Heavy Higgs Searches at the LHC in the light of a Left-Right Symmetric Model

We investigate a Left-Right symmetric model respecting $SU(3)_C \otimes SU(2)_L \otimes U(1)_L \otimes SU(2)_R \otimes U(1)_R$ local gauge symmetry. We study the interactions of the heavy neutral and charged scalars of this model along with their production at the hadron collider and their subsequent decays. We analyze the collider searches of two heavy scalars, one of them is charge neutral and another one is singly charged. In both the cases we consider their associated production at the Large Hadron Collider (LHC) and finally concentrate only on the leptonic final states. We perform both cut-based and multivariate analysis using Boosted Decision Tree algorithm for 14 TeV as well as as 27 TeV LHC run with 3000 fb$^{-1}$ integrated luminosity. As expected, the multivariate analysis shows a better signal-background discrimination compared to the cut-based analysis. In this article, we show that a charged Higgs of mass 750 GeV and 1.2 TeV can be probed with $2.77 \sigma$ ($4.58 \sigma$) and $1.38 \sigma$ ($3.66 \sigma$) significance at 14 (27) TeV run of LHC.Comment: 20 pages, 6 tables, 10 figure

Substrate inhibition imposes fitness penalty at high protein stability

Proteins are only moderately stable. It has long been debated whether this narrow range of stabilities is solely a result of neutral drift towards lower stability or purifying selection against excess stability is also at work - for which no experimental evidence was found so far. Here we show that mutations outside the active site in the essential E. coli enzyme adenylate kinase result in stability-dependent increase in substrate inhibition by AMP, thereby impairing overall enzyme activity at high stability. Such inhibition caused substantial fitness defects not only in the presence of excess substrate but also under physiological conditions. In the latter case, substrate inhibition caused differential accumulation of AMP in the stationary phase for the inhibition prone mutants. Further, we show that changes in flux through Adk could accurately describe the variation in fitness effects. Taken together, these data suggest that selection against substrate inhibition and hence excess stability may have resulted in a narrow range of optimal stability observed for modern proteins.Comment: 30 pages, 6 figures, 1 table, Supplementary figures and tables - 6 page

Systems-Level Response to Point Mutations in a Core Metabolic Enzyme Modulates Genotype-Phenotype Relationship

Linking the molecular effects of mutations to fitness is central to understanding evolutionary dynamics. Here we establish a quantitative relation between the global effect of mutations on the E. coli proteome and bacterial fitness. We created E. coli strains with specific destabilizing mutations in the chromosomal folA gene encoding dihydrofolate reductase (DHFR) and quantified the ensuing changes in the abundances of 2000+ E. coli proteins in mutant strains using tandem mass tags with subsequent LC-MS/MS. mRNA abundances in the same E. coli strains were also quantified. The proteomic effects of mutations in DHFR are quantitatively linked to phenotype: the standard deviations of the distributions of logarithms of relative (to wild-type) protein abundances anti-correlate with bacterial growth rates. Proteomes hierarchically cluster first by media conditions, and within each condition, by the severity of the perturbation to DHFR function. These results highlight the importance of a systems-level layer in the genotype-phenotype relationship.Chemistry and Chemical Biolog

Paradoxical Role of AT-rich Interactive Domain 1A in Restraining Pancreatic Carcinogenesis

Background & Aims: ARID1A is postulated to be a tumor suppressor gene owing to loss-of-function mutations in human pancreatic ductal adenocarcinomas (PDAC). However, its role in pancreatic pathogenesis is not clear despite recent studies using genetically engineered mouse (GEM) models. We aimed at further understanding of its direct functional role in PDAC, using a combination of GEM model and PDAC cell lines. Methods: Pancreas-specific mutant Arid1a-driven GEM model (Ptf1a-Cre; KrasG12D; Arid1af/f or “KAC”) was generated by crossing Ptf1a-Cre; KrasG12D (“KC”) mice with Arid1af/f mice and characterized histologically with timed necropsies. Arid1a was also deleted using CRISPR-Cas9 system in established human and murine PDAC cell lines to study the immediate effects of Arid1a loss in isogenic models. Cell lines with or without Arid1a expression were developed from respective autochthonous PDAC GEM models, compared functionally using various culture assays, and subjected to RNA-sequencing for comparative gene expression analysis. DNA damage repair was analyzed in cultured cells using immunofluorescence and COMET assay. Results: Retention of Arid1a is critical for early progression of mutant Kras-driven pre-malignant lesions into PDAC, as evident by lower Ki-67 and higher apoptosis staining in “KAC” as compared to “KC” mice. Enforced deletion of Arid1a in established PDAC cell lines caused suppression of cellular growth and migration, accompanied by compromised DNA damage repair. Despite early development of relatively indolent cystic precursor lesions called intraductal papillary mucinous neoplasms (IPMNs), a subset of “KAC” mice developed aggressive PDAC in later ages. PDAC cells obtained from older autochthonous “KAC” mice revealed various compensatory (“escaper”) mechanisms to overcome the growth suppressive effects of Arid1a loss. Conclusions: Arid1a is an essential survival gene whose loss impairs cellular growth, and thus, its expression is critical during early stages of pancreatic tumorigenesis in mouse models. In tumors that arise in the setting of ARID1A loss, a multitude of “escaper” mechanisms drive progression

