Orc6 is a component of the replication fork and enables efficient mismatch repair.

In eukaryotes, the origin recognition complex (ORC) is required for the initiation of DNA replication. The smallest subunit of ORC, Orc6, is essential for prereplication complex (pre-RC) assembly and cell viability in yeast and for cytokinesis in metazoans. However, unlike other ORC components, the role of human Orc6 in replication remains to be resolved. Here, we identify an unexpected role for hOrc6, which is to promote S-phase progression after pre-RC assembly and DNA damage response. Orc6 localizes at the replication fork and is an accessory factor of the mismatch repair (MMR) complex. In response to oxidative damage during S phase, often repaired by MMR, Orc6 facilitates MMR complex assembly and activity, without which the checkpoint signaling is abrogated. Mechanistically, Orc6 directly binds to MutSα and enhances the chromatin-association of MutLα, thus enabling efficient MMR. Based on this, we conclude that hOrc6 plays a fundamental role in genome surveillance during S phase.

Probing the Influence of Hybrid Thread Design on Biomechanical Response of Dental Implants: Finite Element Study and Experimental Validation.

This study aimed to perform quantitative biomechanical analysis for probing the effect of varying thread shapes in an implant for improved primary stability in prosthodontics surgery. Dental implants were designed with square (SQR), buttress (BUT), and triangular (TRI) thread shapes or their combinations. Cone-beam computed tomography images of mandible molar zones in human subjects belonging to three age groups were used for virtual implantation of the designed implants, to quantify patient-specific peri-implant bone microstrain, using finite element analyses. The in silico analyses were carried out considering frictional contact to simulate immediate loading with a static masticatory force of 200 N. To validate computational biomechanics results, compression tests were performed on three-dimensional printed implants having the investigated thread architectures. Bone/implant contact areas were also quantitatively assessed. It was observed that, bone/implant contact was maximum for SQR implants followed by BUT and TRI implants. For all the cases, peak microstrain was recorded in the cervical cortical bone. The combination of different thread shapes in the middle or in the apical part (or both) was demonstrated to improve peri-implant microstrain, particularly for BUT and TRI. Considering 1500-2000 microstrain generates in the peri-implant bone during regular physiological functioning, BUT-SQR, BUT-TRI-SQR, TRI-SQR-BUT, SQR, and SQR-BUT-TRI design concepts were suitable for younger; BUT-TRI-SQR, BUT-SQR-TRI, TRI-SQR-BUT, SQR-BUT, SQR-TRI for middle-aged, and BUT-TRI-SQR, BUT-SQR-TRI, TRI-BUT-SQR, SQR, and SQR-TRI for the older group of human patients.

Spatiotemporal gating of SIRT1 functions by O-GlcNAcylation is essential for liver metabolic switching and prevents hyperglycemia.

Inefficient physiological transitions are known to cause metabolic disorders. Therefore, investigating mechanisms that constitute molecular switches in a central metabolic organ like the liver becomes crucial. Specifically, upstream mechanisms that control temporal engagement of transcription factors, which are essential to mediate physiological fed-fast-refed transitions are less understood. SIRT1, a NAD+-dependent deacetylase, is pivotal in regulating hepatic gene expression and has emerged as a key therapeutic target. Despite this, if/how nutrient inputs regulate SIRT1 interactions, stability, and therefore downstream functions are still unknown. Here, we establish nutrient-dependent O-GlcNAcylation of SIRT1, within its N-terminal domain, as a crucial determinant of hepatic functions. Our findings demonstrate that during a fasted-to-refed transition, glycosylation of SIRT1 modulates its interactions with various transcription factors and a nodal cytosolic kinase involved in insulin signaling. Moreover, sustained glycosylation in the fed state causes nuclear exclusion and cytosolic ubiquitin-mediated degradation of SIRT1. This mechanism exerts spatiotemporal control over SIRT1 functions by constituting a previously unknown molecular relay. Of note, loss of SIRT1 glycosylation discomposed these interactions resulting in aberrant gene expression, mitochondrial dysfunctions, and enhanced hepatic gluconeogenesis. Expression of nonglycosylatable SIRT1 in the liver abrogated metabolic flexibility, resulting in systemic insulin resistance, hyperglycemia, and hepatic inflammation, highlighting the physiological costs associated with its overactivation. Conversely, our study also reveals that hyperglycosylation of SIRT1 is associated with aging and high-fat-induced obesity. Thus, we establish that nutrient-dependent glycosylation of SIRT1 is essential to gate its functions and maintain physiological fitness.

