Biology subjects

Shi, H.

Publications and source records attributed to Shi, H..

At least 199 records · Page 11Linked to original sources

bioRxiv2020

A method to map and interpret pleiotropic loci using summary statistics of multiple traits

1The identification of pleiotropic loci and the interpretation of the associations at these loci are essential to understand the shared etiology of related traits. A common approach to map pleiotropic loci is to use an existing meta-analysis method to combine summary statistics of multiple traits. This strategy does not take into account the complex genetic architectures of traits such as genetic correlations and heritabilities. Furthermore, the interpretation is challenging because phenotypes often have different characteristics and units. We propose PLEIO, a summary-statistic-based framework to map and interpret pleiotropic loci in a joint analysis of multiple traits. Our method maximizes power by systematically accounting for the genetic correlations and heritabilities of the traits in the association test. Any set of related phenotypes, binary or quantitative traits with differing units, can be combined seamlessly. In addition, our framework offers interpretation and visualization tools to help downstream analyses. Using our method, we combined 18 traits related to cardiovascular disease and identified 20 novel pleiotropic loci, which showed five different patterns of associations. Our method is available at https://github.com/hanlab-SNU/PLEIO.

bioinformatics↗

bioRxiv2020

Adipose tissue-derived neurotrophic factor 3 regulates sympathetic innervation and thermogenesis in adipose tissue

Activation of brown fat thermogenesis increases energy expenditure and alleviates obesity. Sympathetic nervous system (SNS) is important in brown/beige adipocyte thermogenesis. Here we discover a novel fat-derived “adipokine” neurotrophic factor neurotrophin 3 (NTF3) and its receptor Tropomyosin receptor kinase C (TRKC) as key regulators of SNS growth and innervation in adipose tissue. NTF3 is highly expressed in brown/beige adipocytes, and potently stimulates sympathetic neuron neurite growth. NTF3/TRKC regulates a plethora of pathways in neuronal axonal growth and elongation. Adipose tissue sympathetic innervation is significantly increased in mice with adipocyte-specific NTF3 overexpression, but profoundly reduced in mice with TRKC haploinsufficiency (TRKC+/-). Increasing NTF3 via pharmacological or genetic approach promotes beige adipocyte development, enhances cold-induced thermogenesis and protects against diet-induced obesity (DIO); whereas TRKC+/- mice or SNS TRKC deficient mice are cold intolerant and prone to DIO. Thus, NTF3 is an important fat-derived neurotrophic factor regulating SNS innervation, energy metabolism and obesity.Competing Interest StatementThe authors have declared no competing interest.View Full Text

physiology↗

bioRxiv2020

The role of sodium thiocyanate supplementation during dextran sodium sulphate-stimulated experimental colitis

Ulcerative colitis is a condition characterised by the infiltration of leukocytes into the gastrointestinal wall. Leukocyte-MPO catalyses hypochlorous acid (HOCl) and hypothiocyanous acid (HOSCN) formation from chloride (Cl-) and thiocyanous (SCN-) anions, respectively. While HOCl indiscriminately oxidises biomolecules, HOSCN primarily targets low-molecular weight protein thiols. Oxidative damage mediated by HOSCN may be reversible, potentially decreasing MPO-associated host tissue destruction. This study investigated the effect of SCN- supplementation in a model of acute colitis. Female mice were supplemented dextran sodium sulphate (DSS, 3% w/v) in the presence of 10 mM Cl- or SCN- in drinking water ad libitum, or with salts (NaCl and NaSCN only) or water only (controls). Behavioural studies showed mice tolerated NaSCN and NaCl-treated water with water-seeking frequency. Ion-exchange chromatography showed increased fecal and plasma SCN- levels in thiocyanate supplemented mice; plasma SCN- reached similar fold-increase for smokers. Overall there was no difference in weight loss and clinical score, mucin levels, crypt integrity and extent of cellular infiltration between DSS/SCN- and DSS/Cl- groups. Neutrophil recruitment remained unchanged in DSS-treated mice, as assessed by fecal calprotectin levels. Total thiol and tyrosine phosphatase activity remained unchanged between DSS/Cl- and DSS/SCN- groups, however, colonic tissue showed a trend in decreased 3-chlorotyrosine (1.5-fold reduction, p<0.051) and marked increase in colonic GCLC, the rate-limiting enzyme in glutathione synthesis. These data suggest that SCN- administration can modulate MPO activity towards a HOSCN-specific pathway, however, this does not alter the development of colitis within a DSS murine model.HighlightsSodium thiocyanate (SCN-) supplementation increased plasma and fecal SCN- level.Thiocyanate supplementation diverted HOCl-mediated oxidative damage in mice colon.Thiocyanate supplementation stimulated thiol synthesis in the DSS colitis model.Thiocyanate provides no protection in an acute experimental model of UC.Competing Interest StatementThe authors have declared no competing interest.AbbreviationsCDCrohn’s Disease3-Cl-Tyr3-chlorotyrosineDSSDextran Sodium SulphateGAPDHGlyceraldehyde 3-phosphate dehydrogenaseGCLCGlutamate-Cysteine Ligase Catalytic SubunitGIGastrointestinalGSHGlutathioneGSSGGlutathione DisulfideHOBrHypobromous AcidHOClHypochlorous AcidHCN-Hydrogen; CyanideHOSCNHypothiocyanous AcidIBDInflammatory Bowel DiseaseMPOMyeloperoxidaseNrf2Nuclear factor erythroid 2-related Factor 2PMNsPolymorphonuclear NeutrophilsPTPProtein Tyrosine PhosphatasesROSReactive Oxygen SpeciesSCN-ThiocyanateUCUlcerative ColitisView Full Text

