Chromosome-level genome assembly of the glass catfish(Kryptopterus vitreolus)reveals molecular clues to its transparent phenotype

Glass catfish(Kryptopterus vitreolus)are notable in the aquarium trade for their highly transparent body pattern.This transparency is due to the loss of most reflective iridophores and light-absorbing melanophores in the main body,although certain black and silver pigments remain in the face and head.To date,however,the molecular mechanisms underlying this transparent phenotype remain largely unknown.To explore the genetic basis of this transparency,we constructed a chromosome-level haplotypic genome assembly for the glass catfish,encompassing 32 chromosomes and 23344 protein-coding genes,using PacBio and Hi-C sequencing technologies and standard assembly and annotation pipelines.Analysis revealed a premature stop codon in the putative albinism-related tyrp1b gene,encoding tyrosinase-related protein 1,rendering it a nonfunctional pseudogene.Notably,a synteny comparison with over 30 other fish species identified the loss of the endothelin-3(edn3b)gene in the glass catfish genome.To investigate the role of edn3b,we generated edn3b^(−/−)mutant zebrafish,which exhibited a remarkable reduction in black pigments in body surface stripes compared to wild-type zebrafish.These findings indicate that edn3b loss contributes to the transparent phenotype of the glass catfish.Our high-quality chromosome-scale genome assembly and identification of key genes provide important molecular insights into the transparent phenotype of glass catfish.These findings not only enhance our understanding of the molecular mechanisms underlying transparency in glass catfish,but also offer a valuable genetic resource for further research on pigmentation in various animal species.

Microbial community composition and environmental response characteristics of typical brackish groundwater in the North China Plain

To reveal the microbial community composition of regional shallow porous brackish groundwater and its response characteristics to groundwater environment,the first and second aquifers in Taocheng District,Hengshui City were selected,and 10 groundwater source samples were collected for hydrochemical analysis and microbial 16S RNA gene V4-V5 regional sequencing.The results showed that the shallow brackish groundwater in the study area is weakly alkaline and has high ion content.The hydrochemical types are SO_(4)·Cl-Na·Mg type and HCO3·Cl-Na·Mg type as a whole.The spatial zonation of the abundance and diversity of groundwater microorganisms is obvious.The number of endemic bacteria in groundwater from upstream,midstream to downstream is 11,135 and 22 respectively,with a total of 22 bacteria.Proteobacteria is the most dominant in groundwater level(38.82%-86.88%),and there are obvious differences in different sections.At the genus level,the main dominant species in each group and sample are Pseudomonas and Hydrogenophaga.In terms of composition difference,Pseudohongiella,Pseudorhodobacter and Limnohabitans are the representatives of UR,MR and LR.On the whole,the composition of flora in groundwater in the study area is sensitive and closely related to hydrochemical processes.Species abundance is affected by alkaline and high salinity environmental indicators,while species diversity is related to depth and dissolved oxygen in weak reduction environment.

Modeling of Amperometric Immunosensor for CMOS Integration

A circuit model of the Amperometric immunosensor for use in the biosensor system-on-chip simulation is proposed in this paper.The model parameters are extracted with several methods and verified by MATLAB and SPICE simulation.A CMOS potentiostat circuit required for conditioning the Amperometric immunosensor is also included in the circuit model.The mean square error norm of the simulated curve against the measured one is 8.65×10^(-17) The whole circuit has been fabricated in a 0.35μm CMOS process.

面向变精度仿真数据建模分析的多任务学习方法比较研究

多任务学习(Multi-task Learning,MTL)是利用多个目标任务之间的关联性,实现跨任务知识迁移和共享,从而提高预测精度的一种数据驱动的机器学习范式。基于数值仿真器工程设计问题中经常存在多精度建模分析场景,即采用不同精度的数值仿真器获取数据进行建模。在上述场景中,仿真器的高/低计算精度可以被视为两种目标任务,同时,由于高/低精度数据针对的是同一个研究对象,彼此具有很强的相关性。其中的关键是如何从便宜、丰富的低精度数据中迁移出共享知识以提高基于昂贵、稀少的高精度数据的学习模型的预测质量。本文重点研究基于高斯过程(Gaussian Process,GP)或Kriging模型的多任务统计学习方法及其在高/低精度仿真建模分析方面的应用。首先,本文在典型多精度数值算例上对比分析了单任务Kriging模型,以及三种多任务(精度)模型CoKriging、MTGP(Multi-task Gaussian Process)和SDK(Simple Discrepancy Framework by Kriging,SDK)的特点及预测能力。最后,本文基于多精度仿真数据使用Kriging模型、MTGP模型和CoKriging模型预测RAE2822翼型的空气动力系数。结果表明:将多任务学习应用于多精度工程建模分析可以提高预测的准确度,进而提高产品的设计效率。

