Identification of mixed bacterial DNA contamination in broad-range PCR amplification of 16S rDNA V1 and V3 variable regions by pyrosequencing of cloned amplicons

Using a sensitive and rapid method combining broad-range PCR amplification of bacterial 16S rDNA fragments and pyrosequencing for detection, identification and typing, we have found contaminating bacterial DNA in our reagents used for PCR. Identified bacteria are the water-borne bacterial genera Pseudomonas, Stenotrophomonas, Xanthomonas, Ralstonia and Bacillus. Our results are in concordance with recent reports of contaminated industrial water systems. In light of this conclusion, we believe that there is a need for increased awareness of possible contamination in uncertified widely used molecular biology reagents, including ultra-pure water. Since sequence-based 16S rDNA techniques are used in a variety of settings for bacterial typing and the characterization of microbial communities, we feel that future certification of molecular biology reagents, as free of nucleic acids, would be advantageous.     

New tools and new biology: Recent miniaturized systems for molecular and cellular biology

Recent advances in applied physics and chemistry have led to the development of novel microfluidic systems. Microfluidic systems allow minute amounts of reagents to be processed using μm-scale channels and offer several advantages over conventional analytical devices for use in biological sciences: faster, more accurate and more reproducible analytical performance, reduced cell and reagent consumption, portability, and integration of functional components in a single chip. In this review, we introduce how microfluidics has been applied to biological sciences. We first present an overview of the fabrication of microfluidic systems and describe the distinct technologies available for biological research. We then present examples of microsystems used in biological sciences, focusing on applications in molecular and cellular biology.     

Genetics and molecular biology of methanotrophs

Abstract Over the last 20 years or so, the obligate methane-oxidizing bacteria (methanotrophs) have attracted considerable interest. As they grow on a relatively cheap and abundant carbon source, they appeared ideal organisms for the production of bulk chemicals, single-cell protein and for use in biotransformations. More recently their cooxidation properties have been investigated for bioremediation, including the removal of chlorinated compounds such as trichloroethylene from polluted groundwaters. These studies have resulted in a great deal of information on the physiology and biochemistry of methanotrophs but sadly the molecular biology and genetic studies of these organisms have lagged behind. This has been in part due to the obligate nature of the methanotrophs and the refractory nature of such organisms to conventional genetic analysis. However, the more recent availability of broad-host range plasmids coupled with improvements in molecular biology methods have allowed the development of molecular genetic techniques for methanotrophs. The purpose of this review is to summarize what is known about the genetics and molecular biology of methanotrophs and how this information can be used to complement previous and current biochemical studies on the unique property of these bacteria, i.e. the ability to oxidize methane to methanol. Recent developments in molecular ecology techniques that may be applied to these apparently ubiquitous organism are also considered.     

Genetics and molecular biology of methanotrophs.

Over the last 20 years or so, the obligate methane-oxidizing bacteria (methanotrophs) have attracted considerable interest. As they grow on a relatively cheap and abundant carbon source, they appeared ideal organisms for the production of bulk chemicals, single-cell protein and for use in biotransformations. More recently their cooxidation properties have been investigated for bioremediation, including the removal of chlorinated compounds such as trichloroethylene from polluted groundwaters. These studies have resulted in a great deal of information on the physiology and biochemistry of methanotrophs but sadly the molecular biology and genetic studies of these organisms have lagged behind. This has been in part due to the obligate nature of the methanotrophs and the refractory nature of such organisms to conventional genetic analysis. However, the more recent availability of broad-host range plasmids coupled with improvements in molecular biology methods have allowed the development of molecular genetic techniques for methanotrophs. The purpose of this review is to summarize what is known about the genetics and molecular biology of methanotrophs and how this information can be used to complement previous and current biochemical studies on the unique property of these bacteria, i.e. the ability to oxidize methane to methanol. Recent developments in molecular ecology techniques that may be applied to these apparently ubiquitous organism are also considered.     

