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1.
Biology (Basel) ; 12(6)2023 Jun 16.
Artículo en Inglés | MEDLINE | ID: mdl-37372157

RESUMEN

Differentiation-inducing factors 1 and 2 (DIF-1 and DIF-2) are small lipophilic signal molecules that induce stalk cell differentiation but differentially modulate chemotaxis toward cAMP in the cellular slime mold Dictyostelium discoideum; DIF-1 suppresses chemotactic cell movement in shallow cAMP gradients, whereas DIF-2 promotes it. The receptor(s) for DIF-1 and DIF-2 have not yet been identified. We examined the effects of nine derivatives of DIF-1 on chemotactic cell movement toward cAMP and compared their chemotaxis-modulating activity and stalk cell differentiation-inducing activity in wild-type and mutant strains. The DIF derivatives differentially affected chemotaxis and stalk cell differentiation; for example, TM-DIF-1 suppressed chemotaxis and showed poor stalk-inducing activity, DIF-1(3M) suppressed chemotaxis and showed strong stalk-inducing activity, and TH-DIF-1 promoted chemotaxis. These results suggest that DIF-1 and DIF-2 have at least three receptors: one for stalk cell induction and two for chemotaxis modulation. In addition, our results show that the DIF derivatives can be used to analyze the DIF-signaling pathways in D. discoideum.

2.
Genes (Basel) ; 14(4)2023 04 19.
Artículo en Inglés | MEDLINE | ID: mdl-37107699

RESUMEN

The evolutionary transition from single-celled to multicellular individuality requires organismal fitness to shift from the cell level to a cell group. This reorganization of fitness occurs by re-allocating the two components of fitness, survival and reproduction, between two specialized cell types in the multicellular group: soma and germ, respectively. How does the genetic basis for such fitness reorganization evolve? One possible mechanism is the co-option of life history genes present in the unicellular ancestors of a multicellular lineage. For instance, single-celled organisms must regulate their investment in survival and reproduction in response to environmental changes, particularly decreasing reproduction to ensure survival under stress. Such stress response life history genes can provide the genetic basis for the evolution of cellular differentiation in multicellular lineages. The regA-like gene family in the volvocine green algal lineage provides an excellent model system to study how this co-option can occur. We discuss the origin and evolution of the volvocine regA-like gene family, including regA-the gene that controls somatic cell development in the model organism Volvox carteri. We hypothesize that the co-option of life history trade-off genes is a general mechanism involved in the transition to multicellular individuality, making volvocine algae and the regA-like family a useful template for similar investigations in other lineages.


Asunto(s)
Chlorophyta , Volvox , Filogenia , Volvox/genética , Modelos Biológicos , Diferenciación Celular/genética
3.
Microorganisms ; 10(5)2022 Apr 29.
Artículo en Inglés | MEDLINE | ID: mdl-35630378

RESUMEN

In Rhodobacter capsulatus, the histidine kinase RegB is believed to phosphorylate its cognate transcriptional factor RegA only under anaerobic conditions. However, transcriptome evidence indicates that RegA regulates 47 genes involved in energy storage, energy production, signaling and transcription, under aerobic conditions. In this study, we provide evidence that RegA is a copper binding protein and that copper promotes the dimerization of RegA under aerobic conditions. Inductively coupled plasma mass spectrometry (ICP-MS) analysis indicates that RegA binds Cu1+ and Cu2+ in a 1:1 and 2:1 ratio, respectively. Through LC-MS/MS, ESI-MS and non-reducing SDS-PAGE gels, we show that Cu2+ stimulates disulfide bond formation in RegA at Cys156 in the presence of oxygen. Finally, we used DNase I footprint analysis to demonstrate that Cu2+-mediated covalent dimerized RegA is capable of binding to the ccoN promoter, which drives the expression of cytochrome cbb3 oxidase subunits. This study provides a new model of aerobic regulation of gene expression by RegA involving the formation of an intermolecular disulfide bond.

