Miracle-dz/UniFAR-FTUs huggingface dataset:
A comprehensive human minimal gut metagenome extends the host’s metabolic potential

Accumulating evidence suggests that humans should be considered as holobionts in which the gut microbiota plays essential functions. Initial metagenomic studies reported a pattern of shared genes in the gut microbiome of different individuals, leading to the definition of the minimal gut metagenome as the set of microbial genes necessary for homeostasis, and present in all healthy individuals. Despite its interest, this concept has received little attention following its initial description in terms of various ubiquitous pathways in Western cohorts. This study analyzes the minimal gut metagenome of the most comprehensive dataset available, including individuals from agriculturalist and industrialist societies, also embodying highly diverse ethnic and geographical backgrounds. The outcome, based on metagenomic predictions for community composition data, resulted in a minimal metagenome comprising 3,412 gene clusters, mapping to 1,856 reactions and 128 metabolic pathways predicted to occur across all individuals. These results were substantiated by the analysis of two additional datasets describing the microbial community compositions of larger Western cohorts, as well as a substantial shotgun metagenomics dataset. Subsequent analyses showed the plausible metabolic complementarity provided by the minimal gut metagenome to the human genome.
The Arp2/3 complex and the formin, Diaphanous, are both required to regulate the size of germline ring canals in the developing egg chamber

Intercellular bridges are an essential structural feature found in both germline and somatic cells throughout the animal kingdom. Because of their large size, the germline intercellular bridges, or ring canals, in the developing fruit fly egg chamber are an excellent model to study the formation, stabilization, and expansion of these structures. Within the egg chamber, the germline ring canals connect 15 supporting nurse cells to the developing oocyte, facilitating the transfer of materials required for successful oogenesis. The ring canals are derived from a stalled actomyosin contractile ring; once formed, additional actin and actin-binding proteins are recruited to the ring to support the 20-fold expansion that accompanies oogenesis. These behaviors provide a unique model system to study the actin regulators that control incomplete cytokinesis, intercellular bridge formation, and expansion. By temporally controlling their expression in the germline, we have demonstrated that the Arp2/3 complex and the formin, Diaphanous (Dia), coordinately regulate ring canal size and expansion throughout oogenesis. Dia is required for successful incomplete cytokinesis and the initial stabilization of the germline ring canals. Once the ring canals have formed, the Arp2/3 complex and Dia cooperate to determine ring canal size and maintain their stability. Our data suggest that the nurse cells must maintain a precise balance between the activity of these two nucleators during oogenesis.
Eco-evolutionary dynamics of Plasmodium genotypes under mass drug administration

Mass Drug Administration (MDA) is regarded as a potential strategy for locally interrupting transmission of human malaria under specific circumstances. However, insights on how MDA affects the eco-evolutionary dynamics of different Plasmodium species are not well known. We provide a computational model where the ecologically explicit life cycle of the parasite is implemented. Since the parasite inhabits two different ecological niches – human host and the mosquito – it undergoes different selection pressures during its reproduction. We use the model to perform an evolutionary analysis of the dynamics of resistance alleles under atovaquone, chloroquine and combined atovaquone-chloroquine drug treatments. Our study shows how the reduced viability of resistant parasites in the mosquito affects the spread of resistance and transmission interruption in treated human populations. Overall, results confirm that the disadvantage of drug-resistant genotypes in the mosquito vector is a good tool to achieve malaria control goals under MDA programmes. Author summary Every year there are millions of new malaria cases reported worldwide. The cause of the disease is the infection by Plasmodium, a protozoan which is transmitted between humans through the bite of a mosquito. Antimalarials have existed since long, but Plasmodium has evolved resistance to the treatment, making it necessary to develop new strategies to heal the infected humans. Lately, it has been pointed out that mosquitoes could be our allies when using drugs such as atovaquone, which resistant parasites have difficulties to reproduce in the mosquito. Here we study the scenarios in which these drugs, used in Mass Drug Administration (MDA) programmes, can interrupt the transmission of malaria in local treated populations.
Variability of P26 and P10 genes in Colombian isolates of Potato yellow vein virus (PYVV)

