Miracle-dz/UniFAR-FTUs huggingface dataset:
Changes in Symbiotic Microbiota and Immune Responses in Early Development Stages of Rapana venosa (Valenciennes, 1846) Provide Insights Into Immune System Development in Gastropods

The symbiotic microbiota can stimulate modulation of immune system, which also can promote immune system mature in critical developmental periods. In this study, we have investigated the symbiotic microbiota in Rapana venosa at five early development stages using Illumina high-throughput sequencing, and detected immune responses in larvae. Analysis of the symbiotic microbiota sequences identified that the most abundant phylum was Proteobacteria. Beta diversity analysis indicated that the structure of the symbiotic microbiota dramatically shifted in early development stages. The abundance of immune-related KEGG Orthologs (KOs) also increased in competent larval (J4, 30-day post-hatching) and postlarval after 3 days of metamorphosis (Y5, 33-day post-hatching) stages. Acid phosphatase activity decreased significantly in the Y5 stage, and alkaline phosphatase activity also at a lower level in Y5 stage, whereas lysozyme activities exhibited no remarkable change. Also, the activities of catalase and superoxide dismutase activities decreased dramatically during early development stages of R. venosa. Dramatic changes in the symbiotic microbiota and the immune response mainly occurred in the initially hatched veliger (C1), competent larval (J4) and postlarval (Y5) stages, during which the hosts might experience substantial environmental changes or changes in physiological structure and function. These findings expand our understanding of the stage-specific symbiotic microbiota in R. venosa and the close association between immune system and symbiotic microbiota in mollusks, however, the specific relationship may need more researches are needed to investigated in the future.
Active 650-km Long Fault System and Xolapa Sliver in Southern Mexico

New estimates of long-term velocities of permanent GPS stations in Southern Mexico reveal that the geologically discernible ∼650-km long shear zone, which strikes parallel to the Middle America trench, is active. This left-lateral strike-slip, La Venta–Chacalapa (LVC) fault system, is apparently associated with a motion of the Xolapa terrain and at the present time is the northern boundary of a ∼110–160-km wide forearc sliver with a sinistral motion of 3–6 mm/year with respect to the North America plate. This sliver is the major tectonic feature in the Guerrero and Oaxaca regions, which accommodates most of the oblique component of the convergence between the Cocos and North America plates. Previous studies based purely on the moment tensor coseismic slips exceedingly overestimated the sliver inland extent and allocated its northern margin on or to the north of the Trans-Mexican Volcanic Belt. While the LVC fault system probably slips slowly over geologic scale time and there is not any historic evidence of large earthquakes on the fault so far, its seismic potential could be very high, assuming a feasible order of ∼103 years recurrence cycle. A detailed analysis of long-term position time series of permanent GPS stations in the Guerrero and Oaxaca states, Southern Mexico discards previous models and provides clear evidence of an active LVC fault zone bounding the Xolapa forearc sliver. The southeastward motion of this sliver may have persisted for the last ∼8–10 Million year and played an important role in the tectonic evolution of the region.
In Arabidopsis thaliana Substrate Recognition and Tissue- as Well as Plastid Type-Specific Expression Define the Roles of Distinct Small Subunits of Isopropylmalate Isomerase

In Arabidopsis thaliana, the heterodimeric isopropylmalate isomerase (IPMI) is composed of a single large (IPMI LSU1) and one of three different small subunits (IPMI SSU1 to 3). The function of IPMI is defined by the small subunits. IPMI SSU1 is required for Leu biosynthesis and has previously also been proposed to be involved in the first cycle of Met chain elongation, the first phase of the synthesis of Met-derived glucosinolates. IPMI SSU2 and IPMI SSU3 participate in the Met chain elongation pathway. Here, we investigate the role of the three IPMI SSUs through the analysis of the role of the substrate recognition region spanning five amino acids on the substrate specificity of IPMI SSU1. Furthermore, we analyze in detail the expression pattern of fluorophore-tagged IPMI SSUs throughout plant development. Our study shows that the substrate recognition region that differs between IPMI SSU1 and the other two IMPI SSUs determines the substrate preference of IPMI. Expression of IPMI SSU1 is spatially separated from the expression of IPMI SSU2 and IPMI SSU3, and IPMI SSU1 is found in small plastids, whereas IMPI SSU2 and SSU3 are found in chloroplasts. Our data show a distinct role for IMPI SSU1 in Leu biosynthesis and for IMPI SSU2 and SSU3 in the Met chain elongation pathway.
SMR/Theta Neurofeedback Training Improves Cognitive Performance and EEG Activity in Elderly With Mild Cognitive Impairment: A Pilot Study

