ELIXIR pilot action: Marine metagenomics – towards a domain specific set of sustainable services

Metagenomics, the study of genetic material recovered directly from environmental samples, has the potential to provide insight into the structure and function of heterogeneous microbial communities. There has been an increased use of metagenomics to discover and understand the diverse biosynthetic capacities of marine microbes, thereby allowing them to be exploited for industrial, food, and health care products. This ELIXIR pilot action was motivated by the need to establish dedicated data resources and harmonized metagenomics pipelines for the marine domain, in order to enhance the exploration and exploitation of marine genetic resources. In this paper, we summarize some of the results from the ELIXIR pilot action “Marine metagenomics – towards user centric services”.

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Structure and function of neural networks in the retina

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100102213 ◽

1988 ◽

Vol 46 ◽

pp. 26-27

Author(s):

Peter Sterling

Keyword(s):

Ganglion Cells ◽

Three Dimensional ◽

Structure And Function ◽

Synaptic Connections ◽

Visual Axis ◽

One Dimensional ◽

Cat Retina ◽

Ultrathin Sections ◽

And Function ◽

Insight Into

The synaptic connections in cat retina that link photoreceptors to ganglion cells have been analyzed quantitatively. Our approach has been to prepare serial, ultrathin sections and photograph en montage at low magnification (˜2000X) in the electron microscope. Six series, 100-300 sections long, have been prepared over the last decade. They derive from different cats but always from the same region of retina, about one degree from the center of the visual axis. The material has been analyzed by reconstructing adjacent neurons in each array and then identifying systematically the synaptic connections between arrays. Most reconstructions were done manually by tracing the outlines of processes in successive sections onto acetate sheets aligned on a cartoonist's jig. The tracings were then digitized, stacked by computer, and printed with the hidden lines removed. The results have provided rather than the usual one-dimensional account of pathways, a three-dimensional account of circuits. From this has emerged insight into the functional architecture.

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Computational Approaches to Predict the Non-canonical DNAs

Current Bioinformatics ◽

10.2174/1574893614666190126143438 ◽

2019 ◽

Vol 14 (6) ◽

pp. 470-479 ◽

Cited By ~ 3

Author(s):

Nazia Parveen ◽

Amen Shamim ◽

Seunghee Cho ◽

Kyeong Kyu Kim

Keyword(s):

Computational Methods ◽

Genetic Instability ◽

Computational Prediction ◽

Structure And Function ◽

Sequence Motifs ◽

Computational Approaches ◽

Functional Roles ◽

And Function ◽

Genetic Events ◽

Insight Into

Background: Although most nucleotides in the genome form canonical double-stranded B-DNA, many repeated sequences transiently present as non-canonical conformations (non-B DNA) such as triplexes, quadruplexes, Z-DNA, cruciforms, and slipped/hairpins. Those noncanonical DNAs (ncDNAs) are not only associated with many genetic events such as replication, transcription, and recombination, but are also related to the genetic instability that results in the predisposition to disease. Due to the crucial roles of ncDNAs in cellular and genetic functions, various computational methods have been implemented to predict sequence motifs that generate ncDNA. Objective: Here, we review strategies for the identification of ncDNA motifs across the whole genome, which is necessary for further understanding and investigation of the structure and function of ncDNAs. Conclusion: There is a great demand for computational prediction of non-canonical DNAs that play key functional roles in gene expression and genome biology. In this study, we review the currently available computational methods for predicting the non-canonical DNAs in the genome. Current studies not only provide an insight into the computational methods for predicting the secondary structures of DNA but also increase our understanding of the roles of non-canonical DNA in the genome.

