Miracle-dz/UniFAR-FTUs huggingface dataset:
Seed collection environment: Effects of forest cover reduction on biometrics and seed lot quality of Bowdichia virgilioides Kunth

Considering the growing demand for seed production and seedlings for forest restoration, addressing the implica­tions of landscape changes regarding germination of native species becomes of great value for directing seed collections. The objective of this study is to evaluate the influence of seed collection environment on germination and biometry of fruits and diaspores of Bowdichia virgilioides . Fruits were collected in two forest fragments with distinct characteristics (forest I, open canopy; and forest II, closed canopy), and in isolated trees in pastures. Fruit and seed biometry of the three collection environments was carried out, and a germination test was conducted in a completely randomized design with three treatments (forest I, forest II, and open area) and twenty replicates. Collection site, and therefore changes in forest cover, influences the biometry of fruits and seeds, resulting in lighter seeds and fruits with a smaller size in the fragment with a recent history of disturbance (forest I), as well as the vigor of diaspores of Bowdichia virgilioides. Seeds from forest I expressed a greater vigor, while seeds from the pasture area presented a higher propensity to death and formation of abnormal seedlings. For the production of seedlings and commercialization of seeds for forest restoration, the environment of origin of seeds should be taken into account. It is not recommended to use lots of seedlings from Bowdichia virgilioides seeds from isolated trees, such as those located on pastures and roads.
Effect of Feedback Valence on Family Resemblance Category Learning

This research uses ERPs method to study how different valence of feedback influence family resemblance category learning. The results showed that at the behavioral level, participants in the negative feedback condition received higher test scores than those in the positive feedback condition; at the physiological level, the four kinds of ERPs evoked by both negative and positive feedback are P200, P300, and FRN. Compared with the non-feedback condition, P300 is more sensitive to negative feedback, and negative feedback induces larger amplitude, while P300 is not sensitive to positive feedback. For both negative and positive feedback, when feedback was presented after 200-300ms, the reaction to errors induced FRN production, and FRN produced under negative feedback condition led to more activation. This research has deepened our understanding of the influence of feedback valence on category learning from the brain mechanisms as well.
Past spatial structure of plant communities determines arbuscular mycorrhizal fungal community assembly

Due to the importance of arbuscular mycorrhizal fungi (AMF) in ecosystem productivity, a key ecological question is how do their communities assemble? As plant spatial patterns constitute a mosaic of AM fungi habitats, we hypothesized that AM fungal community assembly is determined by plant community structure, both in space and time. We tested our hypothesis by sampling individuals of two host‐plant species, Brachypodium pinnatum and Elytrigia repens, from experimental communities cultivated in mesocosms, and assessed their AM fungal root colonizers by mass sequencing. We related AM fungal community structure to the distribution of neighbouring plant species at different spatio‐temporal scales. We demonstrated that AM fungal community assembly depends mostly on past plant spatial patterns at a small spatial scale (5 cm), indicating that plants growing at given locations leave a footprint on the AM fungi community. This spatial scale of response was also influenced by the host‐plant species, probably by its clonal propagation. Synthesis. Overall, we highlighted that processes involved in Arbuscular mycorrhizal (AM) fungal community assembly do not operate at the rough scale of the overall plant community mosaic but are instead locally determined, delineating the AM fungal ‘eye‐view’ of the host‐plant community.
Characterization of the human mitochondrial Arginyl-tRNA synthetase and contribution to the général understanding of pathologies linked to mutations on mitochondrial aminoacyl-tRNA synthetases

Human mitochondrial aminoacyl-tRNA synthetases (mt-aaRSs) are housekeeping enzymes involved in the mitochondrial translation. They catalyze the aminoacylation of tRNAs with their cognate amino acids. Mutations in their nuclear genes are correlated with pathologies with a broad spectrum of clinical phenotypes, but with so far no clear explanations about the underlying molecular mechanism(s). The aim of this PhD work follows the long-standing efforts of the host laboratory but expand the interest and knowledge to an unexplored system: the human mitochondrial arginyl-tRNA synthetase (mt-ArgRS). Mutations in the mt-ArgRS lead to Pontocebellar hypoplasia type 6, a severe neuro-developmental pathology. I thus contributed to i) comprehensively analyze the clinical data reported in pathologies related to mutations on mt-aaRSs, resulting in a categorization according to the affected anatomical system; ii) decipher some cellular properties of the mt-ArgRS; and iii) investigate to impact of disease-associated mutations on mt-aaRSs properties. Combined with previous works, the present results expand the knowledge of the mt-aaRSs, shedding new light on the link between mt-aaRSs-mutations and disease.
Regulation of rice sucrose transporter 4 gene expression in response to insect herbivore chewing