PCNA-mediated stabilization of E3 ligase RFWD3 at the replication fork is essential for DNA replication.

RING finger and WD repeat domain-containing protein 3 (RFWD3) is an E3 ligase known to facilitate homologous recombination by removing replication protein A (RPA) and RAD51 from DNA damage sites. Further, RPA-mediated recruitment of RFWD3 to stalled replication forks is essential for interstrand cross-link repair. Here, we report that in unperturbed human cells, RFWD3 localizes at replication forks and associates with proliferating cell nuclear antigen (PCNA) via its PCNA-interacting protein (PIP) motif. PCNA association is critical for the stability of RFWD3 and for DNA replication. Cells lacking RFWD3 show slower fork progression, a prolonged S phase, and an increase in the loading of several replication-fork components on the chromatin. These findings all point to increased frequency of stalled forks in the absence of RFWD3. The S-phase defect is rescued by WT RFWD3, but not by the PIP mutant, suggesting that the interaction of RFWD3 with PCNA is critical for DNA replication. Finally, we observe reduced ubiquitination of RPA in cells lacking RFWD3. We conclude that the stabilization of RFWD3 by PCNA at the replication fork enables the polyubiquitination of RPA and its subsequent degradation for proper DNA replication.

Characterization of zinc solubilization potential of arsenic tolerant Burkholderia spp. isolated from rice rhizospheric soil.

In this study, experiments were conducted to isolate, characterize, and evaluate rice rhizosphere bacteria for their arsenic (As) tolerance ability and zinc (Zn) solubilization potential in culture media and soil. Among 20 bacterial isolates recovered, six were found to solubilize inorganic Zn salt(s) efficiently under in vitro culture conditions. 16S rRNA gene sequence-based phylogenetic analysis indicated the affiliation of efficient Zn solubilizing bacteria (ZSB) to Burkholderia vietnamiensis and Burkholderia seminalis. Zinc solubilizing efficiency (ZSE) of the bacteria varied with the concentrations and types of Zn salts used in the experiments. Increasing trend in ZSE of the bacteria was noticed when the percentage of ZnO increased from 0.1 to 0.5 but the same decreased at 1.0%. Increased Zn solubilization was noticed when bacteria were incubated with lower concentration of Zn3(PO4)2 and ZnCO3. In general, Zn solubilization increased with increasing incubation time in lower volume medium, while some isolates failed to solubilize one or more tested Zn salts. However, enriched concentrated cells of the ZSB in glucose amended medium with 0.5% ZnO showed an increasing trend of Zn solubilization with time and were able to solubilize more than 300 mg/L Zn. This increased rate of Zn release by the ZSB was attributed to marked decline in pH that might be due to the enhanced gluconic acid production from glucose. As evident from the decreased ZSE of the bacteria in the presence of As(V) in particular, it seems arsenic imparts a negative effect on Zn solubilization. The ZSB were also able to increase the rate of Zn release in soil. A microcosm-based soil incubation study amending the enriched bacteria and 0.5% ZnO in soil showed an elevated level of both water-soluble and available Zn compared to un-inoculated control. During Zn solubilization in microcosms, viable cells in terms of colony-forming unit (CFU) declined by the same order of magnitude both in the presence and absence of ZnO that might be due to the nutrients limiting condition aroused during the incubation period rather than Zn toxicity. The bacteria in this study also exhibited plant growth promoting traits, such as growth in nitrogen-free medium, production of indole acetic acid (IAA), and solubilization of potassium and phosphate. Our findings suggested that Burkholderia spp. could be the potential candidates for enhancing Zn dissolution in the soil that might reduce the rate of inorganic Zn fertilization in agricultural soil.

A New Class of Superhalogen Based Anion Receptor in Li-Ion Battery Electrolytes.

