A BASIC microcomputer program to calculate the secondary structure of proteins from their circular dichroism spectrum

A BASIC program (CDPROT) has been developed to calculate thesecondary structure of proteins from their far UV circular dichroismspectrum. This implementation can use different reference spectra,calculated either from model polypeptides or proteins of knowntertiary structure. Apart from obtaining the a-helical, ß-structure,ß-turns or random percentages which would generatethe spectrum of best fit with respect to the experimental measures,CDPROT represents on screen both theoretical and experimentalspectra indicating the root-mean-square error. The provisionof additional reference spectra by the user is also considered,and another program (STOREREF) performs the editing in an adequateformat for CDPROT. Received on March 8, 1988; accepted on June 3, 1988     

Analysing the outer membrane subproteome of Methylococcus capsulatus (Bath) using proteomics and novel biocomputing tools

High-resolution two-dimensional gel electrophoresis and mass spectrometry has been used to identify the outer membrane (OM) subproteome of the Gram-negative bacterium Methylococcus capsulatus (Bath). Twenty-eight unique polypeptide sequences were identified from protein samples enriched in OMs. Only six of these polypeptides had previously been identified. The predictions from novel bioinformatic methods predicting β-barrel outer membrane proteins (OMPs) and OM lipoproteins were compared to proteins identified experimentally. BOMP () predicted 43 β-barrel OMPs (1.45%) from the 2,959 annotated open reading frames. This was a lower percentage than predicted from other Gram-negative proteomes (1.8–3%). More than half of the predicted BOMPs in M. capsulatus were annotated as (conserved) hypothetical proteins with significant similarity to very few sequences in Swiss-Prot or TrEMBL. The experimental data and the computer predictions indicated that the protein composition of the M. capsulatus OM subproteome was different from that of other Gram-negative bacteria studied in a similar manner. A new program, Lipo, was developed that can analyse entire predicted proteomes and give a list of recognised lipoproteins categorised according to their lipo-box similarity to known Gram-negative lipoproteins (). This report is the first using a proteomics and bioinformatics approach to identify the OM subproteome of an obligate methanotroph.     

EvoS: A Prescription for What Ails Pre-Medical Education?

Pre-medical students are certainly a widely varied group, with different motivations and experiences, different skills sets and interests. However, they often tend to approach their undergraduate education as a necessary evil that they must endure in order to achieve their ultimate goals. This article summarizes recent literature addressing some of the questions that have been raised regarding pre-medical education programs. Are students prepared for the intellectual, emotional, and even physical challenges of medical training? What deficiencies are commonly seen in entering medical students? What are students’ perceptions of how well their pre-medical studies helped them? Many of these studies have resulted in a call for more science training, while some have advocated for less, but with an enhanced focus on humanistic studies. We supply a brief outline of our Evolutionary Studies (EvoS) program and reflect upon how participation in this program can enhance pre-medical students’ education. Importantly, we argue that EvoS can expand students’ depth of understanding of science, as well as nurture their ability to think about the needs of their patients and the context of their medical practice.     

Application of FT-IR spectroscopy for control of the medium composition during the biodegradation of nitro aromatic compounds

Previous studies showed that cabbage leaf extract (CLE) added to the growth medium can noticeably promote the degradation of nitro aromatic compounds by specific consortium of bacteria upon their growth. For further development of the approach for contaminated soil remediation it was necessary to evaluate the qualitative and/or quantitative composition of different origin CLE and their relevance on the growth of explosives-degrading bacteria. Six CLE (different by species, cultivars and harvesting time) were tested and used as additives to the growth medium. It was shown that nitro aromatic compounds can be identified in the FT-IR absorption spectra by the characteristic band at 1,527 cm⁻¹, and in CLE by the characteristic band at 1,602 cm⁻¹. The intensity of the CLE band at 1,602 cm⁻¹ correlated with the concentration of total nitrogen (R ² = 0.87) and decreased upon the growth of bacteria. The content of nitrogen in CLE differed (0.22–1.00 vol.%) and significantly influenced the content of total carbohydrates (9.50–16.00% DW) and lipids [3.90–9.90% dry weight (DW)] accumulated in bacterial cells while the content of proteins was similar in all samples. Though this study showed quantitative differences in the composition of the studied CLE and the response of bacterial cells to the composition of the growth media, and proved the potential of this additive for remediation of contaminated soil. It was shown that analysis of CLE and monitoring of the conversion of nitro aromatic compounds can be investigated by FT-IR spectroscopy as well as by conventional chemical methods.     