基于主动学习方法的汽轮机排缸参数分析

It is well known that the efficiency of a steam turbine is affected by the pressure recovery performance of its low-pressure exhaust hood,and therefore,parametric analysis of the exhaust hood is of great importance in the steam turbine design process.In recent years,computationally inexpensive metamodels have been widely used in the parametric analysis of exhaust hood.However,the prediction accuracy of metamodels is highly dependent on the number and distribution of sample points in the design space.The purpose of active learning is selecting informative samples sequentially to obtain an accurate metamodel within a reasonable computational budget.However,the impact of active learning on the accuracy of metamodels such as exhaust hood parameter analysis has not been fully explored.Therefore,this paper investigates and compares four representative active learning methods on the parametric modeling of turbine exhaust hoods,and the comparison results highlight the advantages of active learning and the analysis of the exhaust hood based on the metamodel with the highest accuracy.

Construction of a chromosome-level genome assembly for genome-wide identification of growth-related quantitative trait loci in Sinocyclocheilus grahami(Cypriniformes,Cyprinidae)

The Dianchi golden-line barbel,Sinocyclocheilus grahami(Regan,1904),is one of the“Four Famous Fishes”of Yunnan Province,China.Given its economic value,this species has been artificially bred successfully since 2007,with a nationally selected breed(“S.grahami,Bayou No.1”)certified in 2018.For the future utilization of this species,its growth rate,disease resistance,and wild adaptability need to be improved,which could be achieved with the help of molecular markerassisted selection(MAS).In the current study,we constructed the first chromosome-level genome of S.grahami,assembled 48 pseudo-chromosomes,and obtained a genome size of 1.49 Gb.We also performed QTL-seq analysis of S.grahami using the highest and lowest bulks(i.e.,largest and smallest size)in both a sibling and random population.We screened two quantitative trait loci(QTLs)(Chr3,14.9-39.1 Mb and Chr17,4.1-27.4 Mb)as major growth-related locations.Several candidate genes(e.g.,map2k5,stat1,phf21a,sox6,and smad6)were also identified,with functions related to growth,such as cell differentiation,neuronal development,skeletal muscle development,chondrogenesis,and immunity.These results built a solid foundation for in-depth MAS studies on the growth traits of S.grahami.

带内部支撑结构的低压排汽缸气动性能分析

The static pressure recovery of low-pressure exhaust hood is important for the overall effectiveness of steam turbines.The tubular and plate stiffeners inside the exhaust contribute to the structural safety of exhaust,which affect the aerodynamic performance.Given the complicated exhaust model coupled with the last stage of turbine,this paper intends to investigate the aerodynamic performance of exhaust hood with individual stiffeners using highfidelity numerical simulations in order to figure out the corresponding effects.The results show that(1)the types of stiffeners have different effects on the aerodynamic performance;and(2)different installation positions and types of plate stiffeners have different effects on aerodynamic performance.The above investigations highlight the future demand regarding reasonable layout and quantity of stiffeners to improve the aerodynamic performance of exhaust as well as maintaining the structural safety.

SO_(2)and SOF_(2)simultaneous detection by single mid-infrared laser based on tunable diode laser absorption spectroscopy

In the detection of multi-component gas based on tunable diode laser absorption spectroscopy(TDLAS),the problem of overlapping interference between the absorption lines of each gas is often encountered.For example,when detecting a gas mixture of sulphur dioxide(SO_(2))and thionyl fluoride(SOF_(2)),the characteristic decomposition components of SF6,there is overlapping interference in the absorption lines of the two gases,which makes it difficult to detect the concentration of gases accurately.In view of this problem,a novel method based on support vector regression model used for TDLAS is proposed to detect two gases simultaneously.The detection results show that the correlation coefficients between the concentration of SO_(2)and SOF_(2)and the average value of the second harmonic peak reached 0.992 and 0.993.In addition,through model testing,different concentrations of SO_(2)and SOF_(2)gas mixture are simultaneously detected,and the resulting maximum errors for measuring SO_(2)and SOF_(2)concentrations are less than 7.13×10^(-5)and 0.26×10^(-2).The maximum errors of the measurement results in the verification test are not more than 6.4×10^(-3)and 4.6×10^(-2).Therefore,with assistance of the novel method,the detection of multiple gases by using a single laser is achieved.