Signs,markers, profiles,and signatures: clinical haematology meets the new genetics (1980–2000)

We propose that a fruitful way to understand the extension of molecular biology into clinical practice is through the notion of biomedical platform. In this article, we analyze the development of the new genetics in clinical haematology since the mid‐1980s, focusing on two recent instantiations of the molecular biology platform: RT‐PCR and DNA microarrays. We show how clinical research is more closely entwined with “fundamental” biology than is often imagined and simultaneously caution that the use of techniques in clinical research does not automatically entail their use in routine clinical practice. The article calls attention to the work of articulation and regulation as constitutive aspects of a platform that enters standard clinical use.     

Prospects of nanoparticle–DNA binding and its implications in medical biotechnology

Bio-nanotechnology is a new interdisciplinary R&D area that integrates engineering and physical science with biology through the development of multifunctional devices and systems, focusing biology inspired processes or their applications, in particular in medical biotechnology. DNA based nanotechnology, in many ways, has been one of the most intensively studied fields in recent years that involves the use and the creation of bio-inspired materials and their technologies for highly selective biosensing, nanoarchitecture engineering and nanoelectronics. Increasing researches have been offered to a fundamental understanding how the interactions between the nanoparticles and DNA molecules could alter DNA molecular structure and its biochemical activities. This minor review describes the mechanisms of the nanoparticle–DNA binding and molecular interactions. We present recent discoveries and research progresses how the nanoparticle–DNA binding could vary DNA molecular structure, DNA detection, and gene therapy. We report a few case studies associated with the application of the nanoparticle–DNA binding devices in medical detection and biotechnology. The potential impacts of the nanoparticles via DNA binding on toxicity of the microorganisms are briefly discussed. The nanoparticle–DNA interactions and their impact on molecular and microbial functionalities have only drown attention in recent a few years. The information presented in this review can provide useful references for further studies on biomedical science and technology.     

My perpetual cycle: from student to researcher to teacher to student ..

This contribution stems from the personal experience of the author regarding how he became acquainted with embryology and how he finally entered the field of developmental biology. It reports his feelings as a student of the Histology and Embryology course as it was taught in the late 1970s, and his present efforts in teaching developmental biology to university students. In the Developmental Biology course at Pisa University today, students are taught the tissue, molecular and genetic mechanisms that regulate development of several model systems. Drosophila is introduced at the beginning, because of the great knowledge that it has brought to the unraveling of the molecular aspects of development and because it allows several basic concepts to be introduced, and vertebrate systems follow. Other topics include the classic experiments on amphibian systems, which are explained in the light of recent molecular advances, as well as the genetically more versatile vertebrate systems such as the mouse.     

Chemical and enzymatic synthesis of glycopolymers

The development of efficient, fast, flexible and general synthetic routes to glycopolymers is an ongoing challenge and much progress has been made in recent years. Chemical coupling methods have become increasingly sophisticated to fine-tune reactivity of reagents by fortuitous choices of anomeric activating group and protecting groups. As a result, oligosaccharide synthesis has become more predictable and reliable even to the extent that first examples of saccharide library syntheses in solution and on the solid phase have been published. In biology, the repertoire of biocatalysts that can be used for glycoside synthesis is ever-increasing, and enzyme-catalysed glycosylation steps have been successfully incorporated into synthetic strategies.     

Recent advances in microfluidic technologies for biochemistry and molecular biologys

Advances in the fields of proteomics and genomics have necessitated the development of high-throughput screening methods (HTS) for the systematic transformation of large amounts of biological chemical data into an organized database of knowledge. Microfluidic systems are ideally suited for high-throughput biochemical experimentation since they offer high analytical throughput, consume minute quantities of expensive biological reagents, exhibit superior sensitivity and functionality compared to traditional micro-array techniques and can be integrated within complex experimental work flows. A range of basic biochemical and molecular biological operations have been transferred to chip-based microfluidic formats over the last decade, including gene sequencing, emulsion PCR, immunoassays, electrophoresis, cell-based assays, expression cloning and macromolecule blotting. In this review, we highlight some of the recent advances in the application of microfluidics to biochemistry and molecular biology.     

