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https://www.readbyqxmd.com/read/28636368/probing-the-mechanism-of-lal-32-a-gold-nanoparticle-based-antibiotic-discovered-through-small-molecule-variable-ligand-display
#1
Rose Byrne-Nash, Danielle Lucero, Niki Osbaugh, Roberta J Melander, Christian Melander, Daniel L Feldheim
The unrelenting rise of antimicrobial resistant bacteria has necessitated the search for novel antibiotic solutions. Herein we describe further mechanistic studies on a 2.0 nm diameter gold nanoparticle-based antibiotic (designated LAL-32). This antibiotic exhibits bactericidal activity against the Gram-negative bacterium Escherichia coli at 1.0 μΜ, a concentration significantly lower than several clinically available antibiotics (such as ampicillin and gentamicin), and acute treatment with LAL-32 does not give rise to spontaneous resistant mutants...
June 21, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/28635627/molecular-quantum-similarity-chemical-reactivity-and-database-screening-of-3d-pharmacophores-of-the-protein-kinases-a-b-and-g-from-mycobacterium-tuberculosis
#2
Alejandro Morales-Bayuelo
Mycobacterium tuberculosis remains one of the world's most devastating pathogens. For this reason, we developed a study involving 3D pharmacophore searching, selectivity analysis and database screening for a series of anti-tuberculosis compounds, associated with the protein kinases A, B, and G. This theoretical study is expected to shed some light onto some molecular aspects that could contribute to the knowledge of the molecular mechanics behind interactions of these compounds, with anti-tuberculosis activity...
June 21, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28633355/how-proteins-bind-to-dna-target-discrimination-and-dynamic-sequence-search-by-the-telomeric-protein-trf1
#3
Milosz Wieczór, Jacek Czub
Target search as performed by DNA-binding proteins is a complex process, in which multiple factors contribute to both thermodynamic discrimination of the target sequence from overwhelmingly abundant off-target sites and kinetic acceleration of dynamic sequence interrogation. TRF1, the protein that binds to telomeric tandem repeats, faces an intriguing variant of the search problem where target sites are clustered within short fragments of chromosomal DNA. In this study, we use extensive (>0.5 ms in total) MD simulations to study the dynamical aspects of sequence-specific binding of TRF1 at both telomeric and non-cognate DNA...
June 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28630480/pro-invasive-stimuli-and-the-interacting-protein-hsp70-favour-the-route-of-alpha-enolase-to-the-cell-surface
#4
Giovanni Perconti, Cristina Maranto, Daniele P Romancino, Patrizia Rubino, Salvatore Feo, Antonella Bongiovanni, Agata Giallongo
Cell surface expression of alpha-enolase, a glycolytic enzyme displaying moonlighting activities, has been shown to contribute to the motility and invasiveness of cancer cells through the protein non-enzymatic function of binding plasminogen and enhancing plasmin formation. Although a few recent records indicate the involvement of protein partners in the localization of alpha-enolase to the plasma membrane, the cellular mechanisms underlying surface exposure remain largely elusive. Searching for novel interactors and signalling pathways, we used low-metastatic breast cancer cells, a doxorubicin-resistant counterpart and a non-tumourigenic mammary epithelial cell line...
June 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28626588/uhrf1-is-required-for-basal-stem-cell-proliferation-in-response-to-airway-injury
#5
Handan Xiang, Lifeng Yuan, Xia Gao, Peter B Alexander, Omar Lopez, Calvin Lau, Yi Ding, Mengyang Chong, Tao Sun, Rui Chen, Si-Qi Liu, Haiyang Wu, Ying Wan, Scott H Randell, Qi-Jing Li, Xiao-Fan Wang
Cellular senescence is a cell fate characterized by an irreversible cell cycle arrest, but the molecular mechanism underlying this senescence hallmark remains poorly understood. Through an unbiased search for novel senescence regulators in airway basal cells, we discovered that the epigenetic regulator ubiquitin-like with PHD and ring finger domain-containing protein 1 (UHRF1) is critical for regulating cell cycle progression. Upon injury, basal cells in the mouse airway rapidly induce the expression of UHRF1 in order to stimulate stem cell proliferation and tissue repair...
