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We establish $L_{q,p}$-estimates and solvability for mixed Dirichlet-conormal problems for parabolic equations in a cylindrical Reifenberg-flat domain with a rough time-dependent separation., minor revision, accepted in Calc. Var. Partial Differential Equations. arXiv admin note: text overlap with arXiv:2101.01654

We study Green functions for the pressure of stationary Stokes systems in a (possibly unbounded) domain $\Omega \subset \mathbb{R}^d$, where $d\ge 2$. We construct the Green function when coefficients are merely measurable in one direction and have Dini mean oscillation in the other directions and $\Omega $ is such that the divergence equation is solvable there. We also establish global pointwise bounds for the Green function and its derivatives when coefficients have Dini mean oscillation and $\Omega $ has a $C^{1,\textrm{Dini}}$ boundary. Green functions for the flow velocity of Stokes systems are also considered.

We study the divergence form second-order elliptic equations with mixed Dirichlet-conormal boundary conditions. The unique $W^{1,p}$ solvability is obtained with $p$ being in the optimal range $(4/3,4)$. The leading coefficients are assumed to have small mean oscillations and the boundary of domain is Reifenberg flat. We also assume that the two boundary conditions are separated by some Reifenberg flat set of co-dimension $2$ on the boundary., 29 pages, submitted

We obtain the regularity of solutions in Sobolev spaces for the mixed Dirichlet-conormal problem for parabolic operators in cylindrical domains with time-dependent separations, which is the first of its kind. Assuming the boundary of the domain to be Reifenberg-flat and the separation to be locally sufficiently close to a Lipschitz function of $m$ variables, where $m=0,\ldots,d-2$, with respect to the Hausdorff distance, we prove the unique solvability for $p\in (2(m+2/(m+3),2(m+2)/(m+1)))$. In the case when $m=0$, the range $p\in(4/3,4)$ is optimal in view of the known results for Laplace equations., 34 pages, to appear in SIAM J. Math. Anal. The original submission was divided into two parts as suggested by the referee. This is the first part

The aim of the study was to investigate the potential of a fucoxanthin concentrate prepared from

We prove the solvability in Sobolev spaces of the conormal derivative problem for the stationary Stokes system with irregular coefficients on bounded Reifenberg flat domains. The coefficients are assumed to be merely measurable in one direction, which may differ depending on the local coordinate systems, and have small mean oscillations in the other directions. In the course of the proof, we use a local version of the Poincar\'e inequality on Reifenberg flat domains, the proof of which is of independent interest.

We establish the existence and the pointwise bound of the fundamental solution for the stationary Stokes system with measurable coefficients in the whole space $\mathbb{R}^d$, $d \ge 3$, under the assumption that weak solutions of the system are locally H\"older continuous. We also discuss the existence and the pointwise bound of the Green function for the Stokes system with measurable coefficients on $\Omega$, where $\Omega$ is an unbounded domain such that the divergence equation is solvable. Such a domain includes, for example, half space and an exterior domain., Comment: 32 pages; accepted in Journal of Differential Equation

The uropathogenic Escherichia coli strain CFT073 contains multiple iron and heme transport systems, which facilitate infection of the host urinary tract. To elucidate the molecular and cellular function of ChuY, a hypothetical gene in the heme degradation/utilization pathway, we solved the crystal structure of ChuY at 2.4 Å resolution. ChuY has high structural homology with human biliverdin and flavin reductase. We confirmed that ChuY has flavin mononucleotide (FMN) reductase activity, using NAD(P)H as a cofactor, and shows porphyrin ring binding affinity. A chuY deletion-insertion strain showed reduced survival potential compared to wild-type and complemented strains in mammalian cells. Current results suggest ChuY acts as a reductase in heme homeostasis to maintain the virulence potential of E. coli CFT073.