In the search for new additives (anion receptors) in Li-ion battery electrolytes especially for LiPF6 and LiClO4, we have theoretically designed boron-based complexes by coupling with different heterocyclic ligands. The validation of the formation of modeled compounds involves reproduction of available experimentally reported absolute magnetic shielding and chemical shift values for different boron complexes. As compared to the commonly used tris(pentafluorophenyl) borane, our designed compounds suggest that the complexes like B[C2HBNO(CN)2]3, B[C2HBNS(CN)2]3, and B[C4H3BN(CN)2]3 are promising additives.

Unique reactivity of B in B[Ge9Y3]3 (Y = H, CH3, BO, CN): formation of a Lewis base.

Boron compounds usually exhibit Lewis acidity at the boron center due to the presence of vacant p-orbitals. We show that this chemistry can be altered by an appropriate choice of ligands to decorate the boron center. To elucidate this effect, we studied the interactions of boron with two classes of ligands, one based on penta-substituted phenyl species (C6X5, X = F, BO, CN) and the other based on Zintl-ion-based groups (Ge9Y3, Y = H, CH3, BO, CN). An in-depth analysis of the charges and Fukui function values at the local atomic sites of the substituted boron derivatives B(C6X5)3 and B[Ge9Y3]3 shows that the B-center in the former is electrophilic, while it is nucleophilic in the latter. The chemical stability of the B[Ge9Y3]3 species is shown to be due to the presence of strong 2c-2e bonds between the B and Ge centers. Thus, the general notion of the Lewis acid nature of a boron center depends upon the choice of the ligand.

Elevated level of arsenic negatively influences nifH gene expression of isolated soil bacteria in culture condition as well as soil system.

Comprehensive studies on the effect of arsenic (As) on free-living diazotrophs that play a crucial role in soil fertility by nitrogen fixation are still scanty. Here, we isolated three free-living bacteria from rice field with potential nitrogen-fixing ability and investigated the impact of As on their nifH gene expression and extracellular polysaccharide (EPS) production in culture condition and soil system. 16S rRNA sequence analysis showed that the isolated bacteria were affiliated to ß-Proteobacteria, γ-Proteobacteria and Firmicutes. As(III) exposure to bacterial isolates followed by RT-qPCR analysis revealed that elevated levels of As reduced the expression of nifH gene in selective bacteria, both in culture medium and soil condition. We also noticed reduced production of EPS under higher concentration of As. All the three bacteria showed high tolerance to As(III), able to oxidize As and exhibited significant plant growth-promoting traits. This investigation indicated that an environment exposed with higher concentration of As might perturbed the activity of free-living diazotrophs in agricultural soil system.

Orc5 induces large-scale chromatin decondensation in a GCN5-dependent manner.

In eukaryotes, origin recognition complex (ORC) proteins establish the pre-replicative complex (preRC) at the origins, and this is essential for the initiation of DNA replication. Open chromatin structures regulate the efficiency of preRC formation and replication initiation. However, the molecular mechanisms that control chromatin structure, and how the preRC components establish themselves on the chromatin remain to be understood. In human cells, the ORC is a highly dynamic complex with many separate functions attributed to sub-complexes or individual subunits of the ORC, including heterochromatin organization, telomere and centromere function, centrosome duplication and cytokinesis. We demonstrate that human Orc5, unlike other ORC subunits, when ectopically tethered to a chromatin locus, induces large-scale chromatin decondensation, predominantly during G1 phase of the cell cycle. Orc5 associates with the H3 histone acetyl transferase GCN5 (also known as KAT2A), and this association enhances the chromatin-opening function of Orc5. In the absence of Orc5, histone H3 acetylation is decreased at the origins. We propose that the ability of Orc5 to induce chromatin unfolding during G1 allows the establishment of the preRC at the origins.

Deltahedral Organo-Zintl Superhalogens.

Zintl ions constitute a special type of naked anionic clusters, mainly consisting of Group 13, 14, and 15 elements of the Periodic Table. Due to the presence of multiple negative ions, the chemistry of Zintl ions is unique. They not only form Zintl phases with alkali and alkaline-earth metal cations, but also form organo-Zintl clusters with distinct properties. By first-principles calculations based on density functional theory, we have designed a new deltahedral organo-Zintl cluster with Ge94- as the core and aromatic heterocyclic compounds as ligands. Calculations on such complexes show that they form a special class of system known as a superhalogen (SH), with a high vertical detachment energy of 4.9 eV. The density of states (DOS), partial DOS, and different molecular orbitals give additional information about the bonding features of the complexes.

