Prenatal diagnosis of CLCN4-related neurodevelopmental disorder in fetuses with congenital brain anomalies.

We report two male fetuses born to a healthy unrelated couple, with agenesis of the corpus callosum identified on detailed 20-week ultrasound scans and confirmed by in-utero MRI. Whole-genome sequencing identified a likely pathogenic missense variant in the CLCN4 gene, establishing this as the causative gene in the family. Pathogenic variants in the CLCN4 gene cause a neurodevelopmental disorder (also called Raynaud-Claes syndrome) inherited in an X-linked pattern. The disorder is characterised by developmental delay, intellectual disability, autism spectrum disorder, epilepsy, mental health conditions, and significant feeding difficulties, predominantly, but not exclusively, affecting males. This is the first report of a prenatal phenotype associated with variants in the CLCN4 gene. The diagnosis of the CLCN4-related neurodevelopmental disorder in this family allowed accurate genetic counseling and discussion of reproductive choices. This leaves uncertainty about the possibility of a postnatal neurodevelopmental phenotype in heterozygous females, which we discuss.

Germline mismatch repair (MMR) gene analyses from English NHS regional molecular genomics laboratories 1996-2020: development of a national resource of patient-level genomics laboratory records.

OBJECTIVE: To describe national patterns of National Health Service (NHS) analysis of mismatch repair (MMR) genes in England using individual-level data submitted to the National Disease Registration Service (NDRS) by the NHS regional molecular genetics laboratories. DESIGN: Laboratories submitted individual-level patient data to NDRS against a prescribed data model, including (1) patient identifiers, (2) test episode data, (3) per-gene results and (4) detected sequence variants. Individualised per-laboratory algorithms were designed and applied in NDRS to extract and map the data to the common data model. Laboratory-level MMR activity audit data from the Clinical Molecular Genetics Society/Association of Clinical Genomic Science were used to assess early years' missing data. RESULTS: Individual-level data from patients undergoing NHS MMR germline genetic testing were submitted from all 13 English laboratories performing MMR analyses, comprising in total 16 722 patients (9649 full-gene, 7073 targeted), with the earliest submission from 2000. The NDRS dataset is estimated to comprise >60% of NHS MMR analyses performed since inception of NHS MMR analysis, with complete national data for full-gene analyses for 2016 onwards. Out of 9649 full-gene tests, 2724 had an abnormal result, approximately 70% of which were (likely) pathogenic. Data linkage to the National Cancer Registry demonstrated colorectal cancer was the most frequent cancer type in which full-gene analysis was performed. CONCLUSION: The NDRS MMR dataset is a unique national pan-laboratory amalgamation of individual-level clinical and genomic patient data with pseudonymised identifiers enabling linkage to other national datasets. This growing resource will enable longitudinal research and can form the basis of a live national genomic disease registry.

Morphological transformation from fibers to sheets in embiopteran silk.

Embioptera (webspinners) are insects that construct domiciles using silk produced from their front feet. This silk is the finest known with measured single fiber diameters in the 30-140 nm range. In the wild, some webspinner silk on trees is observed to have a clothlike or shiny sheetlike appearance. Both forms of silk shield the occupants from rain water effectively: presumably valuable in tropical environments. In this article we elucidate the mechanism by which silk fibers are transformed into these structures through interaction with water. We quantify the evaporation rates of single water droplets which have been suspended on unmodified as-spun silk for two Trinidadian arboreal species: Antipaluria urichi (Clothodidae) and Pararhagadochir trinitatis (Scelembiidae). These rates are compared to those of droplets suspended on rose petals due to similar wetting properties (both hydrophobicity and pinning). We observe that on sufficiently thick silk, droplet evaporation rates decrease with time. This behavior is a result of a thin soluble film developing on the drop surface that later becomes a solid residual film. Experimentally verified theoretical models are invoked to support the results.

Ultrasonographic Evaluation of Physiologic Free Intraperitoneal Fluid in Healthy Children: A Prospective Observational Study.