Preparative isolation of polymerase chain reaction products using mixed-mode chromatography

The polymerase chain reaction (PCR) has become one of the most useful techniques in molecular biology laboratories around the world. The purification of the target DNA product is often challenging, however, and most users are restricted to employing available commercial kits. The recent developments in mixed-mode chromatography have shown higher selectivity for a variety of nucleic acid-containing samples. Capto Adhere is a mixed-mode chromatography resin that offers a high-selectivity ligand and is here applied for the purification of amplified DNAs from PCR mixtures in a 10-min single step, with yields above 95%, high linearity, and high precision for different concentrations.     

Integrative approaches to morphogenesis: lessons from dorsal closure

Although developmental biology has been dominated by the genetic analysis of embryonic development, in recent years genetic tools have been combined with new approaches such as imaging of live processes, automated and quantitative image analysis, mechanical perturbation and mathematical modeling, to study the principles underlying the formation of organisms. Here we focus on recent work carried out on Dorsal Closure, a morphogenetic process during Drosophila embryogenesis, to illustrate how this multidisciplinary approach is yielding new and unexpected insights into how cells organize themselves through the activity of their molecular components to give rise to the stereotyped and macroscopic movements observed during development.     

Molecular genetics of cell migration: Dictyostelium as a model system

A central unresolved issue in modern cell biology concerns how eukaryotic cell migration is achieved. Although the underlying mechanics of cell locomotion appear similar in cells ranging from amoebae to leukocytes, the organisms that have been historically studied have not been amenable to the techniques of modern molecular genetics. The recent development of high-efficiency gene targeting technology for Dictyostelium discoideum, coupled with the classic cell migration behavior of this organism, offers an opportunity to resolve many of the controversial issues concerning cell locomotion.     

Chromatin as an expansive canvas for chemical biology

Chromatin is extensively chemically modified and thereby acts as a dynamic signaling platform controlling gene function. Chromatin regulation is integral to cell differentiation, lineage commitment and organism development, whereas chromatin dysregulation can lead to age-related and neurodegenerative disorders as well as cancer. Investigating chromatin biology presents a unique challenge, as the issue spans many disciplines, including cell and systems biology, biochemistry and molecular biophysics. In recent years, the application of chemical biology methods for investigating chromatin processes has gained considerable traction. Indeed, chemical biologists now have at their disposal powerful chemical tools that allow chromatin biology to be scrutinized at the level of the cell all the way down to the single chromatin fiber. Here we present recent examples of how this rapidly expanding palette of chemical tools is being used to paint a detailed picture of chromatin function in organism development and disease.     

新型靶向药物研究的重要分子：可变淋巴细胞受体

自从2004年可变淋巴细胞受体（variable lymphocyte receptor, VLR）在七鳃鳗中首次发现以来,因VLR能识别多种抗原、具有简单的分子结构、物理化学性质稳定、对蛋白质以及聚糖的高亲和力和强特异性等多方面优点,学术界对于VLR的研究和改造十分火热。近年来,随着研究的不断深入,由VLR构建的重组分子广泛用于各领域的基础研究和应用研究。本文对近年来VLR面向下游的最新应用研究进行综述。在肿瘤研究中,VLR可特异性地精准识别碳水化合物,并能够区分只有1个官能团不同的多糖,可作为灵敏抗多糖试剂,用于识别肿瘤细胞上独特的糖复合物,为肿瘤的靶向治疗提供新的策略;VLR也可与其他经典的治疗方法进行结合。例如,将嵌合抗原受体进行改造,经过改造后可表达一种合成受体。这种合成受体可将T细胞的细胞靶向杀伤作用重新定位到所选择的靶点;VLR经重组改造后,也可用于改良分离纯化试剂或在水生生物疾病上发挥作用。这些新开发的VLR的作用有可能作为新型的识别、诊断和治疗试剂。本文将从VLR多样性产生的机制、VLR与糖生物学和生物医药研究上的关系、VLR用于改良分离纯化试剂的作用、VLR在水生生物疾病研究等方面进行阐述,以期为VLR用于疾病药物研发等相关应用提供参考。     