A WD-repeat protein stabilizes ORC binding to chromatin.

Origin recognition complex (ORC) plays critical roles in the initiation of DNA replication and cell-cycle progression. In metazoans, ORC associates with origin DNA during G1 and with heterochromatin in postreplicated cells. However, what regulates the binding of ORC to chromatin is not understood. We have identified a highly conserved, leucine-rich repeats and WD40 repeat domain-containing protein 1 (LRWD1) or ORC-associated (ORCA) in human cells that interacts with ORC and modulates chromatin association of ORC. ORCA colocalizes with ORC and shows similar cell-cycle dynamics. We demonstrate that ORCA efficiently recruits ORC to chromatin. Depletion of ORCA in human primary cells and embryonic stem cells results in loss of ORC association to chromatin, concomitant reduction of MCM binding, and a subsequent accumulation in G1 phase. Our results suggest ORCA-mediated association of ORC to chromatin is critical to initiate preRC assembly in G1 and chromatin organization in post-G1 cells.

Development of effective stochastic potential method using random matrix theory for efficient conformational sampling of semiconductor nanoparticles at non-zero temperatures.

The relationship between structure and property is central to chemistry and enables the understanding of chemical phenomena and processes. Need for an efficient conformational sampling of chemical systems arises from the presence of solvents and the existence of non-zero temperatures. However, conformational sampling of structures to compute molecular quantum mechanical properties is computationally expensive because a large number of electronic structure calculations are required. In this work, the development and implementation of the effective stochastic potential (ESP) method is presented to perform efficient conformational sampling of molecules. The overarching goal of this work is to alleviate the computational bottleneck associated with performing a large number of electronic structure calculations required for conformational sampling. We introduce the concept of a deformation potential and demonstrate its existence by the proof-by-construction approach. A statistical description of the fluctuations in the deformation potential due to non-zero temperature was obtained using infinite-order moment expansion of the distribution. The formal mathematical definition of the ESP was derived using the functional minimization approach to match the infinite-order moment expansion for the deformation potential. Practical implementation of the ESP was obtained using the random-matrix theory method. The developed method was applied to two proof-of-concept calculations of the distribution of HOMO-LUMO gaps in water molecules and solvated CdSe clusters at 300 K. The need for large sample size to obtain statistically meaningful results was demonstrated by performing 105 ESP calculations. The results from these prototype calculations demonstrated the efficacy of the ESP method for performing efficient conformational sampling. We envision that the fundamental nature of this work will not only extend our knowledge of chemical systems at non-zero temperatures but also generate new insights for innovative technological applications.

Effect of reserpine on Pseudomonas aeruginosa quorum sensing mediated virulence factors and biofilm formation.

This study aimed to evaluate the effect of reserpine, a plant-derived indole-alkaloid, against Pseudomonas aeruginosa PAO1 biofilms. The anti-biofilm activity of reserpine was evaluated by crystal violet staining, MTT assay, confocal laser scanning microscopy and scanning electron microscopy. Reserpine effects were also assessed by qRT-PCR of quorum sensing (QS)-regulated genes and biochemical quantification of the QS-mediated virulence factors pyocyanin, rhamnolipids, proteases and elastases. Reserpine reduced biofilm formation, cell motility, virulence factor production, and QS-controlled gene expression. Additionally, molecular docking analysis for AHL synthase LasI and QS transcriptional regulators LasR/MvfR revealed a plausible molecular mechanisms of reserpine QS inhibition. These findings provide insights into the underlying mode of action of reserpine, which may be useful in the development of new drugs against biofilm-related infections.

BEND3 represses rDNA transcription by stabilizing a NoRC component via USP21 deubiquitinase.

