Publications by authors named "Rafiq Islam"

36 Publications

Genetic loci regulating cadmium content in rice grains.

Euphytica 2021 10;217(3):35. Epub 2021 Feb 10.

School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 3UU UK.

It has been estimated that up to 90% of human exposure to cadmium is through food, and that cadmium within rice grains can be a major contributor to that dietary source. In this study genome wide association mapping was conducted on the Bengal and Assam Aus Panel (BAAP) of rice to identify quantitative trait loci and candidate genes for lowering grain cadmium. Field experiments were conducted over two years under two different irrigation systems: continually flooded and alternate wetting and drying (AWD). There was significant effects of water treatment, genotype, and genotype by water treatment interaction. Importantly, AWD increased grain cadmium, on average, by 49.6% and 108.8% in year 1 and 2 respectively. There was between 4.6 and 28 fold variation in cadmium concentration. A total of 58 QTLs were detected but no loci are clearly specific to one water regime despite approximately 20% of variation attributable to genotype by water regime interaction. A number of QTLs were consistent across most water treatments and years. These included QTLs on chromosome 7 (7.23-7.61, 8.93-9.04, and 29.12-29.14 Mbp), chromosome 5 (8.66-8.72 Mbp), and chromosome 9 (11.46-11.64 Mbp). Further analysis of the loci on chromosome 7 (8.93-9.04 Mbp), identified the candidate gene , where cultivars with a deletion upstream of the gene had higher concentrations of cadmium compared to the cultivars that did not have the deletion. The distribution of alleles within the BAAP suggest this QTL is easily detected in this population because it is composed of cultivars. Local genome cluster analysis suggest high Cd alleles are uncommon, but should be avoided in breeding.

Supplementary Information: The online version contains supplementary material available at (10.1007/s10681-020-02752-1).
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http://dx.doi.org/10.1007/s10681-020-02752-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7875855PMC
February 2021

Applications of gold nanoparticles in ELISA, PCR, and immuno-PCR assays: A review.

Anal Chim Acta 2021 Jan 2;1143:250-266. Epub 2020 Sep 2.

Department of Chemistry, 550 University Ave. Charlottetown, PE, C1A 4P3, Canada; Faculty of Sustainable Design Engineering, University of Prince Edward Island, 550 University Ave. Charlottetown, PE, C1A 4P3, Canada. Electronic address:

Development of state-of-the-art assays for sensitive and specific detection of disease biomarkers has received significant interest for early detection and prevention of various diseases. Enzyme Linked Immunosorbent assays (ELISA) and Polymerase Chain Reaction (PCR) are two examples of proteins and nucleic acid detection assays respectively, which have been widely used for the sensitive detection of target analytes in biological fluids. Recently, immuno-PCR has emerged as a sensitive detection method, where high specificity of sandwich ELISA assays is combined with high sensitivity of PCR for trace detection of biomarkers. However, inherent disadvantages of immuno-PCR assays limit their application as rapid and sensitive detection method in clinical settings. With advances in nanomaterials, nanoparticles-based immunoassays have been widely used to improve the sensitivity and simplicity of traditional immunoassays. Owing to facile synthesis, surface functionalization, and superior optical and electronic properties, gold nanoparticles have been at the forefront of sensing and detection technologies and have been extensively studied to improve the efficacies of immunoassays. This review provides a brief history of immuno-PCR assays and specifically focuses on the role of gold nanoparticles to improve the sensitivity and specificity of ELISA, PCR and immuno-PCR assays.
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http://dx.doi.org/10.1016/j.aca.2020.08.030DOI Listing
January 2021

2019 White Paper On Recent Issues in Bioanalysis: FDA BMV Guidance, ICH M10 BMV Guideline and Regulatory Inputs ( - Recommendations on 2018 FDA BMV Guidance, 2019 ICH M10 BMV Draft Guideline and Regulatory Agencies' Input on Bioanalysis, Biomarkers and Immunogenicity).

Bioanalysis 2019 Dec 9;11(23):2099-2132. Epub 2019 Dec 9.

US FDA, Silver Spring, MD, USA.

The 2019 13 Workshop on Recent Issues in Bioanalysis (WRIB) took place in New Orleans, LA on 1-5 April 2019 with an attendance of over 1000 representatives from pharmaceutical/biopharmaceutical companies, biotechnology companies, contract research organizations and regulatory agencies worldwide. WRIB was once again a 5-day, week-long event - a full immersion week of bioanalysis, biomarkers, immunogenicity and gene therapy. As usual, it was specifically designed to facilitate sharing, reviewing, discussing and agreeing on approaches to address the most current issues of interest including both small- and large-molecule bioanalysis involving LCMS, hybrid LBA/LCMS, LBA cell-based/flow cytometry assays and qPCR approaches. This 2019 White Paper encompasses recommendations emerging from the extensive discussions held during the workshop, and is aimed to provide the bioanalytical community with key information and practical solutions on topics and issues addressed, in an effort to enable advances in scientific excellence, improved quality and better regulatory compliance. Due to its length, the 2019 edition of this comprehensive White Paper has been divided into three parts for editorial reasons. This publication (Part 2) covers the recommendations on the 2018 FDA BMV guidance, 2019 ICH M10 BMV draft guideline and regulatory agencies' input on bioanalysis, biomarkers, immunogenicity and gene therapy. Part 1 (Innovation in small molecules and oligonucleotides and mass spectrometry method development strategies for large molecules bioanalysis) and Part 3 (New insights in biomarker assay validation, current and effective strategies for critical reagent management, flow cytometry validation in drug discovery and development and CLSI H62, interpretation of the 2019 FDA immunogenicity guidance and gene therapy bioanalytical challenges) are published in volume 10 of , issues 22 and 24 (2019), respectively.
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http://dx.doi.org/10.4155/bio-2019-0270DOI Listing
December 2019

