Argonaute3-SF3B3 complex controls pre-mRNA splicing to restrain type 2 immunity

Argonaute (AGO) proteins execute microRNA (miRNA)-mediated gene silencing. However, it is unclear whether all 4 mammalian AGO proteins (AGO1, AGO2, AGO3, and AGO4) are required for miRNA activity. We generate Ago1, Ago3, and Ago4-deficient mice (Ago134Δ) and find AGO1/3/4 to be redundant for miRNA biogenesis, homeostasis, or function, a role that is carried out by AGO2. Instead, AGO1/3/4 regulate the expansion of type 2 immunity via precursor mRNA splicing in CD4+ T helper (Th) lymphocytes. Gain- and loss-of-function experiments demonstrate that nuclear AGO3 interacts directly with SF3B3, a component of the U2 spliceosome complex, to aid global mRNA splicing, and in particular the isoforms of the gene Nisch, resulting in a dysregulated Nisch isoform ratio. This work uncouples AGO1, AGO3, and AGO4 from miRNA-mediated RNA interference, identifies an AGO3:SF3B3 complex in the nucleus, and reveals a mechanism by which AGO proteins regulate inflammatory diseases.

Can a shock-induced phonon up-pumping model relate to impact sensitivity of molecular crystals, polymorphs and cocrystals?

Impact sensitivity engineering of high-energy molecular crystals requires accurate predictive models. For this purpose, the promising multi-phonon based approach is selected, assessing a bit more its strengths and weaknesses. Presently used with high-quality phonon calculations of 22 molecular crystals, using a physics-based criterion to determine the phonon bath extent, the resulting intrinsic shock sensitivity index (SSI) is compared to the most common marker of impact sensitivity, h 50, as determined from drop-weight impact tests. Selecting a data subset from experiments performed under very similar conditions (2.5 kg hammer with grit and 30-40 mg samples), the model can predict h 50 values for mono-molecular crystals with very good accuracy, including the ability to discriminate the polymorphs of HMX and CL20. This very good agreement validates an initial indirect up-pumping mechanism occurring under these conditions, where the doorway modes also interact with the phonon bath. However, the phonon bath criterion for mono-molecular crystals does not transfer well to cocrystals. Owing to the vibrational coupling of the co-molecules, it seems a broader phonon bath should be considered. Additionally recalling experimental uncertainty and various experimental factors affecting h 50 values for a given compounds, we recommend that the density of the sample, granularity and morphology be systematically considered and reported along with measurements, which will in turn allow for more systematic data and predictive capabilities for sensitivity models.

Unpacking Land Degradation Neutrality (LDN), An Emerging Paradigm to Conserve Land Systems’ Sustainability in the 21st Century? Meta-analysis of Challenges and Opportunities

The UN Sustainable Development Goals specifically note the growing importance of land degradation management and mitigation strategies, advocating for global collaboration and innovative research and policy outlook. In this reflective summary, we synthesize the current worldview (post-2000) on land degradation neutrality (LDN), an emerging concept in the field of environmental sustainability that advocates a dynamic balance between degradation and restoration, to ensure no net loss in productive land resources. We first introduce the LDN Causal Framework (theoretical framework of LDN), followed by the Logic Model – guideline for on-ground LDN method implementation (comprising preparatory activities, followed by Integrated Land Use Planning (ILUP), and LDN Response Hierarchy (Avoid-Reduce-Reverse)). We draw attention to growing concerns about LDN technical problems: restore vs. rehabilitate; selecting indicator variables, and establishing a baseline. In the final section, we reflect on the social-ecological aspect of LDN – harnessing participatory action (multi-stakeholder engagement) and gender mainstreaming. Overall, LDN presents an umbrella vision for environmental regeneration and land capital management, that requires seamless integration of natural with social sciences, the policy with law, and requires strategic community mobilization.

Improved predictions of thermomechanical properties of molecular crystals from energy and dispersion corrected DFT

Thermal stability and pressure-dependent changes are key to molecular crystals and their properties. The determination of their thermal properties from ab initio methods is, however, a challenging task. While the low-frequency phonon spectrum related to intermolecular vibrations remains difficult to describe, the Quasi-Harmonic Approximation (QHA) also induces for molecular crystals a significant volume deviation, which makes their thermal behavior ill-determined. To overcome these difficulties, we consider a pragmatic energy correction (EC) that has long been used for atomic crystals, and we presently report the first ever use for molecular crystals. Applying the QHA in dispersion-corrected density functional theory (DFT-D) calculations with an ab initio parameterized EC, the resulting model can simultaneously and accurately derive thermal and mechanical properties of high-explosive molecular crystals. When compared to experiments, the mean absolute percent error of previous DFT-based thermomechanical models is 12% for mechanical and 31% for thermal properties. Our model performs significantly better and reduces these uncertainties to 4.1% and 9.8%, respectively. In particular, the agreement between our model and experiments for the thermal properties is three times better. This significant improvement greatly benefits the determination of thermomechanical properties such as the Grüneisen parameter and the shock properties. The method has been successfully applied to molecular crystals showing a large diversity of weak intermolecular interactions (β-1,3,5,7-tetranitro-1,3,5,7-tetrazoctane (HMX), α-1,1-diamino-2,2-dinitroethylene (FOX-7), Triaminotrinitrobenzene (TATB), ε-Hexanitrohexaazaisowurtzitane (CL20), and Pentaerythritol tetranitrate (PETN)-I). Due to its accuracy and transferability, our model is expected to work for a large class of computationally designed molecular crystals and co-crystals, providing a basis for a predictive framework.

