We analyzed the usefulness of rpoA, recA, andpyrH gene sequences for the identification of vibrios. Wesequenced fragments of these loci from a collection of 208representative strains, including 192 ...well-documentedVibrionaceae strains and 16 presumptive Vibrioisolates associated with coral bleaching. In order to determine theintraspecies variation among the three loci, we included severalrepresentative strains per species. The phylogenetic trees constructedwith the different genetic loci were roughly in agreement with formerpolyphasic taxonomic studies, including the 16S rRNA-based phylogeny ofvibrios. The families Vibrionaceae,Photobacteriaceae, Enterovibrionaceae, andSalinivibrionaceae were all differentiated on the basis ofeach genetic locus. Each species clearly formed separated clusters withat least 98, 94, and 94% rpoA, recA, andpyrH gene sequence similarity, respectively. The genusVibrio was heterogeneous and polyphyletic, with Vibriofischeri, V. logei, and V. wodanis groupingcloser to the Photobacterium genus. V. halioticoli-,V. harveyi-, V. splendidus-, and V.tubiashii-related species formed groups within the genusVIBRIO: Overall, the three genetic loci were morediscriminatory among species than were 16S rRNA sequences. In somecases, e.g., within the V. splendidus and V.tubiashii group, rpoA gene sequences were slightly lessdiscriminatory than recA and pyrH sequences. In thesecases, the combination of several loci will yield the most robustidentification. We can conclude that strains of the same species willhave at least 98, 94, and 94% rpoA, recA, andpyrH gene sequence similarity,respectively.
Evidence is strengthening for the morphological evaluation of tumor infiltrating lymphocytes (TILs) in breast cancer. Herein, the concepts for TILs assessment are laid out by pathologists to ...facilitate their wider evaluation and consistent interpretation. The goal of this article is to promote the evaluation of TILs as a biomarker in research, clinical trial settings and day-to-day practice.
The morphological evaluation of tumor-infiltrating lymphocytes (TILs) in breast cancer (BC) is gaining momentum as evidence strengthens for the clinical relevance of this immunological biomarker. Accumulating evidence suggests that the extent of lymphocytic infiltration in tumor tissue can be assessed as a major parameter by evaluation of hematoxylin and eosin (H&E)-stained tumor sections. TILs have been shown to provide prognostic and potentially predictive value, particularly in triple-negative and human epidermal growth factor receptor 2-overexpressing BC.
A standardized methodology for evaluating TILs is now needed as a prerequisite for integrating this parameter in standard histopathological practice, in a research setting as well as in clinical trials. This article reviews current data on the clinical validity and utility of TILs in BC in an effort to foster better knowledge and insight in this rapidly evolving field, and to develop a standardized methodology for visual assessment on H&E sections, acknowledging the future potential of molecular/multiplexed approaches.
The methodology provided is sufficiently detailed to offer a uniformly applied, pragmatic starting point and improve consistency and reproducibility in the measurement of TILs for future studies.
Across the cell cycle, mitochondrial dynamics are regulated by a cycling wave of actin polymerization/depolymerization. In metaphase, this wave induces actin comet tails on mitochondria that propel ...these organelles to drive spatial mixing, resulting in their equitable inheritance by daughter cells. In contrast, during interphase the cycling actin wave promotes localized mitochondrial fission. Here, we identify the F-actin nucleator/elongator FMNL1 as a positive regulator of the wave. FMNL1-depleted cells exhibit decreased mitochondrial polarization, decreased mitochondrial oxygen consumption, and increased production of reactive oxygen species. Accompanying these changes is a loss of hetero-fusion of wave-fragmented mitochondria. Thus, we propose that the interphase actin wave maintains mitochondrial homeostasis by promoting mitochondrial content mixing. Finally, we investigate the mechanistic basis for the observation that the wave drives mitochondrial motility in metaphase but mitochondrial fission in interphase. Our data indicate that when the force of actin polymerization is resisted by mitochondrial tethering to microtubules, as in interphase, fission results.