ABSTRACT Sucrose is an important carbon source for plant tissue repairing and also a signal involved in defense responses to against insect herbivores. Allocation of sucrose toward to undamaged tissues is an herbivory tolerance mechanism. Sucrose transporters (SUTs) are key factors to control sucrose flow in plants. In this study, herbivory effects caused by rice leaffolder [Cnaphalocrocis medinalis (Guenée)] on OsSUT4 expressions were investigated in rice plants, and the results showed OsSUT4 expression was significantly upregulated by larvae infestation and mechanical wounding. The wounding-induced OsSUT4 expression was not systemically demonstrated in undamaged leaves. The larval chewing-induced OsSUT4 expression was obviously reduced by blocking jasmonic acid (JA) and abscisic acid (ABA) biosynthesis. In addition to JA and ABA, data showed H2O2 generated in wounded tissues also role a signal in the regulatory pathway of herbivore-induced OsSUT4 expressions. Our finding provide insights for further study in signal network of herbivory-induced sucrose translocation.
Brain dynamics for confidence-weighted learning

Learning in a changing and uncertain environment is a difficult problem. A popular solution is to predict future observations and then use surprising outcomes to update those predictions. However, humans also have a sense of confidence that characterizes the precision of their predictions. Bayesian models use this confidence to regulate learning: for a given surprise, the update is smaller when confidence is higher. We explored the human brain dynamics sub-tending such a confidence-weighting using magneto-encephalography. During our volatile probability learning task, subjects’ confidence reports conformed with Bayesian inference. Several stimulus-evoked brain responses reflected surprise, and some of them were indeed further modulated by confidence. Confidence about predictions also modulated pupil-linked arousal and beta-range (15-30 Hz) oscillations, which in turn modulated specific stimulus-evoked surprise responses. Our results suggest thus that confidence about predictions modulates intrinsic properties of the brain state to amplify or dampen surprise responses evoked by discrepant observations.
Distribution of Potentially Pathogenic Vibrio parahaemolyticus in Seafood and the Aquatic Environment of Mumbai, India

The occurrence of total and pathogenic Vibrio parahaemolyticus in fresh seafood and the coastal environment of Mumbai, India was examined in this study. Samples comprising of fish, shellfish, coastal sediment and coastal waters were analyzed for V. parahaemolyticus by selective enrichment and isolation. Biochemically identified isolates were tested for the presence of tlh (thermolabile hemolysin), tdh (thermostable direct hemolysin) and trh (tdh-related hemolysin) by polymerase chain reaction (PCR). While Chromogenic Vibrio (CV) agar yielded V. parhaemolyticus from all samples (100%), TCBS agar yielded V. parahaemolyticus from 57.1% of the samples. The incidence of trh V. parahaemolyticus was high, being isolated from 16.4% of the samples analyzed, while the tdh V. parahaemolyticus were isolated from 1.4% of samples. Two tdh, trh isolates from the coastal water were positive by a in pandemic group-specific (GS) PCR. The study suggests that seafood and coastal environment may harbor pathogenic V. parahaemolyticus with characteristics of pandemic clones, although their incidence is very low. Further, sodium taurocholate (ST) broth and chromogenic Vibrio (CV) agar combination is highly suitable for the isolation of total and pathogenic V. parahaemolyticus from seafood and environmental samples.
Search as a simple take-the-best heuristic

