Identification of quantitative trait loci for four morphologic traits under water stress in rice （Oryza sativa L.）

Late season drought coinciding with the rice booting to heading stage affects the development of plant height,panicle exsertion,and flag leaf size,and causes significant yield loss.In this study,a recombinant inbred line population derived from a cross between paddy and upland cultivars was used for data collection of the morphologic traits under well water and drought stress conditions.bought stress was applied at the stage of panicle initiation in the field in 2002 and at the booting stage in PVC pipes in 2003.The data from stress con ditions and their ratios(tait measured under stress condition/trait measured under well water condition)or differences(trait measured under stress condition minus trait measured under well water condition)were used for OTL analysis.Totally,17 and 36 QTLs for these traits were identified in 2002 and 2003,respectively,which explained a range of 2.58%-29.82%Of the phenotypic variation.Among them,six QTLs were commonly identified in the two years,suggesting that the drought stress in the two years was different.The genetic basis of these traits will provide useful information for improving rice late season drought resistance,and their application as indirect indices in rice late season drought resistance screening was also discussed.     

Genetic and environmental interactions determine seizure susceptibility in epileptic EL mice

Gene identification has progressed rapidly for monogenic epilepsies, but complex gene-environmental interactions have hindered progress in gene identification for multifactorial epilepsies. We analyzed the role of environmental risk factors in the inheritance of multifactorial idiopathic generalized epilepsy in the EL mouse. Seizure susceptibility was evaluated in the EL (E) and seizure-resistant ABP/LeJ (A) parental mouse strains and in their AEF1 and AEF2 hybrid offspring using a handling-induced seizure test. The seizure test was administered in three environments (environments I, II and III) that differed with respect to the number of seizure tests administered (one test or four tests) and the age of the mice when tested (young or old). The inheritance of seizure susceptibility appeared dominant after repetitive seizure testing in young or old mice, but recessive after a single test in old mice. Heritability was high (0.67-0.77) in each environment. Significant quantitative trait loci (QTL) that were associated with environments I and III (repetitive testing) were found on chromosomes 2 and 9 and colocalized with previously mapped El2 and El4, respectively. The El2 QTL found in environment I associated only with female susceptibility. A novel QTL, El-N, for age-dependent predisposition to seizures was found on proximal chromosome 9 only in environment II. The findings indicate that environmental risk factors determine the genetic architecture of seizure susceptibility in EL mice and suggest that QTL for complex epilepsies should be defined in terms of the environment in which they are expressed.     

The Saccharomyces cerevisiae W303-K6001 cross-platform genome sequence: insights into ancestry and physiology of a laboratory mutt

Saccharomyces cerevisiae strain W303 is a widely used model organism. However, little is known about its genetic origins, as it was created in the 1970s from crossing yeast strains of uncertain genealogy. To obtain insights into its ancestry and physiology, we sequenced the genome of its variant W303-K6001, a yeast model of ageing research. The combination of two next-generation sequencing (NGS) technologies (Illumina and Roche/454 sequencing) yielded an 11.8 Mb genome assembly at an N50 contig length of 262 kb. Although sequencing was substantially more precise and sensitive than whole-genome tiling arrays, both NGS platforms produced a number of false positives. At a 378× average coverage, only 74 per cent of called differences to the S288c reference genome were confirmed by both techniques. The consensus W303-K6001 genome differs in 8133 positions from S288c, predicting altered amino acid sequence in 799 proteins, including factors of ageing and stress resistance. The W303-K6001 (85.4%) genome is virtually identical (less than equal to 0.5 variations per kb) to S288c, and thus originates in the same ancestor. Non-S288c regions distribute unequally over the genome, with chromosome XVI the most (99.6%) and chromosome XI the least (54.5%) S288c-like. Several of these clusters are shared with Σ1278B, another widely used S288c-related model, indicating that these strains share a second ancestor. Thus, the W303-K6001 genome pictures details of complex genetic relationships between the model strains that date back to the early days of experimental yeast genetics. Moreover, this study underlines the necessity of combining multiple NGS and genome-assembling techniques for achieving accurate variant calling in genomic studies.     

