Complete nucleotide sequence, genomic organization and phylogenetic analysis of Citrus leprosis virus cytoplasmic type

The complete nucleotide sequence of the genomic RNA 1 (8745 nt) and RNA 2 (4986 nt) of Citrus leprosis virus cytoplasmic type (CiLV-C) was determined using cloned cDNA. RNA 1 contains two open reading frames (ORFs), which correspond to 286 and 29 kDa proteins. The 286 kDa protein is a polyprotein putatively involved in virus replication, which contains four conserved domains: methyltransferase, protease, helicase and polymerase. RNA 2 contains four ORFs corresponding to 15, 61, 32 and 24 kDa proteins, respectively. The 32 kDa protein is apparently involved in cell-to-cell movement of the virus, but none of the other putative proteins exhibit any conserved domain. The 5' regions of the two genomic RNAs contain a 'cap' structure and poly(A) tails were identified in the 3'-terminals. Sequence analyses and searches for structural and non-structural protein similarities revealed conserved domains with members of the genera Furovirus, Bromovirus, Tobravirus and Tobamovirus, although phylogenetic analyses strongly suggest that CiLV-C is a member of a distinct, novel virus genus and family, and definitely demonstrate that it does not belong to the family Rhabdoviridae, as previously proposed. Based on these results it was proposed that Citrus leprosis virus be considered as the type member of a new genus of viruses, Cilevirus.

PrimerSNP: a web tool for whole-genome selection of allele-specific and common primers of phylogenetically-related bacterial genomic sequences

Background: The increasing number of genomic sequences of bacteria makes it possible to select unique SNPs of a particular strain/species at the whole genome level and thus design specific primers based on the SNPs. The high similarity of genomic sequences among phylogenetically-related bacteria requires the identification of the few loci in the genome that can serve as unique markers for strain differentiation. PrimerSNP attempts to identify reliable strain-specific markers, on which specific primers are designed for pathogen detection purpose.Results: PrimerSNP is an online tool to design primers based on strain specific SNPs for multiple strains/species of microorganisms at the whole genome level. The allele-specific primers could distinguish query sequences of one strain from other homologous sequences by standard PCR reaction. Additionally, PrimerSNP provides a feature for designing common primers that can amplify all the homologous sequences of multiple strains/species of microorganisms. PrimerSNP is freely available at http://cropdisease.ars.usda.gov/similar to primer.Conclusion: PrimerSNP is a high-throughput specific primer generation tool for the differentiation of phylogenetically-related strains/species. Experimental validation showed that this software had a successful prediction rate of 80.4 - 100% for strain specific primer design.

Use of 37% carbamide peroxide in the walking bleach technique: A case report

Dental bleaching represents an effective, conservative, and relatively low-cost method for improving the appearance of discolored pulpless teeth. Among the bleaching techniques, the walking bleach technique with sodium perborate associated with water or hydrogen peroxide stands out because of its esthetic results and safety. A modified walking bleach technique with the use of 37% carbamide peroxide as the bleaching agent is presented. Additionally, the adverse effects of dental bleaching in the following restorative procedures are discussed, showing the advantages with the use of 37% carbamide peroxide.

The plant energy-dissipating mitochondrial systems: Depicting the genomic structure and the expression profiles of the gene families of uncoupling protein and alternative oxidase in monocots and dicots

The simultaneous existence of alternative oxidases and uncoupling proteins in plants has raised the question as to why plants need two energy-dissipating systems with apparently similar physiological functions. A probably complete plant uncoupling protein gene family is described and the expression profiles of this family compared with the multigene family of alternative oxidases in Arabidopsis thaliana and sugarcane (Saccharum sp.) employed as dicot and monocot models, respectively. In total, six uncoupling protein genes, AtPUMP1-6, were recognized within the Arabidopsis genome and five (SsPUMP1-5) in a sugarcane EST database. The recombinant AtPUMP5 protein displayed similar biochemical properties as AtPUMP1. Sugarcane possessed four Arabidopsis AOx1-type orthologues (SsAOx1a-1d); no sugarcane orthologue corresponding to Arabidopsis AOx2-type genes was identified. Phylogenetic and expression analyses suggested that AtAOx1d does not belong to the AOx1-type family but forms a new (AOx3-type) family. Tissue-enriched expression profiling revealed that uncoupling protein genes were expressed more ubiquitously than the alternative oxidase genes. Distinct expression patterns among gene family members were observed between monocots and dicots and during chilling stress. These findings suggest that the members of each energy-dissipating system are subject to different cell or tissue/organ transcriptional regulation. As a result, plants may respond more flexibly to adverse biotic and abiotic conditions, in which oxidative stress is involved. © The Author [2006]. Published by Oxford University Press [on behalf of the Society for Experimental Biology]. All rights reserved.

