Scientific Reports Biology Table of Contents e-alert: 1 April 2014

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01 April 2014      • Visit Scientific Reports • Submit your manuscript to Scientific Reports     Welcome to your Table of Contents e-alert for Scientific Reports               Biological Sciences               A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing ▶     Jeffrey A. Martin, Nicole V. Johnson, Stephen M. Gross et al.     RNA-sequencing (RNA-seq) enables in-depth exploration of transcriptomes, but typical sequencing depth often limits its comprehensiveness. In this study, we generated nearly 3 …             Pollen sensitivity to ultraviolet-B (UV-B) suggests floral structure evolution in alpine plants ▶     Chan Zhang, Yong-Ping Yang, Yuan-Wen Duan     Various biotic and abiotic factors are known to exert selection pressures on floral traits, but the influence of ultraviolet-B (UV-B) light on the evolution of flower structure …             PSEA: Kinase-specific prediction and analysis of human phosphorylation substrates ▶     Sheng-Bao Suo, Jian-Ding Qiu, Shao-Ping Shi et al.     Protein phosphorylation catalysed by kinases plays crucial regulatory roles in intracellular signal transduction. With the increasing number of kinase-specific phosphorylation …             Predictive combinatorial design of mRNA translation initiation regions for systematic optimization of gene expression levels ▶     Sang Woo Seo, Jae-Seong Yang, Han-Saem Cho et al.     Balancing the amounts of enzymes is one of the important factors to achieve optimum performance of a designed metabolic pathway. However, the random mutagenesis approach is …             Non-random DNA fragmentation in next-generation sequencing ▶     Maria S. Poptsova, Irina A. Il'icheva, Dmitry Yu. Nechipurenko et al.     Next Generation Sequencing (NGS) technology is based on cutting DNA into small fragments, and their massive parallel sequencing. The multiple overlapping segments termed "reads" …             Updating of Attentional and Premotor Allocation Resources as function of previous trial outcome ▶     Antonio Arjona, Miguel Escudero, Carlos M. Gmez     The neural bases of the inter-trial validity/invalidity sequential effects in a visuo-auditory modified version of the Central Cue Posner's Paradigm (CCPP) are analyzed by means …             Alignment-free Visualization of Metagenomic Data by Nonlinear Dimension Reduction ▶     Cedric C. Laczny, Nicols Pinel, Nikos Vlassis et al.     The visualization of metagenomic data, especially without prior taxonomic identification of reconstructed genomic fragments, is a challenging problem in computational biology. An …             Fluorescence-based visualization of autophagic activity predicts mouse embryo viability ▶     Satoshi Tsukamoto, Taichi Hara, Atsushi Yamamoto et al.     Embryo quality is a critical parameter in assisted reproductive technologies. Although embryo quality can be evaluated morphologically, embryo morphology does not correlate …             Real-Time Light Scattering Tracking of Gold Nanoparticles- bioconjugated Respiratory Syncytial Virus Infecting HEp-2 Cells ▶     Xiao-Yan Wan, Lin-Ling Zheng, Peng-Fei Gao et al.     Real-time tracking of virus invasion is crucial for understanding viral infection mechanism, which, however, needs simple and efficient labeling chemistry with improved …             Inertial particle separation by differential equilibrium positions in a symmetrical serpentine micro-channel ▶     Jun Zhang, Sheng Yan, Ronald Sluyter et al.     This paper presents an inertial microfluidic device with a simple serpentine micro-channel to continuously separate particles with high performance. Separation of …             A key role for neuropeptide Y in lifespan extension and cancer suppression via dietary restriction ▶     Takuya Chiba, Yukari Tamashiro, Daeui Park et al.     