Morphology and angiosperm systematics in the molecular era

Several ways in which morphology is used in systematic and evolutionary research in angiosperms are shown and illustrated with examples: 1) searches for special structural similarities, which can be used to find hints for hitherto unrecognized relationships in groups with unresolved phylogenetic position; 2) cladistic studies based on morphology and combined morphological and molecular analyses; 3) comparative morphological studies in new, morphologically puzzling clades derived from molecular studies; 4) studies of morphological character evolution, unusual evolutionary directions, and evolutionary lability based on molecular studies; and 5) studies of organ evolution. Conclusions: Goals of comparative morphology have shifted in the present molecular era. Morphology no longer plays the primary role in phylogenetic studies. However, new opportunities for morphology are opening up that were not present in the premolecular era: 1) phylogenetic studies with combined molecular and morphological analyses; 2) reconstruction of the evolution of morphological features based on molecularly derived cladograms; 3) refined analysis of morphological features induced by inconsistencies of previous molecular and molecular phylogenetic analyses; 4) better understanding of morphological features by judgment in a wider biological context; 5) increased potential for including fossils in morphological analyses; and 6) exploration of the evolution of morphological traits by integration of comparative structural and molecular developmental genetic aspects (Evo-Devo); this field is still in its infancy in botany; its advancement is one of the major goals of evolutionary botany.     

Molecular approaches to the study of myiasis-causing larvae

Among arthropod diseases affecting animals, larval infections - myiases - of domestic and wild animals have been considered important since ancient times. Besides the significant economic losses to livestock worldwide, myiasis-causing larvae have attracted the attention of scientists because some parasitise humans and are of interest in forensic entomology. In the past two decades, the biology, epidemiology, immunology, immunodiagnosis and control methods of myiasis-causing larvae have been focused on and more recently the number of molecular studies have also begun to increase. The 'new technologies' (i.e. molecular biology) are being used to study taxonomy, phylogenesis, molecular identification, diagnosis (recombinant antigens) and vaccination strategies. In particular, more in depth molecular studies have now been performed on Sarcophagidae, Calliphoridae and flies of the Oestridae sister group. This review discusses the most topical issues and recent studies on myiasis-causing larvae using molecular approaches. In the first part, PCR-based techniques and the genes that have already been analysed, or are potentially useful for the molecular phylogenesis and identification of myiasis-causing larvae, are described. The second section deals with the more recent advances concerning taxonomy, phylogenetics, population studies, molecular identification, diagnosis and vaccination.     

Determinants of intra-specific variation in basal metabolic rate

Basal metabolic rate (BMR) provides a widely accepted benchmark of metabolic expenditure for endotherms under laboratory and natural conditions. While most studies examining BMR have concentrated on inter-specific variation, relatively less attention has been paid to the determinants of within-species variation. Even fewer studies have analysed the determinants of within-species BMR variation corrected for the strong influence of body mass by appropriate means (e.g. ANCOVA). Here, we review recent advancements in studies on the quantitative genetics of BMR and organ mass variation, along with their molecular genetics. Next, we decompose BMR variation at the organ, tissue and molecular level. We conclude that within-species variation in BMR and its components have a clear genetic signature, and are functionally linked to key metabolic process at all levels of biological organization. We highlight the need to integrate molecular genetics with conventional metabolic field studies to reveal the adaptive significance of metabolic variation. Since comparing gene expressions inter-specifically is problematic, within-species studies are more likely to inform us about the genetic underpinnings of BMR. We also urge for better integration of animal and medical research on BMR; the latter is quickly advancing thanks to the application of imaging technologies and ‘omics’ studies. We also suggest that much insight on the biochemical and molecular underpinnings of BMR variation can be gained from integrating studies on the mammalian target of rapamycin (mTOR), which appears to be the major regulatory pathway influencing the key molecular components of BMR.     

