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In this study, we describe the engineering of sub-100 nm nanomicelles (DTX-PC NMs) derived from phosphocholine derivative of docetaxel (DTX)-conjugated lithocholic acid (DTX-PC) and poly(ethylene glycol)-tethered lithocholic acid. Administration of DTX-PC NMs decelerate tumor progression and increase the mice survivability compared to Taxotere (DTX-TS), the FDA-approved formulation of DTX. Unlike DTX-TS, DTX-PC NMs do not cause any systemic toxicity and slow the decay rate of plasma DTX concentration in rodents and non-rodent species including non-human primates. We further demonstrate that DTX-PC NMs target demethylation of CpG islands of Sparcl1 (a tumor suppressor gene) by suppressing DNA methyltransferase activity, and increase the expression of Sparcl1 that leads to tumor regression. Therefore, this unique system has the potential to improve the quality of life in cancer patients, and can be translated as a next-generation chemotherapeutic.

The effect of three different interlayer stacking arrangements of bilayer (BL) molybdenum disulfide (MoS2) channel material on the device behavior of p- and n-metal–oxide–semiconductor field-effect transistors (MOSFETs) is extensively investigated using first-principles calculation based on density functional theory, emphasizing electronic properties such as the eigenstates, effective mass, band structure, and total energy of the BL-MoS2 for various stacking arrangements. The corresponding effects on the MOSFET device characteristics are then analyzed. The results indicate that the hole effective masses in both the longitudinal (transport) and transverse direction are highly sensitive to the interlayer stacking arrangement, and the performance of the p-MOSFET can be significantly tuned for a suitable stacking configuration of the BL-MoS2. Indeed, 24.12% and 31.37% improvements in the on-state current and transconductance are observed, respectively, for the p-MOSFET compared with the natural stacking arrangement of BL-MoS2. The ballistic BL-MoS2-based p- and n-MOSFETs with the tuned stacking arrangement demonstrate an on-state current on the order of 103 µA/µm along with an on-state/off-state current ratio greater than 103, a near-ideal (> 65 mV/decade) subthreshold swing, and small (

Germline integrity is critical for progeny fitness. Organisms deploy the DNA damage response (DDR) signalling to protect germline from genotoxic stress, facilitating cell-cycle arrest of germ cells and DNA repair or their apoptosis. Cell-autonomous regulation of germline quality is well-studied; however, how quality is enforced cell non-autonomously on sensing somatic DNA damage is less known. Using Caenorhabditis elegans, we show that DDR disruption, only in the uterus, when insulin-IGF-1 signalling (IIS) is low, arrests germline development and induces sterility in a FOXO/DAF-16 transcription factor (TF)-dependent manner. Without FOXO/DAF-16, germ cells of the IIS mutant escape arrest to produce poor quality oocytes, showing that the TF imposes strict quality control during low IIS. In response to low IIS in neurons, FOXO/DAF-16 works cell autonomously as well as non-autonomously to facilitate the arrest. Activated FOXO/DAF-16 promotes transcription of checkpoint and DDR genes, protecting germline integrity. However, on reducing DDR during low IIS, the TF decreases ERK/MPK-1 signaling below a threshold, and transcriptionally downregulates genes involved in spermatogenesis-to-oogenesis switch as well as cdk-1/Cyclin B to promote germline arrest. Altogether, our study reveals how cell non-autonomous function of FOXO/DAF-16 promotes germline quality and progeny fitness in response to somatic DNA damage.Significance StatementReproductive decisions are supervised processes that take into account various inputs like cellular energy availability and status of damage repair in order to ensure healthy progeny. In this study, we show that the absence of optimal DNA damage repair in the somatic uterine tissues prevents oocyte development by the cell-autonomous as well non-autonomous function of activated FOXO transcription factor DAF-16. Thus, this study elucidates a new surveillance role of FOXO/DAF-16 in somatic tissues that ensures progeny fitness.

Sphingolipid and ganglioside metabolic pathways are crucial components of cell signalling, having established roles in tumor cell proliferation, invasion, and migration. However, regulatory mechanisms controlling sphingolipid and ganglioside biosynthesis in mammalian cells is less known. Here, we show that RICTOR, the regulatory subunit of mTORC2, regulates the synthesis of sphingolipids and gangliosides in luminal breast cancer-specific MCF-7 and BT-474 cells through transcriptional and epigenetic mechanisms. RICTOR regulates glucosylceramide levels by modulating the expression of UDP-Glucose Ceramide Glucosyl transferase (UGCG). We identify Zinc Finger protein X-linked (ZFX) as a RICTOR-responsive transcription factor whose recruitment to the UGCG promoter is regulated by DNA methyltransferases and histone demethylase (KDM5A) that are known AKT substrates. We further demonstrate that RICTOR regulates the synthesis of GD3 gangliosides through ZFX and UGCG, and triggers the activation of EGFR signalling pathway, thereby promoting tumor growth. In line with our findings in cell culture and mice models, we observe an elevated expression of RICTOR, ZFX, and UGCG in Indian luminal breast cancer tissues, and in TCGA and METABRIC datasets. Together, we establish a key regulatory circuit, RICTOR-AKT-ZFX-UGCG-Ganglioside-EGFR-AKT, and elucidate its contribution to breast cancer progression.

