A map of rye chromosome 2R using isozyme and morphological markers

Summary The segregation of isozymic loci for leaf peroxidases (L2Per) has been investigated in backcrosses and F₂ offspring of rye lines having purple seeds (Ps) and monstrosum ears (mo). The Ps, L2Per-3b, mo, and L2Per-2 loci were linked. The Ps and mo loci have been previously located on the 2R chromosome, and the L2Per-3b and L2Per-2 loci have been located on the 2RS chromosome arm. The results favor the gene order Ps ... L2Per-3b ... mo ... L2Per-2 or Ps ... mo... L2Per-3b ... L2Per-2. The position of the loci relative to the centromere is still not known, but the obtained results suggest that the mo locus could be located on the 2RS chromosome arm. On the basis of previously reported linkage groups, the most probable arrangement of the loci located on chromosome 2R is: dw2 ... Ps ... (L2Per-3a ... L2Per-3b ... mo) ... L2Per-2. It has not been possible to know the position of L2Per-4 loci (also located on 2RS chromosome arm) relative to L2Per-3a and L2Per-3b loci.     

Can the problem of hybridization in threatened species be evaluated using a fieldwork research? A case study in snapdragons

Hybridization, natural or artificial, is considered disadvantageous for species biodiversity when it threatens the population integrity of endangered species. Frequently, studies investigating whether hybridization poses a legitimate risk to rare species are based on genetic data obtained in molecular biology laboratories. In this study, we used field research to approach the problem that hybridization could cause for the viability of a population of a rare species and to be able to propose the most appropriate initial conservation strategy. Specifically, using the model genus Antirrhinum, the reproductive barriers between the rare A. pulverulentum and its common congener A. litigiosum have been analysed under the reproductive isolation index (RI). A. pulverulentum had a high value of total RI, indicating that there are barriers to gene flow from A. litigiosum towards this species, and also had a high value for the intrinsic RI, reflecting a low inherent capacity for production of hybrid plants; in addition, the possibility of successful backcrosses between this species with hybrids produced from A. litigiosum ovules were low, given the high intrinsic RI of A. litigiosum. These data indicate the current existence of strong and permanent barriers to hybridization between the two species, suggesting that hybridization does not seem to be a serious problem for the conservation of A. pulverulentum in the studied population, nor for the near future. This study shows how the RI index can provide useful information for conservation purposes and proposes different management recommendations.     

梯棱羊肚菌全基因组SNP/Indel分析及基于Indel标记的遗传连锁图谱构建

基于梯棱羊肚菌Morchella importuna两个子囊孢子培养物的全基因组测序数据,对全基因组范围内的变异位点进行分析。共鉴定到18 438个变异位点,平均每Mbp的变异位点数量为361个;变异位点以单核苷酸多态性SNP为主,共计17 104个,基因组中SNP的频率为335SNPs/Mbp;Indel多态性位点1 334个,以2-10bp的插入缺失为主;73.4% SNP/Indel位于基因间隔区域,外显子区域共检测到3 042个变异位点,占总数的16.50%;对基因功能产生确定影响的移码突变有1 088个,占5.90%,错义突变916个,占比4.97%;不同Scaffold上的SNP/Indel出现频率不同,SNP频率最大的为Scaffold80,平均每Mbp包含2 856个SNP,频率最低为Scaffold60和Scaffold75,分别为16SNPs/Mbp和30SNPs/Mbp;对≥11bp的Indel变异位点进行标记开发和多态性群体分析,成功开发出75对Indel标记。采用原生质体单细胞分离技术,获得了梯棱羊肚菌M04的两个可亲和的同核体菌株M04P01和M04P40,同时采用来自M04子囊果的58个单孢菌株作为作图群体,初步构建了包含75个Indel标记和1个交配型基因的梯棱羊肚菌遗传连锁图谱,共获得12个连锁群,连锁群总长度273.7cM。     

