Sequence identification of 2,375 human brain genes.

We recently described a new approach for the rapid characterization of expressed genes by partial DNA sequencing to generate 'expressed sequence tags'. From a set of 600 human brain complementary DNA clones, 348 were informative nuclear-encoded messenger RNAs. We have now partially sequenced 2,672 new, independent cDNA clones isolated from four human brain cDNA libraries to generate 2,375 expressed sequence tags to nuclear-encoded genes. These sequences, together with 348 brain expressed sequence tags from our previous study, comprise more than 2,500 new human genes and 870,769 base pairs of DNA sequence. These data represent an approximate doubling of the number of human genes identified by DNA sequencing and may represent as many as 5% of the genes in the human genome.     

Identification of Zhoukoudian <Emphasis Type="Italic">Homo erectus</Emphasis> brain asymmetry using 3D laser scanning

Endocasts are important materials used for the study of human brain evolution, and allow examination of the external features of brain anatomy from the inside the cranium. Studies examining brain asymmetries in fossil hominids are usually limited to scoring of differences in hemisphere protrusion rostrally and caudally, or to comparing the width of the hemispheres. In the present study, using 3D laser scanning, we examined asymmetries of the hemisphere volumes and surface areas in the Zhoukoudain (ZKD) Homo erectus, dated to 0.4–0.8 Ma. Compared with modern endocasts, we found that the absolute hemisphere volumes and surface areas exhibited no significant asymmetries in the ZKD or in modern specimens. However, the relative hemisphere volumes against surface areas differed between the two groups. When comparing the relative sizes between the left and right hemispheres, the ZKD specimens exhibited a greater variation than in the modern humans; there were no differences in the two hemispheres in the ZKD specimens, while in the modern endocasts the left hemisphere was significantly greater than the right hemisphere. These data suggest that brain asymmetries originated from relative brain sizes rather than absolute brain volumes during human evolution. These anatomical changes are likely related to the origin of human brain lateralization.     

DNA sequence and comparative analysis of chimpanzee chromosome 22

Human-chimpanzee comparative genome research is essential for narrowing down genetic changes involved in the acquisition of unique human features, such as highly developed cognitive functions, bipedalism or the use of complex language. Here, we report the high-quality DNA sequence of 33.3 megabases of chimpanzee chromosome 22. By comparing the whole sequence with the human counterpart, chromosome 21, we found that 1.44% of the chromosome consists of single-base substitutions in addition to nearly 68,000 insertions or deletions. These differences are sufficient to generate changes in most of the proteins. Indeed, 83% of the 231 coding sequences, including functionally important genes, show differences at the amino acid sequence level. Furthermore, we demonstrate different expansion of particular subfamilies of retrotransposons between the lineages, suggesting different impacts of retrotranspositions on human and chimpanzee evolution. The genomic changes after speciation and their biological consequences seem more complex than originally hypothesized.     

复杂脑网络研究:现状与挑战

以大脑网络研究为例,详细介绍了大脑网络的构建、结构网络、功能网络以及结构与功能的联系等方面的研究进展.基于复杂网络理论,对大脑结构网络和功能网络的分析得到很多重要的拓扑性质,如"小世界"、"无标度"、模块化以及核心脑区的分布等;另外发现认知功能、神经精神疾病与大脑结构和功能网络的拓扑结构变化或异常有关;总结了国内外在此领域的研究成果,提出了大脑网络研究工作面临的挑战,并展望了将来发展方向.     

A genome-wide comparison of recent chimpanzee and human segmental duplications

We present a global comparison of differences in content of segmental duplication between human and chimpanzee, and determine that 33% of human duplications (> 94% sequence identity) are not duplicated in chimpanzee, including some human disease-causing duplications. Combining experimental and computational approaches, we estimate a genomic duplication rate of 4-5 megabases per million years since divergence. These changes have resulted in gene expression differences between the species. In terms of numbers of base pairs affected, we determine that de novo duplication has contributed most significantly to differences between the species, followed by deletion of ancestral duplications. Post-speciation gene conversion accounts for less than 10% of recent segmental duplication. Chimpanzee-specific hyperexpansion (> 100 copies) of particular segments of DNA have resulted in marked quantitative differences and alterations in the genome landscape between chimpanzee and human. Almost all of the most extreme differences relate to changes in chromosome structure, including the emergence of African great ape subterminal heterochromatin. Nevertheless, base per base, large segmental duplication events have had a greater impact (2.7%) in altering the genomic landscape of these two species than single-base-pair substitution (1.2%).     

