AtPIN: Arabidopsis thaliana Protein Interaction Network

Background: Protein-protein interactions (PPIs) constitute one of the most crucial conditions to sustain life in living organisms. To study PPI in Arabidopsis thaliana we have developed AtPIN, a database and web interface for searching and building interaction networks based on publicly available protein-protein interaction datasets. Description: All interactions were divided into experimentally demonstrated or predicted. The PPIs in the AtPIN database present a cellular compartment classification (C(3)) which divides the PPI into 4 classes according to its interaction evidence and subcellular localization. It has been shown in the literature that a pair of genuine interacting proteins are generally expected to have a common cellular role and proteins that have common interaction partners have a high chance of sharing a common function. In AtPIN, due to its integrative profile, the reliability index for a reported PPI can be postulated in terms of the proportion of interaction partners that two proteins have in common. For this, we implement the Functional Similarity Weight (FSW) calculation for all first level interactions present in AtPIN database. In order to identify target proteins of cytosolic glutamyl-tRNA synthetase (Cyt-gluRS) (AT5G26710) we combined two approaches, AtPIN search and yeast two-hybrid screening. Interestingly, the proteins glutamine synthetase (AT5G35630), a disease resistance protein (AT3G50950) and a zinc finger protein (AT5G24930), which has been predicted as target proteins for Cyt-gluRS by AtPIN, were also detected in the experimental screening. Conclusions: AtPIN is a friendly and easy-to-use tool that aggregates information on Arabidopsis thaliana PPIs, ontology, and sub-cellular localization, and might be a useful and reliable strategy to map protein-protein interactions in Arabidopsis. AtPIN can be accessed at http://bioinfo.esalq.usp.br/atpin.

Measurement of banana green life

Introduction. This protocol aims at measuring the storage life potential of banana fruit, and at determining the physiological age of fruit. The principle, key advantages, starting plant material, time required and expected results are presented. Materials and methods. This part describes the required laboratory materials and the five steps necessary for calculating the banana green life duration, which corresponds to the number of days between the fruit harvest and climacteric crisis. Results. The measurement of O-2 and CO2 concentrations allows one to detect the climacteric peak which marks the end of the banana green life.

The Borg Scale as an Important Tool of Self-Monitoring and Self-Regulation of Exercise Prescription in Heart Failure Patients During Hydrotherapy - A Randomized Blinded Controlled Trial

Background: The Borg Scale may be a useful tool for heart failure patients to self-monitor and self-regulate exercise on land or in water (hydrotherapy) by maintaining the heart rate (HR) between the anaerobic threshold and respiratory compensation point. Methods and Results: Patients performed a cardiopulmonary exercise test to determine their anaerobic threshold/respiratory compensation points. The percentage of the mean HR during the exercise session in relation to the anaerobic threshold HR (%EHR-AT), in relation to the respiratory compensation point (%EHR-RCP), in relation to the peak HR by the exercise test (%EHR-Peak) and in relation to the maximum predicted HR (%EHR-Predicted) was calculated. Next, patients were randomized into the land or water exercise group. One blinded investigator instructed the patients in each group to exercise at a level between ""relatively easy and slightly tiring"". The mean HR throughout the 30-min exercise session was recorded. The %EHR-AT and %EHR-Predicted did not differ between the land and water exercisegroups, but they differed in the %EHR-RCP (95 +/- 7 to 86 +/- 7. P<0.001) and in the %EHR-Peak (85 +/- 8 to 78 +/- 9, P=0.007). Conclusions: Exercise guided by the Borg scale maintains the patient's HR between the anaerobic threshold and respiratory compensation point (ie, in the exercise training zone). (Circ J 2009; 73: 1871-1876)

