Machine learning-driven multiscale modeling reveals lipid-dependent dynamics of RAS signaling proteins.

RAS is a signaling protein associated with the cell membrane that is mutated in up to 30% of human cancers. RAS signaling has been proposed to be regulated by dynamic heterogeneity of the cell membrane. Investigating such a mechanism requires near-atomistic detail at macroscopic temporal and spatial scales, which is not possible with conventional computational or experimental techniques. We demonstrate here a multiscale simulation infrastructure that uses machine learning to create a scale-bridging ensemble of over 100,000 simulations of active wild-type KRAS on a complex, asymmetric membrane. Initialized and validated with experimental data (including a new structure of active wild-type KRAS), these simulations represent a substantial advance in the ability to characterize RAS-membrane biology. We report distinctive patterns of local lipid composition that correlate with interfacially promiscuous RAS multimerization. These lipid fingerprints are coupled to RAS dynamics, predicted to influence effector binding, and therefore may be a mechanism for regulating cell signaling cascades.

The etiology of Down syndrome: Maternal MCM9 polymorphisms increase risk of reduced recombination and nondisjunction of chromosome 21 during meiosis I within oocyte.

Altered patterns of recombination on 21q have long been associated with the nondisjunction chromosome 21 within oocytes and the increased risk of having a child with Down syndrome. Unfortunately the genetic etiology of these altered patterns of recombination have yet to be elucidated. We for the first time genotyped the gene MCM9, a candidate gene for recombination regulation and DNA repair in mothers with or without children with Down syndrome. In our approach, we identified the location of recombination on the maternal chromosome 21 using short tandem repeat markers, then stratified our population by the origin of meiotic error and age at conception. We observed that twenty-five out of forty-one single nucleotide polymorphic sites within MCM9 exhibited an association with meiosis I error (N = 700), but not with meiosis II error (N = 125). This association was maternal age-independent. Several variants exhibited aprotective association with MI error, some were neutral. Maternal age stratified characterization of cases revealed that MCM9 risk variants were associated with an increased chance of reduced recombination on 21q within oocytes. The spatial distribution of single observed recombination events revealed no significant change in the location of recombination among women harbouring MCM9 risk, protective, or neutral variant. Additionally, we identified a total of six novel polymorphic variants and two novel alleles that were either risk imparting or protective against meiosis I nondisjunction. In silico analyses using five different programs suggest the risk variants either cause a change in protein function or may alter the splicing pattern of transcripts and disrupt the proportion of different isoforms of MCM9 products within oocytes. These observations bring us a significant step closer to understanding the molecular basis of recombination errors in chromosome 21 nondisjunction within oocytes that leads to birth of child with Down syndrome.

Lifetime of actin-dependent protein nanoclusters.

Protein nanoclusters (PNCs) are dynamic collections of a few proteins that spatially organize in nanometer-length clusters. PNCs are one of the principal forms of spatial organization of membrane proteins, and they have been shown or hypothesized to be important in various cellular processes, including cell signaling. PNCs show remarkable diversity in size, shape, and lifetime. In particular, the lifetime of PNCs can vary over a wide range of timescales. The diversity in size and shape can be explained by the interaction of the clustering proteins with the actin cytoskeleton or the lipid membrane, but very little is known about the processes that determine the lifetime of the nanoclusters. In this paper, using mathematical modeling of the cluster dynamics, we model the biophysical processes that determine the lifetime of actin-dependent PNCs. In particular, we investigated the role of actin aster fragmentation, which had been suggested to be a key determinant of the PNC lifetime, and we found that it is important only for a small class of PNCs. A simple extension of our model allowed us to investigate the kinetics of protein-ligand interaction near PNCs. We found an anomalous increase in the lifetime of ligands near PNCs, which agrees remarkably well with experimental data on RAS-RAF kinetics. In particular, analysis of the RAS-RAF data through our model provides falsifiable predictions and novel hypotheses that will not only shed light on the role of RAS-RAF kinetics in various cancers, but also will be useful in studying membrane protein clustering in general.

Genetic aetiology of Down syndrome birth: novel variants of maternal DNMT3B and RFC1 genes increase risk of meiosis II nondisjunction in the oocyte.