Characteristics of fMRI BOLD signal and its neurophysiological mechanism

The functional magnetic resonance imaging (fMRI) based on blood oxygen level dependent (BOLD) contrast has emerged as one of the most potent noninvasive tools for mapping brain function and has been widely used to explore physiological, pathological changes and mental activity in the brain. Exploring the nature and property of BOLD signal has recently attracted more attentions. Despite that great progress has been made in investigation of the characteristics and neurophysiological basis, the exact nature of BOLD signal remains unclear. In this paper we discuss the characteristics of BOLD signals, the nonlinear BOLD response to external stimuli and the relation between BOLD signals and neural electrophysiological recordings. Furthermore, we develop our new opinions regarding nonlinear BOLD response and make some perspectives on future study.     

Characteristics of fMRI BOLD signal and its neurophysiological mechanism

The functional magnetic resonance imaging (fMRI) based on blood oxygen level dependent (BOLD) contrast has emerged as one of the most potent noninvasive tools for mapping brain function and has been widely used to explore physiological, pathological changes and mental activity in the brain. Exploring the nature and property of BOLD signal has recently attracted more attentions. Despite that great progress has been made in investigation of the characteristics and neurophysiological basis, the exact nature of BOLD signal remains unclear. In this paper we discuss the characteristics of BOLD signals, the nonlinear BOLD response to external stimuli and the relation between BOLD signals and neural electrophysiological recordings. Furthermore, we develop our new opinions regarding nonlinear BOLD response and make some perspectives on future study.     

A robust DNA mechanical device controlled by hybridization topology.

Controlled mechanical movement in molecular-scale devices has been realized in a variety of systems-catenanes and rotaxanes, chiroptical molecular switches, molecular ratchets and DNA-by exploiting conformational changes triggered by changes in redox potential or temperature, reversible binding of small molecules or ions, or irradiation. The incorporation of such devices into arrays could in principle lead to complex structural states suitable for nanorobotic applications, provided that individual devices can be addressed separately. But because the triggers commonly used tend to act equally on all the devices that are present, they will need to be localized very tightly. This could be readily achieved with devices that are controlled individually by separate and device-specific reagents. A trigger mechanism that allows such specific control is the reversible binding of DNA strands, thereby 'fuelling' conformational changes in a DNA machine. Here we improve upon the initial prototype system that uses this mechanism but generates by-products, by demonstrating a robust sequence-dependent rotary DNA device operating in a four-step cycle. We show that DNA strands control and fuel our device cycle by inducing the interconversion between two robust topological motifs, paranemic crossover (PX) DNA and its topoisomer JX2 DNA, in which one strand end is rotated relative to the other by 180 degrees. We expect that a wide range of analogous yet distinct rotary devices can be created by changing the control strands and the device sequences to which they bind.     

脑瘤诱发的组织变化和皮层脑电图分析

健康组织和肿瘤组织具有不同的代谢,结构和热力学特性.脑瘤的代谢和结构无序性导致其有较高的熵产生.两种组织不同的熵产生决定了熵由癌流向健康组织.脑瘤和正常细胞在熵和能量方面的差异诱发皮层不同的脑电信号.研究了28个脑瘤患者的脑电图并和健康人进行比较,观察到脑瘤患者脑电图频率的降低.多数情况中慢alpha和theta波出现在肿瘤投影区,此可能与其高熵产生和向外的熵流有关.研究认为,脑瘤的持续高熵产生和热耗散及其它物理效应使得皮层电产生慢化,从而使肿瘤及其邻近的脑组织显示出频率较低的电活性.     

How did brains evolve?

Three reports on mammalian brain evolution analyse the same comparative data on brain component volumes but come to partially conflicting conclusions. Clark et al. conclude from their analysis of volumetric brain proportions ("cerebro-types") that cerebellum size is invariant across mammalian taxonomic groups, the neocortex and cerebellum do not co-vary in size (in contradiction to ref. 1), and cerebrotype-based measures identify directional changes in brain architecture. Here I provide evidence that calls each of these conclusions into question. The failure of the cerebrotype measure to identify species differences in brain architecture that are independent of gross brain size undermines the proposal by Clark et al. that it could be useful for detecting evolutionary patterns and phylogenetic relationships.     

