Congenital Titinopathy: Comprehensive characterization and pathogenic insights

OBJECTIVE

Comprehensive clinical characterization of congenital titinopathy to facilitate diagnosis and management of this important emerging disorder.

METHODS

Using massively parallel sequencing we identified 30 patients from 27 families with 2 pathogenic nonsense, frameshift and/or splice site TTN mutations in trans. We then undertook a detailed analysis of the clinical, histopathological and imaging features of these patients.

RESULTS

All patients had prenatal or early onset hypotonia and/or congenital contractures. None had ophthalmoplegia. Scoliosis and respiratory insufficiency typically developed early and progressed rapidly, whereas limb weakness was often slowly progressive, and usually did not prevent independent walking. Cardiac involvement was present in 46% of patients. Relatives of 2 patients had dilated cardiomyopathy. Creatine kinase levels were normal to moderately elevated. Increased fiber size variation, internalized nuclei and cores were common histopathological abnormalities. Cap-like regions, whorled or ring fibers, and mitochondrial accumulations were also observed. Muscle magnetic resonance imaging showed gluteal, hamstring and calf muscle involvement. Western blot analysis showed a near-normal sized titin protein in all samples. The presence of 2 mutations predicted to impact both N2BA and N2B cardiac isoforms appeared to be associated with greatest risk of cardiac involvement. One-third of patients had 1 mutation predicted to impact exons present in fetal skeletal muscle, but not included within the mature skeletal muscle isoform transcript. This strongly suggests developmental isoforms are involved in the pathogenesis of this congenital/early onset disorder.

INTERPRETATION

This detailed clinical reference dataset will greatly facilitate diagnostic confirmation and management of patients, and has provided important insights into disease pathogenesis. Ann Neurol 2018;83:1105-1124.

Atomic structures of RNA nanotubes and their comparison with DNA nanotubes

We present a computational framework to model RNA based nanostructures and study their microscopic structures. We model hexagonal nanotubes made of 6 dsRNA (RNTs) connected by double crossover (DX) at different positions. Using several hundred nano-second (ns) long all-atom molecular dynamics simulations, we study the atomic structure, conformational change and elastic properties of RNTs in the presence of explicit water and ions. Based on several structural quantities such as root mean square deviation (RMSD) and root mean square fluctuation (RMSF), we find that the RNTs are almost as stable as DNA nanotubes (DNTs). Although the central portion of the RNTs maintain its cylindrical shape, both the terminal regions open up to give rise to a gating like behavior which can play a crucial role in drug delivery. From the bending angle distribution, we observe that the RNTs are more flexible than DNTs. The calculated persistence length of the RNTs is in the micron range which is an order of magnitude higher than that of a single dsRNA. The stretch modulus of the RNTs from the contour length distribution is in the range of 4-7 nN depending on the sequence. The calculated persistence length and stretch modulus are in the same range of values as in the case of DNTs. To understand the structural properties of RNTs at the individual base-pair level we have also calculated all the helicoidal parameters and analyzed the relative flexibility and rigidity of RNTs having a different sequence. These findings emphasized the fascinating properties of RNTs which will expedite further theoretical and experimental studies in this field.

DNA Translocation through Hybrid Bilayer Nanopores

Pore functionalization has been explored by several groups as a strategy to control DNA translocation through solid-state nanopores. Here we present a hybrid nanopore system consisting of single-layer graphene and a DNA origami layer to achieve base-selective control of DNA translocation rate through aligned nanopores of the two layers. This is achieved by incorporating unpaired dangling bases called overhangs to the origami near the pore region. Molecular dynamics simulations were used to optimize the design of the origami nanopore and the overhangs. Specifically, we considered the influence of the number and spatial distribution of overhangs on translocation times. The simulations revealed that specific interactions between the overhangs and the translocating single-stranded DNA resulted in base-specific residence times.

A theoretical analysis of elastic and optical properties of half Heusler MCoSb (M=Ti, Zr and Hf)

Ab initio calculation of the Elastic and Optical properties of cubic half-Heusler compounds MCoSb (M = Ti, Zr and Hf) are reported using the FP-LAPW approach of the Density Functional Theory. Generalized Gradient Approximation was used as the exchange and correlation potential for investigating these properties. It was found that the Bulk modulus decreases with the increase in temperature and increases with the increase in pressure for all of the three Heusler compounds under study. The Debye's temperature along with compressional, Shear and average elastic wave velocities has also been calculated. The elastic results are compared with the available theoretical and experimental works. The optical investigation of the compounds shows high reflectivity at the infrared region of the photon energy. The imaginary part of the dielectric function reveled the optically non-metallic behavior of the MCoSb compounds, with optical band gap being around 1 eV.

