Disruption and Formation of Surface Salt Bridges Are Coupled to DNA Binding by the Integration Host Factor: A Computational Analysis

Revealing the thermodynamic driving force of protein−DNA interactions is crucial to the understanding of factors that dictate the properties and function of protein−DNA complexes. For the binding of DNA to DNA-wrapping proteins, such as the integration host factor (IHF), Record and co-workers proposed that the disruption of a large number of preexisting salt bridges is coupled with the binding process [Holbrook, J. A., et al. (2001) J. Mol. Biol. 310, 379]. To test this proposal, we have conducted explicit solvent MD simulations (multiple ∼25−50 ns trajectories for each salt concentration) to examine the behavior of charged residues in IHF, especially concerning their ability to form salt bridges at different salt concentrations. Of the 17 cationic residues noted by Record and co-workers, most are engaged in salt bridge interactions for a significant portion of the trajectories, especially in the absence of salt. This observation suggests that, from a structural point of view, their proposal is plausible. However, the complex behaviors of charged residues observed in the MD simulations also suggest that the unusual thermodynamic characteristics of IHF−DNA binding likely arise from the interplay between complex dynamics of charged residues both in and beyond the DNA binding site. Moreover, a comparison of MD simulations at different salt concentrations suggests that the strong dependence of the IHF−DNA binding enthalpy on salt concentration may not be due to a significant decrease in the number of stable salt bridges in apo IHF at high salt concentrations. In addition to the Hofmeister effects quantified in more recent studies of IHF−DNA binding, we recommend consideration of the variation of the enthalpy change of salt bridge disruption at different salt concentrations. Finally, the simulation study presented here explicitly highlights the fact that the electrostatic properties of DNA-binding proteins can be rather different in the apo and DNA-bound states, which has important implications for the design of robust methods for predicting DNA binding sites in proteins

DS_10.1177_0022034518807920 – Supplemental material for Purinergic Signaling Modulates Survival/Proliferation of Human Dental Pulp Stem Cells

Supplemental material, DS_10.1177_0022034518807920 for Purinergic Signaling Modulates Survival/Proliferation of Human Dental Pulp Stem Cells by S. Zhang, D. Ye, L. Ma, Y. Ren, R.T. Dirksen and X. Liu in Journal of Dental Research</p

Optimal Process Design of Commercial-Scale Amine-Based CO₂ Capture Plants

Reactive absorption with an aqueous solution of amines in an absorber/stripper loop is the most mature technology for postcombustion CO₂ capture (PCC). However, most of the commercial-scale CO₂ capture plant designs that have been reported in the open literature are based on values of CO₂ loadings and/or solvent circulation rates without an openly available techno-economic consideration. As a consequence, most of the reported designs may be suboptimal, and some of them appear to be unrealistic from practical and operational viewpoints. In this paper, four monoethanolamine (MEA) based CO₂ capture plants have been optimally designed for both gas-fired and coal-fired power plants based on process and economic analyses. We have found that the optimum lean CO₂ loading for MEA-based CO₂ capture plants that can service commercial-scale power plants, whether natural-gas-fired or coal-fired, is about 0.2 mol/mol for absorber and stripper columns packed with Sulzer Mellapak 250Y structured packing. Also, the optimum liquid/gas ratio for a natural gas combined cycle (NGCC) power plant with a flue gas composition of approximately 4 mol % CO₂ is about 0.96, while the optimum liquid/gas ratio for a pulverized-coal-fired (PC) power plant can range from 2.68 to 2.93 for a flue gas having a CO₂ composition that ranges from 12.38 to 13.50 mol %

Changes in Pig Production in China and Their Effects on Nitrogen and Phosphorus Use and Losses

