Begell House Inc.
Critical Reviews™ in Eukaryotic Gene Expression
CRE
1045-4403
22
3
2012
Novel Insights into Mycobacterium Antigen Ag85 Biology and Implications in Countermeasures for M. tuberculosis
179-187
10.1615/CritRevEukarGeneExpr.v22.i3.10
XieMei
Tang
Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment and Bio-Resource of the Three Gorges Area, School of Life Sciences, Southwest University, Beibei, Chongqing, China
Wanyan
Deng
Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, PR China
Jianping
Xie
Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ecoenvironments in Three Gorges Reservoir Region, Ministry of Education,
School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
Mycobacterium Tuberculosis
Ag85 complex
regulation
vaccination
new drug targets
Tuberculosis remains one of the most prevalent and deadly infectious diseases, largely due to the emergence of multidrug-resistant and extensive drug-resistant Mycobacterium tuberculosis, especially the coinfection with HIV. Mycobacterium Ag85 complex (Ag85A, B, and C), with a carboxylesterase consensus sequence and conserved surface catalysis residues, involves in cell wall biosynthesis and the trigger of the host immune response. The physiological function, structures, distributions, and molecular mechanisms of regulations as well as their implications in novel vaccines and diagnostics against tuberculosis are summarized. Special focus is the regulation underlying the Ag85 expression. This will facilitate in-depth understanding of the role of Ag85 and developing better novel measures against M. tuberculosis infection.
MicroRNAs in Human Lymphoblastoid Cell Lines
189-196
10.1615/CritRevEukarGeneExpr.v22.i3.20
Sung-Mi
Shim
National Biobank of Korea, Center for Genome Science, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, 200 Osongsaengmyung-2-ro, Osong-eup, Chungwon-gun, Chungbuk-do, 363-951, South Korea
Hye-Young
Nam
National Biobank of Korea, Center for Genome Science, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, 200 Osongsaengmyung-2-ro, Osong-eup, Chungwon-gun, Chungbuk-do, 363-951, South Korea
Jae-Eun
Lee
National Biobank of Korea, Center for Genome Science, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, 200 Osongsaengmyung-2-ro, Osong-eup, Chungwon-gun, Chungbuk-do, 363-951, South Korea
Jun-Woo
Kim
National Biobank of Korea, Center for Genome Science, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, 200 Osongsaengmyung-2-ro, Osong-eup, Chungwon-gun, Chungbuk-do, 363-951, South Korea
Bok-Ghee
Han
National Biobank of Korea, Center for Genome Science, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, 200 Osongsaengmyung-2-ro, Osong-eup, Chungwon-gun, Chungbuk-do, 363-951, South Korea
Jae-Pil
Jeon
National Biobank of Korea, Center for Genome Science, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, 200 Osongsaengmyung-2-ro, Osong-eup, Chungwon-gun, Chungbuk-do, 363-951, South Korea
LCL
miRNA
transcription
biobank
Human lymphoblastoid cell lines (LCLs) are generated by EBV-mediated B-cell transformation to provide unlimited genomic resources for human genetics and immunological studies. The LCL is a good in vitro cell model for assessing population differences in the basal expression of genes and miRNAs as well as in cellular responses to various stimulators. Recently, the utility of LCLs was extended to pharmacogenomic studies to discover genetic factors underlying individual variations in response to chemicals and environmental stresses. Although LCLs represent generally lymphoid tissue−specific biological characteristics, genomic signatures of LCLs can distinguish patients with brain-related diseases and nonlymphoid tumors from normal controls. MicroRNA is known to be an epigenetic transcriptional regulator, and its expression is induced in abnormal conditions such as perturbagen-stimulated, virus-infected, or cancer cells. The epigenetic regulation of gene expression mediated by microRNA and DNA methylation is important for understanding the pathogenesis of cancers and complex diseases as well as discovering for therapeutic targets. For integrative genomic analyses, LCLs can be utilized to generate cellular phenotypes and various genomic data (e.g., SNP, CNV, transcriptome, methylome, etc.), which can be linked to clinical information of donors. Here, we discuss miRNA-mediated gene expression in LCLs and its application to disease genomics and global transcriptional regulatory machinery studies.
