Understanding a key gene for thermosensitive genic male sterility in rice

<正>Recently,a joint research team led by Chuxiong Zhuang of South China Agricultural University and Xiaofeng Cao of Institute of Genetics and Development Biology,Chinese Academy of Sciences published their work on the cloning and molecular characterization of the gene thermosensitive genic male sterile 5(tms5)in rice in Nature Communications[1].This is the result of a long-term collaboration representing an important advance in male sterility research in crops.     

Professor Hong-Yuan Yang (1933-2010)

Prof. Hong-Yuan Yang,a renowned botanist,Academician of the Chinese Academy of Sciences and Professor of Wuhan University,passed away at the age of 77 in Wuhan on November 18,2010.     

方兴未艾的古代DNA的研究

保留在古代生物遗骸中的遗传物质DNA是一种重要的遗传资源。古代DNA的研究对于了解包括人类在内的各种生物的起源、进化和迁徙有重要意义。古代DNA的研究有其自身的特点,并且已经取得一系列重要成就。本文综述古代DNA研究的历史、方法和进展。 Abstract：DNA present in ancient samples can be recovered,amplified and analysed.It opens a new window for genetic analysis in many different disciplines,such as anthropology,archaeology,human population genetics,animal and plant evolutionary taxonomy and forensic science.In general,ancient DNA is rare in quantity,damaged in quality.To ensure the reproducibility and reliability of the results,great cares should be taken,such as various measurements against contamination and phylogenetic analysis of ancient DNA sequences.In this paper we review recovery,amplification and analysis of ancient DNA,also discuss the guidelines to ensure the authenticity of ancient DNA and the recent advances in ancient DNA study.     

Insights into complex processes of animal development

Life is very complicated. Recently, a group of review papers on the complexity of various biological behaviors were published by Cell to celebrate its 40th anniversary. The developmental process must be one of the most complex events in multi-cellular organisms. JMCB has published several research papers in the previous Collection ＇Understanding and Mani-pulating Developmental Complexity＇ （Wu, 2013）. This issue publishes more articles focusing on the molecular mechanisms that regulate animal developmental processes, which should provide evidences for a better understanding of the developmental complexity.     

In Memoriam： To our beloved friend,colleague, and Overseas Chinese Entomologists Association （OCEA） member,Professor Que Lan （1959-2014）

Dr. Lan Que was born in 1959 in Wuhan, the capital city of Hubei province, China. It may have been her childhood experience as a 13-year-old girl with a shaking body burning under blankets as she battled with malaria vectored by mosquitoes that fueled her determination to erad- icate this dreaded disease, as she stated many years later in an interview with Grow--Wisconsin＇s Magazine for the Life Sciences （2010, http：//grow.cals.wisc.edu/health/the- exterminator）. Lan＇s enthusiasm for biology, microbiology, entomology, and mosquitoes control quickly became the focus of her higher education and professional career. She received her B.S. in Microbiology from Wuhan University, China, in 1982 and her pursuit of her childhood dream of fighting malaria took her halfway across the world first to Canada, where she earned her M.S. in Biology from Brock University in 1988 and then on to the University of Minnesota in the United States for her Ph.D. in Entomology, which she was awarded in 1993. After 5 years＇ postdoctoral research in Developmental Biology,     

Species identification refined by molecular scatology in a community of sympatric carnivores in Xinjiang,China

Many ecological studies and conservation management plans employ noninvasive scat sampling based on the assumption that species’ scats can be correctly identified in the field. However, in habitats with sympatric similarly sized carnivores, misidentification of scats is frequent and can lead to bias in research results. To address the scat identification dilemma, molecular scatology techniques have been developed to extract DNA from the donor cells present on the outer lining of the scat samples. A total of 100 samples were collected in the winter of 2009 and 2011 in Taxkorgan region of Xinjiang, China. DNA was extracted successfully from 88% of samples and genetic species identification showed that more than half the scats identified in the field as snow leopard(Panthera uncia) actually belonged to fox(Vulpes vulpes). Correlation between scat characteristics and species were investigated, showing that diameter and dry weight of the scat were significantly different between the species. However it was not possible to define a precise range of values for each species because of extensive overlap between the morphological values. This preliminary study confirms that identification of snow leopard feces in the field is misleading. Research that relies upon scat samples to assess distribution or diet of the snow leopard should therefore employ molecular scatology techniques. These methods are financially accessible and employ relatively simple laboratory procedures that can give an indisputable response to species identification from scats.     

