Deformity, etiology, solution, sequence (DESS): Facial analysis in rhinoplasty.

PURPOSE: Rhinoplasty is amongst the most challenging surgeries to perfect and can take decades. This process begins during residency; however, residents often have limited exposure to rhinoplasty during their training and lack a standardized method for systematically analyzing and formulating a surgical plan. The DESS (Deformity, Etiology, Solution, Sequence) is a novel educational format for residents that serves to increase their pre-operative comfort with the surgical evaluation and intraoperative planning for a rhinoplasty. MATERIALS AND METHODS: A qualitative study performed at a tertiary academic institution with an otolaryngology residency program evaluating three consecutive residency classes comprised of four residents per class. A 9-item questionnaire was distributed to measure change in resident comfort after utilizing the DESS during their facial plastics rotation. Questionnaire responses highlighted resident comfort with facial nasal analysis, identifying deformities, suggesting surgical maneuvers, and synthesizing a comprehensive surgical plan. RESULTS: Ten of the twelve residents surveyed responded. Of those that responded, comfort in facial nasal analysis, identification of common nasal deformities, surgical planning, and development of an overall surgical plan were significantly improved after completion of the facial plastic rotation. These residents largely attributed their success to the systematic educational format, with an average score of 4.8/5.0 (SD 0.42). CONCLUSION: While rhinoplasty is a challenging artform to master, systematic approaches to analysis and operative planning are vital for teaching and guiding residents. Through this novel methodology, residents display significant improvement in their comfort with facial nasal analysis and overall surgical preparation.

Population-scale detection of non-reference sequence variants using colored de Bruijn graphs.

MOTIVATION: With the increasing throughput of sequencing technologies, structural variant (SV) detection has become possible across tens of thousands of genomes. Non-reference sequence (NRS) variants have drawn less attention compared with other types of SVs due to the computational complexity of detecting them. When using short-read data, the detection of NRS variants inevitably involves a de novo assembly which requires high-quality sequence data at high coverage. Previous studies have demonstrated how sequence data of multiple genomes can be combined for the reliable detection of NRS variants. However, the algorithms proposed in these studies have limited scalability to larger sets of genomes. RESULTS: We introduce PopIns2, a tool to discover and characterize NRS variants in many genomes, which scales to considerably larger numbers of genomes than its predecessor PopIns. In this article, we briefly outline the PopIns2 workflow and highlight our novel algorithmic contributions. We developed an entirely new approach for merging contig assemblies of unaligned reads from many genomes into a single set of NRS using a colored de Bruijn graph. Our tests on simulated data indicate that the new merging algorithm ranks among the best approaches in terms of quality and reliability and that PopIns2 shows the best precision for a growing number of genomes processed. Results on the Polaris Diversity Cohort and a set of 1000 Icelandic human genomes demonstrate unmatched scalability for the application on population-scale datasets. AVAILABILITY AND IMPLEMENTATION: The source code of PopIns2 is available from https://github.com/kehrlab/PopIns2. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Host individual and gut location are more important in gut microbiota community composition than temporal variation in the marine herbivorous fish Kyphosus sydneyanus.

BACKGROUND: Gut microbiota play a key role in the nutrition of many marine herbivorous fishes through hindgut fermentation of seaweed. Gut microbiota composition in the herbivorous fish Kyphosus sydneyanus (family Kyphosidae) varies between individuals and gut sections, raising two questions: (i) is community composition stable over time, especially given seasonal shifts in storage metabolites of dietary brown algae, and (ii) what processes influence community assembly in the hindgut? RESULTS: We examined variation in community composition in gut lumen and mucosa samples from three hindgut sections of K. sydneyanus collected at various time points in 2020 and 2021 from reefs near Great Barrier Island, New Zealand. 16S rRNA gene analysis was used to characterize microbial community composition, diversity and estimated density. Differences in community composition between gut sections remained relatively stable over time, with little evidence of temporal variation. Clostridia dominated the proximal hindgut sections and Bacteroidia the most distal section. Differences were detected in microbial composition between lumen and mucosa, especially at genus level. CONCLUSIONS: High variation in community composition and estimated bacterial density among individual fish combined with low variation in community composition temporally suggests that initial community assembly involved environmental selection and random sampling/neutral effects. Community stability following colonisation could also be influenced by historical contingency, where early colonizing members of the community may have a selective advantage. The impact of temporal changes in the algae may be limited by the dynamics of substrate depletion along the gut following feeding, i.e. the depletion of storage metabolites in the proximal hindgut. Estimated bacterial density, showed that Bacteroidota has the highest density (copies/mL) in distal-most lumen section V, where SCFA concentrations are highest. Bacteroidota genera Alistipes and Rikenella may play important roles in the breakdown of seaweed into useful compounds for the fish host.

