Biology subjects

Zhang, D.

Publications and source records attributed to Zhang, D..

At least 451 records · Page 25Linked to original sources

bioRxiv2019

Source of additive genetic variance of important traits

Fishers fundamental theorem of natural selection predicts no additive variance of fitness in a natural population. Consistently, observations in a variety of wild populations show virtually no narrow-sense heritability (h2) for traits important to fitness. However, counterexamples are occasionally reported, calling for a deeper understanding on the evolution of additive variance. In this study we propose adaptive divergence followed by population admixture as a source of the additive genetic variance of evolutionarily important traits. We experimentally tested the hypothesis by examining a panel of ~1,000 yeast segregants produced by a hybrid of two yeast strains that experienced adaptive divergence. We measured over 400 yeast cell morphological traits and found a strong positive correlation between h2 and evolutionary importance. Because adaptive divergence followed by population admixture could happen constantly, particularly in some species such as humans, the finding reconciles the observation of abundant additive variances in evolutionarily important traits with Fishers fundamental theorem of natural selection. It also suggests natural selection may effectively promote rather than suppress additive genetic variance in species with wide geographic distribution and strong migratory capacity.

evolutionary biology↗

bioRxiv2019

Germline RNA helicases couple RNA binding to P granule assembly at nuclear periphery

P granules are phase-separated liquid droplets that play important roles in the maintenance of the germ cell fate in C. elegans. The localization and formation of P granules are highly dynamic, but mechanisms that regulate such processes remain poorly understood. Here we show that germline RNA helicases (GLHs) control the formation and disassembly of germ granules through their binding and release of RNAs, respectively. In addition, the FGG repeats in the GLHs promote the formation of germ granules at the perinucleus. Proteomic analyses of a mutation that traps RNA-bound GLH-1 complex revealed transient interactions of GLH-1 with several Argonautes and RNA binding proteins. Finally, we found that defects in perinuclear P granule formation correlate with the fertility defects observed in various GLH mutants. Together, our results highlight the versatile roles of RNA helicases in controlling the formation of liquid droplets in space and time.

cell biology↗

bioRxiv2019

Enzyme-free synthesis of natural phospholipids in water

All living organisms synthesize phospholipids as the primary constituent of their cell membranes. While phospholipids can spontaneously self-assemble in water to form membrane-bound vesicles, their aqueous synthesis requires pre-existing membrane-embedded enzymes. This limitation has led to models in which the first cells used simpler types of membrane building blocks and has hampered integration of phospholipid synthesis into artificial cells. Here we demonstrate that a combination of ion pairing and self-assembly of reactants allows high-yielding synthesis of cellular phospholipids in water. Acylation of 2-lysophospholipids using cationic thioesters occurs in mildly alkaline solutions resulting in the formation of cell-like membranes. A variety of membrane-forming natural phospholipids can be synthesized. Membrane formation takes place in water from natural alkaline sources, such as soda lakes and hydrothermal oceanic vents. When formed vesicles are transferred to more acidic solutions, electrochemical proton gradients are spontaneously established and maintained.

biochemistry↗

bioRxiv2019

Ctf4 organizes sister replisomes and Pol α into a replication factory

The current view is that eukaryotic replisomes are independent. Here we show that Ctf4 tightly dimerizes CMG helicase, with an extensive interface involving Psf2, Cdc45, and Sld5. Interestingly, Ctf4 binds only one Pol -primase. Thus, Ctf4 may have evolved as a trimer to organize two helicases and one Pol -primase into a replication factory. In the 2CMG-Ctf43-1Pol -primase factory model, the two CMGs nearly face each other, placing the two lagging strands toward the center and two leading strands out the sides. The single Pol -primase is centrally located and may prime both sister replisomes. The Ctf4-coupled-sister replisome model is consistent with cellular microscopy studies revealing two sister forks of an origin remain attached and are pushed forward from a protein platform. The replication factory model may facilitate parental nucleosome transfer during replication.