The aim of the present work was to explore the intriguing association of maternal folate regulator gene polymorphisms and mutations with the incidence of chromosome 21 nondisjunction and Down syndrome birth. We tested polymorphisms/mutations of DNMT3B and RFC1 genes for their association with meiotic errors in oocyte among the 1215 Down syndrome child-bearing women and 900 controls. We observed that 23 out of 31 variants of DNMT3B and RFC1 exhibited an association with meiosis II nondisjunction in maternal age-independent manner. Additionally, we have reported 17 novel mutations and 1 novel polymorphic variant that are unique to the Indian Bengali speaking cohort and increased odds in favour of meiosis II nondisjunction. We hypothesize that the risk variants and mutations of DNMT3B and RFC1 genes may cause reduction in two or more recombination events and also cause peri-centromeric single exchange that increases the risk of nondisjunction at any age of women. In silico analyses predicted the probable damages of the transcripts or proteins from the respective genes owing to the said polymorphisms. These findings from the largest population sample tested ever revealed that mutations/polymorphisms of the genes DNMT3B and RFC1 impair recombination that leads to chromosome 21 nondisjunction in the oocyte at meiosis II stage and bring us a significant step closer towards understanding the aetiology of chromosome 21 nondisjunction and birth of a child with Down syndrome to women at any age.

Evaluation of vitamin D profile in juvenile idiopathic arthritis.

OBJECTIVE: To observe the association between serum vitamin D level and disease activity in juvenile idiopathic arthritis (JIA). METHODS: The observational study was conducted at a tertiary care hospital during 2017-2019. Patients suffered from JIA were recruited through purposive sampling which was stratified by the disease activity based on the Juvenile Arthritis Disease Activity Score 27 (JADAS27) criteria. Serum vitamin D was estimated alongside other laboratory parameters. The numerical and categorical variables were analysed with appropriate statistical tests. RESULTS: 40 subjects were studied where inactive disease was observed in nine subjects (22.5%), five subjects (12.5%) were found to be in low disease activity and moderate disease activity groups each, and twenty-one subjects (52.5%) had high disease activity. Considering the total sample size of the study, the mean (SD) JADAS27 score and serum vitamin D level were observed to be 12.02 (11.31) and 23.10 (5.93) respectively. A negative correlation was found between the JADAS27 score and serum vitamin D (r= -0.67). The corrected Chi-square test had revealed significant association between the status of serum vitamin-D and disease activity groups (=16.28; p < .001). CONCLUSIONS: In JIA, higher grade of disease activity was found to be significantly associated with lower serum vitamin D.

Presence or Absence of Ras Dimerization Shows Distinct Kinetic Signature in Ras-Raf Interaction.

Initiations of cell signaling pathways often occur through the formation of multiprotein complexes that form through protein-protein interactions. Therefore, detecting their presence is central to understanding the function of a cell signaling pathway, aberration of which often leads to fatal diseases, including cancers. However, the multiprotein complexes are often difficult to detect using microscopes due to their small sizes. Therefore, currently, their presence can be only detected through indirect means. In this article, we propose to investigate the presence or absence of protein complexes through some easily measurable kinetic parameters, such as activation rates. As a proof of concept, we investigate the Ras-Raf system, a well-characterized cell signaling system. It has been hypothesized that Ras dimerization is necessary to create activated Raf dimers. Although there are circumstantial evidences supporting the Ras dimerization hypothesis, direct proof of Ras dimerization is still inconclusive. In the absence of conclusive direct experimental proof, this hypothesis can only be examined through indirect evidences of Ras dimerization. In this article, using a multiscale simulation technique, we provide multiple criteria that distinguishes an activation mechanism involving Ras dimerization from another mechanism that does not involve Ras dimerization. The provided criteria will be useful in the investigation of not only Ras-Raf interaction but also other two-protein interactions.

Clinical Profile and Therapeutic Response of Scrub Typhus in Children: A Recent Trend from Eastern India.