Age-related changes in polycomb gene regulation disrupt lineage fidelity in intestinal stem cells

Tissue homeostasis requires long-term lineage fidelity of somatic stem cells. Whether and how age-related changes in somatic stem cells impact the faithful execution of lineage decisions remains largely unknown. Here, we address this question using genome-wide chromatin accessibility and transcriptome analysis as well as single-cell RNA-seq to explore stem-cell-intrinsic changes in the aging Drosophila intestine. These studies indicate that in stem cells of old flies, promoters of Polycomb (Pc) target genes become differentially accessible, resulting in the increased expression of enteroendocrine (EE) cell specification genes. Consistently, we find age-related changes in the composition of the EE progenitor cell population in aging intestines, as well as a significant increase in the proportion of EE-specified intestinal stem cells (ISCs) and progenitors in aging flies. We further confirm that Pc-mediated chromatin regulation is a critical determinant of EE cell specification in the Drosophila intestine. Pc is required to maintain expression of stem cell genes while ensuring repression of differentiation and specification genes. Our results identify Pc group proteins as central regulators of lineage identity in the intestinal epithelium and highlight the impact of age-related decline in chromatin regulation on tissue homeostasis.

Restricted epitope specificity determined by variable region germline segment pairing in rodent antibody repertoires

Antibodies from B-cell clonal lineages share sequence and structural properties as well as epitope specificity. Clonally unrelated antibodies can similarly share sequence and specificity properties and are said to be convergent. Convergent antibody responses against several antigens have been described in humans and mice and include different classes of shared sequence features. In particular, some antigens and epitopes can induce convergent responses of clonally unrelated antibodies with restricted heavy (V_H) and light (V_L) chain variable region germline segment usage without similarity in the heavy chain third complementarity-determining region (CDR H3), a critical specificity determinant. Whether these V germline segment-restricted responses reflect a general epitope specificity restriction of antibodies with shared V_H/V_L pairing is not known. Here, we investigated this question by determining patterns of antigen binding competition between clonally unrelated antigen-specific rat antibodies from paired-chain deep sequencing datasets selected based solely on V_H/V_L pairing. We found that antibodies with shared V_H/V_L germline segment pairings but divergent CDR H3 sequences almost invariably have restricted epitope specificity indicated by shared binding competition patterns. This epitope restriction included 82 of 85 clonally unrelated antibodies with 13 different V_H/V_L pairings binding in 8 epitope groups in 2 antigens. The corollary that antibodies with shared V_H/V_L pairing and epitope-restricted binding can accommodate widely divergent CDR H3 sequences was confirmed by in vitro selection of variants of anti-human epidermal growth factor receptor 2 antibodies known to mediate critical antigen interactions through CDR H3. Our results show that restricted epitope specificity determined by V_H/V_L germline segment pairing is a general property of rodent antigen-specific antibodies.

Half metallicity in Cr substituted Fe2TiSn

Band structure tailoring has been a great avenue to achieve the half-metallic electronic ground state in materials. Applying this approach to the full Heusler alloy Fe₂TiSn, Cr is introduced systematically at Ti site that conforms to the chemical formula \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\text{Fe}}_{2} {\text{Ti}}_{{1 - x}} {\text{Cr}}_{x}$$\end{document}Fe2Ti1-xCrxSn. Compositions so obtained have been investigated for its electronic, magnetic, and electrical transport properties with an aim to observe the half-metallic ferromagnetic ground state, anticipated theoretically for Fe₂CrSn. Our experimental study using synchrotron X-ray diffraction reveals that only compositions with \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$x \le$$\end{document}x≤ 0.25 yield phase pure L2\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$_1$$\end{document}1 cubic structures. The non-magnetic ground state of Fe₂TiSn gets dramatically affected upon inclusion of Cr giving rise to a localized magnetic moment in the background of Ruderman–Kittel–Kasuya–Yosida (RKKY) correlations. The ferromagnetic interactions begin to dominate for x = 0.25 composition. Results of its resistivity and magnetoresistance (MR) measurement point towards a half-metallic ground state. The calculation of exchange coupling parameter, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\hbox {J}_{{ij}}$$\end{document}Jij, and orbital projected density of states that indicate a change in hybridization between 3d and 5p orbital, support the observations made from the study of local crystal structure made using the extended X-ray absorption fine structure spectroscopy. Our findings here highlight an interesting prospect of finding half-metallicity via band structure tailoring for wide application in spintronics devices.

Embryonic lethality and defective mammary gland development of activator-function impaired conditional knock-in Erbb3 V943R mice

ERBB3 is a pseudokinase domain-containing member of the ERBB family of receptor tyrosine kinases (RTKs). Following ligand binding, ERBB receptors homo- or hetero-dimerize, leading to a head-to-tail arrangement of the intracellular kinase domains, where the "receiver" kinase domain of one ERBB is activated by the "activator" domain of the other ERBB in the dimer. In ERBB3, a conserved valine at codon 943 (V943) in the kinase C-terminal domain has been shown to be important for its function as an "activator" kinase in vitro. Here we report a knock-in mouse model where we have modified the endogenous Erbb3 allele to allow for tissue-specific conditional expression of Erbb3 ^V943R (Erbb3 ^CKI-V943R ). Additionally, we generated an Erbb3 ^D850N (Erbb3 ^CKI-D850N ) conditional knock-in mouse model where the conserved aspartate in the DFG motif of the pseudokinase domain was mutated to abolish any potential residual kinase activity. While Erbb3 ^D850N/D850N animals developed normally, homozygous Erbb3 ^V943R/V943R expression during development resulted in embryonic lethality. Further, tissue specific expression of Erbb3 ^V943R/V943R in the mammary gland epithelium following its activation using MMTV-Cre resulted in delayed elongation of the ductal network during puberty. Single-cell RNA-seq analysis of Erbb3 ^V943R/V943R mammary glands showed a reduction in a specific subset of fibrinogen-producing luminal epithelial cells.

