DIALIGN is a widely used software tool for multiple DNA and protein sequence alignment. The program combines local and global alignment features and can therefore be applied to sequence data that cannot be correctly aligned by more traditional approaches. DIALIGN is available online through Bielefeld Bioinformatics Server (BiBiServ). The downloadable version of the program offers several new program features. To compare the output of different alignment programs, we developed the program AltA...
Full Text Available Abstract Background Parallel computing is frequently used to speed up computationally expensive tasks in Bioinformatics. Results Herein, a parallel version of the multi-alignment program DIALIGN is introduced. We propose two ways of dividing the program into independent sub-routines that can be run on different processors: (a pair-wise sequence alignments that are used as a first step to multiple alignment account for most of the CPU time in DIALIGN. Since alignments of different sequence pairs are completely independent of each other, they can be distributed to multiple processors without any effect on the resulting output alignments. (b For alignments of large genomic sequences, we use a heuristics by splitting up sequences into sub-sequences based on a previously introduced anchored alignment procedure. For our test sequences, this combined approach reduces the program running time of DIALIGN by up to 97%. Conclusions By distributing sub-routines to multiple processors, the running time of DIALIGN can be crucially improved. With these improvements, it is possible to apply the program in large-scale genomics and proteomics projects that were previously beyond its scope.
Holubová, Martina; Zemenová, Jana; Mikulášková, Barbora; Panajotová, V.; Stöhr, J.; Haluzík, M.; Kuneš, Jaroslav; Železná, Blanka; Maletínská, Lenka
Roč. 229, č. 2 (2016), s. 85-96 ISSN 0022-0795 R&D Projects: GA ČR(CZ) GA15-08679S; GA TA ČR(CZ) TE01020028 Institutional support: RVO:61388963 Keywords : prolactin-releasing peptide * lipidization * diet-induced obesity * ZDF rats * food intake * rat Subject RIV: FB - Endocrinology, Diabetology, Metabolism, Nutrition Impact factor: 4.706, year: 2016
Holubová, M.; Zemenová, J.; Mikulášková, Barbora; Panajotová, V.; Stöhr, J.; Haluzík, M.; Kuneš, Jaroslav; Železná, B.; Maletínská, L.
Roč. 229, č. 2 (2016), s. 85-96 ISSN 0022-0795 R&D Projects: GA TA ČR(CZ) TE01020028; GA ČR(CZ) GA15-08679S Institutional support: RVO:67985823 Keywords : prolactin-releasing peptide * lipidization * diet-induced obesity * ZDF rats * food intake rat Subject RIV: ED - Physiology Impact factor: 4.706, year: 2016
Holubová, Martina; Mikulášková, Barbora; Zemenová, Jana; Panajotová, V.; Stöhr, J.; Kuneš, Jaroslav; Železná, Blanka; Maletínská, Lenka
Roč. 22, Suppl S2 (2016), S173-S174 ISSN 1075-2617. [European Peptide Symposium /34./ and International Peptide Symposium /8./. 04.09.2016-09.09.2016, Leipzig] R&D Projects: GA ČR(CZ) GA15-08679S; GA TA ČR(CZ) TE01020028 Institutional support: RVO:61388963 Keywords : prolactin-releasing peptide * food intake * obesity Subject RIV: CE - Biochemistry
Ortuño, Francisco M; Valenzuela, Olga; Rojas, Fernando; Pomares, Hector; Florido, Javier P; Urquiza, Jose M; Rojas, Ignacio
Multiple sequence alignments (MSAs) are widely used approaches in bioinformatics to carry out other tasks such as structure predictions, biological function analyses or phylogenetic modeling. However, current tools usually provide partially optimal alignments, as each one is focused on specific biological features. Thus, the same set of sequences can produce different alignments, above all when sequences are less similar. Consequently, researchers and biologists do not agree about which is the most suitable way to evaluate MSAs. Recent evaluations tend to use more complex scores including further biological features. Among them, 3D structures are increasingly being used to evaluate alignments. Because structures are more conserved in proteins than sequences, scores with structural information are better suited to evaluate more distant relationships between sequences. The proposed multiobjective algorithm, based on the non-dominated sorting genetic algorithm, aims to jointly optimize three objectives: STRIKE score, non-gaps percentage and totally conserved columns. It was significantly assessed on the BAliBASE benchmark according to the Kruskal-Wallis test (P algorithm also outperforms other aligners, such as ClustalW, Multiple Sequence Alignment Genetic Algorithm (MSA-GA), PRRP, DIALIGN, Hidden Markov Model Training (HMMT), Pattern-Induced Multi-sequence Alignment (PIMA), MULTIALIGN, Sequence Alignment Genetic Algorithm (SAGA), PILEUP, Rubber Band Technique Genetic Algorithm (RBT-GA) and Vertical Decomposition Genetic Algorithm (VDGA), according to the Wilcoxon signed-rank test (P 0.05) with the advantage of being able to use less structures. Structural information is included within the objective function to evaluate more accurately the obtained alignments. The source code is available at http://www.ugr.es/~fortuno/MOSAStrE/MO-SAStrE.zip.
