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Molecular biology

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https://www.readbyqxmd.com/read/29346760/single-cell-transcriptional-profiling-reveals-cellular-diversity-and-intercommunication-in-the-mouse-heart
#1
Daniel A Skelly, Galen T Squiers, Micheal A McLellan, Mohan T Bolisetty, Paul Robson, Nadia A Rosenthal, Alexander R Pinto
Characterization of the cardiac cellulome, the network of cells that form the heart, is essential for understanding cardiac development and normal organ function and for formulating precise therapeutic strategies to combat heart disease. Recent studies have reshaped our understanding of cardiac cellular composition and highlighted important functional roles for non-myocyte cell types. In this study, we characterized single-cell transcriptional profiles of the murine non-myocyte cardiac cellular landscape using single-cell RNA sequencing (scRNA-seq)...
January 16, 2018: Cell Reports
https://www.readbyqxmd.com/read/29346712/synergetic-effects-of-prenatal-and-postnatal-high-sucrose-intake-on-glucose-tolerance-and-hepatic-insulin-resistance-in-rat-offspring
#2
Pengjie Zhang, Di Zhu, Yueming Zhang, Lingjun Li, Xionghui Chen, Wenna Zhang, Ruixiu Shi, Jianying Tao, Bing Han, Zhice Xu
SCOPE: High sucrose intake during pregnancy is linked to type 2 diabetes mellitus and altered insulin resistance. METHODS AND RESULTS: This study attempted to ascertain whether prenatal high sucrose intake (20% sucrose) alleviates the detrimental effects of high postnatal sugar consumption in the offspring, and the molecular mechanisms were investigated using a rat model. High prenatal sucrose exposure increased the body weight of the offspring at 1 to 3 weeks of age...
January 18, 2018: Molecular Nutrition & Food Research
https://www.readbyqxmd.com/read/29346586/plasflow-predicting-plasmid-sequences-in-metagenomic-data-using-genome-signatures
#3
Pawel S Krawczyk, Leszek Lipinski, Andrzej Dziembowski
Plasmids are mobile genetics elements that play an important role in the environmental adaptation of microorganisms. Although plasmids are usually analyzed in cultured microorganisms, there is a need for methods that allow for the analysis of pools of plasmids (plasmidomes) in environmental samples. To that end, several molecular biology and bioinformatics methods have been developed; however, they are limited to environments with low diversity and cannot recover large plasmids. Here, we present PlasFlow, a novel tool based on genomic signatures that employs a neural network approach for identification of bacterial plasmid sequences in environmental samples...
January 13, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29346072/synthesis-biological-evaluation-and-molecular-docking-studies-of-novel-benzimidazole-derivatives
#4
Gagandeep Singh, Amanjot Singh, Raman K Verma, Rajiv Mall, Uzma Azeem
A novel series of N-substituted-benzimidazolyl linked para substituted benzylidene based molecules containing three pharmacologically potent hydrogen bonding parts namely; 2,4-thiazolidinedione (TZD: a 2,4-dicarbonyl), diethyl malonate (DEM: a 1,3-diester and an isooxazolidinedione analog) and methyl acetoacetate (MAA: a β-ketoester) (6a-11b) were synthesized and evaluated for in vitro α-glucosidase inhibition. The structure of the novel synthesized compounds was confirmed through the spectral studies (LC-MS, 1H NMR, 13C NMR, FT-IR)...
December 30, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29346034/coagulopathy-in-severe-sepsis-interconnectivity-of-coagulation-and-the-immune-system
#5
Jason M Samuels, Hunter B Moore, Ernest E Moore
BACKGROUND: Disseminated intravascular coagulation (DIC) remains a challenging complication of infection with inadequate treatment and significant morbidity and mortality rates. METHODS: Review of the English-language literature. RESULTS: Disseminated intravascular coagulation arises from the immune system's response to microbial invasion, as well as the byproducts of cell death that result from severe sepsis. This response triggers the coagulation system through an interconnected network of cellular and molecular signals, which developed originally as an evolutionary mechanism intended to isolate micro-organisms via fibrin mesh formation...