Ribosome biogenesis dictates the translational capacity of cells. Several mechanisms establish and maintain transcriptional output from eukaryotic ribosomal DNA (rDNA) loci. rDNA silencing is one such mechanism that ensures the inactivity and hence the maintenance of a silenced state of a subset of rRNA gene copies. Whereas oncogenic agents stimulate rRNA gene transcription, tumor suppressors decrease rRNA gene transcription. We demonstrate in mammalian cells that BANP, E5R, and Nac1 (BEN) domain 3 (BEND3), a quadruple BEN domain-containing protein, localizes in nucleoli and binds to ribosomal RNA gene promoters to help repress rRNA genes. Loss of BEND3 increases histone H3K4 trimethylation and, correspondingly, decreases rDNA promoter DNA methylation, consistent with a role for BEND3 in rDNA silencing. BEND3 associates with the nucleolar-remodeling complex (NoRC), and SUMOylated BEND3 stabilizes NoRC component TTF-1-interacting protein 5 via association with ubiquitin specific protease 21 (USP21) debiquitinase. Our results provide mechanistic insights into how the novel rDNA transcription repressor BEND3 acts together with NoRC to actively coordinate the establishment of rDNA silencing.

PSIP1/p75 promotes tumorigenicity in breast cancer cells by promoting the transcription of cell cycle genes.

Breast cancer (BC) is a highly heterogeneous disease, both at the pathological and molecular level, and several chromatin-associated proteins play crucial roles in BC initiation and progression. Here, we demonstrate the role of PSIP1 (PC4 and SF2 interacting protein)/p75 (LEDGF) in BC progression. PSIP1/p75, previously identified as a chromatin-adaptor protein, is found to be upregulated in basal-like/triple negative breast cancer (TNBC) patient samples and cell lines. Immunohistochemistry in tissue arrays showed elevated levels of PSIP1 in metastatic invasive ductal carcinoma. Survival data analyses revealed that the levels of PSIP1 showed a negative association with TNBC patient survival. Depletion of PSIP1/p75 significantly reduced the tumorigenicity and metastatic properties of TNBC cell lines while its over-expression promoted tumorigenicity. Further, gene expression studies revealed that PSIP1 regulates the expression of genes controlling cell-cycle progression, cell migration and invasion. Finally, by interacting with RNA polymerase II, PSIP1/p75 facilitates the association of RNA pol II to the promoter of cell cycle genes and thereby regulates their transcription. Our findings demonstrate an important role of PSIP1/p75 in TNBC tumorigenicity by promoting the expression of genes that control the cell cycle and tumor metastasis.

Long noncoding RNA MALAT1 controls cell cycle progression by regulating the expression of oncogenic transcription factor B-MYB.

The long noncoding MALAT1 RNA is upregulated in cancer tissues and its elevated expression is associated with hyper-proliferation, but the underlying mechanism is poorly understood. We demonstrate that MALAT1 levels are regulated during normal cell cycle progression. Genome-wide transcriptome analyses in normal human diploid fibroblasts reveal that MALAT1 modulates the expression of cell cycle genes and is required for G1/S and mitotic progression. Depletion of MALAT1 leads to activation of p53 and its target genes. The cell cycle defects observed in MALAT1-depleted cells are sensitive to p53 levels, indicating that p53 is a major downstream mediator of MALAT1 activity. Furthermore, MALAT1-depleted cells display reduced expression of B-MYB (Mybl2), an oncogenic transcription factor involved in G2/M progression, due to altered binding of splicing factors on B-MYB pre-mRNA and aberrant alternative splicing. In human cells, MALAT1 promotes cellular proliferation by modulating the expression and/or pre-mRNA processing of cell cycle-regulated transcription factors. These findings provide mechanistic insights on the role of MALAT1 in regulating cellular proliferation.

Tidal variation of phytoplankton in the coastal waters of South Andaman, India.

Tidal variations of phytoplankton were studied at two stations i.e., Station 1 (Science Centre) and Station 2 (Junglighat Bay) during the period of December 2010 to February 2011 in the coastal waters of South Andaman Islands, India. Phytoplankton biomass (Chlorophyll-a) was observed low (avg. 0.02- 0.1 mg m(-3)) at the stations during the sampling period. Low values of dissolved oxygen and biochemical oxygen demand were recorded during low tide. In all 114 species belonging to 42 genera of diatoms, 16 genera of dinoflagellates and 4 genera of cyanobacteria were identified. Phytoplankton population density ranged from 827cells I(-1) to 11,790 cells l(-1) and was high during high tide in comparison to low tide. Diatoms were dominant (70.86-88.0%) and contributed more towards phytoplankton biomass followed by dinoflagellates (10.8-19.53%) and cyanobacteria (0.73-9.4%). Dinoflagellates were visualised more in the samples when diatom population had declined. Diversity indices such as species diversity (H') ranged from 0.68-3.1; species richness (d) varied from 2.18-6.54 and Pielou's evenness (J') ranged from 0.24-0.94. H' was more during high tide than at low tide at Station 2. On the other hand, low diversity and equitability in phytoplankton population were observed at Station 1 during the month of January, 2011. It may be due to dominance of mono specific cells of Rhizosolenia sp. The study indicates low production of phytoplankton in coastal waters. Variation of tides may leave implications on sampling, because it has an influence on species diversity and proportion of specific micro algal groups at different times.