Humans commonly engage in a variety of search behaviours, for example when looking for an object, a partner, information, or a solution to a complex problem. The success or failure of a search strategy crucially depends on the structure of the environment and the constraints it imposes on the individuals. Here we focus on environments in which individuals have to explore the solution space gradually and where their reward is determined by one unique solution they choose to exploit. This type of environment has been relatively overlooked in the past despite being relevant to numerous real-life situations, such as spatial search and various problem-solving tasks. By means of a dedicated experimental design, we show that the search behaviour of experimental participants can be well described by a simple heuristic model. Both in rich and poor solution spaces, a take-the-best procedure that ignores all but one cue at a time is capable of reproducing a diversity of observed behavioural patterns. Our approach, therefore, sheds lights on the possible cognitive mechanisms involved in human search.
Tridecaptin synthetase and gene thereof

The present invention is a Gram-positive bacterium Bacillus Companion E681) to separate the tree from the strain kaptin biosynthesis enzyme, a gene encoding this end, a method of manufacturing a tree having kaptin or derivatives thereof using the gene. With the tree to kaptin biosynthetic enzymes of the invention can be used to produce a tree useful in productivity and new antibiotics kaptin.
Efecto de hongos micorrízicos arbusculares en plántulas de maíz (Zea mays L.)

El presente trabajo evaluó el efecto de tres cepas de Hongos Micorrízicos Arbusculares (HMA) provenientes de la finca experimental La Pino de la Universidad Técnica de Manabí sobre el crecimiento, producción de biomasa, y colonización micorrízica en plántulas de maíz (Zea mays L.). Mediante un Diseño Completamente Aleatorizado (DCA) se estudiaron cuatro tratamientos (el control y la inoculación de las tres cepas de HMA Claroideoglomus luteum, Sclerocystis sinuosa y Dominikia spp) con diez repeticiones. La inoculación micorrízica se realizó por el método de inmersión de la raíz, antes de trasplantar las plántulas enmacetas con tierra estéril. Durante veinte días, las plantas se regaron con 100 ml de agua del grifo cada 3 días y se suministró cada cuatro días una solución nutriente (5 ml por maceta de solución de Hoagland) a 1 cm de la raíz. Los resultados demostraron mayor altura y producción de biomasa en las plántulas inoculación de la cepa Sclerocystis sinuosa correspondiente al T2, sin embargo, estas diferencias no fueron estadísticamente significativas. Esta cepa (T2) produjo también mayores porcentajes de colonización micorrízica demostrando diferencias significativas respecto al T1. En general entre las sepas evaluadas, Sclerocystis sinuosa (T2) evidenció mayores índices de eficiencia en las plántulas el maíz.
A Review of the Genetics and Pathogenesis of Syndactyly in Humans and Experimental Animals: A 3-Step Pathway of Pathogenesis

Embryology of normal web space creation and the genetics of syndactyly in humans and experimental animals are well described in the literature. In this review, the author offers a 3-step pathway of pathogenesis for syndactyly. The first step is initiated either by the overactivation of the WNT canonical pathway or the suppression of the Bone Morphogenetic Protein (BMP) canonical pathway. This leads to an overexpression of Fibroblast Growth Factor 8 (FGF8). The final step is the suppression of retinoic acid in the interdigital mesenchyme leading to suppression of both apoptosis and extracellular matrix (ECM) degradation, resulting in syndactyly.
Interspecific hybridizations of Fraxinus L. (F. mandshurica × F. americana and F. mandshurica × F. velutina) and heterosis analysis and selection of F1 progenies

The interspecific hybridizations of Fraxinus mandshurica Rupr. × Fraxinus americana L. (MA) and Fraxinus mandshurica × Fraxinus velutina Torr. (MV) were conducted to solve the problems of poor cold adaption associated with the introduction of Fraxinus in Heilongjiang province. High-voltage electrostatic field (HVEF) treatment to pollen was performed to overcome the prefertilization barriers. The hybrids adapted more strongly and grew better than the pure species (heterosis over higher parent (HHP) of the 9-year volume index was 5.5% for MA and 23.1% for MV) in Heilongjiang province. HVEF treatment greatly improved the number of seeds (0.25- to 5.52-fold) and seedlings (1.63- to 8.71-fold) of the hybrids. Additionally, three excellent female parents (nos. 15, 16, and 17) and seven hybrid combinations of MA (D94, D70, and D100) and MV (D103, D116, D105, and D104) with excellent growth traits were selected. The HHPs of volume index were 39.1%–112.5% for selected hybrids. Additionally, predicted growth trends of the hybrids showed that the hybrids will maintain a 7.7% to 9.3% height advantage over F. mandshurica through ages 10 to 15 years in Mao Ershan. These findings will accelerate the genetic breeding process of Fraxinus species.
Stochastic sampling provides a unifying account of working memory limits