Molecular approaches to field studies of malaria

The third 'Molecular Approaches to Malaria' conference was held in Lorne, Australia, in February 2008 and provided extensive information on the application of molecular tools in field studies on malaria. In recent years, technological advances and capacity building in malaria-endemic countries have permitted molecular tools to be applied much more frequently and successfully with exciting new findings. In this review, Hans-Peter Beck and Kevin Tetteh report on the most recent findings using molecular tools in field studies.     

水生甲虫系统发育研究进展

简要回顾了水生甲虫近十几年来各个分类阶元水平系统关系的研究历史,对代表性的水生甲虫类高级阶元系统发育关系进行了比较分析,总结了普遍存在的共识和争议.在研究进展中还介绍了分子生物学方法在水生甲虫系统发育研究中的尝试,虽然其研究结果还未能完全解决上述问题,但必将是对现有研究方法的补充.     

小麦抗条锈病基因定位及分子标记研究进展

本文综述了小麦抗条锈病基因染色体定位及抗条锈病基因分子标记的研究进展,并对几种分子标记技术的应用潜力作了比较分析,特别是对ＳＳＲ、ＩＳＳＲ、ＡＦＬＰ等新型分子标记在小麦遗传育种中的应用前景作了初步探讨。     

两栖爬行动物的分子系统发生

介绍了两栖爬行动物分子系统发生研究中选用的分子信息的种类及已发表的蛙类,蟾蜍类,龟类,蜥蜴类和蛇类等的分子系统学研究,这些研究中使用的DNA信息主要为mtDNA序列,也使用了一些核DNA序列。其研究的内容涉及目间,科间等高级阶元的系统发生关系,以及属间,种间以及亚种或种群间的系统发生关系。     

Studies on the molecular evolution of the Crocodylia: footprints in the sands of time

A reasonably large number of studies focusing on the molecular evolution of crocodilians have been completed during the past 100 years. Proteins were initially studied before DNA was known to carry the genetic information of cells and organisms, and were subsequently studied to infer changes at the DNA level. More recently, studies on the DNA itself have been completed. We have had the pleasure of taking part in or facilitating many studies conducted over the past 50 years, especially several of the earliest studies done using newly developed molecular techniques. We provide a review of the molecular genetic studies on crocodilians, summarizing the findings of these studies as well as the context in which they were undertaken. This review is a personal look at the history of molecular studies on the evolutionary biology of crocodilians. Our excuse for this focus is that our professors, our students and we have had the opportunity to be among the first to apply many new techniques to studies of crocodilians since 1950, when one of us (HCD) was a graduate student of Roland Coulson and Tom Hernandez. Although we will review much of the material in this subject area, we do not claim that it is complete. Instead, we focus our presentation on work in which we have participated or with which we are particularly familiar. We especially focus on materials relevant to the research presented at the 2(nd) International Crocodilian DNA Workshop, 7-9 November, 2001, at the San Diego Zoo. Thus, the following review also stands as a tribute to our mentors, students, and colleagues.     

农杆菌-植物间基因转移的分子基础

植物病原细菌多以Ⅲ型分泌系统运送毒性因子或无毒基因产物到植物细胞,但根癌农杆菌利用Ⅳ型分泌系统转移致瘤基因片断T-DNA到植物细胞核,并整合到植物基因组,使植物产生肿瘤,作者将介绍vir基因的诱导、T-DNA的加工、T-DNA的转移,以及T-复合体运输的装备等方面的最新研究进展,以探讨农杆菌-植物间基因转移的分子基础,研究该系统转移基因的分子基础将有利于开发和改良植物遗传工程的载体工具;另外,农杆菌-植物作为一种模式植物病害系统,其研究也为植物-病原菌的基础理论研究提供参考。由于有些人体病原细菌也采用Ⅳ型分泌系统运送毒性因子到人体细胞,研究农杆菌-植物间的基因转移系统也有利于医学研究。     

