Profil clinique et évolutif des patients atteints du COVID-19 à Libreville étude rétrospective et mono-centrique / Clinical and evolutionary profile of patients with COVID-19 in Libreville: A Retrospective Cohort study

Introduction : L'étude clinique des patients infectés par le SARS-CoV2 est nécessaire pour la mise en œuvre des mesures préventives de lutte contre la COVID-19. L'objectif de l'étude a été de déterminer le profil clinique et évolutif des patients Covid-19 au CHU de Libreville.Méthodes : Il s'agit d'une étude rétrospective à viser analytique menée en secteur d'infectiologie COVID du SICOV du CHU de Libreville sur une période d'activité allant du 15 mars au 30 juin. La régression logistique univariée et multivariée pour explorer les facteurs de risque associés à la mortalité au SICOV a été utilisée. Résultats : Au total 441 patients COVID-19 étaient inclus dans l'étude, parmi lesquels 398 survivants (90,2%) et 43 décédés (9,8%). La population de moins de 65 ans représentait 88,0% de l'effectif. Le sex-ratio était de 1,34. Par rapport aux 398 survivants, les 43 patients décédés étaient significativement plus âgés (âge médian, 59 ans vs 48 ans ; p <0,001). Les lésions pulmonaires avec atteinte critique > 75% étaient plus importantes chez les patients décédés (29,2% vs 3,0% ; p=0,001). Cependant, après ajustement en analyse multivariée, l'âge supérieur à 65 ans était le seul facteur de risque indépendant de décès (p<0,001 ; OR=4,632 IC95% [2,243 ­ 9,565]).Conclusion : L'âge supérieur à 65 ans était le facteur de risque indépendant de décès, nécessitant un renforcement de mesure de contrôle de l'infection dans cette population

Introduction: The study of the prognostic factors of death of patients infected with SARS-CoV2 is necessary for the implementation of preventive measures against COVID-19. Methods: This is a retrospective study conducted in the COVID infectious disease sector of the SICOV of the University Hospital of Libreville over a period of activity from March 15 to June 30. The clinical course of the survivors and the deceased were compared. Univariate and multivariate logistic regression to explore risk factors associated with SICOV deaths were used.Results: A total of 441 COVID-19 patients were included in the study, of which 398 survivors (90.2%) and 43 died (9.8%). The population under 65 represented 88.0% of the workforce. The sex ratio was 1.34. Compared to the 398 survivors, the 43 patients who died were significantly older (median age, 59 years vs 48 years; p <0.001). Lung lesions with critical impairment > 75% were greater in deceased patients (29.2% vs. 3.0%; p = 0.001). On multivariate analysis, age over 65 was the main independent risk factor for death (p <0.001; OR = 4.632 95% CI [2.243 - 9.565]).Conclusion: Age over 65 was the independent risk factor for death, requiring increased infection control measures in this population

Analysis on epidemiological characteristics of dengue fever and E gene evolution of dengue virus in Guangzhou, 2020 / 中华流行病学杂志

Objective: To assess the incidence of dengue fever and E gene evolution of dengue virus in Guangzhou in 2020 and understand the local epidemiological characteristics of dengue fever and spreading of dengue virus. Methods: The information of dengue fever cases in Guangzhou in 2020 was collected from Notifiable Infectious Disease System of Chinese Center for Disease Control and Prevention Information System. Serum samples from the cases were detected by real-time PCR. The E gene was sequenced and analyzed. Maximum likelihood phylogenetic trees were constructed using software MEGA 5.05. The statistical analysis was conducted using software SPSS 20.0. Results: A total of 33 dengue fever cases were reported in Guangzhou in 2020, including 31 (93.94%) imported cases and 2 (6.06%) local cases. Compared with the data during 2016 to 2019, the number of cases, overall incidence and local incidence all decreased with statistically significant differences (all P<0.05). The imported cases from Southeast Asia constituted 90.32% (28/31) of imported cases. The E gene sequences and the phylogenetic trees of imported and local cases demonstrated close relationship with the virus sequences from Southeast Asian, and they were less homologous with the sequences of dengue virus isolated in Guangzhou in previous years. Conclusions: The incidence of dengue in Guangzhou in 2020 was significantly affected by the imported cases, especially those from Southeast Asian countries. The study result demonstrated that dengue fever was not endemic in Guangzhou and it was caused by imported ones.