4.
Int J Biol Macromol ; 201: 29-36, 2022 Mar 15.
Artículo en Inglés | MEDLINE | ID: mdl-34998872

RESUMEN

Intrinsically disordered proteins (IDPs) are proteins that lack rigid structures yet play important roles in myriad biological phenomena. A distinguishing feature of IDPs is that they often mediate specific biological outcomes via multivalent weak cooperative interactions with multiple partners. Here, we show that several proteins specifically associated with processes that were key in the evolution of complex multicellularity in the lineage leading to the multicellular green alga Volvox carteri are IDPs. We suggest that, by rewiring cellular protein interaction networks, IDPs facilitated the co-option of ancestral pathways for specialized multicellular functions, underscoring the importance of IDPs in the early evolution of complex multicellularity.


Asunto(s)
Proteínas Intrínsecamente Desordenadas , Volvox
5.
J Diabetes ; 14(2): 104-110, 2022 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-34967992

RESUMEN

On 31 October 1920, Sir Frederick Banting, while preparing for a medical student lecture on diabetes, a topic that he knew little about, learned how pancreatic stones resulted in the formation of new islets of Langerhans. He then scribbled down a potential research study of tying off the ducts of the pancreas and collecting the secretions to improve diabetes. These secretions became known as insulin. A century later, 60 different oral medications and 20 different insulins are available for the treatment of diabetes, yet none stimulate new islet formation. One hundred years later, after the discovery of insulin, more than a dozen research teams from around the world have demonstrated that similar studies to Banting's pancreatic ligation studies have resulted in upregulation of the REG gene. There are now more than 200 publications on the role of Reg gene proteins and shorter Reg peptides in initiating new islet formation islet from exocrine pancreatic ducts and protecting against inflammation to islets resulting in islet death. Human data through Phase 2b in both type 1 and 2 diabetes patients with diabetes for an average of 20 years have demonstrated that the use of a shorter bioactive Reg peptide can generate new endogenous insulin production, resulting in significant reductions in hemoglobin A1C and increases in stimulated C-peptide. The observations of Frederick Banting, one century ago, may now lead to the generation of therapeutics that form new islets without the need for transplantation.


Asunto(s)
Diabetes Mellitus Tipo 1 , Diabetes Mellitus Tipo 2 , Islotes Pancreáticos , Diabetes Mellitus Tipo 1/genética , Diabetes Mellitus Tipo 2/metabolismo , Humanos , Insulina/metabolismo , Islotes Pancreáticos/metabolismo , Masculino , Páncreas/metabolismo
6.
Artículo en Inglés | MEDLINE | ID: mdl-33803358

RESUMEN

Background: As more and more people are travelling abroad, there are also increasing numbers who fall ill or have accidents in foreign countries. Some patients must be repatriated. While it has been reported that the number of repatriations is rising steadily, little is known about patients' characteristics, calling for in depth investigations of this patient group. Methods: We have conducted a retrospective study including 447 patients repatriated to the Emergency Department at the University Hospital (Inselspital) in Bern, Switzerland from 2013-2018. Results: Between 2013 and 2018, the number of repatriated patients increased by 42.6%, from 54 to 77 cases. In total, 59% of these patients were male and the median age was 60 years. Overall, 79% of patients were repatriated from European countries, with the top five countries being Italy, France, Spain, Germany and Austria. About half the cases (51.9%) were caused by illness, the other half by accidents. In total, 127 patients had to undergo surgical intervention abroad; another 194 patients underwent surgery after repatriation. The hospitalization rate was 81.4%, with a median length of in-hospital stay of 9 days (IQR 5-14) at the Inselspital. The mortality rate of at the Inselspital hospitalized patients was 4.4%, with 16 patients dying within the first 30 days after repatriation. The median cost per case was 12,005.79 CHF (IQR 4717.66-24,462.79). A multiple regression analysis showed a significant association of total costs with hospitalization (p = 0.001), surgical intervention (p = 0.001), as well as treatment in the intensive care unit (p = 0.001). Conclusions: The number of repatriations has been continuously increasing in recent years and reached a mean value of more than one case per week at the Inselspital (77 cases per year in 2018). The 30 day-mortality rate of 4.4% and the median cost per case are relatively high, demonstrating a neglected Public Health concern. These findings may provide impetus-not only for further research into repatriations but also for Public Health Promotion strategies.