2017: Cell Discovery
https://www.readbyqxmd.com/read/28624993/cancer-stem-cell-marker-glycosylation-nature-function-and-significance
#6
REVIEW
Brody W Mallard, Joe Tiralongo
Glycans are essential for the maintenance of normal biological function, with alterations in glycan expression being a hallmark of cancer. Cancer stem cells (CSCs) are a subset of cells within a tumour capable of self-renewal, cellular differentiation and resistances to conventional therapies. As is the case with stem cells, marker proteins present on the cell surface are frequently used to identify and enrich CSCs, with the expression of these markers statistical correlating with the likelihood of cancer recurrence and overall patient survival...
June 17, 2017: Glycoconjugate Journal
https://www.readbyqxmd.com/read/28615921/data-independent-acquisition-and-parallel-reaction-monitoring-mass-spectrometry-identification-of-serum-biomarkers-for-ovarian-cancer
#7
Navin Rauniyar, Gang Peng, TuKiet T Lam, Hongyu Zhao, Gil Mor, Kenneth R Williams
A data-independent acquisition (DIA)/parallel reaction monitoring (PRM) workflow was implemented to identify improved ovarian cancer biomarkers. Data-independent acquisition on ovarian cancer versus control sera and literature searches identified 50 biomarkers and indicated that apolipoprotein A-IV (ApoA-IV) is the most significantly differentially regulated protein. Parallel reaction monitoring with Targeted Ovarian Cancer Proteome Assay validated differential ApoA-IV expression and quantified 9 other biomarkers...
2017: Biomarker Insights
https://www.readbyqxmd.com/read/28615508/integrative-bioinformatics-analysis-identifies-robo1-as-a-potential-therapeutic-target-modified-by-mir-218-in-hepatocellular-carcinoma
#8
Junqing Wang, Yunyun Zhou, Xiaochun Fei, Xunhua Chen, Rui Chen, Zhenggang Zhu, Yongjun Chen
Patients diagnosed with advanced hepatocellular carcinoma (HCC) presented poor prognosis and short survival time. Althouth accumulating contribution of continuous research has gradually revealed complex tumorigenesis mechanism of HCC with numerous and jumbled biomarkers, those specific ones for HCC diagnose and therapeutic treatment are required illustration. Multiple genes over-expressed in HCC specimens with at least 1.5 fold change were cohorted, compared with the non-cancerous tissues through integrative bioinformatics analysis from Gene Expression Omnibus (GEO) datasets GSE14520 and GSE6764, including 445 and 45 cases of samples spearatly, along with intensive exploration on the Cancer Genome Altas (TCGA) dataset of liver cancer...
May 23, 2017: Oncotarget
https://www.readbyqxmd.com/read/28614919/-effects-of-developmental-exposure-to-dehp-on-learning-and-memory-of-mice
#9
D J Wu, B B Luo, Q W Feng, Q N Wang
Objective: To investigate the effects of developmental exposure to DEHP on learning and memory of mice. Methods: Male littermates of ICR mice randomly assigned to five experimental groups (n=14 for each condition) on PND4 to receive distilled water, vehicle and 10, 50 and 200 mg/ (kg·d) DEHP from PND5 to PND38 by gavage, weighing and recording body weight of mice. Open field task were conducted on PND 26 and Morris water maze task were begun from PND30 to PND 37 to evaluate spontaneous exploration activity and emotion, spatial learning and memory performance of pubertal mice, respectively...
April 20, 2017: Chinese Journal of Industrial Hygiene and Occupational Diseases
https://www.readbyqxmd.com/read/28612535/-prediction-and-analysis-of-epitopes-in-clpp2-of-mycobacterium-tuberculosis
#10
Si-Jing Liu, Ming-Juan Jiang, Qi-Kang Pu, Chen-Yan Ren, Lin Su, Xiang Zhang, Chuan Wang
OBJECTIVES: To predict and analyze the antigenic epitopes in Mycobacterium tuberculosis protein caseinolytic protease P2 (clpP2), and explore its possibility to be applied as a new tuberculosis (TB) vaccine and drug development target. METHODS: Secondary structure of clpP2 based on nucleic sequence was predicted by DNA Star software. The homologous sequence conformation were analyzed by Swiss-Model online software. T cells antigenic epitopes were predicted through VaxiPred, and B cell epitopes were predicted by combining use of several different prediction programs, such as ABCpred, COBEPro and BepiPredPred...
