Bacteriophage and Bacteria in a Flow Reactor

The Levin-Stewart model of bacteriophage predation of bacteria in a chemostat is modified for a flow reactor in which bacteria are motile, phage diffuse, and advection brings fresh nutrient and removes medium, cells and phage. A fixed latent period for phage results in a system of delayed reaction-diffusion equations with non-local nonlinearities. Basic reproductive numbers are obtained for bacteria and for phage which predict survival of each in the bio-reactor. These are expressed in terms of physical and biological parameters. Persistence and extinction results are obtained for both bacteria and phage. Numerical simulations are in general agreement with those for the chemostat model.     

Wood, bark and stem anatomy of New World species of Gnetum

Quantitative and qualitative data are presented for 11 collections of six species. The wide range of character states for the species is presented in the form of a key to emphasize their potential systematic correlations. Distinctive among these are phcllem characteristics. Fibre-tracheids are newly reported for lianoid Gnetum species. Cells previously thought to be like companion cells in secondary phloem are shown to be uniseriate rays, counterparts to uniseriate xylem rays. Laticifers are abundant in most of the species, and are newly described for secondary tissues of Gnetum. Presence of tyloses in laticifers of two species is apparently a new report for vascular plants. Tori are present in two New World Gnetum species, adding to the report in African species. Perforation plates are simple except near or in primary xylem, where they are simple or foraminate. Torus presence and foraminate perforation plate presence are features more reminiscent of Ephedra and other gymnosperms than of angiosperms. The bark of Gnetum is also very similar to that of Ephedra.     

Basic strategies for valid cytometry using image analysis

The present review provides a starting point for setting up an image analysis system for quantitative densitometry and absorbance or fluorescence measurements in cell preparations, tissue sections or gels. Guidelines for instrumental settings that are essential for the valid application of image analysis in cytophotometry and cytofluorometry are described. The general principles of the working mechanism of CCD cameras in combination with general methods to improve the behaviour of the cameras are presented. Optimization of illumination of microscopical and macroscopical objects receives special attention because of its importance for valid cytometry. Sources of errors in quantitative measurements are listed and step-by-step charts for tuning the CCD camera, frame grabber and illumination for the optimal use of the systems are described. Suggestions are given for improvement of image arithmetics in difficult imaging situations, such as low fluorescence signals and high absorbance signals. This revised version was published online in November 2006 with corrections to the Cover Date.     

Phycobiliproteins as a commodity: trends in applied research,patents and commercialization

Phycobiliproteins are a group of colored proteins commonly present in cyanobacteria and red algae possessing a spectrum of applications. They are extensively commercialized for fluorescent applications in clinical and immunological analysis. They are also used as a colorant, and their therapeutic value has also been categorically demonstrated. However, a comprehensive knowledge and technological base for augmenting their commercial utilities is lacking. Hence, this work is focused towards this objective by means of analyzing global patents and commercial activities with application oriented research. Strategic mining of patents was performed from global patent databases resulting in the identification of 297 patents on phycobiliproteins. The majority of the patents are from USA, Japan and Europe. Patents are grouped into fluorescent applications, general applications and production aspects of phycobiliproteins and the features of each group are discussed. Commercial and applied research activities are compared in parallel. It revealed that US patents are mostly related to fluorescent applications while Japanese are on the production, purification and application for therapeutic and diagnostic purposes. Fluorescent applications are well represented in research, patents and commercial sectors. Biomedical properties documented in research and patents are not ventured commercially. Several novel applications are reported only in patents. The paper further pinpoints the plethora of techniques used for cell breakage and for extraction and purification of phycobiliproteins. The analysis identifies the lacuna and suggests means for improvements in the application and production of phycobiliproteins.     

Fibronectin and integrin alpha 5 play requisite roles in cardiac morphogenesis

Fibronectin and its major receptor, integrin α5β1 are required for embryogenesis. These mutants have similar phenotypes, although, defects in integrin α5-deficient mice are milder. In this paper, we examined heart development in those mutants, in which the heart is formed, and discovered that both fibronectin and integrin α5 were required for cardiac morphogenesis, and in particular, for the formation of the cardiac outflow tract. We found that Isl1⁺ precursors are specified and migrate into the heart in fibronectin- or integrin α5-mutant embryos, however, the hearts in these mutants are of aberrant shape, and the cardiac outflow tracts are short and malformed. We show that these defects are likely due to the requirement for cell adhesion to fibronectin for proliferation of myocardial progenitors and for Fgf8 signaling in the pharyngeal region.     

