Systems biology approaches to study the molecular effects of caloric restriction and polyphenols on aging processes

Worldwide population is aging, and a large part of the growing burden associated with age-related conditions can be prevented or delayed by promoting healthy lifestyle and normalizing metabolic risk factors. However, a better understanding of the pleiotropic effects of available nutritional interventions and their influence on the multiple processes affected by aging is needed to select and implement the most promising actions. New methods of analysis are required to tackle the complexity of the interplay between nutritional interventions and aging, and to make sense of a growing amount of -omics data being produced for this purpose. In this paper, we review how various systems biology-inspired methods of analysis can be applied to the study of the molecular basis of nutritional interventions promoting healthy aging, notably caloric restriction and polyphenol supplementation. We specifically focus on the role that different versions of network analysis, molecular signature identification and multi-omics data integration are playing in elucidating the complex mechanisms underlying nutrition, and provide some examples on how to extend the application of these methods using available microarray data.

Electronic supplementary material

The online version of this article (doi:10.1007/s12263-015-0508-9) contains supplementary material, which is available to authorized users.     

Isolation of sixteen autosomal loci and a sex-linked polymorphic microsatellite locus from the Milne-Edwards' sportive lemur (Lepilemur edwardsi)

We isolated 21 microsatellites from the Milne-Edwards' sportive lemur, Lepilemur edwardsi. Eighteen microsatellite sequences possessed sufficient flanking DNA for primer design. Seventeen loci amplified and were found to be polymorphic displaying two to 17 alleles in 32 unrelated individuals from a population from the National Park of Ankarafantsika in northwest Madagascar. One locus (Led-12) was found to be sex linked located on the X chromosome and can be used to sex-type 40% of female L. edwardsi lemurs. These 17 loci were characterized to investigate family structure and the phylogeography of L. edwardsi.     

生物信息学在A型流感病毒研究中的应用

生物信息学是随着人类基因组计划(Human genome project,HGP)的启动而发展起来的一门新兴学科。1995年,在HGP第一个五年总结报告中,给出了较为完整的定义:生物信息学是一门交叉科     

Bootstrap approaches to estimating confidence intervals for molecular dissimilarities and resultant trees

Varied approaches to estimating confidence intervals for immunological and hybridization distances can be uniformly applied to any matrix of distances. One procedure bootstraps the pairwise dissimilarities between the distances of every pair of taxa to all others, creating a derived matrix of distances for which dispersions can be estimated. Another approach bootstraps the sample of differences between pairwise homologous branch lengths concerning each pair of taxa and between asymmetric halves of the matrix, to find a standard error of the dispersions. This allows comparison of the robustness of trees among different sources of data. DNA hybridization, transferrin immunology and protein immunodiffusion matrices all yield much the same result once standard deviations of dissimilarities are acknowledged: namely, unresolvable trichotomies among the human-chimp-gorilla clade and among this clade with orang and gibbon; conventional relationships among hominoids, cercopithecoids, ceboids and strepsirhines; and a polychotomy among anthropoids, strepsirhines, tarsiers, tupaiids and dermopterans.     

Recent approaches to the taxonomy of the Gracilariaceae (Gracilariales,Rhodophyta) and the Gracilaria verrucosa problem

Recognition of species in the Gracilariaceae, often notoriously difficult, is being aided by a combination of classical and modern techniques. We review some recent findings and present new results that may lead to redefinition of Gracilaria verrucosa, the type species of its genus. Plastid DNA restriction profiles (patterns of banding obtained by electrophoresis of DNA after restriction endonuclease digestion) from eleven strains ascribed to G. verrucosa indicated that the concept of this species in northern Europe includes possibly three taxa, one of which is known now to be a species of Gracilariopsis. In contrast, restriction profiles from Argentinian and Japanese strains were closely similar to the predominant pattern for European G. verrucosa. Profiles of several other strains, from the western Atlantic and eastern Pacific, were dissimilar to the European group and to each other. A chromosome number of n = 24 was determined for a representative of the predominant European group, and preliminary results of hybridization trials suggest that these strains, and others with approximately the same plastid DNA restriction pattern, are interfertile.NRCC 30559     

Meiosis and speciation: A study in a speciatingMus terricolor complex

The three chromosomal species of theMus terricolor complex possess 2n = 40 chromosomes. We show that their karyotypes differ in stable heterochromatin variations fixed in homozygous condition as prominent short arms in autosomes 1, 3 and 6. The three chromosomal species exhibit a high incidence of polymorphisms for Robertsonian fusions and pericentric inversions. Breeding experiments and histological analysis of testis show that heterozygosity for pericentric inversions and Robertsonian fusions had no effect on fertility. Meiotic analysis shows normal overall progression of meiosis in the heterozygotes, which is consistent with their normal gametogenesis. Nevertheless, both the inversion and fusion heterozygotes had undergone some alterations in the regular process of homologous synapsis, and it appeared that certain features of the meiotic system circumvented the potential negative effects of these polymorphic chromosomal rearrangements. The results indicate that the attributes of the meiotic system in a given organism could modulate the potential of a chromosomal rearrangement as reproductive barrier. The meiotic modulation hypothesis offers an explanation for the contradictory effects of the similar kinds of chromosomal mutations reported in different species.     

