International Journal of Biological Sciences http://www.biolsci.org International Journal of Biological Sciences RSS feed -- Volume 6 en-us Wed, 21 Jul 2010 04:00:00 GMT Wed, 21 Jul 2010 04:00:00 GMT http://www.biolsci.org/v06p0407.htm Subtle evolutionary changes in the distribution of N-glycosylation sequons in the HIV-1 envelope glycoprotein 120 http://www.biolsci.org/v06p0407.htm Many viruses are known to undergo rapid evolutionary changes under selective pressures. The HIV-1 envelope glycoprotein 120 (gp120) shows extreme selection for NXS/T sequons, the potential sites of N-glycosylation. Although the average number of sequons in gp120 appears to be relatively stable in the recent past, even slight changes in the distribution of sequons may potentially play crucial roles in protein interaction and viral infection. This study tracked the prevalence and distribution of NXS/T sequons in gp120 over a period of 29 years (from 1981 to 2009). The gp120 showed location specific distribution of sequons with higher density in the outer domain of the molecule. The NXT sequon density decreased in the outer domain (despite the increase in the sequon specific amino acid threonine), but increased in the inner domain. By contrast, the NXS sequon density increased specifically in the outer domain. Related changes were also seen in the distribution probabilities of sequons in two domains. The results indicate that the gp120, chiefly in subtype B, is redistributing NXS/T sequons within the molecule with specific selection for NXS sequons. The subtle evolution of sequons in gp120 may have implications in viral resistance and infection.

]]> R. Shyama Prasad Rao, Bernd Wollenweber Ivyspring International Publisher 6 5 407 418 2010-7-21 Research Paper http://www.biolsci.org/v06p0396.htm Sustained Expression of TDP-43 and FUS in Motor Neurons in Rodent's Lifetime http://www.biolsci.org/v06p0396.htm TAR DNA-binding protein (TDP-43) and fused in sarcoma (FUS) are two highly conserved ribonucleoproteins. Pathogenic mutations of the TDP-43 or the FUS gene are all linked to amyotrophic lateral sclerosis (ALS) that is characterized by progressive degeneration of motor neurons. To better understand the correlation of ALS disease genes with the selectivity of chronic motor neuron degeneration, we examined the longitudinal expression of the TDP-43 and the FUS genes in C57BL6 mice and in Sprague-Dawley rats. TDP-43 and FUS were robustly and ubiquitously expressed in the postnatal mice and rats, but were markedly decreased in the adult rodents. In adulthood, TDP-43 and FUS proteins were even undetectable in peripheral organs including skeletal muscles, liver, and kidney, but were constantly expressed at substantial levels in the central nervous system. Motor neurons expressed the TDP-43 and the FUS genes at robust levels throughout rodent's lifetime. Moreover, TDP-43 and FUS were accumulated in the cytoplasm of motor neurons in aged animals. Our findings suggest that TDP-43 and FUS play an important role in development and that constant and robust expression of the genes in motor neurons may render the neurons vulnerable to pathogenic mutation of the TDP-43 or the FUS gene. To faithfully model the pathology of TDP-43- or FUS gene mutations in rodents, we must replicate the expression patterns of the TDP-43 and the FUS gene in animals.

]]> Cao Huang, Pedro Yuxing Xia, Hongxia Zhou Ivyspring International Publisher 6 4 396 406 2010-7-4 Research Paper http://www.biolsci.org/v06p0382.htm E2F-1 binding affinity for pRb is not the only determinant of the E2F-1 activity http://www.biolsci.org/v06p0382.htm E2F-1 is the major cellular target of pRB and is regulated by pRB during cell proliferation. Interaction between pRB and E2F-1 is dependent on the phosphorylation status of pRB. Despite the fact that E2F-1 and pRB have antagonistic activities when they are overexpressed, the role of the E2F-1-pRB interaction in cell growth largely remains unknown. Ideally, it would be better to study the properties of a pRB mutant that fails to bind to E2F, but retains all other activities. To date, no pRB mutation has been characterized in sufficient detail to show that it specifically eliminates E2F binding but leaves other interactions intact. An alternative approach to this issue is to ask whether mutations that change E2F proteins binding affinity to pRB are sufficient to change cell growth in aspect of cell cycle and tumor formation. Therefore, we used the E2F-1 mutants including E2F-1/S332-7A, E2F-1/S375A, E2F-1/S403A, E2F-1/Y411A and E2F-1/L132Q that have different binding affinities for pRB to better understand the roles of the E2F-1 phosphorylation and E2F-1-pRB interaction in the cell cycle, as well as in transformation and gene expression. Data presented in this study suggests that in vivo phosphorylation at amino acids 332-337, 375 and 403 is important for the E2F-1 and pRB interaction in vivo. However, although E2F-1 mutants 332-7, 375 and 403 showed similar binding affinity to pRB, they showed different characteristics in transformation efficiency, G0 accumulation, and target gene experiments.

