DNA damage-induced replication fork regression and processing in Escherichia coli

DNA lesions that block replication are a primary cause of rearrangements, mutations, and lethality in all cells. After ultraviolet (UV)-induced DNA damage in Escherichia coli, replication recovery requires RecA and several other recF pathway proteins. To characterize the mechanism by which lesion-blocked replication forks recover, we used two-dimensional agarose gel electrophoresis to show that replication-blocking DNA lesions induce a transient reversal of the replication fork in vivo. The reversed replication fork intermediate is stabilized by RecA and RecF and is degraded by the RecQ-RecJ helicase-nuclease when these proteins are absent. We propose that fork regression allows repair enzymes to gain access to the replication-blocking lesion, allowing processive replication to resume once the blocking lesion is removed.     

Polymerase exchange during Okazaki fragment synthesis observed in living cells

DNA replication machineries have been studied extensively, but the kinetics of action of their components remains largely unknown. We report a study of DNA synthesis during replication in living Escherichia coli cells. Using single-molecule microscopy, we observed repetitive fluorescence bursts of single polymerase IIIs (Pol IIIs), indicating polymerase exchange at the replication fork. Fluctuations in the amount of DNA-bound single-stranded DNA-binding protein (SSB) reflect different speeds for the leading- and lagging-strand DNA polymerases. Coincidence analyses of Pol III and SSB fluctuations show that they correspond to the lagging-strand synthesis and suggest the use of a new Pol III for each Okazaki fragment. Based on exchanges involving two Pol IIIs, we propose that the third polymerase in the replisome is involved in lagging-strand synthesis.     

Reversible Section of the Brain by a Wall of Cold

A fork made up of hollow tubing may be chronically implanted in the cat's brain. When cooling fluid is pumped through this fork a reversible plane lesion is formed. This technique permits analysis of functional parts of the nervous system in unanesthetized animals.     

Yeast DNA polymerase epsilon participates in leading-strand DNA replication

Multiple DNA polymerases participate in replicating the leading and lagging strands of the eukaryotic nuclear genome. Although 50 years have passed since the first DNA polymerase was discovered, the identity of the major polymerase used for leading-strand replication is uncertain. We constructed a derivative of yeast DNA polymerase epsilon that retains high replication activity but has strongly reduced replication fidelity, particularly for thymine-deoxythymidine 5'-monophosphate (T-dTMP) but not adenine-deoxyadenosine 5'-monophosphate (A-dAMP) mismatches. Yeast strains with this DNA polymerase epsilon allele have elevated rates of T to A substitution mutations. The position and rate of these substitutions depend on the orientation of the mutational reporter and its location relative to origins of DNA replication and reveal a pattern indicating that DNA polymerase epsilon participates in leading-strand DNA replication.     

智利竹鱼拖网最适网囊网目尺寸探讨

根据拖网网囊网目尺寸与鱼体生物学存在关系 ,对智利竹鱼的优势叉长组成、形体特征、初次性腺成熟时的叉长等进行了分析。通过现场测试得出 2 0 0 0年智利竹鱼的优势叉长为 2 5 0～ 30 0mm ;体高、体宽和体周与叉长存在线性关系 ,分别为 2a =0 .185 8L - 3 .5 2 19,2b =0 .1339L - 4.2 99,c =0 .480 3L - 3 .4794。并对智利竹鱼拖网网囊网目尺寸进行了分析与计算 ,认为智利竹鱼拖网网囊的最适网目内径为 115～ 12 0mm。     

智利竹鱼拖网最适网囊网目尺寸探讨

根据拖网网囊网目尺寸与鱼体生物学存在关系 ,对智利竹鱼的优势叉长组成、形体特征、初次性腺成熟时的叉长等进行了分析。通过现场测试得出 2 0 0 0年智利竹鱼的优势叉长为 2 5 0～ 30 0mm ;体高、体宽和体周与叉长存在线性关系 ,分别为 2a =0 .185 8L - 3 .5 2 19,2b =0 .1339L - 4.2 99,c =0 .480 3L - 3 .4794。并对智利竹鱼拖网网囊网目尺寸进行了分析与计算 ,认为智利竹鱼拖网网囊的最适网目内径为 115～ 12 0mm。     

