bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhancing the expression of starch synthase class IV results in increased levels of both transitory and long‐term storage starch
Authors: Gámez‐Arjona Francisco M. , Li Jun , Raynaud Sandy , Baroja‐Fernández Edurne , Muñoz Francisco J. , Ovecka Miroslav , Ragel Paula , Bahaji Abdellatif , Pozueta‐Romero Javier , Mérida Ángel 
Published: June 2011

SummaryStarch is an important renewable raw material with an increasing number of applications. Several attempts have been made to obtain plants that produce modified versions of starch or higher starch yield. Most of the approaches designed to increase the levels of starch have focused on the increment of the amount of ADP‐glucose or ATP available for starch biosynthesis. In this work, we show that the overexpression of starch synthase class IV (SSIV) increases the levels of starch accumulated in the leaves of Arabidopsis by 30%–40%. In addition, SSIV‐overexpressing lines display a higher rate of growth. The increase in starch content as a consequence of enhanced SSIV expression is also observed in long‐term storage starch organs such as potato tubers. Overexpression of SSIV in potato leads to increased tuber starch content on a dry weight basis and to increased yield of starch production in terms of tons of starch/hectare. These results identify SSIV as one of the regulatory steps involved in the control of the amount of starch accumulated in plastids.
Discovery of polymorphisms in starch‐related genes in rice germplasm by amplification of pooled DNA and deeply parallel sequencing†
Authors: Kharabian‐Masouleh Ardashir , Waters Daniel L. E. , Reinke Russell F. , Henry Robert J. 
Published: June 2011

SummaryHigh‐throughput sequencing of pooled DNA was applied to polymorphism discovery in candidate genes involved in starch synthesis. This approach employed semi‐ to long‐range PCR (LR‐PCR) followed by next‐generation sequencing technology. A total of 17 rice starch synthesis genes encoding seven classes of enzymes, including ADP‐glucose pyrophosphorylase (AGPase), granule starch synthase (GBSS), soluble starch synthase (SS), starch branching enzyme (BE), starch debranching enzyme (DBE) and starch phosphorylase (SPHOL) and phosphate translocator (GPT1) from 233 genotypes were PCR amplified using semi‐ to long‐range PCR. The amplification products were equimolarly pooled and sequenced using massively parallel sequencing technology (MPS). By detecting single nucleotide polymorphism (SNP)/Indels in both coding and noncoding areas of the genes, we identified genetic differences and characterized the SNP/Indel variation and distribution patterns among individual starch candidate genes. Approximately, 60.9 million reads were generated, of which 54.8 million (90%) mapped to the reference sequences. The average coverage rate ranged from 12 708 to 38 300 times for SSIIa and SSIIIb, respectively. SNPs and single/multiple‐base Indels were analysed in a total assembled length of 116 403 bp. In total, 501 SNPs and 113 Indels were detected across the 17 starch‐related loci. The ratio of synonymous to nonsynonymous SNPs (Ka/Ks) test indicated GBSSI and isoamylase 1 (ISA1) as the least diversified (most purified) and conservative genes as the studied populations have been through cycles of selection. This report demonstrates a useful strategy for screening germplasm by MPS to discover variants in a specific target group of genes.
Visualization of 3D osteon morphology by synchrotron radiation micro‐CT
Authors: Cooper D. M. L. , Erickson B. , Peele A.G. , Hannah K. , Thomas C. D. L. , Clement J. G. 
Published: June 2011

