The eQTL colocalization and transcriptome‑wide association study identify potentially causal genes responsible for economic traits in Simmental beef cattle

Background A detailed understanding of genetic variants that affect beef merit helps maximize the efficiency of breeding for improved production merit in beef cattle.To prioritize the putative variants and genes,we ran a com-prehensive genome-wide association studies(GWAS)analysis for 21 agronomic traits using imputed whole-genome variants in Simmental beef cattle.Then,we applied expression quantitative trait loci(eQTL)mapping between the genotype variants and transcriptome of three tissues(longissimus dorsi muscle,backfat,and liver)in 120 cattle.Results We identified 1,580 association signals for 21 beef agronomic traits using GWAS.We then illuminated 854,498 cis-eQTLs for 6,017 genes and 46,970 trans-eQTLs for 1,903 genes in three tissues and built a synergistic network by integrating transcriptomics with agronomic traits.These cis-eQTLs were preferentially close to the transcription start site and enriched in functional regulatory regions.We observed an average of 43.5%improvement in cis-eQTL discovery using multi-tissue eQTL mapping.Fine-mapping analysis revealed that 111,192,and 194 variants were most likely to be causative to regulate gene expression in backfat,liver,and muscle,respectively.The transcriptome-wide association studies identified 722 genes significantly associated with 11 agronomic traits.Via the colocalization and Mendelian randomization analyses,we found that eQTLs of several genes were associated with the GWAS signals of agronomic traits in three tissues,which included genes,such as NADSYN1,NDUFS3,LTF and KIFC2 in liver,GRAMD1C,TMTC2 and ZNF613 in backfat,as well as TIGAR,NDUFS3 and L3HYPDH in muscle that could serve as the candidate genes for economic traits.Conclusions The extensive atlas of GWAS,eQTL,fine-mapping,and transcriptome-wide association studies aid in the suggestion of potentially functional variants and genes in cattle agronomic traits and will be an invaluable source for genomics and breeding in beef cattle.

Colocalization of SOM and NOS in the neurons of raphe nucleiinnervating the pharyngeal muscles in the rats: PRV,SOMandNADPH-d triplelabelingstudy

Objective: To investigate the colocalization of Somatostatin (SOM ) and NADPH--diaphorase (NADPHd ) of the neurons in raphe nuclei innervating pharyngeal muscles in the rats. Methods: After PRV was injected into the pharyngeal muscles. PRV and SOM immunofluorescence double labeling procedure was completed at first,then proceeded NADPH -d histochemistry. Results: PRV and SOM double--labled cells were present mainly in the nucleus raphe magnus. but some PRV and SOM double labled neurons were found in the other raphe nuclei as well, such as nucleus raphe pallidus. nucleus raphe obsurus, median raphe nucleus and dorsal raphe nucleus.NADPH -d positive neurons were also observed in the raphe nuclei. PRV. SOM and NADPH-d triple labeling neurons were found in the nucleus raphe magnus. Conclusion: It is suggested that the colocalization of SOM and NADPH--d of the neurons in the raphe nuclei innervating pharyngeal muscles may play an important role in the coordination of the pharyngeal motility.

Identification of novel drug targets for diabetic retinopathy:proteome-wide mendelian randomization and colocalization analyses

