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https://www.readbyqxmd.com/read/28734362/discrimination-of-bacteria-by-rapid-sensing-their-metabolic-volatiles-using-an-aspiration-type-ion-mobility-spectrometer-a-ims-and-gas-chromatography-mass-spectrometry-gc-ms
#1
Ileana Andreea Ratiu, Victor Bocos-Bintintan, Adrian Patrut, Victor Hugo Moll, Matthew Turner, C L Paul Thomas
The objective of our study was to investigate whether one may quickly and reliably discriminate different microorganism strains by direct monitoring of the headspace atmosphere above their cultures. Headspace samples above a series of in vitro bacterial cultures were directly interrogated using an aspiration type ion mobility spectrometer (a-IMS), which produced distinct profiles ("fingerprints") of ion currents generated simultaneously by the detectors present inside the ion mobility cell. Data processing and analysis using principal component analysis showed net differences in the responses produced by volatiles emitted by various bacterial strains...
August 22, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28733422/differences-in-dna-binding-specificity-of-floral-homeotic-protein-complexes-predict-organ-specific-target-genes
#2
Cezary Smaczniak, Jose M Muiño, Dijun Chen, Gerco C Angenent, Kerstin Kaufmann
Floral organ identities in plants are specified by the combinatorial action of homeotic master regulatory transcription factors. How these factors achieve their regulatory specificities is however still largely unclear. Genome-wide in vivo DNA binding data show that homeotic MADS-domain proteins recognize partly distinct genomic regions, suggesting that DNA binding specificity contributes to functional differences of homeotic protein complexes. We used in vitro systematic evolution of ligands by exponential enrichment followed by high throughput DNA sequencing (SELEX-seq) on several floral MADS-domain protein homo- and heterodimers to measure their DNA-binding specificities...
July 21, 2017: Plant Cell
https://www.readbyqxmd.com/read/28732043/investigation-of-horizontal-gene-transfer-of-pathogenicity-islands-in-escherichia-coli-using-next-generation-sequencing
#3
Maxim Messerer, Wolfgang Fischer, Sören Schubert
Horizontal gene transfer (HGT) contributes to the evolution of bacteria. All extraintestinal pathogenic Escherichia coli (ExPEC) harbour pathogenicity islands (PAIs), however relatively little is known about the acquisition of these PAIs. Due to these islands, ExPEC have properties to colonize and invade its hosts efficiently. Even though these PAIs are known to be acquired by HGT, only very few PAIs do carry mobilization and transfer genes required for the transmission by HGT. In this study, we apply for the first time next-generation sequencing (NGS) and in silico analyses in combination with in vitro experiments to decipher the mechanisms of PAI acquisition in ExPEC...
2017: PloS One
https://www.readbyqxmd.com/read/28731826/convergently-evolved-toxic-secondary-metabolites-in-plants-drive-the-parallel-molecular-evolution-of-insect-resistance
#4
Georg Petschenka, Vera Wagschal, Michael von Tschirnhaus, Alexander Donath, Susanne Dobler
Natural selection imposed by natural toxins has led to striking levels of convergent evolution at the molecular level. Cardiac glycosides represent a group of plant toxins that block the Na,K-ATPase, a vital membrane protein in animals. Several herbivorous insects have convergently evolved resistant Na,K-ATPases, and in some species, convergent gene duplications have also arisen, likely to cope with pleiotropic costs of resistance. To understand the genetic basis and predictability of these adaptations, we studied five independent lineages of leaf-mining flies (Diptera: Agromyzidae)...