Background: Neurofeedback (NF) training, as a method of self-regulation of brain activity, may be beneficial in elderly patients with mild cognitive impairment (MCI). In this pilot study, we investigated whether a sensorimotor (SMR)/theta NF training could improve cognitive performance and brain electrical activity in elderly patients with MCI. Methods: Twenty elderly patients with MCI were assigned to 20 consecutive sessions of sensorimotor (SMR)/theta NF training, during 10 weeks, on a basis of two sessions each week. Neuropsychological assessments and questionnaires, as well as electroencephalogram (EEG), were performed and compared between baseline (T0), after the last NF training session at 10 weeks (T1), and 1-month follow-up (T2). Results: Repeated measures ANOVA revealed that from baseline to post-intervention, participants showed significant improvement in the Montreal cognitive assessment (MoCa, F = 4.78; p = 0.012), the delayed recall of the Rey auditory verbal learning test (RAVLT, F = 3.675; p = 0.032), the Forward digit span (F = 13.82; p < 0.0001), the Anxiety Goldberg Scale (F = 4.54; p = 0.015), the Wechsler Adult Intelligence Score–Fourth Edition (WAIS-IV; F = 24.75; p < 0.0001), and the Mac Nair score (F = 4.47; p = 0.016). EEG theta power (F = 4.44; p = 0.016) and alpha power (F = 3.84; p = 0.027) during eyes-closed resting-state significantly increased after the NF training and showed sustained improvement at a 1-month follow-up. Conclusion: Our results suggest that NF training could be effective to reduce cognitive deficits in elderly patients with MCI and improve their EEG activity. If these findings are confirmed by randomized controlled studies with larger samples of patients, NF could be seen as a useful non-invasive, non-pharmacological tool for preventing further decline, rehabilitation of cognitive function in the elderly. Clinical Trial Registration: This pilot study was a preliminary step before the trial registered in www.ClinicalTrials. gov, under the number of NCT03526692.
Screening of Potential Key Transcripts Involved in Planarian Regeneration and Analysis of Its Regeneration Patterns by PacBio Long-Read Sequencing

Dugesia japonica is an excellent animal model for studying the regeneration mechanism due to its characteristics of rapid regeneration and easy breeding. PacBio sequencing was performed on the intact planarians (In) and regenerating planarians of 1 day (1d), 3 days (3d), and 5 days (5d) after amputation. The aim of this study is to deeply profile the transcriptome of D. japonica and to evaluate its regenerate changes. Using robust statistical analysis, we identified 5931, 5115, and 4669 transcripts differentially expressed between 1d and In, 3d and In, 5d and In, respectively. A total of 63 key transcripts were screened from these DETs. These key transcripts enhance the expression in different regenerate stages respectively to regulate specific processes including signal transduction, mitosis, protein synthesis, transport and degradation, apoptosis, neural development, and energy cycling. Finally, according to the biological processes involved in these potential key transcripts, we propose a hypothesis of head regeneration model about D. japonica. In addition, the weighted gene co-expression network analysis provides a new way to screen key transcripts from large amounts of data. Together, these analyses identify a number of potential key regulators controlling proliferation, differentiation, apoptosis, and signal transduction. What’s more, this study provides a powerful data foundation for further research on planarians regeneration.
Mismatch Negativity and Impaired Social Functioning in Long-Term and in First Episode Schizophrenia Spectrum Psychosis