Full Text Available Prolactin-releasing peptide (PrRP is one of the RF-amide peptides and was originally identified in the bovine hypothalamus as a stimulator of prolactin (PRL release. Independently, another RF-amide peptide was found in Japanese crucian carp and named Carassius RFa (C-RFa, which shows high homology to PrRP and stimulates PRL secretion in teleost fish. Therefore, C-RFa has been recognized as fish PrRP. However, recent work has revealed that PrRP and C-RFa in non-mammalian vertebrates are encoded by separate genes originated through duplication of an ancestral gene. Indeed, both PrRP and C-RFa are suggested to exist in teleost, amphibian, reptile, and avian species. Therefore, we propose that non-mammalian PrRP (C-RFa be renamed PrRP2. Despite a common evolutionary origin, PrRP2 appears to be a physiological regulator of PRL, whereas this is not a consistent role for PrRP itself. Further work revealed that the biological functions of PrRP and PrRP2 are not limited solely to PRL release, because they are also neuromodulators of several hypothalamus-pituitary axes and are involved in some brain circuits related to the regulation of food intake, stress, and cardiovascular functions. However, these actions appear to be different among vertebrates. For example, central injection of PrRP inhibits feeding behavior in rodents and teleosts while it stimulates it in chicks. Therefore, both PrRP and PrRP2 have acquired diverse actions through evolution. In this review, we integrate the burgeoning information of structures, expression profiles, and multiple biological actions of PrRP in higher vertebrates, as well as those of PrRP2 in non-mammals.
Murrelle, Lenn; Coggins, Christopher R E; Gennings, Chris; Carchman, Richard A; Carter, Walter H; Davies, Bruce D; Krauss, Marc R; Lee, Peter N; Schleef, Raymond R; Zedler, Barbara K; Heidbreder, Christian
The risk-reducing effect of a potential reduced-risk tobacco product (PRRP) can be investigated conceptually in a long-term, prospective study of disease risks among cigarette smokers who switch to a PRRP and in appropriate comparison groups. Our objective was to provide guidance for establishing the fundamental design characteristics of a study intended to (1) determine if switching to a PRRP reduces the risk of lung cancer (LC) compared with continued cigarette smoking, and (2) compare, using a non-inferiority approach, the reduction in LC risk among smokers who switched to a PRRP to the reduction in risk among smokers who quit smoking entirely. Using standard statistical methods applied to published data on LC incidence after smoking cessation, we show that the sample size and duration required for a study designed to evaluate the potential for LC risk reduction for an already marketed PRRP, compared with continued smoking, varies depending on the LC risk-reducing effectiveness of the PRRP, from a 5-year study with 8000-30,000 subjects to a 15-year study with <5000 to 10,000 subjects. To assess non-inferiority to quitting, the required sample size tends to be about 10 times greater, again depending on the effectiveness of the PRRP. (c) 2009 Elsevier Inc. All rights reserved.
Feb 2, 2012 ... As one of the cell wall-degrading enzymes, polygalacturonase involves in pathogenicity and virulence in a number of host .... plants and bacteria were carried out using ClustalX (version 1.81) .... using plastic molds. Ultrathin ...
Maletínská, Lenka; Tichá, Anežka; Nagelová, Veronika; Špolcová, Andrea; Blechová, Miroslava; Elbert, Tomáš; Železná, Blanka
Roč. 1498, Mar 1 (2013), s. 33-40 ISSN 0006-8993 R&D Projects: GA ČR GAP303/10/1368 Institutional support: RVO:61388963 Keywords : PrRP * NPFF * RF9 * Binding * MAPK/ERK1/2phosphorylation * food intake Subject RIV: FH - Neurology Impact factor: 2.828, year: 2013
Maixnerová, Jana; Špolcová, Andrea; Pýchová, Miroslava; Blechová, Miroslava; Elbert, Tomáš; Řezáčová, M.; Železná, Blanka; Maletínská, Lenka
Roč. 32, č. 4 (2011), s. 811-817 ISSN 0196-9781 R&D Projects: GA ČR GAP303/10/1368 Institutional research plan: CEZ:AV0Z40550506 Keywords : PrRP * pituitary cell lines * food intake Subject RIV: CC - Organic Chemistry Impact factor: 2.434, year: 2011
Maletínská, Lenka; Špolcová, Andrea; Maixnerová, Jana; Blechová, Miroslava; Železná, Blanka
Roč. 32, č. 9 (2011), s. 1887-1892 ISSN 0196-9781 R&D Projects: GA ČR GAP303/10/1368 Institutional research plan: CEZ:AV0Z40550506 Keywords : pituitary cells * PrRP analogs * food intake Subject RIV: CC - Organic Chemistry Impact factor: 2.434, year: 2011
Full Text Available Analogs of anorexigenic neuropeptides, such as prolactin-releasing peptide (PrRP, have a potential as new anti-obesity drugs. In our previous study, palmitic acid attached to the N-terminus of PrRP enabled its central anorexigenic effects after peripheral administration. In this study, two linkers, γ-glutamic acid at Lys11 and a short, modified polyethylene glycol at the N-terminal Ser and/or Lys11, were applied for the palmitoylation of PrRP31 to improve its bioavailability. These analogs had a high affinity and activation ability to the PrRP receptor GPR10 and the neuropeptide FF2 receptor, as well as short-term anorexigenic effect similar to PrRP palmitoylated at the N-terminus. Two-week treatment with analogs that were palmitoylated through linkers to Lys11 (analogs 1 and 2, but not with analog modified both at the N-terminus and Lys11 (analog 3 decreased body and liver weights, insulin, leptin, triglyceride, cholesterol and free fatty acid plasma levels in a mouse model of diet-induced obesity. Moreover, the expression of uncoupling protein-1 was increased in brown fat suggesting an increase in energy expenditure. In addition, treatment with analogs 1 and 2 but not analog 3 significantly decreased urinary concentrations of 1-methylnicotinamide and its oxidation products N-methyl-2-pyridone-5-carboxamide and N-methyl-4-pyridone-3-carboxamide, as shown by NMR-based metabolomics. This observation confirmed the previously reported increase in nicotinamide derivatives in obesity and type 2 diabetes mellitus and the effectiveness of analogs 1 and 2 in the treatment of these disorders.