Optimal clone identifier for genomic shotgun libraries: OC Identifier tool

In DNA microarray experiments, the gene fragments that are spotted on the slides are usually obtained by the synthesis of specific oligonucleotides that are able to amplify genes through PCR. Shotgun library sequences are an alternative to synthesis of primers for the study of each gene in the genome. The possibility of putting thousands of gene sequences into a single slide allows the use of shotgun clones in order to proceed with microarray analysis without a completely sequenced genome. We developed an OC Identifier tool (optimal clone identifier for genomic shotgun libraries) for the identification of unique genes in shotgun libraries based on a partially sequenced genome; this allows simultaneous use of clones in projects such as transcriptome and phylogeny studies, using comparative genomic hybridization and genome assembly. The OC Identifier tool allows comparative genome analysis, biological databases, query language in relational databases, and provides bioinformatics tools to identify clones that contain unique genes as alternatives to primer synthesis. The OC Identifier allows analysis of clones during the sequencing phase, making it possible to select genes of interest for construction of a DNA microarray. ©FUNPEC-RP.

Application of molecular markers on genetic improvement and reproduction in the post-genomic Era: Emerging biotechnologies and perspectives in livestock

Background: New challenges are rising in the animal protein market, and one of the main world challenges is to produce more in shorter time, with better quality and in a sustainable way. Brazil is the largest beef exporter in volume hence the factors affecting the beef meat chain are of major concern in countrýs economy. An emerging class of biotechnological approaches, the molecular markers, is bringing new perspectives to face these challenges, particularly after the publication of the first complete livestock genome (bovine), which has triggered a massive initiative to put in practice the benefits of the so called the Post-Genomic Era. Review: This article aimed at showing the directions and insights in the application of molecular markers on livestock genetic improvement and reproduction as well at organizing the progress so far, pointing some perspectives of these emerging technologies in Brazilian ruminant production context. An overview on the nature of the main molecular markers explored in ruminant production is provided, which describes the molecular bases and detection approaches available for microsatellites (STR) and single nucleotide polymorphisms (SNP). A topic is dedicated to review the history of association studies between markers and important trait variation in livestock, showing the timeline starting on quantitative trait loci (QTL) identification using STR markers and ending in high resolution SNP panels to proceed whole genome scans for phenotype/genotype association. Also the article organizes this information to reveal how QTL prospection using STR could open ground to the feasibility of marker-assisted selection and why this approach is quickly being replaced by studies involving the application of genome-wide association using SNP research in a new concept called genomic selection. Conclusion: The world's scientific community is dedicating effort and resources to apply SNP information in livestock selection through the development of high density panels for genomic association studies, connecting molecular genetic data with phenotypes of economic interest. Once generated, this information can be used to take decisions in genetic improvement programs by selecting animals with the assistance of molecular markers.

Effects of 12-week overground walking training at ventilatory threshold velocity in type 2 diabetic women

This study analyzed the effects of overground walking training at ventilatory threshold (VT) velocity on glycaemic control, body composition, physical fitness and lipid profile in DM2 women. Nineteen sedentary patients were randomly assigned to a control group (CG; n=10, 55.9±2.2 years) or a trained group (TG; n=9, 53.4±2.3 years). Both groups were subjected to anthropometric measures, a 12-h fasting blood sampling and a graded treadmill exercise test at baseline and after a 12-week period, during which TG followed a training program involving overground walking at VT velocity for 20-60min/session three times/week. Significant group×time interactions (P<0.05) in glycated hemoglobin (HbA1c), body mass, body mass index (BMI), peak oxygen uptake (VO 2peak) and exercise duration were observed as effects of training exercise, whereas intervention did not induced significant changes (P>0.05) in fasting blood glucose, submaximal fitness parameters and lipid profile. Our results suggest that overground walking training at VT velocity improves long term glycaemic control, body composition and exercise capacity, attesting for the relevance of this parameter as an effective strategy for the exercise intensity prescription in DM2 population. © 2011 Elsevier B.V.

