A rapid mini-prep method for isolation of ectomycorrhizal DNA from Tuber species

A rapid procedure has been developed to isolate DNA from the ectomycorrhizae of Tuber spp. for use in PCR experiments. The method described is fast and sensitive and can overcome the amplification problems that can arise in the presence of inhibitors. For this reason it can be used to type ectomycorrhizae even starting from a single root tip and make mycorrhizae identification much more rapid.     

Ultra high-speed sorting.

BACKGROUND: Cell sorting has a history dating back approximately 40 years. The main limitation has been that, although flow cytometry is a science, cell sorting has been an art during most of this time. Recent advances in assisting technologies have helped to decrease the amount of expertise necessary to perform sorting. METHODS: Droplet-based sorting is based on a controlled disturbance of a jet stream dependent on surface tension. Sorting yield and purity are highly dependent on stable jet break-off position. System pressures and orifice diameters dictate the number of droplets per second, which is the sort rate limiting step because modern electronics can more than handle the higher cell signal processing rates. RESULTS: Cell sorting still requires considerable expertise. Complex multicolor sorting also requires new and more sophisticated sort decisions, especially when cell subpopulations are rare and need to be extracted from background. High-speed sorting continues to pose major problems in terms of biosafety due to the aerosols generated. CONCLUSIONS: Cell sorting has become more stable and predictable and requires less expertise to operate. However, the problems of aerosol containment continue to make droplet-based cell sorting problematical. Fluid physics and cell viability restraints pose practical limits for high-speed sorting that have almost been reached. Over the next 5 years there may be advances in fluidic switching sorting in lab-on-a-chip microfluidic systems that could not only solve the aerosol and viability problems but also make ultra high-speed sorting possible and practical through massively parallel and exponential staging microfluidic architectures.     

Glyoxal as an alternative fixative to formaldehyde in immunostaining and super‐resolution microscopy

Paraformaldehyde (PFA) is the most commonly used fixative for immunostaining of cells, but has been associated with various problems, ranging from loss of antigenicity to changes in morphology during fixation. We show here that the small dialdehyde glyoxal can successfully replace PFA. Despite being less toxic than PFA, and, as most aldehydes, likely usable as a fixative, glyoxal has not yet been systematically tried in modern fluorescence microscopy. Here, we tested and optimized glyoxal fixation and surprisingly found it to be more efficient than PFA‐based protocols. Glyoxal acted faster than PFA, cross‐linked proteins more effectively, and improved the preservation of cellular morphology. We validated glyoxal fixation in multiple laboratories against different PFA‐based protocols and confirmed that it enabled better immunostainings for a majority of the targets. Our data therefore support that glyoxal can be a valuable alternative to PFA for immunostaining.     

Fine Needle Aspiration For the Diagnosis and Management of Granulomatous Disease

Fine needle aspiration is a quick, minimally invasive and cost-effective technique for the diagnosis of granulomatous disease. Cytological diagnosis can often be specific, with the help of special stains and microbiological culture of aspirated material, particularly in the case of tuberculosis, the most common infective granulomatous disease in this country. At a fine needle aspiration clinic many cases of granulomatous disease, some from unusual sites, have been diagnosed and the use of more invasive investigations has been avoided. The problems involved in cytological diagnosis are discussed using seven cases as examples.     

Production of biogas from solid organic wastes through anaerobic digestion: a review

Anaerobic digestion treatments have often been used for biological stabilization of solid wastes. These treatment processes generate biogas which can be used as a renewable energy sources. Recently, anaerobic digestion of solid wastes has attracted more interest because of current environmental problems, most especially those concerned with global warming. Thus, laboratory-scale research on this area has increased significantly. In this review paper, the summary of the most recent research activities covering production of biogas from solid wastes according to its origin via various anaerobic technologies was presented.     

Time-resolved protein crystallography.

