GeneTools – application for functional annotation and statistical hypothesis testing

Background  

Modern biology has shifted from "one gene" approaches to methods for genomic-scale analysis like microarray technology, which allow simultaneous measurement of thousands of genes. This has created a need for tools facilitating interpretation of biological data in "batch" mode. However, such tools often leave the investigator with large volumes of apparently unorganized information. To meet this interpretation challenge, gene-set, or cluster testing has become a popular analytical tool. Many gene-set testing methods and software packages are now available, most of which use a variety of statistical tests to assess the genes in a set for biological information. However, the field is still evolving, and there is a great need for "integrated" solutions.     

Deciphering membrane protein structures from protein sequences

ABSTRACT: Co-evolving positions within protein sequences have been used as spatial constraints to develop a computational approach for modeling membrane protein structures.     

Inhibitory effects of some esters of 2- and 3-substituted alkoxyphenylcarbamic acids on photosynthetic characteristics

The inhibitory effect of 23N-alkyl-4-piperidylesters (alkyl = ethyl-butyl) (APEA) and 8N-ethyl-2-pyrrolidinylmethylesters (EPMEA) of 2- and 3-substituted alkoxyphenylcarbamic acids (alkoxy = butoxy-heptyloxy-) on photosynthetic Hill reaction activity of spinach chloroplasts and on chlorophyll (Chl) synthesis in green algaeChlorella vulgaris was investigated. Inhibitory activities of these compounds were strongly connected with the lipophilicity of the whole molecule. A lower inhibitory activity of 2-alkoxy-substituted derivatives in relation to the corresponding 3-substituted ones was confirmed. Electron spin resonance (ESR) spectra of spinach chloroplasts demonstrated that the studied compounds affected the structure of photosystem (PS) 2 with the release of Mn²⁺ ions into interior of thylakoid membranes.     

Changes in transmission of Baylisascaris procyonis to intermediate hosts as a function of spatial scale

Physical changes in landscapes alter the abundance and distribution of species. Higher-order effects can occur when changes in ecological processes result in altered interspecific interactions and subsequent changes in a species' abundance or persistence. Baylisascaris procyonis , a roundworm parasite of raccoons ( Procyon lotor ), is pathogenic to numerous small vertebrates that serve as intermediate hosts, including white-footed mice ( Peromyscus leucopus ). Raccoons have responded positively to agriculturally induced changes in landscapes, with potential consequences for intermediate hosts of B . procyonis . We examined white-footed mice from a homogeneous, predominantly forested landscape in south-central Indiana and a heterogeneous, predominantly agricultural landscape in northwestern Indiana for presence of larval B . procyonis . We compared prevalence of infection, intensity of infection, and average number of larvae per mouse between the landscapes, and among forest patches within the highly fragmented agricultural landscape. Prevalence, intensity of infection, and average number of larvae were significantly higher in the highly fragmented landscape. Within the agricultural landscape, regression models predicted probability of infection, intensity of infection, and average number of larvae per mouse per patch as functions of forest patch area and isolation. We conclude that positive responses of raccoons to agriculturally induced fragmentation of forests have resulted in increased encounter rates between white-footed mice and infective stages of B . procyonis between and within landscapes, resulting in increased transmission of the parasite to intermediate hosts.     

Design and implementation of a qualitative simulation model of lambda phage infection

MOTIVATION: Molecular biology databases hold a large number of empirical facts about many different aspects of biological entities. That data is static in the sense that one cannot ask a database 'What effect has protein A on gene B?' or 'Do gene A and gene B interact, and if so, how?'. Those questions require an explicit model of the target organism. Traditionally, biochemical systems are modelled using kinetics and differential equations in a quantitative simulator. For many biological processes however, detailed quantitative information is not available, only qualitative or fuzzy statements about the nature of interactions. RESULTS: We designed and implemented a qualitative simulation model of lambda phage growth control in Escherichia coli based on the existing simulation environment QSim. Qualitative reasoning can serve as the basis for automatic transformation of contents of genomic databases into interactive modelling systems that can reason about the relations and interactions of biological entities.      