Potato yellow vein virus (PYVV) is the causal agent of the potato yellow vein disease and can reduce potato production up to 50%. This virus also infects tomatoes and can remain asymptomatic in plants. PYVV transmission is mediated by vegetative seed, the vector Trialeurodes vaporariorum, and grafts. Its genome has the P26 and P10 genes that are orthologues in the Crinivirus genus, which have been characterized as pathogenic factors and have not been studied in PYVV. We analyzed the variability of P26 and P10 from 45 and 48 sequences, which were obtained by RT-PCR amplification of the total RNA of symptomatic potato leaves from the provinces of Nariño, Cundinamarca, and Boyaca (Colombia). We included sequences of each gene of the PYVV genome of potato and tomato isolates from GenBank. The variability in these genes is influenced by the flow and uncontrolled use of vegetative seed between different provinces, that favor the dispersion of viral variants. In addition, the variability analysis based on maximum likelihood trees, haplotypes, and diversity indices showed that P26 is more variable than P10 and both are more variable in Andigena than in Phureja potatoes. The Tajima and Fu and Li tests revealedthat these genes are subject to negative selection.
A Clock-Phased Sigma Factor Cascade Is Required for Global Circadian Transcriptional Rhythms in Cyanobacteria

The circadian clock of the cyanobacterium Synechococcus elongatus PCC 7942 drives oscillations in global mRNA transcript abundances with 24 h periodicity under continuous light conditions. The transcription factor RpaA controls the timing of circadian gene expression, but the mechanisms underlying RpaA’s indirect control of 90-percent of circadian transcripts are not well understood. Here we show that four RpaA-dependent sigma factors – rpoD2, rpoD6, rpoD5, and sigF2 – are sequentially activated downstream of active RpaA and are required for proper expression of circadian genes. We find that the sigma factors RpoD6, RpoD5, and SigF2 exhibit circadian oscillations with different timing relative to each other at the level of their mRNA expression, protein abundance, and binding enrichment at genomic targets in constant light conditions. We measure global gene expression in strains modified to individually lack rpoD2, rpoD6, rpoD5, and sigF2, and identify how expression of circadian genes – including expression of sigma factor genes – is altered in the absence of each sigma factor. Broadly, our findings suggest that a single transcription factor, RpaA, is sufficient to generate complex circadian expression patterns in part by regulating an interdependent sigma factor cascade.
Birdsbesafe® collar cover reduces bird predation by domestic cats (
 Felis catus
 )

7 The domestic cat (Felis catus) is one of the world’s most damaging invasive species, 8 especially threatening to local bird populations. This study examined the efficacy of the 9 Birdsbesafe® collar cover at reducing predation rates by household cats on avian 10 populations. The vivid colours of the Birdsbesafe® collar cover are assumed to alert nearby 11 birds to the cat’s presence, allowing them to escape safely. Overall, 19 cats were trialled 12 over 8 weeks and the Birdsbesafe® collar cover resulted in a reduction of 78% in the number 13 of birds killed. Further research is required into owner attitudes to collars in order to 14 examine whether these collar-based devices could be widely adopted. 15
Label-free horizontal EMSA for analysis of protein-RNA interactions

We describe a method to analyze the affinity and specificity of interactions between proteins and RNA using horizontal PAGE under non-denaturing conditions. The method permits tracking of migration of anionic and cationic biomolecules and complexes toward anode and cathode, respectively, therefore enabling quantification of bound and free biomolecules of different charges and affinity of their intermolecular interactions. The gel is stained with a fluorescent intercalating dye (SYBR®Gold or ethidium bromide) for visualization of nucleic acids followed by Coomassie® Brilliant Blue R-250 for visualizations of proteins; the dissociation constant is determined separately from the intensity of unshifted and shifted bands visualized by each dye. The method permits calculation of bound and unbound anionic nucleic acid and cationic protein components in the same gel, regardless of charge, under identical conditions, and avoids the need for radioisotope or fluorescent labeling of either component.
Do Conservation Practices Bring Quick Changes to Key Soil Properties for Resource-Limited Farmers?

ABSTRACT Soil conservation practices such as minimum tillage, crop rotation, cover crops, and manure application have strong advocacy. Short-term evidence that these practices are beneficial might improve their adoption by resource-limited producers. A two-year study (2015–2017) was conducted on a privately-owned small, limited-resource farm in southwestern Kentucky to evaluate how cover crops and manure application, alone or in combination, influenced soil nutrient availability, nitrogen mineralization, and crop yield. Three fertilization treatments were used: 1) poultry manure; 2) chemical fertilizers (urea, diammonium phosphate, and potash); and 3) a non-fertilized control. A second set of treatments consisting of presence or absence of winter cover crop was used within each fertilization treatment. The cover crop consisted of a cereal rye (Secale cereale L.), Austrian winter pea (Pisum sativum L.), and crimson clover (Trifolium incarnatum L.) mix. Summer crops consisted of a no-till maize (Zea mays L.) - soybean (Glycine max L.) rotation. Soil samples were taken before and after each summer crop season and analyzed for bulk density, organic carbon content, pH, cation exchange capacity, total phosphorus (P), potassium (K), trace elements, and soil nitrogen (N) mineralization. Cover crops with or without manure enhanced soil N mineralization rates and increased soil extractable P and K, but did not significantly improve yield. Considering the site-specific soil conditions, cover crop and manure use may need longer-term assessment to reveal their effect on the yield and soil quality benefits, especially to resource-limited producers adopting these conservation practices.
Differences in microbiome and virome between cattle and horses in the same farm