January 18, 2018: Surgical Infections
https://www.readbyqxmd.com/read/29345988/measuring-entropy-in-molecular-recognition-by-proteins
#6
A Joshua Wand, Kim A Sharp
Molecular recognition by proteins is fundamental to the molecular basis of biology. Dissection of the thermodynamic landscape governing protein-ligand interactions has proven difficult because determination of various entropic contributions is quite challenging. Nuclear magnetic resonance relaxation measurements, theory, and simulations suggest that conformational entropy can be accessed through a dynamical proxy. Here, we review the relationship between measures of fast side-chain motion and the underlying conformational entropy...
January 18, 2018: Annual Review of Biophysics
https://www.readbyqxmd.com/read/29345901/playing-with-the-molecules-of-life
#7
Douglas D Young, Peter G Schultz
Our understanding of the complex molecular processes of living organisms is growing exponentially. This knowledge, togeth-er with a powerful arsenal of tools for manipulating the structures of biological macromolecules, is allowing chemists to begin to harness and reprogram the remarkable machinery of life. Here we review one such example in which the genetic code itself has been expanded with new building blocks that allow us to probe and manipulate the structures and functions of proteins in ways previously unimaginable...
January 18, 2018: ACS Chemical Biology
https://www.readbyqxmd.com/read/29345351/k313-a-novel-benzoxazole-derivative-exhibits-anti-inflammatory-properties-via-inhibiting-gsk3%C3%AE-activity-in-lps-induced-raw264-7-macrophages
#8
Bo-Bo Zhao, Hui-Jie Guo, Yang Liu, Xing-Yan Luo, Shu-Xia Yang, Yan-Tang Wang, Xiao Leng, Chun-Fen Mo, Qiang Zou
Benzoxazole and its derivatives have been widely studied in recent years due to their various biological properties. A previous study has demonstrated that K313 (1H-indole-2,3-dione 3-(1,3-benzoxazol-2-ylhydrazone)), a novel benzoxazole derivative, inhibits T cell proliferation to yield immunosuppressive effects. However, there are no related reports about its anti-inflammatory effects. In the present study, we investigated the anti-inflammatory properties and the underlying molecular mechanism of K313 in lipopolysaccharide (LPS)-induced RAW264...
January 18, 2018: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/29345288/downregulation-of-mir%C3%A2-205-is-associated-with-glioblastoma-cell-migration-invasion-and-the-epithelial-mesenchymal-transition-by-targeting-zeb1-via-the-akt-mtor-signaling-pathway
#9
Wei Chen, Kuan-Kei Kong, Xin-Ke Xu, Cheng Chen, Hui Li, Fang-Yu Wang, Xiao-Fang Peng, Zhan Zhang, Ping Li, Jun-Liang Li, Fang-Cheng Li
Glioblastoma (GBM) is the most common type of malignant brain tumor. In spite of recent advancements in surgical techniques, chemotherapy, and radiation therapy, patients with GBM often face a dire prognosis. MicroRNAs have been shown to modulate the aggressiveness of various cancers, and have emerged as possible therapeutic agents for the management of GBM. miR‑205 is dysregulated in glioma and act as a prognostic indicator. However, the role of miR‑205 in the development of GBM has not been elucidated...
February 2018: International Journal of Oncology
https://www.readbyqxmd.com/read/29345272/preparation-of-eu-iii-acetylacetonate-doped-well-defined-titania-particles-with-efficient-photoluminescence-properties
#10
Kota Shiba, Takuya Kataoka, Motohiro Tagaya
The aggregation/dispersion of luminescent species is a critical factor that determines their luminescence properties. In this study, europium(iii) acetylacetonate (Eu(acac)3) was doped into a titania matrix to form Eu(acac)3-doped titania particles with well-defined size and shape through a microreactor-based sol-gel approach. The morphology and structure of the as-synthesized products were characterized by Fourier transform infrared spectroscopy, scanning electron microscopy, transmission electron microscopy, scanning transmission electron microscopy and X-ray diffraction measurements...
