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  • 1
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    Effects of dietary fibre source on microbiota composition in the large intestine of suckling piglets (2016)
    Oxford University Press
    Details
    Publication Date: 2016-06-23
    Description: This study aimed to investigate the effects of dietary fibre sources on the gut microbiota in suckling piglets, and to test the hypothesis that a moderate increase of dietary fibre may affect the gut microbiota during the suckling period. Suckling piglets were fed different fibre-containing diets or a control diet from postnatal day 7 to 22. Digesta samples from cecum, proximal colon and distal colon were used for Pig Intestinal Tract Chip analysis. The data showed that the effects of fibre-containing diet on the gut microbiota differed in the fibre source and gut location. The alfalfa diet increased Clostridium cluster XIVb and Sporobacter termitidis in the cecum compared to the pure cellulose diet. Compared to the control diet, the alfalfa diet also increased Coprococcus eutactus in the distal colon, while the pure cellulose diet decreased Eubacterium pyruvativorans in the cecum. The pure cellulose diet increased Prevotella ruminicola compared to the wheat bran diet. Interestingly, the alfalfa group had the lowest abundance of the potential pathogen Streptococcus suis in the cecum and distal colon. These results indicated that a moderate increase in dietary fibres affected the microbial composition in suckling piglets, and that the alfalfa inclusion produced some beneficial effects on the microbial communities.
    Keywords: Environmental Microbiology
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Genome-wide association study in Chinese identifies novel loci for blood pressure and hypertension (2015)
    Oxford University Press
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    Publication Date: 2015-01-13
    Description: Hypertension is a common disorder and the leading risk factor for cardiovascular disease and premature deaths worldwide. Genome-wide association studies (GWASs) in the European population have identified multiple chromosomal regions associated with blood pressure, and the identified loci altogether explain only a small fraction of the variance for blood pressure. The differences in environmental exposures and genetic background between Chinese and European populations might suggest potential different pathways of blood pressure regulation. To identify novel genetic variants affecting blood pressure variation, we conducted a meta-analysis of GWASs of blood pressure and hypertension in 11 816 subjects followed by replication studies including 69 146 additional individuals. We identified genome-wide significant ( P 〈 5.0 x 10 –8 ) associations with blood pressure, which included variants at three new loci ( CACNA1D , CYP21A2 , and MED13L ) and a newly discovered variant near SLC4A7 . We also replicated 14 previously reported loci, 8 ( CASZ1 , MOV10 , FGF5 , CYP17A1 , SOX6 , ATP2B1 , ALDH2 , and JAG1 ) at genome-wide significance, and 6 ( FIGN , ULK4 , GUCY1A3 , HFE , TBX3-TBX5 , and TBX3 ) at a suggestive level of P = 1.81 x 10 –3 to 5.16 x 10 –8 . These findings provide new mechanistic insights into the regulation of blood pressure and potential targets for treatments.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 3
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    PRC2 recruitment and H3K27me3 deposition at FLC require FCA binding of COOLAIR (2019)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2019
    Description: 〈p〉The cold-induced antisense transcript 〈i〉COOLAIR〈/i〉 represses 〈i〉FLOWERING LOCUS C〈/i〉 (〈i〉FLC〈/i〉) transcription with increased H3K27me3 and decreased H3K36me3 levels in response to cold temperatures. However, the molecular connection between 〈i〉COOLAIR〈/i〉 and histone modification factors in the absence of cold treatment remains unclear. We report that the RNA binding protein FCA interacts with the PRC2 subunit CURLY LEAF (CLF) and binds nascent 〈i〉COOLAIR〈/i〉 transcripts to allow deposition of H3K27me3 at 〈i〉FLC〈/i〉. Loss of 〈i〉COOLAIR〈/i〉 function results in a reduction in FCA and CLF enrichment, which, in turn, decreases H3K27me3 levels at 〈i〉FLC〈/i〉. The 〈i〉Arabidopsis〈/i〉 protein phosphatase SSU72 physically interacts with the RRM1 motif of FCA to antagonize FCA binding with 〈i〉COOLAIR〈/i〉. Mutations in 〈i〉SSU72〈/i〉 caused early flowering, reduced 〈i〉FLC〈/i〉 transcription, increased CLF enrichment and H3K27me3, and enhanced affinity between FCA and 〈i〉COOLAIR〈/i〉. Our results suggest that FCA binding of 〈i〉COOLAIR〈/i〉 and SSU72 is critical for PRC2 enrichment and H3K27me3 deposition in 〈i〉Arabidopsis〈/i〉.〈/p〉
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    Trimethylamine N-oxide-derived zwitterionic polymers: A new class of ultralow fouling bioinspired materials (2019)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2019