Zooplankton community size structure and taxonomic composition affects size-selective grazing in natural communities

The body size of an individual zooplankton is well related to its grazing rate and to the range of particle sizes it can ingest, and since cladocerans and copepods feed differently, they follow different relationships. Based on these general patterns in individual organisms, we tested whether the size structure and taxonomic composition of more complex natural zooplankton communities are related to their in situ grazing rate and to the range of algal sizes they graze. We compared community grazing rates on individual algal taxa in two communities dominated by small cladocerans, three communities dominated by large cladocerans and three copepod-dominated communities. Small algae were usually grazed most intensively, but grazing rates were poorly related to algal size alone. The range in size of grazed algae increased with increasing mean zooplankton body size, but differed systematically with their taxonomic composition. Communities dominated by Ceriodaphnia or Holopedium grazed a narrower size range of algae [maximum greatest axial length dimension (GALD)=16–36 μm)] than communities with large biomasses of Bosmina or Daphnia (maximum GALD=28–78 μm). Copepod-dominated communities followed the same general relationship as cladocerans. Daphnia-dominated communities grazed the broadest range of algal sizes, and their total grazing rates were up to 2.4 times their grazing rates on small (<35 μm) “highly edible” algae, a difference of similar magnitude to those found in successful trophic cascade biomanipulations. Received: 31 March 1998 / Accepted: 19 October 1998     

Rapid motif compliance scoring with match weight sets

Most current implementations of motif matching in biologicalsequences have sacrificed the generality of weight matrix scoringfor shorter runfimes. The program MOTIF incorporates a weightmatrix and a rapid, backtracking tree–search algorithmto score motif compliance with greatly enhanced performancewhile placing no constraints on the motif in addition, any positionswithin a motif can be marked as ‘inviolate’, therebyrequiring an exact match. MOTIF allows a choice of regular expressionformats and can use both motif and sequence libraries as eithertargets or queries. Nucleic acid sequences can optionally betranslated by MOTIF in any frame(s) and used against peptidemotifs.     

Cellular imaging assay for early evaluation of an apoptosis inducer

The objective of this study was to propose a feasibility of a cellular imaging assay as an alternative to the conventional cytotoxicity assay, such as MTS assay, for apoptosis monitoring. As an apoptosis monitoring parameter, affinity interaction between phosphatidylserine (PS) and annexin V was chosen. First, the specific binding affinity between annexin V and PS in phospholipid bilayers consisting of various molar (0–15%) composition of PS was measured using a surface plasmon resonance biosensor. As PS composition increased, the binding level of annexin V increased proportionally. Second, various concentrations (0.1–10 μM) of staurosporine were used as to induce apoptosis and introduced to MCF-7 breast carcinoma cells. The cellular fluorescence images from annexin V-FITC conjugate were obtained by confocal microscopy, and their fluorescence intensities were quantified by image scanning. Dose–apoptosis (or cell death) relationships were very similar to those from MTS and FACS assays. In summary, our cellular imaging method could serve as a quicker and simpler alternative to MTS (end point assay) and FACS (flow cytometry) to screen potential apoptosis inducers.     

Fatty acid and phytoplankton compositions of different types of mucilaginous aggregates in thenorthern Adriatic