Stability issues in bioanalysis.

Bioanalysis 2019 Oct;11(20):1813-1814

Celerion, Lincoln, NE 68502, USA.

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http://dx.doi.org/10.4155/bio-2019-0259DOI Listing
October 2019

GCC Consolidated Feedback to ICH on the 2019 ICH M10 Bioanalytical Method Validation Draft Guideline.

Bioanalysis 2019 Sep 30;11(18s):1-228. Epub 2019 Sep 30.

WuXi Apptec, Shanghai, China.

The 13 GCC Closed Forum for Bioanalysis was held in New Orleans, Louisiana, USA on April 5, 2019. This GCC meeting was organized to discuss the contents of the 2019 ICH M10 Bioanalytical Method Validation Draft Guideline published in February 2019 and consolidate the feedback of the GCC members. In attendance were 63 senior-level participants from eight countries representing 44 bioanalytical CRO companies/sites. This event represented a unique opportunity for CRO bioanalytical experts to share their opinions and concerns regarding the ICH M10 Bioanalytical Method Validation Draft Guideline and to build unified comments to be provided to the ICH.
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http://dx.doi.org/10.4155/bio-2019-0207DOI Listing
September 2019

Plasmid DNA nicking- a Novel Activity of Soybean Trypsin Inhibitor and Bovine Aprotinin.

Sci Rep 2019 08 12;9(1):11596. Epub 2019 Aug 12.

Laboratory of Biochemistry, Northwest Missouri State University, 7314 N. Tullis Ave, Kansas City, Missouri, 64158, United States of America.

Protease inhibitors, such as trypsin inhibitor, serum alpha-1 antitrypsin, or liver aprotinin, are a class of proteins that competitively bind and block the catalytic activity of proteolytic enzymes with wide ranging biological functions. A significant number of protease inhibitors have also been shown to possess antimicrobial activity, presumed to contribute in defense against pathogenic microorganisms as plants with higher levels of protease inhibitors tend to exhibit increased resistance towards pathogens. Two proposed mechanisms for the antimicrobial activity are combating microbial proteases that play roles in disease development and disruption of microbial cell wall & membrane necessary for survival. Here we show for the first time a novel activity of soybean trypsin inhibitor and bovine aprotinin that they nick supercoiled, circular plasmid DNA. A number of experiments conducted to demonstrate the observed DNA nicking activity is inherent, rather than a co-purified, contaminating nuclease. The nicking of the plasmid results in markedly reduced efficiencies in transformation of E. coli and transfection of HEK293T cells. Thus, this work reveals yet a new mechanism for the antimicrobial activity by protease inhibitors.
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http://dx.doi.org/10.1038/s41598-019-48068-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6690959PMC
August 2019

12th GCC Closed Forum: critical reagents; oligonucleotides; CoA; method transfer; HRMS; flow cytometry; regulatory findings; stability and immunogenicity.

Bioanalysis 2019 Jun 19;11(12):1129-1138. Epub 2019 Jul 19.

WuXi Apptec, Plainsboro, NJ 08536, USA.

The 12th GCC Closed Forum was held in Philadelphia, PA, USA, on 9 April 2018. Representatives from international bioanalytical Contract Research Organizations were in attendance in order to discuss scientific and regulatory issues specific to bioanalysis. The issues discussed at the meeting included: critical reagents; oligonucleotides; certificates of analysis; method transfer; high resolution mass spectrometry; flow cytometry; recent regulatory findings and case studies involving stability and nonclinical immunogenicity. Conclusions and consensus from discussions of these topics are included in this article.
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http://dx.doi.org/10.4155/bio-2019-0131DOI Listing
June 2019

Recommendations for classification of commercial LBA kits for biomarkers in drug development from the GCC for bioanalysis.

Bioanalysis 2019 Apr 17;11(7):645-653. Epub 2019 Apr 17.

WuXi Apptec, Plainsboro, NJ, USA.