Signaling pathways in insulin- and IGF-I mediated oocyte maturation in lower vertebrates.

The endocrine control of oocyte maturation in fish and amphibians has proved to be a valuable model for investigating the rapid and non-genomic steroid actions at the cell surface. Considerable progress has made over the last decade in elucidating signaling pathways in steroid-induced oocyte maturation. In addition to steroids, various growth factors have also been reported to be involved in this process and progress being made to elucidate their mechanism of actions. Exposure of fully-grown oocytes to steroids or growth factors (insulin/IGFs) initiates various signaling cascade, leading to formation and activation of maturation-promoting factor (MPF), a key enzyme that catalyzes entry into M-phase of meiosis I and II. Whereas the function of MPF in promoting oocyte maturation is ubiquitous, there are differences in signaling pathways between steroids- and growth factors-induced oocyte maturation in amphibian and fish. Here, we have reviewed the recent advances on the signaling pathways in insulin- and IGF-I-induced oocyte maturation in these two groups of non-mammalian vertebrates. New findings demonstrating the involvement of PI3 kinase and MAP kinase in induction of oocyte maturation by insulin and IGF-I are presented.

An Affordable Topography-Based Protocol for Assigning a Residue's Character on a Hydropathy (PARCH) Scale.

The hydropathy of proteins or quantitative assessment of protein-water interactions has been a topic of interest for decades. Most hydropathy scales use a residue-based or atom-based approach to assign fixed numerical values to the 20 amino acids and categorize them as hydrophilic, hydroneutral, or hydrophobic. These scales overlook the protein's nanoscale topography, such as bumps, crevices, cavities, clefts, pockets, and channels, in calculating the hydropathy of the residues. Some recent studies have included protein topography in determining hydrophobic patches on protein surfaces, but these methods do not provide a hydropathy scale. To overcome the limitations in the existing methods, we have developed a Protocol for Assigning a Residue's Character on the Hydropathy (PARCH) scale that adopts a holistic approach to assigning the hydropathy of a residue. The parch scale evaluates the collective response of the water molecules in the protein's first hydration shell to increasing temperatures. We performed the parch analysis of a set of well-studied proteins that include the following─enzymes, immune proteins, and integral membrane proteins, as well as fungal and virus capsid proteins. Since the parch scale evaluates every residue based on its location, a residue may have very different parch values inside a crevice versus a surface bump. Thus, a residue can have a range of parch values (or hydropathies) dictated by the local geometry. The parch scale calculations are computationally inexpensive and can compare hydropathies of different proteins. The parch analysis can affordably and reliably aid in designing nanostructured surfaces, identifying hydrophilic and hydrophobic patches, and drug discovery.

Enhancement of Spontaneous Photon Emission in Inverse Photoemission Transitions in Semiconductor Quantum Dots.

Inverse photoemission (IPE) is a radiative electron capture process where an electron is transiently captured in the conduction band (CB) followed by intraband de-excitation and spontaneous photon emission. IPE in quantum dots (QDs) bypasses optical selection rules for populating the CB and provides insights into the capacity for electron capture in the CB, the propensity for spontaneous photon emission, intraband transition energies where both initial and final states are in the CB, and the generation of photons with frequencies lower than the bandgap. Here, we demonstrate using time-dependent perturbation theory that judicious application of electric fields can significantly enhance the IPE transition in QDs. For a series of CdSe, CdS, PbSe, and PbS QDs, we present evidence of field-induced enhancement of IPE intensities (188% for Cd54Se54), field-dependent control of emitted photon frequencies (Δω = 0.73 eV for Cd54Se54), and enhancement of light-matter interaction using directed Stark fields (103% for Cd54Se54).