Substrate degradation pathways, conserved functions and community composition of the hindgut microbiota in the herbivorous marine fish Kyphosus sydneyanus.

Symbiotic gut microbiota in the herbivorous marine fish Kyphosus sydneyanus play an important role in digestion by converting refractory algal carbohydrate into short-chain fatty acids. Here we characterised community composition using both 16S rRNA gene amplicon sequencing and shotgun-metagenome sequencing. Sequencing was carried out on lumen and mucosa samples (radial sections) from three axial sections taken from the hindgut of wild-caught fish. Both lumen and mucosa communities displayed distinct distributions along the hindgut, likely an effect of the differing selection pressures within these hindgut locations, as well as considerable variation among individual fish. In contrast, metagenomic sequences displayed a high level of functional similarity between individual fish and gut sections in the relative abundance of genes (based on sequencing depth) that encoded enzymes involved in algal-derived substrate degradation. These results suggest that the host gut environment selects for functional capacity in symbionts rather than taxonomic identity. Functional annotation of the enzymes encoded by the gut microbiota was carried out to infer the metabolic pathways used by the gut microbiota for the degradation of important dietary substrates: mannitol, alginate, laminarin, fucoidan and galactan (e.g. agar and carrageenan). This work provides the first evidence of the genomic potential of K. sydneyanus hindgut microbiota to convert highly refractory algal carbohydrates into metabolically useful short-chain fatty acids.

The Influence of Religious Belief on Burnout in Medical Students.

OBJECTIVE: Approximately half of all U.S. medical students are experiencing burnout. A previous study has demonstrated that higher levels of spirituality are associated with less burnout in medical students, yet no studies have examined the relationship between religious affiliation and burnout in medical students. The purpose of this study is to determine if specific religious affiliation and level of religious involvement is associated with less burnout in medical students. METHODS: A cross-sectional online survey was sent to all students attending five different osteopathic and allopathic medical schools in Kansas and Missouri. It contained a validated burnout measure, an item to identify religious affiliation, and items to quantify religious involvement. RESULTS: A response rate of 11.5% (495/4,300) was obtained. An ANOVA showed religious affiliations and burnout scores did not have any statistically significant relationships (F = 0.762, P = 0.619). Additionally, identification as an active participant within a religious affiliation had a statistically significant effect on burnout scores (F = 7.793, P = 0.005). CONCLUSIONS: This is the first study within the U.S. to show that religious affiliation is not associated with medical student burnout and that medical students who consider themselves to be active participants of their religion may be at lower risk of developing burnout, regardless of the faith they practice.

Evaluation of TSEB turbulent fluxes using different methods for the retrieval of soil and canopy component temperatures from UAV thermal and multispectral imagery.