Asunto(s)
Servicio de Urgencia en Hospital , Emigrantes e Inmigrantes , Austria , Europa (Continente) , Femenino , Francia , Alemania , Humanos , Italia , Masculino , Persona de Mediana Edad , Estudios Retrospectivos , España , Suiza/epidemiología
7.
Proc Biol Sci ; 287(1940): 20201414, 2020 12 09.
Artículo en Inglés | MEDLINE | ID: mdl-33259762

RESUMEN

In multicellular organisms with specialized cells, the most significant distinction among cell types is between reproductive (germ) cells and non-reproductive/somatic cells (soma). Although soma contributed to the marked increase in complexity of many multicellular lineages, little is known about its evolutionary origins. We have previously suggested that the evolution of genes responsible for the differentiation of somatic cells involved the co-option of life history trade-off genes that in unicellular organisms enhanced survival at a cost to immediate reproduction. In the multicellular green alga, Volvox carteri, cell fate is established early in development by the differential expression of a master regulatory gene known as regA. A closely related RegA-Like Sequence (RLS1) is present in its single-celled relative, Chlamydomonas reinhardtii. RLS1 is expressed in response to stress, and we proposed that an environmentally induced RLS1-like gene was co-opted into a developmental pathway in the lineage leading to V. carteri. However, the exact evolutionary scenario responsible for the postulated co-option event remains to be determined. Here, we show that in addition to being developmentally regulated, regA can also be induced by environmental cues, indicating that regA has maintained its ancestral regulation. We also found that the absence of a functional RegA protein confers increased sensitivity to stress, consistent with RegA having a direct or indirect role in stress responses. Overall, this study (i) provides mechanistic evidence for the co-option of an environmentally induced gene into a major developmental regulator, (ii) supports the view that major morphological innovations can evolve via regulatory changes and (iii) argues for the role of stress in the evolution of multicellular complexity.


Asunto(s)
Evolución Biológica , Chlorophyta/genética , Evolución Clonal/genética , Estrés Fisiológico/genética
8.
Microorganisms ; 8(4)2020 Apr 14.
Artículo en Inglés | MEDLINE | ID: mdl-32295208

RESUMEN

Bacteria employ regulatory networks to detect environmental signals and respond appropriately, often by adjusting gene expression. Some regulatory networks influence many genes, and many genes are affected by multiple regulatory networks. Here, we investigate the extent to which regulatory systems controlling aerobic-anaerobic energetics overlap with the CtrA phosphorelay, an important system that controls a variety of behavioral processes, in two metabolically versatile alphaproteobacteria, Dinoroseobacter shibae and Rhodobacter capsulatus. We analyzed ten available transcriptomic datasets from relevant regulator deletion strains and environmental changes. We found that in D. shibae, the CtrA phosphorelay represses three of the four aerobic-anaerobic Crp/Fnr superfamily regulator-encoding genes (fnrL, dnrD, and especially dnrF). At the same time, all four Crp/Fnr regulators repress all three phosphorelay genes. Loss of dnrD or dnrF resulted in activation of the entire examined CtrA regulon, regardless of oxygen tension. In R. capsulatus FnrL, in silico and ChIP-seq data also suggested regulation of the CtrA regulon, but it was only with loss of the redox regulator RegA where an actual transcriptional effect on the CtrA regulon was observed. For the first time, we show that there are complex interactions between redox regulators and the CtrA phosphorelays in these bacteria and we present several models for how these interactions might occur.

9.
Cell Signal ; 57: 65-75, 2019 05.
Artículo en Inglés | MEDLINE | ID: mdl-30790701

RESUMEN

In Dictyostelium, the intracellular cAMP-specific phosphodiesterase RegA is a negative regulator of cAMP-dependent protein kinase (PKA), a key determinant in the timing of developmental morphogenesis and spore formation. To assess the role of protein kinases in the regulation of RegA function, this study identified phosphorylation sites on RegA and characterized the role of these modifications through the analysis of phospho-mimetic and phospho-ablative mutations. Mutations affecting residue T676 of RegA, a presumed target of the atypical MAP kinase Erk2, altered the rate of development and impacted cell distribution in chimeric organisms suggesting that phosphorylation of this residue reduces RegA function and regulates cell localization during multicellular development. Mutations affecting the residue S142 of RegA also impacted the rate developmental morphogenesis but in a manner opposite of changes at T676 suggesting the phosphorylation of the S142 residue increases RegA function. Mutations affecting residue S413 residue altered aggregate sizes and delayed developmental progression suggesting that PKA operates in a negative feedback mechanism to increase RegA function. These results suggest that the phosphorylation of different residues on RegA can lead to increased or decreased RegA function and therefore in turn regulate developmental processes such as aggregate formation, cell distribution, and the kinetics of developmental morphogenesis.