Half-Pringle Maneuver: A Useful Tool in Laparoscopic Liver Resection

Introduction: Laparoscopic liver resections are becoming a common procedure, and bleeding remains the major concern during parenchymal transection. Total vascular inflow occlusion can be performed, but ischemic reperfusion injuries can lead to postoperative morbidity. On the other hand, hemihepatic inflow occlusion, leading to hemiliver ischemia, decreases the amount of liver parenchyma submitted to reperfusion damage and offers the advantage of reduced blood loss. Objective: The aim of this work was to describe our experience with laparoscopic the half-Pringle maneuver for segmentar or nonanatomic liver resctions. Patients and Methods: Eight patients submitted to laparoscopic liver resection in a single tertiary center. Results: There were 5 women and 3 men with a mean age of 40.2 years (range, 26-54). Mean tumor size was 4.1 cm (range, 2.6-6.0), and mean hospital stay was 3.1 days (1-5). There were 3 liver adenomas, 2 hepatocellular carcinomas, 1 metastatic melanoma, 1 metastatic colorectal carcinoma, and 1 peripheral colangiocarcinoma. No postoperative complications or mortalities were observed. Conclusions: Results demonstrate that laparoscopic liver resection with the half-Pringle maneuver is feasible and safe and may be included in the technical armamentarium of laparoscopic liver resections for a selected group of patients.

Suppression subtractive hybridization analysis reveals expression of conserved and novel genes in male accessory glands of the ant Leptothorax gredleri

Background: During mating, insect males eject accessory gland proteins (Acps) into the female genital tract. These substances are known to affect female post-mating behavior and physiology. In addition, they may harm the female, e. g., in reducing its lifespan. This is interpreted as a consequence of sexual antagonistic co-evolution. Whereas sexual conflict abounds in non-social species, the peculiar life history of social insects (ants, bees, wasps) with lifelong pair-bonding and no re-mating aligns the reproductive interests of the sexes. Harming the female during mating would negatively affect male fitness and sexual antagonism is therefore not expected. Indeed, mating appears to increase female longevity in at least one ant species. Acps are presumed to play a role in this phenomenon, but the underlying mechanisms are unknown. In this study, we investigated genes, which are preferentially expressed in male accessory glands of the ant Leptothorax gredleri, to determine which proteins might be transferred in the seminal fluid. Results: By a suppression subtractive hybridization protocol we obtained 20 unique sequences (USs). Twelve had mutual best matches with genes predicted for Apis mellifera and Nasonia vitripennis. Functional information (Gene Ontology) was available only for seven of these, including intracellular signaling, energy-dependent transport and metabolic enzyme activities. The remaining eight USs did not match sequences from other species. Six genes were further analyzed by quantitative RT-PCR in three life cycle stages of male ants. A gene with carboxy-lyase activity and one of unpredicted function were significantly overexpressed in accessory glands of sexually mature males. Conclusions: Our study is the first one to investigate differential gene expression in ants in a context related to mating. Our findings indicate that male accessory glands of L. gredleri express a series of genes that are unique to this species, possibly representing novel genes, in addition to conserved ones for which functions can be predicted. Identifying differentially expressed genes might help to better understand molecular mechanisms involved in reproductive processes in eusocial Hymenoptera. While the novel genes could account for rapidly evolving ones driven by intra-sexual conflict between males, conserved genes imply that rather beneficial traits might get fixed by a process described as inter-sexual cooperation between males and females.

Improvement in Quality of Life of An Oncological Patient by Laser Phototherapy

Objective and Background Data: Common side effects of radiotherapy (RT) to the head and neck include oral mucositis, xerostomia, and severe pain. The aim of this study is to report improvement in the quality of life of an oncological patient by laser phototherapy (LPT). Clinical Case and Laser Phototherapy Protocol: The patient, a 15-year-old girl diagnosed with mucoepidermoid carcinoma, underwent surgical excision of a tumor of the left palatomaxilla. After that, she was subjected to 35 sessions of RT (2 Gy/d). Clinical examination revealed the spread of severe ulcerations to the jugal mucosa, gums, lips, hard palate, and tongue (WHO mucositis score 3). She had difficulty in moving her tongue and she was unable to eat any solid food. Oral hygiene orientation and LPT were performed throughout all RT sessions. A continuous diode laser, 660 nm, 40 mW, 6 J/cm(2), 0.24 J per point in contact mode, with spot size of 0.04 cm(2) was used in the entire oral cavity. A high-power diode laser at 1 W, 10 sec per cm of mucositis, approximately 10 J/cm(2), was used in defocused mode only on ulcerative lesions. After the first laser irradiation session, decreases in pain and xerostomia were reported; however, a more significant improvement was seen after five sessions. At that point although the mucositis score was still 2, the patient reported that she was free of pain, and consequently a palatine plate could be made to rehabilitate the entire surgical area. Seventeen laser irradiation sessions were necessary to eliminate all oral mucositis lesions. Conclusion: Normal oral function and consequent improvements in the quality of life of this oncologic patient were observed with LPT.