Chromosomal evolution in Malagasy lemurs: X. chromosomal banding studies of Propithecus diadema edwardsi and Indri indri and phylogenic relationships between all the species of the Indriidae

The R-banded karyotypes of two Indriidae, Propithecus diadema and Indri indri, are described and compared with each other and with those of the other species of this family, previously reported, Avahi laniger and Propithecus verreauxi. These comparisons show that 30 chromosomal rearrangements, including 21 Robertsonian translocations and eight pericentric inversions, differentiate these karyotypes. A phylogenic diagram is proposed, showing the early separation of Avahi and the relatively late divergence of the three other species. A populational evolution has occurred between the three other species, but Indri is clearly separated from the two other species by at least five complex rearrangements, although it shares four Robertsonian translocations with P. verreauxi but not P. diadema.     

Meiotic study of hybrids in the genus Eulemur and taxonomic considerations

A reproductive study was conducted on seven hybrids of Eulemur showing chromosomal multivalents involving at least four chromosomes at the pachytene stage. Three individuals were infertile hybrids and one presented a reduced spermatogenesis. In three out of these four hybrids, multivalents were associated with the sex bivalent in a large number of spermatocytes (23%). The relative importance of the reduction of fertility in males linked to chromosomal multivalent formation as well as the genetic background is discussed with regard to the use of cytogenetic data for systematics. Our findings argue for the classification of Eulemur fulvus collaris and E. f. albocollaris in two separate species. In regard to their repartition area, their separation along a linear north-south axis in Madagascar is discussed. Am. J. Primatol. 42:235–245, 1997. © 1997 Wiley-Liss, Inc.     

Experimental embryologic, biochemical and molecular biology approaches to the identification of embryonic inducers

Problems of the mechanisms of embryonic induction in vertebrate development have been considered on the basis of author's experimental data. Though several polypeptide factors with certain inducing activity have been identified recently, molecular genetic mechanisms of their effect on embryonic target cells remains largely unclear. One of possible causes of very slow progress in this area of developmental biology is an inadequate system of biotesting of inducers at tissue level (ectoderm of early amphibian gastrulae) using histological criteria. A necessity for carrying out similar studies on cellular level and estimating effect of inducers using immunochemical and molecular biological methods has been postulated. Methods allowing to carry out biotesting of inducers on cell suspension or aggregate of a one type of embryonic cells have been proposed. New approaches, combining the methods of experimental embryology and molecular biology, to studies of embryonic inducers, receptors, and their mRNA, have been analyzed.     

河北省绢藓属(Entodon)植物的分类与地理分布

在研究文献和标本的基础上,简要回顾了绢藓属(Entodon C. Muell.)植物在中国以及在河北省的研究背景.对采自河北省的210余号绢藓属植物标本进行了研究鉴定,整理出河北省绢藓属植物14种2变种,其中有河北省新记录2种:细疣绢藓(Entodon verruculosus)和中华绢藓(E. smaragdinus).按照吴征镒先生对中国种子植物属的分布类型划分原则\[1\],河北省绢藓属植物可划分为4个类型,其中,密叶绢藓短柄变种(E. compressus var. zikaiwiensis)、亮叶绢藓(E. aeruginosus)、陕西绢藓(E. schensianus)、中华绢藓、短柄绢藓(E. micropodus)、和细疣绢藓6种为中国特有分布.作者根据标本编制了河北省绢藓属植物分种检索表,并概述了每一种的生境、识别特征和地理分布.最后,对河北省绢藓属植物地理分布的特点进行了简要讨论.     

DNA taxonomy, cryptic speciation and diversification of the Neotropical-African liverwort, Marchesinia brachiata (Lejeuneaceae, Porellales)

The Neotropical-African liverwort Marchesinia brachiata has long been regarded as a polymorphic species. This hypothesis is examined using a dataset including sequences of the nuclear internal transcribed spacer region and the plastidic trnL–trnF region of 39 Marchesinia accessions. Maximum parsimony, maximum likelihood and Bayesian analyses indicate that Marchesinia robusta is nested within M. brachiata s.l. The molecular topologies support at least three partly sympatric biological species within M. brachiata s.l., the Neotropical M. bongardiana and M. languida, and the Neotropical-African M. brachiata s.s. These species are incompletely separated by subtle differences in underleaf shape and leaf dentation. Long branches within M. brachiata s.s. suggest ongoing speciation processes that are not yet reflected in distinguishable morphological variation. Divergence time estimates based on nrITS sequence variation and the liverwort fossil record indicate an establishment of the species M. bongardiana, M. brachiata, M. languida, M. madagassa, and M. robusta in the Late Oligocene and Miocene. The intraspecific diversity shows distinctive patterns with evidence for constant accumulation of genetic diversity in M. robusta and M. brachiata whereas M. bongardiana and M. languida likely went through a recent extinction or expansion process as indicated by the bottleneck pattern of genetic diversity. The tropical American-African disjunction of M. brachiata is the result of dispersal rather than Western Gondwanan vicariance.     

