ProfileGrids as a new visual representation of large multiple sequence alignments: a case study of the RecA protein family

Background  

Multiple sequence alignments are a fundamental tool for the comparative analysis of proteins and nucleic acids. However, large data sets are no longer manageable for visualization and investigation using the traditional stacked sequence alignment representation.     

Creatine supplementation during college football training does not increase the incidence of cramping or injury

The purpose of this study was to examine the effects of creatine supplementation on the incidence of injury observed during 3-years of NCAA Division IA college football training and competition. In an open label manner, athletes participating in the 1998–2000 football seasons elected to take creatine or non-creatine containing supplements following workouts/practices. Subjects who decided to take creatine were administered 15.75 g of creatine for 5 days followed by ingesting an average of 5 g/day thereafter administered in 5–10 g doses. Creatine intake was monitored and recorded by research assistants throughout the study and ranged between 34–56% of players during the course of the study. Subjects practiced or played in environmental conditions ranging from 8–40°C (mean 24.7 ± 9°C) and 19–98% relative humidity (49.3 ± 17%). Injuries treated by the athletic training staff were recorded and categorized as cramping, heat/dehydration, muscle tightness, muscle strains/pulls, non-contact joint injuries, contact injuries, and illness. The number of missed practices due to injury/illness was also recorded. Data are presented as the total number of treated injuries for creatine users/total injuries observed and percentage occurrence rate of injuries for creatine users for all seasons. The incidence of cramping (37/96, 39%), heat/dehydration (8/28, 36%), muscle tightness (18/42, 43%), muscle pulls/strains (25/51, 49%), non-contact joint injuries (44/132, 33%), contact injuries (39/104, 44%), illness (12/27, 44%), number of missed practices due to injury (19/41, 46%), players lost for the season (3/8, 38%), and total injuries/missed practices (205/529, 39%) were generally lower or proportional to the creatine use rate among players. Creatine supplementation does not appear to increase the incidence of injury or cramping in Division IA college football players.     

Historical colonization and demography of the Mediterranean damselfish, Chromis chromis

The desiccation of the Mediterranean Sea during the Messinian Salinity Crisis 6.0-5.3 million years ago (Ma), caused a major extinction of the marine ichthyofauna of the Mediterranean. This was followed by an abrupt replenishment of the Mediterranean from the Atlantic after the opening of the Strait of Gibraltar. In this study, we combined demographic and phylogeographic approaches using mitochondrial and nuclear DNA markers to test the alternative hypotheses of where (Atlantic or Mediterranean) and when (before or after the Messinian Salinity Crisis) speciation occurred in the Mediterranean damselfish, Chromis chromis. The closely related geminate transisthmian pair Chromis multilineata and Chromis atrilobata was used as a way of obtaining an internally calibrated molecular clock. We estimated C. chromis speciation timing both by determining the time of divergence between C. chromis and its Atlantic sister species Chromis limbata (0.93-3.26 Ma depending on the molecular marker used, e.g. 1.23-1.39 Ma for the control region), and by determining the time of coalescence for C. chromis based on mitochondrial control region sequences (0.14-0.21 Ma). The time of speciation of C. chromis was always posterior to the replenishment of the Mediterranean basin, after the Messinian Salinity Crisis. Within the Mediterranean, C. chromis population structure and demographic characteristics revealed a genetic break at the Peloponnese, Greece, with directional and eastbound gene flow between western and eastern groups. The eastern group was found to be more recent and with a faster growing population (coalescent time = 0.09-0.13 Ma, growth = 485.3) than the western group (coalescent time = 0.13-0.20 Ma, growth = 325.6). Our data thus suggested a western origin of C. chromis, most likely within the Mediterranean. Low sea water levels during the glacial periods, the hydrographic regime of the Mediterranean and dispersal restriction during the short pelagic larval phase of C. chromis (18-19 days) have probably played an important role in C. chromis historical colonization.     

