Earthquake-enhanced dissolved carbon cycles in ultra-deep ocean sediments.

Hadal trenches are unique geological and ecological systems located along subduction zones. Earthquake-triggered turbidites act as efficient transport pathways of organic carbon (OC), yet remineralization and transformation of OC in these systems are not comprehensively understood. Here we measure concentrations and stable- and radiocarbon isotope signatures of dissolved organic and inorganic carbon (DOC, DIC) in the subsurface sediment interstitial water along the Japan Trench axis collected during the IODP Expedition 386. We find accumulation and aging of DOC and DIC in the subsurface sediments, which we interpret as enhanced production of labile dissolved carbon owing to earthquake-triggered turbidites, which supports intensive microbial methanogenesis in the trench sediments. The residual dissolved carbon accumulates in deep subsurface sediments and may continue to fuel the deep biosphere. Tectonic events can therefore enhance carbon accumulation and stimulate carbon transformation in plate convergent trench systems, which may accelerate carbon export into the subduction zones.

Technical Performance of a 430-Gene Preventative Genomics Assay to Identify Multiple Variant Types Associated with Adult-Onset Monogenic Conditions, Susceptibility Loci, and Pharmacogenetic Insights.

DNA-based screening in individuals without known risk factors potentially identifies those who may benefit from genetic counseling, early medical interventions, and/or avoidance of late or missed diagnoses. While not currently in widespread usage, technological advances in genetic analysis overcome barriers to access by enabling less labor-intensive and more cost-efficient means to discover variants of clinical importance. This study describes the technical validation of a 430-gene next-generation sequencing based assay, GeneCompassTM, indicated for the screening of healthy individuals in the areas of actionable health risks, pharmaceutical drug response, and wellness traits. The test includes genes associated with Mendelian disorders and genetic susceptibility loci, encompassing 14 clinical areas and pharmacogenetic variants. The custom-designed target enrichment capture and bioinformatics pipelines interrogate multiple variant types, including single nucleotide variants, insertions/deletions (indels), copy number variants, and functional haplotypes (star alleles), including tandem alleles and structural variants. Validation was performed against reference DNA from three sources: 1000 Genomes Project (n = 3), Coriell biobank (n = 105), and previously molecularly characterized biological specimens: blood (n = 15) and saliva (n = 11). Analytical sensitivity and specificity for single nucleotide variants (SNVs) were 97.57% and 99.99%, respectively, and for indels were 74.57% and 97.34%, respectively. This study demonstrates the validity of an NGS assay for genetic screening and the broadening of access to preventative genomics.

Hair regrowth treatment efficacy and resistance in androgenetic alopecia: A systematic review and continuous Bayesian network meta-analysis.

Background: Androgenetic alopecia (AGA) affects almost half the population, and several treatments intending to regenerate a normal scalp hair phenotype are used. This is the first study comparing treatment efficacy response and resistance using standardized continuous outcomes. Objective: To systematically compare the relative efficacy of treatments used for terminal hair (TH) regrowth in women and men with AGA. Methods: A systematic literature review was conducted (from inception to August 11, 2021) to identify randomized, Placebo-controlled trials with ≥ 20 patients and reporting changes in TH density after 24 weeks. Efficacy was analyzed by sex at 12 and 24 weeks using Bayesian network meta-analysis (B-NMA) and compared to frequentist and continuous outcomes profiles. Results: The search identified 2,314 unique articles. Ninety-eight were included for full-text review, and 17 articles met the inclusion criteria for data extraction and analyses. Eligible treatments included ALRV5XR, Dutasteride 0.5 mg/day, Finasteride 1 mg/day, low-level laser comb treatment (LLLT), Minoxidil 2% and 5%, Nutrafol, and Viviscal. At 24 weeks, the B-NMA regrowth efficacy in TH/cm2 and significance (**) in women were ALRV5XR: 30.09**, LLLT: 16.62**, Minoxidil 2%: 12.13**, Minoxidil 5%: 10.82**, and Nutrafol: 7.32**, and in men; ALRV5XR: 21.03**, LLLT: 18.75**, Dutasteride: 18.37**, Viviscal: 13.23, Minoxidil 5%: 13.13**, Finasteride: 12.38, and Minoxidil 2%: 10.54. Two distinct TH regrowth response profiles were found; Continuous: ALRV5XR regrowth rates were linear in men and accelerated in women; Resistant: after 12 weeks, LLLT, Nutrafol, and Viviscal regrowth rates attenuated while Dutasteride and Finasteride plateaued; Minoxidil 2% and 5% lost some regrowth. There were no statistical differences for the same treatment between women and men. B-NMA provided more accurate, statistically relevant, and conservative results than the frequentist-NMA. Conclusion: Some TH regrowth can be expected from most AGA treatments with less variability in women than men. Responses to drug treatments were rapid, showing strong early efficacy followed by the greatest resistance effects from flatlining to loss of regrowth after 12-16 weeks. Finasteride, Minoxidil 2% and Viviscal in men were not statistically different from Placebo. LLLT appeared more efficacious than pharmaceuticals. The natural product formulation ALRV5XR showed better efficacy in all tested parameters without signs of treatment resistance (see Graphical abstract). Systematic review registration: www.crd.york.ac.uk/PROSPERO/display_record.asp?ID=CRD42021268040, identifier CRD42021268040.