Variante Ómicron SARS-CoV-2: una nueva variante de preocupación / Ómicron SARS-CoV-2 variant: anew variant of concern

Ha surgido una nueva variante de preocupación de SARS-CoV-2, cuyos efectos en la evolución de la pandemia parecen inciertos. Sin embargo, ha comenzado a surgir evidencia con respecto al comportamiento viral en cuanto a su transmisibilidad, unión a receptor de la célula hospedadora y escape del sistema inmune. Presentamos una revisión actualizada de los datos existentes en la literatura respecto a los aspectos microbiológicos y epidemiológicos que pueden ayudarnos a comprender las futuras investigaciones en esta variante.(AU)

A new variant of concern for SARS-CoV-2 has emerged, the effects of which on the evolution of the pandemic appear uncertain. However, evidence has begun to emerge regarding viral behavior in terms of its transmissibility, receptor binding on the host cell, and escape from the immune system. We present an updated review of the existing data in the literature regarding the microbiological and epidemiological aspects that can help us understand future research on this variant.(AU)

Evolución de los niveles séricos de proteína C-reactiva y procalcitonina tras resección hepática / Evolution of C-reactive protein and procalcitonin serum levels after hepatic resection

Resumen Objetivo: Evaluar la evolución de los niveles séricos de proteína C-reactiva y procalcitonina tras resección hepática. Materiales y Método: Estudio observacional prospectivo, con pacientes con diferentes tipos de resección hepática, sin infección ni complicaciones mayores posoperatorias. Los niveles de proteína C-reactiva y procalcitonina se midieron el día anterior a la cirugía y diariamente, hasta el 7° día, o hasta el alta, lo primero que ocurriera. Resultados: Se incluyeron 42 pacientes. Los niveles de procalcitonina, a las 24 h, correlacionaban significativamente con la duración de la operación (p = 0,04). A las 48 h, los niveles de proteína C-reactiva fueron mayores en las resecciones hepáticas no lobares que en las lobares (p = 0,049). A las 24 h, los niveles de procalcitonina aumentaron más en las hepatectomías mayores que en las menores (p = 0,017). Los niveles de procalcitonina fueron significativamente menores en los pacientes con abordaje laparoscópico en los 4 primeros días. Conclusión: La resección hepática produce un aumento de los niveles séricos de proteína C-reactiva y procalcitonina, pero con menor intensidad si el abordaje es laparoscópico. Los niveles séricos de proteína C-reactiva tienden a ser mayores en las hepatectomías menos extensas, mientras que los de procalcitonina tienden a ser mayores en las más extensas.

Aim: To evaluate the postoperative evolution of C-reactive protein and procalcitonin after hepatic resection. Materials and Method: Prospective observational study, including patients with different types of hepatic resection, without infectious or major postoperative complications. Procalcitonin and C-reactive protein serum levels were measured on the day prior to surgery and every day after surgery until the seventh postoperative day. Results: Forty-two patients were included. There was a significant correlation between procalcitonin levels at 24 hours after surgery and the overall length of surgery (p = 0.04). C-reactive protein was higher in nonlobar hepatectomies than in lobar hepatectomies 48 hours after surgery (p = 0.049). Procalcitonin was higher in major hepatectomies than in minor hepatectomies 24 hours after surgery (p = 0.017). Procalcitonin levels were significantly lower in patients with laparoscopic approach in the first four postoperative days. Conclusion: Hepatic resection increases the serum levels of C-reactive protein and procalcitonin, but with less intensity if the approach is laparoscopic. C-reactive protein levels tend to be higher in less extensive hepatectomies and procalcitonin levels tend to be higher in more extensive resections.

