Tryptophanyl fluorescence lifetime distribution of hyperthermophilic beta-glycosidase from molecular dynamics simulation: a comparison with the experimental data

A molecular dynamics simulation approach has been utilized to understand the unusual fluorescence emission decay observed for beta-glycosidase from the hyperthermophilic bacterium Solfolobus sulfotaricus (Sbeta gly), a tetrameric enzyme containing 17 tryptophanyl residues for each subunit. The tryptophanyl emission decay of Sbeta gly results from a bimodal distribution of fluorescence lifetimes with a short-lived component centered at 2.5 ns and a long-lived one at 7.4 ns (Bismuto E, Nucci R, Rossi M, Irace G, 1999, Proteins 27:71-79). From the examination of the trajectories of the side chains capable of causing intramolecular quenching for each tryptophan microenvironment and using a modified Stern-Volmer model for the emission quenching processes, we calculated the fluorescence lifetime for each tryptophanyl residue of Sbeta gly at two different temperatures, i.e., 300 and 365 K. The highest temperature was chosen because in this condition Sbeta gly evidences a maximum in its catalytic activity and is stable for a very long time. The calculated lifetime distributions overlap those experimentally determined. Moreover, the majority of trytptophanyl residues having longer lifetimes correspond to those originally identified by inspection of the crystallographic structure. The tryptophanyl lifetimes appear to be a complex function of several variables, such as microenvironment viscosity, solvent accessibility, the chemical structure of quencher side chains, and side-chain dynamics. The lifetime calculation by MD simulation can be used to validate a predicted structure by comparing the theoretical data with the experimental fluorescence decay results.     

Cryptosporidium andersoni n. sp. (Apicomplexa: Cryptosporiidae) from cattle, Bos taurus

A new species of Cryptosporidium is described from the feces of domestic cattle, Bos taurus. Oocysts are structurally similar to those of Cryptosporidium muris described from mice but are larger than those of Cryptosporidium parvum. Oocysts of the new species are ellipsoidal, lack sporocysts, and measure 7.4 x 5.5 microm (range, 6.0-8.1 by 5.0-6.5 microm). The length to width ratio is 1.35 (range, 1.07-1.50). The colorless oocyst wall is < 1 microm thick, lacks a micropyle, and possesses a longitudinal suture at one pole. A polar granule is absent, whereas an oocyst residuum is present. Oocysts were passed fully sporulated and are not infectious to outbred, inbred immunocompetent or immunodeficient mice, chickens or goats. Recent molecular analyses of the rDNA 18S and ITS1 regions and heat-shock protein 70 (HSP-70) genes demonstrate this species to be distinct from C. muris infecting rodents. Based on transmission studies and molecular data, we consider the large form of Cryptosporidium infecting the abomasum of cattle to be a new species and have proposed the name Cryptosporidium andersoni n. sp. for this parasite.     

Evidence for a nutritional disorder of Oxalis acetosella L. on acid forest soils; II. Diagnostic field experiments and nutrient solution studies

Different field experiments were performed to discover the main factor(s) responsible for the poor leaf growth, moderate propagation and leaf chlorosis of Oxalis acetosella in an old Norway spruce stand with acid soil (Höglwald Forest). A previous study had suggested, that Ca (or Mg) deficiency or Mn toxicity could be involved.In a Main Diagnostic Field Experiment with an intact population, Ca and Mg were either applied as sulphate or carbonate to distinguish between nutritional and pH effects. Mn and Si were also applied to aggravate or overcome possible effects of Mn toxicity. Enhancement experiments with different amounts of CaSO₄ were conducted to investigate the Ca dose-effect relationship under field conditions. Additional trials with SrCO₃, BaCO₃ and NaHCO₃ had the goal to raise the soil pH without supply of nutrients.Greenhouse experiments with Oxalis acetosella supplemented the field studies by investigating the Ca and Mn dose-effect relationships under controlled conditions. Growth, vitality and nutrition of Oxalis were studied in a nutrient solution culture at pH 4.0 over a range of concentrations of Ca (20 to 5000 mol L_-1) and Mn (5 to 1000 mol L_-1) respectively. Furthermore, the effects of two contrasting ammonium/nitrate ratios were tested. The nutritional composition of the basal nutrient solution and the microclimate in the greenhouse were as far as possible adjusted to the environmental conditions of the plant in the Höglwald Forest.All these studies led to the conclusion, that the moderate growth and vitality of Oxalis in the Höglwald Forest was mainly due to an insufficient Ca supply, rather than an effect of Mg deficiency, low soil pH or Mn toxicity. The application of CaSO₄ caused a similar stimulation of the growth as CaCO₃. A clearly positive, close CaSO₄ dose-effect relationship was detected in field experiments as well as in the nutrient solution study. The same type of leaf chloroses as in the field was reproduced through low Ca nutrient solutions. Predominant ammonium nutrition may significantly impair Ca uptake.Oxalis acetosella displayed a relatively high leaf tissue tolerance of excessive Mn. There was no indication for a Mn-induced Ca deficiency in the Höglwald Forest. Enhanced Si uptake led to a partial vitalization of Oxalis; the reason for that remained unclear.     

