Isolation and characterization of microsatellite markers in the spiny lobster, Panulirus echinatus Smith, 1869 (Decapoda: Palinuridae) by Illumina MiSeq sequencing.

The isolation and characterization of 17 polymorphic microsatellite loci from the spiny lobster Panulirus echinatus (Decapoda: Palinuridae) by Illumina MiSeq sequencing is described..

MEGASAT: automated inference of microsatellite genotypes from sequence data

MEGASAT is software that enables genotyping of microsatellite loci using next-generation sequencing data. Microsatellites are amplified in large multiplexes, and then sequenced in pooled amplicons. MEGASAT reads sequence files and automatically scores microsatellite genotypes. It uses fuzzy matches to allow for sequencing errors and applies decision rules to account for amplification artefacts, including nontarget amplification products, replication slippage during PCR (amplification stutter) and differential amplification of alleles. An important fea- ture of MEGASAT is the generation of histograms of the length–frequency distributions of amplification products for each locus and each individual. These histograms, analogous to electropherograms traditionally used to score microsatellite genotypes, enable rapid evaluation and editing of automatically scored genotypes. MEGASAT is written in Perl, runs on Windows, Mac OS X and Linux systems, and includes a simple graphical user interface. We demon- strate MEGASAT using data from guppy, Poecilia reticulata. We genotype 1024 guppies at 43 microsatellites per run on an Illumina MiSeq sequencer. We evaluated the accuracy of automatically called genotypes using two methods, based on pedigree and repeat genotyping data, and obtained estimates of mean genotyping error rates of 0.021 and 0.012. In both estimates, three loci accounted for a disproportionate fraction of genotyping errors; conversely, 26 loci were scored with 0–1 detected error (error rate ≤0.007). Our results show that with appropriate selection of loci, automated genotyping of microsatellite loci can be achieved with very high throughput, low genotyping error and very low genotyping costs

Implementation of and Early Outcomes From Anal Cancer Screening at a Community-Engaged Health Care Facility Providing Care to Nigerian Men Who Have Sex With Men.

PurposeAnal cancer risk is substantially higher among HIV-infected men who have sex with men (MSM) as compared with other reproductive-age adults, but screening is rare across sub-Saharan Africa. We report the use of high-resolution anoscopy (HRA) as a first-line screening tool and the resulting early outcomes among MSM in Abuja, Nigeria.MethodsFrom August 2016 to August 2017, 424 MSM enrolled in an anal cancer screening substudy of TRUST/RV368, a combined HIV prevention and treatment cohort. HRA-directed biopsies were diagnosed by histology, and ablative treatment was offered for high-grade squamous intraepithelial lesions (HSIL). HRA proficiency was assessed by evaluating the detection of squamous intraepithelial lesions (SIL) over time and the proportion biopsied. Prevalence estimates of low-grade squamous intraepithelial lesions and HSIL with 95% CIs were calculated. Multinomial logistic regression was used to identify those at the highest risk of SIL.ResultsMedian age was 25 years (interquartile range [IQR], 22-29), median time since sexual debut was 8 years (IQR, 4-12), and 59% (95% CI, 54.2% to 63.6%) were HIV infected. Rate of detection of any SIL stabilized after 200 screenings, and less than 20% had two or more biopsies. Preliminary prevalence estimates of low-grade squamous intraepithelial lesions and HSIL were 50.0% (95% CI, 44.7% to 55.3%) and 6.3% (95% CI, 4.0% to 9.3%). HIV infection, at least 8 years since anal coital debut, concurrency, and external warts were independently statistically associated with SIL.ConclusionProficiency with HRA increased with experience over time. However, HSIL detection rates were low, potentially affected by obstructed views from internal warts and low biopsy rates, highlighting the need for ongoing evaluation and mentoring to validate this finding. HRA is a feasible first-line screening tool at an MSM-friendly health care facility. Years since anal coital debut and external warts could prioritize screening

Accelerated hyperfractionation (AHF) compared to conventional fractionation (CF) in the postoperative radiotherapy of locally advanced head and neck cancer: influence of proliferation

