater visual census, video, and trap sampling

KAUST Repository

Bacheler, NM

2017-04-28

Unbiased counts of individuals or species are often impossible given the prevalence of cryptic or mobile species. We used 77 simultaneous multi-gear deployments to make inferences about relative abundance, diversity, length composition, and habitat of the reef fish community along the southeastern US Atlantic coast. In total, 117 taxa were observed by underwater visual census (UVC), stationary video, and chevron fish traps, with more taxa being observed by UVC (100) than video (82) or traps (20). Frequency of occurrence of focal species was similar among all sampling approaches for tomtate Haemulon aurolineatum and black sea bass Centropristis striata, higher for UVC and video compared to traps for red snapper Lutjanus campechanus, vermilion snapper Rhomboplites aurorubens, and gray triggerfish Balistes capriscus, and higher for UVC compared to video or traps for gray snapper L. griseus and lionfish Pterois spp. For 6 of 7 focal species, correlations of relative abundance among gears were strongest between UVC and video, but there was substantial variability among species. The number of recorded species between UVC and video was correlated (ρ = 0.59), but relationships between traps and the other 2 methods were weaker. Lengths of fish visually estimated by UVC were similar to lengths of fish caught in traps, as were habitat characterizations from UVC and video. No gear provided a complete census for any species in our study, suggesting that analytical methods accounting for imperfect detection are necessary to make unbiased inferences about fish abundance.

Expression of feeding-related peptide receptors mRNA in GT1-7 cell line and roles of leptin and orexins in control of GnRH secretion.

Science.gov (United States)

Yang, Ying; Zhou, Li-bin; Liu, Shang-quan; Tang, Jing-feng; Li, Feng-yin; Li, Rong-ying; Song, Huai-dong; Chen, Ming-dao

2005-08-01

To investigate the expression of feeding-related peptide receptors mRNA in GT1-7 cell line and roles of leptin and orexins in the control of GnRH secretion. Receptors of bombesin3, cholecystokinin (CCK)-A, CCK-B, glucagon-like peptide (GLP)1, melanin-concentrating hormone (MCH)1, orexin1, orexin2, neuromedin-B, neuropeptide Y (NPY)1 and NPY5, neurotensin (NT)1, NT2, NT3, and leptin receptor long form mRNA in GT1-7 cells were detected by reversed transcriptase-polymerase chain reaction. GT1-7 cells were treated with leptin, orexin A and orexin B at a cohort of concentrations for different lengths of time, and GnRH in medium was determined by radioimmunoassay (RIA). Receptors of bombesin 3, CCK-B, GLP1, MCH1, orexin1, neuromedin-B, NPY1, NPY5, NT1, NT3, and leptin receptor long form mRNA were expressed in GT1-7 cells, of which, receptors of GLP1, neuromedin-B, NPY1, and NT3 were highly expressed. No amplified fragments of orexin2, NT2, and CCK-A receptor cDNA were generated with GT1-7 RNA, indicating that the GT1-7 cells did not express mRNA of them. Leptin induced a significant stimulation of GnRH release, the results being most significant at 0.1 nmol/L for 15 min. In contrast to other studies in hypothalamic explants, neither orexin A nor orexin B affected basal GnRH secretion over a wide range of concentrations ranging from 1 nmol/L to 500 nmol/Lat 15, 30, and 60 min. Feeding and reproductive function are closely linked. Many orexigenic and anorexigenic signals may control feeding behavior as well as alter GnRH secretion through their receptors on GnRH neurons.

Changes in androgen receptor mRNA expression in the forebrain and oviduct during the reproductive cycle of female leopard geckos, Eublepharis macularius.

Science.gov (United States)

Rhen, Turk; Sakata, Jon T; Woolley, Sarah; Porter, Raymond; Crews, David

2003-06-01

Successful reproduction requires the coordination of reproductive physiology with behavior. The neural correlates of reproductive behavior have been elucidated in a variety of amphibians, mammals, and birds but relatively few studies have examined reptiles. Here we investigate differences in androgen receptor (AR) mRNA expression in the forebrain and oviduct between previtellogenic and late vitellogenic female leopard geckos, Eublepharis macularius. Plasma concentrations of testosterone (T) are low when females are previtellogenic and sexually unreceptive but increase dramatically during late vitellogenesis when females are receptive. In addition, receptivity can be induced by treatment with exogenous T. The relative abundance of AR-mRNA across various nuclei was greater in late vitellogenic than in previtellogenic females. This general pattern was observed in the medial preoptic area, anterior hypothalamus, external nucleus of the amygdala, dorsolateral aspect of the ventromedial hypothalamus, lateral septum, and periventricular hypothalamus. There were also clear differences in AR-mRNA expression among these nuclei. The pattern of gene expression observed in the brain was reversed within stromal cells of the oviduct where expression of AR-mRNA decreased from the previtellogenic stage to the late vitellogenic stage. Overall, these data demonstrate that T concentration in the plasma, abundance of AR-mRNA in the brain and oviduct, and sexual behavior change coordinately during the reproductive cycle of female leopard geckos. Although the function of AR in the female leopard gecko is not yet clear, our results are in accord with growing evidence that androgens regulate numerous aspects of female physiology and behavior in vertebrates.

mRNA processing in yeast

International Nuclear Information System (INIS)

Stevens, A.

1982-01-01

Investigations in this laboratory center on basic enzymatic reactions of RNA. Still undefined are reactions involved in the conversion of precursors of mRA (pre-mRNA) to mRNA in eukaryotes. The pre-mRNA is called heterogeneous nuclear RNA and is 2 to 6 times larger than mRNA. The conversion, called splicing, involves a removal of internal sequences called introns by endoribonuclease action followed by a rejoining of the 3'- and 5'-end fragments, called exons, by ligating activity. It has not been possible yet to study the enzymes involved in vitro. Also undefined are reactions involved in the turnover or discarding of certain of the pre-mRNA molecules. Yeast is a simple eukaryote and may be expected to have the same, but perhaps simpler, processing reactions as the higher eukaryotes. Two enzymes involved in the processing of pre-mRNA and mRNA in yeast are under investigation. Both enzymes have been partially purified from ribonucleoprotein particles of yeast. The first is a unique decapping enzyme which cleaves [ 3 H]m 7 Gppp [ 14 C]RNA-poly (A) of yeast, yielding [ 3 H]m 7 GDP and is suggested by the finding that the diphosphate product, m 7 GpppA(G), and UDP-glucose are not hydrolyzed. The second enzyme is an endoribonuclease which converts both the [ 3 H] and [ 14 C] labels of [ 3 H]m 7 Gppp[ 14 C]RNA-poly(A) from an oligo(dT)-cellulose bound form to an unbound, acid-insoluble form. Results show that the stimulation involves an interaction of the labeled RNA with the small nuclear RNA. The inhibition of the enzyme by ethidium bromide and its stimulation by small nuclear RNA suggest that it may be a processing ribonuclease, requiring specific double-stranded features in its substrate. The characterization of the unique decapping enzyme and endoribonuclease may help to understand reactions involved in the processing of pre-mRNA and mRNA in eukaryotes

A nondestructive technique to monitor the relative abundance of terrestrial salamanders

Science.gov (United States)

Richard M. DeGraaf; Mariko. Yamasaki

1992-01-01

Salamanders are abundant vertebrates in many forest ecosystems, and their annual biomass production can be important in forest food webs (Pough et al. 1987). Population densities of eastern redback salamanders (Plethodon cinereus) can exceed 2 individuals/m2 in deciduous forests of the United States (Heatwole 1962, Jaeger 1980...

Nitrogen abundance in Comet Halley

International Nuclear Information System (INIS)

Wyckoff, S.; Tegler, S.C.; Engel, L.

1991-01-01

Data on the nitrogen-containing compounds that observed spectroscopically in the coma of Comet Halley are summarized, and the elemental abundance of nitrogen in the Comet Halley nucleus is derived. It is found that 90 percent of elemental nitrogen is in the dust fraction of the coma, while in the gas fraction, most of the nitrogen is contained in NH3 and CN. The elemental nitrogen abundance in the ice component of the nucleus was found to be deficient by a factor of about 75, relative to the solar photosphere, indicating that the chemical partitioning of N2 into NH3 and other nitrogen compounds during the evolution of the solar nebula cannot account completely for the low abundance ratio N2/NH3 = 0.1, observed in the comet. It is suggested that the low N2/NH3 ratio in Comet Halley may be explained simply by physical fractionation and/or thermal diffusion. 88 refs

Endurance exercise induces mRNA expression of oxidative enzymes in human skeletal muscle late in recovery

DEFF Research Database (Denmark)

Leick, Lotte; Plomgaard, Peter S.; Grønløkke, L.

2010-01-01

exercise. To test the hypothesis that mRNA expression of many oxidative enzymes is up-regulated late in recovery (10-24 h) after exercise, male subjects (n=8) performed a 90-min cycling exercise (70% VO(2-max)), with muscle biopsies obtained before exercise (pre), and after 10, 18 and 24 h of recovery....... The mRNA expression of carnitine-palmitoyltransferase (CPT)I, CD36, 3-hydroxyacyl-CoA-dehydrogenase (HAD), cytochrome (Cyt)c, aminolevulinate-delta-synthase (ALAS)1 and GLUT4 was 100-200% higher at 10-24 h of recovery from exercise than in a control trial. Exercise induced a 100-300% increase...... in peroxisome proliferator-activated receptor gamma co-activator (PGC)-1alpha, citrate synthase (CS), CPTI, CD36, HAD and ALAS1 mRNA contents at 10-24 h of recovery relative to before exercise. No protein changes were detected in Cytc, ALAS1 or GLUT4. This shows that mRNA expression of several training...

Role of the mRNA export factor Sus1 in oxidative stress tolerance in Candida albicans.

Science.gov (United States)

Xiao, Chenpeng; Yu, Qilin; Zhang, Bing; Li, Jianrong; Zhang, Dan; Li, Mingchun

2018-02-05

In eukaryotes, the nuclear export of mRNAs is essential for gene expression. However, little is known about the role of mRNA nuclear export in the important fungal pathogen, Candida albicans. In this study, we identified C. albicans Sus1, a nucleus-localized protein that is required for mRNA export. Interestingly, the sus1Δ/Δ displayed hyper-sensitivity to extracellular oxidative stress, enhanced ROS accumulation and severe oxidative stress-related cell death. More strikingly, although the mutant exhibited normal activation of the expression of oxidative stress response (OSR) genes, it had attenuated activity of ROS scavenging system, which may be attributed to the defect in OSR mRNA export in this mutant. In addition, the virulence of the sus1Δ/Δ was seriously attenuated. Taken together, our findings provide evidence that the mRNA export factor Sus1 plays an important role in oxidative stress tolerance and pathogenesis. Copyright © 2018 Elsevier Inc. All rights reserved.

mRNA transfection of mouse and human neural stem cell cultures

OpenAIRE

McLenachan, Samuel; Zhang, D.; Palomo, A.B.; Edel, Michael John; Chen, F.K.

2013-01-01

The use of synthetic mRNA as an alternative gene delivery vector to traditional DNA-based constructs provides an effective method for inducing transient gene expression in cell cultures without genetic modification. Delivery of mRNA has been proposed as a safer alternative to viral vectors in the induction of pluripotent cells for regenerative therapies. Although mRNA transfection of fibroblasts, dendritic and embryonic stem cells has been described, mRNA delivery to neurosphere cultures has ...

Selective mRNA translation coordinates energetic and metabolic adjustments to cellular oxygen deprivation and reoxygenation in Arabidopsis thaliana.

Science.gov (United States)

Branco-Price, Cristina; Kaiser, Kayla A; Jang, Charles J H; Larive, Cynthia K; Bailey-Serres, Julia

2008-12-01

Cellular oxygen deprivation (hypoxia/anoxia) requires an acclimation response that enables survival during an energy crisis. To gain new insights into the processes that facilitate the endurance of transient oxygen deprivation, the dynamics of the mRNA translation state and metabolites were quantitatively monitored in Arabidopsis thaliana seedlings exposed to a short (2 h) or prolonged (9 h) period of oxygen and carbon dioxide deprivation and following 1 h of re-aeration. Hypoxia stress and reoxygenation promoted adjustments in the levels of polyribosomes (polysomes) that were highly coordinated with cellular ATP content. A quantitative comparison of steady-state and polysomal mRNA populations revealed that over half of the cellular mRNAs were restricted from polysome complexes during the stress, with little or no change in abundance. This selective repression of translation was rapidly reversed upon reoxygenation. Comparison of the adjustment in gene transcripts and metabolites demonstrated that profiling of polysomal mRNAs strongly augments the prediction of cellular processes that are altered during cellular oxygen deprivation. The selective translation of a subset of mRNAs promotes the conservation of ATP and facilitates the transition to anaerobic metabolism during low-oxygen stress.

A novel link between Sus1 and the cytoplasmic mRNA decay machinery suggests a broad role in mRNA metabolism

Directory of Open Access Journals (Sweden)

Llopis Ana

2010-03-01

Full Text Available Abstract Background Gene expression is achieved by the coordinated action of multiple factors to ensure a perfect synchrony from chromatin epigenetic regulation through to mRNA export. Sus1 is a conserved mRNA export/transcription factor and is a key player in coupling transcription initiation, elongation and mRNA export. In the nucleus, Sus1 is associated to the transcriptional co-activator SAGA and to the NPC associated complex termed TREX2/THSC. Through these associations, Sus1 mediates the nuclear dynamics of different gene loci and facilitate the export of the new transcripts. Results In this study, we have investigated whether the yeast Sus1 protein is linked to factors involved in mRNA degradation pathways. We provide evidence for genetic interactions between SUS1 and genes coding for components of P-bodies such as PAT1, LSM1, LSM6 and DHH1. We demonstrate that SUS1 deletion is synthetic lethal with 5'→3' decay machinery components LSM1 and PAT1 and has a strong genetic interaction with LSM6 and DHH1. Interestingly, Sus1 overexpression led to an accumulation of Sus1 in cytoplasmic granules, which can co-localise with components of P-bodies and stress granules. In addition, we have identified novel physical interactions between Sus1 and factors associated to P-bodies/stress granules. Finally, absence of LSM1 and PAT1 slightly promotes the Sus1-TREX2 association. Conclusions In this study, we found genetic and biochemical association between Sus1 and components responsible for cytoplasmic mRNA metabolism. Moreover, Sus1 accumulates in discrete cytoplasmic granules, which partially co-localise with P-bodies and stress granules under specific conditions. These interactions suggest a role for Sus1 in gene expression during cytoplasmic mRNA metabolism in addition to its nuclear function.

Pregalactic helium abundance and abundance gradients across our galaxy from planetary nebulae

Energy Technology Data Exchange (ETDEWEB)

D' Odorico, S; Peimbert, M [Universidad Nacional Autonoma de Mexico, Mexico City. Instituto de Astronomia; Sabbadin, F [Padua Univ. (Italy). Istituto di Astronomia

1976-03-01

From the observations of planetary nebulae by Peimbert and Torres-Peimbert we have studied the radial gradients across our galaxy of the helium, oxygen and nitrogen abundance relative to hydrogen. The increase of the oxygen to hydrogen abundance ratio from a radial distance to the galactic center of 14 to 8 kpc is about a factor of 3 while that of the nitrogen to hydrogen ratio is about twice as large. By adopting oxygen as representative of the heavy elements it is found that the helium enrichment is coupled to the heavy metal enrichment by ..delta..Y/..delta..Zapproximately2.9 in close agreement with the value derived from H II regions. The pregalactic N(He)/N(H) value derived from planetary nebulae is 0.073+-0.008 also in agreement with the value derived from H II regions.

The relative influence of prey abundance and co-breeders on the ...

African Journals Online (AJOL)

This study investigates if the reproductive performance of polyandrous Pale Chanting-goshawks, Melierax canorus, is governed by the abundance of dominant rodent-prey species or a co-breeding male participating fully in prey being delivered to the female and young. Polyandrous trios in prey-rich habitat, the only habitat ...

Differential decay of RNA of the CFA/I fimbrial operon and control of relative gene expression.

OpenAIRE

Jordi, B J; op den Camp, I E; de Haan, L A; van der Zeijst, B A; Gaastra, W

1993-01-01

CFA/I fimbriae on human enterotoxigenic Escherichia coli are composed of the CfaB protein, the product of the second gene of the CFA/I operon. We show here that CfaB is expressed at a higher level than other proteins of the CFA/I operon. mRNA encoding the CfaB protein is much more abundant than mRNA encoding CfaA, the first protein, together with CfaB or mRNA encoding CfaA only. Only one promoter, upstream of cfaA, is present. These data indicate that a primary transcript containing cfaA and ...

A promoter within the E6 ORF of human papillomavirus type 16 contributes to the expression of the E7 oncoprotein from a monocistronic mRNA

DEFF Research Database (Denmark)

Glahder, Jacob-Andreas Harald; Hansen, Christina N; Vinther, Jeppe

2003-01-01

RNA that encodes E7 as the first open reading frame (ORF) has been identified. We recently identified a transcription initiation site within the E6 ORF of HPV-16 at nt 542. In the present study we have characterized the P542 promoter, which putatively controls monocistronic expression of E7. The monocistronic m...... from nt 226 to 409. Furthermore, the translation initiation of E7 is most abundant from the monocistronic mRNA. We have also shown that the P542 promoter is downregulated by the transcription factor activator protein 4 (AP-4) and the differentiation-dependent factor hSkn-1a, both binding downstream...... of the transcription initiation site. In conclusion, we have found that P542 is a relatively weak promoter compared with P97 and may be downregulated in differentiated epithelial cells....

Stellar oxygen abundances. I - A resolution to the 7774 A O I abundance discrepancy

Science.gov (United States)

King, Jeremy R.

1993-09-01

We investigate the discrepancy between O/Fe abundance ratios of metal-poor stars derived from the 7774 A O I triplet and O/Fe ratios determined from other oxygen lines. We propose a possible resolution to this discrepancy which also eliminates the correlation of O/Fe and T(eff) found in a recent 7774 A O I analysis. The equivalent widths of Abia & Rebolo (1989) are found to be systematically too high by 25 percent. Arguments are presented that current temperature estimates for halo stars are 150-200 K too low. Using the guidance of both model atmospheres and other empirical color-T(eff) relations, we construct new color temperature relations for metal-poor stars. These relations are tied to the temperature scale of Saxner & Hammarback (1985) for metal-rich stars. We use (b-y) and (V-K) indices to redetermine values of T(eff) for a handful of halo stars. (B-V)-T(eff) relations which do not take into account the effects of metallicity are found to be inadequate. Revised O/Fe ratios are determined using the new temperature scale. The mean abundance ratio of the reanalyzed halo dwarfs is about +0.52. There is no trend of O/Fe with Fe/H or T(eff).

Gray whale distribution relative to benthic invertebrate biomass and abundance: Northeastern Chukchi Sea 2009-2012

Science.gov (United States)

Brower, Amelia A.; Ferguson, Megan C.; Schonberg, Susan V.; Jewett, Stephen C.; Clarke, Janet T.

2017-10-01

The shallow continental shelf waters of the Bering and Chukchi seas are the northernmost foraging grounds of North Pacific gray whales (Eschrichtius robustus). Benthic amphipods are considered the primary prey of gray whales in these waters, although no comprehensive quantitative analysis has been performed to support this assumption. Gray whale relative abundance, distribution, and behavior in the northeastern Chukchi Sea (69°-72°N, 155-169°W) were documented during aerial surveys in June-October 2009-2012. Concurrently, vessel-based benthic infaunal sampling was conducted in the area in July-August 2009-10, September 2011, and August 2012. Gray whales were seen in the study area each month that surveys were conducted, with the majority of whales feeding. Statistical analyses confirm that the highest densities of feeding gray whales were associated with high benthic amphipod abundance, primarily within 70 km of shore from Point Barrow to Icy Cape, in water whales were not seen in 40-km×40-km cells containing benthic sampling stations with 85 m-2 or fewer amphipods. Continuing broad-scale aerial surveys in the Chukchi Sea and prey sampling near feeding gray whales will be an important means to monitor and document ongoing and predicted ecosystem changes.

Clustering in the stellar abundance space

Science.gov (United States)

Boesso, R.; Rocha-Pinto, H. J.

2018-03-01

We have studied the chemical enrichment history of the interstellar medium through an analysis of the n-dimensional stellar abundance space. This work is a non-parametric analysis of the stellar chemical abundance space. The main goal is to study the stars from their organization within this abundance space. Within this space, we seek to find clusters (in a statistical sense), that is, stars likely to share similar chemo-evolutionary history, using two methods: the hierarchical clustering and the principal component analysis. We analysed some selected abundance surveys available in the literature. For each sample, we labelled the group of stars according to its average abundance curve. In all samples, we identify the existence of a main enrichment pattern of the stars, which we call chemical enrichment flow. This flow is set by the structured and well-defined mean rate at which the abundances of the interstellar medium increase, resulting from the mixture of the material ejected from the stars and stellar mass-loss and interstellar medium gas. One of the main results of our analysis is the identification of subgroups of stars with peculiar chemistry. These stars are situated in regions outside of the enrichment flow in the abundance space. These peculiar stars show a mismatch in the enrichment rate of a few elements, such as Mg, Si, Sc and V, when compared to the mean enrichment rate of the other elements of the same stars. We believe that the existence of these groups of stars with peculiar chemistry may be related to the accretion of planetary material on to stellar surfaces or may be due to production of the same chemical element by different nucleosynthetic sites.

Quantitation of TGF-beta1 mRNA in porcine mesangial cells by comparative kinetic RT/PCR: comparison with ribonuclease protection assay and in situ hybridization.

Science.gov (United States)

Ceol, M; Forino, M; Gambaro, G; Sauer, U; Schleicher, E D; D'Angelo, A; Anglani, F

2001-01-01

Gene expression can be examined with different techniques including ribonuclease protection assay (RPA), in situ hybridisation (ISH), and quantitative reverse transcription-polymerase chain reaction (RT/PCR). These methods differ considerably in their sensitivity and precision in detecting and quantifying low abundance mRNA. Although there is evidence that RT/PCR can be performed in a quantitative manner, the quantitative capacity of this method is generally underestimated. To demonstrate that the comparative kinetic RT/PCR strategy-which uses a housekeeping gene as internal standard-is a quantitative method to detect significant differences in mRNA levels between different samples, the inhibitory effect of heparin on phorbol 12-myristate 13-acetate (PMA)-induced-TGF-beta1 mRNA expression was evaluated by RT/PCR and RPA, the standard method of mRNA quantification, and the results were compared. The reproducibility of RT/PCR amplification was calculated by comparing the quantity of G3PDH and TGF-beta1 PCR products, generated during the exponential phases, estimated from two different RT/PCR (G3PDH, r = 0.968, P = 0.0000; TGF-beta1, r = 0.966, P = 0.0000). The quantitative capacity of comparative kinetic RT/PCR was demonstrated by comparing the results obtained from RPA and RT/PCR using linear regression analysis. Starting from the same RNA extraction, but using only 1% of the RNA for the RT/PCR compared to RPA, significant correlation was observed (r = 0.984, P = 0.0004). Moreover the morphometric analysis of ISH signal was applied for the semi-quantitative evaluation of the expression and localisation of TGF-beta1 mRNA in the entire cell population. Our results demonstrate the close similarity of the RT/PCR and RPA methods in giving quantitative information on mRNA expression and indicate the possibility to adopt the comparative kinetic RT/PCR as reliable quantitative method of mRNA analysis. Copyright 2001 Wiley-Liss, Inc.

Relative abundance of resident versus oceanic zooplankton over an interisland reef

International Nuclear Information System (INIS)

Alldredge, A.L.; King, J.M.

1979-01-01

Zooplankton were collected from various substrate types. Densities were determined and results indicated that demersal plankton were abundant on the Japtan reef flat. Behavioral mechanisms were exhibited by many organisms including swimming near the substrate or in the lees of coral heads. Demersal plankton may provide an important food source for nocturnally foraging fishes

Relative Abundance in Bacterial and Fungal Gut Microbes in Obese Children: A Case Control Study.

Science.gov (United States)

Borgo, Francesca; Verduci, Elvira; Riva, Alessandra; Lassandro, Carlotta; Riva, Enrica; Morace, Giulia; Borghi, Elisa

2017-02-01

Differences in relative proportions of gut microbial communities in adults have been correlated with intestinal diseases and obesity. In this study we evaluated the gut microbiota biodiversity, both bacterial and fungal, in obese and normal-weight school-aged children. We studied 28 obese (mean age 10.03 ± 0.68) and 33 age- and sex-matched normal-weight children. BMI z-scores were calculated, and the obesity condition was defined according to the WHO criteria. Fecal samples were analyzed by 16S rRNA amplification followed by denaturing gradient gel electrophoresis (DGGE) analysis and sequencing. Real-time polymerase chain reaction (PCR) was performed to quantify the most representative microbial species and genera. DGGE profiles showed high bacterial biodiversity without significant correlations with BMI z-score groups. Compared to bacterial profiles, we observed lower richness in yeast species. Sequence of the most representative bands gave back Eubacterium rectale, Saccharomyces cerevisiae, Candida albicans, and C. glabrata as present in all samples. Debaryomyces hansenii was present only in two obese children. Obese children revealed a significantly lower abundance in Akkermansia muciniphyla, Faecalibacterium prausnitzii, Bacteroides/Prevotella group, Candida spp., and Saccharomyces spp. (P = 0.031, P = 0.044, P = 0.003, P = 0.047, and P = 0.034, respectively). Taking into account the complexity of obesity, our data suggest that differences in relative abundance of some core microbial species, preexisting or diet driven, could actively be part of its etiology. This study improved our knowledge about the fungal population in the pediatric school-age population and highlighted the need to consider the influence of cross-kingdom relationships.

Consequences of metaphase II oocyte cryopreservation on mRNA content.

Science.gov (United States)

Chamayou, S; Bonaventura, G; Alecci, C; Tibullo, D; Di Raimondo, F; Guglielmino, A; Barcellona, M L

2011-04-01

We studied the consequences of freezing/thawing processes on mRNA contents in MII oocytes after slow-freezing/rapid thawing (SF/RT) and vitrification/warming (V/W) protocols, and compared the results to fresh MII oocytes. We quantified the nuclear transcript mRNA responsible for the translation of proteins belonging either to trans-regulatory protein family or to functional structural proteins such as proteins involved in DNA structural organization (NAP1L1, TOP1, H1F0H1), chromosomal structure maintenance (SMC, SCC3, RAD21, SMC1A, SMC1B, STAG3, REC8), mitochondrial energetic pathways (ATP5GJ, SDHC), cell cycle regulation and processes (CLTA, MAPK6, CKS2) and staminal cell potency-development competence stage (DPPA3, OCT4, FOXJ2). Surplus MII oocytes were donated from patients in IVF cycles and divided in three groups of 15 oocytes. Group 1 was comprised of non-cryopreserved oocytes and Groups 2 and 3 underwent SF/RT and V/W procedures, respectively. There was an overall decrease of mRNA extracted from cryopreserved oocytes compared to control group. Only 39.4% of mRNA content were preserved after SF/RT while 63.3% of mRNA content were maintained after V/W. Oocyte cryopreservation is associated with molecular injury associated with the decrease of stored mRNA. However the V/W protocol is more conservative than SF/RT resulting in a level of mRNA sufficient to maintain biologic functions in the subsequent fertilized oocyte. Copyright © 2011 Elsevier Inc. All rights reserved.

Long-term prairie falcon population changes in relation to prey abundance, weather, land uses, and habitat conditions

Science.gov (United States)

Steenhof, Karen; Kochert, Michael N.; Carpenter, L.B.; Lehman, Robert N.

1999-01-01

We studied a nesting population of Prairie Falcons (Falco mexicanus) in the Snake River Birds of Prey National Conservation Area (NCA) from 1974-1997 to identify factors that influence abundance and reproduction. Our sampling period included two major droughts and associated crashes in Townsend's ground squirrel (Spermophilus townsendii) populations. The number of Prairie Falcon pairs found on long-term survey segments declined significantly from 1976-1997. Early declines were most severe at the eastern end of the NCA, where fires and agriculture have changed native shrubsteppe habitat. More recent declines occurred in the portion of canyon near the Orchard Training Area (OTA), where the Idaho Army National Guard conducts artillery firing and tank maneuvers. Overall Prairie Falcon reproductive rates were tied closely to annual indexes of ground squirrel abundance, but precipitation before and during the breeding season was related inversely to some measures of reproduction. Most reproductive parameters showed no significant trends over time, but during the 1990s, nesting success and productivity were lower in the stretch of canyon near the OTA than in adjacent areas. Extensive shrub loss, by itself, did not explain the pattern of declines in abundance and reproduction that we observed. Recent military training activities likely have interacted with fire and livestock grazing to create less than favorable foraging opportunities for Prairie Falcons in a large part of the NCA. To maintain Prairie Falcon populations in the NCA, managers should suppress wildfires, restore native plant communities, and regulate potentially incompatible land uses.