Effect of temperature and hydrophilic ratio on the structure of poly(N-vinylcaprolactam)-block-poly(dimethylsiloxane)-block-poly(N-vinylcaprolactam) polymersomes

Nanosized polymeric vesicles (polymersomes) assembled from ABA triblock copolymers of poly(N-vinylcaprolactam)-poly(dimethylsiloxane)-poly(N-vinylcaprolactam) (PVCL-PDMS-PVCL) are a promising platform for biomedical applications, as the temperature-responsiveness of the PVCL blocks enables reversible vesicle shrinkage and permeability of the polymersome shell at elevated temperatures. Herein, we explore the effects of molecular weight, polymer block weight ratios, and temperature on the structure of these polymersomes via electron microscopy, dynamic light scattering, small angle neutron scattering (SANS), and all-atom molecular dynamic methods. We show that the shell structure and overall size of the polymersome can be tuned by varying the hydrophilic (PVCL) weight fraction of the polymer: at room temperature, polymers of smaller hydrophilic ratios form larger vesicles that have thinner shells, whereas polymers with higher PVCL content exhibit interchain aggregation of PVCL blocks within the polymersome shell above 50 °C. Model fitting and model-free analysis of the SANS data reveals that increasing the mass ratio of PVCL to the total copolymer weight from 0.3 to 0.56 reduces the temperature-induced change in vesicle diameter by a factor of 3 while simultaneously increasing the change in shell thickness by a factor of 1.5. Finally, by analysis of the shell structures and overall size of polymersomes with various PVCL weight ratios and those without temperature-dependent polymer components, we bring into focus the mechanism of temperature-triggered drug release reported in a previous study. This work provides new fundamental perspectives on temperature-responsive polymersomes and elucidates important structure-property relationships of their constituent polymers.

Anterior hypopituitarism secondary to biopsy-proven IgG4-related hypophysitis in a young man

IgG4-related disease (IgG4-RD) is an immune-mediated fibro-inflammatory condition which can affect various organs including the pituitary gland. The true annual incidence of this condition remains widely unknown. In addition, it is unclear whether IgG4 antibodies are causative or the end result of a trigger. With no specific biomarkers available, the diagnosis of IgG4-related hypophysitis remains a challenge. Additionally, there is a wide differential diagnosis. We report a case of biopsy-proven IgG4-related hypophysitis in a young man with type 2 diabetes mellitus. Learning points: IgG4-related hypophysitis is part of a spectrum of IgG4-related diseases. Clinical manifestations result from anterior pituitary hormone deficiencies with or without diabetes insipidus, which can be temporary or permanent. A combination of clinical, radiological, serological and histological evidence with careful interpretation is required to make the diagnosis. Tissue biopsy remains the gold standard investigation. Disease monitoring and long-term management of this condition is a challenge as relapses occur frequently.

Dynamic Interactions between Lipid-Tethered DNA and Phospholipid Membranes

Lipid-anchored DNA can attach functional cargo to bilayer membranes in DNA nanotechnology, synthetic biology, and cell biology research. To optimize DNA anchoring, an understanding of DNA-membrane interactions in terms of binding strength, extent, and structural dynamics is required. Here we use experiments and molecular dynamics (MD) simulations to determine how the membrane binding of cholesterol-modified DNA depends on electrostatic and steric factors involving the lipid headgroup charge, duplexed or single-stranded DNA, and the buffer composition. The experiments distinguish between free and membrane vesicle-bound DNA and thereby reveal the surface density of anchored DNA and its binding affinity, something which had previously not been known. The K_d values range from 8.5 ± 4.9 to 466 ± 134 μM whereby negatively charged headgroups led to weak binding due to the electrostatic repulsion with respect to the negatively charged DNA. Atomistic MD simulations explain the findings and elucidate the dynamic nature of anchored DNA such as the mushroom-like conformation of single-stranded DNA hovering over the bilayer surface in contrast to a straight-up conformation of double-stranded DNA. The biophysical insight into the binding strength to membranes as well as the molecular accessibility of DNA for hybridization to molecular cargo is expected to facilitate the creation of biomimetic DNA versions of natural membrane nanopores and cytoskeletons for research and nanobiotechnology.

Resting-State Functional Connectivity Changes Associated with Visuospatial Cognitive Deficits in Patients with Mild Alzheimer Disease

BACKGROUND/AIMS

Alzheimer disease (AD) is a neurodegenerative disorder characterized by progressive disconnection of various brain networks leading to neuropsychological impairment. Pathology in the visual association areas has been documented in presymptomatic AD and therefore we aimed at examining the relationship between brain connectivity and visuospatial (VS) cognitive deficits in early AD.

METHODS

Tests for VS working memory, episodic memory and construction were used to classify patients with AD (n = 48) as having severe VS deficits (n = 12, female = 4) or mild deficits (n = 11, female = 4). Resting-state functional magnetic resonance imaging and structural images were acquired as per the standard protocols. Between-group differences in resting-state functional connectivity (rsFC) were examined by dual regression analysis correcting for age, gender, and total brain volume.

RESULTS

Patients with AD having severe VS deficits exhibited significantly reduced rsFC in bilateral lingual gyri of the visual network compared to patients with mild VS deficits.

CONCLUSION

Reduced rsFC in the visual network in patients with more severe VS deficits may be a functional neuroimaging biomarker reflecting hypoconnectivity of the brain with progressive VS deficits during early AD.

