Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of novel EST-SSR markers from the de novo transcriptome sequence and application in persimmon (Diospyros L.)

Introduction The Ebenaceae is an important family of flowering plants belonging to the order Ericales. It consists of ebony and persimmon among about 768 species, distributed across the tropical and warmer temperate regions of the world (Bremer et al., 2009). Persimmon (Diospyros L.) is an important fruit crop and is cultivated extensively in China, Japan, Korea, Italy, Israel and Spain (Yang et al., 2015a). It belongs to the genus Diospyros in the family Ebenaceae. Persimmon included more than 400 species with ploidy levels ranging from diploid (2n = 2x = 30) to nonaploid (2n = 9x = 135) (Jing et al., 2013). Persimmon has existed for 10,000 years in China. China is one of the major gene centers of persimmon species origine. About 650 accessions of persimmon germplasm were Summary Persimmon (Diospyros L.) is one of the most important commercially cultivated fruit crops in the world. However, the research on the molecular biology of persimmon is very less due to the lack of genomic and transcriptome data. In this study, the persimmon transcriptomes were sequenced from a new species of Diospyros L. (Deyangshi). Illumina sequencing generated 44,522,166 high-quality clean reads that were assembled into 48,012 unigenes with an average length of 835 bp. A total of 27,586 unigenes (57.7% of all unigenes) were annotated, and 14,275 unigenes were classified into 24 function classification using Clusters of Orthologous Groups of proteins (COG) database, 71,073 unigenes were assigned to 45 functional groups using Gene Ontology (GO) database, 7,186 annotated sequences were assigned to 124 specific metabolic pathways by Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Furthermore, 8,741 simple sequence repeats (SSRs) were identified from 7,074 unigenes. 100 pairs of primers were selected to evaluate the validity and universality in twenty genotypes of persimmon, and 89 pairs generated clear and abundant bands. This is the first report to develop SSR markers for persimmon by transcriptome information. These data could be used as an important resource for studying the genetics and molecular biology for persimmon in future work.
The efficacy of obesity polygenic risk scores in an autistic population

Polygenic risk scores (PRS) bear great promise in understanding complex diseases and improving clinical diagnoses, but the competency of these risk scores in different populations is known to vary significantly, especially between those of European ancestry and those of other ethnic ancestries. Additionally, the applicability of these risk scores across populations different by disease, instead of ethnicity, is poorly understood. A current and largely unexplored population for the accuracy of PRS is that of individuals with autism. Combined with the increased prevalence of obesity in autistic populations, we seek to evaluate the difference in efficacy of PRS for obesity in autistic versus non-autistic populations. We show that genetic variants strongly associated with obesity in non-autistic populations are significantly less representative of the disease in autistic populations. Rather, these cases of obesity phenocopies in patients with autism may follow a different and non-conventional mechanism of action involving the regulation of oxytocin in the brain among other potential behavioral factors. Our findings elucidate the limits of PRS across populations contrasting by disease and suggest that obesity may be regulated differently in individuals with autism as compared to those without autism.
Regulation of T cell growth

This PhD thesis aims to examine the growth of T cells in response to cytokines of the common gamma chain (yc) family, in particular interleukin (IL)-2 and IL- 15. Cell growth is commonly used to describe cells in exponential division however the growth of a cell is defined by its size and volume, which is directly related to the rate of cell metabolism and protein synthesis. Naive T cells are small and circulate around the body maintaining a minimal rate of metabolic activity and protein synthesis. During an immune response naive T cells undergo rapid proliferation and differentiate into effector cells. These cells produce and secrete large amounts of cytokines and effector molecules allowing them to mediate their immune function. The differentiation of antigen activated T cells to mature effectors takes several days and is regulated by cytokines. These cytokines need to maintain high rates of cell metabolism for a prolonged period. Thus the cytokines that regulate proliferation and differentiation of antigen activated T cells need to sustain cell growth. Data presented in this thesis shows differential roles for gamma chain cytokines, specifically IL-2 and IL-15 in the regulation of protein synthesis and uptake of amino acids, whilst maintaining equal mitogenic capacity. This thesis highlights the possible uncoupling of the rate of cellular division and protein synthesis induced by cytokines and defines a unique role for common gamma chain cytokines in regulation of protein synthesis and ultimately the regulation of cellular function.
Polymerization activity of an alpha-like DNA polymerase requires a conserved 3'-5' exonuclease active site