Genetic parameters for productive life traits and reproductive efficiency traits at 6 years in Nellore cattle

The objective of the present study was to estimate (co)variance components for length of productive life (LPL) and some alternative reproductive traits of 6-year-old Nellore cattle. The data set contained 57,410 records for age at first calving from Nellore females and was edited to remove animal records with uncertain paternity and cows with just one piece of calving information. Only animals with age at first calving ranging from 23 to 48 months and calving intervals between 11 and 24 months were kept for analysis. LPL and life production ( LP) were used to describe productive life. LPL was defined as the number of months a cow was kept in the herd until she was 6 years old, given that she was alive at first calving and LP was defined as total number of calves in that time. Four traits were used to describe reproductive traits: two breeding efficiencies on original scale were estimated using Wilcox and Tomar functions (BEW and BET, respectively), and two breeding efficiencies transformed (ASBEW and ASBET, respectively), using the function [arcsine (square root (BEi/100))]. Estimates of heritability for measures of LPL and LP were low and ranged from 0.04 to 0.05. Estimates of heritability for breeding efficiencies on original and transformed scales oscillated from 0.18 to 0.32. Estimates of genetic correlations ranged from -0.57 to 0.79 for LPL and other traits and from 0.28 to 0.63 for LP and other traits.

Additive genetic relationship of longevity with fertility and production traits in Nellore cattle based on bivariate models

Survival or longevity is an economically important trait in beef cattle. The main inconvenience for its inclusion in selection criteria is delayed recording of phenotypic data and the high computational demand for including survival in proportional hazard models. Thus, identification of a longevity-correlated trait that could be recorded early in life would be very useful for selection purposes. We estimated the genetic relationship of survival with productive and reproductive traits in Nellore cattle, including weaning weight (WW), post-weaning growth (PWG), muscularity (MUSC), scrotal circumference at 18 months (SC18), and heifer pregnancy (HP). Survival was measured in discrete time intervals and modeled through a sequential threshold model. Five independent bivariate Bayesian analyses were performed, accounting for cow survival and the five productive and reproductive traits. Posterior mean estimates for heritability (standard deviation in parentheses) were 0.55 (0.01) for WW, 0.25 (0.01) for PWG, 0.23 (0.01) for MUSC, and 0.48 (0.01) for SC18. The posterior mean estimates (95% confidence interval in parentheses) for the genetic correlation with survival were 0.16 (0.13-0.19), 0.30 (0.25-0.34), 0.31 (0.25-0.36), 0.07 (0.02-0.12), and 0.82 (0.78-0.86) for WW, PWG, MUSC, SC18, and HP, respectively. Based on the high genetic correlation and heritability (0.54) posterior mean estimates for HP, the expected progeny difference for HP can be used to select bulls for longevity, as well as for post-weaning gain and muscle score.

ANALYSIS OF THE PICO DOS DIAS SURVEY HERBIG Ae/Be CANDIDATES

A large sample of Herbig Ae/Be (HAeBe) candidates, distributed in different Galactic regions south to declination +30 degrees, were identified by the Pico dos Dias Survey (a search for young stellar objects based on IRAS colors). Most of the candidates are nearby or associated with star-forming clouds, but several others are considered isolated objects. Aiming to verify the young nature of 93 HAeBe candidates, we searched for additional information that could be useful to confirm if they are pre-main-sequence (PMS) stars or evolved objects, which coincidentally show similar IRAS colors. By adopting a spectral index that is related to the amount of infrared excess and the shape of the spectral energy distribution, we have classified the sample according to three groups, which are analyzed on the basis of (1) circumstellar luminosity; (2) spatial distribution; (3) optical polarization; (4) near-infrared colors; (5) stellar parameters (mass, age, effective temperature); and (5) intensity of emission lines. Our analysis indicates that only 76% of the studied sample, mainly the group with intermediate to low levels of circumstellar emission, can be more confidently considered PMS stars. The nature of the remaining stars, which are in the other group that contains the highest levels of infrared excess, remains to be confirmed. They share the same characteristics of evolved objects, requiring complementary studies in order to correctly classify them. At least seven objects show characteristics typical of post-asymptotic giant branch or proto-planetary nebulae.