AbstractCortical bone histology has been the subject of scientific inquiry since the advent of the earliest microscopes. Histology – literally the study of tissue – is a field nearly synonymous with 2D thin sections. That said, progressive developments in high‐resolution X‐ray imaging are enabling 3D visualization to reach ever smaller structures. Micro‐computed tomography (micro‐CT), employing conventional X‐ray sources, has become the gold standard for 3D analysis of trabecular bone and is capable of detecting the structure of vascular (osteonal) porosity in cortical bone. To date, however, direct 3D visualization of secondary osteons has eluded micro‐CT based upon absorption‐derived contrast. Synchrotron radiation micro‐CT, through greater image quality, resolution and alternative contrast mechanisms (e.g. phase contrast), holds great potential for non‐destructive 3D visualization of secondary osteons. Our objective was to demonstrate this potential and to discuss areas of bone research that can be advanced through the application of this approach. We imaged human mid‐femoral cortical bone specimens derived from a 20‐year‐old male (Melbourne Femur Collection) at the Advanced Photon Source synchrotron (Chicago, IL, USA) using the 2BM beam line. A 60‐mm distance between the target and the detector was employed to enhance visualization of internal structures through propagation phase contrast. Scan times were 1 h and images were acquired with 1.4‐μm nominal isotropic resolution. Computer‐aided manual segmentation and volumetric 3D rendering were employed to visualize secondary osteons and porous structures, respectively. Osteonal borders were evident via two contrast mechanisms. First, relatively new (hypomineralized) osteons were evident due to differences in X‐ray attenuation relative to the surrounding bone. Second, osteon boundaries (cement lines) were delineated by phase contrast. Phase contrast also enabled the detection of soft tissue remnants within the vascular pores. The ability to discern osteon boundaries in conjunction with vascular and cellular porosity revealed a number of secondary osteon morphologies and provided a unique 3D perspective of the superimposition of secondary osteons on existing structures. Improvements in resolution and optimization of the propagation phase contrast promise to provide further improvements in structural detail in the future.
Scan patterns when viewing natural scenes: Emotion, complexity, and repetition
Authors: Bradley Margaret M. , Houbova Petra , Miccoli Laura , Costa Vincent D. , Lang Peter J. 
Published: June 2011

AbstractEye movements were monitored during picture viewing, and effects of hedonic content, perceptual composition, and repetition on scanning assessed. InExperiment 1, emotional and neutral pictures that were figure‐ground compositions or more complex scenes were presented for a 6‐s free viewing period. Viewing emotional pictures or complex scenes prompted more fixations and broader scanning of the visual array, compared to neutral pictures or simple figure‐ground compositions. Effects of emotion and composition were independent, supporting the hypothesis that these oculomotor indices reflect enhanced information seeking.Experiment 2tested an orienting hypothesis by repeatedly presenting the same pictures. Although repetition altered specific scan patterns, emotional, compared to neutral, picture viewing continued to prompt oculomotor differences, suggesting that motivationally relevant cues enhance information seeking in appetitive and defensive contexts.
Calcitonin and calcitonin receptor‐like receptors: common themes with family B GPCRs?
Authors: Barwell James , Gingell Joseph J , Watkins Harriet A , Archbold Julia K , Poyner David R , Hay Debbie L 
Published: June 2011

The calcitonin receptor (CTR) and calcitonin receptor‐like receptor (CLR) are two of the 15 human family B (or Secretin‐like) GPCRs. CTR and CLR are of considerable biological interest as their pharmacology is moulded by interactions with receptor activity‐modifying proteins. They also have therapeutic relevance for many conditions, such as osteoporosis, diabetes, obesity, lymphatic insufficiency, migraine and cardiovascular disease. In light of recent advances in understanding ligand docking and receptor activation in both the family as a whole and in CLR and CTR specifically, this review reflects how applicable general family B GPCR themes are to these two idiosyncratic receptors. We review the main functional domains of the receptors; the N‐terminal extracellular domain, the juxtamembrane domain and ligand interface, the transmembrane domain and the intracellular C‐terminal domain. Structural and functional findings from the CLR and CTR along with other family B GPCRs are critically appraised to gain insight into how these domains may function. The ability for CTR and CLR to interact with receptor activity‐modifying proteins adds another level of sophistication to these receptor systems but means careful consideration is needed when trying to apply generic GPCR principles. This review encapsulates current thinking in the realm of family B GPCR research by highlighting both conflicting and recurring themes and how such findings relate to two unusual but important receptors, CTR and CLR.LINKED ARTICLES This article is part of a themed section on Secretin Family (Class B) G Protein‐Coupled Receptors. To view the other articles in this section visit http://dx.doi.org/10.1111/bph.2012.166.issue‐1
Rapid healing of chronic venous stasis leg ulcers treated by the application of a novel serum‐free cultured autologous epidermis
Authors: Wille John J. , Burdge Jeremy J. , Pitttelkow Mark R. 
Published: June 2011