Interspecific Utility of Microsatellites in Fish: A Case Study of (CT)n and (GT)n Markers in the Shanny Lipophrys pholis (Pisces: Blenniidae) and Their Use in Other Blennioidei

We report the development of new microsatellite markers that can be used for population analyses in the shanny Lipophrys pholis. The procedure involved the construction of a microsatellite-enriched genomic bank. Five (GT)_n and (CT)_n microsatellites have been characterized, four of which are polymorphic. The analysis of one population allowed us to verify their usefulness as markers in population studies. Moreover, interspecific amplifications have been performed using primers defined in other species to amplify Lipophrys pholis, or using the primers defined in Lipophrys pholis to amplify other species. We use these results to discuss the hypothesis that microsatellites are highly conserved in fish. Received May 13, 1999; accepted October 28, 1999.     

Effects of conjugated linoleic acid supplementation during resistance training on body composition,bone density,strength, and selected hematological markers

Conjugated linoleic acids (CLA) are essential fatty acids that have been reported in animal studies to decrease catabolism, promote fat loss, increase bone density, enhance immunity, and serve as an antiatherogenic and anticarcinogenic agent. For this reason, CLA has been marketed as a supplement to promote weight loss and general health. CLA has also been heavily marketed to resistance-trained athletes as a supplement that may help lessen catabolism, decrease body fat, and promote greater gains in strength and muscle mass during training. Although basic research is promising, few studies have examined whether CLA supplementation during training enhances training adaptations and/or affects markers of health. This study evaluated whether CLA supplementation during resistance training affects body composition, strength, and/or general markers of catabolism and immunity. In a double-blind and randomized manner, 23 experienced, resistance-trained subjects were matched according to body mass and training volume and randomly assigned to supplement their diet with 9 g;pdd(-1) of an olive oil placebo or 6 g;pdd(-1) of CLA with 3 g;pdd(-1) of fatty acids for 28 days. Prior to and following supplementation, fasting blood samples, total body mass, and dual-energy X-ray absorptiometry (DEXA) determined body composition, and isotonic bench press and leg press 1 repetition maximums (1RMs) were determined. Results revealed that although some statistical trends were observed with moderate to large effect sizes, CLA supplementation did not significantly affect (p > 0.05) changes in total body mass, fat-free mass, fat mass, percent body fat, bone mass, strength, serum substrates, or general markers of catabolism and immunity during training. These findings indicate that CLA does not appear to possess significant ergogenic value for experienced resistance-trained athletes.     

Development and Characterization of Nisin Nanoparticles as Potential Alternative for the Recurrent Vaginal Candidiasis Treatment

The aim of this work was the development and characterization of nisin-loaded nanoparticles and the evaluation of its potential antifungal activity. Candidiasis is a fungal infection caused by Candida sp. considered as one of the major public health problem currently. The discovery of antifungal agents that present a reduced or null resistance of Candida sp. and the development of more efficient drug release mechanisms are necessary for the improvement of candidiasis treatment. Nisin, a bacteriocin commercially available for more than 50 years, exhibits antibacterial action in food products with potential antifungal activity. Among several alternatives used to modulate antifungal activity of bacteriocins, polymeric nanoparticles have received great attention due to an effective drug release control and reduction of therapeutic dose, besides the minimization of adverse effects by the preferential accumulation in specific tissues. The nisin nanoparticles were prepared by double emulsification and solvent evaporation methods. Nanoparticles were characterized by dynamic light scattering, zeta potential, Fourier transform infrared, X-ray diffraction, differential scanning calorimetry, and scanning electron microscopy. Antifungal activity was accessed by pour plate method and cell counting using Candida albicans strains. The in vitro release profile and in vitro permeation studies were performed using dialysis bag method and pig vaginal mucosa in Franz diffusion cell, respectively. The results revealed nisin nanoparticles (300 nm) with spherical shape and high loading efficiency (93.88?±?3.26%). In vitro test results suggest a promising application of these nanosystems as a prophylactic agent in recurrent vulvovaginal candidiasis and other gynecological diseases.     

