Evolution and diversity of axon guidance Robo receptor family genes

The diversity of axon guidance (AG) receptors reflects gains in complexity of the animal nervous system during evolution. Members of the Roundabout (Robo) family of receptors interact with Slit proteins and play important roles in many developmental processes, including AG and neural crest cell migration. There are four members of the Robo gene family. However, the evolutionary history of Robo family genes remain obscure. We analyzed the distribution of Robo family members in metazoan species ranging in complexity from hydras to humans. We undertook a phylogenetic analysis in metazoans, synteny analysis, and ancestral chromosome mapping in vertebrates, and detected selection pressure and functional divergence among four mammalian Robo paralogs. Based on our analysis, we proposed that the ancestral Robo gene could have undergone a tandem duplication in the vertebrate ancestor; then one round of whole genome duplication events occurred before the divergence of ancestral lamprey and gnathostome, generating four paralogs in early vertebrates. Robo4 paralog underwent segmental loss in the following evolutionary process. Our results showed that Robo3 paralog is under more powerful purifying selection pressure compared with other three paralogs, which could correlate with its unique expression pattern and function. Furthermore, we found four sites under positive selection pressure on the Ig1‐2 domains of Robo4 that might interfere with its binding to Slits ligand. Diverge analysis at the amino acid level showed that Robo4 paralog have relatively greater functional diversifications than other Robo paralogs. This coincides with the fact that Robo4 predominantly functions in vascular endothelial cells but not the nervous system.     

桑黄Zn(II)2Cys6锌簇蛋白转录因子及其在不同碳氮源条件下的表达

Zn(II)2Cys6锌簇蛋白转录因子（C6 zinc）在真菌次生代谢产物合成中发挥重要作用。本研究首先利用本地BLAST,从桑黄Sanghuangporus sanghuang全基因组中获得Zn(II)2Cys6锌簇蛋白转录因子编码基因,并利用生物信息学手段分析编码蛋白保守结构域、一级结构及二级结构,构建蛋白系统发育树,最后利用半定量PCR对它们在不同碳源和氮源培养条件下的表达情况进行检测。结果显示:从桑黄基因组中分析获得的11个Zn(II)2Cys6锌簇蛋白均具有Cy6型锌指基序,属于GAL4型锌簇蛋白转录因子;它们均为不稳定亲水性蛋白,具磷酸化修饰位点,糖基化修饰位点较少或没有,定位于细胞核中;其二级结构主要以无规卷曲和α螺旋为主;系统发育树分析结果显示,桑黄Zn(II)2Cys6锌簇蛋白分为2个大分支,其中Ⅰ类分支转录因子的保守结构域分布于蛋白N-端,Ⅱ类分支转录因子的保守结构域则分布于蛋白C-端;11个桑黄Zn(II)2Cys6锌簇蛋白转录因子在不同培养基培养的菌丝体中呈现差异化表达,其中,肌醇培养基和乳糖培养基能够有效促进大部分锌簇蛋白转录因子的表达;另外,基因簇分析显示桑黄锌簇蛋白SHCZ4可能是NRPS-PKS杂合基因簇体系的途经特异性转录因子。该结果将为桑黄次生代谢产物合成调控相关转录因子的研究以及潜在次生代谢相关基因簇的挖掘提供参考依据。     