]]> Fikret Sahin, Todd L. Sladek Ivyspring International Publisher 6 4 382 395 2010-7-4 Research Paper http://www.biolsci.org/v06p0371.htm Proliferation of Myoblast Skeletal Cells on Three-Dimensional Supermacroporous Cryogels http://www.biolsci.org/v06p0371.htm Cardiac and skeletal muscle tissue engineering provides a smart approach to overcome problems associated with organ transplantation and cardiac tissue and also lays a platform for superior alternative approaches in muscle regeneration. The aim of the study was to demonstrate cryogel scaffold potential in the field of skeletal muscle and cardiac tissue engineering. Poly-hydroxyethyl methacrylate (pHEMA)-gelatin cryogel scaffold was synthesized using cryogelation technique and such a designed material is being reported first time. Rheology study of the pHEMA-gelatin (HG) suggested that the cryogel scaffolds were stable at different temperatures and phase angle remained constant in both dry and wet state. HG cryogel was able to bear increased stress without leading to deformation. Monitoring the hydration of HG scaffold showed shift from a stiff to a more pliable material and upon continuing hydration, shear modulus remained constant with no further change observed. However, the change in phase angle <0.24º indicates a gradual increase in stiffness of the material over time. Scaffold synthesised using such polymer combinations gave cells a native environment for proliferation and surface stiffness have shown to help in differentiation of the cells. Myoskeletal cell lines were cultured on these scaffolds to check the biocompatibility and cell proliferation. Alamar blue assay performed over a period of 3 weeks analysed the metabolic activity of cells which showed more than 60% increase in the total cellular activity. DNA content of cells was found to be directly related to number of cells present at a given time point and this was found to have increased by more than 50% in 3 weeks. Since in 3-D scaffold the surface area is more in comparison to 2-D, hence better cell proliferation is observed. Hoechst and DAPI staining showed tubular structure and alignment of the cells during formation of the tubules shows promising cellular response to the cryogel matrix. The mechanical strength, stiffness and elastic measurements of the scaffold indicated potential application of these materials for skeletal and cardiac tissue engineering.

]]> Deepti Singh, Vijayashree Nayak, Ashok Kumar Ivyspring International Publisher 6 4 371 381 2010-7-3 Research Paper http://www.biolsci.org/v06p0361.htm Regulation of Vid-dependent degradation of FBPase by TCO89, a component of TOR Complex 1 http://www.biolsci.org/v06p0361.htm A pivotal gluconeogenic enzyme in Saccharomyces cerevisuae, fructose-1, 6-bisphosphatase (FBPase) was selectively turned over in vacuole via Vid (vacuole import and degradation) dependent pathway in response to the fresh glucose after chronic glucose starvation. TCO89, a novel and unique component of Tor Complex I (TORCI), was found to physically associate with FBPase and significantly affect FBPase degradation via Vid pathway. Further investigation indicated that Δtco89 mutant strongly impaired FBPase's importing into Vid vesicles and Vid24's association with Vid vesicles. Inactivation of TORCI by rapamycin treatment strongly blocked FBPase degradation. Other components of TORCI were also found to physically associate with FBPase. The P1S mutation of FBPase, reported to block its degradation, was observed to impair the association of FBPase with TORCI components. These results implicated an important regulatory role of TCO89 and TORCI in this pathway.

