VDAC1 (voltage-dependent anion channel 1)

Review on VDAC1 (voltage-dependent anion channel 1), with data on DNA, on the protein encoded, and where the gene is implicated

GenBank

GenBank® is a comprehensive database that contains publicly available nucleotide sequences for more than 300 000 organisms named at the genus level or lower, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the European Molecular Biology Laboratory Nucleotide Sequence Database in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bi-monthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI homepage: www.ncbi.nlm.nih.gov

Cellulose factories : advancing bioenergy production from forest trees

Fast-growing, short-rotation forest trees, such as Populus and Eucalyptus, produce large amounts of cellulose-rich biomass that could be utilized for bioenergy and biopolymer production. Major obstacles need to be overcome before the deployment of these genera as energy crops, including the effective removal of lignin and the subsequent liberation of carbohydrate constituents from wood cell walls. However, significant opportunities exist to both select for and engineer the structure and interaction of cell wall biopolymers, which could afford a means to improve processing and product development. The molecular underpinnings and regulation of cell wall carbohydrate biosynthesis are rapidly being elucidated, and are providing tools to strategically develop and guide the targeted modification required to adapt forest trees for the emerging bioeconomy. Much insight has already been gained from the perturbation of individual genes and pathways, but it is not known to what extent the natural variation in the sequence and expression of these same genes underlies the inherent variation in wood properties of field-grown trees. The integration of data from next-generation genomic technologies applied in natural and experimental populations will enable a systems genetics approach to study cell wall carbohydrate production in trees, and should advance the development of future woody bioenergy and biopolymer crops.http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1469-8137nf201

GenBank

GenBank® is a comprehensive database that contains publicly available nucleotide sequences for more than 250 000 formally described species. These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI home page: www.ncbi.nlm.nih.gov

DRAGON: A Dialogue-Based Robot for Assistive Navigation with Visual Language Grounding

Persons with visual impairments (PwVI) have difficulties understanding and navigating spaces around them. Current wayfinding technologies either focus solely on navigation or provide limited communication about the environment. Motivated by recent advances in visual-language grounding and semantic navigation, we propose DRAGON, a guiding robot powered by a dialogue system and the ability to associate the environment with natural language. By understanding the commands from the user, DRAGON is able to guide the user to the desired landmarks on the map, describe the environment, and answer questions from visual observations. Through effective utilization of dialogue, the robot can ground the user's free-form descriptions to landmarks in the environment, and give the user semantic information through spoken language. We conduct a user study with blindfolded participants in an everyday indoor environment. Our results demonstrate that DRAGON is able to communicate with the user smoothly, provide a good guiding experience, and connect users with their surrounding environment in an intuitive manner.Comment: Webpage and videos are at https://sites.google.com/view/dragon-wayfinding/hom

The Arabidopsis domain of unknown function 1218 (DUF1218) containing proteins, MODIFYING WALL LIGNIN-1 and 2 (At1g31720/MWL-1 and At4g19370/MWL-2) function redundantly to alter secondary cell wall lignin content