超声评分法及肾动脉阻力指数对胎儿肾积水预后的评价价值分析

目的:研究超声评分法及肾动脉阻力指数(RRI)对胎儿肾积水预后的评价价值。方法:将从2016年1月2019年1月经我院超声检查发现的孕晚期肾积水胎儿210例纳入研究,测定其肾实质厚度(RPT)、肾盂前后径(APD)以及肾盂肾盏形态,对上述各项超声检测指标进行评分,累计计算分值。此外,对所有胎儿的积水肾脏肾门部位的RRI值进行测定,并以受试者工作特征(ROC)曲线分析超声评分法与RRI值诊断胎儿肾积水预后类型的价值。结果:所有胎儿出生1年内分别行超声检查以及临床诊断,结果显示210例胎儿,共计420只肾脏,共发生285只肾积水,包括病理性肾积水84只(病理性组),非病理性肾积水201只(非病理性组)。病理性肾积水胎儿超声评分为13分的肾只数占比显著低于非病理性胎儿(P<0.05),而79分的肾只数占比显著高于非病理性胎儿(P<0.05)。病理性肾积水胎儿的平均RRI值为0.74±0.05,显著高于非病理性肾积水胎儿的0.63±0.02,差异有统计学意义(t=26.563,P=0.000)。超声评分法与RRI联合诊断病理性肾积水的曲线下面积(AUC)、敏感度、特异度、准确度均显著高于超声评分法或RRI单独诊断(P<0.05)。结论:超声评分法及RRI诊断对胎儿肾积水预后评价具有较重要的价值,值得临床推广应用。     

Potassium and phosphorus transport and signaling in plants

Nitrogen(N), potassium(K), and phosphorus(P) are essential macronutrients for plant growth and development, and their availability affects crop yield. Compared with N, the relatively low availability of K and P in soils limits crop production and thus threatens food security and agricultural sustainability. Improvement of plant nutrient utilization efficiency provides a potential route to overcome the effects of K and P deficiencies. Investigation of the molecular mechanisms underlying how plants sense, absorb, transport, and use K and P is an important prerequisite to improve crop nutrient utilization efficiency. In this review, we summarize current understanding of K and P transport and signaling in plants, mainly taking Arabidopsis thaliana and rice(Oryza sativa) as examples. We also discuss the mechanisms coordinating transport of N and K, as well as P and N.     

血清DCN、NRG-1、MIF水平与首发未服药精神分裂症患者临床症状和认知功能的相关性分析

目的:探讨血清核心蛋白多糖(DCN)、神经调节蛋白-1(NRG-1)、巨噬细胞迁移抑制因子(MIF)水平与首发未服药精神分裂症患者临床症状和认知功能的相关性。方法:选择2018年1月~2020年11月期间长江大学附属第一医院收治的首发未服药精神分裂症患者80例作为精神分裂症组,同期于长江大学附属第一医院进行体检的健康志愿者80例作为对照组。应用阳性和阴性症状量表(PANSS)评估患者精神病理症状,应用MATRICS共识认知成套测验(MCCB)评估所有受试者认知功能。根据PANSS评分将精神分裂症组分为PANSS评分高分组和低分组,比较两组血清DCN、NRG-1、MIF水平,并分析以上指标水平与PANSS总分、MCCB各项评分的相关性。结果:精神分裂症组患者PANSS总分为(77.18±13.57)分。精神分裂症组MCCB各项评分均低于对照组(P<0.05)。精神分裂症组血清DCN、NRG-1水平低于对照组,MIF水平高于对照组(P<0.05)。PANSS高分组血清DCN、NRG-1水平低于PANSS低分组,MIF水平高于PANSS低分组(P<0.05)。Pearson相关性分析显示,首发未服药精神分裂症患者血清DCN、NRG-1水平与PANSS总分呈负相关,与MCCB各项评分呈正相关,MIF水平与PANSS总分呈正相关,与MCCB各项评分呈负相关(均P<0.05)。结论:首发未服药精神分裂症患者血清DCN、NRG-1、MIF水平异常,且以上指标水平与患者临床症状和认知功能受损有一定联系,提示检测以上指标水平可能为该病患者认知功能及临床症状的评估提供参考。     

Targeted sequencing and integrative analysis of 3,195 Chinese patients with neurodevelopmental disorders prioritized 26 novel candidate genes