January 18, 2018: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/29344964/recent-advances-and-opportunities-in-proteomic-analyses-of-tumor-heterogeneity
#11
REVIEW
Nicholas W Bateman, Thomas P Conrads
Solid tumor malignancies comprise a highly variable admixture of tumor and non-tumor cellular populations, forming a complex cellular ecosystem and tumor microenvironment. This tumor heterogeneity is not incidental and is known to correlate with poor patient prognosis for many cancer types. Indeed, non-malignant cell populations, such as vascular endothelial and immune cells, are known to play key roles supporting and, in some cases, driving aggressive tumor biology and represent targets of emerging therapeutics, such as anti-angiogenesis and immune checkpoint inhibitors...
January 17, 2018: Journal of Pathology
https://www.readbyqxmd.com/read/29344894/systems-biology-approaches-in-cancer-pathology
#12
Aaron DeWard, Rebecca J Critchley-Thorne
The complex network of the tissue system, in both pre-neoplastic tissues and tumors, demonstrates the need for a systems biology approach to cancer pathology, in which quantification of key tissue system processes is combined with informatics tools to produce actionable scores to aid clinical decision-making. A systems biology approach to cancer pathology enables integration of key system features that are relevant to diagnoses, patient outcomes, and responses to therapies. Key tissue system features relevant to cancer pathology include molecular and morphologic abnormalities in epithelia, cellular changes in the stroma such as immune infiltrates, and relationships between components of the system, such as interactions and spatial relationships between epithelial and stromal components, and also between specific immune cell subsets...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344885/microrna-networks-in-breast-cancer-cells
#13
Andliena Tahiri, Miriam R Aure, Vessela N Kristensen
A variety of molecular techniques can be used in order to unravel the molecular composition of cells. In particular, the microarray technology has been used to identify novel biomarkers that may be useful in the diagnosis, prognosis, or treatment of cancer. The microarray technology is ideal for biomarker discovery as it allows for the screening of a large number of molecules at once. In this review, we focus on microRNAs (miRNAs) which are key molecules in cells and regulate gene expression post-transcriptionally...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344860/laser-microdissection-for-human-papillomavirus-hpv-genotyping-attribution-and-methylation-pattern-analyses-of-squamous-intraepithelial-lesions
#14
Monica Molano, Suzanne M Garland, Alyssa M Cornall
Human papillomavirus (HPV) is a nearly ubiquitous infectious organism. It is estimated that 80% of sexually active adults will be exposed to anogenital HPVs in their lifetime, and detection of multiple genotypes in an anogenital sample is common. Detection and genotyping of HPV is usually performed by DNA testing, and less frequently by mRNA testing. HPV genotype testing and characterization of DNA methylation patterns of HPV-related lesions can provide important biological, epidemiological, and potentially relevant clinical information in individuals and populations...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344856/next-generation-sequencing-analysis-of-laser-microdissected-formalin-fixed-and-paraffin-embedded-ffpe-tissue-specimens
#15
Lavinia Mägel, Stephan Bartels, Ulrich Lehmann
In recent years, next-generation sequencing (NGS) became widely used in molecular pathology. Comprehensive mutational profiling improved diagnosis and prognosis, as well as the identification of therapeutically relevant genetic alterations. However, the vast majority of studies analyzing tissue samples use DNA extracted from bulk tissue or only manually microdissected specimens. Laser-assisted microdissection offers the possibility of isolating morphologically defined small tissue compartments (like individual glands) or even of single cells for further molecular analysis...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344854/laser-microdissection-workflow-for-isolating-nucleic-acids-from-fixed-and-frozen-tissue-samples
#16
Yelena G Golubeva, Andrew C Warner
Laser Capture Microdissection has earned a permanent place among modern techniques connecting histology and molecular biology. Laser Capture Microdissection has become an invaluable tool in medical research as a means for collection of specific cell populations isolated from their environment. Such genomic sample enrichment dramatically increases the sensitivity and precision of downstream molecular assays used for biomarker discovery, monitoring disease onset and progression, and in the development of personalized medicine...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344827/molecular-imaging-of-cardiac-remodelling-after-myocardial-infarction
#17
REVIEW
Daniel Curley, Begoña Lavin Plaza, Ajay M Shah, René M Botnar
Myocardial infarction and subsequent heart failure is a major health burden associated with significant mortality and morbidity in western societies. The ability of cardiac tissue to recover after myocardial infarction is affected by numerous complex cellular and molecular pathways. Unbalance or failure of these pathways can lead to adverse remodelling of the heart and poor prognosis. Current clinical cardiac imaging modalities assess anatomy, perfusion, function, and viability of the myocardium, yet do not offer any insight into the specific molecular pathways involved in the repair process...
