Few studies of microbial biogeography address variability across both multiple habitats and multiple seasons. Here we examine the spatial and temporal variability of bacterioplankton community composition of the Columbia River coastal margin using 16S amplicon pyrosequencing of 300 water samples collected in 2007 and 2008. Communities separated into seven groups (ANOSIM, P<0.001): river, estuary, plume, epipelagic, mesopelagic, shelf bottom (depth<350 m) and slope bottom (depth>850 m). The ordination of these samples was correlated with salinity (ρ=−0.83) and depth (ρ=−0.62). Temporal patterns were obscured by spatial variability among the coastal environments, and could only be detected within individual groups. Thus, structuring environmental factors (for example, salinity, depth) dominate over seasonal changes in determining community composition. Seasonal variability was detected across an annual cycle in the river, estuary and plume where communities separated into two groups, early year (April–July) and late year (August–Nov), demonstrating annual reassembly of communities over time. Determining both the spatial and temporal variability of bacterioplankton communities provides a framework for modeling these communities across environmental gradients from river to deep ocean.

The folate and vitamin B12-dependent enzyme methionine synthase (MS) is highly sensitive to cellular oxidative status, and lower MS activity increases production of the antioxidant glutathione, while simultaneously decreasing more than 200 methylation reactions, broadly affecting metabolic activity. MS mRNA levels in postmortem human cortex from subjects across the lifespan were measured and a dramatic progressive biphasic decrease of more than 400-fold from 28 weeks of gestation to 84 years was observed. Further analysis revealed alternative splicing of MS mRNA, including deletion of folate-binding domain exons and age-dependent deletion of exons from the cap domain, which protects vitamin B12 (cobalamin) from oxidation. Although three species of MS were evident at the protein level, corresponding to full-length and alternatively spliced mRNA transcripts, decreasing mRNA levels across the lifespan were not associated with significant changes in MS protein or methionine levels. MS mRNA levels were significantly lower in autistic subjects, especially at younger ages, and this decrease was replicated in cultured human neuronal cells by treatment with TNF-α, whose CSF levels are elevated in autism. These novel findings suggest that rather than serving as a housekeeping enzyme, MS has a broad and dynamic role in coordinating metabolism in the brain during development and aging. Factors adversely affecting MS activity, such as oxidative stress, can be a source of risk for neurological disorders across the lifespan via their impact on methylation reactions, including epigenetic regulation of gene expression.

Experiments using economic games are becoming a major source for the study of human social behavior. These experiments are usually conducted with university students who voluntarily choose to participate. Across the natural and social sciences, there is some concern about how this “particular” subject pool may systematically produce biased results. Focusing on social preferences, this study employs data from a survey-experiment conducted with a representative sample of a city's population (N = 765). We report behavioral data from five experimental decisions in three canonical games: dictator, ultimatum and trust games. The dataset includes students and non-students as well as volunteers and non-volunteers. We separately examine the effects of being a student and being a volunteer on behavior, which allows a ceteris paribus comparison between self-selected students (students*volunteers) and the representative population. Our results suggest that self-selected students are an appropriate subject pool for the study of social behavior.

Inadequate gas conditioning during non-invasive ventilation (NIV) can impair the anatomy and function of nasal mucosa. The resulting symptoms may have a negative effect on patients' adherence to ventilatory treatment, especially for chronic use. Several parameters, mostly technical aspects of NIV, contribute to inefficient gas conditioning. Factors affecting airway humidity during NIV include inspiratory flow, inspiratory oxygen fraction, leaks, type of ventilator, interface used to deliver NIV, temperature and pressure of inhaled gas, and type of humidifier. The correct application of a humidification system may avoid the effects of NIV-induced drying of the airway. This brief review analyses the consequences of airway dryness in patients receiving NIV and the technical tools necessary to guarantee adequate gas conditioning during ventilatory treatment. Open questions remain about the timing of gas conditioning for acute or chronic settings, the choice and type of humidification device, the interaction between the humidifier and the underlying disease, and the effects of individual humidification systems on delivered humidity.