biochemistry↗

bioRxiv2019

DNA unwinding mechanism of a eukaryotic replicative CMG helicase

High-resolution structures have not been reported for replicative helicases at a replication fork at atomic resolution, a prerequisite to understand the unwinding mechanism. The eukaryotic replicative CMG helicase contains a Mcm2-7 motor ring, with the N-tier ring in front and the C-tier motor ring behind. The N-tier ring is structurally divided into a zinc finger (ZF) sub-ring followed by the OB fold ring. Here we report the cryo-EM structure of CMG on forked DNA at 3.9 [A], revealing that parental DNA enters the ZF sub-ring and strand separation occurs at the bottom of the ZF sub-ring, where the lagging strand is blocked and diverted sideways by OB hairpin-loops of Mcm3, Mcm4, Mcm6, and Mcm7. Thus, instead of employing a separation pin, unwinding is achieved via a \"dam-and-diversion tunnel\" for steric exclusion unwinding. The C-tier motor ring contains spirally configured PS1 and H2I loops of Mcms 2, 3, 5, 6 that translocate on the spirally-configured leading strand, and thereby pull the preceding DNA segment through the diversion tunnel for strand separation.

biochemistry↗

bioRxiv2019

A DNA G-quadruplex/i-motif hybrid

DNA can form many structures beyond the canonical Watson-Crick double helix. It is now clear that noncanonical structures are present in genomic DNA and have biological functions. G-rich G-quadruplexes and C-rich i-motifs are the most well-characterized noncanonical DNA motifs that have been detected in vivo with either proscribed or postulated biological roles. Because of their independent sequence requirements, these structures have largely been considered distinct types of quadruplexes. Here, we describe the crystal structure of the DNA oligonucleotide, d(CCAGGCTGCAA), that self-associates to form a quadruplex structure containing two central antiparallel G-tetrads and six i-motif C-C+ base pairs. Solution studies suggest a robust structural motif capable of assembling as a tetramer of individual strands or as a dimer when composed of tandem repeats. This hybrid structure highlights the growing structural diversity of DNA and suggests that biological systems may harbor many functionally important non-duplex structures.

biochemistry↗

bioRxiv2019

VHUT-cryo-FIB, a method to fabricate frozen-hydrated lamella of tissue specimen for in situ cryo-electron tomography

ABSTACTCryo-electron tomography (cryo-ET) provides a promising technique to study high resolution structures of macromolecules in situ, opening a new era of structural biology. One major bottleneck of this technique is to prepare suitable cryo-lamellas of cell/tissue samples. The emergence of cryo-focused ion beam (cryo-FIB) milling technique provides a good solution of this bottleneck. However, there are still large limitations of using cryo-FIB to prepare cryo-lamella of tissue specimen because the thickness of tissue increases the difficulty of specimen freezing and cryo-FIB milling. Here we report a new workflow, VHUT-cryo-FIB (Vibratome - High pressure freezing - Ultramicrotome Trimming - cryo-FIB), aiming for efficient preparation of frozen hydrated tissue lamella for subsequent cryo-ET data collection. This workflow includes tissue slicing using vibratome, high pressure freezing, ultramicrotome cryo-trimming, cryo-FIB milling and the subsequent cryo-electron microscopy (cryo-EM). The modification of equipment in this workflow is highly eliminated. We developed two strategies with a special cryo-holder tip or carrier for loading cryo-lamella into side entry cryo-holder or Autoloader catridge. We tested this workflow using the tissue sample of rat skeleton muscle and spinach leaf and collected high quality cryo-ET tilt series, which enabled us to obtain an in situ structure of spinach ribosome by sub-tomogram averaging.

biophysics↗

bioRxiv2019

Fast and robust ancestry prediction using principal component analysis

Population stratification (PS) is a major confounder in genome-wide association studies (GWAS) and can lead to false positive associations. To adjust for PS, principal component analysis (PCA)-based ancestry prediction has been widely used. Simple projection (SP) based on principal component loading and recently developed data augmentation-decomposition-transformation (ADP), such as LASER and TRACE, are popular methods for predicting PC scores. However, they are either biased or computationally expensive. The predicted PC scores from SP can be biased toward NULL. On the other hand, since ADP requires running PCA separately for each study sample on the augmented data set, its computational cost is high. To address these problems, we develop and propose two alternative approaches, bias-adjusted projection (AP) and online ADP (OADP). Using random matrix theory, AP asymptotically estimates and adjusts for the bias of SP. OADP uses computationally efficient online singular value decomposition, which can greatly reduce the computation cost of ADP. We carried out extensive simulation studies to show that these alternative approaches are unbiased and the computation times can be 10-100 times faster than ADP. We applied our approaches to UK-Biobank data of 488,366 study samples with 2,492 samples from the 1000 Genomes data as the reference. AP and OADP required 7 and 75 CPU hours, respectively, while the projected computation time of ADP is 2,534 CPU hours. Furthermore, when we only used the European reference samples in the 1000 Genomes to infer sub-European ancestry, SP clearly showed bias, unlike the proposed approaches. By using AP and OADP, we can infer ancestry and adjust for PS robustly and efficiently.