浅谈昆虫分类学的研究方向

本文阐述了昆虫分类学的 3个研究方向及其形成过程、各自的研究重心和意义、各自解决的关键问题和工作内容以及 3个研究方向的相互关系。     

Elucidating the molecular mechanisms underlying cellular response to biophysical cues using synthetic biology approaches

ABSTRACT

The use of synthetic surfaces and materials to influence and study cell behavior has vastly progressed our understanding of the underlying molecular mechanisms involved in cellular response to physicochemical and biophysical cues. Reconstituting cytoskeletal proteins and interfacing them with a defined microenvironment has also garnered deep insight into the engineering mechanisms existing within the cell. This review presents recent experimental findings on the influence of several parameters of the extracellular environment on cell behavior and fate, such as substrate topography, stiffness, chemistry and charge. In addition, the use of synthetic environments to measure physical properties of the reconstituted cytoskeleton and their interaction with intracellular proteins such as molecular motors is discussed, which is relevant for understanding cell migration, division and structural integrity, as well as intracellular transport. Insight is provided regarding the next steps to be taken in this interdisciplinary field, in order to achieve the global aim of artificially directing cellular response.     

Establishing the foundation for an applied molecular taxonomy of otters in Southeast Asia

Four species of otters (Mustelidae, Lutrinae) occur in Southeast Asia and are considered to be of conservation concern: Aonyx cinerea (Asian small-clawed otter), Lutra lutra (Eurasian otter), Lutra sumatrana (Hairy-nosed otter), and Lutrogale perspicillata (Smooth-coated otter). Among these, L. sumatrana is endemic to the region, yet little is known about its biology, and the precise distribution of all four species in Southeast Asia is not well known. Furthermore, the taxonomy and systematics of L. sumatrana and L. perspicillata have been the subject of controversy, which has implications for the legal protection and for conservation programs of these taxa. To resolve these controversies, we used a multigene data set comprised of segments from 13 nuclear and 5 mitochondrial loci (11,180 nucleotides) to evaluate the phylogenetic relationships of Asian Old World otters. Phylogenies were also estimated using two mitochondrial loci (1,832 nucleotides) obtained from two or more individuals of the four Southeast Asian species. The results from maximum parsimony, maximum likelihood and Bayesian inference showed that L. sumatrana and L. lutra are sister taxa, whereas L. perspicillata is sister to A. cinerea. Furthermore, the results from the two-mitochondrial gene analyses indicate that L. sumatrana is reciprocally monophyletic with respect to L. lutra, supporting the specific validity of the former taxon. Signs such as tracks and feces are often used in field surveys to provide information on the distribution and abundance of otters, but the accuracy of these methods may be compromised when several closely related species occur sympatrically. Therefore, the two-gene data set was used to develop a provisional set of diagnostic nucleotides that can be potentially used to identify the four species of Southeast Asian otters from noninvasively collected biological samples, such as feces. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Developments in the taxonomy of silica‐scaled chrysophytes – from morphological and ultrastructural to molecular approaches

Taxonomy in silica‐scaled chrysophytes has gone through three morphological phases. From primary studies of the cell morphology in the 18th century, the focus was in the 20th century replaced by studies of the silica structures of the cell envelope. Now, in the latest decades the importance of DNA sequencing has been recognized, not only to support the taxonomic framework but also to obtain new understanding of taxonomic relations among particular taxa. In the first part of this review, we provide a historical overview of the developments in the taxonomy of scale‐bearing chrysophytes. In the second part, we present a phylogenetic reconstruction of chrysophyte algae, updated by newly obtained SSU rDNA and rbcL sequences of several isolated Synura, Mallomonas and Chrysosphaerella species. We detected significant incongruence between the phylogenies obtained from the different datasets, with the SSU rDNA phylogram being the most congruent with the morphological data. Significant saturation of the first rbcL codon position could indicate the presence of positive selection in the rbcL dataset. Within the Synurales, the relationships revealed by the phylogenetic analyses highlight the artificial infragenetic classification of Mallomonas and Synura, and the occurrence of cryptic diversity within a number of traditionally defined species. Finally, three new combinations are proposed based on the phylogenetic analyses: Tessellaria lapponica, Synura asmundiae and S. bjoerkii.