bluuebunny/crossref_metadata_2025_split huggingface dataset:
Production of a pharmaceutical intermediate via biohydroxylation using whole cells ofRhodococcus rubropertinctusN82
Authors: Kimura Takatoshi , Ishikawa Chihiro , Osorio-Lozada Antonio , Robins Karen T , Hibi Makoto , Ogawa Jun 
Published: June 2014

AbstractRhodococcus rubropertinctus N82 possesses unique regiospecific hydroxylation activity in biotransformation of compounds. In this study, the ability of whole cells of the strain R. rubropertinctus N82 in biotransformation was studied. The hydroxylation activity resulted in transforming 6,7-dihydro-4H-thieno[3,2-c]-pyridine-5-carboxylic acid tert-butyl ester (LS1) into 2-hydroxy-6,7-dihydro-4H-thieno[3,2-c]-pyridine-5-carboxylic acid tert-butyl ester (LP1), a pharmaceutical intermediate. By optimizing conditions for the hydroxylating biotransformation using whole cells of R. rubropertinctus N82 as biocatalyst, 3.3 mM LP1 was successfully produced from 4 mM LS1 with a molar yield of 83%. Thus, effective method was newly developed to produce LP1, which is a synthetic intermediate of a platelet inhibitor active pharmaceutical ingredient drug, prasugrel.
Does the brassinosteroid signal pathway in photomorphogenesis overlap with the gravitropic response caused by auxin?
Authors: Jaroensanti Naiyanate , Yoon Jung-Min , Nakai Yuji , Shirai Ikuya , Otani Masato , Park Seung-Hyun , Hayashi Ken-ichiro , Nakajima Masatoshi , Asami Tadao 
Published: June 2014

AbstractBrassinosteroid (BR) and auxin co-regulate plant growth in a process termed cross-talking. Based on the assumption that their signal transductions are partially shared, inhibitory chemicals for both signal transductions were screened from a commercially available library. A chemical designated as NJ15 (ethyl 2-[5-(3,5-dichlorophenyl)-1,2,3,4-tetrazole-2-yl]acetate) diminished the growth promotion of both adzuki bean epicotyls and Arabidopsis seedlings, by the application of either BR or auxin. To understand its target site(s), bioassays with a high dependence on the signal transduction of either BR (BR-signaling) or auxin (AX-signaling) were performed. NJ15 inhibited the photomorphogenesis of Arabidopsis seedlings grown in the dark, which mainly depends on BR-signaling, while NJ15 also inhibited their gravitropic responses mainly depending on AX-signaling. On the study for the structure–activity relationships of NJ15 analogs, they showed strong correlations on the inhibitory profiles between BR- and AX-signalings. These correlations imply that NJ15 targets the downstream pathway after the integration of BR- and AX-signals.
Effects of deer bone extract on the expression of pro-inflammatory cytokine and cartilage-related genes in monosodium iodoacetate-induced osteoarthritic rats
Authors: Lee Hyunji , Choi Hyeon-Son , Park Yooheon , Ahn Chang Won , Jung Sung Ug , Park Soo Hyun , Suh Hyung Joo 
Published: June 2014

Abstract
Deer bone extract has the potential to relieve the discomfort or the articular cartilaginous damage associated with osteoarthritic (OA) and may be useful as a natural supplement for OA treatment without serious side effects. We analyzed the expression of pro-inflammatory cytokine and cartilage-related genes in monosodium iodoacetate-induced OA rats. Increases in the levels of serum pro-inflammatory cytokines, such as interleukin-1β, interleukin-6, and tumor necrosis factor-α were significantly inhibited by the administration of deer bone extract (p &lt; 0.05). Decreases in the expression of collagen type II (COL2) and tissue inhibitors of metalloproteinases (TIMPs) mRNAs in the cartilage were significantly inhibited by deer bone extract treatment (p &lt; 0.05). The deer bone extract significantly suppressed the expression of matrix metalloproteinases (MMPs) mRNAs in the cartilage. The deer bone extract induced the up-regulation of COL2 and TIMP mRNAs and the down-regulation of MMP mRNAs by suppressing the expression of pro-inflammatory cytokine mRNAs.
Pollen Typhae total flavone improves insulin resistance in high-fat diet and low-dose streptozotocin-induced type 2 diabetic rats
Authors: Feng Xiao-Tao , Chen Qun , Xie Zhen , Liang Xiao , Jiang Ze-Hui , Zhao Wei , Leng Jing 
Published: June 2014

