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https://www.readbyqxmd.com/read/28087653/identification-of-regulatory-networks-and-hub-genes-controlling-soybean-seed-set-and-size-using-rna-sequencing-analysis
#1
Juan Du, Shoudong Wang, Cunman He, Bin Zhou, Yong-Ling Ruan, Huixia Shou
To understand the gene expression networks controlling soybean seed set and size, transcriptome analyses were performed in three early seed developmental stages, using two genotypes with contrasting seed size. The two-dimensional data set provides a comprehensive and systems-level view on dynamic gene expression networks underpinning soybean seed set and subsequent development. Using pairwise comparisons and weighted gene coexpression network analyses, we identified modules of coexpressed genes and hub genes for each module...
January 13, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28087515/h-blast-a-fast-protein-sequence-alignment-toolkit-on-heterogeneous-computers-with-gpus
#2
Weicai Ye, Ying Chen, Yongdong Zhang, Yuesheng Xu
MOTIVATION: The sequence alignment is a fundamental problem in bioinformatics. BLAST is a routinely used tool for this purpose with over 118 000 citations in the past two decades. As the size of bio-sequence databases grows exponentially, the computational speed of alignment softwares must be improved. RESULTS: We develop the heterogeneous BLAST (H-BLAST), a fast parallel search tool for a heterogeneous computer that couples CPUs and GPUs, to accelerate BLASTX and BLASTP-basic tools of NCBI-BLAST...
January 13, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28079290/clamped-hybridization-chain-reactions-for-the-self-assembly-of-patterned-dna-hydrogels
#3
Jianbang Wang, Jie Chao, Huajie Liu, Shao Su, Lianhui Wang, Wei Huang, Itamar Willner, Chunhai Fan
DNA hydrogels hold great potential for biological and biomedical applications owing to their programmable nature and macroscopic sizes. However, most previous studies involve spontaneous and homogenous gelation procedures in solution, which often lack precise control. A clamped hybridization chain reaction (C-HCR)-based strategy has been developed to guide DNA self-assembly to form macroscopic hydrogels. Analogous to catalysts in chemical synthesis or seeds in crystal growth, we introduced DNA initiators to induce the gelation process, including crosslinked self-assembly and clamped hybridization in three dimensions with spatial and temporal control...
January 12, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28078380/imaging-features-of-hepatic-sarcomatous-carcinoma-on-computed-tomography-and-gadoxetic-acid-enhanced-magnetic-resonance-imaging
#4
Kyo-Won Gu, Young Kon Kim, Ji Hye Min, Sang Yun Ha, Woo Kyoung Jeong
PURPOSE: To determine the imaging features of hepatic sarcomatous carcinoma including sarcomatous intrahepatic cholangiocarcinoma (S-ICC) and sarcomatous hepatocellular carcinoma (S-HCC) on computed tomography (CT) and gadoxetic acid-enhanced magnetic resonance imaging (MRI). MATERIALS AND METHODS: Twenty-four patients with pathologically confirmed S-ICCs (n = 13), S-HCCs (n = 7), sarcomatous carcinoma (n = 2), carcinosarcoma (n = 1), and sarcomatous combined HCC-CC (n = 1) (size range 2...
January 12, 2017: Abdominal Radiology
https://www.readbyqxmd.com/read/28075555/familial-mutations-may-switch-conformational-preferences-in-%C3%AE-synuclein-fibrils
#5
Liang Xu, Buyong Ma, Ruth Nussinov, Damien Thompson
The pathogenesis of Parkinson's disease is closely associated with the aggregation of the α-synuclein protein. Several familial mutants have been identified and shown to affect the aggregation kinetics of α-synuclein through distinct molecular mechanisms. Quantitative evaluation of the relative stabilities of the wild type and mutant fibrils is crucial for understanding the aggregation process and identifying the key component steps. In this work, we examined two topologically different α-synuclein fibril structures that are either determined by solid-state NMR method or modelled based on solid-state NMR data, and characterized their conformational properties and thermodynamic stabilities using molecular dynamics simulations...
