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Small molecular

Paulius Toliusis, Giedre Tamulaitiene, Rokas Grigaitis, Donata Tuminauskaite, Arunas Silanskas, Elena Manakova, Ceslovas Venclovas, Mark D Szczelkun, Virginijus Siksnys, Mindaugas Zaremba
CglI is a restriction endonuclease from Corynebacterium glutamicum that forms a complex between: two R-subunits that have site specific-recognition and nuclease domains; and two H-subunits, with Superfamily 2 helicase-like DEAD domains, and uncharacterized Z1 and C-terminal domains. ATP hydrolysis by the H-subunits catalyses dsDNA translocation that is necessary for long-range movement along DNA that activates nuclease activity. Here, we provide biochemical and molecular modelling evidence that shows that Z1 has a fold distantly-related to RecA, and that the DEAD-Z1 domains together form an ATP binding interface and are the prototype of a previously undescribed monomeric helicase-like motor...
February 20, 2018: Nucleic Acids Research
Alexander Kudryavtsev, Ekaterina Volkova
We isolated and described a brackish-water amoeba, Clydonella sawyeri n. sp. (Amoebozoa, Vannellida), from the littoral habitat in Kandalaksha Bay (The White Sea, northwestern Russia). Morphology of this amoeba corresponds to the initially proposed diagnosis of the genus Clydonella Sawyer, 1975, although it is sufficiently different from other described species of this genus to warrant a distinct species designation. Phylogenetic analysis based on the small-subunit rRNA gene shows that this species is closely related to the two previously studied ATCC strains identified as Clydonella sp...
February 6, 2018: European Journal of Protistology
George J Dugbartey
Chronic kidney disease (CKD) is a common global health challenge characterized by irreversible pathological processes that reduce kidney function and culminates in development of end-stage renal disease. It is associated with increased morbidity and mortality in addition to increased caregiver burden and higher financial cost. A central player in CKD pathogenesis and progression is renal hypoxia. Renal hypoxia stimulates induction of oxidative and endoplasmic reticulum stress, inflammation and tubulointerstitial fibrosis, which in turn, promote cellular susceptibility and further aggravate hypoxia, thus forming a pathological vicious cycle in CKD progression...
October 19, 2017: Pharmacological Reports: PR
Siyi Gu, Marta Borowska, Christopher T Boughter, Erin J Adams
Despite playing critical roles in the immune response and having significant potential in immunotherapy, γδ T cells have garnered little of the limelight. One major reason for this paradox is that their antigen recognition mechanisms are largely unknown, limiting our understanding of their biology and our potential to modulate their activity. One of the best-studied γδ subsets is the human Vγ9Vδ2 T cell population, which predominates in peripheral blood and can combat both microbial infections and cancers...
February 19, 2018: Seminars in Cell & Developmental Biology
Takashi Matsunaga, Naoya Matsunaga, Naoki Kusunose, Eriko Ikeda, Hiroyuki Okazaki, Keisuke Kakimoto, Kengo Hamamura, Satoru Koyanagi, Shigehiro Ohdo
One approach to increasing pharmacotherapy effects is administering drugs at times of day when they are most effective and/or best tolerated. Circadian variation in expression of pharmacokinetics- and pharmacodynamics-related genes was shown to contribute to dosing time-dependent differences in therapeutic effects of small molecule drugs. However, influence of dosing time of day on effects of high molecular weight formulations, such as drugs encapsulated in liposomes, has not been studied in detail. This study demonstrates that blood pressure rhythm affects dosing time-dependent variation in effects of high molecular weight formulations...
February 19, 2018: Biochemical and Biophysical Research Communications
Jan Leipert, Ingrid Bobis, Sabine Schubert, Helmut Fickenscher, Matthias Leippe, Andreas Tholey
The identification and quantification of molecules involved in bacterial communication are major prerequisites for the understanding of interspecies interactions at the molecular level. We developed a procedure allowing the determination of 2-heptyl-4(1H)-quinolone (HHQ) and 2-heptyl-3-hydroxy-4(1H)-quinolone (PQS) and the virulence factor pyocyanin (PYO) formed by the Gram-negative bacterium Pseudomonas aeruginosa. The method is based on dispersive liquid-liquid microextraction from small supernatant volumes (below 10 μL) followed by quantitative matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS)...
February 22, 2018: Analytical and Bioanalytical Chemistry
James Cockram, Ian Mackay
Fine mapping of quantitative trait loci (QTL) is the route to more detailed molecular characterization and functional studies of the relationship between polymorphism and trait variation. It is also of direct relevance to breeding since it makes QTL more easily integrated into marker-assisted breeding and into genomic selection. Fine mapping requires that marker-trait associations are tested in populations in which large numbers of recombinations have occurred. This can be achieved by increasing the size of mapping populations or by increasing the number of generations of crossing required to create the population...