Over the last decade, the use of biomarker data has become integral to drug development. Biomarkers are not only utilized for internal decision-making by sponsors; they are increasingly utilized to make critical decisions for drug safety and efficacy. As the regulatory agencies are routinely making decisions based on biomarker data, there has been significant scrutiny on the validation of biomarker methods. Contract research organizations regularly use commercially available immunoassay kits to validate biomarker methods. However, adaptation of such kits in a regulated environment presents significant challenges and was one of the key topics discussed during the 12th Global Contract Research Organization Council for Bioanalysis (GCC) meeting. This White Paper reports the GCC members' opinion on the challenges facing the industry and the GCC recommendations on the classification of commercial kits that can be a win-win for commercial kit vendors and end users.
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http://dx.doi.org/10.4155/bio-2019-0072DOI Listing
April 2019

2018 White Paper on Recent Issues in Bioanalysis: focus on flow cytometry, gene therapy, cut points and key clarifications on BAV (Part 3 - LBA/cell-based assays: immunogenicity, biomarkers and PK assays).

Bioanalysis 2018 Dec 29;10(24):1973-2001. Epub 2018 Nov 29.

Amador Bioscience, Pleasanton, CA, USA (formerly of OncoMed, Redwood City, CA, USA).

The 2018 12 Workshop on Recent Issues in Bioanalysis took place in Philadelphia, PA, USA on April 9-13, 2018 with an attendance of over 900 representatives from pharmaceutical/biopharmaceutical companies, biotechnology companies, contract research organizations and regulatory agencies worldwide. WRIB was once again a 5-day full immersion in bioanalysis, biomarkers and immunogenicity. As usual, it was specifically designed to facilitate sharing, reviewing, discussing and agreeing on approaches to address the most current issues of interest including both small- and large-molecule bioanalysis involving LCMS, hybrid LBA/LCMS and LBA/cell-based assays approaches. This 2018 White Paper encompasses recommendations emerging from the extensive discussions held during the workshop and is aimed to provide the bioanalytical community with key information and practical solutions on topics and issues addressed, in an effort to enable advances in scientific excellence, improved quality and better regulatory compliance. Due to its length, the 2018 edition of this comprehensive White Paper has been divided into three parts for editorial reasons. This publication (Part 3) covers the recommendations for large molecule bioanalysis, biomarkers and immunogenicity using LBA and cell-based assays. Part 1 (LCMS for small molecules, peptides, oligonucleotides and small molecule biomarkers) and Part 2 (hybrid LBA/LCMS for biotherapeutics and regulatory agencies' inputs) are published in volume 10 of , issues 22 and 23 (2018), respectively.
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http://dx.doi.org/10.4155/bio-2018-0287DOI Listing
December 2018

11th GCC Closed Forum: cumulative stability; matrix stability; immunogenicity assays; laboratory manuals; biosimilars; chiral methods; hybrid LBA/LCMS assays; fit-for-purpose validation; China Food and Drug Administration bioanalytical method validation.

Bioanalysis 2018 Apr 27;10(7):433-444. Epub 2018 Apr 27.

Worldwide Clinical Trials, Austin, TX, USA.

The 11th Global CRO Council Closed Forum was held in Universal City, CA, USA on 3 April 2017. Representatives from international CRO members offering bioanalytical services were in attendance in order to discuss scientific and regulatory issues specific to bioanalysis. The second CRO-Pharma Scientific Interchange Meeting was held on 7 April 2017, which included Pharma representatives' sharing perspectives on the topics discussed earlier in the week with the CRO members. The issues discussed at the meetings included cumulative stability evaluations, matrix stability evaluations, the 2016 US FDA Immunogenicity Guidance and recent and unexpected FDA Form 483s on immunogenicity assays, the bioanalytical laboratory's role in writing PK sample collection instructions, biosimilars, CRO perspectives on the use of chiral versus achiral methods, hybrid LBA/LCMS assays, applications of fit-for-purpose validation and, at the Global CRO Council Closed Forum only, the status and trend of current regulated bioanalytical practice in China under CFDA's new BMV policy. Conclusions from discussions of these topics at both meetings are included in this report.
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http://dx.doi.org/10.4155/bio-2018-0014DOI Listing
April 2018

2017 White Paper on recent issues in bioanalysis: a global perspective on immunogenicity guidelines & biomarker assay performance (Part 3 - LBA: immunogenicity, biomarkers and PK assays).

Bioanalysis 2017 Dec 5;9(24):1967-1996. Epub 2017 Dec 5.

BioMarin Pharmaceutical, San Rafael, CA, USA.

