Modelling viral and immune system dynamics

During the past 6 years, there have been substantial advances in our understanding of human immunodeficiency virus 1 and other viruses, such as hepatitis B virus and hepatitis C virus, that cause chronic infection. The use of mathematical modelling to interpret experimental results has made a significant contribution to this field. Mathematical modelling is also improving our understanding of T-cell dynamics and the quantitative events that underlie the immune response to pathogens.     

Cognitive and perceptual development during infancy

Over the past seven years, the main advances in our understanding of infant development have involved the application of cognitive neuroscience methods such as neuroimaging and computer modelling. Results obtained using these methods have illuminated further the complex interactions between nature and nurture that underlie early postnatal development.     

Are there general mechanisms of animal home range behaviour? A review and prospects for future research

Home range behaviour is a common pattern of space use, having fundamental consequences for ecological processes. However, a general mechanistic explanation is still lacking. Research is split into three separate areas of inquiry - movement models based on random walks, individual-based models based on optimal foraging theory, and a statistical modelling approach - which have developed without much productive contact. Here we review recent advances in modelling home range behaviour, focusing particularly on the problem of identifying mechanisms that lead to the emergence of stable home ranges from unbounded movement paths. We discuss the issue of spatiotemporal scale, which is rarely considered in modelling studies, as well as highlighting the need to consider more closely the dynamical nature of home ranges. Recent methodological and theoretical advances may soon lead to a unified approach, however, conceptually unifying our understanding of linkages among home range behaviour and ecological or evolutionary processes.     

Sustainable wastewater treatment: How might microbial fuel cells contribute

The need for cost-effective low-energy wastewater treatment has never been greater. Clean water for our expanding and predominantly urban global population will be expensive to deliver, eats into our diminishing carbon-based energy reserves and consequently contributes to green house gases in the atmosphere and climate change. Thus every potential cost and energy cutting measure for wastewater treatment should be explored. Microbial fuel cells (MFCs) could potentially yield such savings but, to achieve this, requires significant advances in our understanding in a few critical areas and in our designs of the overall systems. Here we review the research which might accelerate our progress towards sustainable wastewater treatment using MFCs: system control and modelling and the understanding of the ecology of the microbial communities that catalyse the generation of electricity.     

Gene silencing, cell fate and nuclear organisation

Although advances in molecular biology have allowed us to identify and describe many of the events associated with turning genes on, much less attention has generally been focussed on the related process of gene silencing. This is surprising as heritable gene inactivation plays an important role in determining cell lineage fates during development and defining their temporal order. Recent advances in the area of chromatin and chromosome organisation may have an impact on our understanding of cellular differentiation.     

Schistosomes: the road from host-parasite interactions to vaccines in clinical trials

Insights over recent years into the interactions between helminths, including schistosomes, and the immune system have generated new concepts in immunology and significant advances in vaccine strategies. Here, we report recent advances that substantially increase our understanding of the nature of the host innate and adaptive responses to schistosomes and on strategies elaborated by the parasite to manipulate such responses. We also describe the long road that has allowed us to move from the identification of an anti-schistosome vaccine candidate, a 28kDa glutathione-S-transferase, to its recent evaluation in human clinical trials.     

A consonant model of the tRNA-ribosome complex during the elongation cycle of translation.

Chemical and photochemical affinity techniques have been used extensively to determine the positions of the tRNA binding sites on the Escherichia coli ribosome. Recent advances in our understanding of ribosome structure and function prompted us to critically review the data that have accumulated on tRNA-ribosome cross-links. As a result, we propose a new model of the tRNA-ribosome complex that accounts for nearly all of the pertinent evidence.     

Chemo- and opto-genetic tools for dissecting the role of membrane contact sites in living cells: Recent advances and limitations

Membrane contact sites (MCSs) are morphologically defined intracellular structures where cellular membranes are closely apposed. Recent progress has significantly advanced our understanding of MCSs with the use of new tools and techniques. Visualization of MCSs in living cells by split fluorescence proteins or FRET-based techniques tells us the dynamic property of MCSs. Manipulation of MCSs by chemically-induced dimerization (CID) or light-induced dimerization (LID) greatly contributes to our understanding of their functional aspects including inter-organelle lipid transport mediated by lipid transfer proteins (LTPs). Here we highlight recent advances in these tools and techniques as applied to MCSs, and we discuss their advantages and limitations.     