August 2017: American Naturalist
https://www.readbyqxmd.com/read/28729665/identification-of-proteins-that-specifically-recognize-and-bind-protofibrillar-aggregates-of-amyloid-%C3%AE
#5
Elisabet Wahlberg, M Mahafuzur Rahman, Hanna Lindberg, Elin Gunneriusson, Benjamin Schmuck, Christofer Lendel, Mats Sandgren, John Löfblom, Stefan Ståhl, Torleif Härd
Protofibrils of the 42 amino acids long amyloid-β peptide are transient pre-fibrillar intermediates in the process of peptide aggregation into amyloid plaques and are thought to play a critical role in the pathology of Alzheimer's disease. Hence, there is a need for research reagents and potential diagnostic reagents for detection and imaging of such aggregates. Here we describe an in vitro selection of Affibody molecules that bind to protofibrils of Aβ42cc, which is a stable engineered mimic of wild type Aβ42 protofibrils...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28726847/mapping-genome-wide-transcription-factor-binding-sites-using-dap-seq
#6
Anna Bartlett, Ronan C O'Malley, Shao-Shan Carol Huang, Mary Galli, Joseph R Nery, Andrea Gallavotti, Joseph R Ecker
To enable low-cost, high-throughput generation of cistrome and epicistrome maps for any organism, we developed DNA affinity purification sequencing (DAP-seq), a transcription factor (TF)-binding site (TFBS) discovery assay that couples affinity-purified TFs with next-generation sequencing of a genomic DNA library. The method is fast, inexpensive, and more easily scaled than chromatin immunoprecipitation sequencing (ChIP-seq). DNA libraries are constructed using native genomic DNA from any source of interest, preserving cell- and tissue-specific chemical modifications that are known to affect TF binding (such as DNA methylation) and providing increased specificity as compared with in silico predictions based on motifs from methods such as protein-binding microarrays (PBMs) and systematic evolution of ligands by exponential enrichment (SELEX)...
August 2017: Nature Protocols
https://www.readbyqxmd.com/read/28724752/the-fluid-mechanics-of-transcatheter-heart-valve-leaflet-thrombosis-in-the-neo-sinus
#7
Prem A Midha, Vrishank Raghav, Rahul Sharma, Jose F Condado, Ikechukwu U Okafor, Tanya Rami, Gautam Kumar, Vinod H Thourani, Hasan Jilaihawi, Vasilis Babaliaros, Raj R Makkar, Ajit P Yoganathan
Background -Transcatheter heart valve (THV) thrombosis has been increasingly reported. In these studies, thrombus quantification has been based on 2D assessment of a 3D phenomenon. Methods -Post-procedural four-dimensional, volume-rendered CT (4DCT) data of CoreValve, Evolut R, and SAPIEN 3 transcatheter aortic valve replacement (TAVR) patients enrolled in the RESOLVE trial were included in this analysis. Patients on anticoagulation were excluded. SAPIEN 3 and CoreValve/Evolut R patients with and without hypo-attenuated leaflet thickening (HALT) were included in order to study differences between groups...
July 19, 2017: Circulation
https://www.readbyqxmd.com/read/28722165/dimorphic-ejaculates-and-sperm-release-strategies-associated-with-alternative-mating-behaviors-in-the-squid
#8
Lígia H Apostólico, José E A R Marian
Sperm competition is a powerful postcopulatory selective force influencing male adaptations associated with increasing fertilization success, and it is usually related to the evolution of different strategies of ejaculate expenditure between individuals. Ejaculates may also be influenced by additional selective pressures associated with sperm competition, such as timing between insemination and fertilization, female reproductive tract morphology, and fertilization environment. Also, males that adopt alternative mating tactics may face distinct sperm competition pressures, which may lead to the evolution of intraspecific diversity in ejaculates...
July 18, 2017: Journal of Morphology
https://www.readbyqxmd.com/read/28720900/low-frequency-ultrasound-induced-vegf-suppression-and-synergy-with-dendritic-cell-mediated-anti-tumor-immunity-in-murine-prostate-cancer-cells-in-vitro
#9
Wei Zhang, Wen-De Shou, Yan-Jun Xu, Wen-Kun Bai, Bing Hu
High tumor vascular endothelial growth factor (VEGF) levels are associated with poor treatment outcomes in prostate cancer (PCa), and immune deficiency in the PCa microenvironment, especially suppression of dendritic cell (DC) proliferation, has been confirmed. In this study, we (1) investigated whether VEGF participates in DC suppression in murine PCa cells (RM-1), (2) down-regulated VEGF expression using low-frequency ultrasound and microbubbles (UM), and (3) further explored any synergistic effect on immunological activation...
July 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28720762/quantitative-measurement-of-the-thyroid-uptake-function-of-mouse-by-cerenkov-luminescence-imaging
#10
Chien-Chih Ke, Zi-Ming He, Ya-Ju Hsieh, Chia-Wen Huang, Jia-Je Li, Luen Hwu, Yi-An Chen, Bang-Hung Yang, Chi-Wei Chang, Wen-Sheng Huang, Ren-Shyan Liu
Cerenkov luminescence imaging (CLI) has been an evolutional and alternative approach of nuclear imaging in basic research. This study aimed to measure the (131)I thyroid uptake of mouse using CLI for assessment of thyroid function. Quantification of (131)I thyroid uptake of mice in euthyroid, hypothyroid and hyperthyroid status was performed by CLI and γ-scintigraphy at 24 hours after injection of (131)I. The (131)I thyroid uptake was calculated using the equation: (thyroid counts - background counts)/(counts of injected dose of (131)I) × 100%...