DAPI (4',6-diamidino-2-phenylindole) binds differently to DNA and RNA: minor-groove binding at AT sites and intercalation at AU sites.

The interaction of DAPI and propidium with RNA (polyA.polyU) and corresponding DNA (polydA.polydT) sequences has been compared by spectroscopic, kinetic, viscometric, Tm, and molecular modeling methods. Spectral changes of propidium are similar on binding to the AT and AU sequences but are significantly different for binding of DAPI. Spectral changes for DAPI with the DNA sequence are consistent with the expected groove-binding mode. All spectral changes for complexes of propidium with RNA and DNA and for DAPI with RNA, however, are consistent with an intercalation binding mode. When complexed with RNA, for example, DAPI aromatic protons signals shift significantly upfield, and the DAPI UV-visible spectrum shows significantly larger changes than when complexed with DNA. Slopes of log kd (dissociation rate constants) versus-log [Na+] plots are similar for complexes of propidium with RNA and DNA and for the DAPI-RNA complex and are in the range expected for an intercalation complex. The slope for the DAPI-DNA complex, however, is much larger and is in the range expected for a groove-binding complex. Association kinetics results also support an intercalation binding mode for the DAPI-RNA complex. The viscosity of polyA.polyU solutions increases significantly on addition of both propidium and DAPI, again in agreement with an intercalation binding mode for both molecules with RNA. Molecular modeling studies completely support the experimental findings and indicate that DAPI forms a very favorable intercalation complex with RNA. DAPI also forms a very stable complex in the minor groove of AT sequences of DNA, but the stabilizing interactions are considerably reduced in the wide, shallow minor groove of RNA. Modeling studies,thus,indicate that DAPI interaction energetics are more favorable for minor-groove binding in AT sequences but are more favorable for interaction in RNA.     

Meiotic chromosomes of green frogs (Rana esculenta complex) of the Ukraine territory

In this work meiotic chromosomes of R. ridibunda, R. lessonae and their hybrid form R. esculenta of the Ukraine territory are described for the first time. These chromosomes are connected in diakinesis more often by two chiasma, rarely by one or three chiasma in 13 bivalents. Bivalents with one chiasma in R. ridibunda are typical only for large bivalents, in R. lessonae only for small ones. Three chiasma in parental species are typical only for small bivalents. In the hybrid form R. esculenta chromosomes with two, one and three chiasma are typical both for large bivalents, and for small ones. In the hybrid form (R. esculenta) chiasma frequency noticeably decreases, comparatively with parental species that, possibly, specifies the aberration of normal meiosis realization. The chiasma frequencies of the hybrid form of the eastern and the southern parts of Ukraine are almost the same, but the types of chromosomes are different in such regions. In the eastern region chromosomes of the hybrid form are represented by two or one chiasma, in the southern region by two, one or three chiasma.     

基因型错误对数量性状精细定位的哈迪-温伯格不平衡指数的效应

使用紧密相邻的标记位点且与标记基因频率无关的哈迪-温伯格不平衡(HWD)指数被用来对数量性状位点(QTL)进行精细定位.本文讨论了当存在基因型错误时HWD指数的性质.文章指出,当存在基因型错误时,对于在群体的标记基因频率已知的情形使用的两个HWD指数尽管受基因型错误的影响但仍然有效;而仅仅极端样本的标记基因频率已知的情形下使用的两个HWD指数同时与基因型错误和标记基因频率有关.计算机模拟表明,仅仅极端样本的标记基因频率已知的情形下使用的两个HWD指数在精细定位时会产生偏差,不适宜作精细定位.     

滇川干热河谷种子植物区系成分研究

论及滇川干热河谷种子植物区系成分由科级到种级的研究结果。用于统计分析的植物共1707个种,分属于752个属,165个科．科级区系成分中,除广布科外,明显为主,其次为暖温带科和热带科,热带科有27个科,远比干暖河谷区系中的热带科多。属区系成分中,热带属占明显多数,有523个属,占75．03％,温带属158个,占22．67％,有个中国特有属。种级区系成分中,有中国特有种622个,占37．42％,热带种791个,占47．59％,温带种249个,占14．88％。干热河谷的植物区系标志种很丰富,有437种,分三个等级,其中一级为本河谷特有种,有45种,二级199种,三级193种。热带科、属、种偏多说明本河谷历史上以热带区系为主和近代区系源于热带。干热河谷的特有区系成分和区系的标志种均较好地反映本河谷区系成分组合特征、演化的近代趋势、区系的多样性及其独特性。     