Abstract
Pollen Typhae total flavone (PTF), the extract from Pollen Typhae, is reported to enhance glucose uptake in C2C12 myotubes in vitro, but the convincing evidence is lacking in vivo. In this study, PTF ameliorated insulin resistance and dyslipidemia, but failed to significantly increase body weight in type 2 diabetic rats induced by high-fat diet and low-dose streptozotocin.
The multi-herbal formula Chong-Myung-Tang improves spatial memory and increases cell genesis in the dentate gyrus of aged mice
Authors: Liu Lei , Zhang Mingwei , Zhang Ruifen , Lee Mira , Wang Zhen , Hou Jingang , Sung Chang-Keun 
Published: June 2014

Abstract
Chong-Myung-Tang (CMT) is a multi-herbal formula that has been used to improve memory. However, the potential mechanism remains unknown. The present study investigated the effects of CMT (50, 100, and 200 mg/kg) on spatial memory of aged mice. The behavioral training tests indicated that 200 mg/kg CMT treatment can significantly improve spatial memory of aged mice in the Morris water maze. Moreover, cell survival was examined by injecting bromodeoxyuridine (BrdU) on the first three days. The result showed that 200 mg/kg CMT treatment significantly increased cell survival in the dentate gyrus. Cell proliferation was determined by injecting BrdU 2 h before the mice were killed. The result suggested that CMT treatments had no influence on cell proliferation in the dentate gyrus. Thus, an increase in cell survival in the dentate gyrus stimulated by CMT may be involved in the effect of CMT on spatial memory improvement.
The enhancing effect of fucoidan derived from Undaria pinnatifida on immunoglobulin production by mouse spleen lymphocytes
Authors: Takai Mika , Miyazaki Yoshiyuki , Tachibana Hirofumi , Yamada Koji 
Published: June 2014

Abstract
In this study, we revealed that a Mekabu (Udaria pinnantifida) extract enhanced immunoglobulin (Ig) production of mouse spleen lymphocytes. Furthermore, it was suggested that water-soluble and high molecular weight ingredients in the Mekabu extract have significant enhancing effect on Ig production. Therefore, fucoidan was estimated as the active component.
Late-maturing cooking riceSensyurakuhas excellent properties, equivalent to sake rice, for high-quality sake brewing
Authors: Anzawa Yoshihiko , Satoh Kenji , Satoh Yuko , Ohno Satomi , Watanabe Tsutomu , Katsumata Kazuaki , Kume Kazunori , Watanabe Ken-ichi , Mizunuma Masaki , Hirata Dai 
Published: June 2014

AbstractLow protein content and sufficient grain rigidity are desired properties for the rice used in high-quality sake brewing such as Daiginjo-shu (polishing ratio of the rice, less than 50%). Two kinds of rice, sake rice (SR) and cooking rice (CR), have been used for sake brewing. Compared with those of SR, analyses of CR for high-quality sake brewing using highly polished rice have been limited. Here we described the original screening of late-maturing CR Sensyuraku (SEN) as rice with low protein content and characterization of its properties for high-quality sake brewing. The protein content of SEN was lower than those of SR Gohyakumangoku (GOM) and CR Yukinosei (YUK), and its grain rigidity was higher than that of GOM. The excellent properties of SEN with respect to both water-adsorption and enzyme digestibility were confirmed using a Rapid Visco Analyzer (RVA). Further, we confirmed a clear taste of sake produced from SEN by sensory evaluation. Thus, SEN has excellent properties, equivalent to those of SR, for high-quality sake brewing.
Seal Induced Injuries on Adult Atlantic Salmon Returning to Maine
Authors: Kusnierz Paul C. , Trial Joan G. , Cox Oliver N. , Saunders Rory 
Published: June 2014

