Characterizing the blood microbiota in healthy and febrile domestic cats via 16s rRNA sequencing.

This study aimed to evaluate the blood bacterial microbiota in healthy and febrile cats. High-quality sequencing reads from the 16S rRNA gene variable region V3-V4 were obtained from genomic blood DNA belonging to 145 healthy cats, and 140 febrile cats. Comparisons between the blood microbiota of healthy and febrile cats revealed dominant presence of Actinobacteria, followed by Firmicutes and Proteobacteria, and a lower relative abundance of Bacteroidetes. Upon lower taxonomic levels, the bacterial composition was significantly different between healthy and febrile cats. The families Faecalibacterium and Kineothrix (Firmicutes), and Phyllobacterium (Proteobacteria) experienced increased abundance in febrile samples. Whereas Thioprofundum (Proteobacteria) demonstrated a significant decrease in abundance in febrile. The bacterial composition and beta diversity within febrile cats was different according to the affected body system (Oral/GI, systemic, skin, and respiratory) at both family and genus levels. Sex and age were not significant factors affecting the blood microbiota of febrile cats nor healthy ones. Age was different between young adult and mature adult healthy cats. Alpha diversity was unaffected by any factors. Overall, the findings suggest that age, health status and nature of disease are significant factors affecting blood microbiota diversity and composition in cats, but sex is not.

Bacteriomic Profiles of Rock-Dwelling Lichens from the Venezuelan Guiana Shield and the South African Highveld Plateau.

Lichens are not only fungal-algal symbiotic associations but also matrices for association with bacteria, and the bacterial diversity linked to lichens has been receiving more attention in studies. This study compares the diversity and possible metabolism of lichen-associated bacteria from saxicolous foliose and fruticose taxa Alectoria, Canoparmelia, Crocodia, Menegazzia, Usnea, and Xanthoparmelia from the Venezuelan Guiana Shield and the South African Highveld Plateau. We used DNA extractions from the lichen thalli to amplify the eukaryotic 18S rRNA gene (rDNA) and the V3-V4 region of the bacterial 16S rDNA, of which amplicons were then Sanger- and MiSeq-sequenced, respectively. The V3-V4 sequences of the associated bacteria were grouped into operational taxonomic units (OTUs) ascribed to twelve bacterial phyla previously found in the rock tripe Umbilicaria lichens. The bacterial OTUs emphasized the uniqueness of each region, while, at the species and higher ranks, the regional microbiomes were shown to be somewhat similar. Nevertheless, regional biomarker OTUs were screened to predict relevant metabolic pathways, which implicated different regional metabolic features.

Microbial successional pattern along a glacier retreat gradient from Byers Peninsula, Maritime Antarctica.

The retreat of glaciers in Antarctica has increased in the last decades due to global climate change, influencing vegetation expansion, and soil physico-chemical and biological attributes. However, little is known about soil microbiology diversity in these periglacial landscapes. This study characterized and compared bacterial and fungal diversity using metabarcoding of soil samples from the Byers Peninsula, Maritime Antarctica. We identified bacterial and fungal communities by amplification of bacterial 16 S rRNA region V3-V4 and fungal internal transcribed spacer 1 (ITS1). We also applied 14C dating on soil organic matter (SOM) from six profiles. Physico-chemical analyses and attributes associated with SOM were evaluated. A total of 14,048 bacterial ASVs were obtained, and almost all samples had 50% of their sequences assigned to Actinobacteriota and Proteobacteria. Regarding the fungal community, Mortierellomycota, Ascomycota and Basidiomycota were the main phyla from 1619 ASVs. We found that soil age was more relevant than the distance from the glacier, with the oldest soil profile (late Holocene soil profile) hosting the highest bacterial and fungal diversity. The microbial indices of the fungal community were correlated with nutrient availability, soil reactivity and SOM composition, whereas the bacterial community was not correlated with any soil attribute. The bacterial diversity, richness, and evenness varied according to presence of permafrost and moisture regime. The fungal community richness in the surface horizon was not related to altitude, permafrost, or moisture regime. The soil moisture regime was crucial for the structure, high diversity and richness of the microbial community, specially to the bacterial community. Further studies should examine the relationship between microbial communities and environmental factors to better predict changes in this terrestrial ecosystem.