The 2017 11th Workshop on Recent Issues in Bioanalysis took place in Los Angeles/Universal City, California, on 3-7 April 2017 with participation of close to 750 professionals from pharmaceutical/biopharmaceutical companies, biotechnology companies, contract research organizations and regulatory agencies worldwide. WRIB was once again a 5-day, week-long event - a full immersion week of bioanalysis, biomarkers and immunogenicity. As usual, it was specifically designed to facilitate sharing, reviewing, discussing and agreeing on approaches to address the most current issues of interest including both small- and large-molecule analysis involving LC-MS, hybrid ligand-binding assay (LBA)/LC-MS and LBA approaches. This 2017 White Paper encompasses recommendations emerging from the extensive discussions held during the workshop, and is aimed to provide the bioanalytical community with key information and practical solutions on topics and issues addressed, in an effort to enable advances in scientific excellence, improved quality and better regulatory compliance. Due to its length, the 2017 edition of this comprehensive White Paper has been divided into three parts for editorial reasons. This publication (Part 3) covers the recommendations for large-molecule bioanalysis, biomarkers and immunogenicity using LBA. Part 1 (LC-MS for small molecules, peptides and small molecule biomarkers) and Part 2 (hybrid LBA/LC-MS for biotherapeutics and regulatory agencies' inputs) are published in volume 9 of Bioanalysis, issues 22 and 23 (2017), respectively.
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http://dx.doi.org/10.4155/bio-2017-4974DOI Listing
December 2017

2017 White Paper on recent issues in bioanalysis: aren't BMV guidance/guidelines 'Scientific'? (Part 1 - LCMS: small molecules, peptides and small molecule biomarkers).

Bioanalysis 2017 Nov 17;9(22):1807-1825. Epub 2017 Nov 17.

UK MHRA, London, UK.

The 2017 11th Workshop on Recent Issues in Bioanalysis (11th WRIB) took place in Los Angeles/Universal City, California from 3 April 2017 to 7 April 2017 with participation of close to 750 professionals from pharmaceutical/biopharmaceutical companies, biotechnology companies, contract research organizations and regulatory agencies worldwide. WRIB was once again a 5-day, weeklong event - A Full Immersion Week of Bioanalysis, Biomarkers and Immunogenicity. As usual, it was specifically designed to facilitate sharing, reviewing, discussing and agreeing on approaches to address the most current issues of interest including both small and large molecule analysis involving LCMS, hybrid LBA/LCMS and ligand-binding assay (LBA) approaches. This 2017 White Paper encompasses recommendations emerging from the extensive discussions held during the workshop, and is aimed to provide the bioanalytical community with key information and practical solutions on topics and issues addressed, in an effort to enable advances in scientific excellence, improved quality and better regulatory compliance. Due to its length, the 2017 edition of this comprehensive White Paper has been divided into three parts for editorial reasons. This publication (Part 1) covers the recommendations for Small Molecules, Peptides and Small Molecule Biomarkers using LCMS. Part 2 (Biotherapeutics, Biomarkers and Immunogenicity Assays using Hybrid LBA/LCMS and Regulatory Agencies' Inputs) and Part 3 (LBA: Immunogenicity, Biomarkers and PK Assays) are published in volume 9 of Bioanalysis, issues 23 and 24 (2017), respectively.
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http://dx.doi.org/10.4155/bio-2017-4975DOI Listing
November 2017

The 10th GCC Closed Forum: rejected data, GCP in bioanalysis, extract stability, BAV, processed batch acceptance, matrix stability, critical reagents, ELN and data integrity and counteracting fraud.

Bioanalysis 2017 Apr 24;9(7):505-516. Epub 2017 Mar 24.

WuXi Apptec, Plainsboro, NJ, USA.

The 10th Global CRO Council (GCC) Closed Forum was held in Orlando, FL, USA on 18 April 2016. In attendance were decision makers from international CRO member companies offering bioanalytical services. The objective of this meeting was for GCC members to meet and discuss scientific and regulatory issues specific to bioanalysis. The issues discussed at this closed forum included reporting data from failed method validation runs, GCP for clinical sample bioanalysis, extracted sample stability, biomarker assay validation, processed batch acceptance criteria, electronic laboratory notebooks and data integrity, Health Canada's Notice regarding replicates in matrix stability evaluations, critical reagents and regulatory approaches to counteract fraud. In order to obtain the pharma perspectives on some of these topics, the first joint CRO-Pharma Scientific Interchange Meeting was held on 12 November 2016, in Denver, Colorado, USA. The five topics discussed at this Interchange meeting were reporting data from failed method validation runs, GCP for clinical sample bioanalysis, extracted sample stability, processed batch acceptance criteria and electronic laboratory notebooks and data integrity. The conclusions from the discussions of these topics at both meetings are included in this report.
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http://dx.doi.org/10.4155/bio-2017-5000DOI Listing
April 2017

Characterization and performance of anodic mixed culture biofilms in submersed microbial fuel cells.

Bioelectrochemistry 2017 Feb 13;113:79-84. Epub 2016 Oct 13.

Department of Microbiology, Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA.