China’s pig production has increased manifold in the past 50 years, and this has greatly affected the nitrogen and phosphorus use and losses in the pig production sector. However, the magnitude of these changes are not well-known. Here, we provide an in-depth account of the changes in pig productionN and P use and total N and P losses in the whole pig production chain during the period 1960–2010through simulation modeling and using data from national statistics and farm surveys. For the period of 2010–2030, we explored possible effects of technological and managerial measures aimed at improving the performances of pig production via scenario analysis. We used and further developed the NUtrient flows in Food chains, Environment and Resources use (NUFER) model to calculate the feed requirement and consumption, and N and P losses in different pig production systems for all the years. Between 1960 and 2010, pig production has largely shifted from the so-called backyard system to landless systems. The N use efficiencies at fattener level increased from 18 to 28%, due to the increased animal productivity. However, the N use efficiencies at the whole-system level decreased from 46 to 11% during this period, mainly due to the increase of landless pig farms, which rely on imported feed and have no land-base for manure disposal. The total N and P losses were 5289 and 829 Gg in 2010, which is 30 and 95 times higher than in 1960. In the business as usual scenario, the total N and P losses were projected to increase by 25 and 55% between 2010 and 2030, respectively. Analyses of other scenarios indicate that packages of technological and managerial measures can decrease total N and P losses by 64 and 95%, respectively. Such improvements require major transition in the pig production sector, notably, in manure management, herd management, and feeding practices

Supplementary Materials to the Journal of Insects as Food and Feed JIFF-20220159: <strong>Limited hydrolysis combined with glycation modification of silkworm pupae (</strong><em><strong>Bombyx mori</strong></em><strong>) proteins: structure-function relationship</strong>

   In order to explore the impacts of limited hydrolysis combined with glycation modification on the structure, functional properties, allergenicity, and volatile compounds of silkworm pupae protein, the crude silkworm pupae protein was firstly extracted by alkaline-solution method, followed by Alcalase-treated limited hydrolysis for 10-30 min. Xylose was subsequently added and reacted for 1 h at 95 °C. Afterwards, the structure, functionality, allergenicity, and volatile compounds before and after modification were analysed. The molecular weight of modified silkworm pupae protein was remarkably decreased. The solubility was improved from 4.7 to 28.6%. The foaming ability was elevated by 21%. The in vitro digestibility was elevated by 34.0-44.4%. Furthermore, the abundance of six potential allergic proteins was remarkably reduced. In addition, the contents of off-flavour compounds in modified silkworm pupae proteins substantially decreased. Overall, limited hydrolysis combined with glycation modification can improve the functionality and flavour of silkworm pupae protein, while reduce the allergenicity.</p

Metagenomic reconstructions of caecal microbiome in Landes, Roman and Zhedong White geese

1. The caecal microbiota in geese play a crucial role in determining the host’s health, disease status and behaviour, as evidenced by extensive epidemiological data. The present investigation conducted 10× metagenomic sequencing of caecal content samples obtained from three distinct goose species, namely Landes geese, Roman geese and Zhedong White geese (n = 5), to explore the contribution of the gut microbiome to carbohydrate metabolism. 2. In total, 337GB of Illumina data were generated, which identified 1,048,575 complete genes and construction of 331 metagenomic bins, encompassing 78 species from nine phyla. Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria and Bacteria were identified as the dominant phyla while Prevotella, Bacteroides, Streptococcus, and Subdoligranulum were the most abundant genera in the caecum of geese. 3. The genes were allocated to 375 pathways using the Kyoto Encyclopedia of Genes and Genome (KEGG) analysis. The most abundant classes in the caecum of geese were confirmed to be glycoside hydrolases (GHs), glycosyl transferases (GTs), as identified through the carbohydrate-active enzyme (CAZyme) database mapping. Subdoligranulum variabile and Mediterraneibacter glycyrrhizinilyticus were discovered to potentially facilitate carbohydrate digestion in geese. 4. Notwithstanding, further investigation and validation are required to establish a connection between these species and CAZymes. Based on binning analysis, Mediterraneibacter glycyrrhizinilyticus and Ruminococcus sp. CAG:177 are potential species in LD geese that contribute to the production of fatty liver.</p

Regulation of semaphorin 4D expression and cell proliferation of ovarian cancer by ERalpha and ERbeta