The standard treatment for primary CNS lymphoma (PCNSL) involves high-dose methotrexate-based chemotherapy (HD-MTX) alone or in combination with whole brain radiotherapy (WBRT). The combined modality regimen carries a substantial risk for cognitive impairment, and HD-MTX alone has been used more often recently in part to reduce neurotoxicity. In this study, we assessed cognitive functioning and quality of life in PCNSL survivors treated with WBRT + HD-MTX or HD-MTX alone. Fifty PCNSL patients in disease remission underwent a posttreatment baseline neuropsychological evaluation, and a subset of patients completed a follow-up evaluation. Quality of life and extent of white matter disease and atrophy on MRI were assessed. Comparisons according to treatment type after controlling for age and time since treatment completion showed that patients treated with HD-MTX alone had significantly higher scores on tests of selective attention and memory than patients treated with the combined modality regimen. Patients treated with WBRT + HD-MTX had impairments across most cognitive domains, and these were of sufficient severity to interfere with quality of life, as over 50% were not working due to their illness. Patients treated with HD-MTX alone did not meet criteria for cognitive impairment but scored within 1 SD below the normative sample on most tests. Patients with more extensive white matter disease had lower scores on tests of set-shifting and memory. Cognitive dysfunction was more prevalent in PCNSL survivors treated with WBRT + HD-MTX compared with patients treated with HD-MTX alone.

The sulfonamide antibiotics inhibit dihydropteroate synthase (DHPS), a key enzyme in the folate pathway of bacteria and primitive eukaryotes. However, resistance mutations have severely compromised the usefulness of these drugs. Here, we report structural, computational and mutagenesis studies on the catalytic and resistance mechanisms of DHPS. By performing the enzyme-catalyzed reaction in crystalline DHPS, we have structurally characterized key intermediates along the reaction pathway. Results support an SN1 reaction mechanism via formation of a novel cationic pterin intermediate. We also show that two conserved loops generate a substructure during catalysis that creates a specific binding pocket for p-aminobenzoic acid, one of the two DHPS substrates. This substructure, together with the pterin-binding pocket, explains the roles of the conserved active site residues, and reveals how sulfonamide resistance arises.

The Trypanosomatids parasites Leishmania braziliensis, Leishmania major and Leishmania infantum are important human pathogens. Despite of years of study and genome availability, effective vaccine has not been developed yet, and the chemotherapy is highly toxic. Therefore, it is clear just interdisciplinary integrated studies will have success in trying to search new targets for developing of vaccines and drugs. An essential part of this rationale is related to protein-protein interaction network (PPI) study which can provide a better understanding of complex protein interactions in biological system. Thus, we modeled PPIs for Trypanosomatids through computational methods using sequence comparison against public database of protein or domain interaction for interaction prediction (Interolog Mapping) and developed a dedicated combined system score to address the predictions robustness. The confidence evaluation of network prediction approach was addressed using gold standard positive and negative datasets and the AUC value obtained was 0.94. As result, 39,420, 43,531 and 45,235 interactions were predicted for L. braziliensis, L. major and L. infantum respectively. For each predicted network the top 20 proteins were ranked by MCC topological index. In addition, information related with immunological potential, degree of protein sequence conservation among orthologs and degree of identity compared to proteins of potential parasite hosts was integrated. This information integration provides a better understanding and usefulness of the predicted networks that can be valuable to select new potential biological targets for drug and vaccine development. Network modularity which is a key when one is interested in destabilizing the PPIs for drug or vaccine purposes along with multiple alignments of the predicted PPIs were performed revealing patterns associated with protein turnover. In addition, around 50% of hypothetical protein present in the networks received some degree of functional annotation which represents an important contribution since approximately 60% of Leishmania predicted proteomes has no predicted function.