Structure and electrical properties of DNA nanotubes embedded in lipid bilayer membranes

Engineering the synthetic nanopores through lipid bilayer membrane to access the interior of a cell is a long persisting challenge in biotechnology. Here, we demonstrate the stability and dynamics of a tile-based 6-helix DNA nanotube (DNT) embedded in POPC lipid bilayer using the analysis of 0.2 μs long equilibrium MD simulation trajectories. We observe that the head groups of the lipid molecules close to the lumen cooperatively tilt towards the hydrophilic sugar-phosphate backbone of DNA and form a toroidal structure around the patch of DNT protruding in the membrane. Further, we explore the effect of ionic concentrations to the in-solution structure and stability of the lipid-DNT complex. Transmembrane ionic current measurements for the constant electric field MD simulation provide the I-V characteristics of the water filled DNT lumen in lipid membrane. With increasing salt concentrations, the measured values of transmembrane ionic conductance of the porous DNT lumen vary from 4.3 to 20.6 nS. Simulations of the DNTs with ssDNA and dsDNA overhangs at the mouth of the pore show gating effect with remarkable difference in the transmembrane ionic conductivities for open and close state nanopores.

Goats in the city: prevalence of Giardia duodenalis and Cryptosporidium spp. in extensively reared goats in northern India

BACKGROUND

Various characteristics of goats mean they are highly suitable livestock for backyard rearing by people with limited resources. They are a popular livestock choice in India, where they are often kept to supplement an already scarce income. In these settings, hygiene and sanitation standards tend to be low, and weakens the interface between humans and animals, thus reducing the barrier between them and thereby increasing the likelihood that zoonotic and anthroponotic infections will occur.

RESULTS

This study reports an investigation of the occurrence of Cryptosporidium spp. and Giardia duodenalis in goats being reared in different settings in urban and peri-urban areas in northern India, and addressed the zoonotic potential of these important protozoan parasites shed from goats living close to humans. The overall prevalence of G. duodenalis was 33.8 and 0.5% for Cryptosporidium spp.; the relatively low prevalence of cryptosporidiosis may reflect that most samples were derived from adult animals. The prevalence of G. duodenalis excretion was found to be similar to that reported in other studies. However, although other studies have reported a predominance of non-zoonotic Assemblage E in goats, in this study potentially zoonotic Assemblages predominated [Assemblage A (36%) and Assemblage B (32%)].

CONCLUSIONS

The results of this study indicate that in this area where goats and humans are living in close proximity, there may be sharing of intestinal parasites, which can be detrimental for both host species.

Clinical and neuropsychological profile of persons with mild cognitive impairment, a hospital based study from a lower and middle income country

Mild Cognitive impairment (MCI) is an important pre-dementia stage to be identified towards prevention. We screened a large number of older adults seeking help at hospital and community towards a diagnosis of MCI and this study describe their clinical and neuropsychological profile. Older adults aged 60 years & above seeking help at NIMHANS outpatient & community services were screened for early cognitive deficits. Persons were diagnosed to have MCI according to Petersen's criteria, after detailed clinical and neuropsychological assessments. Age, gender and education matched healthy controls were recruited for comparison. A total of 7469 older adults were screened during the study period (July 2012-December 2014). Less than 1% (n=56) were diagnosed with MCI. Majority were males, from urban background with an average of 13 years of education. They presented mainly with memory disturbances, more than 75% (n=43) were found to have amnestic type of MCI (aMCI). Of the aMCI subjects, majority (80%) had deficits in more than one cognitive domain. They performed significantly worse (p<0.001) on tests of episodic memory, logical memory, attention and executive functions. Neuropsychiatric symptoms were prevalent in 55% of MCI group and influenced their cognitive scores. The findings suggest that persons with MCI perform worse not only on memory tasks but also on some of the attention and executive functions tasks. As observed in earlier studies, amnestic multiple-domain MCI was the most common type of MCI in this study population. Indigenous assessment tools were of significant value in distinguishing MCI from normal ageing.

Checking the detail in retail: Occurrence of Cryptosporidium and Giardia on vegetables sold across different counters in Chandigarh, India

Fresh produce has been recognized as a vehicle of infection for protozoan parasites, particularly Cryptosporidium, and, to a lesser extent, Giardia. For both parasites, outbreaks associated with fresh produce have been documented. Although documented outbreaks tend to be from industrialized countries, contamination of fresh produce with these parasites is a global issue. In developing countries, infections with these parasites are often endemic in the community, and basic infrastructure and hygiene measures may be inadequate, thus the likelihood of contamination of fresh produce with these parasites may be higher. Realization of the importance of this transmission route comes against a backdrop of raw salads and more Western culinary habits gaining a foothold, and fresh produce being encouraged as part of the diet due to their associated health benefits. However, if consumption of uncooked fresh produce is going to increase its market sector in India, it is important that it is safe. In this study, various types of fresh produce obtained from three types of vendors in Chandigarh, a major city in Northern India, were analyzed for contamination with Cryptosporidium oocysts and Giardia cysts using a method that has been previously validated in inter-laboratory spiking experiments. A total of 284 samples of different fresh produce items were analyzed, obtained from the different retailers situated in different societal layers of the city. The overall prevalence of contamination of fresh produce with these parasites was just under 11%, with 6% of the vegetables contaminated with Cryptosporidium oocysts, and 5% with Giardia cysts. Contaminated vegetables included turnip, cabbage, carrot, chili, coriander, cucumber, radishes, and tomatoes. Molecular analyses identified contamination with Cryptosporidium parvum and Giardia duodenalis of Assemblage A and Assemblage D, indicating that contamination from animals may be of relevance. Although the prevalence of contamination is similar to those reported in previous studies, the levels of contamination on some items of fresh produce were relatively high. Although the different socioeconomic areas of Chandigarh from which the samples were obtained was not associated with likelihood of contamination, fresh produce from supermarkets had heavier contamination with Cryptosporidium oocysts than fresh produce purchased through other sales outlets. The results are discussed in relation to the fresh produce chain and sales models in Chandigarh, both in terms of where contamination may occur and the potential importance of fresh produce as a transmission vehicle.