The relative importance of kinetic mechanisms and variable enzyme abundances for the regulation of hepatic glucose metabolism--insights from mathematical modeling.

Science.gov (United States)

Bulik, Sascha; Holzhütter, Hermann-Georg; Berndt, Nikolaus

2016-03-02

Adaptation of the cellular metabolism to varying external conditions is brought about by regulated changes in the activity of enzymes and transporters. Hormone-dependent reversible enzyme phosphorylation and concentration changes of reactants and allosteric effectors are the major types of rapid kinetic enzyme regulation, whereas on longer time scales changes in protein abundance may also become operative. Here, we used a comprehensive mathematical model of the hepatic glucose metabolism of rat hepatocytes to decipher the relative importance of different regulatory modes and their mutual interdependencies in the hepatic control of plasma glucose homeostasis. Model simulations reveal significant differences in the capability of liver metabolism to counteract variations of plasma glucose in different physiological settings (starvation, ad libitum nutrient supply, diabetes). Changes in enzyme abundances adjust the metabolic output to the anticipated physiological demand but may turn into a regulatory disadvantage if sudden unexpected changes of the external conditions occur. Allosteric and hormonal control of enzyme activities allow the liver to assume a broad range of metabolic states and may even fully reverse flux changes resulting from changes of enzyme abundances alone. Metabolic control analysis reveals that control of the hepatic glucose metabolism is mainly exerted by enzymes alone, which are differently controlled by alterations in enzyme abundance, reversible phosphorylation, and allosteric effects. In hepatic glucose metabolism, regulation of enzyme activities by changes of reactants, allosteric effects, and reversible phosphorylation is equally important as changes in protein abundance of key regulatory enzymes.

Abundances and Habitat Sensitivities of Some River Fishes in ...

African Journals Online (AJOL)

Freshwater fishes from a diverse array of 11 families, some dominated by marine species and others containing only a few species, were collected by electrofishing from 84 locations on small rivers in central Thailand and their abundances related to habitat characteristics. Abundances were largest for Channa gachua, ...

Anorexigenic and Orexigenic Hormone Modulation of Mammalian Target of Rapamycin Complex 1 Activity and the Regulation of Hypothalamic Agouti-Related Protein mRNA Expression

Directory of Open Access Journals (Sweden)

Kenneth R. Watterson

2012-03-01

Full Text Available Activation of mammalian target of rapamycin 1 (mTORC1 by nutrients, insulin and leptin leads to appetite suppression (anorexia. Contrastingly, increased AMP-activated protein kinase (AMPK activity by ghrelin promotes appetite (orexia. However, the interplay between these mechanisms remains poorly defined. The relationship between the anorexigenic hormones, insulin and leptin, and the orexigenic hormone, ghrelin, on mTORC1 signalling was examined using S6 kinase phosphorylation as a marker for changes in mTORC1 activity in mouse hypothalamic GT1-7 cells. Additionally, the contribution of AMPK and mTORC1 signalling in relation to insulin-, leptin- and ghrelin-driven alterations to mouse hypothalamic agouti-related protein (AgRP mRNA levels was examined. Insulin and leptin increase mTORC1 activity in a phosphoinositide-3-kinase (PI3K- and protein kinase B (PKB-dependent manner, compared to vehicle controls, whereas increasing AMPK activity inhibits mTORC1 activity and blocks the actions of the anorexigenic hormones. Ghrelin mediates an AMPK-dependent decrease in mTORC1 activity and increases hypothalamic AgRP mRNA levels, the latter effect being prevented by insulin in an mTORC1-dependent manner. In conclusion, mTORC1 acts as an integration node in hypothalamic neurons for hormone-derived PI3K and AMPK signalling and mediates at least part of the assimilated output of anorexigenic and orexigenic hormone actions in the hypothalamus.

VDR mRNA overexpression is associated with worse prognostic factors in papillary thyroid carcinoma

Directory of Open Access Journals (Sweden)

June Young Choi

2017-03-01

Full Text Available The purpose of this study was to assess the relationship between vitamin D receptor gene (VDR expression and prognostic factors in papillary thyroid cancer (PTC. mRNA sequencing and somatic mutation data from The Cancer Genome Atlas (TCGA were analyzed. VDR mRNA expression was compared to clinicopathologic variables by linear regression. Tree-based classification was applied to find cutoff and patients were split into low and high VDR group. Logistic regression, Kaplan–Meier analysis, differentially expressed gene (DEG test and pathway analysis were performed to assess the differences between two VDR groups. VDR mRNA expression was elevated in PTC than that in normal thyroid tissue. VDR expressions were high in classic and tall-cell variant PTC and lateral neck node metastasis was present. High VDR group was also associated with classic and tall cell subtype, AJCC stage IV and lower recurrence-free survival. DEG test reveals that 545 genes were upregulated in high VDR group. Thyroid cancer-related pathways were enriched in high VDR group in pathway analyses. VDR mRNA overexpression was correlated with worse prognostic factors such as subtypes of papillary thyroid carcinoma that are known to be worse prognosis, lateral neck node metastasis, advanced stage and recurrence-free survival.

Aberrant Expression of TNF-α and TGF-β1 mRNA in Spontaneous Abortion

Institute of Scientific and Technical Information of China (English)

Ji-fen HU; Hong-chu BAO; Feng-chuan ZHU; Cai-ling YOU

2004-01-01

Objective To investigate the aberrant expressions of TNF-α and TGF-β1 in peripheral blood mononuclear cells (PBMCs) and placental tissues in patients with early spontaneous abortionMethods Using the technique of semi-quantitative reverse transcript-polymerase chain reaction (RT-PCR), TNF-α mRNA and TGF-β1 mRNA in PBMCs were measured in spontaneous abortion group (30 cases), normal pregnancy group (25 cases) and nonpregnant group (25 cases). The expressive intension of TNF-α protein and TGF-β1 protein in placental tissues was also identified by immunohistochemistry.Results Both levels of TNF-α mRNA and TGF-β1 mRNA expressed in PBMCs were significantly different between the three groups respectively (P＜0. 05). Levels of TNF-α in syncytiotrophoblastic and cytotrophoblastic cells of the two aborted groups were substantially higher than those of the non-pregnant group (P＜0. 01), but the levels of TGF-β1 in syncytiotrophoblastic cells of the two aborted groups were markedly lower than those of the non-pregnant group (P＜0. 01).Conclusion There is potential relation between TGF-β1 at the fetomaternal interface and spontaneous abortion. TGF-β1 may contribute to the maintenance of pregnancy,and low-level expression of TGF-β1 may be associated with pregnancy failure.

In human granulosa cells from small antral follicles, androgen receptor mRNA and androgen levels in follicular fluid correlate with FSH receptor mRNA

DEFF Research Database (Denmark)

Nielsen, M. E.; Rasmussen, I. A.; Kristensen, S. G.

2011-01-01

significantly with the expression of AMHRII, but did not correlate with any of the hormones in the follicular fluid. These data demonstrate an intimate association between AR expression in immature granulosa cells, and the expression of FSHR in normal small human antral follicles and between the follicular......Human small antral follicles (diameter 3-9 mm) were obtained from ovaries surgically removed for fertility preservation. From the individual aspirated follicles, granulosa cells and the corresponding follicular fluid were isolated in 64 follicles, of which 55 were available for mRNA analysis (24...... and to the follicular fluid concentrations of AMH, inhibin-B, progesterone and estradiol. AR mRNA expression in granulosa cells and the follicular fluid content of androgens both showed a highly significant positive association with the expression of FSHR mRNA in granulosa cells. AR mRNA expression also correlated...

Abundance, composition and distribution of simple sequence ...

Indian Academy of Sciences (India)

δ∗(W-29, W-70) = 1.25; δ∗(W-93, W-70 = 0.75)) even though they originate from different geographical regions. We can, therefore, infer that the WSSV sequences are closely related by ancestry. Table 3. Dinucleotide relative abundance in the ...

Yield in almond is related more to the abundance of flowers than the relative number of flowers that set fruit

Directory of Open Access Journals (Sweden)

Sergio Tombesi

2016-11-01

Full Text Available Almond tree yield is a function of the number of flowers on a tree and the percentage of flowers that set fruit. Almonds are borne on spurs (short proleptic shoots that can have both leaves and flowers. Almond tree spur dynamics research has documented that previous year spur leaf area is a predictive parameter for year-to-year spur survival, spur flowering and to a lesser extent spur fruiting, while previous year fruit bearing has a negative impact on subsequent year flowering. However, a question remained about whether yields are more dependent on flower numbers or relative fruit set of the flowers that are present. The aim of the present work was to compare the importance of flower abundance with that of relative fruit set in determining the productivity of a population of tagged spurs in almond trees over a 6-year period. Overall tree yield among years was more sensitive to total number of flowers on a tree rather than relative fruit set. These results emphasize the importance of maintaining large populations of healthy flowering spurs for sustained high production in almond orchards.

Tree hole mosquito species composition and relative abundances differ between urban and adjacent forest habitats in northwestern Argentina.

Science.gov (United States)

Mangudo, C; Aparicio, J P; Rossi, G C; Gleiser, R M

2018-04-01

Water-holding tree holes are main larval habitats for many pathogen vectors, especially mosquitoes (Diptera: Culicidae). Along 3 years, the diversity and composition of mosquito species in tree holes of two neighbouring but completely different environments, a city and its adjacent forest, were compared using generalized linear mixed models, PERMANOVA, SIMPER and species association indexes. The city area (Northwest Argentina) is highly relevant epidemiologically due to the presence of Aedes aegypti L. (main dengue vector) and occurrence of dengue outbreaks; the Yungas rainforests are highly biologically diverse. In total seven mosquito species were recorded, in descending order of abundance: Ae. aegypti, Haemagogus spegazzinii Brèthes, Sabethes purpureus (Theobald), Toxorhynchites guadeloupensis Dyar and Knab, Aedes terrens Walker, Haemagogus leucocelaenus Dyar & Shannon and Sabethes petrocchiae (Shannon and Del Ponte). The seven mosquito species were recorded in both city sites and forested areas; however, their mosquito communities significantly diverged because of marked differences in the frequency and relative abundance of some species: Tx. guadeloupensis and Ae. aegypti were significantly more abundant in forest and urban areas, respectively. Positive significant associations were detected between Ae. aegypti, Hg. spegazzinii and Hg. leucocelaenus. The combined presence of Ae. aegypti, Haemagogus and Sabethes in the area also highlight a potential risk of yellow fever epidemics. Overall results show an impoverished tree hole mosquito fauna in urban environments, reflecting negative effects of urbanization on mosquito diversity.

GeoChip-based insights into the microbial functional gene repertoire of marine sponges (high microbial abundance, low microbial abundance) and seawater

KAUST Repository

Bayer, Kristina

2015-01-08

The GeoChip 4.2 gene array was employed to interrogate the microbial functional gene repertoire of sponges and seawater collected from the Red Sea and the Mediterranean. Complementary amplicon sequencing confirmed the microbial community composition characteristic of high microbial abundance (HMA) and low microbial abundance (LMA) sponges. By use of GeoChip, altogether 20 273 probes encoding for 627 functional genes and representing 16 gene categories were identified. Minimum curvilinear embedding analyses revealed a clear separation between the samples. The HMA/LMA dichotomy was stronger than any possible geographic pattern, which is shown here for the first time on the level of functional genes. However, upon inspection of individual genes, very few specific differences were discernible. Differences were related to microbial ammonia oxidation, ammonification, and archaeal autotrophic carbon fixation (higher gene abundance in sponges over seawater) as well as denitrification and radiation-stress-related genes (lower gene abundance in sponges over seawater). Except for few documented specific differences the functional gene repertoire between the different sources appeared largely similar. This study expands previous reports in that functional gene convergence is not only reported between HMA and LMA sponges but also between sponges and seawater.

GeoChip-based insights into the microbial functional gene repertoire of marine sponges (high microbial abundance, low microbial abundance) and seawater

KAUST Repository

Bayer, Kristina; Moitinho-Silva, Lucas; Brü mmer, Franz; Cannistraci, Carlo V.; Ravasi, Timothy; Hentschel, Ute

2015-01-01

The GeoChip 4.2 gene array was employed to interrogate the microbial functional gene repertoire of sponges and seawater collected from the Red Sea and the Mediterranean. Complementary amplicon sequencing confirmed the microbial community composition characteristic of high microbial abundance (HMA) and low microbial abundance (LMA) sponges. By use of GeoChip, altogether 20 273 probes encoding for 627 functional genes and representing 16 gene categories were identified. Minimum curvilinear embedding analyses revealed a clear separation between the samples. The HMA/LMA dichotomy was stronger than any possible geographic pattern, which is shown here for the first time on the level of functional genes. However, upon inspection of individual genes, very few specific differences were discernible. Differences were related to microbial ammonia oxidation, ammonification, and archaeal autotrophic carbon fixation (higher gene abundance in sponges over seawater) as well as denitrification and radiation-stress-related genes (lower gene abundance in sponges over seawater). Except for few documented specific differences the functional gene repertoire between the different sources appeared largely similar. This study expands previous reports in that functional gene convergence is not only reported between HMA and LMA sponges but also between sponges and seawater.

When should we expect microbial phenotypic traits to predict microbial abundances?

Directory of Open Access Journals (Sweden)

Jeremy W. Fox

2012-08-01

Full Text Available Species’ phenotypic traits may predict their relative abundances. Intuitively, this is because locally-abundant species have traits making them well adapted to local abiotic and biotic conditions, while locally-rare species are not as well-adapted. But this intuition may not be valid. If competing species vary in how well-adapted they are to local conditions, why doesn’t the best-adapted species simply exclude the others entirely? But conversely, if species exhibit niche differences that allow them to coexist, then by definition there is no single best adapted species. Rather, demographic rates depend on species’ relative abundances, so that phenotypic traits conferring high adaptedness do not necessarily confer high abundance. I illustrate these points using a simple theoretical model incorporating adjustable levels of "adaptedness" and "niche differences". Even very small niche differences can weaken or even reverse the expected correlation between adaptive traits and abundance. Conversely, adaptive traits confer high abundance when niche differences are very strong. Future work should be directed towards understanding the link between phenotypic traits and frequency-dependence of demographic rates.

When should we expect microbial phenotypic traits to predict microbial abundances?

Science.gov (United States)

Fox, Jeremy W

2012-01-01

Species' phenotypic traits may predict their relative abundances. Intuitively, this is because locally abundant species have traits making them well-adapted to local abiotic and biotic conditions, while locally rare species are not as well-adapted. But this intuition may not be valid. If competing species vary in how well-adapted they are to local conditions, why doesn't the best-adapted species simply exclude the others entirely? But conversely, if species exhibit niche differences that allow them to coexist, then by definition there is no single best adapted species. Rather, demographic rates depend on species' relative abundances, so that phenotypic traits conferring high adaptedness do not necessarily confer high abundance. I illustrate these points using a simple theoretical model incorporating adjustable levels of "adaptedness" and "niche differences." Even very small niche differences can weaken or even reverse the expected correlation between adaptive traits and abundance. Conversely, adaptive traits confer high abundance when niche differences are very strong. Future work should be directed toward understanding the link between phenotypic traits and frequency-dependence of demographic rates.

Incorporating breeding abundance into spatial assignments on continuous surfaces.

Science.gov (United States)

Rushing, Clark S; Marra, Peter P; Studds, Colin E

2017-06-01

Determining the geographic connections between breeding and nonbreeding populations, termed migratory connectivity, is critical to advancing our understanding of the ecology and conservation of migratory species. Assignment models based on stable isotopes historically have been an important tool for studying migratory connectivity of small-bodied species, but the low resolution of these assignments has generated interest into combining isotopes with other sources in information. Abundance is one of the most appealing data sources to include in isotope-based assignments, but there are currently no statistical methods or guidelines for optimizing the contribution of stable isotopes and abundance for inferring migratory connectivity. Using known-origin stable-hydrogen isotope samples of six Neotropical migratory bird species, we rigorously assessed the performance of assignment models that differentially weight the contribution of the isotope and abundance data. For two species with adequate sample sizes, we used Pareto optimality to determine the set of models that simultaneously minimized both assignment error rate and assignment area. We then assessed the ability of the top models from these two species to improve assignments of the remaining four species compared to assignments based on isotopes alone. We show that the increased precision of models that include abundance is often offset by a large increase in assignment error. However, models that optimally weigh the abundance data relative to the isotope data can result in higher precision and, in some cases, lower error than models based on isotopes alone. The top models, however, depended on the distribution of relative breeding abundance, with patchier distributions requiring stronger downweighting of abundance, and we present general guidelines for future studies. These results confirm that breeding abundance can be an important source of information for studies investigating broad-scale movements of

Abundances of neon, sulfur, and argon in planetary nebulae

International Nuclear Information System (INIS)

Beck, S.C.; Lacy, J.H.; Townes, C.H.; Geballe, T.R.; Baas, F.

1981-01-01

Infrared observations of [Ne II], [S IV], and [Ar III] are used with optical observations to discuss the abundances of Ne, S, and Ar in 18 planetary nebulae. In addition, infrared observations of 18 other nebulae are presented. The derived abundances of S and Ar are each slightly enhanced relative to previous studies

Overexpression of Nitrate Reductase in Tobacco Delays Drought-Induced Decreases in Nitrate Reductase Activity and mRNA1

Science.gov (United States)

Ferrario-Méry, Sylvie; Valadier, Marie-Hélène; Foyer, Christine H.

1998-01-01

Transformed (cauliflower mosaic virus 35S promoter [35S]) tobacco (Nicotiana plumbaginifolia L.) plants constitutively expressing nitrate reductase (NR) and untransformed controls were subjected to drought for 5 d. Drought-induced changes in biomass accumulation and photosynthesis were comparable in both lines of plants. After 4 d of water deprivation, a large increase in the ratio of shoot dry weight to fresh weight was observed, together with a decrease in the rate of photosynthetic CO2 assimilation. Foliar sucrose increased in both lines during water stress, but hexoses increased only in leaves from untransformed controls. Foliar NO3− decreased rapidly in both lines and was halved within 2 d of the onset of water deprivation. Total foliar amino acids decreased in leaves of both lines following water deprivation. After 4 d of water deprivation no NR activity could be detected in leaves of untransformed plants, whereas about 50% of the original activity remained in the leaves of the 35S-NR transformants. NR mRNA was much more stable than NR activity. NR mRNA abundance increased in the leaves of the 35S-NR plants and remained constant in controls for the first 3 d of drought. On the 4th d, however, NR mRNA suddenly decreased in both lines. Rehydration at d 3 caused rapid recovery (within 24 h) of 35S-NR transcripts, but no recovery was observed in the controls. The phosphorylation state of the protein was unchanged by long-term drought. There was a strong correlation between maximal extractable NR activity and ambient photosynthesis in both lines. We conclude that drought first causes increased NR protein turnover and then accelerates NR mRNA turnover. Constitutive NR expression temporarily delayed drought-induced losses in NR activity. 35S-NR expression may therefore allow more rapid recovery of N assimilation following short-term water deficit. PMID:9576799

Differential Gene Expression Associated with Honey Bee Grooming Behavior in Response to Varroa Mites.

Science.gov (United States)

Hamiduzzaman, Mollah Md; Emsen, Berna; Hunt, Greg J; Subramanyam, Subhashree; Williams, Christie E; Tsuruda, Jennifer M; Guzman-Novoa, Ernesto

2017-05-01

Honey bee (Apis mellifera) grooming behavior is an important mechanism of resistance against the parasitic mite Varroa destructor. This research was conducted to study associations between grooming behavior and the expression of selected immune, neural, detoxification, developmental and health-related genes. Individual bees tested in a laboratory assay for various levels of grooming behavior in response to V. destructor were also analyzed for gene expression. Intense groomers (IG) were most efficient in that they needed significantly less time to start grooming and fewer grooming attempts to successfully remove mites from their bodies than did light groomers (LG). In addition, the relative abundance of the neurexin-1 mRNA, was significantly higher in IG than in LG, no groomers (NG) or control (bees without mite). The abundance of poly U binding factor kd 68 and cytochrome p450 mRNAs were significantly higher in IG than in control bees. The abundance of hymenoptaecin mRNA was significantly higher in IG than in NG, but it was not different from that of control bees. The abundance of vitellogenin mRNA was not changed by grooming activity. However, the abundance of blue cheese mRNA was significantly reduced in IG compared to LG or NG, but not to control bees. Efficient removal of mites by IG correlated with different gene expression patterns in bees. These results suggest that the level of grooming behavior may be related to the expression pattern of vital honey bee genes. Neurexin-1, in particular, might be useful as a bio-marker for behavioral traits in bees.

The implicit assumption of symmetry and the species abundance distribution

NARCIS (Netherlands)

Alonso, D.; Ostling, A.; Etienne, R.S.

2008-01-01

Species abundance distributions (SADs) have played a historical role in the development of community ecology. They summarize information about the number and the relative abundance of the species encountered in a sample from a given community. For years ecologists have developed theory to

The implicit assumption of symmetry and the species abundance distribution

NARCIS (Netherlands)

Alonso, David; Ostling, Annette; Etienne, Rampal S.

Species abundance distributions (SADs) have played a historical role in the development of community ecology. They summarize information about the number and the relative abundance of the species encountered in a sample from a given community. For years ecologists have developed theory to

Nuclear Imprisonment: Viral Strategies to Arrest Host mRNA Nuclear Export

Directory of Open Access Journals (Sweden)

Beatriz M. A. Fontoura

2013-07-01

Full Text Available Viruses possess many strategies to impair host cellular responses to infection. Nuclear export of host messenger RNAs (mRNA that encode antiviral factors is critical for antiviral protein production and control of viral infections. Several viruses have evolved sophisticated strategies to inhibit nuclear export of host mRNAs, including targeting mRNA export factors and nucleoporins to compromise their roles in nucleo-cytoplasmic trafficking of cellular mRNA. Here, we present a review of research focused on suppression of host mRNA nuclear export by viruses, including influenza A virus and vesicular stomatitis virus, and the impact of this viral suppression on host antiviral responses.

Nuclear Imprisonment: Viral Strategies to Arrest Host mRNA Nuclear Export

Science.gov (United States)

Kuss, Sharon K.; Mata, Miguel A.; Zhang, Liang; Fontoura, Beatriz M. A.

2013-01-01

Viruses possess many strategies to impair host cellular responses to infection. Nuclear export of host messenger RNAs (mRNA) that encode antiviral factors is critical for antiviral protein production and control of viral infections. Several viruses have evolved sophisticated strategies to inhibit nuclear export of host mRNAs, including targeting mRNA export factors and nucleoporins to compromise their roles in nucleo-cytoplasmic trafficking of cellular mRNA. Here, we present a review of research focused on suppression of host mRNA nuclear export by viruses, including influenza A virus and vesicular stomatitis virus, and the impact of this viral suppression on host antiviral responses. PMID:23872491

Relative Abundance of Carsonella ruddii (Gamma Proteobacterium) in Females and Males of Cacopsylla pyricola (Hemiptera: Psyllidae) and Bactericera cockerelli (Hemiptera: Triozidae)

Science.gov (United States)

Cooper, W. Rodney; Garczynski, Stephen F.; Horton, David R.

2015-01-01

Carsonella ruddii (Gamma Proteobacterium) is an obligate bacterial endosymbiont of psyllids that produces essential amino acids that are lacking in the insect’s diet. Accurate estimations of Carsonella populations are important to studies of Carsonella-psyllid interactions and to developing ways to target Carsonella for control of psyllid pests including pear psylla, Cacopsylla pyricola (Förster) (Hemiptera: Psyllidae) and potato psyllid, Bactericera cockerelli (Šulc) (Hemiptera: Triozidae). We used two methods, namely fluorescence in situ hybridization and quantitative polymerase chain reaction (qPCR), to estimate relative abundance of Carsonella in bacteriocytes and whole bodies of psyllids, respectively. Using these two methods, we compared Carsonella populations between female and male insects. Estimations using fluorescence in situ hybridization indicated that Carsonella was more abundant in bacteriocytes of female C. pyricola than in those of males, but Carsonella abundance in bacteriocytes did not differ between sexes of B. cockerelli. Analyses by qPCR using whole-body specimens indicated Carsonella was more abundant in females than in males of both psyllids. Neither fluorescence in situ hybridization nor qPCR indicated that Carsonella populations differed in abundance among adults of different ages (0–3 wk after adult eclosion). Using fluorescence in situ hybridization, Carsonella was observed in ovarioles of newly emerged females and formed an aggregation in the posterior end of mature oocytes. Results of our study indicate that female psyllids harbor greater populations of Carsonella than do males and that sex should be controlled for in studies which require estimations of Carsonella populations. PMID:26056318

Origin of the solar system s-process abundances

International Nuclear Information System (INIS)

Malaney, R.A.; Boothroyd, A.I.

1987-01-01

In the search for the origin of the solar system s-process abundances much attention has been focused on the intershell zones of thermally pulsing asymptotic giant branch (AGB) stars. It has recently been suggested that, relative to the poor fits obtained from intermediate-mass AGB models, low-mass AGB models may result in much better fits to the observed solar system abundances. This suggestion was motivated by the high intershell base temperatures indicated by recent low-mass AGB calculations. Using new data, presented for the peak intershell base temperature in such stars, the s-process enhancements occurring in the intershell zones of low-mass AGB stars are calculated. A nonsolar distribution of s-process abundances is reported for all realistic AGB models studied. Other possible astrophysical sites for the origin of the solar system s-process abundances are discussed. 35 references

Low-level lasers on microRNA and uncoupling protein 2 mRNA levels in human breast cancer cells

Science.gov (United States)

Canuto, K. S.; Teixeira, A. F.; Rodrigues, J. A.; Paoli, F.; Nogueira, E. M.; Mencalha, A. L.; Fonseca, A. S.

2017-06-01

MicroRNA is short non-coding RNA and is a mediator of post-transcriptional regulation of gene expression. In addition, uncoupling proteins (UCPs) regulate thermogenesis, metabolic and energy balance, and decrease reactive oxygen species production. Both microRNA and UCP2 expression can be altered in cancer cells. At low power, laser wavelength, frequency, fluence and emission mode deternube photobiological responses, which are the basis of low-level laser therapy. There are few studies on miRNA and UCP mRNA levels after low-level laser exposure on cancer cells. In this work, we evaluate the micrRNA (mir-106b and mir-15a) and UCP2 mRNA levels in human breast cancer cells exposed to low-level lasers. MDA-MB-231 human breast cancer cells were exposed to low-level red and infrared lasers, total RNA was extracted for cDNA synthesis and mRNA levels by real time quantitative polymerase chain reaction were evaluated. Data show that mir-106b and mir-15a relative levels are not altered, but UCP2 mRNA relative levels are increased in MDA-MB-231 human breast cancer cells exposed to low-level red and infrared lasers at fluences used in therapeutic protocols.

Accumulation of catechins in tea in relation to accumulation of mRNA from genes involved in catechin biosynthesis.

Science.gov (United States)

Eungwanichayapant, P D; Popluechai, S

2009-02-01

Catechins are a group of polyphenols found in tea (Camellia sinensis var. sinensis) at high levels. They are beneficial for health. From the study on accumulation of catechins in shoots and mature leaves of a tea cultivar, Oolong No. 17, using high-performance liquid chromatography (HPLC), it was found that the amounts of most catechins in the shoots were higher than those in the mature leaves, with an exception of catechins gallate (CG) that was found in trace amounts in both the shoots and mature leaves. mRNA accumulation of genes involved in catechin synthesis was studied using reverse transcriptase-polymerase chain reaction (RT-PCR). The results showed that the mRNA accumulation of the genes were higher in the shoots than in the mature leaves. These genes included genes of phenylalanine ammonia-lyase 1 (PAL1; EC 4.3.1.5), chalcone synthase (CHS; EC 2.3.1.74), dihydroflavonol 4-reductase (DFR; EC 1.1.1.219), leucoanthocyanidin reductase (LCR; EC 1.17.1.3), and flavanone 3-hydroxylase (F3H; EC 1.14.11.9).

Differential trypanosome surface coat regulation by a CCCH protein that co-associates with procyclin mRNA cis-elements.