Due to the shortage of effective antibiotics against drug-resistant Staphylococcus aureus, new targets are urgently required to develop next-generation antibiotics. We investigated mannitol-1-phosphate dehydrogenase of S. aureus USA300 (SaM1PDH), a key enzyme regulating intracellular mannitol levels, and explored the possibility of using SaM1PDH as a target for developing antibiotic. Since mannitol is necessary for maintaining the cellular redox and osmotic potential, the homeostatic imbalance caused by treatment with a SaM1PDH inhibitor or knockout of the gene encoding SaM1PDH results in bacterial cell death through oxidative and/or mannitol-dependent cytolysis. We elucidated the molecular mechanism of SaM1PDH and the structural basis of substrate and inhibitor recognition by enzymatic and structural analyses of SaM1PDH. Our results strongly support the concept that targeting of SaM1PDH represents an alternative strategy for developing a new class of antibiotics that cause bacterial cell death not by blocking key cellular machinery but by inducing cytolysis and reducing stress tolerance through inhibition of the mannitol pathway., Mannitol-1-phosphate dehydrogenase (M1PDH) is a key enzyme in Staphylococcus aureus mannitol metabolism, but its roles in pathophysiological settings have not been established. We performed comprehensive structure-function analysis of M1PDH from S. aureus USA300, a strain of community-associated methicillin-resistant S. aureus, to evaluate its roles in cell viability and virulence under pathophysiological conditions. On the basis of our results, we propose M1PDH as a potential antibacterial target. In vitro cell viability assessment of ΔmtlD knockout and complemented strains confirmed that M1PDH is essential to endure pH, high-salt, and oxidative stress and thus that M1PDH is required for preventing osmotic burst by regulating pressure potential imposed by mannitol. The mouse infection model also verified that M1PDH is essential for bacterial survival during infection. To further support the use of M1PDH as an antibacterial target, we identified dihydrocelastrol (DHCL) as a competitive inhibitor of S. aureus M1PDH (SaM1PDH) and confirmed that DHCL effectively reduces bacterial cell viability during host infection. To explain physiological functions of SaM1PDH at the atomic level, the crystal structure of SaM1PDH was determined at 1.7-Å resolution. Structure-based mutation analyses and DHCL molecular docking to the SaM1PDH active site followed by functional assay identified key residues in the active site and provided the action mechanism of DHCL. Collectively, we propose SaM1PDH as a target for antibiotic development based on its physiological roles with the goals of expanding the repertory of antibiotic targets to fight antimicrobial resistance and providing essential knowledge for developing potent inhibitors of SaM1PDH based on structure-function studies.

We prove weighted $L_{p,q}$-estimates for divergence type higher order elliptic and parabolic systems with irregular coefficients on Reifenberg flat domains. In particular, in the parabolic case the coefficients do not have any regularity assumptions in the time variable. As functions of the spatial variables, the leading coefficients are permitted to have small mean oscillations. The weights are in the class of Muckenhoupt weights $A_p$. We also prove the solvability of the systems in weighted Sobolev spaces., Comment: the solvability results are improved, references updated; accepted in Calculus of Variations and Partial Differential Equations

We present a new regularity criterion for suitable weak solutions of the one-dimensional surface growth initial-value problem in terms of mixed Lebesgue norms.

Bacterial two-component signal transduction systems are used to adapt to fluctuations in the environment. YycG, a key two-component histidine kinase in Staphylococcus aureus, plays an essential role in cell viability and regulates cell wall metabolism, biofilm formation, virulence, and antibiotic resistance. For these reasons, YycG is considered a compelling target for the development of novel antibiotics. However, to date, the signaling mechanism of YycG and its stimulus are poorly understood mainly because of a lack of structural information on YycG. To address this deficiency, we determined the crystal structure of the extracellular domain of S. aureus YycG (YycGex) at 2.0-Å resolution. The crystal structure indicated two subunits with an extracellular Per-Arnt-Sim (PAS) topology packed into a dimer with interloop interactions. Disulfide scanning using cysteine-substituted mutants revealed that YycGex possessed dimeric interfaces not only in the loop but also in the helix α1. Cross-linking studies using intact YycG demonstrated that it was capable of forming high molecular weight oligomers on the cell membrane. Furthermore, we also observed that two auxiliary proteins of YycG, YycH and YycI, cooperatively interfered with the multimerization of YycG. From these results, we propose that signaling through YycG is regulated by multimerization and binding of YycH and YycI. These structural studies, combined with biochemical analyses, provide a better understanding of the signaling mechanism of YycG, which is necessary for developing novel antibacterial drugs targeting S. aureus.