Dissecting the structure-function relationship in lysozyme domain of mycobacteriophage D29-encoded peptidoglycan hydrolase

Most bacteriophages rapidly infect and kill bacteria and, therefore, qualify as the next generation therapeutics for rapidly emerging drug-resistant bacteria such as Mycobacterium tuberculosis. We have previously characterized the mycobacteriophage D29-generated endolysin, Lysin A, for its activity against mycobacteria. Here, we present a detailed characterization of the lysozyme domain (LD) of D29 Lysin A that hydrolyzes peptidoglycan of both gram-positive and gram-negative bacteria with high potency. By characterizing an exhaustive LD protein variant library, we have identified critical residues important for LD activity and stability. We further complement our in vitro experiments with detailed in silico investigations. We present LD as a potent candidate for developing phage-based broad-spectrum therapeutics.

Anti-Mullerian hormone (AMH) and embryo quality assessed by time-lapse imaging (TLI): a cross-sectional observational study

PURPOSE

Serum anti-Mullerian hormone shows a strong positive correlation to the quantitative ovarian reserve but its correlation to embryo quality is unclear. This study assessed the association between serum AMH as a marker of ovarian reserve and embryo quality, using the technology of time-lapse imaging of the embryos in women undergoing in vitro fertilisation (IVF) treatment.

METHODS

304 embryos from 198 women undergoing IVF were included in the study. Serum AMH was assessed for all women. Embryo quality was assessed with the known implantation data (KID) score generated by the time-lapse imaging system.

RESULTS

There was no statistically significant difference in mean serum AMH among different KID score categories (p = 0.135). This remained non-significant after controlling for confounding variables (p = 0.305).

CONCLUSIONS

The results of our study show no significant association between serum AMH and embryo quality in women undergoing IVF treatment when embryo quality was assessed using the KID scores generated by time-lapse imaging which is a better method of embryo assessment rather than conventional morphological assessment.

Improving genetic diagnosis in Mendelian disease with transcriptome sequencing

Exome and whole-genome sequencing are becoming increasingly routine approaches in Mendelian disease diagnosis. Despite their success, the current diagnostic rate for genomic analyses across a variety of rare diseases is approximately 25 to 50%. We explore the utility of transcriptome sequencing [RNA sequencing (RNA-seq)] as a complementary diagnostic tool in a cohort of 50 patients with genetically undiagnosed rare muscle disorders. We describe an integrated approach to analyze patient muscle RNA-seq, leveraging an analysis framework focused on the detection of transcript-level changes that are unique to the patient compared to more than 180 control skeletal muscle samples. We demonstrate the power of RNA-seq to validate candidate splice-disrupting mutations and to identify splice-altering variants in both exonic and deep intronic regions, yielding an overall diagnosis rate of 35%. We also report the discovery of a highly recurrent de novo intronic mutation in COL6A1 that results in a dominantly acting splice-gain event, disrupting the critical glycine repeat motif of the triple helical domain. We identify this pathogenic variant in a total of 27 genetically unsolved patients in an external collagen VI-like dystrophy cohort, thus explaining approximately 25% of patients clinically suggestive of having collagen VI dystrophy in whom prior genetic analysis is negative. Overall, this study represents a large systematic application of transcriptome sequencing to rare disease diagnosis and highlights its utility for the detection and interpretation of variants missed by current standard diagnostic approaches.

Probing the structure and in silico stability of cargo loaded DNA icosahedra using MD simulations

Platonic solids such as polyhedra based on DNA have been deployed for multifarious applications such as RNAi delivery, biological targeting and bioimaging. All of these applications hinge on the capability of DNA polyhedra for molecular display with high spatial precision. Therefore high resolution structural models of such polyhedra are critical to widen their applications in both materials and biology. Here, we present an atomistic model of a well-characterized DNA icosahedron, with demonstrated versatile functionalities in biological systems. We study the structure and dynamics of this DNA icosahedron using fully atomistic molecular dynamics (MD) simulation in explicit water and ions. The major modes of internal motion have been identified using principal component analysis. We provide a quantitative estimate of the radius of gyration (R_g), solvent accessible surface area (SASA) and volume of the icosahedron which is essential to estimate its maximal cargo carrying capacity. Importantly, our simulation of gold nanoparticles (AuNPs) encapsulated within DNA icosahedra revealed enhanced stability of the AuNP loaded DNA icosahedra compared to empty icosahedra. This is consistent with the experimental results that show high yields of cargo-encapsulated DNA icosahedra that have led to its diverse applications for precision targeting. These studies reveal that the stabilizing interactions between the cargo and the DNA scaffold powerfully position DNA polyhedra as targetable nanocapsules for payload delivery. These insights can be exploited for precise molecular display for diverse biological applications.