Effects of fatigue induced by prolonged gait when walking on the elderly

Purpose. Fatigue has been pointed as a fall risk in the elderly; however, the effects of prolonged gait on neuromuscular recruitment and on its pattern remain unknown. The aim of this study was to evaluate the effects of prolonged gait on neuromuscular recruitment levels and spatial-temporal gait variables. Methods. Eight healthy older women (age: 72.63 ± 6.55 years) walked at their preferred walking speed for twenty minutes on a treadmill. The Root Mean Square (RMS) from the vastus-lateralis, femoral biceps, tibialis anterior and lateral gastrocnemius muscles were determined at the first and last minute of the test during the moments of Heel Strike (HS), Terminal Stance and Terminal Swing (TS). In addition, coactivation in the knee and ankle as well as the stride cadence and length were measured in the test. The two RMS data (taken at the first and last minute) were compared by means of a Student's t-test. Results. Twenty minutes of walking induced fatigue in the subjects, as observed through an increase in RMS, notably during the HS and TS. Coactivation was also influenced by the prolonged gait test. The only gait phase where a risk of falling was enhanced was the HS. Nonetheless, subjects developed strategies to maintain a safe motor pattern, which was evidenced by an increase in stride length and a decrease in stride cadence. Conclusion. Tests lasting just twenty minutes on a treadmill were enough to induce fatigue in older adults. However, the level of fatigue was not enough to present a danger or fall risk to elderly individuals.

Aerobic fitness evaluation during walking tests identifies the maximal lactate steady state

Objective. The aim of this study was to verify the possibility of lactate minimum (LM) determination during a walking test and the validity of such LM protocol on predicting the maximal lactate steady-state (MLSS) intensity. Design. Eleven healthy subjects (24.2 ± 4.5 yr; 74.3 ± 7.7 kg; 176.9 ± 4.1 cm) performed LM tests on a treadmill, consisting of walking at 5.5 km h -1 and with 20-22% of inclination until voluntary exhaustion to induce metabolic acidosis. After 7 minutes of recovery the participants performed an incremental test starting at 7% incline with increments of 2% at each 3 minutes until exhaustion. A polynomial modeling approach (LMp) and a visual inspection (LMv) were used to identify the LM as the exercise intensity associated to the lowest [bLac] during the test. Participants also underwent to 24 constant intensity tests of 30 minutes to determine the MLSS intensity. Results. There were no differences among LMv (12.6 ± 1.7 %), LMp (13.1 ± 1.5 %), and MLSS (13.6 ± 2.1 %) and the Bland and Altman plots evidenced acceptable agreement between them. Conclusion. It was possible to identify the LM during walking tests with intensity imposed by treadmill inclination, and it seemed to be valid on identifying the exercise intensity associated to the MLSS. Copyright © 2012 Guilherme Morais Puga et al.

How bioinformatics enables livestock applied sciences in the genomic era

This review paper presents the three main approaches currently used in livestock genomic sciences where the bioinfomatics plays a critical role. They are named as Genomic Selection (GS), Genome Wide Association Study (GWAS) and Signatures of Selection (SS). The subsides for the construction of this article were generated in a current project (started in 2011), so called Zebu Genome Consortium (ZGC), which joins researchers from different institutions and countries, aiming to scientifically explore genomic information of Bos taurus indicus cattle breeds and deliver useful information to breeders and academic community, specially from the tropical regions of the world. © 2012 Springer-Verlag.

Adaptive walking in alzheimer's disease

The aim of this study is to analyze dual-task effects on free and adaptive gait in Alzheimer's disease (AD) patients. Nineteen elders with AD participated in the study. A veteran neuropsychiatrist established the degree of AD in the sample. To determine dual-task effects on free and adaptive gait, patients performed five trials for each experimental condition: free and adaptive gait with and without a dual-task (regressive countdown). Spatial and temporal parameters were collected through an optoelectronic tridimensional system. The central stride was analyzed in free gait, and the steps immediately before (approaching phase) and during the obstacle crossing were analyzed in adaptive gait. Results indicated that AD patients walked more slowly during adaptive gait and free gait, using conservative strategies when confronted either with an obstacle or a secondary task. Furthermore, patients sought for stability to perform the tasks, particularly for adaptive gait with dual task, who used anticipatory and online adjustments to perform the task. Therefore, the increase of task complexity enhances cognitive load and risk of falls for AD patients. © 2012 Diego Orcioli-Silva et al.