Directory of Open Access Journals (Sweden)

Pegine Walrad

2009-02-01

Full Text Available The genome of Trypanosoma brucei is unusual in being regulated almost entirely at the post-transcriptional level. In terms of regulation, the best-studied genes are procyclins, which encode a family of major surface GPI-anchored glycoproteins (EP1, EP2, EP3, GPEET that show differential expression in the parasite's tsetse-fly vector. Although procyclin mRNA cis-regulatory sequences have provided the paradigm for post-transcriptional control in kinetoplastid parasites, trans-acting regulators of procyclin mRNAs are unidentified, despite intensive effort over 15 years. Here we identify the developmental regulator, TbZFP3, a CCCH-class predicted RNA binding protein, as an isoform-specific regulator of Procyclin surface coat expression in trypanosomes. We demonstrate (i that endogenous TbZFP3 shows sequence-specific co-precipitation of EP1 and GPEET, but not EP2 and EP3, procyclin mRNA isoforms, (ii that ectopic overexpression of TbZFP3 does not perturb the mRNA abundance of procyclin transcripts, but rather that (iii their protein expression is regulated in an isoform-specific manner, as evidenced by mass spectrometric analysis of the Procyclin expression signature in the transgenic cell lines. The TbZFP3 mRNA-protein complex (TbZFP3mRNP is identified as a trans-regulator of differential surface protein expression in trypanosomes. Moreover, its sequence-specific interactions with procyclin mRNAs are compatible with long-established predictions for Procyclin regulation. Combined with the known association of TbZFP3 with the translational apparatus, this study provides a long-sought missing link between surface protein cis-regulatory signals and the gene expression machinery in trypanosomes.

High Brain Ammonia Tolerance and Down-Regulation of Na+:K+:2Cl- Cotransporter 1b mRNA and Protein Expression in the Brain of the Swamp Eel, Monopterus albus, Exposed to Environmental Ammonia or Terrestrial Conditions

Science.gov (United States)

Ip, Yuen K.; Hou, Zhisheng; Chen, Xiu L.; Ong, Jasmine L. Y.; Chng, You R.; Ching, Biyun; Hiong, Kum C.; Chew, Shit F.

2013-01-01

Na+:K+:2Cl- cotransporter 1 (NKCC1) has been implicated in mediating ischemia-, trauma- or ammonia-induced astrocyte swelling/brain edema in mammals. This study aimed to determine the effects of ammonia or terrestrial exposure on ammonia concentrations in the plasma and brain, and the mRNA expression and protein abundance of nkcc/Nkcc in the brain, of the swamp eel Monopterus albus . Ammonia exposure led to a greater increase in the ammonia concentration in the brain of M. albus than terrestrial exposure. The brain ammonia concentration of M. albus reached 4.5 µmol g-1 and 2.7 µmol g-1 after 6 days of exposure to 50 mmol l-1 NH4Cl and terrestrial conditions, respectively. The full cDNA coding sequence of nkcc1b from M. albus brain comprised 3276 bp and coded for 1092 amino acids with an estimated molecular mass of 119.6 kDa. A molecular characterization indicated that it could be activated through phosphorylation and/or glycosylation by osmotic and/or oxidative stresses. Ammonia exposure for 1 day or 6 days led to significant decreases in the nkcc1b mRNA expression and Nkcc1b protein abundance in the brain of M. albus. In comparison, a significant decrease in nkcc1b mRNA expression was observed in the brain of M. albus only after 6 days of terrestrial exposure, but both 1 day and 6 days of terrestrial exposure resulted in significant decreases in the protein abundance of Nkcc1b. These results are novel because it has been established in mammals that ammonia up-regulates NKCC1 expression in astrocytes and NKCC1 plays an important role in ammonia-induced astrocyte swelling and brain edema. By contrast, our results indicate for the first time that M. albus is able to down-regulate the mRNA and protein expression of nkcc1b/Nkcc1b in the brain when confronted with ammonia toxicity, which could be one of the contributing factors to its extraordinarily high brain ammonia tolerance. PMID:24069137

Abundance of sea kraits correlates with precipitation.

Directory of Open Access Journals (Sweden)

Harvey B Lillywhite

Full Text Available Recent studies have shown that sea kraits (Laticauda spp.--amphibious sea snakes--dehydrate without a source of fresh water, drink only fresh water or very dilute brackish water, and have a spatial distribution of abundance that correlates with freshwater sites in Taiwan. The spatial distribution correlates with sites where there is a source of fresh water in addition to local precipitation. Here we report six years of longitudinal data on the abundance of sea kraits related to precipitation at sites where these snakes are normally abundant in the coastal waters of Lanyu (Orchid Island, Taiwan. The number of observed sea kraits varies from year-to-year and correlates positively with previous 6-mo cumulative rainfall, which serves as an inverse index of drought. Grouped data for snake counts indicate that mean abundance in wet years is nearly 3-fold greater than in dry years, and this difference is significant. These data corroborate previous findings and suggest that freshwater dependence influences the abundance or activity of sea kraits on both spatial and temporal scales. The increasing evidence for freshwater dependence in these and other marine species have important implications for the possible impact of climate change on sea snake distributions.

Aging alters mRNA expression of amyloid transporter genes at the blood-brain barrier.

Science.gov (United States)

Osgood, Doreen; Miller, Miles C; Messier, Arthur A; Gonzalez, Liliana; Silverberg, Gerald D

2017-09-01

Decreased clearance of potentially toxic metabolites, due to aging changes, likely plays a significant role in the accumulation of amyloid-beta (Aβ) peptides and other macromolecules in the brain of the elderly and in the patients with Alzheimer's disease (AD). Aging is the single most important risk factor for AD development. Aβ transport receptor proteins expressed at the blood-brain barrier are significantly altered with age: the efflux transporters lipoprotein receptor-related protein 1 and P-glycoprotein are reduced, whereas the influx transporter receptor for advanced glycation end products is increased. These receptors play an important role in maintaining brain biochemical homeostasis. We now report that, in a rat model of aging, gene transcription is altered in aging, as measured by Aβ receptor gene messenger RNA (mRNA) at 3, 6, 9, 12, 15, 20, 30, and 36 months. Gene mRNA expression from isolated cerebral microvessels was measured by quantitative polymerase chain reaction. Lipoprotein receptor-related protein 1 and P-glycoprotein mRNA were significantly reduced in aging, and receptor for advanced glycation end products was increased, in parallel with the changes seen in receptor protein expression. Transcriptional changes appear to play a role in aging alterations in blood-brain barrier receptor expression and Aβ accumulation. Copyright © 2017 Elsevier Inc. All rights reserved.

Maternal separation induces hippocampal changes in cadherin-1 (CDH-1) mRNA and recognition memory impairment in adolescent mice.

Science.gov (United States)

de Azeredo, Lucas Araújo; Wearick-Silva, Luis Eduardo; Viola, Thiago Wendt; Tractenberg, Saulo Gantes; Centeno-Silva, Anderson; Orso, Rodrigo; Schröder, Nadja; Bredy, Timothy William; Grassi-Oliveira, Rodrigo

2017-05-01

In rodents, disruption of mother-infant attachment induced by maternal separation (MS) is associated with recognition memory impairment and long-term neurobiological consequences. Particularly stress-induced modifications have been associated to disruption of cadherin (CDH) adhesion function, which plays an important role in remodeling of neuronal connection and synaptic plasticity. This study investigated the sex-dependent effect of MS on recognition memory and mRNA levels of classical type I and type II CDH and the related β -catenin (β -Cat) in the hippocampus and prefrontal cortex of late adolescent mice. We provided evidence that the BALB/c mice exposed to MS present deficit in recognition memory, especially females. Postnatal MS induced higher hippocampal CDH-2 and CDH-8 mRNA levels, as well as an upregulation of CDH-1 in the prefrontal cortex in both males and females. MS-reared female mice presented lower CDH-1 mRNA levels in the hippocampus. In addition, hippocampal CDH-1 mRNA levels were positively correlated with recognition memory performance in females. MS-reared male mice exhibited higher β -Cat mRNA levels in the hippocampus. Considering sex-specific effects on CDH mRNA levels, it has been demonstrated mRNA changes in CDH-1, β -Cat, and CDH-6 in the hippocampus, as well as CDH-1, CDH-8 and CDH-11 in the prefrontal cortex. Overall, these findings suggest a complex interplay among MS, CDH mRNA expression, and sex differences in the PFC and hippocampus of adolescent mice. Copyright © 2017 Elsevier Inc. All rights reserved.

Multiple correlation analyses revealed complex relationship between DNA methylation and mRNA expression in human peripheral blood mononuclear cells.

Science.gov (United States)

Xie, Fang-Fei; Deng, Fei-Yan; Wu, Long-Fei; Mo, Xing-Bo; Zhu, Hong; Wu, Jian; Guo, Yu-Fan; Zeng, Ke-Qin; Wang, Ming-Jun; Zhu, Xiao-Wei; Xia, Wei; Wang, Lan; He, Pei; Bing, Peng-Fei; Lu, Xin; Zhang, Yong-Hong; Lei, Shu-Feng

2018-01-01

DNA methylation is an important regulator on the mRNA expression. However, a genome-wide correlation pattern between DNA methylation and mRNA expression in human peripheral blood mononuclear cells (PBMCs) is largely unknown. The comprehensive relationship between mRNA and DNA methylation was explored by using four types of correlation analyses and a genome-wide methylation-mRNA expression quantitative trait locus (eQTL) analysis in PBMCs in 46 unrelated female subjects. An enrichment analysis was performed to detect biological function for the detected genes. Single pair correlation coefficient (r T1 ) between methylation level and mRNA is moderate (-0.63-0.62) in intensity, and the negative and positive correlations are nearly equal in quantity. Correlation analysis on each gene (T4) found 60.1% genes showed correlations between mRNA and gene-based methylation at P correlation (R T4  > 0.8). Methylation sites have regulation effects on mRNA expression in eQTL analysis, with more often observations in region of transcription start site (TSS). The genes under significant methylation regulation both in correlation analysis and eQTL analysis tend to cluster to the categories (e.g., transcription, translation, regulation of transcription) that are essential for maintaining the basic life activities of cells. Our findings indicated that DNA methylation has predictive regulation effect on mRNA with a very complex pattern in PBMCs. The results increased our understanding on correlation of methylation and mRNA and also provided useful clues for future epigenetic studies in exploring biological and disease-related regulatory mechanisms in PBMC.

Viperin mRNA is a novel target for the human RNase MRP/RNase P endoribonuclease.

Science.gov (United States)

Mattijssen, Sandy; Hinson, Ella R; Onnekink, Carla; Hermanns, Pia; Zabel, Bernhard; Cresswell, Peter; Pruijn, Ger J M

2011-07-01

RNase MRP is a conserved endoribonuclease, in humans consisting of a 267-nucleotide RNA associated with 7-10 proteins. Mutations in its RNA component lead to several autosomal recessive skeletal dysplasias, including cartilage-hair hypoplasia (CHH). Because the known substrates of mammalian RNase MRP, pre-ribosomal RNA, and RNA involved in mitochondrial DNA replication are not likely involved in CHH, we analyzed the effects of RNase MRP (and the structurally related RNase P) depletion on mRNAs using DNA microarrays. We confirmed the upregulation of the interferon-inducible viperin mRNA by RNAi experiments and this appeared to be independent of the interferon response. We detected two cleavage sites for RNase MRP/RNase P in the coding sequence of viperin mRNA. This is the first study providing direct evidence for the cleavage of a mRNA by RNase MRP/RNase P in human cells. Implications for the involvement in the pathophysiology of CHH are discussed.

LDL receptor-related protein 1 regulates the abundance of diverse cell-signaling proteins in the plasma membrane proteome.

Science.gov (United States)

Gaultier, Alban; Simon, Gabriel; Niessen, Sherry; Dix, Melissa; Takimoto, Shinako; Cravatt, Benjamin F; Gonias, Steven L

2010-12-03

LDL receptor-related protein 1 (LRP1) is an endocytic receptor, reported to regulate the abundance of other receptors in the plasma membrane, including uPAR and tissue factor. The goal of this study was to identify novel plasma membrane proteins, involved in cell-signaling, that are regulated by LRP1. Membrane protein ectodomains were prepared from RAW 264.7 cells in which LRP1 was silenced and control cells using protease K. Peptides were identified by LC-MS/MS. By analysis of spectral counts, 31 transmembrane and secreted proteins were regulated in abundance at least 2-fold when LRP1 was silenced. Validation studies confirmed that semaphorin4D (Sema4D), plexin domain-containing protein-1 (Plxdc1), and neuropilin-1 were more abundant in the membranes of LRP1 gene-silenced cells. Regulation of Plxdc1 by LRP1 was confirmed in CHO cells, as a second model system. Plxdc1 coimmunoprecipitated with LRP1 from extracts of RAW 264.7 cells and mouse liver. Although Sema4D did not coimmunoprecipitate with LRP1, the cell-surface level of Sema4D was increased by RAP, which binds to LRP1 and inhibits binding of other ligands. These studies identify Plxdc1, Sema4D, and neuropilin-1 as novel LRP1-regulated cell-signaling proteins. Overall, LRP1 emerges as a generalized regulator of the plasma membrane proteome.

Explaining variation in adult Anopheles indoor resting abundance: the relative effects of larval habitat proximity and insecticide-treated bed net use.

Science.gov (United States)

McCann, Robert S; Messina, Joseph P; MacFarlane, David W; Bayoh, M Nabie; Gimnig, John E; Giorgi, Emanuele; Walker, Edward D

2017-07-17

Spatial determinants of malaria risk within communities are associated with heterogeneity of exposure to vector mosquitoes. The abundance of adult malaria vectors inside people's houses, where most transmission takes place, should be associated with several factors: proximity of houses to larval habitats, structural characteristics of houses, indoor use of vector control tools containing insecticides, and human behavioural and environmental factors in and near houses. While most previous studies have assessed the association of larval habitat proximity in landscapes with relatively low densities of larval habitats, in this study these relationships were analysed in a region of rural, lowland western Kenya with high larval habitat density. 525 houses were sampled for indoor-resting mosquitoes across an 8 by 8 km study area using the pyrethrum spray catch method. A predictive model of larval habitat location in this landscape, previously verified, provided derivations of indices of larval habitat proximity to houses. Using geostatistical regression models, the association of larval habitat proximity, long-lasting insecticidal nets (LLIN) use, house structural characteristics (wall type, roof type), and peridomestic variables (cooking in the house, cattle near the house, number of people sleeping in the house) with mosquito abundance in houses was quantified. Vector abundance was low (mean, 1.1 adult Anopheles per house). Proximity of larval habitats was a strong predictor of Anopheles abundance. Houses without an LLIN had more female Anopheles gambiae s.s., Anopheles arabiensis and Anopheles funestus than houses where some people used an LLIN (rate ratios, 95% CI 0.87, 0.85-0.89; 0.84, 0.82-0.86; 0.38, 0.37-0.40) and houses where everyone used an LLIN (RR, 95% CI 0.49, 0.48-0.50; 0.39, 0.39-0.40; 0.60, 0.58-0.61). Cooking in the house also reduced Anopheles abundance across all species. The number of people sleeping in the house, presence of cattle near the house

GALAXIES IN ΛCDM WITH HALO ABUNDANCE MATCHING: LUMINOSITY-VELOCITY RELATION, BARYONIC MASS-VELOCITY RELATION, VELOCITY FUNCTION, AND CLUSTERING

International Nuclear Information System (INIS)

Trujillo-Gomez, Sebastian; Klypin, Anatoly; Primack, Joel; Romanowsky, Aaron J.

2011-01-01

It has long been regarded as difficult if not impossible for a cosmological model to account simultaneously for the galaxy luminosity, mass, and velocity distributions. We revisit this issue using a modern compilation of observational data along with the best available large-scale cosmological simulation of dark matter (DM). We find that the standard cosmological model, used in conjunction with halo abundance matching (HAM) and simple dynamical corrections, fits—at least on average—all basic statistics of galaxies with circular velocities V circ > 80 km s –1 calculated at a radius of ∼10 kpc. Our primary observational constraint is the luminosity-velocity (LV) relation—which generalizes the Tully-Fisher and Faber-Jackson relations in allowing all types of galaxies to be included, and provides a fundamental benchmark to be reproduced by any theory of galaxy formation. We have compiled data for a variety of galaxies ranging from dwarf irregulars to giant ellipticals. The data present a clear monotonic LV relation from ∼50 km s –1 to ∼500 km s –1 , with a bend below ∼80 km s –1 and a systematic offset between late- and early-type galaxies. For comparison to theory, we employ our new ΛCDM 'Bolshoi' simulation of DM, which has unprecedented mass and force resolution over a large cosmological volume, while using an up-to-date set of cosmological parameters. We use HAM to assign rank-ordered galaxy luminosities to the DM halos, a procedure that automatically fits the empirical luminosity function and provides a predicted LV relation that can be checked against observations. The adiabatic contraction of DM halos in response to the infall of the baryons is included as an optional model ingredient. The resulting predictions for the LV relation are in excellent agreement with the available data on both early-type and late-type galaxies for the luminosity range from M r = –14 to M r = –22. We also compare our predictions for the 'cold' baryon mass (i

Assessing mRNA nuclear export in mammalian cells by microinjection.

Science.gov (United States)

Lee, Eliza S; Palazzo, Alexander F

2017-08-15

The nuclear export of mRNAs is an important yet little understood part of eukaryotic gene expression. One of the easiest methods for monitoring mRNA export in mammalian tissue culture cells is through the microinjection of DNA plasmids into the nucleus and monitoring the distribution of the transcribed product over time. Here we describe how to setup a microscope equipped with a micromanipulator used in cell microinjections, and we explain how to perform a nuclear mRNA export assay and obtain the nuclear export rate for any given mRNA. Copyright © 2017 Elsevier Inc. All rights reserved.

Pretranslational regulation of Na-K-ATPase in cultured canine kidney cells by low K

Energy Technology Data Exchange (ETDEWEB)

Bowen, J.W.; McDonough, A.

1987-02-01

Long-term upregulation of the sodium pump (Na-K-adenosine triphosphatase (Na-K-ATPase)) entails an increase in the number of enzyme molecules. The authors incubated Madin-Darby canine kidney (MDCK) cells in low K medium and studied the time course and magnitude of change in the relative abundance of the two Na-K-ATPase subunits ( and US ), in the synthesis rate of the subunits, and in the relative abundance of - and US -mRNA. When cells were incubated in medium containing 0.25 mM K , intracellular Na increased. The relative abundance of Na-K-ATPase subunits, measured with ( SVI)-labelled immunoblots of cell homogenates, increases such that after 24 h was 1.71 +/- 0.33 and US was 1.67 +/- 0.22 times control. After 8 h of K depletion, -synthesis rate, measured by immunoprecipitation of pulse-labelled cells, increased to 2.30 +/- 0.50 and beta increased to 2.07 +/- 0.42 times control. The - and US -subunit mRNA abundance, measured by hybridizing - and US -cDNA probes to total RNA, increased within 30 min to 1.93 +/- 0.24 and 2.29 +/- 0.64 times control, respectively. They conclude that regulatory adjustments of Na-K-ATPase abundance involve an increase in translation after a rapid and coordinate increase in the concentrations of - and US -subunit mRNA.

Modelling tick abundance using machine learning techniques and satellite imagery

DEFF Research Database (Denmark)

Kjær, Lene Jung; Korslund, L.; Kjelland, V.

satellite images to run Boosted Regression Tree machine learning algorithms to predict overall distribution (presence/absence of ticks) and relative tick abundance of nymphs and larvae in southern Scandinavia. For nymphs, the predicted abundance had a positive correlation with observed abundance...... the predicted distribution of larvae was mostly even throughout Denmark, it was primarily around the coastlines in Norway and Sweden. Abundance was fairly low overall except in some fragmented patches corresponding to forested habitats in the region. Machine learning techniques allow us to predict for larger...... the collected ticks for pathogens and using the same machine learning techniques to develop prevalence maps of the ScandTick region....

Evaluation of alternative age-based methods for estimating relative abundance from survey data in relation to assessment models

DEFF Research Database (Denmark)

Berg, Casper Willestofte; Nielsen, Anders; Kristensen, Kasper

2014-01-01

Indices of abundance from fishery-independent trawl surveys constitute an important source of information for many fish stock assessments. Indices are often calculated using area stratified sample means on age-disaggregated data, and finally treated in stock assessment models as independent...... observations. We evaluate a series of alternative methods for calculating indices of abundance from trawl survey data (delta-lognormal, delta-gamma, and Tweedie using Generalized Additive Models) as well as different error structures for these indices when used as input in an age-based stock assessment model...... the different indices produced. The stratified mean method is found much more imprecise than the alternatives based on GAMs, which are found to be similar. Having time-varying index variances is found to be of minor importance, whereas the independence assumption is not only violated but has significant impact...

Can occupancy-abundance models be used to monitor wolf abundance?

Directory of Open Access Journals (Sweden)

M Cecilia Latham

Full Text Available Estimating the abundance of wild carnivores is of foremost importance for conservation and management. However, given their elusive habits, direct observations of these animals are difficult to obtain, so abundance is more commonly estimated from sign surveys or radio-marked individuals. These methods can be costly and difficult, particularly in large areas with heavy forest cover. As an alternative, recent research has suggested that wolf abundance can be estimated from occupancy-abundance curves derived from "virtual" surveys of simulated wolf track networks. Although potentially more cost-effective, the utility of this approach hinges on its robustness to violations of its assumptions. We assessed the sensitivity of the occupancy-abundance approach to four assumptions: variation in wolf movement rates, changes in pack cohesion, presence of lone wolves, and size of survey units. Our simulations showed that occupancy rates and wolf pack abundances were biased high if track surveys were conducted when wolves made long compared to short movements, wolf packs were moving as multiple hunting units as opposed to a cohesive pack, and lone wolves were moving throughout the surveyed landscape. We also found that larger survey units (400 and 576 km2 were more robust to changes in these factors than smaller survey units (36 and 144 km2. However, occupancy rates derived from large survey units rapidly reached an asymptote at 100% occupancy, suggesting that these large units are inappropriate for areas with moderate to high wolf densities (>15 wolves/1,000 km2. Virtually-derived occupancy-abundance relationships can be a useful method for monitoring wolves and other elusive wildlife if applied within certain constraints, in particular biological knowledge of the surveyed species needs to be incorporated into the design of the occupancy surveys. Further, we suggest that the applicability of this method could be extended by directly incorporating some of its

Distribuição e abundância relativa de bagres marinhos (Siluriformes, Ariidae na Baía de Sepetiba, Rio de Janeiro Distribution and relative abundance of the marine catfish (Siluriformes, Ariidae in Sepetiba Bay, Rio de Janeiro

Directory of Open Access Journals (Sweden)

Márcia Cristina Costa de Azevedo

1998-12-01

Full Text Available Marine catfish (Ariidae are abundant resources in otter trawl fisheries carried out at Sepetiba Bay, Rio de Janeiro (Lat. 22º54, 23º04'S; Long. 43º34 44º10'W. Relative abundance and distribution were assessed, based in 158 fishing sampling at seven sites in the Bay, between July-1993 e June-1996. Five species were recorded in the following abundance rank order: Genidens genidens (Valenciennes, 1839, Caihorops spixii (Agassiz,1829, Sciadeichthys lunisculis (Valenciennes, 1840, Nelunia barba (Lacépède, 1803, and Bagre marinus (Mitchill, 1814, the latter have been caught in only two samples. Marine catfish showed higher abundance in the inner Bay, with indication of spatial segregation. G genidens was abundant in ali sites of lhe inner Bay, C. spixii e N. barba, near to rivers mouths, andS lunisculis, being widespread in ali studied area. Sazonality was not evident, with few exceplions in some of the three annual cycles; G. genidens and S. luniscutis were more abundant in biomass in summer 1994/95 (G. genidens and 1993/94 (S. luniscutis. G. genidens e N. barba show higher abundance (CPUE and biomass between July-93 and June-95 and C. spixii e S. luniscutis between July-95 and June-96. Total association index indicates a overall positive association among ali species, with. higher Jaccard and Sorensen similarities coefficient for the pairs C. spixii/G. genidens, G. genidens/S. luniscutis, e C. spixii/S. luniscutis. Pearson linear correlation and Sperman rank indicate that G. genidens and N. barba are inversely correlated to C. spixii and S. luniscutis. Spatial segregation strategy may be explaining the coexistence of the marine catfish at Sepetiba Bay.

Relative Abundance and Diversity of Bacterial Methanotrophs at the Oxic?Anoxic Interface of the Congo Deep-Sea Fan

OpenAIRE

Bessette, Sandrine; Moalic, Yann; Gautey, S?bastien; Lesongeur, Fran?oise; Godfroy, Anne; Toffin, Laurent

2017-01-01

Sitting at ∼5,000 m water depth on the Congo-Angola margin and ∼760 km offshore of the West African coast, the recent lobe complex of the Congo deep-sea fan receives large amounts of fluvial sediments (3–5% organic carbon). This organic-rich sedimentation area harbors habitats with chemosynthetic communities similar to those of cold seeps. In this study, we investigated relative abundance, diversity and distribution of aerobic methane-oxidizing bacteria (MOB) communities at the oxic–anoxic in...

Single step production of Cas9 mRNA for zygote injection.

Science.gov (United States)

Redel, Bethany K; Beaton, Benjamin P; Spate, Lee D; Benne, Joshua A; Murphy, Stephanie L; O'Gorman, Chad W; Spate, Anna M; Prather, Randall S; Wells, Kevin D

2018-03-01

Production of Cas9 mRNA in vitro typically requires the addition of a 5´ cap and 3´ polyadenylation. A plasmid was constructed that harbored the T7 promoter followed by the EMCV IRES and a Cas9 coding region. We hypothesized that the use of the metastasis associated lung adenocarcinoma transcript 1 (Malat1) triplex structure downstream of an IRES/Cas9 expression cassette would make polyadenylation of in vitro produced mRNA unnecessary. A sequence from the mMalat1 gene was cloned downstream of the IRES/Cas9 cassette described above. An mRNA concentration curve was constructed with either commercially available Cas9 mRNA or the IRES/ Cas9/triplex, by injection into porcine zygotes. Blastocysts were genotyped to determine if differences existed in the percent of embryos modified. The concentration curve identified differences due to concentration and RNA type injected. Single step production of Cas9 mRNA provides an alternative source of Cas9 for use in zygote injections.

Concerted elevation of acyl-coenzyme A:diacylglycerol acyltransferase (DGAT) activity through independent stimulation of mRNA expression of DGAT1 and DGAT2 by carbohydrate and insulin.

Science.gov (United States)

Meegalla, Rupalie L; Billheimer, Jeffrey T; Cheng, Dong

2002-11-01

Glucose and insulin are anabolic signals which upregulate the transcriptions of a series of lipogenic enzymes to convert excess carbohydrate into triglycerides for efficient energy storage. These enzymes include ATP-citrate lyase (ACL), acetyl-coenzyme A carboxylase (ACC), fatty acid synthase (FAS), and glycerol-3-phosphate acyltransferase (G3PA). Acyl-coenzyme A:diacylglycerol acyltransferase (DGAT) is important to synthesize fatty acids into triglycerides. Two DGATs from different gene families have recently been identified. In the current study, we report that glucose preferentially enhances DGAT1 mRNA expression, whereas insulin specifically increases the level of DGAT2 mRNA. Treatment of adipocytes with glucose and insulin together results in higher DGAT activity in the membrane than cells treated with either of the agents alone, indicating that glucose and insulin have additive effect on DGAT activation. In mice treated with fast/refeeding protocol, DGAT2 mRNA decreased upon fasting and was replenished upon refeeding in adipose tissue and liver. This pattern of change was not observed for DGAT1. Inasmuch as DGAT1 mRNA is less abundant in liver, we suggest that DGAT1 is more involved in fat absorption in the intestine and in basal level triglyceride synthesis in adipose tissue where it is more highly expressed. In contrast, DGAT2 is more likely to play important roles in assembly of de novo synthesized fatty acids into VLDL particles in the liver.

Nonsense mutations in the human β-globin gene affect mRNA metabolism

International Nuclear Information System (INIS)

Baserga, S.J.; Benz, E.J. Jr.

1988-01-01

A number of premature translation termination mutations (nonsense mutations) have been described in the human α- and β-globin genes. Studies on mRNA isolated from patients with β 0 -thalassemia have shown that for both the β-17 and the β-39 mutations less than normal levels of β-globin mRNA accumulate in peripheral blood cells. (The codon at which the mutation occurs designates the name of the mutation; there are 146 codons in human β-globin mRNA). In vitro studies using the cloned β-39 gene have reproduced this effect in a heterologous transfection system and have suggested that the defect resides in intranuclear metabolism. The authors have asked if this phenomenon of decreased mRNA accumulation is a general property of nonsense mutations and if the effect depends on the location or the type of mutation. Toward this end, they have studied the effect of five nonsense mutations and two missense mutations on the expression of human β-globin mRNA in a heterologous transfection system. In all cases studied, the presence of a translation termination codon correlates with a decrease in the steady-state level of mRNA. The data suggest that the metabolism of a mammalian mRNA is affected by the presence of a mutation that affects translation

β-glucuronidase use as a single internal control gene may confound analysis in FMR1 mRNA toxicity studies.