ADP-ribosylhydrolases: from DNA damage repair to COVID-19 / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

Adenosine diphosphate (ADP)-ribosylation is a unique post-translational modification that regulates many biological processes, such as DNA damage repair. During DNA repair, ADP-ribosylation needs to be reversed by ADP-ribosylhydrolases. A group of ADP-ribosylhydrolases have a catalytic domain, namely the macrodomain, which is conserved in evolution from prokaryotes to humans. Not all macrodomains remove ADP-ribosylation. One set of macrodomains loses enzymatic activity and only binds to ADP-ribose (ADPR). Here, we summarize the biological functions of these macrodomains in DNA damage repair and compare the structure of enzymatically active and inactive macrodomains. Moreover, small molecular inhibitors have been developed that target macrodomains to suppress DNA damage repair and tumor growth. Macrodomain proteins are also expressed in pathogens, such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, these domains may not be directly involved in DNA damage repair in the hosts or pathogens. Instead, they play key roles in pathogen replication. Thus, by targeting macrodomains it may be possible to treat pathogen-induced diseases, such as coronavirus disease 2019 (COVID-19).

Enzyme ancestral sequence reconstruction and directed evolution / 生物工程学报

The amino acid sequence of ancestral enzymes from extinct organisms can be deduced through in silico approach termed ancestral sequence reconstruction (ASR). ASR usually has six steps, which are the collection of nucleic acid/amino acid sequences of modern enzymes, multiple sequence alignment, phylogenetic tree construction, computational deduction of ancestral enzyme sequence, gene cloning, and characterization of enzyme properties. This method is widely used to study the adaptation and evolution mechanism of molecules to the changing environmental conditions on planetary time scale. As enzymes play key roles in biocatalysis, this method has become a powerful method for studying the relationship among the sequence, structure, and function of enzymes. Notably, most of the ancestral enzymes show better temperature stability and mutation stability, making them ideal protein scaffolds for further directed evolution. This article summarizes the computer algorithms, applications, and commonly used computer software of ASR, and discusses the potential application in directed evolution of enzymes.

Genome-wide characterization of the abscisic acid-, stress- and ripening-induced (ASR) gene family in wheat (Triticum aestivum L)

BACKGROUND: Abscisic acid-, stress-, and ripening-induced (ASR) genes are a class of plant specific transcription factors (TFs), which play important roles in plant development, growth and abiotic stress responses. The wheat ASRs have not been described in genome-wide yet. METHODS: We predicted the transmembrane regions and subcellular localization using the TMHMM server, and Plant-mPLoc server and CELLO v2.5, respectively. Then the phylogeny tree was built by MEGA7. The exon-intron structures, conserved motifs and TFs binding sites were analyzed by GSDS, MEME program and PlantRegMap, respectively. RESULTS: In wheat, 33ASR genes were identified through a genome-wide survey and classified into six groups. Phylogenetic analyses revealed that the TaASR proteins in the same group tightly clustered together, compared with those from other species. Duplication analysis indicated that the TaASR gene family has expanded mainly through tandem and segmental duplication events. Similar gene structures and conserved protein motifs of TaASRs in wheat were identified in the same groups. ASR genes contained various TF binding cites associated with the stress responses in the promoter region. Gene expression was generally associated with the expected group-specific expression pattern in five tissues, including grain, leaf, root, spike and stem, indicating the broad conservation of ASR genes function during wheat evolution. The qRT-PCR analysis revealed that several ASRs were up-regulated in response to NaCl and PEG stress. CONCLUSION: We identified ASR genes in wheat and found that gene duplication events are the main driving force for ASR gene evolution in wheat. The expression of wheat ASR genes was modulated in responses to multiple abiotic stresses, including drought/osmotic and salt stress. The results provided important information for further identifications of the functions of wheat ASR genes and candidate genes for high abiotic stress tolerant wheat breeding.

Paleo-polyploidization in Lycophytes / 基因组蛋白质组与生物信息学报·英文版

Lycophytes and seed plants constitute the typical vascular plants. Lycophytes have been thought to have no paleo-polyploidization although the event is known to be critical for the fast expansion of seed plants. Here, genomic analyses including the homologous gene dot plot analysis detected multiple paleo-polyploidization events, with one occurring approximately 13-15 million years ago (MYA) and another about 125-142 MYA, during the evolution of the genome of Selaginella moellendorffii, a model lycophyte. In addition, comparative analysis of reconstructed ancestral genomes of lycophytes and angiosperms suggested that lycophytes were affected by more paleo-polyploidization events than seed plants. Results from the present genomic analyses indicate that paleo-polyploidization has contributed to the successful establishment of both lineages-lycophytes and seed plants-of vascular plants.