Knowledge of genes essential for the life-extending effect of dietary restriction (DR) in mammals is incomplete. In this study, we found that neuropeptide Y (Npy), which mediates …             Isolation of microplastics in biota-rich seawater samples and marine organisms ▶     Matthew Cole, Hannah Webb, Pennie K. Lindeque et al.     Microplastic litter is a pervasive pollutant present in aquatic systems across the globe. A range of marine organisms have the capacity to ingest microplastics, resulting in …             Validation of microinjection methods for generating knockout mice by CRISPR/Cas-mediated genome engineering ▶     Takuro Horii, Yuji Arai, Miho Yamazaki et al.     The CRISPR/Cas system, in which the Cas9 endonuclease and a guide RNA complementary to the target are sufficient for RNA-guided cleavage of the target DNA, is a powerful new …             Variants near CHRNB3-CHRNA6 are associated with DSM-5 cocaine use disorder: evidence for pleiotropy ▶     Brooke Sadler, Gabe Haller, Arpana Agrawal et al.     In the U.S.A., cocaine is the second most abused illicit drug. Variants within the CHRNB3-A6 gene cluster have been associated with cigarette consumption in several GWAS. These …             Nitrogen and water availability to tomato plants triggers bottom-up effects on the leafminer Tuta absoluta ▶     Peng Han, Anne-Violette Lavoir, Jacques Le Bot et al.     This study examined the effects of various levels of nitrogen inputs (optimal, insufficient and excessive) and water inputs (optimal, low drought and high drought) to tomato …             Discovery of a super-strong promoter enables efficient production of heterologous proteins in cyanobacteria ▶     Jie Zhou, Haifeng Zhang, Hengkai Meng et al.     Cyanobacteria are oxygenic photosynthetic prokaryotes that play important roles in the global carbon cycle. Recently, engineered cyanobacteria capable of producing various small …             Increased expression of p62/SQSTM1 in prion diseases and its association with pathogenic prion protein ▶     Takujiro Homma, Daisuke Ishibashi, Takehiro Nakagaki et al.     Prion diseases are neurodegenerative disorders characterized by the aggregation of abnormally folded prion protein (PrPSc). In this study, we focused on the mechanism of clearance …             Green Light Synergistally Enhances Male Sweetpotato Weevil Response to Sex Pheromone ▶     Grant T. McQuate     Sweetpotato, commercially grown in over 100 countries, is one of the ten most important staple crops in the world. Sweetpotato weevil is a major pest of sweetpotato in most areas …             Tumor Lysing Genetically Engineered T Cells Loaded with Multi-Modal Imaging Agents ▶     Parijat Bhatnagar, Mian Alauddin, James A. Bankson et al.     Genetically-modified T cells expressing chimeric antigen receptors (CAR) exert anti-tumor effect by identifying tumor-associated antigen (TAA), independent of major …             A potent and Kv1.3-selective analogue of the scorpion toxin HsTX1 as a potential therapeutic for autoimmune diseases ▶     M. Harunur Rashid, Redwan Huq, Mark R. Tanner et al.     HsTX1 toxin, from the scorpion Heterometrus spinnifer, is a 34-residue, C-terminally amidated peptide cross-linked by four disulfide bridges. Here we describe new HsTX1 analogues …             Exogenous expression of marine lectins DlFBL and SpRBL induces cancer cell apoptosis possibly through PRMT5-E2F-1 pathway ▶     Liqin Wu, Xinyan Yang, Xuemei Duan et al.     Lectins are widely existed in marine bioresources, and some purified marine lectins were found toxic to cancer cells. In this report, genes encoding Dicentrarchus labrax …             Statistical physics approach to quantifying differences in myelinated nerve fibers ▶     César H. Comin, João R. Santos, Dario Corradini et al.     We present a new method to quantify differences in myelinated nerve fibers. These differences range from morphologic characteristics of individual fibers to differences in …             CRISPR/Cas9 mediated multiplex genome editing and heritable mutagenesis of BmKu70 in Bombyx mori ▶     Sanyuan Ma, Jiasong Chang, Xiaogang Wang et al.     