Miracle-dz/UniFAR-FTUs huggingface dataset:
De novo assembly and characterization of transcriptome towards understanding molecular mechanism associated with MYMIV-resistance in Vigna mungo - A computational study

The fast climate change affects yield in Vigna mungo via enhancing both biotic and abiotic stresses. Out of all factors, the yellow mosaic disease has the most damaging effect. However, due to lack of reference genome of Vigna mungo, the complete mechanism associated with MYMIV (Mungbean Yellow Mosaic Indian Virus) resistance in Vigna mungo remain elusive to date. Considering this, the authors made an attempt to release new transcriptome and its annotation by employing computational approaches. Quality assessment of the generated transcriptomes reveals that it successfully aligned with 99.03% of the raw reads and hence can be employed for future research. Functional annotation of the transcriptome reveals that 31% and ∼14% of the total transcripts encode lncRNAs and protein-coding sequences, respectively. Further, analysis reveals that, out of total transcripts, only 4536 and 78808 are significantly down and up-regulated during MYMIV infection in Vigna mungo, respectively. These significant transcripts are mainly associated with ribosome, spliceosome, glycolysis /gluconeogenesis, RNA transport, oxidative phosphorylation, protein processing in the endoplasmic reticulum, MAPK signaling pathway - plant, methionine and cysteine metabolism, purine metabolism and RNA degradation. Unlike the previous study, this is for the first time, the present study identified these pathways may play key role in MYMIV resistance in Vigna mungo. Thus, information and transcriptomes data available in the present study make a significant contribution to understanding the genomic structure of Vigna mungo, enabling future analyses as well as downstream applications of gene expression, sequence evolution, and genome annotation.
Poisson balanced spiking networks

An important problem in computational neuroscience is to understand how networks of spiking neurons can carry out various computations underlying behavior. Balanced spiking networks (BSNs) provide a powerful framework for implementing arbitrary linear dynamical systems in networks of integrate-and-fire neurons (Boerlin et al. [1]). However, the classic BSN model requires near-instantaneous transmission of spikes between neurons, which is biologically implausible. Introducing realistic synaptic delays leads to an pathological regime known as “ping-ponging”, in which different populations spike maximally in alternating time bins, causing network output to overshoot the target solution. Here we document this phenomenon and provide a novel solution: we show that a network can have realistic synaptic delays while maintaining accuracy and stability if neurons are endowed with conditionally Poisson firing. Formally, we propose two alternate formulations of Poisson balanced spiking networks: (1) a “local” framework, which replaces the hard integrate-and-fire spiking rule within each neuron by a “soft” threshold function, such that firing probability grows as a smooth nonlinear function of membrane potential; and (2) a “population” framework, which reformulates the BSN objective function in terms of expected spike counts over the entire population. We show that both approaches offer improved robustness, allowing for accurate implementation of network dynamics with realistic synaptic delays between neurons. Moreover, both models produce positive correlations between similarly tuned neurons, a feature of real neural populations that is not found in the original BSN. This work unifies balanced spiking networks with Poisson generalized linear models and suggests several promising avenues for future research.
Human NK cell deficiency as a result of biallelic mutations in MCM10

Human natural killer cell deficiency (NKD) arises from inborn errors of immunity that lead to impaired NK cell development, function or both. Through the understanding of the biological perturbations in individuals with NKD, requirements for the generation of terminally mature functional innate effector cells can be elucidated. Here we report a novel cause of NKD resulting from compound heterozygous mutations in MCM10 that impaired NK cell maturation in a child with fatal susceptibility to CMV. MCM10 has not been previously associated with monogenic disease and plays a critical role in the activation and function of the eukaryotic DNA replisome. By modeling MCM10 deficiency in human NK cell lines and primary NK cell precursors, we demonstrate that MCM10 is required for NK cell terminal maturation and acquisition of immunological system function.
RNA sequencing by direct tagmentation of RNA/DNA hybrids