基于环境DNA的合浦榄根村退化红树林底栖动物多样性的研究

本研究基于环境DNA研究合浦榄根村红树林底栖生物的多样性和生物量,探究因海岸工程造成红树林退化后的底栖生物的变化。实验设置死亡红树林、严重退化红树林（以上合称退化红树林）、尚存活红树林以及对照组红树林4种样地,提取红树林沉积物环境总DNA,并设计特异性引物,利用荧光定量PCR法比较优势物种的相对生物量差异;高通量测序后通过生物信息学分析各样地的物种组成结构。定量实验结果显示,退化红树林中两种甲壳类动物生物量相对较低,两种贝类的生物量在各样地没有显著差异。基于高通量测序的环境DNA揭示死亡红树林、严重退化红树林、尚存活红树林以及对照组红树林的群落结构、优势物种存在差异;退化红树林中,软体动物门丰度减少,环节动物门和刺胞动物门增多。聚类结果显示,尚存活红树林与对照组红树林的群落结构相关性最近,随后是严重退化红树林,死亡红树林的相关性最远。本研究结果反映海岸工程造成退化红树林中底栖动物生物多样性和生物量均产生了变化,同时证明环境DNA是研究红树林大型底栖动物生物多样性和生物量变化的有效手段。     

Multifractal analysis of resting state fMRI series in default mode network: age and gender effects

Age-related changes of resting state in default mode network （DMN） may provide new clues to the developing mechanism of normal brain as well as early diagnosis and therapy of some neuropsychiatric disorders. The application of multifractal theory to functional magnetic resonance imaging （fMRI） signals has recently raised increasing attention. We aim to explore the multifractal characteristics underlying the resting state functional magnetic resonance imaging （rs-fMRI） series extracted from DMN, and two issues are mainly discussed： （1） whether there exist multifractals in rs-fMRI series; （2） whether it is possible to distinguish between the different ages or genders by means of multifractal characteristics. Results demon- strated the existence of multifractals in rs-fMRI series in DMN. In addition, slight differences between young subjects and middle-aged or elderly subjects can be successfully detected by △asα, a modified measure we proposed. Furthermore, it is revealed that the rs-fMRI series from young subjects possess smaller averaged scale index and weaker long range correlation, while those from middle-aged or elderly people present increasing averaged scale index andstronger long range correlation. Whereas no significant statistical differences has been found between male and female group. Our results, therefore, highlight the potential useful- ness of multifractal analysis in fMRI series of a certain brain region, and provide important insights into healthy aging in DMN.     

基于独立成分分析的抑郁症脑网络属性分析

使用ICA与图论相结合的方法来研究抑郁症的脑网络拓扑属性差异可以为抑郁症的诊断提供依据。针对以ICA成分为节点构建的二值化网络中轻度抑郁症患者与正常人的传统属性差异不明显的问题,提出将二值化网络改进为加权网络,并引入信息维数这个属性。通过计算信息维数对比患者与正常人的显著差异,找到差异显著的独立成分,并进行溯源分析。实验结果表明,抑郁症患者的信息维数都明显高于正常人,说明抑郁症患者脑网络的复杂度更高,并且二者的差异显著脑区定位为左侧额叶中上回与左侧颞叶中回。     

微波辐射对中枢神经系统功能及其调控的影响

从神经行为、电生理、血脑屏障通透性、生物学机制以及量效关系等方面阐述了近年来微波辐射对中枢神经系统功能及调控的影响。研究表明,微波热效应可引起中枢神经系统功能及生物学机制的变化,如DNA、即早基因、热休克蛋白、神经递质及信号转导等的改变,但对微波非热效应引起的效应仍存在争议,有待进一步探讨。     

Similar level of polyteny in bands and interbands of Drosophila giant chromosomes

The giant polytene chromosomes of Drosophila melanogaster have long been of interest to the geneticist because of the visible map of the genome provided by their characteristic banding patterns. An issue in the understanding of the molecular basis of chromosome banding has been whether the chromosomal DNA is replicated to the same extent in bands and interbands. Although various suggestions have been put forward the point has remained controversial. We have isolated 315 kilobases (kb) of contiguous Drosophila genomic DNA which spans an interval of approximately 13 bands and interbands of the polytene chromosomes. We report here the measurement of the relative level of DNA replication in polytene chromosomes of 84 adjacent restriction fragments of our cloned DNA. We conclude that there are no significant differences in the level of polyteny within the large band and between bands and interbands of this region. This result supports the 'folded fibre' model of polytene chromosome organization, rather than models involving disproportionate replication along the banding pattern.