scholarly journals A Random Sequencing Approach for the Analysis of the Trypanosoma cruzi Genome: General Structure, Large Gene and Repetitive DNA Families, and Gene Discovery

2000 ◽  
Vol 10 (12) ◽  
pp. 1996-2005
Author(s):  
Fernán Agüero ◽  
Ramiro E. Verdún ◽  
Alberto Carlos C. Frasch ◽  
Daniel O. Sánchez
Keyword(s):  
Trypanosoma Cruzi ◽  
Repetitive Dna ◽  
Sequence Data ◽  
Random Sequence ◽  
General Structure ◽  
Gc Content ◽  
Haploid Genome ◽  
Additional Information ◽  
Link Type ◽  
New Genes

A random sequence survey of the genome of Trypanosoma cruzi, the agent of Chagas disease, was performed and 11,459 genomic sequences were obtained, resulting in ∼4.3 Mb of readable sequences or ∼10% of the parasite haploid genome. The estimated total GC content was 50.9%, with a high representation of A and T di- and trinucleotide repeats. Out of the estimated 5000 parasite genes, 947 putative new genes were identified. Another 1723 sequences corresponded to genes detected previously in T. cruzi through expression sequence tag analysis. 7735 sequences had no matches in the database, but the presence of open reading frames that passed Fickett's test suggests that some might contain coding DNA. The survey was highly redundant, with ∼35% of the sequences included in a few large sequence families. Some of them code for protein families present in dozens of copies, including proteins essential for parasite survival and retrotransposons. Other sequence families include repetitive DNA present in thousands of copies per haploid genome. Some families in the latter group are new, parasite-specific, repetitive DNAs. These results suggest that T. cruzi could constitute an interesting model to analyze gene and genome evolution due to its plasticity in terms of sequence amplification and divergence. Additional information can be found at http://www.iib.unsam.edu.ar/tcruzi.gss.html.[The sequence data described in this paper have been submitted to the dbGSS database under the following GenBank accession nos.:AQ443439–AQ443513, AQ443743–AQ445667, AQ902981–AQ911366,AZ049857–AZ051184, and AZ302116–AZ302563.]

scholarly journals Retroposed New Genes Out of the X in Drosophila

2002 ◽  
Vol 12 (12) ◽  
pp. 1854-1859
Author(s):  
Esther Betrán ◽  
Kevin Thornton ◽  
Manyuan Long
Keyword(s):  
Population Genetics ◽  
Molecular Mechanisms ◽  
Sequence Data ◽  
Evolutionary Process ◽  
Significant Excess ◽  
Link Type ◽  
New Genes ◽  
Asymmetric Pattern ◽  
Unpublished Information

New genes that originated by various molecular mechanisms are an essential component in understanding the evolution of genetic systems. We investigated the pattern of origin of the genes created by retroposition in Drosophila. We surveyed the wholeDrosophila melanogaster genome for such new retrogenes and experimentally analyzed their functionality and evolutionary process. These retrogenes, functional as revealed by the analysis of expression, substitution, and population genetics, show a surprisingly asymmetric pattern in their origin. There is a significant excess of retrogenes that originate from the X chromosome and retropose to autosomes; new genes retroposed from autosomes are scarce. Further, we found that most of these X-derived autosomal retrogenes had evolved a testis expression pattern. These observations may be explained by natural selection favoring those new retrogenes that moved to autosomes and avoided the spermatogenesis X inactivation, and suggest the important role of genome position for the origin of new genes.[The sequence data from this study have been submitted to GenBank under accession nos. AY150701–AY150797. The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: M.-L. Wu, F. Lemeunier, and P. Gibert.]

scholarly journals Comparative Sequence Analysis of the X-Inactivation Center Region in Mouse, Human, and Bovine