July 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28719838/identification-of-a-prototypical-single-stranded-uracil-dna-glycosylase-from-listeria-innocua
#11
Jing Li, Ye Yang, Jose Guevara, Liangjiang Wang, Weiguo Cao
A recent phylogenetic study on UDG superfamily estimated a new clade of family 3 enzymes (SMUG1-like), which shares a lower homology with canonic SMUG1 enzymes. The enzymatic properties of the newly found putative DNA glycosylase are unknown. To test the potential UDG activity and evaluate phylogenetic classification, we isolated one SMUG1-like glycosylase representative from Listeria innocua (Lin). A biochemical screening of DNA glycosylase activity in vitro indicates that Lin SMUG1-like glycosylase is a single-strand selective uracil DNA glycosylase...
July 8, 2017: DNA Repair
https://www.readbyqxmd.com/read/28719188/phage-selection-of-cyclic-peptides-for-application-in-research-and-drug-development
#12
Kaycie Deyle, Xu-Dong Kong, Christian Heinis
Cyclic peptides can bind to protein targets with high affinities and selectivities, which makes them an attractive modality for the development of research reagents and therapeutics. Additional properties, including low inherent toxicity, efficient chemical synthesis, and facile modification with labels or immobilization reagents, increase their attractiveness. Cyclic peptide ligands against a wide range of protein targets have been isolated from natural sources such as bacteria, fungi, plants, and animals...
July 18, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28716960/bacterial-tubulin-a-b-exhibit-polarized-growth-mixed-polarity-bundling-and-destabilization-by-gtp-hydrolysis
#13
César Díaz-Celis, Viviana I Risca, Felipe Hurtado, Jessica K Polka, Scott D Hansen, Daniel Maturana, Rosalba Lagos, R Dyche Mullins, Octavio Monasterio
Bacteria of the genus Prosthecobacter express homologs of eukaryotic α- and β-tubulin, called BtubA and BtubB, that have been observed to assemble into filaments in presence of GTP. BtubA/B polymers are proposed to be composed in vitro by two to six protofilaments, in contrast to in vivo where they have been reported to form 5-protofilaments tubes named bacterial microtubules (bMTs). The btubAB genes likely entered the Prosthecobacter lineage via horizontal gene transfer and may derive from an early ancestor of the modern eukaryotic microtubule (MT)...
July 17, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28715205/polymerase-chain-transcription-exponential-synthesis-of-rna-and-modified-rna
#14
Tingjian Chen, Floyd E Romesberg
There is increasing demand for RNA and modified RNA oligonucleotides, but in contrast to DNA oligonucleotides, they are typically prohibitively expensive to chemically synthesize, and unlike longer RNAs, they are only inefficiently produced by in vitro transcription, especially when modified. To address these challenges, we previously reported the evolution of a thermostable DNA polymerase, SFM4-3, that more efficiently accepts substrates with 2'-substituents. We now show that SFM4-3 efficiently transcribes RNA or 2'-F-modified RNA and that it also efficiently PCR amplifies oligonucleotides of mixed RNA and DNA composition...
July 17, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28712706/discovery-of-novel-2-4-aryl-2-methylpiperazin-1-yl-pyrimidin-4-ones-as-glycogen-synthase-kinase-3%C3%AE-inhibitors
#15
Toshiyuki Kohara, Kazuki Nakayama, Kazutoshi Watanabe, Shin-Ichi Kusaka, Daiki Sakai, Hiroshi Tanaka, Kenji Fukunaga, Shinji Sunada, Mika Nabeno, Ken-Ichi Saito, Jun-Ichi Eguchi, Akiko Mori, Shinji Tanaka, Tomoko Bessho, Keiko Takiguchi-Hayashi, Takashi Horikawa
We herein describe the results of further evolution of glycogen synthase kinase (GSK)-3β inhibitors from our promising compounds containing a 3-methylmorpholine moiety. Transformation of the morpholine moiety into a piperazine moiety resulted in potent GSK-3β inhibitors. SAR studies focused on the nitrogen atom of the piperazine moiety revealed that a phenyl group afforded potent inhibitory activity toward GSK-3β. Docking studies indicated that the phenyl group on the piperazine nitrogen atom and the methyl group on the piperazine make cation-π and CH-π interactions with GSK-3β respectively...