Diet regulates complex life‐history traits such as longevity. For optimal lifespan, organisms employ intricate adaptive mechanisms whose molecular underpinnings are less known. We show that Caenorhabditis elegans FLR‐4 kinase prevents lifespan differentials on the bacterial diet having higher Vitamin B12 levels. The flr‐4 mutants are more responsive to the higher B12 levels of Escherichia coli HT115 diet, and consequently, have enhanced flux through the one‐carbon cycle. Mechanistically, a higher level of B12 transcriptionally downregulates the phosphoethanolamine methyltransferase pmt‐2 gene, which modulates phosphatidylcholine (PC) levels. Pmt‐2 downregulation activates cytoprotective gene expression through the p38‐MAPK pathway, leading to increased lifespan only in the mutant. Evidently, preventing bacterial B12 uptake or inhibiting one‐carbon metabolism reverses all the above phenotypes. Conversely, supplementation of B12 to E. coli OP50 or genetically reducing PC levels in the OP50‐fed mutant extends lifespan. Together, we reveal how worms maintain adaptive capacity to diets having varying micronutrient content to ensure a normal lifespan., Multiple genes interact to maintain physiological homeostasis when Caenorhabditis elegans feeds on the varied diet it encounters in its ecological niche. Worms harboring a kinase‐dead version of the FLR‐4 protein are more responsive to the higher dietary Vitamin B12 present in Escherichia coli HT115. This boosts the flux through the one‐carbon metabolism, leading to reduction in phosphatidylcholine levels. Since the mutant FLR‐4 fails to prevent p38‐MAPK activation, these animals have better health and life span.

Meta-analysis of transcripts in colon adenocarcinoma patient tissues led to the identification of a DNA damage responsive miR signature called DNA damage sensitive miRs (DDSMs). DDSMs were experimentally validated in the cancerous colon tissues obtained from an independent cohort of colon cancer patients and in multiple cellular systems with high levels of endogenous DNA damage. All the tested DDSMs were transcriptionally upregulated by a common intestine-specific transcription factor, CDX2. Reciprocally, DDSMs were repressed via the recruitment of HDAC1/2-containing complexes onto the CDX2 promoter. These miRs downregulated multiple key targets in the DNA damage response (DDR) pathway, namely BRCA1, ATM, Chk1 (also known as CHEK1) and RNF8. CDX2 directly regulated the DDSMs, which led to increased tumor volume and metastasis in multiple preclinical models. In colon cancer patient tissues, the DDSMs negatively correlated with BRCA1 levels, were associated with decreased probability of survival and thereby could be used as a prognostic biomarker. This article has an associated First Person interview with the first author of the paper.

Significance The endoplasmic reticulum (ER) deteriorates with age and fails to mount an effective stress response against misfolded proteins (UPRER), leading to protein folding disorders. However, preconditioning the ER using a mild ER stress (ER hormesis) can protect against future insults. We show that dietary restriction, an intervention that protects against protein misfolding disorders and increases life span across species, uses ER hormesis as a mechanism of action. Simply mimicking the ER hormesis in Caenorhabditis elegans by transient treatment with pharmacological reagents leads to delayed age-onset failure of UPRER, better capacity to process misfolded proteins, and increased life span. We also show that this process may be conserved in a mammalian cellular model of neurodegenerative disease., Unfolded protein response (UPR) of the endoplasmic reticulum (UPRER) helps maintain proteostasis in the cell. The ability to mount an effective UPRER to external stress (iUPRER) decreases with age and is linked to the pathophysiology of multiple age-related disorders. Here, we show that a transient pharmacological ER stress, imposed early in development on Caenorhabditis elegans, enhances proteostasis, prevents iUPRER decline with age, and increases adult life span. Importantly, dietary restriction (DR), that has a conserved positive effect on life span, employs this mechanism of ER hormesis for longevity assurance. We found that only the IRE-1–XBP-1 branch of UPRER is required for the longevity effects, resulting in increased ER-associated degradation (ERAD) gene expression and degradation of ER resident proteins during DR. Further, both ER hormesis and DR protect against polyglutamine aggregation in an IRE-1–dependent manner. We show that the DR-specific FOXA transcription factor PHA-4 transcriptionally regulates the genes required for ER homeostasis and is required for ER preconditioning-induced life span extension. Finally, we show that ER hormesis improves proteostasis and viability in a mammalian cellular model of neurodegenerative disease. Together, our study identifies a mechanism by which DR offers its benefits and opens the possibility of using ER-targeted pharmacological interventions to mimic the prolongevity effects of DR.

