Biology subjects

Wu, J.

Publications and source records attributed to Wu, J..

At least 883 records · Page 49Linked to original sources

bioRxiv2018

Genome-wide survey and expression analysis of the SLAC/SLAH gene family in pear (Pyrus bretschneideri) and other members of the Rosaceae

S-type anion channels (SLAC/SLAHs), which play important roles in plant anion (such as nitrate and chloride) transport, growth and development, abiotic stress responses and hormone signaling. However, there is far less information about this family in Rosaceae species. We performed a genome-wide analysis and identified SLAC/SLAH gene family members in pear (Pyrus bretschneideri) and four other species of Rosaceae (Malus domestica, Prunus persica, Fragaria vesca and Prunus mume). A total of 21 SLAC/SLAH genes were identified from the five Rosaceae species. Based on the structural characteristics and a phylogenetic analysis of these genes, the SLAC/SLAH gene family could be classified into three main groups (I, II and III). The evolutionary analysis showed that the SLAC/SLAH gene family was comparatively conserved during the evolution of Rosaceae species. Transcriptome data demonstrated that PbrSLAC/SLAH genes were detected in all parts of the pear. However, PbrSLAC1 showed a higher expression level in leaf, while PbrSLAH2/3 was mainly expressed in roots. In addition, PbrSLAC/SLAH genes were only located on the plasma membrane in transient expression experiments in Arabidopsis protoplasts cells. These results provide valuable information that increases our understanding of the evolution, expression and functions of the SLAC/SLAH gene family in higher plants.

bioinformatics↗

bioRxiv2018

Large-scale gene losses underlie the genome evolution of parasitic plant Cuscuta australis

Dodders (Cuscuta spp., Convolvulaceae) are globally distributed root- and leafless parasitic plants that parasitize a wide range of hosts. The physiology, ecology, and evolution of these obligate parasites are still poorly understood. A high-quality reference genome (size 266.74 Mb and contig N50 of 3.63 Mb) of Cuscuta australis was assembled. Our analyses reveal that Cuscuta experienced accelerated evolution, and Cuscuta and the convolvulaceous morning glory (Ipomoea) shared a common whole-genome triplication event before their divergence. Importantly, C. australis genome harbors only 19805 protein-coding genes, and 11.7% of the conserved orthologs in autotrophic plants are lost in C. australis. Many of these gene loss events likely result from the plants parasitic lifestyle and large changes in its body plan. Moreover, comparison of the gene expression patterns in Cuscuta prehaustoria/haustoria and various tissues of closely related autotrophic plants suggests that Cuscuta haustorium genes largely evolved from roots. The C. australis genome provides important resources for studying the evolution of parasitism, regressive evolution, and evo-devo in plant parasites.

genomics↗

bioRxiv2018

Time-dependent mnemonic vulnerability induced by new-learning

Reactivation renders consolidated memory labile again, and the ensuing temporary reconsolidation process is highly susceptible to mnemonic modification. Here, we show that memories in such an unstable state could be reprogrammed by sheer behavioral means, bypassing the need for pharmacological intervention. In two experiments using a \"face-location associationc\" paradigm in which participants experienced a \"Learning - New-learning - Final-test\" programme, we demonstrate that reactivated memory traces were robustly hampered when the new learning was strategically administered within a critical 20-minute time window. Using fMRI, we further advance our theoretical understanding that this lability can be mechanistically explained by the differential activation in the hippocampal-amygdala memory system implicated by the new-learning whereas the mnemonic intrusion caused by newly learned memories is efficaciously reconciled by the left inferior frontal gyrus. Our findings provide important implications for educational and clinical practices in devising effective strategies for memory integration.

neuroscience↗

bioRxiv2018

Characterization of Diverse Homoserine Lactone Synthases in Escherichia coli

Quorum sensing networks have been identified in over one hundred bacterial species to date. A subset of these networks regulate group behaviors, such as bioluminescence, virulence, and biofilm formation, by sending and receiving small molecules called homoserine lactones (HSLs). Bioengineers have incorporated quorum sensing pathways into genetic circuits to connect logical operations. However, the development of higher-order genetic circuitry is inhibited by crosstalk, in which one quorum sensing network responds to HSLs produced by a different network. Here, we report the construction and characterization of a library of ten synthases including some that are expected to produce HSLs that are incompatible with the Lux pathway, and therefore show no crosstalk. We demonstrated their function in a common lab chassis, Escherichia coli BL21, and in two contexts, liquid and solid agar cultures, using decoupled Sender and Receiver pathways. We observed weak or strong stimulation of a Lux Receiver by longer-chain or shorter-chain HSL-generating Senders, respectively. We also considered the under-investigated risk of unintentional release of incompletely deactivated HSLs in biological waste. We found that HSL-enriched media treated with bleach is still bioactive, while autoclaving deactivates LuxR induction. This work represents the most extensive comparison of quorum sensing synthases to date and greatly expands the bacterial signaling toolkit while recommending practices for disposal based on empirical, quantitative evidence.