Functional characterization of SMARCA4 variants identified by targeted exome-sequencing of 131,668 cancer patients

Genomic studies performed in cancer patients and tumor-derived cell lines have identified a high frequency of alterations in components of the mammalian switch/sucrose non-fermentable (mSWI/SNF or BAF) chromatin remodeling complex, including its core catalytic subunit, SMARCA4. Cells exhibiting loss of SMARCA4 rely on its paralog, SMARCA2, making SMARCA2 an attractive therapeutic target. Here we report the genomic profiling of solid tumors from 131,668 cancer patients, identifying 9434 patients with one or more SMARCA4 gene alterations. Homozygous SMARCA4 mutations were highly prevalent in certain tumor types, notably non-small cell lung cancer (NSCLC), and associated with reduced survival. The large sample size revealed previously uncharacterized hotspot missense mutations within the SMARCA4 helicase domain. Functional characterization of these mutations demonstrated markedly reduced remodeling activity. Surprisingly, a few SMARCA4 missense variants partially or fully rescued paralog dependency, underscoring that careful selection criteria must be employed to identify patients with inactivating, homozygous SMARCA4 missense mutations who may benefit from SMARCA2-targeted therapy.

Integrated genomic analysis reveals mutated ELF3 as a potential gallbladder cancer vaccine candidate

Gallbladder cancer (GBC) is an aggressive gastrointestinal malignancy with no approved targeted therapy. Here, we analyze exomes (n = 160), transcriptomes (n = 115), and low pass whole genomes (n = 146) from 167 gallbladder cancers (GBCs) from patients in Korea, India and Chile. In addition, we also sequence samples from 39 GBC high-risk patients and detect evidence of early cancer-related genomic lesions. Among the several significantly mutated genes not previously linked to GBC are ETS domain genes ELF3 and EHF, CTNNB1, APC, NSD1, KAT8, STK11 and NFE2L2. A majority of ELF3 alterations are frame-shift mutations that result in several cancer-specific neoantigens that activate T-cells indicating that they are cancer vaccine candidates. In addition, we identify recurrent alterations in KEAP1/NFE2L2 and WNT pathway in GBC. Taken together, these define multiple targetable therapeutic interventions opportunities for GBC treatment and management.

T11TS immunotherapy potentiates the repressed calcineurin-NFAT signalling pathway of T cells in Cryptococcus neoformans infected rats: a cue towards T-cell activation for antifungal immunity

AIMS

To examine the modulation of the interacting partners of the calcineurin (CaN)-NFAT pathway in T cells during Cryptococcus neoformans fungal infection and post-T11TS immunotherapy.

METHODS AND RESULTS

Wistar rats were infected with C. neoformans and followed by immunotherapy with immune-potentiator T11TS. T cells were analysed by flow cytometry, immunoblotting and nuclear translocation study. The signalling proteins LCK, FYN, LAT, PLCγ1 and CaN in T cells were regulated by C. neoformans infection resulting in reduced nuclear translocation of NFAT and IL-2 expression. Following T11TS immunotherapy, the expressions of the above-mentioned proteins were boosted and thus resulting in the clearance of C. neoformans from lung and spleen.

CONCLUSIONS

The precise mechanism of suppression of the T-cell function by C. neoformans is still unknown. Previously, we have shown that T11TS positively regulates the function of T cells to abrogate glioma and other immunosuppressive conditions. T11TS immunotherapy increased the expression of the above signalling partners of the CaN-NFAT pathway in T cells and improved nuclear retention of NFAT. As a result, an increased IL-2 expression leads to activation and proliferation of T cells.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our results demonstrate the role of T11TS in restoring the CaN-NFAT signalling pathway in T cells. It identifies T11TS as an immunotherapeutic agent with potential clinical outcomes to counteract C. neoformans infection.

The Indian cobra reference genome and transcriptome enables comprehensive identification of venom toxins

Snakebite envenoming is a serious and neglected tropical disease that kills ~100,000 people annually. High-quality, genome-enabled comprehensive characterization of toxin genes will facilitate development of effective humanized recombinant antivenom. We report a de novo near-chromosomal genome assembly of Naja naja, the Indian cobra, a highly venomous, medically important snake. Our assembly has a scaffold N50 of 223.35 Mb, with 19 scaffolds containing 95% of the genome. Of the 23,248 predicted protein-coding genes, 12,346 venom-gland-expressed genes constitute the ‘venom-ome’ and this included 139 genes from 33 toxin families. Among the 139 toxin genes were 19 ‘venom-ome-specific toxins’ (VSTs) that showed venom-gland-specific expression, and these probably encode the minimal core venom effector proteins. Synthetic venom reconstituted through recombinant VST expression will aid in the rapid development of safe and effective synthetic antivenom. Additionally, our genome could serve as a reference for snake genomes, support evolutionary studies and enable venom-driven drug discovery.

Analysis of a near-chromosomal genome assembly and transcriptome profiling of the Indian cobra identifies genes expressed in the venom glands. These data should help develop a new antivenom.

Evaluating the quality of the 1000 genomes project data

BACKGROUND

Data from the 1000 Genomes project is quite often used as a reference for human genomic analysis. However, its accuracy needs to be assessed to understand the quality of predictions made using this reference. We present here an assessment of the genotyping, phasing, and imputation accuracy data in the 1000 Genomes project. We compare the phased haplotype calls from the 1000 Genomes project to experimentally phased haplotypes for 28 of the same individuals sequenced using the 10X Genomics platform.

RESULTS

We observe that phasing and imputation for rare variants are unreliable, which likely reflects the limited sample size of the 1000 Genomes project data. Further, it appears that using a population specific reference panel does not improve the accuracy of imputation over using the entire 1000 Genomes data set as a reference panel. We also note that the error rates and trends depend on the choice of definition of error, and hence any error reporting needs to take these definitions into account.

CONCLUSIONS

The quality of the 1000 Genomes data needs to be considered while using this database for further studies. This work presents an analysis that can be used for these assessments.

Massively parallel single-cell B-cell receptor sequencing enables rapid discovery of diverse antigen-reactive antibodies

Obtaining full-length antibody heavy- and light-chain variable regions from individual B cells at scale remains a challenging problem. Here we use high-throughput single-cell B-cell receptor sequencing (scBCR-seq) to obtain accurately paired full-length variable regions in a massively parallel fashion. We sequenced more than 250,000 B cells from rat, mouse and human repertoires to characterize their lineages and expansion. In addition, we immunized rats with chicken ovalbumin and profiled antigen-reactive B cells from lymph nodes of immunized animals. The scBCR-seq data recovered 81% (n = 56/69) of B-cell lineages identified from hybridomas generated from the same set of B cells subjected to scBCR-seq. Importantly, scBCR-seq identified an additional 710 candidate lineages not recovered as hybridomas. We synthesized, expressed and tested 93 clones from the identified lineages and found that 99% (n = 92/93) of the clones were antigen-reactive. Our results establish scBCR-seq as a powerful tool for antibody discovery.