In this work, the bi-layer (2L) Molybdenum Di-Sulfide i.e. MoS 2 at different stacking orientation are investigated under applied biaxial strain using first principle calculations. The 2L-MoS 2 has been considered in their natural stacking orientation for 2H-phase as well as in three other artificial stacking orientations achieved through appropriate in-plane rotations and translations of one atomic layer with respect to the other. Furthermore, each stacking orientations of MoS 2 are subjected to biaxial compressive and tensile strains and subsequent modulation of electronic properties in each of these cases are extensively analyzed. In this context, emphasize has been given on the effective masses and energy band-gaps of 2L-MoS 2 structures. The influence of strain on the energy band structures has been analyzed in details from the orbital projections of electronic states near the conduction band minima and valence band maxima.

Global dysregulation of RNA splicing and imbalanced sphingolipid metabolism has emerged as promoters of cancer cell transformation. Here, we present specific signature of alternative splicing (AS) events of sphingolipid genes for each breast cancer subtype from the TCGA-BRCA dataset. We show that ceramide synthase 2 (CERS2) undergoes a unique cassette exon event specifically in Luminal B subtype tumors. We validated this exon 8 skipping event in Luminal B cancer cells compared to normal epithelial cells, and in patient-derived tumor tissues compared to matched normal tissues. Differential AS-based survival analysis shows that this AS event of CERS2 is a poor prognostic factor for Luminal B patients. As Exon 8 corresponds to catalytic Lag1p domain, overexpression of AS transcript of CERS2 in Luminal B cancer cells leads to a reduction in the level of very-long-chain ceramides compared to overexpression of protein-coding (PC) transcript of CERS2. We further demonstrate that this AS event-mediated decrease of very-long-chain ceramides leads to enhanced cancer cell proliferation and migration. Therefore, our results show subtype-specific AS of sphingolipid genes as a regulatory mechanism that deregulates sphingolipids like ceramides in breast tumors, and can be explored further as a suitable therapeutic target.

The proposed manuscript demonstrates designs and analyzes the frequency band response of cavity backed substrate integrated waveguide (SIW) antenna. Single X shaped slot is used to achieve the satellite communication frequency band. The designed antenna resonates at satellite communication frequency band of 11.2 GHz with a gain of 2.7 dBi.

In the proposed paper, dual band cavity backed substrate integrated waveguide (SIW) antenna is designed and analyzed. The dual frequency operation is achieved using L-shaped slots. The designed antenna resonates at satellite communication frequency band of 8.9 GHz and 11.1 GHz with gain of 7.1 dBi and 2.2 dBi at resonance respectively.

Dietary restriction (DR) increases life span and improves health in most model systems tested, including non-human primates. In C. elegans, as in other models, DR leads to reprogramming of metabolism, improvements in mitochondrial health, large changes in gene expression, including increase in expression of cytoprotective genes, better proteostasis etc. Understandably, multiple global transcriptional regulators like transcription factors FOXO/DAF-16, FOXA/PHA-4, HSF1/HSF-1 and NRF2/SKN-1 are important for DR longevity. Considering the wide-ranging effects of p53 on organismal biology, we asked whether the C. elegans ortholog, CEP-1 is required for DR-mediated longevity assurance. We employed the widely-used TJ1 strain of cep-1(gk138). We show that cep-1(gk138) suppresses the life span extension of two genetic paradigms of DR, but two non-genetic modes of DR remain unaffected in this strain. We find that in cep-1(gk138), two aspects of DR, increased autophagy and the up-regulation of expression of cytoprotective xenobiotic detoxification program (cXDP) genes are dampened. Importantly, we find that background mutation(s) in the strain may be the actual cause for the phenotypic differences that we observed and cep-1 may not be directly involved in genetic DR-mediated longevity assurance in worms. Identifying these mutation(s) may reveal a novel regulator of longevity required specifically by genetic modes of DR.

In this work, for the first time, the tri-layer sandwiched Van der Waals heterostructures of SnS2 and MoSe2 are investigated using first principle calculations. In such heterostructures, a monolayer of SnS2 (MoSe2) is sandwiched between two MoSe2 (SnS2) layers. Subsequently, such heterostructures are considered in two different stacking orders, i.e. ABA and AAA corresponding to the natural stacking of bulk MoSe2 and SnS2, respectively. The structural and electronic properties of such tri-layer heterostructures are extensively analyzed in comparison with the homogeneous SnS2 and MoSe2 tri-layers. In this context, emphasis has been given on the bond length and bond angles of metal and chalcogen atoms at the sandwiched layers of heterostructures. Finally, the influences of the homogenous and heterogeneous sandwiched layers on the energy band structures have been analyzed in detail from the orbital projections of electronic states at the conduction band and valence band.