OBJECTIVE: The aim of this study was to assess the clinico-laboratory parameters, complications and therapeutic responses in children with scrub typhus in Eastern India. MATERIALS AND METHODS: In this prospective, observational study, all children (age, <12 years) with suspected scrub typhus with a compatible clinical scenario were enrolled consecutively over six months. Cases confirmed by means of a positive IgM serology or a positive Weil-Felix reaction (OXK = 1/80 or above) were administered enteral doxycycline (4.5 mg/kg/day). RESULTS: Out of 94 recruited children, 61 had confirmed scrub typhus (mean age = 6.1 years, M:F = 1.1:1) with or without complications and having a considerably higher incidence of neurological presentation (meningoencephalistis n = 21, 34.4%). The most frequent manifestations included vomiting (n = 39, 63.9%), abdominal pain (n = 33, 54.1%), lymphadenopathy (n = 36, 59%), hepatosplenomegaly (n = 32, 52.5%), pedal edema (n = 32, 52.5%) and eschar formation (n = 30, 49.2%). Low hemoglobin levels, leukocytosis, thrombocytopenia, hypoalbuminemia, hyponatremia, increased liver enzymes and increased C-reactive protein were associated with delayed defervescence (>48 h). CONCLUSION: Scrub meningoencephalitis, with a notably higher incidence, showed favorable therapeutic response. Prompt and empiric doxycycline therapy could be lifesaving.

Risk of Down syndrome birth: Consanguineous marriage is associated with maternal meiosis-II nondisjunction at younger age and without any detectable recombination error.

Consanguineous marriage was examined as a risk factor for Down syndrome birth. We genotyped Down syndrome family trios using short tandem repeat markers on 21q-to interpret the parental and meiotic stage of origin of errors as well as to record recombination profile along long arm of chromosome 21. We then compared nonconsanguineous (N = 811) group with-the consanguineous (N =157) marriages. We report for the first time that consanguineous marriage is associated with an increased risk for nondisjunction of chromosome 21 in oocytes-during the second meiotic division. We observed the absence of recombination more frequently in younger mothers in nonconsanguineous meiosis I cases. This was in contrast to an equal distribution of nonrecombinant cases across the age categories in the meiosis I consanguineous group. Moreover, the non-consanguineous group exhibited preferential telomeric recombination in meiosis I error among younger women and centromeric recombination in meiosis II errors in older women. In contrast, the consanguineous group exhibited medially placed recombination events in both meiosis I and meiosis II nondisjunction errors. Additionally, we recorded reduced maternal age at conception in the-consanguineous group. These findings suggest novel risk factors associated that increase the risk of chromosome 21 nondisjunction in the families with consanguinity.

Animal Bites and Rabies Prophylaxis in Rural Children: Indian Perspective.

A prospective observational study was conducted in a tertiary care hospital to study clinicoepidemiological profile of potentially rabid animal bite cases from rural India. Total of 308 children (median age 6 years) admitted to hospital, were recruited over 1 year and followed up till completion of antirabies vaccine course. Dog was the commonest (77.27%) offending animal. Of the exposures, 66.88% were scratches, 88.96% were unprovoked and 27.27% were categorized as Class III. The median times to wound toileting and reporting to health facility were 1 and 6 h, respectively. Majority received prompt PEP in hospital, and RIG was administered in 34.55% of Class II and 90.48% of Class III exposures. Compared with their older counterparts, children aged <5 years suffered more bites on face and trunk and more Class III exposures. The rabies prophylaxis scenario is encouraging, when compared with earlier studies, but there are gaps to be addressed.

Spirometric Assessment in Juvenile Idiopathic Arthritis.

OBJECTIVE: To estimate the prevalence of abnormal spirometry in Juvenile idiopathic arthritis (JIA) patients and to evaluate its relation with subtype, gender, disease activity and methotrexate therapy. METHODS: A cross-sectional study was carried out involving 5-12 years old JIA patients. Forced vital capacity (FVC), Forced expiratory volume in 1 second (FEV1), FEV1/FVC ratio, Forced expiratory flow between 25-75% of vital capacity (FEF25-75%) and peak expiratory flow rate (PEFR) were measured. RESULT: Out of 33 patients, 18 were male. Six patients had oligoarthritis, 16 had polyarthritis and 11 had systemic JIA. Seventeen patients had clinically inactive disease and 16 received methotrexate. None had respiratory symptoms. Thirteen patients had decreased FVC with normal FEV1/FVC. One had decreased FEV1 and FEV1/FVC with normal FVC. Decreased FEF25-75% was found in 4 and decreased PEFR in 8 patients. JIA subtypes differed significantly with regard to prevalence of decreased FVC and FEV1. CONCLUSION: Abnormal spirometry was present in 13 patients and affected all subsets in terms of subtypes, gender, disease activity and methotrexate therapy.