Advances in synchrotron radiation technology have allowed exposure times from protein crystals of the order of milliseconds to be used routinely, and in exceptional circumstances exposure times of 100 ps have been obtained. However, many data sets take seconds to record because of the slow time scale of film change or crystal reorientation or translation when more than one exposure is required. This problem has been addressed by Amemiya et al. (1989). There has been considerable progress in methods to initiate reactions in protein crystals, especially the development of photolabile caged compounds but also temperature jump, pH jump, and diffusion. Although flash lamps deliver pulses of 100 mJ/ms, often several pulses are required to release sufficient product, and reaction initiation can take several seconds. Laser illumination can provide more powerful input, but the laser must be accommodated within the restricted space at the synchrotron station. The requirement to maintain synchrony among the molecules in the crystal lattice as the reaction proceeds and to ensure that the lifetime of intermediates is longer than data collection rates emphasizes the need for chemical characterization of the reaction under study. As Ringe advocated in the studies with chymotrypsin, it may be more profitable to devise conditions under which certain intermediates along the reaction pathway accumulate in the crystal and to record these in a series of discrete steps rather than continuous monitoring of the reaction. The Laue method is limited to those proteins that give well-ordered crystals and problems of transient disorder on initiation of reaction and problems of radiation damage need to be overcome or avoided by suitable experimental protocols.(ABSTRACT TRUNCATED AT 250 WORDS)     

Practical aspects of using the microbatch method in screening conditions for protein crystallization

The microbatch technique is a simple and efficient method for screening for protein crystallization conditions both by hand and using automated systems. Many of the problems associated with more commonly used methods such as vapour diffusion can be overcome using this method. Despite its promise microbatch has not been widely utilized as a viable screening procedure. This review aims to describe the method from a practical point of view with an emphasis on screening crystallization conditions, outlining current progress and discussion of the advantages compared to other methods.     

Tandem couture

Receptor subunits in the Cys-loop superfamily assemble to form channels as hom opentamers or heteropentamers, expanding functional diversity through modularity. Expression of two or more compatible subunit types can lead to various receptor assemblies or subtypes. However, what may be good for diversity in vivo may be undesirable for the bench scientist, because we often wish to reduce our analyses to a single receptor subtype. By linking two or more subunits, creating tandems or concatamers, we can control stoichiometry and limit expression to exactly one receptor subtype. In this fashion, receptors with mixed subunit subtypes and heterozygous mutations can be separated from a mixture and can be described in detail. However, several recent studies have shown that this may be more easily conceived than accomplished, because several unforeseen problems have arisen. Concatamers can degrade, linkers can sometimes be clipped after or during translation, and one subunit may “loop out” or even become part of a second (now linked) pentamer with different characteristics. Some strategies have been developed to overcome these drawbacks, and the resultant new information that has begun to emerge has revitalized the study of these receptors in heterologous expression systems.     

Comparative footprinting of DNA-binding proteins

MOTIVATION: Comparative modelling is a computational method used to tackle a variety of problems in molecular biology and biotechnology. Traditionally it has been applied to model the structure of proteins on their own or bound to small ligands, although more recently it has also been used to model protein-protein interfaces. This work is the first to systematically analyze whether comparative models of protein-DNA complexes could be built and be useful for predicting DNA binding sites. RESULTS: First, we describe the structural and evolutionary conservation of protein-DNA interfaces, and the limits they impose on modelling accuracy. Second, we find that side-chains from contacting residues can be reasonably modeled and therefore used to identify contacting nucleotides. Third, the DNASITE protocol is implemented and different parameters are benchmarked on a set of 85 regulators from Escherichia coli. Results show that comparative footprinting can make useful predictions based solely on structural data, depending primarily on the interface identity with respect to the template used. AVAILABILITY: DNASITE code available on request from the authors.     