Science.gov (United States)

Kraan, Claudine M; Cornish, Kim M; Bui, Quang M; Li, Xin; Slater, Howard R; Godler, David E

2018-01-01

Relationships between Fragile X Mental Retardation 1 (FMR1) mRNA levels in blood and intragenic FMR1 CGG triplet expansions support the pathogenic role of RNA gain of function toxicity in premutation (PM: 55-199 CGGs) related disorders. Real-time PCR (RT-PCR) studies reporting these findings normalised FMR1 mRNA level to a single internal control gene called β-glucuronidase (GUS). This study evaluated FMR1 mRNA-CGG correlations in 33 PM and 33 age- and IQ-matched control females using three normalisation strategies in peripheral blood mononuclear cells (PBMCs): (i) GUS as a single internal control; (ii) the mean of GUS, Eukaryotic Translation Initiation Factor 4A2 (EIF4A2) and succinate dehydrogenase complex flavoprotein subunit A (SDHA); and (iii) the mean of EIF4A2 and SDHA (with no contribution from GUS). GUS mRNA levels normalised to the mean of EIF4A2 and SDHA mRNA levels and EIF4A2/SDHA ratio were also evaluated. FMR1mRNA level normalised to the mean of EIF4A2 and SDHA mRNA levels, with no contribution from GUS, showed the most significant correlation with CGG size and the greatest difference between PM and control groups (p = 10-11). Only 15% of FMR1 mRNA PM results exceeded the maximum control value when normalised to GUS, compared with over 42% when normalised to the mean of EIF4A2 and SDHA mRNA levels. Neither GUS mRNA level normalised to the mean RNA levels of EIF4A2 and SDHA, nor to the EIF4A2/SDHA ratio were correlated with CGG size. However, greater variability in GUS mRNA levels were observed for both PM and control females across the full range of CGG repeat as compared to the EIF4A2/SDHA ratio. In conclusion, normalisation with multiple control genes, excluding GUS, can improve assessment of the biological significance of FMR1 mRNA-CGG size relationships.

Clinical values of AFP, GPC3 mRNA in peripheral blood for prediction of hepatocellular carcinoma recurrence following OLT: AFP, GPC3 mRNA for prediction of HCC.

Science.gov (United States)

Wang, Yuliang; Shen, Zhongyang; Zhu, Zhijun; Han, Ruifa; Huai, Mingsheng

2011-03-01

Hepatocellular carcinoma (HCC) is one of the most common malignancies worldwide. Annually, about 200,000 patients died of HCC in China. Liver transplantation (LT) holds great theoretical appeal in treating HCC. However, the high recurrence rate after transplantation is the most important limiting factor for long-term survival. To assess the value of alpha-fetoprotein (AFP) messenger RNA (mRNA), Glypican-3 (GPC3) mRNA-expressing cells in the peripheral blood (PB) for prediction of HCC recurrence following orthotopic liver transplantation (OLT). 29 patients with HCC who underwent OLT with a minimum clinical follow-up of 12 months were included in this retrospective study. We detected AFP mRNA, GPC3 mRNA-expressing cells in the PB by TaqMan real-time reverse transcriptase-polymerase chain reaction (RT-PCR), pre-, intra- and post-operatively. The early recurrence of patients was evaluated. 8 (28%), 15 (52%), and 9 (31%) patients had AFP mRNA detected pre-, intra-, and post-operatively, respectively. With 12 months of follow-up, HCC recurred in 7 (24%) patients. Univariate analysis revealed that positive pre- and post-operative AFP mRNA, TNM stage as well as vascular invasion were significant predictors for the HCC recurrence. Multivariate analysis revealed that being positive for AFP mRNA pre-operatively remained a significant risk factor for HCC recurrence after OLT. GPC3 mRNA was expressed in all PB samples. There was no significant difference in the expression levels of GPC3 mRNA between the HCC and control groups. There were no significant differences in GPC3 mRNA expression values between those patients with and without tumor recurrence. The pre-operative detection of circulating AFP mRNA-expressing cells could be a useful predictor for HCC recurrence following OLT. GPC3 mRNA-expressing cells in PB seem to have no diagnostic value.

Dissociation of SERPINE1 mRNA from the translational repressor proteins Ago2 and TIA-1 upon platelet activation.

Science.gov (United States)

Corduan, Aurélie; Plé, Hélène; Laffont, Benoit; Wallon, Thérèse; Plante, Isabelle; Landry, Patricia; Provost, Patrick

2015-05-01

Platelets play an important role in haemostasis, as well as in thrombosis and coagulation processes. They harbour a wide variety of messenger RNAs (mRNAs), that can template de novo protein synthesis, and an abundant array of microRNAs, which are known to mediate mRNA translational repression through proteins of the Argonaute (Ago) family. The relationship between platelet microRNAs and proteins capable of mediating translational repression, however, remains unclear. Here, we report that half of platelet microRNAs is associated to mRNA-regulatory Ago2 protein complexes, in various proportions. Associated to these Ago2 complexes are platelet mRNAs known to support de novo protein synthesis. Reporter gene activity assays confirmed the capacity of the platelet microRNAs, found to be associated to Ago2 complexes, to regulate translation of these platelet mRNAs through their 3'UTR. Neither the microRNA repertoire nor the microRNA composition of Ago2 complexes of human platelets changed upon activation with thrombin. However, under conditions favoring de novo synthesis of Plasminogen Activator Inhibitor-1 (PAI-1) protein, we documented a rapid dissociation of the encoding platelet SERPINE1 mRNA from Ago2 protein complexes as well as from the translational repressor protein T-cell-restricted intracellular antigen-1 (TIA-1). These findings are consistent with a scenario by which lifting of the repressive effects of Ago2 and TIA-1 protein complexes, involving a rearrangement of proteinmRNA complexes rather than disassembly of Ago2microRNA complexes, would allow translation of SERPINE1 mRNA into PAI-1 in response to platelet activation.

Presence of High-Risk HPV mRNA in Relation to Future High-Grade Lesions among High-Risk HPV DNA Positive Women with Minor Cytological Abnormalities.

Directory of Open Access Journals (Sweden)

Hanna Johansson

Full Text Available Continuous expression of E6- and E7-oncogenes of high-risk human papillomavirus (HPV types is necessary for the development and maintenance of the dysplastic phenotype. The aim of the study was to determine the sensitivity and specificity of the APTIMA HPV mRNA assay (Hologic in predicting future development of high-grade cervical intraepithelial neoplasia (CIN among high-risk HPV-DNA-positive women with atypical squamous cells of undetermined significance (ASCUS or low-grade squamous epithelial lesion (LSIL cytology.Archived SurePath cervical samples of women ≥ 35 years of age with high-risk HPV DNA-positive ASCUS (n = 211 or LSIL, (n = 131 were tested for the presence of high-risk HPV E6/E7 mRNA using the APTIMA HPV assay, and the women were monitored for development of histopathologically verified CIN2+.Twenty-nine percent (61/211 of the women in the ASCUS group, and 34.3% (45/131 in the LSIL group developed CIN2+ within 4.5 years of follow-up. The prevalence of HPV mRNA was 90.0% (95% CI 85.9-94.0 among women with ASCUS and 95.4% (95% CI 91.8-99.0 among women with LSIL. The presence of HPV E6/E7 mRNA was associated with future development of CIN2+ among women with ASCUS and LSIL (p=0.02. The mRNA assay demonstrated high sensitivity in predicting future CIN2+ and CIN3 for index ASCUS (96.7%; 95% CI 87.6-99.4 and 100%; 95% CI 82.2-100, respectively and LSIL (97.8%, 95% CI 86.8-99.9 and 100%, 95% CI 79.9-100, respectively. The corresponding specificity was low, 12.7% (95% CI 7.9-19.3 and 5.8% (95% CI 2.2-13.6, for future CIN2+, respectively. The negative predictive value of the HPV mRNA assay for detecting future CIN3 was 100%, since no mRNA-negative woman developed CIN3 (0/27 as compared to 13.6% (43/315 of the mRNA-positive women (p = 0.03.The APTIMA mRNA assay demonstrated high sensitivity but low specificity in predicting future CIN2+ among women with minor cytological abnormalities. The assay had high negative predictive value for future

Presence of High-Risk HPV mRNA in Relation to Future High-Grade Lesions among High-Risk HPV DNA Positive Women with Minor Cytological Abnormalities

Science.gov (United States)

Johansson, Hanna; Bjelkenkrantz, Kaj; Darlin, Lotten; Dilllner, Joakim; Forslund, Ola

2015-01-01

Objective Continuous expression of E6- and E7-oncogenes of high-risk human papillomavirus (HPV) types is necessary for the development and maintenance of the dysplastic phenotype. The aim of the study was to determine the sensitivity and specificity of the APTIMA HPV mRNA assay (Hologic) in predicting future development of high-grade cervical intraepithelial neoplasia (CIN) among high-risk HPV-DNA-positive women with atypical squamous cells of undetermined significance (ASCUS) or low-grade squamous epithelial lesion (LSIL) cytology. Methods Archived SurePath cervical samples of women ≥ 35 years of age with high-risk HPV DNA-positive ASCUS (n = 211) or LSIL, (n = 131) were tested for the presence of high-risk HPV E6/E7 mRNA using the APTIMA HPV assay, and the women were monitored for development of histopathologically verified CIN2+. Results Twenty-nine percent (61/211) of the women in the ASCUS group, and 34.3% (45/131) in the LSIL group developed CIN2+ within 4.5 years of follow-up. The prevalence of HPV mRNA was 90.0% (95% CI 85.9-94.0) among women with ASCUS and 95.4% (95% CI 91.8-99.0) among women with LSIL. The presence of HPV E6/E7 mRNA was associated with future development of CIN2+ among women with ASCUS and LSIL (p=0.02). The mRNA assay demonstrated high sensitivity in predicting future CIN2+ and CIN3 for index ASCUS (96.7%; 95% CI 87.6-99.4 and 100%; 95% CI 82.2-100, respectively) and LSIL (97.8%, 95% CI 86.8-99.9 and 100%, 95% CI 79.9-100, respectively). The corresponding specificity was low, 12.7% (95% CI 7.9-19.3) and 5.8% (95% CI 2.2-13.6), for future CIN2+, respectively. The negative predictive value of the HPV mRNA assay for detecting future CIN3 was 100%, since no mRNA-negative woman developed CIN3 (0/27) as compared to 13.6% (43/315) of the mRNA-positive women (p = 0.03). Conclusion The APTIMA mRNA assay demonstrated high sensitivity but low specificity in predicting future CIN2+ among women with minor cytological abnormalities. The assay had

Primary induction of vitellogenin mRNA in the rooster by 17beta-estradiol.

Science.gov (United States)

Burns, A T; Deeley, R G; Gordon, J I; Udell, D S; Mullinix, K P; Goldberger, R F

1978-01-01

We have studied the kinetics of vitellogenin mRNA accumulation in rooster liver after a primary injection of 17beta-estradiol. The levels of vitellogenin mRNA have been determined both by hybridization of total cellular RNA to vitellogenin cDNA and by translation of vitellogenin mRNA in a wheat germ cell-free system. The results obtained by both methods of analysis are in good agreement and indicate that vitellogenin mRNA is present in the liver of normal roosters at a level of 0-5 molecules per liver cell and increases in amount during the 3 days following injection of estrogen, reaching a level of almost 6000 molecules per cell at the peak of the response. The level of vitellogenin mRNA declined exponentially during the next 14 days with a half-life of 29 hr, reaching a level of less than 10 molecules per cell at 17 days after injection of the hormone. The levels of vitellogenin mRNA after stimulation with estrogen have been correlated with the in vivo rate of synthesis of the vitellogenin polypeptide. The results indicate that the rate of vitellogenin synthesis is closely correlated with the level of vitellogenin mRNA. On the basis of these findings, we conclude that vitellogenin mRNA does not exist in the liver in an untranslated form after withdrawal from estrogen. PMID:273910

SULFUR ABUNDANCES IN THE ORION ASSOCIATION B STARS

International Nuclear Information System (INIS)

Daflon, Simone; Cunha, Katia; De la Reza, Ramiro; Holtzman, Jon; Chiappini, Cristina

2009-01-01

Sulfur abundances are derived for a sample of 10 B main-sequence star members of the Orion association. The analysis is based on LTE plane-parallel model atmospheres and non-LTE line formation theory by means of a self-consistent spectrum synthesis analysis of lines from two ionization states of sulfur, S II and S III. The observations are high-resolution spectra obtained with the ARCES spectrograph at the Apache Point Observatory. The abundance distribution obtained for the Orion targets is homogeneous within the expected errors in the analysis: A(S) = 7.15 ± 0.05. This average abundance result is in agreement with the recommended solar value (both from modeling of the photospheres in one-dimensional and three-dimensional, and meteorites) and indicates that little, if any, chemical evolution of sulfur has taken place in the last ∼4.5 billion years. The sulfur abundances of the young stars in Orion are found to agree well with results for the Orion Nebulae, and place strong constraints on the amount of sulfur depletion onto grains as being very modest or nonexistent. The sulfur abundances for Orion are consistent with other measurements at a similar galactocentric radius: combined with previous results for other OB-type stars produce a relatively shallow sulfur abundance gradient with a slope of -0.037 ± 0.012 dex kpc -1 .

Photometric abundances of cepheid variables in the galaxy and the small magellanic cloud

International Nuclear Information System (INIS)

Harris, H.C.

1980-01-01

Washington system colors and V magnitudes are described for classical and Type II cepheids. The sample includes 102 classical cepheids and 63 Type II cepheids with a wide range of positions in the Galaxy and 45 classical cepheids in the Small Magellanic Cloud. Period-color relations are derived of each type of cepheid and, with period-magnitude relations, are used to determine reddenings and distances. The colors are interpreted in terms of abundances of heavy elements, with a calibration based on observed stars with known abundances and on model-atmosphere colors. The classical cepheids in the Galaxy show a gradient in the Galactic disk of d[A/H]/dR = -0.07 kpc -1 , approximately linear over 10 kpc, small scatter in the abundances of most stars at a given galactocentric radius, and a few stars indicating peculiar abundances. The Type II cepheids show a wide range of abundances with only a small fraction representing a true halo population, a gradient in the abundance distribution with distance from the galactic plane, and at most a weak gradient with distance from the galactic center outside of 2 kpc. Their origin and relation to the metal-rich RR Lyraes is discussed. The cepheids in the SMC show a mean value relative to the Sun of [A/H] = -0.54, with weak evidence that short-period stars are more metal-poor, but with no correlation with projected position in the SMC. The consistency of their colors, temperatures, abundances, and reddenings is discussed

Lower glutamic acid decarboxylase 65kD mRNA and protein levels in the prefrontal cortex in schizoaffective disorder but not schizophrenia

Science.gov (United States)

Glausier, JR; Kimoto, S; Fish, KN; Lewis, DA

2014-01-01

Background Altered GABA signaling in the prefrontal cortex (PFC) has been associated with cognitive dysfunction in schizophrenia and schizoaffective disorder. PFC levels of the GABA-synthesizing enzyme glutamic acid decarboxylase 67kD (GAD67) has been consistently reported to be lower in these disorders, but the status of the second GABA-synthesizing enzyme, GAD65, remains unclear. Methods GAD65 mRNA levels were quantified in PFC area 9 by quantitative polymerase chain reaction from 62 subjects with schizophrenia or schizoaffective disorder and 62 matched healthy comparison subjects. GAD65 relative protein levels were quantified in a subset of subject pairs by confocal immunofluorescence microscopy. Results Mean GAD65 mRNA levels were 13.6% lower in schizoaffective disorder subjects, but did not differ in schizophrenia subjects, relative to their matched healthy comparison subjects. In the subjects with schizoaffective disorder, mean GAD65 protein levels were 19.4% lower and were correlated with GAD65 mRNA levels. Lower GAD65 mRNA and protein measures within schizoaffective disorder subjects was not attributable to factors commonly comorbid with the diagnosis. Conclusions In concert with previous studies, these findings suggest that schizoaffective disorder is associated with lower levels of both GAD65 and GAD67 mRNA and protein in the PFC, whereas subjects with schizophrenia have lower mean levels of only GAD67 mRNA and protein. Because cognitive function is generally better preserved in subjects with schizoaffective disorder relative to subjects with schizophrenia, these findings may support an interpretation that GAD65 down-regulation provides a homeostatic response complementary to GAD67 down-regulation expression that serves to reduce inhibition in the face of lower PFC network activity. PMID:24993056

Reprogramming the Dynamin 2 mRNA by Spliceosome-mediated RNA Trans-splicing

Directory of Open Access Journals (Sweden)

Delphine Trochet

2016-01-01

Full Text Available Dynamin 2 (DNM2 is a large GTPase, ubiquitously expressed, involved in membrane trafficking and regulation of actin and microtubule cytoskeletons. DNM2 mutations cause autosomal dominant centronuclear myopathy which is a rare congenital myopathy characterized by skeletal muscle weakness and histopathological features including nuclear centralization in absence of regeneration. No curative treatment is currently available for the DNM2-related autosomal dominant centronuclear myopathy. In order to develop therapeutic strategy, we evaluated here the potential of Spliceosome-Mediated RNA Trans-splicing technology to reprogram the Dnm2-mRNA in vitro and in vivo in mice. We show that classical 3′-trans-splicing strategy cannot be considered as accurate therapeutic strategy regarding toxicity of the pre-trans-splicing molecules leading to low rate of trans-splicing in vivo. Thus, we tested alternative strategies devoted to prevent this toxicity and enhance frequency of trans-splicing events. We succeeded to overcome the toxicity through a 5′-trans-splicing strategy which also allows detection of trans-splicing events at mRNA and protein levels in vitro and in vivo. These results suggest that the Spliceosome-Mediated RNA Trans-splicing strategy may be used to reprogram mutated Dnm2-mRNA but highlight the potential toxicity linked to the molecular tools which have to be carefully investigated during preclinical development.

Changes in rRNA levels during stress invalidates results from mRNA blotting: Fluorescence in situ rRNA hybridization permits renormalization for estimation of cellular mRNA levels

DEFF Research Database (Denmark)

Hansen, M.C.; Nielsen, A.K.; Molin, Søren

2001-01-01

obtained by these techniques are compared between experiments in which differences in growth rates, strains, or stress treatments occur, the normalization procedure may have a significant impact on the results. In this report we present a solution to the normalization problem in RNA slot blotting...... the relative level of rRNA per cell, and slot blotting to rRNA probes, which estimates the level of rRNA per extracted total RNA, the amount of RNA per cell was calculated in a series of heat shock experiments with the gram-positive bacterium Lactococcus lactis. It was found that the level of rRNA per cell...... decreased to 30% in the course of the heat shock. This lowered ribosome level led to a decrease in the total RNA content, resulting in a gradually increasing overestimation of the mRNA levels throughout the experiment. Using renormalized cellular mRNA levels, the HrcA-mediated regulation of the genes...

Constraints on the Mass–Richness Relation from the Abundance and Weak Lensing of SDSS Clusters

Science.gov (United States)

Murata, Ryoma; Nishimichi, Takahiro; Takada, Masahiro; Miyatake, Hironao; Shirasaki, Masato; More, Surhud; Takahashi, Ryuichi; Osato, Ken

2018-02-01

We constrain the scaling relation between optical richness (λ) and halo mass (M) for a sample of Sloan Digital Sky Survey (SDSS) red-sequence Matched-filter Probabilistic Percolation (redMaPPer) galaxy clusters within the context of the Planck cosmological model. We use a forward modeling approach where we model the probability distribution of optical richness for a given mass, P({ln}λ | M). To model the abundance and the stacked lensing profiles, we use an emulator specifically built to interpolate the halo mass function and the stacked lensing profile for an arbitrary set of halo mass and redshift, which is calibrated based on a suite of high-resolution N-body simulations. We apply our method to 8312 SDSS redMaPPer clusters with 20 ≤ λ ≤ 100 and 0.10 ≤ z λ ≤ 0.33 and show that the lognormal distribution model for P(λ | M), with four free parameters, well reproduces the measured abundances and lensing profiles simultaneously. The constraints are characterized by the mean relation, (M)=A+B{ln}(M/{M}pivot}), with A={3.207}-0.046+0.044 and B={0.993}-0.055+0.041 (68% CL), where the pivot mass scale M pivot = 3 × 1014 h ‑1 M ⊙, and the scatter {σ }lnλ | M}={σ }0+q{ln}(M/{M}pivot}) with {σ }0={0.456}-0.039+0.047 and q=-{0.169}-0.026+0.035. We find that a large scatter in halo masses is required at the lowest-richness bins (20 ≤ λ ≲ 30) in order to reproduce the measurements. Without such a large scatter, the model prediction for the lensing profiles tends to overestimate the measured amplitudes. This might imply a possible contamination of intrinsically low-richness clusters due to the projection effects. Such a low-mass halo contribution is significantly reduced when applying our method to the sample of 30 ≤ λ ≤ 100.

Anomalous behavior of tellurium abundances

Energy Technology Data Exchange (ETDEWEB)

Cohen, B L

1984-01-01

The cosmic abundance of Te is larger than for any element with atomic number greater than 40, but it is one of the least abundant elements in the earth's lithosphere and it is one of the five elements never reported in sea water. On the other hand, it is the fourth most abundant element in the human body (after Fe, Zn and Rb), and is unusually abundant in human food. It is shown that the high abundance in human food combined with the low abundance in soil requires that it be picked up by plant roots very much more efficiently than any other trace element.

The effects of dietary Myrtle (Myrtus communis) on skin mucus immune parameters and mRNA levels of growth, antioxidant and immune related genes in zebrafish (Danio rerio).

Science.gov (United States)

Safari, Roghieh; Hoseinifar, Seyed Hossein; Van Doan, Hien; Dadar, Maryam

2017-07-01

Myrtle (Myrtus communis L., Myrtaceae) is a significant plant which naturally distributed around the globe. Although numerous studies have demonstrated the benefits of myrtle in different species, studies using the oral route are rare in the literature. In the present study, we evaluated the effect of myrtle intake on the antioxidant, immune, appetite and growth related genes as well as mucosal immune responses in zebrafish (Danio rerio) model. Zebrafish were fed control or myrtle (5, 10 and 20 g kg -1 myrtle) supplemented diets for sixty days. The results showed that, oral administration of Myrtle significantly improved mucosal immune responses (the activity of lysozyme, total Ig and protease). Furthermore, fish fed 20 g kg -1 showed remarkably higher antioxidant (sod and cat) enzymes gene expression compared other treatment. There were significant difference between myrtle fed fish and control group regarding tnf-alpha and lyz expression. Also, evaluation of growth (gh and igf1) related genes revealed remarkable upregulation in 20 g kg -1 myrtle treatment compared other myrtle treatments and control group. Similar results was observed regarding the mRNA levels of appetite related genes (ghrl) in zebrafish fed 20 g kg -1 myrtle. The present results indicated that dietary administration of myrtle improved mucosal immune parameters and altered mRNA levels of selected genes. These results on zebrafish model also highlights the potential use of Myrtle supplements as additive in human diets. Copyright © 2017 Elsevier Ltd. All rights reserved.

High ALK mRNA expression has a negative prognostic significance in rhabdomyosarcoma

Science.gov (United States)

Bonvini, P; Zin, A; Alaggio, R; Pawel, B; Bisogno, G; Rosolen, A

2013-01-01

Background: Anaplastic lymphoma kinase (ALK) is a receptor tyrosine kinase aberrantly expressed in cancer, but its clinical and functional importance remain controversial. Mutation or amplification of ALK, as well as its expression levels assessed by conventional immunohistochemistry methods, has been linked to prognosis in cancer, although with potential bias because of the semi-quantitative approaches. Herein, we measured ALK mRNA expression in rhabdomyosarcoma (RMS) and determined its clinical impact on patients' stratification and outcome. Methods: Specimens were obtained from RMS patients and cell lines, and ALK expression was analysed by quantitative RT–PCR, western blotting, IHC, and copy number analysis. Results: High ALK mRNA expression was detected in the vast majority of PAX3/7-FOXO1-positive tumours, whereas PAX3/7-FOXO1-negative RMS displayed considerably lower amounts of both mRNA and protein. Notably, ALK mRNA distinguished unfavourable PAX3/7-FOXO1-positive tumours from PAX3/7-FOXO1-negative RMS (Ptumour size (PALK mRNA levels were of prognostic relevance by Cox univariate regression analysis and correlated with increased risk of relapse (P=0.001) and survival (P=0.01), whereas by multivariate analysis elevated ALK mRNA expression resulted a negative prognostic marker when clinical stage was not included. Conclusion: Quantitative assessment of ALK mRNA expression helps to improve risk stratification of RMS patients and identifies tumours with adverse biological characteristics and aggressive behaviour. PMID:24149177

mRNA transfection of mouse and human neural stem cell cultures.

Directory of Open Access Journals (Sweden)

Samuel McLenachan

Full Text Available The use of synthetic mRNA as an alternative gene delivery vector to traditional DNA-based constructs provides an effective method for inducing transient gene expression in cell cultures without genetic modification. Delivery of mRNA has been proposed as a safer alternative to viral vectors in the induction of pluripotent cells for regenerative therapies. Although mRNA transfection of fibroblasts, dendritic and embryonic stem cells has been described, mRNA delivery to neurosphere cultures has not been previously reported. Here we sought to establish an efficient method for delivering mRNA to primary neurosphere cultures. Neurospheres derived from the subventricular zone of adult mice or from human embryonic stem cells were transfected with EGFP mRNA by lipofection and electroporation. Transfection efficiency and expression levels were monitored by flow cytometry. Cell survival following transfection was examined using live cell counting and the MTT assay. Both lipofection and electroporation provided high efficiency transfection of neurospheres. In comparison with lipofection, electroporation resulted in increased transfection efficiencies, but lower expression per cell and shorter durations of expression. Additional rounds of lipofection renewed EGFP expression in neurospheres, suggesting this method may be suitable for reprogramming applications. In summary, we have developed a protocol for achieving high efficiency transfection rates in mouse and human neurosphere cell culture that can be applied for future studies of gene function studies in neural stem cells, such as defining efficient differentiation protocols for glial and neuronal linages.

mRNA Transfection of Mouse and Human Neural Stem Cell Cultures

Science.gov (United States)

McLenachan, Samuel; Zhang, Dan; Palomo, Ana Belén Alvarez; Edel, Michael J.; Chen, Fred K.

2013-01-01

The use of synthetic mRNA as an alternative gene delivery vector to traditional DNA-based constructs provides an effective method for inducing transient gene expression in cell cultures without genetic modification. Delivery of mRNA has been proposed as a safer alternative to viral vectors in the induction of pluripotent cells for regenerative therapies. Although mRNA transfection of fibroblasts, dendritic and embryonic stem cells has been described, mRNA delivery to neurosphere cultures has not been previously reported. Here we sought to establish an efficient method for delivering mRNA to primary neurosphere cultures. Neurospheres derived from the subventricular zone of adult mice or from human embryonic stem cells were transfected with EGFP mRNA by lipofection and electroporation. Transfection efficiency and expression levels were monitored by flow cytometry. Cell survival following transfection was examined using live cell counting and the MTT assay. Both lipofection and electroporation provided high efficiency transfection of neurospheres. In comparison with lipofection, electroporation resulted in increased transfection efficiencies, but lower expression per cell and shorter durations of expression. Additional rounds of lipofection renewed EGFP expression in neurospheres, suggesting this method may be suitable for reprogramming applications. In summary, we have developed a protocol for achieving high efficiency transfection rates in mouse and human neurosphere cell culture that can be applied for future studies of gene function studies in neural stem cells, such as defining efficient differentiation protocols for glial and neuronal linages. PMID:24386231

mRNA transfection of mouse and human neural stem cell cultures.