OBJECTIVES: The detection of intraperitoneal free fluid (FF) is an important finding in the sonographic evaluation of the pediatric abdomen, especially in the context of blunt abdominal trauma. One specific challenge is differentiating physiologic from pathologic FF. The purpose of this study was to determine with ultrasound the prevalence, location, and volume of intraperitoneal FF in healthy pediatric patients and its relation to pubertal status and gender. METHODS: Healthy children between the ages of 1 and 17 years who presented to the emergency department with non-abdominal complaints were evaluated for physiologic intra-abdominal fluid. Point-of-Care Ultrasound (POCUS) was performed, utilizing the Focused Assessment with Sonography in Trauma (FAST) examination. RESULTS: A total of 325 pediatric patients were analyzed. Intraperitoneal FF was found in 52 children (16.0%, 95% CI: 12.0-20.0%). The pelvis was the only region where FF was located. The prevalence of FF was nearly equivalent between male and female children (15.4% vs 16.7%, P = .76). There was a higher prevalence of FF identified in the prepubertal subgroup compared to the pubertal group (20.0% vs 11.3%, P = .03). Seventy-seven percent of children with FF had a fluid volume of less than 1 mL. CONCLUSIONS: Physiologic FF of less than 1 mL within the pelvis is a common finding in the pediatric population. There was no difference in the rate of FF identified by gender, but there was a higher prevalence of FF among prepubertal children.

Supervised Learning for Predictive Pore Size Classification of Regenerated Cellulose Membranes Based on Atomic Force Microscopy Measurements.

Nanoporous dialysis membranes made of regenerated cellulose are used as molecular weight cutoff standards in bioseparations. In this study, mesoporous standards with Stokes' radii (50 kDa/2.7 nm, 100 kDa/3.4 nm and 1000 kDa/7.3 nm) and overlapping skewed distributions were characterized using AFM, with the specific aim of generating pore size classifiers for biomimetic membranes using supervised learning. Gamma transformation was used prior to conducting discriminant analysis in terms of the area under the receiver operating curve (AUC) and classification accuracy (Acc). Monte Carlo simulations were run to generate datasets (n = 10) on which logistic regression was conducted using a constant ratio of 80:20 (measurement:algorithm training), followed by algorithm validation by WEKA. The proposed algorithm can classify the 1000 kDa vs. 100 kDa (AUC > 0.8) correctly, but discrimination is weak for the 100 kDa vs. 50 kDa (AUC < 0.7), the latter being attributed to the instrument accuracy errors below 5 nm. As indicated by the results of the cross-validation study, a test size equivalent to 70% (AUCtapping = 0.8341 ± 0.0519, Acctapping = 76.8% ± 5.9%) and 80% (AUCfluid = 0.7614 ± 0.0314, Acctfluid = 76.2% ± 1.0%) of the training sets for the tapping and fluid modes are needed for correct classification, resulting in predicted reduction of scan times.

A Multiscale Characterization of Two Tropical Embiopteran Species: Nano- and Microscale Features of Silk, Silk-Spinning Behavior, and Environmental Correlates of their Distributions.

Embioptera display the unique ability to spin silk with their front feet to create protective domiciles. Their body form is remarkably uniform throughout the order, perhaps because they all live within the tight confines of silken tubes. This study contributes to an understanding of the ecology of Embioptera, an order that is rarely studied in the field. We conducted a census to quantify the habitats of two species with overlapping distributions on the tropical island of Trinidad in a search for characteristics that might explain their distinct ecologies. One species, Antipaluria urichi (Saussure) (Embioptera: Clothodidae), lives in larger colonies with more expansive silk in habitats throughout the island, especially in the rainforest of the Northern Range Mountains. The other, Pararhagadochir trinitatis (Saussure) (Embioptera: Scelembiidae), was found only in lowland locations. We quantified silk-spinning behavior and productivity of the two species and found that A. urichi spins thicker silk sheets per individual and emphasizes spin-steps that function to create a domicile that is more expansive than that produced by P. trinitatis. Their silks also interact differently when exposed to water: the smaller-diameter silk fibers of P. trinitatis form more continuous films on the surface of the domicile after being wetted and dried than that seen in A. urichi silk. This tendency gives P. trinitatis silk a shiny appearance in the field compared to the more cloth-like silk of A. urichi. How these silks function in the field and if the differences are partially responsible for the distinct distributions of the two species remain to be determined.