January 11, 2017: ACS Chemical Neuroscience
https://www.readbyqxmd.com/read/28075047/growing-larger-with-domestication-a-matter-of-physiology-morphology-or-allocation
#6
R Milla, S Matesanz
• Domestication might affect plant size. We investigated whether herbaceous crops are larger than their wild progenitors, and the traits that influence size variation. • We grew six crop plants and their wild progenitors under common garden conditions. We measured the aboveground biomass gain by individual plants during the vegetative stage. We then tested whether the photosynthesis rate, biomass allocation to leaves, leaf size, and specific leaf area (SLA) accounted for variations in whole-plant photosynthesis, and ultimately in aboveground biomass...
January 11, 2017: Plant Biology
https://www.readbyqxmd.com/read/28071733/an-automated-method-for-large-scale-monitoring-of-seed-dispersal-by-ants
#7
Audrey Bologna, Etienne Toffin, Claire Detrain, Alexandre Campo
Myrmecochory is the process of seed dispersal by ants; however, it is highly challenging to study, mainly because of the small size of both partners and the comparatively large range of dispersal. The mutualistic interaction between ants and seeds involves the former retrieving diaspores, consuming their elaiosome (a nutrient-rich appendage), and the rejection of seeds from the nest. Here, we introduce a semi-automated method based on stitching high resolution images together, allowing the study of myrmecochory in a controlled environment over time...
January 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28070272/impact-of-temperature-shifts-on-the-joint-evolution-of-seed-dormancy-and-size
#8
Yang Liu, Sébastien Barot, Yousry A El-Kassaby, Nicolas Loeuille
Seed dormancy and size are two important life-history traits that interplay as adaptation to varying environmental settings. As evolution of both traits involves correlated selective pressures, it is of interest to comparatively investigate the evolution of the two traits jointly as well as independently. We explore evolutionary trajectories of seed dormancy and size using adaptive dynamics in scenarios of deterministic or stochastic temperature variations. Ecological dynamics usually result in unbalanced population structures, and temperature shifts or fluctuations of high magnitude give rise to more balanced ecological structures...
January 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28069694/myocardial-tissue-engineering-with-cells-derived-from-human-induced-pluripotent-stem-cells-and-a-native-like-high-resolution-3-dimensionally-printed-scaffold
#9
Ling Gao, Molly Kupfer, Jangwook Jung, Libang Yang, Patrick Zhang, Yong Sie, Quyen Tran, Visar Ajeti, Brian Freeman, Vladimir Fast, Paul Campagnola, Brenda Ogle, Jianyi Zhang
RATIONALE: Conventional three-dimensional (3D) printing techniques cannot produce structures of the size at which individual cells interact. OBJECTIVE: Here, we used multiphoton-excited, 3-dimensional printing (MPE-3DP) to generate a native-like, extracellular matrix (ECM) scaffold with submicron resolution, and then seeded the scaffold with cardiomyocytes (CMs), smooth-muscle cells (SMCs), and endothelial cells (ECs) that had been differentiated from human induced-pluripotent stem cells (iPSCs) to generate a human, iPSC-derived cardiac muscle patch (hCMP), which was subsequently evaluated in a murine model of myocardial infarction (MI)...
January 9, 2017: Circulation Research
https://www.readbyqxmd.com/read/28068913/microrna-157-targeted-spl-genes-regulate-floral-organ-size-and-ovule-production-in-cotton
#10
Nian Liu, Lili Tu, Lichen Wang, Haiyan Hu, Jiao Xu, Xianlong Zhang
BACKGROUND: microRNAs (miRNAs) have been involved in regulation of diverse spectrum of plant development processes in many species. In cotton, few miRNAs have been well characterised in floral organ development. Floral organ, which should be finely tuned, is a crucial factor affecting the yield of cotton. Therefore, it is well worth revealing the function of miRNAs in regulation of floral organ development. Here, we report the role of miRNA156/157 in regulation of floral organ size in cotton...