Comparative Genome Analysis of Scutellaria baicalensis and Scutellaria barbata Reveals the Evolution of Active Flavonoid Biosynthesis / 基因组蛋白质组与生物信息学报·英文版

Scutellaria baicalensis (S. baicalensis) and Scutellaria barbata (S. barbata) are common medicinal plants of the Lamiaceae family. Both produce specific flavonoid compounds, including baicalein, scutellarein, norwogonin, and wogonin, as well as their glycosides, which exhibit antioxidant and antitumor activities. Here, we report chromosome-level genome assemblies of S. baicalensis and S. barbata with quantitative chromosomal variation (2n = 18 and 2n = 26, respectively). The divergence of S. baicalensis and S. barbata occurred far earlier than previously reported, and a whole-genome duplication (WGD) event was identified. The insertion of long terminal repeat elements after speciation might be responsible for the observed chromosomal expansion and rearrangement. Comparative genome analysis of the congeneric species revealed the species-specific evolution of chrysin and apigenin biosynthetic genes, such as the S. baicalensis-specific tandem duplication of genes encoding phenylalanine ammonia lyase and chalcone synthase, and the S. barbata-specific duplication of genes encoding 4-CoA ligase. In addition, the paralogous duplication, colinearity, and expression diversity of CYP82D subfamily members revealed the functional divergence of genes encoding flavone hydroxylase between S. baicalensis and S. barbata. Analyzing these Scutellaria genomes reveals the common and species-specific evolution of flavone biosynthetic genes. Thus, these findings would facilitate the development of molecular breeding and studies of biosynthesis and regulation of bioactive compounds.

Genome Size Evolution Mediated by Gypsy Retrotransposons in Brassicaceae / 基因组蛋白质组与生物信息学报·英文版

The dynamic activity of transposable elements (TEs) contributes to the vast diversity of genome size and architecture among plants. Here, we examined the genomic distribution and transposition activity of long terminal repeat retrotransposons (LTR-RTs) in Arabidopsis thaliana (Ath) and three of its relatives, Arabidopsis lyrata (Aly), Eutrema salsugineum (Esa), and Schrenkiella parvula (Spa), in Brassicaceae. Our analyses revealed the distinct evolutionary dynamics of Gypsyretrotransposons, which reflects the different patterns of genome size changes of the four species over the past million years. The rate of Gypsy transposition in Aly is approximately five times more rapid than that of Ath and Esa, suggesting an expanding Aly genome. Gypsy insertions in Esa are strictly confined to pericentromeric heterochromatin and associated with dramatic centromere expansion. In contrast, Gypsy insertions in Spa have been largely suppressed over the last million years, likely as a result of a combination of an inherent molecular mechanism of preferential DNA removal and purifying selection at Gypsy elements. Additionally, species-specific clades of Gypsy elements shaped the distinct genome architectures of Aly and Esa.

Evolvement of a five-way translocation t(5;9;22;6;17) from a four-way Philadelphia translocation t(5;9;22;6) in a rare case of chronic myeloid leukemia / 中华医学遗传学杂志

OBJECTIVE@#To trace a rare case of chronic myeloid leukemia (CML) with a four-way Philadelphia chromosome variant by cytogenetic analysis in order to provide a basis for the selection of treatment.@*METHODS@#Bone marrow morphology, chromosomal karyotyping, fluorescence in situ hybridization (FISH) and real-time quantitative PCR (RQ-PCR) were used for the diagnosis and staging of the disease. Point mutations in the tyrosine kinase domain of ABL1 gene were detected by Sanger sequencing.@*RESULTS@#The patient was initially diagnosed as CML in chronic phase (CML-CP) with a chromosomal karyotype of 46,XX,t(5;9;22;6)(q13;q34;q11;q25), while FISH revealed presence of a variant Philadelphia chromosome translocation. Clonal evolution has occurred after 38 months of tyrosine kinase inhibitor (TKI) treatment, when cytogenetic analysis revealed coexisting t(5;9;22;6)(q13;q34;q11;q25) and t(5;9;22;6;17)(q13;q34;q11;q25;q11). After 57 months of TKIs treatment, only the t(5;9;22;6;17) clone was detected. Three months later, hyperdiploidy with additional abnormalities were detected in addition to t(5;9;22;6;17). Three mutations, including p.Tyr253Phe, p.Thr315Ile and p.Gly250Glu, were identified in the tyrosine kinase domain of the ABL1 gene during the course of disease. The patient did not attain cytogenetic and molecular response to TKIs.@*CONCLUSION@#The four-way variant translocation may be genetically unstable. Clonal evolution and genetic mutations are likely to occur during TKIs treatment, resulting in poor response to drug therapy. This observation, however, needs to be confirmed by large-scale studies.

