Miracle-dz/UniFAR-FTUs huggingface dataset:
Multiscale Simulation Reveals Passive Proton Transport Through SERCA on the Microsecond Timescale

The sarcoplasmic reticulum Ca2+-ATPase (SERCA) transports two Ca2+ ions from the cytoplasm to the reticulum lumen at the expense of ATP hydrolysis. In addition to transporting Ca2+, SERCA facilitates bidirectional proton transport across the sarcoplasmic reticulum to maintain the charge balance of the transport sites and to balance the charge deficit generated by the exchange of Ca2+. Previous studies have shown the existence of a transient water-filled pore in SERCA that connects the Ca2+-binding sites with the lumen, but the capacity of this pathway to sustain passive proton transport has remained unknown. In this study, we used the multiscale reactive molecular dynamics (MS-RMD) method and free energy sampling to quantify the free energy profile and timescale of the proton transport across this pathway while also explicitly accounting for the dynamically coupled hydration changes of the pore. We find that proton transport from the central binding site to the lumen has a microsecond timescale, revealing a novel passive cytoplasm-to-lumen proton flow beside the well-known inverse proton countertransport occurring in active Ca2+ transport. We propose that this proton transport mechanism is operational and serves as a functional conduit for passive proton transport across the sarcoplasmic reticulum. SIGNIFICANCE Multiscale reactive molecular dynamics combined with free energy sampling was applied to study proton transport through a transient water pore connecting the Ca2+-binding site to the lumen in SERCA. This is the first computational study of this large biomolecular system that treats the hydrated excess proton and its transport through water structures and amino acids explicitly. When also correctly accounting for the hydration fluctuations of the pore, it is found that a transiently hydrated channel can transport protons on a microsecond timescale. These results quantitatively support the hypothesis of the proton intake into the sarcoplasm via SERCA, in addition to the well-known proton pumping by SERCA to the cytoplasm along with Ca2+ transport.
Bacterial retrons encode tripartite toxin/antitoxin systems

Retrons are genetic retroelements, commonly found in bacterial genomes and recently repurposed as genome editing tools. Their encoded reverse transcriptase (RT) produces a multi-copy single-stranded DNA (msDNA). Despite our understanding of their complex biosynthesis, the function of msDNAs and therefore, the physiological role of retrons has remained elusive. We establish that the retron-Sen2 in Salmonella Typhimurium encodes a toxin, which we have renamed as RcaT (Retron cold-anaerobic Toxin). RcaT is activated when msDNA biosynthesis is perturbed and its toxicity is higher at ambient temperatures or during anaerobiosis. The RT and msDNA form together the antitoxin unit, with the RT binding RcaT, and the msDNA enabling the antitoxin activity. Using another E. coli retron, we establish that this toxin/antitoxin function is conserved, and that RT-toxin interactions are cognate. Altogether, retrons constitute a novel family of tripartite toxin/antitoxin systems.
Dengue virus strain 2 capsid protein switches the annealing pathway and reduces the intrinsic dynamics of the conserved 5’ untranslated region

The capsid protein of Dengue Virus strain 2 (DENV2C) is a structural protein with RNA chaperone activity that promotes multiple nucleic acid structural rearrangements, critical for transcription of the single-stranded positive-sense DENV2 genomic RNA. Annealing of the conserved 5’ untranslated region (5’UTR) to either its complementary sequence or to the 3’ untranslated region (3’UTR) occurs during (+)/(−) ds-RNA formation and (+) RNA circularization, respectively, both essential steps during DENV RNA replication. We investigated the effect of DENV2C on the annealing mechanism of two hairpin structures from the 5’UTR region (21-nt upstream AUG region (5’UAR) and 23-nt capsid-coding hairpin (5’cHP)) to their complementary sequences during (+)/(−) ds-RNA formation and (+) RNA circularization. Using fluorescence spectroscopy, DENV2C was found to switch annealing reactions nucleated mainly through kissing-loop intermediates to stem-stem interactions during (+)/(−) ds-RNA formation while it promotes annealing mainly through kissing-loop interactions during the (+) RNA circularization. Using FRET-FCS and trFRET, we determined that DENV2C exerts RNA chaperone activities by modulating intrinsic dynamics and by reducing the kinetically trapped unfavorable conformations of the 5’UTR sequence. Thus, DENV2C is likely to facilitate genome folding into functional conformations required for replication, playing a role in modulating (+)/(−) ds-RNA formation and (+) RNA circularization.
Smooth muscle-specific MMP17 (MT4-MMP) defines the intestinal ECM niche