Towards defining the core Saccharum microbiome: input from five genotypes.

BACKGROUND: Plant microbiome and its manipulation inaugurate a new era for plant biotechnology with the potential to benefit sustainable crop production. Here, we used the large-scale 16S rDNA sequencing analysis to unravel the dynamic, structure, and composition of exophytic and endophytic microbial communities in two hybrid commercial cultivars of sugarcane (R570 and SP80-3280), two cultivated genotypes (Saccharum officinarum and Saccharum barberi) and one wild species (Saccharum spontaneum). RESULTS: Our analysis identified 1372 amplicon sequence variants (ASVs). The microbial communities' profiles are grouped by two, root and bulk soils and stem and leave when these four components are compared. However, PCoA-based data supports that endophytes and epiphytes communities form distinct groups, revealing an active host-derived mechanism to select the resident microbiota. A strong genotype-influence on the assembly of microbial communities in Saccharum ssp. is documented. A total of 220 ASVs persisted across plant cultivars and species. The ubiquitous bacteria are two potential beneficial bacteria, Acinetobacter ssp., and Serratia symbiotica. CONCLUSIONS: The results presented support the existence of common and cultivar-specific ASVs in two commercial hybrids, two cultivated canes and one species of Saccharum across tissues (leaves, stems, and roots). Also, evidence is provided that under the experimental conditions described here, each genotype bears its microbial community with little impact from the soil conditions, except in the root system. It remains to be demonstrated which aspect, genotype, environment or both, has the most significant impact on the microbial selection in sugarcane fields.

Glaucoma detection in Latino population through OCT's RNFL thickness map using transfer learning.

PURPOSE: Glaucoma is the leading cause of irreversible blindness worldwide. It is estimated that over 60 million people around the world have this disease, with only part of them knowing they have it. Timely and early diagnosis is vital to delay/prevent patient blindness. Deep learning (DL) could be a tool for ophthalmologists to give a more informed and objective diagnosis. However, there is a lack of studies that apply DL for glaucoma detection to Latino population. Our contribution is to use transfer learning to retrain MobileNet and Inception V3 models with images of the retinal nerve fiber layer thickness map of Mexican patients, obtained with optical coherence tomography (OCT) from the Instituto de la Visión, a clinic in the northern part of Mexico. METHODS: The IBM Foundational Methodology for Data Science was used in this study. The MobileNet and Inception V3 topologies were chosen as the analytical approaches to classify OCT images in two classes, namely glaucomatous and non-glaucomatous. The OCT files were collected from a Zeiss OCT machine at the Instituto de la Visión, and classified by an expert into the two classes under study. These images conform a dataset of 333 files in total. Since this research work is focused on RNFL thickness map images, the OCT files were cropped to obtain only the RNFL thickness map images of the corresponding eye. This action was carried out for images in both classes, glaucomatous and non-glaucomatous. Since some images were damaged (with black spots in which data was missing), these images were cut-out and cut-off. After the preparation process, 50 images per class were used for training. Fifteen images per class, different than the ones used in the training stage, were used for running predictions. In total, 260 images were used in the experiments, 130 per eye. Four models were generated, two trained with MobileNet, one for the left eye and one for the right eye, and another two trained with Inception V3. TensorFlow was used for running transfer learning. RESULTS: The evaluation results of the MobileNet model for the left eye are, accuracy: 86%, precision: 87%, recall: 87%, and F1 score: 87%. The evaluation results of the MobileNet model for the right eye are, accuracy: 90%, precision: 90%, recall: 90%, and F1 score: 90%. The evaluation results of the Inception V3 model for the left eye are, accuracy: 90%, precision: 90%, recall: 90%, and F1 score: 90%. The evaluation results of the Inception V3 model for the right eye are, accuracy: 90%, precision: 90%, recall: 90%, and F1 score: 90%. CONCLUSION: In average, the evaluation results for right eye images were the same for both models. The Inception V3 model showed slight better average results than the MobileNet model in the case of classifying left eye images.

