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81.
Wajid Bilal Anwar Faria Wajid Imran Nisar Haseeb Meraj Sharoze Zafar Ali Al-Shawaqfeh Mustafa Kamal Ekti Ali Riza Khatoon Asia Suchodolski Jan S. 《Functional & integrative genomics》2022,22(1):3-26
Functional & Integrative Genomics - This humble effort highlights the intricate details of metagenomics in a simple, poetic, and rhythmic way. The paper enforces the significance of the... 相似文献
82.
Iqbal Aneela Khan Raham Sher Shehryar Kashmala Imran Anum Ali Faryal Attia Syeda Shah Shahen Mii Masahiro 《Plant Cell, Tissue and Organ Culture》2019,137(1):1-10
Plant Cell, Tissue and Organ Culture (PCTOC) - Four serotypes of the dengue virus that can cause severe disease in humans greatly increases the complexity of vaccine development. In this study, we... 相似文献
83.
Siddiqui Rehan Ahmed Simjee Shabana Usman Kabir Nurul Ateeq Muhammad Shah M. Raza Hussain Syed Saad 《Molecular and cellular biochemistry》2019,450(1-2):43-52
Molecular and Cellular Biochemistry - The protective activity of N-(2-hydroxyphenyl)acetamide (NA-2) and NA-2-coated gold nanoparticles (NA-2-AuNPs) in glycerol-treated model of acute kidney injury... 相似文献
84.
Sajjad Ahmad Bilal Shaker Faisal Ahmad Saad Raza 《Journal of biomolecular structure & dynamics》2019,37(11):2897-2912
Acinetobacter baumannii is an alarming nosocomial pathogen that is resistant to multiple drugs. The pathogen is forefront of scientific attention because of high mortality and morbidity found for its complications in the past decade. As a consequence, identification of novel drug candidates and subsequent designing of novel chemical scaffolds is an imperative need of time. In the present study, we used a recently reported structure of BfmR enzyme and performed structure based virtual screening, MD simulation and binding free energies calculations. MD simulation revealed a profound movement of the best-characterized inhibitor towards the α4-β5-α5 face of the enzyme receiver domain, thus indicating its high affinity for this site compared to phosphorylation. Furthermore, it was observed that the enzyme and enzyme-inhibitor complex have high structure stability with mean RMSD of 1.2 and 1.1 Å, respectively. Binding free energy calculations for the complex unraveled high stability with MMGBSA score of ?26.21?kcal/mol and MMPBSA score of ?1.47?kcal/mol. Van der Waal energy was found highly favorable with value of ?30.25?kcal/mol and dominated significantly the overall binding energy. Furthermore, a novel WaterSwap assay was used to circumvent the limitations of MMGB/PBSA that complements the inhibitor affinity for enzyme active pocket as depicted by the low convergence of Bennett, TI and FEP algorithms. Results yielded from this study will not only give insight into the phenomena of inhibitor movement towards the enzyme receiver domain, but will also provide a useful baseline for designing derivatives with improved biological and pharmacokinetics profiles.
Communicated by Ramaswamy H. Sarma 相似文献
85.
Raphael Petegrosso Zhuliu Li Molly A. Srour Yousef Saad Wei Zhang Rui Kuang 《Proteins》2019,87(6):478-491
The global connectivities in very large protein similarity networks contain traces of evolution among the proteins for detecting protein remote evolutionary relations or structural similarities. To investigate how well a protein network captures the evolutionary information, a key limitation is the intensive computation of pairwise sequence similarities needed to construct very large protein networks. In this article, we introduce label propagation on low-rank kernel approximation (LP-LOKA) for searching massively large protein networks. LP-LOKA propagates initial protein similarities in a low-rank graph by Nyström approximation without computing all pairwise similarities. With scalable parallel implementations based on distributed-memory using message-passing interface and Apache-Hadoop/Spark on cloud, LP-LOKA can search protein networks with one million proteins or more. In the experiments on Swiss-Prot/ADDA/CASP data, LP-LOKA significantly improved protein ranking over the widely used HMM-HMM or profile-sequence alignment methods utilizing large protein networks. It was observed that the larger the protein similarity network, the better the performance, especially on relatively small protein superfamilies and folds. The results suggest that computing massively large protein network is necessary to meet the growing need of annotating proteins from newly sequenced species and LP-LOKA is both scalable and accurate for searching massively large protein networks. 相似文献
86.
Nireeksha Sudhir Rama Varma Marah Damdoum Mohammed Amjed Alsaegh Mithra N. Hegde Suchetha N. Kumari Srinivasan Ramamurthy Jayaraj Narayanan Eisha Imran Juzer Shabbir Zohaib Khurshid 《Current issues in molecular biology》2021,43(1):116
The role of inflammatory mediators in dental pulp is unique. The local environment of pulp responds to any changes in the physiology that are highly fundamental, like odontoblast cell differentiation and other secretory activity. The aim of this review is to assess the role of cathelicidins based on their capacity to heal wounds, their immunomodulatory potential, and their ability to stimulate cytokine production and stimulate immune-inflammatory response in pulp and periapex. Accessible electronic databases were searched to find studies reporting the role of cathelicidins in pulpal inflammation and regeneration published between September 2010 and September 2020. The search was performed using the following databases: Medline, Scopus, Web of Science, SciELO and PubMed. The electronic search was performed using the combination of keywords “cathelicidins” and “dental pulp inflammation”. On the basis of previous studies, it can be inferred that LL-37 plays an important role in odontoblastic cell differentiation and stimulation of antimicrobial peptides. Furthermore, based on these outcomes, it can be concluded that LL-37 plays an important role in reparative dentin formation and provides signaling for defense by activating the innate immune system. 相似文献
87.
