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Behrouz Golichenari, Rahim Nosrati, Aref Farokhi-Fard, Khalil Abnous, Farzam Vaziri, Javad Behravan
Tuberculosis is a major global health problem caused by the bacterium Mycobacterium tuberculosis (Mtb) complex. According to WHO reports, 53 million TB patients died from 2000 to 2016. Therefore, early diagnosis of the disease is of great importance for global health care programs. The restrictions of traditional methods have encouraged the development of innovative methods for rapid, reliable, and cost-effective diagnosis of tuberculosis. In recent years, aptamer-based biosensors or aptasensors have drawn great attention to sensitive and accessible detection of tuberculosis...
June 11, 2018: Biosensors & Bioelectronics
Muhammad Ali, Dario Rangel Shaw, Lei Zhang, Mohamed Fauzi Haroon, Yuko Narita, Abdul-Hamid Emwas, Pascal E Saikaly, Satoshi Okabe
Anaerobic ammonium-oxidizing (anammox) bacteria are well known for their aggregation ability. However, very little is known about cell surface physicochemical properties of anammox bacteria and thus their aggregation abilities have not been quantitatively evaluated yet. Here, we investigated the aggregation abilities of three different anammox bacterial species: "Candidatus Brocadia sinica", "Ca. Jettenia caeni" and "Ca. Brocadia sapporoensis". Planktonic free-living enrichment cultures of these three anammox species were harvested from the membrane bioreactors (MBRs)...
June 12, 2018: Water Research
Franz W R Hippler, Dirceu Mattos-Jr, Rodrigo M Boaretto, Lorraine E Williams
Nitrate uptake by plants is mediated by specific transport proteins in roots (NRTs), which are also dependent on the activity of proton pumps that energize the reaction. Nitrogen (N) metabolism in plants is sensitive to copper (Cu) toxicity conditions. To understand how Cu affects the uptake and assimilation processes, this study assesses the inhibitory effects of elevated Cu levels on the expression of genes related to N absorption, transport and assimilation in roots of Arabidopsis. Plants were grown hydroponically for 45 days, being exposed to a range of Cu concentrations in the last 72 h or alternatively exposed to 5...
June 14, 2018: Journal of Plant Physiology
Shahryar Khoshtinat Nikkhoi, Fatemeh Rahbarizadeh, Davoud Ahmadvand, Seyed Moein Moghimi
The variable domain of the heavy chain antibodies (VHHs) is the smallest (15 kDa) intact single domain antigen-binding fragment. VHHs often exhibit sub-nanomolar affinity for their designated targets and therefore are receiving increasing attention in molecular targeting and nanomedicine engineering. We cloned and expressed four non-overlapping anti-HER2 VHHs in a prokaryotic expression system that yielded periplasmic expression of disulfide-bonded VHHs. Purified VHHs, before and after thiolation, were characterized by Western blot and their functionality against the ecto-domain of HER2 receptor was confirmed by ELISA and flow cytometry...
June 19, 2018: European Journal of Pharmaceutical Sciences
Diego A T Pires, Luisa M R Arake, Luciano P Silva, Alejandro Lopez-Castillo, Maura V Prates, Claudia J Nascimento, Carlos Bloch
A previously undescribed six residues long peptide His-Arg-Phe-Leu-Arg-His was identified and purified from the skin secretion of the amphibian Phyllomedusa centralis. A synthetic analogue carboxyamidated HRFLRH-NH2 showed structural changes induced by CO2 and metal ions in aqueous solution when analyzed by NMR. The present work reports NMR structures for the carboxyamidated hexapeptide in the presence CO2 , Zn2+ and Cd2+ , suggesting possible affinity regions on the polypeptide chain for each ligand. The NMR structures were optimized by DFT to identify probable biding sites of these species in the polypeptide structure...
June 19, 2018: Peptides
Rogério O Faleiros, Daniela P Garçon, Malson N Lucena, John C McNamara, Francisco A Leone
The evolutionary history of the Crustacea reveals ample adaptive radiation and the subsequent occupation of many osmotic niches resulting from physiological plasticity in their osmoregulatory mechanisms. We evaluate osmoregulatory ability in the intertidal, thinstripe hermit crab Clibanarius symmetricus after short-term exposure (6 h) or long-term acclimation (10 days) to a wide salinity range, also analyzing kinetic behavior and α-subunit mRNA expression of the gill (Na+ , K+ )-ATPase. The crab strongly hyper-regulates its hemolymph at 5 and 15‰S (Salinity, g L-1 ) but weakly hyper-regulates up to ≈27‰S...
June 19, 2018: Comparative Biochemistry and Physiology. Part A, Molecular & Integrative Physiology
Sanjay K Choubey, Jeyaraman Jeyakanthan
Histone deacetylase 2 (HDAC2) is an emerging target of Alzheimer's disease. Four featured pharmacophore model (ADRR) with one H-bond acceptor (A), one H-bond donor (D), and two aromatic rings (R) was generated using experimentally reported compounds, ((E-5[3-benzenesulfonamido) phenyl]-N-hydroxypent-2-en-4-ynamide)) and (N'-hydroxy-N-phenyloctanediamide) with IC50 values of 0.16 ± 0.11 nM and 62 ± 0.15 nM, respectively. Quantum Polarized Ligand Docking and Binding Free Energy calculation was performed for the top three identified leads RH01652, JFD02573, and HTS00800 from HitFinder database...