Body mass‐corrected molecular rate for bird mitochondrial DNA

Mitochondrial DNA remains one of the most widely used molecular markers to reconstruct the phylogeny and phylogeography of closely related birds. It has been proposed that bird mitochondrial genomes evolve at a constant rate of ~0.01 substitution per site per million years, that is that they evolve according to a strict molecular clock. This molecular clock is often used in studies of bird mitochondrial phylogeny and molecular dating. However, rates of mitochondrial genome evolution vary among bird species and correlate with life history traits such as body mass and generation time. These correlations could cause systematic biases in molecular dating studies that assume a strict molecular clock. In this study, we overcome this issue by estimating corrected molecular rates for birds. Using complete or nearly complete mitochondrial genomes of 475 species, we show that there are strong relationships between body mass and substitution rates across birds. We use this information to build models that use bird species’ body mass to estimate their substitution rates across a wide range of common mitochondrial markers. We demonstrate the use of these corrected molecular rates on two recently published data sets. In one case, we obtained molecular dates that are twice as old as the estimates obtained using the strict molecular clock. We hope that this method to estimate molecular rates will increase the accuracy of future molecular dating studies in birds.     

Influence of metabolic network structure and function on enzyme evolution

Background  

Most studies of molecular evolution are focused on individual genes and proteins. However, understanding the design principles and evolutionary properties of molecular networks requires a system-wide perspective. In the present work we connect molecular evolution on the gene level with system properties of a cellular metabolic network. In contrast to protein interaction networks, where several previous studies investigated the molecular evolution of proteins, metabolic networks have a relatively well-defined global function. The ability to consider fluxes in a metabolic network allows us to relate the functional role of each enzyme in a network to its rate of evolution.     

活细胞单分子实时视见研究

我们对细胞生物学与分子生物学中有关分子事件和相互作用的认识,大部分都是集团平均水平研究的结果,并且基于所有的分子在给定时间内以完全相同的方式运动这样一种不真实的假设。现在,激光技术和全内反射显微镜的应用,以及绿色荧光蛋白(green fluorescent proteins,GFPs)等新的分子荧光探针的出现,使得显示活细胞单个生物分子的运动行为和轨迹成为可能。单分子水平的研究将会加深人们对分子和细胞生物学的基本概念的认识。     

Southern Ocean diversity: new paradigms from molecular ecology

Southern Ocean biodiversity reflects past climate, oceanographic, and tectonic changes. Molecular data from contemporary populations carry signatures of these processes. Here, we review new molecular studies on Southern Ocean benthic fauna. Many of these studies focus on species with extensive geographic or bathymetric distributions, and resolve taxonomic questions. Reviewing all available data, we show that, in addition to reflecting life-history characteristics, the molecular signals found in these studies provide an insight into how species survived the last glacial maximum (LGM). We identify molecular signatures that are characteristic of surviving glacial cycles in small refugia on the continental shelf and distinguish them from molecular signatures that are indicative of surviving glacial cycles in the deep sea.     

From the mechanisms of genetic transposition to the functional genomics

Pioneer works on studying molecular mechanisms of mutagenesis were published in the journal Genetika in the 1960s. In the laboratory of S.I. Alikhanian, studies on molecular mechanisms of genetic transposition were initiated in the late 1960s on the model of bacteriophage transposon Mu (Mutator). Parallel to these studies conducted in the laboratory of plant molecular genetics (Institute of Molecular Genetics, Academy of Sciences of the USSR), which was later named the Laboratory of Functional Genomics (Vavilov Institute of General Genetics, Russian Academy of Sciences), studies on transposition of Ti-plasmid T-DNA of Agrobacterium tumefaciens and works on construction of transgenic plants began in this laboratory. Transgenic plants with the expressed bacterial genes provided a model for the functional genomics. This topic is considered here in detail.     

