ENCODE

Puromycin-sensitive aminopeptidases have long been implicated in cell-cycle regulation, but the mechanism remains unknown. Here we show that mutations in the gene encoding the C. elegans puromycin-sensitive aminopeptidase, PAM-1 , cause chromosome segregation defects and an elongated mitosis in the one-cell embryo. Depleting a known regulator of the spindle assembly checkpoint (SAC), MDF-2 (MAD2 in humans), restores normal mitotic timing to pam-1 mutants but exacerbates the chromosome segregation defects. Thus, PAM-1 is required for proper attachment of chromosomes to the mitotic spindle and its absence triggers the SAC...

Glycosyl-phosphatidylinositol (GPI) anchored proteins are implicated in remodeling of the yeast cell wall during growth and division. Schizosaccharomyces pombe proteins, Psu1 , Dfg501 , and Dfg502 are predicted GPI anchored proteins with likely cell wall modifying activity. Here, we isolated and characterized null and temperature-sensitive alleles that will allow further analysis of the function of these proteins and S. pombe cell wall formation. Our data confirm that Psu1 is necessary for cell separation, maintaining proper cell shape, and viability...

Rare, germline loss-of-function variants in a handful of genes that encode DNA repair proteins have been shown to be associated with epithelial ovarian cancer with a stronger association for the high-grade serous hiostotype. The aim of this study was to collate exome sequencing data from multiple epithelial ovarian cancer case cohorts and controls in order to systematically evaluate the role of coding, loss-of-function variants across the genome in epithelial ovarian cancer risk. We assembled exome data for a total of 2,573 non-mucinous cases (1,876 high-grade serous and 697 non-high grade serous) and 13,925 controls...

Pathogens encapsulate or encode their own suite of enzymes to facilitate replication in the host. The pathogen-derived enzymes possess specialized activities that are essential for pathogen replication and have naturally been candidates for drug targets. Phenotypic assays detecting the activities of pathogen-derived enzymes and characterizing their inhibition under drugs offer an opportunity for pathogen detection, drug resistance testing for individual patients, and as a research tool for new drug development...

INTRODUCTION: Bacillus amyloliquefaciens DGL1, isolated from the arid sandy areas in Dagler, Qinghai Province, China, promotes the growth of Avena sativa variety "Qing Yan 1". METHODS: To elucidate the transcriptomic changes in the oat root system following interaction with DGL1 and to reveal the molecular mechanism by which DGL1 promotes oat growth, treatment and control groups of oat roots at 2, 4, 8, and 12 h after inoculation with a suspension of strain DGL1 were analyzed using Illumina high-throughput transcriptome sequencing technology...

Brain state classification by applying deep learning techniques on neuroimaging data has become a recent topic of research. However, unlike domains where the data is low dimensional or there are large number of available training samples, neuroimaging data is high dimensional and has few training samples. To tackle these issues, we present a sparse feedforward deep neural architecture for encoding and decoding the structural connectome of the human brain. We use a sparsely connected element-wise multiplication as the first hidden layer and a fixed transform layer as the output layer...

UNLABELLED: Acanthopanax gracilistylus is a deciduous plant in the family Araliaceae, which is commonly used in Chinese herbal medicine, as the root bark has functions of nourishing the liver and kidneys, removing dampness and expelling wind, and strengthening the bones and tendons. Kaurenoic acid (KA) is the main effective substance in the root bark of A. gracilistylus with strong anti-inflammatory effects. To elucidate the KA biosynthesis pathway, second-generation (DNA nanoball) and third-generation (Pacific Biosciences) sequencing were performed to analyze the transcriptomes of the A...

Cystinosis is a rare autosomal recessive disorder caused by mutations in the CTNS gene that encodes cystinosin, a ubiquitous lysosomal cystine/H+ antiporter. The hallmark of the disease is progressive accumulation of cystine and cystine crystals in virtually all tissues. At the kidney level, human cystinosis is characterized by the development of renal Fanconi syndrome and progressive glomerular and interstitial damage leading to end-stage kidney disease in the second or third decade of life. The exact molecular mechanisms involved in the pathogenesis of renal disease in cystinosis are incompletely elucidated...

BACKGROUND AND AIMS: X lymphoproliferative syndrome type 1 (XLP1) is a rare inborn error of immunity due to mutations of SH2D1A , encoding for slam-associated protein (SAP). The clinical phenotype includes severe mononucleosis, hemophagocytic lymphohistiocytosis (HLH), and B-cell lymphomas. METHODS: We report the case of a child affected with XLP1 who presented with an incomplete HLH, triggered by Epstein-Barr virus (EBV) and treated with rituximab, involving orbits and paranasal sinuses...

B cell transcriptomic signatures hold promise for the early prediction of vaccine-induced humoral immunity and vaccine protective efficacy. We performed a longitudinal study in 232 healthy adult participants before/after a 3rd dose of MMR (MMR3) vaccine. We assessed baseline and early transcriptional patterns in purified B cells and their association with measles-specific humoral immunity after MMR vaccination using two analytical methods ("per gene" linear models and joint analysis). Our study identified distinct early transcriptional signatures/genes following MMR3 that were associated with measles-specific neutralizing antibody titer and/or binding antibody titer...