Science.gov (United States)

McLenachan, Samuel; Zhang, Dan; Palomo, Ana Belén Alvarez; Edel, Michael J; Chen, Fred K

2013-01-01

The use of synthetic mRNA as an alternative gene delivery vector to traditional DNA-based constructs provides an effective method for inducing transient gene expression in cell cultures without genetic modification. Delivery of mRNA has been proposed as a safer alternative to viral vectors in the induction of pluripotent cells for regenerative therapies. Although mRNA transfection of fibroblasts, dendritic and embryonic stem cells has been described, mRNA delivery to neurosphere cultures has not been previously reported. Here we sought to establish an efficient method for delivering mRNA to primary neurosphere cultures. Neurospheres derived from the subventricular zone of adult mice or from human embryonic stem cells were transfected with EGFP mRNA by lipofection and electroporation. Transfection efficiency and expression levels were monitored by flow cytometry. Cell survival following transfection was examined using live cell counting and the MTT assay. Both lipofection and electroporation provided high efficiency transfection of neurospheres. In comparison with lipofection, electroporation resulted in increased transfection efficiencies, but lower expression per cell and shorter durations of expression. Additional rounds of lipofection renewed EGFP expression in neurospheres, suggesting this method may be suitable for reprogramming applications. In summary, we have developed a protocol for achieving high efficiency transfection rates in mouse and human neurosphere cell culture that can be applied for future studies of gene function studies in neural stem cells, such as defining efficient differentiation protocols for glial and neuronal linages.

Protein Structure and the Sequential Structure of mRNA

DEFF Research Database (Denmark)

Brunak, Søren; Engelbrecht, Jacob

1996-01-01

entries in the Brookhaven Protein Data Bank produced 719 protein chains with matching mRNA sequence, amino acid sequence, and secondary structure assignment, By neural network analysis, we found strong signals in mRNA sequence regions surrounding helices and sheets, These signals do not originate from......A direct comparison of experimentally determined protein structures and their corresponding protein coding mRNA sequences has been performed, We examine whether real world data support the hypothesis that clusters of rare codons correlate with the location of structural units in the resulting...... protein, The degeneracy of the genetic code allows for a biased selection of codons which may control the translational rate of the ribosome, and may thus in vivo have a catalyzing effect on the folding of the polypeptide chain, A complete search for GenBank nucleotide sequences coding for structural...

Kinetics of lipid-nanoparticle-mediated intracellular mRNA delivery and function

Science.gov (United States)

Zhdanov, Vladimir P.

2017-10-01

mRNA delivery into cells forms the basis for one of the new and promising ways to treat various diseases. Among suitable carriers, lipid nanoparticles (LNPs) with a size of about 100 nm are now often employed. Despite high current interest in this area, the understanding of the basic details of LNP-mediated mRNA delivery and function is limited. To clarify the kinetics of mRNA release from LNPs, the author uses three generic models implying (i) exponential, (ii) diffusion-controlled, and (iii) detachment-controlled kinetic regimes, respectively. Despite the distinct differences in these kinetics, the associated transient kinetics of mRNA translation to the corresponding protein and its degradation are shown to be not too sensitive to the details of the mRNA delivery by LNPs (or other nanocarriers). In addition, the author illustrates how this protein may temporarily influence the expression of one gene or a few equivalent genes. The analysis includes positive or negative regulation of the gene transcription via the attachment of the protein without or with positive or negative feedback in the gene expression. Stable, bistable, and oscillatory schemes have been scrutinized in this context.

Monitoring waterbird abundance in wetlands: The importance of controlling results for variation in water depth

Science.gov (United States)

Bolduc, F.; Afton, A.D.

2008-01-01

Wetland use by waterbirds is highly dependent on water depth, and depth requirements generally vary among species. Furthermore, water depth within wetlands often varies greatly over time due to unpredictable hydrological events, making comparisons of waterbird abundance among wetlands difficult as effects of habitat variables and water depth are confounded. Species-specific relationships between bird abundance and water depth necessarily are non-linear; thus, we developed a methodology to correct waterbird abundance for variation in water depth, based on the non-parametric regression of these two variables. Accordingly, we used the difference between observed and predicted abundances from non-parametric regression (analogous to parametric residuals) as an estimate of bird abundance at equivalent water depths. We scaled this difference to levels of observed and predicted abundances using the formula: ((observed - predicted abundance)/(observed + predicted abundance)) ?? 100. This estimate also corresponds to the observed:predicted abundance ratio, which allows easy interpretation of results. We illustrated this methodology using two hypothetical species that differed in water depth and wetland preferences. Comparisons of wetlands, using both observed and relative corrected abundances, indicated that relative corrected abundance adequately separates the effect of water depth from the effect of wetlands. ?? 2008 Elsevier B.V.

[Relative abundance and microhabitat use by the frog Geobatrachus walkeri (Anura: Strabomantidae) in two habitats of Sierra Nevada de Santa Marta, Colombia].

Science.gov (United States)

Martínez Baños, Vera; Pacheco Florez, Vanesa; Ramírez-Pinilla, Martha P

2011-06-01

Geobatrachus walkeri belongs to a monotypic frog genus endemic to the San Lorenzo area, Sierra Nevada de Santa Marta, Colombia. This species has been categorized as endangered because of its small distribution area and the decline in the extent and quality of its habitat. It inhabits two forest types with different composition and structure, the native secondary forest and a pine plantation (dominated by Pinus patula). To compare the relative abundance and microhabitat use of this species in these habitat types, 30 quadrants/environment were distributed randomly. The individual number, microhabitat use and other aspects of its natural history were registered using visual encounter surveys in both sites, including non-sampled areas in the quadrants. The relative abundance of frogs was significantly different between habitats and among seasons. The highest abundance of G. walkeri relative to the total area was found in the pine plantation, being 2.3 times higher than in the natural forest. More frogs were significantly found during the rainy season; nevertheless, active individuals were also found during the dry season. Significant differences were found in the microhabitat use with respect to the forest type and season. The most frequently microhabitat used in the two forest types was the pine leaf-litter; besides, in the native forest, the microhabitat occupied more frequently presented medium and large size stones. Geobatrachus walkeri is a successful species in pine plantations, associated permanently to its leaf-litter environment where it seems to develop its entire life cycle. The clear modifications in the soils and water, derived from the introduction of the pine plantation in this area, seem not to have negatively affected the conservation and successful maintenance of this species.

Abundance Ratios in Dwarf Elliptical Galaxies

NARCIS (Netherlands)

Sen, Seyda; Peletier, Reynier F.; Toloba, Elisa; Mentz, Jaco J.

The aim of this study is to determine abundance ratios and star formation histories (SFH) of dwarf ellipticals in the nearby Virgo cluster. We perform a stellar population analysis of 39 dEs and study them using index-index and scaling relations. We find an unusual behaviour where [Na/Fe] is

Collision-Induced Dissociation of Deprotonated Peptides. Relative Abundance of Side-Chain Neutral Losses, Residue-Specific Product Ions, and Comparison with Protonated Peptides.

Science.gov (United States)

Liang, Yuxue; Neta, Pedatsur; Yang, Xiaoyu; Stein, Stephen E

2018-03-01

High-accuracy MS/MS spectra of deprotonated ions of 390 dipeptides and 137 peptides with three to six residues are studied. Many amino acid residues undergo neutral losses from their side chains. The most abundant is the loss of acetaldehyde from threonine. The abundance of losses from the side chains of other amino acids is estimated relative to that of threonine. While some amino acids lose the whole side chain, others lose only part of it, and some exhibit two or more different losses. Side-chain neutral losses are less abundant in the spectra of protonated peptides, being significant mainly for methionine and arginine. In addition to the neutral losses, many amino acid residues in deprotonated peptides produce specific negative ions after peptide bond cleavage. An expanded list of fragment ions from protonated peptides is also presented and compared with those of deprotonated peptides. Fragment ions are mostly different for these two cases. These lists of fragments are used to annotate peptide mass spectral libraries and to aid in the confirmation of specific amino acids in peptides. Graphical Abstract ᅟ.

Relationship between abundance and morphology of benthic foraminifera Epistominella exigua: Palaeoclimatic implications

Digital Repository Service at National Institute of Oceanography (India)

Saraswat, R.; Deopujari, A.; Nigam, R.; Henriques, P.J.

The relationship between abundance (relative as well as absolute abundance) and morphology (size of the shell, numbers and proloculus size) of benthic foraminifera Epistominella exigua has been studied in a core to understand the influence...

Abundance, biting behaviour and parous rate of anopheline mosquito species in relation to malaria incidence in gold-mining areas of southern Venezuela.

Science.gov (United States)

Moreno, J E; Rubio-Palis, Y; Páez, E; Pérez, E; Sánchez, V

2007-12-01

A longitudinal entomological and epidemiological study was conducted in five localities of southern Venezuela between January 1999 and April 2000 to determine the abundance, biting behaviour and parity of anopheline mosquitoes (Diptera: Culicidae) in relation to climate variables and malaria incidence. A total of 3685 female anopheline mosquitoes, representing six species, were collected. The most abundant species were Anopheles marajoara Galvão & Damasceno (60.7%) and Anopheles darlingi Root (35.1%), which together represented 95.8% of the total anophelines collected. Abundance and species distribution varied by locality. Malaria prevalence varied from 12.5 to 21.4 cases per 1000 population. Transmission occurred throughout the year; the annual parasite index (API) for the study period was 813.0 cases per 1000 population, with a range of 71.6-2492 per 1000 population, depending on locality. Plasmodium vivax (Grassi & Feletti) (Coccidia: Plasmodiidae) accounted for 78.6% of cases, Plasmodium falciparum (Welch) for 21.4% and mixed infections (Pv+Pf) for 0.05) between mosquito abundance and rainfall. Correlations between malaria incidence by parasite species and mosquito abundance were not significant (P > 0.05). Monthly parous rates were similar for An. marajoara and An. darlingi throughout the year, with two peaks that coincided with the dry-rainy transition period and the period of less rain. Peaks in the incidence of malaria cases were observed 1 month after major peaks in biting rates of parous anophelines. Anopheles darlingi engages in biting activity throughout the night, with two minor peaks at 23.00-00.00 hours and 03.00-04.00 hours. Anopheles marajoara has a different pattern, with a biting peak at 19.00-21.00 hours and 76.6% of biting occurring before midnight. Although both vectors bite indoors and outdoors, they showed a highly significant (P < 0.01) degree of exophagic behaviour. The present study constitutes the first effort to characterize the

Latitudinal patterns in the abundance of major marine bacterioplankton groups

DEFF Research Database (Denmark)

Wietz, Matthias; Gram, Lone; Jørgensen, Bo

2010-01-01

relative abundance 37%, average absolute abundance 3.7×105 cells mL-1) including SAR11 (30%/3×105), Gammaproteobacteria (14%/1.2×105), and Bacteroidetes (12%/1.3×105) globally dominated the bacterioplankton. The SAR86 clade (4.6%/4.1×104) and Actinobacteria (4.5%/4×104) were detected ubiquitously, whereas...

Regulation of mRNA Translation Is a Novel Mechanism for Phthalate Toxicity.

Directory of Open Access Journals (Sweden)

Jun Ling

Full Text Available Phthalates are a group of plasticizers that are widely used in many consumer products and medical devices, thus generating a huge burden to human health. Phthalates have been known to cause a number of developmental and reproductive disorders functioning as endocrine modulators. They are also involved in carcinogenesis with mechanisms less understood. To further understand the molecular mechanisms of phthalate toxicity, in this study we reported a new effect of phthalates on mRNA translation/protein synthesis, a key regulatory step of gene expression. Butyl benzyl phthalate (BBP was found to directly inhibit mRNA translation in vitro but showed a complicated pattern of affecting mRNA translation in cells. In human kidney embryonic cell (HEK-293T, BBP increased cap-dependent mRNA translation at lower concentrations but showed inhibitory effect at higher concentrations. Cap-independent translation was not affected. On the other hand, mono (2-ethylhexyl phthalate (MEHP as a major metabolite of another important phthalate di (2-ethylhexyl phthalate (DEHP inhibited both can-dependent and -independent mRNA translation in vivo. In contrast, BBP and MEHP exhibited an overall promoting effect on mRNA translation in cancer cells. Mechanistic studies identified that the level and phosphorylation of eIF4E-BP (eIF4E binding protein and the amount of eIF4GI in eIF4F complex were altered in accordance with the effect of BBP on translation. BBP was also identified to directly bind to eIF4E, providing a further mechanism underlying the regulation of mRNA by phthalate. At the cellular level BBP inhibited normal cell growth but slightly promoted cancer cells (HT29 growth. Overall, this study provides the first evidence that phthalates can directly regulate mRNA translation as a novel mechanism to mediate their biological toxicities.

Diet and condition of mesopredators on coral reefs in relation to shark abundance.

Directory of Open Access Journals (Sweden)

Shanta C Barley

Full Text Available Reef sharks may influence the foraging behaviour of mesopredatory teleosts on coral reefs via both risk effects and competitive exclusion. We used a "natural experiment" to test the hypothesis that the loss of sharks on coral reefs can influence the diet and body condition of mesopredatory fishes by comparing two remote, atoll-like reef systems, the Rowley Shoals and the Scott Reefs, in northwestern Australia. The Rowley Shoals are a marine reserve where sharks are abundant, whereas at the Scott Reefs numbers of sharks have been reduced by centuries of targeted fishing. On reefs where sharks were rare, the gut contents of five species of mesopredatory teleosts largely contained fish while on reefs with abundant sharks, the same mesopredatory species consumed a larger proportion of benthic invertebrates. These measures of diet were correlated with changes in body condition, such that the condition of mesopredatory teleosts was significantly poorer on reefs with higher shark abundance. Condition was defined as body weight, height and width for a given length and also estimated via several indices of condition. Due to the nature of natural experiments, alternative explanations cannot be discounted. However, the results were consistent with the hypothesis that loss of sharks may influence the diet and condition of mesopredators and by association, their fecundity and trophic role. Regardless of the mechanism (risk effects, competitive release, or other, our findings suggest that overfishing of sharks has the potential to trigger trophic cascades on coral reefs and that further declines in shark populations globally should be prevented to protect ecosystem health.

Diet and condition of mesopredators on coral reefs in relation to shark abundance.

Science.gov (United States)

Barley, Shanta C; Meekan, Mark G; Meeuwig, Jessica J

2017-01-01

Reef sharks may influence the foraging behaviour of mesopredatory teleosts on coral reefs via both risk effects and competitive exclusion. We used a "natural experiment" to test the hypothesis that the loss of sharks on coral reefs can influence the diet and body condition of mesopredatory fishes by comparing two remote, atoll-like reef systems, the Rowley Shoals and the Scott Reefs, in northwestern Australia. The Rowley Shoals are a marine reserve where sharks are abundant, whereas at the Scott Reefs numbers of sharks have been reduced by centuries of targeted fishing. On reefs where sharks were rare, the gut contents of five species of mesopredatory teleosts largely contained fish while on reefs with abundant sharks, the same mesopredatory species consumed a larger proportion of benthic invertebrates. These measures of diet were correlated with changes in body condition, such that the condition of mesopredatory teleosts was significantly poorer on reefs with higher shark abundance. Condition was defined as body weight, height and width for a given length and also estimated via several indices of condition. Due to the nature of natural experiments, alternative explanations cannot be discounted. However, the results were consistent with the hypothesis that loss of sharks may influence the diet and condition of mesopredators and by association, their fecundity and trophic role. Regardless of the mechanism (risk effects, competitive release, or other), our findings suggest that overfishing of sharks has the potential to trigger trophic cascades on coral reefs and that further declines in shark populations globally should be prevented to protect ecosystem health.

Impact of target mRNA structure on siRNA silencing efficiency: A large-scale study.

Science.gov (United States)

Gredell, Joseph A; Berger, Angela K; Walton, S Patrick

2008-07-01

The selection of active siRNAs is generally based on identifying siRNAs with certain sequence and structural properties. However, the efficiency of RNA interference has also been shown to depend on the structure of the target mRNA, primarily through studies using exogenous transcripts with well-defined secondary structures in the vicinity of the target sequence. While these studies provide a means for examining the impact of target sequence and structure independently, the predicted secondary structures for these transcripts are often not reflective of structures that form in full-length, native mRNAs where interactions can occur between relatively remote segments of the mRNAs. Here, using a combination of experimental results and analysis of a large dataset, we demonstrate that the accessibility of certain local target structures on the mRNA is an important determinant in the gene silencing ability of siRNAs. siRNAs targeting the enhanced green fluorescent protein were chosen using a minimal siRNA selection algorithm followed by classification based on the predicted minimum free energy structures of the target transcripts. Transfection into HeLa and HepG2 cells revealed that siRNAs targeting regions of the mRNA predicted to have unpaired 5'- and 3'-ends resulted in greater gene silencing than regions predicted to have other types of secondary structure. These results were confirmed by analysis of gene silencing data from previously published siRNAs, which showed that mRNA target regions unpaired at either the 5'-end or 3'-end were silenced, on average, approximately 10% more strongly than target regions unpaired in the center or primarily paired throughout. We found this effect to be independent of the structure of the siRNA guide strand. Taken together, these results suggest minimal requirements for nucleation of hybridization between the siRNA guide strand and mRNA and that both mRNA and guide strand structure should be considered when choosing candidate si

On theoretical models of gene expression evolution with random genetic drift and natural selection.

Directory of Open Access Journals (Sweden)

Osamu Ogasawara

2009-11-01

Full Text Available The relative contributions of natural selection and random genetic drift are a major source of debate in the study of gene expression evolution, which is hypothesized to serve as a bridge from molecular to phenotypic evolution. It has been suggested that the conflict between views is caused by the lack of a definite model of the neutral hypothesis, which can describe the long-run behavior of evolutionary change in mRNA abundance. Therefore previous studies have used inadequate analogies with the neutral prediction of other phenomena, such as amino acid or nucleotide sequence evolution, as the null hypothesis of their statistical inference.In this study, we introduced two novel theoretical models, one based on neutral drift and the other assuming natural selection, by focusing on a common property of the distribution of mRNA abundance among a variety of eukaryotic cells, which reflects the result of long-term evolution. Our results demonstrated that (1 our models can reproduce two independently found phenomena simultaneously: the time development of gene expression divergence and Zipf's law of the transcriptome; (2 cytological constraints can be explicitly formulated to describe long-term evolution; (3 the model assuming that natural selection optimized relative mRNA abundance was more consistent with previously published observations than the model of optimized absolute mRNA abundances.The models introduced in this study give a formulation of evolutionary change in the mRNA abundance of each gene as a stochastic process, on the basis of previously published observations. This model provides a foundation for interpreting observed data in studies of gene expression evolution, including identifying an adequate time scale for discriminating the effect of natural selection from that of random genetic drift of selectively neutral variations.

Simultaneous isolation of mRNA and native protein from minute samples of cells

DEFF Research Database (Denmark)

Petersen, Tonny Studsgaard; Andersen, Claus Yding

2014-01-01

Precious biological samples often lack a sufficient number of cells for multiple procedures, such as extraction of mRNA while maintaining protein in a non-denatured state suitable for subsequent characterization. Here we present a new method for the simultaneous purification of mRNA and native...... in their native state for traditional protein assays. We validated the procedure using neonatal rat ovaries and small numbers of human granulosa cells, demonstrating the extraction of mRNA suitable for gene expression analysis with simultaneous isolation of native proteins suitable for downstream characterization...... proteins from samples containing small numbers of cells. Our approach utilizes oligodeoxythymidylate [oligo(dT)25]-coated paramagnetic beads in an optimized reaction buffer to isolate mRNA comparable in quantity and quality to mRNA isolated with existing methods, while maintaining the proteins...

Physical change in cytoplasmic messenger ribonucleoproteins in cells treated with inhibitors of mRNA transcription

International Nuclear Information System (INIS)

Dreyfuss, G.; Adam, S.A.; Choi, Y.D.

1984-01-01

Exposure of intact cells to UV light brings about cross-linking of polyadenylated mRNA to a set of cytoplasmic proteins which are in direct contact with the mRNA in vivo. Substantial amounts of an additional protein of molecular weight 38,000 become cross-linked to the mRNA when cells are treated with inhibitors of mRNA synthesis (actinomycin D, camptothecin, and 5,6-dichloro-1-beta-D-ribofuranosyl benzimidazole) or after infection with vesicular stomatitis virus. Cordycepin, which inhibits polyadenylation but not mRNA synthesis, has no such effect. Inhibitors of protein synthesis and of rRNA synthesis are also without effect on 38K cross-linking to mRNA. The onset of the effect of inhibitors of mRNA synthesis on the UV cross-linkable interaction between mRNA and 38K is rapid and reaches a maximal level in less than 60 min, and it is completely and rapidly reversible. In cells treated with actinomycin D, the amount of 38K which becomes cross-linked to mRNA is proportional to the extent of inhibition of mRNA synthesis. The association of 38K with mRNA during transcriptional arrest does not require protein synthesis because simultaneous treatment with the protein synthesis inhibitor emetine does not interfere with it. The effectors which promote the interaction of 38K with mRNA do not affect the proteins which are in contact with polyadenylated heterogeneous nuclear RNA and do not markedly affect protein synthesis in the cell. The 38K protein can be isolated with the polyribosomal polyadenylated fraction from which it was purified, and monoclonal antibodies against it were prepared

How ants drop out: ant abundance on tropical mountains.

Science.gov (United States)

Longino, John T; Branstetter, Michael G; Colwell, Robert K

2014-01-01

In tropical wet forests, ants are a large proportion of the animal biomass, but the factors determining abundance are not well understood. We characterized ant abundance in the litter layer of 41 mature wet forest sites spread throughout Central America (Chiapas, Guatemala, Honduras, Nicaragua, and Costa Rica) and examined the impact of elevation (as a proxy for temperature) and community species richness. Sites were intentionally chosen to minimize variation in precipitation and seasonality. From sea level to 1500 m ant abundance very gradually declined, community richness declined more rapidly than abundance, and the local frequency of the locally most common species increased. These results suggest that within this elevational zone, density compensation is acting, maintaining high ant abundance as richness declines. In contrast, in sites above 1500 m, ant abundance dropped abruptly to much lower levels. Among these high montane sites, community richness explained much more of the variation in abundance than elevation, and there was no evidence of density compensation. The relative stability of abundance below 1500 m may be caused by opposing effects of temperature on productivity and metabolism. Lower temperatures may decrease productivity and thus the amount of food available for consumers, but slower metabolisms of consumers may allow maintenance of higher biomass at lower resource supply rates. Ant communities at these lower elevations may be highly interactive, the result of continuous habitat presence over geological time. High montane sites may be ephemeral in geological time, resulting in non-interactive communities dominated by historical and stochastic processes. Abundance in these sites may be determined by the number of species that manage to colonize and/or avoid extinction on mountaintops.

How ants drop out: ant abundance on tropical mountains.

Directory of Open Access Journals (Sweden)

John T Longino

Full Text Available In tropical wet forests, ants are a large proportion of the animal biomass, but the factors determining abundance are not well understood. We characterized ant abundance in the litter layer of 41 mature wet forest sites spread throughout Central America (Chiapas, Guatemala, Honduras, Nicaragua, and Costa Rica and examined the impact of elevation (as a proxy for temperature and community species richness. Sites were intentionally chosen to minimize variation in precipitation and seasonality. From sea level to 1500 m ant abundance very gradually declined, community richness declined more rapidly than abundance, and the local frequency of the locally most common species increased. These results suggest that within this elevational zone, density compensation is acting, maintaining high ant abundance as richness declines. In contrast, in sites above 1500 m, ant abundance dropped abruptly to much lower levels. Among these high montane sites, community richness explained much more of the variation in abundance than elevation, and there was no evidence of density compensation. The relative stability of abundance below 1500 m may be caused by opposing effects of temperature on productivity and metabolism. Lower temperatures may decrease productivity and thus the amount of food available for consumers, but slower metabolisms of consumers may allow maintenance of higher biomass at lower resource supply rates. Ant communities at these lower elevations may be highly interactive, the result of continuous habitat presence over geological time. High montane sites may be ephemeral in geological time, resulting in non-interactive communities dominated by historical and stochastic processes. Abundance in these sites may be determined by the number of species that manage to colonize and/or avoid extinction on mountaintops.

Population density approach for discrete mRNA distributions in generalized switching models for stochastic gene expression.

Science.gov (United States)

Stinchcombe, Adam R; Peskin, Charles S; Tranchina, Daniel

2012-06-01

We present a generalization of a population density approach for modeling and analysis of stochastic gene expression. In the model, the gene of interest fluctuates stochastically between an inactive state, in which transcription cannot occur, and an active state, in which discrete transcription events occur; and the individual mRNA molecules are degraded stochastically in an independent manner. This sort of model in simplest form with exponential dwell times has been used to explain experimental estimates of the discrete distribution of random mRNA copy number. In our generalization, the random dwell times in the inactive and active states, T_{0} and T_{1}, respectively, are independent random variables drawn from any specified distributions. Consequently, the probability per unit time of switching out of a state depends on the time since entering that state. Our method exploits a connection between the fully discrete random process and a related continuous process. We present numerical methods for computing steady-state mRNA distributions and an analytical derivation of the mRNA autocovariance function. We find that empirical estimates of the steady-state mRNA probability mass function from Monte Carlo simulations of laboratory data do not allow one to distinguish between underlying models with exponential and nonexponential dwell times in some relevant parameter regimes. However, in these parameter regimes and where the autocovariance function has negative lobes, the autocovariance function disambiguates the two types of models. Our results strongly suggest that temporal data beyond the autocovariance function is required in general to characterize gene switching.

Expressions of interferon-inducible genes IFIT1 and IFIT4 mRNA in PBMCs of patients with systemic lupus erythematosus

International Nuclear Information System (INIS)

Liu Chunyan; Chen Xingguo; Wang Zizheng

2009-01-01

To investigate the expression levels of interferon-inducible genes (IFIT1, IFIT4) in the peripheral blood mononuclear cells (PBMCs) of patients with systemic lupus erythematosus (SLE), and the relations between these genes expression levels and disease activity, the expression levels of IFIT1 and IFIT4 mRNA in the 95 patients with SLE and 48 normal controls were detected by Sybr green dye based real-time quantitative PCR method, and these genes expression levels were compared with anti-double strand DNA antibody. The associations between the expression levels of IFIT1, IFIT4 mRNA, anti-double strand DNA antibody and SLEDAI scores in patients with SLE were analyzed. The results showed that the expression levels of IFIT1, IFIT4 mRNA in the SLE patients were significantly higher than those of the normal controls (P<0.01). The expression levels of IFIT1, IFIT4 mRNA in the active SLE patients were higher than those of the inactive SLE patients (P<0.05). The real time expression levels of IFIT1 and IFIT4 mRNA showed positive correlations with each other (P<0.05) in patients with SLE. There was positively correlation between the expression levels of IFIT1, IFIT4 mRNA and the anti-double strand DNA antibody (P<0.05). The expression levels of IFIT1, IFIT4 mRNA in patients with SLE were significantly higher than those of the normal controls, and positively associated with SLEDAI scores, so they were helpful in evaluating SLE disease activity and severity. To inhibit the expressions of IFIT1, IFIT4 mRNA may provide a novel target for SLE treatment. (authors)

Compilation of solar abundance data

International Nuclear Information System (INIS)

Hauge, Oe.; Engvold, O.

1977-01-01

Interest in the previous compilations of solar abundance data by the same authors (ITA--31 and ITA--39) has led to this third, revised edition. Solar abundance data of 67 elements are tabulated and in addition upper limits for the abundances of 5 elements are listed. References are made to 167 papers. A recommended abundance value is given for each element. (JIW)

Abundances in planetary nebulae near the galactic centre .1. Abundance determinations

NARCIS (Netherlands)

Ratag, MA; Pottasch, [No Value; Dennefeld, M; Menzies, J

1997-01-01

Abundance determinations of about 110 planetary nebulae, which are likely to be in the Galactic Bulge are presented. Plasma diagnostics have been performed by making use of the available forbidden line ratios combined with radio continuum measurements. Chemical abundances of He, O, N, Ne, S, Ar, and

Astrocyte cultures derived from human brain tissue express angiotensinogen mRNA

International Nuclear Information System (INIS)

Milsted, A.; Barna, B.P.; Ransohoff, R.M.; Brosnihan, K.B.; Ferrario, C.M.