Strand-specific postreplicative processing of mammalian telomeres

Telomeres are specialized nucleoprotein structures that stabilize the ends of linear eukaryotic chromosomes. In mammalian cells, abrogation of telomeric repeat binding factor TRF2 or DNA-dependent protein kinase (DNA-PK) activity causes end-to-end chromosomal fusion, thus establishing an essential role for these proteins in telomere function. Here we show that TRF2-mediated end-capping occurs after telomere replication. The postreplicative requirement for TRF2 and DNA-PKcs, the catalytic subunit of DNA-PK, is confined to only half of the telomeres, namely, those that were produced by leading-strand DNA synthesis. These results demonstrate a crucial difference in postreplicative processing of telomeres that is linked to their mode of replication.     

基于线性混合效应模型的镰鲳叉长-体质量关系的异质性分析

根据2016—2018年3月初(冬季)、5月(春季)、8月(夏季)、11月(秋季)4个季节在浙江南部近海的温台地区底拖网调查数据,通过构建广义线性模型(GLM)和9个线性混合效应模型,对镰鲳(Pampus echinogaster)的叉长-体质量关系(W=aLb)及其异质性进行了分析。结果表明:浙江南部近海的镰鲳叉长范围为53.00~238.00 mm,平均叉长128.54 mm,优势叉长组为110.00~160.00 mm;体质量范围为3.80~420.50 g,平均体质量63.61 g,优势体质量为60.00~180.00 g。根据赤池信息准则(AIC),最佳的生长拟合模型为同时存在季节和年份对镰鲳生长参数a,b的随机效应的组合模型;均方根误差结果同样表明该模型的性能最优。在最优模型中,参数a的固定值为1.75×10^-5,参数b的固定值为3.083,表示镰鲳为正异速增长,肥满度较高。最优线性混合模型结果显示:a值在秋季最大,其次是夏季和冬季,而春季最小;b值与其相反。从不同年份来看:a值在2016年最大,2018年和2017年次之;b值在2017年最大,2018年和2016年次之。本研究分析了年份、季节与镰鲳的叉长-体质量关系,通过混合效应模型,显示出年份和季节对镰鲳的叉长-体质量关系具有较为显著的影响,表明该模型在镰鲳的叉长-体质量关系的异质性研究中具有重要的参考价值,并为其资源的合理开发和管理提供科学依据。     

Ubiquitin-binding domains in Y-family polymerases regulate translesion synthesis

Translesion synthesis (TLS) is the major pathway by which mammalian cells replicate across DNA lesions. Upon DNA damage, ubiquitination of proliferating cell nuclear antigen (PCNA) induces bypass of the lesion by directing the replication machinery into the TLS pathway. Yet, how this modification is recognized and interpreted in the cell remains unclear. Here we describe the identification of two ubiquitin (Ub)-binding domains (UBM and UBZ), which are evolutionarily conserved in all Y-family TLS polymerases (pols). These domains are required for binding of poleta and poliota to ubiquitin, their accumulation in replication factories, and their interaction with monoubiquitinated PCNA. Moreover, the UBZ domain of poleta is essential to efficiently restore a normal response to ultraviolet irradiation in xeroderma pigmentosum variant (XP-V) fibroblasts. Our results indicate that Ub-binding domains of Y-family polymerases play crucial regulatory roles in TLS.     

ATR homolog Mec1 promotes fork progression,thus averting breaks in replication slow zones

Budding yeast Mec1, homolog of mammalian ATR, is an essential protein that mediates S-phase checkpoint responses and meiotic recombination. Elimination of Mec1 function leads to genomewide fork stalling followed by chromosome breakage. Breaks do not result from stochastic collapse of stalled forks or other incidental lesions; instead, they occur in specific regions of the genome during a G2 chromosomal transition. Break regions are found to be genetically encoded replication slow zones (RSZs), a newly discovered yeast chromosomal determinant. Thus, Mec1 has important functions in normal S phase and the genome instability of mec1 (and, analogously, ATR-/-) mutants stems from defects in these basic roles.     