Maniscalco, James W.; Zheng, Huiyuan; Gordon, Patrick J.; Rinaman, Linda
Previous reports indicate that caloric restriction attenuates anxiety and other behavioral responses to acute stress, and blunts the ability of stress to increase anterior pituitary release of adrenocorticotropic hormone. Since hindbrain glucagon-like peptide-1 (GLP-1) neurons and noradrenergic prolactin-releasing peptide (PrRP) neurons participate in behavioral and endocrine stress responses, and are sensitive to the metabolic state, we examined whether overnight food deprivation blunts stre...
Zhang, Zefeng; Lin, Hao; Li, Ming
Multiple sequence alignment is a classical and challenging task for biological sequence analysis. The problem is NP-hard. The full dynamic programming takes too much time. The progressive alignment heuristics adopted by most state of the art multiple sequence alignment programs suffer from the 'once a gap, always a gap' phenomenon. Is there a radically new way to do multiple sequence alignment? This paper introduces a novel and orthogonal multiple sequence alignment method, using multiple optimized spaced seeds and new algorithms to handle these seeds efficiently. Our new algorithm processes information of all sequences as a whole, avoiding problems caused by the popular progressive approaches. Because the optimized spaced seeds are provably significantly more sensitive than the consecutive k-mers, the new approach promises to be more accurate and reliable. To validate our new approach, we have implemented MANGO: Multiple Alignment with N Gapped Oligos. Experiments were carried out on large 16S RNA benchmarks showing that MANGO compares favorably, in both accuracy and speed, against state-of-art multiple sequence alignment methods, including ClustalW 1.83, MUSCLE 3.6, MAFFT 5.861, Prob-ConsRNA 1.11, Dialign 2.2.1, DIALIGN-T 0.2.1, T-Coffee 4.85, POA 2.0 and Kalign 2.0.
Hjulsager, Charlotte Kristiane; Breum, Solvej Østergaard; Larsen, Lars Erik
, named from their geographic origin of identification. Great diversity within the two genotypes exists, and further division of PRRSV EU type into at least 3 subtypes has been suggested (Stadejek et al. 2006, 2008). In Denmark PRRSV EU type was first identified in 1992 and a few years later the US type......-PCR, essentially as described by Egli et al. 2001, on RNA extracted with RNeasy Mini Kit (QIAGEN). Complete open reading frames (ORF) ORF5 and ORF7 were PCR amplified as described (Oleksiewicz et al. 1998) and sequenced. Sequences were aligned and Neighbour-Joining trees were constructed with ClustalX. Trees were...
Maniscalco, James W; Zheng, Huiyuan; Gordon, Patrick J; Rinaman, Linda
Previous reports indicate that caloric restriction attenuates anxiety and other behavioral responses to acute stress, and blunts the ability of stress to increase anterior pituitary release of adrenocorticotropic hormone. Since hindbrain glucagon-like peptide-1 (GLP-1) neurons and noradrenergic prolactin-releasing peptide (PrRP) neurons participate in behavioral and endocrine stress responses, and are sensitive to the metabolic state, we examined whether overnight food deprivation blunts stress-induced recruitment of these neurons and their downstream hypothalamic and limbic forebrain targets. A single overnight fast reduced anxiety-like behavior assessed in the elevated-plus maze and acoustic startle test, including marked attenuation of light-enhanced startle. Acute stress [i.e., 30 min restraint (RES) or 5 min elevated platform exposure] robustly activated c-Fos in GLP-1 and PrRP neurons in fed rats, but not in fasted rats. Fasting also significantly blunted the ability of acute stress to activate c-Fos expression within the anterior ventrolateral bed nucleus of the stria terminalis (vlBST). Acute RES stress suppressed dark-onset food intake in rats that were fed ad libitum, whereas central infusion of a GLP-1 receptor antagonist blocked RES-induced hypophagia, and reduced the ability of RES to activate PrRP and anterior vlBST neurons in ad libitum-fed rats. Thus, an overnight fast "silences" GLP-1 and PrRP neurons, and reduces both anxiety-like and hypophagic responses to acute stress. The partial mimicking of these fasting-induced effects in ad libitum-fed rats after GLP-1 receptor antagonism suggests a potential mechanism by which short-term negative energy balance attenuates neuroendocrine and behavioral responses to acute stress. The results from this study reveal a potential central mechanism for the "metabolic tuning" of stress responsiveness. A single overnight fast, which markedly reduces anxiety-like behavior in rats, reduces or blocks the ability of
Keast, Shellie L; Pham, Timothy; Teel, Ashley; Nesser, Nancy J
Patient review and restriction programs (PRRPs), used by state Medicaid programs to limit potential abuse and misuse of opioids and related controlled medications, often restrict members to a single pharmacy for controlled medications. While most states use a restricted pharmacy access model, not all states include restricted prescriber access. Oklahoma Medicaid (MOK) added a restricted prescriber access feature to its PRRP in July 2014. To evaluate the incremental effect that the addition of a prescriber restriction to MOK's pharmacy-only PRRP had on the pharmacy and resource utilization of the enrolled members. MOK members with at least 6 months of enrollment in the pharmacy-only PRRP were restricted to a maximum of 3 prescribers for controlled substances in July 2014 and were identified as "cases." Using a propensity score