人乳头瘤病毒-6 L1蛋白B-细胞优势表位作为多肽疫苗的研究

本研究分析了人乳头瘤病毒-6型L1外壳蛋白之B-细胞优势表位,并拟以此为基础制作表位多肽疫苗。研究中采用Goldkey和PC／Gene软件系统综合分析HPV6之L1蛋白B-细胞优势表位后,Fmoc固相合成表位多肽,通过HPLC纯化和毛细管电泳分析其纯度。与佐剂完全乳化后,免疫小鼠,进行动物水平的免疫效果评价。取免疫小鼠血清,与HPV-6 DNA阳性的尖锐湿疣患者疣体组织上清液结合,以鉴定免疫小鼠所产生抗体的特异性。发现L1蛋白第425-439位和第486-500位具有较高的免疫原性,可明显诱导小鼠血清抗体滴度升高,且该抗体与人尖锐湿疣疣体组织上清液呈阳性反应。说明所选这两个肽段为HPV6之L1蛋白的B-细胞优势表位,但诱导产生的抗体是否具有功能特异性,正在做进一步研究。     

Retracted: Screening of candidate genes and fine mapping of drought tolerance quantitative trait loci on chromosome 4 in rice (Oryza sativa L.) under drought stress

Due to severe water resource shortage, genetics of and breeding for DT (drought tolerance) in rice (Oryza sativa L.) have become one of the hot research topics. Identification of grain yield QTLs (quantitative trait loci) directly related to the DT trait of rice can provide useful information for breeding new drought‐resistant and water‐saving rice varieties via marker‐assisted selection. A population of 105 advanced BILs (backcross introgression lines) derived from a cross between Zhenshan97B and IRAT109 in Zhenshan97B background were grown under drought stress in a field experiment and phenotypic traits were investigated. The results showed that in the target interval of RM273‐RM255 on chromosome 4, three main‐effect QTLs related to panicle length, panicle number, and spikelet number per panicle were identified (LOD [logarithm of the odds] > 2.0). The panicle length‐related QTL had two loci located in the neighboring intervals of RM17308‐RM17305 and RM17349‐RM17190, which explained 18.80% and 20.42%, respectively, of the phenotypic variation, while the panicle number‐related QTL was identified in the interval of RM1354‐RM17308, explaining 11.47% of the phenotypic variation. As far as the spikelet number per panicle‐related QTL was concerned, it was found to be located in the interval of RM17308‐RM17305, which explained 28.08% of the phenotypic variation. Using the online Plant‐GE query system, a total of 13 matched ESTs (expressed sequence tags) were found in the target region, and of the 13 ESTs, 12 had corresponding predicted genes. For instance, the two ESTs CB096766 and CA765747 were corresponded to the same predicted gene LOC_Os04g46370, while the other four ESTs, CA754286, CB000011, CX056247, and CX056240, were corresponded to the same predicted gene LOC_Os04g46390.     

A multiparent advanced generation inter-cross population for genetic analysis in wheat

We present the first results from a novel multiparent advanced generation inter-cross (MAGIC) population derived from four elite wheat cultivars. The large size of this MAGIC population (1579 progeny), its diverse genetic composition and high levels of recombination all contribute to its value as a genetic resource. Applications of this resource include interrogation of the wheat genome and the analysis of gene-trait association in agronomically important wheat phenotypes. Here, we report the utilization of a MAGIC population for the first time for linkage map construction. We have constructed a linkage map with 1162 DArT, single nucleotide polymorphism and simple sequence repeat markers distributed across all 21 chromosomes. We benchmark this map against a high-density DArT consensus map created by integrating more than 100 biparental populations. The linkage map forms the basis for further exploration of the genetic architecture within the population, including characterization of linkage disequilibrium, founder contribution and inclusion of an alien introgression into the genetic map. Finally, we demonstrate the application of the resource for quantitative trait loci mapping using the complex traits plant height and hectolitre weight as a proof of principle.     

Deciphering Spatial Protein–Protein Interactions in Brain Using Proximity Labeling

Cellular biomolecular complexes including protein–protein, protein–RNA, and protein–DNA interactions regulate and execute most biological functions. In particular in brain, protein–protein interactions (PPIs) mediate or regulate virtually all nerve cell functions, such as neurotransmission, cell–cell communication, neurogenesis, synaptogenesis, and synaptic plasticity. Perturbations of PPIs in specific subsets of neurons and glia are thought to underly a majority of neurobiological disorders. Therefore, understanding biological functions at a cellular level requires a reasonably complete catalog of all physical interactions between proteins. An enzyme-catalyzed method to biotinylate proximal interacting proteins within 10 to 300 nm of each other is being increasingly used to characterize the spatiotemporal features of complex PPIs in brain. Thus, proximity labeling has emerged recently as a powerful tool to identify proteomes in distinct cell types in brain as well as proteomes and PPIs in structures difficult to isolate, such as the synaptic cleft, axonal projections, or astrocyte–neuron junctions. In this review, we summarize recent advances in proximity labeling methods and their application to neurobiology.     