대한민국 식품의약품안전처(식약처)는 포름알데하이드 분석법으로 2,4-dinitrophenylhydrazine (DNPH) 유도체화-고성능액체크로마토그래프법(HPLC)을 고시하고 있다. 본 연구는 고시법의 복잡한 시료 전처리 과정을 개선하여 화장품 분석에 편리하게 사용할 수 있는 유도체화법을 개발하고자 수행되었다. 전처리법을 간단하게 하기 위하여 pH, 시간 및 온도 등 반응조건을 최적화하였다. 이 전처리법은 초산염 완충액(pH5.0)을 사용한 검액의 pH 조정, 디클로로메탄을 사용한 액-액 분획 그리고 감압농축기를 사용한 증발건조와 같이 식약처 고시법의 복잡한 과정이 필요 없다. 유도체화 과정을 통하여 생성된 formaldehyde dinitrophenylhydrazone (formaldehyde-DNP)는 식약처의 시험방법을 약간 변형한 역상 HPLC법으로 분리하고 정량하였다. 2 ∼ 40 ppm 농도 범위의 표준액들을 가지고 수행한 검량선 작성 결과, 본 시험법은 상관계수 값이 0.9999로 좋은 직선성을 보여주었다. 본 실험의 최소검출한계(LOD)와 최소정량한계(LOQ)는 각각 0.2ppm과 0.5 ppm이었다. 또한 회수율 실험결과는 실험방법이 매우 정확하고 재현성이 높음을 보여주었다. 따라서 본 연구에서 제안된 시험법은 화장품 중 포름알데하이드를 신속하게 분석하는데 적용될 수 있을 것이다.

We prove the existence and pointwise bounds of the Green functions for stationary Stokes systems with measurable coefficients in two dimensional domains. We also establish pointwise bounds of the derivatives of the Green functions under a regularity assumption on the $L_1$-mean oscillations of the coefficients., minor revision; accepted in Journal of Mathematical Analysis and Applications

We study the stationary Stokes system in divergence form. The coefficients are assumed to be merely measurable in one direction and have Dini mean oscillations in the other directions. We prove that if $(u,p)$ is a weak solution of the system, then $(Du,p)$ is bounded and its certain linear combinations are continuous. We also prove a weak type-$(1,1)$ estimate for $(Du,p)$ under a stronger assumption on the $L^1$-mean oscillation of the coefficients. The corresponding results up to the boundary on a half ball are also established. These results are new even for elliptic equations and systems., minor revision; accepted in Journal of Differential Equations

We study Green functions for stationary Stokes systems satisfying the conormal derivative boundary condition. We establish existence, uniqueness, and various estimates for the Green function under the assumption that weak solutions of the Stokes system are continuous in the interior of the domain. Also, we establish the global pointwise bound for the Green function under the additional assumption that weak solutions of the conormal derivative problem for the Stokes system are locally bounded up to the boundary. We provide some examples satisfying such continuity and boundedness properties., Comment: minor revision; accepted in Journal of Mathematical Fluid Mechanics

Urinary-tract infections (UTIs), which are some of the most common infectious diseases in humans, can cause sepsis and death without proper treatment. Therefore, it is necessary to understand their pathogenicity for proper diagnosis and therapeutics. UropathogenicEscherichia coli, the major causative agents of UTIs, contain several genes that are absent in nonpathogenic strains and are therefore considered to be relevant to UTI pathogenicity. c4763 is one of the uropathogenicE. coli-specific proteins, but its function is unknown. To investigate the function of c4763 and its possible role in UTI pathogenicity, its crystal structure was determined at a resolution of 1.45 Å by a multiple-wavelength anomalous diffraction method. c4763 is a homodimer with 129 residues in one subunit that contains a GGCT-like domain with five α-helices and seven β-strands. c4763 shows structural similarity to the C-terminal domain of allophanate hydrolase fromKluyveromyces lactis, which is involved in the degradation of urea. These results suggest that c4763 might be involved in the utilization of urea, which is necessary for bacterial survival in the urinary tract. Further biochemical and physiological investigation will elucidate its functional relevance in UTIs.