genetics↗

bioRxiv2019

Effects of melatonin on germination and amino acid content in different wheat varieties seeds under polyethylene glycol stress

In this research, the effects of melatonin on germination and amino acid content in wheat (Triticum aestivum L.) seeds under polyethylene glycol (PEG-6000) stress were investigated. The results revealed that 10 M melatonin could aggravate the adverse effects of drought stress on germination percentage, germination index, and germination potential of two wheat varieties (JM22 and HG35). However, 300 M melatonin could obviously alleviate the negative effect of water stress on germination and increase radicle length, radicle number and plumule length of germinated seeds. Principal component analysis showed that amino acid content apparently changed in germination and the variation amplitude was different due to melatonin concentrations and wheat varieties. Lys content in wheat seed under 300 M melatonin plus PEG treatment increased compared with that under PEG. Meanwhile, Lys content was significantly and positively correlated with germination percentage, germination index, germination potential, radicle length, and plumule length, respectively. Our results suggested Lys play an important role in the regulation of melatonin on drought resistance of wheat seed during germination. This may be of value for saving water resources in North China Plain.

physiology↗

bioRxiv2019

Protein interactions of Magnaporthe oryzae protein kinase CK2 and secondary data analysis of a large number of transcriptomes suggest chaperone-like activity is integral to its function

CK2, a serine/threonine (S/T) kinase present in eukaryotic cells is known to have a vast number of substrates. We have recently shown that it localizes to nuclei and at pores between hyphal compartments in M. oryzae. We performed a pulldown-proteomics of M. oryzae CK2 catalytic subunit MoCKa to detect interacting proteins. The MoCKa pulldown was enriched for septa and nucleoli proteins and intrinsically disordered proteins (IDPs) containing a CK2 phosphorylation motif proposed to destabilize and unfold alpha helixes. This points to a function for CK2 phosphorylation and corresponding phosphatase dephosphorylation in the formation of functional protein-protein aggregates and protein-RNA/DNA binding. To test this as widely as possible we used secondary data downloaded from databases from a large range of M. oryzae experiments and also for a relatively closely related plant pathogenic fungus, Fusarium graminearum. We found that CKa expression was strongly positively correlated with S/T phosphatases as well as with disaggregase (HSP104, YDJ1, SSA1) and an autophagy indicating protein (ATG8). The latter points to increased protein aggregate formation at high levels of CKa expression. Our results suggest a general role for CK2 in aggregation and disaggregation of IDPs and their binding to proteins, DNA and RNA interactions.

cell biology↗

bioRxiv2019

Evolutionary decomposition of genetic effects

Genic functions have long been confounded by pleiotropic mutational effects. To understand such genetic effects, we examine HAP4, a well-studied transcription factor in Saccharomyces cerevisiae that functions by forming a tetramer with HAP2, HAP3, and HAP5. Deletion of HAP4 results in highly pleiotropic gene expression responses, some of which are clustered in related cellular processes (clustered effects) while most are distributed randomly across diverse cellular processes (distributed effects). Strikingly, the distributed effects that account for much of HAP4 pleiotropy tend to be non-heritable in a population, suggesting they have little evolutionary consequences. Indeed, these effects are poorly conserved in closely related yeasts. We further show substantial overlaps of clustered effects, but not distributed effects, among the four genes encoding the HAP2/3/4/5 tetramer. This pattern holds for other biochemically characterized yeast protein complexes or metabolic pathways. Examination of a set of cell morphological traits of the deletion lines yields consistent results. Hence, only some gene deletion effects support related biochemical understandings with the rest being pleiotropic and evolutionarily decoupled from the genes normal functions.