基于LBB方法估算北部湾竹䇲鱼种群参数

为探究北部湾竹?鱼(Trachurus japonicus)不同组距的划分对其种群参数和资源评估的影响,利用2006—2018年北部湾竹?鱼叉长数据重构长度频率,通过逻辑斯蒂曲线拟合和长度贝叶斯生物量估算(length-based Bayesian biomass estimation method,LBB)方法,估算竹?鱼的初次性成熟叉长(L₅₀)、渐进叉长(L_∞)、相对自然死亡率(M/k)、相对捕捞死亡率(F/k)、相对总死亡率(Z/k)、最适开捕叉长(L_{c_opt})、开发率(E)和相对生物量(B/B₀)等种群参数。分析在不同组距情况下种群参数的差异。结果表明:初次性成熟叉长范围为157~162 mm;北部湾竹?鱼种群参数平均值分别为L_∞=248 mm、M/k=1.38、F/k=6.92、Z/k=8.28和L_{c_opt}=156 mm;北部湾竹?鱼相对生物量B/B₀低于0.5,E大于0.5;不同组距重构长度频率估算的种群参数结果有差异,且随组距的增大波动较为明显。研究表明,竹?鱼生物量相对低且处于过度开发状态,建议今后以样本数量、长度组成和生物特性共同确定某种鱼类长度分组组距。     

Multiple sclerosis: distribution of T cell subsets within active chronic lesions

The distribution of T cells and T cell subsets was examined within the human central nervous system in active lesions from seven patients with chronic multiple sclerosis. The monoclonal antibodies anti-T11, anti-T4, and anti-T8 were used to detect total (whole) T cells, helper T cells, and suppressor-cytotoxic T cells, respectively, and a monoclonal antibody against human Ia was used for macrophages and B cells. Lesion progression was associated with large numbers of T4+ cells at the lesion margin and these extended great distances into the adjacent normal-appearing white matter. T8+ cells were most commonly concentrated around the lesion margin and displayed a preferential perivascular distribution. Within the lesion center, only a few T cells were found. Ia+ macrophages were most numerous within the centers of active lesions and were always present in the adjacent normal white matter. The monoclonal antibodies to T cells did not cross-react with glial cells including oligodendrocytes. These results indicate that T4+ cells are actively involved in lesion extension and Ia+ cells, in demyelination.     

印度洋中南部长鳍金枪鱼生物学特性的研究

根据2008年9月—2009年4月印度洋中南部金枪鱼延绳钓渔场所捕获的长鳍金枪鱼Thunnus alalun-ga数据,对该鱼种的生物学特征进行了分析。结果表明：1）叉长为74~120 cm,优势叉长为105~110cm,约占总数的47.8%,平均叉长为（107.2±4.99）cm。2）长鳍金枪鱼叉长（LF,cm）与加工后重（WD,kg）的关系可表达为WD=1.7146×10-5LF3.0197（总体）,WDM=7×10-5L2F.M7229（雄性）,WDF=2×10-6L3F.F5354（雌性）。3）调查期间,长鳍金枪鱼性腺成熟度以Ⅳ级为主,约占总数的43.1%。4）当长鳍金枪鱼叉长小于100 cm时,摄食等级以0级和2级为主;当叉长为100~120 cm时,空胃率达39%以上,且随叉长的增长而递增。当叉长为91~110 cm时,摄食饱满指数随叉长增长而上升;当叉长为111~120 cm时,饱满指数随叉长递增而降低。     

Structure of the RNA polymerase domain of E. coli primase

All cellular organisms use specialized RNA polymerases called "primases" to synthesize RNA primers for the initiation of DNA replication. The high-resolution crystal structure of a primase, comprising the catalytic core of the Escherichia coli DnaG protein, was determined. The core structure contains an active-site architecture that is unrelated to other DNA or RNA polymerase palm folds, but is instead related to the "toprim" fold. On the basis of the structure, it is likely that DnaG binds nucleic acid in a groove clustered with invariant residues and that DnaG is positioned within the replisome to accept single-stranded DNA directly from the replicative helicase.     