Most DNA polymerases are multifunctional proteins that possess both polymerizing and exonucleolytic activities. For Escherichia coli DNA polymerase I and its relatives, polymerase and exonuclease activities reside on distinct, separable domains of the same polypeptide. The catalytic subunits of the a-like DNA polymerase family share regions of sequence homology with the 3'-5' exonuclease active site of DNA polymerase I; in certain a-like DNA polymerases, these regions of homology have been shown to be important for exonuclease activity. This finding has led to the hypothesis that a-like DNA polymerases also contain a distinct 3'-5' exonuclease domain. We have introduced conservative substitutions into a 3'-5' exonuclease active site homology in the gene encoding herpes simplex virus DNA polymerase, an a-like polymerase. Two mutants were severely impaired for viral DNA replication and polymerase activity. The mutants were not detectably affected in the ability of the polymerase to interact with its accessory protein, UL42, or to colocalize in infected cell nuclei with the major viral DNA-binding protein, ICP8, suggesting that the mutation did not exert global effects on protein folding. The results raise the possibility that there is a fundamental difference between a-like DNA polymerases and E. coli DNA polymerase I, with less distinction between 3'-5' exonuclease and polymerase functions in a-like DNA polymerases. Mutagenesis Exo
Evaluation of nest habitat, site preferences and architecture of the critically endangered White-bellied Heron Ardea insignis in Bhutan

Summary This research evaluated the nesting habitat, nest-site preferences, and nest architecture of the critically endangered White-bellied Heron Ardea insignis in Bhutan. There are fewer than 60 wild birds left in the world, distributed in Bhutan, India, and Myanmar with fewer than five active breeding pairs in Bhutan. From 2003 to 2018, 20 successful and two unsuccessful nests were located from which at least 76 juveniles were expected to have fledged. The population in Bhutan has remained at 22–30 individuals for the last decade. Site-specific data were collected from 22 nests, and additional vegetation and environmental data were collected from 14 nests and random sites. We used 20-m diameter circular plots to evaluate the site preferences. Ground vegetation, litter and rock cover were evaluated using four 1-m2 quadrats in both nest and random sites. Nesting habitat was analysed to compare characteristics of nesting sites to random sites. Our results suggest that the White-bellied Heron builds a simple platform nest within average distance of 74 m from water bodies on the tallest isolated trees at an average height of 18.3 m on an elevated site with a clear overview of surroundings and are sensitive to even slight disturbance. Our results also suggest that the bird has a preference for an east-facing aspect at an average slope of approximately 40° between the altitudes of 400–1,450 m. Our observations also suggest that the bird has abandoned all nesting sites used prior to 2015, and the frequency of nest re-use has decreased. Protecting each nest site from hazards, avoiding disturbance, maintaining safe feeding habitats and flight routes are essential to ensure continued breeding in current sites and survival of this population. Further research to better understand the habitat requirements for the White-bellied Heron is vital.
Production of interspecific hybrids between Japanese gentians and wild species of Gentiana

Wide hybridization, which is a powerful tool to broaden genetic variation, has been used in breeding of many crops. However, in ornamental gentian few wide hybridizations have been reported. Interspecific hybridizations between two gentian cultivated species (Gentiana scabra and G. triflora) and 11 wild species, which were classified in five sections, were carried out using ovule culture. When G. scabra was used as a female parent, normal seedlings and hybrid plants were obtained from eight and five interspecific combinations, respectively. The yield of seedling produced from ovule culture depended on interspecific combinations, ranging from 0.3 to 427.7 normal seedling per flower. In the hybridization of G. triflora with five wild species, normal seedlings and plants were produced in five and four interspecific combinations, respectively. The yield of normal seedling ranging from 0.4 to 228.3 was different between not only interspecific combinations but also reciprocal crosses. Two cultivated species are classified in sect. Pneumonanthe, and successful production of hybrids was obtained from the hybridization with species classified in sections Pneumonanthe or Cruciata. The hybrid nature of the produced plants was confirmed by molecular marker and morphology. The production of interspecific hybrids opens a novel prospect in ornamental gentian breeding.
The accumulation of chloroplast small RNAs in unicellular alga Chlamydomonas reinhardtii is affected by nitrogen deprivation