Structural and wetting properties of nature's finest silks (order Embioptera).

Insects from the order Embioptera (webspinners) spin silk fibres which are less than 200 nm in diameter. In this work, we characterized and compared the diameters of single silk fibres from nine species-Antipaluria urichi, Pararhagadochir trinitatis, Saussurembia calypso, Diradius vandykei, Aposthonia ceylonica, Haploembia solieri, H. tarsalis, Oligotoma nigra and O. saundersii. Silk from seven of these species have not been previously quantified. Our studies cover five of the 10 named taxonomic families and represent about one third of the known taxonomic family-level diversity in the order Embioptera. Naturally spun silk varied in diameter from 43.6 ± 1.7 nm for D. vandykei to 122.4 ± 3.2 nm for An. urichi. Mean fibre diameter did not correlate with adult female body length. Fibre diameter is more similar in closely related species than in more distantly related species. Field observations indicated that silk appears shiny and smooth when exposed to rainwater. We therefore measured contact angles to learn more about interactions between silk and water. Higher contact angles were measured for silks with wider fibre diameter and higher quantity of hydrophobic amino acids. High static contact angles (ranging up to 122° ± 3° for An. urichi) indicated that silken sheets spun by four arboreal, webspinner species were hydrophobic. A second contact angle measurement made on a previously wetted patch of silk resulted in a lower contact angle (average difference was greater than 27°) for all four species. Our studies suggest that silk fibres which had been previously exposed to water exhibited irreversible changes in hydrophobicity and water adhesion properties. Our results are in alignment with the 'super-pinning' site hypothesis by Yarger and co-workers to describe the hydrophobic, yet water adhesive, properties exhibited by webspinner silk fibres. The physical and chemical insights gained here may inform the synthesis and development of smaller diameter silk fibres with unique water adhesion properties.

Comparative modeling and molecular docking analysis of white, brown and soft rot fungal laccases using lignin model compounds for understanding the structural and functional properties of laccases.

Extrinsic catalytic properties of laccase enable it to oxidize a wide range of aromatic (phenolic and non-phenolic) compounds which makes it commercially an important enzyme. In this study, we have extensively compared and analyzed the physico-chemical, structural and functional properties of white, brown and soft rot fungal laccases using standard protein analysis software. We have computationally predicted the three-dimensional comparative models of these laccases and later performed the molecular docking studies using the lignin model compounds. We also report a customizable rapid and reliable protein modelling and docking pipeline for developing structurally and functionally stable protein structures. We have observed that soft rot fungal laccases exhibited comparatively higher structural variation (higher random coil) when compared to brown and white rot fungal laccases. White and brown rot fungal laccase sequences exhibited higher similarity for conserved domains of Trametes versicolor laccase, whereas soft rot fungal laccases shared higher similarity towards conserved domains of Melanocarpus albomyces laccase. Results obtained from molecular docking studies showed that aminoacids PRO, PHE, LEU, LYS and GLN were commonly found to interact with the ligands. We have also observed that white and brown rot fungal laccases showed similar docking patterns (topologically monomer, dimer and trimer bind at same pocket location and tetramer binds at another pocket location) when compared to soft rot fungal laccases. Finally, the binding efficiencies of white and brown rot fungal laccases with lignin model compounds were higher compared to the soft rot fungi. These findings can be further applied in developing genetically efficient laccases which can be applied in growing biofuel and bioremediation industries.

Purification and characterisation of anti-pneumococcal capsular polysaccharide IgG immunoglobulins.