2000 ◽  
Vol 12 (6) ◽  
pp. 894-908 ◽  
Author(s):  
Corinne Chureau ◽  
Marine Prissette ◽  
Agnès Bourdet ◽  
Valérie Barbe ◽  
Laurence Cattolico ◽  
...  
Keyword(s):  
Transcriptional Activity ◽  
Sequence Data ◽  
Cpg Islands ◽  
Comparative Sequence Analysis ◽  
X Inactivation ◽  
Asymmetric Distribution ◽  
Repeat Elements ◽  
Link Type ◽  
New Genes ◽  
Intergenic Regions

We have sequenced to high levels of accuracy 714-kb and 233-kb regions of the mouse and bovine X-inactivation centers (Xic), respectively, centered on the Xist gene. This has provided the basis for a fully annotated comparative analysis of the mouse Xic with the 2.3-Mb orthologous region in human and has allowed a three-way species comparison of the core central region, including theXist gene. These comparisons have revealed conserved genes, both coding and noncoding, conserved CpG islands and, more surprisingly, conserved pseudogenes. The distribution of repeated elements, especially LINE repeats, in the mouse Xic region when compared to the rest of the genome does not support the hypothesis of a role for these repeat elements in the spreading of X inactivation. Interestingly, an asymmetric distribution of LINE elements on the two DNA strands was observed in the three species, not only within introns but also in intergenic regions. This feature is suggestive of important transcriptional activity within these intergenic regions. In silico prediction followed by experimental analysis has allowed four new genes, Cnbp2, Ftx, Jpx, and Ppnx, to be identified and novel, widespread, complex, and apparently noncoding transcriptional activity to be characterized in a region 5′ of Xist that was recently shown to attract histone modification early after the onset of X inactivation.[The sequence data described in this paper have been submitted to the EMBL data library under accession nos. AJ421478, AJ421479, AJ421480, andAJ421481. Online supplemental data are available athttp://pbil.univ-lyon1.fr/datasets/Xic2002/data.html andwww.genome.org.]

The Development of ASHS HortBase—A Global Information System

HortScience ◽  
1998 ◽  
Vol 33 (3) ◽  
pp. 552e-552
Author(s):  
James L. Green
Keyword(s):  
Information System ◽  
Information Needs ◽  
Standing Committee ◽  
Task Forces ◽  
Additional Information ◽  
Link Type ◽  
Dispersed System ◽  
Global Information System ◽  
Information File ◽  
International Standing

In 1997, the ASHS Board of Directors established ASHS HortBase as a Standing Committee of the Society. The ASHS HortBase Committee, a six-member Standing Committee and Chair, is charged to implement and maintain ASHS HortBase. The members of the ASHS HortBase Committee will be chair and chair-elect of the three HortBase Task Forces: 1) Finance and Marketing; 2) Standards—authoring, reviewing, and publishing; and 3) Technology. ASHS HortBase is a dispersed, dynamic horticultural information system (network) on the WWW comprised of peer—reviewed, concise, interlinked information modules to meet the information needs of instructors and students, gardeners and growers. A strong advantage and distinguishing characteristic of ASHS HortBase is our dynamic pool of potential authors, reviewers, and users (ASHS Extension, Industry, and Teaching membership) to continually evolve and update the peer-reviewed information in HortBase. We have the scholastic international standing to provide peer review and validation of the information and to recognition to the authors, coupled with the marketing to stimulate wide use of their information modules. ASHS HortBase is a dispersed system (dispersed development and server costs). The “dispersed cost” for information file development and updating and delivery on the respective authors' dispersed servers disperses the major costs of the HortBase information system. Additional information on ASHS HortBase and the papers presented at the 4-h Colloquium on HortBase at ASHS-97 can be found at http://[email protected] or contact me ([email protected], phone 541.737.5452, fax 541.737.3479).

Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 316-324 ◽  
Author(s):  
Jongsik Chun ◽  
Fred A. Rainey
Keyword(s):  
Genomic Sequence ◽  
Sequence Data ◽  
Original Research ◽  
Rrna Gene ◽  
New Taxon ◽  
Genome Sequences ◽  
Microbial World ◽  
Content Type ◽  
Link Type ◽  
Type Strains

The polyphasic approach used today in the taxonomy and systematics of the Bacteria and Archaea includes the use of phenotypic, chemotaxonomic and genotypic data. The use of 16S rRNA gene sequence data has revolutionized our understanding of the microbial world and led to a rapid increase in the number of descriptions of novel taxa, especially at the species level. It has allowed in many cases for the demarcation of taxa into distinct species, but its limitations in a number of groups have resulted in the continued use of DNA–DNA hybridization. As technology has improved, next-generation sequencing (NGS) has provided a rapid and cost-effective approach to obtaining whole-genome sequences of microbial strains. Although some 12 000 bacterial or archaeal genome sequences are available for comparison, only 1725 of these are of actual type strains, limiting the use of genomic data in comparative taxonomic studies when there are nearly 11 000 type strains. Efforts to obtain complete genome sequences of all type strains are critical to the future of microbial systematics. The incorporation of genomics into the taxonomy and systematics of the Bacteria and Archaea coupled with computational advances will boost the credibility of taxonomy in the genomic era. This special issue of International Journal of Systematic and Evolutionary Microbiology contains both original research and review articles covering the use of genomic sequence data in microbial taxonomy and systematics. It includes contributions on specific taxa as well as outlines of approaches for incorporating genomics into new strain isolation to new taxon description workflows.

scholarly journals Analysis of Codon Usage Patterns in Giardia duodenalis Based on Transcriptome Data from GiardiaDB

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1169
Author(s):  
Xin Li ◽  
Xiaocen Wang ◽  
Pengtao Gong ◽  
Nan Zhang ◽  
Xichen Zhang ◽  
...  
Keyword(s):  
Codon Usage ◽  
Genetic Manipulation ◽  
Molecular Genetic ◽  
Gc Content ◽  
Giardia Duodenalis ◽  
Codon Usage Pattern ◽  
Protein Size ◽  
New Genes ◽  
Optimal Codons ◽  
Usage Patterns

Giardia duodenalis, a flagellated parasitic protozoan, the most common cause of parasite-induced diarrheal diseases worldwide. Codon usage bias (CUB) is an important evolutionary character in most species. However, G. duodenalis CUB remains unclear. Thus, this study analyzes codon usage patterns to assess the restriction factors and obtain useful information in shaping G. duodenalis CUB. The neutrality analysis result indicates that G. duodenalis has a wide GC3 distribution, which significantly correlates with GC12. ENC-plot result—suggesting that most genes were close to the expected curve with only a few strayed away points. This indicates that mutational pressure and natural selection played an important role in the development of CUB. The Parity Rule 2 plot (PR2) result demonstrates that the usage of GC and AT was out of proportion. Interestingly, we identified 26 optimal codons in the G. duodenalis genome, ending with G or C. In addition, GC content, gene expression, and protein size also influence G. duodenalis CUB formation. This study systematically analyzes G. duodenalis codon usage pattern and clarifies the mechanisms of G. duodenalis CUB. These results will be very useful to identify new genes, molecular genetic manipulation, and study of G. duodenalis evolution.

scholarly journals The pentose phosphate pathway in Trypanosoma cruzi: a potential target for the chemotherapy of Chagas disease

2007 ◽  
Vol 79 (4) ◽  
pp. 649-663 ◽  
Author(s):  
Mariana Igoillo-Esteve ◽  
Dante Maugeri ◽  
Ana L. Stern ◽  
Paula Beluardi ◽  
Juan J. Cazzulo
Keyword(s):  
Oxidative Stress ◽  
Trypanosoma Cruzi ◽  
Pentose Phosphate Pathway ◽  
Single Copy ◽  
Pentose Phosphate ◽  
Site Directed Mutagenesis ◽  
Haploid Genome ◽  
Salt Bridges ◽  
Phosphogluconate Dehydrogenase ◽  
Genes Encoding