synthetic biology↗

bioRxiv2018

Verified the effectiveness of AsCpf1 system in a variety of vertebrate species

CRISPR/Cpf1 system is a novel genomic editing tool. Because of its more sophisticated components, and lower off-target rate, it has the potential to become a better gene-editing tool. Previous reports showed that CRISPR/Cpf1 could work effectively in multiple species. But our data show that AsCpf1 activity has a big difference in different vertebrates. Using in vitro experiments, we finally learned that the difference between species is due to temperature.

developmental biology↗

bioRxiv2018

Crystallizing the Parkinson’s Disease Protein LRRK2 Under Microgravity Conditions

Mutations in the gene coding for leucine-rich repeat kinase 2 (LRRK2) are a considerable cause for Parkinsons disease (PD). However, the high- resolution 3D structure of the protein is still lacking. This structure will not only help to understand PD etiology but will also enable rational drug design. We have established a reliable method to produce LRRK2 crystals for the first time. However, the limited resolution of the diffraction data prevented structure determination using crystallographic methods. Herein we describe our efforts to improve the crystal quality by crystallizing under microgravity conditions aboard the International Space Station (ISS). Our method features diffusive sample mixing in capillaries and controlled crystal formation by transporting the samples in a frozen state. The crystallisation was successfully repeated under microgravity conditions. However, comparison of earth-grown and microgravity-grown LRRK2 crystals did not reveal any differences in diffraction quality. Here we present the established protocol and our experience adapting crystallization condition to the requirements necessary for successful crystallization of large and sensitive biomolecules under microgravity.

biochemistry↗

bioRxiv2018

Activity of Antimicrobial Peptides Decreases with Increased Cell Membrane Crossing Free Energy Cost

Antimicrobial peptides (AMPs) are a promising alternative to mitigating bacterial infections in light of increasing bacterial resistance to antibiotics. However, predicting, understanding, and controlling the antibacterial activity of AMPs remains a significant challenge. While peptide intramolecular interactions are known to modulate AMP antimi-crobial activity, peptide intermolecular interactions remain elusive in their impact on peptide bioactivity. Herein, we test the relationship between AMP intermolecular interactions and antibacterial efficacy by controlling AMP intermolecular hydrophobic and hydrogen bonding interactions. Molecular dynamics simulations and Gibbs free energy calculations in concert with experimental assays show that increasing intermolecular interactions via inter-peptide aggregation increases the energy cost for the peptide to cross the bacterial cell membrane, which in turn decreases the AMP antibacterial activity. Our findings provide a route for predicting and controlling the antibacterial activity of AMPs against Gramnegative bacteria via reductions of intermolecular AMP interactions.

biophysics↗

bioRxiv2018

Identification of Variable and Joining germline genes and alleles for Rhesus macaque from B-cell receptor repertoires

The Rhesus macaque is a valuable preclinical animal model to estimate vaccine effectiveness, and is also important for understanding antibody maturation and B-cell repertoire evolution responding to vaccination; however, incomplete mapping of rhesus immunoglobulin germline genes hinders the research efforts. To address this deficiency, we sequenced B-cell receptor (BCR) repertoires of 75 India Rhesus macaques. Using a bioinformatic method that has been validated with BCR repertoire analysis of three human donors, we were able to infer rhesus Variable (V) and Joint(J) germline alleles, identifying a total of 122 V and 20 J germline alleles. Importantly, 91 V and 13 J alleles were novel, and 40 V and 13 J genes were found at a novel genome region that has not been previously recorded. The novelty of these newly identified alleles was supported by two observations. Firstly, 50 V and 5 J novel alleles were observed in whole genome sequencing data of 10 Rhesus macaques. Secondly, using alignment reference including the novel alleles, the mutation rate of rearranged repertoires was significant declined in 9 other irrelevant samples, and all our identified novel V and J alleles were 100% identity mapped by rearranged repertoire data. These newly identified novel alleles, along with previous reported alleles, provide an important reference for future investigations of rhesus immune repertoire evolution, in response to vaccination or infection. In addition, the method outlined in our study offered an example to future efforts in identifying novel immunoglobulin alleles.