OBJECTIVES: The production of reference materials for quantifying pneumococcal antibody concentrations relies upon large scale vaccination. An alternative simple, reproducible protocol has been developed for the affinity purification of 23 serotype anti-pneumococcal capsular polysaccharide (PCP) IgG immunoglobulins. DESIGN & METHODS: The purification protocol utilised IgG fractionation, capsular polysaccharide (CPS) adsorption, and affinity chromatography using Pneumovax®-Sepharose. Purification efficiency and method reproducibility were assessed by comparison of 4 batches of anti-PCP IgG. Immunoglobulin composition was determined using nephelometry and functionality was evaluated using VaccZyme™ ELISAs. RESULTS: Anti-PCP IgG preparations were ≥95% pure by SDS-PAGE analysis with no contaminating IgA or IgM immunoglobulins or IgG antigen specific antibodies towards haemophilus influenzae b, diphtheria toxoid or tetanus toxoid. The predominant IgG subclass in the preparation was IgG2. CONCLUSIONS: This novel purification procedure produced highly specific anti-PCP IgG preparations that compared well to both Lot 89SF and 007sp international serum standards and could be used as an alternative method for the production of reference materials.

Decadal Declines of Mercury in Adult Bluefish (1972-2011) from the Mid-Atlantic Coast of the U.S.A.

Concentrations of total mercury were measured in muscle of adult bluefish (Pomatomus saltatrix) collected in 2011 off North Carolina and compared with similar measurements made in 1972. Concentrations of mercury decreased by 43% in the fish between the two time periods, with an average rate of decline of about 10% per decade. This reduction is similar to estimated reductions of mercury observed in atmospheric deposition, riverine input, seawater, freshwater lakes, and freshwater fish across northern North America. Eight other studies between 1973 and 2007 confirm the decrease in mercury levels in bluefish captured in the Mid-Atlantic Bight. These findings imply that (1) reductions in the release of mercury across northern North America were reflected rather quickly (decades) in the decline of mercury in adult bluefish; (2) marine predatory fish may have been contaminated by anthropogenic sources of mercury for over 100 years; and (3) if bluefish are surrogates for other predators in the Mid-Atlantic Bight, then a reduction in the intake of mercury by the fish-consuming public has occurred. Finally, with global emissions of mercury continuing to increase, especially from Asia, it is important that long-term monitoring programs be conducted for mercury in marine fish of economic importance.

Potential predictive ability of the orthopaedic trauma association open fracture classification.

OBJECTIVE: Is the OTA open fracture classification (OTA-OFC) potentially predictive of early amputation and specific clinical treatments? DESIGN: Retrospective chart review of prospectively collected data. SETTING: Level I trauma center, Seattle, WA. PATIENTS/PARTICIPANTS: Three hundred fifty-six patients with open fractures of the femur, tibia, malleoli, humerus, radius/ulna, pelvis, acetabulum, foot, or clavicle. INTERVENTION: No intervention. MAIN OUTCOME MEASUREMENTS: Vacuum-assisted closure placement, 3+ irrigation and debridements, antibiotic bead placement, and early amputation. RESULTS: The OTA-OFC is related to the type of treatment used to treat an open fracture. The model demonstrated that the strongest potential predictor of vacuum-assisted closure use is the severity of the skin injury; multiple debridements (≥ 2) is best predicted by the severity of the skin injury and muscle injury; bone loss was the strongest potential predictor of antibiotic bead placement; and the strongest predictors of early amputation are skin injury, contamination, and arterial injury. CONCLUSIONS: Exploratory analysis of these data demonstrates that variations in muscle damage, skin injury, bone loss, arterial injury, and contamination sustained in an open fracture are related to different treatments in the total study population and for anatomical regions. The information provided by this study demonstrates that the OTA-OFC may have predictive abilities relative to how an open fracture is treated. LEVEL OF EVIDENCE: Prognostic level II. See Instructions for Authors for a complete description of levels of evidence.

Microarray based analysis of 3p25-p26 deletions (3p- syndrome).