February 23, 2018: Advances in Biochemical Engineering/biotechnology
Danni Zhou, Xiaoming Wang, Guokang Chen, Suli Sun, Yang Yang, Zhendong Zhu, Canxing Duan
Fusarium verticillioides , F. proliferatum , and F. meridionale were identified as the predominant fungi among 116 Fusarium isolates causing maize ear and kernel rot, a destructive disease in Chongqing areas, China. The toxigenic capability and genotype were determined by molecular amplification and toxin assay. The results showed that the key toxigenic gene FUM1 was detected in 47 F. verticillioides and 19 F. proliferatum isolates. Among these, F. verticillioides and F. proliferatum isolates mainly produced fumonisin B₁, ranging from 3...
February 22, 2018: Toxins
Adriana Caracciolo, Dandan Lu, Nadia Balucani, Gianmarco Vanuzzo, Domenico Stranges, Xingan Wang, Jun Li, Hua Guo, Piergiorgio Casavecchia
A combined experimental/theoretical study is performed to advance our understanding of the dynamics of the prototypical tetra-atom, complex-forming reaction OH + CO→ H + CO2 , which is also of great practical relevance in combustion, Earth atmosphere and, potentially, Mars' atmosphere and interstellar chemistry. New crossed molecular beam experiments with mass spectrometric detection are analyzed together with the results from previous experiments and compared with quasi-classical trajectory (QCT) calculations on a new, full-dimensional potential energy surface (PES)...
February 22, 2018: Journal of Physical Chemistry Letters
Shahrazad Moh'd Ahmad Malek, Francesco Sciortino, Peter H Poole, Ivan Saika-Voivod
We calculate the components of the microscopic pressure tensor as a function of radial distance r from the centre of a spherical water droplet, modelled using the TIP4P/2005 potential. To do so, we modify a coarse-graining method for calculating the microscopic pressure [T. Ikeshoji, B. Hafskjold, and H. Furuholt, Mol. Simul. 29, 101 (2003)] in order to apply it to a rigid molecular model of water. As test cases, we study nanodroplets ranging in size from 776 to 2880 molecules at 220 K. Beneath a surface region comprising approximately two molecular layers, the pressure tensor becomes approximately isotropic and constant with r...
February 22, 2018: Journal of Physics. Condensed Matter: An Institute of Physics Journal
Zhou Wei, Yang Jun-Qi
The Rho subfamily of GTPase belongs to the Ras superfamily of small GTP binding protein, it is a nucleotide dependent protein, which plays a "molecular switch" function in the signal transduction process and control of numerous signaling pathways. Rho protein has many biological effects on cytoskeleton or target proteins as a signal converter in signal transduction, such as the regulation of membrane transport function, cell migration, cell adhesion, and cell proliferation. It also plays a very important role in the infection and immune inflammation of the body...
December 26, 2017: Zhongguo Xue Xi Chong Bing Fang Zhi za Zhi, Chinese Journal of Schistosomiasis Control
Rakesh Kumar, Dhananjay Jade, Dinesh Gupta
5-HydroxyTriptamine 2A antagonists are potential targets for treatment of various cerebrovascular and cardiovascular disorders. In this study we have developed and performed a unique screening pipeline for filtering ZINC database compounds on the basis of similarities to known antagonists to determine novel small molecule antagonists of 5-HydroxyTriptamine 2A. The screening pipeline is based on 2D similarity, 3D dissimilarity and a combination of 2D/3D similarity. The shortlisted compounds were docked to a 5-HydroxyTriptamine 2A homology based model, and complexes with low binding energies (287 complexes) were selected for molecular dynamics (MD) simulations in a lipid bilayer...
February 22, 2018: Journal of Biomolecular Structure & Dynamics
Tao Huang, Xinglong Luan, Qi Xia, Shaofeng Pan, Qi An, Yaling Wu, Yihe Zhang
The molecularly selective regulation of molecular fluxes in a biomaterial that delivers simultaneously multiple chemical species is still beyond the touch of materials scientists. We developed a delivery material using layer-by-layer (LbL) technique that discriminatively regulates the delivery flux of bioactive small molecules, represented by a peptide containing RGD fragment and the chemotherapy drug DOX. Molecularly selective flux regulations in layer-by-layer films are realized using fast reversible supramolecular bindings between cyclodextrin and its guests...