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Crystal structure and function of an unusual dimeric Hsp20.1 provide insight into the thermal protection mechanism of small heat shock proteins

Biochemical and Biophysical Research Communications ◽

10.1016/j.bbrc.2015.01.134 ◽

2015 ◽

Vol 458 (2) ◽

pp. 429-434 ◽

Cited By ~ 2

Author(s):

Liang Liu ◽

Jiyun Chen ◽

Bo Yang ◽

Yonghua Wang

Keyword(s):

Crystal Structure ◽

Heat Shock ◽

Heat Shock Proteins ◽

Thermal Protection ◽

Small Heat Shock Proteins ◽

Structure And Function ◽

Protection Mechanism ◽

Shock Proteins ◽

And Function ◽

Insight Into

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Sensing Extracellular Calcium – An Insight into the Structure and Function of the Calcium-Sensing Receptor (CaSR)

Advances in Experimental Medicine and Biology - Calcium Signaling ◽

10.1007/978-3-030-12457-1_41 ◽

2019 ◽

pp. 1031-1063 ◽

Cited By ~ 6

Author(s):

Sergei Chavez-Abiega ◽

Iris Mos ◽

Patricia P. Centeno ◽

Taha Elajnaf ◽

Wolfgang Schlattl ◽

...

Keyword(s):

Structure And Function ◽

Extracellular Calcium ◽

Calcium Sensing Receptor ◽

Calcium Sensing ◽

And Function ◽

Insight Into

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Function of Genetic Material. Structure and Function of Regulatory Sequences

Progress in Botany ◽

10.1007/978-3-642-75154-7_14 ◽

1989 ◽

pp. 225-236 ◽

Cited By ~ 1

Author(s):

Rolf Blaich

Keyword(s):

Genetic Material ◽

Structure And Function ◽

Material Structure ◽

Regulatory Sequences ◽

And Function

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Structure and function of USP5: Insight into physiological and pathophysiological roles

Pharmacological Research ◽

10.1016/j.phrs.2019.104557 ◽

2020 ◽

Vol 157 ◽

pp. 104557 ◽

Cited By ~ 1

Author(s):

Fengling Ning ◽

Hong Xin ◽

Junqiu Liu ◽

Chao Lv ◽

Xin Xu ◽

...

Keyword(s):

Structure And Function ◽

And Function ◽

Insight Into

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ENaC structure and function in the wake of a resolved structure of a family member

AJP Renal Physiology ◽

10.1152/ajprenal.00259.2011 ◽

2011 ◽

Vol 301 (4) ◽

pp. F684-F696 ◽

Cited By ~ 89

Author(s):

Ossama B. Kashlan ◽

Thomas R. Kleyman

Keyword(s):

Plasma Membrane ◽

Ion Channel ◽

Functional Data ◽

Ion Selectivity ◽

External Environment ◽

Structure And Function ◽

Close Proximity ◽

Channel Assembly ◽

And Function ◽

Insight Into

Our understanding of epithelial Na+ channel (ENaC) structure and function has been profoundly impacted by the resolved structure of the homologous acid-sensing ion channel 1 (ASIC1). The structure of the extracellular and pore regions provide insight into channel assembly, processing, and the ability of these channels to sense the external environment. The absence of intracellular structures precludes insight into important interactions with intracellular factors that regulate trafficking and function. The primary sequences of ASIC1 and ENaC subunits are well conserved within the regions that are within or in close proximity to the plasma membrane, but poorly conserved in peripheral domains that may functionally differentiate family members. This review examines functional data, including ion selectivity, gating, and amiloride block, in light of the resolved ASIC1 structure.

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Structural and mechanistic insight into alkane hydroxylation by Pseudomonas putida AlkB

Biochemical Journal ◽

10.1042/bj20131648 ◽

2014 ◽

Vol 460 (2) ◽

pp. 283-293 ◽

Cited By ~ 13

Author(s):

Hernan Alonso ◽

Oded Kleifeld ◽

Adva Yeheskel ◽

Poh C. Ong ◽

Yu C. Liu ◽

...

Keyword(s):

Ab Initio ◽

Pseudomonas Putida ◽

Structure And Function ◽

Alkane Hydroxylation ◽

Mechanistic Insight ◽

Unknown Structure ◽

And Function ◽

Alkane Hydroxylases ◽

Insight Into

Integral membrane non-haem di-iron alkane hydroxylases (AlkBs) are enzymes of unknown structure that allow bacteria to grow on alkanes. Catalysis-linked modifications with the inhibitor 1-octyne, mutagenesis studies and ab initio modelling provided novel insights into the structure and function of AlkB.

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