192 research outputs found

    Database of Trypanosoma cruzi repeated genes: 20 000 additional gene variants

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    <p>Abstract</p> <p>Background</p> <p>Repeats are present in all genomes, and often have important functions. However, in large genome sequencing projects, many repetitive regions remain uncharacterized. The genome of the protozoan parasite <it>Trypanosoma cruzi </it>consists of more than 50% repeats. These repeats include surface molecule genes, and several other gene families. In the <it>T. cruzi </it>genome sequencing project, it was clear that not all copies of repetitive genes were present in the assembly, due to collapse of nearly identical repeats. However, at the time of publication of the <it>T. cruzi </it>genome, it was not clear to what extent this had occurred.</p> <p>Results</p> <p>We have developed a pipeline to estimate the genomic repeat content, where shotgun reads are aligned to the genomic sequence and the gene copy number is estimated using the average shotgun coverage. This method was applied to the genome of <it>T. cruzi </it>and copy numbers of all protein coding sequences and pseudogenes were estimated. The 22 640 results were stored in a database available online. 18% of all protein coding sequences and pseudogenes were estimated to exist in 14 or more copies in the <it>T. cruzi </it>CL Brener genome. The average coverage of the annotated protein coding sequences and pseudogenes indicate a total gene copy number, including allelic gene variants, of over 40 000.</p> <p>Conclusion</p> <p>Our results indicate that the number of protein coding sequences and pseudogenes in the <it>T. cruzi </it>genome may be twice the previous estimate. We have constructed a database of the <it>T. cruzi </it>gene repeat data that is available as a resource to the community. The main purpose of the database is to enable biologists interested in repeated, unfinished regions to closely examine and resolve these regions themselves using all available shotgun data, instead of having to rely on annotated consensus sequences that often are erroneous and possibly misleading. Five repetitive genes were studied in more detail, in order to illustrate how the database can be used to analyze and extract information about gene repeats with different characteristics in <it>Trypanosoma cruzi</it>.</p

    Pseudomonas putida toksiin-antitoksiin sĂŒsteem GraTA: regulatsioon ja osalus stressitaluvuses

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    VĂ€itekirja elektrooniline versioon ei sisalda publikatsioone.Elu on stressirohke, eriti ĂŒheraksetel organismidel nagu bakterid. Sageli tundub, et parim viis stressiga toimetulekuks on rahulikult oodata tingimuste paranemist. Selline kĂ€itumismall on kasutust leidnud ka mikroobide maailmas. Bakteritel on palju erinevaid kasvu reguleerimise vĂ”imalusi, mille hulka on viimasel ajal arvatud ka toksiin-antitoksiin (TA) sĂŒsteemid. TA-sĂŒsteemid koosnevad kahest komponendist: rakule eluliselt olulisi protsesse vĂ”i rakukesta kahjustavast toksiinist ja teda neutraliseerivast antitoksiinist. Selliste geenide olemasolu bakterite genoomis on esmapilgul mĂ”istatuslik, sest miks peaks bakter tootma iseendale toksilist valku? Hiljutised uuringud mikroobide mudelorganismis Escherichia coli on nĂ€idanud, et toksiinid pĂ”hjustavad bakterite ĂŒleminekut uinuvasse olekusse, mida iseloomustab bakterite ainevahetuse aeglustumine ja peatunud kasv. Sellised mikroobid tekitavad suuri probleeme meditsiinis, kuna on vĂ€ga paljude stressiolukordade, kaasa arvatud paljude antibiootikumide toime suhtes tundetumad ja vĂ”imelised ĂŒle elama tingimusi, mis kiirelt kasvavaid baktereid tapaks. Kui mudelorganismis E. coli on TA sĂŒsteemide osalus bakteri stressitaluvuses hĂ€sti kirjeldatud, siis teistes bakteriliikides ei ole neid potentsiaalselt toksilisi sĂŒsteeme nii sĂŒstemaatiliselt uuritud. SeetĂ”ttu ei ole ka selge, kas erinevates bakterites toimivad TA sĂŒsteemid erinevalt vĂ”i mingi ĂŒldise mehhanismi alusel. KĂ€esolev töö kirjeldab keskkonnabakteri Pseudomonas putida kasvukiirust mĂ”jutavat GraTA sĂŒsteemi. Tavaliselt takistab antitoksiin GraA vĂ€ga efektiivselt toksiini GraT aktiivsust, kuid antitoksiinist vabanenult suudab toksiin mĂ”jutada selle bakteri stressitaluvust. Toksiini mĂ”ju on kahetine, sest olenevalt stressi tĂŒĂŒbist vĂ”ib toksiin nii suurendada kui ka vĂ€hendada bakteri stressitaluvust. SeetĂ”ttu on bakterile vĂ€ga oluline, et potentsiaalselt kahjulik TA sĂŒsteem aktiveeruks vaid kindlatel stressitingimustel.Life is full of stress, especially for small unicellular organisms like bacteria. For bacteria, just like for us, the best option to survive harsh conditions is sometimes to just lie still and wait for things to get better. Bacteria have many mechanisms to regulate growth, among them also the intriguing toxin-antitoxin (TA) systems. These systems consist of two components: a toxic protein that can harm the vital functions or compartments of a cell, and an antitoxin that can inhibit the toxin’s action. The presence of the TA systems in bacterial chromosomes is puzzling at first sight: why should a bacterium waste energy and resources to produce a toxin against itself? Recent research in the model organism Escherichia coli has shown that the toxic proteins cause a dormant, hibernation-like state, which is characterized by reduced metabolism and ceased growth. These bacteria cause great medical concerns as they are highly persistent to different stresses, including antibiotics, and survive conditions that would kill rapidly growing bacteria. After the stress has passed, the antitoxins inactivate the toxins and bacteria can resume growth. So, TA systems contribute to stress survival of bacteria, at least of E. coli. The contribution of TA systems to stress tolerance has been studied less systematically in other bacteria and no universal mechanism for the TA-mediated stress management has emerged so far. The current work describes a growth-rate-affecting TA system GraTA in the environmental bacterium Pseudomonas putida and shows that the toxin is kept under strict regulation by the antitoxin. Yet, when toxin is freed from the antitoxin, it inhibits the protein production in a cold-sensitive manner. The GraT toxin plays a controversial role in stress tolerance as it can both increase and decrease the tolerance to certain chemicals. This vividly highlights both the benefits and costs that the TA systems can have for bacteria