Objective The ecosystem of an animal farm is composed of various elements, such as animals, farmers, plants, feed, soil, and microorganisms. A domesticated animal’s health is largely connected with the reservoir of bacteria and viruses in animal farms. Although a few studies have focused on exploring the gut microbiome of animals, communities of microbiota and viruses in feedlots have not been thoroughly investigated. Methods Here, we collected feces and dust samples (4 groups: cattle feces, C_F; horse feces, H_F; cattle dust, C_D; and horse dust, H_D) from cattle and horse farms sharing the same housing and investigated their microbiome/virome communities by Illumina sequencing. Results Dust groups (C_D and H_D) showed higher microbial diversity than feces groups (C_F and H_F) regardless of animal species. From the microbial community analysis, all the samples from the four groups have major phyla such as Proteobacteria (min 37.1% to max 42.8%), Firmicutes (19.1% to 24.9%), Bacteroidetes (10.6% to 22.1%), and Actinobacteria (6.1% to 20.5%). The abundance of Streptococcus, which commonly recognized as equine pathogens, was significantly higher in the horse group (H_D and H_F). Over 99% among the classified virome reads were classified as Caudovirales, a group of tailed bacteriophages, in all four groups. Foot-and-mouth disease virus and equine adenovirus, which cause deadly diseases in cattle and horse, respectively, were not detected. Conclusion Our results will provide baseline information to understand different gut and environmental microbial ecology between two livestock species.
Novel haplotype combinations reveal enhanced seedling vigor traits in rice that can accurately predict dry biomass accumulation in seedlings

Seedling vigor is of vital importance for the initial plant establishment of direct-seeded rice. Here, 166 recombinant inbred lines were employed to assess eight seedling vigor traits over the first 25 days of germination. Significant correlations were found between most traits, and statistical analysis has revealed, for the first time, a linear relationship that uses seedling height and fresh weight to accurately predict the accumulation of dry biomass. Further, a subset of 20 lines, spanning the phenotypic range of the larger population, were genotyped by using 16 simple sequence repeats (SSR) markers known to be associated with seedling vigor traits. Markers RM317 and RM348 linked with significantly different phenotypes, including seedling height and fresh weight. One combination, haplotype II-1 (RM317 (I/II) and RM348 (1/2)), consistently produced superior values for seedling height, root length, and leaf length. The new prediction tool for seedling dry weight, namely the haplotype of RM317 and RM348, will have a wide range of applications in breeding strategies by using marker-assisted selection to produce elite lines that optimize genetic composition contributing to seedling vigor.
Correlates of non-random patterns of capsule switching in pneumococcus

Background Pneumococcus is a diverse pathogen, with >90 serotypes, each of which has a distinct polysaccharide capsule. Pneumococci can switch capsules, evading vaccine pressure. Certain serotype pairs are more likely to switch, but the drivers of these patterns are not well understood. Methods We used the PubMLST and Global Pneumococcal Sequencing (GPS) databases to quantify the number of genetic lineages on which different serotype pairs co-occur. We also quantified the genetic diversity of each serotype. Regression models evaluated the relationship between shared polysaccharide structural components and the frequency of serotype switching and diversity. Results A number of serotype pairs co-occurred on the same genetic lineage more commonly than expected. Co-occurrence of between-serogroup pairs was more common when both serotypes had glucose as a component of the capsule (and, potentially, glucuronic acid). Diversity also varied markedly by serotype and was lower for serotypes with glucuronic acid in the capsule and higher for those with galactose in the capsule. Conclusions Certain pairs of serotypes are more likely to occur on the same genetic background, and these patterns were correlated with shared polysaccharide components. This might indicate adaptation of strains to produce capsules with particular characteristics.
Recurrent neural network models of multi-area computation underlying decision-making

Cognition emerges from coordinated computations across multiple brain areas. However, elucidating these computations within and across brain regions is challenging because intra- and inter-area connectivity are typically unknown. To study coordinated computation, we trained multi-area recurrent neural networks (RNNs) to discriminate the dominant color of a checker-board and output decision variables reflecting a direction decision, a task previously used to investigate decision-related dynamics in dorsal premotor cortex (PMd) of monkeys. We found that multi-area RNNs, trained with neurophysiological connectivity constraints and Dale’s law, recapitulated decision-related dynamics observed in PMd. The RNN solved this task by a dynamical mechanism where the direction decision was computed and outputted, via precisely oriented dynamics, on an axis that was nearly orthogonal to checkerboard color inputs. This orthogonal direction information was preferentially propagated through alignment with inter-area connections; in contrast, color information was filtered. These results suggest that cortex uses modular computation to generate minimal sufficient representations of task information. Finally, we used multi-area RNNs to produce experimentally testable hypotheses for computations that occur within and across multiple brain areas, enabling new insights into distributed computation in neural systems.
Idea Paper: Predicting culturability of microbes from population dynamics under field conditions

