鸣禽前脑听觉和鸣唱系统zenk基因的诱导表达

鸣曲和鸣唱行为可以诱导鸣禽前脑不同区域的zenk基因表达.鸣禽听到同类鸣曲时在听觉系统会出现zenk表达,并在致聋后这种诱导消失.而鸣禽鸣唱时,在鸣唱系统同样有zenk基因的表达,且不依赖于听觉反馈,因为致聋鸟只要发声就可以诱导表达.大量的研究表明,zenk基因在听区的诱导表达不仅可对同类鸣曲进行识别,而且在教习曲模板的记忆方面发挥重要作用.鸣唱系统zenk基因诱导表达则主要与鸣曲的产生与维持有关.zenk基因在两个系统中的诱导表达将听觉感知与鸣唱运动紧密联系起来.     

Quantifying Histological Features of Cancer Biospecimens for Biobanking Quality Assurance Using Automated Morphometric Pattern Recognition Image Analysis Algorithms

Biorepository-supported translational research depends on high-quality, well-annotated specimens. Histopathology assessment contributes insight into how representative lesions are for research objectives. Feasibility of documenting histological proportions of tumor and stroma was studied in an effort to enhance information regarding biorepository tissue heterogeneity. Using commercially available software, unique spatial-spectral algorithms were developed for applying automated pattern recognition morphometric image analysis to quantify histologic tumor and nontumor tissue areas in biospecimen tissue sections. Measurements were acquired successfully for 75/75 (100%) lymphomas, 76/77 (98.7%) osteosarcomas, and 60/70 (85.7%) melanomas. The percentage of tissue area occupied by tumor varied among patients and tumor types and was distributed around medians of 94% [interquartile range (IQR)=14%] for lymphomas, 84% for melanomas (IQR=24%), and 39% for osteosarcomas (IQR=44%). Within-patient comparisons from a subset, including multiple individual patient specimens, revealed ≤12% median coefficient of variation (CV) for lymphomas and melanomas. Phenotypic heterogeneity of osteosarcomas resulted in 33% median CV. Uniformly applied, tumor-specific pattern recognition software permits automated tissue-feature quantification. Furthermore, dispersion analyses of area measurements across collections, as well as of multiple specimens from individual patients, support using limited tissue slices to gauge features for some tumor types. Quantitative image analysis automation is anticipated to minimize variability associated with routine biorepository pathologic evaluations and enhance biomarker discovery by helping to guide the selection of study-appropriate specimens.     

Molecular Recognition Features in Zika Virus Proteome

Viruses have compact genomes that encode limited number of proteins in comparison to other biological entities. Interestingly, viral proteins have shown natural abundance of either completely disordered proteins that are recognized as intrinsically disorder proteins (IDPs) or partially disordered segments known as intrinsically disordered protein regions (IDPRs). IDPRs are involved in interactions with multiple binding partners to accomplish signaling, regulation, and control functions in cells. Tuning of IDPs and IDPRs are mediated through post-translational modification and alternative splicing. Often, the interactions of IDPRs with their binding protein partner(s) lead to transition from the state of disorder to ordered form. Such interaction-prone protein IDPRs are identified as molecular recognition features (MoRFs). Molecular recognition is an important initial step for the biomolecular interactions and their functional proceedings. Although previous studies have established occurrence of the IDPRs in Zika virus proteome, which provide the functional diversity and structural plasticity to viral proteins, the MoRF analysis has not been performed as of yet. Many computational methods have been developed for the identification of the MoRFs in protein sequences including ANCHOR, MoRFpred, DISOPRED3, and MoRFchibi_web server. In the current study, we have investigated the presence of MoRF regions in structural and non-structural proteins of Zika virus using an aforementioned set of computational techniques. Furthermore, we have experimentally validated the intrinsic disorderness of NS2B cofactor region of NS2B–NS3 protease. NS2B has one of the longest MoRF regions in Zika virus proteome. In future, this study may provide valuable information while investigating the virus host protein interaction networks.     