ABSTRACTThe efficacy and durability of wound closure was examined in a prospective randomized unbalanced clinical trial using the application of a living serum‐free cultured epidermal autograft in conjunction with wound‐area debridement and a four‐layer compression wrap (N=10) compared with wound‐area debridement and a four‐layer compression wrap in patients with hard‐to‐heal leg ulcers arising from confirmed venous stasis (N=5). All 15 patients who presented with full‐thickness venous ulceration were treated weekly for 8 weeks, with a 12‐week final evaluation. The average time to wound closure for the grafted wounds was 4.1 weeks for 80% (8/10) of the cases that closed in 12 weeks compared with 12 weeks for the one closed in the control case. All of the grafted wounds remained closed at 12‐month follow‐up and one more healed at 30 weeks postenrollment. In the control group, one additional wound healed at 21 weeks postenrollment after the placement of an autograft. No serious adverse events were reported and subjective pain assessment was substantially reduced immediately after graft application. The graft treatment significantly improved outcome and provided durable wound closure. The data suggest that this adaption of this procedure may reduce the management costs of these wound types.
Enhancement of flap survival and changes in angiogenic gene expression after AAV2‐mediated VEGF gene transfer to rat ischemic flaps
Authors: Wang Xiao Tian , Avanessian Bella , Ma Qiangzhong , Durfee Heather , Tang Yu Qing , Liu Paul Y. 
Published: June 2011

ABSTRACTNecrosis of surgically transferred flaps due to ischemia is a serious wound problem. We evaluated the improvement of flap survival and changes in angiogenic gene expression profiles after transfer of the VEGF gene by means of adeno‐associated virus type 2 (AAV2) vector to rat ischemic flaps. Thirty rats were divided into one experimental group, one AAV2‐GFP group, and one saline group. AAV2‐VEGF or AAV2‐GFP were injected intradermally into the rat dorsum in the AAV2‐VEGF or AAV2‐GFP group. The saline group received saline injection. A 3 × 10 cm flap was raised in each rat two weeks post‐injection. One week after surgery, flap viability was evaluated. Angiogenesis real‐time PCR array was performed to analyze the expression of angiogenesis‐associated genes. The AAV2‐VEGF treatment significantly improved flap survival (p<0.05). Immunohistochemical staining showed increased VEGF expression in AAV2‐VEGF treated flaps. The PCR array identified remarkable changes in 6 out of the 84 angiogenesis‐associated genes in AAV2‐VEGF treated flaps. Particularly, EGF, PDGF‐A and VEGF‐B genes were up‐regulated in these flaps. In contrast, FGF2 gene expression was down‐regulated. In conclusion, AAV2‐VEGF improves flap survival and affects the expression of a series of endogenous growth factor genes, which likely play critical roles in the enhancement of ischemic flap survival.
Sequential use of human‐derived medium supplements favours cardiovascular tissue engineering
Authors: Vis Paul W. Riem , Sluijter Joost P. G. , Soekhradj‐Soechit R. Sarita , van Herwerden Lex A. , Kluin Jolanda , Bouten Carlijn V. C. 
Published: June 2011

AbstractFor clinical application of tissue engineering strategies, the use of animal‐derived serum in culture medium is not recommended, because it can evoke immune responses in patients. We previously observed that human platelet‐lysate (PL) is favourable for cell expansion, but generates weaker tissue as compared to culture in foetal bovine serum (FBS). We investigated if human serum (HS) is a better human supplement to increase tissue strength. Cells were isolated from venous grafts of 10 patients and expanded in media supplemented with PL or HS, to determine proliferation rates and expression of genes related to collagen production and maturation. Zymography was used to assess protease expression. Collagen contraction assays were used as a two‐dimensional (2D) model for matrix contraction. As a prove of principle, 3D tissue culture and tensile testing was performed for two patients, to determine tissue strength. Cell proliferation was lower in HS‐supplemented medium than in PL medium. The HS cells produced less active matrix metallo‐proteinase 2 (MMP2) and showed increased matrix contraction as indicated by gel contraction assays and 3D‐tissue culture. Tensile testing showed increased strength for tissues cultured in HS when compared to PL. This effect was more pronounced if cells were sequentially cultured in PL, followed by tissue culture in HS. These data suggest that sequential use of PL and HS as substitutes for FBS in culture medium for cardiovascular tissue engineering results in improved cell proliferation and tissue mechanical properties, as compared to use of PL or HS apart.
Role of Slug transcription factor in human mesenchymal stem cells
Authors: Torreggiani Elena , Lisignoli Gina , Manferdini Cristina , Lambertini Elisabetta , Penolazzi Letizia , Vecchiatini Renata , Gabusi Elena , Chieco Pasquale , Facchini Andrea , Gambari Roberto , Piva Roberta 
Published: June 2011