Structural determinants of the dominant conformational epitopes of phospholipase A2 receptor in primary membranous nephropathy

Anti-phospholipase A2 receptor autoantibody (PLA2R-Ab) plays a critical role in the pathogenesis of primary membranous nephropathy (PMN), an autoimmune kidney disease characterized by immune deposits in the glomerular subepithelial spaces and proteinuria. However, the mechanism of how PLA2R-Abs interact with the conformational epitope(s) of PLA2R has remained elusive. PLA2R is a single transmembrane helix receptor containing ten extracellular domains that begin with a CysR domain followed by a FnII and eight CTLD domains. Here, we examined the interactions of PLA2R-Ab with the full PLA2R protein, N-terminal domain truncations, and C-terminal domain deletions under either denaturing or physiological conditions. Our data demonstrate that the PLA2R-Abs against the dominant epitope (the N-terminal CysR-CTLD1 triple domain) possess weak cross-reactivities to the C-terminal domains beyond CTLD1. Moreover, both the CysR and CTLD1 domains are required to form a conformational epitope for PLA2R-Ab interaction, with FnII serving as a linker domain. Upon close examination, we also observed that patients with newly diagnosed PMN carry two populations of PLA2R-Abs in sera that react to the denatured CysR-CTLD3 (the PLA2R-Ab₁) and denatured CysR-CTLD1 (the PLA2R-Ab₂) domain complexes on Western blots, respectively. Furthermore, the PLA2R-Ab₁ appeared at an earlier time point than PLA2R-Ab₂ in patients, whereas the increased levels of PLA2R-Ab₂ coincided with the worsening of proteinuria. In summary, our data support that an integrated folding of the three PLA2R N-terminal domains, CysR, FnII, and CTLD1, is a prerequisite to forming the PLA2R conformational epitope and that the dominant epitope-reactive PLA2R-Ab₂ plays a critical role in PMN clinical progression.     

Genome physical mapping with large-insert bacterial clones by fingerprint analysis: methodologies, source clone genome coverage, and contig map quality

Genome physical mapping with large-insert clones by fingerprint analysis is becoming an active area of genomics research. Here, we report two new capillary electrophoresis-based fingerprinting methods for genome physical mapping and the effects of different fingerprinting methods and source clone genome coverage on quality physical map construction revealed by computer simulations and laboratory experiments. It was shown that the manual sequencing gel-based two-enzyme fingerprinting method consistently generated larger and more accurate contigs, followed by the new capillary electrophoresis-based three-enzyme method, the new capillary electrophoresis-based five-enzyme (SNaPshot) method, the agarose gel-based one-enzyme method, and the automatic sequencing gel-based four-enzyme method, in descending order, when 1% or fewer questionable clones were allowed. Analysis of clones equivalent to 5x, 8x, 10x, and 15x genomes using the fingerprinting methods revealed that as the number of clones increased from 5x to 10x, the contig length rapidly increased for all methods. However, when the number of clones was increased from 10x to 15x coverage, the contig length at best increased at a lower rate or even decreased. The results will provide useful knowledge and strategies for effective construction of quality genome physical maps for advanced genomics research.     

森林碳汇研究热点与趋势——基于知识图谱分析

森林在全球碳循环中发挥着重要作用,森林碳汇是陆地碳汇的重要组成部分,其研究的知识领域在国际社会中已较为成熟。以Web of Science中1990-2021年4973篇相关的文献为研究对象,运用文献计量工具CiteSpace绘制文献共被引和关键词共现网络知识图谱,以此清楚分析森林碳汇研究的发展趋势。研究发现：（1）森林碳汇研究的发文量持续增长,文献数量的变化趋势证明森林碳汇仍是国内外的研究热点。（2）森林碳汇研究主线变化从运用大量方法测量森林碳平衡,到对森林碳汇稳定区域估计的理论归纳,再到将理论用于实践并全面实现对全球碳汇规模的监控。阶段的热点问题从森林是否为碳汇到森林碳汇的形成机制,再到实现监控管理下的可持续森林碳汇。（3）国内森林碳汇研究主线变化从研究测量碳储量的方法,到运用大量方法测量中国森林碳平衡,再到中国森林碳汇稳定区域估计的理论归纳。阶段的热点问题从中国森林碳储量的变化,转变为中国森林是否为碳汇,最后聚焦到中国森林碳汇的形成机制。如今国内研究趋势逐渐与国际接轨,中国在国际森林碳汇研究领域中的学术地位日益提升。在未来,中国需要增加对森林生态系统调查和监测强度,构建"天-空-地"一体化的碳汇计算体系,进而实现对碳汇规模的准确监控。并且需要准确且全面评估森林碳汇对我国实现"碳中和"目标的贡献,推动我国"碳中和"目标的实现。