Asunto(s)
3',5'-AMP Cíclico Fosfodiesterasas/metabolismo , Proteínas Bacterianas/metabolismo , Dictyostelium/metabolismo , Morfogénesis/fisiología , Animales , Diferenciación Celular/fisiología , AMP Cíclico/metabolismo , Proteínas Quinasas Dependientes de AMP Cíclico/metabolismo , Dictyostelium/genética , Mutación/genética , Hidrolasas Diéster Fosfóricas/metabolismo , Fosforilación/fisiología , Proteínas Quinasas/metabolismo , Proteínas Protozoarias/metabolismo
10.
Microb Genom ; 3(9): e000125, 2017 09.
Artículo en Inglés | MEDLINE | ID: mdl-29114403

RESUMEN

Anoxygenicphotosynthetic prokaryotes have simplified photosystems that represent ancient lineages that predate the more complex oxygen evolving photosystems present in cyanobacteria and chloroplasts. These organisms thrive under illuminated anaerobic photosynthetic conditions, but also have the ability to grow under dark aerobic respiratory conditions. This study provides a detailed snapshot of transcription ground states of both dark aerobic and anaerobic photosynthetic growth modes in the purple photosynthetic bacterium Rhodobactercapsulatus. Using 18 biological replicates for aerobic and photosynthetic states, we observed that 1834 genes (53 % of the genome) exhibited altered expression between aerobic and anaerobic growth. In comparison with aerobically grown cells, photosynthetically grown anaerobic cells showed decreased transcription of genes for cobalamin biosynthesis (-45 %), iron transport and homeostasis (-42 %), motility (-32 %), and glycolysis (-34 %). Conversely and more intuitively, the expression of genes involved in carbon fixation (547 %), bacteriochlorophyll biosynthesis (162 %) and carotenogenesis (114 %) were induced. We also analysed the relative contributions of known global redox transcription factors RegA, FnrL and CrtJ in regulating aerobic and anaerobic growth. Approximately 50 % of differentially expressed genes (913 of 1834) were affected by a deletion of RegA, while 33 % (598 out of 1834) were affected by FnrL, and just 7 % (136 out of 1834) by CrtJ. Numerous genes were also shown to be controlled by more than one redox responding regulator.


Asunto(s)
Proteínas Bacterianas/genética , Proteínas de Unión al ADN/genética , Regulación Bacteriana de la Expresión Génica , Fotosíntesis/genética , Proteínas del Complejo del Centro de Reacción Fotosintética/genética , Rhodobacter capsulatus/genética , Factores de Transcripción/genética , Anaerobiosis/genética , Bacterioclorofilas/genética , Ciclo del Carbono/genética , Carotenoides/genética , ADN Bacteriano , Perfilación de la Expresión Génica , Glucólisis/genética , Homeostasis/genética , Oxidación-Reducción , Vitamina B 12/genética
11.
J Biotechnol ; 257: 78-86, 2017 Sep 10.
Artículo en Inglés | MEDLINE | ID: mdl-28687513