pathology↗

bioRxiv2020

2'-O-methylation alters the RNA secondary structural ensemble

2-O-methyl (Nm) is a highly abundant post-transcriptional RNA modification that plays important biological roles through mechanisms that are not entirely understood. There is evidence that Nm can alter the biological activities of RNAs by biasing the ribose sugar pucker equilibrium toward the C3-endo conformation formed in canonical duplexes. However, little is known about how Nm might more broadly alter the dynamic ensembles of non-canonical RNA motifs. Here, using NMR and the HIV-1 transactivation response (TAR) element as a model system, we show that Nm preferentially stabilizes alternative secondary structures in which the Nm-modified nucleotides are paired, increasing both the abundance and lifetime of a low-populated short-lived excited state by up to 10-fold. The extent of stabilization increased with number of Nm modifications and was also dependent on Mg2+. Through phi ({Phi}) value analysis, the Nm modification also provided rare insights into the structure of the transition state for conformational exchange. Our results suggest that Nm could alter the biological activities of Nm-modified RNAs by modulating their secondary structural ensembles as well as establish the utility of Nm as a tool for the discovery and characterization of RNA excited state conformations.

biochemistry↗

bioRxiv2020

Hoogsteen base pairs increase the susceptibility of double-stranded DNA to cytotoxic damage

As the Watson-Crick faces of nucleobases are protected in double-stranded DNA (dsDNA), it is commonly assumed that deleterious alkylation damage to the Watson-Crick faces of nucleobases predominantly occurs when DNA becomes single-stranded during replication and transcription. However, damage to the Watson-Crick faces of nucleobases has been reported in dsDNA in vitro through mechanisms that are not understood. In addition, the extent of protection from methylation damage conferred by dsDNA relative to single-stranded DNA (ssDNA) has not been quantified. Watson-Crick base-pairs in dsDNA exist in dynamic equilibrium with Hoogsteen base-pairs that expose the Watson-Crick faces of purine nucleobases to solvent. Whether this can influence the damage susceptibility of dsDNA remains unknown. Using dot-blot and primer extension assays, we measured the susceptibility of adenine-N1 to methylation by dimethyl sulfate (DMS) when in an A-T Watson-Crick versus Hoogsteen conformation. Relative to unpaired adenines in a bulge, Watson-Crick A-T base-pairs in dsDNA only conferred ~130-fold protection against adenine-N1 methylation and this protection was reduced to ~40-fold for A(syn)-T Hoogsteen base-pairs embedded in a DNA-drug complex. Our results indicate that Watson-Crick faces of nucleobases are accessible to alkylating agents in canonical dsDNA and that Hoogsteen base-pairs increase this accessibility. Given the higher abundance of dsDNA relative to ssDNA, these results suggest that dsDNA could be a substantial source of cytotoxic damage. The work establishes DMS probing as a method for characterizing A(syn)-T Hoogsteen base pairs in vitro and also lays the foundation for a sequencing approach to map A(syn)-T Hoogsteen and unpaired adenines genome-wide in vivo.