CRISPR/Cas9, a bacterial adaptive immune system derived genome-editing technique, has become to be one of the most compelling topics in biotechnology. Bombyx mori is an …             Active transport of vesicles in neurons is modulated by mechanical tension ▶     Wylie W. Ahmed, Taher A. Saif     Effective intracellular transport of proteins and organelles is critical in cells, and is especially important for ensuring proper neuron functionality. In neurons, most proteins …             Identification and Characterization of a Suite of Tumor Targeting Peptides for Non-Small Cell Lung Cancer ▶     Michael J. McGuire, Bethany Powell Gray, Shunzi Li et al.     Tumor targeting ligands are emerging components in cancer therapies. Widespread use of targeted therapies and molecular imaging is dependent on increasing the number of high …             Noncanonical Wnt5a enhances Wnt/-catenin signaling during osteoblastogenesis ▶     Masanori Okamoto, Nobuyuki Udagawa, Shunsuke Uehara et al.     Wnt regulates bone formation through -catenin-dependent canonical and -independent noncanonical signaling pathways. However, the cooperation that exists between the two signaling …             Pretreatment with chemotherapeutics for enhanced nanoparticles accumulation in tumor: the potential role of G2 cycle retention effect ▶     Huile Gao, Guanlian Hu, Qianyu Zhang et al.     Ligands were anchored onto nanoparticles (NPs) to improve the cell internalization and tumor localization of chemotherapeutics. However, the clinical application was shadowed by …             Ecto-5-Nucleotidase (CD73) Regulates Host Inflammatory Responses and Exacerbates Murine Salmonellosis ▶     M. Samiul Alam, Jennifer L. Kuo, Peter B. Ernst et al.     Food-borne Salmonella spp., are a major cause of hospitalization and death. Adenosine, an important immune regulator of inflammation, limits tissue damage during infection. CD39 …             Detection of Termites and Other Insects Consumed by African Great Apes using Molecular Fecal Analysis ▶     Ibrahim Hamad, Eric Delaporte, Didier Raoult et al.     The consumption of insects by apes has previously been reported based on direct observations and/or trail signs in feces. However, DNA-based diet analyses may have the potential …             Sequential acquisition of multi-dimensional heteronuclear chemical shift correlation spectra with 1H detection ▶     Peter Bellstedt, Yvonne Ihle, Christoph Wiedemann et al.     RF pulse schemes for the simultaneous acquisition of heteronuclear multi-dimensional chemical shift correlation spectra, such as {HA(CA)NH & HA(CACO)NH}, {HA(CA)NH & H(N)CAHA} and …             Endodermal differentiation of human pluripotent stem cells to insulin-producing cells in 3D culture ▶     Hiroki Takeuchi, Norio Nakatsuji, Hirofumi Suemori     Insulin-producing cells (IPCs) derived from human pluripotent stem cells (hPSCs) may be useful in cell therapy and drug discovery for diabetes. Here, we examined various growth …             Herceptin Resistance Database for Understanding Mechanism of Resistance in Breast Cancer Patients ▶     Sahil Ahmad, Sudheer Gupta, Rahul Kumar et al.     Monoclonal antibody Trastuzumab/Herceptin is considered as frontline therapy for Her2-positive breast cancer patients. However, it is not effective against several patients due to …             Modelling mutational landscapes of human cancers in vitro ▶     Magali Olivier, Annette Weninger, Maude Ardin et al.     Experimental models that recapitulate mutational landscapes of human cancers are needed to decipher the rapidly expanding data on human somatic mutations. We demonstrate that …             Chinese Grain for Green Program led to highly increased soil organic carbon levels: A meta-analysis ▶     Xinzhang Song, Changhui Peng, Guomo Zhou et al.     