Plasmid rolling-circle replication: recent developments

It is now well established that a large majority of small, multicopy plasmids of Gram-positive bacteria use the rolling-circle (RC) mechanism for their replication. Furthermore, the host range of RC plasmids now includes Gram-negative organisms as well as archaea. RC plasmids can be broadly classified into at least five families, individual members of which are spread among widely different bacteria. There is significant homology in the basic replicons of plasmids belonging to a particular family, and there is compelling evidence that such plasmids have evolved from common ancestors. Major advances have recently been made in our understanding of plasmid RC replication, including the characterization of the biochemical activities of the plasmid initiator proteins and their interaction with the double-strand origin, the domain structure of the initiator proteins and the molecular basis for the function of single-strand origins in plasmid lagging strand synthesis. Over the past several years, there has been a 'renaissance' in studies on RC replication as a result of the discovery that many plasmids replicate by this mechanism, and studies in the next few years are likely to reveal new and novel mechanisms used by RC plasmids for their regulated replication.     

Gene synthesis technology: recent developments and future prospects

Gene synthesis is a potentially powerful tool in molecular biology that has not yet reached widespread use because of the relatively high cost and labor-intensive nature of the process. This paper reviews some recent technological developments and current research activities of this laboratory which promise to greatly reduce the cost of gene synthesis and to increase the speed and efficiency of the process. We recently developed an improved device for "segmented" synthesis of oligonucleotides, which utilizes porous Teflon wafers containing derivatized controlled pore glass supports to simultaneously synthesize up to 100 different DNA sequences. The stepwise coupling efficiency with the "wafer synthesis device" is as high as that attained with current automated "gene machines" producing 1-4 oligonucleotides at a time, whereas the reagent usage is only 20-50% that of the current DNA synthesizers. At present, we are optimizing the conditions for rapid, efficient assembly of genes on a solid-phase support, wherein ordered, stepwise annealing/washing is performed to segmentally elongate a "starting" oligonucleotide attached to a solid-phase support. We expect that the wafer synthesis device (operated at reduced scale of synthesis), together with solid-phase gene assembly, will permit the synthesis and assembly of an average size gene (1 kb) in one week at a cost of less than $1000. These developments should make gene synthesis a routine and powerful tool in molecular biology.     

Replication of human hepatitis delta virus: recent developments

In a natural setting, hepatitis delta virus (HDV) is only found in patients that are also infected with hepatitis B virus (HBV). In hepatocytes infected with these two viruses, HDV RNA genomes are assembled using the envelope proteins of HBV. Since 1986, we have known that HDV has a small single-stranded RNA genome with a unique circular conformation that is replicated using a host RNA polymerase. These and other features make HDV and its replication unique, at least among agents that infect animals. This mini-review focuses on advances gained over the last 2-3 years, together with an evaluation of HDV questions that are either unsolved or not yet solved satisfactorily.     

Auxin receptors: recent developments

Rapid advances have been made in the study of auxin binding proteins (ABPs) in the last five years. In particular, an ABP in maize membranes has been cloned, sequenced and both monoclonal and polyclonal antibodies to this ABP have been developed. Structural and functional analysis has begun and there is good electrophysiological evidence that ABP in the plasma membrane functions as a receptor, probably involved in auxin-induced cell expansion. The role of the large amount of ABP in the endoplasmic reticulum is less clear, as is the relationship to soluble ABPs. At present there is only some circumstantial evidence relating any ABP to cell division. Receptors for synthetic inhibitors of auxin transport (phytotropins) are also of interest in relation to auxin action, but are less well characterised. Identification of new naturally-occurring phytotropins could lead to novel plant growth regulators.     

PROSITE: recent developments.

PROSITE is a compilation of sites and patterns found in protein sequences; it can be used as a method of determining the function of uncharacterized proteins translated from genomic or cDNA sequences.     

Hesperidin and its aglycone hesperetin in breast cancer therapy: A review of recent developments and future prospects