The biomarkers (fatty acid proportions and ratios characteristicof phytoplankton and bacteria) and phytoplankton species insmall (0.5–2.0 cm) and large (0.5–5 m) marine aggregateswere determined in samples collected in the northern AdriaticSea, during a mucilage event in 1997, as well as in 1993, 1994and 1998, when events were not observed. Types of aggregateswere identified according to various biomarker relationships,particularly those related to bacterial and phytoplankton activitiesand changes in the diatom species composition. Aged mucilaginousaggregates (in summer 1997) showed fatty acid proportions (16P/18P,3.9–7.7) characteristic of the highest phytoplankton activities,and also showed the highest bacterial fatty acid proportions(13.3–17.1%) and ratios (C15:br/C15:0, 4.4–6.0).They showed an different diatom community (dominated by Cylindrothecaclosterium) from that in surrounding waters. These characteristicssuggest a continuous renewal of the aggregate organic matter,supporting the hypothesis that aggregate is a ‘selfsustaining’community. In contrast, both freshly formed marine snow, dominantduring periods without mucilage events, and freshly formed mucilaginousaggregates presented biomarker proportions and ratios similarto those of suspended matter (bacterial fatty acids 3–6.7%,C15:br/C15:0 1.2–4.6, 16P/180.4–4.0), and diatomcomposition similar to that of the ambient water. This indicatesthat marine snow sinks more rapidly than large aggregates, beforesignificant changes can occur in its plankton composition. Otheraging aggregate types showed intermediate characteristics, suggestingthat their residence times in the water column were still sufficientto develop organic production–decomposition cycles thatmodified to various extents their biochemical composition.     

Algorithm and computer program Pro--Anal for analysis of relationship between structure and activity in a family of proteins or peptides

In this paper we introduce a computer algorithm and programPro—Anal for analysis of the structure-activity relationshipin a family of evolutionarily related (and/or artificially mutated)proteins/peptides. The program uses aligned amino acid sequenceswith data of their activity (pK, K_m, ED₅₀ or any other) andsearches for correlations between data on activity and variousphysico-chemical characteristics of different regions in primarystructures. In automatic mode, the program generates and verifieshypotheses on the disposition of a sequential modulating regionin a protein, and key characteristics of the region. In manualmode, users can generate and analyze their own hypotheses. Theprogram is implemented on IBM PC or compatible computers. Itis designed to be easily handled by the occasional computeruser and yet it is powerful enough for experienced professionals.Pro—Anal operation is demonstrated on the example of findingmodulating centers in a family of disintegrins—proteinsfrom snake venoms which inhibit fibrinogen interaction withplatelet receptors. In another example it is shown that theimmunogenicity of peptides is connected with their positivecharge.     

Studies on species diversity of Larix chinensis community ecotone

The communities of Larix chinensis and their ecotone in Qinling Mountains were investigated by sampling belt method. Species richness, Simpson diversity, Shannon-Weiner diversity, PIE and Pielou evenness indices of vascular plants in their communities and ecotone were calculated. Structure and composition of the communities in 6 sampling belts within the sites were analyzed. The results showed that the edge effect was obvious in the ecotone with a less changing environment (such as soil and terrain) and acute variation of composition and structure, while inconspicuous or even none in the ecotone with worse environmental condition (such as great space fluctuation). It is apparent that the edge effect of community was affected by soil and terrain, but not by microclimate. __________ Translated from Guibaia, 2005, 25 (2)[译自: 广西植物, 2005,25(2)]     

Isotopic enrichment in a phloem-feeding insect: influences of nutrient and water availability

The isotopic enrichment between an animal and its diet can vary among and within living systems, but the sources of variation are not yet fully understood. Some studies have found that diet quality or an animal’s nutritional status can influence the degree of trophic enrichment, while others have dismissed nutrition as a contributing factor. We evaluated the effects of nutrient and water availability on carbon and nitrogen isotopic enrichment in a specialized plant–herbivore system. Aphids are largely sedentary and rely exclusively on nitrogen-poor phloem sap of their host for nutrition. We grew potato aphids [Macrosiphum euphorbiae (Aphididae)] on an accepted host, pumpkin [Cucurbita pepo L. (Cucurbitaceae)], in a glasshouse environment. Twelve pumpkin plants growing under high- and low-watering regimes were inoculated at 4 weeks of age with aphids. During the course of the experiment we collected leaves, phloem sap, aphids and honeydew (i.e., aphid exudates). We found no trophic enrichment between aphids and their phloem sap diet, but significant carbon enrichment of honeydew relative to aphids (2.5‰) and phloem sap (2.1‰). Honeydew was also enriched in nitrogen compared to the phloem sap (1.2‰). Watering treatment had a substantial impact on trophic enrichment. Correlations among tissues, an indication of uniform trophic enrichment among samples, were significant only for the carbon isotopic composition, and then only for plants and aphids grown in the low-water treatment. Diet quality also influenced the degree of isotopic enrichment; trophic enrichment for both carbon and nitrogen isotopic composition increased as diet quality (C/N) declined. We conclude that the degree of trophic enrichment is variable due, in part, to diet quality, but that the scale of variation is small.     