The Grain for Green Program (GGP), initiated in 1999, is the largest ecological restoration project in central and western China. Here, for the first time, we performed a …             Degradation of 4-chloro-3-nitrophenol via a novel intermediate, 4-chlororesorcinol by Pseudomonas sp. JHN ▶     Pankaj Kumar Arora, Alok Srivastava, Vijay Pal Singh     A 4-chloro-3-nitrophenol (4C3NP)-mineralizing bacterium, Pseudomonas sp. JHN was isolated from a waste water sample collected from a chemically-contaminated area, India by an …             GeneSense: a new approach for human gene annotation integrated with protein-protein interaction networks ▶     Zhongzhong Chen, Tianhong Zhang, Jun Lin et al.     Virtually all cellular functions involve protein-protein interactions (PPIs). As an increasing number of PPIs are identified and vast amount of information accumulated, …             High-yield novel leech hyaluronidase to expedite the preparation of specific hyaluronan oligomers ▶     Peng Jin, Zhen Kang, Na Zhang et al.     Hyaluronidases (HAases), particularly leech HAases, have attracted intense attention due to their broad applications in medical treatments and great potential for the enzymatic …             Snail modulates the assembly of fibronectin via α5 integrin for myocardial migration in zebrafish embryos ▶     Liangjun Qiao, Hongwei Gao, Ting Zhang et al.     The Snail family member snail encodes a zinc finger-containing transcriptional factor that is involved in heart formation. Yet, little is known about how Snail regulates heart …             Super-resolution microscopy reveals decondensed chromatin structure at transcription sites ▶     Yejun Wang, Shovamayee Maharana, Michelle D. Wang et al.     Remodeling of the local chromatin structure is essential for the regulation of gene expression. While a number of biochemical and bioimaging experiments suggest decondensed …             Type IV collagen α1-chain noncollagenous domain blocks MMP-2 activation both in-vitro and in-vivo ▶     Yakkanti Akul Sudhakar, Raj Kumar Verma, Smita C. Pawar     α1(IV)NC1 inhibits angiogenesis by regulating MAPK activation, this biological function was partly attributed α1(IV)NC1 binding to α1β1-integrin. However, its potent …             Highly dynamic animal contact network and implications on disease transmission ▶     Shi Chen, Brad J. White, Michael W. Sanderson et al.     Contact patterns among hosts are considered as one of the most critical factors contributing to unequal pathogen transmission. Consequently, networks have been widely applied in …             Heat stress induces apoptosis through transcription-independent p53-mediated mitochondrial pathways in human umbilical vein endothelial cell ▶     Z. T. Gu, H. Wang, L. Li et al.     Cells apoptosis induced by intense heat stress is the prominent feature of heat-related illness. However, little is known about the biological effects of heat stress on cells …             Structure of the substrate-binding b′ domain of the Protein disulfide isomerase-like protein of the testis ▶     Sara Bastos-Aristizabal, Guennadi Kozlov, Kalle Gehring     Protein Disulfide Isomerase-Like protein of the Testis (PDILT) is a testis-specific member of the PDI family. PDILT displays similar domain architecture to PDIA1, the founding …             A novel, visible light-induced, rapidly cross-linkable gelatin scaffold for osteochondral tissue engineering ▶     Tetsuro Mazaki, Yasuyuki Shiozaki, Kentaro Yamane et al.     Osteochondral injuries remain difficult to repair. We developed a novel photo-cross-linkable furfurylamine-conjugated gelatin (gelatin-FA). Gelatin-FA was rapidly cross-linked by …             Accelerating Forest Growth Enhancement due to Climate and Atmospheric Changes in British Colombia, Canada over 1956-2001 ▶     Chaoyang Wu, Robbie A. Hember, Jing M. Chen et al.     Changes in climate and atmospheric CO2 and nitrogen (N) over the last several decades have induced significant effects on forest carbon (C) cycling. However, contributions of …             Hydrogel microfluidics for the patterning of pluripotent stem cells ▶     S. Cosson, M. P. 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