Demonstration of Athena X-IFU Compatible 40-Row Time-Division-Multiplexed Readout

Time-division multiplexing (TDM) is the backup readout technology for the X-ray Integral Field Unit (X-IFU), a 3,168-pixel X-ray transition-edge sensor (TES) array that will provide imaging spectroscopy for ESA's Athena satellite mission. X-0IFU design studies are considering readout with a multiplexing factor of up to 40. We present data showing 40-row TDM readout (32 TES rows + 8 repeats of the last row) of TESs that are of the same type as those being planned for X-IFU, using measurement and analysis parameters within the ranges specified for X-IFU. Singlecolumn TDM measurements have best-fit energy resolution of (1.91 ± 0.01) eV for the Al Kα complex (1.5 keV), (2.10 ± 0.02) eV for Ti Kα (4.5 keV), (2.23 ± 0.02) eV for Mn Kα (5.9 keV), (2.40 ± 0.02) eV for Co Kα (6.9 keV), and (3.44 ± 0.04) eV for Br Kα (11.9 keV). Three-column measurements have best-fit resolution of (2.03 ± 0.01) eV for Ti Kα and (2.40 ± 0.01) eV for Co Kα. The degradation due to the multiplexed readout ranges from 0.1 eV at the lower end of the energy range to 0.5 eV at the higher end. The demonstrated performance meets X-IFU's energy-resolution and energy-range requirements. True 40-row TDM readout, without repeated rows, of kilopixel scale arrays of X-IFU-like TESs is now under development.

Intrinsic apoptosis shapes the tumor spectrum linked to inactivation of the deubiquitinase BAP1

Malignancies arising from mutation of tumor suppressors have unexplained tissue proclivity. For example, BAP1 encodes a widely expressed deubiquitinase for histone H2A, but germline mutations are predominantly associated with uveal melanomas and mesotheliomas. We show that BAP1 inactivation causes apoptosis in mouse embryonic stem cells, fibroblasts, liver, and pancreatic tissue but not in melanocytes and mesothelial cells. Ubiquitin ligase RNF2, which silences genes by monoubiquitinating H2A, promoted apoptosis in BAP1-deficient cells by suppressing expression of the prosurvival genes Bcl2 and Mcl1. In contrast, BAP1 loss in melanocytes had little impact on expression of prosurvival genes, instead inducing Mitf Thus, BAP1 appears to modulate gene expression by countering H2A ubiquitination, but its loss only promotes tumorigenesis in cells that do not engage an RNF2-dependent apoptotic program.

Optimization of Time- and Code-Division-Multiplexed Readout for Athena X-IFU

Readout of a large, spacecraft-based array of superconducting transition-edge sensors (TESs) requires careful management of the layout area and power dissipation of the cryogenic-circuit components. We present three optimizations of our time- (TDM) and code-division-multiplexing (CDM) systems for the X-ray Integral Field Unit (X-IFU), a several-thousand-pixel-TES array for the planned Athena-satellite mission. The first optimization is a new readout scheme that is a hybrid of CDM and TDM. This C/TDM architecture balances CDM's noise advantage with TDM's layout compactness. The second is a redesign of a component: the shunt resistor that provides a dc-voltage bias to the TESs. A new layout and a thicker Pd-Au resistive layer combine to reduce this resistor's area by more than a factor of 5. Third, we have studied the power dissipated by the first-stage SQUIDs (superconducting quantum-interference devices) and the readout noise versus the critical current of the first-stage SqUIDs. As a result, the X-IFU TDM and C/TDM SQUIDs will have a specified junction critical current of 5 μA. Based on these design optimizations and TDM experiments described by Durkin, et al. (these proceedings), TDM meets all requirements to be X-IFU's backup-readout option. Hybrid C/TDM is another viable option that could save spacecraft resources.

Unraveling the physical properties and superparamagnetism in anti-site disorder controlled Fe2TiSn

With an aim to control the anti-site disorder between Fe and Ti atoms in the full Heusler alloy, Fe[Formula: see text]TiSn, we substitute a small percentage of Ti at Fe site to form the Fe[Formula: see text]Ti[Formula: see text]Sn ([Formula: see text]) series. Using the incident x-rays tuned to the Fe K-edge absorption energy, we record the high resolution synchrotron x-ray diffraction profiles and unambiguously show the reduction in anti-site disorder. In particular, the Fe-Ti anti-site disorder decreases up to an excess Ti content of 0.07; further increase of Ti content leads to disorder between Ti-Sn sites. Detailed characterization vis-á-vis the excess Ti content has been carried out in terms of its thermal and electrical transport, and magnetic properties. Signatures of strong spin fluctuation are seen in all the physical properties reported here. The much disputed high value of the Sommerfeld constant has been shown to be a resultant of such strong spin fluctuations, thus ruling out the long standing controversy of heavy fermionic nature of Fe[Formula: see text]TiSn. Magnetization and the Seebeck coefficient show clear dependence on the disorder. Both dc and ac magnetic measurements reveal the low temperature superparamagnetic nature of this system, comprising of large magnetic clusters [Formula: see text]3 nm in size.