Microbial fuel cells (MFCs) were designed for laboratory scale experiments to study electroactive biofilms in anodic chambers. Anodic biofilms and current generation during biofilm growth were examined using single chambered MFCs submersed in algal catholyte. A culture of the marine green alga Nanochloropsis salina was used as a biocatholyte, and a rumen fluid microbiota was the anodic chamber inoculum. Electrical impedance spectroscopy was performed under varying external resistance once a week to identify mass transport limitations at the biofilm-electrolyte interface during the four-week experiment. The power generation increased from 249 to 461mWm during the time course. Confocal laser scanning microscopy imaging showed that the depth of the bacterial biofilm on the anode was about 65μm. There were more viable bacteria on the biofilm surface and near the biofilm-electrolyte interface as compared to those close to the anode surface. The results suggest that biofilm growth on the anode creates a conductive layer, which can help overcome mass transport limitations in MFCs.
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http://dx.doi.org/10.1016/j.bioelechem.2016.10.003DOI Listing
February 2017

2016 White Paper on recent issues in bioanalysis: focus on biomarker assay validation (BAV) (Part 1 - small molecules, peptides and small molecule biomarkers by LCMS).

Bioanalysis 2016 Nov 7;8(22):2363-2378. Epub 2016 Oct 7.

Novartis, Emeryville, CA, USA.

The 2016 10 Workshop on Recent Issues in Bioanalysis (10 WRIB) took place in Orlando, Florida with participation of close to 700 professionals from pharmaceutical/biopharmaceutical companies, biotechnology companies, contract research organizations, and regulatory agencies worldwide. WRIB was once again a 5-day, weeklong event - A Full Immersion Week of Bioanalysis including Biomarkers and Immunogenicity. As usual, it was specifically designed to facilitate sharing, reviewing, discussing and agreeing on approaches to address the most current issues of interest including both small and large molecule analysis involving LCMS, hybrid LBA/LCMS, and LBA approaches, with the focus on biomarkers and immunogenicity. This 2016 White Paper encompasses recommendations emerging from the extensive discussions held during the workshop, and is aimed to provide the bioanalytical community with key information and practical solutions on topics and issues addressed, in an effort to enable advances in scientific excellence, improved quality and better regulatory compliance. This white paper is published in 3 parts due to length. This part (Part 1) discusses the recommendations for small molecules, peptides and small molecule biomarkers by LCMS. Part 2 (Hybrid LBA/LCMS and regulatory inputs from major global health authorities) and Part 3 (large molecule bioanalysis using LBA, biomarkers and immunogenicity) will be published in the Bioanalysis journal, issue 23.
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http://dx.doi.org/10.4155/bio-2016-4992DOI Listing
November 2016

9th GCC closed forum: CAPA in regulated bioanalysis; method robustness, biosimilars, preclinical method validation, endogenous biomarkers, whole blood stability, regulatory audit experiences and electronic laboratory notebooks.

Bioanalysis 2016 Mar 26;8(6):487-95. Epub 2016 Feb 26.

WuXi/XBL, 107 Morgan Lane, Plainsboro, NJ, USA.

The 9th GCCClosed Forum was held just prior to the 2015 Workshop on Recent Issues in Bioanalysis (WRIB) in Miami, FL, USA on 13 April 2015. In attendance were 58 senior-level participants, from eight countries, representing 38 CRO companies offering bioanalytical services. The objective of this meeting was for CRO bioanalytical representatives to meet and discuss scientific and regulatory issues specific to bioanalysis. The issues selected at this year's closed forum include CAPA, biosimilars, preclinical method validation, endogenous biomarkers, whole blood stability, and ELNs. A summary of the industry's best practices and the conclusions from the discussion of these topics is included in this meeting report.
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http://dx.doi.org/10.4155/bio.16.16DOI Listing
March 2016

Nuclear Localization Signal and p53 Binding Site in MAP/ERK Kinase Kinase 1 (MEKK1).

J Cell Biochem 2015 Dec;116(12):2903-14

Laboratory of Biochemistry, Garrett-Strong Science Building 3100, 800 University Drive, Northwest Missouri State University, Maryville, Missouri, 64468.

Previously, we showed that Mekk1 translocates to the nucleus, interacts with tumor suppressor protein p53, and co-represses PKD1 transcription via an atypical p53 binding site on the minimal PKD1 promoter (JBC 285:38,818-38,831, 2010). In this study, we report the mechanisms of Mekk1 nuclear transport and p53 binding. Using GFP-linked constitutively active-Mekk1 (CA-Mekk1) and a deletion strategy, we identified a nuclear localization signal (HRDVK) located at amino acid (aa) residues 1,349-1,353 in the C-terminal Mekk1 catalytic domain. Deletion of this sequence in CA-Mekk1 and full-length Mekk1 significantly reduced their nuclear translocation in both HEK293T and COS-1 cells. Using co-immunoprecipitation, we identified an adjacent sequence (GANLID, aa 1,354-1,360) in Mekk1 responsible for p53 binding. Deletion of this sequence markedly reduced the interaction of Mekk1 with p53. Mekk1 does not appear to affect phosphorylation of Ser15, located in the Mdm2 interaction site, or other Ser residues in p53. However, Mekk1 mediates p53 protein stability in the presence of Mdm2 and reduces p53 ubiquitination, suggesting an interference with Mdm2-mediated degradation of p53 by the ubiquitin-proteasome pathway.
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http://dx.doi.org/10.1002/jcb.25238DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4600025PMC
December 2015

Expression of root-related transcription factors associated with flooding tolerance of soybean (Glycine max).