股票卖空机制与企业研发投资

本文以2007-2014年中国上市公司为样本,基于中国融券卖空的自然实验环境,采用双重差分模型检验了股票卖空机制对企业研发投资的影响。结果发现:(1)股票卖空机制抑制了中国企业研发投资的增长;(2)股票卖空交易对企业研发投资的抑制效应在治理机制不完善的上市公司更加显著;(3)股票卖空机制是通过提高企业被收购的威胁,促使企业采取真实的盈余管理等作用渠道抑制了企业的研发投资;(4)允许卖空的上市公司更可能出现研发投资效率不足。

股票卖空压力能否抑制高管的在职消费?--基于中国融资融券的自然实验证据

本文检验中国资本市场融资融券制度所施加的股票卖空压力对企业高管在职消费的影响。以2007-2014年中国上市公司财务数据为样本,基于自然实验框架的双重差分模型进行检验,结果发现,允许卖空的上市公司,其高管在职消费水平与不能卖空的上市公司相比显著降低;进一步的研究则发现,股票卖空压力是通过缓解信息不对称程度和减少委托代理问题来抑制高管的在职消费。本文实证结果说明股票卖空对高管在职消费来说是一种潜在的外部治理机制。

Involvement of NF-κB and the CX3CR1 Signaling Network in Mechanical Allodynia Induced by Tetanic Sciatic Stimulation

Tetanic stimulation of the sciatic nerve （TSS） triggers long-term potentiation in the dorsal horn of the spinal cord and long-lasting pain hypersensitivity. CX3CL1- CX3CR1 signaling is an important pathway in neuronal- microglial activation. Nuclear factor nB （NF-KB） is a key signal transduction molecule that regulates neuroinflamma- tion and neuropathic pain. Here, we set out to determine whether and how NF-~B and CX3CR1 are involved in the mechanism underlying the pathological changes induced by TSS. After unilateral TSS, significant bilateral mechanical allodynia was induced, as assessed by the von Frey test. The expression of phosphorylated NF-nB （pNF-nB） and CX3CR1 was significantly up-regulated in the bilateral dorsal horn. Immunofluorescence staining demonstrated that pNF-κB and NeuN co-existed, implying that the NF-κB pathway is predominantly activated in neurons following TSS. Administration of either the NF-κB inhibitor ammo- nium pyrrolidine dithiocarbamate or a CX3CR1-neutralizing antibody blocked the development and maintenance of neuropathic pain. In addition, blockade of NF-κB down- regulated the expression of CX3CL1-CX3CR1 signaling,and conversely the CX3CRl-neutralizing antibody also down-regulated pNF-rd3. These findings suggest an involvement of NF-κB and the CX3CR1 signaling network in the development and maintenance of TSS-induced mechanical allodynia. Our work suggests the potential clinical application of NF-κB inhibitors or CX3CR 1-neutralizing antibodies in treating pathological pain.

Divergence, evolution and adaptation in ray-finned fish genomes

With the rapid development of next-generation sequencing technologies and bioinformatics, over 50 ray-finned fish genomes by far have been sequenced with high quality. The genomic work provides abundant genetic resources for deep understanding of divergence, evolution and adaptation in the fish genomes. They are also instructive for identification of candidate genes for functional verification, molecular breeding, and development of novel marine drugs. As an example of other omics data, the Fish-T1 K project generated a big database of fish transcriptomes to integrate with these published fish genomes for potential applications. In this review, we highlight the above-mentioned recent investigations and core topics on the ray-finned fish genome research, with a main goal to obtain a deeper understanding of fish biology for theoretical and practical applications.