Background:Diabetic retinopathy(DR)urgently needs novel and effective therapeutic targets.Integrated analyses of plasma proteomic and genetic markers can clarify the causal relevance of proteins and discover novel targets for diseases,but no systematic screening for DR has been performed.Methods:Summary statistics of plasma protein quantitative trait loci(pQTL)were derived from two extensive genome-wide analysis study(GWAS)datasets and one systematic review,with over 100 thousand participants covering thousands of plasma proteins.DR data were sourced from the largest FinnGen study,comprising 10,413 DR cases and 308,633 European controls.Genetic instrumental variables were identified using multiple filters.In the two-sample MR analysis,Wald ratio and inverse variance-weighted(IVW)MR were utilized to investigate the causality of plasma proteins with DR.Bidirectional MR,Bayesian Co-localization,and phenotype scanning were employed to test for potential reverse causality and confounding factors in the main MR analyses.By systemically searching druggable gene lists,the ChEMBL database,DrugBank,and Gene Ontology database,the druggability and relevant functional pathways of the identified proteins were systematically evaluated.Results:Genetically predicted levels of 24 proteins were significantly associated with DR risk at a false discovery rate<0.05 including 11 with positive associations and 13 with negative associations.For each standard deviation increase in plasm protein levels,the odds ratios(ORs)for DR varied from 0.51(95%CI:0.36-0.73;P=2.22×10-5)for tubulin polymerization-promoting protein family member 3(TPPP3)to 2.02(95%CI:1.44-2.83;P=5.01×10-5)for olfactomedin like 3(OLFML3).Bidirectional MR indicated there was no reverse causality that interfered with the results of the main MR analyses.Four proteins exhibited strong co-localization evidence(PH4≥0.8):cytoplasmic tRNA synthetase(WARS),acrosin binding protein(ACRBP),and intercellular adhesion molecule 1(ICAM1)were negatively associated with DR risk,while neurogenic locus notch homolog protein 2(NOTCH2)showed a positive association.No confounding factors were detected between pQTLs and DR according to the phenotypic scan.Drugability assessments highlighted 6 proteins already in drug development endeavor and 18 novel drug targets,with metalloproteinase inhibitor 3(TIMP)currently in phase I clinical trials for DR.GO analysis identified 18 of 24 plasma proteins enriching 22 pathways related to cell differentiation and proliferation regulation.Conclusions:Twenty-four promising drug targets for DR were identified,including four plasma proteins with particular co-localization evidence.These findings offer new insights into DR's etiology and therapeutic targeting,exemplifying the value of genomic and proteomic data in drug target discovery.

ezQTL:A Web Platform for Interactive Visualization and Colocalization of QTLs and GWAS Loci

Genome-wide association studies(GWAS)have identified thousands of genomic loci associated with complex diseases and traits,including cancer.The vast majority of common traitassociated variants identified via GWAS fall in non-coding regions of the genome,posing a challenge in elucidating the causal variants,genes,and mechanisms involved.Expression quantitative trait locus(eQTL)and other molecular QTL studies have been valuable resources in identifying candidate causal genes from GWAS loci through statistical colocalization methods.While QTL colocalization is becoming a standard analysis in post-GWAS investigation,an easy web tool for users to perform formal colocalization analyses with either user-provided or public GWAS and eQTL datasets has been lacking.Here,we present ezQTL,a web-based bioinformatic application to interactively visualize and analyze genetic association data such as GWAS loci and molecular QTLs under different linkage disequilibrium(LD)patterns(1000 Genomes Project,UK Biobank,or user-provided data).This application allows users to perform data quality control for variants matched between different datasets,LD visualization,and two-trait colocalization analyses using two state-of-the-art methodologies(eCAVIAR and HyPrColoc),including batch processing.ezQTL is a free and publicly available cross-platform web tool,which can be accessed online at https://analysistools.cancer.gov/ezqtl.

两个色原酮衍生物的二维谱研究

应用２ＤＮＭＲ技术研究了土茯苓中两个新色原酮衍生物的结构，证实二维谱技术（ＣＯＬＯＣ，１Ｈ－１ＨＣＯＳＹ，２ＤＩＮＡＤＥＱＵＡＴＥ）可用于确定该类化合物的取代基位置．同时也有助于确定该类化合物的１３Ｃ、１ＨＮＭＲ谱的详细归属．

用COLOC谱研究线型二氢吡喃香豆素Pd—C—I酰基连接位置

用ＣＯＬＯＣ技术并结合１Ｈ－１ＨＣＯＳＹ谱对线型二氢吡喃香豆素类化合物Ｐｄ—Ｃ—Ｉ的化学结构进行了深入研究．证实该类化合物酰基连接位置可用ＣＯＬＯＣ谱确定．这对这类化合物的结构研究和构效关系的探讨均有重要意义，另外利用２ＤＮＭＲ修正了文献中对Ｐｄ—Ｃ—Ｉ部分碳氢信号归属的错误．