Phylogenetic comparative analysis of RNA structure on Macintosh computers

A Macintosh Hypertalk program (Hypercard ‘stack’)for use in phylogenetic comparative analysis of RNA structureis described. The program identifies covariations and compensatorychanges in RNA sequence alignments, for use in the constructionof secondary structure models or the identification of tertiaryinteractions. The results of an analysis are presented eitheras a list of positions in the alignment which covary, or asa 2-dimensional matrix in which potential helices in the secondarystructure appear as diagonal patterns. Received on January 7, 1991; accepted on March 19, 1991     

Influence of Drying–Rewetting Frequency on Soil Bacterial Community Structure

Soil drying and rewetting represents a common physiological stress for the microbial communities residing in surface soils. A drying–rewetting cycle may induce lysis in a significant proportion of the microbial biomass and, for a number of reasons, may directly or indirectly influence microbial community composition. Few studies have explicitly examined the role of drying–rewetting frequency in shaping soil microbial community structure. In this experiment, we manipulated soil water stress in the laboratory by exposing two different soil types to 0, 1, 2, 4, 6, 9, or 15 drying–rewetting cycles over a 2-month period. The two soils used for the experiment were both collected from the Sedgwick Ranch Natural Reserve in Santa Ynez, CA, one from an annual grassland, the other from underneath an oak canopy. The average soil moisture content over the course of the incubation was the same for all samples, compensating for the number of drying–rewetting cycles. At the end of the 2-month incubation we extracted DNA from soil samples and characterized the soil bacterial communities using the terminal restriction fragment length polymorphism (T-RFLP) method. We found that drying–rewetting regimes can influence bacterial community composition in oak but not in grass soils. The two soils have inherently different bacterial communities; only the bacteria residing in the oak soil, which are less frequently exposed to moisture stress in their natural environment, were significantly affected by drying–rewetting cycles. The community indices of taxonomic diversity and richness were relatively insensitive to drying–rewetting frequency. We hypothesize that drying–rewetting induced shifts in bacterial community composition may partly explain the changes in C mineralization rates that are commonly observed following exposure to numerous drying–rewetting cycles. Microbial community composition may influence soil processes, particularly in soils exposed to a significant level of environmental stress.     

Effects of N-starvation and C-source on Bradyrhizobium japonicum exopolysaccharide production and composition, and bacterial infectivity to soybean roots

The exopolysaccharide (EPS) is an extracellular molecule that in Bradyrhizobium japonicum affects bacterial efficiency to nodulate soybean. Culture conditions such as N availability, type of C-source, or culture age can modify the amount and composition of EPS. To better understand the relationship among these conditions for EPS production, we analyzed their influence on EPS in B. japonicum USDA 110 and its derived mutant ΔP22. This mutant has a deletion including the 3′ region of exoP, exoT, and the 5′ region of exoB, and produces a shorter EPS devoid of galactose. The studies were carried out in minimal media with the N-source at starving or sufficient levels, and mannitol or malate as the only C-source. Under N-starvation there was a net EPS accumulation, the levels being similar in the wild type and the mutant with malate as the C-source. By contrast, the amount of EPS diminished in N-sufficient conditions, being poyhydroxybutyrate accumulated with culture age. Hexoses composition was the same in both N-situations, either with mannitol or malate as the only C-source, in contrast to previous observations made with different strains. This result suggests that the change in EPS composition in response to the environment is not general in B. japonicum. The wild type EPS composition was 1 glucose:0.5 galactose:0.5 galacturonic acid:0.17 mannose. In ΔP22 the EPS had no galactose but had galacturonic acid, thus indicating that it was not produced from oxidation of UDP-galactose. Infectivity was lower in ΔP22 than in USDA 110. When the mutant infectivity was compared between N-starved or N-sufficient cultures, the N-starved were not less infective, despite the fact that the amounts of altered EPS produced by this mutant under N-starvation were higher than in N-sufficiency. Since this altered EPS does not bind soybean lectin, the interaction of EPS with this protein was not involved in increasing ΔP22 infectivity under N-starvation.     