The thermal-based Two-Source Energy Balance (TSEB) model partitions the evapotranspiration (ET) and energy fluxes from vegetation and soil components providing the capability for estimating soil evaporation (E) and canopy transpiration (T). However, it is crucial for ET partitioning to retrieve reliable estimates of canopy and soil temperatures and net radiation, as the latter determines the available energy for water and heat exchange from soil and canopy sources. These two factors become especially relevant in row crops with wide spacing and strongly clumped vegetation such as vineyards and orchards. To better understand these effects, very high spatial resolution remote-sensing data from an unmanned aerial vehicle were collected over vineyards in California, as part of the Grape Remote sensing and Atmospheric Profile and Evapotranspiration eXperiment and used in four different TSEB approaches to estimate the component soil and canopy temperatures, and ET partitioning between soil and canopy. Two approaches rely on the use of composite T rad, and assume initially that the canopy transpires at the Priestley-Taylor potential rate. The other two algorithms are based on the contextual relationship between optical and thermal imagery partition T rad into soil and canopy component temperatures, which are then used to drive the TSEB without requiring a priori assumptions regarding initial canopy transpiration rate. The results showed that a simple contextual algorithm based on the inverse relationship of a vegetation index and T rad to derive soil and canopy temperatures yielded the closest agreement with flux tower measurements. The utility in very high-resolution remote-sensing data for estimating ET and E and T partitioning at the canopy level is also discussed.

Catch composition and aspects of the biology of sharks caught by Thai commercial fisheries in the Andaman Sea.

Catch composition, landing patterns and biological aspects of sharks caught by commercial fishing fleet operating in the Andaman Sea were recorded from landing sites in Ranong province of Thailand over a period of 1 year. Of the 64 species previously reported in the existing Thailand checklist, only 17 species were recorded in this study. Shark landings from the Andaman Sea appear now to be dominated largely by bamboo sharks Chiloscyllium spp. (Hemiscylliidae), which contribute c. 65% of the total number of sharks recorded. The carcharhinid sharks comprised c. 30·5% to the total catch, while the remaining c. 4·5% of landings comprised sharks from the families Squalidae, Stegostomatidae, Sphyrnidae and Triakidae. The catch composition is remarkably different from the previous landing survey in 2004, in that the current study found noticeable declines in landings of slow-growing, late- maturing and low-fecundity species (especially sphyrnid and carcharhinid species). The absences of many species and changes in life-stage composition suggest that the populations of these groups may be close to collapse. The results from this study emphasize the urgency for additional research and monitoring efforts and also the need for management incentives in order to manage shark fisheries effectively in the Andaman Sea.

Preclinical atherosclerosis at the time of pre-eclamptic pregnancy and up to 10 years postpartum: systematic review and meta-analysis.

OBJECTIVES: Pre-eclampsia (PE) is a pregnancy-specific hypertensive disorder that has been associated with cardiovascular risk factors and vascular changes, such as acute atherosis in placental blood vessels, similar to early-stage atherosclerosis. The objective of this study was to determine whether women with PE have increased atherosclerotic burden, as determined by the carotid intima-media thickness (CIMT), compared with women without PE. METHODS: We conducted a systematic review and meta-analysis of studies that reported CIMT, a non-invasive, ultrasound-based measure of subclinical atherosclerosis, in women who did vs those who did not have PE. Studies were eligible if they had been conducted during pregnancy or during the first decade postpartum, and if CIMT was measured in the common carotid artery. Studies published before 7 March 2016 were identified through PubMed, EMBASE and Web of Science. Two reviewers used predefined forms and protocols to evaluate independently the eligibility of studies based on titles and abstracts and to perform full-text screening, data abstraction and quality assessment. Heterogeneity was assessed using the I2 statistic. Standardized mean difference (SMD) was used as a measure of effect size. RESULTS: Fourteen studies were included in the meta-analysis. Seven studies were carried out during pregnancy complicated by PE, 10 were carried out up to 10 years postpartum and three included measurements obtained at both time periods. Women who had PE had significantly higher CIMT than did those who did not have PE, both at the time of diagnosis (SMD, 1.10 (95% CI, 0.73-1.48); P < 0.001) and in the first decade postpartum (SMD, 0.58 (95% CI, 0.36-0.79); P < 0.001). CONCLUSIONS: Atherosclerotic load is present at the time of PE and may be a mechanism associated with the disease. Measurement of CIMT may offer an opportunity for the early identification of premenopausal women with atherosclerotic burden after a PE pregnancy. Copyright © 2016 ISUOG. Published by John Wiley & Sons Ltd.