Small RNAs generated from the chloroplast genome may play a role in gene regulation. Given that chloroplast function is affected by nitrogen deprivation, there is yet an attempt to link chloroplast small RNAs to this stress condition. This study aims to determine the response of chloroplast small RNAs under nitrogen deprivation and their putative mode of action. A comparative transcriptomic approach was carried out to analyze the differential accumulation of chloroplast small RNAs from Chlamydomonas reinhardtii cells grown in nitrogen-deprived versus nitrogen-based medium. A total of 101 chloroplast small RNA candidates were successfully annotated. Growth in nitrogen-deprived medium revealed 17 significantly upregulated and 12 downregulated chloroplast small RNAs. These chloroplast small RNAs originated from different genomic locations such as untranslated, intergenic or antisense regions as well as the ends of tRNA and rRNA genes. The differentially accumulated csRNAs from 3’-untranslated regions were all upregulated. In contrast, the csRNAs from the ends of tRNA and rRNA genes were all downregulated during nitrogen deprivation. Fluctuations of the chloroplast small RNA levels indicated their importance in the chloroplasts during changes in nitrogen levels. The primary sequences of three selected chloroplast small RNA were found to be conserved in the chloroplast genomes of a few microalgae, again reflecting their functional importance. The findings from this study provided new insights into the involvement of non-coding RNAs in chloroplast during metabolic stress.
Improved protein structure prediction using predicted interresidue orientations

Significance Protein structure prediction is a longstanding challenge in computational biology. Through extension of deep learning-based prediction to interresidue orientations in addition to distances, and the development of a constrained optimization by Rosetta, we show that more accurate models can be generated. Results on a set of 18 de novo-designed proteins suggests the proposed method should be directly applicable to current challenges in de novo protein design. The prediction of interresidue contacts and distances from coevolutionary data using deep learning has considerably advanced protein structure prediction. Here, we build on these advances by developing a deep residual network for predicting interresidue orientations, in addition to distances, and a Rosetta-constrained energy-minimization protocol for rapidly and accurately generating structure models guided by these restraints. In benchmark tests on 13th Community-Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP13)- and Continuous Automated Model Evaluation (CAMEO)-derived sets, the method outperforms all previously described structure-prediction methods. Although trained entirely on native proteins, the network consistently assigns higher probability to de novo-designed proteins, identifying the key fold-determining residues and providing an independent quantitative measure of the “ideality” of a protein structure. The method promises to be useful for a broad range of protein structure prediction and design problems.
A Germinal Center-Associated Microenvironmental Signature Reflects Malignant Phenotype and Outcome of Diffuse Large B-cell Lymphoma

Diffuse large B-cell lymphoma (DLBCL) is the most common B-cell malignancy with varying prognosis after the gold standard rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP). Several prognostic models have been established by focusing primarily on characteristics of lymphoma cells themselves including cell-of-origin, genomic alterations, and gene/protein expressions. However, the prognostic impact of lymphoma microenvironment and its association with characteristics of lymphoma cells are not fully understood. Using highly-sensitive transcriptome profiling of untreated DLBCL tissues, we here assess the clinical impact of lymphoma microenvironment on the clinical outcomes and pathophysiological, molecular signatures in DLBCL. The presence of normal germinal center (GC)-microenvironmental cells, including follicular T cells, macrophage/dendritic cells, and stromal cells, in lymphoma tissue indicates a positive therapeutic response. Our prognostic model, based on quantitation of transcripts from distinct GC-microenvironmental cell markers, clearly identified patients with graded prognosis independently of existing prognostic models. We observed increased incidences of genomic alterations and aberrant gene expression associated with poor prognosis in DLBCL tissues lacking GC-microenvironmental cells relative to those containing these cells. These data suggest that the loss of GC-associated microenvironmental signature dictates clinical outcomes of DLBCL patients reflecting the accumulation of “unfavorable” molecular signatures.
Protein structure featurization via standard image classification neural networks