The new tuberculosis (TB) lead ecumicin (1), a cyclic tridecapeptide, was isolated from Nonomuraea sp. MJM5123, following a high-throughput campaign for anti-TB activity. The large molecular weight of 1599 amu detected by LC-HR-MS precluded the initial inference of its molecular formula. The individual building blocks were identified by extensive NMR experiments. The resulting two possible planar structures were distinguished by LC-MS(2). Determination of absolute configuration and unambiguous structural confirmation were carried out by X-ray crystallography and Marfey's analysis.

In this study, to evaluate the anti-obesity effects of mulberry leaf tea and its fermented product by Monascus pilosus , we investigated body and organ weight, blood and liver biomarkers in mice fed 1% tea infusionsinstead of water for 8 weeks. Mice were divided into three groups such as a normal control (NC), unfermented mulberry leaf tea infusion (UMI) and fermented mulberry leaf tea infusion (FMI). Although it is not significant, teainfusion groups showed reduction of body weight gains compared with NC group. Moreover, contents of LDL-cholesterol and lipid peroxide (LPO), altherogenic index, and xanthin oxidase (XO) activity were significantlydecreased, and glutathione S-transferase (GST) activity was significantly elevated. The results from this study suggested that UMI and FMI may have an anti-obesity activity, upregulate antioxidant enzymes and reduce levelsof oxidants related to liver damage. Key Words : Antiobese, Fermentation, Monascus pilosuss, Mulberry leaf tea, ROS-scavenging enzymes

In this study, we investigated the preventive effects of the mulberry leaf tea fermented by Monascus pilosus on high fat-induced obesity, hyperlipidemia, and fatty liver in mice. Non-fermented mulberry leaf tea powder (UM) and fermented mulberry leaf tea powder (FM) were supplemented with high-fat diet at 2% (wt/wt) dosage for 8 weeks. Both UM and FM lowered body weight gain, feed efficiency ratio, epididymal fat, serum triglyceride, total cholesterol and LDL-cholesterol increased markedly with high fat diet (HC) in mice. FM showed more significant effects when it was compared with UM. In addition, Hepatic lipid peroxides and xanthin oxidase activities of the UM and FM were significantly lower than those of HC, despite the lack of a big difference in the amount of hepatic GSH. Activities of ROS scavenging enzymes and serum alanine aminotransferase activity were also examined as a parameter of hepatic damage. The UM and FM groups showed a recovery to NC group from significant changes induced by HC. Finally, histopathological analyses of liver samples revealed a decrease of lipid accumulation in hepatocytes in the UM and FM groups. These results suggest that UM and

Miglitol, a well-known therapeutic intervention agents for diabetes, exhibits competitive inhibitory activityagainst α-glucosidase and it is usually produced through three sequential steps including chemical and bioconversionprocesses. Gluconobactor oxydans ( G. oxydans ) belonging to acetic acid bacteria biologically, converts 1-deoxy-1 -(2-hydroxyethylamino)-D-glucitol (P1) into a key intermidiate, 6-(2-hydroxyetyl) amino-6-deoxy-α-L-sorbofuranose (P2) by incomplete oxidation. In this study, we identified and optimized fermentation conditions of CK-2165, that was selected in soil samples by comparing the bioconversion yield. CK-2165 strain was found to be closely relatedto G. oxydans based on the result of phylogenetic analysis using 16S rDNA sequence. Utilization of API 20 kits revealed that this strain could use glucose, mannose, inositol, sorbitol, rhamnose, sucrose, melibiose, amygdalin andarabinose as carbon sources. The culture conditions were optimized for industrial production and several important factors affecting bioconversion rate were also tested using mycelial cake. Cell harvested at the late-stationary phaseshowed the highest bioconversion yield and MgSO

Human tyrosinase (hTyr) catalyzes the first and rate limiting step in the biosynthesis of a skin color determinant, melanin. Although a number of cosmetic companies have tried to develop hTyr inhibitors for severaldecades, absence of 3D structure of hTyr make it impossible to design or screen inhibitors by structure-based approach. Therefore, we built a 3D structure by comparative modeling technique based on the crystal structure of tyrosinase from Bacillus megaterium to provide structural information and to search new hit compounds from database. Our model revealed that two copper atoms of active site located deep inside and were coordinated withsix strictly conserved histidine residues coming from four-helix-bundle. Substrate binding site had narrow funnel likeshape and its entrance was wide and exposed to solvent. In addition, hTyr-tyrosine and hTyr-kojic acid, a well-knowninhibitor, complexes were modeled with the guide of solvent accessible surface generated by in-house software. Our model demonstrated that only phenol group or its analogs could fill the binding site near the nuclear copper center,because inside of binding site had narrow shape relatively. In conclusion, the results of this study may provide helpfulinformation for designing and screening new anti-melanogenic agents.요 약