Smooth muscle is an essential component of the intestine, both to maintain its structure and produce peristaltic and segmentation movements. However, very little is known about other putative roles that smooth muscle may have. Here, we show that smooth muscle is the dominant supplier of BMP antagonists, which are niche factors that are essential for intestinal stem cell maintenance. Furthermore, muscle-derived factors can render epithelium reparative and fetal-like, which includes heightened YAP activity. Mechanistically, we find that the matrix metalloproteinase MMP17, which is exclusively expressed by smooth muscle, is required for intestinal epithelial repair after inflammation- or irradiation-induced injury. Furthermore, we provide evidence that MMP17 affects intestinal epithelial reprogramming indirectly by cleaving the matricellular protein PERIOSTIN, which itself is able to activate YAP. Together, we identify an important signaling axis that firmly establishes a role for smooth muscle as a modulator of intestinal epithelial regeneration and the intestinal stem cell niche.
Using cost-effective surveys from platforms of opportunity to assess cetacean occurrence patterns for marine park management in the heart of the Coral Triangle

The Wakatobi National Park (WNP) at the heart of Coral Triangle is an important area for cetaceans in Indonesia. Currently there is insufficient information on spatio-temporal occurrence patterns of cetaceans to inform effective conservation strategies. This study used platforms of opportunity from May 2004 to May 2012 as a cost-effective way to address this knowledge gap. A database was created of cetacean sightings per surveyed days at sea, allowing for an analysis of species diversity and habitat use around the islands. A total of 11 cetacean species were identified. Spinner and bottlenose dolphins were sighted most often, followed by melon-headed and sperm whales. Spinner dolphin showed a wide distribution in the area, whilst bottlenose dolphin and melon-headed whale occupied the waters between the main islands and south atolls. Sperm whales occurred mostly in waters to the north of the main islands and as melon-headed whales were mostly found in deep waters. Most cetacean sightings occurred in the zones designated for human use, indicating where potential conflicts might occur. No sightings were found in the Park core zone, indicating a mismatch between WNP design and the ecological needs of the cetaceans. A sub-sample of the data from dedicated fishing monitoring trips was used to derive a sighting frequency. Occurrence of both small and large cetaceans was highest during inter-monsoonal seasons, possibly related to an increase of prey availability due to seasonal upwelling and increase in survey activity. Inter-annual occurrence of cetaceans was variable, with no large cetaceans being sighted in 2010-2012, likely due to reduced survey efforts. In areas with limited resources for designated surveys, the use of platforms of opportunity can be a cost-effective tool to provide valuable data on cetacean occurrence. It helps identify potentially important areas as well as highlight where to direct designated research efforts. We discuss the implications of our findings for the conservation management of these cetaceans and give suggestions for improved marine park management.
A Mutation in the Drosophila melanogaster eve Stripe 2 Minimal Enhancer Is Buffered by Flanking Sequences

Enhancers are DNA sequences composed of transcription factor binding sites that drive complex patterns of gene expression in space and time. Until recently, studying enhancers in their genomic context was technically challenging. Therefore, minimal enhancers, the shortest pieces of DNA that can drive an expression pattern that resembles a gene’s endogenous pattern, are often used to study features of enhancer function. However, evidence suggests that some enhancers require sequences outside the minimal enhancer to maintain function under environmental perturbations. We hypothesized that these additional sequences also prevent misexpression caused by a transcription factor binding site mutation within a minimal enhancer. Using the Drosophila melanogaster even-skipped stripe 2 enhancer as a case study, we tested the effect of a Giant binding site mutation (gt-2) on the expression patterns driven by minimal and extended enhancer reporter constructs. We found that, in contrast to the misexpression caused by the gt-2 binding site mutation in the minimal enhancer, the same gt-2 binding site mutation in the extended enhancer did not have an effect on expression. The buffering of expression levels, but not expression pattern, is partially explained by an additional Giant binding site outside the minimal enhancer. Mutating the gt-2 binding site in the endogenous locus had no significant effect on stripe 2 expression. Our results indicate that rules derived from mutating enhancer reporter constructs may not represent what occurs in the endogenous context.
Comparative Genomic Analysis of Fifty-Two Staphylococcus aureus Isolates Identified from Uncharacterized Staphylococcus Genomes in the NCBI database