genetics↗

bioRxiv2019

Quantitative Personality Predictions from a Brief EEG Recording

The assessment of personality is crucial not only for scientific inquiries but also for real-world applications such as personnel selection. However, most existing ways to quantify personality traits rely on self-reported scales, which are susceptible to biases such as self-presentational concerns. In this study, we propose and evaluate a novel implicit measure of personality that uses machine learning (ML) algorithms to predict an individuals levels in the Big Five personality traits from 5 minutes of electroencephalography (EEG) recordings. Results from a large test sample of 196 volunteers indicated that the personality scores derived from the proposed measure converged significantly with a commonly used questionnaire, predicted behavioral indices and psychological adjustment in a manner similar to self-reported scores, and were relatively stable across time. These evaluations suggest that the proposed measure can serve as a viable alternative to conventional personality questionnaires in practice.

neuroscience↗

bioRxiv2019

Genome analysis and Hi-C assisted assembly of Elaeagnus angustifolia L., a deciduous tree belonging to Elaeagnaceae

Elaeagnus angustifolia L. is a deciduous tree of the Elaeagnaceae family. It is widely used in the study of abiotic stress tolerance in plants and for the improvement of desertification-affected land due to its characteristics of drought resistance, salt tolerance, cold resistance, wind resistance, and other environmental adaptation. Here, we report the complete genome sequencing using the Pacific Biosciences (PacBio) platform and Hi-C assisted assembly of E. angustifolia. A total of 44.27 Gb raw PacBio sequel reads were obtained after filtering out low-quality data, with an average length of 8.64 Kb. And 39.56 Gb clean reads was obtained, with a sequencing coverage of 75x, and Q30 ratio > 95.46%. The 510.71 Mb genomic sequence was mapped to the chromosome, accounting for 96.94% of the total length of the sequence, and the corresponding number of sequences was 269, accounting for 45.83% of the total number of sequences. The genome sequence study of E. angustifolia can be a valuable source for the comparative genome analysis of the Elaeagnaceae family members, and can help to understand the evolutionary response mechanisms of the Elaeagnaceae to drought, salt, cold and wind resistance, and thereby provide effective theoretical support for the improvement of desertification-affected land.

genetics↗

bioRxiv2019

Delta phase resetting mediates non-rhythmic temporal prediction

The phase of neural oscillatory activity aligns to the predicted onset of upcoming stimulation. Whether such phase alignments represent phase resets of underlying neural oscillations or just rhythmically evoked activity, and whether they can be observed in a rhythm-free visual context, however, remains unclear. Here, we recorded the magnetoencephalogram while participants were engaged in a temporal prediction task judging the visual or tactile reappearance of a uniformly moving stimulus. The prediction conditions were contrasted with a control condition to dissociate phase adjustments of neural oscillations from stimulus-driven activity. We observed stronger delta band inter-trial phase consistency (ITPC) in a network of sensory, parietal and frontal brain areas, but no power increase reflecting stimulus-driven or prediction-related processes. Delta ITPC further correlated with prediction performance in the cerebellum and visual cortex. Our results provide evidence that phase alignments of low-frequency neural oscillations underlie temporal predictions in a non-rhythmic visual and crossmodal context.

neuroscience↗

bioRxiv2019

Dysregulated Alternative Splicing Landscape Identifies Intron Retention as a Hallmark and Spliceosome as a Therapeutic Vulnerability in Aggressive Prostate Cancer

Dysregulation of mRNA alternative splicing (AS) has been implicated in development and progression of hematological malignancies. Here we describe the first comprehensive AS landscape in the spectrum of human prostate cancer (PCa) development, progression and therapy resistance. We find that the severity of splicing dysregulation correlates with disease progression and establish intron retention (IR) as a hallmark of PCa stemness and aggressiveness. Systematic interrogation of 274 splicing-regulatory genes (SRGs) uncovers prevalent SRG mutations associated with, mainly, copy number variations leading to mis-expression of ~68% of SRGs during PCa evolution. Consequently, we identify many SRGs as prognostic markers associated with splicing disruption and patient outcome. Interestingly, androgen receptor (AR) controls a splicing program distinct from its transcriptional regulation. The spliceosome modulator, E7107, reverses cancer aggressiveness and abolishes the growth of castration-resistant PCa (CRPC) models. Altogether, we establish aberrant AS landscape caused by dysregulated SRGs as a novel therapeutic vulnerability for CRPC.\n\nStatement of significanceWe present the first comprehensive AS landscape during PCa evolution and link genomic and transcriptional alterations in SRGs to global splicing dysregulation. AR regulates splicing in pri-PCa and CRPC distinct from its transcriptional regulation. Intron retention is a hallmark for and spliceosome represents a therapeutic vulnerability in aggressive PCa.