LIFE CYCLE AND POPULATION STRUCTURE OF AEGLA PAULENSIS (DECAPODA: ANOMURA: AEGLIDAE)

We describe growth, longevity, sex ratio, reproductive period, and recruitment of Aegla paulensis from Jaragua Stale Park, Sao Paulo, Brazil (23 degrees 27'27.9 '' S; 46 degrees 45'32.3 '' W). The population was sampled monthly (September 2007 through August 2009) with the aid of traps. Over five thousand individuals were captured, sexed, measured (carapace length = CL) and inspected for reproductive traits (females only), and then released back to the sampling site. The pattern of the reproductive cycle was strongly seasonal (austral mid autumn through late winter), with a single recruitment pulse per year. The obtained von Bertalanffy growth equations were CL = 21.25[1-e(-0.041(t + 1.250))] and CL = 16.52[1-e(-0.049(t + 1.823))] for males and females, respectively. Males (mean CL +/- SD = 11.86 +/- 2.79 mm) attain larger sizes than females (mean CL +/- SD = 10.84 +/- 2.36 mm). Aegla paulensis reproduces twice during an estimated life span of 40.2 months for females and 33.9 months for males. Temporal variation of sex ratio showed a distinctive pattern characterized by a sequence of three distinct periods that repeated from one year to another, and which suggested that a behavioral component influence the proportion of sex in adult specimens sampled with traps during reproductive and non-reproductive periods.

Life-History Evolution on Tropidurinae Lizards: Influence of Lineage, Body Size and Climate

The study of life history variation is central to the evolutionary theory. In many ectothermic lineages, including lizards, life history traits are plastic and relate to several sources of variation including body size, which is both a factor and a life history trait likely to modulate reproductive parameters. Larger species within a lineage, for example tend to be more fecund and have larger clutch size, but clutch size may also be influenced by climate, independently of body size. Thus, the study of climatic effects on lizard fecundity is mandatory on the current scenario of global climatic change. We asked how body and clutch size have responded to climate through time in a group of tropical lizards, the Tropidurinae, and how these two variables relate to each other. We used both traditional and phylogenetic comparative methods. Body and clutch size are variable within Tropidurinae, and both traits are influenced by phylogenetic position. Across the lineage, species which evolved larger size produce more eggs and neither trait is influenced by temperature components. A climatic component of precipitation, however, relates to larger female body size, and therefore seems to exert an indirect relationship on clutch size. This effect of precipitation on body size is likely a correlate of primary production. A decrease in fecundity is expected for Tropidurinae species on continental landmasses, which are predicted to undergo a decrease in summer rainfall.

Detection of polymorphisms of the mtDNA control region of Caretta caretta (Testudines: Cheloniidae) by PCR-SSCP

Marine turtles are increasingly being threatened worldwide by anthropogenic activities. Better understanding of their life cycle, behavior and population structure is imperative for the design of adequate conservation strategies. The mtDNA control region is a fast-evolving matrilineal marker that has been employed in the study of marine turtle populations. We developed and tested a simple molecular tracing system for Caretta caretta mtDNA haplotypes by polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP). Using this technique, we were able to distinguish the SSCP patterns of 18 individuals of the haplotypes CC-A4, CC-A24 and CCxLO, which are commonly found in turtles sampled on the Brazilian coast. When we analyzed 15 turtles with previously unknown sequences, we detected two other haplotypes, in addition to the other four. Based on DNA sequencing, they were identified as the CC-A17 and CC-A1 haplotypes. Further analyses were made with the sea turtles, Chelonia mydas (N = 8), Lepidochelys olivacea (N = 3) and Eretmochelys imbricata (N = 1), demonstrating that the PCR-SSCP technique is able to distinguish intra-and interspecific variation in the family Cheloniidae. We found that this technique can be useful for identifying sea turtle mtDNA haplotypes, reducing the need for sequencing.