A flexible-molecule force field to model and study hexanitrohexaazaisowurtzitane (CL-20) – polymorphism under extreme conditions

The quantum-chemistry based force field (FF) developed for HMX by Smith and Bharadwaj (SB) [G. D. Smith and R. K. Bharadwaj, J. Phys. Chem. B, 1999, 103(18), 3570–3575] is transferred to another nitramine of different stoichiometry: hexanitrohexaazaisowurtzitane (CL-20 or HNIW). The modification of a single parameter alongside a very small number of add-ons related to carbon–carbon bonds, angles and dihedrals lead to two SB FF variants denoted SB-CL20 and SB-CL20 + CCNN. These flexible-molecule FFs should inherit the predictive capabilities of SB FF. For this purpose, we perform Molecular Dynamics simulations at ambient temperature and selected pressures. The modeled structures of the various CL-20 polymorphs are consistent with experimental data. Focusing on the ε-polymorph, we determine an equation of state which consolidates the general trend underpinned by most published results, and we confirm the increasing stiffness of the crystal under pressures up to 90 GPa. Moreover, we link some subtle pressure-induced changes of the elastic and structural properties to the flexibility and mobility of well-identified nitro groups. Finally, the simulations of the γ ↔ ζ phase transition suggest different multiple-step direct and reverse thermodynamic paths.

The quantum-chemistry based force field developed by Smith and Bharadwaj is transferred to hexanitrohexaazaisowurtzitane (CL20), revealing pressure-induced alterations of ε-CL20.

Actionable Activating Oncogenic ERBB2/HER2 Transmembrane and Juxtamembrane Domain Mutations

Deregulated HER2 is a target of many approved cancer drugs. We analyzed 111,176 patient tumors and identified recurrent mutations in HER2 transmembrane domain (TMD) and juxtamembrane domain (JMD) that include G660D, R678Q, E693K, and Q709L. Using a saturation mutagenesis screen and testing of patient-derived mutations we found several activating TMD and JMD mutations. Structural modeling and analysis showed that the TMD/JMD mutations function by improving the active dimer interface or stabilizing an activating conformation. Further, we found that HER2 G660D employed asymmetric kinase dimerization for activation and signaling. Importantly, anti-HER2 antibodies and small-molecule kinase inhibitors blocked the activity of TMD/JMD mutants. Consistent with this, a G660D germline mutant lung cancer patient showed remarkable clinical response to HER2 blockade.

Nonsmoked Tobacco Addiction Playing a Major Role in Oral Mucosal Changes in Northern Indian Population Over Smoked and Alcohol Use

Background: Oral cavity is prone for myriad of changes with advancing age as well result of environmental and life style related factors like consumption of tobacco (smoke or smokeless) and alcohol. Aim: The aim of this study was to quantify and compare the association of oral mucosal changes (OMC) with nonsmoked tobacco over smoked tobacco and alcohol. Methods: Data of 11,145 subjects from 106 health screening camps, organized in Uttar Pradesh and Rajasthan between April 2015 to June 2017 was analyzed to unveil and determine the mode of addiction and prevalence of OMC. Bivariate and multivariable models were tested for comparison and identification of factors associated with an increasing risk of developing OMC. Results: The primary symptoms were mouth ulcer in 5.6% and trismus (1.0%). The overall proportions of tobacco chewing, smoking and alcohol addiction were 12.5%, 10.7% and 2.5% respectively. The highest prevalence of smoking noted in the age-group 55-64 years (14.4%), for tobacco chewing and alcohol consumption in the age-group 25-34 years was 15.6% and 4.2% respectively ( P < 0.001). The prevalence of mouth ulcers were 20.7% among smokers and 27.8% among tobacco chewers ( P < 0.001) while the percentage of trismus 26.1% among smokers and 53.0% among tobacco chewers ( P < 0.001). Conclusion: Results of this study can be used for creating awareness among the population regarding the hazards of tobacco use. More number of studies needs to be conducted all over India to understand the prevalence and the biologic behavior of these oral premalignant lesions and its progression to invasive diseases.

Disparity Between Metro-Centric Cancer Care and Rural Outreach in India: Situational Analysis and Future Trends in Context of Developing Countries

Background: Radiation therapy is used in two-third of all patients diagnosed with cancer in any form and it has become an integral part of modern treatment strategies for many types of cancers in recent decade. Semi-urban and rural places in India lack healthcare facilities and so as the cancer care facilities. Aim: To identify the propensity of a metro-centric oncologic care in developing countries undermining the need of availability of facilities in smaller towns and cities. Methods: Data for state-wise population for 2016 and 2026 was projected using cohort component method. For the projection of cancer incidence and prevalence in 2016 and 2026, we assumed that the state-level prevalence and incidence of cancer in the year 2015 will not change over time in 2016. Data collected through telephonic interviews from the radiotherapy centers listed by Atomic Energy Regulatory Board (AERB), India. Further, we assumed few scenarios of cancer incidence and prevalence increase and projected state wise cancer burden in 2026. Results: With almost 70% population of India residing in districts and cities lacking quality health care, the situation of cancer care is much grave. India is currently equipped with only 394 RTU (Radiation Therapy Unit) against requirement of almost 1300 RTU, amounting to 0.38 RTU per million populations as per World Health Organization. The public sponsored healthcare infrastructure for cancer treatment, and research is centralized with all the resources centered in metro/major cities. Eight metro cities of India with a combined population of 140.6 million hold control of 188 RTU under their boundaries. Thus, while habitants of these eight metro cities, constituting only 10.9% of the national population, avail treatment benefit from 38% of total RTU capacity of India, rest of Indian population at 1143.8 million strengths is left prey to the wrath of cancer with just 306 machines at disposal. In comparison, the developed nations as the United States of America, Australia, and the United Kingdom fare far better in RTU availability for treatment of diagnosed cancer patients, with RTU per million population density of 12.45, 10.12 and 5.04 respectively. Similar scenario has been seen in other LMICs in world like Congo, Mongolia, Sudan, Nigeria, Nepal etc. Conclusion: We observed that wide disparity exists in India concerning RTU and cancer facility availability and density per million populations in between metro cities and rest of India and a dire need of improvement to fight against cancer which is very similar to the situation in developing countries.

Reaction Characteristics of Antiprothrombin Antibody on the Activation of Prothrombin (Sheep)

1. Prothrombin was purified by a series of steps and subsequently on DEAE-Cellu- lose chromatography and specific antibody to pure prothrombin was prepared.