Attempts to characterize the limits of human working memory have differed on whether internal representations are discrete or continuous, with models of each type competing to best capture the errors observers make in delayed reproduction of elementary stimulus features. Here we show discretization only weakly discriminates between models; the critical distinction is instead between deterministic (fixed) and stochastic (randomly varying) limits, with only the latter compatible with observed human performance and the underlying biological system. Reconceptualizing existing models in terms of sampling reveals strong commonalities between seemingly opposing accounts: adding stochasticity to a discrete model brings it into closer correspondence with theories of neural coding, and puts its quality of fit on a par with continuous models, but also eliminates the stability and dependencies between items implied by a fixed set of “slots”. A probabilistic limit on the number of items successfully retrieved is an emergent property of stochastic sampling, with no explicit mechanism required to enforce it. These findings resolve discrepancies between previous accounts and establish a unified computational framework for further investigating working memory.
Development of NQ-E, Nutrition Quotient for Korean elderly: item selection and validation of factor structure

본 연구는 생애주기별 영양지수 중 노인 대상 영양지수(Nutrition Quotient for Elderly, NQ-E) 개발을 목표로 수행되었다. 노인의 식행동과 영양섭취 관련 문헌, 국민건강 영양조사 자료, 국가 영양정책 및 권고사항, 전문가 대상 심층면접을 통해 식품섭취영역에서 18개 문항, 식행동 식습관 영역에서 23개 문항의 총 41.
TMT-Opsins differentially modulate medaka brain function in a context-dependent fashion

Vertebrate behavior is strongly influenced by light. Photoreceptors, encoded by Opsins, are present inside the vertebrate brain and peripheral tissues. Their non-visual functions are largely enigmatic. We focus on tmt-opsin1b and 2, c-Opsins with ancestral-type sequence features, conserved across several vertebrate phyla and with partly similar expression. Their loss-of-function mutations differentially modulate medakafish behavior in a context-dependent manner. Specifically, differences in light conditions have differential effects depending on age and frequency of the light changes, part of which are mediated by TMT-Opsin1b acting outside the eyes, while the pre-pro-hormone sst1b is regulated by daylength via TMT-opsin1b in an eye-dependent manner. Analyses of tmt-opsin1b;tmt-opsin2 double mutants reveals partial complementation of single mutant behavioral and molecular phenotypes. Our work starts to disentangle the highly complex interactions of vertebrate non-visual Opsins, suggesting that tmt-opsin-expressing cells together with other Opsins provide detailed light information to the organism for behavioral fine-tuning. One Sentence Summary Two medakafish non-visual c-type Opsins interact non-additively, impacting the levels of the preprohormone sst1b, as well as the voltage-gated sodium channel subunit scn12aa and- at least in part independently of the eyes- the amount of larval day-time rest.
Extensive genetic differentiation between recently evolved sympatric Arctic charr morphs

Abstract The availability of diverse ecological niches can promote adaptation of trophic specializations and related traits, as has been repeatedly observed in evolutionary radiations of freshwater fish. The role of genetics, environment, and history in ecologically driven divergence and adaptation, can be studied on adaptive radiations or populations showing ecological polymorphism. Salmonids, especially the Salvelinus genus, are renowned for both phenotypic diversity and polymorphism. Arctic charr (Salvelinus alpinus) invaded Icelandic streams during the glacial retreat (about 10,000 years ago) and exhibits many instances of sympatric polymorphism. Particularly, well studied are the four morphs in Lake Þingvallavatn in Iceland. The small benthic (SB), large benthic (LB), planktivorous (PL), and piscivorous (PI) charr differ in many regards, including size, form, and life history traits. To investigate relatedness and genomic differentiation between morphs, we identified variable sites from RNA‐sequencing data from three of those morphs and verified 22 variants in population samples. The data reveal genetic differences between the morphs, with the two benthic morphs being more similar and the PL‐charr more genetically different. The markers with high differentiation map to all linkage groups, suggesting ancient and pervasive genetic separation of these three morphs. Furthermore, GO analyses suggest differences in collagen metabolism, odontogenesis, and sensory systems between PL‐charr and the benthic morphs. Genotyping in population samples from all four morphs confirms the genetic separation and indicates that the PI‐charr are less genetically distinct than the other three morphs. The genetic separation of the other three morphs indicates certain degree of reproductive isolation. The extent of gene flow between the morphs and the nature of reproductive barriers between them remain to be elucidated.
Transcriptome Analysis to Identify Putative Genes Involved in Flowering Time Under Different Photoperiods in ‘Hong jin gou’ Common Bean