biochemistry↗

bioRxiv2020

An RNA dynamic ensemble at atomic resolution

Biomolecules do not fold into a single 3D structure but rather form dynamic ensembles of many inter-converting conformations1. Knowledge of dynamic ensembles is key for understanding how biomolecules fold and function, and for rationally manipulating their activities in drug discovery and synthetic biology2-4. However, solving dynamic ensembles of biomolecules at atomic resolution is a major challenge in structural biology because the information required to specify the position of all atoms in thousands of conformations in an ensemble far exceeds the information content of experimental measurements. Here we addressed the data gap and dramatically simplified and accelerated RNA ensemble determination by using structure prediction tools that leverage the growing database of RNA structures to generate a conformational library. Library refinement with NMR residual dipolar couplings enabled determination of an atomic-resolution ensemble for HIV-1 TAR as confirmed by quantum-mechanical calculations of NMR chemical shifts, comparison to a crystal structure of a substate, and through the successful redistribution of the ensemble by design using atomic mutagenesis. The ensemble provides an unprecedented view of how bulge residues cooperatively flip out and undergo sugar repuckering to allow the adjoining helices to stack. The generality of this approach will make determination of atomic-resolution RNA ensembles routine.

biophysics↗

bioRxiv2020

Revealing the high propensity of RNAs to non-specifically bind drug-like small molecules

Identifying small molecules that selectively bind a single RNA target while discriminating against all other cellular RNAs is an important challenge in RNA-targeted drug discovery. Much effort has been directed toward identifying drug-like small molecules that minimize electrostatic and stacking interactions that lead to non-specific binding of aminoglycosides and intercalators to a variety of RNAs. Many such compounds have been reported to bind RNAs and inhibit their cellular activities, however the ability of such compounds to discriminate against RNA stem-loops commonly found in the transcriptome has not been thoroughly assessed in all cases. Here, we examined the propensities of three drug-like compounds, previously shown to bind and inhibit the cellular activity of three distinct RNAs, to non-specifically bind two HIV-1 stem-loop RNAs: the transactivation response element (TAR) and stem IIB in the rev response element (RREIIB). All three compounds bound to TAR and RREIIB in vitro, and two inhibited TAR-dependent transactivation and RRE-dependent viral export in cell-based assays while also exhibiting substantial off-target interactions consistent with non-specific cellular activity. A survey of X-ray and NMR structures of RNA-small molecule complexes revealed that drug-like molecules form hydrogen bonds with functional groups commonly accessible in canonical stem-loop RNA motifs, much like aminoglycosides, and in contrast to ligands that specifically bind riboswitches. Our results support extending the group of non-selective RNA-binders beyond aminoglycosides and intercalators to encompass drug-like compounds with capacity for non-specific hydrogen-bonding and reinforce the importance of assaying for off-target interactions and RNA selectivity in vitro and in cells when assessing novel RNA-binders.

biochemistry↗

bioRxiv2020

Coordination between E. coli Cell Size and Cell Cycle Mediated by DnaA

Sixty years ago, bacterial cell size was found as an exponential function of growth rate. Fifty years ago, a more general relationship was proposed, in which the cell mass was equal to the initiation mass multiplied by the ratio of the total time of the C and D periods to the doubling time. This relationship has recently been experimentally confirmed by perturbing doubling time, C period, D period or the initiation mass. However, the underlying molecular mechanism remains unclear. Here, we developed a mechanistic and kinetic model to describe how the initiator protein DnaA mediates the initiation of DNA replication in E. coli. In the model, we introduced an initiation probability function involving competitive binding of DnaA-ATP (active) and DnaA-ADP (inactive) at replication origin to determine the initiation of replication. In addition, we considered RNAP availability, ppGpp inhibition, DnaA autorepression, DnaA titration by chromosomal sites, hydrolysis of DnaA-ATP along with DNA replication, reactivation of DnaA-ADP and established a kinetic description of these DnaA regulatory processes. We simulated DnaA kinetics and obtained a self-consistent cell size and a regular DnaA oscillation coordinated with the cell cycle at steady state. The relationship between the cell size obtained by the simulation and the growth rate, C period, D period or initiation mass reproduces the results of the experiment. This model also predicts how the number of DnaA and the initiation mass vary with the perturbation parameters (including those reflecting the mutation or interference of DnaA regulatory processes), which is comparable to experimental data. The results suggest that the regulatory mechanisms of DnaA level and activity are associated with the invariance of initiation mass and the cell size general relationship for matching frequencies of replication initiation and cell division. This study may provide clues for concerted control of cell size and cell cycle in synthetic biology.