Significance RNA sequencing is widely used to measure gene expression in biomedical research; therefore, improvements in the simplicity and accuracy of the technology are desirable. All existing RNA sequencing methods rely on the conversion of RNA into double-stranded DNA through reverse transcription followed by second-strand synthesis. The latter step requires additional enzymes and purification, and introduces sequence-dependent bias. Here, we show that Tn5 transposase, which randomly binds and cuts double-stranded DNA, can directly fragment and prime the RNA/DNA heteroduplexes generated by reverse transcription. The primed fragments are then subject to PCR amplification. This provides an approach for simple and accurate RNA characterization and quantification. Transcriptome profiling by RNA sequencing (RNA-seq) has been widely used to characterize cellular status, but it relies on second-strand complementary DNA (cDNA) synthesis to generate initial material for library preparation. Here we use bacterial transposase Tn5, which has been increasingly used in various high-throughput DNA analyses, to construct RNA-seq libraries without second-strand synthesis. We show that Tn5 transposome can randomly bind RNA/DNA heteroduplexes and add sequencing adapters onto RNA directly after reverse transcription. This method, Sequencing HEteRo RNA-DNA-hYbrid (SHERRY), is versatile and scalable. SHERRY accepts a wide range of starting materials, from bulk RNA to single cells. SHERRY offers a greatly simplified protocol and produces results with higher reproducibility and GC uniformity compared with prevailing RNA-seq methods.
Relationship of the cellular structure of teak wood (Tectona grandis L. f.) with different ages and growth sites

Introduccion: Las caracteristicas celulares de la madera determinan las condiciones de procesamiento y uso de las especies forestales. Objetivo: Estudiar la variacion de las caracteristicas anatomicas en la parte interna y externa del duramen de Tectona grandis L. f. de diferentes edades y procedencias. Materiales y metodos: Se seleccionaron arboles de Campeche (9 y 15 anos), Tabasco (15 anos) y Chiapas (21 anos). Se hicieron cortes (10 y 20 µm de espesor) de las caras anatomicas (transversal, radial y tangencial) de la madera y se observaron en microscopio de campo claro. Las imagenes se capturaron con el software Matrox PC-VCR version 02.10. 10. Los elementos celulares se midieron con el software ArcView GIS 3.2. Resultados y discusion: La madera de teca tuvo de 6 a 8 vasos·mm-². La madera de Campeche (9 y 15 anos) presento el mayor diametro de vasos en la parte interna y externa del duramen; en su parte interna, tuvo el mayor ancho de radios. En ambas partes del duramen, la madera de 9 anos de Campeche tuvo mayor altura de radios; la madera de Chiapas de 21 anos presento mayor longitud y diametro de fibras; y la madera de 15 anos de Tabasco produjo el mayor espesor de pared de fibras. Conclusiones: La edad y procedencia inciden sobre la estructura celular de la madera de teca
Effectiveness of botanical hydrocolloid of grass jelly leaf and seaweed to delay ripening of banana

Banana has an important purpose as the source of vitamins, minerals, and other substances in supporting nutritional adequacy. However, there is an obstacle in the supply chain of banana from producers to consumers with prime quality because of the nature of banana which is perishable. Therefore, it is necessary to implement any mean to delay the ripening of banana so that the process can be inhibited and the quality of banana maintained, among which is the fruit skin surface coating technology. The aim of this study was to determine the appropriate material and concentration of botanical hydrocolloid to delay ripening of bananas. This research was conducted in November to December 2014 in the Agronomy Laboratory of University of Mercu Buana Yogyakarta. The research is a single factor experiment arranged in a completely randomized design with three replications. The treatments tested were both hydrocolloid material of seaweed (Euchema spinosum) concentration of 1.5%, 2%, 2.5% and grass jelly (Stephania hernandifolia) with concentration of 2.5%, 5%, 7.5%. The result showed that based on either the percentage of fruit weight loss, fruit skin discoloration, hardness (texture), or total dissolved solids, the grass jelly hydrocolloid with the concentration of 7.5% is the best application in delaying the ripening of banana. The coating of banana with grass jelly hydrocolloid concentration of 7,5% is capable of inhibiting ripening of bananas for 11 days.
Bridging of nucleosome-proximal DNA double-strand breaks by PARP2 enhances its interaction with HPF1