Based on the assumption that an accelerated proliferation process prevails in tumour cell residues after surgery, the possibility that treatment acceleration would offer a therapeutic advantage in postoperative radiotherapy of locally advanced head and neck cancer was investigated. The value of Tpot in predicting the treatment outcome and in selecting patients for accelerated fractionation was tested. Seventy patients with (T2/N1–N2) or (T3-4/any N) squamous cell carcinoma of the oral cavity, larynx and hypopharynx who underwent radical surgery, were randomized to either (a) accelerated hyperfractionation: 46.2 Gy per 12 days, 1.4 Gy per fraction, three fractions per day with 6 h interfraction interval, treating 6 days per week or (b) Conventional fractionation: 60 Gy per 6 weeks, 2 Gy per fraction, treating 5 days per week. The 3-year locoregional control rate was significantly better in the accelerated hyperfractionation (88±4%) than in the CF (57±9%) group, P=0.01 (and this was confirmed by multivariate analysis), but the difference in survival (60±10% vs 46±9%) was not significant (P=0.29). The favourable influence of a short treatment time was further substantiated by demonstrating the importance of the gap between surgery and radiotherapy and the overall treatment time between surgery and end of radiotherapy. Early mucositis progressed more rapidly and was more severe in the accelerated hyperfractionation group; reflecting a faster rate of dose accumulation. Xerostomia was experienced by all patients with a tendency to be more severe after accelerated hyperfractionation. Fibrosis and oedema also tended to be more frequent after accelerated hyperfractionation and probably represent consequential reactions. Tpot showed a correlation with disease-free survival in a univariate analysis but did not prove to be an independent factor. Moreover, the use of the minimum and corrected P-values did not identify a significant cut-off. Compared to conventional fractionation, accelerated hyperfractionation did not seem to offer a survival advantage in fast tumours though a better local control rate was noted. This limits the use of Tpot as a guide for selecting patients for accelerated hyperfractionation. For slowly growing tumours, tumour control and survival probabilities were not significantly different in the conventional fractionation and accelerated hyperfractionation groups. A rapid tumour growth was associated with a higher risk of distant metastases (P=0.01). In conclusion, tumour cell repopulation seems to be an important determinant of postoperative radiotherapy of locally advanced head and neck cancer despite lack of a definite association between Tpot and treatment outcome. In fast growing tumours accelerated hyperfractionation provided an improved local control but without a survival advantage. To gain a full benefit from treatment acceleration, the surgery-radiotherapy gap and the overall treatment time should not exceed 6 and 10 weeks respectively

Genome-wide discovery and characterization of microsatellite markers from Melipona fasciculata (Hymenoptera: Apidae), cross-amplifi cation and a snapshot assessment of the genetic diversity in two stingless bee populations.

Brazilian native meliponines are currently threatened by increased human impacts. The assessment of their genetic variation by microsatellite DNA markers can assist in the conservation of populations and help in the planning and establishment of effi cient management strategies. The purpose of this study was to develop the fi rst set of microsatellite markers for Melipona fasciculata, selected from partial genome assembly of Illumina paired-end reads. Primer pairs were designed for each detected locus at their fl anking regions. Bee samples were genotyped from two different populations of Northeastern Brazil for marker characterization and validation..

Genomics reveal population structure, evolutionary history, and signatures of selection in the northern bottlenose whale, Hyperoodon ampullatus

Funding: This work was supported by Fisheries and Oceans Canada (DFO) Maritimes and National Geographic emerging explorer grant to L.J.F, with support by and Natural Sciences and Engineering Research Council of Canada (NSERC) and Killam Nova Scotia Doctoral Scholarships. Work was also supported by US Office of Naval Research and US Strategic Environmental Research and Development Program (SERDP), DFO, University of Windsor, Crown-Indigenous Relations and Northern Affairs Canada, Nunavut Fisheries Association, Government of Nunavut, and NSERC. Funding and resources for sequencing the northern bottlenose whale genome was supported by the CanSeq150 program of Canada’s Genomics Enterprise.Information on wildlife population structure, demographic history, and adaptations are fundamental to understanding species evolution and informing conservation strategies. To study this ecological context for a cetacean of conservation concern, we conducted the first genomic assessment of the northern bottlenose whale, Hyperoodon ampullatus, using whole-genome resequencing data (n = 37) from five regions across the North Atlantic Ocean. We found a range-wide pattern of isolation-by-distance with a genetic subdivision distinguishing three subgroups: the Scotian Shelf, western North Atlantic, and Jan Mayen regions. Signals of elevated levels of inbreeding in the Endangered Scotian Shelf population indicate this population may be more vulnerable than the other two subgroups. In addition to signatures of inbreeding, evidence of local adaptation in the Scotian Shelf was detected across the genome. We found a long-term decline in effective population size for the species, which poses risks to their genetic diversity and may be exacerbated by the isolating effects of population subdivision. Protecting important habitat and migratory corridors should be prioritized to rebuild population sizes that were diminished by commercial whaling, strengthen gene flow, and ensure animals can move across regions in response to environmental changes.Publisher PDFPeer reviewe