90 years of perseverance and achievements in biological education and research

<正>This special issue commemorates the 90th anniversary(1925-2015)of Peking University’s School of Life Sciences.As one of China’s centers for education and research in biological sciences,the school’s past 90 years have been eventful,ranging from times of prosperity to periods of war     

Progress in the Study of Molecular Genetic Improvements of Poplar in China

The poplar is one of the most economically important and intensively studied tree species owing to its wide application in the timber industry and as a model material for the study of woody plants. The natural resource of poplars in China is replete. Over the past 10 years, the application of molecular biological techniques to genetic improvements in poplar species has been widely studied in China. Recent advances in molecular genetic improvements of poplar, including cDNA library construction, gene cloning and identification, genetic engineering, gene expression, genetic linkage map construction, mapping of quantitative trait loci （QTL） and molecular-assisted selection, are reviewed in the present paper. In addition, the application of modern biotechnology to molecular improvements in the genetic traits of the poplar and some unsolved problems are discussed.     

Acta Biochimica et Biophysica Sinica

Acta Biochimica et Biophysica Sinica (Acta Biochim Biophys Sin, ISSN 0582-9879) is a leading scientific journalpublishing original papers, short communications and mini reviews in the fields of biochemistry molecular biology andbiophysics in China. It has been published monthly for 35 years. Acta Biochim Biophys Sin is sponsored by theInstitute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, the Chinese Academy ofSciences, published by Shanghai Scientific and Technical Publishers, and supported by National Natural ScienceFoundation of China and the Chinese Academy of Sciences. Acta Biochim Biophys Sin has a wide circulation amongthe scientists and students of biological sciences and basic medicine in China, and has been subscribed in variouscolleges, universities, institutes, information centers of scientific research units and libraries in China, Europe, Japan,USA and so on. Acta Biochim Biophys Sin has attracted attention of many outstanding scientists both at home and     

Shu-szi Sin:A Chinese pioneer biologist,ancient agronomist,and educator

Shu-szi Sin(辛树帜,1894-1977)(Fig.1),a Chinese pioneer biologist and ancient agronomist,initiated the earliest sci-entific biological investigation of the Dayao mountain in both Guangxi and Guangdong provinces,discovering more than 20 new species that have been acknowledged internation-ally.He was one of the founders and initiators of the China Botanical Society and the China Zoological Society.Mr.Sin was also a great educator.Among one of those who first introduced the scientific method into agricultural history research,Mr.Sin helped to set up the National Northwest Agriculture and Forestry College(now Northwest A&F University)and the Lanzhou University.He devoted himself to the development of higher education in Northwest China.     

Ancient genomics

The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field''s focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when testing specific hypotheses related to the past.     

More on contamination: the use of asymmetric molecular behavior to identify authentic ancient human DNA

Authentication of ancient human DNA results is an exceedingly difficult challenge due to the presence of modern contaminant DNA sequences. Nevertheless, the field of ancient human genetics generates huge scientific and public interest, and thus researchers are rarely discouraged by problems concerning the authenticity of such data. Although several methods have been developed to the purpose of authenticating ancient DNA (aDNA) results, while they are useful in faunal research, most of the methods have proven complicated to apply to ancient human DNA. Here, we investigate in detail the reliability of one of the proposed criteria, that of appropriate molecular behavior. Using real-time polymerase chain reaction (PCR) and pyrosequencing, we have quantified the relative levels of authentic aDNA and contaminant human DNA sequences recovered from archaeological dog and cattle remains. In doing so, we also produce data that describes the efficiency of bleach incubation of bone powder and its relative detrimental effects on contaminant and authentic ancient DNA. We note that bleach treatment is significantly more detrimental to contaminant than to authentic aDNA in the bleached bone powder. Furthermore, we find that there is a substantial increase in the relative proportions of authentic DNA to contaminant DNA as the PCR target fragment size is decreased. We therefore conclude that the degradation pattern in aDNA provides a quantifiable difference between authentic aDNA and modern contamination. This asymmetrical behavior of authentic and contaminant DNA can be used to identify authentic haplotypes in human aDNA studies.     

The use of protein characteristics to assess the retrievability of ancient DNA from ancient bones

The ability to retrieve DNA from ancient specimens has been one of the greatest achievements of the past decade, and has opened a totally new field of research with applications in seemingly distant domains such as archeobotany, the molecular phylogeny of extinct genomes, human paleopathology and the genetic of ancient human populations. However, extraction of ancient DNA has often a very low rate of success, prompting researchers to develop screening methods for the selection of promising specimens. With this goal in mind, we studied the amino acid content of nine human bones of ancient origin. We demonstrate that a single HPLC chromatogram is indicative of the integrity of ancient bone proteins. Among five specimens containing amplifiable DNA, four exhibited a protein content similar to that of contemporary bone protein content. Three of the four specimens, from which we were unable to extract any amplifiable DNA, had an amino acid content strikingly different from that of contem-porary bone. A non-parametric statistical test, Kendall's tau, was used to show that protein content and PCR products, are probably correlated (at a 95% confidence level). In addition, the D/L Asp and D/L Glu racemization ratios obtained are indicative of the presence of ancient organic compounds. We propose that protein analysis should be systematically performed in studies where there are many samples in order to select the specimens that are most likely to contain retrievable ancient DNA.     