A temperature-dependent delay optimization model for a multilayered graphene nanoribbon (MLGNR) with top contact (TC-GNR), side contact (SC-GNR), and Cu-based nano-interconnects using a wire sizing method was applied to determine the delay for different interconnects widths (11 nm, 16 nm, and 22 nm) and lengths (10 μm, 50 μm, and 100 μm), being the first such model for TC-GNR, SC-GNR, and Cu interconnects applied at three different chip operating temperatures (233 K, 300 K, and 378 K). The results reveal that the SC-GNR requires ~ 3–6× and ~ 2–3× fewer repeaters w.r.t. the TC-GNR or Cu interconnect, and that the SC-GNR and Cu interconnects can achieve ~ 4–5× and ~ 2–2.5× reduction in repeater dimension compared with the TC-GNR interconnect. Meanwhile, the SC-GNR interconnect can achieve 73× less propagation delay w.r.t. the TC-GNR interconnect for interconnect width of 22 nm, interconnect length of 10 μm, and two different chip operating temperatures of 233 K and 300 K. Similarly, the Cu interconnect can achieve 6× less propagation delay w.r.t. the TC-GNR interconnect at interconnect width of 22 nm and 16 nm, interconnect length of 10 μm, and 300 K.

The paper presents an ab initio study of the 2-D insulators and their effect on the performance of a magnetic tunnel junction memory (MTJ) device. MTJ devices has been considered as an alternate to the charge based data storage cells due to its spin-polarised operation and high scaling probability. The use of 2-D insulators like X-(OH)2 (X: Ca and Mg) and h-BN (hexagonal-Boron Nitride) in such device would be interesting. The authors have calculated the band structures, density of states and effective mass of electrons and holes for the mono-layer of these three non-conventional 2-D insulators using the first principle calculations in density functional theory framework using Quantumwise ATK tool. The ab initio calculation yielded band gap (Eg) of 4.633, 4.685 and 4.249 eV for h-BN, Ca(OH)2 and Mg(OH)2, respectively. The effective mass of electrons was calculated as 0.621, 0.604 and 0.478 for single layer h-BN, Ca(OH)2 and Mg(OH)2, respectively. While for holes it is 0.834, 0.446 and 0.407, respectively for h-BN, Ca(OH)2 and Mg(OH)2. The MTJ device properties as tunneling-magneto resistance, differential TMR, parallel and anti-parallel resistance, differential resistance and spin transfer torque components (in-plane and out-of-plane) with these materials as composite dielectric has been reported in this paper using MTJ Lab tool. The performance of MTJ memory device with h-BN based composite dielectric is found better.

The metabolic state of an organism instructs gene expression modalities, leading to changes in complex life history traits, such as longevity. Dietary restriction (DR), which positively affects health and life span across species, leads to metabolic reprogramming that enhances utilisation of fatty acids for energy generation. One direct consequence of this metabolic shift is the upregulation of cytoprotective (CyTP) genes categorized in the Gene Ontology (GO) term of “Xenobiotic Detoxification Program” (XDP). How an organism senses metabolic changes during nutritional stress to alter gene expression programs is less known. Here, using a genetic model of DR, we show that the levels of polyunsaturated fatty acids (PUFAs), especially linoleic acid (LA) and eicosapentaenoic acid (EPA), are increased following DR and these PUFAs are able to activate the CyTP genes. This activation of CyTP genes is mediated by the conserved p38 mitogen-activated protein kinase (p38-MAPK) pathway. Consequently, genes of the PUFA biosynthesis and p38-MAPK pathway are required for multiple paradigms of DR-mediated longevity, suggesting conservation of mechanism. Thus, our study shows that PUFAs and p38-MAPK pathway function downstream of DR to help communicate the metabolic state of an organism to regulate expression of CyTP genes, ensuring extended life span., Metabolic reprogramming during Dietary Restriction (DR) activates cytoprotective gene expression. Here the authors show that PUFAs generated during DR signal via the p38-MAPK pathway to enhance cytoprotective gene expression, contributing to increased longevity.

We investigate the effects of uniaxial tensile and compressive strain on the material and transport properties of semiconducting Carbon Nanotube and the device properties of Blue-Phosphorene-CNT heterojunction devices. We see that the material and transport properties of the semiconducting CNT can be tuned through the application of uniaxial strain. The device properties of the heterojunction can also be modulated by strain. The variation in the current is significant in tensile strain zone.