A Voting-Based Sequential Pattern Recognition Method

We propose a novel method for recognizing sequential patterns such as motion trajectory of biological objects (i.e., cells, organelle, protein molecules, etc.), human behavior motion, and meteorological data. In the proposed method, a local classifier is prepared for every point (or timing or frame) and then the whole pattern is recognized by majority voting of the recognition results of the local classifiers. The voting strategy has a strong benefit that even if an input pattern has a very large deviation from a prototype locally at several points, they do not severely influence the recognition result; they are treated just as several incorrect votes and thus will be neglected successfully through the majority voting. For regularizing the recognition result, we introduce partial-dependency to local classifiers. An important point is that this dependency is introduced to not only local classifiers at neighboring point pairs but also to those at distant point pairs. Although, the dependency makes the problem non-Markovian (i.e., higher-order Markovian), it can still be solved efficiently by using a graph cut algorithm with polynomial-order computations. The experimental results revealed that the proposed method can achieve better recognition accuracy while utilizing the above characteristics of the proposed method.     

Wood Recognition Using Image Texture Features

Inspired by theories of higher local order autocorrelation (HLAC), this paper presents a simple, novel, yet very powerful approach for wood recognition. The method is suitable for wood database applications, which are of great importance in wood related industries and administrations. At the feature extraction stage, a set of features is extracted from Mask Matching Image (MMI). The MMI features preserve the mask matching information gathered from the HLAC methods. The texture information in the image can then be accurately extracted from the statistical and geometrical features. In particular, richer information and enhanced discriminative power is achieved through the length histogram, a new histogram that embodies the width and height histograms. The performance of the proposed approach is compared to the state-of-the-art HLAC approaches using the wood stereogram dataset ZAFU WS 24. By conducting extensive experiments on ZAFU WS 24, we show that our approach significantly improves the classification accuracy.     

Acoustic Features Used in Song Discrimination by the Veery

To investigate which song features are used for discrimination by the veery (Catharus fuscescens), we synthesized songs by computer and manipulated or deleted various features. These songs were then played to territorial males in their natural habitat. Differences in response to these stimuli indicated the relative importance of the manipulated song components. We found that certain features must be maintained in order to elicit a territorial response similar to that elicited by the natural song. These features were the frequency changes between and within syllables, the dominant higher frequency band (or voice), the intra-syllable syntax, and the rapid repetitive amplitude and frequency modulations. Manipulations of inter-syllable syntax independent of frequency changes between syllables, broad changes in amplitude, and the lower frequency band, did not have a significant effect on response. We thus concluded that they are not essential as cues for discrimination or species identification. Re-recordings of songs broadcast along transects indicate that song components used in encoding species identity are those which transmit well across veery territories.     

仿生模式识别在细菌基因组水平转移基因预测中的应用

水平转移基因的预测对于生物进化过程的理解和物种之间遗传物质进行定性和定量的估计都有重要的意义.本文提出一种利用仿生模式识别原理来对细茵基因组水平转移基因进行预测的方法.仿生模式识别是基于同调连续性原理一特征空间中同类样本的连续性特性,强调用"认识"模式取代传统的模式"分类"与划分,它更接近于人类"认识"事物的特性.仿生模式识别理论已经成功应用于多镜头人脸身份确认,人脸识别,图像复原,语音识别等领域.我们采用超香肠神经元网络对水平转移基因进行识别,结果显示,仿生模式识别方法优于目前预测结果最好的八联核苷酸频率的打分算法,和基于支撑向量机的识别算法.特别是在对大肠杆菌(Eschefichia coli K12)基因组,识别率分别提高了42.3%和30.5%.     

面向代谢组学的模式识别技术应用与展望

代谢组学是后基因时代新兴的一门研究生物体内所有小分子代谢物的组学学科,是系统生物学的有机组成部分。由于代谢组学是基于数据驱动的学科,因此如何有效利用数据预处理、模式识别等信息处理技术从代谢组学复杂的高维样本中挖掘深层次的“知识”是代谢组学乃至整个系统生物学的关键问题。对模式识别技术在代谢组学中的应用作了全面的综述。总结代谢组学数据特性及其对模式识别技术的特殊要求,揭示面向代谢组学的模式识别技术所遇到的困难并在此基础上提出相应的解决办法。     