Enhanced resolution of sedimentation coefficient distribution profiles by extrapolation to infinite time

Sedimentation velocity experiments can be used to identify two or more independent non-interacting macromolecules, which differ in their size by only a few percent. The procedure requires the extrapolation of differential apparent sedimentation coefficient distributions obtained at different running time to t → ∞ and works because it eliminates or greatly reduces diffusion effects. Here, we present an improved time extrapolation function of sedimentation distribution profiles originally presented by Stafford (In: Harding, Rowe, Horton (eds.) Analytical ultracentrifugation in biochemistry and polymer science, 1992). We describe a computing procedure with the program lamm to analyze concentration profiles obtained by absorbance or interference optics that utilizes suitable smoothing methods for noisy data sets and present examples which include time invariant noises.     

Hybridity of carrageenans water- and alkali-extracted from Chondracanthus chamissoi, Mazzaella laminarioides, Sarcothalia crispata, and Sarcothalia radula

Carrageenans water- and alkali-extracted from Chondracanthus chamissoi, Mazzaella laminarioides, Sarcothalia crispata, and Sarcothalia radula were degraded by Pseudoalteromonas carrageenovora κ-carrageenase and Alteromonas fortis ι-carrageenase. The composition of the high molecular weight fraction (i.e., enzyme-resistant fraction) as well as the standard and hybrid oligosaccharide content highlighted differences between the species-specific carrageenans in terms of composition and distribution of the carrabiose moieties. Inspection of the distribution of μ- and ν-carrabiose, the biosynthetic precursors of κ- and ι-carrabiose, revealed their localization in κ-carrabiose- or ι-carrabiose-rich segments, respectively.     

The late jurassic ‘Massenkalk fazies’ of Southern Germany: calcareous sand piles rather than organic reefs

Summary Upper Jurassic (Malm δ to ζ1) massive limestones (‘algal-sponge-reefs, sponge-reefs, reef-complexes, reefs, algal-sponge-bioherms, biolithites, Massenkalk, bioherms, Stillwasser-Mudmounds’) were analyzed in the Southern Swabian Alb, the Southern Franconian Alb and in drilling wells in the Molasse basin (Southern Bavaria). This analysis was carried out within the frame of a multidisciplinary DFG-study with the objective of decifering the controls on the development of Upper Jurassic spongiolites, their three-dimensional distribution, their characteristic faunal composition, and the diagenetic trends of the different primary facies. The data base consists of detailed facies mapping in the areas of the Eybtal and the Blautal (1300 samples) as well as comparative studies in the Upper Donautal (Swabian Alb) and the Southern Franconian Alb (400 samples). All together about 500 thin sections were studied. The distribution of the most important components (ooids, intraclasts, peloids, corals, sponges, sponge spicules, cyanobacterial crusts, brachiopods, molluscs, echinoids, bryozoans, serpulids,Terebella, Tubiphytes), and diagenetic features (dolomite, dedolomite, silicification, stylolites, clay flasers, hematite patches) results in a spatial distribution pattern of facies types. The largest part (70 %) of the massive limestones consists of a peloid-lithoclast-ooid sand facies rich in completely or partly micritized ooids. These ooids, especially in beds of the Malm δ to ε, might be the clue to a reinterpretation of the water depth. True biogenic constructions occur (about 30 % of the volume; sponge-algalmudmounds, algal-sponge-boundstones, and brachiopod-algal-sponge-mounds) within and at the margins of this facies and are interpreted as platform sands. The spatial distribution of the buildups in relation to the sand facies was probably controlled by hydrodynamic conditions. In addition, zoned sponge-algal-mounds occur in intraplatform channels and nodular sponge-algal-mudmounds in the marly basin sediments between platform sand areas. Breccias and slumpings in beds older than the Malm ζ have to be reinterpreted. Most of the breccias found originated from the flanks of the sand platforms, reflecting the faunal composition of the algal-sponge-boundstones which stabilized the flanks. Breccias of this composition occur throughout the Malm δ-ζ1 and differ markedly in their composition from the sand facies. The boundary breccia (Malm ε/ζ1) is interpreted as marking a regressive maximum. The increasing growth of buildups, rich in brachiopods in the Malm ζ1, is ascribed to an increase of reef growth at the beginning of a transgression. Detailed facies analyses necessary for the reconstruction of the spatial distribution of different facies types are in progress. Most of the older data on faunal distributions cannot be used for detailed facies analysis because they differentiated only between massive facies and bedded facies. Therefore Upper Jurassic limestones of Southern Germany should be restudied in order to recognize the volumetric importance of sand facies and buildups within massive limestones.     

