A modified Chou and Fasman protein structure algorithm

A FORTRAN program PRSTRC has been developed for protein secondarystructure prediction, which is a modified Chou and Fasman (1978)analysis. This implementation carries out a running averageof amino acid structure occurrence frequencies, utilizes a simpleset of nucleation conditions, and allows user control over nucleationthreshold and cutoff parameters. The algorithm includes predictionof the newly defined secondary structure elements: omega loops(1986). It also generates a charge distribution and hydropathyprofile. Output includes a simple graphic display for a printer,or a CRT using color addition. Correct structures are predictedfor T. dyscritum hemerythrin and the variable domain of mouseimmunoglobin k-chain. Received on November 17, 1986; accepted on June 10, 1987     

A rapid computer technique for analysing molecular interactions

A rapid method for analysing enzyme — substrate interactionsusing a discriminant analysis program is described. This technqueidentifies the structural features of substrate molecules whichare important in determining metabolic activity. Two model systems,nucleoside diphosphatase activity of Golgi membranes and theinteraction of yeast hexokinase with a range of D-sugars, areused as illustrations of the technique. The conclusions fromboth models are consistent with those previously obtained fromanalytical techniques. Received on January 21, 1986; accepted on April 1, 1986     

Hyperbolic regression analysis for kinetics, electrophoresis, ELISA, RIA, Bradford, Lowry, and other applications

Hyperbolic regression analysis is an effective method for fittingexperimental data points obtained from a variety of experimentsin molecular biology, including enzyme kinetics, agarose gelelectrophoresis of DNA fragments, SDS—polyacrylamide gelelectrophoresis of proteins, enzyme–linked immunosorbentassays (ELISA), radioimmunoassays (RIA), Bradford protein quantitationassays, Lowry protein assays, and other applications. Hyperbolicregression yields excellent fitted curves without the biasesthat are introduced by carrying out linear regression on doublereciprocal coordinates, and it produces one simple equation,encompassing all the data points, that can be used easily ina pocket calculator to estimate the values of unknown samplesfrom the known standards. Received on February 9, 1986; accepted on April 11, 1986     

Epidemiological analysis of testicular malignant neoplasm incidence and mortality in Poland 1963-1986

Epidemiological analysis of both morbidity and mortality rates for testicular cancer in Poland between 1963 and 1986 was carried out. A particular attention was drawn to the period between 1981 and 1986, when a program of combined chemotherapy and surgery was introduced in Poland. The study aimed at analysing an effect of this combined treatment on mortality rate for testicular cancer. Between 1963 and 1986, a constant increase in morbidity for the testicular cancer was noted. Mortality rate increased between 1963 and 1983. This trend was inhibited between 1984 and 1986. "Splitting" of the morbidity and mortality curves was observed between 1984 and 1986. A decrease in mortality rate was noted at the constant morbidity for testicular tumors. It was particularly clear in younger age groups (15-39 years), as well as older age groups (60-64 years and over 75 years). A decrease in mortality rate for testicular tumors within 1984-1986 may be attributed to the introduction of combined treatment in Poland.     

DNAMAT: an efficient graphic matrix sequence homology algorithm and its application to structural analysis

We present a fast algorithm to produce a graphic matrix representationof sequence homology. The algorithm is based on lexicographicalordering of fragments. It preserves most of the options of asimple naive algorithm with a significant increase in speed.This algorithm was the basis for a program, called DNAMAT, thathas been extensively tested during the last three years at theWeizmann Institute of Science and has proven to be very useful.In addition we suggest a way to extend our approach to analysea series of related DNA or RNA sequences, in order to determinecertain common structural features. The analysis is done by‘summing’ a set of dot-matrices to produce an overallmatrix that displays structural elements common to most of thesequences. We give an example of this procedure by analysingtRNA sequences. Received on June 26, 1986; accepted on September 28, 1986     

A Comparative Analysis of the Stillbirth Incidence in Radioactively Contaminated Areas of Bryansk Oblast after the Chernobyl Accident (1986–2016)

Biology Bulletin - Abstract—Based on the official statistics for 1986–2016, this paper presents the findings of a comparative analysis of the rate of stillbirth in boys and girls in...     