Mismatch negativity (MMN) is elicited by infrequent physical parameter sound changes. MMN to pitch-deviants (pMMN) and duration-deviants (dMMN) are severely reduced in long-term schizophrenia (Sz). Although symptom factors (positive, negative, cognitive) are inconsistently associated with MMN amplitude in Sz, several studies have shown smaller dMMN is associated with impaired social functioning in Sz. MMN is less reduced at the first psychotic episode in the schizophrenia spectrum (FESz). Meta-analyses demonstrate that pMMN is not reduced, while dMMN is moderately impaired. Correlations of pMMN and dMMN with symptom factors in FESz are also equivocal. Associations with social functioning have not been reported. FESz and matched controls (n = 40/group), and Sz and matched controls (n = 50/group) were assessed for baseline and current cognitive functioning, symptoms, and social functioning, and pMMN and dMMN were recorded. Sz showed reductions in pMMN (p = 0.001) and dMMN (p = 0.006) amplitude. By contrast, pMMN (p = 0.27) and dMMN (p = 0.84) were not reduced in FESz. However, FESz showed associations between both MMNs and negative symptoms and social functioning. More impaired MMNs in FESz were associated with increased negative symptoms and impaired social functioning, both current and in the year prior to the emergence of psychosis. These data suggest that the extent of pathological process occurring before first psychosis as reflected in compromised social behavior prior to first break and reduced interpersonal communication and increased alogia at first break is indexed by pMMN and dMMN, putative biomarkers of disease progression sensitive to functional impairment.
Human Norovirus Proteins: Implications in the Replicative Cycle, Pathogenesis, and the Host Immune Response

Human noroviruses (HuNoVs) are the cause of more than 95% of epidemic non-bacterial gastroenteritis worldwide, with some lethal cases. These viral agents affect people of all ages. However, young children and older adults are the highest-risk groups, being affected with the greatest rate of hospitalizations and morbidity cases. HuNoV structural proteins, especially VP1, have been studied extensively. In contrast, the functions of the non-structural proteins of the virus have been undescribed in depth. Studies on HuNoV non-structural proteins have mostly been made by expressing them individually in in vitro cultures, providing insights of their functions and the role that they play in HuNoV replication and pathogenesis. This review examines exhaustively the functions of both HuNoV structural and non-structural proteins and their possible role within the viral replicative cycle and the pathogenesis of the virus. It also highlights recent findings regarding the host's innate and adaptive immune responses against HuNoV, which are of great relevance for diagnostics and vaccine development so as to prevent infections caused by these fastidious viruses.
A New Species of Osedax (Siboglinidae: Annelida) From Colonization Experiments in the Arctic Deep Sea

Large parcels of organic matter in the deep sea, such as whale carcasses, harbor a very specialized fauna, most famously the bone-eating worms in the genus Osedax (Annelida, Siboglinidae). Although Osedax was first described only 15 years ago, there are already 26 described species from the Pacific, Atlantic, and Southern Oceans. The high discovery rate of new Osedax species indicates that there is still a lot of undescribed diversity. In this study we describe the most northerly species of Osedax to date, Osedax fenrisi sp. nov. from 73°N on the Arctic Mid-Ocean Ridge. We also present an updated molecular phylogeny of Osedax based on cytochrome oxidase subunit I and 18S rRNA, including all described species in the genus. The molecular results support that O. fenrisi sp. nov. is distinct from the previously known species of Osedax. Both morphological characters and the molecular phylogeny support the placement of O. fenrisi sp. nov. in clade V. The most striking morphological character shared with other described species in this clade (Osedax rubiplumus, Osedax roseus, and Osedax bryani) is the presence of long pinnules inserted on the outside of the palps.
Rich resource environment of fish farms facilitates phenotypic variation and virulence in an opportunistic fish pathogen