2. The effect of Anti-prothrombin antibody was tested on the activation of prothrombin. The generated thrombin was assayed for its clotting function as well as for esterase activity on TAMe (Tosyl-Arginine-Methyl ester) as substrate.

3. Anti-prothrombin antibody inhibits the clotting function of generated thrombin completely but its esterase function is only partially affected.

Comprehensive genomic analysis identifies pathogenic variants in maturity-onset diabetes of the young (MODY) patients in South India

BACKGROUND

Maturity-onset diabetes of the young (MODY) is an early-onset, autosomal dominant form of non-insulin dependent diabetes. Genetic diagnosis of MODY can transform patient management. Earlier data on the genetic predisposition to MODY have come primarily from familial studies in populations of European origin.

METHODS

In this study, we carried out a comprehensive genomic analysis of 289 individuals from India that included 152 clinically diagnosed MODY cases to identify variants in known MODY genes. Further, we have analyzed exome data to identify putative MODY relevant variants in genes previously not implicated in MODY. Functional validation of MODY relevant variants was also performed.

RESULTS

We found MODY 3 (HNF1A; 7.2%) to be most frequently mutated followed by MODY 12 (ABCC8; 3.3%). They together account for ~ 11% of the cases. In addition to known MODY genes, we report the identification of variants in RFX6, WFS1, AKT2, NKX6-1 that may contribute to development of MODY. Functional assessment of the NKX6-1 variants showed that they are functionally impaired.

CONCLUSIONS

Our findings showed HNF1A and ABCC8 to be the most frequently mutated MODY genes in south India. Further we provide evidence for additional MODY relevant genes, such as NKX6-1, and these require further validation.

Possible half-metallicity and variable range hopping transport in Sb-substituted Fe2TiSn Heusler alloys

The investigation of the magnetotransport properties on [Formula: see text] [Formula: see text]Sb _x with 0 [Formula: see text] 0.6 are presented in this paper. The substitution of Sb in place of Sn decreases the anti-site disorder as evident from x-ray diffraction patterns as well as from transport properties measurement. The much-disputed upturn in low temperature electrical resistivity of [Formula: see text]TiSn has been demonstrated to be a result of weak localization induced by anti-site disorder. With increased Sb substitution (⩾25%) the metallic transport behavior of [Formula: see text]TiSn changes to semiconductor-like. At low temperature, carrier transport in such compositions occurs via the variable range hopping mechanism. Moreover, a systematic increase in the anomalous Hall voltage is observed with increasing Sb-content, attributable to a side jump or Berry phase curvature effect. Electrical resistivity in the entire temperature regime hints towards half metallicity of the system. Our ab initio electronic structure calculations using generalised gradient approximation formalism further supports the results of our magnetotransport study.

Silencing of retrotransposons by SETDB1 inhibits the interferon response in acute myeloid leukemia

Cancer cells can rewire genetic and epigenetic regulatory networks to promote cell proliferation and evade the immune system. Using a focused CRISPR/Cas9 genetic screen, Cuellar et al. identify a novel role for the SETDB1 histone methyltransferase in regulating the antiviral response in AML cells via the suppression of transposable elements.

A propensity for rewiring genetic and epigenetic regulatory networks, thus enabling sustained cell proliferation, suppression of apoptosis, and the ability to evade the immune system, is vital to cancer cell propagation. An increased understanding of how this is achieved is critical for identifying or improving therapeutic interventions. In this study, using acute myeloid leukemia (AML) human cell lines and a custom CRISPR/Cas9 screening platform, we identify the H3K9 methyltransferase SETDB1 as a novel, negative regulator of innate immunity. SETDB1 is overexpressed in many cancers, and loss of this gene in AML cells triggers desilencing of retrotransposable elements that leads to the production of double-stranded RNAs (dsRNAs). This is coincident with induction of a type I interferon response and apoptosis through the dsRNA-sensing pathway. Collectively, our findings establish a unique gene regulatory axis that cancer cells can exploit to circumvent the immune system.

A tunable coupler for superconducting microwave resonators using a nonlinear kinetic inductance transmission line

We present a tunable coupler scheme that allows us to tune the coupling strength between a feedline and a superconducting resonator in situ over a wide range. In this scheme, we shunt the feedline with a 50-Ω lumped-element nonlinear transmission line made from a 20 nm NbTiN film. By injecting a DC current, the nonlinear kinetic inductance changes and the effective impedance shunting the resonator periodically varies from a short to an open, which tunes the coupling strength and coupling quality factor Qc . We have demonstrated Qc tuning over a factor of 40, between Qc ~ 5.5 × 104 and Qc ~ 2.3 × 106, for a 4.5 GHz resonator by applying a DC current less than 3.3 mA. Our tunable coupler scheme is easy to implement and may find broad applications in superconducting detector and quantum computing/information experiments.

Comprehensive genomic analysis of malignant pleural mesothelioma identifies recurrent mutations, gene fusions and splicing alterations

We analyzed transcriptomes (n = 211), whole exomes (n = 99) and targeted exomes (n = 103) from 216 malignant pleural mesothelioma (MPM) tumors. Using RNA-seq data, we identified four distinct molecular subtypes: sarcomatoid, epithelioid, biphasic-epithelioid (biphasic-E) and biphasic-sarcomatoid (biphasic-S). Through exome analysis, we found BAP1, NF2, TP53, SETD2, DDX3X, ULK2, RYR2, CFAP45, SETDB1 and DDX51 to be significantly mutated (q-score ≥ 0.8) in MPMs. We identified recurrent mutations in several genes, including SF3B1 (∼2%; 4/216) and TRAF7 (∼2%; 5/216). SF3B1-mutant samples showed a splicing profile distinct from that of wild-type tumors. TRAF7 alterations occurred primarily in the WD40 domain and were, except in one case, mutually exclusive with NF2 alterations. We found recurrent gene fusions and splice alterations to be frequent mechanisms for inactivation of NF2, BAP1 and SETD2. Through integrated analyses, we identified alterations in Hippo, mTOR, histone methylation, RNA helicase and p53 signaling pathways in MPMs.

