PHOPSPHORYLATION AND UBIQUITIN MODIFICATION AT DNA DAMAGE SITES IN RESPONSE TO DOUBLE-STRAND BREAKS

Genomes of all organisms are continuously damaged by numerous exogenous and endogenous sources leading to different kinds of DNA lesions, which if not repaired efficiently may trigger wide-scale genomic instability, a hallmark of cancer development. To overcome this, cells have evolved a sophisticated sensory network called the DNA damage response (DDR) comprised of a large number of distinct protein complexes categorized as sensor, mediator, transducer and effector proteins that amplify the DNA damage signal and activate cell cycle checkpoint to initiate DNA repair or trigger apoptosis where the defect is beyond repair. This intricate signaling pathway is tightly regulated by modulating DDR factors recruitment, retention and dissociation from the sites of DNA damage in a spatiotemporal manner mediated by numerous reversible post-translational modification (PTMs) including phosphorylation, ubiquitination, SUMOylation, methylation, acetylation, poly(ADP-ribosyl)ation, and Neddylation. In this study, I examined the role of phosphorylation and ubiquitination in regulating the DDR signaling at the DNA damage sites. DNA double-strand breaks triggers a phosphorylation-mediated signaling at the damage sites leading to histone ubiquitination in Lys63-linked manner that recruits BRCA1-A complex to the damage sites. The A complex is comprised of BRCA1, Rap80, NBA1, BRE, BRCC36 and the adaptor protein Abraxas, which has been shown previously to constitutively interact with BRCA1-BRCT (BRCA1 C- terminal) domain through its C-terminal phosphorylated S406 residue. In this study, we found that DNA damage-induced Abraxas phosphorylation at neighboring S404 residue induces stable BRCA1 dimerization through its BRCT domain. Both crystal structure and in vivo analysis confirmed that phosphorylation at Abraxas S404 residue is essential for stable BRCA1-BRCT dimer formation and mutation in the S404 residue leads to impaired accumulation of BRCA1 to damaged chromatin. In addition, we found two germline mutations in the BRCA1-BRCT dimerization interface disrupt stable dimer formation both in vitro and in vivo. Although phosphorylation has been shown to be the major PTM at the DSB sites, over the last decade, ubiquitination has also emerged as a key regulatory player in the DDR. Irradiation (IR)-induced DNA damage catalyzes Lys63-linked polyubiquitination of histones, H2A and H2A.X that leads to accumulation of BRCA1- A complex to DSBs. In my second study, we sought to determine whether non- lys63-linked ubiquitination also exists at the DSBs regulating the DDR pathway. My findings indicate that along with Lys63-linked ubiquitination, chromatin-bound proteins are also modified with Lys11-linked polyubiquitination at DNA damage sites in an ATM-dependent manner by Ube2S/Ube2C E2 conjugating and RNF8 E3 ligase enzymes and deubiquitinated by OTUD7B (Cezanne) enzyme. I further showed that histones H2A and H2A.X is modified with Lys11-linked polyubiquitination in a DNA damage-dependent manner that is essential for inhibiting transcriptional silencing at proximity to DSB sites to maintain genomic stability. Overall, my findings provide insights into how post-translational modifications regulate DDR factors dynamics at DSB sites and play a crucial role in maintaining genomic integrity

Financial Planning and Challenges for College Libraries in Present Era

This article indicates the various financial problems associated with the college library budget. It studies the meaning of budget and examined the various techniques of budgeting that may be use in the libraries for fund acquisition and allocation. It draws the necessary steps to be taken for library budget preparation and finally concluded with the role of librarian for better utilization of limited fund.Fund crisis, Budget planning, Library budget, Fund allocation, Library financeIAC

Bacteriophage Mu C protein is a new member of unusual leucine zipper-HTH class of proteins