古DNA实时荧光定量PCR实验中标准品的制备

实时荧光定量PCR技术通过对PCR每一循环扩增产物的实时检测,可对模板的精确拷贝数进行绝对定量,从而用于古DNA实验中提取和扩增条件的比较和优化.本研究采用异硫氰酸胍碱裂解-SiO2吸附的方法,从采自黑龙江省的晚更新世斑鬣狗化石材料中提取得到了斑鬣狗线粒体基因组古DNA.经常规PCR扩增后,将纯化的扩增产物克隆到微生物体内使其大量复制,再用M13通用引物扩增出含少量外源DNA的古DNA目标片段,从而建立了适用于古DNA荧光定量PCR扩增的标准品的制备方法.经检测分析,运用该方法制备的标准品性质稳定,能够准确地指示反应体系中较为精确的古DNA模板拷贝数,从而反映古DNA的提取和扩增效率,用于比较并优化古DNA提取和扩增条件.     

Spiking of contemporary human template DNA with ancient DNA extracts induces mutations under PCR and generates nonauthentic mitochondrial sequences

Proof of authenticity is the greatest challenge in palaeogenetic research, and many safeguards have become standard routine in laboratories specialized on ancient DNA research. Here we describe an as-yet unknown source of artifacts that will require special attention in the future. We show that ancient DNA extracts on their own can have an inhibitory and mutagenic effect under PCR. We have spiked PCR reactions including known human test DNA with 14 selected ancient DNA extracts from human and nonhuman sources. We find that the ancient DNA extracts inhibit the amplification of large fragments to different degrees, suggesting that the usual control against contaminations, i.e., the absence of long amplifiable fragments, is not sufficient. But even more important, we find that the extracts induce mutations in a nonrandom fashion. We have amplified a 148-bp stretch of the mitochondrial HVRI from contemporary human template DNA in spiked PCR reactions. Subsequent analysis of 547 sequences from cloned amplicons revealed that the vast majority (76.97%) differed from the correct sequence by single nucleotide substitutions and/or indels. In total, 34 positions of a 103-bp alignment are affected, and most mutations occur repeatedly in independent PCR amplifications. Several of the induced mutations occur at positions that have previously been detected in studies of ancient hominid sequences, including the Neandertal sequences. Our data imply that PCR-induced mutations are likely to be an intrinsic and general problem of PCR amplifications of ancient templates. Therefore, ancient DNA sequences should be considered with caution, at least as long as the molecular basis for the extract-induced mutations is not understood.     

Detection of DNA in Ancient Bones Using Histochemical Methods

We describe histochemical techniques for detecting DNA within the osteocytic lacunae of ancient bones. The bones examined were fragments of femurs from two human individuals found in the Pompeian C. I. Polybius house and fragments of metacarpals from two horses (Equus sp.) found in the Pompeian “Casti Amanti” house. Both buildings were buried by the 79 A. D. Vesuvius eruption. Fragments of femurs from a modern horse, a modern swine and a modern amphibian also were studied as controls. Some bone sections were stained with two different DNA-specific fluorochromes, 4′ -′ 6-diamidino-2-phenylindole (DAPI) and chromomycin A3 (CMA), while others were stained by the Feulgen reaction. All of the techniques gave a positive reaction within the osteocytic lacunae. Histological analysis of the undecalcified, ground and unstained sections agreed well with results of bone sections stained with either the fluorochromes or the Feulgen reaction. Bones showing good histology also were positive by our DNA-specific stain. Histochemical and histological analyses correlated well with the success of DNA extraction and amplification. Using conventional DNA-specific histochemical techniques in conjunction with histological analysis can be useful in the study of DNA extracted from ancient bone remains while reducing both the amount of time and cost.     