DUF1218 is a land plant-specific innovation and has previously been shown to be associated with cell wall biology, vasculature patterning and abiotic/biotic stress response. The Arabidopsis genome encodes 15 members, two of which (At1g31720 and At4g27435) are preferentially expressed in the secondary cell wall depositing inflorescence stems. To further our understanding of the roles of DUF1218-containing proteins in secondary cell wall biology, we functionally characterized At1g31720 (herein referred to as MODIFYING WALL LIGNIN-1 or MWL-1). Since related gene family members may contribute to functional redundancy, we also characterized At4g19370 (MWL-2), the most closely related gene to MWL-1 in the protein family. Subcellular localization revealed that both Arabidopsis proteins are targeted to the cell periphery. The single T-DNA knockout lines, mwl-1 and mwl-2, and independent overexpression lines showed no significant differences in plant growth or changes in total lignin content relative to wild-type (WT) control plants. However, the double homozygous mutant, mwl-1/mwl-2, had smaller rosettes with a significant decrease in rosette fresh weight and stem height relative to the WT control at four weeks and six weeks, respectively. Moreover, mwl-1/mwl-2 showed a significant reduction in total lignin content (by ca. 11% relative to WT) and an increase in syringyl/guaiacyl (S/G) monomer ratio relative to the control plants. Our study has identified two additional members of the DUF1218 family in Arabidopsis as novel contributors to secondary cell wall biology, specifically lignin biosynthesis, and these proteins appear to function redundantly.S1 Fig. Phylogenetic and bioinformatics analysis of all members of the Arabidopsis domain of unknown function 1218 (DUF1218) family, and expression profiling of the candidate members, MODIFYING WALL LIGNIN-1 (MWL-1, At1g31720) and MWL-2 (At4g19370). (A) Neighbor-joining phylogenetic tree of Arabdiopsis DUF1218-containing proteins. ClustalW was used to align protein sequences from TAIR and the alignment thereafter used to construct the tree using p-distance and pairwise deletion with 1000 bootstrap replicates in MEGA5 [16]. Prediction of subcellular localization, signal peptide and number of transmembrane domains was done using SUBA3 [31], Signal-3L [18] and TMHMM[19] respectively, with default settings. Highlighted in pink are the related MWL-1 and 2 sequences. (B) Arabidopsis expression profiles for MWL-1 and MWL-2 across different tissues during development, exctracted from The Bio-Analytic Resource for Plant Biology (http://bar. utoronto.ca/welcome.htm) [20]. Preferential expression is seen at distinct developmental stages, however, there is overlap in the secondary cell wall depositing, 2nd internode region. (DOCX)S2 Fig. Gene ontology enrichment of MWL-1 top 300 co-expressed genes in Arabidopsis. Co-expressed genes were extracted from ATTED-II [10]. GO-full was conducted in Cytoscape 2.8.2 [22] using BiNGO 2.44 [21], while overrepresentation summary enrichment was performed with the REVIGO server [23]. (DOCX)S3 Fig. Phenotypic analysis of At1g31720 (MWL-1) single T-DNA knockout line mutants and MWL-1 overexpression lines. (A) RT-PCR detection of endogenous MWL-1 transcript in the wildtype (WT) plants and absence in the single knockout mutant. (B) Semi-quantitative RT-PCR analysis of MWL-1 overexpression lines 1 to 3 showing detection of MWL-1 transgene in the transgenic lines. Actin2 was used as a control gene and RT-PCR was performed on cDNA from stem tissue. Actin2 and MWL-1 gene-specific oligonucleotide sequences can be found in S1 Table. Rosette size (C) and mass (D) of MWL-1 single T-DNA knockout line and overexpression lines 1–3 relative to (WT) control line at four weeks. Qualitative (E) and quantitative (F) stem length of MWL-1 single T-DNA knockout line and overexpression lines relative to WT control at six weeks. For rosette mass n = 3 and for quantitative stem length n = 66. Error bars indicate the standard error. Scale bar, 3 cm. Based on a two-tailed Student’s t-test (P-value 0.05) no significant differences were seen in the growth and development of the single mutant and transgenic OE lines in comparison to the WT controls.S4 Fig. Phenotypic analysis of At4g19370 (MWL-2) single T-DNA knockout line mutants and MWL-2 overexpression lines. (A) RT-PCR detection of endogenous MWL-2 transcript in the wildtype (WT) plants and absence in the single knockout mutant. (B) Semi-quantitative RT-PCR analysis of MWL-2 overexpression lines 1 to 3 showing detection of MWL-2 transgene in the transgenic lines except for OE1 which could be indicative of positional effect (position in the genome), or co-suppression dominant repression. Actin2 was used as a control gene and RT-PCR was performed on stem tissue. Actin2 and MWL-2 gene-specific oligonucleotide sequences can be found in S1 Table. Rosette size (C) and mass (D) of MWL-2 single T-DNA knockout line and overexpression lines 1–3 relative to (WT) control line at four weeks. Qualitative (E) and quantitative (F) stem length of MWL-2 single T-DNA knockout line and overexpression lines relative to WT control at six weeks. For rosette mass n = 3 and for quantitative stem length n = 66. Error bars indicate the standard error while significant difference from the WT based on a two-tailed Student’s t-test (P-value 0.05) is indicated by . Scale bar, 3 cm. No significant differences were seen in the growth and development of the single mutant and transgenic OE lines in comparison to the WT controls except for OE-Line 2. (DOCX)S5 Fig. Transverse sections of six-week-old stem tissue stained with phloroglucinol from At1g31720 (MWL-1) and At4g19370 (MWL-2) T-DNA knockout mutant and overexpression (OE) lines. Transverse sections from wildtype (WT) (A), At1g31720 mutant (B), At4g19370 mutant (C), At1g31720 x At4g19370 double knockdown mutant (D), OEAt1g31720 line 1 (E), line 2 (F), line 3 (G), OEAt4g19370 line 1(H), line 2 (I), line 3 (J). Scale bar, 100μm (indicated in red). No discernible differences were seen in the transverse sections of the single and double mutant as well as the transgenic OE lines in comparison to the WT controls. (DOCX)S1 Table. List of oligonucleotides used in the study. (DOCX)S2 Table. Top 300 Arabidopsis co-expressed genes for MWL-1 (At1g31720) from ATTED-II represented as MR value. (DOCX)S3 Table. Top 300 Arabidopsis co-expressed genes for MWL-2 (At4g19370) from ATTED-II represented as MR value. (DOCX)S4 Table. Structural cell wall carbohydrates and lignin content from MWL-1 and MWL-2 overexpression, single and double knockout lines compared to its respective wildtype (WT) control. (DOCX)Sappi through the Forest Molecular Genetics (FMG) Programme, the Technology and Human Resources for Industry Programme (THRIP, UID 80118), and the National Research Foundation (NRF, UID 71255 and 86936) of South Africa. RM acknowledges an NRF Ph.D. Prestige and Equity Scholarship.http://www.plosone.orgam2016Chemical EngineeringGenetic