Induction of endoplasmic reticulum-derived oxidative stress by an occult infection related S surface antigen variant

AIM: To investigate the mechanism of endoplasmic reticulum(ER) stress induction by an occult infection related hepatitis B virus S surface antigen(HBsAg)variant.METHODS: We used an HBsAg variant with lower secretion capacity, which was a KD variant from a Korean subject who was occultly infected with the genotype C. We compared the expression profiles of ER stress-related proteins between HuH-7 cells transfected with HBsAg plasmids of a wild-type and a KD variant using Western blot.RESULTS: Confocal microscopy indicated that the KD variant had higher levels of co-localization with ER than the wild-type HBsAg. The KD variant upregulated ER stress-related proteins and induced reactive oxygen species(ROS) compared to the wildtype via an increase in calcium. The KD variant also down-regulated anti-oxidant proteins(HO-1, catalase and SOD) compared to the wild-type, which indicates positive amplification loops of the ER-ROS axis. The KD variant also induced apoptotic cell death via the upregulation of caspase proteins(caspase 6, 9 and 12).Furthermore, the KD variant induced a higher level of nitric oxide than wild-type HBsAg via the up-regulation of the iNOS protein.CONCLUSION: Our data indicate that occult infection related HBsAg variants can lead to ER-derived oxidative stress and liver cell death in HuH-7 cells.

Coexisting tubular adenoma with a neuroendocrine carcinoma of colon allowing early surgical intervention and implicating a shared stem cell origin

High-grade colonic neuroendocrine carcinomas (NECs) are uncommon but extremely aggressive. Their co-existence with tubular adenoma (TA) has rarely been reported. We present a 68-year-old man who was found on routine colonoscopy to have multiple colorectal TAs and an ulcerated lesion in the ascending colon. Microscopically, a poorly-differentiated invasive carcinoma juxtaposed with a TA was identified. Differential diagnosis included a poorly-differentiated adenocarcinoma, medullary carcinoma, high-grade NEC and lymphoma. The immunohistochemical profile showed positive staining for keratins, synaptophysin and chromogranin but negative for LCA, CDX2, CK7, CK20, TTF-1 and PSA, supporting the NEC diagnosis. Upon subsequent laparoscopic right hemicolectomy, the tumor was identified as a 3.0 cm umbilicated and ulcerated mass with an adjacent TA. Both TA and NEC showed positive staining for β-catenin indicating a shared colonic origin. The mitotic counts (77/10 high power fields) and a high proliferation rate (75% by Ki-67) corroborated a high-grade stratification. Mutational analysis indicated a wild-type BRAF and KRAS with mismatch repair proficiency. The AJCC (7th edition) pathologic stage is pT3, pN0, pMx. The patient received adjuvant chemotherapy with cisplatin/etoposides for three cycles and will be followed up for a year to detect recurrence. In conclusion, the co-existence of TA with high grade-NEC in our case allowed early identification and intervention of the otherwise asymptomatic but aggressive tumor. In addition, the finding of a high-grade NEC within a large TA in this case suggests a link between the two lesions and could represent a shared stem cell origin.

Mitochondrial division inhibitor 1 protects cortical neurons from excitotoxicity:a mechanistic pathway

Mitochondrial division inhibitor 1（Mdivi-1） is a selective cell-permeable inhibitor of dynamin-related protein-1（Drp1） and mitochondrial division.To investigate the effect of Mdivi-1 on cells treated with glutamate,cerebral cortex neurons isolated from neonatal rats were treated with 10 m M glutamate for 24 hours.Normal cultured cells and dimethyl sulfoxide-cultured cells were considered as controls.Apoptotic cells were detected by flow cytometry.Changes in mitochondrial morphology were examined by electron microscopy.Drp1,Bax,and casp ase-3 expression was evaluated by western blot assays and immunocytochemistry.Mitochondrial membrane potential was detected using the JC-1 probe.Twenty-four hours after 10 m M glutamate treatment,Drp1,Bax and caspase-3 expression was upregulated,Drp1 and Bax were translocated to mitochondria,mitochondrial membrane potential was decreased and the rate of apoptosis was increased.These effects were inhibited by treatment with 50 μM Mdivi-1 for 2 hours.This finding indicates that Mdivi-1 is a candidate neuroprotective drug that can potentially mitigate against neuronal injury caused by glutamate-induced excitotoxicity.