Recombinant Laccase: II. Medical Biosensor
197-203
10.1615/CritRevEukarGeneExpr.v22.i3.30
Nicola Luigi
Bragazzi
Nanoworld Institute Fondazione EL.B.A Nicolini (FEN), Pradalunga, Largo Redaelli 7, Bergamo 24100, Italy; Biophysics and Nanobiotechnology Laboratories (BNL), Department of Experimental Medicine (DIMES), University of Genoa, Via Antonio Pastore 3, Genoa
Eugenia
Pechkova
Nanoworld Institute Fondazione ELBA Nicolini, Pradalunga, Bergamo 24100, Italy ; Biophysics and Nanobiotechnology Laboratories, Department of Experimental Medicine, University of Genova, Genoa 16121-16167, Italy; European Synchrotron Radiation Facility
Dora
Scudieri
Biophysics and Nanobiotechnology Laboratories, Department of Experimental Medicine, University of Genova, Genoa 16121-16167, Italy
Tercio Bezerra Correia
Terencio
Biophysics and Nanobiotechnology Laboratories, Department of Experimental Medicine, University of Genova, Genoa 16121-16167, Italy
Manuela
Adami
Nanoworld Institute Fondazione ELBA Nicolini, Pradalunga, Bergamo 24100, Italy
Claudio
Nicolini
Nanoworld Institute Fondazione ELBA Nicolini, Pradalunga, Bergamo 24100, Italy; Biophysics and Nanobiotechnology Laboratories, Department of Experimental Medicine, University of Genova, Genoa 16121-16167, Italy; European Synchrotron Radiation Facility
cyclic voltammetry
chronoamperometry
UV spectrophotometry
laccase
Rigidoporus lignosus
clomipramine
Langmuir-Blodgett (LB) technology was used to build a high-sensitivity enzyme-based biosensor for medical purposes. Recombinant fungal laccase from Rigidoporous lignosus, as previously described, was used to catalyze a widely used antidepressant in a micromolar range, namely, clomipramine. The topological properties of the laccase thin film were characterized via LB π-A isotherm and AFM (mean roughness 8.22 nm, compressibility coefficient 37.5 m/N). The sensitivity of the biosensor was investigated via UV spectroscopy, and linearity was found in the absorbance peak shift at 400 nm at drug concentration varying up to 20 uM. The enzyme kinetics was subsequently investigated with potentiometric and amperometric measurements, and we found electronic transfer of at least 1 electron, ks 0.57 s−1, diffusion coefficient 3 × 10−6 cm2/s, Kcat t 6825.92 min−1, KM 4.1 uM, Kcat /KM 2.8 ×
107 mol−1 s−1, sensitivity of 440 nA/uM, maximum velocity 1706.48 nA/s, and response time less than 5 s. The amperometric and potentiometric measurements were repeated after a month, confirming the stability of the biosensor.
Nmp4/CIZ Closes the Parathyroid Hormone Anabolic Window
205-218
10.1615/CritRevEukarGeneExpr.v22.i3.40
Joseph
Bidwell
Department of Anatomy and Cell Biology, Indiana University School of Medicine, Indianapolis IN, 46202
Paul
Childress
Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46202
Marta B.
Alvarez
Department of Anatomy and Cell Biology, Indiana University School of Dentistry, Indianapolis, IN 46202
Mark
Hood, Jr.,
Department of Anatomy and Cell Biology, Indiana University School of Medicine, Indianapolis IN, 46202
Yongzheng
He
Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, 46202; Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46202
Fredrick M.
Pavalko
Department of Cellular & Integrative Physiology, Indiana University School of Medicine, Indianapolis, IN 46202
Melissa A.
Kacena
Department of Orthopaedic Surgery, Indiana University School of Medicine, Indianapolis, IN 46202
Feng-Chun
Yang
Department of Anatomy and Cell Biology, Indiana University School of Medicine, Indianapolis IN, 46202; Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, 46202
BMP2
osteoblasts
osteoclast
osteoporosis
osteoprogenitors
p130Cas
Chronic degenerative diseases are increasing with the aging U.S. population. One consequence of this phenomenon is the need for long-term osteoporosis therapies. Parathyroid hormone (PTH), the only FDA-approved treatment that adds bone to the aged skeleton, loses its potency within two years of initial treatment but the mechanism regulating its limited "anabolic window" is unknown. We have discovered that disabling the nucleocytoplasmic shuttling transcription factor nuclear matrix protein 4/cas interacting zinc finger protein (Nmp4/CIZ) in mice extends the PTH bone-forming capacity. Nmp4 was discovered during our search for nuclear matrix transcription factors that couple this hormone's impact on osteoblast cytoskeletal and nuclear organization with its anabolic capacity. CIZ was independently discovered as a protein that associates with the focal adhesion-associated mechanosensor p130Cas. The Nmp4/CIZ-knockout (KO) skeletal phenotype exhibits a modestly enhanced bone mineral density but manifests an exaggerated response to both PTH and to BMP2 and is resistant to disuse-induced bone loss. The cellular basis of the global Nmp4/CIZ-KO skeletal phenotype remains to be elucidated but may involve an expansion of the bone marrow osteoprogenitor population along with modestly enhanced osteoblast and osteoclast activities supporting anabolic bone turnover. As a shuttling Cys2His2 zinc finger protein, Nmp4/CIZ acts as a repressive transcription factor perhaps associated with epigenetic remodeling complexes, but the functional significance of its interaction with p130Cas is not known. Despite numerous remaining questions, Nmp4/CIZ provides insights into how the anabolic window is regulated, and itself may provide an adjuvant therapy target for the treatment of osteoporosis by extending PTH anabolic efficacy.
