Begell House Inc.
Critical Reviews™ in Eukaryotic Gene Expression
CRE
1045-4403
24
3
2014
ALDOB Acts as a Novel HBsAg-Binding Protein and Its Coexistence Inhibits Cisplatin-Induced HepG2 Cell Apoptosis
181-191
10.1615/CritRevEukaryotGeneExpr.2014010087
Jing
Wu
Department of Gastroenterology, Zhongshan Hospital, Xiamen University, Xiamen, Fujian Province, China
Can
Dan
Medical College of Xiamen University, Xiamen, Fujian Province, China, 361005
Hong-Bo
Zhao
Department of Gastroenterology, Zhongshan Hospital, Xiamen University, Xiamen, Fujian Province, China
Chuan-Xing
Xiao
Department of Gastroenterology, Zhongshan Hospital, Xiamen University, Xiamen, Fujian Province, China
Yun-Peng
Liu
Department of Gastroenterology, Zhongshan Hospital, Xiamen University, Xiamen, Fujian Province, China
Li-Juan
Si
Department of Gastroenterology, Zhongshan Hospital, Xiamen University, Xiamen, Fujian Province, China
Jian-Lin
Ren
Department of Gastroenterology, Zhongshan Hospital, Xiamen University, Xiamen, Fujian Province, China
Bayasi
Guleng
Department of Gastroenterology, Zhongshan Hospital, Xiamen University, Xiamen, Fujian Province, China; Medical College of Xiamen University, Xiamen, Fujian Province, China, 361005
ALDOB
HBs binding protein
HepG2 cell apoptosis
Chronic infection with hepatitis B virus is a cause of end-stage liver disease and hepatocellular carcinoma (HCC). We previously screened fructose-bisphosphate aldolase B (ALDOB) as a candidate binding protein of hepatitis B surface antigen (HBsAg) using a yeast 2-hybrid assay. In this study we aimed to confirm ALDOB as a binding protein of the S region of the HbsAg (HBs) and to investigate the function and involved mechanism between its interactions during HCC development. Our results demonstrated that both of exogenous and endogenous ALDOB proteins bind to HBs and colocalize in the cytoplasm in vitro. The coexistence of HBs and ALDOB inhibit apoptosis of cisplatin-induced HepG2 cells. Furthermore, western blot analysis showed the coexistence of HBs and ALDOB enhance the phosphorylations of AKT and its downstream of GSK-3β (phosphorylation); decreased expression of the pro-apoptotic proteins Bax, Bid, Bim, and Puma; and increased expression of the prosur-vival proteins Bcl-2, Bcl-xl, and Mcl-1 in HepG2 cells. These findings suggest that interaction between HBs and ALDOB might be applied as a potential therapeutic target during the treatment of HBV-related hepatitis or HCC.
Significance of Hypoxia in the Physiological Function of Intervertebral Disc Cells
193-204
10.1615/CritRevEukaryotGeneExpr.2014010485
Jiang-Wei
Chen
Department of Orthopedic Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
Bo
Li
Department of Orthopedic Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
Yue-Hua
Yang
Department of Orthopedic Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
Sheng-Dan
Jiang
Department of Orthopedic Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
Lei-Sheng
Jiang
Department of Orthopedic Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
hypoxia
intervertebral disc
cell
hypoxia-inducible factor
physiology
The intervertebral disc (IVD) is the largest avascular structure in the body, and IVD cells reside in vivo in an environment that is considered to be hypoxic. However, the role of oxygen in IVD cell biology remains an issue of debate. By reviewing the available literature about the effect of oxygen tension on regulating the phenotype, energy metabolism, matrix production, and survival of IVD cells, as well as on the expression and function of hypoxia-inducible factor in IVD cells, we conclude that hypoxia is essential in maintaining the physiological function of IVD cells. Modulating the oxygen tension of the IVD or the activity of hypoxia-inducible factor in IVD cells may be a promising strategy for the prevention and treatment of IVD degeneration.