Reports of unrelated individuals with autism spectrum disorder (ASD) and similar clinical features having overlapping de novo interstitial deletions at 2p15–p16.1 suggest that this region harbors a gene(s) important to the development of autism. We molecularly characterized two such deletions, selecting two genes in this region, exportin 1 (XPO1) and orthodenticle homolog 1 (OTX1) for association studies in three North American cohorts (Autism Spectrum Disorder – Canadian American Research Consortium (ASD–CARC), New York, and Autism Genetic Resource Exchange (AGRE)) and one Italian cohort (Società Italiana per la Ricerca e la Formazione sull'Autismo (SIRFA)) of families with ASD. In XPO1, rs6735330 was associated with autism in all four cohorts (P<0.05), being significant in ASD–CARC cohorts (P-value following false discovery rate correction for multiple testing (PFDR)=1.29 × 10−5), the AGRE cohort (PFDR=0.0011) and the combined families (PFDR=2.34 × 10−9). Similarly, in OTX1, rs2018650 and rs13000344 were associated with autism in ASD–CARC cohorts (PFDR=8.65 × 10−7 and 6.07 × 105, respectively), AGRE cohort (PFDR=0.0034 and 0.015, respectively) and the combined families (PFDR=2.34 × 10−9 and 0.00017, respectively); associations were marginal or insignificant in the New York and SIRFA cohorts. A significant association (PFDR=2.63 × 10−11) was found for the rs2018650G–rs13000344C haplotype. The above three SNPs were associated with severity of social interaction and verbal communication deficits and repetitive behaviors (P-values <0.01). No additional deletions were identified following screening of 798 ASD individuals. Our results indicate that deletion 2p15–p16.1 is not commonly associated with idiopathic ASD, but represents a novel contiguous gene syndrome associated with a constellation of phenotypic features (autism, intellectual disability, craniofacial/CNS dysmorphology), and that XPO1 and OXT1 may contribute to ASD in 2p15–p16.1 deletion cases and non-deletion cases of ASD mapping to this chromosome region.

Regulation of RNA polymerase II transcription initiation is apparently absent in trypanosomes. Instead, these eukaryotes control gene expression mainly at the post-transcriptional level. Regulation is exerted through the action of numerous RNA-binding proteins that modulate mRNA processing, turnover, translation and localization. In this work we show that the RNA-binding protein DRBD3 resides in the cytoplasm, but localizes to the nucleus upon oxidative challenge and to stress granules under starvation conditions. DRBD3 associates with other proteins to form a complex, the composition of which is altered by cellular stress. Interestingly, target mRNAs remain bound to DRBD3 under stress conditions. Our results suggest that DRBD3 transports regulated mRNAs within the cell in the form of ribonucleoprotein complexes that are remodeled in response to environmental cues.

A minilaparoscopic combined approach for inguinal hernia appears to be safe and feasible for a more simple endoscopic hernia repair.

Introduction:

Endoscopic surgical repair of inguinal hernia is currently conducted using 2 techniques: the totally extraperitoneal (TEP) and the transabdominal (TAPP) hernia repair. The TEP procedure is technically advantageous, because of the use of no mesh fixation and the elimination of the peritoneal flap, leading to less postoperative pain and faster recovery. The drawback is that TEP is not performed as frequently, because of its complexity and longer learning curve. In this study, we propose a hybrid technique that could potentially become the gold standard of minimally invasive inguinal hernia surgery. This will be achieved by combining established advantages of TEP and TAPP associated with the precision and cosmetics of minilaparoscopy (MINI).

Materials and Surgical Technique:

Between January and July 2011, 22 patients were admitted for endoscopic inguinal hernia repair. The combined technique was initiated with TAPP inspection and direct visualization of a minilaparoscopic trocar dissection of the preperitoneum space. A10-mm trocar was then placed inside the previously dissected preperitoneal space, using the same umbilical TAPP skin incision. Minilaparoscopic retroperitoneal dissection was completed by TEP, and the surgical procedure was finalized with intraperitoneal review and correction of the preperitoneal work.

Discussion:

The minilaparoscopic TEP-TAPP combined approach for inguinal hernia is feasible, safe, and allows a simple endoscopic repair. This is achieved by combining features and advantages of both TAPP and TEP techniques using precise and sophisticated MINI instruments. Minilaparoscopic preperitoneal dissection allows a faster and easier creation of the preperitoneal space for the TEP component of the procedure.

Background

Nuña bean is a type of ancient common bean (Phaseolus vulgaris L.) native to the Andean region of South America, whose seeds possess the unusual property of popping. The nutritional features of popped seeds make them a healthy low fat and high protein snack. However, flowering of nuña bean only takes place under short-day photoperiod conditions, which means a difficulty to extend production to areas where such conditions do not prevail. Therefore, breeding programs of adaptation traits will facilitate the diversification of the bean crops and the development of new varieties with enhanced healthy properties. Although the popping trait has been profusely studied in maize (popcorn), little is known about the biology and genetic basis of the popping ability in common bean. To obtain insights into the genetics of popping ability related traits of nuña bean, a comprehensive quantitative trait loci (QTL) analysis was performed to detect single-locus and epistatic QTLs responsible for the phenotypic variance observed in these traits.