January 17, 2018: Basic Research in Cardiology
https://www.readbyqxmd.com/read/29344776/dawning-of-a-new-era-in-trp-channel-structural-biology-by-cryo-electron-microscopy
#18
REVIEW
M Gregor Madej, Christine M Ziegler
Cryo-electron microscopy (cryo-EM) permits the determination of atomic protein structures by averaging large numbers of individual projection images recorded at cryogenic temperatures-a method termed single-particle analysis. The cryo-preservation traps proteins within a thin glass-like ice layer, making literally a freeze image of proteins in solution. Projections of randomly adopted orientations are merged to reconstruct a 3D density map. While atomic resolution for highly symmetric viruses was achieved already in 2009, the development of new sensitive and fast electron detectors has enabled cryo-EM for smaller and asymmetrical proteins including fragile membrane proteins...
January 17, 2018: Pflügers Archiv: European Journal of Physiology
https://www.readbyqxmd.com/read/29344683/the-root-transcriptome-of-achyranthes-bidentata-and-the-identification-of-the-genes-involved-in-the-replanting-benefit
#19
Yan Hui Yang, Ming Jie Li, Yan Jie Yi, Rui Fang Li, Cheng Dong, Zhong Yi Zhang
The transcriptome profiling in replanting roots revealed that expression pattern changes of key genes promoted important metabolism pathways, antioxidant and pathogen defense systems, adjusted phytohormone signaling and inhibited lignin biosynthesis. The yield of the medicinal plant Achyranthes bidentata could be significantly increased when replanted into a field cultivated previously for the same crop, but the biological basis of this so-called "replanting benefit" is unknown. Here, the RNA-seq technique was used to identify candidate genes responsible for the benefit...
January 17, 2018: Plant Cell Reports
https://www.readbyqxmd.com/read/29344293/ligand-activation-of-ppar%C3%AE-by-ligustrazine-suppresses-pericyte-functions-of-hepatic-stellate-cells-via-smrt-mediated-transrepression-of-hif-1%C3%AE
#20
Feng Zhang, Shuai Lu, Jianlin He, Huanhuan Jin, Feixia Wang, Li Wu, Jiangjuan Shao, Anping Chen, Shizhong Zheng
Rationale: Hepatic stellate cells (HSCs) are liver-specific pericytes regulating vascular remodeling during hepatic fibrosis. Here, we investigated how ligustrazine affects HSC pericyte functions. Methods: Rat HSC-T6 and human HSC-LX2 cells were cultured, and multiple molecular experiments including real-time PCR, Western blot, flow cytometry, immunofluorescence, electrophoretic mobility shift assay and co-immunoprecipitation were used to elucidate the underlying mechanisms. Molecular simulation and site-directed mutagenesis were performed to uncover the target molecule of ligustrazine...
2018: Theranostics
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