Background: A Korean herbal medicine, KOTMIN13, composed of Inula japonica Thunberg, Trichosanthes kirilowii Maximowicz var. japonica kitamura, Peucedanum praeruptorum Dunn, and Allium macrostemon Bge, has been used for anti-allergic and anti-asthmatic treatment in oriental clinics, but its activity has not been investigated. Materials and Methods: To evaluate the anti-inflammatory activity of KOTMIN13 for in vitro study, LPS-stimulated RAW 264.7 cells were used to induce the production and expression of inflammatory mediators and its mechanisms. 12-O-Tetradecanoylphorobol-13 aceate (TPA)-induced ear edema and carrageenan-induced paw edema models were also used to evaluate the effect of KOTMIN13 on acute inflammation in vivo. Results: KOTMIN13 reduced the release of inflammatory mediators [nitric oxide, prostaglandin E2, interleukin (IL)-1β, and IL-6] and the protein expression of inducible nitric oxide synthase and cyclooxygenase-2 in LPS-stimulated RAW 264.7 cells. Mechanism studies showed the attenuation of LPS-induced NF-κB activation by KOTMIN13 via IκBα degradation abrogation and a subsequent decrease in nuclear p65 levels. Activation of mitogen-activated protein kinases (ERK, JNK, and p38) was also suppressed. Furthermore, KOTMIN13 ameliorated the development of TPA-induced ear edema and carrageenan-induced paw edema in acute inflammatory edema mouse models. Conclusion: Our study demonstrates that KOTMIN13 inhibits inflammatory mediators through the inhibitions of NF-κB and MAPK activities in LPS-induced RAW 264.7 cells, as well as acute inflammation in edema models, indicating that KOTMIN13 is an effective suppressor for anti-inflammatory activities. SUMMARY KOTMIN13 decrease the production of No, PGE2, and proinflammatory cytokine (TNF-∝, IL-1β,IL-6).KOTMIN13 Suppressed the degradation of NF-kβ and IKβα and the phosorylation of MAP Kinases.Topical application of KOTMIN13 reduced mouse ear edema.Oral administration of KOTMIN13 decreased carrageenan-induced paw edema. Abbreviations used: NO: nitric oxide; PGE2: prostaglandin E2; iNOS: inducible NO synthase; COX-2: cyclooxygenase-2; TNF-α: tumor necrosis factor-α; IL: interleukin; NF-κB: nuclear factor kappaB; MAPK: mitogen-activated protein kinases; ERK: extracellular signal regulated kinase; JNK: c-jun N terminal kinase; TPA: 12-O-tetradecanoylphorbol-13-acetate

In Korea, the effort to include students with disabilities in the educational accountability system has just begun. This paper reviews how Korean students with disabilities have been tested using the National Assessment of Educational Achievement (NAEA) and what issues have emerged as a result of the testing. Analysis of the 2009 and 2010 NAEA data reveals that only a small proportion of students with disabilities participated in these tests and that those who did participate showed low academic achievement compared with general education students. In addition, even though alternate assessments are conducted by special education teachers to assess the academic performance of students with disabilities, national academic assessments in Korea do not include a system for alternate assessment. Based on findings of the analysis, several suggestions are made for improvement in Korea’s educational accountability system for students with disabilities.

Endorepellin, the C-terminal region of perlecan, inhibits angiogenesis by disrupting actin cytoskeleton and focal adhesions. The C-terminal laminin-like globular domain (LG3) of endorepellin directs most of this antiangiogenic activity. To investigate the angiostatic mechanism and to identify structural determinants, we have solved crystal structures of the LG3 domain in both apo- and calcium-bound forms at resolutions of 1.5 Å and 2.8 Å, respectively. The conserved core has the jellyroll fold characteristic of LG domains. The calcium-induced structural changes seem very restricted, and the calcium binding site appears to be preformed, suggesting that the bound calcium ion, rather than structural rearrangements, contributes to antiangiogenesis. We have identified H4268 on the EF loop as a key residue for the biochemical function of LG3, since its mutation abolishes antiangiogenic activity, and mutant LG3 can no longer form a direct interaction with integrin. Taken together, we propose that these two distinct structural elements contribute to the angiostatic effect of endorepellin.