    Description: 〈p〉Materials that resist nonspecific protein adsorption are needed for many applications. However, few are able to achieve ultralow fouling in complex biological milieu. Zwitterionic polymers emerge as a class of highly effective ultralow fouling materials due to their superhydrophilicity, outperforming other hydrophilic materials such as poly(ethylene glycol). Unfortunately, there are only three major classes of zwitterionic materials based on poly(phosphorylcholine), poly(sulfobetaine), and poly(carboxybetaine) currently available. Inspired by trimethylamine 〈i〉N〈/i〉-oxide (TMAO), a zwitterionic osmolyte and the most effective protein stabilizer, we here report TMAO-derived zwitterionic polymers (PTMAO) as a new class of ultralow fouling biomaterials. The nonfouling properties of PTMAO were demonstrated under highly challenging conditions. The mechanism accounting for the extraordinary hydration of PTMAO was elucidated by molecular dynamics simulations. The discovery of PTMAO polymers demonstrates the power of molecular understanding in the design of new biomimetic materials and provides the biomaterials community with another class of nonfouling zwitterionic materials.〈/p〉
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    Intrinsic magnetic topological insulators in van der Waals layered MnBi2Te4-family materials (2019)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2019
    Description: 〈p〉The interplay of magnetism and topology is a key research subject in condensed matter physics, which offers great opportunities to explore emerging new physics, such as the quantum anomalous Hall (QAH) effect, axion electrodynamics, and Majorana fermions. However, these exotic physical effects have rarely been realized experimentally because of the lack of suitable working materials. Here, we predict a series of van der Waals layered MnBi〈sub〉2〈/sub〉Te〈sub〉4〈/sub〉-related materials that show intralayer ferromagnetic and interlayer antiferromagnetic exchange interactions. We find extremely rich topological quantum states with outstanding characteristics in MnBi〈sub〉2〈/sub〉Te〈sub〉4〈/sub〉, including an antiferromagnetic topological insulator with the long-sought topological axion states on the surface, a type II magnetic Weyl semimetal with one pair of Weyl points, as well as a collection of intrinsic axion insulators and QAH insulators in even- and odd-layer films, respectively. These notable predictions, if proven experimentally, could profoundly change future research and technology of topological quantum physics.〈/p〉
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
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  • 6
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    Fingerprinting protein structures effectively and efficiently (2014)
    Oxford University Press
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    Publication Date: 2014-03-28
    Description: Motivation:  One common task in structural biology is to assess the similarities and differences among protein structures. A variety of structure alignment algorithms and programs has been designed and implemented for this purpose. A major drawback with existing structure alignment programs is that they require a large amount of computational time, rendering them infeasible for pairwise alignments on large collections of structures. To overcome this drawback, a fragment alphabet learned from known structures has been introduced. The method, however, considers local similarity only, and therefore occasionally assigns high scores to structures that are similar only in local fragments. Method:  We propose a novel approach that eliminates false positives, through the comparison of both local and remote similarity, with little compromise in speed. Two kinds of contact libraries (ContactLib) are introduced to fingerprint protein structures effectively and efficiently. Each contact group of the contact library consists of one local or two remote fragments and is represented by a concise vector. These vectors are then indexed and used to calculate a new combined hit-rate score to identify similar protein structures effectively and efficiently. Results:  We tested our method on the high-quality protein structure subset of SCOP30 containing 3297 protein structures. For each protein structure of the subset, we retrieved its neighbor protein structures from the rest of the subset. The best area under the Receiver-Operating Characteristic curve, archived by ContactLib, is as high as 0.960. This is a significant improvement compared with 0.747, the best result achieved by FragBag. We also demonstrated that incorporating remote contact information is critical to consistently retrieve accurate neighbor protein structures for all- query protein structures. Availability and implementation:   https://cs.uwaterloo.ca/~xfcui/contactlib/ . Contact:   shuaicli@cityu.edu.hk or mli@uwaterloo.ca
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 7
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    Matrix completion via an alternating direction method (2012)
    Oxford University Press
    Details
    Publication Date: 2012-01-20
    Description: The matrix completion problem is to complete an unknown matrix from a small number of entries, and it captures many applications in diversified areas. Recently, it was shown that completing a low-rank matrix can be successfully accomplished by solving its convex relaxation problem using the nuclear norm. This paper shows that the alternating direction method (ADM) is applicable for completing a low-rank matrix including the noiseless case, the noisy case and the positive semidefinite case. The ADM approach for the matrix completion problem is easily implementable and very efficient. Numerical comparisons of the ADM approach with some state-of-the-art methods are reported.