No Coolidge Effect in Decorated Crickets

Female decorated crickets, Gryllodes sigillatus , obtain genetic benefits by mating with different males and, when given a choice, prefer novel males over previous mates. It is unknown, however, whether males exhibit a similar preference for novel females. Although female crickets control copulation, there are at least two ways in which males can exercise choice: (1) the amount of courtship directed towards prospective mates and (2) the size of the spermatophore transferred to the female at mating. To determine whether males devote more courtship effort to novel females while controlling for female behavioral cues, male courtship effort toward two dead females, one, a previous mate and the other, a novel female, was measured. To determine whether males manufacture larger spermatophores when paired with novel females, males were mated to novel or previous mates, and the different components of the spermatophore weighed. Males did not spend more time courting dead novel females than previous mates. There was no difference in the latency to remating of males confined with novel females and those paired with previous mates, and there was no difference in the mass of spermatophores transferred to novel and familiar females. Contrary to previous studies in other taxa, this study suggests that male crickets do not prefer novel mates and thus, are not subject to the Coolidge effect. Although mating with novel females may be beneficial to males, selection on males to identify and discriminate against previous mates may be relaxed because of a strong female preference for novel males.     

Mitochondrial DNA Transmission Genetics in Crickets

This paper presents the results of a single generation study of the transmission genetics of mitochondrial DNA in the field cricket Gryllus firmus. In this species, individuals heteroplasmic for at least two different-sized mitochondrial genomes can be collected easily from natural populations. The frequencies of mtDNA size variants in heteroplasmic females and samples of their offspring were estimated by densitometry of autoradiographs. The variance in mitochondrial genotype frequencies among the offspring of heteroplasmic females indicates that, through genetic drift, fixation would take several hundred animal generations. Differences between the observations and data on mtDNA transmission in yeast and cows are discussed in light of the differences in organelle sampling regime and early developmental events in these species. Our data also show shifts in genotype frequencies in the transmission from mother to offspring that suggest a bias in favor of smaller genomes. The nature of mtDNA size variation in natural populations of crickets is discussed in reference to a mutation-selection balance.     

Genetic Control of Acoustic Behavior in Crickets

Evidence is presented that acoustic behavior in field cricketsis under firm genetic control. The calling song of adult malesis highly stereotyped and species specific. Hybrids can be madeby crossing two species of Teleogryllus with dissimilar callingsongs. The calling songs of the hybrids are uniquely differentfrom that of either parental species, and in addition the songsof the two reciprocal hybrids are different from each other.Genetic control of song production is polygenic and multichromosomal;sex-linkage of some song determinants is also indicated. Femalephonoresponse to calling song was measured on a Y-maze. Speciesspecificity of phonoresponse was confirmed and in addition,hybrid females prefer hybrid song to either parental song. Thepossibility that calling song production in the male and itsreception in the female are genetically coupled is discussed.     

基于打分矩阵的多类蛋白质折叠子的预测

依据蛋白质折叠子中氨基酸保守性,以氨基酸、氨基酸的极性、氨基酸的电性以及氨基酸的亲—疏水性为参数,从蛋白质的氨基酸序列出发,采用"一对多"的分类策略,通过构建打分矩阵和选取氨基酸序列模式片断,利用5种相似性打分函数对27类折叠子进行识别,最好的预测精度达到83.46%。结果表明,打分矩阵是预测多类蛋白质折叠子有效的方法。     

Seeing the Song: Left Auditory Structures May Track Auditory-Visual Dynamic Alignment

Auditory and visual signals generated by a single source tend to be temporally correlated, such as the synchronous sounds of footsteps and the limb movements of a walker. Continuous tracking and comparison of the dynamics of auditory-visual streams is thus useful for the perceptual binding of information arising from a common source. Although language-related mechanisms have been implicated in the tracking of speech-related auditory-visual signals (e.g., speech sounds and lip movements), it is not well known what sensory mechanisms generally track ongoing auditory-visual synchrony for non-speech signals in a complex auditory-visual environment. To begin to address this question, we used music and visual displays that varied in the dynamics of multiple features (e.g., auditory loudness and pitch; visual luminance, color, size, motion, and organization) across multiple time scales. Auditory activity (monitored using auditory steady-state responses, ASSR) was selectively reduced in the left hemisphere when the music and dynamic visual displays were temporally misaligned. Importantly, ASSR was not affected when attentional engagement with the music was reduced, or when visual displays presented dynamics clearly dissimilar to the music. These results appear to suggest that left-lateralized auditory mechanisms are sensitive to auditory-visual temporal alignment, but perhaps only when the dynamics of auditory and visual streams are similar. These mechanisms may contribute to correct auditory-visual binding in a busy sensory environment.