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  • 1
    Publication Date: 2009-03-28
    Description: Similarities in the behavior of diverse animal species that form large groups have motivated attempts to establish general principles governing animal group behavior. It has been difficult, however, to make quantitative measurements of the temporal and spatial behavior of extensive animal groups in the wild, such as bird flocks, fish shoals, and locust swarms. By quantifying the formation processes of vast oceanic fish shoals during spawning, we show that (i) a rapid transition from disordered to highly synchronized behavior occurs as population density reaches a critical value; (ii) organized group migration occurs after this transition; and (iii) small sets of leaders significantly influence the actions of much larger groups. Each of these findings confirms general theoretical predictions believed to apply in nature irrespective of animal species.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Makris, Nicholas C -- Ratilal, Purnima -- Jagannathan, Srinivasan -- Gong, Zheng -- Andrews, Mark -- Bertsatos, Ioannis -- Godo, Olav Rune -- Nero, Redwood W -- Jech, J Michael -- New York, N.Y. -- Science. 2009 Mar 27;323(5922):1734-7. doi: 10.1126/science.1169441.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA. makris@mit.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19325116" target="_blank"〉PubMed〈/a〉
    Keywords: Animal Migration ; Animals ; Atlantic Ocean ; *Behavior, Animal ; Ecosystem ; Fishes/*physiology ; Population Density ; Reproduction ; Spatial Behavior ; *Swimming ; Time Factors
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2010-10-23
    Description: Appropriate preferences for light or dark conditions can be crucial for an animal's survival. Innate light preferences are not static in some animals, including the fruit fly Drosophila melanogaster, which prefers darkness in the feeding larval stage but prefers light in adulthood. To elucidate the neural circuit underlying light preference, we examined the neurons involved in larval phototactic behavior by regulating neuronal functions. Modulating activity of two pairs of isomorphic neurons in the central brain switched the larval light preference between photophobic and photophilic. These neurons were found to be immediately downstream of pdf-expressing lateral neurons, which are innervated by larval photoreceptors. Our results revealed a neural mechanism that could enable the adjustment of animals' response strategies to environmental stimuli according to biological needs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gong, Zhefeng -- Liu, Jiangqu -- Guo, Chao -- Zhou, Yanqiong -- Teng, Yan -- Liu, Li -- New York, N.Y. -- Science. 2010 Oct 22;330(6003):499-502. doi: 10.1126/science.1195993.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China. zfgong@moon.ibp.ac.cn〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20966250" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Behavior, Animal/*radiation effects ; Brain/cytology/physiology ; Drosophila melanogaster/cytology/growth & development/*radiation effects ; Green Fluorescent Proteins ; Larva/physiology/radiation effects ; *Light ; Neural Pathways ; Neurons/*physiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2012-06-16
    Description: Active DNA demethylation is an important part of epigenetic regulation in plants and animals. How active DNA demethylation is regulated and its relationship with histone modification patterns are unclear. Here, we report the discovery of IDM1, a regulator of DNA demethylation in Arabidopsis. IDM1 is required for preventing DNA hypermethylation of highly homologous multicopy genes and other repetitive sequences that are normally targeted for active DNA demethylation by Repressor of Silencing 1 and related 5-methylcytosine DNA glycosylases. IDM1 binds methylated DNA at chromatin sites lacking histone H3K4 di- or trimethylation and acetylates H3 to create a chromatin environment permissible for 5-methylcytosine DNA glycosylases to function. Our study reveals how some genes are indicated by multiple epigenetic marks for active DNA demethylation and protection from silencing.