Langmuir-Blodgett Nanotemplate and Radiation Resistance in Protein Crystals: State of the Art
219-232
10.1615/CritRevEukarGeneExpr.v22.i3.50
Luca
Belmonte
Nanobiotechnology and Biophysics Laboratories (NBL), Department of Experimental Medicine (DIMES), University of Genoa, Genoa, Italy; Nanoworld Institute Fondazione EL.B.A Nicolini (FEN), Pradalunga, Bergamo, Italy
Eugenia
Pechkova
Nanoworld Institute Fondazione ELBA Nicolini, Pradalunga, Bergamo 24100, Italy ; Biophysics and Nanobiotechnology Laboratories, Department of Experimental Medicine, University of Genova, Genoa 16121-16167, Italy; European Synchrotron Radiation Facility
Shailesh
Tripathi
Nanoworld Institute, Fondazione EL.B.A. Nicolini, Largo Redaelli 7, Pradalunga, Bergamo and Laboratories of Biophysics and Nanobiotechnology, Department of Experimental Medicine, University of Genova, Via Pastore 3, 16132 Genova Italy
Dora
Scudieri
Biophysics and Nanobiotechnology Laboratories, Department of Experimental Medicine, University of Genova, Genoa 16121-16167, Italy
Claudio
Nicolini
University of Genoa
X-ray diffraction
radiation damage
protein crystallography
langmuir-Blodgett nanotemplate
A state-of-the-art review of the role of the Langmuir-Blodgett nanotemplate on protein crystal structures is here presented. Crystals grown by nanostructured template appear more radiation resistant than the classical ones, even in the presence of a third-generation highly focused beam at the European Synchrotron Radiation Facility. The electron density maps and the changes in parameters such as total diffractive power, B-factor, and pairwise R-factor have been discussed. Protein crystals, grown by the Langmuir-Blodgett nanotemplate-based method, proved to be more radiation resistant compared to crystals grown by the classical hanging drop method in terms of both global and specific damage.
Tuberculosis and Sexual Inequality: The Role of Sex Hormones in Immunity
233-241
10.1615/CritRevEukarGeneExpr.v22.i3.60
Yuzhong
Zhao
Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China; School of Chemistry & Environmental Scienc
He
Ying
Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment and Bio-Resource of the Three Gorges Area, School of Life Sciences, Southwest University. Chongqing 400700, China
Jiang
Demei
Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment and Bio-Resource of the Three Gorges Area, School of Life Sciences, Southwest University. Chongqing 400700, China
Jianping
Xie
Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ecoenvironments in Three Gorges Reservoir Region, Ministry of Education,
School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
TB immunity
sex steroids
influence
The role of sex hormones is profound and diverse. The gender and age differences in TB incidences suggest a role of hormones. These data, together with their relevance to the epidemiology of tuberculosis, are gathered and analyzed in this review. The underlying network of hormones functionalities in TB is also proposed.