The receptor activator of nuclear factor-κB (RANK) and its ligand RANKL, which belong to the tumor necrosis factor (TNF) receptor-ligand family, mediate osteoclastogenesis. The crystal structure of the RANKL ectodomain (eRANKL) in complex with the RANK ectodomain (eRANK) combined with biochemical assays of RANK mutants indicated that three RANK loops (Loop1, Loop2, and Loop3) bind to the interface of a trimeric eRANKL. Loop3 is particularly notable in that it is structurally distinctive from other TNF-family receptors and forms extensive contacts with RANKL. The disulfide bond (C125-C127) at the tip of Loop3 is important for determining the unique topology of Loop3, and docking E126 close to RANKL, which was supported by the inability of C127A or E126A mutants of RANK to bind to RANKL. Inhibitory activity of RANK mutants, which contain loops of osteoprotegerin (OPG), a soluble decoy receptor to RANKL, confirmed that OPG shares the similar binding mode with RANK and OPG. Loop3 plays a key role in RANKL binding. Peptide inhibitors designed to mimic Loop3 blocked the RANKL-induced differentiation of osteoclast precursors, suggesting that they could be developed as therapeutic agents for the treatment of osteoporosis and bone-related diseases. Furthermore, some of the RANK mutations associated with autosomal recessive osteopetrosis (ARO) resulted in reduced RANKL-binding activity and failure to induce osteoclastogenesis. These results, together with structural interpretation of eRANK-eRANKL interaction, provided molecular understanding for pathogenesis of ARO.

UDP-glucose pyrophosphorylases (UGPase; EC 2.7.7.9) catalyze the conversion of UTP and glucose-1-phosphate to UDP-glucose and pyrophosphate and vice versa. Prokaryotic UGPases are distinct from their eukaryotic counterparts and are considered appropriate targets for the development of novel antibacterial agents since their product, UDP-glucose, is indispensable for the biosynthesis of virulence factors such as lipopolysaccharides and capsular polysaccharides. In this study, the crystal structures of UGPase from Helicobacter pylori (HpUGPase) were determined in apo- and UDP-glucose/Mg(2+)-bound forms at 2.9 A and 2.3 A resolutions, respectively. HpUGPase is a homotetramer and its active site is located in a deep pocket of each subunit. Magnesium ion is coordinated by Asp130, two oxygen atoms of phosphoryl groups, and three water molecules with octahedral geometry. Isothermal titration calorimetry analyses demonstrated that Mg(2+) ion plays a key role in the enzymatic activity of UGPase by enhancing the binding of UGPase to UTP or UDP-glucose, suggesting that this reaction is catalyzed by an ordered sequential Bi Bi mechanism. Furthermore, the crystal structure explains the specificity for uracil bases. The current structural study combined with functional analyses provides essential information for understanding the reaction mechanism of bacterial UGPases, as well as a platform for the development of novel antibacterial agents.

Saccharomyces cerevisiae nTPx is a thioredoxin-dependent thiol peroxidase that is localized in the nucleus. nTPx belongs to the C-type atypical 2-Cys peroxiredoxin family members, which are frequently called BCPs or PrxQs. A double mutant (C107S/C112S) of nTPx overexpressed in Escherichia coli was spontaneously degraded upon freezing and thawing and its truncated form (residues 57-215; MW = 17837 Da) was crystallized with PEG 3350 and mercury(II) acetate as precipitants using the hanging-drop vapour-diffusion method. Diffraction data were collected to 1.8 A resolution using X-ray synchrotron radiation. The crystals belong to the trigonal space group P3(2), with unit-cell parameters a = b = 37.54, c = 83.26 A. The asymmetric unit contains one molecule of truncated mutant nTPx, with a corresponding VM of 1.91 A3 Da(-1) and a solvent content of 35.5%.