    Print ISSN: 0272-4979
    Electronic ISSN: 1464-3642
    Topics: Mathematics
    Published by Oxford University Press
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  • 8
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    CDD: NCBI's conserved domain database (2015)
    Oxford University Press
    Details
    Publication Date: 2015-01-16
    Description: NCBI's CDD, the Conserved Domain Database, enters its 15 th year as a public resource for the annotation of proteins with the location of conserved domain footprints. Going forward, we strive to improve the coverage and consistency of domain annotation provided by CDD. We maintain a live search system as well as an archive of pre-computed domain annotation for sequences tracked in NCBI's Entrez protein database, which can be retrieved for single sequences or in bulk. We also maintain import procedures so that CDD contains domain models and domain definitions provided by several collections available in the public domain, as well as those produced by an in-house curation effort. The curation effort aims at increasing coverage and providing finer-grained classifications of common protein domains, for which a wealth of functional and structural data has become available. CDD curation generates alignment models of representative sequence fragments, which are in agreement with domain boundaries as observed in protein 3D structure, and which model the structurally conserved cores of domain families as well as annotate conserved features. CDD can be accessed at http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml .
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    Direct activation of human and mouse Oct4 genes using engineered TALE and Cas9 transcription factors (2014)
    Oxford University Press
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    Publication Date: 2014-04-15
    Description: The newly developed transcription activator-like effector protein (TALE) and clustered regularly interspaced short palindromic repeats/Cas9 transcription factors (TF) offered a powerful and precise approach for modulating gene expression. In this article, we systematically investigated the potential of these new tools in activating the stringently silenced pluripotency gene Oct4 ( Pou5f1 ) in mouse and human somatic cells. First, with a number of TALEs and sgRNAs targeting various regions in the mouse and human Oct4 promoters, we found that the most efficient TALE-VP64s bound around –120 to –80 bp, while highly effective sgRNAs targeted from –147 to –89-bp upstream of the transcription start sites to induce high activity of luciferase reporters. In addition, we observed significant transcriptional synergy when multiple TFs were applied simultaneously. Although individual TFs exhibited marginal activity to up-regulate endogenous gene expression, optimized combinations of TALE-VP64s could enhance endogenous Oct4 transcription up to 30-fold in mouse NIH3T3 cells and 20-fold in human HEK293T cells. More importantly, the enhancement of OCT4 transcription ultimately generated OCT4 proteins. Furthermore, examination of different epigenetic modifiers showed that histone acetyltransferase p300 could enhance both TALE-VP64 and sgRNA/dCas9-VP64 induced transcription of endogenous OCT4 . Taken together, our study suggested that engineered TALE-TF and dCas9-TF are useful tools for modulating gene expression in mammalian cells.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 10
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    Label-free biomedical imaging with high sensitivity by stimulated Raman scattering microscopy (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-12-20
    Description: Label-free chemical contrast is highly desirable in biomedical imaging. Spontaneous Raman microscopy provides specific vibrational signatures of chemical bonds, but is often hindered by low sensitivity. Here we report a three-dimensional multiphoton vibrational imaging technique based on stimulated Raman scattering (SRS). The sensitivity of SRS imaging is significantly greater than that of spontaneous Raman microscopy, which is achieved by implementing high-frequency (megahertz) phase-sensitive detection. SRS microscopy has a major advantage over previous coherent Raman techniques in that it offers background-free and readily interpretable chemical contrast. We show a variety of biomedical applications, such as differentiating distributions of omega-3 fatty acids and saturated lipids in living cells, imaging of brain and skin tissues based on intrinsic lipid contrast, and monitoring drug delivery through the epidermis.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3576036/" 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/PMC3576036/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Freudiger, Christian W -- Min, Wei -- Saar, Brian G -- Lu, Sijia -- Holtom, Gary R -- He, Chengwei -- Tsai, Jason C -- Kang, Jing X -- Xie, X Sunney -- CA113605/CA/NCI NIH HHS/ -- DP1 OD000277/OD/NIH HHS/ -- DP1 OD000277-05/OD/NIH HHS/ -- R01 CA113605/CA/NCI NIH HHS/ -- R01 CA113605-01A2/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2008 Dec 19;322(5909):1857-61. doi: 10.1126/science.1165758.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19095943" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line, Tumor ; Corpus Callosum/chemistry/cytology ; Dimethyl Sulfoxide/administration & dosage/pharmacokinetics ; Eicosapentaenoic Acid/metabolism ; Epidermis/chemistry/metabolism/ultrastructure ; Humans ; Imaging, Three-Dimensional/*methods ; Lipids/*analysis ; Mice ; Microscopy/*methods ; Neurons/ultrastructure ; Sensitivity and Specificity ; Skin/chemistry/ultrastructure ; *Spectrum Analysis, Raman ; Tretinoin/administration & dosage/pharmacokinetics ; Vitamin A/analysis/chemistry
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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