A uva de mesa do Vale do São Francisco no mercado de frutas nobres do Recife.

A pesquisa objetiva a sistematização do processo de comercialização de uvas de mesa produzidas na região semi-árida do Vale do São Francisco e comercializadas no mercado informal de frutas nobres, entendido como setor como setor isento de tributação, representado por comerciantes cadastrados na Prefeitura de Recife.Trabalho apresentado na Reunião de Projeto de Economia Rural da UFRPE em parceria com a Embrapa Semiárido

Gating kinetics and pharmacological properties of small conductance calcium-activated potassium channels.

peer reviewedSmall conductance calcium-activated potassium (SK) channels are a promising treatment target in atrial fibrillation. However, the functional properties that differentiate SK inhibitors remain poorly understood. The objective of this study was to determine how two unrelated SK channel inhibitors, apamin and AP14145, impact SK channel function in excised inside-out single channel recordings. Surprisingly, both apamin and AP14145 exert much of their inhibition by inducing a class of very long-lived channel closures (apamin: τ c,vl=11.8±7.1 s, and AP14145: τ c,vl=10.3±7.2 s), which were never observed under control conditions. Both inhibitors also induced changes to the three closed and two open durations typical of normal SK channel gating. AP14145 shifted the open duration distribution to favor longer open durations, whereas apamin did not alter open state kinetics. AP14145 also prolonged the two shortest channel closed durations (AP14145: τ c,s=3.50±0.81 ms, and τ c,i=32.0±6.76 ms vs. control: τ c,s=1.59±0.19 ms, and τ c,i=13.5±1.17 ms), thus slowing overall gating kinetics within bursts of channel activity. In contrast, apamin accelerated intra-burst gating kinetics by shortening the two shortest closed durations (τ c,s=0.75±0.10 ms and τ c,i=5.08±0.49 ms), and inducing periods of flickery activity. Finally, AP14145 introduced a unique form of inhibition by decreasing unitary current amplitude. SK channels exhibited two clearly distinguishable amplitudes (control: Ahigh=0.76±0.03 pA, and Alow=0.54±0.03 pA). AP14145 both reduced the fraction of patches exhibiting the higher amplitude (AP14145: 4/9 patches vs. control: 16/16 patches), and reduced the mean low amplitude (0.38±0.03 pA). Here we have demonstrated that both inhibitors introduce very long channel closures, but that each also exhibits unique effects on other components of SK gating kinetics and unitary current. The combination of these effects is likely to be critical for understanding the functional differences of each inhibitor in the context of cyclical Ca2+-dependent channel activation in vivo

Caracterização geral dos projetos irrigados do Vale do São Francisco com ênfase na fruticultura.

O estudo objetiva a sistematização de informações, enfatizando a fruticultura como fonte de geração de desenvolvimento do submédio do São Francisco pela implantação da agricultura irrigada, atuando como elemento catalisador do desenvolvimento regional pela transformação de um ambiente adverso caracterizado pela irregularidade das chuvas em polos de produção de culturas com elevado valor comercial. Levantamento de dados secundários, procedendo a seleção de informações de caráter de maior relevância ao objetivo do estudo e, posterior reflexão e análise. A implantação dos projetos de irrigação pela iniciativa pública gerou um novo desenho geográfico no semi-árido nordestino com a introdução da agricultura irrigada, em especial, a produção frutícola, pela melhoria dos níveis de renda, por ser uma atividade intensiva na utilização de mão de obra, promovendo a fixação do homem no campo através da interiorização do desenvolvimento regional.Trabalho apresentado na Reunião de Projeto de Economia Rural da UFRPE em parceria com a Embrapa Semiárido