Abstract
Seals (Phocidae) are known predators of Atlantic Salmon Salmo salar from their entry into the estuary as smolts until their return to freshwater as adults. We developed a written protocol for identifying seal induced injuries on adult Atlantic Salmon returning to Maine rivers. The protocol, which includes photos and category definitions, has been used since 2006 by Maine Department of Marine Resources biologists when handling adult Atlantic Salmon at the Veazie Dam fishway on the Penobscot River and at other adult capture facilities in Maine. The written protocol has ensured that reporting is consistent among years and rivers; photos of wounds serve as quality assurance for the protocol. For adults returning to the Penobscot River in 2006 and 2007, seal induced injuries were more likely to be found on two sea winter fish; to appear as gashes or arched wounds; to be open rather than healed; and to occur on the center third of the body below the lateral line. Larger two sea winter fish (&gt;67 cm FL) returning to the Penobscot River early in the run (May–early July) were more likely to have a seal induced injury. Injury rates increased from 1978 to 2010; this increase was correlated with seal aerial counts for the Gulf of Maine and Penobscot Bay. From 2006 to 2010, the annual seal induced injury rate for Atlantic Salmon in six Maine rivers (including the Penobscot River) ranged from 0.00 to 0.30 across rivers. Rates of injury on Atlantic Salmon for all years combined did not differ among the six rivers, but low power likely affected our ability to detect any differences.
Received July 25, 2013; accepted February 5, 2014
Impact of fluorescence-guided surgery on the improvement of clinical outcomes in glioblastoma patients
Authors: Kim Sung Kwon , Choi Seung Hong , Kim Yong Hwy , Park Chul-Kee 
Published: June 2014

Abstract

Background
To evaluate the clinical impact of fluorescence-guided surgery (FGS) in glioblastoma, we analyzed the clinical data of 80 consecutive patients operated on by a single surgeon with or without 5-aminolevulinic acid (5-ALA).

Methods
We compared 3-dimensional volumetric extent of resection and clinical outcomes between 40 consecutive patients undergoing resection using a white-light (WL) microscope and 40 subsequent consecutive patients undergoing resection using FGS with 5ALA.

Results
By introducing FGS, there was a significant difference in the mean volumetric extent of the resection rate of T1-enhancing lesions (84.7% in the white-light group and 97.0% in the 5-ALA group, P = .002). The complete resection rate was improved from 43% to 80%, and the proportion of resections that were <80% was reduced from 26% to 4% by FGS. The median progression-free survival was significantly better in the 5-ALA group (18.0 months vs. 6.0 months; P = .001). Although the immediate postoperative functional status was slightly worse in the 5-ALA group, this trend had reversed itself by 3 months postoperatively.

Conclusions
The present study adds practical evidence of the clinical impact of 5-ALA FGS on glioblastomas from the surgeon's standpoint.
Accurate prediction of transmembraneβ-barrel proteins from sequences
Authors: Hayat Sikander , Sander Chris , Elofsson Arne , Marks Debora S. 
Published: June 2014

AbstractTransmembraneβ-barrels are known to play major roles in substrate transport and protein biogenesis in gram-negative bacteria, chloroplasts and mitochondria. However, the exact number of transmembraneβ-barrel families is unknown and experimental structure determination is challenging. In theory, if one knows the number of strands in theβ-barrel, then the 3D structure of the barrel could be trivial, but current topology predictions do not predict accurate structures and are unable to give information beyond theβ-strands in the barrel. Recent work has shown successful prediction of globular and alpha-helical membrane proteins from sequence alignments, by using high ranked evolutionary couplings between residues as distance constraints to fold extended polypeptides. However, these methods, have not addressed the calculation of preciseβ-sheet hydrogen bonding that defines transmembraneβ-barrels, and would be required to fold these proteins successfully. Hence we developed a method (EVFold_BB) that can successfully model transmembraneβ-barrels by combining evolutionary couplings together with topology predictions. EVFold_BB is validated by the accurate all-atom 3D modeling of 18 proteins, representing all known membraneβ-barrel families that have sufficient sequences available. To demonstrate the potential of our approach we predict the unknown 3D structure of the LptD protein, the plausibility of its accuracy is supported by the blindly predicted benchmarks, and is consistent with experimental observations. Our approach can naturally be extended to all unknownβ-barrel proteins with sufficient sequence information.SignificanceEVFold_BB predicts fast, accurate 3D models of large membraneβ-barrels that are notoriously hard to solve experimentally. The major advance is the use of evolutionary couplings from sequence alignments together with theβ-strand prediction to ascertain accurate hydrogen bond between theβ-strands that gives rise to the canonical barrel shapes. The method will enable biological research into outer-membrane proteins.
Converging structural and functional connectivity of orbitofrontal, dorsolateral prefrontal, and posterior parietal cortex in the human striatum
Authors: Jarbo Kevin , Verstynen Timothy D. 
Published: June 2014