AbstractThe pathways that control mesenchymal stem cells (MSCs) differentiation are not well understood, and although some of the involved transcription factors (TFs) have been characterized, the role of others remains unclear. We used human MSCs from tibial plateau (TP) trabecular bone, iliac crest (IC) bone marrow and Wharton’s jelly (WJ) umbilical cord demonstrating a variability in their mineral matrix deposition, and in the expression levels of TFs including Runx2, Sox9, Sox5, Sox6, STAT1 and Slug, all involved in the control of osteochondroprogenitors differentiation program. Because we reasoned that the basal expression level of some TFs with crucial role in the control of MSC fate may be correlated with osteogenic potential, we considered the possibility to affect the hMSCs behaviour by using gene silencing approach without exposing cells to induction media. In this study we found that Slug‐silenced cells changed in morphology, decreased in their migration ability, increased Sox9 and Sox5 and decreased Sox6 and STAT1 expression. On the contrary, the effect of Slug depletion on Runx2 was influenced by cell type. Interestingly, we demonstrated a direct in vivo regulatory action of Slug by chromatin immunoprecipitation, showing a specific recruitment of this TF in the promoter of Runx2 and Sox9 genes. As a whole, our findings have important potential implication on bone tissue engineering applications, reinforcing the concept that manipulation of specific TF expression levels may elucidate MSC biology and the molecular mechanisms, which promote osteogenic differentiation.
Angiotensin II receptor type 1 blockade decreases CTGF/CCN2‐mediated damage and fibrosis in normal and dystrophic skeletal muscles
Authors: Cabello‐Verrugio Claudio , Morales María Gabriela , Cabrera Daniel , Vio Carlos P. , Brandan Enrique 
Published: June 2011

AbstractConnective tissue growth factor (CTGF/CCN‐2) is mainly involved in the induction of extracellular matrix (ECM) proteins. The levels of CTGF correlate with the degree and severity of fibrosis in many tissues, including dystrophic skeletal muscle. The CTGF overexpression in tibialis anterior skeletal muscle using an adenoviral vector reproduced many of the features observed in dystrophic muscles including muscle damage and regeneration, fibrotic response and decrease in the skeletal muscle strength. The renin–angiotensin system is involved in the genesis and progression of fibrotic diseases through its main fibrotic components angiotensin‐II and its transducer receptor AT‐1. The use of AT‐1 receptor blockers (ARB) has been shown to decrease fibrosis. In this paper, we show the effect of AT‐1 receptor blockade on CTGF‐dependent biological activity in skeletal muscle cells as well as the response to CTGF overexpression in normal skeletal muscle. Our results show that in myoblasts ARB decreased CTGF‐mediated increase of ECM protein levels, extracellular signal regulated kinases 1/2 (ERK‐1/2) phosphorylation and stress fibres formation. In tibialis anterior muscle overexpressing CTGF using an adenovirus, ARB treatment decreased CTGF‐mediated increase of ECM molecules, α‐SMA and ERK‐1/2 phosphorylation levels. Quite remarkable, ARB was able to prevent the loss of contractile force of tibialis anterior muscles overexpressing CTGF. Finally, we show that ARB decreased the levels of fibrotic proteins, CTGF and ERK‐1/2 phosphorylation augmented in a dystrophic skeletal muscle from mdx mice. We propose that ARB is a novel pharmacological tool that can be used to decrease the fibrosis induced by CTGF in skeletal muscle associated with muscular dystrophies.
Characterization of human‐type monoclonal antibodies against reduced form of hemin binding protein 35 from Porphyromonas gingivalis
Authors: Shibata Y. , Okano S. , Shiroza T. , Tahara T. , Nakazawa K. , Kataoka S. , Ishida I. , Kobayashi T. , Yoshie H. , Abiko Y. 
Published: June 2011