Application of Reflectance Spectroscopy for Analysis of Higher Plant Pigments

Nondestructive techniques developed by the authors for assessment of chlorophylls, carotenoids, and anthocyanins in higher plant leaves and fruits are presented. The spectral features of leaf reflectance in the visible and near infrared regions are briefly considered. For pigment analysis only reflectance values at several specific wavelengths are required. The chlorophyll (Chl) content over a wide range of its changes can be assessed during leaf ontogeny using reflectance near 700 nm and, in the absence of anthocyanins, at 550 nm. The approaches used for elimination of Chl interference in the analysis of carotenoids (reflectance at 520 nm) and anthocyanins (at 550 nm) are described. The suitability of reflectance spectroscopy for estimates of carotenoid/chlorophyll ratios during leaf senescence and fruit ripening is demonstrated. The algorithms developed for pigment analysis are presented, and the conditions of their applicability are considered. Further perspectives for the application of reflectance spectroscopy including remote sensing for estimation of plant pigment content and physiological states are discussed.     

Methods for prevention of mass development of the cyanobacterium Microcystis aeruginosa Kutz emend. Elenk. in aquatic ecosystems

Methods for prevention of mass development of the cyanobacterium Microcystis aeruginosa Kutz emend. Elenk. in continental water bodies and industrial water supply systems are reviewed. The physicochemical, chemical, and biological methods for prevention of M. aeruginosa development in water bodies and water supply systems are considered; examples of successful inhibition of M. aeruginosa growth in laboratory experiments are demonstrated. The scientific problems are outlined that are to be solved for perfecting techniques for prevention of M. aeruginosa mass development in open water bodies and in closed water supply systems.     

Biotope prioritisation in the Central Apennines (Italy): species rarity and cross-taxon congruence

The conservation status of invertebrates is usually lesser known than that of vertebrates, and strategies to identify biotopes to preserve invertebrate diversity are typically based on a single surrogate taxon, or even on the use of vertebrates as surrogates. Aim of this research is to illustrate a method for biotope prioritisation that can be easily adapted to different animal groups and geographical contexts. A two-step protocol for biotope prioritisation is proposed on the basis of a multidimensional characterisation of species vulnerability. Firstly, species vulnerability is estimated from rarity measures which include geographical range, abundance and biotope specialisation. Then, these values of vulnerability are used to rank biotopes. The method was applied here to the tenebrionid beetles, the butterflies, the birds and the mammals of the Central Apennines, a montane area of high conservation concern for South Europe. This study provides evidence for the importance of including insects in conservation decisions, because vertebrates are poor surrogates for insects. Conservation efforts in the reserves included in the study area are mostly focused on vertebrates, for which woodlands are considered particularly important. However high altitude open biotopes are crucial for both tenebrionids and butterflies, and preservation of such kind of biotopes would be beneficial also for vertebrates. The approach applied here demonstrates that (1) vertebrates are poor surrogates for insects, and (2) measures of species rarity, typically used in vertebrate conservation, can be obtained also for insects, for which a veritable amount of data are hidden in specialised literature and museum collections.     

Differential and integral W-values for ionization in gaseous water under electron and proton irradiation: consistency of inelastic collision cross sections.

Differential and integral W-values for ionization in gaseous water for electron and proton irradiation have been analyzed from the theoretical point of view for consistency between ionization and total inelastic collision cross sections. For low-energy electrons, which are ubiquitous for all primary radiations, the experimental or compiled cross sections from different sources are sometimes not consistent with one another. A practical, self-consistent procedure is outlined in such cases. The high-energy asymptotic W-values for differential and integral ionization are calculated to be 33.7 and 34.7 eV, respectively, for electron irradiation and 34.6 and 32.5 eV, respectively, for proton irradiation. The computed variations of the W-values with energy are generally in good agreement with experiment. Integral primary W-values due only to the interactions between the incident particle and the water vapor are calculated to be 43.5 and 45.0 eV for electrons and protons, respectively, in the high-energy asymptotic limit.     