超声内镜辅助下内镜黏膜下切除术对食管癌前病变患者肿瘤标志物及应激反应指标的影响

目的:探讨超声内镜(EUS)辅助下内镜黏膜下切除术(EMR)对食管癌前病变患者肿瘤标志物及应激反应指标的影响。方法:选择山东大学齐鲁医院青岛院区消化内科于2016年3月至2018年4月期间收治的食管癌前病变患者137例,采用随机数字表法将患者分为常规组(n=68,常规胃镜下行EMR)和EUS组(n=69,EUS辅助下行EMR),比较两组患者临床指标,比较两组术前、术后血清肿瘤标志物及应激反应指标水平,比较两组术前、术后1周相关遗传学分子水平。结果:EUS组手术时间、术后流质饮食时间均短于常规组(P0.05),并发食管黏膜小穿孔例数、使用钛夹止血例数均少于常规组(P0.05)。两组患者术后肿瘤特异性生长因子(TSGF)、细胞角蛋白19血清片段21-1(CYFRA21-1)、鳞状上皮细胞癌抗原(SCC-Ag)均较术前升高,但EUS组低于常规组(P0.05)。两组患者术后肾上腺素(E)、去甲肾上腺素(NE)、肾素(R)、血管紧张素Ⅱ(AngⅡ)、醛固酮均较术前升高,但EUS组低于常规组(P0.05)。两组患者术后1周细胞周期素E(Cyclin E)、转化生长因子-α(TGF-α)均较术前降低,且EUS组低于常规组(P0.05)。结论:相比于常规胃镜,经EUS辅助下EMR治疗食管癌前病变可有效改善患者的临床指标,减轻患者应激反应,有利于降低血清肿瘤标志物及遗传学分子水平。     

The growth ring concept: seeking a broader and unambiguous approach covering tropical species

The concept of growth rings is little discussed in the literature and their treatment remains somewhat confusing in terms of the diversity of structures described. This situation has a major impact on the study of growth rings in tropical species, in which variations and complexity are greater and accuracy of identification less good. The rigid conceptual delimitations used by dendrochronologists and wood anatomists of temperate regions cannot be applied to the study of growth rings in most tropical species, which has led to neglect of this subject. With the objective of discussing the concept of growth rings, the present study consists of a survey of anatomical, periodicity, causal and evolutionary aspects of the treatment of these structures as evidenced in previous studies, and the evaluation of their application and limitations to the development of this concept. Anatomical aspects arise through radial integrity, or the presence of early and late wood; the degree of distinction of the rings, which may vary from well to poorly defined; and tangential continuity, meaning that rings may form a complete circle in the transverse section of the trunk, or instead be tangentially discontinuous, lens‐shaped or in wedges. In addition there are a diversity of anatomical markers which enable us to recognize growth rings. Regarding periodicity, the rings may be annual, infra‐annual or supra‐annual. Causal aspects include genetic, endogenous and environmental components. Evolutionary aspects continue to be insufficiently investigated, and although most comparative studies treat growth rings recognized by different markers as though they were a single character, it remains questionable whether they can be regarded as homologous or the result of homoplasy. We conclude that the elaboration of a robust but broad definition which can include all the variation observed in growth rings of tropical species is a complex task, which is only possible by overcoming the restrictions adopted by dendrochronologists and wood anatomists of temperate regions for whom growth rings are essentially annual, strongly demarcated, tangentially continuous and restricted to the most pronounced markers.     

A metabolome‐based core hybridisation strategy for the prediction of rice grain weight across environments

Marker‐based prediction holds great promise for improving current plant and animal breeding efficiencies. However, the predictabilities of complex traits are always severely affected by negative factors, including distant relatedness, environmental discrepancies, unknown population structures, and indeterminate numbers of predictive variables. In this study, we utilised two independent F₁ hybrid populations in the years 2012 and 2015 to predict rice thousand grain weight (TGW) using parental untargeted metabolite profiles with a partial least squares regression method. A stable predictive model for TGW was built based on hybrids from the population in 2012 (r = 0.75) but failed to properly predict TGW for hybrids from the population in 2015 (r = 0.27). After integrating hybrids from both populations into the training set, the TGW of hybrids could be predicted but was largely dependent on population structures. Then, core hybrids from each population were determined by principal component analysis and the TGW of hybrids in both environments were successfully predicted (r > 0.60). Moreover, adjusting the population structures and numbers of predictive analytes increased TGW predictability for hybrids in 2015 (r = 0.72). Our study demonstrates that the TGW of F₁ hybrids across environments can be accurately predicted based on parental untargeted metabolite profiles with a core hybridisation strategy in rice. Metabolic biomarkers identified from early developmental stage tissues, which are grown under experimental conditions, may represent a workable approach towards the robust prediction of major agronomic traits for climate‐adaptive varieties.     

Inhibiting the urokinase‐type plasminogen activator receptor system recovers STZ‐induced diabetic nephropathy