Distal deletion of chromosome 3p25-pter (3p- syndrome) produces a distinct clinical syndrome characterized by low birth weight, mental retardation, telecanthus, ptosis, and micrognathia. Congenital heart disease (CHD), typically atrioventricular septal defect (AVSD) occurs in about a third of patients. Previously we reported on an association between the presence of CHD and the proximal extent of the deletion such that a CHD susceptibility gene was mapped between D3S1263 and D3S3594. In addition, we and others have suggested several candidate genes for the psychomotor retardation usually seen with constitutional 3p25 deletions. In order to further investigate genotype-phenotype correlations in 3p- syndrome we analyzed 14 patients with cytogenetically detectable deletions of 3p25 (including one patient with a normal phenotype) using Affymetrix 250K SNP microarrays. Deletion size varied from approximately 6 to 12 Mb. Assuming complete penetrance, a candidate critical region for a CHD susceptibility gene was refined to approximately 200 kb and a candidate critical region for mental retardation was mapped to an approximately 1 Mb interval containing SRGAP3 but other 3p neurodevelopmental genes including CHL1, CNTN4, LRRN1, and ITPR1 mapped outside the candidate critical interval. We suggest that current evidence suggests that SRGAP3 is the major determinant of mental retardation in distal 3p deletions.

Genotype-phenotype correlations in VHL exon deletions.

Von Hippel-Lindau (VHL) syndrome is a dominantly inherited familial cancer syndrome caused by mutations in the VHL gene. VHL syndrome displays marked variation in expression and analysis of genotype-phenotype correlations have led to the concept of four subtypes of VHL syndrome (Types 1, 2A-C). Type 2 subtypes of VHL syndrome are characterized by the presence of pheochromocytoma and the three Type 2 subtypes are associated with differing risks of hemangioblastoma and renal cell carcinoma (RCC). Type 2 VHL syndrome is usually associated with surface missense mutations. Type 1 VHL syndrome is most commonly caused by germline exon deletions and truncating mutations and is characterized by susceptibility to hemangioblastomas and RCC but not pheochromocytoma. Recently, it has been suggested that large VHL gene deletions involving C3orf10 (HSPC300) might be associated with a low risk of RCC. We have reviewed the molecular and clinical characteristics of 127 individuals with germline VHL gene deletions. Large VHL gene deletions associated with a contiguous loss of C3orf10 were associated with a significantly lower lifetime risk of RCC than deletions that did not involve C3orf10. The risks of hemangioblastomas were similar in both groups. These results add to the growing body of evidence suggesting that patients with VHL syndrome caused by large VHL deletions that include C3orf10 may be designated as having a specific subtype (Type 1B) of the disorder.

Photosynthetic maximum quantum yield increases are an essential component of the Southern Ocean phytoplankton response to iron.

It is well established that an increase in iron supply causes an increase in total oceanic primary production in many regions, but the physiological mechanism driving the observed increases has not been clearly identified. The Southern Ocean iron enrichment experiment, an iron fertilization experiment in the waters closest to Antarctica, resulted in a 9-fold increase in chlorophyll (Chl) concentration and a 5-fold increase in integrated primary production. Upon iron addition, the maximum quantum yield of photosynthesis (phi(m)) rapidly doubled, from 0.011 to 0.025 mol C.mol quanta(-1). Paradoxically, this increase in light-limited productivity was not accompanied by a significant increase in light-saturated productivity (P(max)(b)). P(max)(b), maximum Chl normalized productivity, was 1.34 mg C.mg Chl(-1).h(-1) outside and 1.49 mg C.mg Chl(-1).h(-1) inside the iron-enriched patch. The importance of phi(m) as compared with P(max)(b) in controlling the biological response to iron addition has vast implications for understanding the ecological response to iron. We show that an iron-driven increase in phi(m) is the proximate physiological mechanism affected by iron addition and can account for most of the increases in primary production. The relative importance of phi(m) over P(max)(b) in this iron-fertilized bloom highlights the limitations of often-used primary productivity algorithms that are driven by estimates of P(max)(b) but largely ignore variability in phi(m) and light-limited productivity. To use primary productivity models that include variability in iron supply in prediction or forecasting, the variability of light-limited productivity must be resolved.

The effect of advection on the nutrient reservoir in the North Atlantic subtropical gyre.