Many applications in the biomedical domain involve the detailed molecular and functional characterization of macro-molecules such as proteins. Where possible, this involves the knowledge of detailed 3D coordinates of every atom within a protein. At the same time, machine learning has become the basis of much innovation within this domain in recent years. There are, however, a few challenges in applying machine learning to 3D protein structures, such as variability in size and high dimensionality of the data. It would therefore be beneficial to be able to map every protein structure to a smaller fixed-dimensional representation that is directly learned from the structure without manual curation. In addition, it would be valuable for biomedical researchers if such approaches would require little method development and instead draw from cutting-edge research such as image classification via deep neural networks. Here, such an approach is outlined that first re-formats protein structures as 2D color images and then applies off-the-shelf neural networks for image classification. It is shown that such neural networks can be trained to effectively encode the CATH protein classification database and that feature vectors extracted from such networks, once trained, can be transferred to a completely new task that is likely to benefit from molecular protein information, namely that of small molecule binding.
The complete chloroplast genome of Mahonia eurybracteata subsp. Ganpinensis (H.Lév.) T. S. Ying & Boufford (Berberidaceae)

Abstract Mahonia eurybracteata subsp. ganpinensis (H.Lév.) T.S. Ying & Boufford. is an evergreen shrub of Berberidaceae and has the potentials for horticultural and medicinal development. In the present paper, the complete chloroplast genome of Mahonia eurybracteata subsp. ganpinensis (H.Lév.) T.S. Ying & Boufford. was sequenced. The complete chloroplast genome was 165,562 bp in length, containing a large single copy region (73,394 bp), a small single copy region (18,698 bp) and two inverted repeat regions (36,735 bp). The genome consisted of 113 genes, including 79 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Phylogenetic analysis showed that M. eurybracteata subsp. ganpinensis and M. bealei were firstly clustered into a branch and the two Mahonia species were most closely related to the genus Berberis of Berberidaceae.
Zika virus infects pericytes in the choroid plexus and enters the central nervous system through the blood-cerebrospinal fluid barrier

Zika virus (ZIKV) can infect and cause microcephaly and Zika-associated neurological complications in the developing fetal and adult brains. In terms of pathogenesis, a critical question is how ZIKV overcomes the barriers separating the brain from the circulation and gains access to the central nervous system (CNS). Despite the importance of ZIKV pathogenesis, the route ZIKV utilizes to cross CNS barriers remains unclear. Here we show that in mouse models, ZIKV-infected cells initially appeared in the periventricular regions of the brain, including the choroid plexus and the meninges, prior to infection of the cortex. The appearance of ZIKV in cerebrospinal fluid (CSF) preceded infection of the brain parenchyma. We show that ZIKV infects pericytes in the choroid plexus, and that ZIKV infection of pericytes is dependent on AXL receptor tyrosine kinase. Using an in vitro Transwell system, we highlight the possibility of ZIKV to move from the blood side to CSF side, across the choroid plexus epithelial layers, via a nondestructive pathway (e.g., transcytosis). Finally, we demonstrate that brain infection is significantly attenuated by neutralization of the virus in the CSF, indicating that ZIKV in the CSF at the early stage of infection might be responsible for establishing a lethal infection of the brain. Taken together, our results suggest that ZIKV invades the host brain by exploiting the blood-CSF barrier rather than the blood-brain barrier. AUTHOR SUMMARY Zika virus invades the human brains and causes Zika-associated neurological complications; however, the mechanism(s) by which Zika virus accesses the central nerves system remain unclear. Understanding of the cellular and molecular mechanisms will shed light on development of novel therapeutic and prophylactic targets for Zika virus and other neurotropic viruses. Here we use in vivo and in vitro models to understand how Zika virus enters the brain. In mouse models, we found that Zika virus infects pericytes in the choroid plexus at very early stages of infection and neutralization of Zika virus in the cerebrospinal fluid significantly attenuate the brain infection. Further we show evidence that Zika virus can cross the epithelial cell layers in the choroid plexus from the blood side. Our research highlights that ZIKV invades the host brain by exploiting the blood-CSF barrier rather than the blood-brain barrier.
OpenSim Moco: Musculoskeletal optimal control