The structure of a pectin-bound complex of rhamnogalacturonase was modeled to identify the amino acid residues involved in catalysis and substrate binding. The "hairy" region of pectin, represented by six repeating stretches of (1-->4)-D-galacturonate-(1-->2)-L-rhamnose dimer, was flexibly docked into the putative binding site of rhamnogalacturonase from Aspergillus aculeatus whose X-ray structure is known. A search of the complex configurational space was performed using AutoDock for the dimeric and tetrameric sugar units in which the -1 galacturonate residue has various ring conformations. Then the plausible AutoDock solutions were manually extended to the dodecameric pectin models. Subsequently, the resulting complex models were subjected to solvated molecular dynamics using AMBER. In the best model, the substrate has an extended pseudo-threefold helix with the -1 ring in a 4H3 half-chair that approaches the transition state conformation. The catalytic machinery is clearly defined: Asp197 is a general acid and the activated water bound between Asp177 and Glu198 is a nucleophile. The active site is similar, with a small yet significant difference, to that of polygalacturonase that degrades the pectic "smooth" region of linear homopolymer of D-(1-->4)-linked galacturonic acid. Rhamnogalacturonase has ten binding subsites ranging from -3 to +7, while polygalacturonase has eight subsites from -5 to +3. The model suggests that the eight amino acids including three arginine and three lysine residues, all of which are invariantly conserved in the rhamnogalacturonase family of proteins, are important in substrate binding. The present study may aid in designing mutational studies to characterize rhamnogalacturonase.

Thioredoxin-dependent thiol peroxidase (Tpx) from Escherichia coli represents a group of antioxidant enzymes that are widely distributed in pathogenic bacterial species and which belong to the peroxiredoxin (Prx) family. Bacterial Tpxs are unique in that the location of the resolving cysteine (CR) is different from those of other Prxs. E. coli Tpx (EcTpx) shows substrate specificity toward alkyl hydroperoxides over H2O2 and is the most potent reductant of alkyl hydroperoxides surpassing AhpC and BCP, the other E. coli Prx members. Here, we present the crystal structure of EcTpx in the oxidized state determined at 2.2-A resolution. The structure revealed that Tpxs are the second type of atypical 2-Cys Prxs with an intramolecular disulfide bond formed between the peroxidatic (CP, Cys61) and resolving (Cys95) cysteine residues. The extraordinarily long N-terminal chain of EcTpx folds into a β-hairpin making the overall structure very compact. Modeling suggests that, in atypical 2-Cys Prxs, the CR-loop as well as the CP-loop may alternately assume the fully folded or locally unfolded conformation depending on redox states, as does the CP-loop in typical 2-Cys Prxs. EcTpx exists as a dimer stabilized by hydrogen bonds. Its substrate binding site extends to the dimer interface. A modeled structure of the reduced EcTpx in complex with 15-hydroperoxyeicosatetraenoic acid suggests that the size and shape of the binding site are particularly suited for long fatty acid hydroperoxides consistent with its greater reactivity.

The purpose of this study was to examine the antiobesity effects of Monascus pilosus-fermented black soybean (F-BS) in C57BL/6 mice with high-fat diet (HFD)-induced obesity. F-BS (oral, 0.5 and 1.0 g/kg per body weight, twice per day) ameliorated obesity by reducing body and liver weight increases, and regulating blood glucose and cholesterol levels in C57BL/6 mice fed a control or HFD with oral administration of F-BS for 12 weeks. F-BS suppressed the growth of epididymal, retroperitoneal, and perirenal fat pads by preventing increases in the adipocyte size. Moreover, the levels of blood glucose, total cholesterol, and leptin were significantly lowered by F-BS administration in a dose-dependent manner. These results indicated that F-BS is a beneficial food supplement for preventing obesity, controlling blood glucose, and lowering cholesterol. Future research strategies should address the mechanisms that selectively regulate obesity, including hyperglycemia and hypercholesterolemia.