1990-01-01

The authors have identified human cultured cell lines that are useful for studying angiotensinogen gene expression and its regulation in the central nervous system. A model cell system of human central nervous system origin expressing angiotensinogen has not previously been available. Expression of angiotensinogen mRNA appears to be a basal property of noninduced human astrocytes, since astrocytic cell lines derived from human glioblastomas or nonneoplastic human brain tissue invariably produced angiotensinogen mRNA. In situ hybridization histochemistry revealed that angiotensinogen mRNA production was not limited to a subpopulation of astrocytes because >99% of cells in these cultures contained angiotensinogen mRNA. These cell lines will be useful in studies of the molecular mechanisms controlling angiotensin synthesis and the role of biologically active angiotensin in the human brain by allowing the authors to examine regulation of expression of the renin-angiotensin system in human astrocyte cultures

A selective splicing variant of hepcidin mRNA in hepatocellular carcinoma cell lines

International Nuclear Information System (INIS)

Toki, Yasumichi; Sasaki, Katsunori; Tanaka, Hiroki; Yamamoto, Masayo; Hatayama, Mayumi; Ito, Satoshi; Ikuta, Katsuya; Shindo, Motohiro; Hasebe, Takumu; Nakajima, Shunsuke; Sawada, Koji; Fujiya, Mikihiro; Torimoto, Yoshihiro; Ohtake, Takaaki; Kohgo, Yutaka

2016-01-01

Hepcidin is a main regulator of iron metabolism, of which abnormal expression affects intestinal absorption and reticuloendothelial sequestration of iron by interacting with ferroportin. It is also noted that abnormal iron accumulation is one of the key factors to facilitate promotion and progression of cancer including hepatoma. By RT-PCR/agarose gel electrophoresis of hepcidin mRNA in a hepatocellular carcinoma cell line HLF, a smaller mRNA band was shown in addition to the wild-type hepcidin mRNA. From sequencing analysis, this additional band was a selective splicing variant of hepcidin mRNA lacking exon 2 of HAMP gene, producing the transcript that encodes truncated peptide lacking 20 amino acids at the middle of preprohepcidin. In the present study, we used the digital PCR, because such a small amount of variant mRNA was difficult to quantitate by the conventional RT-PCR amplification. Among seven hepatoma-derived cell lines, six cell lines have significant copy numbers of this variant mRNA, but not in one cell line. In the transient transfection analysis of variant-type hepcidin cDNA, truncated preprohepcidin has a different character comparing with native preprohepcidin: its product is insensitive to digestion, and secreted into the medium as a whole preprohepcidin form without maturation. Loss or reduction of function of HAMP gene by aberrantly splicing may be a suitable phenomenon to obtain the proliferating advantage of hepatoma cells. - Highlights: • An aberrant splicing variant of hepcidin mRNA lacking exon 2 of HAMP gene. • Absolute quantification of hepcidin mRNA by digital PCR amplification. • Hepatoma-derived cell lines have significant copies of variant-type hepcidin mRNA. • Truncated preprohepcidin is secreted from cells without posttranslational cleavage.

A selective splicing variant of hepcidin mRNA in hepatocellular carcinoma cell lines

Energy Technology Data Exchange (ETDEWEB)

Toki, Yasumichi [Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, Hokkaido 078-8510 (Japan); Sasaki, Katsunori, E-mail: k-sasaki@asahikawa-med.ac.jp [Department of Gastrointestinal Immunology and Regenerative Medicine, Asahikawa Medical University, Hokkaido 078-8510 (Japan); Tanaka, Hiroki [Department of Legal Medicine, Asahikawa Medical University, Hokkaido 078-8510 (Japan); Yamamoto, Masayo; Hatayama, Mayumi; Ito, Satoshi; Ikuta, Katsuya; Shindo, Motohiro; Hasebe, Takumu; Nakajima, Shunsuke; Sawada, Koji; Fujiya, Mikihiro [Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, Hokkaido 078-8510 (Japan); Torimoto, Yoshihiro [Oncology Center, Asahikawa Medical University Hospital, Hokkaido 078-8510 (Japan); Ohtake, Takaaki; Kohgo, Yutaka [Department of Gastroenterology, International University of Health and Welfare Hospital, Tochigi 329-2763 (Japan)

2016-08-05

Hepcidin is a main regulator of iron metabolism, of which abnormal expression affects intestinal absorption and reticuloendothelial sequestration of iron by interacting with ferroportin. It is also noted that abnormal iron accumulation is one of the key factors to facilitate promotion and progression of cancer including hepatoma. By RT-PCR/agarose gel electrophoresis of hepcidin mRNA in a hepatocellular carcinoma cell line HLF, a smaller mRNA band was shown in addition to the wild-type hepcidin mRNA. From sequencing analysis, this additional band was a selective splicing variant of hepcidin mRNA lacking exon 2 of HAMP gene, producing the transcript that encodes truncated peptide lacking 20 amino acids at the middle of preprohepcidin. In the present study, we used the digital PCR, because such a small amount of variant mRNA was difficult to quantitate by the conventional RT-PCR amplification. Among seven hepatoma-derived cell lines, six cell lines have significant copy numbers of this variant mRNA, but not in one cell line. In the transient transfection analysis of variant-type hepcidin cDNA, truncated preprohepcidin has a different character comparing with native preprohepcidin: its product is insensitive to digestion, and secreted into the medium as a whole preprohepcidin form without maturation. Loss or reduction of function of HAMP gene by aberrantly splicing may be a suitable phenomenon to obtain the proliferating advantage of hepatoma cells. - Highlights: • An aberrant splicing variant of hepcidin mRNA lacking exon 2 of HAMP gene. • Absolute quantification of hepcidin mRNA by digital PCR amplification. • Hepatoma-derived cell lines have significant copies of variant-type hepcidin mRNA. • Truncated preprohepcidin is secreted from cells without posttranslational cleavage.

Creatine kinase and alpha-actin mRNA levels decrease in diabetic rat hearts

International Nuclear Information System (INIS)

Popovich, B.; Barrieux, A.; Dillmann, W.H.

1987-01-01

Diabetic cardiomyopathy is associated with cardiac atrophy and isoenzyme redistribution. To determine if tissue specific changes occur in mRNAs coding for α-actin and creatine kinase (CK), they performed RNA blot analysis. Total ventricular RNA from control (C) and 4 wk old diabetic (D) rats were hybridized with 32 P cDNA probes for α-actin and CK. A tissue independent cDNA probe, CHOA was also used. Signal intensity was quantified by photodensitometry. D CK mRNA was 47 +/- 16% lower in D vs C. Insulin increases CK mRNA by 20% at 1.5 hs, and completely reverses the deficit after 4 wks. D α-actin mRNA is 66 +/- 18% lower in D vs C. Insulin normalized α-actin mRNA by 5 hs. CHOA mRNA is unchanged in D vs C, but D + insulin CHOA mRNA is 30 +/- 2% lower than C. In rats with diabetic cardiomyopathy, muscle specific CK and α-actin mRNAs are decreased. Insulin treatment reverses these changes

[Relative abundance, population structure, habitat preferences and activity patterns of Tapirus bairdii (Perissodactyla: Tapiridae), in Chimalapas forest, Oaxaca, Mexico].

Science.gov (United States)

Lira-Torres, Iván; Briones-Salas, Miguel; Sánchez-Rojas, Gerardo

2014-12-01

Baird's tapir (Tapirus bairdii) is endangered primarily because of habitat loss and fragmentation, and overhunting throughout its distribution range. One of the priority land areas for the conservation of this species is the Northern part of its range in the Chimalapas forest, Oaxaca. The aim of this research was to determine the relative abundance, population struc- ture, habitat preferences and activity patterns of Baird's tapir (Tapirus bairdii) in the Chimalapas forest, Oaxaca, Mexico, through the non-invasive technique of camera-trap sampling. A total of five sampling sessions were undertaken among 2009-2013, and used a total of 30 camera-traps in each period. The determinant factor of the sampling design was the hunting between two study areas. A total sampling effort of 9000 trap-days allowed to estimate an index of relative abundance (IRA) of 6.77 tapir photographs/1,000 trap-days (n = 61). IRA varied significantly between sampling stations (Mann-Whitney, p dry season in tropical rain forest without hunting (χ2, p tropical rain forest and secondary vegetation habitats showed higher photo frequency than expected from random (χ2, p forest appears to be the second most important terrestrial priority ecoregion, just after the Mayan Forest (Campeche, Chiapas, Quintana Roo), for the conservation of tapir populations, not only for Mexico but also for Central America.

APOGEE Chemical Abundances of the Sagittarius Dwarf Galaxy

International Nuclear Information System (INIS)

Hasselquist, Sten; Holtzman, Jon; Shetrone, Matthew; Smith, Verne; Nidever, David L.; McWilliam, Andrew; Fernández-Trincado, J. G.; Tang, Baitian; Beers, Timothy C.; Majewski, Steven R.; Anguiano, Borja; Tissera, Patricia B.; Alvar, Emma Fernández; Carigi, Leticia; Delgado Inglada, Gloria; Allende Prieto, Carlos; Battaglia, Giuseppina; García-Hernández, D. A.; Almeida, Andres; Frinchaboy, Peter

2017-01-01

The Apache Point Observatory Galactic Evolution Experiment provides the opportunity of measuring elemental abundances for C, N, O, Na, Mg, Al, Si, P, K, Ca, V, Cr, Mn, Fe, Co, and Ni in vast numbers of stars. We analyze thechemical-abundance patterns of these elements for 158 red giant stars belonging to the Sagittarius dwarf galaxy (Sgr). This is the largest sample of Sgr stars with detailed chemical abundances, and it is the first time that C, N, P, K, V, Cr, Co, and Ni have been studied at high resolution in this galaxy. We find that the Sgr stars with [Fe/H] ≳ −0.8 are deficient in all elemental abundance ratios (expressed as [X/Fe]) relative to the Milky Way, suggesting that the Sgr stars observed today were formed from gas that was less enriched by Type II SNe than stars formed in the Milky Way. By examining the relative deficiencies of the hydrostatic (O, Na, Mg, and Al) and explosive (Si, P, K, and Mn) elements, our analysis supports the argument that previous generations of Sgr stars were formed with a top-light initial mass function, one lacking the most massive stars that would normally pollute the interstellar medium with the hydrostatic elements. We use a simple chemical-evolution model, flexCE, to further support our claim and conclude that recent stellar generations of Fornax and the Large Magellanic Cloud could also have formed according to a top-light initial mass function.

APOGEE Chemical Abundances of the Sagittarius Dwarf Galaxy

Energy Technology Data Exchange (ETDEWEB)

Hasselquist, Sten; Holtzman, Jon [New Mexico State University, Las Cruces, NM 88003 (United States); Shetrone, Matthew [University of Texas at Austin, McDonald Observatory, Fort Davis, TX 79734 (United States); Smith, Verne; Nidever, David L. [National Optical Astronomy Observatories, Tucson, AZ 85719 (United States); McWilliam, Andrew [The Observatories of the Carnegie Institute of Washington, 813 Santa Barbara Street, Pasadena, CA 91101 (United States); Fernández-Trincado, J. G.; Tang, Baitian [Departamento de Astronomía, Casilla 160-C, Universidad de Concepción, Concepción (Chile); Beers, Timothy C. [Department of Physics and JINA Center for the Evolution of the Elements, University of Notre Dame, Notre Dame, IN 46556 (United States); Majewski, Steven R.; Anguiano, Borja [Department of Astronomy, University of Virginia, Charlottesville, VA 22904-4325 (United States); Tissera, Patricia B. [Department of Physics, Universidad Andres Bello, 700 Fernandez Concha (Chile); Alvar, Emma Fernández; Carigi, Leticia; Delgado Inglada, Gloria [Instituto de Astronomía, Universidad Nacional Autnoma de México, Apdo. Postal 70264, Ciudad de México, 04510 (Mexico); Allende Prieto, Carlos; Battaglia, Giuseppina; García-Hernández, D. A. [Instituto de Astrofísica de Canarias, E-38205 La Laguna, Tenerife (Spain); Almeida, Andres [Departamento de Física, Facultad de Ciencias, Universidad de La Serena, Cisternas 1200, La Serena (Chile); Frinchaboy, Peter, E-mail: sten@nmsu.edu, E-mail: holtz@nmsu.edu, E-mail: shetrone@astro.as.utexas.edu, E-mail: vsmith@email.noao.edu [Texas Christian University, Fort Worth, TX 76129 (United States); and others

2017-08-20

The Apache Point Observatory Galactic Evolution Experiment provides the opportunity of measuring elemental abundances for C, N, O, Na, Mg, Al, Si, P, K, Ca, V, Cr, Mn, Fe, Co, and Ni in vast numbers of stars. We analyze thechemical-abundance patterns of these elements for 158 red giant stars belonging to the Sagittarius dwarf galaxy (Sgr). This is the largest sample of Sgr stars with detailed chemical abundances, and it is the first time that C, N, P, K, V, Cr, Co, and Ni have been studied at high resolution in this galaxy. We find that the Sgr stars with [Fe/H] ≳ −0.8 are deficient in all elemental abundance ratios (expressed as [X/Fe]) relative to the Milky Way, suggesting that the Sgr stars observed today were formed from gas that was less enriched by Type II SNe than stars formed in the Milky Way. By examining the relative deficiencies of the hydrostatic (O, Na, Mg, and Al) and explosive (Si, P, K, and Mn) elements, our analysis supports the argument that previous generations of Sgr stars were formed with a top-light initial mass function, one lacking the most massive stars that would normally pollute the interstellar medium with the hydrostatic elements. We use a simple chemical-evolution model, flexCE, to further support our claim and conclude that recent stellar generations of Fornax and the Large Magellanic Cloud could also have formed according to a top-light initial mass function.

ABUNDANCES IN THE LOCAL REGION. II. F, G, AND K DWARFS AND SUBGIANTS

Energy Technology Data Exchange (ETDEWEB)

Luck, R. Earle, E-mail: rel2@case.edu [Department of Astronomy, Case Western Reserve University 10900 Euclid Avenue, Cleveland, OH 44106-7215 (United States)

2017-01-01

Parameters and abundances have been derived for 1002 stars of spectral types F, G, and K, and luminosity classes IV and V. After culling the sample for rotational velocity and effective temperature, 867 stars remain for discussion. Twenty-eight elements are considered in the analysis. The α , iron-peak, and Period 5 transition metal abundances for these stars show a modest enhancement over solar averaging about 0.05 dex. The lanthanides are more abundant, averaging about +0.2 dex over solar. The question is: Are these stars enhanced, or is the Sun somewhat metal-poor relative to these stars? The consistency of the abundances derived here supports an argument for the latter view. Lithium, carbon, and oxygen abundances have been derived. The stars show the usual lithium astration as a function of mass/temperature. There are more than 100 planet-hosts in the sample, and there is no discernible difference in their lithium content, relative to the remaining stars. The carbon and oxygen abundances show the well-known trend of decreasing [x/Fe] ratio with increasing [Fe/H].

Abundances of neutron-capture elements in G 24-25

DEFF Research Database (Denmark)

Liu, S.; Nissen, Poul Erik; Schuster, W. J.

2012-01-01

for a peculiar halo star G24-25 with [Fe/H] = -1.4 in order to probe its origin. Methods. The equivalent widths of unblended lines are measured from high resolution NOT/FIES spectra and used to derive abundances based on Kurucz model atmospheres. In the case of CH, Pr, Eu, Gd, and Pb lines, the abundances...... are derived by fitting synthetic profiles to the observed spectra. Abundance analyses are performed both relative to the Sun and to a normal halo star G16-20 that has similar stellar parameters as G24-25. Results. We find that G24-25 is a halo subgiant star with an unseen component. It has large...

Influenza A Virus NS1 Protein Promotes Efficient Nuclear Export of Unspliced Viral M1 mRNA.

Science.gov (United States)

Pereira, Carina F; Read, Eliot K C; Wise, Helen M; Amorim, Maria J; Digard, Paul

2017-08-01

Influenza A virus mRNAs are transcribed by the viral RNA-dependent RNA polymerase in the cell nucleus before being exported to the cytoplasm for translation. Segment 7 produces two major transcripts: an unspliced mRNA that encodes the M1 matrix protein and a spliced transcript that encodes the M2 ion channel. Export of both mRNAs is dependent on the cellular NXF1/TAP pathway, but it is unclear how they are recruited to the export machinery or how the intron-containing but unspliced M1 mRNA bypasses the normal quality-control checkpoints. Using fluorescent in situ hybridization to monitor segment 7 mRNA localization, we found that cytoplasmic accumulation of unspliced M1 mRNA was inefficient in the absence of NS1, both in the context of segment 7 RNPs reconstituted by plasmid transfection and in mutant virus-infected cells. This effect was independent of any major effect on steady-state levels of segment 7 mRNA or splicing but corresponded to a ∼5-fold reduction in the accumulation of M1. A similar defect in intronless hemagglutinin (HA) mRNA nuclear export was seen with an NS1 mutant virus. Efficient export of M1 mRNA required both an intact NS1 RNA-binding domain and effector domain. Furthermore, while wild-type NS1 interacted with cellular NXF1 and also increased the interaction of segment 7 mRNA with NXF1, mutant NS1 polypeptides unable to promote mRNA export did neither. Thus, we propose that NS1 facilitates late viral gene expression by acting as an adaptor between viral mRNAs and the cellular nuclear export machinery to promote their nuclear export. IMPORTANCE Influenza A virus is a major pathogen of a wide variety of mammalian and avian species that threatens public health and food security. A fuller understanding of the virus life cycle is important to aid control strategies. The virus has a small genome that encodes relatively few proteins that are often multifunctional. Here, we characterize a new function for the NS1 protein, showing that, as well as

Change in avian abundance predicted from regional forest inventory data

Science.gov (United States)

Twedt, Daniel J.; Tirpak, John M.; Jones-Farrand, D. Todd; Thompson, Frank R.; Uihlein, William B.; Fitzgerald, Jane A.

2010-01-01

An inability to predict population response to future habitat projections is a shortcoming in bird conservation planning. We sought to predict avian response to projections of future forest conditions that were developed from nationwide forest surveys within the Forest Inventory and Analysis (FIA) program. To accomplish this, we evaluated the historical relationship between silvicolous bird populations and FIA-derived forest conditions within 25 ecoregions that comprise the southeastern United States. We aggregated forest area by forest ownership, forest type, and tree size-class categories in county-based ecoregions for 5 time periods spanning 1963-2008. We assessed the relationship of forest data with contemporaneous indices of abundance for 24 silvicolous bird species that were obtained from Breeding Bird Surveys. Relationships between bird abundance and forest inventory data for 18 species were deemed sufficient as predictive models. We used these empirically derived relationships between regional forest conditions and bird populations to predict relative changes in abundance of these species within ecoregions that are anticipated to coincide with projected changes in forest variables through 2040. Predicted abundances of these 18 species are expected to remain relatively stable in over a quarter (27%) of the ecoregions. However, change in forest area and redistribution of forest types will likely result in changed abundance of some species within many ecosystems. For example, abundances of 11 species, including pine warbler (Dendroica pinus), brown-headed nuthatch (Sitta pusilla), and chuckwills- widow (Caprimulgus carolinensis), are projected to increase within more ecoregions than ecoregions where they will decrease. For 6 other species, such as blue-winged warbler (Vermivora pinus), Carolina wren (Thryothorus ludovicianus), and indigo bunting (Passerina cyanea), we projected abundances will decrease within more ecoregions than ecoregions where they will

Abundance estimation and Conservation Biology

Directory of Open Access Journals (Sweden)

Nichols, J. D.

2004-06-01

Full Text Available Abundance is the state variable of interest in most population–level ecological research and in most programs involving management and conservation of animal populations. Abundance is the single parameter of interest in capture–recapture models for closed populations (e.g., Darroch, 1958; Otis et al., 1978; Chao, 2001. The initial capture–recapture models developed for partially (Darroch, 1959 and completely (Jolly, 1965; Seber, 1965 open populations represented efforts to relax the restrictive assumption of population closure for the purpose of estimating abundance. Subsequent emphases in capture–recapture work were on survival rate estimation in the 1970’s and 1980’s (e.g., Burnham et al., 1987; Lebreton et al.,1992, and on movement estimation in the 1990’s (Brownie et al., 1993; Schwarz et al., 1993. However, from the mid–1990’s until the present time, capture–recapture investigators have expressed a renewed interest in abundance and related parameters (Pradel, 1996; Schwarz & Arnason, 1996; Schwarz, 2001. The focus of this session was abundance, and presentations covered topics ranging from estimation of abundance and rate of change in abundance, to inferences about the demographic processes underlying changes in abundance, to occupancy as a surrogate of abundance. The plenary paper by Link & Barker (2004 is provocative and very interesting, and it contains a number of important messages and suggestions. Link & Barker (2004 emphasize that the increasing complexity of capture–recapture models has resulted in large numbers of parameters and that a challenge to ecologists is to extract ecological signals from this complexity. They offer hierarchical models as a natural approach to inference in which traditional parameters are viewed as realizations of stochastic processes. These processes are governed by hyperparameters, and the inferential approach focuses on these hyperparameters. Link & Barker (2004 also suggest that

Abundance estimation and conservation biology

Science.gov (United States)

Nichols, J.D.; MacKenzie, D.I.

2004-01-01

Abundance is the state variable of interest in most population–level ecological research and in most programs involving management and conservation of animal populations. Abundance is the single parameter of interest in capture–recapture models for closed populations (e.g., Darroch, 1958; Otis et al., 1978; Chao, 2001). The initial capture–recapture models developed for partially (Darroch, 1959) and completely (Jolly, 1965; Seber, 1965) open populations represented efforts to relax the restrictive assumption of population closure for the purpose of estimating abundance. Subsequent emphases in capture–recapture work were on survival rate estimation in the 1970’s and 1980’s (e.g., Burnham et al., 1987; Lebreton et al.,1992), and on movement estimation in the 1990’s (Brownie et al., 1993; Schwarz et al., 1993). However, from the mid–1990’s until the present time, capture–recapture investigators have expressed a renewed interest in abundance and related parameters (Pradel, 1996; Schwarz & Arnason, 1996; Schwarz, 2001). The focus of this session was abundance, and presentations covered topics ranging from estimation of abundance and rate of change in abundance, to inferences about the demographic processes underlying changes in abundance, to occupancy as a surrogate of abundance. The plenary paper by Link & Barker (2004) is provocative and very interesting, and it contains a number of important messages and suggestions. Link & Barker (2004) emphasize that the increasing complexity of capture–recapture models has resulted in large numbers of parameters and that a challenge to ecologists is to extract ecological signals from this complexity. They offer hierarchical models as a natural approach to inference in which traditional parameters are viewed as realizations of stochastic processes. These processes are governed by hyperparameters, and the inferential approach focuses on these hyperparameters. Link & Barker (2004) also suggest that our attention

Exploratory Bioinformatics Study of lncRNAs in Alzheimer’s Disease mRNA Sequences with Application to Drug Development

Directory of Open Access Journals (Sweden)

T. Holden

2013-01-01

Full Text Available Long noncoding RNA (lncRNA within mRNA sequences of Alzheimer’s disease genes, namely, APP, APOE, PSEN1, and PSEN2, has been analyzed using fractal dimension (FD computation and correlation analysis. We examined lncRNA by comparing mRNA FD to corresponding coding DNA sequences (CDSs FD. APP, APOE, and PSEN1 CDSs select slightly higher FDs compared to the mRNA, while PSEN2 CDSs FDs are lower. The correlation coefficient for these sequences is 0.969. A comparative study of differentially expressed MAPK signaling pathway lncRNAs in pancreatic cancer cells shows a correlation of 0.771. Selection of higher FD CDSs could indicate interaction of Alzheimer’s gene products APP, APOE, and PSEN1. Including hypocretin sequences (where all CDSs have higher fractal dimensions than mRNA in the APP, APOE, and PSEN1 sequence analyses improves correlation, but the inclusion of erythropoietin (where all CDSs have higher FD than mRNA would suppress correlation, suggesting that HCRT, a hypothalamus neurotransmitter related to the wake/sleep cycle, might be better when compared to EPO, a glycoprotein hormone, for targeting Alzheimer’s disease drug development. Fractal dimension and entropy correlation have provided supporting evidence, consistent with evolutionary studies, for using a zebrafish model together with a mouse model, in HCRT drug development.

Effects of corticosteroid on the expressions of neuropeptide and cytokine mRNA and on tenocyte viability in lateral epicondylitis

Directory of Open Access Journals (Sweden)

Han Soo

2012-10-01

Full Text Available Abstract Background The purpose of this study was to determine the reaction mechanism of corticosteroid by analyzing the expression patterns of neuropeptides (substance P (SP, calcitonin gene related peptide (CGRP and of cytokines (interleukin (IL-1α, tumor growth factor (TGF-β after corticosteroid treatment in lateral epicondylitis. In addition, we also investigated whether corticosteroid influenced tenocyte viability. Methods The corticosteroid triamcinolone acetonide (TAA was applied to cultured tenocytes of lateral epicondylitis, and the changes in the mRNA expressions of neuropeptides and cytokines and tenocyte viabilities were analyzed at seven time points. Quantitative real-time polymerase chain reaction and an MTT assay were used. Results The expression of SP mRNA was maximally inhibited by TAA at 24 hours but recovered at 72 hours, and the expressions of CGRP mRNA and IL-1α mRNA were inhibited at 24 and 3 hours, respectively. The expression of TGF-β mRNA was not significant. Tenocyte viability was significantly reduced by TAA at 24 hours. Conclusions We postulate that the reaction mechanism predominantly responsible for symptomatic relief after a corticosteroid injection involves the inhibitions of neuropeptides and cytokines, such as, CGRP and IL-1α. However the tenocyte viability was compromised by a corticosteroid.

FoxP3 mRNA splice forms in synovial CD4+ T cells in rheumatoid arthritis and psoriatic arthritis

DEFF Research Database (Denmark)

Ryder, L Rebekka; Bartels, Else Marie; Woetmann, Anders

2012-01-01

Our aim was to elucidate the relative amount of the different splice forms of FoxP3 mRNA in CD4+ T cells in peripheral blood (PB) compared to synovial fluid (SF) in RA and PsA patients. FoxP3 mRNA was measured using a quantitative real-time PCR method. CD4+ T cells were isolated from 17 paired...... samples of PB and SF from RA and PsA patients, and PB from 10 controls. FoxP3fl and FoxP3Δ2 mRNA was significantly increased (6.7 and 2.1-fold, respectively) in PB CD4+ T cells from RA patients compared to controls. FoxP3fl and Δ2 mRNA in SF CD4+ T cells was increased compared to controls in sero......-negative RA and PsA, but not in sero-positive RA patients, who had a high FoxP3 expression in both PB and SF. The FoxP3Δ2Δ7 mRNA was barely detectable in patient samples, and not at all in healthy individuals. We provide evidence of an increased expression of FoxP3 splice forms in synovial CD4+ T cells from...

Cosmological evolution of the nitrogen abundance

Science.gov (United States)

Vangioni, Elisabeth; Dvorkin, Irina; Olive, Keith A.; Dubois, Yohan; Molaro, Paolo; Petitjean, Patrick; Silk, Joe; Kimm, Taysun

2018-06-01

The abundance of nitrogen in the interstellar medium is a powerful probe of star formation processes over cosmological time-scales. Since nitrogen can be produced both in massive and intermediate-mass stars with metallicity-dependent yields, its evolution is challenging to model, as evidenced by the differences between theoretical predictions and observations. In this work, we attempt to identify the sources of these discrepancies using a cosmic evolution model. To further complicate matters, there is considerable dispersion in the abundances from observations of damped Lyα absorbers (DLAs) at z ˜ 2-3. We study the evolution of nitrogen with a detailed cosmic chemical evolution model and find good agreement with these observations, including the relative abundances of (N/O) and (N/Si). We find that the principal contribution of nitrogen comes from intermediate-mass stars, with the exception of systems with the lowest N/H, where nitrogen production might possibly be dominated by massive stars. This last result could be strengthened if stellar rotation which is important at low metallicity can produce significant amounts of nitrogen. Moreover, these systems likely reside in host galaxies with stellar masses below 108.5 M⊙. We also study the origin of the observed dispersion in nitrogen abundances using the cosmological hydrodynamical simulations Horizon-AGN. We conclude that this dispersion can originate from two effects: difference in the masses of the DLA host galaxies, and difference in their position inside the galaxy.

Spectroscopic abundance analyses of the 3He stars HD 185330 and 3 Cen A

Science.gov (United States)

Sadakane, Kozo; Nishimura, Masayoshi

2018-04-01

Abundances of 21 elements in two 3He stars, HD 185330 and 3 Cen A, have been analysed relative to the well-studied sharp-lined B3 V star ι Her. Six elements (P, Ti, Mn, Fe, Ni, and Br) are over-abundant in these two peculiar stars, while six elements (C, O, Mg, Al, S, and Cl) are under-abundant. Absorption lines of the two rarely observed heavy elements Br II and Kr II are detected in both stars and these elements are both over-abundant. The centroid wavelengths of the Ca II infrared triplet lines in these stars are redshifted relative to those lines in ι Her and the presence of heavy isotopes of Ca (mass number 44-46) in these two stars is confirmed. In spite of these similarities, there are several remarkable differences in abundance pattern between these two stars. N is under-abundant in HD 185330, as in many Hg-Mn stars, while it is significantly over-abundant in 3 Cen A. P and Ga are both over-abundant in 3 Cen A, while only P is over-abundant and no trace of absorption line of Ga II can be found in HD 185330. Large over-abundances of Kr and Xe are found in both stars, while the abundance ratio Kr/Xe is significantly different between them (-1.4 dex in HD 185330 and +1.2 dex in 3 Cen A). Some physical explanations are needed to account for these qualitative differences.

