Homology in classical and molecular biology

Hypotheses of homology are the basis of comparative morphology and comparative molecular biology. The kinds of homologous and nonhomologous relations in classical and molecular biology are explored through the three tests that may be applied to a hypothesis of homology: congruence, conjunction, and similarity. The same three tests apply in molecular comparisons and in morphology, and in each field they differentiate eight kinds of relation. These various relations are discussed and compared. The unit or standard of comparison differs in morphology and in molecular biology; in morphology it is the adult or life cycle, but with molecules it is the haploid genome. In morphology the congruence test is decisive in separating homology and nonhomology, whereas with molecular sequence data similarity is the decisive test. Consequences of this difference are that the boundary between homology and nonhomology is not the same in molecular biology as in morphology, that homology and synapomorphy can be equated in morphology but not in all molecular comparisons, and that there is no detected molecular equivalent of convergence. Since molecular homology may reflect either species phylogeny or gene phylogeny, there are more kinds of homologous relation between molecular sequences than in morphology. The terms paraxenology and plerology are proposed for two of these kinds--respectively, the consequence of multiple xenology and of gene conversion.     

酿酒酵母细胞衰老机理的研究进展

酿酒酵母的细胞衰老研究作为生命科学领域的前沿课题,对解析高等真核生物衰老的分子机制具有重要意义。迄今为止,在酵母中已经确立的衰老模式有两种,即复制型衰老和时序型衰老。细胞衰老的影响因子较多,涉及到很多过程,所以研究起来非常复杂。综述了两种细胞衰老机制的研究进展。     

Emergence,therefore antireductionism? A critique of emergent antireductionism

Emergent antireductionism in biological sciences states that even though all living cells and organisms are composed of molecules, molecular wholes are characterized by emergent properties that can only be understood from the perspective of cellular and organismal levels of composition. Thus, an emergence claim (molecular wholes are characterized by emergent properties) is thought to support a form of antireductionism (properties of higher-level molecular wholes can only be understood by taking into account concepts, theories and explanations dealing with higher-level entities). I argue that this argument is flawed: even if molecular wholes are characterized by emergent properties and even if many successful explanations in biology are not molecular, there is no entailment between the two claims.     

Molecular genetics of chronic neutrophilic leukemia,chronic myelomonocytic leukemia and atypical chronic myeloid leukemia

According to the 2008 World Health Organization classification, chronic neutrophilic leukemia, chronic myelomonocytic leukemia and atypical chronic myeloid leukemia are rare diseases. The remarkable progress in our understanding of the molecular genetics of myeloproliferative neoplasms and myelodysplastic/myeloproliferative neoplasms has made it clear that there are some specific genetic abnormalities in these 3 rare diseases. At the same time, there is considerable overlap among these disorders at the molecular level. The various combinations of genetic abnormalities indicate a multi-step pathogenesis, which likely contributes to the marked clinical heterogeneity of these disorders. This review focuses on the current knowledge and challenges related to the molecular pathogenesis of chronic neutrophilic leukemia, chronic myelomonocytic leukemia and atypical chronic myeloid leukemia and relationships between molecular findings, clinical features and prognosis.     

Characterization of Endotrypanum (Kinetoplastida: Trypanosomatidae), a unique parasite infecting the neotropical tree sloths (Edentata)

This article reviews current concepts of the biology of Endotrypanum spp. Data summarized here on parasite classification and taxonomic divergence found among these haemoflagellates come from our studies of molecular characterization of Endotrypanum stocks (representing an heterogenous population of reference strains and isolates from the Brazilian Amazon region) and from scientific literature. Using numerical zymotaxonomy we have demonstrated genetic diversity among these parasites. The molecular trees obtained revealed that there are, at least, three groups (distinct species?) of Endotrypanum, which are distributed in Central and South America. In concordance with this classification of the parasites there are further newer molecular data obtained using distinct markers. Moreover, comparative studies (based on the molecular genetics of the organisms) have shown the phylogenetic relationships between some Endotrypanum and related kinetoplastid lineages.     