method, cases were matched to controls from the MOK non-PRRP enrolled population based on demographics and baseline health care utilization. Data from January 1, 2014, through December 31, 2014, were evaluated. Each member's monthly health care resource utilization, defined in terms of medical and pharmacy costs, prescription counts, and opioid use per member per month (PMPM), was analyzed. A difference-indifferences (DID) regression estimated the change in resource utilization following the July 2014 policy change. This study included 378 controls and 126 cases after propensity matching. No differences were noted for daily morphine equivalents, benzodiazepine prescriptions, or maintenance prescriptions. There were decreases in mean PMPM use for both groups for short-acting opioid (SAO) claims (P evidence that overall opioid claims were affected, the addition of prescriber restrictions may have resulted in an incremental change to SAO, prescriber, and pharmacy use in the PRPP population. Use of PRRPs may be an effective tool in reducing inappropriate use of prescription opioids within payer systems. The question remains whether these changes
Zhang, Zefeng; Lin, Hao; Li, Ming
Multiple sequence alignment is a classical and challenging task. The problem is NP-hard. The full dynamic programming takes too much time. The progressive alignment heuristics adopted by most state-of-the-art works suffer from the "once a gap, always a gap" phenomenon. Is there a radically new way to do multiple sequence alignment? In this paper, we introduce a novel and orthogonal multiple sequence alignment method, using both multiple optimized spaced seeds and new algorithms to handle these seeds efficiently. Our new algorithm processes information of all sequences as a whole and tries to build the alignment vertically, avoiding problems caused by the popular progressive approaches. Because the optimized spaced seeds have proved significantly more sensitive than the consecutive k-mers, the new approach promises to be more accurate and reliable. To validate our new approach, we have implemented MANGO: Multiple Alignment with N Gapped Oligos. Experiments were carried out on large 16S RNA benchmarks, showing that MANGO compares favorably, in both accuracy and speed, against state-of-the-art multiple sequence alignment methods, including ClustalW 1.83, MUSCLE 3.6, MAFFT 5.861, ProbConsRNA 1.11, Dialign 2.2.1, DIALIGN-T 0.2.1, T-Coffee 4.85, POA 2.0, and Kalign 2.0. We have further demonstrated the scalability of MANGO on very large datasets of repeat elements. MANGO can be downloaded at http://www.bioinfo.org.cn/mango/ and is free for academic usage.
Alvite, Gabriela; Canclini, Lucía; Corvo, Ileana; Esteves, Adriana
This work describes two new fatty acid binding proteins (FABPs) identified in the parasite platyhelminth Mesocestoides vogae (syn. corti). The corresponding polypeptide chains share 62% identical residues and overall 90% similarity according to CLUSTALX default conditions. Compared with Cestoda FABPs, these proteins share the highest similarity score with the Taenia solium protein. M. vogae FABPs are also phylogenetically related to the FABP3/FABP4 mammalian FABP subfamilies. The native proteins were purified by chromatographical procedures, and apparent molecular mass and isoelectric point were determined. Immunolocalization studies determined the localization of the expression of these proteins in the larval form of the parasite. The genomic exon-intron organization of both genes is also reported, and supports new insights on intron evolution. Consensus motifs involved in splicing were identified.
Xu, Liang; Dou, Deqiang; Wang, Bing; Yang, Yanyun; Kang, Tingguo
To study the correlation between ITS sequence of Arctium lappa and Fructus Arctii quality of different origin. The samples of Fructu arctii materials were collected from 26 different producing areas. Their ITS sequence were determined after polymerase chain reaction (PCR) and quality were evaluated through the determination of arctiin content by HPLC. Genetic diversity, genotype and correlation were analyzed by ClustalX (1.81), Mage 4.0, SPSS 13.0 statistical software. ITS sequence of A. was obtained from 26 samples, and was registered in the GenBank. Corresponding arctiin content of Fructus arctii and 1000-grain weight were determined. A. lappa genotype correlated with Fructus arctii quality by statistical analysis. The research provided a foundation for revealing the molecular mechanism of Fructus arctii geoherbs.
Full Text Available The genera Bostryx and Scutalus (Orthalicidae: Bulimulinae are endemics from South America. They are mainly distributed on the western slopes of the Peruvian Andes. The goal of the present work was to assess their evolutionary position among the stylommatophoran gastropods based on the 16S rRNA mitochondrial marker. Four sequences were obtained, and along with 28 sequences of other Stylommatophora retrieved from the GenBank, were aligned with ClustalX. The phylogenetic reconstruction was carried out using the methods of Neighbor-Joining, Maximum Parsimony, Maximum Likelihood and Bayesian inference. The multiple sequence alignment had 371 sites, with indels. The two genera of the family Orthalicidae for the first time included in a molecular phylogeny (Bostryx and Scutalus, formed a monophyletic group along with another member of the superfamily Orthalicoidea (Placostylus, result that is comparable with that obtained with nuclear markers. Their evolutionary relationship with other land snails is also discussed.