重金属超富集植物及植物修复技术研究进展

植物修复技术（Phytoremediation)是近年来发展起来的一种主要用于清除土壤重金属污染的绿色生态技术,重金属超富集植物（hyperaccumulator)及植物修复技术是当前学术界研究的热点领域,目前虽已有Cd、Co、Cr、Cu、Mn、Ni、Pb、Zn等超富集植物发现的报道,但尚无一例报道来自于中国,中国具有广袤的国土面积、丰富的植物类型和多种（处）古老的矿山开采与冶炼场所,在中国开展超富集植物的寻找,研究与开发工作,将会有重要突破,并具有重要的理论与实践意义,本文拟就国内外在这一领域的研究进展作一简要综述。     

X-RAY MICROANALYSIS IN CELL BIOLOGY AND CELL PATHOLOGY

Electron probe X-ray microanalysis has been used for the last 25 years by biologists to obtain information about the distribution of elements at the cell and tissue level. During this period, progress has mainly been made through the development of more adequate techniques for specimen preparation (mainly low temperature techniques) and quantitative analysis, so that accurate analysis of the physiologically important cellular ions can be carried out. Use ofin vitrosystems and cell cultures may further increase the number of problems to which X-ray microanalysis can be applied. Among the numerous applications of X-ray microanalysis in cell biology and cell pathology, applications in the areas of epithelial ion transport, the role of calcium in secretory and contractile cells, and the role of ions in cell proliferation and cancer are discussed in more detail.     

The genetics of nontuberculous mycobacterial infection

The molecular aetiology of familial susceptibility to disseminated mycobacterial disease, usually involving weakly pathogenic strains of mycobacteria, has now been elucidated in more than 30 families. Mutations have been identified in five genes in the interleukin-12-dependent interferon-gamma pathway, highlighting the importance of this pathway in human mycobacterial immunity. Knowledge derived from the study of these rare patients contributes to our understanding of the immune response to common mycobacterial pathogens such as Mycobacterium tuberculosis and Mycobacterium leprae, which remain major public health problems globally. This knowledge can be applied to the rational development of novel therapies and vaccines for these important mycobacterial diseases.     

Reflections and meditations upon complex chromosomal exchanges

The application of FISH chromosome painting techniques, especially the recent mFISH (and its equivalents) where all 23 human chromosome pairs can be distinguished, has demonstrated that many chromosome-type structural exchanges are much more complicated (involving more "break-rejoins" and arms) than has hitherto been assumed. It is clear that we have been greatly under-estimating the damage produced in chromatin by such agents as ionising radiation. This article gives a brief historical summary of observations leading up to this conclusion, and after outlining some of the problems surrounding the formation of complex chromosomes exchanges, speculates about possible solutions currently being proposed.     

Ecology after 100 years: Progress and pseudo-progress

Has the science of ecology fulfilled the promises made by the originators of ecological science at the start of the last century? What should ecology achieve? Have good policies for environmental management flowed out of ecological science? These important questions are rarely discussed by ecologists working on detailed studies of individual systems. Until we decide what we wish to achieve as ecologists we cannot define progress toward those goals. Ecologists desire to achieve an understanding of how the natural world operates, how humans have modified the natural world, and how to alleviate problems arising from human actions. Ecologists have made impressive gains over the past century in achieving these goals, but this progress has been uneven. Some sub-disciplines of ecology are well developed empirically and theoretically, while others languish for reasons that are not always clear. Fundamental problems can be lost to view as ecologists fiddle with unimportant pseudo-problems. Bandwagons develop and disappear with limited success in addressing problems. The public demands progress from all the sciences, and as time moves along and problems get worse, more rapid progress is demanded. The result for ecology has too often been poor, short-term science and poor management decisions. But since the science is rarely repeated and the management results may be a generation or two down the line, it is difficult for the public or for scientists to decide how good or bad the scientific advice has been. In ecology over the past 100 years we have made solid achievements in behavioural ecology, population dynamics, and ecological methods, we have made some progress in understanding community and ecosystem dynamics, but we have made less useful progress in developing theoretical ecology, landscape ecology, and natural resource management. The key to increasing progress is to adopt a systems approach with explicit hypotheses, theoretical models, and field experiments on a scale defined by the problem. With continuous feedback between problems, possible solutions, relevant theory and experimental data we can achieve our scientific goals.     