Long life of Gauss-Bonnet corrected black holes

Dictated by the string theory and various higher dimensional scenarios, black holes in D > 4-dimensional space-times must have higher curvature corrections. The first and dominant term is quadratic in curvature, and called the Gauss-Bonnet (GB) term. We shall show that although the Gauss-Bonnet correction changes black hole's geometry only softly, the emission of gravitons is suppressed by many orders even at quite small values of the GB coupling. The huge suppression of the graviton emission is due to the multiplication of the two effects: the quick cooling of the black hole when one turns on the GB coupling and the exponential decreasing of the gray-body factor of the tensor type of gravitons at small and moderate energies. At higher D the tensor gravitons emission is dominant, so that the overall lifetime of black holes with Gauss-Bonnet corrections is many orders larger than was expected. This effect should be relevant for the future experiments at the Large Hadron Collider (LHC).

Cryptic species, life cycles, and the phylogeny of Clytia (Cnidaria: Hydrozoa: Campanulariidae)

Medusae and polyps of Clytia are abundantly found in coastal marine environments and one species in the genus-Clytia hemisphaerica (Linnaeus, 1767)-has become an important experimental model. Yet, only 10 species in the genus have had their life cycle investigated. Most species of Clytia are also poorly described, and detailed life cycle and morphological studies are needed for accurate species-level identifications. Here, we investigated the life cycle of Clytia elsaeoswaldae Stechow, 1914, a species described for the tropical western Atlantic and subsequently considered conspecific to the nearly-cosmopolitan species Clytia gracilis (Sars, 1850) and Clytia hemisphaerica, originally described for the temperate North Atlantic. Based on observations of mature medusae and multiple colonies from southeastern Brazil and the U. S. Virgin Islands (type locality), our results show that C. elsaeoswaldae is morphologically distinct from C. gracilis and C. hemisphaerica. The morphological results are corroborated by a multigene phylogenetic analysis of the genus Clytia, which shows that C. gracilis-like species form a polyphyletic group of several species. These results suggest that the nearly-cosmopolitan distribution attributed to some species of Clytia may be due to the non-recognition of morphologically similar species with more restricted ranges.

Shelf and estuarine transport mechanisms affecting the supply of competent larvae in a suite of brachyuran crabs with different life histories

Supply of competent larvae to the benthic habitat is a major determinant of population dynamics in coastal and estuarine invertebrates with an indirect life cycle. Larval delivery may depend not only on physical transport mechanisms, but also on larval behavior and physiological progress to the competent stage. Yet, the combined analysis of such factors has seldom been attempted. We used time-series analyses to examine tide- and wind-driven mechanisms responsible for the supply of crab megalopae to an estuarine river under a major marine influence in SW Spain, and monitored the vertical distribution of upstream moving megalopae, their net flux and competent state. The species Panopeus africanus (estuarine), Brachynotus sexdentatus (euryhaline) and Nepinnotheres pinnotheres (coastal) comprised 80% of the whole sample, and responded in a similar way to tide and wind forcing. Tidal range was positively correlated to supply, with maxima 0 to 1 d after spring tides, suggesting selective tidal stream transport. Despite being extensively subjected to upwelling, downwind drift under the effect of westerlies, not Ekman transport, explained residual supply variation at our sampling area. Once in the estuary, net flux and competence state matched the expected trends. Net upstream flux increased from B. sexdentatus to P. africanus, favoring transport to a sheltered coastal habitat (N. pinnotheres), or to the upper estuary (P. africanus). Competence state was highest in N. pinnotheres, intermediate in B. sexdentatus and lowest in P. africanus, as expected if larvae respond to cues from adequate benthic habitat. P. africanus megalopae were found close to the bottom, not above, rendering slower upstream transport than anticipated.