LCA of concrete and steel building frames

The effects on the external environment of seven concrete and steel building frames representative of present-day building technology in Sweden were analysed using LCA methodology. Objects of the study included frame construction and supplementary materials. Several-storey offices and dwellings were studied. The functional unit was defined as one average m² of floor area during the lifetime of the building. Inventory data were elaborated for concrete and steel production, the building site, service life, demolition and final disposal. Parameters included were raw material use, energy use, emissions to air, emissions to water and waste generation. The inventory results were presented and evaluated as such, in addition to an interpretation by using three quantitative impact assessment methods. Parameters that weighed heavily were use of fossil fuels, CO₂, electricity, SO_x ² NO_x ² alloy materials and waste, depending on what assessment method was used. Over the life cycle, building production from cradle to gate accounted for about the same contribution to total environmental loads as maintenance and replacement of heat losses through external walls during service life, whereas demolition and final disposal accounted for a considerably lower contribution.     

浅水草型湖泊──扁担塘中桡足类的群落结构（英文）

本文研究了一浅水草型湖泊──扁担塘中桡足类的群落结构,包括种类组成、种群动态及现存量。在一周年的研究中,共发现14种浮游桡足类（9种剑水蚤和5种哲水蚤）。根据年平均密度,剑水蚤的优势种为：Mesocyclops notius,Cyclops vincinuis vincinus和Thermocyclops brevifurcatus,而哲水蚤的优势种为Meodiaptomus yantsekiangensis和Sinocalanus dorrii。通过比较长江沿岸的5个湖泊的桡足类的种类组成发现,桡足类的种类数并不与湖泊面积大小成正比,这与Dodson通过研究欧洲及北美湖泊中的枝角类得出的结论并不一致。此外,虽然这5个湖泊中的桡足类的种类数多达35种,但每个湖泊中的优势种都非常相似地集中到少数几个属或种,而其它均为偶尔性种类。     

Dietary boron intakes of selected populations in the United States

Knowledge of daily boron (B) intakes will assist researchers in establishing B requirements and elucidating the metabolic role of B in humans. B concentrations in commonly consumed foods were utilized to approximate the B intake of selected US populations. Triplicate food samples were digested at low temperatures with 16M HNO₃ and 30% H₂O₂, and analyzed by inductively coupled plasma spectroscopy (ICP). Milk and dairy products, juices, and beverages were the largest contributors to dietary B. Total B content of average daily diets ranged from 548 μg for toddlers (2 yr old) to 883 μg for mature males (60–65 yr old), excluding tap water contributions. Toddlers consumed 3.7 times more B than mature males when adjusted for body weight (body wt) and consumed the diet with the highest boron density (1.8 μg/kJ or 0.43 μg/kcal). Adolescent females consumed a diet with the lowest B density (1.12 μg/kJ or 0.26 μg/kcal). Food B concentrations applied to diet records (1020 μg/d) and ICP analysis of the corresponding food composites (1170 μg/d) were comparable (p < 0.05). Current estimations of B in US diets are consistent with reports in the literature stating that normal adult daily B intakes are approx 1 mg. Presented at the symposium “Second International Symposium on the Health Effects of Boron and Its Compounds” held in Irvine, CA, on October 23, 1997. This symposium was presented by the University of California, Irvine. The publication of the symposium was supported by U.S. Borax Inc. Guest editors for this symposium were B. Dwight Culver (University of California, Irvine, CA) and James R. Coughlin (Coughlin and Associates, Newport Coast, CA). US Department of Agriculture, Agricultural Research Service, Northern Plains Area is an equal opportunity/affirmative action employer, and all agency services are available without discrimination.     