February 22, 2018: Chemistry, An Asian Journal
G Gillessen-Kaesbach, B Albrecht, T Eggermann, M Elbracht, D Mitter, S Morlot, C M A van Ravenswaaij-Arts, S Schulz, G Strobl-Wildemann, K Buiting, J Beygo
Temple syndrome (TS14, #616222) is a rare imprinting disorder characterised by phenotypic features including pre- and postnatal growth retardation, muscular hypotonia and feeding difficulties in infancy, early puberty and short stature with small hands and feet and often truncal obesity. It is caused by maternal uniparental disomies, paternal deletions and primary imprinting defects that affect the chromosomal region 14q32 and lead to a disturbed expression of imprinted genes in this region. Here we present detailed clinical data of eight patients with Temple syndrome, four with an imprinting defect, two with an imprinting defect in a mosaic state as well as one complete and one segmental maternal uniparental disomy of chromosome 14...
February 22, 2018: Clinical Genetics
V Stühler, S Kruck, T Todenhöfer, A Stenzl, J Bedke
After surgical resection of renal cell carcinoma by laparoscopic or open partial or complete nephrectomy, medical aftercare based on the current guidelines should be provided. This seems desirable, especially because one third of patients after initial curative tumor resection develop recurrence over time. In this article, the current recommendations for follow-up will be systematically presented based on the accepted German S3 guideline and the European Association of Urology (EAU) guideline. Another point of this article will be the presentation of the currently applied risk scores to predict prognosis with a focus on molecular markers...
February 21, 2018: Der Urologe. Ausg. A
Yang Yang, Yi Meng, Hang Zhang, Xiaoyan Shen, Rutian Li, Lixia Yu, Baorui Liu, Lifeng Wang
Epithelial growth factor receptor (EGFR)-tyrosine kinase inhibitors are the standard first-line treatment for patients with metastatic non-small cell lung cancer (NSCLC) expressing sensitive EGFR-mutants. Other drugs target different driver mutants, including the serine/threonine-protein kinase B-raf (BRAF) inhibitor dabrafenib, which has exhibited promising efficacy for treating patients with metastatic BRAF-mutated NSCLC. Therefore, identifying patients carrying mutations that may be treated using targeted therapies is important...
March 2018: Oncology Letters
Bo Song, Bingyao Li, Xiaoyan Wang, Wei Shen, Sungjin Park, Cynthia Collings, Anran Feng, Steve J Smith, Jonathan D Walton, Shi-You Ding
Background: The high cost of enzymes is one of the key technical barriers that must be overcome to realize the economical production of biofuels and biomaterials from biomass. Supplementation of enzyme cocktails with lytic polysaccharide monooxygenase (LPMO) can increase the efficiency of these cellulase mixtures for biomass conversion. The previous studies have revealed that LPMOs cleave polysaccharide chains by oxidization of the C1 and/or C4 carbons of the monomeric units. However, how LPMOs enhance enzymatic degradation of lignocellulose is still poorly understood...
2018: Biotechnology for Biofuels
Qianfeng Liu, Jiasong Fang, Jiangtao Li, Li Zhang, Bin-Bin Xie, Xiu-Lan Chen, Yu-Zhong Zhang
Marine microorganisms and their extracellular enzymes (ECEs) play an important role in the remineralization of organic material by hydrolyzing high-molecular-weight substrates to sizes sufficiently small to be transported through cell membrane, yet the diversity of the enzyme-producing bacteria and the types of ECEs involved in the degradation process are largely unknown. In this work, we investigated the diversity of cultivable bacteria and their ECEs and the potential activities of aminopeptidase in the water column at eight different depths of the New Britain Trench...
2018: Frontiers in Microbiology
Safikur Rahman, Ayyagari Archana, Arif Tasleem Jan, Rinki Minakshi
Alzheimer's disease (AD), a neurodegenerative disorder, is most common cause of dementia witnessed among aged people. The pathophysiology of AD develops as a consequence of neurofibrillary tangle formation which consists of hyperphosphorylated microtubule associated tau protein and senile plaques of amyloid-β (Aβ) peptide in specific brain regions that result in synaptic loss and neuronal death. The feeble buffering capacity of endoplasmic reticulum (ER) proteostasis in AD is evident through alteration in unfolded protein response (UPR), where UPR markers express invariably in AD patient's brain samples...
2018: Frontiers in Aging Neuroscience
Lu Zhang, Sang Bum Kim, Krishna Luitel, Jerry W Shay
TASIN-1 (Truncated APC Selective INhibitor-1) is a recently identified small molecule that selectively kills colorectal cancer cells that express truncated APC by reducing cellular cholesterol levels. However, the downstream mechanism responsible for its cytotoxicity is not well understood. In this study, we show that TASIN-1 leads to apoptotic cell death via inducing ER stress-dependent JNK activation in human truncated APC colon cancer cells, accompanied by production of reactive oxygen species (ROS). In addition, TASIN-1 inhibits Akt activity through a cholesterol-dependent manner...
February 21, 2018: Molecular Cancer Therapeutics
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