Phenotypic variation allows adaptation of opportunistic pathogens to variable conditions in the outside-host environment with strong effects on their epidemiology and pathogenicity in hosts. Here we found that the isolates of an opportunistic fish pathogen Flavobacterium columnare from fish farming environment had higher phenotypic variation between two morphotypes in growth, as compared to the isolates from the natural water environment. The rough morphotypes had higher growth rate than the rhizoid morphotypes especially in the higher resource concentrations and in the higher temperature, but only if the isolate was originating from the fish farms. Rhizoid morphotype was more virulent than the rough type regardless of their origin. However, the virulence of the rough type increased sharply with the size of the fish, and the bacterial isolates from the gills of diseased fish were rhizoid type, indicating a reversal of the rough morphotype into rhizoid in contact with the fish. The high growth rate of the rough morphotype combined with the morphotype reversibility could increase the probability of columnaris epidemics at fish farms. Our findings suggest that intensive farming imposes different selection pressures on bacterial survival in the outside-host environment and its transmission compared to the natural water environment.
IPSE, a parasite-derived, host immunomodulatory infiltrin protein, alleviates resiniferatoxin-induced bladder pain

The transient receptor potential cation channel subfamily V member 1 (TRPV1) receptor is an important mediator of nociception and its expression is enriched in nociceptive neurons. TRPV1 signaling has been implicated in bladder pain and is a potential analgesic target. Resiniferatoxin is the most potent known agonist of TRPV1. Acute exposure of the rat bladder to resiniferatoxin has been demonstrated to result in pain-related freezing and licking behaviors that are alleviated by virally encoded IL-4. The interleukin-4-inducing principle of Schistosoma mansoni eggs (IPSE) is a powerful inducer of IL-4 secretion, and is also known to alter host cell transcription through a nuclear localization sequence-based mechanism. We previously reported that IPSE ameliorates ifosfamide-induced bladder pain in an IL-4- and nuclear localization sequence-dependent manner. We hypothesized that pre-administration of IPSE to resiniferatoxin-challenged mice would dampen pain-related behaviors. IPSE indeed lessened resiniferatoxin-triggered freezing behaviors in mice. This was a nuclear localization sequence-dependent phenomenon, since administration of a nuclear localization sequence mutant version of IPSE abrogated IPSE’s analgesic effect. In contrast, IPSE’s analgesic effect did not seem IL-4-dependent, since use of anti-IL-4 antibody in mice given both IPSE and resiniferatoxin did not significantly affect freezing behaviors. RNA-Seq analysis of resiniferatoxin- and IPSE-exposed bladders revealed differential expression of TNF/NF-κb-related signaling pathway genes. In vitro testing of IPSE uptake by urothelial cells and TRPV1-expressing neuronal cells showed uptake by both cell types. Thus, IPSE’s nuclear localization sequence-dependent therapeutic effects on TRPV1-mediated bladder pain may act on TRPV1-expressing neurons and/or may rely upon urothelial mechanisms.
A cautionary note on the use of haplotype callers in Phylogenomics

Next-generation-sequencing haplotype callers are commonly used in studies to call variants from newly-sequenced species. However, due to the current availability of genomic resources, it is still common practice to use only one reference genome for a given genus, or even one reference for an entire clade of a higher taxon. The problem with traditional haplotype callers such as the one from GATK, is that they are optimized for variant calling at the population level, but not at the phylogenetic level. Thus, the consequences for downstream analyses can be substantial. Here, through simulations, we compare the performance between the haplotype callers of GATK and ATLAS, and present their differences at various phylogenetic scales. We show how the haplotype caller of GATK substantially underestimates the number of variants at the phylogenetic level, but not at the population level. We also quantified the level at which the accuracy of heterozygote calls declines with increasing distance to the reference genome. Such decrease is very sharp in GATK, while ATLAS maintains a high accuracy in variant calling, even at moderately-divergent species from the reference. We further suggest that efforts should be taken towards acquiring more reference genomes per species, before pursuing high-scale phylogenomic studies.
Assessing the reliability of species distribution projections in climate change research