Similarities and Varieties: A Brief Sketch on the Reception of Darwinism and Sociobiology in Japan

This paper discusses the reception of Darwinian evolutionary theory and sociobiology in Japan. Darwinism was introduced into Japan in the late 19th century and Japanese people readily accepted the concept of evolution because, lacking Christianity, there was no religious opposition. However, the theory of evolution was treated as a kind of social scientific tool, i.e., social Spencerism and eugenics. Although evolutionary biology was developed during the late 19th and the early 20th century, orthodox Darwinian theory was neglected for a long time. In the mid 1980s, sociobiology was introduced but it was ignored and criticized by a large part of the ecologist-evolutionist community in Japan. This hostile attitude was due to the absence of Darwinism among these scientists. Compared with the reception of sociobiology in English-speaking countries, there were both similarities and differences in Japan.     

Structure and function of a novel endonuclease acting on branched DNA substrates

We show that Pyrococcus abyssi PAB2263 (dubbed NucS (nuc lease for s s DNA) is a novel archaeal endonuclease that interacts with the replication clamp PCNA. Structural determination of P. abyssi NucS revealed a two‐domain dumbbell‐like structure that in overall does not resemble any known protein structure. Biochemical and structural studies indicate that NucS orthologues use a non‐catalytic ssDNA‐binding domain to regulate the cleavage activity at another site, thus resulting into the specific cleavage at double‐stranded DNA (dsDNA)/ssDNA junctions on branched DNA substrates. Both 3′ and 5′ extremities of the ssDNA can be cleaved at the nuclease channel that is too narrow to accommodate duplex DNA. Altogether, our data suggest that NucS proteins constitute a new family of structure‐specific DNA endonucleases that are widely distributed in archaea and in bacteria, including Mycobacterium tuberculosis.     

The chick embryo: hatching a model for contemporary biomedical research

Animal models play a crucial role in fundamental and medical research. Progress in the fields of drug discovery, regenerative medicine and cancer research among others are heavily dependent on in vivo models to validate in vitro observations, and develop new therapeutic approaches. However, conventional rodent and large animal experiments face ethical, practical and technical issues that limit their usage. The chick embryo represents an accessible and economical in vivo model, which has long been used in developmental biology, gene expression analysis and loss/gain of function experiments. It is also an established model for tissue/cell transplantation, and because of its lack of immune system in early development, the chick embryo is increasingly recognised as a model of choice for mammalian biology with new applications for stem cell and cancer research. Here, we review novel applications of the chick embryo model, and discuss future developments of this in vivo model for biomedical research.     

Development of advanced host cell protein enrichment and detection strategies to enable process relevant spike challenge studies

An orthogonal chromatography methodology for the enrichment of host cell protein (HCP) species relative to monoclonal antibody (mAb) products was developed and applied for the successful enrichment of HCP from post‐Protein A process pools for seven different mAb products. An advanced two‐dimensional liquid chromatography/mass spectrometry platform (2D‐LC/MS^E) was utilized to demonstrate that the HCP enriched material was representative, in terms of species content, to pre‐enriched process pools. The HCP enrichment methodology was scaled up for two different mAb products, and this process relevant enriched HCP material was used to conduct advanced spike challenge studies to demonstrate the utility of the approach for the understanding of (1) quantitative HCP clearance, (2) individual species clearance, and (3) species clearance redundancy across polishing chromatography steps. The combined ability to enrich process relevant HCP, detect individual HCP species with 2D‐LC/MS^E technology, and conduct advanced challenge studies with process relevant material surmounts prior limitations to high integrity process challenge study implementation, and facilitates significant process understanding for development of risk‐based control strategies and strategic process design. This also demonstrates implementation of a foundational strategy for conducting spike‐challenge studies using process‐relevant impurities isolated from processes of interest using orthogonal approaches. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 31:983–989, 2015