Imported SARS-CoV-2 Variant P.1 in Traveler Returning from Brazil to Italy.

We report an imported case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant P.1 detected in an asymptomatic traveler who arrived in Italy on an indirect flight from Brazil. This case shows the risk for introduction of SARS-CoV-2 variants from indirect flights and the need for continued SARS-CoV-2 surveillance.

Identification and characterization of the V3 promoter of the ST3GAL4 gene.

The ST3GAL4 gene encodes the enzyme Galß1-4GlcNAc α2,3 sialyltransferase (ST3Gal IV). This enzyme participates in the synthesis of the sialyl Lewis x antigen. In different cancer types altered expression of this antigen has been reported. The transcriptional regulation of this gene is very complex, different mRNA variants (V1-V10) have been reported and are originated by the activity of different promoters and alternative splicing. Only the promoter that gives rise to the V3 variant has not been previously reported. The objective of this work was to identify and characterize the V3 promoter of the ST3GAL4 gene. For this, the putative V3 promoter of the ST3GAL4 gene was delimited by in silico analysis. The complete promoter and smaller versions were cloned in a reporter plasmid. The constructs were transfected in the HaCaT cells and the promoter activity was evaluated by luciferase reporter assays. The cloned region showed promoter activity, and the basal activity was not dependent on TATA boxes. However, the GC boxes, an initiator element (Inr) and downstream promoter element (DPE) could contribute to basal activity. The promoter contains several binding sites for the nuclear factor of activated T-cells (NFAT) that could participate in inducible activity during the immune response. The minimal promoter corresponds to a fragment of approximately 300 bp, located in the position -347 b to -40 b. The characterization of the V3 promoter of the ST3GAL4 gene completes the study of the four promoters of this gene, this contributes to the understanding of its complex transcription regulation.

Safety ranges in V3 segment of the vertebral artery for surgical procedures at the craniocervical junction / Rangos de seguridad en el segmento V3 de la arteria vertebral para procedimientos quirúrgicos en la unión craneocervical

The aim of this study was to establish safety ranges for the third vertebral artery segment (V3) for craneocervical procedures. Injury to V3 represents a potentially catastrophic complication. Its tortuous path and complex relationship with neighboring structures, increasing the risk. Ten male adult cadavers (20 vertebral arteries) with arterial infiltration of red latex were studied. The length, angles and anatomical measurements were obtained between the selected surgical landmarks and the portions of V3 segment. The horizontal portion has a length of 32.7 ± 3.6 mm with an angulation of 115.1 ± 8.3 degrees. The mean distances of the horizontal portion were: from the midline to the V3 groove of C1 posterior arch (24.7 ± 6.3 mm); from C1 pars interarticularis to the V3 distal loop of V3 (8.9 ± 1.4 mm). The vertical portion has a length 32.5 ± 5.6 mm with an angulation of the proximal loop of 113.6 ± 5.8 degrees. The mean distances between the C2 spinous process to the medial surface of the distal loop (43.8 ± 4.2 mm); from the C1-C2 joint to the V3 vertical portion (9.5 ± 1.5 mm); from C2 pars interarticularis to V3 in the C2 transverse foramen (6.5 ± 3.4 mm); from C2 pars interarticularis to V3 in the C1 transverse foramen (17.5 ± 4.5 mm). We reported four potential sites where V3 can be injured during four different surgical procedures: exposure of the posterior arch of C1, and pars interarticularis of C1 in the horizontal portion and exposure of the C1C2 joint, and placement of C1-C2 transarticular screws one in the vertical portion. We provide measurements of redundancy and safety ranges to reduce the risk of injury to the V3 segment during craniocervical surgical procedures.