Molecular techniques in phytoplankton research: from allozyme electrophoresis to genomics

Molecular techniques have become a valuable tool in phytoplankton studies over the past decades. The appropriate choice of a technique from an increasing array of methods can be rather complex, because different techniques are suitable for different questions or problems in ecology and evolution. Each technique has its particular strengths and weaknesses and is based upon different (theoretical) assumptions. Our aim is to give a better insight in the (correct) use of various molecular techniques in phytoplankton research, with special emphasis on the fields of strain identification, differentiation of populations and the establishment of phylogenetic relationships. The basic steps in the development of molecular techniques like allozyme electrophoresis, RFLP, DGGE, SSCP, RAPD, AFLP and microsatellites, and the application of these techniques in phytoplankton research, are discussed. Furthermore, recent developments in molecular biology, that have so far only found limited application in phytoplankton studies, such as single-cell PCR, PCR assays combined with molecular probes (Heteroduplex Mobility Assays or DNA arrays), Real-time PCR, complete genome sequencing, multi-gene expression studies using microarrays, and Single Nucleotide Polymorphism (SNPs), are discussed. We emphasise the relevance of fundamental and applied molecular studies on phytoplankton for a wider community of ecologists and evolutionary biologists.     

Tetrahydroisoquinolines functionalized with carbamates as selective ligands of D2 dopamine receptor

A series of tetrahydroisoquinolines functionalized with carbamates is reported here as highly selective ligands on the dopamine D2 receptor. These compounds were selected by means of a molecular modeling study. The studies were carried out in three stages: first an exploratory study was carried out using combined docking techniques and molecular dynamics simulations. According to these results, the bioassays were performed; these experimental studies corroborated the results obtained by molecular modeling. In the last stage of our study, a QTAIM analysis was performed in order to determine the main molecular interactions that stabilize the different ligand-receptor complexes. Our results show that the adequate use of combined simple techniques is a very useful tool to predict the potential affinity of new ligands at dopamine D1 and D2 receptors. In turn the QTAIM studies show that they are very useful to evaluate in detail the molecular interactions that stabilize the different ligand-receptor complexes; such information is crucial for the design of new ligands.     

Protein aggregation in silico

Protein aggregation is a challenge to the successful manufacture of protein therapeutics; it can impose severe limitations on purification yields and compromise formulation stability. Advances in computer power, and the wealth of computational studies pertaining to protein folding, have facilitated the development of molecular simulation as a tool to investigate protein misfolding and aggregation. Here, we highlight the successes of protein aggregation studies carried out in silico, with a particular emphasis on studies related to biotechnology. To conclude, we discuss future prospects for the field, and identify several biotechnology-related problems that would benefit from molecular simulation.     

Prognostic molecular markers in pediatric liver disease – Are there any?

Pediatric liver disease (PLD) is a major cause of severe morbidity and prolonged hospitalizations in children. Stratifying patients in terms of prognosis remains challenging. The limited knowledge about molecular mechanisms causing and accompanying PLD remains the main obstacle in a search for reliable prognostic biomarkers. A systematic search of MEDLINE via PubMed and Embase via OVID was conducted on studies published between August 2007 and August 2017. Molecular markers with a prognostic potential in terms of survival, need for liver transplantation or disease progression/regression were selected. In general, identified studies were single center smaller case-control studies or case series with a low level of evidence and a high risk of bias. Only 23 studies comprising 898 patients could be included, mostly focusing on biliary atresia, non-alcoholic fatty liver disease, viral hepatitis, and LT; and markers related to morphogenesis and fibrosis. Furthermore, molecular markers in metabolic pathways and inflammation shown to be relevant, however requiring further validation. Hence, further biological and clinical studies are needed to gain greater molecular insight into PLD.     

Determination of cell fate in sea urchin embryos

Classical embryological studies have provided a great deal of information on the autonomy and stability of cell fate determination in early sea urchin embryos. However, these studies were limited by the tools available at the time, and the interpretation of the results of these experiments was limited by the lack of information available at the molecular level. Recent studies which have re-examined classical experiments at the molecular level have provided important new insights into the mechanism of determination in sea urchins, and require us to re-evaluate some long standing theories on the process of differentiation.