“Sex, drugs and the brain”: The interaction between drugs of abuse and sexual behavior in the female rat

Preclinical and clinical research investigating female sexual motivation has lagged behind research on male sexual function. The present review summarizes recent advances in our understanding of the specific roles of various brain areas, as well as our understanding of the role of dopaminergic neurotransmission in sexual motivation of the female rat. A number of behavioral paradigms that can be used to thoroughly evaluate sexual behavior in the female rat are first discussed. Although traditional assessment of the reflexive, lordosis posture has been useful in understanding the neuroanatomical and neurochemical systems that contribute to copulatory behavior, the additional behavioral paradigms described in this review have helped us expand our understanding of appetitive and consumatory behavioral patterns that better assess sexual motivation - the equivalent of “desire” in humans. A summary of numerous lesion studies indicates that different areas of the brain, including forebrain and midbrain structures, work together to produce the complex repertoire of female sexual behavior. In addition, by investigating the effects of commonly addictive drugs, we are beginning to elucidate the role of dopaminergic neurotransmission in female sexual motivation. Consequently, research in this area may contribute to meaningful advances in the treatment of human female sexual dysfunction.     

Microbes,the gut and ankylosing spondylitis

It is increasingly clear that the interaction between host and microbiome profoundly affects health. There are 10 times more bacteria in and on our bodies than the total of our own cells, and the human intestine contains approximately 100 trillion bacteria. Interrogation of microbial communities by using classic microbiology techniques offers a very restricted view of these communities, allowing us to see only what we can grow in isolation. However, recent advances in sequencing technologies have greatly facilitated systematic and comprehensive studies of the role of the microbiome in human health and disease. Comprehensive understanding of our microbiome will enhance understanding of disease pathogenesis, which in turn may lead to rationally targeted therapy for a number of conditions, including autoimmunity.     

Approaching the molecular origins of collective dynamics in oscillating cell populations

From flocking birds, to organ generation, to swarming bacterial colonies, biological systems often exhibit collective behaviors. Here, we review recent advances in our understanding of collective dynamics in cell populations. We argue that understanding population-level oscillations requires examining the system under consideration at three different levels of complexity: at the level of isolated cells, homogenous populations, and spatially structured populations. We discuss the experimental and theoretical challenges this poses and highlight how new experimental techniques, when combined with conceptual tools adapted from physics, may help us overcome these challenges.     

Model for studying virus attachment. II. Binding of biotinylated human T cell leukemia virus type I to human blood mononuclear cells potential targets for human T cell leukemia virus type I infection.

Purified human T cell leukemia virus type I (HTLV-I) was biotinylated and used to study its attachment to human PBMC. The use of biotinylated HTLV-I (biot-HTLV-I) in conjunction with mouse mAb specific for selected cell-surface molecules and flow cytometric analysis allowed us to positively identify virus-binding cells among a heterogeneous blood mononuclear cell population. Biot-HTLV-I efficiently bound not only to T cells, but also to B cells and monocytes. Preincubation of monocytes with excess of unlabeled HTLV-I significantly reduced the attachment of biot-HTLV-I. HTLV-I not only bound to, but also infected, B cells, as suggested by: i) in situ hybridization of a 35S-labeled full length HTLV-I DNA probe with EBV-transformed B cells, previously cocultured with HTLV-I-producing (G11MJ) T cells, and ii) hybridization of the same nick-translated 32P-labeled DNA probe with blotted DNA from similar HTLV-I-infected EBV-transformed B cells. HTLV-I infection did not affect the ability of B cells to secrete IgG. These findings suggest that HTLV-I cannot only infect cells of the T lineage, but can also infect B cells.     

“On A Piece of Chalk”-Updated1

ABSTRACT. Many advances have been made in our knowledge of the biology of foraminifera over the past several decades. Fine structural, biophysical, and molecular biological studies have shown that the most prominent components of their distinctive bidirectional granuloreliculopods are bundles of micro tubules linked by crossbridges to each other, as well as to membrane-bound organelles and the plasma membrane. the microtubules ratchet past each other as dynein transduces the free energy of ATP to produce pseudopodal movements. In spite of the fact that there are over 40,000 described species of living and fossil species of foraminifera, there have been many recent exciting discoveries of new species and groups. New casting techniques are providing us with greater understanding of the complexities and functional aspects of form in the group. Significant advances are being made in understanding the distribution and energetics of deep-sea forms. Larger and planktonic foraminifera are the hosts for a particularly diverse range of endosymbiotic algae, including dinoflagellates, chlorophytes, unicellular rhodophytes, and diatoms. Chloroplast husbandry also occurs. Significant research effort has been expended yielding us considerable insight into various aspects of the endosymbiotic phenomenon. A unified conceptual framework has been drawn to help us understand the life cycle options found in foraminifera.     