    Pseudomonas putida toksiini GraT mĂ”ju bakteri fĂŒsioloogiale

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    VĂ€itekirja elektrooniline versioon ei sisalda publikatsiooneLooduses peavad bakterid olema vĂ”imelised toime tulema keskkonnatingimuste muutumisega ĂŒpris laiades piirides. Selles on bakteritele abiks paljud raku elutegevust ja kasvu kontrollivad sĂŒsteemid. Eriti omapĂ€rasteks bakteri kasvu regulaatoriteks arvatakse olevat toksiin-antitoksiin (TA) sĂŒsteemid. Enamasti koosnevad need kahest vĂ€ikesest valgust: toksiin on vĂ”imeline inhibeerima bakteri elutĂ€htsaid protsesse, kuid tavatingimustel takistab seda temaga seondunud antitoksiin. Selleks, et mĂ”ista konkreetse TA sĂŒsteemi olulisust ja mĂ”ju bakterile, on vaja kirjeldada nii toksiini otsest sihtmĂ€rki rakus kui ka bakteri fĂŒsioloogilist vastust toksiini toimele. Selle töö eesmĂ€rgiks oli tuvastada mullabakteri Pseudomonas putida ĂŒhe TA toksiini, GraT, sihtmĂ€rk rakus ning kirjeldada toksiini mĂ”ju raku elutegevusele. GraT on omapĂ€rane toksiin, kuna selle efekt on temperatuuritundlik ning sĂŒveneb kĂŒlmas. Töö tuvastas, et GraT lagundab transleeritavaid mRNA-sid. GraT struktuuri analĂŒĂŒs viitab, et toksiinidele ebatĂŒĂŒpiliselt on valgu esimene viiendik paindlik ja ilma kindla struktuurita. Samuti tuvastati, et GraT toksilisust vĂ”imendab teiste valkude voltumist abistav ĆĄaperonvalk DnaK, mis vĂ”ib olla seotud GraT paindliku regiooni voltumisega. GraT fĂŒsioloogilisi efekte jĂ€lgiti mudelsĂŒsteemis, kus toksiini toodetakse looduslikust genoomsest lookusest, millest puudub antitoksiin. VĂ”rreldes tihti rakendatavate toksiini kunstliku ĂŒletootmise sĂŒsteemidega, on kasutatud mudel paremaks lĂ€henduseks toksiini loomulikule aktivatsioonile. GraT mĂ”jul tĂ€heldati kahetist efekti bakteri stressitaluvusele: mĂ”ningate stressiallikate puhul see suureneb, kuid teiste puhul vĂ€heneb. Lisaks hĂ€irib GraT ribosoomide biogeneesi, mida pole sarnaste toksiinide kohta varem kirjeldatud. GraT mĂ”ju all kasvavate rakkude valgulise koostise analĂŒĂŒs nĂ€itas, et bakter ĂŒritab GraT toksilisust leevendada, suurendades ribosoomide biosĂŒnteesi abivalkude hulka ja vĂ€hendades sĂŒsinikumetabolismi intensiivsust. Kuigi GraT roll P. putida elus ei ole endiselt selge, kirjeldati GraT puhul mitmeid TA toksiinidele ebaharilikke omadusi, mis tĂ€iendavad meie arusaamu nende ebatavaliste regulaatorite mitmekesisusest.Free-living bacteria must cope with very different environmental conditions. This is enabled by many systems that control their growth and metabolism. Toxin-antitoxin (TA) systems are thought to be a peculiar example of such regulators. These usually consist of two small proteins: the toxin blocks vital cellular processes but is normally inhibited by antitoxin binding. To understand the importance of a TA system in bacterial life, it is necessary to pinpoint the toxin’s molecular target and to also describe the physiological response to the toxicity. This thesis aimed to identify the target of GraT, a TA toxin in the soil bacterium Pseudomonas putida, and to study the toxin’s effect on bacterial physiology. GraT is an intriguing toxin, as its effect is more pronounced at lower growth temperatures. This work identified that GraT degrades translated mRNAs. Structural analysis of GraT suggests that, atypically for TA toxins, the first one fifth of the protein is disordered. Additionally, it was seen that the chaperone DnaK enhances GraT toxicity, which may be linked to folding the GraT disordered region. The physiological effects of GraT were studied in a model where the toxin is produced from its native locus that lacks the antitoxin gene. Compared to the common systems of artificial toxin overexpression, the applied model is a better estimation of natural toxin activation. GraT was found to have a dual effect on P. putida stress tolerance: the bacterium is more sensitive to some stressors while more resilient against others. Additionally, GraT inhibits ribosome biogenesis, which has not been described before for similar toxins. Analysing the protein composition of cells growing under GraT stress showed that bacteria work to alleviate GraT toxicity by upregulating ribosome assembly factors and downregulating carbon metabolism. Even though the role of GraT in P. putida biology is still uncertain, the thesis described several GraT features unusual for TA toxins and thus enriched our knowledge of TA systems’ diversit