Detection of melatonin receptor mRNA in human muscle

International Nuclear Information System (INIS)

Li Lei

2004-01-01

To verify the expression of melatonin receptor mRNA in human, muscle, muscle beside vertebrae was collected to obtain total RNA and the mRNA of melatonin receptor was detected by RT-PCR method. The electrophoretic results of RT-PCR products by mt 1 and MT 2 primer were all positive and the sequence is corresponding with human melatonin receptor cDNA. It suggests that melatonin may act on the muscle beside vertebrae directly and regulate its growth and development. (authors)

OXYGEN ABUNDANCES IN CEPHEIDS

International Nuclear Information System (INIS)

Luck, R. E.; Andrievsky, S. M.; Korotin, S. N.; Kovtyukh, V. V.

2013-01-01

Oxygen abundances in later-type stars, and intermediate-mass stars in particular, are usually determined from the [O I] line at 630.0 nm, and to a lesser extent, from the O I triplet at 615.7 nm. The near-IR triplets at 777.4 nm and 844.6 nm are strong in these stars and generally do not suffer from severe blending with other species. However, these latter two triplets suffer from strong non-local thermodynamic equilibrium (NLTE) effects and thus see limited use in abundance analyses. In this paper, we derive oxygen abundances in a large sample of Cepheids using the near-IR triplets from an NLTE analysis, and compare those abundances to values derived from a local thermodynamic equilibrium (LTE) analysis of the [O I] 630.0 nm line and the O I 615.7 nm triplet as well as LTE abundances for the 777.4 nm triplet. All of these lines suffer from line strength problems making them sensitive to either measurement complications (weak lines) or to line saturation difficulties (strong lines). Upon this realization, the LTE results for the [O I] lines and the O I 615.7 nm triplet are in adequate agreement with the abundance from the NLTE analysis of the near-IR triplets.

The ApaH-like phosphatase TbALPH1 is the major mRNA decapping enzyme of trypanosomes.

Directory of Open Access Journals (Sweden)

Susanne Kramer

2017-06-01

Full Text Available 5'-3' decay is the major mRNA decay pathway in many eukaryotes, including trypanosomes. After deadenylation, mRNAs are decapped by the nudix hydrolase DCP2 of the decapping complex and finally degraded by the 5'-3' exoribonuclease. Uniquely, trypanosomes lack homologues to all subunits of the decapping complex, while deadenylation and 5'-3' degradation are conserved. Here, I show that the parasites use an ApaH-like phosphatase (ALPH1 as their major mRNA decapping enzyme. The protein was recently identified as a novel trypanosome stress granule protein and as involved in mRNA binding. A fraction of ALPH1 co-localises exclusively with the trypanosome 5'-3' exoribonuclease XRNA to a special granule at the posterior pole of the cell, indicating a connection between the two enzymes. RNAi depletion of ALPH1 is lethal and causes a massive increase in total mRNAs that are deadenylated, but have not yet started 5'-3' decay. These data suggest that ALPH1 acts downstream of deadenylation and upstream of mRNA degradation, consistent with a function in mRNA decapping. In vitro experiments show that recombinant, N-terminally truncated ALHP1 protein, but not a catalytically inactive mutant, sensitises the capped trypanosome spliced leader RNA to yeast Xrn1, but only if an RNA 5' polyphosphatase is included. This indicates that the decapping mechanism of ALPH1 differs from the decapping mechanism of Dcp2 by leaving more than one phosphate group at the mRNA's 5' end. This is the first reported function of a eukaryotic ApaH-like phosphatase, a bacterial-derived class of enzymes present in all phylogenetic super-groups of the eukaryotic kingdom. The substrates of eukaryotic ApaH-like phosphatases are unknown. However, the substrate of the related bacterial enzyme ApaH, diadenosine tetraphosphate, is highly reminiscent of a eukaryotic mRNA cap.

Differential regulation of renal cyclooxygenase mRNA by dietary salt intake

DEFF Research Database (Denmark)

Jensen, B L; Kurtz, A

1997-01-01

RNA correlated directly with salt intake. We conclude that dietary salt intake influences renal cyclooxygenase mRNAs zone-specifically with opposite responses between cortex and medulla. Cortical COX II-mediated prostaglandin formation is probably important in low salt states whereas medullary COX I......Experiments were done to investigate the influence of dietary salt intake on renal cyclooxygenase (COX) I and II mRNA levels. To this end rats were fed either a low NaCl diet (LS; 0.02% NaCl wt/wt) or a high NaCl diet (HS diet; 4% NaCl wt/wt) for 5, 10 and 20 days. After 10 days Na excretion...... differed 760-fold, plasma renin activity and renin mRNA were increased eight- and threefold in LS compared to HS animals. Total renal COX I mRNA decreased 50% following the LS diet and did not change after the HS diet. Conversely, COX II mRNA declined after HS intake and transiently increased after salt...

Application of General Circulation Models to Assess the Potential Impact of Climate Change on Potential Distribution and Relative Abundance of Melanoplus sanguinipes (Fabricius (Orthoptera: Acrididae in North America

Directory of Open Access Journals (Sweden)

O. Olfert

2011-01-01

Full Text Available Climate is the dominant factor determining the distribution and abundance of most insect species. In recent years, the issue of climatic changes caused by human activities and the effects on agriculture has raised concern. General circulation model scenarios were applied to a bioclimatic model of Melanoplus sanguinipes to assess the potential impact of global warming on its distribution and relative abundance. Native to North America and widely distributed, M. sanguinipes is one of the grasshopper species of the continent most responsible for economic damage to grain, oilseed, pulse, and forage crops. Compared to predicted range and distribution under current climate conditions, model results indicated that M. sanguinipes would have increased range and relative abundance under the three general circulation model scenarios in more northern regions of North America. Conversely, model output predicted that the range of this crop pest could contract in regions where climate conditions became limiting.

Larval abundance and its relation to macrofouling settlement pattern in the coastal waters of Kalpakkam, southeastern part of India.

Science.gov (United States)

Sahu, Gouri; Satpathy, K K; Mohanty, A K; Biswas, Sudeepta; Achary, M Smita; Sarkar, S K

2013-02-01

The present work revealed that salinity, water temperature, and food availability were the most crucial factors affecting the abundance of larvae and their settlement as macrofouling community in the coastal waters of Kalpakkam. Quantitative as well as qualitative results showed that late post-monsoon (April-May) and pre-monsoon (June-September) periods were found to be suitable periods for larval growth, development, and survival to adult stages for most of the organisms. Clustering of physico-chemical and biological (including larval and adult availability) data yielded two major clusters; one formed by northeast (NE) monsoon months (October-January) and the other by post-monsoon/summer (February-May) months, whereas; pre-monsoon months (June-September) were distributed between these two clusters. Among all the major macrofouler groups, only bivalves established a successful relationship between its larval abundance and adult settlement. Principal component analysis indicated good associations of bivalve larvae with polychaete larvae and adult bivalves with adult barnacles. However, biotic relation between ascidians and bryozoans was observed both in the larval as well as adult community.

Myeloperoxidase mRNA detection for lineage determination of leukemic blasts: retrospective analysis.

Science.gov (United States)

Crisan, D; Anstett, M J

1995-07-01

Myeloperoxidase (MPO) mRNA is an early myeloid marker; its detection in the morphologically and immunophenotypically primitive blasts of acute undifferentiated leukemia (AUL) establishes myeloid lineage and allows reclassification as acute myelogenous leukemia with minimal differentiation (AML-MO). We have previously reported a procedure for MPO mRNA detection by RT-PCR (reverse transcription-polymerase chain reaction) and an adaptation for use of routine hematology smears. This variant procedure allows retrospective analysis of mRNA and is used in the present study to evaluate the lineage of leukemic blasts in seven cases with morphology and cytochemistry consistent with AUL. All hematology smears used in this study were air-dried, unstained or Wright-stained and stored at room temperature for periods varying between 3 days and 2 years. MPO mRNA was detected in six cases, establishing the myeloid lineage of the blasts and the diagnosis of AML-MO. In the remaining case, the blasts were MPO mRNA negative, confirming the diagnosis of AUL. The RT-PCR procedure for retrospective mRNA analysis is useful in the clinical setting, due to its high specificity and sensitivity, speed (less than 24 h), safety (no radioactivity) and convenient use of routine hematology smears; it is particularly attractive in clinical situations when fresh or frozen specimens are no longer available at the time when the need for molecular diagnostics becomes apparent.

Chemical Abundance Analysis of Moving Group W11450 (Latham 1)

Science.gov (United States)

O'Connell, Julia E.; Martens, Kylee; Frinchaboy, Peter M.

2016-12-01

We present elemental abundances for all seven stars in Moving Group W11450 (Latham 1) to determine if they may be chemically related. These stars appear to be both spatially and kinematically related, but no spectroscopic abundance analysis exists in literature. Abundances for eight elements were derived via equivalent width analyses of high-resolution (R ˜ 60,000), high-signal-to-noise ratio ( ˜ 100) spectra obtained with the Otto Struve 2.1 m telescope and the Sandiford Echelle Spectrograph at McDonald Observatory. The large star-to-star scatter in metallicity, -0.55 ≤ [Fe/H] ≤slant 0.06 dex (σ = 0.25), implies these stars were not produced from the same chemically homogeneous molecular cloud, and are therefore not part of a remnant or open cluster as previously proposed. Prior to this analysis, it was suggested that two stars in the group, W11449 and W11450, are possible wide binaries. The candidate wide binary pair show similar chemical abundance patterns with not only iron but with other elements analyzed in this study, suggesting the proposed connection between these two stars may be real.

H II region in NGC 6744: Spectrophotometry and chemical abundances

International Nuclear Information System (INIS)

Talent, D.L.

1982-01-01

Spectrophotometry of emission lines in the lambdalambda3700--6800 spectral range is presented for An H II region in an outer arm of NGC6744, a southern hemisphere galaxy of type SAB(r)bc II. The electron temperature, derived from the [O III] lines and assuming N/sub e/ = 100 cm -3 , was found to be 9,630 +- 450 K. Ionic abundances, derived in the usual fashion from the measured line strengths, were corrected to total relative number abundances by application of the standard ionization correction factor (ICF) scheme and by comparison to models. The derived abundances, relative to log Hequivalent12.00, are log He = 10.96 +- 0.06, log N = 7.34 +- 0.26, log O log O = 8.44 +- 0.10, log Ne = 7.80 +- 0.16, and log S = 6.75 +- 0.28. The NGC 6744 H II region abundances, and various ratios, are compared to similar data for H II regions in the SMC, LMC, and the Perseus arm of the Galaxy,. From the comparison it is suggested that the histories of nucleosynthesis in the outer regions of NGC 6744 and the Galaxy could have been quite similar

Analysis of a herpetofaunal community from an altered marshy area in Sicily; with special remarks on habitat use (niche breadth and overlap), relative abundance of lizards and snakes, and the correlation between predator abundance and tail loss in lizards

NARCIS (Netherlands)

Luiselli, L.; Angelici, F.M.; Di Vittorio, M.; Spinnato, A.; Politano, E.

2005-01-01

A field survey was conducted in a highly degraded barren environment in Sicily in order to investigate herpetofaunal community composition and structure, habitat use (niche breadth and overlap) and relative abundance of a snake predator and two species of lizard prey. The site was chosen because it

Correlation of the A-FABP Gene Polymorphism and mRNA Expression with Intramuscular Fat Content in Three-Yellow Chicken and Hetian-Black Chicken.

Science.gov (United States)

Wang, Yong; Chen, Hongwei; Han, Diangang; Chen, Ying; Muhatai, Gemingguli; Kurban, Tursunjan; Xing, Jinming; He, Jianzhong

2017-01-02

The adipocyte-type fatty acid-binding protein (A-FABP) is considered a candidate gene for fat metabolism; thus, it affects fat deposition in chickens. The present study was designed to examine the polymorphism and mRNA abundance of the A-FABP gene with intramuscular fat (IMF) in the pectoralis muscles (PM) and leg muscles (LM) of Three-yellow Chicken (TYC) and Hetian-black Chicken (HTBC). In total, 60 TYCs and 60 HTBCs were sacrificed using exsanguination at market age. The IMF contents of the PM and LM in the HTBC were significantly higher than those in the TYC. Three genotypes of the A-FABP gene first exon, AA, AB, and BB, were examined by polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP), and a C51 T mutational site, which is a silent substitution mutation, was revealed. The IMF contents of the AA genotype in the PM of the HTBC were significantly higher than those in the AB genotype; thus, the C51 T mutable site is a gene marker for selecting a higher IMF content in the PM of the HTBC. The relative expression of the A-FABP mRNA in the LM of the HTBC, which was measured by quantitative real-time PCR, was significantly higher than in the TYC. A significantly positive association was detected between A-FABP expression with the IMF contents of the PM and LM of both the TYC and the HTBC. These results provide basic data that might be helpful to further research the role of the A-FABP gene in fat deposition and fatty acid metabolism in chickens.

A glimpse at mRNA dynamics reveals cellular domains and rapid trafficking through granules

NARCIS (Netherlands)

Gemert, Alice Myriam Christi van

2011-01-01

mRNA transport and targeting are essential to gene expression regulation. Specific mRNA sequences can bind several proteins and together form RiboNucleoProtein particles (RNP). The various proteins within the RNP determine mRNA fate: translation, transport or decay. RNP composition varies with

Host trait combinations drive abundance and canopy distribution of atmospheric bromeliad assemblages.

Science.gov (United States)

Chaves, Cleber Juliano Neves; Dyonisio, Júlio César; Rossatto, Davi Rodrigo

2016-01-01

Epiphytes are strongly dependent on the conditions created by their host's traits and a certain degree of specificity is expected between them, even if these species are largely abundant in a series of tree hosts of a given environment, as in the case of atmospheric bromeliads. Despite their considerable abundance in these environments, we hypothesize that stochasticity alone cannot explain the presence and abundance of atmospheric bromeliads on host trees, since host traits could have a greater influence on the establishment of these bromeliads. We used secondary and reforested seasonal forests and three distinct silvicultures to test whether species richness, phylogenetic diversity and functional diversity of trees can predict the differential presence, abundance and distribution of atmospheric bromeliads on hosts. We compared the observed parameters of their assemblage with null models and performed successive variance hierarchic partitions of abundance and distribution of the assemblage to detect the influence of multiple traits of the tree hosts. Our results do not indicate direct relationships between the abundance of atmospheric bromeliads and phylogenetic or functional diversity of trees, but instead indicate that bromeliads occurred on fewer tree species than expected by chance. We distinguished functional tree patterns that can improve or reduce the abundance of atmospheric bromeliads, and change their distribution on branches and trunk. While individual tree traits are related to increased abundance, species traits are related to the canopy distribution of atmospheric bromeliad assemblages. A balance among these tree functional patterns drives the atmospheric bromeliad assemblage of the forest patches. Published by Oxford University Press on behalf of the Annals of Botany Company.

Bumble bee nest abundance, foraging distance, and host-plant reproduction: implications for management and conservation.

Science.gov (United States)

Geib, Jennifer C; Strange, James P; Galenj, Candace

2015-04-01

Recent reports of global declines in pollinator species imply an urgent need to assess the abundance of native pollinators and density-dependent benefits for linked plants. In this study, we investigated (1) pollinator nest distributions and estimated colony abundances, (2) the relationship between abundances of foraging workers and the number of nests they represent, (3) pollinator foraging ranges, and (4) the relationship between pollinator abundance and plant reproduction. We examined these questions in an alpine ecosystem in the Colorado Rocky Mountains, focusing on four alpine bumble bee species (Bombus balteatus, B. flavifrons, B. bifarius, and B. sylvicola), and two host plants that differ in their degrees of pollinator specialization (Trifolium dasyphyllum and T. parryi). Using microsatellites, we found that estimated colony abundances among Bombus species ranged from ~18 to 78 colonies/0.01 km2. The long-tongued species B. balteatus was most common, especially high above treeline, but the subalpine species B. bifarius was unexpectedly abundant for this elevation range. Nests detected among sampled foragers of each species were correlated with the number of foragers caught. Foraging ranges were smaller than expected for all Bombus species, ranging from 25 to 110 m. Fruit set for the specialized plant, Trifolium parryi, was positively related to the abundance of its Bombus pollinator. In contrast, fruit set for the generalized plant, T. dasyphyllum, was related to abundance of all Bombus species. Because forager abundance was related to nest abundance of each Bombus species and was an equally effective predictor of plant fecundity, forager inventories are probably suitable for assessing the health of outcrossing plant populations. However, nest abundance, rather than forager abundance, better reflects demographic and genetic health in populations of eusocial pollinators such as bumble bees. Development of models incorporating the parameters we have measured

Human apolipoprotein B (apoB) mRNA: Identification of two distinct apoB mRNAs, an mRNA with the apoB-100 sequence and an apoB mRNA containing a premature in-frame translational stop codon, in both liver and intestine

International Nuclear Information System (INIS)

Higuchi, K.; Hospattankar, A.V.; Law, S.W.; Meglin, N.; Cortright, J.; Brewer, H.B. Jr.

1988-01-01

Human apolipoprotein B (apoB) is present in plasma as two separate isoproteins, designated apoB-100 (512 kDa) and apoB-48 (250 kDa). ApoB is encoded by a single gene on chromosome 2, and a single nuclear mRNA is edited and processed into two separate apoB mRNAs. A 14.1-kilobase apoB mRNA codes for apoB-100, and the second mRNA, which codes for apoB-48, contains a premature stop codon generated by a single base substitution of cytosine to uracil at nucleotide 6,538, which converts the translated CAA codon coding for the amino acid glutamine at residue 2,153 in apoB-100 to a premature in-frame stop codon (UAA). Two 30-base synthetic oligonucleotides, designated apoB-Stop and apoB-Gln, were synthesized containing the complementary sequence to the stop codon (UAA) and glutamine codon (CAA), respectively. The combined results from these studies establish that both human intestine and liver contain the two distinct apoB mRNAs, an mRNA that codes for apoB-100 and an apoB mRNA that contains the premature stop codon, which codes for apoB-48. The premature in-frame stop codon is not tissue specific and is present in both human liver and intestine

Landscape Effects on the Presence, Abundance and Diversity of Mosquitoes in Mediterranean Wetlands.

Directory of Open Access Journals (Sweden)

David Roiz

Full Text Available Environment determines the distribution of mosquito-borne diseases in that it influences the vector-host-pathogen transmission cycle, including vector distribution, abundance and diversity. In this study, we analyse the relationship between environmental variables estimated by remote sensing and the spatial distribution (presence, abundance and diversity of seven mosquito species vectors of West Nile and other pathogens (Usutu, avian malaria and dirofilariasis in the Doñana Natural Park, Spain. Traps were distributed over an area of 54,984 ha divided into six ecological units: marshland, sand dunes, scrubland, ricefields, crops and fishponds. We collected mosquitoes once a month from up to 112 locations using BG-Sentinel traps baited with BG-lure and CO2 during March-November 2010. Hydroperiod, NDVI and Inundation surface were estimated at several resolution scales (100, 250, 500, 1000 and 2000 metres from corrected and normalized Landsat Images. We sampled 972,346 female mosquitoes, the most abundant species being Culex theileri, Ochlerotatus caspius, Culex modestus, Culex perexiguus, Culex pipiens, Anopheles atroparvus and Ochlerotatus detritus. Our results suggest that: (1 hydroperiod, inundation surface and NDVI are strongly related to the spatial distribution of mosquitoes; (2 the spatial scales used to measure these variables affected quantification of these relationships, the larger scale being more informative; (3 these relationships are species-specific; (4 hydroperiod is negatively related to mosquito presence and richness; (5 Culex abundance is positively related to hydroperiod; (6 NDVI is positively related to mosquito diversity, presence and abundance, except in the case of the two salt marsh species (Oc. caspius and Oc. detritus; and (7 inundation surfaces positively condition the abundance and richness of most species except the salt marsh mosquitoes. Remote sensing data provided reliable information for monitoring mosquito

Pubertal Escape From Estradiol Negative Feedback in Ewe Lambs Is Not Accounted for by Decreased ESR1 mRNA or Protein in Kisspeptin Neurons.

Science.gov (United States)

Bedenbaugh, Michelle N; D'Oliveira, Marcella; Cardoso, Rodolfo C; Hileman, Stanley M; Williams, Gary L; Amstalden, Marcel

2018-01-01

In this study, we investigated whether decreased sensitivity to estradiol negative feedback is associated with reduced estrogen receptor α (ESR1) expression in kisspeptin neurons as ewe lambs approach puberty. Lambs were ovariectomized and received no implant (OVX) or an implant containing estradiol (OVX+E). In the middle arcuate nucleus (mARC), ESR1 messenger RNA (mRNA) was greater in OVX than OVX+E lambs but did not differ elsewhere. Post hoc analysis of luteinizing hormone (LH) secretion from OVX+E lambs revealed three patterns of LH pulsatility: low [1 to 2 pulses per 12 hours; low frequency (LF), n = 3], moderate [6 to 7 pulses per 12 hours; moderate frequency (MF), n = 6], and high [>10 pulses per 12 hours; high frequency (HF), n = 5]. The percentage of kisspeptin neurons containing ESR1 mRNA in the preoptic area did not differ among HF, MF, or LF groups. However, the percentage of kisspeptin neurons containing ESR1 mRNA in the mARC was greater in HF (57%) than in MF (36%) or LF (27%) lambs and did not differ from OVX (50%) lambs. A higher percentage of kisspeptin neurons contained ESR1 protein in all regions of the arcuate nucleus (ARC) in OVX compared with OVX+E lambs. There were no differences in ESR1 protein among the HF, MF, or LF groups in the preoptic area or ARC. Contrary to our hypothesis, increases in LH pulsatility were associated with enhanced ESR1 mRNA abundance in kisspeptin neurons in the ARC, and absence of estradiol increased the percentage of kisspeptin neurons containing ESR1 protein in the ARC. Therefore, changes in the expression of ESR1, particularly in kisspeptin neurons in the ARC, do not explain the pubertal escape from estradiol negative feedback in ewe lambs. Copyright © 2018 Endocrine Society.

Complexity on Acute Myeloid Leukemia mRNA Transcript Variant

Directory of Open Access Journals (Sweden)

Carlo Cattani

2011-01-01

Full Text Available This paper deals with the sequence analysis of acute myeloid leukemia mRNA. Six transcript variants of mlf1 mRNA, with more than 2000 bps, are analyzed by focusing on the autocorrelation of each distribution. Through the correlation matrix, some patches and similarities are singled out and commented, with respect to similar distributions. The comparison of Kolmogorov fractal dimension will be also given in order to classify the six variants. The existence of a fractal shape, patterns, and symmetries are discussed as well.

Low-level lasers alter mRNA levels from traditional reference genes used in breast cancer cells

Science.gov (United States)

Teixeira, A. F.; Canuto, K. S.; Rodrigues, J. A.; Fonseca, A. S.; Mencalha, A. L.

2017-07-01

Cancer is among the leading causes of mortality worldwide, increasing the importance of treatment development. Low-level lasers are used in several diseases, but some concerns remains on cancers. Reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) is a technique used to understand cellular behavior through quantification of mRNA levels. Output data from target genes are commonly relative to a reference that cannot vary according to treatment. This study evaluated reference genes levels from MDA-MB-231 cells exposed to red or infrared lasers at different fluences. Cultures were exposed to red and infrared lasers, incubated (4 h, 37 °C), total RNA was extracted and cDNA synthesis was performed to evaluate mRNA levels from ACTB, GUSB and TRFC genes by RT-qPCR. Specific amplification was verified by melting curves and agarose gel electrophoresis. RefFinder enabled data analysis by geNorm, NormFinder and BestKeeper. Specific amplifications were obtained and, although mRNA levels from ACTB, GUSB or TRFC genes presented no significant variation through traditional statistical analysis, Excel-based tools revealed that the use of these reference genes are dependent of laser characteristics. Our data showed that exposure to low-level red and infrared lasers at different fluences alter the mRNA levels from ACTB, GUSB and TRFC in MDA-MB-231 cells.

Search for antisense copies of beta-globin mRNA in anemic mouse spleen

Directory of Open Access Journals (Sweden)

Taylor John M

2001-03-01

Full Text Available Abstract Background Previous studies by Volloch and coworkers have reported that during the expression of high levels of β-globin mRNA in the spleen of anemic mice, they could also detect small but significant levels of an antisense (AS globin RNA species, which they postulated might have somehow arisen by RNA-directed RNA synthesis. For two reasons we undertook to confirm and possibly extend these studies. First, previous studies in our lab have focussed on what is an unequivocal example of host RNA-directed RNA polymerase activity on the RNA genome of human hepatitis delta virus. Second, if AS globin species do exist they could in turn form double-stranded RNA species which might induce post-transcriptional gene silencing, a phenomenon somehow provoked in eukaryotic cells by AS RNA sequences. Results We reexamined critical aspects of the previous globin studies. We used intraperitoneal injections of phenylhydrazine to induce anemia in mice, as demonstrated by the appearance and ultimate disappearance of splenomegaly. While a 30-fold increase in globin mRNA was detected in the spleen, the relative amount of putative AS RNA could be no more than 0.004%. Conclusions Contrary to earlier reports, induction of a major increase in globin transcripts in the mouse spleen was not associated with a detectable level of antisense RNA to globin mRNA.

Bacterial 16S rRNA gene analysis revealed that bacteria related to Arcobacter spp. constitute an abundant and common component of the oyster microbiota (Tiostrea chilensis).

Science.gov (United States)

Romero, J; García-Varela, M; Laclette, J P; Espejo, R T

2002-11-01

To explore the bacterial microbiota in Chilean oyster (Tiostrea chilensis), a molecular approach that permits detection of different bacteria, independently of their capacity to grow in culture media, was used. Bacterial diversity was assessed by analysis of both the 16S rDNA and the 16S-23S intergenic region, obtained by PCR amplifications of DNA extracted from depurated oysters. RFLP of the PCR amplified 16S rDNA showed a prevailing pattern in most of the individuals analyzed, indicating that a few bacterial species were relatively abundant and common in oysters. Cloning and sequencing of the 16S rDNA with the prevailing RFLP pattern indicated that this rRNA was most closely related to Arcobacter spp. However, analysis by the size of the amplified 16S-23S rRNA intergenic regions revealed not Arcobacter spp. but Staphylococcus spp. related bacteria as a major and common component in oyster. These different results may be caused by the absence of target for one of the primers employed for amplification of the intergenic region. Neither of the two bacteria species found in large abundance was recovered after culturing under aerobic, anaerobic, or microaerophilic conditions. This result, however, is expected because the number of bacteria recovered after cultivation was less than 0.01% of the total. All together, these observations suggest that Arcobacter-related strains are probably abundant and common in the Chilean oyster bacterial microbiota.

Impairment of FOS mRNA stabilization following translation arrest in granulocytes from myelodysplastic syndrome patients.

Science.gov (United States)

Feng, Xiaomin; Shikama, Yayoi; Shichishima, Tsutomu; Noji, Hideyoshi; Ikeda, Kazuhiko; Ogawa, Kazuei; Kimura, Hideo; Takeishi, Yasuchika; Kimura, Junko

2013-01-01

Although quantitative and qualitative granulocyte defects have been described in myelodysplastic syndromes (MDS), the underlying molecular basis of granulocyte dysfunction in MDS is largely unknown. We recently found that FOS mRNA elevation under translation-inhibiting stimuli was significantly smaller in granulocytes from MDS patients than in healthy individuals. The aim of this study is to clarify the cause of the impaired FOS induction in MDS. We first examined the mechanisms of FOS mRNA elevation using granulocytes from healthy donors cultured with the translation inhibitor emetine. Emetine increased both transcription and mRNA stability of FOS. p38 MAPK inhibition abolished the emetine-induced increase of FOS transcription but did not affect FOS mRNA stabilization. The binding of an AU-rich element (ARE)-binding protein HuR to FOS mRNA containing an ARE in 3'UTR was increased by emetine, and the knockdown of HuR reduced the FOS mRNA stabilizing effect of emetine. We next compared the emetine-induced transcription and mRNA stabilization of FOS between MDS patients and healthy controls. Increased rates of FOS transcription by emetine were similar in MDS and controls. In the absence of emetine, FOS mRNA decayed to nearly 17% of initial levels in 45 min in both groups. In the presence of emetine, however, 76.7±19.8% of FOS mRNA remained after 45 min in healthy controls, versus 37.9±25.5% in MDS (Pknowledge, this is the first report demonstrating attenuation of stress-induced FOS mRNA stabilization in MDS granulocytes.