Background Staphylococcus aureus is a major bacterial pathogen that causes a variety of diseases, ranging from wound infections to severe bacteremia or food poisoning. The course and severity of the disease are mainly dependent on the bacterium genotype as well as host factors. Whole-genome sequencing (WGS) is currently the most extensive genotyping method available, followed by bioinformatic sequence analysis. Methods A total of 253 uncharacterized staphylococcus genome sequences were downloaded from the National Center for Biotechnology Information (NCBI) (August 2012 to March 2020) from different studies. Samples were clustered based on core and accessory pairwise distances between isolates and then analyzed by multilocus sequence typing tool (MLST). Staphylococcal Cassette Chromosome mec (SCCmec), spa typing, variant calling, core genome alignment, and recombination sites prediction were performed on detected S. aureus isolates. S. aureus isolates were also analyzed for the presence of genes coding for virulence factors and antibiotic resistance. Results and conclusion Uncategorized genome sequences were clustered into 24 groups. About 182 uncharacterized Staphylococcus genomes were identified at the species level based on MLST, including 32 S. lugdunensis genome sequence, thus doubling the number of the publicly accessible S. lugdunensis genome sequence in Genbank. MLST identified another four species (S. epidermidis (33/253), S. lugdunensis (32/253), S. haemolyticus (41/253), S. hominis (24/253) and S. aureus (52/253)). Among the 52 S. aureus isolates, 21 (40.38%) isolates carried mecA gene, with 57.14% classified as SCCmec IV. The results of this study provide knowledge that facilitates evolutionary studies of staphylococcal species and other bacteria at the genome level.
TITLE PAGE Title: Prevalence and Virulence Gene Profiles of Escherichia coli O157 from Cattle Slaughtered in Buea, Cameroon Authors and affiliations:

Background: Escherichia coli O157 is an emerging foodborne pathogen of great public health concern. It has been associated with bloody diarrhoea, haemorrhagic colitis and haemolytic uremic syndrome in humans. Most human infections have been traced to cattle and the consumption of contaminated cattle products. In order to understand the risk associated with the consumption of cattle products, this study sought to investigate the prevalence and identify virulence genes in E. coli O157 from cattle in Cameroon. Method: A total of 512 rectal samples were obtained and analysed using conventional bacteriological methods (enrichment on modified Tryptone Soy Broth and selective plating on Cefixime-Tellurite Sorbitol Mac-Conkey Agar) for the isolation of E. coli O157. Presumptive E. coli O157 isolates were confirmed serologically using E. COLIPROTM O157 latex agglutination test and molecularly using PCR targeting the rfb gene in the isolates. Characterisation of the confirmed E. coli O157 strains was done by amplification of stx1, stx2, eaeA and hlyA virulence genes using both singleplex and multiplex PCR. Results: E. coli O157 was detected in 56 (10.9%) of the 512 samples examined. The presence of the virulence genes stx2, eaeA and hylA was demonstrated in 96.4% (54/56) of the isolates and stx1 in 40 (71.4%) of the 54. The isolates exhibited three genetic profiles (I-III) with I (stx1, stx2, eaeA and hlyA) being the most prevalent (40/56; 71.4%) while two isolates had none of the virulence genes tested. Conclusion: A proportion of cattle slaughtered in abattoirs in Buea are infected with pathogenic E. coli O157 and could be a potential source of human infections. We recommend proper animal food processing measures and proper hygiene be prescribed and implemented to reduce the risk of beef contamination.
Role of apoptosis and epithelial cells in Hydra spermatogenesis and histocompatibility reactions