Determining Omics Spatiotemporal Dimensions Using Exciting New Nanoscopy Techniques to Assess Complex Cell Responses to DNA Damage: PART A−Radiomics
205-223
10.1615/CritRevEukaryotGeneExpr.2014010313
Martin
Falk
Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
Michael
Hausmann
Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany
Emilie
Lukasova
Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
Abin
Biswas
Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany; Department of Radiation Oncology, University Medical Center Mannheim, University of Heidelberg, Heidelberg, Germany
Georg
Hildenbrand
Department of Radiation Oncology, University Medical Center Mannheim, Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany
Marie
Davidkova
Nuclear Physics Institute, Academy of Sciences of the Czech Republic, Rez, Czech Republic
Evgeny
Krasavin
Joint Institute for Nuclear Research, Dubna, Moscow, Russia
Zdenek
Kleibl
Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
Iva
Falkova
Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
Lucie
Jezkova
Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic; Joint Institute for Nuclear Research, Dubna, Moscow, Russia; Institute of Chemical Technology Prague, Prague, Czech Republic
Lenka
Stefancikova
Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
Jan
Sevcik
Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
Michal
Hofer
Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
Alena
Bacikova
Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
Pavel
Matula
Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic; Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University, Brno, Czech Republic
Alla
Boreyko
Joint Institute for Nuclear Research, Dubna, Moscow, Russia
Jana
Vachelova
Nuclear Physics Institute, Academy of Sciences of the Czech Republic, Rez, Czech Republic
Anna
Michaelidesova
Nuclear Physics Institute, Academy of Sciences of the Czech Republic, Rez, Czech Republic; Proton Therapy Center, Prague, Czech Republic
Stanislav
Kozubek
Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
Omics
ionizing radiation
low-dose dilemma
biological complexity and variability
higher-order chromatin structure
DNA damage response
formation of chromosomal translocations
confocal microscopy
localization nanoscopy
Recent ground-breaking developments in Omics have generated new hope for overcoming the complexity and variability of biological systems while simultaneously shedding more light on fundamental radiobiological questions that have remained unanswered for decades. In the era of Omics, our knowledge of how genes and proteins interact in the frame of complex networks to preserve genome integrity has been rapidly expanding. Nevertheless, these functional networks must be observed with strong correspondence to the cell nucleus, which is the main target of ionizing radiation. Nuclear architecture and nuclear processes, including DNA damage responses, are precisely organized in space and time. Information regarding these intricate processes cannot be achieved using high-throughput Omics approaches alone, but requires sophisticated structural probing and imaging. Based on the results obtained from studying the relationship between higher-order chromatin structure, DNA double-strand break induction and repair, and the formation of chromosomal translocations, we show the development of Omics solutions especially for radiation research (radiomics) (discussed in this article) and how confocal microscopy as well as novel approaches of molecular localization nanoscopy fill the gaps to successfully place the Omics data in the context of space and time (discussed in our other article in this issue, "Determining Omics Spatiotemporal Dimensions Using Exciting New Nanoscopy Techniques to Assess Complex Cell Responses to DNA Damage: Part B−Structuromics"). Finally, we introduce a novel method of specific chromatin nanotargeting and speculate future perspectives, which may combine nanoprobing and structural nanoscopy to observe structure–function correlations in living cells in real time. Thus, the Omics networks obtained from function analyses may be enriched by real-time visualization of Structuromics.
Determining Omics Spatiotemporal Dimensions Using Exciting New Nanoscopy Techniques to Assess Complex Cell Responses to DNA Damage: Part B− Structuromics
225-247
10.1615/CritRevEukaryotGeneExpr.v24.i3.40
Martin
Falk
Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
Michael
Hausmann
Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany
Emilie
Lukasova
Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
Abin
Biswas
Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany; Department of Radiation Oncology, University Medical Center Mannheim, University of Heidelberg, Heidelberg, Germany
Georg
Hildenbrand
Department of Radiation Oncology, University Medical Center Mannheim, Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany
Marie
Davidkova
Nuclear Physics Institute, Academy of Sciences of the Czech Republic, Rez, Czech Republic
Evgeny
Krasavin
Joint Institute for Nuclear Research, Dubna, Moscow, Russia
Zdenek
Kleibl
Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
Iva
Falkova
Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
Lucie
Jezkova
Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic; Joint Institute for Nuclear Research, Dubna, Moscow, Russia; Institute of Chemical Technology Prague, Prague, Czech Republic
Lenka
Stefancikova
Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
Jan
Sevcik
Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
Michal
Hofer
Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
Alena
Bacikova
Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
Pavel
Matula
Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic; Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University, Brno, Czech Republic
Alla
Boreyko
Joint Institute for Nuclear Research, Dubna, Moscow, Russia
Jana
Vachelova
Nuclear Physics Institute, Academy of Sciences of the Czech Republic, Rez, Czech Republic
Anna
Michaelidesova
Nuclear Physics Institute, Academy of Sciences of the Czech Republic, Rez, Czech Republic; Proton Therapy Center, Prague, Czech Republic
Stanislav
Kozubek
Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
Omics
ionizing radiation
low-dose dilemma
biological complexity and variability
higher-order chromatin structure
DNA damage response
formation of chromosomal translocations
confocal microscopy
localization nanoscopy
Recent groundbreaking developments in Omics and bioinformatics have generated new hope for overcoming the complexity and variability of (radio)biological systems while simultaneously shedding more light on fundamental radiobiological questions that have remained unanswered for decades. In the era of Omics, our knowledge of how genes and dozens of proteins interact in the frame of complex signaling and repair pathways (or, rather, networks) to preserve the integrity of the genome has been rapidly expanding. Nevertheless, these functional networks must be observed with strong correspondence to the cell nucleus, which is the main target of ionizing radiation. Information regarding these intricate processes cannot be achieved using high-throughput Omics approaches alone; it requires sophisticated structural probing and imaging. In the first part of this review, the article "Giving Omics Spatiotemporal Dimensions Using Exciting New Nanoscopy Techniques to Assess Complex Cell Responses to DNA Damage: Part A−Radiomics," we showed the development of different Omics solutions and how they are contributing to a better understanding of cellular radiation response. In this Part B we show how high-resolution confocal microscopy as well as novel approaches of molecular localization nanoscopy fill the gaps to successfully place Omics data in the context of space and time. The dynamics of double-strand breaks during repair processes and chromosomal rearrangements at the microscale correlated to aberration induction are explained. For the first time we visualize pan-nuclear nucleosomal rearrangements and clustering at the nanoscale during repair processes. Finally, we introduce a novel method of specific chromatin nanotargeting based on a computer database search of uniquely binding oligonucleotide combinations (COMBO-FISH). With these challenging techniques on hand, we speculate future perspectives that may combine specific COMBO-FISH nanoprobing and structural nanoscopy to observe structure-function correlations in living cells in real-time. Thus, the Omics networks obtained from function analyses may be enriched by real-time visualization of Structuromics.