The protonation equilibria of selected glycine dipeptides in ethanol-water mixture: solvent composition effect

Knowledge of the protonation constants of small dipeptide is important, interesting and necessary for complete understanding of the physiochemical behavior of dipeptide. In this study, the protonation constants of some aliphatic dipeptides (Gly–Gly, Gly–Val, Gly–Leu, Gly–Thr, Gly–Phe and Gly–Met) were studied in water and ethanol–water mixtures [20% ethanol–80% water, 40% ethanol–60% water, 60% ethanol–40% water, (v/v)] at 25 ± 0.1°C under nitrogen atmosphere and ionic strength at 0.10 mol dm⁻³ by potentiometry. The constants of the systems were calculated by using BEST computer program, and distribution species diagrams were produced using the SPE computer program. The protonation constants were influenced by changes in solvent composition, and their variations were discussed in terms of solvent and structural properties. The concentration distribution of the various species in ethanol–water mixtures was evaluated.     

Similarities in protein amino acid composition in connection with principles of protein evolution

The amino acid composition of human alcohol dehydrogenase (ADH) was compared with alcohol dehydrogenases from different organisms and with other proteins. Similar amino acid sequences in human ADH (template protein) and in other proteins were determined by means of an original computer program. Analysis of amino acid motifs reveals that the ADHs from evolutionary more close organisms have more common amino acid sequences. The quantity measure of amino acid similarity was the number of similar motifs in analyzed protein per protein length. This value was measured for ADHs and for different proteins. For ADHs, this quotient was higher than for proteins with different functions; for vertebrates it correlated with evolutionary closeness. The similar operation of motif comparison was made with the help of program complex “MEME”. The analysis of ADHs revealed 4 motifs common to 6 of 10 tested organisms and no such motifs for proteins of different function. The conclusion is that general amino composition is more important for protein function than amino acid order and for enzymes of similar function it better correlates with evolutionary distance between organisms.     

Organisms can essentially be classified according to two codon patterns

We recently classified 23 bacteria into two types based on their complete genomes; “S-type” as represented by Staphylococcus aureus and “E-type” as represented by Escherichia coli. Classification was characterized by concentrations of Arg, Ala or Lys in the amino acid composition calculated from the complete genome. Based on these previous classifications, not only prokaryotic but also eukaryotic genome structures were investigated by amino acid compositions and nucleotide contents. Organisms consisting of 112 bacteria, 15 archaea and 18 eukaryotes were classified into two major groups by cluster analysis using GC contents at the three codon positions calculated from complete genomes. The 145 organisms were classified into “AT-type” and “GC-type” represented by high A or T (low G or C) and high G or C (low A or T) contents, respectively, at every third codon position. Reciprocal changes between G or C and A or T contents at the third codon position occurred almost synchronously in every codon among the organisms. Correlations between amino acid concentrations (Ala, Ile and Lys) and the nucleotide contents at the codon position were obtained in both “AT-type” and “GC-type” organisms, but with different regression coefficients. In certain correlations of amino acid concentrations with GC contents, eukaryotes, archaea and bacteria showed different behaviors; thus these kingdoms evolved differently. All organisms are basically classifiable into two groups having characteristic codon patterns; organisms with low GC and high AT contents at the third codon position and their derivatives, and organisms with an inverse relationship.