Lia Di Saymon Akther Edgaras Bezrucenkovas Larisa Ivanova Brian Sulkow Bing Wu Saad Mneimneh Maria Gomes-Solecki Wei-Gang Qiu 《The ISME journal》2022,16(2):447
Natural populations of pathogens and their hosts are engaged in an arms race in which the pathogens diversify to escape host immunity while the hosts evolve novel immunity. This co-evolutionary process poses a fundamental challenge to the development of broadly effective vaccines and diagnostics against a diversifying pathogen. Based on surveys of natural allele frequencies and experimental immunization of mice, we show high antigenic specificities of natural variants of the outer surface protein C (OspC), a dominant antigen of a Lyme Disease-causing bacterium (Borrelia burgdorferi). To overcome the challenge of OspC antigenic diversity to clinical development of preventive measures, we implemented a number of evolution-informed strategies to broaden OspC antigenic reactivity. In particular, the centroid algorithm—a genetic algorithm to generate sequences that minimize amino-acid differences with natural variants—generated synthetic OspC analogs with the greatest promise as diagnostic and vaccine candidates against diverse Lyme pathogen strains co-existing in the Northeast United States. Mechanistically, we propose a model of maximum antigen diversification (MAD) mediated by amino-acid variations distributed across the hypervariable regions on the OspC molecule. Under the MAD hypothesis, evolutionary centroids display broad cross-reactivity by occupying the central void in the antigenic space excavated by diversifying natural variants. In contrast to vaccine designs based on concatenated epitopes, the evolutionary algorithms generate analogs of natural antigens and are automated. The novel centroid algorithm and the evolutionary antigen designs based on consensus and ancestral sequences have broad implications for combating diversifying pathogens driven by pathogen–host co-evolution.Subject terms: Population genetics, Bacterial genetics 相似文献
88.
Mohamed T. El-Saadony Ahmed M. Saad Hend A. Elakkad Amira M. El-Tahan Omniah A. Alshahrani Mashaeal S. Alshilawi Hanan El-Sayed Shimaa A. Amin Alshaymaa I. Ahmed 《Saudi Journal of Biological Sciences》2022,29(1):346
This work aims to enhance the flavor of functional cucumber juice using herbal extracts of peppermint, basil, lavender, and lemongrass ethanolic extracts and extend its lifetime by controlling the chemical and microbial fluctuations. Cucumber juices were processed as; non-supplemented (J-Con), J-PME, J-BE, J-LE, and J-LEE supplemented with peppermint, basil, lavender, and lemongrass ethanolic extracts, respectively. Peppermint extract was significantly scavenged 88% of DPPH radicals and inhibited the growth of tested gram-positive, gram-negative bacteria and fungi followed by the lemongrass extract. The antioxidant activity of cucumber juices increased due to polyphenols and aroma compounds in the added extracts. However, the antioxidant content was decreased after two months of storage at 4 °C, due to the decrease in polyphenols. The flavor compounds were determined using GC mass, wherein hydrocarbons, acids, alcohols, and carbonyl compounds were the main aroma contents in cucumber juices, and their contents decreased with storage time. Peppermint and lemongrass extracts were significantly (p ≤ 0.05) increased the whiteness of J-PME, and J-LEE, respectively. The highest score of flavor and taste was observed in J-PME that scored 8.3 based on panelists'' reports followed by J-LEE. The PME was significantly maintained 91% of the odor and color of J-PME as compared to other juices. 相似文献
89.
90.
Pericellular proteolysis by leukocytes and tumor cells on substrates: focal activation and the role of urokinase-type plasminogen activator 总被引:12,自引:1,他引:11
Kindzelskii AL Amhad I Keller D Zhou MJ Haugland RP Garni-Wagner BA Gyetko MR Todd RF Petty HR 《Histochemistry and cell biology》2004,121(4):299-310
Previous studies have shown that the urokinase-type plasminogen activator receptor (uPAR) is localized to the adherence sites of leukocytes and tumor cells suggesting that pericellular proteolysis may accompany focal activation of adherence. To assess for focused pericellular proteolytic activity, we prepared two-dimensional substrates coated with FITC-casein or Bodipy FL-BSA. These molecules are poorly fluorescent, but become highly fluorescent after proteolytic degradation. Fluorescent peptide products were observed at adherence sites of stationary human neutrophils and at lamellipodia of polarized neutrophils. During cell migration, multiple regions of proteolysis appeared sequentially beneath the cell. Similarly, proteolytic action was restricted to adherence sites of resting HT1080 tumor cells but localized to the invadopodia of active cells. Using an extracellular fluorescence quenching method, we demonstrate that these fluorescent peptide products are extracellular. The uPA/uPAR system played an important role in the observed proteolytic activation. Plasminogen activator inhibitor-1 significantly reduced focal proteolysis. Sites of focal proteolysis matched the membrane distribution of uPAR. When uPA was dissociated from uPAR by acid washing, substantially reduced pericellular proteolysis was found. uPAR-negative T47D tumor cells did not express significant levels of substrate proteolysis. However, transfectant clones expressing uPAR (for example, T47D-26) displayed high levels of fluorescence indicating proteolysis at adherence sites. To provide further evidence for the role of the uPA/uPAR system in pericellular proteolysis, peritoneal macrophages from uPA knock-out (uPA–/–) and control (uPA+/+) mice were studied. Pericellular proteolysis was dramatically reduced in uPA-negative peritoneal macrophages. Thus, we have: (1) developed a novel methodology to detect pericellular proteolytic function, (2) demonstrated focused activation of proteolytic enzymatic activity in several cell types, (3) demonstrated its usefulness in real-time studies of cell migration, and (4) showed that the uPA/uPAR system is an important contributor to focal pericellular proteolysis. 相似文献