When dispersal fails: unexpected genetic separation in Gibraltar macaques (Macaca sylvanus)

Barbary macaques (Macaca sylvanus), now restricted in the wild to a few isolated forested areas of Morocco and Algeria, are present in a free‐ranging colony on Gibraltar. For many decades, the Gibraltar colony was exposed to multiple bottlenecks due to highly nonrandom removal of animals, followed by repeated introductions of animals from North Africa. Moreover, because of complete isolation, Gibraltar's several social groups of macaques provide an ideal system to study the genetic consequences of dispersal in cercopithecines in situ. Predictions of genetic consequences due to male‐biased dispersal in cercopithecines will be different for autosomal and maternally inherited genetic markers, such as the control region of the mitochondrial DNA. We used a panel of 14 highly polymorphic microsatellite loci and part of the hypervariable region I of the mitochondrial control region to estimate genetic structure between five social groups in Gibraltar. Surprisingly, for autosomal markers, both classical summary statistics and an individual‐based method using a Bayesian framework detected significant genetic structure between social groups in Gibraltar, despite much closer proximity than wild Algerian and Moroccan populations. Mitochondrial data support this finding, as a very substantial portion of the total genetic variation (70.2%) was found between social groups. Using two Bayesian approaches, we likewise identified not only a small number of male first‐generation immigrants (albeit less than expected for cercopithecines) but also unexpectedly a few females. We hypothesize that the culling of males that are more likely to disperse might slow down genetic homogenization among neighbouring groups, but may also and more perversely produce selection on certain behavioural traits. This may have important repercussions for conservation, as it could lead to evolutionary changes that are not due to inbreeding or genetic drift.     

Distribution and prevalence of Echinococcus multilocularis in wild predators in Nebraska,Kansas, and Wyoming

To further determine the distribution and prevalence of Echinococcus multilocularis in the central United States, 245 wild canids (125 red foxes, 120 coyotes) and 33 bobcats were collected from Nebraska, Kansas, and Wyoming and examined for this parasite. Animals examined included 11 red foxes from the western panhandle of Nebraska; 5 red foxes and 30 coyotes from southern Nebraska; 56 red foxes and 1 coyote from northeastern Nebraska; 20 red foxes, 63 coyotes, and 13 bobcats from northern Kansas; 2 red foxes, 26 coyotes, and 20 bobcats from southern Kansas; and 31 red foxes from east-central Wyoming. Of these, 27 of 72 (37.5%) red foxes from Nebraska were positive, including 2 of 11 (18.2%) from the western panhandle and 25 of 56 (44.6%) from the northeastern part of the state. Mean intensity of infection was 282 worms (range, 1-5,150). New distribution records were established for E. multilocularis in western Nebraska as well as for several northeastern counties. These findings support previous estimates that the southernmost front of the parasite's range extends along the southern border of Wyoming, eastward through central Nebraska and central Illinois into Indiana and Ohio.     

Ocular, naso-maxillary, and neural anomalies in raccoons, Procyon lotor (L.)

Congenital ocular and related anomalies were studied in two unrelated young raccoons. One animal was anophthalmic and had severe anomalies of the central nervous system, consisting of meningoencephalocele, pachygyria, hydranencephaly, cerebellar cavitation, syringomyelia, and other defects. A second animal was microphthalmic with congenital defects of the nose, maxilla and teeth. Ocular lesions were severe and included chorioretinal coloboma, retinal folds, disorganized neuroectodermal cell layers, spherophakia, cataract and other defects. The nose had unilateral abnormal epithelium, hair follicles, sweat glands and sebaceous glands, and a lack of parietal cartilage on the affected side.     

Pathology of pentastomid infections (Sebekia mississippiensis) in fish

Differential pathogenesis was observed in two species of fish naturally infected with the pentastome Sebekia mississippiensis. Mosquitofish (Gambusia affinis) showed a mild inflammatory response to developing nymphs, whereas swordtails (Xiphophorus helleri) had an extensive granulomatous inflammatory reaction with accompanying hemorrhage, myositis, and myodegeneration. This suggested that certain species of tropical fish reared in the southeastern United States may be at risk to potentially harmful infections with this parasite.