Ríos-Lugo, María J; Jiménez-Ortega, Vanesa; Cano-Barquilla, Pilar; Mateos, Pilar Fernández; Spinedi, Eduardo J; Cardinali, Daniel P; Esquifino, Ana I
Previous studies indicate that the administration of melatonin caused body weight and abdominal visceral fat reductions in rodent models of hyperadiposity. The objective of the present study performed in high-fat fed rats was to evaluate the activity of melatonin on gene expression of some medial basal hypothalamus (MBH) signals involved in feeding behavior regulation, including neuropeptide Y (NPY), proopiomelanocortin (POMC), prolactin-releasing peptide (PrRP), leptin- and insulin-receptors (R) and insulin-R substrate (IRS)-1 and -2. Blood levels of leptin and adiponectin were also measured. Adult Wistar male rats were divided into four groups (n=16 per group): (i) control diet (3% fat); (ii) high-fat (35%) diet; (iii) high-fat diet+melatonin; (iv) control diet+melatonin. Rats had free access to high-fat or control chow and one of the following drinking solutions: (a) tap water; (b) 25 μg/mL of melatonin. After 10 weeks, the high-fat fed rats showed augmented MBH mRNA levels of NPY, leptin-R, PrRP, insulin-R, IRS-1 and IRS-2. The concomitant administration of melatonin counteracted this increase. Feeding of rats with a high-fat diet augmented expression of the MBH POMC gene through an effect insensitive to melatonin treatment. The augmented levels of circulating leptin and adiponectin seen in high-fat fed rats were counteracted by melatonin as was the augmented body weight: melatonin significantly attenuated a body weight increase in high-fat fed rats without affecting chow or water consumption. Melatonin augmented plasma leptin and adiponectin in control rats. The results indicate that an effect on gene expression of feeding behavior signals at the central nervous system (CNS) may complement a peripheral rise of the energy expenditure produced by melatonin to decrease body weight in high-fat fed rats.
Izzo, Lisa K.; Maynard, George A.; Zydlewski, Joseph D.
The Penobscot River Restoration Project (PRRP), to be completed in 2016, involved an extensive plan of dam removal, increases in hydroelectric capacity, and fish passage modifications to increase habitat access for diadromous species. As part of the PRRP, Great Works and Veazie dams were removed, making Milford Dam the first impediment to federally endangered Atlantic Salmon Salmo salar. Upstream habitat access for Atlantic Salmon is dependent upon successful and timely passage at Milford Dam because nearly all suitable spawning habitat is located upstream. In 2014 and 2015, a total of 73 adult salmon were radio-tagged to track their upstream movements through the Penobscot River to assess potential delays at (1) the dam remnants, (2) the confluence of the Stillwater Branch and the main stem of the Penobscot River below the impassable Orono Dam, and (3) the Milford Dam fish lift (installed in 2014). Movement rates through the dam remnants and the Stillwater confluence were comparable to open river reaches. Passage efficiency of the fish lift was high in both years (95% and 100%). However, fish experienced long delays at Milford Dam, with approximately one-third of fish taking more than a week to pass in each year, well below the Federal Energy Regulatory Commission passage standard of 95% within 48 h. Telemetry indicates most fish locate the fishway entrance within 5 h of arrival and were observed at the entrance at all hours of the day. These data indicate that overall transit times through the lower river were comparable to reported movement rates prior to changes to the Penobscot River due to the substantial delays seen at Milford Dam. The results of this study show that while adult Atlantic Salmon locate the new fish lift entrance quickly, passage of these fish was significantly delayed under 2014–2015 operations.
Otim, M.O.; Bisgaard, M.; Christensen, H.; Jorgensen, P.; Handberg, K.
Molecular techniques were used to characterize 16 Newcastle disease (ND) Virus (NDV) isolates from ND outbreaks in chickens in eastern Uganda in 2001, and evaluate ND epidemiology, with emphasis on molecular aspects. F and HN genes, which are the major determinants of virulence, were studied. Strain pathogenicity was derived from genetic analysis of the F gene sequence and intracerebral pathogenicity index (ICPI). Comparative genetic and phylogenetic tree analyses were performed on the HN genes of the isolates and some strains selected from GenBank. ClustalX 1.81 and Phylip were used for gene alignment analysis and the final phylogeny was produced by the neighbour-joining method. F gene cleavage site sequence analysis, phylogenetic analysis and biological characterization showed that the strains were very virulent and closely related, being of common ancestry. All the Ugandan NDV isolates formed separate clades from the currently known genotypes, suggesting that they are a novel genotype, unrelated to those that have caused previous pandemics. (author)
Zhang, Jirong; Lei, Fumin
In the present study, we used nucleotide and protein sequences of avian influenza virus H5N1, which were obtained in Asia and Africa, analyzed HA proteins using ClustalX1.83 and MEGA4.0, and built a genetic evolutionary tree of HA nucleotides. The analysis revealed that the receptor specificity amino acid of A/HK/213/2003, A/Turkey/65596/2006 and etc mutated into QNG, which could bind with á-2, 3 galactose and á-2, 6 galactose. A mutation might thus take place and lead to an outbreak of human infections of avian influenza virus. The mutations of HA protein amino acids from 2004 to 2009 coincided with human infections provided by the World Health Organization, indicating a "low-high-highest-high-low" pattern. We also found out that virus strains in Asia are from different origins: strains from Southeast Asia and East Asia are of the same origin, whereas those from West Asia, South Asia and Africa descend from one ancestor. The composition of the phylogenetic tree and mutations of key site amino acids in HA proteins reflected the fact that the majority of strains are regional and long term, and virus diffusions exist between China, Laos, Malaysia, Indonesia, Azerbaijan, Turkey and Iraq. We would advise that pertinent vaccines be developed and due attention be paid to the spread of viruses between neighboring countries and the dangers of virus mutation and evolution. © 2010 ISZS, Blackwell Publishing and IOZ/CAS.