Int J Mol Sci 2014 Sep 29;15(10):17622-43. Epub 2014 Sep 29.

Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA.

Much research has been conducted on the changes in gene expression of the model plant Arabidopsis to low-oxygen stress. Flooding results in a low oxygen environment in the root zone. However, there is ample evidence that tolerance to soil flooding is more than tolerance to low oxygen alone. In this study, we investigated the physiological response and differential expression of root-related transcription factors (TFs) associated with the tolerance of soybean plants to soil flooding. Differential responses of PI408105A and S99-2281 plants to ten days of soil flooding were evaluated at physiological, morphological and anatomical levels. Gene expression underlying the tolerance response was investigated using qRT-PCR of root-related TFs, known anaerobic genes, and housekeeping genes. Biomass of flood-sensitive S99-2281 roots remained unchanged during the entire 10 days of flooding. Flood-tolerant PI408105A plants exhibited recovery of root growth after 3 days of flooding. Flooding induced the development of aerenchyma and adventitious roots more rapidly in the flood-tolerant than the flood-sensitive genotype. Roots of tolerant plants also contained more ATP than roots of sensitive plants at the 7th and 10th days of flooding. Quantitative transcript analysis identified 132 genes differentially expressed between the two genotypes at one or more time points of flooding. Expression of genes related to the ethylene biosynthesis pathway and formation of adventitious roots was induced earlier and to higher levels in roots of the flood-tolerant genotype. Three potential flood-tolerance TFs which were differentially expressed between the two genotypes during the entire 10-day flooding duration were identified. This study confirmed the expression of anaerobic genes in response to soil flooding. Additionally, the differential expression of TFs associated with soil flooding tolerance was not qualitative but quantitative and temporal. Functional analyses of these genes will be necessary to reveal their potential to enhance flooding tolerance of soybean cultivars.
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http://dx.doi.org/10.3390/ijms151017622DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4227181PMC
September 2014

Bioanalytical challenges of biosimilars.

Authors:
Rafiq Islam

Bioanalysis 2014 Feb;6(3):349-56

Celerion, 621 Rose St, Lincoln, NE 68502, USA.

Biologics such as monoclonal antibodies and recombinant proteins represent a significant portion of the pharmaceutical market. With many of the first generation biologics' patents expiring, an increasing number of biosimilars will be submitted for approval in the near future. The successful development of a biosimilar requires the demonstration of biosimilarity in terms of efficacy, safety and purity to an innovator-approved product. While regulatory frameworks have been established for the approval of biosimilars in several countries, there is not an established guidance for bioanalytical testing of biosimilars. Although there are regulatory guidances and White Papers on testing requirements for biologics in general, there is a need to address the bioanalytical challenges and solutions that apply specifically to the analysis of biosimilars in biological samples. This paper will focus on components of the PK and immunogenicity assays that are critical to biosimilar drug development.
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http://dx.doi.org/10.4155/bio.13.307DOI Listing
February 2014

Simultaneous detection and quantification of select nitromusks, antimicrobial agent, and antihistamine in fish of grocery stores by gas chromatography-mass spectrometry.

Chemosphere 2014 Jul 28;107:187-193. Epub 2013 Dec 28.

Department of Natural Sciences, Northwest Missouri State University, 800 University Drive, Maryville, MO 64468, USA.

Continually detected biologically persistent nitromusks; galaxolide (HHCB), tonalide (AHTN) and musk ketone (MK), antimicrobial triclosan (TCS), and antihistamine diphenhydramine (DPH) were examined for the first time in edible fillets originating from eight fish species grown in salt- and fresh-water. The sampled fish collected from local grocery stores were homogenized, extracted, pre-concentrated and analyzed by gas chromatography-mass spectrometry (GC-MS) using selected ion monitoring (SIM). The presence of the target compounds in fish extracts was confirmed based on similar mass spectral features and retention behavior with standards. Internal standard based calibration plots were used for quantification. The HHCB, AHTN, TCS and DPH were consistently observed with concentration of 0.163-0.892, 0.068-0.904, 0.189-1.182, and 0.942-7.472 ng g(-1), respectively. These values are at least 1-3 orders of magnitude lower than those obtained in environmental fish specimens. The MK was not detected in any fish.
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http://dx.doi.org/10.1016/j.chemosphere.2013.12.032DOI Listing
July 2014

Regulation of HFE expression by poly(ADP-ribose) polymerase-1 (PARP1) through an inverted repeat DNA sequence in the distal promoter.

Biochim Biophys Acta 2013 Dec 29;1829(12):1257-1265. Epub 2013 Oct 29.

Biochemistry Laboratory, Northwest Missouri State University, Maryville, MO 64468.