Autism Spectrum Disorder: the Present Perspective

The last decade has witnessed a surge of awareness about autism among the public and professionals. Much revealing research is being done on this issue and the knowledge base has improved substantially and a set of professionals are specializing on the subject, focusing on its causative factors and management. Autism being a disorder stemming from early childhood and the prevalence rate rising alarmingly over the years, Pediatricians are expected to play a vital role in early detection and early intervention in management of the problem. But, unfortunately, autism is not yet considered to be under the purview of pediatricians. As pediatricians, we are often perplexed when faced with such a different child in our office and either overlook the problem or hurry to hand him over to a psychiatrist, not trying to really identify and understand the problem as a medical entity ourselves. Hence better awareness among pediatricians is the need of the day. As specialists have worked with autism over the decades, it has become clear that: autism is a disorder that involves early development, presently there is no medical answer to autism, and the only management strategy hinges largely on effective training. The earlier the training begins the better it is for the child. It is of paramount importance to start training and bring about changes by the time the child is 18 months old. This throws up interesting new challenges to the profession of pediatrics. To identify the early warning signs of autism, it is important that Pediatricians are able to recognize the signs and symptoms of autistic spectrum disorders (ASD), have a strategy for assessing them systematically, be familiar with available tools for screening as well as developmental and educational resources.DOI: http://dx.doi.org/10.3126/jcmsn.v10i3.12775 Journal of College of Medical Sciences-Nepal, 2014, Vol-10, No-3, 37-47

Spectrum of diverse genomic alterations define non-clear cell renal carcinoma subtypes

To further understand the molecular distinctions between kidney cancer subtypes, we analyzed exome, transcriptome and copy number alteration data from 167 primary human tumors that included renal oncocytomas and non-clear cell renal cell carcinomas (nccRCCs), consisting of papillary (pRCC), chromophobe (chRCC) and translocation (tRCC) subtypes. We identified ten significantly mutated genes in pRCC, including MET, NF2, SLC5A3, PNKD and CPQ. MET mutations occurred in 15% (10/65) of pRCC samples and included previously unreported recurrent activating mutations. In chRCC, we found TP53, PTEN, FAAH2, PDHB, PDXDC1 and ZNF765 to be significantly mutated. Gene expression analysis identified a five-gene set that enabled the molecular classification of chRCC, renal oncocytoma and pRCC. Using RNA sequencing, we identified previously unreported gene fusions, including ACTG1-MITF fusion. Ectopic expression of the ACTG1-MITF fusion led to cellular transformation and induced the expression of downstream target genes. Finally, we observed upregulation of the anti-apoptotic factor BIRC7 in MiTF-high RCC tumors, suggesting a potential therapeutic role for BIRC7 inhibitors.

Abstract 4428: Oncogenic ERBB3 mutations in human cancers

The human epidermal growth factor receptor (HER) family of tyrosine kinases are deregulated in multiple cancers either through amplification, overexpression or mutation. ERBB3/HER3, the only ERBB family member with an impaired kinase domain, upon ligand binding heterodimerizes with ERBB2 to promote signaling. While amplification and overexpression of ERBB3 is observed in some cancers, occurrence and relevance of ERBB3 somatic mutations in oncogenesis is not established. Here we report the identification of ERBB3 somatic mutations in ∼11% of colon and gastric cancers. We found that the ERBB3 mutants together with ERBB2 promote oncogenic signaling and transformed colonic and breast epithelial cells in a ligand independent manner. Further, we found that multiple target therapeutics that acts on ERBB3, ERBB2 or their downstream signaling components are effective in blocking ERBB3-mutant mediated oncogenic signaling and disease progression in vivo. Identification of activating ERBB3 mutations along with the established contribution of ERBB3 to acquired resistance to EGFR/ERBB2-targeted drugs provides a rational to therapeutically target ERBB3.

Citation Format: Bijay S. Jaiswal, Noelyn M. Kljavin, Eric Stawiski, Steffen Durinck, Subhra Chaudhuri, Charles Eigenbrot, Gabriele Schaefer, Frederic J. de Sauvage, Somasekar Seshagiri. Oncogenic ERBB3 mutations in human cancers. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4428. doi:10.1158/1538-7445.AM2014-4428

Oncogenic ERBB3 mutations in human cancers

The human epidermal growth factor receptor (HER) family of tyrosine kinases is deregulated in multiple cancers either through amplification, overexpression, or mutation. ERBB3/HER3, the only member with an impaired kinase domain, although amplified or overexpressed in some cancers, has not been reported to carry oncogenic mutations. Here, we report the identification of ERBB3 somatic mutations in ~11% of colon and gastric cancers. We found that the ERBB3 mutants transformed colonic and breast epithelial cells in a ligand-independent manner. However, the mutant ERBB3 oncogenic activity was dependent on kinase-active ERBB2. Furthermore, we found that anti-ERBB antibodies and small molecule inhibitors effectively blocked mutant ERBB3-mediated oncogenic signaling and disease progression in vivo.

Ecoepidemics overcoming the species barrier and being subject to harvesting

An ecoepidemiological model in which the disease can be transmitted from one population to another one is considered. Linear harvesting on all the populations is considered. By means of numerical simulations, the role of the epidemiological parameters as well as that of harvesting are investigated. Some relevant consequences of harvesting on the system dynamics are discovered.

Dynamics of a robust photo-induced insulator-metal transition driven by coherent and broad-band light in epitaxial films of La(0.625-y)Pr(y)Ca(0.375)MnO(3)

A dramatic drop of ≈5 orders of magnitude in the resistance (R) of La(0.175)Pr(0.45)Ca(0.375)MnO(3) epitaxial films upon exposure to optical photons derived from both continuous and pulsed lasers, as well as broad-band sources at temperatures (T) < 30 K is reported. The strength of change is a sensitive function of both the incident photon flux and temperature. Under isothermal conditions the photo-generated low resistance state persists eternally after removal of light. This non-equilibrium state is metallic, as revealed by the positive dR/dT for T ≤ T(p) (≈120 K). This electrically conducting state is presumably ferromagnetic as T(p) coincides with the temperature where a weak ferromagnetism sets in on cooling the insulating film from room temperature. To rule out the possibility of photon-induced local heating of the sample as a mechanism of the observed effects, photo-illumination experiments were performed under identical conditions on thin films of two non-charge-ordered manganites deposited on substrates of similar thermal conductivity. Our model for the observed transition encompasses a global charge-ordered state in which ferromagnetic metallic clusters of fraction p much less than the critical fraction p(c) for percolation exists at low temperatures. Photo-induced melting of the charge-ordered state increases this fraction beyond p(c) in a cumulative manner as successive pulses of light fall on the sample.