July 5, 2017: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28711790/six-phenylalanine-ammonia-lyases-from-camellia-sinensis-evolution-expression-and-kinetics
#16
Yingling Wu, Wenzhao Wang, Yanzhi Li, Xinlong Dai, Guoliang Ma, Dawei Xing, Mengqing Zhu, Liping Gao, Tao Xia
Phenylalanine ammonia-lyase (PAL), the branch point enzyme controlling the flow of primary metabolism into second metabolism, converts the L-phenylalanine (L-Phe) to yield cinnamic acid. Based on the sequencing data available from eight transcriptome projects, six PAL genes have been screened out, cloned, and designated as CsPALa-CsPALf. The phylogenetic tree showed that CsPALs were divided into three subgroups, PALa and PALb, PALc and PALd, and PALe and PALf. All six CsPALs exhibited indiscriminate cytosolic locations in epidermis cells and mesophyll cells...
June 29, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/28711549/a-case-of-hypocholesterolemia-and-steatosis-in-a-carrier-of-a-pcsk9-loss-of-function-mutation-and-polymorphisms-predisposing-to-nonalcoholic-fatty-liver-disease
#17
Mathilde Di Filippo, Benoit Vokaer, Nabil G Seidah
We report a new case of hypobetalipoproteinemia in a 44-year-old man of Peruvian origin exhibiting a heterozygous PCSK9 missense mutation (c.946 G>T, p. Gly316Cys). In vitro functional studies demonstrated that this mutation leads to a loss of function of PCSK9 on low-density lipoprotein receptor degradation. This patient exhibited liver steatosis; he was neither diabetic, nor obese or alcoholic, but is a carrier of 2 polymorphisms, p.Ile148Met (rs738409) and p.Glu167Lys (rs58542926) on PNPLA3 and TM6SF2 gene, respectively, previously shown to be associated with nonalcoholic steatosis and fibrosis evolution...
June 13, 2017: Journal of Clinical Lipidology
https://www.readbyqxmd.com/read/28708490/effect-of-season-and-age-on-indian-red-jungle-fowl-gallus-gallus-murghi-semen-characteristics-a-4-year-retrospective-study
#18
B A Rakha, M S Ansari, S Akhter, E Blesbois
The reproductive potential of the adult males is expected to vary with age/season and largely differ not only in closely related avian species but even in subspecies, breeds and/or strains of the same species. Thus, it is pre-requisite to have knowledge of seminal parameters to achieve maximum production potential of at-risk species for ex situ in vitro conservation programs. A 4-year study was designed to evaluate the effect of age and season (spring, summer, autumn and winter) on semen characteristics of Indian red jungle fowl (Gallus gallus murghi) in a retrospective manner...
May 24, 2017: Theriogenology
https://www.readbyqxmd.com/read/28705674/molecular-bases-of-antifungal-resistance-in-filamentous-fungi
#19
Cheshta Sharma, Anuradha Chowdhary
Invasive mould infections due to Aspergillus species, Fusarium spp., Scedosporium spp. and other filamentous fungi remain a significant cause of morbidity and mortality in immunocompromised patients. Antifungal therapy is required for successful patient management; however, limited antifungal drugs and emergence of drug resistance pose a challenge to the clinicians for the effective management of the disease. The evolution of multidrug resistant strains due to selective pressure and the intrinsically resistant pathogenic species are a major concern...
July 10, 2017: International Journal of Antimicrobial Agents
https://www.readbyqxmd.com/read/28702529/assessing-chemotherapeutic-effectiveness-using-a-paper-based-tumor-model
#20
Matthew W Boyce, Gabriel J LaBonia, Amanda B Hummon, Matthew R Lockett
In vitro models for screening new cancer chemotherapeutics often rely on two-dimensional cultures to predict therapeutic potential. Unfortunately, the predictive power of these models is limited, as they fail to recapitulate the complex three-dimensional environments in tumors that promote a chemoresistant phenotype. In this study, we describe the preparation and characterization of paper-based cultures (PBCs) engineered to assess chemotherapeutic effectiveness in three dimensional, diffusion-limited environments...
July 12, 2017: Analyst
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