June 22, 2018: Journal of Receptor and Signal Transduction Research
Marco Tjioe, Hyeon Ryoo, Yuji Ishitsuka, Pinghua Ge, Carol Bookwalter, Walter Huynh, Richard J McKenney, Kathleen M Trybus, Paul R Selvin
We develop Magnetic Cytoskeleton Affinity (MiCA) purification, which allows for rapid isolation of molecular motors conjugated to large multivalent quantum dots, in miniscule quantities, which is especially useful for single-molecule applications. When purifying labeled molecular motors, an excess of fluorophores or labels is usually used. However, large labels tend to sediment during the centrifugation step of microtubule affinity purification, a traditionally powerful technique for motor purification. This is solved with MiCA, and purification time is cut from 2 hours to 20 minutes, a significant time-savings when it needs to be done daily...
June 22, 2018: Bioconjugate Chemistry
Noor A Shaik, Zuhier A Awan, Prashant K Verma, Ramu Elango, Babajan Banaganapalli
The life-threatening group of irregular cardiac rhythmic disorders also known as Cardiac Arrhythmias (CA) are caused by mutations in highly conserved Calmodulin (CALM/CaM) genes. Herein, we present a multidimensional approach to diagnose changes in phenotypic, stability, and Ca2+ ion binding properties of CA-causing mutations. Mutation pathogenicity was determined by diverse computational machine learning approaches. We further modeled the mutations in 3D protein structure and analyzed residue level phenotype plasticity...
June 22, 2018: Journal of Cellular Biochemistry
Franziska Sueck, Miklós Poór, Zelma Faisal, Christoph G W Gertzen, Benedikt Cramer, Beáta Lemli, Sándor Kunsági-Máté, Holger Gohlke, Hans-Ulrich Humpf
Ochratoxin A (OTA) is a toxic secondary metabolite produced by several fungal species of the genus Penicillium and Aspergillus . 2′ R -Ochratoxin A (2′ R -OTA) is a thermal isomerization product of OTA formed during food processing at high temperatures. Both compounds are detectable in human blood in concentrations between 0.02 and 0.41 µg/L with 2′ R -OTA being only detectable in the blood of coffee drinkers. Humans have approximately a fifty-fold higher exposure through food consumption to OTA than to 2′ R -OTA...
June 22, 2018: Toxins
Sun-Hee Ahn, Jin-Kyung Lee, Nam Doo Kim, Seok-Ho Kim, Sunwoo Lee, Seunggon Jung, Kee-Oh Chay, Tae-Hoon Lee
Interleukin-1β (IL-1β) is a prominent pro-inflammatory cytokine that is implicated in a variety of autoimmune diseases and plays an important role in host defense against infections. IL-1β activity increases with its increasing binding capacity to IL-1 receptors (IL-1Rs). Thus, numerous studies have targeted the discovery of molecules modulating the interactions between IL-1β and IL-1R1. We have conducted an IL-1R1 structure-based virtual screening to identify small molecules that could alter IL-1β activity, using in silico computational analysis...
June 22, 2018: International Journal of Molecular Sciences
Seungeun Lee, Kumju Youn, GyuTae Lim, Jinhyuk Lee, Mira Jun
Alzheimer’s disease (AD) is the most prevalent neurodegenerative disease, distinctively characterized by senile plaques, neurofibrillary tangles, and synaptic loss, finally resulting in neuronal death. β-Site amyloid precursor protein (APP) cleaving enzyme 1 (BACE1) and cholinesterases have been identified as therapeutic targets for AD, and the discovery of their inhibitors is of critical importance for developing preventive strategies for AD. To discover natural multi-target compounds possessing BACE1, acetylcholinesterase (AChE), and butyrylcholinesterase (BChE) inhibitory properties, major citrus flavanones including hesperetin, naringenin, and hesperidin were evaluated...
June 22, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Shuai Liu, Jixiang Yang, Huiting Jia, Hao Zhou, Jiatong Chen, Tianying Guo
Virus-inspired mimics for gene therapy have attracted increasing attention, because viral vectors show robust efficacy owing to the high infectious nature and efficient endosomal escape. Nonetheless, until now synthetic materials fail to achieve high "infectivity", especially the mimicking of virus spikes for "infection" is underappreciated. Herein, a virus spike mimic by a zinc (Zn) coordinative ligand that shows high affinity towards phosphate-rich cell membranes is reported. Surprisingly, this ligand also demonstrates superior functionality of destabilizing endosomes...
June 22, 2018: ACS Applied Materials & Interfaces
Veronique A J Smits, Elisa Cabrera, Raimundo Freire, David A Gillespie
Claspin was discovered as a Chk1-interacting protein necessary for Chk1 phosphorylation and activation by the upstream kinase, ATR, in response to DNA synthesis inhibition in Xenopus oocyte extracts. Subsequent investigations have defined a molecular model in which Claspin acts as an adaptor or scaffold protein to facilitate activation of Chk1 by ATR within a multi-protein complex that forms on single-stranded DNA at stalled replication forks and sites of DNA damage. Interestingly, Claspin is an unstable protein whose degradation via the proteasome is tightly regulated via ubiquitination and controlled by multiple ubiquitin ligases and de-ubiquitinases...