Poly(ADP-ribose) Polymerase 2 (PARP2) is one of three DNA-dependent PARPs involved in the detection of DNA damage. Upon binding to DNA double-strand breaks, PARP2 uses nicotinamide adenine dinucleotide to synthesize poly(ADP-ribose) (PAR) onto itself and other proteins, including histones. PAR chains in turn promote the DNA damage response by recruiting downstream repair factors. These early steps of DNA damage signaling are relevant for understanding how genome integrity is maintained and how their failure leads to genome instability or cancer. There is no structural information on DNA double-strand break detection in the context of chromatin. Here we present a cryo-EM structure of two nucleosomes bridged by human PARP2 and confirm that PARP2 bridges DNA ends in the context of nucleosomes bearing short linker DNA. We demonstrate that the conformation of PARP2 bound to damaged chromatin provides a binding platform for the regulatory protein Histone PARylation Factor 1 (HPF1), and that the resulting HPF1•PARP2•nucleosome complex is enzymatically active. Our results contribute to a structural view of the early steps of the DNA damage response in chromatin.
EFFECT OF DIFFERENT FERTILIZERS IN YIELD AND NODULATION OF COWPEA (VIGNA UNGUICULATA) UNDER MULCHED AND UN-MULCHED FIELD CONDITION IN CHITWAN DISTRICT, NEPAL

To study the effects on nodulation and yield of Cowpea (Vigna Unguiculata), a research had been conducted in the sandy loam soil of the horticulture farm of Agriculture and Forestry University in 2018. The experiment was laid out in factorial 2×5 Randomized complete block design with ten treatments and 3 replications which consists; 1st factor – mulched and un-mulched condition, 2nd factor – Rhizobium inoculation (R) at 1gm/ 16.66 gm seed, Phosphorus (P) at recommended dose of 120kg/ha ,use of R plus P(RP),RP plus Molybdenum (RPMo) at 2 gm Molybdenum per kg seed and control with no such application. The analysis of the findings showed that mulched and RPMo treatment were found significantly superior than other treatments in case of main effects of yield attributes like plant height, canopy diameter and stem number. The highest fresh weight of pods per plant i.e. 312.61 gm and 312.53 gm and no of nodules per plant i.e. 121.63 and 129.33 were found in mulched and RPMo treatment, significant at p
Crop signal markers facilitate crop detection and weed removal from lettuce and tomato by an intelligent cultivator

Abstract Increasing weed control costs and limited herbicide options threaten vegetable crop profitability. Traditional interrow mechanical cultivation is very effective at removing weeds between crop rows. However, weed control within the crop rows is necessary to establish the crop and prevent yield loss. Currently, many vegetable crops require hand weeding to remove weeds within the row that remain after traditional cultivation and herbicide use. Intelligent cultivators have come into commercial use to remove intrarow weeds and reduce cost of hand weeding. Intelligent cultivators currently on the market such as the Robovator, use pattern recognition to detect the crop row. These cultivators do not differentiate crops and weeds and do not work well among high weed populations. One approach to differentiate weeds is to place a machine-detectable mark or signal on the crop (i.e., the crop has the mark and the weed does not), thereby facilitating weed/crop differentiation. Lettuce and tomato plants were marked with labels and topical markers, then cultivated with an intelligent cultivator programmed to identify the markers. Results from field trials in marked tomato and lettuce found that the intelligent cultivator removed 90% more weeds from tomato and 66% more weeds from lettuce than standard cultivators without reducing yields. Accurate crop and weed differentiation described here resulted in a 45% to 48% reduction in hand-weeding time per hectare. Nomenclature: lettuce, Lactuca sativa L. ; tomato, Solanum lycopersicum L
S1P-S1PR1 activity controls VEGF-A signaling during lymphatic vessel development