Al-Qurainy, F.; Al-Hemaidi, F.M.; Khan, S.; Ali, M.A.; Tarroum, M.; Ashraf, M.
Sodium azide (NaN/sub 3/) is a well known chemical mutagen which can effectively cause point mutation in plant genome. The mutagenicity by this potential mutagen was assessed in the regenerated mutant shoots of Artemisia annua using internal transcribed spacer (ITS) sequences of n rDNA. Insertions and/or deletions were detected in n rDNA-ITS sequences of all mutant shoots and compared with control ones using the ClustalX program. The regenerated shoots TS1 and TS2 had deleted bases, whereas TS3, TS4 and TS5 had insertions, because NaN/sub 3/ replaced the cytosine (C) by thymine (T) (C - T) (shoots; TS1 and TS4) and thymine (T) replaced by guanine (G) (T - G) (shoot; TS5), respectively. Artemisinin content was also measured in the regenerated six-week-old shoots of A. annua. All regenerated shoots had enhanced level of this compound as compared to that in the controls, being highest in the regenerated shoot TS3. (author)
Full Text Available Energy efficiency has been considered as the most important issue in wireless sensor networks. As in many applications, wireless sensors are scattered in a wide harsh area, where the battery replacement or charging will be quite difficult and it is the most important challenge. Therefore, the design of energy saving mechanism becomes mandatory in most recent research. In this paper, a new energy efficient clustered routing protocol is proposed: the proposed protocol is based on analyzing the data collected from the sensors in a base-station. Based on this analysis the cluster head will be selected as the one with the most useful data. Then, a variable time slot is specified to each sensor to minimize the transmission of repetitive and un-useful data. The proposed protocol Data-Based Energy Efficient Clustered Routing Protocol for Wireless Sensors Networks (DCRP was compared with the famous energy efficient LEACH protocol and also with one of the recent energy efficient routing protocols named Position Responsive Routing Protocol (PRRP. DCRP has been used in monitoring the floods in Tabuk area –Saudi Arabia. It shows comparatively better results.
Saravana Mohan Mariappan
Full Text Available Los robots son sistemas electromecánicos que necesitan enfoque mecatrónico antes de fabricarlos, esto con el fin de reducir el costo de desarrollo. En este trabajo se presenta un nuevo intento de modelado PRRP (prismáticos-revoluto-revoluto-prismático, una configuración redundante SCARA (Brazo robótico articulado de respuesta selectiva, herramienta de perforación milti-eje (MSDT usando el software CAD de SolidWorks y el estudio dinámico con la ayuda de MATLAB/SimMechanics de perforación. Un SCARA con MSDT se utiliza para perforar varios agujeros en las placas de circuito impreso (PCB y la chapa metálica. En este trabajo, el modelo de CAD 3D del robot propuesto se convierte en un diagrama de bloque SimMechanics exportando a MATLAB/SimMechanics segunda generación de tecnología de modelado y simulación. Entonces se realiza una simulación SimMechanics y utilizando su capacidad de detección de movimiento la velocidad de parámetros dinámicos y la torsión del manipulador se observa la estructura del robot variable modificado. Los resultados de la simulación indican un cambio considerable en el rendimiento dinámico para diferentes parámetros de diseño.
Seri Masran, Siti Nor Ain; Ab Majid, Abdul Hafiz
The tropical bed bug is scientifically recognized as a significant public health problem. While there is an increased awareness about their resurgence by medical and life science committees, efficient bed bug management still remains unresolved. The solution may soon arise, as information about bed bugs' infestation dynamics and systematics are becoming more distinguishable. Recent developments in studies about bed bugs are based on molecular intervention by determining their genetic variation and phylogeography. The aim of this study is to assess the phylogenetic relationships and genetic diversity among the populations of tropical bed bugs inhabiting Malaysia. A molecular genotyping study was conducted with 22 tropical bed bug populations composed of three individuals per population. The mitochondrial (COI) gene was used as a marker. The data obtained were analyzed using the T-Coffee, ClustalX, MEGA 6.0, and PAUP software. The results showed one main monophyletic clade that consisted of two groups: Ch01 and Ch02. Ch02 consists of samples from the Bandar Hilir population, differing from the other populations studied by one singleton base. However, as there were no changes in the amino acid, this singleton genetic variation was considered to have no effect on genetic differentiation. Ch01 shows similarity with some sequence of Cimex hemipterus (F.) from Thailand, suggesting an international diversity connection. The disparity index apparently suggests that all isolates are homogeneous populations and are supported by the low value of the mean pairwise distance between isolates. This study will increase the knowledge about phylogeographic diversity of tropical bed bug in Malaysia. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: firstname.lastname@example.org.