    The SIB Swiss Institute of Bioinformatics’ resources : focus on curated databases

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    The SIB Swiss Institute of Bioinformatics provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article

    Fv1 restriction properties beyond the murine leukemia virus

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    Restriction factors are cellular proteins that constitute one of the defence mechanisms developed by the host to fight viral infections. Friend virus susceptibility-1 (Fv1) is the prototypic restriction factor known for blocking murine leukemia virus (MLV) replication by targeting the viral capsid protein. This gene was found to be highly polymorphic between murine species as well as being under strong positive selection and having different restriction specificities. The origin of Fv1 remains unclear, however, its acquisition is known to have happened before the emergence of MLVs. It is, therefore, reasonable to speculate that non-MLV retroviruses have been involved in shaping Fv1 evolution. The aim of this PhD project was to further understand how Fv1 evolves and interacts with retroviruses. A number of retroviruses from different genera were tested against a panel of Fv1s from different wild mice. Novel restriction activities were found for the gammaretroviruses Gibbon Ape Leukemia Virus and Feline Leukemia Virus as well as for two newly discovered endogenous retroviruses. More interestingly, the alpharetrovirus Rous Sarcoma Virus and the betaretrovirus Mouse Mammary Tumour Virus could be restricted by two Fv1s. These Fv1s showed no sign of gammaretrovirus restriction. Mapping studies pointed to the Fv1 C-terminal domain variable regions VA and VD as the interacting domains involved in these new specificities. Fine mapping revealed that single residue determinants were different for each virus. It was also shown that loss of activity is possible with very limited changes. To investigate the stage of the life cycle blocked for these viruses, qPCR assays were performed in Fv1 transduced cells to detect late reverse transcription and nuclear entry. The results confirmed that infection is blocked at the post-entry level after reverse transcription and before integration, as previously observed with MLV. Taken together with previous published data, these findings support the hypothesis that Fv1 is a very plastic system and that it might have evolved in response to non-gamma retroviruses from different genera that would have predated MLVs.  Open Acces

    The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases.

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    The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article

    The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

    Get PDF
    The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article

    Medicago PhosphoProtein Database: a repository for Medicago truncatula phosphoprotein data

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    The ability of legume crops to fix atmospheric nitrogen via a symbiotic association with soil rhizobia makes them an essential component of many agricultural systems. Initiation of this symbiosis requires protein phosphorylation-mediated signaling in response to rhizobial signals named Nod factors. Medicago truncatula (Medicago) is the model system for studying legume biology, making the study of its phosphoproteome essential. Here, we describe the Medicago PhosphoProtein Database (MPPD; http://phospho.medicago.wisc.edu), a repository built to house phosphoprotein, phosphopeptide, and phosphosite data specific to Medicago. Currently, the MPPD holds 3,457 unique phosphopeptides that contain 3,404 non-redundant sites of phosphorylation on 829 proteins. Through the web-based interface, users are allowed to browse identified proteins or search for proteins of interest. Furthermore, we allow users to conduct BLAST searches of the database using both peptide sequences and phosphorylation motifs as queries. The data contained within the database are available for download to be investigated at the user’s discretion. The MPPD will be updated continually with novel phosphoprotein and phosphopeptide identifications, with the intent of constructing an unparalleled compendium of large-scale Medicago phosphorylation data

    New Tools for Dengue Diagnostics

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    Dengue caused by four antigenically distinct serotype remains a serious health concern around the world, particularly in the tropical areas. Clinical signs and symptoms of this disease are indistinguishable from other infectious disease; therefore, laboratory diagnosis is very crucial for confirming the disease that will be useful for the patient’s management. In laboratory, dengue can be confirmed using cell culture, RNA detection, and serological detection based on ELISA and immunochromatographic test. However, each of these methods has certain practical limitations. Therefore, researchers from all over the world have been working to address these limitations. In this chapter, we will highlight the current research toward the development of novel point-of-care test for the diagnosis of dengue in acute and convalescent phase
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