Resumen Objetivos: La preeclampsia (PE) es un trastorno hipertensivo específico del embarazo que ha sido asociada con factores de riesgo cardiovascular y cambios vasculares, tales como aterosis aguda en los vasos sanguíneos de la placenta, similares a las primeras etapas de la aterosclerosis. El objetivo de este estudio fue determinar si las mujeres con PE han aumentado la carga aterosclerótica, según lo determinado por el espesor del complejo íntima-media de la arteria carótida (CIMT, por sus siglas en inglés), en comparación con las mujeres sin PE. MÉTODOS: Se realizó una revisión sistemática y un metaanálisis de estudios que reportaron el CIMT, una medida no invasiva de la aterosclerosis subclínica obtenida mediante ecografía, comparando mujeres con PE y mujeres sin ella. Solo se incluyeron estudios llevados a cabo durante el embarazo o durante la primera década después del parto, y en los que se midió el CIMT en la arteria carótida común. Se usaron las bases de datos de PubMed, EMBASE y Web of Science para identificar estudios publicados antes del 7 marzo de 2016. Dos revisores utilizaron formularios y protocolos preestablecidos para evaluar de forma independiente la elegibilidad de los estudios, a partir de los títulos y los resúmenes, y para realizar un cribado del texto completo, un resumen de los datos y una evaluación de calidad. La heterogeneidad se evaluó mediante el test estadístico I2 . Se usó la diferencia de medias estandarizada (SMD, por sus siglas en inglés) como una medida de la magnitud del efecto. Resultados: En el metaanálisis se incluyeron catorce estudios. Siete de los estudios se llevaron a cabo durante embarazos complicados por PE, 10 se realizaron hasta 10 años después del parto y tres incluyeron mediciones tomadas en ambos períodos. Las mujeres con PE tuvieron un CIMT significativamente mayor que aquellas que no la tenían, tanto en el momento del diagnóstico (SMD 1,10 (I 95%, 0,73-1,48), P <0,001) como en la primera década después del parto (SMD 0,58 (IC 95%, 0,36-0,79), P <0,001). Conclusiones: La carga aterosclerótica está presente en el momento de la PE y podría ser un mecanismo asociado con esta enfermedad. La medición del CIMT puede ofrecer una oportunidad para la identificación temprana de mujeres premenopáusicas con carga aterosclerótica después de un embarazo con PE. : (pre-eclampsia,PE),,,。-(carotid intima-media thickness,CIMT),PEPE,。 : PEPECIMTmeta,CIMT、。:10CIMT。PubMed、EMBASEWeb of Science,201637。,,、。I2 。(SMD)。 : meta14。7PE,1010,3。PEPE,[SMD,1.10(95% CI,0.73~1.48);P<0.001]10[SMD,0.58(95% CI,0.36~0.79);P<0.001] CIMT。 : PE,。CIMT,PE。.

Optimization of isoxazoline amide benzoxaboroles for identification of a development candidate as an oral long acting animal ectoparasiticide.

Novel isoxazoline amide benzoxaboroles were designed and synthesized to optimize the ectoparasiticide activity of this chemistry series against ticks and fleas. The study identified an orally bioavailable molecule, (S)-N-((1-hydroxy-3,3-dimethyl-1,3-dihydrobenzo[c][1,2]oxaborol-6-yl)methyl)-2-methyl-4-(5-(3,4,5-trichlorophenyl)-5-(trifluoromethyl)-4,5-dihydroisoxazol-3-yl)benzamide (23), with a favorable pharmacodynamics profile in dogs (Cmax=7.42ng/mL; Tmax=26.0h; terminal half-life t1/2=127h). Compound 23, a development candidate, demonstrated 100% therapeutic effectiveness within 24h of treatment, with residual efficacy of 97% against American dog ticks (Dermacentor variabilis) on day 30 and 98% against cat fleas (Ctenocephalides felis) on day 32 after a single oral dose at 25mg/kg in dogs.