Full Text Available Abstract Background There is an increasing demand to assemble and align large-scale biological sequence data sets. The commonly used multiple sequence alignment programs are still limited in their ability to handle very large amounts of sequences because the system lacks a scalable high-performance computing (HPC environment with a greatly extended data storage capacity. Results We designed ClustalXeed, a software system for multiple sequence alignment with incremental improvements over previous versions of the ClustalX and ClustalW-MPI software. The primary advantage of ClustalXeed over other multiple sequence alignment software is its ability to align a large family of protein or nucleic acid sequences. To solve the conventional memory-dependency problem, ClustalXeed uses both physical random access memory (RAM and a distributed file-allocation system for distance matrix construction and pair-align computation. The computation efficiency of disk-storage system was markedly improved by implementing an efficient load-balancing algorithm, called "idle node-seeking task algorithm" (INSTA. The new editing option and the graphical user interface (GUI provide ready access to a parallel-computing environment for users who seek fast and easy alignment of large DNA and protein sequence sets. Conclusions ClustalXeed can now compute a large volume of biological sequence data sets, which were not tractable in any other parallel or single MSA program. The main developments include: 1 the ability to tackle larger sequence alignment problems than possible with previous systems through markedly improved storage-handling capabilities. 2 Implementing an efficient task load-balancing algorithm, INSTA, which improves overall processing times for multiple sequence alignment with input sequences of non-uniform length. 3 Support for both single PC and distributed cluster systems.
Dijkman, B; Wellens, H J
Dual chamber implantable cardioverter defibrillator (ICD) technology extended ICD therapy to more than termination of hemodynamically unstable ventricular tachyarrhythmias. It created the basis for dual chamber arrhythmia management in which dependable detection is important for treatment and prevention of both ventricular and atrial arrhythmias. Dual chamber detection algorithms were investigated in two Medtronic dual chamber ICDs: the 7250 Jewel AF (33 patients) and the 7271 Gem DR (31 patients). Both ICDs use the same PR Logic algorithm to interpret tachycardia as ventricular tachycardia (VT), supraventricular tachycardia (SVT), or dual (VT+ SVT). The accuracy of dual chamber detection was studied in 310 of 1,367 spontaneously occurring tachycardias in which rate criterion only was not sufficient for arrhythmia diagnosis. In 78 episodes there was a double tachycardia, in 223 episodes SVT was detected in the VT or ventricular fibrillation zone, and in 9 episodes arrhythmia was detected outside the boundaries of the PR Logic functioning. In 100% of double tachycardias the VT was correctly diagnosed and received priority treatment. SVT was seen in 59 (19%) episodes diagnosed as VT. The causes of inappropriate detection were (1) algorithm failure (inability to fulfill the PR
Thomas S Bibby
Full Text Available BACKGROUND: Photosynthetic light-harvesting proteins are the mechanism by which energy enters the marine ecosystem. The dominant prokaryotic photoautotrophs are the cyanobacterial genera Prochlorococcus and Synechococcus that are defined by two distinct light-harvesting systems, chlorophyll-bound protein complexes or phycobilin-bound protein complexes, respectively. Here, we use the Global Ocean Sampling (GOS Project as a unique and powerful tool to analyze the environmental diversity of photosynthetic light-harvesting genes in relation to available metadata including geographical location and physical and chemical environmental parameters. METHODS: All light-harvesting gene fragments and their metadata were obtained from the GOS database, aligned using ClustalX and classified phylogenetically. Each sequence has a name indicative of its geographic location; subsequent biogeographical analysis was performed by correlating light-harvesting gene budgets for each GOS station with surface chlorophyll concentration. CONCLUSION/SIGNIFICANCE: Using the GOS data, we have mapped the biogeography of light-harvesting genes in marine cyanobacteria on ocean-basin scales and show that an environmental gradient exists in which chlorophyll concentration is correlated to diversity of light-harvesting systems. Three functionally distinct types of light-harvesting genes are defined: (1 the phycobilisome (PBS genes of Synechococcus; (2 the pcb genes of Prochlorococcus; and (3 the iron-stress-induced (isiA genes present in some marine Synechococcus. At low chlorophyll concentrations, where nutrients are limited, the Pcb-type light-harvesting system shows greater genetic diversity; whereas at high chlorophyll concentrations, where nutrients are abundant, the PBS-type light-harvesting system shows higher genetic diversity. We interpret this as an environmental selection of specific photosynthetic strategy. Importantly, the unique light-harvesting system isiA is found
Full Text Available Cancer of the cervix is associated with infection by certain types of human papillomavirus (HPV. The gene variants differ in immune responses and oncogenic potential. The E6 and E7 proteins encoded by high-risk HPV play a key role in cellular transformation. HPV-33 and HPV-58 types are highly prevalent among Chinese women. To study the gene intratypic variations, polymorphisms and positive selections of HPV-33 and HPV-58 E6/E7 in southwest China, HPV-33 (E6, E7: n = 216 and HPV-58 (E6, E7: n = 405 E6 and E7 genes were sequenced and compared to others submitted to GenBank. Phylogenetic trees were constructed by Maximum-likelihood and the Kimura 2-parameters methods by MEGA 6 (Molecular Evolutionary Genetics Analysis version 6.0. The diversity of secondary structure was analyzed by PSIPred software. The selection pressures acting on the E6/E7 genes were estimated by PAML 4.8 (Phylogenetic Analyses by Maximun Likelihood version4.8 software. The positive sites of HPV-33 and HPV-58 E6/E7 were contrasted by ClustalX 2.1. Among 216 HPV-33 E6 sequences, 8 single nucleotide mutations were observed with 6/8 non-synonymous and 2/8 synonymous mutations. The 216 HPV-33 E7 sequences showed 3 single nucleotide mutations that were non-synonymous. The 405 HPV-58 E6 sequences revealed 8 single nucleotide mutations with 4/8 non-synonymous and 4/8 synonymous mutations. Among 405 HPV-58 E7 sequences, 13 single nucleotide mutations were observed with 10/13 non-synonymous mutations and 3/13 synonymous mutations. The selective pressure analysis showed that all HPV-33 and 4/6 HPV-58 E6/E7 major non-synonymous mutations were sites of positive selection. All variations were observed in sites belonging to major histocompatibility complex and/or B-cell predicted epitopes. K93N and R145 (I/N were observed in both HPV-33 and HPV-58 E6.