A Pascal microcomputer program for prediction of protein secondary structure and hydropathic segments

This paper describes a simple Pascal microcomputer program forprediction of protein secondary structure according to the Chouand Fasman algorithm. In addition, it performs an analysis ofthe hydropathic character of the residues for prediction ofexternal/internal regions of the polypeptide chain. Also itsearches for probable glycosylation and phosphorylation sites. Received on July 26, 1985; accepted on May 6, 1986     

Growth and production of O+ bream (Abramis brama), O+ roach (Rutilus rutilus) and O+ carp (Cyprinus carpio) in 10 drainable 0.1 Ha ponds

In ten 0.1 ha drainable ponds O⁺ cyprinids were stocked to assess their impact on the aquatic community. Bream and roach were stocked in early June, 1986, and carp in early July, 1986. The ponds were drained mid November, 1986. The relationship between the fish community and its food resource was estimated in terms of production and consumption with use of the data on growth and mortality of the fish. The average gross production of the fish species in the ten ponds (48.4 kg during the experiment) was dominated by the carp (58.5%). A minimum estimate of the food consumption of the O⁺ cyprinids is 760 kJ.m^–2. The average production of bream and roach was much lower than that of carp due to a higher mortality and a more specialized feeding pattern. The gross productions of carp, bream and roach in the ten ponds were not significantly related, although stomach analysis showed diet overlap between the carp and the bream.     

METAMOD: software for steady-state modelling and control analysis of metabolic pathways on the BBC microcomputer

METAMOD, a BBC microcomputer-based software package for steady-statemodelling and control analysis of model metabolic pathways,is described, The package consists of two programs. METADEFallows the user to define the pathway in terms of reactions,rate equations and initial concentrations of metabolites. METACALuses one of two algorithms to calculate the steady-state concentrationsand fluxes. One algorithm uses the current ratio of productionand consumption rates of variable metabolites to adjust iterativelytheir concentrations in such a way that they converge towardsthe steady state. The other algorithm solves the roots of thesystem equations by means of a quasi-Newtonian procedure. Controlanalysis allows the calculation of elasticity, control and responsecoefficients, by means of finite difference approximation. METAMODis interactive and easy to use, and suitable for teaching andresearch purposes. Received on January 17, 1986; accepted on June 2, 1986     

The relationship between chinook conditions and women's physical and mental well-being

The objective of this study was (1) to determine the relationship between chinook conditions and physical and psychological symptoms in women aged 20–49 years, and (2) to examine the possibility of subgroups of chinook-sensitive women. The evidence for this relationship is at present merely anecdotal. The study carried out in 1985–1986 in Calgary comprises the secondary analysis of a large survey of various health and health-related factors, including different symptoms, of urban women aged 20–49 years. The interview date was used to link these data to days on which pre-chinook, chinook, post-chinook and non-chinook conditions occurred. Between November 1, 1985 and February 28, 1986, 182 women were interviewed on pre-chinook days, 74 on chinook days, 229 on post-chinook days and 886 on non-chinook days. Autonomic reactions and skin disorders were found to be significantly related to chinook conditions. None of the psychological symptoms was related to chinook conditions. However, a significant relationship was found between symptoms and chinook conditions in women with a history of emotional disorders. This type of information is important to educate chinook-sensitive women and health professionals as well as for hospital emergency departments in order to be able to prepare for potential increases in workload.     

黑河流域酒泉绿洲景观生态安全格局分析

以1986年和2000年的酒泉市遥感数据为基础资料,利用GIS软件生成研究区的景观类型图,计算各景观斑块的面积、数目、形状等空间特征和基于景观空间邻接的绿洲生态安全指标,进而在空间格局方面对绿洲的生态安全进行评价,以了解在人类活动影响下酒泉绿洲的生态安全状况,为该地区生态环境保护提供科学依据。结果表明：（1）从1986年到2000年,绿洲不断扩张,各绿洲斑块类型面积呈增加趋势,同时强烈的人类活动也造成了沙地和裸土面积的增加;（2）从1986年到2000年,受沙化威胁程度最大的斑块类型由耕地变成了草地,而城乡居民用地始终是受胁程度最小的斑块类型;除了城乡居民用地,各绿洲斑块类型受沙化的潜在威胁程度是增加的,人类有目的性的干扰活动改变了干旱区有限水资源的分布与分配,社会经济发展的同时导致了生态环境的退化;（3）与1986年相比,2000年各绿洲斑块类型受盐碱化威胁呈减弱趋势,表明注水洗盐改良土壤使得局部地区生态系统向良性方向演替。干旱区绿洲生态环境有脆弱性和易变性的特点,加强区域景观生态建设和生态安全控制有利于将景观演化导入良性循环。     