RESUMEN

The biotechnologically important Gram-negative ß-proteobacterium Ralstonia eutropha H16 is able to grow lithoautotrophically by utilizing CO2 and H2 as sole carbon and energy sources, respectively. CO2 is fixed by the CBB cycle, which is encoded in duplicate on the genome of R. eutropha H16. The transcription of both cbb operons is controlled by the transcription regulator CbbR dependent on intracellular PEP levels as a response to the carbon-state of the cell. As demonstrated in this study transcription control of both cbb operons appears to be more complex and additionally involves, next to CbbR, the transcription regulator RegA as part of the global transcription regulation system RegA/RegB. The identification of a highly conserved RegA/RegB homologue in R. eutropha H16 and experimental evidence gathered in this study reveal that RegA plays a crucial role in the transcription control of both cbb promoters. RegA is able to induce cbb promoter activity and controls transcription in combination with CbbR dependent on cellular PEP concentrations. These results clearly demonstrate that RegA plays an important role in cbb operon transcription regulation and may also be relevant for the control of other energy-utilizing and energy-generating pathways of R. eutropha H16. In addition to promoting a more complete understanding of the CO2 fixation mechanism of R. eutropha H16 these findings also provide crucial insights for the utilization of this bacterium in biotechnological applications with respect to CO2 fixation.


Asunto(s)
Proteínas Bacterianas/metabolismo , Cupriavidus necator/genética , Cupriavidus necator/metabolismo , Proteínas de Unión al ADN/metabolismo , Operón/genética , Factores de Transcripción/genética , Factores de Transcripción/metabolismo , Secuencia de Aminoácidos , Proteínas Bacterianas/genética , Dióxido de Carbono/metabolismo , Cromosomas Bacterianos , Proteínas de Unión al ADN/genética , Escherichia coli/genética , Regulación Bacteriana de la Expresión Génica , Genes Bacterianos , Redes y Vías Metabólicas/genética , Regiones Promotoras Genéticas/genética , Alineación de Secuencia , Transducción de Señal , Transcripción Genética
12.
Front Microbiol ; 8: 1277, 2017.
Artículo en Inglés | MEDLINE | ID: mdl-28747899

RESUMEN

The chemical attack of ore by ferric iron and/or sulfuric acid releases valuable metals. The products of these reactions are recycled by iron and sulfur oxidizing microorganisms. These acidophilic chemolithotrophic prokaryotes, among which Acidithiobacillus ferrooxidans, grow at the expense of the energy released from the oxidation of ferrous iron and/or inorganic sulfur compounds (ISCs). In At. ferrooxidans, it has been shown that the expression of the genes encoding the proteins involved in these respiratory pathways is dependent on the electron donor and that the genes involved in iron oxidation are expressed before those responsible for ISCs oxidation when both iron and sulfur are present. Since the redox potential increases during iron oxidation but remains stable during sulfur oxidation, we have put forward the hypothesis that the global redox responding two components system RegB/RegA is involved in this regulation. To understand the mechanism of this system and its role in the regulation of the aerobic respiratory pathways in At. ferrooxidans, the binding of different forms of RegA (DNA binding domain, wild-type, unphosphorylated and phosphorylated-like forms of RegA) on the regulatory region of different genes/operons involved in ferrous iron and ISC oxidation has been analyzed. We have shown that the four RegA forms are able to bind specifically the upstream region of these genes. Interestingly, the phosphorylation of RegA did not change its affinity for its cognate DNA. The transcriptional start site of these genes/operons has been determined. In most cases, the RegA binding site(s) was (were) located upstream from the -35 (or -24) box suggesting that RegA does not interfere with the RNA polymerase binding. Based on the results presented in this report, the role of the RegB/RegA system in the regulation of the ferrous iron and ISC oxidation pathways in At. ferrooxidans is discussed.