SummaryReductive stress leads to the loss of disulfide bond formation and induces the unfolded protein response of the endoplasmic reticulum (UPRER), necessary to regain proteostasis in the compartment. Here we show that peroxide accumulation during reductive stress attenuates UPRER amplitude by altering translation without any discernible effect on transcription. Through a comprehensive genetic screen in Saccharomyces cerevisiae, we identify modulators of reductive stress-induced UPRER and demonstrate that oxidative quality control (OQC) genes modulate this cellular response in the presence of chronic but not acute reductive stress. Using a combination of microarray and relative quantitative proteomics, we uncover a non-canonical translation attenuation mechanism that acts in a bipartite manner to selectively downregulate highly expressed proteins, decoupling the cell’s transcriptional and translational response during reductive ER stress. Finally, we demonstrate that PERK, a canonical translation attenuator in higher eukaryotes, helps in bypassing a ROS-dependent, non-canonical mode of translation attenuation.

In this work, we present a computational study on the possibility of strain engineering in monolayer Black Phosphorus (black P) and Blue Phosphorus (blue P) based MOSFETs. The material properties like band structure, carrier effective masses, carrier densities at band extrema are evaluated using Generalized Gradient Approximation (GGA) in Density Functional Theory (DFT).Thereafter self-consistent Non-Equilibrium Greens Function (NEGF) simulations are carried out to study the device performance metrics (such as output characteristics, ON currents, transconductance etc.) of such strained black P and blue P based MOSFETs. Our simulations show that carrier effective masses in blue P are more sensitive to strain applied in both zigzag and armchair directions. Blue P is more responsive in strain engineering for n-MOS and p-MOS. Except for black P based FETs with strain in armchair direction, overall the blue P (black P) n-MOSFET (p-MOSFET) show moderate to significant improvement in performance with tensile (compressive) strain in the transport directions., 16 pages

Summary Insulin/IGF-1-like signalling (IIS) and dietary restriction (DR) are the two major modulatory pathways controlling longevity across species. Here, we show that both pathways license a common chromatin modifier, ZFP-1/AF10. The downstream transcription factors of the IIS and select DR pathways, DAF-16/FOXO or PHA-4/FOXA, respectively, both transcriptionally regulate the expression of zfp-1. ZFP-1, in turn, negatively regulates the expression of DAF-16/FOXO and PHA-4/FOXA target genes, apparently forming feed-forward loops that control the amplitude as well as the duration of gene expression. We show that ZFP-1 mediates this regulation by negatively influencing the recruitment of DAF-16/FOXO and PHA-4/FOXA to their target promoters. Consequently, zfp-1 is required for the enhanced longevity observed during DR and on knockdown of IIS. Our data reveal how two distinct sensor pathways control an overlapping set of genes, using different downstream transcription factors, integrating potentially diverse and temporally distinct nutritional situations.

Chromatin immunoprecipitation (ChIP) coupled to quantitative real-time PCR (ChIP-qPCR) or Next-Generation Sequencing (ChIP-seq) enables us to study the dynamics of chromatin recruitment of transcription factors (TFs). The popular model system Caenorhabditis elegans has provided us with fundamental understanding of the role of Insulin/IGF-1-like signaling (IIS) in metabolism and aging. The FOXO TF DAF-16 is the major output of the pathway that regulates most of the phenotypes associated with the IIS pathway. Here, we describe a ChIP protocol to study FOXO recruitment dynamics in whole C. elegans extracts. We discuss detailed practical procedures, including optimization, growth, harvesting, formaldehyde fixation, sonication of worms, TF immunoprecipitation for further downstream processing using qPCR as well as NGS for the analysis of FOXO-bound DNA.

Chromatin immunoprecipitation (ChIP) coupled to quantitative real-time PCR (ChIP-qPCR) or Next-Generation Sequencing (ChIP-seq) enables us to study the dynamics of chromatin recruitment of transcription factors (TFs). The popular model system Caenorhabditis elegans has provided us with fundamental understanding of the role of Insulin/IGF-1-like signaling (IIS) in metabolism and aging. The FOXO TF DAF-16 is the major output of the pathway that regulates most of the phenotypes associated with the IIS pathway. Here, we describe a ChIP protocol to study FOXO recruitment dynamics in whole C. elegans extracts. We discuss detailed practical procedures, including optimization, growth, harvesting, formaldehyde fixation, sonication of worms, TF immunoprecipitation for further downstream processing using qPCR as well as NGS for the analysis of FOXO-bound DNA.

In this work by means of ab-initio calculations and Non equilibrium Green's function (NEGF) simulation we look to investigate the effect of strain in MoS 2 armchair nanoribbon (ANR)-metal junctions. We consider a (10, 0) MoS 2 ANR and various metals as Ti, Cr, Al and Ag for contact material. The effect of strain both in plain and out of plain direction is considered. We calculated the work function variations, band-gaps and carrier effective masses with Density Functional Theory (DFT) calculation and evaluated the Schottky barriers with the Schottky-Mott formula. The currents through these barriers were then evaluated with NEGF calculations. Our results show a wide possibility of output current enhancement with Schottky barrier height modulation with the proper choice of strain and contact material combinations.