The effect of anti-emetic doses of dexamethasone on postoperative blood glucose levels in non-diabetic and diabetic patients: a prospective randomised controlled study.

There are few data regarding postoperative hyperglycaemia in non-diabetic compared with diabetic patients following postoperative nausea and vomiting prophylaxis with dexamethasone. Eighty-five non-diabetic patients and patients with type-2 diabetes were randomly allocated to receive intravenous dexamethasone (8 mg) or ondansetron (4 mg). Blood glucose levels were measured at baseline and then 2, 4 and 24 h following induction of anaesthesia. In non-diabetic patients, the mean (SD) maximum blood glucose was higher in those who received dexamethasone compared with ondansetron (9.1 (2.2) mmol.l(-1) vs. 7.8 (1.4) mmol.l(-1) , p = 0.04). In diabetic patients, the mean (SD) maximum blood glucose was also higher in those who received dexamethasone compared with ondansetron (14.0 (2.5) mmol.l(-1) vs. 10.7 (2.4) mmol.l(-1) , p < 0.01). Multivariate analysis demonstrated that dexamethasone administration was a significant predictor of maximum postoperative blood glucose increase (p < 0.01) after adjusting for potential confounders. There was no interaction between baseline blood glucose level, or presence or absence of diabetes, and dexamethasone administration. We conclude that dexamethasone increases postoperative blood glucose levels in both non-diabetics and diabetics.

Return to sport following acute lateral ligament repair of the ankle in professional athletes.

PURPOSE: Recent literature supports early reconstruction of severe acute lateral ligament injuries in professional athletes, suggesting earlier rehabilitation and reduced recurrent instability incidence. Not previously reported, predicting the time to return to training and play is important to both athlete and club. We evaluate the effectiveness and complications of lateral ligament reconstruction in professional athletes. We aim to estimate the time to return to training and sports in both isolated injuries and patients with additional injuries. METHODS: A consecutive series of 42 athletes underwent modified Broström repair for clinically and radiologically confirmed acute grade III lateral ligament injury. Of 42, 30 had isolated complete rupture of ATFL and CFL. Of 42, 12 had additional injuries (osteochondral lesions, deltoid ligament injuries). All patients received minimum of 2 years post-operative assessment. RESULTS: The median return to training and sports for isolated injuries was 63 days (49-110) and 77 days (56-127), respectively. However, for concomitant injury results were 86 days (63-152) and 105 days (82-178). This delay was significant (p < 0.001). Despite no difference in pre- and post-op VAS scores between the groups, those with combined injuries had significantly lower FAOS pain and symptoms sub-scores post-operatively (p = 0.027, p < 0.001). Two superficial infections responded to oral antibiotics. No patient developed recurrent instability. All returned to their pre-injury level of professional sports. CONCLUSION: Lateral ligament reconstruction is a safe and effective treatment for acute severe ruptures providing a stable ankle and expected return to sports at approximately 10 weeks. Despite return to the same level of competition, club and player should be aware that associated injuries may delay return and symptoms may continue. These results may act as a guide to predict the expected time to return to training and to sport after surgical repair of acute injuries and also the influence of associated injuries in prolonging rehabilitation. LEVEL OF EVIDENCE: III.

Life histories of two deep-water Australian endemic elasmobranchs: Argus skate Dipturus polyommata and eastern spotted gummy shark Mustelus walkeri.