The freshwater cnidarian polyp hydra is the simplest organism hitherto known to possess components of the apoptotic machinery. However, little is known about the functions of apoptosis in hydra. Here I present evidence for the role of apoptosis in hydra spermatogenesis and histocompatibility. Cells undergoing programmed cell death were detected by vital acridine orange staining and TUNEL assay. Sperm precursors were shown to undergo apoptosis mostly at early stages of spermatogenesis. Role of apoptosis as a mechanism to adjust the number of sperm precursors at different stages of spermatogenesis is discussed. Surprisingly, epithelial cells, previously thought to function merely as physical support of the testes, were found to play an active role during spermatogenesis as phagocytes. Similar to Sertoli cells in mammals they may provide signals to differentiating sperm. Apoptosis was also found to be induced at the graft border in hydra interspecies grafts. Though self / non-self recognition was proposed previously to play a crucial role in such heterografts, no evidence for existence of allorecognition system was found. Hydra seems to have lost this system secondarily during evolution. Ultrastructural studies of the graft site revealed morphologically disturbed mesoglea separating H. vulgaris ectoderm and H. oligactis endoderm. Apoptosis is proposed to result due to incompatibility between tissues of these two species. Role of incompatibility mechanisms such as anoikis or inability to properly recognize survival signals from a different species is discussed.
Critical information thresholds underlying concurrent face recognition functions

Humans rapidly and automatically recognise faces on multiple different levels, yet little is known about how the brain achieves these manifold categorisations concurrently. We bring a new perspective to this emerging issue by probing the relative informational dependencies of two of the most important aspects of human face processing: categorisation of the stimulus as a face (generic face recognition) and categorisation of its familiarity (familiar face recognition). Recording electrophysiological responses to a large set of natural images progressively increasing in image duration (Expt. 1) or spatial frequency content (Expt. 2), we contrasted critical sensory thresholds for these recognition functions as driven by the same face encounters. Across both manipulations, individual observer thresholds were consistently lower for distinguishing faces from other objects than for distinguishing familiar from unfamiliar faces. Moreover, familiar face recognition displayed marked inter-individual variability compared to generic face recognition, with no systematic relationship evident between the two thresholds. Scalp activation was also more strongly right-lateralised at the generic face recognition threshold than at the familiar face recognition threshold. These results suggest that high-level recognition of a face as a face arises based on minimal sensory input (i.e., very brief exposures/coarse resolutions), predominantly in right hemisphere regions. In contrast, the amount of additional sensory evidence required to access face familiarity is highly idiosyncratic and recruits wider neural networks. These findings underscore the neurofunctional distinctions between these two recognition functions, and constitute an important step forward in understanding how the human brain recognises various dimensions of a face in parallel. Significance Statement The relational dynamics between different aspects of face recognition are not yet well understood. We report relative informational dependencies for two concurrent, ecologically relevant face recognition functions: distinguishing faces from objects, and recognising people we know. Our electrophysiological data show that for a given face encounter, the human brain requires less sensory input to categorise that stimulus as a face than to recognise whether the face is familiar. Moreover, where sensory thresholds for distinguishing faces from objects are remarkably consistent across observers, they vary widely for familiar face recognition. These findings shed new light on the multifaceted nature of human face recognition by painting a more comprehensive picture of the concurrent evidence accumulation processes initiated by seeing a face.
Development of zygotic and germline gene drives in mice

CRISPR-based synthetic gene drives have the potential to deliver a more effective and humane method of invasive vertebrate pest control than current strategies. Relatively efficient CRISPR gene drives have been developed in insects and yeast but not in mammals. Here we investigated the efficiency of CRISPR/Cas9-based gene drives in Mus musculus by constructing “split drive” systems with Cas9 under the control of zygotic (CAG) or germline (Vasa) promoters. While both systems generated double stranded breaks at their intended target site in vivo, no homing was detectable. Our data indicate that robust and specific Cas9 expression during meiosis is a critical requirement for the generation of efficient CRISPR-based synthetic gene drives in rodents.
Genomic Features of Parthenogenetic Animals