Breast cancer (BC) has high incidence and mortality rates, making it a major global health issue. BC treatment has been challenging due to the presence of drug resistance and the limited availability of therapeutic options for triple-negative and metastatic BC, thereby urging the exploration of more effective anti-cancer agents. Hesperidin and its aglycone hesperetin, two flavonoids from citrus species, have been extensively evaluated for their anti-cancer potentials. In this review, available literatures on the chemotherapeutic and chemosensitising activities of hesperidin and hesperetin in preclinical BC models are reported. The safety and bioavailability of hesperidin and hesperetin as well as the strategies to enhance their bioavailability are also discussed. Overall, hesperidin and hesperetin can inhibit cell proliferation, migration and BC stem cells as well as induce apoptosis and cell cycle arrest in vitro. They can also inhibit tumour growth, metastasis and neoplastic changes in tissue architecture in vivo. Moreover, the co-administration of hesperidin or hesperetin with doxorubicin, letrozole or tamoxifen can enhance the efficacies of these clinically available agents. These chemotherapeutic and chemosensitising activities of hesperidin and hesperetin have been linked to several mechanisms, including the modulation of signalling pathways, glucose uptake, enzymes, miRNA expression, oxidative status, cell cycle regulatory proteins, tumour suppressor p53, plasma and liver lipid profiles as well as DNA repair mechanisms. However, poor water solubility, extensive phase II metabolism and apical efflux have posed limitations to the bioavailability of hesperidin and hesperetin. Various strategies for bioavailability enhancement have been studied, including the utilisation of nano-based drug delivery systems and the co-administration of hesperetin with other flavonoids. In particular, nanoformulated hesperidin and hesperetin possess greater chemotherapeutic and chemosensitising activities than free compounds. Despite promising preclinical results, further safety and efficacy evaluation of hesperidin and hesperetin as well as their nanoformulations in clinical trials is required to ascertain their potentials to be developed as clinically useful agents for BC treatment.     

Biotechnological advances in guava (Psidium guajava L.): recent developments and prospects for further research

Guava (Psidium guajava L.), an important fruit crop of several tropical and sub-tropical countries, is facing several agronomic and horticultural problems such as susceptibility to many pathogens, particularly guava wilting caused by Fusarium oxysporium psidii, low fruit growth, short shelf life of fruits, high seed content, and stress sensitivity. Conventional breeding techniques have limited scope in improvement of guava owing to long juvenile period, self incompatibility, and heterozygous nature. Conventional propagation methods, i.e., cutting, grafting or stool layering, for improvement of guava already exist, but the long juvenile period has made them time consuming and cumbersome. Several biotechnological approaches such as genetic transformation may be effective practical solutions for such problems and improvement of guava. The improvement of fruit trees through genetic transformation requires an efficient regeneration system. During the past 2–3 decades, different approaches have been made for in vitro propagation of guava. An overview on the in vitro regeneration of guava via organogenesis, somatic embryogenesis, and synthetic seeds is presented. Organogenesis in several different genotypes through various explant selection from mature tree and seedling plants has been achieved. Factors affecting somatic embryogenesis in guava have been reviewed. Production of synthetic seeds using embryogenic propagules, i.e., somatic embryos and non-embryogenic vegetative propagules, i.e., shoot tips and nodal segments have also been achieved. Development of synthetic seed in guava may be applicable for propagation, short-term storage, and germplasm exchange, and distribution. An initial attempt for genetic transformation has also been reported. The purpose of this review is to focus upon the current information on in vitro propagation and biotechnological advances made in guava.     

Neutral theory and the species abundance distribution: recent developments and prospects for unifying niche and neutral perspectives

Published in 2001, The Unified Neutral Theory of Biodiversity and Biogeography (UNTB) emphasizes the importance of stochastic processes in ecological community structure, and has challenged the traditional niche‐based view of ecology. While neutral models have since been applied to a broad range of ecological and macroecological phenomena, the majority of research relating to neutral theory has focused exclusively on the species abundance distribution (SAD). Here, we synthesize the large body of work on neutral theory in the context of the species abundance distribution, with a particular focus on integrating ideas from neutral theory with traditional niche theory. First, we summarize the basic tenets of neutral theory; both in general and in the context of SADs. Second, we explore the issues associated with neutral theory and the SAD, such as complications with fitting and model comparison, the underlying assumptions of neutral models, and the difficultly of linking pattern to process. Third, we highlight the advances in understanding of SADs that have resulted from neutral theory and models. Finally, we focus consideration on recent developments aimed at unifying neutral‐ and niche‐based approaches to ecology, with a particular emphasis on what this means for SAD theory, embracing, for instance, ideas of emergent neutrality and stochastic niche theory. We put forward the argument that the prospect of the unification of niche and neutral perspectives represents one of the most promising future avenues of neutral theory research.     