Two Australian endemic elasmobranchs, the Argus skate Dipturus polyommata and the eastern spotted gummy shark Mustelus walkeri, were collected from the by-catch of a prawn Melicertus plebejus trawl fishery off Queensland. Age and growth parameters were estimated from growth band counts in vertebral sections of 220 D. polyommata and 44 M. walkeri. Dipturus polyommata males and females had an observed maximum age of 10 years and reached maximum sizes of 369 and 371 mm total length (LT ), respectively. Mustelus walkeri lived longer, with the oldest female aged 16 years and measuring 1050 mm stretched total length (LST ), and oldest male aged 9 years and 805 mm LST . Dipturus polyommata grew relatively fast with a von Bertalanffy growth completion parameter of k = 0·208 year(-1) with males reaching maturity at 4·0 years (c. 278 mm LT ) and females at 5·1 years (c. 305 mm LT ). Mustelus walkeri grew more slowly with k = 0·033 year(-1) with males estimated to mature at 7-9 years (670-805 mm LST ) and females at 10-14 years (833-1012 mm LST ). Length at birth inferred from neonate D. polyommata was 89-111 mm LT while for M. walkeri it was estimated to be 273 LST based on the value of L0 from the von Bertalanffy growth model. Both species appeared to have continuous reproductive cycles and low fecundity with an average ovarian fecundity of eight follicles for D. polyommata and a litter size of five to seven pups for M. walkeri. Based on these life-history traits, D. polyommata is more resilient to fishing pressure than M. walkeri.

Discovery of an orally bioavailable isoxazoline benzoxaborole (AN8030) as a long acting animal ectoparasiticide.

A novel series of isoxazoline benzoxaborole small molecules was designed and synthesized for a structure-activity relationship (SAR) investigation to assess the ectoparasiticide activity against ticks and fleas. The study identified an orally bioavailable molecule, (S)-3,3-dimethyl-5-(5-(3,4,5-trichlorophenyl)-5-(trifluoromethyl)-4,5-dihydroisoxazol-3-yl)benzo[c][1,2]oxaborol-1(3H)-ol (38, AN8030), which was long lasting in dogs (t1/2=22 days). Compound 38 demonstrated 97.6% therapeutic effectiveness within 24 h of treatment, with residual efficacy of 95.3% against American dog ticks (Dermacentor variabilis) on day 30% and 100% against cat fleas (Ctenocephalides felis) on day 32 after a single oral dose at 50 mg/kg in dogs.

Species composition and aspects of the biology of Orectolobiformes from Indonesian waters.

The biological aspects of members of the order Orectolobiformes exploited in Indonesian waters are given. Seven species belonging to five families were recorded in the catches at various landing sites in southern Indonesia. Of these, Chiloscyllium punctatum was the most abundant species landed, contributing >50% of the number of orectolobiforms recorded. The biological data obtained varied greatly between the species listed. The total length (LT ) at maturity for some species, e.g. C. punctatum and Nebrius ferrugineus, varied from that which has been previously recorded for those species in other regions. This highlights the need for regional-specific biological data for fisheries managers and conservation assessors.

Age, growth and maturity of the pelagic thresher Alopias pelagicus and the scalloped hammerhead Sphyrna lewini.

Indonesia has the greatest reported chondrichthyan catches worldwide, with c.110,000 t caught annually. The pelagic thresher (Alopias pelagicus) and scalloped hammerhead (Sphryna lewini) together comprise about 25% of the total catches of sharks landed in Indonesia. Age and growth parameters were estimated for A. pelagicus and S. lewini from growth-band counts of thin-cut vertebral sections. Alopias pelagicus (n = 158) and S. lewini (n = 157) vertebrae were collected from three Indonesian fish markets over a 5 year period. A multi-model analysis was used to estimate growth parameters for both species. The models of best fit for males and females for A. pelagicus was the three-parameter logistic (L∞ = 3169 mm LT , k = 0·2) and the two-parameter von Bertalanffy models (L∞ = 3281 mm LT , k = 0·12). Age at maturity was calculated to be 10·4 and 13·2 years for males and females, respectively, and these are the oldest estimated for this species. The samples of S. lewini were heavily biased towards females, and the model of best fit for males and females was the three-parameter Gompertz (L∞ = 2598 mm LT , k = 0·15) and the two-parameter Gompertz (L∞ = 2896 mm LT , k= 0·16). Age at maturity was calculated to be 8·9 and 13·2 years for males and females, respectively. Although numerous age and growth studies have previously been undertaken on S. lewini, few studies have been able to obtain adequate samples from all components of the population because adult females, adult males and juveniles often reside in different areas. For the first time, sex bias in this study was towards sexually mature females, which are commonly lacking in previous biological studies on S. lewini. Additionally, some of the oldest aged specimens and highest age at maturity for both species were observed in this study. Both species exhibit slow rates of growth and late age at maturity, highlighting the need for a re-assessment of the relative resilience of these two globally threatened sharks at current high levels of fishing mortality throughout the eastern Indian Ocean.