Assessing the genetic diversity of the critically endangered Chinese sturgeon Acipenser sinensis using mitochondrial markers and genome-wide single-nucleotide polymorphisms from RAD-seq

As a living fossil, the endangered Chinese sturgeon(Acipenser sinensis) has been considered a national treasure in China. Here,the famous Gezhouba Dam and Three Gorges Dam on the Yangtze River were built in 1988 and 2006, for economic purposes.The natural population of Chinese sturgeon has declined since then, as these dams block its migratory route to the original spawning grounds in the middle reaches of the Yangtze River. In 2013 and 2014, there was an absence of spawning where it typically happened near the Gezhouba Dam. Nevertheless, from April to June in 2015, over 1,000 larvae with different body lengths(10–35 cm) were detected along the Shanghai Yangtze Estuary; but only little is currently known about the population genetic structure of the Chinese sturgeon. Herein, we inferred population genetic parameters from 462 available Chinese sturgeon specimens based on a 421-bp fragment of the mitochondrial DNA(mtDNA) D-loop region and 1,481,620 SNPs(singlenucleotide polymorphisms) generated by restriction site-associated DNA sequencing(RAD-seq). For the D-loop dataset, 15 haplotypes were determined. Randomly picked 23 individuals, representing the 15 D-loop haplotype groups, were subsequently used for further RAD-seq validation. The average nucleotide diversity calculated from the mtDNA and RAD datasets was 0.0086 and 0.000478, respectively. The overall effective female population size was calculated to be 1,255 to 2,607, and the long-term effective population size was estimated to range from 11,950 to 119,500. We observed that the genetic variability and the effective female population size of the current population in the Yangtze River are severely low, which are similar to the data reported over 10 years ago. The deduced relatively small effective population of female fish, limiting the genetic connectivity among Chinese sturgeon, should be considered a serious threat to this endangered species.

Solid-liquid-core optical fiber biosensor for highly sensitive and selective detection of 4-chlorophenol in water

A novel solid-liquid-core fiber-optic biosensor was fabricated for highly sensitive and selective detection of 4-chlorophenol in water.The sensor comprised horseradish peroxidase(HRP)-coated U-shaped liquidcore optical fiber(LCOF)and 4-chlorophenol permselective polymer membrane.The U-shaped LCOF was flled with ethanol suspension of SiO_(2)particles and the polymer membrane was composed of molecularly imprinted polymer,sulfonated polyethersulfone,and polysulfone.The morphology,composition,and surface luminous properties of the sensing region were examined.The effects of the diameter and content of SiO_(2)particles and temperature of 4-chlorophenol solutions on the sensitivity of the biosensors were investigated.Further,the sensitivity,selectivity,response time,and limit of detection(LOD)of the biosensors was investigated.In addition,the effects of fiber core materials on the light transmission in sensing region were investigated and a biosensor sensing model was established.The proposed sensor exhibited high selectivity for 4-chlorophenol with satisfactory sensitivity,LOD,and response time:-1.18(μg/L)^(-1),30μg/L,and 400 s,respectively.The results are expected to aid in the development of methods for enhancing sensitivity of fiber-optic sensors and surface luminous intensity of optical fibers.

China is initiating the Aquatic 10-100-1,000 Genomics Program

On June 17 of 2016,a group of scientists from Chinese Academy of Fishery Sciences（CAFS）and Shenzhen BGI Fisheries Sci＆Tech Co.Ltd.（BGI Fisheries）met together in Shenzhen,China to launch a novel project,the China Aquatic 10-100-1,000 Genomics Program,to conduct molecular breeding of-10 aquaculture species and sequence genomes of-100 and transcriptomes of-1,000 aquatic species.

High-Throughput Prediction and Design of Novel Conopeptides for Biomedical Research and Development

Cone snail venoms have been considered a valuable treasure for international scientists and businessmen, mainly due to theirpharmacological applications in development of marine drugs for treatment of various human diseases. To date, around 800Conus species are recorded, and each of them produces over 1,000 venom peptides (termed as conopeptides or conotoxins).This reflects the high diversity and complexity of cone snails, although most of their venoms are still uncharacterized.Advanced multiomics (such as genomics, transcriptomics, and proteomics) approaches have been recently developed to minediverse Conus venom samples, with the main aim to predict and identify potentially interesting conopeptides in an efficientway. Some bioinformatics techniques have been applied to predict and design novel conopeptide sequences, related targets, andtheir binding modes. This review provides an overview of current knowledge on the high diversity of conopeptides andmultiomics advances in high-throughput prediction of novel conopeptide sequences, as well as molecular modeling and designof potential drugs based on the predicted or validated interactions between these toxins and their molecular targets.