Trypanosoma cruzi is highly sensitive to oxidative stress caused by reactive oxygen species. Trypanothione, the parasite's major protection against oxidative stress, is kept reduced by trypanothione reductase, using NADPH; the major source of the reduced coenzyme seems to be the pentose phosphate pathway. Its seven enzymes are present in the four major stages in the parasite's biological cycle; we have cloned and expressed them in Escherichia coli as active proteins. Glucose 6-phosphate dehydrogenase, which controls glucose flux through the pathway by its response to the NADP/NADPH ratio, is encoded by a number of genes per haploid genome, and is induced up to 46-fold by hydrogen peroxide in metacyclic trypomastigotes. The genes encoding 6-phosphogluconolactonase, 6-phosphogluconate dehydrogenase, transaldolase and transketolase are present in the CL Brener clone as a single copy per haploid genome. 6-phosphogluconate dehydrogenase is very unstable, but was stabilized introducing two salt bridges by site-directed mutagenesis. Ribose-5-phosphate isomerase belongs to Type B; genes encoding Type A enzymes, present in mammals, are absent. Ribulose-5-phosphate epimerase is encoded by two genes. The enzymes of the pathway have a major cytosolic component, although several of them have a secondary glycosomal localization, and also minor localizations in other organelles.

scholarly journals Machine learning can differentiate venom toxins from other proteins having non-toxic physiological functions

2016 ◽  
Vol 2 ◽  
pp. e90 ◽  
Author(s):  
Ranko Gacesa ◽  
David J. Barlow ◽  
Paul F. Long
Keyword(s):  
Machine Learning ◽  
Sequence Data ◽  
Biological Data ◽  
Biological Databases ◽  
Web Based ◽  
Physiological Functions ◽  
Link Type ◽  
Venom Toxins ◽  
Venomous Animals ◽  
Toxin Protein

Ascribing function to sequence in the absence of biological data is an ongoing challenge in bioinformatics. Differentiating the toxins of venomous animals from homologues having other physiological functions is particularly problematic as there are no universally accepted methods by which to attribute toxin function using sequence data alone. Bioinformatics tools that do exist are difficult to implement for researchers with little bioinformatics training. Here we announce a machine learning tool called ‘ToxClassifier’ that enables simple and consistent discrimination of toxins from non-toxin sequences with >99% accuracy and compare it to commonly used toxin annotation methods. ‘ToxClassifer’ also reports the best-hit annotation allowing placement of a toxin into the most appropriate toxin protein family, or relates it to a non-toxic protein having the closest homology, giving enhanced curation of existing biological databases and new venomics projects. ‘ToxClassifier’ is available for free, either to download (https://github.com/rgacesa/ToxClassifier) or to use on a web-based server (http://bioserv7.bioinfo.pbf.hr/ToxClassifier/).

scholarly journals MHC-Linked Olfactory Receptor Loci Exhibit Polymorphism and Contribute to Extended HLA/OR-Haplotypes

2000 ◽  
Vol 10 (12) ◽  
pp. 1968-1978 ◽  
Author(s):  
Anke Ehlers ◽  
Stephan Beck ◽  
Simon A. Forbes ◽  
John Trowsdale ◽  
Armin Volz ◽  
...  
Keyword(s):  
Olfactory Receptor ◽  
Sequence Data ◽  
Allelic Variation ◽  
Mate Preferences ◽  
Coding Region ◽  
Link Type ◽  
Or Gene ◽  
Hla Haplotypes ◽  
A Minor ◽  
Or Genes