Detection of DNA in Ancient Bones Using Histochemical Methods

We describe histochemical techniques for detecting DNA within the osteocytic lacunae of ancient bones. The bones examined were fragments of femurs from two human individuals found in the Pompeian C. I. Polybius house and fragments of metacarpals from two horses (Equus sp.) found in the Pompeian “Casti Amanti” house. Both buildings were buried by the 79 A. D. Vesuvius eruption. Fragments of femurs from a modern horse, a modern swine and a modern amphibian also were studied as controls. Some bone sections were stained with two different DNA-specific fluorochromes, 4' -' 6-diamidino-2-phenylindole (DAPI) and chromomycin A3 (CMA), while others were stained by the Feulgen reaction. All of the techniques gave a positive reaction within the osteocytic lacunae. Histological analysis of the undecalcified, ground and unstained sections agreed well with results of bone sections stained with either the fluorochromes or the Feulgen reaction. Bones showing good histology also were positive by our DNA-specific stain. Histochemical and histological analyses correlated well with the success of DNA extraction and amplification. Using conventional DNA-specific histochemical techniques in conjunction with histological analysis can be useful in the study of DNA extracted from ancient bone remains while reducing both the amount of time and cost.     

湖泊沉积植物古DNA的现代过程

对植被历史变化过程的研究是理解现代植被组成、分布及其对全球变化响应的基础。近年来, 随着分子古生态学的发展, 分析沉积介质中的陆生植物古DNA信号, 以研究植被及植物多样性演变的历史过程正在成为研究热点, 湖泊沉积植物古DNA已成为古植被和古生态学研究的成熟代用指标。然而与第四纪孢粉分析相比较, 湖泊沉积植物古DNA的现代过程依然不明确, 成为其进一步发展和应用的限制因素。基于此, 该文综述了湖泊沉积植物古DNA技术研究进展, 尝试阐明湖泊沉积植物古DNA的现代过程, 包括植物DNA的来源、沉积和保存过程及其影响因素, 以及植物DNA与现代植被的关系等。已有研究表明, 湖泊沉积植物古DNA主要来自湖泊周边或流域范围, 其丰度和组成除受到源植物生物量的影响外, 同样受到沉积物的搬运和沉积过程中DNA降解作用、土壤以及沉积物中颗粒的吸附过程和稀释作用等因素的影响。湖泊沉积物中植物DNA的保存则主要受到微生物活动、湖水的化学性质(电导率和pH值)、湖泊深度、沉积物组成等一系列生物与非生物因素的共同影响。湖泊沉积植物古DNA可以揭示其沉积时代的植物群落类型以及气候环境信息, 但目前并不能够用来定量重建古植被变化过程。鉴于湖泊沉积植物古DNA现代过程的复杂性, 对研究结果的解释要格外小心。与孢粉分析相比, 湖泊沉积植物古DNA研究仍处于起步阶段, 但随着分子生物技术的进步、实验设计的优化、物种条形码的扩充及参考数据库的完善等, 以DNA宏条形码和宏基因组学为主要技术手段的植物古DNA技术, 必将推动我国植物古生态研究的进一步发展。     

Mutations induced by ancient DNA extracts?

We have investigated whether some factor in ancient DNA extractsinduces site-specific mutations in modern DNA. We find no evidencefor higher mutation rates when extracts from three differentPleistocene mammals are added to modern DNA than when wateror extraction blanks are added. We also fail to find evidencethat any such factor affects ancient DNA sequences determinedfrom the same extracts. This as well as the patterns of nucleotidesubstitutions seen in DNA sequences determined from hundredsof other specimens leads us to doubt that a previously unknownmutagenic factor can be a general feature of extracts from oldtissues.     

Mitochondrial DNA variation in the Viking age population of Norway

The medieval Norsemen or Vikings had an important biological and cultural impact on many parts of Europe through raids, colonization and trade, from about AD 793 to 1066. To help understand the genetic affinities of the ancient Norsemen, and their genetic contribution to the gene pool of other Europeans, we analysed DNA markers in Late Iron Age skeletal remains from Norway. DNA was extracted from 80 individuals, and mitochondrial DNA polymorphisms were detected by next-generation sequencing. The sequences of 45 ancient Norwegians were verified as genuine through the identification of damage patterns characteristic of ancient DNA. The ancient Norwegians were genetically similar to previously analysed ancient Icelanders, and to present-day Shetland and Orkney Islanders, Norwegians, Swedes, Scots, English, German and French. The Viking Age population had higher frequencies of K*, U*, V* and I* haplogroups than their modern counterparts, but a lower proportion of T* and H* haplogroups. Three individuals carried haplotypes that are rare in Norway today (U5b1b1, Hg A* and an uncommon variant of H*). Our combined analyses indicate that Norse women were important agents in the overseas expansion and settlement of the Vikings, and that women from the Orkneys and Western Isles contributed to the colonization of Iceland.