Microalbuminuria: An inexpensive, non invasive bedside tool to predict outcome in critically ill patients

This study was conducted to evaluate whether microalbuminuria on admission and after 24 hrs of admission to intensive care unit (ICU) predicts outcome as well as the Acute Physiology and Chronic Health Evaluation (APACHE) II severity illness score, the current accepted method of doing so. The study was carried out in a 20 bed mixed medical-surgical ICU of a tertiary care hospital. Of 525 consecutive adult patients with ICU stay of more than 24 hrs, 238 were included for the study. Patients with pregnancy, menstruation, anuria, macroscopic hematuria, urinary tract infection, marked proteinuria due to renal and post-renal structural diseases, were excluded. Spot urine samples were collected on admission to ICU and 24 hrs thereafter. Urine albumincreatinine ratio (ACR) was measured on ICU admission (ACR1) and after 24 hrs (ACR2) and expressed in mg/g. Patient demographics were noted on admission. For disease severity scoring, APACHE II scores were calculated. Each patient was followed up throughout their ICU stay for a maximum of 28 days and the following outcome data were obtained: ICU length of stay and ICU mortality. Of the 238 patients, 196 survived while 42 patients died in the ICU. Non-survivors had a significantly higher median ACR2 [162.7 mg/g (IQR 69.5-344.3)] in comparison to the survivors who had a median ACR2 = 54.4 mg/g (IQR 19.0-129.1) (P< 0.0001). The median ACR1 [161.0 mg/g (IQR 29.0-369.3)] of non-survivors was higher than the median ACR1 [80.4 mg/g (IQR 35.1-167.6)] of survivors but failed to reach statistical significance (P= 0.0948). In a receiver operating characteristic curve (ROC) analysis, ACR2 emerged as the best indicator of mortality [(area under curve (AUC) of ACR2 = 0.71 > AUC (ACR1) =0.58 > AUC (ΔACR) =0.55] similar to the currently used APACHE II scores (AUC = 0.78) (P=0.3). At a cutoff of 101 mg/g, ACR2 had a sensitivity of 69%, specificity of 67%, positive predictive value of 31% and a negative predictive value of 91% for predicting mortality in the critically ill patients. Absence of significant microalbuminuria at 24 hrs of ICU admission may help to predict survival in the ICU.

Abstract 305: Frequent PIK3R1 somatic mutations promote oncogenic signaling

We performed a systematic analysis of human fresh frozen tumors for somatic mutations in the RAS-effector pathways and have identified frequent mutations (&gt;8%) in PIK3R1 (p85α) regulatory subunit of PI3K (p110) enzyme complex. Mutations in other members of the PI3K regulatory subunits, along with mutations in additional components of the pathway were also identified in this study. An integrated analysis of somatic mutations and genomic copy number variations identified by comparative genome hybridization revealed distinct mutation patterns across tumor types. In order to understand the functional consequence of p85α mutations, we generated mutant p85α constructs and tested them for activity in biochemical and cellular assays. In this studies, we found that all the mutants that contain an intact p110-binding domain were able to interact with p110α, p110β and p110δ. Also, all these mutants stabilized expression of p110 class IA members when tested in pan-p85 null fibroblasts, indicating that the p110-stabilizing activity of p85 mutants was still intact. However, in un-stimulated cells, some of the p85α mutants were not as effective as wild-type p85α in inhibiting the activity of p110. Furthermore, these p85α somatic mutants activated AKT signaling leading to cell survival. Additionally, cells expressing the p85α mutants when transplanted in vivo promote a leukemia-like disease leading to decreased overall survival of the mice compared to wild-type p85α. These data demonstrate an alternate mechanism for activation of class IA PI3Ks in tumors through somatic mutations in p85α that abrogates its p110 regulatory activity while maintaining its p110-stabilizing activity. The frequent occurrence of p85α mutations and its ability to promote survival signaling suggest that tumors with such mutations are likely candidates for inhibitors that target the components of the PI3K pathway.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 305.

A study of coupling interactions in finite arbitrarily-shaped grooves in electromagnetic scattering problem

A study of coupling between finite number of general-shaped grooves in electromagnetic plane-wave scattering problem is presented. The formulation for a single groove [1] is extended to two grooves. The importance of inclusion of coupling interaction between two grooves in scattering analysis is presented and its dependence on the grooves separation distance and the angle of incident of the electromagnetic field is demonstrated quantitatively. For larger angle of incident and smaller separation distance between grooves indicate larger discrepancy between between simulation results with and without inclusion of the coupling effects. Although the results presented here considers two grooves, the formulation can be extended to arbitrary number of grooves.

Somatic mutations in p85alpha promote tumorigenesis through class IA PI3K activation

Members of the mammalian phosphoinositide-3-OH kinase (PI3K) family of proteins are critical regulators of various cellular process including cell survival, growth, proliferation, and motility. Oncogenic activating mutations in the p110alpha catalytic subunit of the heterodimeric p110/p85 PI3K enzyme are frequent in human cancers. Here we show the presence of frequent mutations in p85alpha in colon cancer, a majority of which occurs in the inter-Src homology-2 (iSH2) domain. These mutations uncouple and retain p85alpha's p110-stabilizing activity, while abrogating its p110-inhibitory activity. The p85alpha mutants promote cell survival, AKT activation, anchorage-independent cell growth, and oncogenesis in a p110-dependent manner.