immunology↗

bioRxiv2018

Candidate urine biomarker discovery from only five pairs of samples before and after tumor resection in glioma patients

Biomarkers are measurable changes associated with the disease. Without the control of homeostatic mechanisms, urine accumulates systemic body changes and thus serves as an excellent early biomarker source. However, urine is affected by many factors other than disease. Although many candidate biomarkers have been identified in animal models, a large number of clinical samples might still be required for the disease related changes. A self-controlled study should be able to avoid the interferences of individual differences among patients. Gliomas are the most common primary malignant brain tumors and have a very poor prognosis. Early diagnosis of gliomas and the monitoring of tumor recurrence are crucial to improve glioma patient outcomes. Here we set to try if biomarker candidates can be identified by comparing urine samples from five glioma patients collected at the time of tumor diagnosis and after surgical removal of the tumor. Using label-free liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) quantification, twenty-seven urinary proteins were significantly changed after tumor resection (fold change [≥] 1.5, P-value < 0.05, and similar changes in all 5 patients), many of which have been previously associated with gliomas, such as CEACAM1, ANXA7, CALR, CRYAB, CD276, pIgR and cathepsin D. Functions of these proteins were significantly enriched in the regulation of tissue remodeling, autophagy, the inhibition of gene expression, the positive regulation of natural killer cell-mediated cytotoxicity and angiogenesis, which are associated with glioma development. Our results suggested that using the self-control of before and after tumor resection is an effective method to identify differential proteins associated with the disease, even with a small number of patients.

cancer biology↗

bioRxiv2017

Clustering enzymes using E.coli inner cell membrane as scaffold in metabolic pathway

Clustering enzymes in the same metabolism pathway is a natural strategy to enhance the productivity. Several systems have been designed to artificially cluster desired enzymes in the cell, such as synthetic protein scaffold and nucleic acid scaffold. However, these scaffolds require complicated construction process and have limited slots for target enzymes. Following this direction, we designed a scaffold system based on natural cell membrane. Target enzymes (FabZ, FabG, FabI and TesA in fatty acid synthesis II pathway) are anchored on the E.coli inner membrane, showing the enhanced metabolism flux without the requirement of the further artificial interactions to force the clustering. Furthermore, anchoring the enzymes on the membrane enhances the products exportation, which further increases the productivity. Together, the proposed system has potential applications in producing valuable biomaterials.

synthetic biology↗

bioRxiv2017

Longitudinal Analysis of Particulate Air Pollutants and Adolescent Delinquent Behavior in Southern California

Animal experiments and cross-sectional human studies have linked particulate matter (PM) with increased behavioral problems. We conducted a longitudinal study to examine whether the trajectories of delinquent behavior are affected by PM2.5 (PM with aerodynamic diameter [≤]2.5 m) exposures before and during adolescence. We used the parent-reported Child Behavior Checklist at age 9-18 with repeated measures every ~2-3 years (up to 4 behavioral assessments) on 682 children from the Risk Factors for Antisocial Behavior Study conducted in a multi-ethnic cohort of twins born in 1990-1995. Based on prospectively-collected residential addresses and a spatiotemporal model of ambient air concentrations in Southern California, monthly PM2.5 estimates were aggregated to represent long-term (1-, 2-, 3-year average) exposures preceding baseline and cumulative average exposure until the last assessment. Multilevel mixed-effects models were used to examine the association between PM2.5 exposure and individual trajectories of delinquent behavior, adjusting for within-family/within-individual correlations and potential confounders. We also examined whether psychosocial factors modified this association. The results suggest that PM2.5 exposure at baseline and cumulative exposure during follow-up was significantly associated (p<0.05) with increased delinquent behavior. The estimated effect sizes (per interquartile increase of PM2.5 by 3.12-5.18 {micro}g/m3) were equivalent to the difference in delinquency scores between adolescents who are 3.5-4 years apart in age. The adverse effect was stronger in families with unfavorable parent-to-child relationships, increased parental stress or maternal depressive symptoms. Overall, these findings suggest long-term PM2.5 exposure may increase delinquent behavior of urban-dwelling adolescents, with the resulting neurotoxic effect aggravated by psychosocial adversities.

epidemiology↗

bioRxiv2017

Socioeconomic Disparities and Sexual Dimorphism in Neurotoxic Effects of Ambient Fine Particles on Youth IQ: A Longitudinal Analysis