Vibrio sp. YB1T (=ATCC BAA-450T =LMG 20984T), the aetiological agent of tissue lysis of the coral Pocillopora damicornis, was characterized as a novel Vibrio species on the basis of 16S rDNA ...sequence, DNA-DNA hybridization data (G + C content is 45.6 mol%), AFLP and GTG5-PCR genomic fingerprinting patterns and phenotypic properties, including the cellular fatty acid profile. The predominant fatty acids were 16:0 and 18:1 omega7c. The name Vibrio coralliilyticus sp. nov. is proposed for the novel coral-pathogenic species. In addition to strain YB1T, which was isolated from the Indian Ocean, five additional strains of V. coralliilyticus have been isolated, three from diseased P. damicornis in the Red Sea, one from diseased oyster larvae (Kent, UK) and one from bivalve larvae (Brazil). The six V. coralliilyticus strains showed high genotypic and phenotypic similarities and all were pathogenic to P. damicornis. The closest phylogenetic neighbours to V. coralliilyticus are Vibrio tubiashii, Vibrio nereis and Vibrio shilonii.
The unique combination of depth, salinity, and water masses make the South Atlantic Ocean an ecosystem of special relevance within the global ocean. Yet, the microbiome of this ecosystem has received ...less attention than other regions of the global Ocean. This has hampered our understanding of the diversity and metabolic potential of the microorganisms that dwell in this habitat. To fill this knowledge gap, we analyzed a collection of 31 metagenomes from the Atlantic Ocean that spanned the epipelagic, mesopelagic and bathypelagic zones (surface to 4000 m). Read-centric and gene-centric analysis revealed the unique taxonomic and functional composition of metagenomes from each depth zone, which was driven by differences in physical and chemical parameters. In parallel, a total of 40 metagenome-assembled genomes were obtained, which recovered one third of the total community. Phylogenomic reconstruction revealed that many of these genomes are derived from poorly characterized taxa of Bacteria and Archaea. Genomes derived from heterotrophic bacteria of the aphotic zone displayed a large apparatus of genes suited for the utilization of recalcitrant organic compounds such as cellulose, chitin and alkanes. In addition, we found genomic evidence suggesting that mixotrophic bacteria from the bathypelagic zone could perform carbon fixation through the Calvin-Benson-Bassham cycle, fueled by sulfur oxidation. Finally, we found that the viral communities shifted throughout the water column regarding their targeted hosts and virus-to-microbe ratio, in response to shifts in the composition and functioning their microbial counterparts. Our findings shed light on the microbial and viral drivers of important biogeochemical processes that take place in the South Atlantic Ocean.
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•Metagenomics was applied to unravel the prokaryote and viral diversity in the South Atlantic Ocean.•Metagenome assembled genomes obtained belonged to novel taxa of Bacteria and Archaea from the mesopelagic and bathypelagic•The metabolic apparatus bacteria of the aphotic zone revealed a capacity for the use of recalcitrant organic matter•The metabolic apparatus of mixotrophic bacteria highlighted the relevance of the Calvin-Benson-Bassham cycle•A model was proposed for the roles of taxa of prokaryotes and viruses to biological processes in the South Atlantic Ocean.
We present the discovery of three new transiting hot Jupiters by the WASP-South project, WASP-161 b, WASP-163 b, and WASP-170 b. Follow-up radial velocities obtained with the Euler/CORALIE ...spectrograph and transit light curves obtained with the TRAPPIST-North, TRAPPIST-South, SPECULOOS-South, NITES, and Euler telescopes have enabled us to determine the masses and radii for these transiting exoplanets. WASP-161 b completes an orbit around its V = 11.1 F6V-type host star in 5.406 days, and has a mass Mp = 2.5 0.2MJup and radius Rp = 1.14 0.06 RJup. WASP-163 b orbits around its host star (spectral type G8V and the magnitude V = 12.5) every 1.609 days, and has a mass of MP = 1.9 0.2 MJup and a radius of Rp = 1.2 0.1 RJup. WASP-170 b has a mass of 1.7 0.2 MJup and a radius of 1.14 0.09 RJup and is on a 2.344 day orbit around a G1V-type star of magnitude V = 12.8. Given their irradiations (∼109 erg s−1 cm−2) and masses, the three new planets' sizes are in good agreement with classical models of irradiated giant planets.