Prevalence of Obstructive Sleep Apnea Risk According to the STOP-BANG Questionnaire in an Oral Surgery Office-Based Anesthesia Patient Population.

PURPOSE: Patients with obstructive sleep apnea (OSA) are at an increased risk for perioperative and postoperative complications after receiving intravenous (IV) sedation or postoperative analgesia. We previously showed that most oral and maxillofacial surgery (OMS) providers do not screen for OSA using a quantifiable method. The purpose of this study was to determine the prevalence of OSA risk in the OMS office-based anesthesia patient population using the snoring, tiredness, observed apnea, high blood pressure, body mass index, age, neck circumference, and gender (STOP-BANG) questionnaire. PATIENTS AND METHODS: After deeming patients (n = 153) suitable for outpatient IV sedation using our existing institutional ambulatory preanesthesia protocol, 2 OMS providers administered the STOP-BANG questionnaire to classify patient risk for OSA. The questionnaire is a concise, validated predictor for OSA risk and consists of 8 yes or no questions. RESULTS: Of the 153 patients, 141 (92.16%) were at a low risk for moderate to severe OSA, 11 (7.19%) were at a moderate risk, and 1 (0.65%) was at a high risk. Overall, 12 (7.84%) patients were shown to be at risk for OSA. We estimate with 95% confidence that between 5.7 and 10% of all OMS office-based anesthesia patients are at risk for OSA. The IV sedation plans for 4 (2.61%) patients were changed after including OSA risk with the existing preanesthesia protocol. CONCLUSIONS: A statistically significant proportion (95% confidence interval, 0.0567 to 0.100) of the OMS office-based anesthesia patient population is at an increased risk for moderate to severe OSA. These results outline the importance of screening for OSA before office-based anesthesia administration. OMS providers can easily use the STOP-BANG questionnaire to assess OSA risk, modify anesthesia management, and improve patient safety.

Clinical analysis of germline copy number variation in DMD using a non-conjugate hierarchical Bayesian model.

BACKGROUND: Detection of copy number variants (CNVs) is an important aspect of clinical testing for several disorders, including Duchenne muscular dystrophy, and is often performed using multiplex ligation-dependent probe amplification (MLPA). However, since many genetic carrier screens depend instead on next-generation sequencing (NGS) for wider discovery of small variants, they often do not include CNV analysis. Moreover, most computational techniques developed to detect CNVs from exome sequencing data are not suitable for carrier screening, as they require matched normals, very large cohorts, or extensive gene panels. METHODS: We present a computational software package, geneCNV ( http://github.com/vkozareva/geneCNV ), which can identify exon-level CNVs using exome sequencing data from only a few genes. The tool relies on a hierarchical parametric model trained on a small cohort of reference samples. RESULTS: Using geneCNV, we accurately inferred heterozygous CNVs in the DMD gene across a cohort of 15 test subjects. These results were validated against MLPA, the current standard for clinical CNV analysis in DMD. We also benchmarked the tool's performance against other computational techniques and found comparable or improved CNV detection in DMD using data from panels ranging from 4,000 genes to as few as 8 genes. CONCLUSIONS: geneCNV allows for the creation of cost-effective screening panels by allowing NGS sequencing approaches to generate results equivalent to bespoke genotyping assays like MLPA. By using a parametric model to detect CNVs, it also fulfills regulatory requirements to define a reference range for a genetic test. It is freely available and can be incorporated into any Illumina sequencing pipeline to create clinical assays for detection of exon duplications and deletions.

Engineering the production of conjugated fatty acids in Arabidopsis thaliana leaves.