Transcription activator protein C of bacteriophage Mu activates transcription of the late genes, including mom, during the lytic cycle of the phage. C binding to its site leads to the alteration in DNA topology of the promoter elements resulting in RNA polymerase (RNAP) recruitment. At the next step, the transactivator enhances promoter clearance of RNAP from Pmom. The C protein binds DNA with a very high affinity using a carboxylterminal helix turn helix (HTH) motif which has similarity with the HTH from paired domain of Drosophila prd protein. Previous studies established that the protein is dimeric in free and DNA bound forms. We describe now the unique dimerization interface of the protein. Two heptad repeats of hydrophobic amino acids found in the protein were considered to be the candidates for dimerization region. Site-directed mutational analysis revealed that the amino-terminal coiled coil region is not the dimerization determinant. In contrast, similar mutagenesis studies indicated a role for the leucine zipper motif, located in the middle region of the protein, in dimerization. Mixed oligomerization assays confirmed the importance of leucine zipper in C dimer formation establishing the presence of an uncommon zipper-HTH domain in the transactivator

Head-to-Head and Tail-to-Tail Domain Wall in Hafnium Zirconium Oxide: A First Principles Analysis of Domain Wall Formation and Energetics

180{\deg} domains walls (DWs) of Head-to-Head/Tail-to-Tail (H-H/T-T) type in ferroelectric (FE) materials are of immense interest for a comprehensive understanding of the FE attributes as well as harnessing them for new applications. Our first principles calculation suggests that such DW formation in Hafnium Zirconium Oxide (HZO) based FEs depends on the unique attributes of the HZO unit cell, such as polar-spacer segmentation. Cross pattern of the polar and spacer segments in two neighboring domains along the polarization direction (where polar segment of one domain aligns with the spacer segment of another) boosts the stability of such DWs. We further show that low density of oxygen vacancies at the metal-HZO interface and high work function of metal electrodes are conducive for T-T DW formation. On the other hand, high density of oxygen vacancy and low work function of metal electrode favor H-H DW formation. Polarization bound charges at the DW get screened when band bending from depolarization field accumulates holes (electrons) in T-T (H-H) DW. For a comprehensive understanding, we also investigate their FE nature and domain growth mechanism. Our analysis suggests that a minimum thickness criterion of domains has to be satisfied for the stability of H-H/T-T DW and switching of the domains through such DW formation.Comment: 10 figure

Direction-Dependent Lateral Domain Walls in Ferroelectric Hafnium Zirconium Oxide and their Gradient Energy Coefficients: A First Principles Study

To understand and harness the physical mechanisms of ferroelectric Hafnium Zirconium Oxide (HZO)-based devices, there is a need for a clear understanding of the domain interactions, domain density, nucleation, domain wall motion, negative capacitance effects, and other multi-domain characteristics. All these crucial attributes strongly depend on the coupling between neighboring domains in HZO which is quantified by gradient energy coefficient (g). Furthermore, HZO has unique orientation-dependent lateral multidomain configurations, which plays a key role for directional dependence of g. To develop an in-depth understanding of these effects, there is a need for a thorough analysis of g in HZO, including its orientation and strain-dependence. In this work, we analyze the energetics of multidomain configurations, domain growth mechanism and gradient energy coefficients of HZO corresponding to lateral domain walls using first-principle Density Functional Theory (DFT) calculations. The dependence of g on domain width and strain is also analyzed to provide a comprehensive understanding of this crucial parameter. Our results indicate that one lateral direction exhibits the following characteristics: (i) domain growth occurs unit-cell-by-unit-cell, (ii) the value of g is negative and in the order of $10^{-12} Vm^{3}C^{-1}$, and (iii) g is much sensitive to strain. In contrast, in the other lateral direction, the following attributes are observed: (i) domain growth occurs in quanta of half-unit-cell, (ii) g is positive and in the order of $10^{-10} Vm^{3}C^{-1}$ and (iii) g shows negligible sensitivity to strain (up to the 1% strain limit considered in this work)

Perception of prevention of Japanese Encephalitis with emphasis on its vaccination programme: a community based study in a slum of Kolkata