Results

A mapping population of 185 recombinant inbred lines (RILs) derived from a cross between two Andean common bean genotypes was evaluated for three popping related traits, popping dimension index (PDI), expansion coefficient (EC), and percentage of unpopped seeds (PUS), in five different environmental conditions. The genetic map constructed included 193 loci across 12 linkage groups (LGs), covering a genetic distance of 822.1 cM, with an average of 4.3 cM per marker. Individual and multi-environment QTL analyses detected a total of nineteen single-locus QTLs, highlighting among them the co-localized QTLs for the three popping ability traits placed on LGs 3, 5, 6, and 7, which together explained 24.9, 14.5, and 25.3% of the phenotypic variance for PDI, EC, and PUS, respectively. Interestingly, epistatic interactions among QTLs have been detected, which could have a key role in the genetic control of popping.

Conclusions

The QTLs here reported constitute useful tools for marker assisted selection breeding programs aimed at improving nuña bean cultivars, as well as for extending our knowledge of the genetic determinants and genotype x environment interaction involved in the popping ability traits of this bean crop.

Symbiotic microorganisms may be directly transferred from parents to offspring or acquired from a particular environment that animals may be able to select. If benefits for hosts vary among microbial strains, natural selection may favour hosts holding the most beneficial one. Enterococci symbionts living in the hoopoe (Upupa epops) uropygial gland are able to synthesise bacteriocins (antimicrobial peptides that inhibit the growth of competitor bacteria). We explored variability in genetic profile (through RAPD-PCR analyses) and antimicrobial properties (by performing antagonistic tests against ten bacterial indicator strains) of the different isolates obtained from the uropygial glands of hoopoe females and nestlings. We found that the genetic profile of bacterial isolates was related to antimicrobial activity, as well as to individual host identity and the nest from which samples were obtained. This association suggest that variation in the inhibitory capacity of Enterococci symbionts should be under selection.

BRAF is a serine/threonine protein kinase activating the MAP kinase/ERK-signaling pathway. About 50 % of melanomas harbors activating BRAF mutations (over 90 % V600E). BRAFV600E has been implicated in different mechanisms underlying melanomagenesis, most of which due to the deregulated activation of the downstream MEK/ERK effectors. The first selective inhibitor of mutant BRAF, vemurafenib, after highly encouraging results of the phase I and II trial, was compared to dacarbazine in a phase III trial in treatment-naïve patients (BRIM-3). The study results showed a relative reduction of 63 % in risk of death and 74 % in risk of tumor progression. Considering all trials so far completed, median overall survival reached approximately 16 months for vemurafenib compared to less than 10 months for dacarbazine treatment. Vemurafenib has been extensively tested on melanoma patients expressing the BRAFV600E mutated form; it has been demonstrated to be also effective in inhibiting melanomas carrying the V600K mutation. In 2011, both FDA and EMA therefore approved vemurafenib for metastatic melanoma carrying BRAFV600 mutations. Some findings suggest that continuation of vemurafenib treatment is potentially beneficial after local therapy in a subset of patients with disease progression (PD). Among who continued vemurafenib >30 days after local therapy of PD lesion(s), a median overall survival was not reached, with a median follow-up of 15.5 months from initiation of BRAF inhibitor therapy. For patients who did not continue treatment, median overall survival from the time of disease progression was 1.4 months. A clinical phase I/II trial is evaluating the safety, tolerability and efficacy of vemurafenib in combination with the CTLA-4 inhibitor mAb ipilimumab. In the BRIM-7 trial vemurafenib is tested in association with GDC-0973, a potent and highly selective inhibitor of MEK1/2. Preliminary data seem to indicate that an additional inhibitor of mutated BRAF, GSK2118436, might be also active on a wider range of BRAF mutations (V600E-K-D-R); actually, treatment with such a compound is under evaluation in a phase III study among stage III-IV melanoma patients positive for BRAF mutations. Overall, BRAF inhibitors were well tolerated; common adverse events are arthralgia, rash, fatigue, alopecia, keratoacanthoma or cutaneous squamous-cell carcinoma, photosensitivity, nausea, and diarrhea, with some variants between different inhibitors.