El objetivo de este estudio fue establecer rangos de seguridad en el tercer segmento de arteria vertebral (V3) para cirugías de la región craneocervicales. La lesión de V3 representa una complicación potencialmente catastrófica. Su tortuoso trayecto y compleja relación con las estructuras aledañas, aumenta el riesgo. Se estudiaron diez cadáveres adultos masculinos (20 arterias vertebrales) con infiltración arterial de látex rojo. La longitud, ángulos y medidas anatómicas se obtuvieron respecto a los puntos de referencia quirúrgicos y las porciones del segmento V3. La porción horizontal tiene una longitud de 32,7 ± 3,6 mm con una angulación de 115,1 ± 8,3 grados. Las distancias medias de la porción horizontal fueron: desde la línea media hasta el surco V3 del arco posterior C1 (24,7 ± 6,3 mm); desde C1 pars interarticularis hasta el bucle distal V3 de V3 (8,9 ± 1,4 mm). La parte vertical tiene una longitud de 32,5 ± 5,6 mm con una angulación del bucle proximal de 113,6 ± 5,8 grados. Las distancias medias entre el proceso espinoso C2 y la superficie medial del bucle distal (43,8 ± 4,2 mm); desde la unión C1-C2 hasta la porción vertical V3 (9,5 ± 1,5 mm); de C2 pars interarticularis a V3 en el foramen transversal C2 (6,5 ± 3,4 mm); de C2 pars interarticularis a V3 en el foramen transversal C1 (17,5 ± 4,5 mm). Informamos cuatro sitios potenciales donde la V3 puede lesionarse durante cuatro procedimientos quirúrgicos diferentes: exposición del arco posterior de C1 y pars interarticularis de C1 en la porción horizontal y exposición de la articulación C1-C2, y colocación de C1-C2 Tornillos transarticulares uno en la porción vertical. Proporcionamos mediciones de los rangos de redundancia y seguridad para reducir el riesgo de lesiones en el segmento V3 durante procedimientos quirúrgicos craneocervicales.

Controversies about the visual areas located at the anterior border of area V2 in primates.

Anatomical and electrophysiological studies have provided us with detailed information regarding the extent and topography of the primary (V1) and secondary (V2) visual areas in primates. The consensus about the V1 and V2 maps, however, is in sharp contrast with controversies regarding the organization of the cortical areas lying immediately rostral to V2. In this review, we address the contentious issue of the extent of the third visual area (V3). Specifically, we will argue for the existence of both ventral (V3v) and dorsal (V3d) segments of V3, which are located, respectively, adjacent to the anterior border of ventral and dorsal V2. V3v and V3d would together constitute a single functional area with a complete representation of both upper and lower visual hemifields. Another contentious issue is the organization of the parietal-occipital (PO) area, which also borders the rostral edge of the medial portion of dorsal V2. Different from V1, V2, and V3, which exhibit a topography based on the defined lines of isoeccentricity and isopolar representation, area PO only has a systematic representation of polar angles, with an emphasis on the peripheral visual field (isoeccentricity lines are not well defined). Based on the connectivity patterns of area PO with distinct cytochrome oxidase modules in V2, we propose a subdivision of the dorsal stream of visual information processing into lateral and medial domains. In this model, area PO constitutes the first processing instance of the dorsal-medial stream, coding for the full-field flow of visual cues during navigation. Finally, we compare our findings with those in other species of Old and New World monkeys and argue that larger animals, such as macaque and capuchin monkeys, have similar organizations of the areas rostral to V2, which is different from that in smaller New World monkeys.