Neurodevelopmental disorders(NDDs) are a set of complex disorders characterized by diverse and cooccurring clinical symptoms. The genetic contribution in patients with NDDs remains largely unknown.Here, we sequence 519 NDD-related genes in 3,195 Chinese probands with neurodevelopmental phenotypes and identify 2,522 putative functional mutations consisting of 137 de novo mutations(DNMs) in 86 genes and 2,385 rare inherited mutations(RIMs) with 22 X-linked hemizygotes in 13 genes, 2 homozygous mutations in 2 genes and 23 compound heterozygous mutations in 10 genes. Furthermore, the DNMs of16,807 probands with NDDs are retrieved from public datasets and combine in an integrated analysis with the mutation data of our Chinese NDD probands by taking 3,582 in-house controls of Chinese origin as background. We prioritize 26 novel candidate genes. Notably, six of these genes d ITSN1, UBR3, CADM1,RYR3, FLNA, and PLXNA3 d preferably contribute to autism spectrum disorders(ASDs), as demonstrated by high co-expression and/or interaction with ASD genes confirmed via rescue experiments in a mouse model. Importantly, these genes are differentially expressed in the ASD cortex in a significant manner and involved in ASD-associated networks. Together, our study expands the genetic spectrum of Chinese NDDs,further facilitating both basic and translational research.     

Genomes of 12 fig wasps provide insights into the adaptation of pollinators to fig syconia

Figs and fig pollinators are one of the few classic textbook examples of obligate pollination mutualism. The specific dependence of fig pollinators on the relatively safe living environment with sufficient food sources in the enclosed fig syconia implies that they are vulnerable to habitat changes. However, there is still no extensive genomic evidence to reveal the evolutionary footprint of this long-term mutually beneficial symbiosis in fig pollinators. In fig syconia, there are also non-pollinator species. The non-pollinator species differ in their evolutionary and life histories from pollinators. We conducted comparative analyses on 11 newly sequenced fig wasp genomes and one previously published genome. The pollinators colonized the figs approximately 66.9 million years ago, consistent with the origin of host figs. Compared with nonpollinators, many more genes in pollinators were subject to relaxed selection. Seven genes were absent in pollinators in response to environmental stress and immune activation. Pollinators had more streamlined gene repertoires in the innate immune system, chemosensory toolbox, and detoxification system. Our results provide genomic evidence for the differentiation between pollinators and nonpollinators. The data suggest that owing to the long-term adaptation to the fig, some genes related to functions no longer required are absent in pollinators.     

A whole-genome association approach for large-scale interspecies traits

Science China Life Sciences -     

Comprehensive landscape and interference of clonal haematopoiesis mutations for liquid biopsy: A Chinese pan-cancer cohort

Tumour-derived DNA found in the plasma of cancer patients provides the probability to detect somatic mutations from circulating cell-free DNA (cfDNA) in plasma samples. However, clonal hematopoiesis (CH) mutations affect the accuracy of liquid biopsy for cancer diagnosis and treatment. Here, we integrated landscape of CH mutations in 11,725 pan-cancer patients of Chinese and explored effects of CH on liquid biopsies in real-world. We first identified 5933 CHs based on panel sequencing of matched DNA of white blood cell and cfDNA on 301 genes for 5100 patients, in which CH number of patients had positive correlation with their diagnosis age. We observed that canonical genes related to CH, including DNMT3A, TET2, ASXL1, TP53, ATM, CHEK2 and SF3B1, were dominant in the Chinese cohort and 13.29% of CH mutations only appeared in the Chinese cohort compared with the Western cohort. Analysis of CH gene distribution bias indicated that CH tended to appear in genes with functions of tyrosine kinase regulation, PI3K-Akt signalling and TP53 activity, suggesting unfavourable effects of CH mutations in cancer patients. We further confirmed effect of driver genes carried by CH on somatic mutations in liquid biopsy of cancer patients. Forty-eight actionable somatic mutations in 17 driver genes were considered CH genes in 92 patients (1.80%) of the Chinese cohort, implying potential impacts of CH on clinical decision-making. Taken together, this study exhibits strong evidence that gene mutations from CH interfere accuracy of liquid biopsies using cfDNA in cancer diagnosis and treatment in real-world.