After more than 30 years, landmark progress has been made in the treatment of cancer, and melanoma in particular, with the success of new molecules such as ipilimumab, vemurafenib and active specific immunization.

After the first congress in December 2010, the second edition of “Melanoma Research: a bridge from Naples to the World” meeting, organized by Paolo A. Ascierto (INT, Naples, Italy), Francesco M. Marincola (NIH, Bethesda, USA), and Nicola Mozzillo (INT, Naples, Italy) took place in Naples, on 5–6 December 2011. We have identified four new topics of discussion: Innovative Approaches in Prevention, Diagnosis and Surgical Treatment, New Pathways and Targets in Melanoma: An Update about Immunotherapy, and Combination Strategies.

This international congress gathered more than 30 international faculty members and was focused on recent advances in melanoma molecular biology, immunology and therapy, and created an interactive atmosphere which stimulated discussion of new approaches and strategies in the field of melanoma.

This study evaluated the impact of age and pneumococcal vaccination on the density of pneumococcal nasopharyngeal carriage. Among colonized individuals, density decreased with increasing age. Time-trends analysis revealed that pneumococcal vaccination appeared to lower the density of nasopharyngeal carriage.

Background. This study evaluated the impact of age and pneumococcal vaccination on the density of pneumococcal nasopharyngeal carriage.

Methods. A cluster-randomized trial was conducted in rural Gambia. In 11 villages (the vaccine group), all residents received 7-valent pneumococcal conjugate vaccine (PCV-7), while in another 10 villages (the control group), only children <30 months old or born during the study period received PCV-7. Cross-sectional surveys (CSSs) were conducted to collect nasopharyngeal swabs before vaccination (baseline CSS) and 4, 12, and 22 months after vaccination. Pneumococcal density was defined using a semiquantitative classification (range, 1–4) among colonized individuals. An age-trend analysis of density was conducted using data from the baseline CSS. Mean pneumococcal density was compared in CSSs conducted before and after vaccination.

Results. Mean bacterial density among colonized individuals in the baseline CSS was 2.57 for vaccine-type (VT) and non–vaccine-type (NVT) pneumococci; it decreased with age (P < .001 for VT and NVT). There was a decrease in the density of VT carriage following vaccination in individuals older than 5 years (from 2.44 to 1.88; P = .001) and in younger individuals (from 2.57 to 2.11; P = .070) in the vaccinated villages. Similar decreases in density were observed with NVT within vaccinated and control villages. No significant differences were found between vaccinated and control villages in the postvaccination comparisons for either VT or NVT.

Conclusions. A high density of carriage among young subjects might partly explain why children are more efficient than adults in pneumococcal transmission. PCV-7 vaccination lowered the density of VT and of NVT pneumococcal carriage in the before-after vaccination analysis.

Clinical Trials Registration. ISRCTN51695599.

Background

Ipilimumab and vemurafenib have both been shown to improve survival in phase III trials of patients with metastatic melanoma. Although vemurafenib is associated with a rapid onset of activity, responses are often of limited duration. Conversely, responses to ipilimumab take time to develop, but can be durable. Currently, limited data exist on the sequencing of these agents in patients with the BRAFV600 mutation. The aim of this analysis was to identify factors that could potentially be used to optimise the order in which ipilimumab and BRAF inhibitors are administered in this patient population.

Methods

This was a retrospective, single-institution, analysis of patients treated with vemurafenib 960 mg or dabrafenib 150 mg twice-daily and ipilimumab 3 mg/kg every 3 weeks for 4 doses as part of a clinical trial or expanded access program. Eligible patients tested positive for the BRAFV600 mutation and had sequentially received treatment with vemurafenib or dabrafenib followed by ipilimumab, or vice versa.