Musculoskeletal simulations of movement can provide insights needed to help humans regain mobility after injuries and design robots that interact with humans. Here, we introduce Open-Sim Moco, a software toolkit for optimizing the motion and control of musculoskeletal models built in the OpenSim modeling and simulation package. OpenSim Moco uses the direct collocation method, which is often faster and can handle more diverse problems than other methods for musculoskeletal simulation but requires extensive technical expertise to implement. Moco frees researchers from implementing direct collocation themselves, allowing them to focus on their scientific questions. The software can handle the wide range of problems that interest biomechanists, including motion tracking, motion prediction, parameter optimization, model fitting, electromyography-driven simulation, and device design. Moco is the first musculoskeletal direct collocation tool to handle kinematic constraints, which are common in musculoskeletal models. To show Moco’s abilities, we first solve for muscle activity that produces an observed walking motion while minimizing muscle excitations and knee joint loading. Then, we predict a squat-to-stand motion and optimize the stiffness of a passive assistive knee device. We designed Moco to be easy to use, customizable, and extensible, thereby accelerating the use of simulations to understand human and animal movement.
The complete chloroplast genome sequence of Pellacalyx yunnanensis: an endangered species in China

Abstract Pellacalyx yunnanensis is an endangered plant species occurring in Yunnan province of China. The first complete chloroplast genome (cpDNA) sequence of P. yunnanensis was determined from Illumina HiSeq pair-end sequencing data in this study. The cpDNA is 163,743 bp in length, contains a large single-copy region (LSC) of 91,075 bp and a small single-copy region (SSC) of 18,668 bp, which were separated by a pair of inverted repeats (IR) regions of 27,000 bp. The genome contains 128 genes, including 83 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content of the whole genome is 35.7%, and the corresponding values of the LSC, SSC, and IR regions are 33.0%, 29.6%, and 42.3%, respectively. Further phylogenomic analysis showed that P. yunnanensis clustered in a unique clade in family Rhizophoraceae.
Growth and Development of Basil Species in Response to Temperature

Basil (Ocimum sp.) is the most popular fresh culinary herb, but the effects of air temperature on growth and development of basil have not been well characterized. Our objective was to quantify the effects of air temperature on growth and development of three basil species. Seedlings of sweet basil (Ocimum basilicum ‘Nufar’), holy basil (O. tenuiflorum), and lemon basil (O. ×citriodorum ‘Lime’ and O. basilicum ‘Sweet Dani’) were placed in five different growth chambers with target air temperatures of 11, 17, 23, 29, or 35 °C. After 3 weeks, chlorophyll fluorescence (Fv/Fm), plant height, node and branch number, fresh and dry weight, and flowering data were recorded. For all species, Fv/Fm increased as temperature increased to 17 or 23 °C, then plateaued, whereas height increased with temperature to 23 or 29 °C. Also, the percentage of plants with flowers or flower buds increased with temperature to 17 or 23 °C for all species, with the exception of sweet basil, of which all plants were vegetative and node appearance rate was calculated. Sweet basil node appearance increased from 0.03 to 0.30 node/day as the temperature increased from 11 to 29 °C. Fresh weight gain increased with increasing temperature to 29 °C, but then decreased at 35 °C. Data from plants grown within the linear air temperature range were used to develop models for calculating the base temperature (Tb) and predicting growth in response to air temperature. These models can be applied by commercial producers to schedule crops and predict yields.