Edible Vaccine: A New Platform for the Development of Malaria Vaccine
243-248
10.1615/CritRevEukarGeneExpr.v22.i3.70
Choudhary Sudheer
Kumar
School of Biotechnology, Rajiv Gandhi Proudyogiki Vishwavidhyalaya (State Technological University of Madhya Pradesh), Airport Bypass Road, Bhopal (M.P.) 462033, India
Gupta
Deepesh
School of Biotechnology, Rajiv Gandhi Proudyogiki Vishwavidhyalaya (State Technological University of Madhya Pradesh), Airport Bypass Road, Bhopal (M.P.) 462033, India
Yadav
Mahavir
School of Biotechnology, Rajiv Gandhi Proudyogiki Vishwavidhyalaya (State Technological University of Madhya Pradesh), Airport Bypass Road, Bhopal (M.P.) 462033, India
Tiwari
Archana
School of Biotechnology, Rajiv Gandhi Proudyogiki Vishwavidhyalaya (State Technological University of Madhya Pradesh), Airport Bypass Road, Bhopal (M.P.) 462033, India
edible vaccine
malaria
antibodies
transgenic plant
The plasmodium vivax is the most prevalent malaria parasite. The world essentially needs a malaria vaccine to alleviate the human suffering associated with the parasitic disease that kills more than one million people annually. The use of plants for the expression of the proteins of disease-causing vehicle in transgenic plants has been increasingly used in the development of experimental vaccines, largely oriented to the improvement of edible vaccines. Currently, through modern biotechnology, there has been a revival in obtaining a new edible vaccine against the malaria parasite from plant sources. Through genetic alteration, it is now recognized that plants are potentially a new source of recombinant proteins including vaccines, antibodies, blood substitutes, and other therapeutic entities. Plant-derived antibodies and other proteins are mostly valuable since they are free of mammalian viral vectors and human pathogens. Although significant progress has been achieved in the research for edible vaccine in Plasmodium falciparum, limited progress has been made in the Plasmodium vivax component that might be eligible for edible vaccine development. We describe the overall strategy recommended by plants, which include high biomass production and low cost of cultivation, relatively fast "gene to protein" time, low capital and operating costs, outstanding scalability, eukaryotic posttranslational modifications, and a relatively high protein yield.
Tumor Suppressor Maspin as a Rheostat in HDAC Regulation to Achieve the Fine-Tuning of Epithelial Homeostasis
249-258
10.1615/CritRevEukarGeneExpr.v22.i3.80
Alexander
Kaplun
Department of Pathology, Karmanos Cancer Institute, Wayne State University School of Medicine, 4100 John R Street, Detroit, MI 48201
Sijana
Dzinic
Department of Pathology, Karmanos Cancer Institute, Wayne State University School of Medicine, 4100 John R Street, Detroit, MI 48201
M. Margarida
Bernardo
Department of Pathology, Karmanos Cancer Institute, Wayne State University School of Medicine, 4100 John R Street, Detroit, MI 48201
Shijie
Sheng
Department of Pathology, Karmanos Cancer Institute, Wayne State University School of Medicine, 4100 John R Street, Detroit, MI 48201
maspin
HDAC
tumor suppressor
re-differentiation
epigenetic regulation
E-cadherin
MEF2
Nanog
TGFβ
Abl
Maspin, a class II tumor suppressor, is often downregulated during tumor progression and its depletion from the nucleus is associated with poor prognosis. Recently, we reported that reintroduction of maspin is sufficient for redifferentiation of prostate cancer cells to epithelial phenotype, a reversal of epithelial-to-mesenchymal transition. We have linked this effect of maspin with its ability to directly inhibit HDAC1, thereby influencing the acetylation state of transcription factors and other proteins. Maspin overexpression leads to changes in the expression level of a large number of proteins and these changes are often microenvironment specific. In this review, we summarize the epigenetic effects of maspin and provide comprehensive bioinformatic analysis of microarray-derived gene expression changes caused by maspin in different microenvironments. The analysis was performed on multiple levels, including identification of statistically enriched gene ontology groups, detection of overreprepresented transcription factors binding sites in promoters of differentially expressed genes, followed by searching for key nodes of regulatory networks controlling these transcription factors. The results are consistent with our hypothesis that maspin serves as an endogenous regulator of HDAC activity and suggest that the effect of maspin is primarily mediated by TGFβ, β-catenin/E-cadherin pathways, and network key nodes such as Abl kinase, p62, IL1, and caspases 6 and 8.
Roles of Peptidoglycan Recognition Protein (PGRP) in Immunity and Implications for Novel Anti-infective Measures
259-268
10.1615/CritRevEukarGeneExpr.v22.i3.90
Zhen
Zhang
Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
Quan Xin
Long
Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment and Bio-Resource of the Three Gorges Area, School of Life Sciences, Southwest University, Chongqing 400715, China
Jianping
Xie
Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ecoenvironments in Three Gorges Reservoir Region, Ministry of Education,
School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
PGRP
immunity function
distribution
transcript regulation
structure
evolution
Peptidoglycan recognition protein (PGRP) is an important host innate immunity arm capable of peptidoglycan and allied bacteria recognition. PGRP belongs to host pattern recognition receptors (PRRs) responsible for pathogen associated molecular patterns recognition, such as lipopolysaccharide, lipoteichoic acid, PGN, and mannose. As an essential host PRR, PGRP is well conserved from insects to mammals. The distribution, structure, function, regulation of gene expression, and evolution of PGRP from insects and mammals were summarized to furnish insights into this important molecule family.