Prevalence of HIV, hepatitis B and hepatitis C infections among patients with thalassemia attending a tertiary care (rural) hospital.

Introduction: The Sunderban area of West Bengal is home to tribal and religious minorities inhabiting various islands. There is a high prevalence of thalassemia among poverty-stricken residents of this region living with meagre health care facilities. This work was planned to determine the proportion of four viral transfusion-transmitted infections (TTIs): HIV-1, HIV-2, hepatitis B virus (HBV) and hepatitis C virus (HCV) among thalassemia patients attending the sole rural medical college in the region. Materials and Methods: Thalassemia patients (n = 359, age ranging from 1 year to 60 years) attending the thalassemia clinic or being admitted to the indoor facilities for better management were included in the study. Only patients diagnosed with high-performance liquid chromatography (HPLC) and with classical clinical features were included in the study. Blood samples of these patients were tested for HIV as per NACO protocol. For HBV and HCV, samples were first tested serologically; reactive samples were collected and sent in the cold chain to a higher centre for nucleic acid amplification testing (NAAT) for qualitative and quantitative estimation. Clinical and laboratory data was collected, patients were followed up for complications and hospitalisation during the study period, and statistical analysis was performed. Results: Majority of our patients had E-beta-thalassemia (245, 59.81%), followed by beta-thalassemia major (102, 28.30%). NAAT-confirmed HCV infection (14.21%) infection was the most common, followed by HBV (2.51%), and lastly by HIV-1 (0.58%) infection. Among infected thalassemia patients, the mean HCV RNA was 741063 ± 438514.67 IU/ml while the mean HBV DNA level was 4082863 ± 7298514 IU/ml. Co-infections of HIV-1 and HCV and that of HBV and HCV were noted in one patient each (0.28%). HCV-related liver disease (14.21%) and growth retardation (10.31%) were the most typical complication noted, and death occurred in five patients (1.39%) during the study period. Conclusion: Primary care physicians should know HCV infection is the most common TTI among thalassemia patients in rural eastern India.

Origin of rigidity in dry granular solids.

Solids are distinguished from fluids by their ability to resist shear. In traditional solids, the resistance to shear is associated with the emergence of broken translational symmetry as exhibited by a nonuniform density pattern. In this work, we focus on the emergence of shear rigidity in a class of solids where this paradigm is challenged. Dry granular materials have no energetically or entropically preferred density modulations. We show that, in contrast to traditional solids, the emergence of shear rigidity in these granular solids is a collective process, which is controlled solely by boundary forces, the constraints of force and torque balance, and the positivity of the contact forces. We develop a theoretical framework based on these constraints, which connects rigidity to broken translational symmetry in the space of forces, not positions of grains. We apply our theory to experimentally generated shear-jammed states and show that these states are indeed characterized by a persistent, non-uniform density modulation in force space, which emerges at the shear-jamming transition.

Immune thrombocytopenic purpura in a child with thyroid hormone resistance - a rare presentation.

Resistance to thyroid hormone (RTH) is a rare entity characterized by a decreased target tissue responsiveness of thyroid hormones. Although immune thrombocytopenic purpura (ITP) has been reported with different thyroid disorders in the literature, its coexistence with RTH is not known. A 9-year-old girl presented with ITP and features of hypothyroidism in the form of goiter and growth retardation. She was subsequently found to have RTH. High-dose thyroid hormone replacement was required to overcome the resistance that not only ameliorated the features of hypothyroidism but also brought an apparent remission of ITP.

Link updating strategies influence consensus decisions as a function of the direction of communication.

Consensus decision-making in social groups strongly depends on communication links that determine to whom individuals send, and from whom they receive, information. Here, we ask how consensus decisions are affected by strategic updating of links and how this effect varies with the direction of communication. We quantified the coevolution of link and opinion dynamics in a large population with binary opinions using mean-field numerical simulations of two voter-like models of opinion dynamics: an incoming model (IM) (where individuals choose who to receive opinions from) and an outgoing model (OM) (where individuals choose who to send opinions to). We show that individuals can bias group-level outcomes in their favour by breaking disagreeing links while receiving opinions (IM) and retaining disagreeing links while sending opinions (OM). Importantly, these biases can help the population avoid stalemates and achieve consensus. However, the role of disagreement avoidance is diluted in the presence of strong preferences-highly stubborn individuals can shape decisions to favour their preferences, giving rise to non-consensus outcomes. We conclude that collectively changing communication structures can bias consensus decisions, as a function of the strength of preferences and the direction of communication.