Ovarian cancer is one of the most common malignancies in women. Semaphorin 4D (sema 4D) is involved in the progress of multiple cancers. In the presence of estrogen-like ligands, estrogen receptors (ERα and ERβ) participate in the progress of breast and ovarian cancers by transcriptional regulation. The aim of the study was to investigate the role of sema 4D and elucidate the regulatory pattern of ERα and ERβ on sema 4D expression in ovarian cancers. Sema 4D levels were up-regulated in ovarian cancer SKOV-3 cells. Patients with malignant ovarian cancers had significantly higher sema 4D levels than controls, suggesting an oncogene role of sema 4D in ovarian cancer. ERα expressions were up-regulated in SKOV-3 cells compared with normal ovarian IOSE80 epithelial cells. Conversely, down-regulation of ERβ was observed in SKOV-3 cells. Forced over-expression of ERα and ERβ in SKOV-3 cells was manipulated to establish ERα+ and ERβ+ SKOV-3 cell lines. Incubation of ERα+ SKOV-3 cells with ERs agonist 17β-estradiol (E2) significantly enhanced sema 4D expression and rate of cell proliferation. Incubated with E2, ERβ+ SKOV-3 cells showed lower sema 4D expression and cell proliferation. Blocking ERα and ERβ activities with ICI182-780 inhibitor, sema 4D expressions and cell proliferation of ERα+ and ERβ+ SKOV-3 cells were recovered to control levels. Taken together, the data showed that sema 4D expression was positively correlated with the progress of ovarian cancer. ERα positively regulated sema 4D expression and accelerated cell proliferation. ERβ negatively regulated sema 4D expression and inhibited cell multiplication.</div

DS_10.1177_0022034519864519 – Supplemental material for MiR-361-3p/Nfat5 Signaling Axis Controls Cementoblast Differentiation

Supplemental material, DS_10.1177_0022034519864519 for MiR-361-3p/Nfat5 Signaling Axis Controls Cementoblast Differentiation by H.Q. Liao, H. Liu, H.L. Sun, J.B. Xiang, X.X. Wang, C.X. Jiang, L. Ma and Z.G. Cao in Journal of Dental Research</p

sj-docx-1-jdr-10.1177_00220345211054744 – Supplemental material for Ckip-1 Mediates P. gingivalis–Suppressed Cementoblast Mineralization

Supplemental material, sj-docx-1-jdr-10.1177_00220345211054744 for Ckip-1 Mediates P. gingivalis–Suppressed Cementoblast Mineralization by X. Huang, L. Ma, X. Wang, H. Wang, Y. Peng, X. Gao, H. Huang, Y. Chen, Y. Zhang and Z. Cao in Journal of Dental Research</p

Mechanism of the First Lithiation/Delithiation Process in the Anode Material CoFeOPO₄@C for Li-Ion Batteries

A cobalt iron oxyphosphate CoFeOPO₄@C (abbreviated as CFP@C) anode was prepared via a solid-state route, and its electrochemical performance was investigated vs Li⁺/Li over a wide voltage range of 0.01–3.0 V at different current rates C/<i>n</i> (<i>n</i> = 20, 10, 5, 2, and 1). This anode material is able to intercalate more than six lithium ions into the structure at the C/10 current rate, delivering a specific capacity of 748.23 mAh g^–1, which is much higher than the theoretical capacity (593.7 mAh g^–1) calculated when the insertion of a five lithium ions is considered. A reversible capacity of 200 mAhg^–1 was maintained after 30 cycles. Raman spectroscopy confirmed the incorporation of carbon layers into the CoFeOPO₄@C composite. Scanning electronic microscopy revealed that CFP@C particles have an angular-flake shape with particle sizes ranging between 1 and 5 μm. <i>In situ</i> X-ray absorption spectroscopy of Fe and Co at the K-edge showed that both transition metals are active during the whole discharge and charge. <i>In operando</i> high-energy X-ray diffraction revealed that this material undergoes a gradual evolution of the structure with lower crystallinity after the first discharge. Correlating electrochemical performance to the structural and electronic features indicated that the cycling mechanism of the CFP@C anode material exhibits a combination of intercalation and conversion processes