cancer biology↗

bioRxiv2019

Controlling emulsification for organic solvent-based tissue clearing

Organic solvent-based tissue clearing techniques are hampered by the quenching of fluorescent proteins, partially due to routine complete dehydration. Unexpectedly, we discovered that complete dehydration is unnecessary for organic solvents to clear tissues and that the hidden purpose has been to prevent emulsification. After controlling emulsification of organic solvent-cleared but incompletely dehydrated mouse brain, we achieved sufficient tissue transparency that allowed light-sheet imaging while well-preserving the fluorescence of fluorescent proteins.

neuroscience↗

bioRxiv2019

Integration of eQTL and Parkinson’s disease GWAS data implicates 11 disease genes

Substantial genome-wide association study (GWAS) work in Parkinsons disease (PD) has led to an increasing number of loci shown reliably and robustly to be associated with the increased risk of the disease. Prioritising causative genes and pathways from these studies has proven problematic. Here, we present a comprehensive analysis of PD GWAS data with expression and methylation quantitative trait loci (eQTL/mQTL) using Colocalisation analysis (Coloc) and transcriptome-wide association analysis (TWAS) to uncover putative gene expression and splicing mechanisms driving PD GWAS signals. Candidate genes were further characterised by determining cell-type specificity, weighted gene co-expression (WGNCA) and protein-protein interaction (PPI) networks.\n\nGene-level analysis of expression revealed 5 genes (WDR6, CD38, GPNMB, RAB29, TMEM163) that replicated using both Coloc and TWAS analyses in both GTEx and Braineac expression datasets. A further 6 genes (ZRANB3, PCGF3, NEK1, NUPL2, GALC, CTSB) showed evidence of disease-associated splicing effects. Cell-type specificity analysis revealed that gene expression was overall more prevalent in glial cell-types compared to neurons. The WGNCA analysis showed that NUPL2 is a key gene in 3 modules implicated in catabolic processes related with protein ubiquitination (protein ubiquitination (p=7.47e-10) and ubiquitin-dependent protein catabolic process (p = 2.57e-17) in nucleus accumbens, caudate and putamen, while TMEM163 and ZRANB3 were both important in modules indicating regulation of signalling (p=1.33e-65] and cell communication (p=7.55e-35) in the frontal cortex and caudate respectively. PPI analysis and simulations using random networks demonstrated that the candidate genes interact significantly more with known Mendelian PD and parkinsonism proteins than would be expected by chance. The proteins core proteins this network were enriched for regulation of the ERBB receptor tyrosine protein kinase signalling pathways.\n\nTogether, these results point to a number of candidate genes and pathways that are driving the associations observed in PD GWAS studies.

neuroscience↗

bioRxiv2019

The Catalytic Core of DEMETER Guides Active DNA Demethylation in Arabidopsis

The Arabidopsis DEMETER (DME) DNA glycosylase demethylates the maternal genome in the central cell prior to fertilization, and is essential for seed viability. DME preferentially targets small transposons that flank coding genes, influencing their expression and initiating plant gene imprinting. DME also targets intergenic and heterochromatic regions, and how it is recruited to these differing chromatin landscapes is unknown. The C-terminal DME catalytic core consists of three conserved regions required for catalysis in vitro. We show that the catalytic core of DME guides active demethylation at endogenous targets, rescuing the developmental and genomic hypermethylation phenotypes of DME mutants. However, without the N-terminus, heterochromatin demethylation is significantly impeded, and abundant CG-methylated genic sequences are ectopically demethylated. We used comparative analysis to reveal that the conserved DME N-terminal domains are only present in the flowering plants, whereas the domain architecture of DME-like proteins in non-vascular plants mainly resembles the catalytic core, suggesting that it might represent the ancestral form of the 5mC DNA glycosylase found in all plant lineages. We propose a bipartite model for DME protein action and suggest that the DME N-terminus was acquired late during land plant evolution to improve specificity and facilitate demethylation at heterochromatin targets.

plant biology↗