Progress in source tracking of SARS-CoV-2 / 南方医科大学学报

Coronavirus disease 2019 (COVID-19) pandemic has caused a total of 55 928 327 confirmed cases and 1 344 003 deaths as of November 19, 2020. But so far the origin of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes this pandemic has remained undetermined. The purpose of this study is to review the current research of SARS-CoV-2 and the existing problems therein, which may provide inspiration for further researches. Existing evidence suggested that SARS-CoV-2 may be derived from bat coronavirus 40-70 years ago. During the evolution, this virus underwent extensive variations in the process of mutations and natural selection. Different genomic regions of SARS-CoV-2 may have different selection pressures, but all of which increase the difficulty of tracing the origin of this virus. A wide variety of animals have been considered as potential hosts of SARS-CoV-2, including cats, lions, tigers, dogs and minks. SARS-CoV-2 has a chance to transmit from humans to animals and can be transmitted among animals. Current research evidence has shown that China is not the original source of SARS-CoV-2. It is still unclear how the virus spreads to human, and efforts are still need to be made to explore the origin of SARS-CoV-2, its hosts and intermediate hosts, and the mechanism of its transmission across different species of animals.

Spike protein in the detection and treatment of novel coronavirus / 生物医学工程学杂志

Recently a COVID-19 pneumonia pandemic caused by a novel coronavirus 2019-nCoV has broken out over the world. In order to better control the spread of the pandemic, there's an urgent need to extensively study the virus' origin and the mechanisms for its infectivity and pathogenicity. Spike protein is a special structural protein on the surface of coronavirus. It contains important information about the evolution of the virus and plays critical roles in the processes of cellular recognition and entry. In the past decades, spike protein has always been one of the most important objects in research works on coronaviruses closely related to human life. In this review we introduce these research works related to spike proteins, hoping it will provide reasonable ideas for the control of the current pandemic, as well as for the diagnosis and treatment of COVID-19.

In silico cloning and bioinformatics analysis of HSP21 in Manihot esculenta / 生物工程学报

HSP21 gene is a key gene to respond high temperature stress in plant and plays an important role in preventing protein denaturation, protecting cell structure and maintaining normal growth and development. Therefore, cloning HSP21 gene is the basis for revealing the molecular mechanism of resistance to high temperature stress in cassava. To obtain cassava HSP21 homologous gene and analyze the properties of predicted protein, electronic cloning technology was used to assemble and derivate new gene in this study, and bioinformatics analysis method was used to analyze the primary to highest structure, hydrophilicity/hydrophobicity, signal peptide, protein homology and phylogenetic evolution of expressed protein. HSP21 gene was 969 bp, its open reading frame was 705 bp, and the predicted protein contains 234 amino acids. The predicted protein is a non-transmembrane protein that is alkaline and hydrophilic, and is mainly localized in the chloroplast. Through multiple sequence alignment and phylogenetic analysis, it was found that the cassava HSP21 protein has high homology with other plants such as Hevea brasiliensis, Ricinus communis, and Jatropha curcas. The results could provide reference for the study of cloning and transformation of this gene.