Is breathing in infants chaotic? Dimension estimates for respiratory patterns during quiet sleep

Wedescribe an analysis of dynamic behavior apparent in times-seriesrecordings of infant breathing during sleep. Three principal techniqueswere used: estimation of correlation dimension, surrogate dataanalysis, and reduced linear (autoregressive) modeling (RARM). Correlation dimension can be used to quantify the complexity of timeseries and has been applied to a variety of physiological andbiological measurements. However, the methods most commonly used toestimate correlation dimension suffer from some technical problems thatcan produce misleading results if not correctly applied. We used a newtechnique of estimating correlation dimension that has fewer problems.We tested the significance of dimension estimates by comparingestimates with artificial data sets (surrogate data). On the basis ofthe analysis, we conclude that the dynamics of infant breathing duringquiet sleep can best be described as a nonlinear dynamic system withlarge-scale, low-dimensional and small-scale, high-dimensionalbehavior; more specifically, a noise-driven nonlinear system with atwo-dimensional periodic orbit. Using our RARM technique, we identifiedthe second period as cyclic amplitude modulation of the same period asperiodic breathing. We conclude that our data are consistent withrespiration being chaotic.

     

Nanotechnology and pharmaceutical inhalation aerosols

Pharmaceutical inhalation aerosols have been playing a crucial role in the health and well being of millions of people throughout the world for many years. The technology's continual advancement, the ease of use and the more desirable pulmonary-rather-than-needle delivery for systemic drugs has increased the attraction for the pharmaceutical aerosol in recent years. But administration of drugs by the pulmonary route is technically challenging because oral deposition can be high, and variations in inhalation technique can affect the quantity of drug delivered to the lungs. Recent advances in nanotechnology, particularly drug delivery field have encouraged formulation scientists to expand their reach in solving tricky problems related to drug delivery. Moreover, application of nanotechnology to aerosol science has opened up a new category of pharmaceutical aerosols (collectively known as nanoenabled-aerosols) with added advantages and effectiveness. In this review, some of the latest approaches of nano-enabled aerosol drug delivery system (including nano-suspension, trojan particles, bioadhesive nanoparticles and smart particle aerosols) that can be employed successfully to overcome problems of conventional aerosol systems have been introduced.     

基于独立元分析的MEG(脑磁图)数据分析和处理

独立元分析(independent component analysis,ICA)可用于分离混迭的MEG(Magnetoencephalography)多通道信号中的信号源。从ICA分解的结果中消除干扰源和噪声,并将剩余分量投影回MEG多通道数据空间,可得到净化的MEG信号,表示各个信号源的各独立元分别投影回多通道,可对各活动源进行空间定位。特别是,响应于外界刺激的诱发活动源亦可从重叠的MEG多通道信号中得到分离,这对脑功能研究及脑医学临床应用极有吸引力。提出了一个简单有效的基于ICA的MEG数据分析和处理方法,研究和分析了一些实际应用问题,特别是给出了听觉诱发响应的一些有意义的分析结果。     

Unprofessional Physicians—Some Correlative Data

In the background of those physicians who have problems in medical practice serious enough to attract attention by the licensing body, there are factors that apparently can help predict such behavior. As a candidate for medical school the applicant more likely to have future problems has the following profile: (1) older than the average applicant with a lower grade point average; (2) more likely to have used tobacco; (3) did not receive a baccalaureate degree; (4) no military service; (5) turned in a sloppy handwritten application form, and (6) received a less than ideal character reference by the college from which applying. Furthermore, after admission to medical school the person more prone to future problems tends to be a poorer student than his peers and to receive a poorer rating in his first postgraduate year. The Loma Linda University graduate who has had such problems is also more likely to have settled in Southern California and to be in general practice.     

Sample preparation for the analysis of membrane proteomes by mass spectrometry

The low abundance and highly hydrophobic nature of most membrane proteins make their analysis more difficult than that for common soluble proteins. Successful membrane protein identification is largely dependent on the sample preparation including the enrichment and dissolution of the membrane proteins. A series of conventional and newly developed methods has been applied to the enrichment of low-abundance membrane proteins at membrane and/or protein levels and to the dissolution of hydrophobic membrane proteins. However, all the existing methods have inherent advantages and limitations. Up to now, there has been no unique method that can universally be employed to solve all the problems and more efforts are needed in improving sample preparation for the analysis of membrane proteomes.