Chemical characterization of rainwater at a high-altitude site "Nainital" in the central Himalayas, India

The present study investigates the chemical composition of rainwater (RW) from a high-altitude site "Nainital" (1958 m above msl) in the central Himalaya region, to understand the influence of local, regional, and long-range transport of pollutants. A total of 55 (2 in pre-monsoon and 53 in monsoon) RW samples were collected during the study period (June-September 2012) and were analyzed for major anions and cations using an ion chromatograph. The pH of precipitation events ranged from 4.95 to 6.50 (average 5.6 ± 0.3) was observed during the monsoon period (near to the acidic), whereas during the pre-monsoon, the pH was 6.25 ± 0.49 (alkaline) over the study region; it is due the mixture of anthropogenic as well as the natural chemical constituents. The average ionic concentration (sum of measured chemical constituents) was ∼3 times higher during the pre-monsoon (986 ± 101 μeq/1) compared to that in the monsoon season (373 ± 37 μeq/1). This is mainly due to the presence of more natural aerosols in the pre-monsoon season which is also reflected in the pH of rainwater (average 6.25 ± 0.50) as well as ionic concentration. The chemical composition suggests that Ca²⁺ was the major contributor (34%) among cations, followed by Na⁺ (10%), K⁺ (8%), and Mg²⁺ (9%), whereas Cl^-, NO₃^-, and SO₄^2- contributed ∼13, 11, and 9%, respectively, among anions. The average ratio of acidic species (SO₄^2-/NO₃^-) is 1.56, suggesting 61 and 39% contribution of SO₄^2- and NO₃^-, respectively, which is very close to the estimated contribution of H₂SO₄ (60-70%) and HNO₃ (30-40%) in the precipitation samples. Neutralization factors for Ca²⁺, Mg²⁺, and NH₄⁺ in RW at Nainital are 4.94, 1.21, and 0.37, respectively, indicating their crucial role in neutralization of acidic species. The non-sea-salt (NSS) contribution to total Ca²⁺, K⁺, and Mg²⁺ is estimated to be ∼98, 97, and 74%, respectively, suggesting the dominance of crustal sources for cations. In contrast, the NSS contribution to the total Cl^- and SO₄^2- is 16 and 69% indicating their anthropogenic origin, respectively. Principle component analysis also suggests that the first factor (i.e., natural sources, mainly dust, and sea-salts) accounts for ∼33% variance, whereas the second factor (i.e., fossil fuel and biomass burning) accounts for ∼18% variance of the measured ionic composition. The remaining contributions are attributed to the mixed emission sources and transport of pollutants from Indo-Gangetic Plain (IGP) and western parts of India. The results of the present study reveal a significant contribution of crustal and anthropogenic sources in the RW and neutralization processes in the central Himalaya.

A Multimodal Structural and Functional Neuroimaging Study of Amnestic Mild Cognitive Impairment

Examination of brain structural and functional abnormalities in amnestic mild cognitive impairment (aMCI) has the potential to enhance our understanding of the initial pathophysiological changes in dementia. We examined gray matter volumes and white matter microstructural integrity, as well as resting state functional connectivity (rsFC) in patients with aMCI (N = 48) in comparison to elderly cognitively healthy comparison subjects (N = 48). Brain volumetric comparisons were carried out using voxel-based morphometric analysis of T1-weighted images using the FMRIB Software Library. White matter microstructural integrity was examined using whole-brain tract-based spatial statistics analysis of fractional anisotropy maps generated from diffusion tensor imaging data. Finally, rsFC differences between the samples were examined by Multivariate Exploratory Linear Optimised Decomposition into Independent Components of the resting state functional magnetic resonance imaging time series, followed by between-group comparisons of selected networks using dual regression analysis. Patients with aMCI showed significant gray matter volumetric reductions in bilateral parahippocampal gyri as well as multiple other brain regions including frontal, temporal, and parietal cortices. Additionally, reduced rsFC in the anterior subdivision of the default mode network (DMN) and increased rsFC in the executive network were noted in the absence of demonstrable impairment of white matter microstructural integrity. We conclude that the demonstrable neuroimaging findings in aMCI include significant gray matter volumetric reductions in the fronto-temporo-parietal structures as well as resting state functional connectivity disturbances in DMN and executive network. These findings differentiate aMCI from healthy aging and could constitute the earliest demonstrable neuroimaging findings of incipient dementia.

Endoscopic pilonidal abscess treatment: a novel approach for the treatment of pilonidal abscess

INTRODUCTION Pilonidal abscess is a common surgical emergency. Conventional treatment with incision and drainage is associated with significant postoperative morbidity. We report our initial experience of using minimally invasive endoscopic technique for the treatment of pilonidal abscesses, referred to as endoscopic pilonidal abscess treatment (EPAT). MATERIALS AND METHODS A prospective database of all patients undergoing EPAT between January 2015 and March 2016 at Whiston Hospital was maintained. Data regarding patient demographics, peroperative variables and postoperative follow-up were recorded. RESULTS Nineteen patients were included, male to female ratio was 53 : 47 and median age of the cohort was 24 years (interquartile range 22-25 years). EPAT was the primary procedure for 10 patients and 9 had EPAT for recurrent pilonidal abscesses. There were no readmissions and none needed further surgery within 6 weeks of having the procedure. In all patients, complete wound healing was achieved within 6 weeks; all reported minimal postoperative pain (median postoperative visual analogue scale score 1) and immediate return to the activities of daily life. Four of the nineteen patients (21%) required definitive intervention for pilonidal disease in the follow-up period. CONCLUSIONS EPAT is a novel, minimally invasive technique for the treatment of acute pilonidal abscesses. It is safe, associated with reduced postoperative morbidity, recurrence rate and quick wound healing. Initial encouraging results require further investigations on a larger group of patients in a multicentre setting.