AbstractModification of spatial attention via reinforcement learning (Lee & Shomstein, 2013) requires the integration of reward, attention, and executive processes. Corticostriatal pathways are an ideal neural substrate for this integration because these projections exhibit a globally parallel (Alexander, De Long, and Strick, 1985), but locally overlapping (Haber, 2003), topographical organization. Here, we explored whether there are unique striatal regions that exhibit convergent anatomical connections from orbitofrontal cortex (OFC), dorsolateral prefrontal cortex (DLPFC), and posterior parietal cortex. Deterministic fiber tractography on diffusion spectrum imaging data from neurologically healthy adults (N=60) was used to map fronto-and parieto-striatal projections. In general, projections from cortex were organized in a rostral-caudal gradient along the striatal nuclei; however, we also identified two bilateral convergence zones—one in the caudate nucleus and another in the putamen—that consisted of voxels with projections from OFC, DLPFC, and parietal regions. The distributed cortical connectivity of these striatal convergence zones was confirmed with follow-up functional connectivity analysis from resting state fMRI data from 55 of the participants, in which a high percentage (62-80%) of structurally connected voxels also showed significant functional connectivity. These results delineate a neurologically plausible network of converging corticostriatal projections that may support the integration of reward, executive control, and spatial attention that occurs during spatial reinforcement learning.
Genetic Evidence That Chain Length and Branch Point Distributions Are Linked Determinants of Starch Granule Formation in Arabidopsis
Authors: Pfister Barbara , Lu Kuan-Jen , Eicke Simona , Feil Regina , Lunn John E. , Streb Sebastian , Zeeman Samuel C. 
Published: June 2014

Abstract
The major component of starch is the branched glucan amylopectin. Structural features of amylopectin, such as the branching pattern and the chain length distribution, are thought to be key factors that enable it to form semicrystalline starch granules. We varied both structural parameters by creating Arabidopsis (Arabidopsis thaliana) mutants lacking combinations of starch synthases (SSs) SS1, SS2, and SS3 (to vary chain lengths) and the debranching enzyme ISOAMYLASE1-ISOAMYLASE2 (ISA; to alter branching pattern). The isa mutant accumulates primarily phytoglycogen in leaf mesophyll cells, with only small amounts of starch in other cell types (epidermis and bundle sheath cells). This balance can be significantly shifted by mutating different SSs. Mutation of SS1 promoted starch synthesis, restoring granules in mesophyll cell plastids. Mutation of SS2 decreased starch synthesis, abolishing granules in epidermal and bundle sheath cells. Thus, the types of SSs present affect the crystallinity and thus the solubility of the glucans made, compensating for or compounding the effects of an aberrant branching pattern. Interestingly, ss2 mutant plants contained small amounts of phytoglycogen in addition to aberrant starch. Likewise, ss2ss3 plants contained phytoglycogen, but were almost devoid of glucan despite retaining other SS isoforms. Surprisingly, glucan production was restored in the ss2ss3isa triple mutants, indicating that SS activity in ss2ss3 per se is not limiting but that the isoamylase suppresses glucan accumulation. We conclude that loss of only SSs can cause phytoglycogen production. This is readily degraded by isoamylase and other enzymes so it does not accumulate and was previously unnoticed.
Plant functional diversity drives niche‐size‐structure of dominant microbial consumers along a poor to extremely rich fen gradient
Authors: Jassey Vincent E. J. , Lamentowicz Łukasz , Robroek Bjorn J. M. , Gąbka Maciej , Rusińska Anna , Lamentowicz Mariusz 
Published: June 2014

Summary

Plant community composition is recognized more and more for playing an important role in ecosystem processes, such as C cycling. In particular, plant functional type (PFT) composition seems to have a key regulatory role, yet the underlying mechanisms in the interaction between PFTs and ecosystem processes are still to be identified.

Here, we assess the link between PFTs and dominant microbial consumers along a calcareous poor to extremely rich fen gradient in western Poland. We particularly focussed on dominant microbial consumers (testate amoebae), which can exert large effects on the functioning of peatlands. Using moving‐window analyses and path‐relation networks subjected to structural equation modelling (SEM), we investigated linkages among abiotic factors, PFTs and testate amoebae.

We show that along the poor to extremely rich fen gradient, the dependence of testate amoebae to PFTs is higher than their dependence to abiotic factors. We also found that the link between testate amoebae and PFTs differs between size assemblages of testate amoebae. While large testate amoeba species (i.e. high trophic level) were highly linked to Sphagnum mosses cover, small species (i.e. low trophic level) were linked to brown mosses. Distinction between shallow‐rooted and deep‐rooted vascular plants also showed that shallow‐rooted plants play a role on testate amoeba community structure at the ‘poor’ side of the gradient.