The urokinase‐type plasminogen activator (uPA) receptor (uPAR) participates to the mechanisms causing renal damage in response to hyperglycaemia. The main function of uPAR in podocytes (as well as soluble uPAR ‐(s)uPAR‐ from circulation) is to regulate podocyte function through αvβ3 integrin/Rac‐1. We addressed the question of whether blocking the uPAR pathway with the small peptide UPARANT, which inhibits uPAR binding to the formyl peptide receptors (FPRs) can improve kidney lesions in a rat model of streptozotocin (STZ)‐induced diabetes. The concentration of systemically administered UPARANT was measured in the plasma, in kidney and liver extracts and UPARANT effects on dysregulated uPAR pathway, αvβ3 integrin/Rac‐1 activity, renal fibrosis and kidney morphology were determined. UPARANT was found to revert STZ‐induced up‐regulation of uPA levels and activity, while uPAR on podocytes and (s)uPAR were unaffected. In glomeruli, UPARANT inhibited FPR2 expression suggesting that the drug may act downstream uPAR, and recovered the increased activity of the αvβ3 integrin/Rac‐1 pathway indicating a major role of uPAR in regulating podocyte function. At the functional level, UPARANT was shown to ameliorate: (a) the standard renal parameters, (b) the vascular permeability, (c) the renal inflammation, (d) the renal fibrosis including dysregulated plasminogen‐plasmin system, extracellular matrix accumulation and glomerular fibrotic areas and (e) morphological alterations of the glomerulus including diseased filtration barrier. These results provide the first demonstration that blocking the uPAR pathway can improve diabetic kidney lesion in the STZ model, thus suggesting the uPA/uPAR system as a promising target for the development of novel uPAR‐targeting approaches.     

基于质谱的蛋白质N末端乙酰化程度定量方法的研究

随着质谱技术及各种定量方法的不断完善和发展,定量蛋白质组学的方法不断地被应用到各类生物学研究中。蛋白质组学定性定量数据的处理主要通过一些多功能的商业化或者开源软件来进行,如常用的数据分析软件Proteome Discoverer和Maxquant。但是在通过化学标记对蛋白质N末端乙酰化程度进行定量这一方面,Proteome Discoverer和Maxquant在一定程度上存在准确性不高和完整度不够的问题。于是本研究针对自己的实验特点,通过Java算法编写了相应的定量程序Acequant来完成N末端乙酰化程度的相对定量。本研究将该程序在已有相关报道的He La cell上进行了验证,Acequant共定量到1 587个蛋白质N末端,而Proteome Discoverer和Maxquant分别只定量到42个和306个N末端。同时,手动验证原始图谱也证实了Acequant定量的准确性更好。于是,本研究将此方法进一步应用到秀丽隐杆线虫N末端乙酰化的研究中,并初步发现了线虫整体的N末端乙酰化状态,为进一步的N末端研究提供了支持。     

Successful sexual reproduction of the scleractinian coral Porites panamensis: Evidence of planktonic larvae and recruitment

Porites panamensis is a hermatypic brooder coral endemic to, and distributed along, the Eastern Tropical Pacific, and is considered a species vulnerable to local effects because it has limited capacity for long‐distance dispersal (and low genetic diversity). Although larvae of P. panamensis have been previously shown to recruit to artificial settlement platforms, they have never been observed in the water column. The present study describes the reproductive behavior of P. panamensis, with a focus on using molecular tools to document evidence for a larval planktonic stage and for successful recruitment. Larvae collected from the water column, and recruitment on natural and artificial substrata were documented. Phylogenetic analysis of two ribosomal markers, 18s rRNA and ITS (ITS1‐5.8‐ITS2), and one mitochondrial marker, cytochrome oxidase subunit 1 (cox1), confirmed the taxonomic identity of larvae, and showed that larvae and recruits have genotypes similar to adults of P. panamensis. Lipid vacuoles and Symbiodinium sp. were present in the gastrodermis of all larvae. A total of 12 and 371 recruits settled on artificial and natural substrates, respectively, and the recruitment rate differed significantly over time. By documenting the reproductive success of the species, we show the potential for existing individuals both to maintain the population in the study area and to contribute to maintenance of the coral reef community in the coming decades.     

Genetic diversity of autochthonous pig breeds analyzed by microsatellite markers and mitochondrial DNA D-loop sequence polymorphism

The evaluation of the genetic structure of autochthonous pig breeds is very important for conservation of local pig breeds and preservation of diversity. In this study, 18 microsatellite loci were used to detect genetic relationship between autochthonous pig breeds [Black Slavonian (BS), Turopolje pig (TP), and Croatian wild boar] and to determine phylogenetic relationship among Croatian autochthonous pig breeds and certain Asian and European pigs using the mitochondrial DNA (mtDNA) D-loop sequence polymorphism. Relatively high degree of genetic variation was found between the observed populations. The analysis of mtDNA showed that haplotypes of the studied pig populations are different from the other European and Chinese haplotypes. BS pigs showed some similarities with Mangalitsa and Duroc breeds. The genetic distances of TP can be explained by high degree of inbreeding during the past century. Despite the European origin of Croatian pig breeds with some impact of Chinese breeds in the past, the results of present study show that genetic diversity is still pronounced within investigated breeds. Furthermore, the genetic diversity is even more pronounced between Croatian breeds and other European and Chinese pig breeds. Thus, conservation of Croatian pig breeds will contribute to overall genetic diversity preservation of pig breeds.