Flowering time influences pod yield and quality of common bean (Phaseolus vulgaris); however, our knowledge of flowering time genes and flowering mechanisms in common bean remain limited. We performed RNA-sequencing (RNA-seq) analyses [long-day (LD) condition and short-day (SD) condition] to identify the flowering time genes and analyzed differentially expressed genes to examine their expression levels in relation to flowering time in ‘Hong Jin Gou’ common bean, a cultivar highly sensitive to photoperiod. The circadian patterns of related genes were identified using quantitative real-time polymerase chain reaction (qRT-PCR). Flowering time in ‘Hong Jin Gou’ was influenced by day length: SD conditions promoted flowering. A total of eight flowering time–related genes were identified, which were classified into photoperiod pathways. Homologs of pseudo-response regulator 5, pseudo-response regulator 7, and gigantea were more highly expressed under SD conditions than under LD conditions. Homologs of late elongated hypocotyl and timing of cab expression 1 were differentially expressed under light and dark conditions. Early flowering 3 is a key regulator of the pathway, which coordinates light and circadian clock inputs in leaves to trigger the expression of downstream genes. The present study provides critical information that could facilitate further investigations on the genetic mechanism of flowering time in common bean.
Structural Basis of Enhanced Facilitated Diffusion of DNA Binding Proteins in Crowded Cellular Milieu

DNA binding proteins (DBPs) rapidly recognize and specifically associate with their target DNA sites inside cell nucleus that contains up to 400 g/L macromolecules, most of which are proteins. While the fast association between DBPs and DNA is explained by a facilitated diffusion mechanism, where DBPs adopt a weighted combination of 3D diffusion and 1D sliding and hopping modes of transportation, the role of cellular environment that contains many nonspecifically interacting proteins and other biomolecules is mostly overlooked. By performing large scale computational simulations with an appropriately tuned model of protein and DNA in the presence of nonspecifically interacting bulk and DNA bound crowders (genomic crowders), we demonstrate the structural basis of the enhanced facilitated diffusion of DBPs inside a crowded cellular milieu through novel 1D scanning mechanisms. In the presence of bulk crowders, we identify the protein to float along the DNA under the influence of protein-crowder nonspecific interactions. The search mode is distinctly different compared to usual 1D sliding and hopping dynamics where protein diffusion is regulated by the DNA electrostatics. In contrast, the presence of genomic crowders expedite the target search process by transporting the protein over DNA segments through the formation of a transient protein-crowder bridged complex. By analyzing the ruggedness of the associated potential energy landscape, we underpin the molecular origin of the kinetic advantages of these search modes and show that they successfully explain the experimentally observed acceleration of facilitated diffusion of DBPs by molecular crowding agents and crowder concentration dependent enzymatic activity of transcription factors. Our findings provide crucial insights into gene regulation kinetics inside the crowded cellular milieu. SIGNIFICANCE 10-40% of the intracellular volume is occupied by proteins, and other biomolecules, collectively known as macromolecular crowders. Their presence has been found to promote faster translocation of DNA binding proteins (DBPs) during the search of their target DNA sites for crucial cellular processes. Using molecular simulations, we probe the underlying structural basis and underscore the existence of novel DNA scanning mechanisms actuated by protein-crowder nonspecific interactions. We show that the observed search modes are kinetically beneficial and can successfully explain the acceleration of facilitated diffusion of DBPs by molecular crowding agents and crowderconcentration dependent enzymatic activity of transcription factors.Our study sheds new light on the long-standing facilitated diffusion problem of DBPs in the crowded cellular environment for regulating gene expression.