Isolation and cultivation of microbes from environmental samples have been fundamental and important for species identification and investigating functions and ecology of target microbes. While cultivation and isolation of microbes are not easy, the natural environment can “culture” any endemic microbes, and thus key information for culturing and isolating microbes may be encoded in the natural population dynamics of microbes. In this paper, I present the idea that culturability of microbes may be inferred by quantifying dynamics properties of microbes using nonlinear time series analytical tools. To briefly demonstrate the idea, I analyzed high-frequency, quantitative microbial time series obtained for artificial rice plots established at Kyoto University, Japan. I selected bacterial phyla that included sufficient numbers of microbial taxa, and analyzed 398 microbial taxa using empirical dynamic modeling. The nine phyla analyzed generally followed a similar pattern: many microbial taxa fell into the “Simple” dynamics category, and a small proportion of taxa were categorized in “Simple but nonlinear” or “Nearly random” dynamics categories. The present analysis suggested that many microbes in the study system might be cultivated by modifying a relatively small number of conditions. However, the present idea as well as the result is preliminary and premature, and more precise taxonomic information (i.e., species-level identification) and a culturability dataset will help to validate the idea. If the present idea was found to be valid, a priori evaluation of the culturability of microbes would become possible, which would avoid unnecessary costs (labor, time and money) of attempts to cultivate microbes.
An Update on Probiotic Safety and Efficacy

Probiotics are live microorganisms that have recently gained popularity for being beneficial to human health and digestion. There are several forms of probiotics, perhaps the more widely used form is the lactic acid producer. Studies with the strongest clinical evidence have shown beneficial effects of probiotics for acute infectious diarrhea in children, antibiotic-associated diarrhea, among several others. Some studies have shown promising prophylactic effects for necrotizing enterocolitis, the common cold, irritable bowel syndrome, cancer, mucosal immunity, allergies, and urinary tract infections. While probiotics are generally known to be safe, there are occasional reports of adverse effects. Chief among the safety concerns is the ability of these organisms to invade the blood stream causing bacteremia or fungemia. Another concern relates to modifying the gut immune system, the largest immune organ, at a young age if probiotics are given to infants. With regards to lactic acid-producing probiotics, there is concern that accumulation of lactic acid in the body and the development of lactic acidosis can cause clinically significant problems. This article will provide an update on the safety and efficacy of probiotics and summarize the current literature about probiotics, including the issue of quality control.
Cumulative Effects of Social Stress on Reward-Guided Actions and Prefrontal Cortical Activity

When exposed to chronic social stress, animals display behavioral changes that are relevant to depressive-like phenotypes. However, the cascading relationship between incremental stress exposure and neural dysfunctions over time remains incompletely understood. Here we characterize the longitudinal effect of social defeat on goal-directed actions and prefrontal cortical activity in mice, using a head-fixed sucrose preference task and two-photon calcium imaging. Behaviorally, stress-induced loss of reward sensitivity intensifies over days. Motivational anhedonia, the failure to translate positive reinforcements into future actions, requires multiple sessions of stress exposure to become fully established. For neural activity, individual layer 2/3 pyramidal neurons in the Cg1 and M2 subregions of the medial prefrontal cortex have heterogeneous responses to stress. Changes in ensemble activity differ significantly between susceptible and resilient animals after the first defeat session, and continue to diverge following successive stress episodes before reaching persistent abnormal levels. Collectively, these results demonstrate that the cumulative impact of an ethologically relevant stress can be observed at the level of cellular activity of individual prefrontal neurons. The distinct neural responses associated with resilience versus susceptibility raises the hypothesis that the negative impact of social stress is neutralized in resilient animals, in part through an adaptive reorganization of prefrontal cortical activity.
Static and Dynamic Evaluation of an UWB Localization System for Industrial Applications

Many applications in the context of Industry 4.0 require precise localization. However, indoor localization remains an open problem, especially in complex environments such as industrial environments. In recent years, we have seen the emergence of Ultra WideBand (UWB) localization systems. The aim of this article is to evaluate the performance of a UWB system to estimate the position of a person moving in an indoor environment. To do so, we implemented an experimental protocol to evaluate the accuracy of the UWB system both statically and dynamically. The UWB system is compared to a ground truth obtained by a motion capture system with a millimetric accuracy.