High-performance liquid chromatography of proteins by gel permeation chromatography

The ability of two high-performance liquid chromatography gel permeation columns to separate proteins was evaluated. These columns gave satisfactory molecular weight separations for some, but not all, proteins tested. These results indicate that there are limitations in confidence of molecular weight determinations made by this technique.     

The effect of reducing agents on the structure of mammalian beta-adrenergic receptors

Under reducing conditions (5% beta-mercaptoethanol) the mammalian beta-adrenergic receptor binding site from both beta 1 (porcine heart membranes) and beta 2 receptors (hamster lung and rat erythrocyte membranes) appears to reside on peptides of Mr 62,000-65,000 as determined by photoaffinity labeling with p-azido-m-[125I]iodobenzylcarazolol and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. When similar experiments are performed in these same systems under a variety of non-reducing conditions, there are minimal changes in the apparent molecular weight of both the beta 1- and beta 2-adrenergic receptor binding subunits and no specifically labeled higher molecular weight proteins are observed suggesting that there are no disulfide linked subunits in mammalian beta-adrenergic receptors.     

Structural features in the heptad substructure and longer range repeats of two-stranded alpha-fibrous proteins

Considerable sequence data have been collected from the intermediate filament proteins and other alpha-fibrous proteins including myosin, tropomyosin, paramyosin, desmoplakin and M-protein. The data show that there is a clear preference for some amino acids to occur in specific positions within the heptad substructure that characterizes the sequences which form the coiled-coil rod domain in this class of proteins. The results also indicate that although there are major similarities between the various proteins there are also key differences. In all cases, however, significant regularities in the linear disposition of the acidic and the basic residues in the coiled-coil segments can be related to modes of chain and molecular aggregation. In particular a clear trend has been observed which relates the mode of molecular aggregation to the number of interchain ionic interactions per heptad pair.     

Future of DNA-based insect monitoring

Insects are crucial for ecosystem health but climate change and pesticide use are driving massive insect decline. To mitigate this loss, we need new and effective monitoring techniques. Over the past decade there has been a shift to DNA-based techniques. We describe key emerging techniques for sample collection. We suggest that the selection of tools should be broadened, and that DNA-based insect monitoring data need to be integrated more rapidly into policymaking. We argue that there are four key areas for advancement, including the generation of more complete DNA barcode databases to interpret molecular data, standardisation of molecular methods, scaling up of monitoring efforts, and integrating molecular tools with other technologies that allow continuous, passive monitoring based on images and/or laser imaging, detection, and ranging (LIDAR).     

Molecular Illustration in Research and Education: Past,Present, and Future

Two-dimensional illustration is used extensively to study and disseminate the results of structural molecular biology. Molecular graphics methods have been and continue to be developed to address the growing needs of the structural biology community, and there are currently many effective, turn-key methods for displaying and exploring molecular structure. Building on decades of experience in design, best-practice resources are available to guide creation of illustrations that are effective for research and education communities.     

Evaluation of cross-linked polypeptides in SDS gel electrophoresis

The behavior of covalently cross-linked protein oligomers in polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate has been compared with that of reduced polypeptides of known molecular weight. Over a limited range of molecular weights the two groups of proteins behave similarly with marked differences in mobility apparent only above 150,000 daltons. However, at all molecular weights there is a tendency for the cross-linked proteins to migrate faster than standard proteins; this could lead to overestimation of apparent molecular weights by 5–15% when the oligomers are used as ealibrating standards.     