Dea-Ayuela, María Auxiliadora; Pérez-Castillo, Yunierkis; Meneses-Marcel, Alfredo; Ubeira, Florencio M; Bolas-Fernández, Francisco; Chou, Kuo-Chen; González-Díaz, Humberto
The toxicity and inefficacy of actual organic drugs against Leishmaniosis justify research projects to find new molecular targets in Leishmania species including Leishmania infantum (L. infantum) and Leishmaniamajor (L. major), both important pathogens. In this sense, quantitative structure-activity relationship (QSAR) methods, which are very useful in Bioorganic and Medicinal Chemistry to discover small-sized drugs, may help to identify not only new drugs but also new drug targets, if we apply them to proteins. Dyneins are important proteins of these parasites governing fundamental processes such as cilia and flagella motion, nuclear migration, organization of the mitotic splinde, and chromosome separation during mitosis. However, despite the interest for them as potential drug targets, so far there has been no report whatsoever on dyneins with QSAR techniques. To the best of our knowledge, we report here the first QSAR for dynein proteins. We used as input the Spectral Moments of a Markov matrix associated to the HP-Lattice Network of the protein sequence. The data contain 411 protein sequences of different species selected by ClustalX to develop a QSAR that correctly discriminates on average between 92.75% and 92.51% of dyneins and other proteins in four different train and cross-validation datasets. We also report a combined experimental and theoretic study of a new dynein sequence in order to illustrate the utility of the model to search for potential drug targets with a practical example. First, we carried out a 2D-electrophoresis analysis of L. infantum biological samples. Next, we excised from 2D-E gels one spot of interest belonging to an unknown protein or protein fragment in the region Mdata base with the highest similarity score to the MS of the protein isolated from L. infantum. We used the QSAR model to predict the new sequence as dynein with probability of 99.99% without relying upon alignment. In order to confirm the previous function annotation we
Mashinistova, A. V.; Elchin, A. A.; Gorbunova, N. V.; Muratov, V. S.; Kydralieva, K. A.; Khudaibergenova, B. M.; Shabaev, V. P.; Jorobekova, Sh. J.
, which had the highest degree of homology with the strains under study, applying the program ClustalX 1.83. Building of rootless phylogenetic trees of the studying bacteria was carried out with the help of the program Njplot. Acknowledgement. This research was supported by the grant of ISTC KR-993.2.
李艳星; 郭平毅; 孙建光
[Objective]The objectives of this study are to isolate, identify and analyze phylogenetics of endophytic diazotrophs from tuber and root crops, test plant growth promoting (PGP) characteristics of the isolates, and to explore population property and host distributions of endophytic diazotrophs from tuber and root crops. [Method] Surface sterilization and low nitrogen medium were used to isolate endophytic diazotrophs. nifH detection based on PCR amplification to confirm isolates as nitrogen-fixing bacteria. 16S rRNA was amplified with PCR, blasted in EzTaxon after sequencing, and analyzed with Clustalx-MEGA to make phylogenetic tree. PGP characteristics were evaluated by testing 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity, indole acetic acid (IAA) production and antagonism to Fusarium spp. [Result] Total 219 endophytic bacterial isolates were obtained from 14 tuber and root samples including radish, carrot, potato, ginger, beet, lotus, yam, taro, cabbage, and sweet potato. All isolates were verified as nitrogen-fixing bacteria after nifH inspection and identified as 79 species of 24 genera based on 16S rRNA. The 79 species are Acinetobacter harbinensis, Arthrobacter arilaitensis, Ar. bergerei, Ar. nicotianae, Ar. nicotinovorans, Ar. nitroguajacolicus, Bacillus amyloliquefaciens, Ba. aryabhattai, Ba. circulans, Ba. fengqiuensis, Ba. firmus, Ba. flexus, Ba. halosaccharovorans, Ba. idriensis, Ba. licheniformis, Ba. litoralis, Ba. luciferensis, Ba. marisflavi, Ba. megaterium, Ba. methylotrophicus, Ba. oceanisediminis, Ba. safensis, Ba. simplex, Ba. sonorensis, Ba. stratosphericus, Ba. subterraneus, Ba. tequilensis, Ba. thaonhiensis, Ba. thioparans, Brevibacillus brevis, Br. formosus, Br. nitrificans, Br. frigoritolerans, Chryseobacterium indoltheticum, Ch. lactis, Citrobacter youngae, Delftia lacustris, Domibacillus indicus, Enterobacter asburiae, E. ludwigii, E. mori, E. xiangfangensis, Fictibacillus barbaricus, Fi. enclensis, Fi. nanhaiensis, Fi