Quantum dot-loaded monofunctionalized DNA icosahedra for single-particle tracking of endocytic pathways

Functionalization of quantum dots (QDs) with a single biomolecular tag using traditional approaches in bulk solution has met with limited success. DNA polyhedra consist of an internal void bounded by a well-defined three-dimensional structured surface. The void can house cargo and the surface can be functionalized with stoichiometric and spatial precision. Here, we show that monofunctionalized QDs can be realized by encapsulating QDs inside DNA icosahedra and functionalizing the DNA shell with an endocytic ligand. We deployed the DNA-encapsulated QDs for real-time imaging of three different endocytic ligands-folic acid, galectin-3 (Gal3) and the Shiga toxin B-subunit (STxB). Single-particle tracking of Gal3- or STxB-functionalized QD-loaded DNA icosahedra allows us to monitor compartmental dynamics along endocytic pathways. These DNA-encapsulated QDs, which bear a unique stoichiometry of endocytic ligands, represent a new class of molecular probes for quantitative imaging of endocytic receptor dynamics.

Variants in the Oxidoreductase PYROXD1 Cause Early-Onset Myopathy with Internalized Nuclei and Myofibrillar Disorganization

This study establishes PYROXD1 variants as a cause of early-onset myopathy and uses biospecimens and cell lines, yeast, and zebrafish models to elucidate the fundamental role of PYROXD1 in skeletal muscle. Exome sequencing identified recessive variants in PYROXD1 in nine probands from five families. Affected individuals presented in infancy or childhood with slowly progressive proximal and distal weakness, facial weakness, nasal speech, swallowing difficulties, and normal to moderately elevated creatine kinase. Distinctive histopathology showed abundant internalized nuclei, myofibrillar disorganization, desmin-positive inclusions, and thickened Z-bands. PYROXD1 is a nuclear-cytoplasmic pyridine nucleotide-disulphide reductase (PNDR). PNDRs are flavoproteins (FAD-binding) and catalyze pyridine-nucleotide-dependent (NAD/NADH) reduction of thiol residues in other proteins. Complementation experiments in yeast lacking glutathione reductase glr1 show that human PYROXD1 has reductase activity that is strongly impaired by the disease-associated missense mutations. Immunolocalization studies in human muscle and zebrafish myofibers demonstrate that PYROXD1 localizes to the nucleus and to striated sarcomeric compartments. Zebrafish with ryroxD1 knock-down recapitulate features of PYROXD1 myopathy with sarcomeric disorganization, myofibrillar aggregates, and marked swimming defect. We characterize variants in the oxidoreductase PYROXD1 as a cause of early-onset myopathy with distinctive histopathology and introduce altered redox regulation as a primary cause of congenital muscle disease.

Nanoscale Structure and Elasticity of Pillared DNA Nanotubes

We present an atomistic model of pillared DNA nanotubes (DNTs) and their elastic properties which will facilitate further studies of these nanotubes in several important nanotechnological and biological applications. In particular, we introduce a computational design to create an atomistic model of a 6-helix DNT (6HB) along with its two variants, 6HB flanked symmetrically with two double helical DNA pillars (6HB+2) and 6HB flanked symmetrically by three double helical DNA pillars (6HB+3). Analysis of 200 ns all-atom simulation trajectories in the presence of explicit water and ions shows that these structures are stable and well behaved in all three geometries. Hydrogen bonding is well maintained for all variants of 6HB DNTs. From the equilibrium bending angle distribution, we calculate the persistence lengths of these tubes. The measured persistence lengths of these nanotubes are ∼10 μm, which is 2 orders of magnitude larger than that of dsDNA. We also find a gradual increase of persistence length with an increasing number of pillars, in quantitative agreement with previous experimental findings. To have a quantitative understanding of the stretch modulus of these tubes, we carried out nonequilibrium steered molecular dynamics (SMD). The linear part of the force-extension plot gives a stretch modulus in the range 6500 pN for 6HB without pillars, which increases to 11 000 pN for tubes with three pillars. The values of the stretch modulus calculated using contour length distribution obtained from equilibrium MD simulations are similar to those obtained from nonequilibrium SMD simulations. The addition of pillars makes these DNTs very rigid.