The aim of this paper is to investigate Green's function for parabolic and elliptic systems satisfying a possibly nonlocal Robin-type boundary condition. We construct Green's function for parabolic systems with time-dependent coefficients satisfying a possibly nonlocal Robin-type boundary condition assuming that weak solutions of the system are locally H\"{o}lder continuous in the interior of the domain, and as a corollary we construct Green's function for elliptic system with a Robin-type condition. Also, we obtain Gaussian bound for Robin Green's function under an additional assumption that weak solutions of Robin problem are locally bounded up to the boundary. We provide some examples satisfying such a local boundedness property, and thus have Gaussian bounds for their Green's functions., Comment: 41 pages, accepted in Journal of Functional Analysis

Escherichia coliSdiA is a quorum-sensing (QS) receptor that responds to autoinducers produced by other bacterial species to control cell division and virulence. Crystal structures reveal thatE. coliSdiA, which is composed of an N-terminal ligand-binding domain and a C-terminal DNA-binding domain (DBD), forms a symmetrical dimer. Although each domain shows structural similarity to other QS receptors, SdiA differs from them in the relative orientation of the two domains, suggesting that its ligand-binding and DNA-binding functions are independent. Consistently, in DNA gel-shift assays the binding affinity of SdiA for theftsQP2 promoter appeared to be insensitive to the presence of autoinducers. These results suggest that autoinducers increase the functionality of SdiA by enhancing the protein stability rather than by directly affecting the DNA-binding affinity. Structural analyses of the ligand-binding pocket showed that SdiA cannot accommodate ligands with long acyl chains, which was corroborated by isothermal titration calorimetry and thermal stability analyses. The formation of an intersubunit disulfide bond that might be relevant to modulation of the DNA-binding activity was predicted from the proximal position of two Cys residues in the DBDs of dimeric SdiA. It was confirmed that the binding affinity of SdiA for theuvrYpromoter was reduced under oxidizing conditions, which suggested the possibility of regulation of SdiA by multiple independent signals such as quorum-sensing inducers and the oxidation state of the cell.

We study the Neumann Green's function for second order parabolic systems in divergence form with time-dependent measurable coefficients in a cylindrical domain $\mathcal{Q}=\Omega\times (-\infty,\infty)$, where $\Omega\subset \mathbb{R}^n$ is an open connected set such that a multiplicative Sobolev embedding inequality holds there. Such a domain includes, for example, a bounded Sobolev extension domain, a special Lipschitz domain, and an unbounded domain with compact Lipschitz boundary. We construct the Neumann Green's function in $\mathcal{Q}$ under the assumption that weak solutions of the systems satisfy an interior H\"older continuity estimate. We also establish global Gaussian bounds for Neumann Green's function under an additional assumption that weak solutions with zero Neumann data satisfy a local boundedness estimate. In the scalar case, such a local boundedness estimate is a consequence of De Giorgi-Moser-Nash theory holds for equations with bounded measurable coefficients in Sobolev extension domains, while in the vectorial case, one may need to impose further regularity assumptions on the coefficients of the system as well as on the domain to obtain such an estimate. We present a unified approach valid for both the scalar and vectorial cases and discuss some applications of our results including the construction of Neumann functions for second order elliptic systems with measurable coefficients in two dimensional domains., Comment: 28 pages, 0 figure; accepted in Journal of Differential Equation

Escherichia coli p20 is a thioredoxin-dependent thiol peroxidase. This protein represents a novel group of antioxidant enzymes that are widely expressed in various pathogenic bacteria and show distant yet significant sequence homology with peroxiredoxins. E. coli p20, overexpressed in E. coli, was crystallized with PEG 4000 and 2-propanol as precipitants using the hanging-drop vapour-diffusion method. Diffraction data were collected to 2.2 A resolution using synchrotron radiation. The crystals belong to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 38.97, b = 58.97, c = 127.59 A. The asymmetric unit contains two p20 molecules, with a corresponding V(M) of 2.06 A(3) Da(-1) and a solvent content of 40.4%.

We study Neumann functions for divergence form, second order elliptic systems with bounded measurable coefficients in a bounded Lipschitz domain or a Lipschitz graph domain. We establish existence, uniqueness, and various estimates for the Neumann functions under the assumption that weak solutions of the system enjoy interior H\"older continuity. Also, we establish global pointwise bounds for the Neumann functions under the assumption that weak solutions of the system satisfy a certain natural local boundedness estimate. Moreover, we prove that such a local boundedness estimate for weak solutions of the system is in fact equivalent to the global pointwise bound for the Neumann function. We present a unified approach valid for both the scalar and the vectorial cases., Comment: 23 pages, 0 figure; accepted in Trans. Amer. Math. Soc