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3575687/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3575687/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Qian, Weiqiang -- Miki, Daisuke -- Zhang, Heng -- Liu, Yunhua -- Zhang, Xi -- Tang, Kai -- Kan, Yunchao -- La, Honggui -- Li, Xiaojie -- Li, Shaofang -- Zhu, Xiaohong -- Shi, Xiaobing -- Zhang, Kangling -- Pontes, Olga -- Chen, Xuemei -- Liu, Renyi -- Gong, Zhizhong -- Zhu, Jian-Kang -- R01 GM059138/GM/NIGMS NIH HHS/ -- R01 GM070795/GM/NIGMS NIH HHS/ -- R01GM059138/GM/NIGMS NIH HHS/ -- R01GM070795/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Jun 15;336(6087):1445-8. doi: 10.1126/science.1219416.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Shanghai Center for Plant Stress Biology and Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22700931" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation ; Arabidopsis/*genetics/*metabolism ; Arabidopsis Proteins/chemistry/genetics/*metabolism ; Chromatin/metabolism ; DNA Glycosylases/metabolism ; *DNA Methylation ; DNA, Plant/*metabolism ; Gene Silencing ; Genes, Plant ; Histone Acetyltransferases/chemistry/genetics/*metabolism ; Histones/metabolism ; Methylation ; Mutation ; Nuclear Proteins/genetics/metabolism ; Protein Structure, Tertiary ; Transgenes
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2012-08-08
    Description: Contact: zyhe@dlut.edu.cn
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 5
    Publication Date: 2018-03-06
    Description: Fuchs’ endothelial corneal dystrophy (FECD) is the most common repeat expansion disorder. FECD impacts 4% of U.S. population and is the leading indication for corneal transplantation. Most cases are caused by an expanded intronic CUG tract in the TCF4 gene that forms nuclear foci, sequesters splicing factors and impairs splicing. We investigated the sense and antisense RNA landscape at the FECD gene and find that the sense-expanded repeat transcript is the predominant species in patient corneas. In patient tissue, sense foci number were negatively correlated with age and showed no correlation with sex. Each endothelial cell has ∼2 sense foci and each foci is single RNA molecule. We designed antisense oligonucleotides (ASOs) to target the mutant-repetitive RNA and demonstrated potent inhibition of foci in patient-derived cells. Ex vivo treatment of FECD human corneas effectively inhibits foci and reverses pathological changes in splicing. FECD has the potential to be a model for treating many trinucleotide repeat diseases and targeting the TCF4 expansion with ASOs represents a promising therapeutic strategy to prevent and treat FECD.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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  • 6
    Publication Date: 2013-06-14
    Description: Endogenous and exogenous factors can induce DNA damage, leading to increased risk of cancer. Nucleotide excision repair (NER) is considered as the most versatile DNA repair pathway to deal with a variety of different DNA lesions. ERCC1 and ERCC2 are the two important proteins in NER pathway. In this study, we investigated the association of three functional single nucleotide polymorphisms (SNPs) ( ERCC1 rs11615, ERCC2 rs13181 and ERCC2 rs1799793) with the clinical outcome of 940 gastric cancer patients in a Chinese population. Multiplex SNaPshot technology was used to genotype these three SNPs. Our results revealed that individuals with ERCC2 rs13181TG/GG genotypes had a decreased risk of death compared with those with TT genotype [log-rank P = 0.008; adjusted hazard ratio = 0.68, 95% confidence interval = 0.51–0.91] and this protective effect was more pronounced among the subgroups of patients with tumour size ≤ 5cm (0.59, 0.39–0.89), non-cardia gastric tumour (0.69, 0.48–0.98), no lymph node metastasis (0.55, 0.32–0.96), no distant metastasis (0.70, 0.52–0.95) and chemotherapy (0.39, 0.21–0.72). We conclude that ERCC2 rs13181 polymorphism could play different roles in the overall survival of gastric cancer. Further larger studies should be conducted to validate our findings.