O diagnóstico das síndromes mielodisplásicas: revisão da literatura / The diagnosis of myelodysplastic syndromes: literature review

A síndrome mielodisplásica (SMD) é uma doença de diagnóstico complexo e, com bases nas contribuições encontradas na literatura, reunimos as principais ferramentas diagnósticas disponíveis na atualidade e sua aplicação, bem como o avanço nos métodos de diagnóstico, contribuindo para melhor compreensão da doença e futuras pesquisas. Este trabalho teve como objetivo apresentar as características da SMD, e apontar os exames realizados para o diagnóstico e seu avanço laboratorial, expondo as novas tecnologias para diagnóstico. Para realizar uma revisão bibliográfica, foi realizado um levantamento de artigos científicos publicados a partir de banco de dados confiáveis como PubMed, Bireme e SciELO, de 2000 a 2016. Foram utilizados os seguintes termos para a pesquisa: síndrome mielodisplásica, displasia e diagnóstico. Incluindo-se publicações no idioma Inglês e Português. A SMD, por se tratar de uma doença clonal ou não clonal, deve ser avaliada desde uma análise de sangue periférico, no qual observa-se uma alteração, e com o isso realizar uma investigação baseando-se em dados clínicos, histopatológicos, citogenéticos e na evolução do paciente. Sendo assim, requer profissionais altamente capacitados e que acompanhem a evolução dos critérios para o diagnóstico.

Origination and selection of ABCDE and AGL6 subfamily MADS-box genes in gymnosperms and angiosperms

BACKGROUND: The morphological diversity of flower organs is closely related to functional divergence within the MADS-box gene family. Bryophytes and seedless vascular plants have MADS-box genes but do not have ABCDE or AGAMOUS-LIKE6 (AGL6) genes. ABCDE and AGL6 genes belong to the subgroup of MADS-box genes. Previous works suggest that the B gene was the first ABCDE and AGL6 genes to emerge in plant but there are no mentions about the probable origin time of ACDE and AGL6 genes. Here, we collected ABCDE and AGL6 gene 381 protein sequences and 361 coding sequences from gymnosperms and angiosperms and reconstructed a complete Bayesian phylogeny of these genes. In this study, we want to clarify the probable origin time of ABCDE and AGL6 genes is a great help for understanding the role of the formation of the flower, which can decipher the forming order of MADS-box genes in the future. RESULTS: These genes appeared to have been under purifying selection and their evolutionary rates are not significantly different from each other. Using the Bayesian evolutionary analysis by sampling trees (BEAST) tool, we estimated that: the mutation rate of the ABCDE and AGL6 genes was 2.617 × 10-3 substitutions/site/million years, and that B genes originated 339 million years ago (MYA), CD genes originated 322 MYA, and A genes shared the most recent common ancestor with E/AGL6 296 MYA, respectively. CONCLUSIONS: The phylogeny of ABCDE and AGL6 genes subfamilies differed. The APETALA1 (AP1 or A gene) subfamily clustered into one group. The APETALA3/PISTILLATA (AP3/PI or B genes) subfamily clustered into two groups: the AP3 and PI clades. The AGAMOUS/SHATTERPROOF/SEEDSTICK (AG/SHP/STK or CD genes) subfamily clustered into a single group. The SEPALLATA (SEP or E gene) subfamily in angiosperms clustered into two groups: the SEP1/2/4 and SEP3 clades. The AGL6 subfamily clustered into a single group. Moreover, ABCDE and AGL6 genes appeared in the following order: AP3/PI → AG/SHP/STK → AGL6/SEP/AP1. In this study, we collected candidate sequences from gymnosperms and angiosperms. This study highlights important events in the evolutionary history of the ABCDE and AGL6 gene families and clarifies their evolutionary path.

Evolutionary relationship analysis of Middle East respiratory syndrome coronavirus 4a and 4b protein coding sequences

The 4a and 4b proteins of the Middle East respiratory syndrome coronavirus (MERS-CoV) have been described for their antagonism on host innate immunity. However, unlike clustering patterns of the complete gene sequences of human and camel MERS-CoVs, the 4a and 4b protein coding regions did not constitute species-specific phylogenetic groups. Moreover, given the estimated evolutionary rates of the complete, 4a, and 4b gene sequences, the 4a and 4b proteins might be less affected by species-specific innate immune pressures. These results suggest that the 4a and 4b proteins of MERS-CoV may function against host innate immunity in a manner independent of host species and/or evolutionary clustering patterns.