Tumor heterogeneity: morphological, molecular and clinical implications

Malignant tumors are characterized by their great heterogeneity and variability. There are hundreds of different types of malignant tumors that harbour many oncogenic alterations. The tumor heterogeneity has important morphological, molecular and clinical implications. Except for some hematopoietic and lymphoproliferative processes and small cell infant tumors, there are not specific molecular alterations for most human tumors. In this review we summarize the most important aspects of carcinogenesis and chemoradiosensitivity of malignant cells. In this regard, some oncogenes such as neu, ras and bcl-2 have been associated with cellular resistance to treatment with anticancer agents. The knowledge of oncogenic alterations involved in each tumor can be important to correlate the morphological features, the genetic background, the prognosis and the clinical response to treatment with anticancer agents. Based on the molecular background of the tumor there are new cancer gene therapy protocols. For example using adenovirus Ela in tumors with overexpression of neu oncogene, inhibitors of tyrosine kinase specific for the PDGF receptor in glioma, inhibitors of farnesil transferase to prevent ras activity in tumors with mutations in the ras gene.     

The relationship between molecular weight and quaternary structure of globular proteins

The relationship between the molecular weight and the number of subunits in oligomeric globular proteins consisting of identical subunits has been analyzed. It has been shown that the molecular weights of the subunits are distributed about a mean value of 48,000 and consequently that the molecular weights of the native oligomeric proteins are distributed in clearly distinguishable molecular weight regions. This observation allows the probability of a particular oligomeric structure to be predicted from a measurement of the oligomer molecular weight alone, which is useful in a number of types of study of protein structure, particularly comparative studies. Calculations have been performed which suggest that there is no thermodynamic limitation, in terms of the subunit interactions themselves, to the size of an oligomeric protein with a given number of subunits. Rather, an individual polypeptide chain itself has inherent size limitations, which consequently limits the molecular weight of the corresponding oligomer.     

Differential enzyme targeting as an evolutionary adaptation to herbivory in carnivora

Not all members of the order Carnivora are carnivorous. Some are omnivorous, and a few, such as the giant panda, Ailuropoda melanoleuca, are almost exclusively herbivorous. Although a number of adaptations to increased plant-eating are recognized within Carnivora, few have been studied at the molecular level. One molecular adaptation to diet that is spread widely across Mammalia is the differential intracellular targeting of the intermediary metabolic enzyme alanine:glyoxylate aminotransferase (AGT), which tends to be mitochondrial in carnivores, peroxisomal in herbivores, and both mitochondrial and peroxisomal in omnivores. In the present study, we have analyzed the targeting of AGT in Carnivora in relation to species' natural diets. We show not only that there has been an adaptive shift in AGT targeting from the mitochondrion toward the peroxisome as diets have shifted from being mainly carnivorous to ones that are more omnivorous and herbivorous but also that in one lineage, namely that of the giant panda, there is evidence for positive selection pressure at the molecular level on the AGT mitochondrial targeting sequence to decrease its efficiency, thereby allowing more AGT to be targeted to the peroxisomes.     

酶分子设计常用策略和进展

酶分子的生物学功能很大程度上是由其三维空间结构和所处溶剂环境共同决定的。因此,优化酶分子的结构性质以及探索其性质最优的溶剂环境是改善酶分子功能以及进行理性设计的一个可行途径。从实际应用的角度来看,分子设计方法可以为酶工程提供一种有效的解决方案。目前,酶分子设计有两个重要的研究方向,包括提高酶分子的催化活力和优化其稳定性。同时,对酶分子设计方法的研究也有助于对蛋白质生物学机理的探索。在近些年的学术界酶分子设计案例中,生物信息学方法得到广泛的应用。本文系统地总结基于生物信息学的酶分子设计方法的背景、策略和一些经典案例。     

Biochemical markers predicting response to radiation- and radiochemo-therapy in cancer patients

Ongoing studies carried out worldwide using banks of tumor and non-tumor samples give evidence that perspective markers predicting response of individual patients to intended radiation therapy may be found among some apoptotic indexes, spectrum of specialized proteins, and DNA-based microarray molecular profiling analysis as well determination of single nucleotide polymorphisms in genome of the patients. In the last years there is increasing interest in radiogenomics and characterization of gene expression profiles by DNA (micro)array technique that can predict radioresponse of tumor and non-tumor tissues. So far there are only a few reliable molecular markers predicting response of tumor and non-tumor tissues to radiation.     