High throughput and quantitative enzymology in the genomic era

Accurate predictions from models based on physical principles are the ultimate metric of our biophysical understanding. Although there has been stunning progress toward structure prediction, quantitative prediction of enzyme function has remained challenging. Realizing this goal will require large numbers of quantitative measurements of rate and binding constants and the use of these ground-truth data sets to guide the development and testing of these quantitative models. Ground truth data more closely linked to the underlying physical forces are also desired. Here, we describe technological advances that enable both types of ground truth measurements. These advances allow classic models to be tested, provide novel mechanistic insights, and place us on the path toward a predictive understanding of enzyme structure and function.     

Three-dimensional culture models of mammary gland

The mammary gland is a complex tissue comprised of a branching network of ducts embedded within an adipocyterich stroma. The ductal epithelium is a bi-layer of luminal and myoepithelial cells, the latter being in contact with a basement membrane. During pregnancy, tertiary branching occurs and lobuloalveolar structures, which produce milk during lactation, form in response to hormonal and cytokine signals. Postlactational regression is characterized by extensive cell death and tissue remodeling. These complex developmental events have been difficult to mimic in cell culture although many useful culture models exist. Recently, considerable advances in three-dimensional modelling of the mammary gland have been made with the use of collagen and other biomaterials for the study of branching morphogenesis and tumorigenesis, techniques which may enable rapid advances in our understanding of both basic biology and the study of cancer therapeutics.     

作物生长模拟模型研究和应用

作物生长模拟模型研究和应用宇振荣（北京农业大学农业生态环境系,１０００９４）ＳｔｕｄｉｅｓｏｎＣｒｏｐＧｒｏｗｔｈＭｏｄｅｌｌｉｎｇａｎｄＩｔｓＡｐｐｌｉｃａｔｉｏｎ．￥ＹｕＺｈｅｎｒｏｎｇ（ＤｅｐａｒｔｍｅｎｔｏｆＡｇｒｏ－Ｅ－ｃｏｌｏｇｉｃａｌＥ...     

Placebos and painkillers: is mind as real as matter?

Considerable progress has been made in our understanding of the neurobiological mechanisms of the placebo effect, and most of our knowledge originates from the field of pain and analgesia. Today, the placebo effect represents a promising model that could allow us to shed new light on mind-body interactions. The mental events induced by placebo administration can activate mechanisms that are similar to those activated by drugs, which indicates a similarity between psychosocial and pharmacodynamic effects. These new neurobiological advances are already changing our conception of how clinical trials and medical practice must be viewed and conducted.     

Mathematical modelling of mycelia: a question of scale

Recent advances in systems biology have driven many aspects of biological research in a direction heavily weighted towards computational, quantitative and predictive analysis, based on, or assisted by mathematical modelling. In particular, mathematical modelling has played a significant role in the development of our understanding of the growth and function of the fungal mycelium. One of the main problems that faces modellers in this context is the choice of scale. In the study of fungal mycelia, the question of scale is expressed in an extreme manner: Their indeterminate growth habit ensures that the investigation of the growth and function of mycelial fungi has to consider scales ranging from the (sub) micron to the kilometer. An excellent and extensive review of the applications of mathematical modelling to fungal growth, conducted up to the mid-1990s, can be found in Prosser (1995). In this article, we will concentrate on work since that date, with the emphasis being on recent developments in understanding fungal mycelia at all scales.     

Mouse models for ATR deficiency

ATM and ATR orchestrate overlapping DNA damage responses in reply to different forms of DNA strand discontinuities. But, knockout mouse models suggest that ATR is essential for viability in contrast to ATM. Recently, more sophisticated mouse models have been published including a conditional ATR-knockdown system and by modelling the human ATR-Seckel syndrome-causative mutation. Here, I will overview and contrast these models highlighting the advances both represent in our understanding of how defects in the ATR-dependent DNA damage response can impact on normal development, tissue homeostasis, ageing and cancer.     

Origin of sucrose metabolism in higher plants: when,how and why?

Since the discovery of sucrose biosynthesis, considerable advances have been made in understanding its regulation and crucial role in the functional biology of plants. However, important aspects of this metabolism are still an enigma. Studies in cyanobacteria and the publication of the sequences of several complete genomes have recently significantly increased our knowledge of the structures of proteins involved in sucrose metabolism and given us new insights into their origin and further evolution.