In this work, we investigate the layer dependency of Mos2channel material based Double Gate Schottky barrier MOSFET. In order to evaluate the transport properties due to this effect accurately, we have calculated the electronic properties of multilayer Mos2using density functional theory and incorporated those parameters in our analytical model for double Gate Schottky barrier MOSFET. A full description of the electron transport due to tunneling through the Schottky barrier and thermionic emission of electrons is computed in our model. Our results demonstrate that monolayer Mos2shows good device characteristics for logic applications, with ON/OFF ratio $\sim 10^{7}$ . As far as the layer dependency is concerned, more than two times higher drain current is achievable for the device made of the monolayer based channel than that of the five-layer based channel of Mos2. In Mos2, drive current, transconductance significantly reduced with increasing number of layer. The results obtained with our model concur with experimental reports.

The report focuses on an optimization scheme of advanced MOSFETs for designing power efficient circuits. For the purpose the physics-based compact model HiSIM2 is applied so that the relationship between device and circuit characteristics can be investigated properly. It is demonstrated that the short-channel effect, which is usually measured by the threshold-voltage shift compared to the long-channel MOSFET, provides the consistent measure as the short-channel effect on device performance degradation. However, the circuitry performances degradation such as the power loss cannot be predicted sufficiently by the short channel effect alone. It is demonstrated that the power efficient circuit design can be achieved by minimizing the additional leakage current caused by the short-channel contribution.

// Neeraj Kumar 1,2 , Vaibhav Jain 1,* , Anupama Singh 1,* , Urmila Jagtap 1 , Sonia Verma 1 and Arnab Mukhopadhyay 1 1 Molecular Aging Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India 2 Current address: Centre for Human Genetics and Molecular Medicine, School of Health Sciences , Central University of Punjab, Bathinda, India * These authors have contributed equally to this work Correspondence to: Neeraj Kumar, email: // Arnab Mukhopadhyay, email: // Keywords : DAF-16, FOXO, ChIP-seq, C. elegans, transcription, Gerotarget Received : August 31, 2015 Accepted : October 20, 2015 Published : November 02, 2015 Abstract Lowering insulin-IGF-1-like signalling (IIS) activates FOXO transcription factors (TF) to extend life span across species. To study the dynamics of FOXO chromatin occupancy under this condition in C. elegans , we report the first recruitment profile of endogenous DAF-16 and show that the response is conserved. DAF-16 predominantly acts as a transcriptional activator and binding within the 0.5 kb promoter-proximal region results in maximum induction of downstream targets that code for proteins involved in detoxification and longevity. Interestingly, genes that are activated under low IIS already have higher DAF-16 recruited to their promoters in WT. DAF-16 binds to variants of the FOXO consensus sequence in the promoter proximal regions of genes that are exclusively targeted during low IIS. We also define a set of ‘core’ direct targets, after comparing multiple studies, which tend to co-express and contribute robustly towards IIS-associated phenotypes. Additionally, we show that nuclear hormone receptor DAF-12 as well as zinc-finger TF EOR-1 may bind DNA in close proximity to DAF-16 and distinct TF classes that are direct targets of DAF-16 may be instrumental in regulating its indirect targets. Together, our study provides fundamental insights into the transcriptional biology of FOXO/DAF-16 and gene regulation downstream of the IIS pathway.

This paper presents a theoretical study of tunneling current density and the leakage current through multi-layer (stacked) trapping layer in the gate dielectric in MOS non-volatile memory devices. Two different 2D materials ($$\hbox {MoS}_{2}$$MoS2 and black phosphorous) with a combination of high-k dielectric ($$\hbox {HfO}_{2}$$HfO2) have been used for the study with differently ordered stacks i.e., as trapping layer and substrate. The material properties of 2D materials like density of states, effective mass and band structure has been evaluated using density functional theory simulations. Using the Maxwell---Garnett effective medium theory we have calculated the effective barrier height, effective bandgap, effective dielectric constant and effective mass of the gate dielectric stacks. By applying WKB approximation in the multi-layer trapping layer we have studied the effect of the direct and Fowler---Nordheim tunneling currents. The leakage current in all the different stack combinations used has also been evaluated. The results obtained have shown to match the required dynamics of a memory device.