Mounting evidence indicates that early-life exposure to particulate air pollutants pose threats to childrens cognitive development, but studies about the neurotoxic effects associated with exposures during adolescence remain unclear. We examined whether exposure to ambient fine particles (PM2.5) at residential locations affects intelligence quotient (IQ) during pre-/early-adolescence (ages 9-11) and emerging adulthood (ages 18-20) in a demographically-diverse population (N = 1,360) residing in Southern California. Increased ambient PM2.5 levels were associated with decreased IQ scores. This association was more evident for Performance IQ (PIQ), but less for Verbal IQ, assessed by the Wechsler Abbreviated Scale of Intelligence. For each inter-quartile (7.73 g/m3) increase in one-year PM2.5 preceding each assessment, the average PIQ score decreased by 3.08 points (95% confidence interval = [-6.04, -0.12]) accounting for within-family/within-individual correlations, demographic characteristics, family socioeconomic status (SES), parents cognitive abilities, neighborhood characteristics, and other spatial confounders. The adverse effect was 150% greater in low SES families and 89% stronger in males, compared to their counterparts. Better understanding of the social disparities and sexual dimorphism in the adverse PM2.5-IQ effects may help elucidate the underlying mechanisms and shed light on prevention strategies.

epidemiology↗

bioRxiv2017

Small Molecule Inhibitors of the Human Histone Lysine Methyltransferase NSD2 / WHSC1 / MMSET Identified from a Quantitative High-Throughput Screen with Nucleosome Substrate

The activity of the histone lysine methyltransferase NSD2 is thought to play a driving role in oncogenesis. Both overexpression of NSD2 and point mutations that increase its catalytic activity are associated with a variety of human cancers. While NSD2 is an attractive therapeutic target, no potent, selective and cell-active inhibitors have been reported to date, possibly due to the challenging nature of developing high-throughput assays for NSD2. To establish a platform for the discovery and development of selective NSD2 inhibitors, multiple assays were optimized and implemented. Quantitative high-throughput screening was performed with full-length wild-type NSD2 and a nucleosome substrate against a diverse collection of known bioactives comprising 16,251 compounds. Actives from the primary screen were further interrogated with orthogonal and counter assays, as well as activity assays with the clinically relevant NSD2 mutants E1099K and T1150A. Five confirmed inhibitors were selected for follow-up, which included a radiolabeled validation assay, surface plasmon resonance studies, methyltransferase profiling, and histone methylation in cells. The identification of NSD2 inhibitors that bind the catalytic SET domain and demonstrate activity in cells validates the workflow, providing a template for identifying selective NSD2 inhibitors.

cancer biology↗

bioRxiv2017

SALP, a new single-stranded DNA library preparation method especially useful for the high-throughput characterization of chromatin openness states

Based on a novel kind of single strand adaptor (SSA), this study developed a new method to construct next-generation sequencing (NGS) library, named as SALP, representing Single strand Adaptor Library Preparation. The key creativity of the method lies in the design and verification of a special adaptor that can be efficiently linked to the 3' end of single-stranded DNA, which is a double-stranded oligonucleotide with a 3' overhang of 3 random nucleotides. This method can start with the denatured DNAs or chromatins fragmented by different methods such as Tn5 tagmentation, enzyme digestion and sonication. When applied to Tn5-tagmented chromatin, SALP overcomes the key limitation of the current ATAC-seq method and develops a high-throughput NGS library construction and sequencing approach, SALP-seq, which can be used to comparatively characterize the chromatin openness state of multiple cells simply and unbiasly. In this way, the comparative chromatin openness states of four different cell lines, including GM12878, HepG2, HeLa and 293T, were successfully characterized. This study also demonstrated that SALP-seq could characterize the chromatin openness states with 105 to 500 cells, indicating the high sensitivity of SALP-seq in characterizing chromatin state of cells. SALP should have wide applications in the future biological sciences and biomedicine.

genomics↗

bioRxiv2017

Early urinary candidate biomarkers in a rat model of experimental autoimmune encephalomyelitis