biophysics↗

bioRxiv2020

Clinically applicable histopathological diagnosis system for gastric cancer detection using deep learning

Gastric cancer is among the most malignant tumours with the highest incidence and mortality rates. The early detection and accurate histopathological diagnosis of gastric cancer are essential factors that can help increase the chances of successful treatment. While the worldwide shortage of pathologists has imposed burdens on current histopathology services, it also offers a unique opportunity for the use of artificial intelligence assistance systems to alleviate the workload and increase diagnostic accuracy. To the best of our knowledge, there has not been a clinically applicable histopathological assistance system with high accuracy that can generalize to whole slide images created with diverse digital scanner models from different hospitals. Here, we report a clinically applicable artificial intelligence assistance system developed at the Chinese PLA General Hospital, China, using a deep convolutional neural network trained with 2,123 pixel-level annotated H&E-stained whole slide images. The model achieved a sensitivity near 100% and an average specificity of 80.6% on a real-world test dataset, which included 3,212 whole slide images digitalized with three scanner models. We showed that the system could aid pathologists in improving diagnostic accuracy and preventing misdiagnoses. Moreover, we demonstrated that our system could perform robustly with 1,582 whole slide images from two other medical centres. Our study suggests the feasibility and benefits of using histopathological artificial intelligence assistance systems in routine practice scenarios.Competing Interest StatementXiaoqing Zhang is the founder of Thorough Images. Shuhao Wang is the co-founder and chief technology officer (CTO) of Thorough Images. Calvin Ku, Cancheng Liu, Zhuo Sun, Gang Xu, Yuefeng Wang are algorithm researchers of Thorough Images. All remaining authors have declared no conflicts of interest.View Full Text

pathology↗

bioRxiv2020

A variant in SMOC2, inhibiting BMP signaling by competitively binding to BMPR1B, causes multiple epiphyseal dysplasia

Previously study showed that SMOC, a matricellular protein, inhibits BMP signaling downstream of its receptor via activation of mitogen-activated protein kinase (MAPK) signaling. In our study, exome sequencing revealed a missense mutation (c.1076T>G, p.Leu359Arg) in EC domain of SMOC2 in a Chinese family with multiple epiphyseal disease (MED). The pathogenicity of this SMOC2 variant was verified by Smoc2L359R/L359R knock-in mice. Of note, decreasing phosphorylation of SMAD1/5/9 was detected in growth plates and primary chondrocytes from Smoc2L359R/L359R mice. Furthermore, binding affinity of mutant SMOC2 with collagen IX and HSPG in the extracellular matrix of cartilage were reduced while binding affinity with BMPRIB was intact. In addition, in contrast to previously results, that SMOC2 cannot antagonize BMP activity in the presence of a constitutively activated BMP receptor. These results support that SMOC2 with p.Leu359Arg variant act as an antagonist of canonical BMP pathway by competitively binding with BMP receptors.

genomics↗

bioRxiv2020

The role of Fnr paralogs for controlling anaerobic metabolism in diazotroph Paenibacillus polymyxa WLY78