Organic and inorganic components of aerosols over the central Himalayas: winter and summer variations in stable carbon and nitrogen isotopic composition

The aerosol samples were collected from a high elevation mountain site, Nainital, in India (1958 m asl) during September 2006 to June 2007 and were analyzed for water-soluble inorganic species, total carbon, nitrogen, and their isotopic composition (δ(13)C and δ(15)N, respectively). The chemical and isotopic composition of aerosols revealed significant anthropogenic influence over this remote free-troposphere site. The amount of total carbon and nitrogen and their isotopic composition suggest a considerable contribution of biomass burning to the aerosols during winter. On the other hand, fossil fuel combustion sources are found to be dominant during summer. The carbon aerosol in winter is characterized by greater isotope ratios (av. -24.0‰), mostly originated from biomass burning of C4 plants. On the contrary, the aerosols in summer showed smaller δ(13)C values (-26.0‰), indicating that they are originated from vascular plants (mostly of C3 plants). The secondary ions (i.e., SO4 (2-), NH4 (+), and NO3 (-)) were abundant due to the atmospheric reactions during long-range transport in both seasons. The water-soluble organic and inorganic compositions revealed that they are aged in winter but comparatively fresh in summer. This study validates that the pollutants generated from far distant sources could reach high altitudes over the Himalayan region under favorable meteorological conditions.

Association of ARV7 expression with molecular and clinical characteristics in prostate cancer

109

Background: Prostate cancer (PC) is the most common cancer in men over the age of 60 and the second leading cause of cancer mortality in the United States. Clinicopathological parameters such as Gleason score, tumor volume, surgical margins, prostate-specific antigen (PSA), Ki-67 index and clinical stage are used as prognostic markers for clinical outcomes. Identification of novel molecular markers could improve our understanding of the clinical behavior of this disease. Androgen receptor isoforms, in particular variant 7 (ARV7 or AR3) have been recently studied for elucidating their potential role in PC progression, associated with epithelial-mesenchymal transition (EMT), disease aggressiveness, increased proliferation and therapeutic resistance. Our study is analyzing the association of ARV7 mRNA expression to clinical characteristics and is analyzing the genomic data to identify differentially altered genes by ARV expression status, summarized as a potential functional network. Methods: We obtained the TCGA public dataset of prostate adenocarcinoma tumors (N=499) that included the clinical data, gene and isoform expression and mutation data. Cases were categorized into ARV7 over-expressing (ARV+) and normal or low expression (ARV –/N) by using a cut-off of upper 25th percentile of the background genomic expression. Analysis was performed in R and Perl by using custom-made scripts. Differentially altered genes and pathways were identified and were summarized as potential functional networks. Results: We categorized 30 out of the 499 tumors as ARV+. ARV7 over-expression was found to be significantly associated with older age at diagnosis (>70), advanced clinical stage, nodal involvement, high Gleason score and a poor therapeutic response. We also observed a trend towards shorter disease-free survival among ARV+ tumors. In addition, ARV+ tumors showed significantly higher number of mutations in 20 key regulatory pathways including Jak-STAT signaling, homologous recombination, ErbB and Wnt signaling pathways. Conclusions: ARV7 overexpression is associated with genomic alterations in key regulatory pathways and poorer clinical outcome in PC patients.

Novel pppGpp binding site at the C-terminal region of the Rel enzyme from Mycobacterium smegmatis

Mycobacterium tuberculosis elicits the stringent response under unfavorable growth conditions, such as those encountered by the pathogen inside the host. The hallmark of this response is production of guanosine tetra- and pentaphosphates, collectively termed (p)ppGpp, which have pleiotropic effects on the bacterial physiology. As the stringent response is connected to survival under stress, it is now being targeted for developing inhibitors against bacterial persistence. The Rel enzyme in mycobacteria has two catalytic domains at its N-terminus that are involved in the synthesis and hydrolysis of (p)ppGpp, respectively. However, the function of the C-terminal region of the protein remained unknown. Here, we have identified a binding site for pppGpp in the C-terminal region of Rel. The binding affinity of pppGpp was quantified by isothermal titration calorimetry. The binding site was determined by crosslinking using the nucleotide analog azido-pppGpp, and examining the crosslink product by mass spectrometry. Additionally, mutations in the Rel protein were created to confirm the site of pppGpp binding by isothermal titration calorimetry. These mutants showed increased pppGpp synthesis and reduced hydrolytic activity. We believe that binding of pppGpp to Rel provides a feedback mechanism that allows the protein to detect and adjust the (p)ppGpp level in the cell. Our work suggests that such sites should also be considered while designing inhibitors to target the stringent response.

SYNTHESIS AND BIOLOGICAL EVALUATION OF N-(SUBSTITUTED PHENYL)-2-(5H-[1,2,4]TRIAZINO[5,6-b]INDOL-3-YLSULFANYL)ACETAMIDES AS ANTIMICROBIAL, ANTIDEPRESSANT AND ANTICONVULSANT AGENTS

A new series of N-Aryl-2-(5H-[1,2,4]triazino[5,6-b]indol-3-ylsulfanyl)acetamides were synthesized by condensation of tricyclic compound 2,5-dihydro-3H-[1,2,4]triazino[5,6-b]indole-3-thione with chloro N-phenylacetamides. The tricyclic compound was obtained by condensation of Isatin with thiosemicarbazide. Chloro N-phenylacetamides were obtained from different substituted anilines. Their structures were characterized by IR, 1H NMR, LC-MS and elemental analyses. Newly synthesized compounds were screened for antimicrobial, antidepressant and anticonvulsant activities. Preliminary results indicated that most of the compounds showed lesser MIC value than the standard drug used when tested for antimicrobial activity. Some of the compounds were endowed with very good antidepressant and anticonvulsant activity.