Advanced glycation end products (AGEs) are formed when glucose reacts nonenzymatically with proteins; these modifications are implicated in aging and pathogenesis of many age-related diseases including type II diabetes, atherosclerosis, and neurodegenerative disorders. Thus, pharmaceutical interventions that can reduce AGEs may delay age-onset diseases and extend lifespan. Using LC-MS(E), we show that rifampicin (RIF) reduces glycation of important cellular proteins in vivo and consequently increases lifespan in Caenorhabditis elegans by up to 60%. RIF analog rifamycin SV (RSV) possesses similar properties, while rifaximin (RMN) lacks antiglycation activity and therefore fails to affect lifespan positively. The efficacy of RIF and RSV as potent antiglycating agents may be attributed to the presence of a p-dihydroxyl moiety that can potentially undergo spontaneous oxidation to yield highly reactive p-quinone structures, a feature absent in RMN. We also show that supplementing rifampicin late in adulthood is sufficient to increase lifespan. For its effect on longevity, rifampicin requires DAF-18 (nematode PTEN) as well as JNK-1 and activates DAF-16, the FOXO homolog. Interestingly, the drug treatment modulates transcription of a different subset of DAF-16 target genes, those not controlled by the conserved Insulin-IGF-1-like signaling pathway. RIF failed to increase the lifespan of daf-16 null mutant despite reducing glycation, showing thereby that DAF-16 may not directly affect AGE formation. Together, our data suggest that the dual ability to reduce glycation in vivo and activate prolongevity processes through DAF-16 makes RIF and RSV effective lifespan-extending interventions.

Diet profoundly affects metabolism and incidences of age-related diseases. Animals adapt their physiology to different food-types, modulating complex life-history traits like aging. The molecular mechanisms linking adaptive capacity to diet with aging are less known. We identify FLR-4 kinase as a novel modulator of aging in C. elegans, depending on bacterial diet. FLR-4 functions to prevent differential activation of the p38MAPK pathway in response to diverse food-types, thereby maintaining normal life span. In a kinase-dead flr-4 mutant, E. coli HT115 (K12 strain), but not the standard diet OP50 (B strain), is able to activate p38MAPK, elevate expression of cytoprotective genes through the nuclear hormone receptor NHR-8 and enhance life span. Interestingly, flr-4 and dietary restriction utilize similar pathways for longevity assurance, suggesting cross-talks between cellular modules that respond to diet quality and quantity. Together, our study discovers a new C. elegans gene-diet pair that controls the plasticity of aging., Author summary For animals living in the wild, being able to utilize a wide range of diet is evolutionarily advantageous as they can survive even when their optimal diet is depleted. Since diet is known to influence the rate of aging, animals seem to have evolved intricate mechanisms to maintain homeostasis and normal life span, but the molecular mechanisms are less understood. Using a small nematode, C. elegans as a model, we show that the adaptive capacity to different diet is maintained by a kinase gene. When this gene is mutated, worms start living longer on one strain of bacterial diet but not on the other. We identify the molecular cascade required for this food-type-dependent longevity. We show that this cascade of events significantly overlaps with the pathway that determine food quantity-dependent life span enhancement. Our study thus elucidates a part of the molecular monitoring system that regulates longevity dependent on the available quality and quantity of diet.

In this work, we investigate the contact and channel material dependency of the transport properties of Siticene and Armchair CNT based heterostructure devices. The Density of States (DOS) of the heterojunction materials and transport properties like Device Density of States, transmission eigenstate, transmission pathway, transmission spectrum and I-V characteristics of two structures — CNT-Si-CNT and Si-CNT-Si are investigated. We see that CNT-Silicene-CNT heterojunction gives higher current and it is more conducive for FET device application. This device also shows better transport properties in terms of transmission Eigenstate, Transmission pathway and IV characteristics.

Magnetic tunnel junctions (MTJ) have emerged as a possible alternative to charge based data storage cells. With the development in 2-dimensional materials, non-conventional insulators like 2D hexagonal boron nitride (hBN), Ca(OH) 2 and Mg(OH) 2 have emerged as possible dielectrics in future nanoscale devices. Thus it could be interesting to investigate the application of these materials as insulators in MTJ devices. In this work, we have studied the effect of Ca(OH) 2 , hBN and Mg(OH)2 based composite oxides in a MTJ device. The barrier height of the composite oxide and effective mass of the same has been calculated using Maxwell-Garnett model. With the MTJ Lab tool available at nanohub, device characteristics were calculated. We have studied various MTJ parameters like parallel and anti-parallel resistance and differential resistance, tunnelling magneto resistance (TMR) and differential TMR (DTMR), and the variation of spin transfer torque (STT) components (In-Plane and Out-of-Plane STT) with voltage.

Dietary restriction (DR) increases life span and delays the onset of age-related diseases across species. However, the molecular mechanisms have remained relatively unexplored in terms of gene regulation. In C. elegans, a popular model for aging studies, the FOXA transcription factor PHA-4 is a robust genetic regulator of DR, although little is known about how it regulates gene expression. We profiled the transcriptome and miRNAome of an eat-2 mutant, a genetic surrogate of DR, by Next Generation sequencing and find that most of the miRNAs are upregulated in the young-adult worms, none significantly downregulated. Interestingly, PHA-4 can potentially regulate the expression of most of these miRNA genes. Remarkably, many of the PHA-4-regulated genes that are induced during DR are also targets of the PHA-4-upregulated miRNAs, forming a large feed-forward gene regulatory network. The genes targeted by the feed-forward loops (FFLs) are enriched for functions related to ubiquitin-mediated decay, lysosomal autophagy, cellular signalling, protein folding etc., processes that play critical roles in DR and longevity. Together our data provides a framework for understanding the complex and unique regulatory network employed during DR, suggesting that PHA-4 employs such FFLs to fine-tune gene expression and instil robustness in the system during energy crisis.