M31 GLOBULAR CLUSTER ABUNDANCES FROM HIGH-RESOLUTION, INTEGRATED-LIGHT SPECTROSCOPY

International Nuclear Information System (INIS)

Colucci, Janet E.; Bernstein, Rebecca A.; Cameron, Scott; McWilliam, Andrew; Cohen, Judith G.

2009-01-01

We report the first detailed chemical abundances for five globular clusters (GCs) in M31 from high-resolution (R ∼ 25,000) spectroscopy of their integrated light (IL). These GCs are the first in a larger set of clusters observed as part of an ongoing project to study the formation history of M31 and its GC population. The data presented here were obtained with the HIRES echelle spectrograph on the Keck I telescope and are analyzed using a new IL spectra analysis method that we have developed. In these clusters, we measure abundances for Mg, Al, Si, Ca, Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Y, and Ba, ages ≥10 Gyr, and a range in [Fe/H] of -0.9 to -2.2. As is typical of Milky Way GCs, we find these M31 GCs to be enhanced in the α-elements Ca, Si, and Ti relative to Fe. We also find [Mg/Fe] to be low relative to other [α/Fe], and [Al/Fe] to be enhanced in the IL abundances. These results imply that abundances of Mg, Al (and likely O, Na) recovered from IL do display the inter- and intra-cluster abundance variations seen in individual Milky Way GC stars, and that special care should be taken in the future in interpreting low- or high-resolution IL abundances of GCs that are based on Mg-dominated absorption features. Fe-peak and the neutron-capture elements Ba and Y also follow Milky Way abundance trends. We also present high-precision velocity dispersion measurements for all five M31 GCs, as well as independent constraints on the reddening toward the clusters from our analysis.

Characterization of a major late herpes simplex virus type 1 mRNA.

Science.gov (United States)

Costa, R H; Devi, B G; Anderson, K P; Gaylord, B H; Wagner, E K

1981-05-01

A major, late 6-kilobase (6-kb) mRNa mapping in the large unique region of herpes simplex virus type 1 (HSV-1) was characterized by using two recombinant DNA clones, one containing EcoRI fragment G (0.190 to 0.30 map units) in lambda. WES.B (L. Enquist, M. Madden, P. Schiop-Stansly, and G. Vandl Woude, Science 203:541-544, 1979) and one containing HindIII fragment J (0.181 to 0.259 map units) in pBR322. This 6-kb mRNA had its 3' end to the left of 0.231 on the prototypical arrangement of the HSV-1 genome and was transcribed from right to left. It was bounded on both sides by regions containing a large number of distinct mRNA species, and its 3' end was partially colinear with a 1.5-kb mRNA which encoded a 35,000-dalton polypeptide. The 6-kb mRNA encoded a 155,000-dalton polypeptide which was shown to be the only one of this size detectable by hybrid-arrested translation encoded by late polyadenylated polyribosomal RNA. The S1 nuclease mapping experiments indicated that there were no introns in the coding sequence for this mRNA and that its 3' end mapped approximately 800 nucleotides to the left of the BglII site at 0.231, whereas its 5' end extended very close to the BamHI site at 0.266.

Investigation of plutonium abundance and age analysis

Energy Technology Data Exchange (ETDEWEB)

Huailong, Wu; Jian, Gong; Fanhua, Hao [China Academy of Engineering Physics, Mianyang (China). Inst. of Nuclear Physics and Chemistry

2007-06-15

Based on spectra analysis software, all of the plutonium material peak counts are analyzed. Relatively efficiency calibration is done by the non-coupling peaks of {sup 239}Pu. By using the known isotopes half life and yield, the coupling peaks counts are allocated by non-coupling peaks, consequently the atom ratios of each isotope are gotten. The formula between atom ratio and abundance or age is deduced by plutonium material isotopes decay characteristic. And so the abundance and age of plutonium material is gotten. After some re- peat measurements for a plutonium equipment are completed, a comparison between our analysis results and PC-FRAM and the owner's reference results are done. (authors)

2'-O-methylation in mRNA disrupts tRNA decoding during translation elongation.

Science.gov (United States)

Choi, Junhong; Indrisiunaite, Gabriele; DeMirci, Hasan; Ieong, Ka-Weng; Wang, Jinfan; Petrov, Alexey; Prabhakar, Arjun; Rechavi, Gideon; Dominissini, Dan; He, Chuan; Ehrenberg, Måns; Puglisi, Joseph D

2018-03-01

Chemical modifications of mRNA may regulate many aspects of mRNA processing and protein synthesis. Recently, 2'-O-methylation of nucleotides was identified as a frequent modification in translated regions of human mRNA, showing enrichment in codons for certain amino acids. Here, using single-molecule, bulk kinetics and structural methods, we show that 2'-O-methylation within coding regions of mRNA disrupts key steps in codon reading during cognate tRNA selection. Our results suggest that 2'-O-methylation sterically perturbs interactions of ribosomal-monitoring bases (G530, A1492 and A1493) with cognate codon-anticodon helices, thereby inhibiting downstream GTP hydrolysis by elongation factor Tu (EF-Tu) and A-site tRNA accommodation, leading to excessive rejection of cognate aminoacylated tRNAs in initial selection and proofreading. Our current and prior findings highlight how chemical modifications of mRNA tune the dynamics of protein synthesis at different steps of translation elongation.

Quantitative PCR--new diagnostic tool for quantifying specific mRNA and DNA molecules

DEFF Research Database (Denmark)

Schlemmer, B O; Sorensen, B S; Overgaard, J

2004-01-01

of a subset of ligands from the EGF system is increased in bladder cancer. Furthermore, measurement of the mRNA concentration gives important information such as the expression of these ligands correlated to the survival of the patients. In addition to the alterations at the mRNA level, changes also can occur...... at the DNA level in the EGF system. Thus, it has been demonstrated that the number of genes coding for the human epidermal growth factor receptor 2 (HER2) is increased in a number of breast tumors. It is now possible to treat breast cancer patients with a humanized antibody reacting with HER2...... of mRNA or DNA in biological samples. In this study quantitative PCR was used to investigate the role of the EGF (epidermal growth factor) system in cancer both for measurements of mRNA concentrations and for measurements of the number of copies of specific genes. It is shown that the mRNA expression...

Applying the breaks on gene expression - mRNA deadenylation by Pop2p

DEFF Research Database (Denmark)

Andersen, Kasper Røjkjær; Jonstrup, Anette Thyssen; Van, Lan Bich

When driving a car, control of the brakes is just as important as control of the accelerator pedal. Likewise, in gene expression, regulation of mRNA degradation is as important as regulation of its synthesis (Mühlemann, 2005). The rate-determining step of mRNA decay in eukaryotes seems to be the ......When driving a car, control of the brakes is just as important as control of the accelerator pedal. Likewise, in gene expression, regulation of mRNA degradation is as important as regulation of its synthesis (Mühlemann, 2005). The rate-determining step of mRNA decay in eukaryotes seems...... to be the shortening of the poly(A) tail (deadenylation), as this step is slower than the subsequent decapping and degradation of the mRNA body. The Mega-Dalton Ccr4-Not complex contains two exonucleases, Ccr4p and Pop2p, responsible for this process. It is not known at present why two conserved nucleases are needed...

Indigenous abundances of siderophile elements in the lunar highlands: implications for the origin of the Moon

International Nuclear Information System (INIS)

Delano, J.W.; Ringwood, A.E.

1978-01-01

Substantial indigeneous abundances of siderophile elements have been found to be present in the lunar highlands. The abundances of 13 siderophile elements in the parental magma were estimated by using a simple model. It is shown that metal/silicate fractionation within the Moon cannot have been the cause of the siderophile element abundances in the parental highlands magma and primitive, low-Ti mare basalts. The relative abundances of the indigenous siderophile elements in highlands and mare samples seem, instead, to be the result of complex processes which operated prior to the Moon's accretion. The abundances of the relatively involatile, siderophile elements in the parental highlands magma are strikingly similar to the abundances observed in terrestrial oceanic tholeiites. Furthermore, the abundances of the relatively volatile, siderophile elements in the parental highlands magma are also systematically related to the corresponding abundances in terrestrial oceanic tholeiites. In fact, the parental magma of the lunar highlands can be essentially regarded as having been a volatile-depleted terrestrial oceanic tholeite. The origin of the moon is discussed in the context of the results. The probability that depletion of siderophile elements occurred in an earlier generation of differentiated planetesimals similar to those which formed the basaltic achondrites, stony-irons, and irons is examined but can be dismissed on several grounds. It seems that the uniquely terrestrial 'siderophile signature' within the Moon can be explained only if the Moon was derived from the Earth's mantle subsequent to core-formation. (Auth.)

APOGEE Chemical Abundances of the Sagittarius Dwarf Galaxy System

Science.gov (United States)

Hasselquist, Sten; Shetrone, Matthew D.; Smith, Verne V.; Holtzman, Jon A.; McWilliam, Andrew; APOGEE Team

2018-06-01

The Apache Point Observatory Galactic Evolution Experiment provides the opportunity of measuring elemental abundances for C, N, O, Na, Mg, Al, Si, P, K, Ca, V, Cr, Mn, Fe, Co, and Ni in vast numbers of stars. We analyze the chemical-abundance patterns of these elements for 158 red giant stars belonging to the Sagittarius dwarf galaxy (Sgr). This is the largest sample of Sgr stars with detailed chemical abundances, and it is the first time that C, N, P, K, V, Cr, Co, and Ni have been studied at high resolution in this galaxy. We find that the Sgr stars with [Fe/H] > -0.8 are deficient in all elemental abundance ratios (expressed as [X/Fe]) relative to the Milky Way, suggesting that the Sgr stars observed today were formed from gas that was less enriched by Type II SNe than stars formed in the Milky Way. By examining the relative deficiencies of the hydrostatic (O, Na, Mg, and Al) and explosive (Si, P, K, and Mn) elements, our analysis supports the argument that previous generations of Sgr stars were formed with a top-light initial mass function, one lacking the most massive stars that would normally pollute the interstellar medium with the hydrostatic elements. We use a simple chemical-evolution model, flexCE, to further support our claim and conclude that recent stellar generations of Fornax and the Large Magellanic Cloud could also have formed according to a top-light initial mass function. We then exploit the unique chemical abundance patters of the Sgr core to trace stars belonging to the Sgr tidal streams elsewhere in the Milky Way.

HLA-G allelic variants are associated with differences in the HLA-G mRNA isoform profile and HLA-G mRNA levels

DEFF Research Database (Denmark)

Hviid, Thomas Vauvert F; Hylenius, Sine; Rørbye, Christina

2003-01-01

between mother and fetus in several ways. Finally, the expression of membrane-bound HLA-G and soluble HLA-G has been proposed to influence the outcome of pregnancy, and an aberrant HLA-G expression in pre-eclamptic placentas and spontaneous abortions has been reported. Here, an association between certain...... HLA-G polymorphisms and the mRNA levels of the different alternatively spliced HLA-G isoforms in first trimester trophoblast cell populations is reported. Several alternatively spliced HLA-G mRNA isoforms, including a 14-bp polymorphism in the 3'UTR end (exon 8) of the HLA-G gene, are expressed...

Effect of in vitro estrogenic pesticides on human oestrogen receptor α and β mRNA levels

DEFF Research Database (Denmark)

Theander Grünfeld, Heidi; Bonefeld-Jørgensen, Eva Cecilie

2004-01-01

of the ERα mRNA level, but only significantly for prochloraz, dieldrin, and tolchlofos-methyl. Alone no pesticides affected the ERβ mRNA level significantly, but chlorpyrifos increased the mRNA level weakly. Co-exposure with E2 elicited a significant increased ERβ mRNA level by prochloraz, fenarimol...

Regulation of mRNA translation influences hypoxia tolerance

International Nuclear Information System (INIS)

Koritzinsky, M.; Wouters, B.G.; Koumenis, C.

2003-01-01

Hypoxia is a heterogenous but common characteristic of human tumours and poor oxygenation is associated with poor prognosis. We believe that the presence of viable hypoxic tumor cells reflects in part an adaptation and tolerance of these cells to oxygen deficiency. Since oxidative phosphorylation is compromized during hypoxia, adaptation may involve both the upregulation of glycolysis as well as downregulation of energy consumption. mRNA translation is one of the most energy costly cellular processes, and we and others have shown that global mRNA translation is rapidly inhibited during hypoxia. However, some mRNAs, including those coding for HIF-1 α and VEGF, remain efficiently translated during hypoxia. Clearly, the mechanisms responsible for the overall inhibition of translation during hypoxia does not compromize the translation of certain hypoxia-induced mRNA species. We therefore hypothesize that the inhibition of mRNA translation serves to promote hypoxia tolerance in two ways: i) through conservation of energy and ii) through differential gene expression involved in hypoxia adaptation. We have recently identified two pathways that are responsible for the global inhibition of translation during hypoxia. The phosphorylation of the eukaryotic initiation factor eIF2 α by the ER resident kinase PERK results in down-regulation of protein synthesis shortly after the onset of hypoxia. In addition, the initiation complex eIF4F is disrupted during long lasting hypoxic conditions. The identification of the molecular pathways responsible for the inhibition of overall translation during hypoxia has rendered it possible to investigate their importance for hypoxia tolerance. We have found that mouse embryo fibroblasts that are knockout for PERK and therefore not able to inhibit protein synthesis efficiently during oxygen deficiency are significantly less tolerant to hypoxia than their wildtype counterparts. We are currently also investigating the functional significance

Abundances in planetary nebulae : Including ISO results

NARCIS (Netherlands)

Pottasch, [No Value; Beintema, DA; Sales, JB; Feibelman, WA; Kwok, S; Dopita, M; Sutherland, R

2003-01-01

The far infrared nebular spectrum provides a valuable complement to the observed lines in other spectral regions. There are several reasons for this, the most important being the large increase in the number of ions observed, and the fact that the abundances found from these lines are relatively

An investigation of nutrient-dependent mRNA translation in Drosophila larvae

Directory of Open Access Journals (Sweden)

Sabarish Nagarajan

2014-10-01

Full Text Available The larval period of the Drosophila life cycle is characterized by immense growth. In nutrient rich conditions, larvae increase in mass approximately two hundred-fold in five days. However, upon nutrient deprivation, growth is arrested. The prevailing view is that dietary amino acids drive this larval growth by activating the conserved insulin/PI3 kinase and Target of rapamycin (TOR pathways and promoting anabolic metabolism. One key anabolic process is protein synthesis. However, few studies have attempted to measure mRNA translation during larval development or examine the signaling requirements for nutrient-dependent regulation. Our work addresses this issue. Using polysome analyses, we observed that starvation rapidly (within thirty minutes decreased larval mRNA translation, with a maximal decrease at 6–18 hours. By analyzing individual genes, we observed that nutrient-deprivation led to a general reduction in mRNA translation, regardless of any starvation-mediated changes (increase or decrease in total transcript levels. Although sugars and amino acids are key regulators of translation in animal cells and are the major macronutrients in the larval diet, we found that they alone were not sufficient to maintain mRNA translation in larvae. The insulin/PI3 kinase and TOR pathways are widely proposed as the main link between nutrients and mRNA translation in animal cells. However, we found that genetic activation of PI3K and TOR signaling, or regulation of two effectors – 4EBP and S6K – could not prevent the starvation-mediated translation inhibition. Similarly, we showed that the nutrient stress-activated eIF2α kinases, GCN2 and PERK, were not required for starvation-induced inhibition of translation in larvae. These findings indicate that nutrient control of mRNA translation in larvae is more complex than simply amino acid activation of insulin and TOR signaling.

Interleukin-21 mRNA expression during virus infections

DEFF Research Database (Denmark)

Holm, Christian; Nyvold, Charlotte Guldborg; Paludan, Søren Riis

2006-01-01

and activational effects of IL-21 on different leukocytes come into play in vivo in an immune response has so far not been fully investigated. We show here for the first time in vivo, that IL-21 mRNA is produced in the spleen when mice are challenged with herpes simplex virus type 2 (HSV-2) or lymphocytic...... choriomeningitis virus (LCMV). We show in HSV-2 challenged mice that this production takes place in CD4+ T cell fractions and is absent in CD4+ T cell-depleted fractions. We also show that the peak of IL-21 mRNA production in both the HSV-2 and LCMV-challenged mice coincides with the onset of the adaptive immune...

The Abundance of Large Arcs From CLASH

Science.gov (United States)

Xu, Bingxiao; Postman, Marc; Meneghetti, Massimo; Coe, Dan A.; Clash Team

2015-01-01

We have developed an automated arc-finding algorithm to perform a rigorous comparison of the observed and simulated abundance of large lensed background galaxies (a.k.a arcs). We use images from the CLASH program to derive our observed arc abundance. Simulated CLASH images are created by performing ray tracing through mock clusters generated by the N-body simulation calibrated tool -- MOKA, and N-body/hydrodynamic simulations -- MUSIC, over the same mass and redshift range as the CLASH X-ray selected sample. We derive a lensing efficiency of 15 ± 3 arcs per cluster for the X-ray selected CLASH sample and 4 ± 2 arcs per cluster for the simulated sample. The marginally significant difference (3.0 σ) between the results for the observations and the simulations can be explained by the systematically smaller area with magnification larger than 3 (by a factor of ˜4) in both MOKA and MUSIC mass models relative to those derived from the CLASH data. Accounting for this difference brings the observed and simulated arc statistics into full agreement. We find that the source redshift distribution does not have big impact on the arc abundance but the arc abundance is very sensitive to the concentration of the dark matter halos. Our results suggest that the solution to the "arc statistics problem" lies primarily in matching the cluster dark matter distribution.

Multiple marker abundance profiling

DEFF Research Database (Denmark)

Hooper, Cornelia M.; Stevens, Tim J.; Saukkonen, Anna

2017-01-01

proteins and the scoring accuracy of lower-abundance proteins in Arabidopsis. NPAS was combined with subcellular protein localization data, facilitating quantitative estimations of organelle abundance during routine experimental procedures. A suite of targeted proteomics markers for subcellular compartment...

Abundance of plankton population densities in relation to bottom soil textural types in aquaculture ponds

Directory of Open Access Journals (Sweden)

F. Siddika

2012-06-01

Full Text Available Plankton is an important food item of fishes and indicator for the productivity of a water body. The present study was conducted to evaluate the effects of bottom soil textural conditions on abundance of plankton in aquaculture pond. The experiment was carried out using three treatments, i.e., ponds bottom with sandy loam (T1, with loam (T2 and with clay loam (T3. The ranges of water quality parameters analyzed were suitable for the growth of plankton during the experimental period. Similarly, chemical properties of soil were also within suitable ranges and every parameter showed higher ranges in T2. A total 20 genera of phytoplankton were recorded belonged to Chlorophyceae (7, Cyanophyceae (5, Bacillariophyceae (5, Euglenophyceae (2 and Dinophyceae (1. On the other hand, total 13 genera of zooplankton were recorded belonged to Crustacea (7 and Rotifera (6. The highest ranges of phytoplankton and zooplankton densities were found in T2 where low to medium-type bloom was observed during the study period. Consequently, the mean abundance of plankton (phytoplankton and zooplankton density was significantly highest in T2. The highest abundance of plankton in the T2 indicated that pond bottom with loamy soil is suitable for the growth and production of plankton in aquaculture ponds.

Evaluation of mRNA markers for estimating blood deposition time: Towards alibi testing from human forensic stains with rhythmic biomarkers.

Science.gov (United States)

Lech, Karolina; Liu, Fan; Ackermann, Katrin; Revell, Victoria L; Lao, Oscar; Skene, Debra J; Kayser, Manfred

2016-03-01

Determining the time a biological trace was left at a scene of crime reflects a crucial aspect of forensic investigations as - if possible - it would permit testing the sample donor's alibi directly from the trace evidence, helping to link (or not) the DNA-identified sample donor with the crime event. However, reliable and robust methodology is lacking thus far. In this study, we assessed the suitability of mRNA for the purpose of estimating blood deposition time, and its added value relative to melatonin and cortisol, two circadian hormones we previously introduced for this purpose. By analysing 21 candidate mRNA markers in blood samples from 12 individuals collected around the clock at 2h intervals for 36h under real-life, controlled conditions, we identified 11 mRNAs with statistically significant expression rhythms. We then used these 11 significantly rhythmic mRNA markers, with and without melatonin and cortisol also analysed in these samples, to establish statistical models for predicting day/night time categories. We found that although in general mRNA-based estimation of time categories was less accurate than hormone-based estimation, the use of three mRNA markers HSPA1B, MKNK2 and PER3 together with melatonin and cortisol generally enhanced the time prediction accuracy relative to the use of the two hormones alone. Our data best support a model that by using these five molecular biomarkers estimates three time categories, i.e. night/early morning, morning/noon, and afternoon/evening with prediction accuracies expressed as AUC values of 0.88, 0.88, and 0.95, respectively. For the first time, we demonstrate the value of mRNA for blood deposition timing and introduce a statistical model for estimating day/night time categories based on molecular biomarkers, which shall be further validated with additional samples in the future. Moreover, our work provides new leads for molecular approaches on time of death estimation using the significantly rhythmic mRNA

Abundances in the diffuse interstellar medium

International Nuclear Information System (INIS)

Harris, A.W.

1988-04-01

The wealth of interstellar absorption line data obtained with the Copernicus and IUE satellites has opened up a new era in studies of the interstellar gas. It is now well established that certain elements, generally those with high condensation temperatures, are substantially under-abundant in the gas-phase relative to total solar or cosmic abundances. This depletion of elements is due to the existence of solid material in the form of dust grains in the interstellar medium. Surprisingly, however, recent surveys indicate that even volatile elements such as Zn and S are significantly depleted in many sight lines. Developments in this field which have been made possible by the large base of UV interstellar absorption line data built up over recent years are reviewed and the implications of the results for our understanding of the physical processes governing depletion are discussed. (author)

The distribution, relative abundance, and seasonal phenology of Ceratitis capitata, Ceratitis rosa, and Ceratitis cosyra (Diptera: Tephritidae) in South Africa.

Science.gov (United States)

De Villiers, Marelize; Manrakhan, Aruna; Addison, Pia; Hattingh, Vaughan

2013-10-01

Ceratitis capitata (Wiedemann), Ceratitis rosa Karsch, and Ceratitis cosyra (Walker) are fruit fly species (Diptera: Tephritidae) of economic importance in South Africa. These pests cause direct damage to a number of commercially produced fruit and are of phytosanitary concern. A study was conducted to determine the distribution, relative abundance, and seasonal occurrence of the three species in different climatic regions of South Africa. The relative abundance and seasonal phenology of C. capitata and C. rosa were also compared between production areas and home gardens in Stellenbosch, Western Cape. Yellow bucket traps baited with Biolure were used to trap the flies over a 2-yr period in the different sampling areas. Different fruit types were sampled in Stellenbosch to determine fruit fly infestation. C. capitata was found to have a widespread distribution in South Africa, whereas C. rosa were absent from or only present in low numbers in the drier regions. C. cosyra was restricted to the North East and East coast, following a similar pattern to the distribution of marula, Sclerocarrya birrea, an important wild host. Fruit in home gardens provided a breeding ground for C. capitata and C. rosa and a source for infestation of orchards when fruit started to mature, highlighting the need for an area-wide strategy for the control of fruit flies.

Exogenous mRNA encoding tetanus or botulinum neurotoxins expressed in Aplysia neurons

NARCIS (Netherlands)

Mochida, Sumiko; Poulain, Bernard; Eisel, Ulrich; Binz, Thomas; Kurazono, Hisao; Niemann, Heiner; Tauc, Ladislav; Bullock, Theodore H.

1990-01-01

Injection of exogenous mRNA purified from various tissue preparations into cellular translation systems such as Xenopus oocytes has allowed expression of complex proteins (e.g., receptors for neurotransmitters). No evidence for expression of injected exogenous mRNA, however, has been reported in

Distribution And Seasonal Abundance Of Anopheline Mosquito ...

African Journals Online (AJOL)

The essence of this study was to identify Anopheles mosquito species in Nguru, Yobe State and to determine their distribution and relative abundance in the months of the year. Insecticide and aspirator were used to collect mosqutoes in human dwellngs and preserved in 2% formalin for identcation using dissectng ...

Novel subtractive transcription-based amplification of mRNA (STAR method and its application in search of rare and differentially expressed genes in AD brains

Directory of Open Access Journals (Sweden)

Walker P Roy

2006-11-01

Full Text Available Abstract Background Alzheimer's disease (AD is a complex disorder that involves multiple biological processes. Many genes implicated in these processes may be present in low abundance in the human brain. DNA microarray analysis identifies changed genes that are expressed at high or moderate levels. Complementary to this approach, we described here a novel technology designed specifically to isolate rare and novel genes previously undetectable by other methods. We have used this method to identify differentially expressed genes in brains affected by AD. Our method, termed Subtractive Transcription-based Amplification of mRNA (STAR, is a combination of subtractive RNA/DNA hybridization and RNA amplification, which allows the removal of non-differentially expressed transcripts and the linear amplification of the differentially expressed genes. Results Using the STAR technology we have identified over 800 differentially expressed sequences in AD brains, both up- and down- regulated, compared to age-matched controls. Over 55% of the sequences represent genes of unknown function and roughly half of them were novel and rare discoveries in the human brain. The expression changes of nearly 80 unique genes were further confirmed by qRT-PCR and the association of additional genes with AD and/or neurodegeneration was established using an in-house literature mining tool (LitMiner. Conclusion The STAR process significantly amplifies unique and rare sequences relative to abundant housekeeping genes and, as a consequence, identifies genes not previously linked to AD. This method also offers new opportunities to study the subtle changes in gene expression that potentially contribute to the development and/or progression of AD.

Influenza polymerase encoding mRNAs utilize atypical mRNA nuclear export.

Science.gov (United States)

Larsen, Sean; Bui, Steven; Perez, Veronica; Mohammad, Adeba; Medina-Ramirez, Hilario; Newcomb, Laura L

2014-08-28

Influenza is a segmented negative strand RNA virus. Each RNA segment is encapsulated by influenza nucleoprotein and bound by the viral RNA dependent RNA polymerase (RdRP) to form viral ribonucleoproteins responsible for RNA synthesis in the nucleus of the host cell. Influenza transcription results in spliced mRNAs (M2 and NS2), intron-containing mRNAs (M1 and NS1), and intron-less mRNAs (HA, NA, NP, PB1, PB2, and PA), all of which undergo nuclear export into the cytoplasm for translation. Most cellular mRNA nuclear export is Nxf1-mediated, while select mRNAs utilize Crm1. Here we inhibited Nxf1 and Crm1 nuclear export prior to infection with influenza A/Udorn/307/1972(H3N2) virus and analyzed influenza intron-less mRNAs using cellular fractionation and reverse transcription-quantitative polymerase chain reaction (RT-qPCR). We examined direct interaction between Nxf1 and influenza intron-less mRNAs using immuno purification of Nxf1 and RT-PCR of associated RNA. Inhibition of Nxf1 resulted in less influenza intron-less mRNA export into the cytoplasm for HA and NA influenza mRNAs in both human embryonic kidney cell line (293 T) and human lung adenocarcinoma epithelial cell line (A549). However, in 293 T cells no change was observed for mRNAs encoding the components of the viral ribonucleoproteins; NP, PA, PB1, and PB2, while in A549 cells, only PA, PB1, and PB2 mRNAs, encoding the RdRP, remained unaffected; NP mRNA was reduced in the cytoplasm. In A549 cells NP, NA, HA, mRNAs were found associated with Nxf1 but PA, PB1, and PB2 mRNAs were not. Crm1 inhibition also resulted in no significant difference in PA, PB1, and PB2 mRNA nuclear export. These results further confirm Nxf1-mediated nuclear export is functional during the influenza life cycle and hijacked for select influenza mRNA nuclear export. We reveal a cell type difference for Nxf1-mediated nuclear export of influenza NP mRNA, a reminder that cell type can influence molecular mechanisms. Importantly, we

Isolation of full-length putative rat lysophospholipase cDNA using improved methods for mRNA isolation and cDNA cloning

International Nuclear Information System (INIS)

Han, J.H.; Stratowa, C.; Rutter, W.J.

1987-01-01

The authors have cloned a full-length putative rat pancreatic lysophospholipase cDNA by an improved mRNA isolation method and cDNA cloning strategy using [ 32 P]-labelled nucleotides. These new methods allow the construction of a cDNA library from the adult rat pancreas in which the majority of recombinant clones contained complete sequences for the corresponding mRNAs. A previously recognized but unidentified long and relatively rare cDNA clone containing the entire sequence from the cap site at the 5' end to the poly(A) tail at the 3' end of the mRNA was isolated by single-step screening of the library. The size, amino acid composition, and the activity of the protein expressed in heterologous cells strongly suggest this mRNA codes for lysophospholipase