Plant virus ecology and epidemiology: historical perspectives,recent progress and future prospects

After clarifying the relationship between the closely related concepts of ecology and epidemiology as they are used in plant virology, this article provides a historical perspective on the subject before discussing recent progress and future prospects. Ecology focuses on virus populations interacting with host populations within a variable environment, while epidemiology focuses on the complex association between virus and host plant, and factors that influence spread. The evolution and growth of plant virus ecology and epidemiology since its inception to the present day, and the major milestones in its development, are illustrated by examples from influential historical reviews published in the Annals of Applied Biology over the last 100 years. Original research papers published in the journal are used to illustrate important ecological and epidemiological principles and new developments in both fields. Both areas are multifaceted with many factors influencing host plants, and virus and vector behaviour. The highly diverse scenarios that arise from this process influence the virus population and the spatiotemporal dynamics of virus distribution and spread. The review then describes exciting progress in research in the areas of molecular epidemiology and ecology, and understanding virus–vector interactions. Application of new molecular techniques has greatly accelerated the rate of progress in understanding virus populations and the way changes in these populations influence epidemics. Viruses cause direct and plant‐mediated indirect effects on insect vectors by modifying their life cycles, fitness and behaviour, and one of the most fascinating recent fields of research concerns plant‐mediated indirect virus manipulation of insect vector behaviour that encourages virus spread. Next, the review describes the current state of knowledge about spread of plant viruses at the critical agro‐ecological interface between managed and natural vegetation. There is an urgent need to understand how viruses move in both directions between the two and be able to anticipate these kinds of events. To obtain an understanding of, and ability to foresee, such events will require a major research effort into the future. The review finishes by discussing the implications of climate change and rapid technological innovation for the types of research needed to avoid virus threats to future world food supplies and plant biodiversity. There has been lamentably little focus on research to determine the magnitude of the threat from diseases caused in diverse plant virus pathosystems under different climate change scenarios. Increasing technological innovation offers many opportunities to help ensure this situation is addressed, and provide plant virus ecology and epidemiology with a very exciting future.     

Cancer gene and immunotherapy: recent developments

Gene and immunotherapeutic approaches to treat human malignant tumors are reviewed. Special attention is given to the different strategies of cancer gene therapy and to recent aspects of cytokine-supported tumor immunotherapy or tumor-specific vaccination. The limitations of these therapy approaches are critically discussed especially with respect to immune escape mechanisms.     

Mitochondrial biogenesis: recent developments and insights

Biosynthesis of a functional mitochondrion requires the coordinate expression of genes in both mitochondrial and nuclear DNAs. In yeast, three mitochondrial genes are split and RNA splicing plays a pivotal role in their expression. The recent finding that some introns are capable of self-splicing activity in vitro has permitted analysis of the mechanisms involved in RNA catalysis and may eventually shed light on the evolution of splicing mechanisms in general. Most mitochondrial proteins are encoded by nuclear genes, synthesized in the cytoplasm and imported by the organelle. The availability of cloned genes coding for several constituent subunits of the ubiquinol-cytochrome c reductase, which are imported by mitochondria, has allowed study of selected steps in the addressing of proteins to mitochondria and their intercompartmental sorting within the organelle. Recent developments are discussed.     

Synteny: recent advances and future prospects

Their small sizes have meant that the Arabidopsis and rice genomes are the best-studied of all plant genomes. Although even closely related plant species can show large variations in genome size, extensive genome colinearity has been established at the genetic level and recently also at the gene level. This allows the transfer of information and resources assembled for rice and Arabidopsis to be used in the genome analysis of many other plants.     

Ion channels: recent progress and prospects

Determination of the crystal structure of the KcsA potassium channel and its subsequent refinement at 2 A resolution have stimulated much interest in modelling of ion channels. Here we review the recent developments in ion channels research, focusing especially on the question of structure-function relationships, and discuss how permeation models based on Brownian and molecular dynamics simulations can be used fruitfully in this endeavour.     

Some recent developments in the molecular epidemiology of Epstein-Barr virus infections

We have applied two different recombinant DNA techniques to the study of the epidemiology of Epstein-Barr virus infections. In the first application, cloned subfragments of viral DNA were used as probes to detect EBV DNA in a variety of lymphoproliferative disorders and in lymphoid cell lines. Patients who are epidemiologically unrelated harbor EBV genotypes which can readily be distinguished from each other. Patients who are epidemiologically related (such as mothers and infants) have similar EBV genotypes. Some patients, especially those who are immunocompromised, are infected with two distinct genotypes. In the second application, we have examined the immune response to specific EBV antigens expressed from small cloned viral DNA subfragments. We have identified a group of patients with presumed chronic EBV infection who selectively fail to recognize one subcomponent of the EB nuclear antigen complex.     

Nanovaccines: recent developments in vaccination

In the past 100 years, vaccination has contributed immensely to public health by preventing a number of infectious diseases. Attenuated, killed or part of the microorganism is employed to stimulate the immune system against it. Progress in biotechnology has provided protective immunity through DNA vaccines. In recent years, nanovaccine is a novel approach to the methodology of vaccination. Nanomaterials are delivered in the form of microspheres, nanobeads or micro-nanoprojections. Painless, effective and safe needle-free routes such as the intranasal or the oral route, or patches of microprojections to the skin are some of the approaches which are in the experimental stage at present but may have a great future ahead in nanovaccination.