Clusters of olfactory receptor (OR) genes are found on most human chromosomes. They are one of the largest mammalian multigene families. Here, we report a systematic study of polymorphism of OR genes belonging to the largest fully sequenced OR cluster. The cluster contains 36 OR genes, of which two belong to the vomeronasal 1 (V1-OR) family. The cluster is divided into a major and a minor region at the telomeric end of the HLA complex on chromosome 6. These OR genes could be involved in MHC-related mate preferences. The polymorphism screen was carried out with 13 genes from the HLA-linked OR cluster and three genes from chromosomes 7, 17, and 19 as controls. Ten human cell lines, representing 18 different chromosome 6s, were analyzed. They were from various ethnic origins and exhibited different HLA haplotypes. All OR genes tested, including those not linked to the HLA complex, were polymorphic. These polymorphisms were dispersed along the coding region and resulted in up to seven alleles for a given OR gene. Three polymorphisms resulted either in stop codons (genes hs6M1-4P,hs6M1-17) or in a 16–bp deletion (gene hs6M1-19P), possibly leading to lack of ligand recognition by the respective receptors in the cell line donors. In total, 13 HLA-linked OR haplotypes could be defined. Therefore, allelic variation appears to be a general feature of human OR genes.[The sequence data reported in this paper have been submitted to EMBL under accession nos. AC006137, AC004178, AJ132194, AL022727, AL031983,AL035402, AL035542, Z98744, CAB55431, AL050339, AL035402, AL096770,AL133267, AL121944, Z98745, AL021808, and AL021807.]

BIOLOGICAL CHARACTERISTICS OF BACTERIOPHAGE PHAGUM B.C. 11 UGSHA

2020 ◽  
pp. 174-183
Author(s):  
K. V. Martynova ◽  
Keyword(s):  
Sequence Data ◽  
Raw Materials ◽  
Secondary Growth ◽  
Gc Content ◽  
Bacillus Coagulans ◽  
Passage Time ◽  
Biological Properties ◽  
Lytic Activity ◽  
Bacterial Strains ◽  
Technological Parameters

The article presents the results of research on the biological properties of the bacteriophage Phagum B. c. 11 UGSHA. Bioinformatic sequence data of Bacillus coagulans phage Phagum B. c. 11 UGSHA: length: 42609 bp, GC content: 37,1 %, molecular weight: 27 014 203,97 Da, the molarity of 1 μg/μl: 0.04 μm, the number of molecules in 1 g: 2.23 x 1010, And 260 of 1 μg/mql after 100-fold dilution: 0,259. Experimentally technological parameters of cultivation system phage/host were selected(0.2 ml of bacteriophage to 0.2 ml of the indicator culture B. coagulans), passage time-6 hours at the cultivation temperature- 35±20С. It is recommended to use Millipore membrane filters of 0.22 μm GV for cleaning Phagum B. c. 11 UGSHA. It was determined that the lytic activity by Appelman was 10-9, by Grazia the indicator was4,0+0,1×1010 ((BFU / ml); Phagum B. c. 11 UGSHA had strict specificity in relation to B. coagulans strains; morphology of plaque-forming units (rounded shape with a transparent center, zones of incomplete lysis, diameter 1-4 mm, secondary growth was not observed). It is empirically established that Phagum B. c. 11 UGSHA did not lose its lytic activity after 3 months when stored at a temperature of 2-40С, and after 12 months the indicator decreased to 108. The studied biological properties of bacteriophage Phagum B. c. 11 UGSHA isolated from fresh tomatoes with signs of spoiling, specific for 46 out of 50 bacterial strains of Bacillus coagulans, allow us to recommend Phagum B. c. 11 UGSHA for the production of phage biopreparations used not only in the laboratory for the indication and identification of Bacillus coagulans bacteria specific to it, but also for decontamination of food raw materials and food products, prevention of food poisoning, since the data of our genetic and proteomic mapping allow us to conclude that the Phagum B. c. 11 UGSHA bacteriophage does not contain pathogenicity locuses and their homologues.

Sign in / Sign up

Export Citation Format

Share Document