Regulation of replication fork progression through histone supply and demand

DNA replication in eukaryotes requires nucleosome disruption ahead of the replication fork and reassembly behind. An unresolved issue concerns how histone dynamics are coordinated with fork progression to maintain chromosomal stability. Here, we characterize a complex in which the human histone chaperone Asf1 and MCM2-7, the putative replicative helicase, are connected through a histone H3-H4 bridge. Depletion of Asf1 by RNA interference impedes DNA unwinding at replication sites, and similar defects arise from overproduction of new histone H3-H4 that compromises Asf1 function. These data link Asf1 chaperone function, histone supply, and replicative unwinding of DNA in chromatin. We propose that Asf1, as a histone acceptor and donor, handles parental and new histones at the replication fork via an Asf1-(H3-H4)-MCM2-7 intermediate and thus provides a means to fine-tune replication fork progression and histone supply and demand.     

PULMONARY EDEMA AS A CONSEQUENCE OF HYPOTHALAMIC LESIONS IN RATS

Rats were observed for the incidence of pulmonary edema after the placement of hypothalamic lesions by radio frequency thermocoagulation or d-c electrolysis. In the animals with electrolytic lesions, 31 percent died with pulmonary edema and marked signs were observed in another 20 percent. Moderate transient signs appeared in only 3.7 percent of the animals with radio-frequency lesions, and there were no deaths attributable to this syndrome in this group. These results suggest that this syndrome is an irritative consequence of the electrolytic lesion process rather than a "release" phenomenon.     

水稻类病变(Lesion Resembling Disease)突变体对光照和温度的诱导反应

【目的】对水稻lrd表达的光温诱导反应进行研究,明确水稻lrd表达光诱导波段和温度的抑制或促进作用。【方法】利用自有的6个水稻lrd突变体,用LED单色光源诱激和人工气候箱中不同温度梯度处理,观察类病斑的发生情况和统计病斑个数,比较诱导的效果。【结果】lrd31类病斑表达受紫外光诱导,lrd36的表达受黄光诱导,lrd37和lrd35的表达受蓝光诱导,而lrd32和lrd40在所有处理的光源下均表达类病斑;lrd32、lrd36和lrd37等3种温度下都正常产生病斑,低温明显促进病斑的发生。lrd35和lrd40在高温下不表达,在中温下可正常表达,低温下也表现促进作用,但lrd31只有在中温下正常表达,低温和高温抑制病斑出现。【结论】不同的lrd基因型所需的光诱导反应波段是不相同的。温度是抑制或促进lrd表达的另一个重要环境因子,一般是较低的温度促进lrd表达,高温抑制lrd表达。     

THE PROTECTION OF PANCREATIC LIPASE BY ACACIA GUM

In this preliminary note we describe the results obtained by inoculation of the skin of the scrotum of four black rabbits with serous fluid expressed from an initial pinta lesion. The inoculation was made intradermally, as superficially as possible, with serous fluid rich in treponemata and diluted with normal salt solution. A papule appeared at the point of inoculation in one of the four rabbits on the 105th day. One hundred and fifteen days after inoculation the papule presented a circular erosion on an indurated base. The serous fluid expressed from this lesion contained numerous treponemata on dark-field examination, and these were easily impregnated by the Fontana-Tribondeau method. A volunteer inoculated with serous fluid expressed from the rabbit's lesion developed a typical initial pinta lesion at the point of inoculation, thus proving that the scrotal lesion of the rabbit was produced by Treponema carateum or Treponema herrejoni, the causal agent of pinta, mal del pinto or carate. Four rabbits inoculated with serous fluid from the scrotal lesion of the rabbit have not yet developed visible lesions.