Shibata Y, Okano S, Shiroza T, Tahara T, Nakazawa K, Kataoka S, Ishida I, Kobayashi T, Yoshie H, Abiko Y. Characterization of human‐type monoclonal antibodies against reduced form of hemin binding protein 35 from Porphyromonas gingivalis. J Periodont Res 2011; 46: 673–681. © 2011 John Wiley & Sons A/SBackground and Objective:  The gram‐negative anaerobe Porphyromonas gingivalis has been implicated as an important pathogen in the development of adult periodontitis, and its colonization of subgingival sites is critical in the pathogenic process. We previously identified a 35 kDa surface protein (hemin binding protein 35; HBP35) from P. gingivalis that exhibited coaggregation activity, while additional analysis suggested that this protein possessed an ability to bind heme molecules. For development of passive immunotherapy for periodontal diseases, human‐type monoclonal antibodies have been prepared using HBP35 as an antigen in TransChromo mice. In the present study, we focused on a single antibody, TCmAb‐h13, which is known to inhibit heme binding to recombinant HBP35. The aim of our investigation was to clarify the redox‐related function of HBP35 and consider the benefits of human‐type monoclonal antibodies.Material and Methods:  To examine the antigen recognition capability of TCmAbs with immunoblotting and Biacore techniques, we used the native form as well as several Cys‐to‐Ser variants of recombinant HBP35.Results:  We found that the redox state of recombinant HBP35 was dependent on two Cys residues, 48C and 51C, in the thioredoxin active center (WCGxCx). Furthermore, TCmAb‐h13 recognized the reduced forms of recombinant HBP35, indicating its inhibitory effect on P. gingivalis growth.Conclusion:  Hemin binding protein 35 appears to be an important molecule involved in recognition of the redox state of environmental conditions. In addition, TCmAb‐h13 had an inhibitory effect on heme binding to recombinant HBP35, thereby interfering with P. gingivalis growth.
Body composition measured by dual‐energy X‐ray absorptiometry half‐body scans in obese children
Authors: Breithaupt P , Colley RC , Adamo KB 
Published: June 2011

AbstractAim:  To perform a methods comparison of a left or right half‐body scan versus whole‐body scan for measuring body composition in a sample of obese children.Methods:  A group of obese children (n = 58; ≥95th BMI percentile; 8–18 years) were required to undergo a dual‐energy X‐ray absorptiometry (DXA) body composition measurement as part of an ongoing cohort study; 34 fit within the imaging field of the DXA scanner and were eligible for inclusion in the present analysis. Percent fat, total mass, fat mass, lean mass and bone mineral content (BMC) were estimated from half‐body scans and compared with the whole‐body results. Assessment was completed using GE enCORE 11.40 software.Results:  In comparing left‐ and right‐side scans to whole‐body scans, there was significant correlation for all body composition variables (p ≤ 0.005, R2 = 0.996–1.0). Bland Altman analyses also showed high levels of agreement between half‐body estimates and whole‐body measurements.Conclusion:  This study supports using a half‐body scan methodology for percent fat, total mass, fat mass, lean mass, and BMC as a valid alternative to full‐body analysis in obese children and youth.
N-Terminal Probrain Natriuretic Peptide as a Biomarker of Cardioembolic Stroke
Authors: Fonseca Ana Catarina , Matias Joaquim Sampaio , e Melo Teresa Pinho , Falcão Filipa , Canhão Patrícia , Ferro José M. 
Published: June 2011

Background and purpose N-terminal probrain natriuretic peptide, which is mainly produced by the heart, is increased in acute stroke. We aimed to determine if N-terminal probrain natriuretic peptide could be a biomarker for ischemic stroke with a cardioembolic cause. Methods Consecutive sample of acute stroke patients admitted to a Stroke Unit. Ischemic stroke subtype was classified using the TOAST classification. Blood samples were drawn within 72 h after stroke onset. Serum N-terminal probrain natriuretic peptide concentration was measured using an electrochemiluminescence immunoassay. Mean values of N-terminal probrain natriuretic peptide were compared between patients with hemorrhagic stroke vs. ischemic stroke, cardioembolic stroke vs. noncardioembolic stroke, cardioembolic stroke with atrial fibrillation vs. noncardioembolic stroke using t-test. Receiver operating characteristic curves were used to test the ability of N-terminal probrain natriuretic peptide values to identify cardioembolic stroke and cardioembolic stroke with atrial fibrillation. Results Ninety-two patients were included (66 with ischemic stroke) with a mean age of 58·6 years. Twenty-eight (42·4%) ischemic strokes had a cardioembolic cause. Mean N-terminal probrain natriuretic peptide values for cardioembolic stroke were significantly higher ( P < 0·001) (491·6; 95% confidence interval 283·7–852·0 pg/ml) than for noncardioembolic ischemic stroke (124·7; 86·3–180·2 pg/ml). The area under the receiver operating characteristic curve for N-terminal probrain natriuretic peptide in cardioembolic stroke was 0·77. The cut-off point with the highest sensitivity and specificity was set at 265·5 pg/ml (71·4% and 73·7% respectively). The area under the curve of N-terminal probrain natriuretic peptide for cardioembolic stroke related to atrial fibrillation was 0·92, cut-off was set at 265·5 pg/ml (sensitivity 94·4%, specificity 72·9%). Conclusion N-terminal probrain natriuretic peptide is a biomarker with a good accuracy to predict ischemic stroke of cardioembolic cause, namely associated with atrial fibrillation.