13.
Artículo en Inglés | MEDLINE | ID: mdl-28573107

RESUMEN

For aerobic human pathogens, adaptation to hypoxia is a critical factor for the establishment of persistent infections, as oxygen availability is low inside the host. The two-component system RegB/A of Brucella suis plays a central role in the control of respiratory systems adapted to oxygen deficiency, and in persistence in vivo. Using an original "in vitro model of persistence" consisting in gradual oxygen depletion, we compared transcriptomes and proteomes of wild-type and ΔregA strains to identify the RegA-regulon potentially involved in the set-up of persistence. Consecutive to oxygen consumption resulting in growth arrest, 12% of the genes in B. suis were potentially controlled directly or indirectly by RegA, among which numerous transcriptional regulators were up-regulated. In contrast, genes or proteins involved in envelope biogenesis and in cellular division were repressed, suggesting a possible role for RegA in the set-up of a non-proliferative persistence state. Importantly, the greatest number of the RegA-repressed genes and proteins, including aceA encoding the functional IsoCitrate Lyase (ICL), were involved in energy production. A potential consequence of this RegA impact may be the slowing-down of the central metabolism as B. suis progressively enters into persistence. Moreover, ICL is an essential determinant of pathogenesis and long-term interactions with the host, as demonstrated by the strict dependence of B. suis on ICL activity for multiplication and persistence during in vivo infection. RegA regulates gene or protein expression of all functional groups, which is why RegA is a key regulator of B. suis in adaptation to oxygen depletion. This function may contribute to the constraint of bacterial growth, typical of chronic infection. Oxygen-dependent activation of two-component systems that control persistence regulons, shared by several aerobic human pathogens, has not been studied in Brucella sp. before. This work therefore contributes significantly to the unraveling of persistence mechanisms in this important zoonotic pathogen.


Asunto(s)
Proteínas Bacterianas/genética , Proteínas Bacterianas/fisiología , Brucella suis/genética , Brucella suis/metabolismo , Regulación Bacteriana de la Expresión Génica/genética , Hipoxia/metabolismo , Isocitratoliasa/genética , Regulón/genética , Adaptación Fisiológica , Animales , Secuencia de Bases , Brucella suis/crecimiento & desarrollo , Brucella suis/patogenicidad , Brucelosis/metabolismo , Brucelosis/microbiología , ADN Bacteriano , Modelos Animales de Enfermedad , Regulación hacia Abajo , Metabolismo Energético , Femenino , Genes Bacterianos/genética , Isocitratoliasa/metabolismo , Redes y Vías Metabólicas/genética , Ratones , Ratones Endogámicos BALB C , Mutación , Nitrito Reductasas/análisis , Oxidorreductasas/análisis , Oxígeno/metabolismo , Consumo de Oxígeno/fisiología , Proteoma/análisis , ARN Bacteriano/aislamiento & purificación , Regulación hacia Arriba , Virulencia/genética
14.
Evolution ; 68(7): 2014-25, 2014 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-24689915

RESUMEN

To understand the hierarchy of life in evolutionary terms, we must explain why groups of one kind of individual, say cells, evolve into a new higher level individual, a multicellular organism. A fundamental step in this process is the division of labor into nonreproductive altruistic soma. The regA gene is critical for somatic differentiation in Volvox carteri, a multicellular species of volvocine algae. We report the sequence of regA-like genes and several syntenic markers from divergent species of Volvox. We show that regA evolved early in the volvocines and predict that lineages with and without soma descended from a regA-containing ancestor. We hypothesize an alternate evolutionary history of regA than the prevailing "proto-regA" hypothesis. The variation in presence of soma may be explained by multiple lineages independently evolving soma utilizing regA or alternate genetic pathways. Our prediction that the genetic basis for soma exists in species without somatic cells raises a number of questions, most fundamentally, under what conditions would species with the genetic potential for soma, and hence greater individuality, not evolve these traits. We conclude that the evolution of individuality in the volvocine algae is more complicated and labile than previously appreciated on theoretical grounds.


Asunto(s)
Evolución Molecular , Duplicación de Gen , Genes de Plantas , Volvox/genética , Diferenciación Celular , Filogenia , Volvox/citología
15.
Infect Genet Evol ; 19: 337-48, 2013 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-23660484