January 10, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28067252/two-step-amyloid-aggregation-sequential-lag-phase-intermediates
#11
Fabio Castello, Jose M Paredes, Maria J Ruedas-Rama, Miguel Martin, Mar Roldan, Salvador Casares, Angel Orte
The self-assembly of proteins into fibrillar structures called amyloid fibrils underlies the onset and symptoms of neurodegenerative diseases, such as Alzheimer's and Parkinson's. However, the molecular basis and mechanism of amyloid aggregation are not completely understood. For many amyloidogenic proteins, certain oligomeric intermediates that form in the early aggregation phase appear to be the principal cause of cellular toxicity. Recent computational studies have suggested the importance of nonspecific interactions for the initiation of the oligomerization process prior to the structural conversion steps and template seeding, particularly at low protein concentrations...
January 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28066993/developing-a-biomimetic-tooth-bud-model
#12
Elizabeth E Smith, Weibo Zhang, Nathan R Schiele, Ali Khademhosseini, Catherine K Kuo, Pamela C Yelick
A long-term goal is to bioengineer, fully functional, living teeth for regenerative medicine and dentistry applications. Biologically based replacement teeth would avoid insufficiencies of the currently used dental implants. Using natural tooth development as a guide, a model was fabricated using post-natal porcine dental epithelial (pDE), porcine dental mesenchymal (pDM) progenitor cells, and human umbilical vein endothelial cells (HUVEC) encapsulated within gelatin methacrylate (GelMA) hydrogels. Previous publications have shown that post-natal DE and DM cells seeded onto synthetic scaffolds exhibited mineralized tooth crowns composed of dentin and enamel...
January 8, 2017: Journal of Tissue Engineering and Regenerative Medicine
https://www.readbyqxmd.com/read/28065925/small-genomes-and-large-seeds-chromosome-numbers-genome-size-and-seed-mass-in-diploid-aesculus-species-sapindaceae
#13
Anna Krahulcová, Pavel Trávníček, František Krahulec, Marcel Rejmánek
BACKGROUND AND AIMS: Aesculus L. (horse chestnut, buckeye) is a genus of 12-19 extant woody species native to the temperate Northern Hemisphere. This genus is known for unusually large seeds among angiosperms. While chromosome counts are available for many Aesculus species, only one has had its genome size measured. The aim of this study is to provide more genome size data and analyse the relationship between genome size and seed mass in this genus. METHODS: Chromosome numbers in root tip cuttings were confirmed for four species and reported for the first time for three additional species...
January 8, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28064561/the-effects-of-water-absorption-and-roasting-conditions-on-fracture-properties-and-internal-structure-of-sesame-seeds
#14
Nakako Katsuno, Makoto Fujimura, Akira Hanya, Takahisa Nishizu
We investigated the effects of soaking, residence time before roasting and roasting conditions on the fracture properties and structure of the cross-section of sesame seeds. Soaking time affected only the size of the side voids of the seed cross-section. The fracture force and strain of the roasted seeds decreased as residence time increased. The center void of the roasted seeds, important for seed crispness increased as residence time increased. In contrast, the side void of the roasted seeds only increased with residence time during the first 10 min...
January 9, 2017: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/28062196/radiotherapeutic-and-surgical-management-of-iris-melanoma-a-review
#15
REVIEW
Marko Popovic, Iqbal Ike K Ahmed, Julia DiGiovanni, Carol L Shields
We compare outcomes following radiotherapeutic and surgical management of iris melanoma. Endpoints included local tumor recurrence, metastases, and common complications. From an initial search that yielded 231 articles, we found 17 relevant studies with 761 eyes. The gender distribution was balanced with a mean age of 52 years. Most studies focused on either proton beam (49.4%) or plaque (31.4%) radiotherapy. Rates of local recurrence (range: 0-8%) and metastatic development (0-5%) were favorable following radiotherapy; however, common complications included cataract (36-73%), glaucoma (3-92%) and corneal conditions (0-33%)...