Hereditary hemochromatosis (HH) is a common autosomal recessive disorder of iron overload among Caucasians of northern European descent. Over 85% of all cases with HH are due to mutations in the hemochromatosis protein (HFE) involved in iron metabolism. Although the importance in iron homeostasis is well recognized, the mechanism of sensing and regulating iron absorption by HFE, especially in the absence of iron response element in its gene, is not fully understood. In this report, we have identified an inverted repeat sequence (ATGGTcttACCTA) within 1700bp (-1675/+35) of the HFE promoter capable to form cruciform structure that binds PARP1 and strongly represses HFE promoter. Knockdown of PARP1 increases HFE mRNA and protein. Similarly, hemin or FeCl3 treatments resulted in increase in HFE expression by reducing nuclear PARP1 pool via its apoptosis induced cleavage, leading to upregulation of the iron regulatory hormone hepcidin mRNA. Thus, PARP1 binding to the inverted repeat sequence on the HFE promoter may serve as a novel iron sensing mechanism as increased iron level can trigger PARP1 cleavage and relief of HFE transcriptional repression.
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http://dx.doi.org/10.1016/j.bbagrm.2013.10.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3889151PMC
December 2013

CMV promoter is repressed by p53 and activated by JNK pathway.

Plasmid 2013 May 1;69(3):223-30. Epub 2013 Feb 1.

Laboratory of Biochemistry, Garrett-Strong Science Building 3100, Northwest Missouri State University, Maryville, MO 64468, USA.

Viral promoters are widely utilized in commercial and customized vectors to drive expression of genes of interest including reporter, effector and transfection control, because of their high transcription efficiency in a variety of primary and transformed cell lines. However, we observed altered rate of transcription for these promoters under conditions such as presence of an effector protein. These variations in viral promoter driven expressions can potentially lead to incorrect conclusion, especially in comparative and quantitative experiments. We found significantly reduced viral promoter activity in cells overexpressing tumor suppressor protein p53, whereas markedly induced transcription in cells overexpressing MAP/ERK kinase kinase 1 (Mekk 1). Using deletion constructs generated from the CMV promoter, we found the transcription reduction by p53 is possibly mediated through the TATA motif present in proximal CMV promoter. The activation of the CMV promoter by Mekk 1, on the other hand, is attributed to the proximal CRE binding site in the promoter. These findings may be of interest to investigators who use CMV (or other viral) promoter driven vectors for either comparative or quantitative gene expression, or effect on promoter activity.
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http://dx.doi.org/10.1016/j.plasmid.2013.01.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3650106PMC
May 2013

Recommendations on biomarker bioanalytical method validation by GCC.

Bioanalysis 2012 Oct;4(20):2439-46

Quotient Bioresearch, Fordham, UK.

The 5th GCC in Barcelona (Spain) and 6th GCC in San Antonio (TX, USA) events provided a unique opportunity for CRO leaders to openly share opinions and perspectives, and to agree upon recommendations on biomarker bioanalytical method validation.
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http://dx.doi.org/10.4155/bio.12.197DOI Listing
October 2012

Cytotoxicity analysis of active components in bitter melon (Momordica charantia) seed extracts using human embryonic kidney and colon tumor cells.

Nat Prod Commun 2012 Sep;7(9):1203-8

Laboratory of Biochemistry, Northwest Missouri State University, 800 University Drive, Maryville, MO 64468, USA.

Bitter melon (Momordica charantia) seed extracts (BMSE) have been used as traditional medicine for treating various ailments, although in many cases, the active component(s) are unidentified. In this study, bitter melon seeds were extracted in water, ethanol, or ethanol: water (1:1). The aqueous seed extracts (BMSE-W) exhibited marked cytotoxicity towards human embryonic kidney 293T (HEK293T) and human colon tumor 116 (HCT1116) cells. The activity in BMSE-W was unaffected by heat and proteinases treatments, and eluted in the total volume of size-exclusion HPLC, suggesting the small, organic nature of the active component(s). Gas chromatographic-mass spectrometic (GC-MS) analysis of the HPLC fractions identified methoxy-phenyl oxime (MPO) as a major active component. Acetophenone oxime, a commercially available structural homolog of MPO, demonstrated cytotoxicity comparable with that of the BMSE-W. The oxime functional group was found to be critical for activity. Increased poly-(ADP-ribose)-polymerase and beta-actin cleavage, and chromatin condensation observed in treated cells suggested apoptosis as a plausible cause for the cytotoxicity. This study, for the first time, identified a cytotoxic oxime in BMSE-W.
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September 2012

Recommendations on bioanalytical method stability implications of co-administered and co-formulated drugs by Global CRO Council for Bioanalysis (GCC).

Bioanalysis 2012 Sep;4(17):2117-26

Advion Bioanalytical Laboratories, Quintiles, NY, USA.

An open letter written by the Global CRO Council for Bioanalysis (GCC) describing the GCC survey results on stability data from co-administered and co-formulated drugs was sent to multiple regulatory authorities on 14 December 2011. This letter and further discussions at different GCC meetings led to subsequent recommendations on this topic of widespread interest within the bioanalytical community over the past 2 years.
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http://dx.doi.org/10.4155/bio.12.192DOI Listing
September 2012

4th Global CRO Council for Bioanalysis: coadministered drugs stability, EMA/US FDA guidelines, 483s and carryover.