RESUMEN

BACKGROUND: To investigate differences in pathogenesis, diagnosis and resistance pathways between HIV-1 subtypes, an accurate subtyping tool for large datasets is needed. We aimed to evaluate the performance of automated subtyping tools to classify the different subtypes and circulating recombinant forms using pol, the most sequenced region in clinical practice. We also present the upgraded version 3 of the Rega HIV subtyping tool (REGAv3). METHODOLOGY: HIV-1 pol sequences (PR+RT) for 4674 patients retrieved from the Portuguese HIV Drug Resistance Database, and 1872 pol sequences trimmed from full-length genomes retrieved from the Los Alamos database were classified with statistical-based tools such as COMET, jpHMM and STAR; similarity-based tools such as NCBI and Stanford; and phylogenetic-based tools such as REGA version 2 (REGAv2), REGAv3, and SCUEAL. The performance of these tools, for pol, and for PR and RT separately, was compared in terms of reproducibility, sensitivity and specificity with respect to the gold standard which was manual phylogenetic analysis of the pol region. RESULTS: The sensitivity and specificity for subtypes B and C was more than 96% for seven tools, but was variable for other subtypes such as A, D, F and G. With regard to the most common circulating recombinant forms (CRFs), the sensitivity and specificity for CRF01_AE was ~99% with statistical-based tools, with phylogenetic-based tools and with Stanford, one of the similarity based tools. CRF02_AG was correctly identified for more than 96% by COMET, REGAv3, Stanford and STAR. All the tools reached a specificity of more than 97% for most of the subtypes and the two main CRFs (CRF01_AE and CRF02_AG). Other CRFs were identified only by COMET, REGAv2, REGAv3, and SCUEAL and with variable sensitivity. When analyzing sequences for PR and RT separately, the performance for PR was generally lower and variable between the tools. Similarity and statistical-based tools were 100% reproducible, but this was lower for phylogenetic-based tools such as REGA (~99%) and SCUEAL (~96%). CONCLUSIONS: REGAv3 had an improved performance for subtype B and CRF02_AG compared to REGAv2 and is now able to also identify all epidemiologically relevant CRFs. In general the best performing tools, in alphabetical order, were COMET, jpHMM, REGAv3, and SCUEAL when analyzing pure subtypes in the pol region, and COMET and REGAv3 when analyzing most of the CRFs. Based on this study, we recommend to confirm subtyping with 2 well performing tools, and be cautious with the interpretation of short sequences.


Asunto(s)
Infecciones por VIH/virología , VIH-1/clasificación , VIH-1/genética , Tipificación Molecular/métodos , Análisis por Conglomerados , Biología Computacional , Bases de Datos Genéticas , Infecciones por VIH/epidemiología , Humanos , Filogenia , Vigilancia en Salud Pública , Reproducibilidad de los Resultados , Sensibilidad y Especificidad
16.
Biosci. j. (Online) ; 23(2)abr.-jun. 2007. graf, ilus
Artículo en Portugués | LILACS | ID: lil-469383

RESUMEN

Objetivou-se estudar o efeito de diferentes turnos de rega e níveis de irrigação sobre a composição bromatológica e a digestibilidade "in vitro' da matéria seca (DIVMS) de Panicum maximum Jacq. cv. Tanzânia-1. Uma bancada experimental foi montada sob ambiente protegido, onde foram colocados recipientes cultivados com a gramínea. As irrigações foram realizadas com turnos de rega de um, quatro e sete dias e lâminas d'água para restabelecer 50, 75 e 100% da disponibilidade total de água no solo. Foram avaliados os teores de proteína bruta (PB), fibra em detergente neutro (FDN), fibra em detergente ácido (FDA) e DIVMS após o último corte. Foi verificado que o teor de PB foi maior quanto menor foi a quantidade de água aplicada. Os valores de DIVMS foram inversamente proporcionais aos teores de FDA. Conclui-se que o turno de rega pouco influencia nos fatores estudados e que a irrigação elevando o teor de água do solo próximo a capacidade de campo, diminui e aumenta os teores de PB e FDA, respectivamente.


The aim of this work was to study the effect of different frequency and levels of irrigation on chemical composition and ?in vitro? dry matter digestibility (IVDMD) of tanz?nia grass (Panicum maximum Jacq. Cv Tanzania-1). The experiment was carried out under greenhouse conditions where drums were filled with soil and cultivated with tanzania grass. The irrigations were performed with a frequency of one, four and seven days, in order to reestablish soil water content to 50, 75 and 100% of the total available water in the soil. During the experiment were evaluated the crude protein (CD), neutral detergent fiber (NDF), acid detergent fiber (ADF) and IVDMD after the last cut. The CD increased as the irrigation depth decreased. The values of IVDMD of were inversely proportional to that of the ADF. The results show that irrigation frequency does not influency in the monitored variables and the irrigation could be.


Asunto(s)
Riego Agrícola , Suelo , Pastizales , Poaceae , Panicum
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