Sphingosine-1-phosphate (S1P), a lipid signaling molecule produced by endothelial cells, is required for development and homeostasis of blood vessels. However, its role during lymphatic vessel development is unclear. We show in murine newborns that pharmacologically enhanced S1P signaling increases VEGF-A-dependent LEC proliferation. In contrast, S1PR1 inhibition, mediated by the antagonist NIBR0213 or LEC-specific genetic deletion of S1pr1, promotes filopodia formation and vessel branching, independent of VEGF-A. To investigate the S1P and VEGF-A signaling crosstalk observed in vivo, we used LECs cultured in vitro. We demonstrate that S1P activates endogenous S1PR1 in a constitutive, autocrine manner. Importantly, S1P-S1PR1 activity was required for VEGF-A-induced LEC proliferation and strongly supported ERK1/2 activation and VEGFR-2 trafficking to the perinuclear area. In conclusion, S1P-S1PR1 signaling promotes VEGF-A-dependent LEC proliferation and limits migratory and filopodia-forming responses. Hence, S1P-S1PR1 signaling is required for balanced growth factor-induced lymphangiogenesis and correctly patterned lymphatic vessels during postnatal development.
Heritability and genetic variability estimates in F3 populations of bread wheat (Triticum aestivum L.)

The wheat breeders are concentrating to improve the yield potential of bread wheat by developing new varieties with desirable genetic makeup in order to overcome the consumption pressure of the everincreasing human population. For resolving this situation, research was carried out on eight F3 populations along with their six parents grown in the Experimental Field. The experiment was carried out in a Randomized Complete Block Design with four replications. The characters studied were; plant height (cm), peduncle length (cm), tiller plant, spike length (cm), spikelets spike, grains spike, seed index (g), grain yield plant (g), biological yield plant (g) and harvest index (%). The analysis of variance revealed significant differences among genotypes, hybrids and parents vs. hybrids for all the traits studied. Such results signified the worth of breeding material for further exploitation. The present research indicated that based on average performance, F3 populations performed better than their parents for most of the traits studied. It means transgressive segregants were present in F3 populations. If the selection of such potential plants is successful, then they may be utilized for further improvement of bread wheat. The genetic parameters of F3 progenies indicated that cross TJ-83 x TD-1 displayed higher heritability estimates coupled with more genetic gains for plant height, spike length, spikelets per spike and grains per spike; TJ-83 x Sarsabz for tillers per plant and biological yield plant; TJ-83 x Moomal for peduncle length, grain yield per plant and harvest index and Moomal x TD-1 for seed index. These F3 populations may be kept on priority for selection from subsequent filial generations to improve the studied traits in bread wheat.
Global kinome silencing combined with 3D invasion screening of the tumor microenvironment identifies fibroblast-expressed PIK3Cδ involvement in triple-negative breast cancer progression

As there is growing evidence for the tumor microenvironment’s (TME) role in tumorigenesis, we sought to investigate the role of fibroblast-expressed kinases in triple negative breast cancer (TNBC). Using a high-throughput kinome screen combined with 3D invasion assays, we identified fibroblast-expressed PIK3Cδ (f-PIK3Cδ) as a key regulator of progression. Although PIK3Cδ has been mainly described in leucocytes, we detected high expression in primary fibroblasts derived from TNBC patients, while PIK3Cδ was undetectable in cancer epithelial cell lines. Genetic and pharmacologic gain- and loss-of functions experiments verified the contribution of f-PIK3Cδ in TNBC cell invasion. By employing an integrated secretomics and transcriptomics analysis, we revealed a paracrine mechanism via which f-PIK3Cδ confers its pro-tumorigenic effects. Inhibition of f-PIK3Cδ promoted the secretion of factors, including PLGF and BDNF, which subsequently led to upregulation of NR4A1 in TNBC cells where it acts as a tumor suppressor. Inhibition of PIK3Cδ in an orthotopic BC mouse model reduced tumor growth only after inoculation with fibroblasts, indicating a role of f-PIK3Cδ in cancer progression. Similar results were observed in the MMTV-PyMT transgenic BC mouse model, in addition to a decrease on tumor metastasis emphasizing the potential immune-independent effects of PIK3Cδ inhibition. Finally, analysis of BC patient cohorts and TCGA datasets identified f-PIK3Cδ (protein and mRNA levels) as an independent prognostic factor for overall and disease free survival, highlighting it as a therapeutic target for TNBC.
A neornithischian dinosaur from the Middle Jurassic Xintiangou Formation of Yunyang, Chongqing, China: the earliest record in Asia