Multiple sclerosis is a chronic autoimmune demyelinating disease of the central nervous system and is difficult to diagnose in early stages. Without homeostatic control, urine was reported to have the ability to accumulate early changes in the body. We expect that urinary proteome can reflect early changes in the nervous system. In this study, the early urinary proteome changes in a most employed multiple sclerosis rat model (experimental autoimmune encephalomyelitis (EAE)) were analyzed to explore early urinary candidate biomarkers, and early treatment of methylprednisolone were used to evaluate the therapeutic effect. Compare with controls, twenty-five urinary proteins were altered at day 7 when there were no clinical symptoms and no obvious histological changes. Among them, twenty-three have human homologs and fourteen were reported to be differently expressed in the serum/cerebrospinal fluid/brain tissues of multiple sclerosis patients or animal models. Functional analysis showed that the dysregulated proteins were associated with asparagine degradation, neuroinflammation and lipid metabolism. After the early treatment of methylprednisolone, the incidence of encephalomyelitis in the intervention group was only 1/13. This study demonstrates that urine may be a good source of biomarkers for the early detection of multiple sclerosis and early treatment can significantly delay disease progression. These findings may provide important information for early diagnosis and intervention of multiple sclerosis in the future.

biochemistry↗

bioRxiv2017

Quinary structure kinetically controls protein function and dysfunction

Protein self-assemblies modulate protein activities over biological time scales that can exceed the lifetimes of the proteins or even the cells that harbor them. We hypothesized that these time scales relate to kinetic barriers inherent to the nucleation of ordered phases. To investigate nucleation barriers in living cells, we developed Distributed Amphifluoric FRET (DAmFRET). DAmFRET exploits a photoconvertible fluorophore, heterogeneous expression, and large cell numbers to quantify via flow cytometry the extent of a proteins self-assembly as a function of cellular concentration. We show that kinetic barriers limit the nucleation of ordered self-assemblies, and that the persistence of the barriers with respect to concentration relates to structure. Supersaturation resulting from sequence-encoded nucleation barriers gave rise to prion behavior, and enabled a prion-forming protein, Sup35 PrD, to partition into dynamic intracellular condensates or to form toxic aggregates. Our results suggest that nucleation barriers govern cytoplasmic inheritance, subcellular organization, and proteotoxicity.\n\nHighlightsO_LIDistributed Amphifluoric FRET (DAmFRET) quantifies nucleation in living cells\nC_LIO_LIDAmFRET rapidly distinguishes prion-like from non-prion phase transitions\nC_LIO_LINucleation barriers allow switch-like temporal control of protein activity\nC_LIO_LISequence-intrinsic features determine the concentration-dependence of nucleation barriers\nC_LI

biophysics↗

bioRxiv2017

Sub-threshold resonance organizes activity and optimizes learning in neural networks.

Network oscillations across and within brain areas are critical for learning and performance in memory tasks. While a large amount of work has focused on the generation of neural oscillations, their effects on neuronal populations spiking activity and information encoding is less known. Here, we use computational modeling and in vivo recording to demonstrate that a shift in sub-threshold resonance can interact with oscillating input to ensure that networks of neurons properly encode new information represented in external inputs to the weights of recurrent synaptic connections. Using a neuronal network model, we find that due to an input-current dependent shift in their resonance response, individual neurons in a network will arrange their phases of firing to represent varying strengths of their respective inputs. As networks encode information, neurons fire more synchronously, and this effect limits the extent to which further \"learning\" (in the form of changes in synaptic strength) can occur. We also demonstrate that sequential patterns of neuronal firing can be accurately stored in the network; these sequences are later reproduced without external input (in the context of sub-threshold oscillations) in both the forward and reverse directions (as has been observed following learning in vivo). To test whether a similar mechanism could act in vivo, we show that periodic stimulation of hippocampal neurons coordinates network activity and functional connectivity in a frequency-dependent manner. We conclude that sub-threshold resonance provides a plausible network-level mechanism to accurately encode and retrieve information without over-strengthening connections between neurons.

neuroscience↗

bioRxiv2017

Urinary candidate biomarkers in an experimental autoimmune myocarditis rat model

Urine is a better source than plasma for biomarker studies, as it can accumulate all changes in the body. Various candidate urinary biomarkers of physiological conditions, kidney disease and even brain dysfunction, have been detected in urine; however, urine has rarely been used to reflect cardiac diseases. As the clinical presentations of myocarditis are heterogeneous, reliable and sensitive diagnostic biomarkers of myocarditis are very important. In this study, candidate urinary biomarkers in the myosin-induced autoimmune myocarditis rat models were characterized using the isobaric tandem mass tag labeling approach coupled with high-resolution mass spectrometry. Compared with controls, forty-six urinary proteins were significantly changed in the myocarditis rats; among them, ten had previously been associated with myocarditis, twelve corresponding gene products have been annotated as mainly cardiovascular network genes by the Ingenuity Pathway Analysis, and four urinary proteins were validated by western blot.

molecular biology↗