A comparative study of territoriality in intertidal and subtidal blennioids (Teleostei, Blennioidei)

This paper presents a comparative analysis of territoriality in three intertidal (Lipophrys pholis, Coryphoblennius galerita, Salaria pavo) and two subtidal (Tripterygion delaisi, Parablennius pilicornis) blennioid fishes. Focal-animal observations of males guarding eggs showed that: (i) intertidal species had smaller territories that were less frequently patrolled; (ii) in subtidal species feeding was limited to the territory, while in intertidal fishes a substantial proportion of the feeding acts occurred outside the defended area; (iii) intertidal species spent less time out of the nest and showed a lower level of locomotory activity; (iv) subtidal species were subjected to a higher number of territorial intrusions with more species intruding their territory, some of them potential egg predators; (v) subtidal species performed several water column displays that played a significant role in courtship, while in intertidal fishes these displays are almost absent. Signalling without the presence of a female was almost absent in intertidal species. It is argued that intertidal fishes minimize the time spent out of the nest and the loss of contact with the substrate, features that may be of high survival value in conditions of strong turbulence. Although intertidal species have a reduced time available for feeding, this may be compensated by lower levels of locomotory activity, territorial defense and risk of egg predation. This revised version was published online in August 2006 with corrections to the Cover Date.     

Androgenization of Dominant Males in a Cichlid Fish: Androgens Mediate the Social Modulation of Sexually Dimorphic Traits

We present data on the relationship between social status and male secondary sex traits, both morphological and ethological, in Oreochromis mossambicus at the onset of sexual maturation. There is a differential expression of morphological (dorsal fin height, anal fin height, mandible width and premaxilla length) and behavioural (nuptial coloration, per cent time defending a territory, spawning pit volume, pit hovering and courtship rate) traits according to social status, with dominants presenting the highest expression of these dimorphic traits. Social status also affects the development of the genital papillae, which is considered to be a good predictor of androgen levels in cichlid fishes. The results support a causal model in which social status modulate androgen levels that in turn modulate the expression of behavioural and morphological male traits.     

Juvenile recruitment, growth and maturation of Lipophrys pholis (Pisces: Blenniidae), from the west coast of Portugal

Data on the juvenile recruitment, growth and size at maturation of Lipophrys pholis in Portuguese waters are compared with the information available on the biology of this species at higher latitudes. In Portugal, recruitment extends for a much longer period, young fish grow faster and sexual maturation is earlier than at higher latitudes. There is a delay of 2–3 months between the appearance of the first eggs on the shore and the recruitment of the first juveniles to the pools.     

Breeding ecology and nest aggregations in a population of Salaria pavo (Pisces: Blenniidae) in an area where nest sites are very scarce

In this paper we present data on the breeding ecology and patterns of nest aggregation in a population of Salaria pavo (Pisces: Blenniidae), in an area where hard substrates are very scarce. The study site was at Ria Formosa, an extensive littoral lagoon on the south coast of Portugal. The only hard materials available are bricks, tiles, stones and debris that clam culturists use to delimit their fields. The males of S. pavo establish nests intertidally in the holes of the bricks where they guard the eggs. Data were collected at low tide inspections of these artificial ridges and underwater behavioural observations during high tide. The main results are: (i) the same male can establish sequentially more than one nest in the same breeding season; the number of males that stay within the bricks increases before the start of the breeding season and declines towards its end; (ii) there is a large excess of mature males that do not establish nests and they are significantly smaller than the nesting males, suggesting very strong competition for nest sites; (iii) the nests of several males occur in adjacent holes of the same brick, sometimes being entirely surrounded by other nests. Thus, in this population, there is virtually no defended territory around the nest, a situation not known for other blenniid species. This pattern of nest aggregation implies both strong competition among males and reduction of aggression between neighbour parental fishes. This can be explained by the extreme scarcity and spatial distribution of available nest sites.