Determination o viral tropism by genotyping an phenotyping assays in Braziliaan hiv-1-infected patients / Determinação do tropismo viral por ensaios genotípicos e fenotípicos em pacientes brasileiros infectados por HIV-1

The clinical application of CCR5 antagonists involves first determining the coreceptor usage by the infecting viral strain. Bioinformatics programs that predict coreceptor usage could provide an alternative method to screen candidates for treatment with CCR5 antagonists, particularly in countries with limited financial resources. Thus, the present study aims to identify the best approach using bioinformatics tools for determining HIV-1 coreceptor usage in clinical practice. Proviral DNA sequences and Trofile results from 99 HIV-1-infected subjects under clinical monitoring were analyzed in this study. Based on the Trofile results, the viral variants present were 81.1% R5, 21.4% R5X4 and 1.8% X4. Determination of tropism using a Geno2pheno[coreceptor] analysis with a false positive rate of 10% gave the most suitable performance in this sampling: the R5 and X4 strains were found at frequencies of 78.5% and 28.4%, respectively, and there was 78.6% concordance between the phenotypic and genotypic results. Further studies are needed to clarify how genetic diversity amongst virus strains affects bioinformatics-driven approaches for determining tropism. Although this strategy could be useful for screening patients in developing countries, some limitations remain that restrict the wider application of coreceptor usage tests in clinical practice.

A aplicação clínica dos antagonistas de CCR5 envolve em primeiro lugar determinar o uso de co-receptor pela cepa viral infectante. Programas de bioinformática que prevêem o uso co-receptor poderiam fornecer um método alternativo para selecionar candidatos para o tratamento com os antagonistas do CCR5, particularmente em países com poucos recursos financeiros. Assim, o presente estudo teve por objetivo identificar a melhor abordagem utilizando ferramentas de bioinformática para determinar qual o tipo de co-receptor do HIV-1 que poderia ser usado na prática clínica. Sequências de DNA proviral e Trofile resultados a partir de 99 pacientes infectados pelo HIV-1 sob monitorização clínica foram avaliadas. Com base nos resultados do Teste Trofile, as variantes virais presentes eram R5 (81,1%), R5X4 (21,4%) e X4 (1,8%). Determinação do tropismo pela análise do Geno2pheno, com taxa de falso positivos de 10% apresentou desempenho mais adequado para esta amostragem: as cepas R5 e X4 foram encontradas em frequências de 78,5% e 28,4%, respectivamente, e foi de 78,6% a concordância entre os resultados fenotípicos e genotípicos. Mais estudos são necessários para esclarecer como a diversidade genética entre as cepas do vírus afeta abordagens baseadas na determinação do tropismo pelas ferramentas de bioinformática. Embora esta estratégia possa ser útil para o rastreio de pacientes em países em desenvolvimento, permanecem algumas limitações que restringem a aplicação mais ampla para utilização de testes de co-receptor na prática clínica.

Variability of the conserved V3 loop tip motif in HIV-1 subtype B isolates collected from Brazilian and French patients

The diversity of the V3 loop tip motif sequences of HIV-1 subtype B was analyzed in patients from Botucatu (Brazil) and Montpellier (France). Overall, 37 tetrameric tip motifs were identified, 28 and 17 of them being recognized in Brazilian and French patients, respectively. The GPGR (P) motif was predominant in French but not in Brazilian patients (53.5 percent vs 31.0 percent), whereas the GWGR (W) motif was frequent in Brazilian patients (23.0 percent) and absent in French patients. Three tip motif groups were considered: P, W, and non-P non-W groups. The distribution of HIV-1 isolates into the three groups was significantly different between isolates from Botucatu and from Montpellier (P < 0.001). A higher proportion of CXCR4-using HIV-1 (X4 variants) was observed in the non-P non-W group as compared with the P group (37.5 percent vs 19.1 percent), and no X4 variant was identified in the W group (P < 0.001). The higher proportion of X4 variants in the non-P non-W group was essentially observed among the patients from Montpellier, who have been infected with HIV-1 for a longer period of time than those from Botucatu. Among patients from Montpellier, CD4+ cell counts were lower in patients belonging to the non-P non-W group than in those belonging to the P group (24 cells/µL vs 197 cells/µL; P = 0.005). Taken together, the results suggest that variability of the V3 loop tip motif may be related to HIV-1 coreceptor usage and to disease progression. However, as analyzed by a bioinformatic method, the substitution of the V3 loop tip motif of the subtype B consensus sequence with the different tip motifs identified in the present study was not sufficient to induce a change in HIV-1 coreceptor usage.