Although dietary restriction (DR) is known to extend lifespan across species, from yeast to mammals, the signalling events downstream of food/nutrient perception are not well understood. In Caenorhabditis elegans, DR is typically attained either by using the eat-2 mutants that have reduced pharyngeal pumping leading to lower food intake or by feeding diluted bacterial food to the worms. In this study, we show that knocking down a mammalian MEKK3-like kinase gene, mekk-3 in C. elegans, initiates a process similar to DR without compromising food intake. This DR-like state results in upregulation of beta-oxidation genes through the nuclear hormone receptor NHR-49, a HNF-4 homolog, resulting in depletion of stored fat. This metabolic shift leads to low levels of reactive oxygen species (ROS), potent oxidizing agents that damage macromolecules. Increased beta-oxidation, in turn, induces the phase I and II xenobiotic detoxification genes, through PHA-4/FOXA, NHR-8 and aryl hydrocarbon receptor AHR-1, possibly to purge lipophilic endotoxins generated during fatty acid catabolism. The coupling of a metabolic shift with endotoxin detoxification results in extreme longevity following mekk-3 knock-down. Thus, MEKK-3 may function as an important nutrient sensor and signalling component within the organism that controls metabolism. Knocking down mekk-3 may signal an imminent nutrient crisis that results in initiation of a DR-like state, even when food is plentiful.

Ncb2, the β subunit of NC2 complex, a heterodimeric regulator of transcription was earlier shown to be involved in the activated transcription of CDR1 gene in azole resistant isolate (AR) of Candida albicans. This study examines its genome-wide role by profiling Ncb2 occupancy between genetically matched pair of azole sensitive (AS) and AR clinical isolates. A comparison of Ncb2 recruitment between the two isolates displayed that 29 genes had higher promoter occupancy of Ncb2 in the AR isolate. Additionally, a host of genes exhibited exclusive occupancy of Ncb2 at promoters of either AR or AS isolate. The analysis also divulged new actors of multi-drug resistance, whose transcription was activated owing to the differential occupancy of Ncb2. The conditional, sequence-specific positional escape of Ncb2 from the core promoter in AS isolate and its preferential recruitment to the core promoter of certain genes in AR isolates was most noteworthy means of transcription regulation. Together, we show that positional rearrangement of Ncb2 resulting in either activation or repression of gene expression in response to drug-induced stress, represents a novel regulatory mechanism that opens new opportunities for therapeutic intervention to prevent development of drug tolerance in C. albicans cells.

OSIPP3 gene (coding for pectin methylesterase inhibitor protein) was isolated from a pre-pollinated inflorescence-specific cDNA library by differential screening of stage-specific libraries from Oryza sativa. OSIPP3 is present in the genome of rice as a single copy gene. OSIPP3 gene was expressed exclusively in the pre-pollinated spikelets of rice. Upstream regulatory region (URR) of OSIPP3 was isolated and a series of 5'-deletions were cloned upstream of GUS reporter gene and were used to transform Arabidopsis. OSIPP3_del1 and del2 transgenic plants showed GUS expression in root, anther and silique, while OSIPP3_del3 showed GUS activity only in anthers and siliques. Pollen-specific expression was observed in case of plants harboring OSIPP3_del4 construct. It can, therefore, be concluded that the OSIPP3 URR between -178 and +108 bp is necessary for conferring pollen-specific expression in Arabidopsis.

Signal transduction pathways are tightly regulated by phosphorylation-dephosphorylation cycles and yet the mammalian genome contains far more genes that encode for protein kinases than protein phosphatases. Therefore, to target specific substrates, many phosphatases associate with distinct regulatory subunits and thereby modulate multiple cellular processes. One such example is the C. elegans PP2A regulatory subunit PPTR-1 that negatively regulates the insulin/insulin-like growth factor signaling pathway to modulate longevity, dauer diapause, fat metabolism and stress resistance. PPTR-1, as well as its mammalian homolog B56beta, specifically target the PP2A enzyme to AKT and mediate the dephosphorylation of this important kinase at a conserved threonine residue. In C. elegans, the major consequence of this modulation is activation of the FOXO transcription factor homolog DAF-16, which in turn regulates transcription of its many target genes involved in longevity and stress resistance. Understanding the function of B56 subunits may have important consequences in diseases such as Type 2 diabetes and cancer where the balance of Akt phosphorylation is deregulated.