A study of structural and functional connectivity in early Alzheimer's disease using rest fMRI and diffusion tensor imaging

BACKGROUND/OBJECTIVES

Alzheimer's disease (AD) is a progressive neurodegenerative condition where in early diagnosis and interventions are key policy priorities in dementia services and research. We studied the functional and structural connectivity in mild AD to determine the nature of connectivity changes that coexist with neurocognitive deficits in the early stages of AD.

METHODS

Fifteen mild AD subjects and 15 cognitively healthy controls (CHc) matched for age and gender, underwent detailed neurocognitive assessment and magnetic resonance imaging (MRI) of resting state functional MRI (rs-fMRI) and diffusion tensor imaging (DTI). Rest fMRI was analyzed using dual regression approach and DTI by voxel wise statistics.

RESULTS

Patients with mild AD had significantly lower functional connectivity (FC) within the default mode network and increased FC within the executive network. The mild AD group scored significantly lower in all domains of cognition compared with CHc. But fractional anisotropy did not significantly (p < 0.05) differ between the groups.

CONCLUSION

Resting state functional connectivity alterations are noted during initial stages of cognitive decline in AD, even when there are no significant white matter microstructural changes.

Integration of somatic mutation, expression and functional data reveals potential driver genes predictive of breast cancer survival

MOTIVATION

Genome and transcriptome analyses can be used to explore cancers comprehensively, and it is increasingly common to have multiple omics data measured from each individual. Furthermore, there are rich functional data such as predicted impact of mutations on protein coding and gene/protein networks. However, integration of the complex information across the different omics and functional data is still challenging. Clinical validation, particularly based on patient outcomes such as survival, is important for assessing the relevance of the integrated information and for comparing different procedures.

RESULTS

An analysis pipeline is built for integrating genomic and transcriptomic alterations from whole-exome and RNA sequence data and functional data from protein function prediction and gene interaction networks. The method accumulates evidence for the functional implications of mutated potential driver genes found within and across patients. A driver-gene score (DGscore) is developed to capture the cumulative effect of such genes. To contribute to the score, a gene has to be frequently mutated, with high or moderate mutational impact at protein level, exhibiting an extreme expression and functionally linked to many differentially expressed neighbors in the functional gene network. The pipeline is applied to 60 matched tumor and normal samples of the same patient from The Cancer Genome Atlas breast-cancer project. In clinical validation, patients with high DGscores have worse survival than those with low scores (P = 0.001). Furthermore, the DGscore outperforms the established expression-based signatures MammaPrint and PAM50 in predicting patient survival. In conclusion, integration of mutation, expression and functional data allows identification of clinically relevant potential driver genes in cancer.

AVAILABILITY AND IMPLEMENTATION

The documented pipeline including annotated sample scripts can be found in http://fafner.meb.ki.se/biostatwiki/driver-genes/.

CONTACT

yudi.pawitan@ki.se

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Structure, stability and elasticity of DNA nanotubes

DNA nanotubes: an extension to DNA crossover molecules.

Two-stage electrochemical treatment of bio-digested distillery spent wash using stainless steel and aluminum electrodes

The objective of this study was to determine the effectiveness of two-stage electro-coagulation (EC) process using multi-parameter optimization for treating bio-digested distillery spent wash by stainless steel (SS) and aluminum (Al) electrodes. Operating parameters have been optimized and treatment efficiency of SS and Al electrodes have been compared by central composite design of response surface analysis in terms of COD, color and total organic carbon (TOC) removal. Individual and interactive effects of four independent parameters namely initial pH (pHo: 2-10 and 4-10 for SS and Al electrodes, respectively), current density (j: 30.86-154.32 A m(-2)), inter-electrode distance (g: 0.5-2.5 cm) and electrolysis time (t: 30-150 min) on the COD, color and TOC removal efficiency were evaluated for both the electrodes. SS electrode was found to be more effective for the removal of COD, color and TOC with removal efficiencies of 70%, 93% and 72%, respectively, as compared to Al electrode, which showed respective removal efficiencies of 59%, 80% and 55%. A two-stage EC process was also conducted to study the predominance of different types of electrodes, and to increase the efficiency of EC process. Results shows that SS followed by Al electrode (with total COD, color and TOC removal efficiency of 81%, 94% and 78%, respectively) was found to be more effective than Al followed by SS electrode combination (with total COD, color and TOC removal efficiency of 78%, 89% and 76%, respectively). Present study shows that EC process can be used as an additional step to bio-methanation process so as to meet effluent discharge standards in distilleries.

Membrane autopsy based bio-fouling investigation of distillery spent wash RO treatment plant

In this paper, a thorough investigation has been done to evaluate the effects of different pollutants on membrane performance by autopsy. Autopsy was performed on fresh and fouled reverse osmosis (RO) membrane elements from a distillery spent wash treatment plant by different analyses, such as field emission scanning electron microscopy, atomic force microscopy, Fourier transform infrared spectroscopy and X-ray diffraction, to identify the cause of poor performance of an RO plant. Results obtained from the analysis of membranes indicate that a mixture of colloids and organic matters (polysaccharides and amines) along with the presence of multivalent ions (Ca, Mg, Fe and SO4) causes membrane fouling, which in turn affects membrane performance. Possible measures to improve treated effluent quality and mitigate fouling have been suggested for this particular case study.