Phylogeny and evo-devo: characters, homology, and the historical analysis of the evolution of development

The concept of homology continues to attract more and more commentary. In systematic and evolutionary biology the meaning of homology as synapomorphic similarity inherited from a common ancestor has gained wide acceptance over the last three or four decades. In recent years, however, developmental biologists, in particular, have argued for a new approach to, and new definition for, homology that revolves around the desire to make it more process-oriented and more mechanistic. These efforts raise questions about the relationship between developmental and evolutionary biology as well as how the evolution of development is to be studied. It is argued in this paper that this new approach to homology seemingly decouples developmental biology from the study of the evolution of development rather than to facilitate that study. In contrast, applying the notion of historical, phylogenetic homology to developmental data is inherently comparative and therefore evolutionary.     

The renaissance of aminoacyl-tRNA synthesis

The role of tRNA as the adaptor in protein synthesis has held an enduring fascination for molecular biologists. Over four decades of study, taking in numerous milestones in molecular biology, led to what was widely held to be a fairly complete picture of how tRNAs and amino acids are paired prior to protein synthesis. However, recent developments in genomics and structural biology have revealed an unexpected array of new enzymes, pathways and mechanisms involved in aminoacyl-tRNA synthesis. As a more complete picture of aminoacyl-tRNA synthesis now begins to emerge, the high degree of evolutionary diversity in this universal and essential process is becoming clearer.     

A molecular biological approach to synaptic plasticity and learning

Until the more recent advances made in molecular biology, attempts to link synaptic plasticity and learning have focused on using LTP as a marker of learning-induced synaptic plasticity, where one has expected to observe the same magnitude of change in synaptic strength as that observed with artificial stimulation. To a large extent this approach has been frustrated by the fact that it is generally assumed that the representation of the memory traces is distributed thoughout widespread networks of cells. By implication it is more likely that one would observe small distributed changes within a network; a formidable task to measure. In this review we describe how the advances in molecular biology give us both the tools to investigate the mechanisms of synaptic plasticity and to apply these to investigations of the underlying mechanisms in learning and the formation of memories that have until now remained out of our grasp.     

Host-cell invasion by malaria parasites: insights from Plasmodium and Toxoplasma

Recent years have seen tremendous progress in our understanding of malaria parasite molecular biology. To a large extent, this progress follows significant developments in genetic, molecular and chemical tools available to study the malaria parasites and related Apicomplexa, in particular Toxoplasma gondii. One area of major advancement has been in understanding parasite host-cell invasion, a process that utilizes several essential molecular mechanisms that are conserved across the different lifecycle stages. Here, we summarize some of the most recent experimental data that shed light on the events underlying preparation and execution of malaria parasite invasion and how these insights might relate to the development of new antimalarial drugs.     

CRISPR/Cas9 for plant genome editing: accomplishments,problems and prospects

The increasing burden of the world population on agriculture requires the development of more robust crops. Dissecting the basic biology that underlies plant development and stress responses will inform the design of better crops. One powerful tool for studying plants at the molecular level is the RNA-programmed genome editing system composed of a clustered regularly interspaced short palindromic repeats (CRISPR)-encoded guide RNA and the nuclease Cas9. Here, some of the recent advances in CRISPR/Cas9 technology that have profound implications for improving the study of plant biology are described. These tools are also paving the way towards new horizons for biotechnologies and crop development.     

Molecular control of vertebrate limb development, evolution and congenital malformations

The vertebrate limb is a powerful model system for studying the cellular and molecular interactions that determine morphological pattern during embryonic development. Recent advances in our understanding of these interactions have shed new light on the molecular mechanisms of vertebrate limb development, evolution and congenital malformations. The transfer of information has, until recently, been largely one way, with developmental studies informing our understanding of the fossil record and clinical limb anomalies; however, evolutionary and clinical studies are now beginning to shed light onto one another and onto basic developmental processes. In this review, we discuss recent advances in these fields and how they are interacting to improve our understanding of vertebrate limb biology.