Fnr is a transcriptional regulator that controls the expression of a variety of genes in response to oxygen limitation in bacteria. Genome sequencing revealed four genes (fnr1, fnr3, fnr5 and fnr7) coding for Fnr proteins in Paenibacillus polymyxa WLY78. Fnr1 and Fnr3 showed more similarity to each other than to Fnr5 and Fnr7. Also, Fnr1 and Fnr3 exhibited high similarity with Bacillus cereus Fnr and Bacillus subtilis Fnr in sequence and structures. Deletion analysis showed that the four fnr genes, especially fnr1 and fnr3, have significant impacts on the growth and nitrogenase activity. Single deletion of fnr1 or fnr3 led to 50% reduction in nitrogenase activity and double deletion of fnr1 and fnr3 resulted to 90% reduction in activity. Both of the aerobically purified His-tagged Fnr1 and His-tagged Fnr3 in Escherichia coli could bind to the specific DNA promoter. Genome-wide transcription analysis showed that Fnr1 and Fnr3 indirectly activated expression of nif (nitrogen fixation) genes and Fe transport genes under anaerobic condition. Fnr1 and Fnr3 inhibited expression of the genes involved in aerobic respiratory chain and activated expression of genes responsible for anaerobic electron acceptor genes. IMPORTANCEPaenibacillus is a genus of Gram-positive, facultative anaerobic and endospore-forming bacteria. The members of nitrogen-fixing Paenibacillus have great potential use as a bacterial fertilizer in agriculture. However, the functions of fnr gene(s) in nitrogen fixation and other metabolisms in Paenibacillus spp. are not known. Here, we revealed that copy numbers vary largely among different Paenibacillus species and strains. Deletion and complementation analysis demonstrated that fnr1 and fnr3 have significant impacts on the growth and nitrogenase activity. Both of the aerobically purified His-tagged Fnr1 and His-tagged Fnr3 purified in Escherichia coli could bind to the specific DNA promoter as Bacillus cereus Fnr did. Fnr1 and Fnr3 indirectly activated nif expression under anaerobic condition. Fnr1 and Fnr3 directly or indirectly activated or inhibited expression of many important genes involved in respiration, energy metabolism, Fe uptake and potentially specific electron transport for nitrogenase under anaerobic condition. This study not only reveals the roles of fnr genes in nitrogen fixation and anaerobic metabolism, but also provides insight into the evolution and regulatory mechanisms of fnr in Paenibacillus.

microbiology↗

bioRxiv2019

Recombinant HcGAPDH Protein Expressed on Probiotic Bacillus subtilis Spores Protects Sheep from Haemonchus contortus Infection by Inducing both Humoral and Cell-mediated Responses

Probiotic Bacillales have been shown effective in controlling pathogens. In particular, live probiotic bacteria are thought to improve the composition of gastrointestinal microbiota, and to reduce pathogen colonization. However, how probiotics regulate immune responses and protect the host from parasitic infection remains largely unknown. In this study, we investigated whether Bacillales can be used against Haemonchus contortus, a parasitic nematode that infects small ruminants in sheep and goats worldwide. Using 16S ribosomal RNA sequencing, we found that Bacillales was highly depleted in the abomasal microbiota of sheep infected with H. contortus. We constructed a recombinant Bacillus subtilis strain (rBSCotB-HcG) that express glyceraldehyde-3-phosphate dehydrogenase of H. contortus (HcGAPDH) on its spore surface. However, mice orally administrated with the rBSCotB-HcG strain showed strong Th1-dominated immune responses; and sheep administrated per os with rBSCotB-HcG showed increased proliferation of peripheral blood mononuclear cells, elevated anti-HcGAPDH IgG levels in sera, and higher anti-HcGAPDH sIgA levels in intestinal mucus. In addition, treatment of H. contortus infected sheep with rBSCotB-HcG (Hc+rBSCotB-HcG) promoted the abundance of probiotic species in the abomasal microbiota; it also improved the average weight gain of the sheep by 27.7%. These Hc+rBSCotB-HcG sheep have reduced number of eggs per gram of feces (by 84.1%) and worm burdens (by 71.5%), with alleviated abomasal damage by H. contortus. Collectively, our data demonstrate the protective roles of CotB-HcGAPDH-expressing B. subtilis spores against H. contortus infection, suggesting a potential value of using this probiotic-based strategy in controlling parasitic nematodes of socioeconomic importance. ImportanceSequencing of the infected sheep s stomach flora revealed potential probiotics that could control H. contortus infection, and further genetically engineered recombinant probiotic spores expressing parasite protein, and validated their good immunogenicity in a mouse model. In the sheep infection model, the recombinant probiotics have proven to be effective against parasite infections.

microbiology↗

bioRxiv2019

Prognostic significances of interleukin-17-producing cells and Th17 cells in malignant cancers: a meta-analysis of the literatures