Restricted movements and mangrove dependency of the nervous shark Carcharhinus cautus in nearshore coastal waters.

This study used a network of acoustic receivers deployed around a no-take zone in Mangrove Bay, within the Ningaloo Reef Marine Park in Western Australia, to study residency and habitat preference of a small coastal shark, the nervous shark Carcharhinus cautus. Twelve C. cautus were tagged with acoustic tags and monitored for up to 579 days. Based on individuals detected within the receiver array for at least 2 months, C. cautus had small core (50% kernel utilization distribution, KUD) and home ranges (95% KUD) of 0.66 and 3.64 km2, respectively, and showed a strong habitat preference for mangroves, which are only found in the no-take zone. This resulted in C. cautus spending most of their detected time within the no-take zone boundaries (mean = 81.5%), showing that such a protected area could be beneficial to protect this species from extensive fishing pressure and local depletion, where required. Not all C. cautus remained within the acoustic array, however, suggesting that individual variations occur and that not all individuals would benefit from such protection. This study provides important information about the habitat, residency and movements of C. cautus that can be used for management and conservation. The strong affinity and residency of C. cautus within a mangrove-fringing coastline, emphasizes the importance of mangrove habitat to the species and suggests that such preferences can be used to design appropriate no-take zones for this species or others with similar habitat preferences.

From cheek swabs to consensus sequences: an A to Z protocol for high-throughput DNA sequencing of complete human mitochondrial genomes.

BACKGROUND: Next-generation DNA sequencing (NGS) technologies have made huge impacts in many fields of biological research, but especially in evolutionary biology. One area where NGS has shown potential is for high-throughput sequencing of complete mtDNA genomes (of humans and other animals). Despite the increasing use of NGS technologies and a better appreciation of their importance in answering biological questions, there remain significant obstacles to the successful implementation of NGS-based projects, especially for new users. RESULTS: Here we present an 'A to Z' protocol for obtaining complete human mitochondrial (mtDNA) genomes - from DNA extraction to consensus sequence. Although designed for use on humans, this protocol could also be used to sequence small, organellar genomes from other species, and also nuclear loci. This protocol includes DNA extraction, PCR amplification, fragmentation of PCR products, barcoding of fragments, sequencing using the 454 GS FLX platform, and a complete bioinformatics pipeline (primer removal, reference-based mapping, output of coverage plots and SNP calling). CONCLUSIONS: All steps in this protocol are designed to be straightforward to implement, especially for researchers who are undertaking next-generation sequencing for the first time. The molecular steps are scalable to large numbers (hundreds) of individuals and all steps post-DNA extraction can be carried out in 96-well plate format. Also, the protocol has been assembled so that individual 'modules' can be swapped out to suit available resources.

Bacteroidia and Clostridia are equipped to degrade a cascade of polysaccharides along the hindgut of the herbivorous fish Kyphosus sydneyanus.