Southern and Northern analysis

This review on Southern and Northern analysis, rather than providing step-by-step protocols, focuses on a critical evaluation of the existing experimental methods and modifications thereof. Principal parameters influencing electrophoresis of DNA/RNA in agarose gels are outlined and at the same time alterations in these parameters for optimal resolution of DNA of varying length are discussed. Further, methods for evaluating the quality of DNA/RNA size separation in agarose gels are described. Since efficient transfer of DNA/RNA from the gel onto a membrane support is critical in both methods, several experimental approaches for transfer are compared. Also discussed in this review are alternative methods for radioactive and non-radioactive labelling of DNA probes. Finally, detailed protocols are provided for an effective hybridization of Southern and Northern blots.     

中国秋海棠属植物的传统利用

秋海棠属植物除了具有较高的观赏价值外,在中国还作为药用、食用、饮料和饲料等被利用。本文应用民族植物学研究方法,通过野外调查、文献和标本收集整理和研究,共记载了中国产26种秋海棠属植物被作为药用、食用、饮料和饲料加以利用。在所记载的26种国产秋海棠属植物中,有24种作药用,8种作食用(蔬菜)或饮料,5种作饲料。3种作饮料的种类在其自然分布地被广泛利用。9种秋海棠作为多种用途加以利用,其中8种既被作为药用、食用和饮料,也被作为饲料加以利用。本研究还表明,国产秋海棠属植物中,有些种类由于过度采集利用或其它因素已变得稀有或濒危。由此提出,合理开发利用和有效保护应成为今后中国秋海棠属植物研究的重要内容。     

Hydrogen bonding in DNA base complexes.

Experimental intermolecular frequencies in the DNA base complexes 1-methylthymine (1-MT) and cytosine monohydrate (CMH) are analyzed in terms of simple analytic interatomic potentials. Calculations with two different values for the constants of the nonbonded interactions are considered, and the hydrogen bond potentials are determined for each of these models. The observed frequencies in 1-MT are reasonably well described, although corresponding potentials are very different in the two models. The observed frequencies in CMH are less well described, although corresponding hydrogen bond potentials are similar in the two models. Hydration interactions are found to be important in CMH and the role of the water molecule is discussed. Possible reasons for the shortcomings of this simple analysis are considered.     

Urban indicators for UK butterflies

Most people live in urban environments and there is a need to produce abundance indices to assist policy and management of urban greenspaces and gardens. While regional indices are produced, with the exception of birds, studies of the differences between urban and rural areas are rare. We explore these differences for UK butterflies, with the intention to describe changes that are relevant to people living in urban areas, in order to better connect people with nature in support of conservation, provide a measure relevant to human well-being, and assess the biodiversity status of the urban environment.Transects walked under the UK Butterfly Monitoring Scheme are classified as urban or rural, using a classification for urban morphological zones. We use models from the Generalised Abundance Index family to produce urban and rural indices of relative abundance for UK butterfly species. Composite indices are constructed for various subsets of species. For univoltine and bivoltine species, where we are able to fit phenomenological models, we estimate measures of phenology and identify urban/rural differences. Trends in relative abundance over the period 1995–2014 are more negative in urban areas compared to rural areas for 25 out of 28 species. For the composite indices, all trends are negative, and they are significantly more negative for urban areas than for rural areas. Analysis of phenological parameters shows butterflies tend to emerge earlier in urban than in rural areas. In addition, some fly longer in urban than in rural areas, whereas in other cases the opposite is the case, and hypotheses are proposed to account for these features.Investigating new urban/rural indicators has revealed national declines that are stronger for urban areas. For continued monitoring, there is a need for an urban butterfly indicator, and for this to be evaluated and reported annually. We explain how this may be interpreted, and the relevance for other monitoring schemes. The results of this paper, including the phenological findings, shed new light on the potentially deleterious effects of urbanisation and climate change, which require suitable monitoring and reporting to support policy and management, for example of urban greenspaces and gardens.     

Cell culture from sponges: pluripotency and immortality

Sponges are a source of compounds with potential pharmaceutical applications. In this article, methods of sponge cell culture for production of these bioactive compounds are reviewed, and new approaches for overcoming the problem of metabolite supply are examined. The use of embryos is proposed as a new source of sponge material for cell culture. Stem cells are present in high amounts in embryos and are more versatile and resistant to infections than adult cells. Additionally, genetic engineering and cellular research on apoptotic mechanisms are promising new fields that might help to improve cell survival in sponge-cell lines. We propose that one topic for future research should be how to reduce apoptosis, which appears to be very high in sponge cell cultures.