Three-dimensional stacks acquired with confocal or two-photon microscopy are crucial for studying neuroanatomy. However, high-resolution image stacks acquired at multiple depths are time-consuming and susceptible to photobleaching. In vivo microscopy is further prone to motion artifacts. In this work, we suggest that deep neural networks with sine activation functions encoding implicit neural representations (SIRENs) are suitable for predicting intermediate planes and correcting motion artifacts, addressing the aforementioned shortcomings...

Automatic and precise polyp segmentation in colonoscopy images is highly valuable for diagnosis at an early stage and surgery of colorectal cancer. Nevertheless, it still posed a major challenge due to variations in the size and intricate morphological characteristics of polyps coupled with the indistinct demarcation between polyps and mucosas. To alleviate these challenges, we proposed an improved dual-aggregation polyp segmentation network, dubbed Dua-PSNet, for automatic and accurate full-size polyp prediction by combining both the transformer branch and a fully convolutional network (FCN) branch in a parallel style...

The development of efficient genetically encoded indicators and actuators has opened up the possibility of reading and manipulating neuronal activity in living tissues with light. To achieve precise and reconfigurable targeting of large numbers of neurons with single-cell resolution within arbitrary volumes, different groups have recently developed all-optical strategies based on two-photon excitation and spatio-temporal shaping of ultrashort laser pulses. However, such techniques are often complex to set up and typically operate at a single wavelength only...

The two-photon all-optical physiology system has attracted great interest in deciphering neuronal circuits in vivo , benefiting from its advantages in recording and modulating neuronal activities at single neuron resolutions. However, the interference, or crosstalk, between the imaging and photostimulation beams introduces a significant challenge and may impede the future application of voltage indicators in two-photon all-optical physiology system. Here, we propose the time multiplexed excitation method to distinguish signals from neuronal activities and crosstalks from photostimulation...

Immune evasion is critical for fungal virulence. However, how the human opportunistic pathogen Candida glabrata ( Cg ) accomplishes this is unknown. Here, we present the first genome-wide nucleosome map of the macrophage-internalized Cg consisting of ∼12,000 dynamic and 70,000 total nucleosomes. We demonstrate that CgSnf2 (SWI/SNF chromatin remodeling complex-ATPase subunit)-mediated chromatin reorganization in macrophage-internalized Cg upregulates and downregulates the immunosuppressive seven-gene mannosyltransferase-cluster ( CgMT-C ) and immunostimulatory cell surface adhesin-encoding EPA1 gene, respectively...

Collagen is a major component of the tissue matrix, and soybean can regulate the tissue immune response. Both materials have been used to fabricate biomaterials for tissue repair. In this study, adult and fetal human astrocytes were grown in a soy protein isolate (SPI)-collagen hybrid gel or on the surface of a cross-linked SPI-collagen membrane. Hybrid materials reduced the cell proliferation rate compared to materials generated by collagen alone. However, the hybrid materials did not significantly change the cell motility compared to the control collagen material...

Mitochondria have multiple functions such as supplying energy, regulating the redox status, and producing proteins encoded by an independent genome. They are closely related to the physiology and pathology of many organs and tissues, among which the brain is particularly prominent. The brain demands 20% of the resting metabolic rate and holds highly active mitochondrial activities. Considerable research shows that mitochondria are closely related to brain function, while mitochondrial defects induce or exacerbate pathology in the brain...

BACKGROUND: Repressor element 1 (RE1) silencing transcription factor (REST) is a transcriptional repressor abundantly expressed in aging human brains. It is known to regulate genes associated with oxidative stress, inflammation, and neurological disorders by binding to a canonical form of sequence motif and its non-canonical variations. Although analysis of genomic sequence motifs is crucial to understand transcriptional regulation by transcription factors (TFs), a comprehensive characterization of various forms of RE1 motifs in human cell lines has not been performed...

Klebsiella pneumoniae is a Gram-negative Enterobacteriaceae that is classified by the World Health Organisation (WHO) as a Priority One ESKAPE pathogen. South and Southeast Asian countries are regions where both healthcare associated infections (HAI) and community acquired infections (CAI) due to extended-spectrum β-lactamase (ESBL)-producing and carbapenem-resistant K. pneumoniae (CRKp) are of concern. As K. pneumoniae can also exist as a harmless commensal, the spread of resistance genotypes requires epidemiological vigilance...

BACKGROUND: Leaf rust (LR) is among the most destructive fungal diseases of rye (Secale cereale L.). Despite intensive research using various analytical and methodological approaches, such as quantitative trait locus (QTL) mapping, candidate gene expression analysis, and transcriptome sequencing, the genetic basis of the rye immune response to LR remains unclear. RESULTS: A genome-wide association study was employed to detect QTLs controlling the immune response to LR of rye...