Our results further show a dominant role for calcium content and the structure of the bryophyte community on testate amoeba size assemblages at the poor to extremely rich fen scale, both for diversity and abundance of testate amoebae.

Synthesis. Variations in plant functional type composition drive niche‐size‐structure of testate amoebae along the (calcareous) poor to extremely rich fen gradient. Furthermore, strong relationships between moss types and testate amoeba size‐structure suggest that mosses specifically influence testate amoeba development through autogenic effects. Therefore, moss cover composition is key to microbial consumers and may be the driving factor determining microbial network structure and associated ecosystem processes, such as carbon cycling.
Functional attributes of savanna soils: contrasting effects of tree canopies and herbivores on bulk density, nutrients and moisture dynamics
Authors: Holdo Ricardo M. , Mack Michelle C. 
Published: June 2014

Summary

Savannas are highly heterogeneous tree‐grass mixtures, and the structural variation imposed by a discontinuous canopy cover results in spatial variation in soil properties such as plant‐available nutrients, temperature and soil moisture. Many savannas are also dominated by large vertebrate herbivores, which impose a different suite of effects on soil properties related to consumption, excretion and physical disturbance.

In nutrient‐poor, water‐limited systems, variation in soil resource availability may play a fundamental role in structuring plant communities, but the relative and interactive effects of key drivers of heterogeneity have received little attention in savanna ecosystems.

We investigated the independent and interactive effects of herbivores and tree canopy cover on multiple soil properties up to a depth of 10 cm, including bulk density, soil C pools, total and plant‐available nutrients, moisture dynamics and temperature at two contrasting sites in Kruger National Park, South Africa. We analysed samples from locations under and between adult tree canopies and inside and outside long‐term herbivore exclosures using a nested design.

We found strong positive effects of tree canopies on total and labile pools of soil C and N and negative effects on plant‐available P and soil temperature. Tree canopy effects on soil moisture availability were small but clearly detectable. During precipitation events, trees increased moisture inputs on granite soils but decreased moisture inputs on basalt soils compared to open sites.

Conversely, we found mixed evidence for herbivore effects on soil chemistry and temperature, but a clearer effect on soil moisture, with areas outside exclosures experiencing higher soil moisture retention, particularly immediately following precipitation events. Soil bulk density, a driver of both nutrient and soil moisture dynamics, was lower under trees and when herbivores were excluded.

Synthesis. Our results suggest that variation in tree cover is the dominant biotic driver of C, N and P dynamics in these savanna systems in the top 10 cm of soil, that herbivores primarily affect soil moisture content, and that canopy and herbivore effects tend to be additive rather than synergistic.
Bbmsn2 acts as a pH‐dependent negative regulator of secondary metabolite production in the entomopathogenic fungus Beauveria bassiana
Authors: Luo Zhibing , Li Yujie , Mousa Jarrod , Bruner Steven , Zhang Yongjun , Pei Yan , Keyhani Nemat O. 
Published: June 2014

SummaryFungal secondary metabolites are chemical compounds important for development, environmental adaptation and for potential biotechnological and pharmaceutical applications. Oosporein, a red‐pigmented benzoquinone, produced by many fungal insect pathogenic Beauveria spp., shows remarkable functional diversity, displaying antimicrobial, antiviral and even anti‐proliferative activities. A homologue of the msn2/seb1 transcription factor was identified in a Beauveria bassiana random T‐DNA insertion library. Targeted gene‐knockout of Bbmsn2 resulted in reduced growth and increased sensitivity to Calcofluor White, H2O2 and Congo Red. However, when normalized to growth at 26°C, the ΔBbmsn2 mutant was more tolerant to high temperature (32°C) than the wild type parent. The ΔBbmsn2 mutant also displayed a pH‐dependent growth phenotype, with little growth seen at pH < 5.0 but, better growth at alkaline conditions (pH > 8.0). Unexpectedly, a pH‐dependent deregulation of a red pigment, identified as oosporein, was seen in the ΔBbmsn2 mutant. The ΔBbmsn2 strain was impaired in virulence in both topical and intrahaemocoel injection bioassays against Galleria mellonella. ΔBbmsn2 proliferation in the host haemolymph and conidiation on the host cadaver was reduced. These data indicate that Bbmsn2 acts as a negative regulator of oosporein production and contributes to virulence and growth in response to external pH in B. bassiana.