TET1 is a tumor suppressor of hematopoietic malignancy

The methylcytosine dioxygenase TET1 (‘ten-eleven translocation 1’) is an important regulator of 5-hydroxymethylcytosine (5hmC) in embryonic stem cells. The diminished expression of TET proteins and loss of 5hmC in many tumors suggests a critical role for the maintenance of this epigenetic modification. Here we found that deletion of Tet1 promoted the development of B cell lymphoma in mice. TET1 was required for maintenance of the normal abundance and distribution of 5hmC, which prevented hypermethylation of DNA, and for regulation of the B cell lineage and of genes encoding molecules involved in chromosome maintenance and DNA repair. Whole-exome sequencing of TET1-deficient tumors revealed mutations frequently found in non-Hodgkin B cell lymphoma (B-NHL), in which TET1 was hypermethylated and transcriptionally silenced. Our findings provide in vivo evidence of a function for TET1 as a tumor suppressor of hematopoietic malignancy.National Institutes of Health (U.S.) (5RO1HD045022)National Institutes of Health (U.S.) (5R37CA084198

Stem and progenitor cells in myelodysplastic syndromes show aberrant stage-specific expansion and harbor genetic and epigenetic alterations

Even though hematopoietic stem cell (HSC) dysfunction is presumed in myelodysplastic syndrome (MDS), the exact nature of quantitative and qualitative alterations is unknown. We conducted a study of phenotypic and molecular alterations in highly fractionated stem and progenitor populations in a variety of MDS subtypes. We observed an expansion of the phenotypically primitive long-term HSCs (lineage ؊ /CD34 ؉ /CD38 ؊ /CD90 ؉ ) in MDS, which was most pronounced in higher-risk cases. These MDS HSCs demonstrated dysplastic clonogenic activity. Examination of progenitors revealed that lower-risk MDS i

Lactate-Mediated Epigenetic Reprogramming Regulates Formation of Human Pancreatic Cancer-Associated Fibroblasts

Even though pancreatic ductal adenocarcinoma (PDAC) is associated with fibrotic stroma, the molecular pathways regulating the formation of cancer associated fibroblasts (CAFs) are not well elucidated. An epigenomic analysis of patient-derived and de-novo generated CAFs demonstrated widespread loss of cytosine methylation that was associated with overexpression of various inflammatory transcripts including CXCR4. Co-culture of neoplastic cells with CAFs led to increased invasiveness that was abrogated by inhibition of CXCR4. Metabolite tracing revealed that lactate produced by neoplastic cells leads to increased production of alpha-ketoglutarate (aKG) within mesenchymal stem cells (MSCs). In turn, aKG mediated activation of the demethylase TET enzyme led to decreased cytosine methylation and increased hydroxymethylation during de novo differentiation of MSCs to CAF. Co-injection of neoplastic cells with TET-deficient MSCs inhibited tumor growth in vivo. Thus, in PDAC, a tumor-mediated lactate flux is associated with widespread epigenomic reprogramming that is seen during CAF formation

Dark Matter perspective of Left-Right symmetric gauge model

We consider an incarnation of left-right symmetric model with a local gauge symmetry of $SU(3)_C \otimes SU(2)_L \otimes U(1)_L \otimes SU(2)_R \otimes U(1)_R$. Heavy scalars and fermions present in the {\bf 27} of $E_6$ are included in the matter sector along with the Standard Model fermions. Two such colour singlet fermions, $N$ and $l_S$, transforming as bi-doublet and singlet under $SU(2)$s respectively, can be potential candidates for Dark Matter (DM). Assignment of $U(1)$ charges for the matter fields restricts some of the exotic fermions to interact with the SM fermions. We study in some details the prospect of such fermionic dark matters by calculating relic densities and direct detection cross-sections by treating these particles as stand alone relic particles in turn. $N$, when treated as relic particle, would produce a direct-detection cross-section very high compared to the experimental upper limits. However, the interaction rate of $N$ can be controlled by introducing a dimension-6 operator involving two $N$ fields and two SM fermions and appropriately choosing the coupling constant. This in turn, makes the interaction rate of $N$ very high and yields a small relic density. On the other hand, $l_S$ for some chosen mass window, can give us right amount of relic, but its direct detection cross-section is too small. Keeping these in mind, we propose two-component model of DM, where both $N$ and $l_S$ contribute to the relic density, albeit with unequal proportion while the direct detection cross-section limits can be satisfied mainly by $N$ in presence of an extra dimension-6 interaction. We derive limits on such an interaction from XENON experiment.Comment: 16 pages, 8 figures, 1 tabl

Packing in molten globules and native states

Close packing of hydrophobic residues in the protein interior is an important determinant of protein stability. Cavities introduced by large to small substitutions are known to destabilize proteins. Conversely, native states of proteins and protein fragments can be stabilized by filling in existing cavities. Molten globules (MGs) were initially used to describe a state of protein which has well-defined secondary structure but little or no tertiary packing. Subsequent studies have shown that MGs do have some degree of native-like topology and specific packing. Wet molten globules (WMGs) with hydrated cores and considerably decreased packing relative to the native state have been studied extensively. Recently there has been renewed interest in identification and characterization of dry molten globules (DMGs). These are slightly expanded forms of the native state which show increased conformational flexibility, native-like main-chain hydrogen bonding and dry interiors. The generality of occurrence of DMGs during protein unfolding and the extent and nature of packing in DMGs remain to be elucidated. Packing interactions in native proteins and MGs can be probed through mutations. Next generation sequencing technologies make it possible to determine relative populations of mutants in a large pool. When this is coupled to phenotypic screens or cell-surface display, it becomes possible to rapidly examine large panels of single-site or multi-site mutants. From such studies, residue specific contributions to protein stability and function can be estimated in a highly parallelized fashion. This complements conventional biophysical methods for characterization of packing in native states and molten globules

Gene Dosage Experiments in Enterobacteriaceae Using Arabinose-regulated Promoters

This protocol is used to assay the effect of protein over-expression on fitness of E. coli. It is based on a plasmid expression of a protein of interest from an arabinose-regulated pBAD promoter followed by the measurement of the intracellular protein abundance by Western blot along with the measurement of growth parameters of E. coli cell expressing this protein