Results

In total, 34 BRAF-mutation positive patients were eligible, comprising six patients who received ipilimumab followed by a BRAF inhibitor, and 28 patients treated with a BRAF inhibitor who subsequently received ipilimumab. Of these 28 patients, 12 (43 %) had rapid disease progression resulting in death and were unable to complete ipilimumab treatment as per protocol. These patients were classified as having rapid disease progression. Median overall survival for rapid progressors was 5.7 months (95 % CI: 5.0–6.3), compared with 18.6 months (95 % CI: 3.2–41.3; p < 0.0001) for those patients who were able to complete ipilimumab treatment. Baseline factors associated with rapid progression were elevated lactate dehydrogenase, a performance status of 1 and the presence of brain metastases. Patients were more likely to have rapid disease progression if they had at least two of these risk factors at baseline.

Conclusions

Our analysis suggests it may be possible to identify those patients at high risk of rapid disease progression upon relapse with a BRAF inhibitor who might not have time to subsequently complete ipilimumab treatment. We hypothesise that these BRAF-mutation positive patients may benefit from being treated with ipilimumab first.

Background

In a number of organisms sex-biased genes are non-randomly distributed between autosomes and the shared sex chromosome X (or Z). Studies on Anopheles gambiae have produced conflicting results regarding the underrepresentation of male-biased genes on the X chromosome and it is unclear to what extent sexual antagonism, dosage compensation or X-inactivation in the male germline, the evolutionary forces that have been suggested to affect the chromosomal distribution of sex-biased genes, are operational in Anopheles.

Results

We performed a meta-analysis of sex-biased gene expression in Anopheles gambiae which provides evidence for a general underrepresentation of male-biased genes on the X-chromosome that increased in significance with the observed degree of sex-bias. A phylogenomic comparison between Drosophila melanogaster, Aedes aegypti and Culex quinquefasciatus also indicates that the Anopheles X chromosome strongly disfavours the evolutionary conservation of male-biased expression and that novel male-biased genes are more likely to arise on autosomes. Finally, we demonstrate experimentally that transgenes situated on the Anopheles gambiae X chromosome are transcriptionally silenced in the male germline.

Conclusion

The data presented here support the hypothesis that the observed demasculinization of the Anopheles X chromosome is driven by X-chromosome inactivation in the male germline and by sexual antagonism. The demasculinization appears to be the consequence of a loss of male-biased expression, rather than a failure in the establishment or the extinction of male-biased genes.

Malaria remains a devastating disease despite efforts at control and prevention. Extensive studies using mostly rodent infection models reveal that successful Plasmodium parasite transmission by the African mosquito vector Anopheles gambiae depends on finely tuned vector-parasite interactions. Here we investigate the transcriptional response of A. gambiae to geographically related Plasmodium falciparum populations at various infection intensities and different infection stages. These responses are compared with those of mosquitoes infected with the rodent parasite Plasmodium berghei. We demonstrate that mosquito responses are largely dependent on the intensity of infection. A major transcriptional suppression of genes involved in the regulation of midgut homeostasis is detected in low-intensity P. falciparum infections, the most common type of infection in Africa. Importantly, genes transcriptionally induced during these infections tend to be phylogenetically unique to A. gambiae. These data suggest that coadaptation between vectors and parasites may act to minimize the impact of infection on mosquito fitness by selectively suppressing specific functional classes of genes. RNA interference (RNAi)-mediated gene silencing provides initial evidence for important roles of the mosquito G protein-coupled receptors (GPCRs) in controlling infection intensity-dependent antiparasitic responses.

Coastal solar saltworks of Brazil are exploited for sea salt, which becomes progressively concentrated by evaporation. This study aimed to review the current and new potential uses of these systems, in order to provide more dynamic for this activity. The first evaporation ponds are also used for artisanal fisheries, ensuring the livelihood of many families. All the brine rich in secondary salts (bittern) can be widely used by the chemical industry, while the Brazil shows an incipient production of "flower of salt", a salt with distinct characteristics with higher market value than sodium chloride. On the other hand, the saltponds have a high potential for management and obtaining of large populations of Artemia spp., purifying the brine through the action as biological filter. This microcrustacean occurs naturally in intermediate salinity ponds, being commonly used in aquaculture. Species of microalgae and halobacteria found in the saltworks are employed for extraction of beta-carotene and glycerol, used in an extensive list of products with high commercial value. These ecosystems represent refuge zones for many species of migratory birds, becoming imperative to promote the conservation of these hypersaline wetlands.