June 22, 2018: FEBS Journal
Thomas W Kirby, Lars C Pedersen, Scott A Gabel, Natalie R Gassman, Robert E London
Despite the essential roles of pol X family enzymes in DNA repair, information about the structural basis of their nuclear import is limited. Recent studies revealed the unexpected presence of a functional NLS in DNA polymerase β, indicating the importance of active nuclear targeting, even for enzymes likely to leak into and out of the nucleus. The current studies further explore the active nuclear transport of these enzymes by identifying and structurally characterizing the functional NLS sequences in the three remaining human pol X enzymes: terminal deoxynucleotidyl transferase (TdT), DNA polymerase μ (pol μ), and DNA polymerase λ (pol λ)...
June 22, 2018: Traffic
Lina Podda, Andrea Santo, Efisio Mattana, Olga Mayoral, Gianluigi Bacchetta
Invasions by alien Carpobrotus spp. have been recognized as one of the most severe threats to Mediterranean-climate coastal ecosystems and Carpobrotus is considered one of the most widespread invasive alien genera in the Mediterranean Basin. The aims of this study were to characterize seed germination of both C. edulis and its hybrid C. affine acinaciformis, in terms of photoperiod, temperature and salinity. Inter- and intra-specific variability in the responses to photoperiod (12/12 h light and total darkness), constant temperatures (5, 10, 15, 20, 25°C) and an alternating temperature regime (25/10°C), salt stress (0, 125, 250, 500 mM NaCl) and the recovery of seed germination were evaluated for two seed lots of C...
June 22, 2018: Plant Biology
Breeanna Mintmier, Jennifer M McGarry, Courtney Sparacino-Watkins, Joseph Sallmen, Katrin Fischer-Schrader, Axel Magalon, Joseph R McCormick, John F Stolz, Günter Schwarz, Daniel J Bain, Partha Basu
Campylobacter jejuni, a human gastrointestinal pathogen, uses nitrate for growth under microaerophilic conditions using periplasmic nitrate reductase (Nap). The catalytic subunit, NapA, contains two prosthetic groups, an iron sulfur cluster and a molybdenum cofactor. Here we describe the cloning, expression, purification, Michaelis-Menten kinetics (kcat of 5.91 ± 0.18 s-1 and a KM (nitrate) of 3.40 ± 0.44 μM) in solution using methyl viologen as an electron donor. The data suggest that the high affinity of NapA for nitrate could support growth of C...
June 19, 2018: FEMS Microbiology Letters
Derek M Mason, Cédric R Weber, Cristina Parola, Simon M Meng, Victor Greiff, William J Kelton, Sai T Reddy
Antibody engineering is often performed to improve therapeutic properties by directed evolution, usually by high-throughput screening of phage or yeast display libraries. Engineering antibodies in mammalian cells offer advantages associated with expression in their final therapeutic format (full-length glycosylated IgG); however, the inability to express large and diverse libraries severely limits their potential throughput. To address this limitation, we have developed homology-directed mutagenesis (HDM), a novel method which extends the concept of CRISPR/Cas9-mediated homology-directed repair (HDR)...
June 21, 2018: Nucleic Acids Research
Saurabh P Singh, Vandna Kukshal, Paolo De Bona, Edwin Antony, Roberto Galletto
Rim1 is the mitochondrial single-stranded DNA binding protein in Saccharomyces cerevisiae and functions to coordinate replication and maintenance of mtDNA. Rim1 can form homo-tetramers in solution and this species has been assumed to be solely responsible for ssDNA binding. We solved structures of tetrameric Rim1 in two crystals forms which differ in the relative orientation of the dimers within the tetramer. In testing whether the different arrangement of the dimers was due to formation of unstable tetramers, we discovered that while Rim1 forms tetramers at high protein concentration, it dissociates into a smaller oligomeric species at low protein concentrations...
June 21, 2018: Nucleic Acids Research
Richard T Waldron, Hsin-Yuan Su, Honit Piplani, Joseph Capri, Whitaker Cohn, Julian P Whitelegge, Kym F Faull, Sugunadevi Sakkiah, Ravinder Abrol, Wei Yang, Bo Zhou, Michael R Freeman, Stephen J Pandol, Aurelia Lugea
Background & Aims: Heavy alcohol drinking is associated with pancreatitis, whereas moderate intake lowers the risk. Mice fed ethanol long term show no pancreas damage unless adaptive/protective responses mediating proteostasis are disrupted. Pancreatic acini synthesize digestive enzymes (largely serine hydrolases) in the endoplasmic reticulum (ER), where perturbations (eg, alcohol consumption) activate adaptive unfolded protein responses orchestrated by spliced X-box binding protein 1 (XBP1)...
2018: Cellular and Molecular Gastroenterology and Hepatology
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