The rich fossil record of equids has made them a model for evolutionary processes. Here we present a 1.12-times coverage draft genome from a horse bone recovered from permafrost dated to ...approximately 560-780 thousand years before present (kyr BP). Our data represent the oldest full genome sequence determined so far by almost an order of magnitude. For comparison, we sequenced the genome of a Late Pleistocene horse (43 kyr BP), and modern genomes of five domestic horse breeds (Equus ferus caballus), a Przewalski's horse (E. f. przewalskii) and a donkey (E. asinus). Our analyses suggest that the Equus lineage giving rise to all contemporary horses, zebras and donkeys originated 4.0-4.5 million years before present (Myr BP), twice the conventionally accepted time to the most recent common ancestor of the genus Equus. We also find that horse population size fluctuated multiple times over the past 2 Myr, particularly during periods of severe climatic changes. We estimate that the Przewalski's and domestic horse populations diverged 38-72 kyr BP, and find no evidence of recent admixture between the domestic horse breeds and the Przewalski's horse investigated. This supports the contention that Przewalski's horses represent the last surviving wild horse population. We find similar levels of genetic variation among Przewalski's and domestic populations, indicating that the former are genetically viable and worthy of conservation efforts. We also find evidence for continuous selection on the immune system and olfaction throughout horse evolution. Finally, we identify 29 genomic regions among horse breeds that deviate from neutrality and show low levels of genetic variation compared to the Przewalski's horse. Such regions could correspond to loci selected early during domestication.
ABSTRACT
We report the discovery and characterization of WASP-180Ab, a hot Jupiter confirmed by the detection of its Doppler shadow and by measuring its mass using radial velocities. We find the 0.9 ... ± 0.1 MJup, 1.24 ± 0.04 RJup planet to be in a misaligned, retrograde orbit around an F7 star with Teff = 6500 K and a moderate rotation speed of vsin i⋆ = 19.9 km s−1. The host star is the primary of a V = 10.7 binary, where a secondary separated by ∼5 arcsec (∼1200 au) contributes ∼ 30 per cent of the light. WASP-180Ab therefore adds to a small sample of transiting hot Jupiters known in binary systems. A 4.6-d modulation seen in the WASP data is likely to be the rotational modulation of the companion star, WASP-180B.
Guanabara Bay is a tropical estuarine ecosystem that receives massive anthropogenic impacts from the metropolitan region of Rio de Janeiro. This ecosystem suffers from an ongoing eutrophication ...process that has been shown to promote the emergence of potentially pathogenic bacteria, giving rise to public health concerns. Although previous studies have investigated how environmental parameters influence the microbial community of Guanabara Bay, they often have been limited to small spatial and temporal gradients and have not been integrated into predictive mathematical models. Our objective was to fill this knowledge gap by building models that could predict how temperature, salinity, phosphorus, nitrogen and transparency work together to regulate the abundance of bacteria, chlorophyll and Vibrio (a potential human pathogen) in Guanabara Bay. To that end, we built artificial neural networks to model the associations between these variables. These networks were carefully validated to ensure that they could provide accurate predictions without biases or overfitting. The estimated models displayed high predictive capacity (Pearson correlation coefficients ≥0.67 and root mean square error ≤ 0.55). Our findings showed that temperature and salinity were often the most important factors regulating the abundance of bacteria, chlorophyll and Vibrio (absolute importance ≥5) and that each of these has a unique level of dependence on nitrogen and phosphorus for their growth. These models allowed us to estimate the Guanabara Bay microbiome's response to changes in environmental conditions, which allowed us to propose strategies for the management and remediation of Guanabara Bay.
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•Artificial Neural Networks accurately modelled the microbiome from Guanabara Bay.•Temperature and Salinity are main factors controlling the Microbiome.•Phosphorus, Nitrogen and Transparency are of lesser importance.•Small increases in temperature are predicted to promote the growth of pathogens.
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