March 2017: Sichuan da Xue Xue Bao. Yi Xue Ban, Journal of Sichuan University. Medical Science Edition
https://www.readbyqxmd.com/read/28611186/success-failure-and-transparency-in-biomarker-based-drug-development-a-case-study-of-cholesteryl-ester-transfer-protein-inhibitors
#11
Spencer Phillips Hey, Jessica M Franklin, Jerry Avorn, Aaron S Kesselheim
BACKGROUND: Although biomarkers are used as surrogate measures for drug targeting and approval and are generally based on plausible biological hypotheses, some are found to not correlate well with clinical outcomes. Over-reliance on inadequately validated biomarkers in drug development can lead to harm to trial subjects and patients and to research waste. To shed greater light on the process and ethics of biomarker-based drug development, we conducted a systematic portfolio analysis of cholesterol ester transfer protein inhibitors, a drug class designed to improve lipid profiles and prevent cardiovascular events...
June 2017: Circulation. Cardiovascular Quality and Outcomes
https://www.readbyqxmd.com/read/28610996/from-cheminformatics-to-structure-based-design-web-services-and-desktop-applications-based-on-the-naomi-library
#12
Stefan Bietz, Therese Inhester, Florian Lauck, Kai Sommer, Mathias M von Behren, Rainer Fährrolfes, Florian Flachsenberg, Agnes Meyder, Eva Nittinger, Thomas Otto, Matthias Hilbig, Karen T Schomburg, Andrea Volkamer, Matthias Rarey
Nowadays, computational approaches are an integral part of life science research. Problems related to interpretation of experimental results, data analysis, or visualization tasks highly benefit from the achievements of the digital era. Simulation methods facilitate predictions of physicochemical properties and can assist in understanding macromolecular phenomena. Here, we will give an overview of the methods developed in our group that aim at supporting researchers from all life science areas. Based on state-of-the-art approaches from structural bioinformatics and cheminformatics, we provide software covering a wide range of research questions...
June 10, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28610419/gene-expression-profiling-of-chemokines-and-their-receptors-in-low-and-high-grade-astrocytoma
#13
Ira Sharma, Avninder Singh, Karam Chand Sharma, Sunita Saxena
Background: Despite intense interest in molecular characterization and searches for novel therapeutic targets, the glioblastoma remains a formidable clinical challenge. Among many contributors to gliomagenesis, chemokines have drawn special attention due to their involvement in a plethora of biological processes and pathological conditions. In the present study we aimed to elucidate any pro-gliomagenic chemokine axis and probable roles in development of glioblastoma multiforme (GBM). Method: An array of 84 chemokines, chemokine receptors and related genes were studied by real time PCR with comparison between low grade astrocytoma (diffuse astrocytoma – grade II) and high grade astrocytoma (glioblastoma multiforme – grade IV)...
May 1, 2017: Asian Pacific Journal of Cancer Prevention: APJCP
https://www.readbyqxmd.com/read/28605995/dna-trinucleotide-gaa-repeats-in-human-genome-hint-for-disease-pathogenesis
#14
Himanshu Narayan Singh, Barbara Scheiber-Mojdehkar, Moganty R Rajeswari
Short DNA triplet repeats are generally considered to 'benign' in nature, however, it can lead to abnormal genetic features by inducing hyper expansion including mutational hotspots, unusual DNA structure etc. Thus, the expanded DNA base triplets in human genome are expected to play crucial role in disease pathogenesis. One such triplet repeat expansion of (GAA) is observed in FXN gene which is well established to cause neurological disease "Friedreich's ataxia". To explore the association of repeats in other genes if any, we performed a systematic search in the entire human genome...
June 12, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28605292/targeting-the-gram-negative-bacteria-peptidoglycan-synthase-mray-as-a-new-approach-for-monoclonal-antibody-anti-bacterial-activity
#15
Jun Cao, Fei Yi, Qiufeng Tian, Guanghui Dang, Wei Si, Siguo Liu, Shenye Yu
The use of antibiotics to target bacteria is a well-validated approach for controlling infections in animals and humans. Peptidoglycan biosynthesis is a crucial process in bacteria, and the conserved peptidoglycan synthase MraY is an attractive target for drug design. However, due to the lack of detailed MraY structural information, antibiotics targeting MraY have not yet been developed. In the present study, two hydrophilic regions of MraY from Escherichia coli were expressed as a fusion protein and used to raise a monoclonal antibody in mice...