January 3, 2017: Survey of Ophthalmology
https://www.readbyqxmd.com/read/28056183/cell-seeded-autologous-chondrocyte-implantation
#16
Andreas H Gomoll, Amy Phan, Marissa Mastrocola, Luiz Felipe Ambra, Nehal Shah
BACKGROUND: The use of autologous chondrocyte implantation (ACI) remains limited, even though multiple studies have demonstrated success rates exceeding 75%. The procedure is perceived as invasive and technically challenging, presenting barriers to more widespread adoption. Purpose/Hypothesis: The objective of this study was to investigate whether outcomes and the failure rate of a simplified ACI technique (cs-ACI) were comparable with those of the more complicated traditional technique of a chondrocyte suspension injected under a collagen membrane (cACI)...
December 1, 2016: American Journal of Sports Medicine
https://www.readbyqxmd.com/read/28051180/human-heart-valve-derived-scaffold-improves-cardiac-repair-in-a-murine-model-of-myocardial-infarction
#17
Long Wan, Yao Chen, Zhenhua Wang, Weijun Wang, Sebastian Schmull, Jun Dong, Song Xue, Hans Imboden, Jun Li
Cardiac tissue engineering using biomaterials with or without combination of stem cell therapy offers a new option for repairing infarcted heart. However, the bioactivity of biomaterials remains to be optimized because currently available biomaterials do not mimic the biochemical components as well as the structural properties of native myocardial extracellular matrix. Here we hypothesized that human heart valve-derived scaffold (hHVS), as a clinically relevant novel biomaterial, may provide the proper microenvironment of native myocardial extracellular matrix for cardiac repair...
January 4, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28049374/needle-track-seeding-after-percutaneous-radiofrequency-ablation-of-hepatocellular-carcinoma-14-year-experience-at-a-single-center
#18
Zhong-Yi Zhang, Wei Yang, Kun Yan, Ying Dai, Wei Wu, Jung-Chieh Lee, Min-Hua Chen
PURPOSE: To determine the incidence, risk factors and prognosis associated with needle track seeding after percutaneous radiofrequency ablations(RFA) for hepatocellular carcinoma(HCC) with a long-term follow-up. MATERIALS AND METHODS: 741 HCC patients undergoing percutaneous RFA were retrospectively analyzed. Mean follow-up interval was 34.3±26.8 months. All seeding neoplasms were diagnosed by imaging modalities with or without pathological evaluation. Risk factors, including Child-Pugh grading, tumor size, number, location, serum AFP level, track number, biopsy before RFA and electrode type were performed by univariate analysis...
January 3, 2017: International Journal of Hyperthermia
https://www.readbyqxmd.com/read/28048746/su-f-t-46-the-effect-of-inter-seed-attenuation-and-tissue-composition-in-prostate-125i-brachytherapy-dose-calculations
#19
K Tamura, F Araki, T Ohno
PURPOSE: To investigate the difference of dose distributions with/without the effect of inter-seed attenuation and tissue compositions in prostate (125) I brachytherapy dose calculations, using Monte Carlo simulations of Particle and Heavy Ion Transport code System (PHITS). METHODS: The dose distributions in (125) I prostate brachytherapy were calculated using PHITS for non-simultaneous and simultaneous alignments of STM1251 sources in water or prostate phantom for six patients...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28048540/we-de-201-04-cross-validation-of-knowledge-based-treatment-planning-for-prostate-ldr-brachytherapy-using-principle-component-analysis
#20
J Roper, B Ghavidel, V Chanyavanich, K Godette, E Schreibmann
PURPOSE: To validate a knowledge-based algorithm for prostate LDR brachytherapy treatment planning. METHODS: A dataset of 100 cases was compiled from an active prostate seed implant service. Cases were randomized into 10 subsets. For each subset, the 90 remaining library cases were registered to a common reference frame and then characterized on a point by point basis using principle component analysis (PCA). Each test case was converted to PCA vectors using the same process and compared with each library case using a Mahalanobis distance to evaluate similarity...
June 2016: Medical Physics
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