Acupuncture, Connective Tissue, and Peripheral Sensory Modulation
249-253
10.1615/CritRevEukaryotGeneExpr.2014008284
Helene M.
Langevin
Department of Neurological Sciences, University of Vermont, Burlington, VT, Osher Center for Integrative Medicine, Division of Preventive Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
acupuncture
connective tissue
purinergic signaling
ATP
adenosine
fibroblasts
mechanotransduction
Although considerable controversy surrounds the legitimacy of acupuncture as a treatment, a growing literature on the physiological effects of acupuncture needling in animals and humans is providing new insights into basic cellular mechanisms including connective tissue mechanotransduction and purinergic signaling. This review summarizes these findings and proposes a model combining connective tissue plasticity and peripheral sensory modulation in response to the sustained stretching of tissue that results from acupuncture needle manipulation.
Cytoskeleton Dynamics in the Retina
255-268
10.1615/CritRevEukaryotGeneExpr.2014010561
Akshay
Anand
Neuroscience Research Lab, Post Graduate Institute of Medical Education and Research, Chandigarh, India
Sridhar
Bammidi
Department of Neurology, PGIMER, Chandigarh 160012, India
Parul
Bali
Department of Biophysics, Panjab University, Chandigarh 160014, India
microtubule
intermediate filament
microfilament
cytoskeleton
Background: Cytoskeleton is one of the essential forms of protein, important in the existence of both eukaryotic as well as prokaryotic cells. Its transformation plays a vital role in cell division and intracellular transportation by facilitating intracellular vesicular traffic. Among the various tissue types in the body, the neural tissue exhibits the maximum heterogeneity, and hence the role of cytoskeleton at both developmental and functional levels becomes paramount. Cytoskeleton dynamics have been established in the neural physiology, but only at the level of axonal development and growth. Retina has not been adequately studied in the context of cytoskeletal proteins. Methods: We reviewed the last 10 years of literature with reference to the development, growth, degeneration, and regeneration of the retina and the role of cytoskeleton in each aspect. We have focused on various changes that the retina undergoes at the cytosolic and cytoskeletal levels in the course of degeneration as well as regeneration. Findings: For this review, we compiled research articles pertaining to the role of cytoskeletal and other associated proteins involved in development of retina, which used various animal models. The effect of SNPs in the cytoskeletal proteins and their impact in retinal degeneration is also discussed. Conclusion: Studies describing the role of cytoskeleton in the anatomy and physiology of retina and its layers, although they are few, collectively provide an opportunity to understand retinal development in the context of cytoskeleton dynamics.
Mycobacterium Biofilms: Factors Involved in Development, Dispersal, and Therapeutic Strategies Against Biofilm-Relevant Pathogens
269-279
10.1615/CritRevEukaryotGeneExpr.2014010545
Xiaohong
Xiang
Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, State Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Scien
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
Minqiang
Liu
Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, State Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Scien
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
Keywords
Mycobacterium
tuberculosis
development
dispersal
antibiotics
biofilm
resistance
drug target
Many bacteria can develop biofilm (BF), a multicellular structure largely combining bacteria and their extracellular polymeric substances (EPS). The formation of biofilm results in an alternative existence in which microbes ensure their survival in adverse environments. Biofilm-relevant infections are more persistent, resistant to most antibiotics, and more recalcitrant to host immunity. Mycobacterium tuberculosis, the causative agent of tuberculosis, can develop biofilm, though whether M. tuberculosis can form biofilm within tuberculosis patients has yet to be determined. Here, we summarize the factors involved in the development and dispersal of mycobacterial biofilms, as well as underlying regulatory factors and inhibitors against biofilm to deepen our understanding of their development and to elucidate potential novel modes of action for future antibiotics. Key factors in biofilm formation identified as drug targets represent a novel and promising avenue for developing better antibiotics.