Abstract Evolution without sex is predicted to impact genomes in numerous ways. Case studies of individual parthenogenetic animals have reported peculiar genomic features that were suggested to be caused by their mode of reproduction, including high heterozygosity, a high abundance of horizontally acquired genes, a low transposable element load, or the presence of palindromes. We systematically characterized these genomic features in published genomes of 26 parthenogenetic animals representing at least 18 independent transitions to asexuality. Surprisingly, not a single feature was systematically replicated across a majority of these transitions, suggesting that previously reported patterns were lineage-specific rather than illustrating the general consequences of parthenogenesis. We found that only parthenogens of hybrid origin were characterized by high heterozygosity levels. Parthenogens that were not of hybrid origin appeared to be largely homozygous, independent of the cellular mechanism underlying parthenogenesis. Overall, despite the importance of recombination rate variation for the evolution of sexual animal genomes, the genome-wide absence of recombination does not appear to have had the dramatic effects which are expected from classical theoretical models. The reasons for this are probably a combination of lineage-specific patterns, the impact of the origin of parthenogenesis, and a survivorship bias of parthenogenetic lineages.
Agonists of orally expressed TRP channels stimulate salivary secretion and modify the salivary proteome

Natural compounds that can stimulate salivary secretion are of interest in developing treatments for xerostomia, the perception of a dry mouth, that affects between 10 and 30% of the adult and elderly population. Chemesthetic transient receptor potential (TRP) channels are expressed in the surface of the oral mucosa. The TRPV1 agonists capsaicin and piperine have been shown to increase salivary flow when introduced into the oral cavity but the sialogogic properties of other TRP channel agonists have not been investigated. In this study we have determined the influence of different TRP channel agonists on the flow and protein composition of saliva. Mouth rinsing with the TRPV1 agonist nonivamide or menthol, a TRPM8 agonist, increased whole mouth saliva (WMS) flow and total protein secretion compared to unstimulated saliva, the vehicle control mouth rinse or cinnamaldehyde, a TRPA1 agonist. Nonivamide also increased the flow of labial minor gland saliva but parotid saliva flow rate was not increased. The influence of TRP channel agonists on the composition and function of the salivary proteome was investigated using a multi-batch quantitative mass spectrometry method novel to salivary proteomics. Inter-personal and inter-mouth rinse variation was observed in the secreted proteomes and, using a novel bioinformatics method, inter-day variation was identified with some of the mouth rinses. Significant changes in specific salivary proteins were identified after all mouth rinses. In the case of nonivamide, these changes were attributed to functional shifts in the WMS secreted, primarily the over representation of salivary and non-salivary cystatins which was confirmed by immunoassay. This study provides new evidence of the impact of TRP channel agonists on the salivary proteome and the stimulation of salivary secretion by a TRPM8 channel agonist, which suggests that TRP channel agonists are potential candidates for developing treatments for sufferers of xerostomia.
Oxalic acid content of rice root exudates determine the degree of positive chemotaxis in Pseudomonas fluorescens

The positive chemotaxis of Pseudomonas fluorescens isolates viz., PFR-3, an rhizosphere isolate and PFP-6, an phyllosphere isolate of rice, towards the various fractions viz., crude, individual and combined fractions, of rice root exudates was studied under in vitro condition. It was observed that the purified, recombined fractions (Anionic + Cationic + Neutral) of rice root exudates exerted more chemoattraction towards Pseudomonas isolates followed by recombined any two fractions and individual fractions of rice root exudates. Among the individual fractions, the anionic fraction of rice root exudates recorded more chemotatic ratio for Pseudomonas fluorescens followed by cationic and neutral fraction. Among the compounds present in the anionic fraction of rice root exudates, it was observed that oxalic acid exerted more chemoattraction towards Pseudomonas fluorescens isolates at all concentrations tested when compared to other organic acids. The phyllosphere isolate of Pseudomonas fluorescens viz., PFP-6 was found to have more chemotatic response towards rice root exudates than the rhizosphere isolate. It was concluded that the anionic fraction, as one of the component, of rice root exudates play a key role in chemotaxis of Pseudomonas fluorescens and oxalic acid, as one of the compound, play a determinant role in fixing the degree of positive chemotaxis of Pseudomonas fluorescens towards rice root exudates. © 2010 IJRSR. All rights reserved.