A non-linear regression program in BASIC for estimating Km and Vmax

This paper gives a program in BASIC for calculating the kineticparameters K_m and V_max for an enzyme reaction from a set ofpaired values of reaction velocity at given substrate concentrations.An initial estimate of the two parameters is made using a weightedlinear regression, these values are then used in an iterativeprocess to fit the data to the Michaelis–Menten equationand give final values of K_m and V_max with their associated standarderrors. Received on July 15, 1986; accepted on November 13, 1986     

Climate-driven changes on phytoplankton–zooplankton coupling and nutrient availability in high mountain lakes of Southern Europe

1. The effect of climate variability on phytoplankton and zooplankton dynamics and nutrient availability was studied in two high mountain fishless lakes (La Caldera and Río Seco) of contrasting morphology, hydrology and dissolved inorganic nitrogen : soluble reactive phosphate (DIN : SRP) ratios during 1986 and after a 10‐year‐long drought in 1996 and 1997. 2. Thaw was delayed and water temperatures were lower in both lakes in 1996 than in 1986 and 1997. However, the lake‐specific DIN : SRP ratio was maintained in the 3 years studied, reflecting its local control. 3. On other hand, the presumptive limiting nutrient in each lake, P in La Caldera and N in Río Seco, showed higher concentrations in 1996 versus 1986 and 1997. Significant positive correlations between temperature and chlorophyll a were found in both lakes in 1996 but these relationships were negative or not significant in 1986 and 1997. Zooplankton biomass showed lower values in 1996 than in 1986 or 1997. 4. These findings can be explained by a decoupling of the phytoplankton–zooplankton interaction because of a constraint on zooplankton growth by low temperatures in the coldest year studied. This observation furnishes evidence that regional climatic control on the phytoplankton–zooplankton link can modulate the overall demand for nutrients.     

Bayes's Theorem and the Analysis of Binomial Random Variables

A very practical application of Bayes's theorem, for the analysis of binomial random variables, is presented. Previous papers (Walters, 1985; Walters, 1986a) have already demonstrated the reliability of the technique for one, or two random variables, and the extension of the approach to several random variables is described. Two biometrical examples are used to illustrate the method.     

Association between Dopamine Receptor D2 (DRD2) Variations rs6277 and rs1800497 and Cognitive Performance According to Risk Type for Psychosis: A Nested Case Control Study in a Finnish Population Sample

Background

There is limited research regarding the association between genes and cognitive intermediate phenotypes in those at risk for psychotic disorders.

Methods

We measured the association between established psychosis risk variants in dopamine D2 receptor (DRD2) and cognitive performance in individuals at age 23 years and explored if associations between cognition and these variants differed according to the presence of familial or clinical risk for psychosis. The subjects of the Oulu Brain and Mind Study were drawn from the general population-based Northern Finland 1986 Birth Cohort (NFBC 1986). Using linear regression, we compared the associations between cognitive performance and two candidate DRD2 polymorphisms (rs6277 and rs1800497) between subjects having familial (n=61) and clinical (n=45) risk for psychosis and a random sample of participating NFBC 1986 controls (n=74). Cognitive performance was evaluated using a comprehensive battery of tests at follow-up.

Results

Principal components factor analysis supported a three-factor model for cognitive measures. The minor allele of rs6277 was associated with poorer performance on a verbal factor (p=0.003) but this did not significantly interact with familial or clinical risk for psychosis. The minor allele of rs1800497 was associated with poorer performance on a psychomotor factor (p=0.038), though only in those at familial risk for psychotic disorders (interaction p=0.049).

Conclusion

The effect of two DRD2 SNPs on cognitive performance may differ according to risk type for psychosis, suggesting that cognitive intermediate phenotypes differ according to the type (familial or clinical) risk for psychosis.     