Background and purposeAs a proinflammatory factor, interleukin-17 (IL-17) can play a role in both tumor promotion and suppression. IL-17 is traditionally regarded as secreting mainly by CD4+ T helper cells (Th17 cells), while other immune subsets have been proved to produce IL-17, called IL-17+ cells. Considerable studies have drawn controversial conclusions about association between IL-17+/Th17 cells and prognosis of cancer patients. This meta-analysis was performed to systematically and quantitatively analyze prognostic values of IL-17+ cells and Th17 cells in cancer patients. MethodsA comprehensive retrieval was conducted in Pubmed (MEDLINE) and EMBASE databases. Pooled risk ratios (RRs) or hazard ratios (HRs) and corresponding 95% confidence intervals (CI) were calculated to evaluate the prognostic values of IL-17+ cells and Th17 cells in cancer patients. ResultsA total of 42 studies with 5039 patitents were included. High IL-17+ cells was significantly associated with tumor recurrence (RR = 4.23, 95% CI [1.58, 11.35]), worse disease free survival (DFS) (HR = 1.84, 95% CI [1.22, 2.77]) and overall survival (OS) (HR = 1.39, 95% CI [1.04, 1.87]), especially in cancers of digestive system. Besides, no significant difference was observed between high IL-17+ cells and histological grade, lymph node metastasis, tumor volume, clinical stages or distant metastasis. Moreover, there was no significant difference in OS between high and low Th17 cells in cancer patients (HR = 0.93, 95% CI [0.58, 1.49]). ConclusionsThis meta-analysis suggests high IL-17+ cells could be an indicator for worse survival in patients with malignant cancers, especially with cancers of digestive system. Although high Th17 cells appears to have non-statistically significance on prognosis, more clinical studies should be implemented to investigate the underlying function of Th17 cells within tumor microenvironment. This study put forward a new insight for potential application of anti-IL-17 target therapy in cancer therapeutics.

cancer biology↗

bioRxiv2019

Localizing components of shared transethnic genetic architecture of complex traits from GWAS summary data

Despite strong transethnic genetic correlations reported in the literature for many complex traits, the non-transferability of polygenic risk scores across populations suggests the presence of population-specific components of genetic architecture. We propose an approach that models GWAS summary data for one trait in two populations to estimate genome-wide proportions of population-specific/shared causal SNPs. In simulations across various genetic architectures, we show that our approach yields approximately unbiased estimates with in-sample LD and slight upward-bias with out-of-sample LD. We analyze 9 complex traits in individuals of East Asian and European ancestry, restricting to common SNPs (MAF > 5%), and find that most common causal SNPs are shared by both populations. Using the genome-wide estimates as priors in an empirical Bayes framework, we perform fine-mapping and observe that high-posterior SNPs (for both the population-specific and shared causal configurations) have highly correlated effects in East Asians and Europeans. In population-specific GWAS risk regions, we observe a 2.8x enrichment of shared high-posterior SNPs, suggesting that population-specific GWAS risk regions harbor shared causal SNPs that are undetected in the other GWAS due to differences in LD, allele frequencies, and/or sample size. Finally, we report enrichments of shared high-posterior SNPs in 53 tissue-specific functional categories and find evidence that SNP-heritability enrichments are driven largely by many low-effect common SNPs.

genomics↗

bioRxiv2019

Developmental plasticity of hearing sensitivity in red-eared slider Trachemys scripta elegans

Developmental plasticity of hearing sensitivity (DPHS) has been verified in some groups of vertebrates. Turtles face a trade-off between terrestrial and aquatic hearing in different acoustic environments throughout ontogeny. However, how chelonian hearing sensitivity changes throughout ontogeny is still unclear. To verify DPHS in turtles, auditory brainstem responses (ABR) were compared using hearing thresholds and latencies in female red-eared slider (Trachemys scripta elegans) aged 1 week, 1 month, 1 year, and 5 years, and the results showed hearing sensitivity bandwidths of approximately 200-1100, 200-1100, 200-1300, and 200-1400 Hz, respectively. The lowest threshold sensitivity was approximately 600{square}Hz. Below 600 Hz, ABR threshold decreased rapidly with increasing age (1 week to 1 year), with significant differences between age groups, but no significant difference between the 1- and 5-year age groups (stimulus frequency, 200-600 Hz). Above 600 Hz, ABR threshold was the lowest in the 5-year age group. These findings show that aging was accompanied by hearing sensitivity changes, suggesting rapid, frequency-segmented development during ontogeny. This variability in hearing sensitivity differs from that reported in other vertebrates, and allows adaptation to acoustically distinct environments throughout ontogeny. Our findings further elucidate the developmental patterns of the vertebrate auditory system.