The gut microbiota of the marine herbivorous fish Kyphosus sydneyanus are thought to play an important role in host nutrition by supplying short-chain fatty acids (SCFAs) through fermentation of dietary red and brown macroalgae. Here, using 645 metagenome-assembled genomes (MAGs) from wild fish, we determined the capacity of different bacterial taxa to degrade seaweed carbohydrates along the gut. Most bacteria (99%) were unclassified at the species level. Gut communities and CAZyme-related transcriptional activity were dominated by Bacteroidia and Clostridia. Both classes possess genes CAZymes acting on internal polysaccharide bonds, suggesting their role initiating glycan depolymerization, followed by rarer Gammaproteobacteria and Verrucomicrobiae. Results indicate that Bacteroidia utilize substrates in both brown and red algae, whereas other taxa, namely, Clostridia, Bacilli, and Verrucomicrobiae, utilize mainly brown algae. Bacteroidia had the highest CAZyme gene densities overall, and Alistipes were especially enriched in CAZyme gene clusters (n = 73 versus just 62 distributed across all other taxa), pointing to an enhanced capacity for macroalgal polysaccharide utilization (e.g., alginate, laminarin, and sulfated polysaccharides). Pairwise correlations of MAG relative abundances and encoded CAZyme compositions provide evidence of potential inter-species collaborations. Co-abundant MAGs exhibited complementary degradative capacities for specific substrates, and flexibility in their capacity to source carbon (e.g., glucose- or galactose-rich glycans), possibly facilitating coexistence via niche partitioning. Results indicate the potential for collaborative microbial carbohydrate metabolism in the K. sydneyanus gut, that a greater variety of taxa contribute to the breakdown of brown versus red dietary algae, and that Bacteroidia encompass specialized macroalgae degraders.

Cardiovascular safety of the dipetidyl peptidase-4 inhibitor alogliptin in type 2 diabetes mellitus.

AIM: As there have been concerns that some classes or agents for the treatment of type 2 diabetes may increase CV risk, we evaluated the cardiovascular profile of the dipeptidyl peptidase-4 inhibitor alogliptin. METHODS: We evaluated the incidence of CV events in patients treated with alogliptin, placebo or comparator antihyperglycaemic drugs in the clinical trial database for alogliptin using the composite major adverse cardiovascular event (MACE) endpoints of CV death, non-fatal myocardial infarction and non-fatal stroke. RESULTS: The pooled analysis included 4168 patients exposed to alogliptin 12.5 and 25 mg daily for 2023 patient-years compared to 691 patients treated with placebo for 263 patient-years and 1169 patients treated with other antidiabetic agents (metformin, sulfonylureas and thiazolidinediones) for 703 patient-years. CV events were adjudicated by an expert endpoint committee blinded to treatment allocation. The incidence rates of the combined MACE were not significantly different between patients treated with alogliptin and comparator therapies (hazard ratio=0.635, 95% confidence interval, 0.0, 1.41). Additionally, other types of serious CV events were not significantly different between patients treated with alogliptin and comparator therapies. CONCLUSION: These analyses have not shown a signal of increased CV risk with alogliptin in patients with type 2 diabetes. Future results from the adequately powered EXAMINE trial will definitively assess the CV safety profile of aloglipin in patients with type 2 diabetes mellitus.

Adhesion molecules, endothelin-1 and lung function in seven population-based cohorts.

CONTEXT: Endothelial function is abnormal in chronic obstructive pulmonary disease (COPD); whether endothelial dysfunction causes COPD is unknown. OBJECTIVE: Test associations of endothelial biomarkers with FEV1 using instrumental variables. METHODS: Among 26 907 participants with spirometry, ICAM-1, P-selectin, E-selectin and endothelin-1 were measured in subsets. RESULTS: ICAM-1 and P-selectin were inversely associated with FEV1 among European-Americans (-29 mL and -34 mL per standard deviation of log-transformed biomarker, p < 0.001), as was endothelin-1 among African-Americans (-22 mL, p = 0.008). Genetically-estimated ICAM-1 and P-selectin were not significantly associated with FEV1. The instrumental variable for endothelin-1 was non-informative. CONCLUSION: Although ICAM-1, P-selectin and endothelin-1 were inversely associated with FEV1, associations for ICAM-1 and P-selectin do not appear causal.