The seeds of many nondomesticated plant species synthesize oils containing high amounts of a single unusual fatty acid, many of which have potential usage in industry. Despite the identification of enzymes for unusual oxidized fatty acid synthesis, the production of these fatty acids in engineered seeds remains low and is often hampered by their inefficient exclusion from phospholipids. Recent studies have established the feasibility of increasing triacylglycerol content in plant leaves, which provides a novel approach for increasing energy density of biomass crops. Here, we determined whether the fatty acid composition of leaf oil could be engineered to accumulate unusual fatty acids. Eleostearic acid (ESA) is a conjugated fatty acid produced in seeds of the tung tree (Vernicia fordii) and has both industrial and nutritional end-uses. Arabidopsis thaliana lines with elevated leaf oil were first generated by transforming wild-type, cgi-58 or pxa1 mutants (the latter two of which contain mutations disrupting fatty acid breakdown) with the diacylglycerol acyltransferases (DGAT1 or DGAT2) and/or oleosin genes from tung. High-leaf-oil plant lines were then transformed with tung FADX, which encodes the fatty acid desaturase/conjugase responsible for ESA synthesis. Analysis of lipids in leaves revealed that ESA was efficiently excluded from phospholipids, and co-expression of tung FADX and DGAT2 promoted a synergistic increase in leaf oil content and ESA accumulation. Taken together, these results provide a new approach for increasing leaf oil content that is coupled with accumulation of unusual fatty acids. Implications for production of biofuels, bioproducts, and plant-pest interactions are discussed.

Carrier Screening is a Deficient Strategy for Determining Sperm Donor Eligibility and Reducing Risk of Disease in Recipient Children.

AIMS: DNA-based carrier screening is a standard component of donor eligibility protocols practiced by U.S. sperm banks. Applicants who test positive for carrying a recessive disease mutation are typically disqualified. The aim of our study was to examine the utility of a range of screening panels adopted by the industry and the effectiveness of the screening paradigm in reducing a future child's risk of inheriting disease. METHODS: A cohort of 27 donor applicants, who tested negative on an initial cystic fibrosis carrier test, was further screened with three expanded commercial carrier testing panels. These results were then compared to a systematic analysis of the applicants' DNA using next-generation sequencing (NGS) data. RESULTS: The carrier panels detected serious pediatric disease mutations in one, four, or six donor applicants. Because each panel screens distinct regions of the genome, no single donor was uniformly identified as carrier positive by all three panels. In contrast, systematic NGS analysis identified all donors as carriers of one or more mutations associated with severe monogenic pediatric disease. These included 30 variants classified as "pathogenic" based on clinical observation and 66 with a high likelihood of causing gene dysfunction. CONCLUSION: Despite tremendous advances in variant identification, understanding, and analysis, the vast majority of disease-causing mutation combinations remain undetected by commercial carrier screening panels, which cover a narrow, and often distinct, subset of genes and mutations. The biological reality is that all donors and recipients carry serious recessive disease mutations. This challenges the utility of any screening protocol that anchors donor eligibility to carrier status. A more effective approach to reducing recessive disease risk would consider joint comprehensive analysis of both donor and recipient disease mutations. This type of high-resolution recessive disease risk analysis is now available and affordable, but industry practice must be modified to incorporate its use.

Targeted mutation screening panels expose systematic population bias in detection of cystic fibrosis risk.

PURPOSE: Carrier screening for mutations contributing to cystic fibrosis (CF) is typically accomplished with panels composed of variants that are clinically validated primarily in patients of European descent. This approach has created a static genetic and phenotypic profile for CF. An opportunity now exists to reevaluate the disease profile of CFTR at a global population level. METHODS: CFTR allele and genotype frequencies were obtained from a nonpatient cohort with more than 60,000 unrelated personal genomes collected by the Exome Aggregation Consortium. Likely disease-contributing mutations were identified with the use of public database annotations and computational tools. RESULTS: We identified 131 previously described and likely pathogenic variants and another 210 untested variants with a high probability of causing protein damage. None of the current genetic screening panels or existing CFTR mutation databases covered a majority of deleterious variants in any geographical population outside of Europe. CONCLUSIONS: Both clinical annotation and mutation coverage by commercially available targeted screening panels for CF are strongly biased toward detection of reproductive risk in persons of European descent. South and East Asian populations are severely underrepresented, in part because of a definition of disease that preferences the phenotype associated with European-typical CFTR alleles.