Acute kidney injury following multiple wasp stings.

BACKGROUND: Common manifestations of hypersensitivity reactions to toxins of stinging insects range from local swelling to angioedema and anaphylaxis. Sometimes it may result in unusual manifestations like intravascular hemolysis, disseminated intravascular coagulation, rhabdomyolysis, etc. Acute kidney injury (AKI) due to immune-mediated acute interstitial nephritis is an extremely uncommon manifestation of insect stings. CASE-DIAGNOSIS/TREATMENT: A 9-year-old boy who developed renal failure from acute interstitial nephritis 7 days after getting stung by a swarm of wasps at multiple sites is described. He regained normal renal function after eight sessions of hemodialysis. CONCLUSIONS: Acute interstitial nephritis resulting in AKI may be either due to immune-mediated tubulointerstitial injury or acute cellular injury caused by obstruction by pigments like hemoglobin and myoglobin. Timely and appropriate supportive management usually cures the patient without any residual damage. The objective of reporting this case is to draw the attention of fellow clinicians towards the possibility of this unusual but life-threatening delayed complication in multiple wasp stings, even if there are no significant immediate reactions.

Understanding etiology of chromosome 21 nondisjunction from gene × environment models.

Maternal risk factors and their interactions with each other that associate chromosome 21 nondisjunction are intriguing and need incisive study to be resolved. We determined recombination profile of nondisjoined chromosome 21 and maternal genotypes for four selected polymorphic variants from the folate regulators genes stratifying the women according to the origin of segregation error and age at conception. We conducted association study for genotype and maternal addiction to smokeless chewing tobacco, usually chopped tobacco leaves or paste of tobacco leaves with the incidence of Down syndrome birth. Additionally, we designed various logistic regression models to explore the effects of maternal genotype, maternal habit of smokeless chewing tobacco, maternal age at conception and all possible interactions among them on chromosome 21 nondisjunction. We found folate regulator gene mutations are associated with maternal meiosis II error. Regression models revealed smokeless chewing tobacco and folate polymorphic/mutant risk genotype interact with each other to increase the risk of reduced and single peri-centromeric recombination events on chromosome 21 that nondisjoined at meiosis II in the oocytes and the effect is maternal age independent. We inferred maternal folate polymorphic/mutant risk genotypes and habit of smokeless chewing tobacco interact with each other and increase the risk of meiosis II error in oocytes in maternal age-independent manner.

Immunogenicity and safety of the first indigenously developed Indian tetravalent influenza vaccine (split virion) in healthy children (6 months to 17 years of age): a randomized, multicenter, phase III clinical trial.

This phase III clinical trial was conducted to evaluate the immunogenicity and safety of the Tetravalent Influenza Vaccine (Split virion) I.P. (TetIV), containing two strains each of influenza A and B, developed indigenously in the country for the first time by M/s Cadila Healthcare Limited, India for use in the pediatric population (6 months -17 years of age), and compare it to that of a licensed seasonal Trivalent Influenza Vaccine (TriIV) of Sanofi Pasteur India Private Limited, containing two influenza A and one influenza B strains. Three hundred six subjects of either sex, 6 months to 17 years of age, were randomized in a 1:1 ratio to receive either TetIV or TriIV. Immunogenicity assessments (antibodies against A/H1N1, A/H3N2, B/Phuket, and B/Brisbane) were performed using the hemagglutination inhibition assay at baseline and 28 days after the last vaccination. TetIV was found to fulfill the criteria set by the United States Food and Drug Administration on the requirements of clinical data for licensure of seasonal inactivated influenza vaccines for the pediatric population. The seroconversion rates with TetIV were 94.6% for A/H1N1, 93.9% for A/H3N2, 91.2% for B/Brisbane, and 87.2% for B/Phuket strains. TetIV showed non-inferiority and superiority in immune response, as compared to TriIV, against the shared strains and an additional B strain, respectively. Both the vaccines were tolerated well by all the study participants, and an addition of the fourth strain in TetIV did not compromise the safety as compared to that of TriIV. The most common adverse event reported in both groups was fever.