Enduring alterations in hippocampal astrocytesynaptic proximity following adolescent alcohol exposure: reversal by gabapentin

Adolescent alcohol abuse is a substantive public health problem that has been the subject of intensive study in recent years.Despite reports of a wide range of effects of adolescent intermittent ethanol(AIE)exposure on brain and behavior,little is known about the mechanisms that may underlie those effects,and even less about treatments that might reverse them.Recent studies from our laboratory have indicated that AIE produced enduring changes in astrocyte function and synaptic activity in the hippocampal formation,suggesting the possibility of an alteration in astrocyte-neuronal connectivity and function.We utilized astrocyte-specific,membrane restricted viral labeling paired with immunohistochemistry to perform confocal single cell astrocyte imaging,three-dimensional reconstruction,and quantification of astrocyte morphology in hippocampal area CA1 from adult rats after AIE.Additionally,we assessed the colocalization of astrocyte plasma membrane labeling with immunoreactivity for AMPA-(α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid)glutamate receptor 1,an AMPA receptor subunit and established neuronal marker of excitatory synapses,as a metric of astrocyte-synapse proximity.AIE significantly reduced the colocalization of the astrocyte plasma membrane with synaptic marker puncta in adulthood.This is striking in that it suggests not only an alteration of the physical association of astrocytes with synapses by AIE,but one that lasts into adulthood-well after the termination of alcohol exposure.Perhaps even more notable,the AIE-induced reduction of astrocyte-synapse interaction was reversed by sub-chronic treatment with the clinically used agent,gabapentin(Neurontin),in adulthood.This suggests that a medication in common clinical use may have the potential to reverse some of the enduring effects of adolescent alcohol exposure on brain function.All animal experiments conducted were approved by the Duke University Institutional Animal Care and Use Committee(Protocol Registry Number A159-18-07)on July 27,2018.

Role of Interleukin 17A in Aortic Valve Inflammation in Apolipoprotein E-deficient Mice

Summary:Interleukin 17A(IL 17A)is reported to be involved in many inflammatory processes,but its role in aortic valve diseases remains unknown.We examined the role of IL17A based on an ApoE^-/-mouse model with strategies as fed with high-fat diet or treated with ILI7A monoclonal antibody(mAb).12 weeks of high-fat diet feeding can elevate cytokines secretion,inflammatory cells infiltration and myofibroblastic transition of valvular interstitial cells(VICs)in aortic valve.Moreover,diet-induction accelerated interleukin 17 receptor A(IL17RA)activation in VICs.In an IL17A inhibition model,the treatment group was intra-peritoneally injected with anti-IL17A mAb while controls received irrelevant antibody.Functional blockade of IL17A markedly reduced cellular infiltration and transition in aortic valve.To investigate potential mechanisms,NF-kB was co-stained in IL17RA^+VICs and IL17RA macrophages,and further confirmed by Western blotting in VICs.High-fat diet could activate NF-kB nuclear translocation in IL17RA^+VICs and IL17RA^+macrophages and this process was depressed after IL17A mAb-treatment.In conclusion,high-fat diet can lead to IL17A upregulation,VICs myofibroblastic transition and inflammatory cells infiltration in the aortic value of ApoE^-/-mice.Blocking IL17A with IL17A mAb can alleviate aortic valve inflammatory states.