June 12, 2017: Human Vaccines & Immunotherapeutics
https://www.readbyqxmd.com/read/28604122/blood-stage-malaria-vaccines-post-genome-strategies-for-the-identification-of-novel-vaccine-candidates
#16
Edward H Ntege, Eizo Takashima, Masayuki Morita, Hikaru Nagaoka, Tomoko Ishino, Takafumi Tsuboi
An efficacious malaria vaccine is necessary to advance the current control measures towards malaria elimination. To-date, only RTS,S/AS01, a leading pre-erythrocytic stage vaccine completed phase 3 trials, but with an efficacy of 28-36% in children, and 18-26% in infants, that waned over time. Blood-stage malaria vaccines protect against disease, and are considered effective targets for the logical design of next generation vaccines to improve the RTS,S field efficacy. Therefore, novel blood-stage vaccine candidate discovery efforts are critical, albeit with several challenges including, high polymorphisms in vaccine antigens, poor understanding of targets of naturally protective immunity, and difficulties in the expression of high AT-rich plasmodial proteins...
June 19, 2017: Expert Review of Vaccines
https://www.readbyqxmd.com/read/28601044/mass-spectrometry-as-a-tool-for-biomarkers-searching-in-gynecological-oncology
#17
REVIEW
Paulina Banach, Wiktor Suchy, Paweł Dereziński, Jan Matysiak, Zenon J Kokot, Ewa Nowak-Markwitz
Tumors of the female reproductive tract are an important target for the development of diagnostic, prognostic and therapeutic strategies. Recent research has turned to proteomics based on mass spectrometry techniques, to achieve more effective diagnostic results. Mass spectrometry (MS) enables identification and quantification of multiple molecules simultaneously in a single experiment according to mass to charge ratio (m/z). Several proteomic strategies may be applied to establish the function of a particular protein/peptide or to identify a novel disease and specific biomarkers related to it...
June 7, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28600543/innate-and-adaptive-immunity-are-progressively-activated-in-parallel-with-renal-injury-in-the-5-6-renal-ablation-model
#18
Camilla Fanelli, Simone C A Arias, Flavia G Machado, Jessica K Okuma, Denise M A C Malheiros, Hatylas Azevedo, Carlos A Moreira-Filho, Niels O S Camara, Clarice K Fujihara, Roberto Zatz
The mechanisms triggering renal inflammation in chronic kidney disease (CKD) are unclear. We performed a detailed analysis of the time course of innate and adaptive immunity activation in the 5/6 renal ablation (Nx) model. Munich-Wistar rats undergoing Nx were studied 15, 60 and 120 days after ablation. Hypertension, albuminuria, creatinine retention, interstitial expansion and infiltration by macrophages and T-lymphocytes were already evident 15 days after Nx. PCR-array was used to screen for altered gene expression, whereas gene and protein expressions of TLR4, CASP1, IL-1β and NLRP3 were individually assessed...
June 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28599476/identification-of-gene-markers-associated-with-metastasis-in-clear-cell-renal-cell-carcinoma
#19
Hailing Yang, Pengfei Huo, Guozhang Hu, Bo Wei, Dalian Kong, Hongjun Li
The present study aimed to screen potential target genes for the early diagnosis and treatment of early metastatic clear cell renal cell carcinoma (ccRCC) using the microarray data of early metastatic and non-metastatic ccRCC samples. The DNA microarray dataset GSE47352 was downloaded from Gene Expression Omnibus and included 4 early metastatic and 5 non-metastatic ccRCC samples. Differentially expressed genes (DEGs) were screened using the limma package. Then, pheatmap package was used to conduct two-way clustering for the DEGs...
June 2017: Oncology Letters
https://www.readbyqxmd.com/read/28596971/soluble-urokinase-receptor-and-the-kidney-response-in-diabetes-mellitus
#20
REVIEW
Ranadheer R Dande, Vasil Peev, Mehmet M Altintas, Jochen Reiser
Diabetic nephropathy (DN) is the leading cause of end-stage renal disease (ESRD) worldwide. DN typically manifests by glomerular hyperfiltration and microalbuminuria; then, the disease progresses to impaired glomerular filtration rate, which leads to ESRD. Treatment options for DN include the strict control of blood glucose levels and pressure (e.g., intraglomerular hypertension). However, the search for novel therapeutic strategies is ongoing. These include seeking specific molecules that contribute to the development and progression of DN to potentially interfere with these "molecular targets" as well as with the cellular targets within the kidney such as podocytes, which play a major role in the pathogenesis of DN...
2017: Journal of Diabetes Research
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