animal behavior and cognition↗

bioRxiv2019

Increasing vitrification temperature improves the cryo-electron microscopy reconstruction

At the initial stage of the cryo-electron microcopy (cryo-EM) samples irradiated by electrons, the cryo-EM samples suffer from a rapid \"burst\" phase (first 3~4 e-/[A]2) of beam induced motion (BIM) which is too fast to be corrected by existing motion correction software, and lowers the quality of the initial frames. Therefore, these least radiation damaged, but ruined frames are commonly excluded or down-weighted during data processing, which reduces the undamaged signals in the reconstruction and decreases the reconstruction resolution by weakening the averaging power. Here, we show that increasing the freezing temperature of cryo-EM samples suppresses the BIM in this phase. The quality of initial frames is partially recovered after BIM correction and is better than that of subsequent frames in certain frames. Incorporating these initial frames into the reconstruction increases the resolution, at an equivalent of ~60% extra data. Moreover, these frames are least radiation damaged, thus preserves the high quality cryo-EM density of radiation sensitive residues. Such density is usually damaged or very weak in the canonical 3D reconstruction. In addition, we found that a different kind of radiation damage neglected previously occurs in the per-frame reconstruction after the exposure of 2.5 e-/[A]2. Such radiation damage distorts the density of atoms. The deformation can be avoided by only including the frames from the first 2.5 e-/[A]2 into the reconstruction. Overall, the high temperature freezing not only provides extra undamaged signal to the reconstruction, but also increases the resolution of the reconstruction.

biophysics↗

bioRxiv2019

Precise regulation of the relative rates of surface area and volume synthesis in dynamic environments

Bacterial cells constantly face complex environmental changes in their natural habitats. While steady-state cell size correlates with nutrient-determined growth rate, it remains unclear how cells regulate their morphology during rapid environmental changes. Here, we systematically quantified cellular dimensions throughout passage cycles of stationary-phase cells diluted into fresh medium and grown back to saturation, and found that cells exhibit characteristic dynamics in surface area to volume ratio (SA/V). SA/V dynamics were conserved across many genetic/chemical perturbations, as well as across species and growth temperatures. We developed a model with a single fitting parameter, the time delay between surface and volume synthesis, that quantitatively explained our SA/V observations, and showed that the time delay was indeed due to differential expression of volume and surface-related genes. The first division after dilution occurred at a tightly controlled SA/V, a previously unrecognized size-control mechanism highlighting the relevance of SA/V. Finally, our time-delay model successfully predicted the quantitative changes in SA/V dynamics due to altered surface area synthesis rates or time delays from translation inhibition. Our minimal model thus provides insight into how cells regulate their morphologies through differential regulation of surface area and volume synthesis and potentiates deep understanding of the connections between growth rate and cell shape in complex environments.

microbiology↗

bioRxiv2019

Population-specific causal disease effect sizes in functionally important regions impacted by selection

Many diseases and complex traits exhibit population-specific causal effect sizes with trans-ethnic genetic correlations significantly less than 1, limiting trans-ethnic polygenic risk prediction. We developed a new method, S-LDXR, for stratifying squared trans-ethnic genetic correlation across genomic annotations, and applied S-LDXR to genome-wide association summary statistics for 31 diseases and complex traits in East Asians (EAS) and Europeans (EUR) (average NEAS=90K, NEUR=267K) with an average trans-ethnic genetic correlation of 0.85 (s.e. 0.01). We determined that squared trans-ethnic genetic correlation was 0.82x (s.e. 0.01) smaller than the genome-wide average at SNPs in the top quintile of background selection statistic, implying more population-specific causal effect sizes. Accordingly, causal effect sizes were more population-specific in functionally important regions, including conserved and regulatory regions. In analyses of regions surrounding specifically expressed genes, causal effect sizes were most population-specific for skin and immune genes and least population-specific for brain genes. Our results could potentially be explained by stronger gene-environment interaction at loci impacted by selection, particularly positive selection.

genetics↗