Genomic identification and characterization of the elite strains Bradyrhizobium yuanmingense BR 3267 and Bradyrhizobium pachyrhizi BR 3262 recommended for cowpea inoculation in Brazil

ABSTRACT The leguminous inoculation with nodule-inducing bacteria that perform biological nitrogen fixation is a good example of an "eco-friendly agricultural practice". Bradyrhizobium strains BR 3267 and BR 3262 are recommended for cowpea (Vigna unguiculata) inoculation in Brazil and showed remarkable responses; nevertheless neither strain was characterized at species level, which is our goal in the present work using a polyphasic approach. The strains presented the typical phenotype of Bradyrhizobium with a slow growth and a white colony on yeast extract-mannitol medium. Strain BR 3267 was more versatile in its use of carbon sources compared to BR 3262. The fatty acid composition of BR 3267 was similar to the type strain of Bradyrhizobium yuanmingense; while BR 3262 was similar to Bradyrhizobium elkanii and Bradyrhizobium pachyrhizi. Phylogenetic analyses based on 16S rRNA and three housekeeping genes placed both strains within the genus Bradyrhizobium: strain BR 3267 was closest to B. yuanmingense and BR 3262 to B. pachyrhizi. Genome average nucleotide identity and DNA-DNA reassociation confirmed the genomic identification of B. yuanmingense BR 3267 and B. pachyrhizi BR 3262. The nodC and nifH gene analyses showed that strains BR 3267 and BR 3262 hold divergent symbiotic genes. In summary, the results indicate that cowpea can establish effective symbiosis with divergent bradyrhizobia isolated from Brazilian soils.

Inducible cellulase production from an organic solvent tolerant Bacillus sp. SV1 and evolutionary divergence of endoglucanase in different species of the genus Bacillus

Abstract Bacteria are important sources of cellulases with various industrial and biotechnological applications. In view of this, a non-hemolytic bacterial strain, tolerant to various environmental pollutants (heavy metals and organic solvents), showing high cellulolytic index (7.89) was isolated from cattle shed soil and identified as Bacillus sp. SV1 (99.27% pairwise similarity with Bacillus korlensis). Extracellular cellulases showed the presence of endoglucanase, total cellulase and β-glucosidase activities. Cellulase production was induced in presence of cellulose (3.3 times CMCase, 2.9 times FPase and 2.1 times β-glucosidase), and enhanced (115.1% CMCase) by low-cost corn steep solids. An in silico investigation of endoglucanase (EC 3.2.1.4) protein sequences of three Bacillus spp. as query, revealed their similarities with members of nine bacterial phyla and to Eukaryota (represented by Arthropoda and Nematoda), and also highlighted of a convergent and divergent evolution from other enzymes of different substrate [(1,3)-linked beta-d-glucans, xylan and chitosan] specificities. Characteristic conserved signature indels were observed among members of Actinobacteria (7 aa insert) and Firmicutes (9 aa insert) that served as a potential tool in support of their relatedness in phylogenetic trees.

Evolution of equine influenza viruses (H3N8) during a Brazilian outbreak, 2015

Abstract Equine influenza is one of the major respiratory infectious diseases in horses. An equine influenza virus outbreak was identified in vaccinated and unvaccinated horses in a veterinary school hospital in São Paulo, SP, Brazil, in September 2015. The twelve equine influenza viruses isolated belonged to Florida Clade 1. The hemagglutinin and neuraminidase amino acid sequences were compared with the recent isolates from North and South America and the World Organisation for Animal Health recommended Florida Clade 1 vaccine strain. The hemagglutinin amino acid sequences had nine substitutions, compared with the vaccine strain. Two of them were in antigenic site A (A138S and G142R), one in antigenic site E (R62K) and another not in antigenic site (K304E). The four substitutions changed the hydrophobicity of hemagglutinin. Three distinct genetic variants were identified during the outbreak. Eleven variants were found in four quasispecies, which suggests the equine influenza virus evolved during the outbreak. The use of an out of date vaccine strain or updated vaccines without the production of protective antibody titers might be the major contributing factors on virus dissemination during this outbreak.