苯并二氢呋喃类木脂素NMR谱的研究

用2DHMR技术研究了从水飞蓟素（Silymarin）中分离的一个苯并二氢呋喃类木脂素的结构，证实该类化合物的取代基位置可用COLOC谱确定．同时研究了该类化合物以DMSO-d6为溶剂的PMR谱的特征．另外对Balanophonin的PMR谱进行了详细归属．

核磁COLOC技术在一类多取代苯结构鉴定中的应用一类多取代苯结构的COLOC鉴定

通过非环前体的分子内成环反应，可合成一类多取代苯，对这类产物进行结构鉴定，有助于了解整个反应历程和机理。但取代基增多，势必导致各结构因素变得复杂，难以从各芳碳的经验计算式去推测各取代基所处的相对位置，而以一般的光、波谱方法也较难获得这类结构信息。实验表明，核磁ＣＯＬＯＣ技术是确定这类产物各取代基相对位置较为合适的方法，本文以ＮＭＲ技术对这类产物进行了结构鉴定，并讨论了ＣＯＬＯＣ技术在确定其各取代基相对位置中的作用；同时通过对产物的结构确认，讨论了产物取代基间的相互作用所导致其芳碳化学位移实测值与经验计算值之间的差异，以及含氟基团对邻位芳碳的碳氟间三键偶合作用。

模糊空间的colocation模式挖掘研究

近年来空间colocation模式挖掘由传统数据扩展到了不确定数据、模糊数据领域,但在模糊数据层面上,只有少量关于对象模糊的研究,而对于模糊空间这一论域的研究还是空白。基于经典的colocation模式挖掘的理论,针对性地提出了面向模糊空间的colocation模式挖掘及相关定义,增加了模糊数据领域内研究的深度和广度,并根据模糊数学理论结合空间colocation挖掘的特点,在模糊距离隶属度函数未知的情况下建立了具有较好适用性的FS基本算法。该算法一改以往在经典数据集上需要验证"团实例"的复杂做法,大大提高了算法性能。在已知模糊距离隶属度函数时,给出一个同时适用于经典数据以及模糊数据的增加数据完整性的通用方法;引进模糊方位,给出完全有别于以往的FS补充算法,增加了数据的完整性,并能实现模糊数据空间向经典数据空间的转换。

PERTURBATIONAL FINITE VOLUME METHOD FOR THE SOLUTION OF 2-D NAVIER-STOKES EQUATIONS ON UNSTRUCTURED AND STRUCTURED COLOCATED MESHES

Based on the first-order upwind and second-order central type of finite volume (UFV and CFV) scheme, upwind and central type of perturbation finite volume (UPFV and CPFV) schemes of the Navier-Stokes equations were developed. In PFV method, the mass fluxes of across the cell faces of the control volume (CV) were expanded into power series of the grid spacing and the coefficients of the power series were determined by means of the conservation equation itself. The UPFV and CPFV scheme respectively uses the same nodes and expressions as those of the normal first-order upwind and second-order central scheme, which is apt to programming. The results of numerical experiments about the flow in a lid-driven cavity and the problem of transport of a scalar quantity in a known velocity field show that compared to the first-order UFV and second-order CFV schemes, upwind PFV scheme is higher accuracy and resolution, especially better robustness. The numerical computation to flow in a lid-driven cavity shows that the under-relaxation factor can be arbitrarily selected ranging from (0.3) to (0.8) and convergence perform excellent with Reynolds number variation from 10~2 to 10~4.

Joint Ofshore Wind and Wave Energy Resources in the Caribbean Sea

Complementarities between wind and wave energies have many signifcant advantages that are unavailable with the sole deployment of either.Using all available wind speed,signifcant wave height,and wave period buoy observations over a 10-year period(i.e.,2009–2019),colocated wind and wave energy resources are estimated.Although buoy records are imper-fect,results show that the inner Caribbean Sea(CS)under the infuence of the Caribbean low-level jet has the highest wind energy resource at~1500 W/m^(2),followed by the outer CS at~600 W/m^(2) and Atlantic Ocean(AO)at~550–600 W/m^(2) at a 100 m height.Wave energy was most abundant in the AO at 14 kW/m,followed by the inner CS at 13 kW/m and outer CS at 5 kW/m.The average and dominant wave energies can reach a maximum of 10 and 14 kW/m,respectively.Asymmetry between wind and wave energy resources is observed in the AO,where wave energy is higher than the low wind speed/energy would suggest.Swell is responsible for this discrepancy;thus,it must be considered not only for wave energy extraction but also for wind turbine fatigue,stability,and power extraction efciency.