Aim Forecasting changes in species distribution under future scenarios is one of the most prolific areas of application for species distribution models (SDMs). However, no consensus yet exists on the reliability of such models for drawing conclusions on species distribution response to changing climate. In this study we provide an overview of common modelling practices in the field and assess model predictions reliability using a virtual species approach. Location Global Methods We first provide an overview of common modelling practices in the field by reviewing the papers published in the last 5 years. Then, we use a virtual species approach and three commonly applied SDM algorithms (GLM, MaxEnt and Random Forest) to assess the estimated (cross-validated) and actual predictive performance of models parameterized with different modelling settings and violations of modelling assumptions. Results Our literature review shows that most papers that model species distribution under climate change rely on single models (65%) and small samples (< 50 presence points, 62%), use presence-only data (85%), and binarize models’ output to estimate range shift, contraction or expansion (74%). Our virtual species approach reveals that the estimated predictive performance tends to be over-optimistic compared to the real predictive performance. Further, the binarization of predicted probabilities of presence reduces models’ predictive ability considerably. Sample size is one of the main predictors of real accuracy, but has little influence on estimated accuracy. Finally, the inclusion of irrelevant predictors and the violation of modelling assumptions increases estimated accuracy but decreases real accuracy of model projections, leading to biased estimates of range contraction and expansion. Main conclusions Our study calls for extreme caution in the application and interpretation of SDMs in the context of biodiversity conservation and climate change research, especially when modelling a large number of species where species-specific model settings become impracticable.
2-amino-1,3-benzothiazole-6-carboxamide Preferentially Binds the Tandem Mismatch Motif r(UY:GA)

RNA helices are often punctuated with non-Watson-Crick features that can be the target of chemical compounds, but progress towards identifying small molecules specific for non-canonical elements has been slow. We have used a tandem UU:GA mismatch motif (5’-UG-3’:5’-AU-3’) embedded within the helix of an RNA hairpin as a model to identify compounds that bind the motif specifically. The three-dimensional structure of the RNA hairpin and its interaction with a small molecule compound identified through a virtual screen are presented. The G-A of the mismatch forms a sheared pair upon which the U-U base pair stacks. The hydrogen bond configuration of the U-U pair involves the O2 of the U adjacent to the G and the O4 of the U adjacent to the A. The G-A and U-U pairs are flanked by A-U and G-C base pairs, respectively, and the mismatch exhibits greater stability than when the motif is within the context of other flanking base pairs or when the 5’-3’ orientation of the G-A and U-U is swapped. Residual dipolar coupling constants were used to generate an ensemble of structures against which a virtual screen of 64,480 small molecules was performed to identify candidate compounds that the motif specifically binds. The tandem mismatch was found to be specific for one compound, 2-amino-1,3-benzothiazole-6-carboxamide, which binds with moderate affinity but extends the motif to include the flanking A-U and G-C base pairs. The finding that affinity for the UU:GA mismatch is flanking sequence dependent emphasizes the importance of motif context and potentially increases the number of small non-canonical features within RNA that can be specifically targeted by small molecules.
Myosin-driven actin-microtubule networks exhibit self-organized contractile dynamics

Microtubules enable organized myosin-driven contraction by providing flexural rigidity and enhanced connectivity to actin networks. The cytoskeleton is a dynamic network of proteins, including actin, microtubules, and their associated motor proteins, that enables essential cellular processes such as motility, division, and growth. While actomyosin networks are extensively studied, how interactions between actin and microtubules, ubiquitous in the cytoskeleton, influence actomyosin activity remains an open question. Here, we create a network of co-entangled actin and microtubules driven by myosin II. We combine dynamic differential microscopy, particle image velocimetry, and particle tracking to show that both actin and microtubules undergo ballistic contraction with unexpectedly indistinguishable characteristics. This contractility is distinct from faster disordered motion and rupturing that active actin networks exhibit. Our results suggest that microtubules enable self-organized myosin-driven contraction by providing flexural rigidity and enhanced connectivity to actin networks. Beyond the immediate relevance to cytoskeletal dynamics, our results shed light on the design of active materials that can be precisely tuned by the network composition.