Arrangement of high molecular weight associated proteins on purified mammalian brain microtubules

The arrangement of the high molecular weight proteins associated with the walls of reconstituted mammalian brain microtubules has been investigated by electron microscopy of negatively stained preparations. The images are found to be consistent with an arrangement whereby the high molecular weight molecules are spaced 12 tubulin dimers apart, i.e., 960 A, along each protofilament of the microtubule, in agreement with the relative stoichiometry of tubulin and high molecular weight protein. Molecules on neighbouring protofilaments seem to be staggered so that they give rise to a helical superlattice, which can be superimposed on the underlying tubulin lattice. In micrographs of disintegrating tubules there is some indication of lateral interactions between neighbouring high molecular weight molecules. When the microtubules are depolymerized into a mixture of short spirals and rings, the high molecular weight proteins appear to remain attached to their respective protofilaments.     

Nature and consequences of mammalian brain and CSF efflux transporters: four decades of progress

In the last 40 years, especially with the application of new neurochemical and molecular biological techniques, there has been explosive progress in understanding how certain ligands and drugs are transported across the blood-brain barrier and choroid plexus out of brain and CSF. In the CNS, there are several separate efflux transporters with very broad specificity that are responsible for much of the efflux transport. This review focuses on three such transporters: organic acid transporter-3, peptide transporter-2 and P-glycoprotein for which there is substantial new information including 'knockout' models in mice and, in one case, dogs. Moreover, the structural biology and transport mechanism of P-glycoprotein at 3.8 angstroms is described. The overall objective is to show how this new knowledge provides a more thorough understanding (e.g., of molecular mechanisms) of efflux transport and in several cases leads to clinically relevant information that allows better treatment of certain CNS disorders (e.g., meningitis and brain cancer).     

Developmental paradigms in terminal lung development

Late lung development comprises the formation of the terminal sac followed by the subdivision of the terminal sac by septa into alveoli and results in the formation of the gas-exchange surface of the lung. This developmentally regulated process involves a complex epithelium-mesenchyme interaction via evolutionarily conserved molecular signaling pathways. In addition, there is a continuous process of vascular growth and development. Currently there are large gaps in our understanding of the molecular mechanisms involved in the formation of the gas-exchange surface. In this review, we attempt to integrate and reconcile the morphologic features in late lung development with what is known about the molecular basis for these processes. We describe the formation of the terminal sac and the subsequent formation of the septa, which divide the terminal sac into alveoli, in terms of the classically described developmental stages of induction, morphogenesis and differentiation. We believe that evolutionarily conserved pathways regulate this process and that morphogen gradients are likely to be a central mechanism. In addition, we highlight the importance of the molecular mechanisms involved in the simultaneous development of the vascular bed and its importance in the late development of the lungs.     

Atrial natriuretic factor: atrial conversion of high to low molecular weight forms

The atrial natriuretic factor elutes by gel filtration in high and low molecular weight fractions. Extraction and elution of rat atria in 1.0 M acetic acid yielded a predominance of the high molecular weight form(s); whereas when these procedures were carried out in 0.1 M acetic acid, there was a predominance of the low molecular weight forms. When partially purified high molecular weight natriuretic activity was eluted in 0.1 M acetic acid, the high molecular weight form(s) remained intact. When partially purified high molecular weight natriuretic activity was mixed with crude atrial extract in 0.1 M acetic acid, there was an apparent conversion to the low molecular weight forms. Extraction of rat atria in boiling 0.1 M acetic acid blocked this conversion. It is concluded that rat atria contain a heat labile factor that converts high molecular weight natriuretic activity to the low molecular weight forms.