Genetic and acquired blistering disorders of pediatric age group: An experience from Eastern India.

INTRODUCTION: Blistering or vesiculobullous disorders in pediatric population are either immunobullous or mechanobullous. Spectrum was analyzed using demographic details, clinical features, histopathology, direct immunofluorescence (DIF) and Immunofluorescence mapping (IFM). METHODOLOGY: This was a single institution based observational study in children below 18 years. The demographic details were collected using proforma containing particulars of the patient, history, complaints, and other parameters. Punch biopsy of the skin lesion was done. Biopsy samples were examined under light microscope followed by DIF using fluorescent conjugated polyclonal antibody against immunoglobulins IgG, IgM, IgA, and complement C3. The salt-split technique was also used in particular cases. IFM was done using anticytokeratin (CK) 5 & 14, antilaminin 332, anticollagen VII, and anticollagen IV antibodies. RESULTS: Out of total 50 cases, linear IgA bullous dermatosis (LABD) was the commonest. The average concordance between clinical and final diagnosis (histopathological examination + DIF) was 87.5% and discordance was 12.5%. The agreement between histopathological examination and DIF was found to be substantially significant (κ = 0.6892). IFM depicted epidermolysis bullosa simplex with reduced CK 14 expression, dystrophic epidermolysis bullosa with reduced Collagen VII expression and junctional epidermolysis bullosa with absent laminin 5 expression. CONCLUSION: The spectrum of bullous lesions in childhood was properly delineated and subcategorization of EB was done. Histopathological examination showed the hallmarks that were conclusive in most of the cases except in LABD and EB. DIF and IFM proved indispensable in those cases. Thus, DIF is not a substitute for histopathology but complementary to it.

Synchronization of an ensemble of oscillators regulated by their spatial movement.

Synchronization for a collection of oscillators residing in a finite two dimensional plane is explored. The coupling between any two oscillators in this array is unidirectional, viz., master-slave configuration. Initially the oscillators are distributed randomly in space and their autonomous time-periods follow a Gaussian distribution. The duty cycles of these oscillators, which work under an on-off scenario, are normally distributed as well. It is realized that random hopping of oscillators is a necessary condition for observing global synchronization in this ensemble of oscillators. Global synchronization in the context of the present work is defined as the state in which all the oscillators are rendered identical. Furthermore, there exists an optimal amplitude of random hopping for which the attainment of this global synchronization is the fastest. The present work is deemed to be of relevance to the synchronization phenomena exhibited by pulse coupled oscillators such as a collection of fireflies.

How Anionic Lipids Affect Spatiotemporal Properties of KRAS4B on Model Membranes.

RAS proteins are small membrane-anchored GTPases that regulate key cellular signaling networks. It has been recently shown that different anionic lipid types can affect the spatiotemporal properties of RAS through dimerization/clustering and signaling fidelity. To understand the effects of anionic lipids on key spatiotemporal properties of RAS, we dissected 1 ms of data from all-atom molecular dynamics simulations for KRAS4B on two model anionic lipid membranes that have 30% of POPS mixed with neutral POPC and 8% of PIP2 mixed with POPC. We unveiled the orientation space of KRAS4B, whose kinetics were slower and more distinguishable on the membrane containing PIP2 than the membrane containing POPS. Particularly, the PIP2-mixed membrane can differentiate a third kinetic orientation state from the other two known orientation states. We observed that each orientation state may yield different binding modes with an RAF kinase, which is required for activating the MAPK/ERK signaling pathway. However, an overall occluded probability, for which RAF kinases cannot bind KRAS4B, remains unchanged on the two different membranes. We identified rare fast diffusion modes of KRAS4B that appear coupled with orientations exposed to cytosolic RAF. Particularly, on the membrane having PIP2, we found nonlinear correlations between the orientation states and the conformations of the cationic farnesylated hypervariable region, which acts as an anchor in the membrane. Using diffusion coefficients estimated from the all-atom simulations, we quantified the effect of PIP2 and POPS on the KRAS4B dimerization via Green's function reaction dynamics simulations, in which the averaged dimerization rate is 12.5% slower on PIP2-mixed membranes.