ABSTRACT A new neornithischian dinosaur, Sanxiasaurus modaoxiensis gen. et sp. nov., is described based on a partial postcranial skeleton from the Middle Jurassic Xintiangou Formation of Yunyang, Chongqing Municipality, China. It is the first neornithischian dinosaur from the Middle Jurassic Xintiangou Formation of Sichuan Basin, and also the earliest record of a neornithischian dinosaur in Asia. It differs from other neornithischians in possessing the following unique combination of characters: at least four sacrals; humerus strongly bowed laterally along its length; obturator process located at mid-length of ischial shaft; lesser trochanter of femur broadened, wing shaped and subequal in anteroposterior width to greater trochanter; distal tibia with elongate posterolateral process. Phylogenetic analysis shows that Sanxiasaurus modaoxiensis is positioned near the base of neornithischia. This find extends the Asia neornithischian stratigraphic horizon to the lower Middle Jurassic.
Inhibition of planarian regeneration

This study investigated the extent to which an inhibitory substance, located primarily in the head of the planarian, Dugesia tigrina, prevented brain regeneration in decapitated planaria. Dimethyl Sulfoxide was used in conjunction with the extracted planarian brain inhibitor in hopes of enhancing the action of the inhibitory substance. When decapitated planaria regenerated a new head in culture media containing the extract of homogenized planarian heads, there was a significant decrease in the length of the regenerated brain. Less inhibition of brain regeneration was noted in decapitated planaria which regenerated in media containing an extract of homogenized planarian tails. The removal of the brain from the intact animal also removed the inhibitor of brain development and the organism was free to regenerate a new brain to replace the lost one. This inhibitory substance acts as the controller or one of the controllers of brain regeneration and development in Dugesia tigrina, and by studying it more closely a better understanding of planarian regeneration can be attained.
Evaluation of haplotype callers for next-generation sequencing of viruses

Currently, the standard practice for assembling next-generation sequencing (NGS) reads of viral genomes is to summarize thousands of individual short reads into a single consensus sequence, thus confounding useful intra-host diversity information for molecular phylodynamic inference. It is hypothesized that a few viral strains may dominate the intra-host genetic diversity with a variety of lower frequency strains comprising the rest of the population. Several software tools currently exist to convert NGS sequence variants into haplotypes. However, previous studies suggest that current approaches of haplotype reconstruction greatly underestimate intra-host diversity. Here, we tested twelve NGS haplotype reconstruction methods using viral populations simulated under realistic evolutionary dynamics. Parameters for the simulated data spanned known fast evolving viruses (e.g., HIV-1) diversity estimates to test the limits of the haplotype reconstruction methods and ensured coverage of predicted intra-host viral diversity levels. Using those parameters, we simulated HIV-1 viral populations of 216-1,185 haplotypes per host at a frequency <7%. All twelve investigated haplotype callers showed variable performance and produced drastically different results that were mainly driven by differences in mutation rate and, to a lesser extent, in effective population size. Most methods were able to accurately reconstruct haplotypes when genetic diversity was low. However, under higher levels of diversity (e.g., those seen intra-host HIV-1 infections), haplotype reconstruction accuracy was highly variable and, on average, poor. High diversity levels led to severe underestimation of, with a few tools greatly overestimating, the true number of haplotypes. PredictHaplo and PEHaplo produced estimates close to the true number of haplotypes, although their haplotype reconstruction accuracy was worse than that of the other ten tools. We conclude that haplotype reconstruction from NGS short reads is unreliable due to high genetic diversity of fast-evolving viruses. Local haplotype reconstruction of longer reads to phase variants may provide a more reliable estimation of viral variants within a population. Highlights Haplotype callers for NGS data vary greatly in their performance. Haplotype callers performance is mainly determined by mutation rate. Haplotype callers performance is less sensitive to effective population size. Most haplotype callers perform well with low diversity and poorly with high diversity. PredictHaplo performs best if genetic diversity is in the range of HIV diversity.