Introduction Japanese Encephalitis (JE) is a mosquito borne disease with epidemic potential. There is no specific treatment available till date and apart from vector control, vaccination of individuals is considered as a safe and effective measure for prevention. Vaccination campaign among 1-15 years is being carried out with full vigour from 2015 onwards in West Bengal. Objectives This study was conducted to assess the knowledge of the care givers of 1-15 years old children about JE and its prevention and to find out the factors associated with vaccination status of the children. Methods A cross sectional, community based study was conducted from May-June 2016 in a slum of Chetla, Kolkata, which is within the service area of Urban Health Unit and Training Centre (UHU&TC), Chetla of All India Institute of Hygiene and Public Health, Kolkata, where the campaign prior to the study was completed in March 2016. Care givers of 90 children of aged 1-15 years were interviewed with a pre-designed, pre-tested, structured schedule. Results Mean age of the surveyed children was 6.34 years (SD 3.76) and 88% of them were vaccinated during the campaign. 56.7% of the caregivers had poor knowledge about JE and 84.95% were sensitized about the campaign by relatives/friends followed by health workers (33.7%). Low socio-economic status and good knowledge of JE had significant association with vaccination of the child after adjusting with other factors (age and sex of the child, education and occupation of parents, type of family). Conclusions Enhancement of knowledge and awareness about JE with appropriate health education programmes and special emphasis on sensitization campaigns for JE vaccination at both mass and individual level would prevent emergence of JE epidemics in future

Impacts of Organic and Conventional Management on the Nutritional Level of Vegetables

The nutrient concentration of fruits and vegetables in the U.S.A. has declined in the past 50–70 years. Crop management practices utilizing on-farm inputs are thought to increase crop nutritional quality, but few studies have evaluated this under long-term side-by-side trials. An experiment was conducted from 2004 to 2005 at Rodale Institute’s long-term Farming Systems Trial to investigate the nutritional quality of vegetables under organic manure (MNR) and conventional (CNV) farming systems, with or without arbuscular mycorrhizal fungi (AMF) treatment. AMF reduced the vitamin C content in carrots in both systems in 2004, but the reduction was 87% in CNV and 28% in MNR. AMF also reduced antioxidants in carrots in both CNV and MNR. This trend was likely due to the suppression of native AMF colonization by the non-native AMF inoculum used. Between 2004 and 2005, MNR increased the vitamin C in green peppers by 50% while CNV decreased the vitamin C in red peppers by 48%. Tomatoes under MNR had a 40% greater vitamin C content compared to CNV in 2005. The vegetable yield declined between 2004 and 2005, except for tomato, where the yield increased by 51% and 44% under CNV and MNR, respectively. In general, MNR tended to increase the nutrient concentration of vegetables compared with CNV, while the AMF effects were inconclusive

Development of half metallicity within mixed magnetic phase of Cu1−x_{1-x}Cox_xMnSb alloy

Cubic Half-Heusler Cu$_{1-x}$Co$_x$MnSb (0 $\leq$ $x$ $\leq$ 0.1) compounds have been investigated both experimentally and theoretically for their magnetic, transport and electronic properties in search of possible half metallic antiferromagnetism. The systems (Cu,Co)MnSb are of particular interest as the end member alloys CuMnSb and CoMnSb are semi metallic (SM) antiferromagnetic (AFM) and half metallic (HM) ferromagnetic (FM), respectively. Clearly, Co-doping at the Cu-site of CuMnSb introduces changes in the carrier concentration at the Fermi level that may lead to half-metallic ground state but there remains a persistent controversy whether the AFM to FM transition occurs simultaneously. Our experimental results reveal that the AFM to FM magnetic transition occurs through a percolation mechanism where Co-substitution gradually suppresses the AFM phase and forces FM polarization around every dopant cobalt. As a result a mixed magnetic phase is realized within this composition range while a nearly HM band structure is developed already at the 10% Co-doping. Absence of T$^2$ dependence in the resistivity variation at low T-region serves as an indirect proof of opening up an energy gap at the Fermi surface in one of the spin channels. This is further corroborated by the ab-initio electronic structure calculations that suggests a nearly ferromagnetic half-metallic ground state is stabilized by Sb-p holes produced upon Co doping