Though critically important in sustaining the ocean's biological pump, the cycling of nutrients in the subtropical gyres is poorly understood. The supply of nutrients to the sunlit surface layer of the ocean has traditionally been attributed solely to vertical processes. However, horizontal advection may also be important in establishing the availability of nutrients. Here we show that the production and advection of North Atlantic Subtropical Mode Water introduces spatial and temporal variability in the subsurface nutrient reservoir beneath the North Atlantic subtropical gyre. As the mode water is formed, its nutrients are depleted by biological utilization. When the depleted water mass is exported to the gyre, it injects a wedge of low-nutrient water into the upper layers of the ocean. Contrary to intuition, cold winters that promote deep convective mixing and vigorous mode water formation may diminish downstream primary productivity by altering the subsurface delivery of nutrients.

Application of multiplex ligation-dependent probe analysis to define a small deletion encompassing PMP22 exons 4 and 5 in hereditary neuropathy with liability to pressure palsies.

Hereditary neuropathy with liability to pressure palsies arises as a result of defects at the chromosome 17p11.2-12 locus and in 84% of cases a 1.5 Mb deletion containing the PMP22 gene is detected by analysis that utilises polymorphic (CA)n repeat markers which flank this gene. We report the clinical and electrophysiological findings observed in a kindred with three members affected by HNPP due to a deletion containing exons 4 and 5 of the PMP22 gene. This small deletion cannot be detected using standard analysis with polymorphic (CA)n repeat markers and a definitive diagnosis was made by multiplex ligation-dependent probe analysis of PMP22 exons 1A-5. MLPA can be readily utilised as a routine diagnostic laboratory test to detect the common HNPP 1.5 Mb deletion, as well as the reciprocal 1.5 Mb insertion observed in CMT1A, but has the advantage over other diagnostic techniques of being able to define single exon deletions.

Southern Ocean iron enrichment experiment: carbon cycling in high- and low-Si waters.

The availability of iron is known to exert a controlling influence on biological productivity in surface waters over large areas of the ocean and may have been an important factor in the variation of the concentration of atmospheric carbon dioxide over glacial cycles. The effect of iron in the Southern Ocean is particularly important because of its large area and abundant nitrate, yet iron-enhanced growth of phytoplankton may be differentially expressed between waters with high silicic acid in the south and low silicic acid in the north, where diatom growth may be limited by both silicic acid and iron. Two mesoscale experiments, designed to investigate the effects of iron enrichment in regions with high and low concentrations of silicic acid, were performed in the Southern Ocean. These experiments demonstrate iron's pivotal role in controlling carbon uptake and regulating atmospheric partial pressure of carbon dioxide.

The low-light reduction in the quantum yield of photosynthesis: potential errors and biases when calculating the maximum quantum yield.

Photosynthesis-irradiance (P-E) curves are widely used to describe photosynthetic efficiency and potential. Contemporary models assume maximal photosynthetic quantum yield (phi) at low irradiances. But P-E observations made with both oxygen evolution and carbon uptake techniques show that this is not always the case. Using new and published data in conjunction with modeling exercises, we demonstrate that regardless of the mechanism there can be reductions in phi at low irradiances that are not readily observable using conventional P-E analyses. We also show that analytical errors, such as inaccurate estimation of dark oxygen consumption or carbon uptake, can markedly affect the structure of phi-E curves with negligible effect on P-E curve structure. Whether from respiration ;corrections' or other mechanisms, these deviations in phi at low light levels from the maximum quantum yield of photosynthesis (phi(max)) can lead to significant errors (> 50%) in the estimation of the linear portion of the P-E curve and ultimately phi(max). Non-linear models of P-E, such as the rectangular hyperbola, quadratic, exponential and hyperbolic tangent that are commonly used to estimate the initial slope (alpha) of the P-E curve assume that phi is maximal at low light levels and therefore can err in the estimation of phi(max) when phi is reduced at low light levels. Using a diverse data set of 622 P-E curves with a total of 7623 points, we show that although model skills are high (r (2) = 0.96 +/- 0.05, 0.97 +/- 0.04, 0.97 +/- 0.04 and 0.97 +/- 0.04, respectively), a large fraction of the model-predicted phi(max) differ by greater than 10% from true phi(max) values (91%, 50%, 82% and 46%, respectively). Data from these observations and modeling exercises lead us to suggest that phi(max) be determined by directly estimating the true maximum of a phi-E curve rather than using the more conventional methodology employing the initial slope of the P-E curve.