Chromosome mapping of repetitive sequences in Anostomidae species: Implications for genomic and sex chromosome evolution

Background: Members of the Anostomidae family provide an interesting model system for the study of the influence of repetitive elements on genome composition, mainly because they possess numerous heterochromatic segments and a peculiar system of female heterogamety that is restricted to a few species of the Leporinus genus. The aim of this study was to isolate and identify important new repetitive DNA elements in Anostomidae through restriction enzyme digestion, followed by cloning, characterisation and chromosome mapping of this fragment. To identify repetitive elements in other Leporinus species and expand on studies of repetitive elements in Anostomidae, hybridisation experiments were also performed using previously described probes of LeSpeI repetitive elements. Results: The 628-base pair (bp) LeSpeII fragment was hybridised to metaphase cells of L. elongatus individuals as well as those of L. macrocephalus, L. obtusidens, L. striatus, L. lacustris, L. friderici, Schizodon borellii and S. isognathus. In L. elongatus, both male and female cells contained small clusters of LeSpeII repetitive elements dispersed on all of the chromosomes, with enrichment near most of the terminal portions of the chromosomes. In the female sex chromosomes of L. elongatus (Z2,Z2/W1W 2), however, this repeated element was absent. In the remaining species, a dispersed pattern of hybridisation was observed on all chromosomes irrespective of whether or not they were sex chromosomes. The repetitive element LeSpeI produced positive hybridisations signals only in L. elongatus, L. macrocephalus and L. obtusidens, i.e., species with differentiated sex chromosomes. In the remaining species, the LeSpeI element did not produce hybridisation signals. Conclusions: Results are discussed in terms of the effects of repetitive sequences on the differentiation of the Anostomidae genome, especially with respect to sex chromosome evolution. LeSpeII showed hybridisation patterns typical of Long Interspersed Elements (LINEs). The differential distribution of this element may be linked to sex chromosome differentiation in L. elongatus species. The relationship between sex chromosome specificity and the LeSpeI element is confirmed in the species L. elongatus, L. macrocephalus and L. obtusidens. © 2012 da Silva et al.; licensee BioMed Central Ltd.

Association between energy cost of walking, muscle activation, and biomechanical parameters in older female fallers and non-fallers

Objective: To determine the nervous activation, muscle strength, and biomechanical parameters that influence the cost of walking in older fallers and non-fallers. Methods: Maximal voluntary isokinetic torque was measured for the hip, knee and ankle of older women. Oxygen consumption was measured at rest and during 8 min of walking at self-selected speed. An additional minute of walking was performed to collect kinematic variables and the electromyographic signal of trunk, hip, knee, and ankle muscles, which was analyzed by the linear envelope. Cost of walking was calculated by subtracting resting body mass-normalized oxygen consumption from walking body mass-normalized oxygen consumption. Stride time and length, and ankle and hip range of motion were calculated from kinematic data. Findings: Older adult fallers had 28% lower knee extensor strength (p = 0.02), 47% lower internal oblique activation at heel contact (p = 0.03), and higher coactivation between tibialis anterior and gastrocnemius lateralis in each of the gait phases (p < 0.05). For fallers, a higher activation of gluteus maximus was associated with a higher cost of walking (r = 0.55, p < 0.05 and r = 0.71, p < 0.01, before and after heel contact, respectively). For non-fallers, an association between cost of walking and age (r = 0.60, p = 0.01) and cost of walking and thigh muscle coactivation (r = 0.53, p = 0.01) existed. Interpretation: This study demonstrated that there may be links between lower-extremity muscle weakness, muscle activation patterns, altered gait, and increased cost of walking in older fallers. © 2013 Elsevier Ltd. All rights reserved.

Coordination of spinal motion in the transverse and frontal planes during walking in people with and without recurrent low back pain

STUDY DESIGN. Observational cohort study. OBJECTIVE. To investigate spinal coordination during preferred and fast speed walking in pain-free subjects with and without a history of recurrent low back pain (LBP). SUMMARY OF BACKGROUND DATA. Dynamic motion of the spine during walking is compromised in the presence of back pain (LBP), but its analysis often presents some challenges. The coexistence of significant symptoms may change gait because of pain or adaptation of the musculoskeletal structures or both. A history of LBP without the overlay of a current symptomatic episode allows a better model in which to explore the impact on spinal coordination during walking. METHODS. Spinal and lower limb segmental motions were tracked using electromagnetic sensors. Analyses were conducted to explore the synchrony and spatial coordination of the segments and to compare the control and subjects with LBP. RESULTS. We found no apparent differences between the groups for either overall amplitude of motion or most indicators of coordination in the lumbar region; however, there were significant postural differences in the mid-stance phase and other indicators of less phase locking in controls compared with subjects with LBP. The lower thoracic spinal segment was more affected by the history of back pain than the lumbar segment. CONCLUSION. Although small, there were indicators that alterations in spinal movement and coordination in subjects with recurrent LBP were due to adaptive changes rather than the presence of pain. © 2013, Lippincott Williams & Wilkins.