Variability of the conserved v3 loop tip motif in hiv-1 subtype B isolates collected from brazilian and French patients.

The diversity of the V3 loop tip motif sequences of HIV-1 subtype B was analyzed in patients from Botucatu (Brazil) and Montpellier (France). Overall, 37 tetrameric tip motifs were identified, 28 and 17 of them being recognized in Brazilian and French patients, respectively. The GPGR (P) motif was predominant in French but not in Brazilian patients (53.5% vs 31.0%), whereas the GWGR (W) motif was frequent in Brazilian patients (23.0%) and absent in French patients. Three tip motif groups were considered: P, W, and non-P non-W groups. The distribution of HIV-1 isolates into the three groups was significantly different between isolates from Botucatu and from Montpellier (P < 0.001). A higher proportion of CXCR4-using HIV-1 (X4 variants) was observed in the non-P non-W group as compared with the P group (37.5% vs 19.1%), and no X4 variant was identified in the W group (P < 0.001). The higher proportion of X4 variants in the non-P non-W group was essentially observed among the patients from Montpellier, who have been infected with HIV-1 for a longer period of time than those from Botucatu. Among patients from Montpellier, CD4+ cell counts were lower in patients belonging to the non-P non-W group than in those belonging to the P group (24 cells/µL vs 197 cells/µL; P = 0.005). Taken together, the results suggest that variability of the V3 loop tip motif may be related to HIV-1 coreceptor usage and to disease progression. However, as analyzed by a bioinformatic method, the substitution of the V3 loop tip motif of the subtype B consensus sequence with the different tip motifs identified in the present study was not sufficient to induce a change in HIV-1 coreceptor usage.

Variability of the conserved V3 loop tip motif in HIV-1 subtype B isolates collected from Brazilian and French patients

The diversity of the V3 loop tip motif sequences of HIV-1 subtype B was analyzed in patients from Botucatu (Brazil) and Montpellier (France). Overall, 37 tetrameric tip motifs were identified, 28 and 17 of them being recognized in Brazilian and French patients, respectively. The GPGR (P) motif was predominant in French but not in Brazilian patients (53.5% vs 31.0%), whereas the GWGR (W) motif was frequent in Brazilian patients (23.0%) and absent in French patients. Three tip motif groups were considered: P, W, and non-P non-W groups. The distribution of HIV-1 isolates into the three groups was significantly different between isolates from Botucatu and from Montpellier (P 0.001). A higher proportion of CXCR4-using HIV-1 (X4 variants) was observed in the non-P non-W group as compared with the P group (37.5% vs 19.1%), and no X4 variant was identified in the W group (P 0.001). The higher proportion of X4 variants in the non-P non-W group was essentially observed among the patients from Montpellier, who have been infected with HIV-1 for a longer period of time than those from Botucatu. Among patients from Montpellier, CD4+ cell counts were lower in patients belonging to the non-P non-W group than in those belonging to the P group (24 cells/µL vs 197 cells/µL; P = 0.005). Taken together, the results suggest that variability of the V3 loop tip motif may be related to HIV-1 coreceptor usage and to disease progression. However, as analyzed by a bioinformatic method, the substitution of the V3 loop tip motif of the subtype B consensus sequence with the different tip motifs identified in the present study was not sufficient to induce a change in HIV-1 coreceptor usage.