    Print ISSN: 0267-8357
    Electronic ISSN: 1464-3804
    Topics: Biology , Medicine
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  • 7
    Publication Date: 2012-12-14
    Description: Long non-coding RNAs (lncRNAs) that have no protein-coding capacity make up a large proportion of the transcriptome of various species. Many lncRNAs are expressed within the animal central nervous system in spatial- and temporal-specific patterns, indicating that lncRNAs play important roles in cellular processes, neural development, and even in cognitive and behavioral processes. However, relatively little is known about their in vivo functions and underlying molecular mechanisms in the nervous system. Here, we report a neural-specific Drosophila lncRNA, CASK regulatory gene ( CRG ), which participates in locomotor activity and climbing ability by positively regulating its neighboring gene CASK (Ca 2+ /calmodulin-dependent protein kinase). CRG deficiency led to reduced locomotor activity and a defective climbing ability—phenotypes that are often seen in CASK mutant. CRG mutant also showed reduced CASK expression level while CASK over-expression could rescue the CRG mutant phenotypes in reciprocal. At the molecular level, CRG was required for the recruitment of RNA polymerase II to the CASK promoter regions, which in turn enhanced CASK expression. Our work has revealed new functional roles of lncRNAs and has provided insights to explore the pathogenesis of neurological diseases associated with movement disorders.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 8
    Publication Date: 2014-04-23
    Description: Hybridization and polyploidization are prominent processes in plant evolution. Hybrids and allopolyploids typically exhibit radically altered gene expression patterns relative to their parents, a phenomenon termed "transcriptomic shock." To distinguish the effects of hybridization from polyploidization on coregulation of divergent alleles, we analyzed expression of parental copies (homoeologs) of 11,608 genes using RNA-seq-based transcriptome profiling in reciprocal hybrids and tetraploids constructed from subspecies japonica and indica of Asian rice ( Oryza sativa L.). The diploid hybrids and their derived allopolyploids differ dramatically in morphology, despite having the same suite of genes and genic proportions. Allelic and homoeolog-specific transcripts were unequivocally diagnosed in the hybrids and tetraploids based on parent-specific SNPs. Compared with the in silico hybrid (parental mix), the range of progenitor expression divergence was significantly reduced in both reciprocally generated F1 hybrids, presumably due to the ameliorating effects of a common trans environment on divergent cis -factors. In contrast, parental expression differences were greatly elaborated at the polyploid level, which we propose is a consequence of stoichiometric disruptions associated with the numerous chromosomal packaging and volumetric changes accompanying nascent polyploidy. We speculate that the emergent property of "whole genome doubling" has repercussions that reverberate throughout the transcriptome and downstream, ultimately generating altered phenotypes. This perspective may yield insight into the nature of adaptation and the origin of evolutionary novelty accompanying polyploidy.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
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  • 9
    Publication Date: 2017-08-26
    Description: Although statistical mechanics describes thermal equilibrium states, these states may or may not emerge dynamically for a subsystem of an isolated quantum many-body system. For instance, quantum systems that are near-integrable usually fail to thermalize in an experimentally realistic time scale, and instead relax to quasi-stationary prethermal states that can be described by statistical mechanics, when approximately conserved quantities are included in a generalized Gibbs ensemble (GGE). We experimentally study the relaxation dynamics of a chain of up to 22 spins evolving under a long-range transverse-field Ising Hamiltonian following a sudden quench. For sufficiently long-range interactions, the system relaxes to a new type of prethermal state that retains a strong memory of the initial conditions. However, the prethermal state in this case cannot be described by a standard GGE; it rather arises from an emergent double-well potential felt by the spin excitations. This result shows that prethermalization occurs in a broader context than previously thought, and reveals new challenges for a generic understanding of the thermalization of quantum systems, particularly in the presence of long-range interactions.
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
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  • 10
    Publication Date: 2013-11-02
    Description: The effect of a cationic-neutral diblock polypeptide on the conformation of single DNA molecules confined in rectangular nanochannels is investigated with fluorescence microscopy. An enhanced stretch along the channel is observed with increased binding of the cationic block of the polypeptide to DNA. A maximum stretch of 85% of the contour length can be achieved inside a channel with a cross-sectional diameter of 200 nm and at a 2-fold excess of polypeptide with respect to DNA charge. With site-specific fluorescence labelling, it is demonstrated that this maximum stretch is sufficient to map large-scale genomic organization. Monte Carlo computer simulation shows that the amplification of the stretch inside the nanochannels is owing to an increase in bending rigidity and thickness of bottlebrush-coated DNA. The persistence lengths and widths deduced from the nanochannel data agree with what has been estimated from the analysis of atomic force microscopy images of dried complexes on silica.
    Keywords: Phsyical and Biochemical Characterisation of DNA
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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