SOFIA FORCAST Grism Study of the Mineralogy of Dust in the Winds of Proto-planetary Nebulae: RV Tauri Stars and SRd Variables

We present a SOFIA FORCAST grism spectroscopic survey to examine the mineralogy of the circumstellar dust in a sample of post-asymptotic giant branch (post-AGB) yellow supergiants that are believed to be the precursors of planetary nebulae. Our mineralogical model of each star indicates the presence of both carbon-rich and oxygenrich dust species—contrary to simple dredge-up models—with a majority of the dust in the form of amorphous carbon and graphite. The oxygen-rich dust is primarily in the form of amorphous silicates. The spectra do not exhibit any prominent crystalline silicate emission features. For most of the systems, our analysis suggests that the grains are relatively large and have undergone significant processing, supporting the hypothesis that the dust is confined to a Keplerian disk and that we are viewing the heavily processed, central regions of the disk from a nearly face-on orientation. These results help to determine the physical properties of the post-AGB circumstellar environment and to constrain models of post-AGB mass loss and planetary nebula formatio

Academic reading format preferences and behaviors among university students worldwide: A comparative survey analysis

This study reports the descriptive and inferential statistical findings of a survey of academic reading format preferences and behaviors of 10,293 tertiary students worldwide. The study hypothesized that country-based differences in schooling systems, socioeconomic development, culture or other factors might have an influence on preferred formats, print or electronic, for academic reading, as well as the learning engagement behaviors of students. The main findings are that country of origin has little to no relationship with or effect on reading format preferences of university students, and that the broad majority of students worldwide prefer to read academic course materials in print. The majority of participants report better focus and retention of information presented in print formats, and more frequently prefer print for longer texts. Additional demographic and post-hoc analysis suggests that format preference has a small relationship with academic rank. The relationship between task demands, format preferences and reading comprehension are discussed. Additional outcomes and implications for the fields of education, psychology, computer science, information science and human-computer interaction are considered