Bioanalysis 2012 Apr;4(7):763-8

The Global CRO Council for Bioanalysis (GCC) was formed in September 2010. Since then, the representatives of the member companies come together periodically to openly discuss bioanalysis and the regulatory challenges unique to the outsourcing industry. The 4th GCC Closed Forum brought together experts from bioanalytical CROs to share and discuss recent issues in regulated bioanalysis, such as the impact of coadministered drugs on stability, some differences between European Medicines Agency and US FDA bioanalytical guidance documents and lessons learned following recent Untitled Letters. Recent 483s and agency findings, as well as issues on method carryover, were also part of the topics discussed.
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http://dx.doi.org/10.4155/bio.12.48DOI Listing
April 2012

Identification of bound nitro musk-protein adducts in fish liver by gas chromatography-mass spectrometry: biotransformation, dose-response and toxicokinetics of nitro musk metabolites protein adducts in trout liver as biomarkers of exposure.

Aquat Toxicol 2012 Jan 28;106-107:164-72. Epub 2011 Nov 28.

Department of Chemistry/Physics, Center for Innovation and Entrepreneurship, Northwest Missouri State University, 800 University Drive, Maryville, MO 64468, USA.

Ubiquitous occurrences of synthetic nitro musks are evident in the literature. The in vivo analysis of musk xylene (MX) and musk ketone (MK)-protein adducts in trout liver has been performed by gas chromatography-mass spectrometry using selected ion monitoring (GC-SIM-MS). Biotransformation, dose-response and toxicokinetics studies of 2-amino-MX (2-AMX), 2-amino-MK (2-AMK) and 4-amino-MX (4-AMX) metabolites, covalently bound to cysteine amino acids in proteins in fish liver, formed by enzymatic nitro-reduction of MX and MK, have been described. Trouts were exposed to single exposures of 0.010, 0.030, 0.10, and 0.30 mg/g MX and/or MK. Forty-two fish liver samples were collected from exposed- and control-fish subsequent to exposure intervals of 1 day, 3 days, and 7 days and were composited as per exposure schedules and times. Alkaline hydrolysis released bound metabolites from exposed liver composites that were extracted into n-hexane and then concentrated and analyzed by GC-SIM-MS. The presence of the metabolites in liver extracts was confirmed based on agreement of similar mass spectral properties and retention times with standards. In the dose-response study, the maximum adduct formation was 492.0 ng/g for 2-AMX, 505.5 ng/g for 2-AMK and 12588.5 ng/g for 4-AMX in liver at 0.03 mg/g MX and MK fish in 1 day after exposure. For toxicokinetics investigation, the highest amount of the target metabolites was found to be the same concentration as observed in the dose-response study for 1 day after exposure with 0.03 mg/g MX and MK fish and the half-lives of the metabolites were estimated to be 2-9 days based on assumption of first-order kinetics. Average recoveries exceeded 95% with a relative standard deviation (RSD) around 9%, and the limit of detection (LOD) ranged from 0.91 to 3.8 ng/g based on a signal to noise ratio of 10 (S/N=10) could be achieved for the metabolites. No metabolites were detected in the controls and exposed non-hydrolyzed liver extracts. This is the first report on dose-response and toxicokinetics of nitro musk-cysteine-protein adducts in fish liver.
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http://dx.doi.org/10.1016/j.aquatox.2011.11.010DOI Listing
January 2012

MAP/ERK kinase kinase 1 (MEKK1) mediates transcriptional repression by interacting with polycystic kidney disease-1 (PKD1) promoter-bound p53 tumor suppressor protein.

J Biol Chem 2010 Dec 5;285(50):38818-31. Epub 2010 Oct 5.

Department of Chemistry/Physics, Northwest Missouri State University, Maryville, Missouri 64468, USA.

Mitogen-activated protein kinase (MAPK) cascades regulate a wide variety of cellular processes that ultimately depend on changes in gene expression. We have found a novel mechanism whereby one of the key MAP3 kinases, Mekk1, regulates transcriptional activity through an interaction with p53. The tumor suppressor protein p53 down-regulates a number of genes, including the gene most frequently mutated in autosomal dominant polycystic kidney disease (PKD1). We have discovered that Mekk1 translocates to the nucleus and acts as a co-repressor with p53 to down-regulate PKD1 transcriptional activity. This repression does not require Mekk1 kinase activity, excluding the need for an Mekk1 phosphorylation cascade. However, this PKD1 repression can also be induced by the stress-pathway stimuli, including TNFα, suggesting that Mekk1 activation induces both JNK-dependent and JNK-independent pathways that target the PKD1 gene. An Mekk1-p53 interaction at the PKD1 promoter suggests a new mechanism by which abnormally elevated stress-pathway stimuli might directly down-regulate the PKD1 gene, possibly causing haploinsufficiency and cyst formation.
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http://dx.doi.org/10.1074/jbc.M110.145284DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2998141PMC
December 2010