Efficient tensor decomposition method for noncircular source in colocated coprime MIMO radar

An effective method via tensor decomposition is proposed to deal with the joint direction-of-departure(DOD)and direction-of-arrival(DOA)estimation of noncircular sources in colocated coprime MIMO radar.By decomposing the transmitter and receiver into two sparse subarrays,noncircular property of source can be used to construct new extended received signal model for two sparse subarrays.The new received model can double the virtual array aperture due to the elliptic covariance of imping sources is nonzero.To further exploit the multidimensional structure of the noncircular received model,we stack the subarray output and its conjugation according to mode-1 unfolding and mode-2 unfolding of a third-order tensor,respectively.Thus,the corresponding extended tensor model consisted of noncircular information for DOA and DOD can be obtained.Then,the higher-order singular value decomposition technique is utilized to estimate the accurate signal subspace and angular parameter can be automatically paired via the rotational invariance relationship.Specifically,the ambiguous angle can be eliminated and the true targets can be achieved with the aid of the coprime property.Furthermore,a closed-form expression for the deterministic CRB under the NC sources scenario is also derived.Simulation results verify the superiority of the proposed estimator.

An overview of detecting gene-trait associations by integrating GWAS summary statistics and eQTLs

Detecting genes that affect specific traits(such as human diseases and crop yields)is important for treating complex diseases and improving crop quality.A genome-wide association study(GWAS)provides new insights and directions for understanding complex traits by identifying important single nucleotide polymorphisms.Many GWAS summary statistics data related to various complex traits have been gathered recently.Studies have shown that GWAS risk loci and expression quantitative trait loci(e QTLs)often have a lot of overlaps,which makes gene expression gradually become an important intermediary to reveal the regulatory role of GWAS.In this review,we review three types of gene-trait association detection methods of integrating GWAS summary statistics and e QTLs data,namely colocalization methods,transcriptome-wide association study-oriented approaches,and Mendelian randomization-related methods.At the theoretical level,we discussed the differences,relationships,advantages,and disadvantages of various algorithms in the three kinds of gene-trait association detection methods.To further discuss the performance of various methods,we summarize the significant gene sets that influence highdensity lipoprotein,low-density lipoprotein,total cholesterol,and triglyceride reported in 16 studies.We discuss the performance of various algorithms using the datasets of the four lipid traits.The advantages and limitations of various algorithms are analyzed based on experimental results,and we suggest directions for follow-up studies on detecting gene-trait associations.

Identification of new aptamer BC-3 targeting RPS7 from rapid screening for bladder carcinoma

Aptamers,short single DNA or RNA oligonucleotides,have shown immense application potential as molecular probes for the early diagnosis and therapy of cancer.However,conventional cell-SELEX technologies for aptamer discovery are time-consuming and laborious.Here we discovered a new aptamer BC-3 by using an improved rapid X-Aptamer selection process for human bladder carcinoma,for which there is no specific molecular probe yet.We show that BC-3 exhibited excellent affinity in bladder cancer cells but not normal cells.We demonstrate that BC-3 displayed high selectivity for tumor cells over their normal counterparts in vitro,in mice,and in patient tumor tissue specimens.Further endocytosis pathway analysis revealed that BC-3 internalized into bladder cancer cells via clathrin-mediated endocytosis.Importantly,we identified ribosomal protein S7(RPS7)as the binding target of BC-3 via an integrated methodology(mass spectrometry,colocalization assay,and immunoblotting).Together,we report that a novel aptamer BC-3 is discovered for bladder cancer and its properties in the disease are unearthed.Our findings will facilitate the discovery of novel diagnostic and therapeutic strategies for bladder cancer.

Gaining access to acetyl-CoA by peroxisomal surface display

Synthetic biology is constantly making progress for producing compounds on demand.Recently,Yocum and collaborators have developed an outstanding approach based on the anchoring of biosynthetic enzymes to the peroxisomal membrane.This allowed access to an untapped resource of acetyl-CoA and stimulated the synthesis of a valuable polyketide.