Interactions between vegetation development and island formation in the Alpine river Tagliamento

Abstract. Early-successional stages of woody vegetation on gravel bars were studied in an island-braided section of the River Tagliamento in northeastern Italy. We mapped landscape-level changes in the study area (125 ha) by GIS-based analysis of aerial photographs for two time periods (1984–1986, 1986–1991); we surveyed island vegetation, and estimated island age by tree ring analysis. The study area experienced considerable changes between 1984 and 1991 due to at least two major floods in 1987 and 1990. The development of woody vegetation on bars follows three distinct phases: (1) gravel bars plus large woody debris (LWD), (2) pioneer islands, and (3) established islands. Established islands have sections dominated by shrubs of Salix elaeagnos, S. purpurea, S. daphnoides and S. triandra, and tree-dominated sections with Populus nigra, Salix alba and Alnus incana. Large woody debris seems to play a key role for plant colonization on gravel bars. The succession from bars to established islands took about 10 - 20 yr, and the probability of an island being washed away decreased with island age. Erosion produced new LWD which again initiated successional processes in the active zone of the river. Most species were already present in the early-successional stages, although the number of species increased with island development. Established islands were characterized by a distinctive species composition, including an assemblage of species less tolerant of inundation. The results are discussed within the framework of island dynamics and its significance for restoration of early-successional habitats in more regulated rivers.     

Effect of Planting Date,Alachlor, and Fenamiphos on Heterodera glycines Development

The effects of alachlor (2.25 kg a.i./ha) and fenamiphos (2.25 kg a.i./ha) on the penetration and development of Heterodera glycines were examined on Glycine max cultivars Deltapine 105 planted 29 April, 29 May, and 29 June 1986 and Deltapine 105 and Centennial planted 15 May, 15 June, and 15 July 1987. Penetration was lowest on the third planting of soybeans and on fenamiphos-treated plants. Development from second-stage juveniles to adult females required 270 (1986) and 260 (1987) DD20/32 on roots from the first planting control and alachlor treatments. Fenamiphos, alone or with alachlor, retarded development in Deltapine 105 (1986) and in Centennial (1987). Males matured in roots from the second planting in 190 (1986) and 180 (1987) DD20/32 regardless of treatment or cultivar. No development occurred in roots from the third planting until 400 DD20/32 in 1986, but in 1987 development was similar to that in roots from the second planting. Nematode development was similar in alachlor-treated and control roots regardless of planting date. Fenamiphos restricted nematode penetration on most planting dates and slowed development. Simultaneous applications of alachlor and fenamiphos usually also inhibited development.     

Programs for evaluating and characterising bacterial taxonomic data

Three programs are described for evaluating and characterisingdata collected during numerical taxonomic studies of bacteria.The program VARIANCE compares replicate cultures and evaluatesthe reproducibility of each character. Also it identifies thosecharacters that should be excluded from subsequent taxonomicanalysis because of their poor reproducibility. GPROPS summarisesthe properties of clusters of strains that have been definedfrom a cluster analysis, it can produce a probabilistic identificationmatrix and compares each strain within a cluster with the HypotheticalMean Organism (HMO) of that cluster. OVCLUST is an implementationof the program described by Sneath (1979) which calculates overlapstatistics between major clusters. These programs are designedto complement the CLUSTAN package (Wishart, 1982) which is oftenused for cluster analysis of bacterial taxonomic data. The programswere written in FORTRAN 77 and implemented on an IBM PC usingMS–DOS. Received on November 13, 1986; accepted on January 8, 1987     

Physical mechanism for inactivation of metallo-enzymes by characteristic X-rays: analysis of the data of Jawad and Watt

Table 1 summarizes the mean numbers of events and interactions of various types which we calculate to occur per single dihydro-orotic dehydrogenase enzyme when irradiated in solution with D37 = 99 Gy of 8.04 keV X-rays under the experimental conditions of Jawad and Watt (1986). There are clearly many orders or magnitude too few direct interactions of X-ray photons, or electrons, with the enzymes for these processes to be responsible for the mean of one inactivating event per enzyme which must occur at the D37 dose. Jawad and Watt (1986) concluded that the enzyme inactivation was predominantly due to direct interaction of an X-ray photon with a non-metal atom of the enzyme, but our analysis shows that this is not possible by five orders of magnitude. Of the possible mechanisms (a)-(d), the only one which remains feasible in this experimental system is the indirect action of radiolysis products from the solution (d). Diffusion distances of the order of 0.1 micron may be quite adequate for such inactivation. The situation would be very different for enzymes or other molecules within mammalian cells where diffusion distances are very much smaller (probably of the order of a few nanometres). Our analysis leaves unexplained the fairly small (20 per cent) change in effectiveness reported by Jawad and Watt (1986) for X-ray energy above, as compared to below, the K-absorption edge of Fe. The experimental observation is directly dependent on the accuracy of the dosimetry at these two energies; we have made no attempt to evaluate this.