]]> Yan Yan, Bin Kang Ivyspring International Publisher 6 4 361 370 2010-7-2 Research Paper http://www.biolsci.org/v06p0350.htm Differential transcriptional analysis between red and white skeletal muscle of Chinese Meishan pigs http://www.biolsci.org/v06p0350.htm In order to better understand and elucidate the major determinants of red and white muscle phenotypic properties, the global gene expression profiling was performed in white (longissimus doris) and red (soleus) skeletal muscle of Chinese Meishan pigs using the Affymetrix Porcine Genechip. 550 transcripts at least 1.5-fold difference were identified at p < 0.05 level, with 323 showing increased expression and 227 decreased expression in red muscle. Quantitative real-time PCR validated the differential expression of eleven genes (α-Actin, ART3, GATA-6, HMOX1, HSP, MYBPH, OCA2, SLC12A4, TGFB1, TGFB3 and TNX). Twenty eight signaling pathways including ECM-receptor interaction, focal adhesion, TGF-beta signaling pathway, MAPK signaling pathway, Wnt signaling pathway, mTOR signaling pathway, insulin signaling pathway and cell cycle, were identified using KEGG pathway database. Our findings demonstrate previously unrecognized changes in gene transcription between red and white muscle, and some potential cascades identified in the study merit further investigation.

]]> Yang Li, Zaiyan Xu, Hongying Li, Yuanzhu Xiong, Bo Zuo Ivyspring International Publisher 6 4 350 360 2010-6-27 Research Paper http://www.biolsci.org/v06p0333.htm Water Buffalo Genome Science Comes of Age http://www.biolsci.org/v06p0333.htm The water buffalo is vital to the lives of small farmers and to the economy of many countries worldwide. Not only are they draught animals, but they are also a source of meat, horns, skin and particularly the rich and precious milk that may be converted to creams, butter, yogurt and many cheeses. Genome analysis of water buffalo has advanced significantly in recent years. This review focuses on currently available genome resources in water buffalo in terms of cytogenetic characterization, whole genome mapping and next generation sequencing. No doubt, these resources indicate that genome science comes of age in the species and will provide knowledge and technologies to help optimize production potential, reproduction efficiency, product quality, nutritional value and resistance to diseases. As water buffalo and domestic cattle, both members of the Bovidae family, are closely related, the vast amount of cattle genetic/genomic resources might serve as shortcuts for the buffalo community to further advance genome science and biotechnologies in the species.

]]> Vanessa N. Michelizzi, Michael V. Dodson, Zengxiang Pan, M Elisabete J Amaral, Jennifer J. Michal, Derek J. McLean, James E. Womack, Zhihua Jiang Ivyspring International Publisher 6 4 333 349 2010-6-17 Review http://www.biolsci.org/v06p0327.htm Generation of Fgfr3 Conditional Knockout Mice http://www.biolsci.org/v06p0327.htm Fibroblast growth factor receptor 3 (FGFR3), highly conserved in both humans and murine, is one of key tyrosine kinase receptors for FGF. FGFR3 is expressed in different tissues, including cartilage, brain, kidney, and intestine at different development stages. Conventional knockout of Fgfr3 alleles leads to short life span, and overgrowth of bone. In clinic, human FGFR3 mutations are responsible for three different types of chondrodysplasia syndromes including achondroplasia (ACH), hypochondroplasia (HCH) and thanatophoric dysplasia (TD). For better understanding of the roles of FGFR3 in different tissues at different stages of development and in pathological conditions, we generated Fgfr3 conditional knockout mice in which loxp sites flank exons 9-10 in the Fgfr3 allele. We also demonstrated that Cre-mediated recombination using Col2a1-Cre, a Cre line expressed in chondrocyte during bone development, results in specific deletion of the gene in tissues containing cartilage. This animal model will be useful to study distinct roles of FGFR3 in different tissues at different ages.

]]> Nan Su, Xiaoling Xu, Cuiling Li, Qifen He, Ling Zhao, Can Li, Siyu Chen, Fengtao Luo, Lingxian Yi, Xiaolan Du, Haiyang Huang, Chuxia Deng, Lin Chen Ivyspring International Publisher 6 4 327 332 2010-6-15 Research Paper http://www.biolsci.org/v06p0316.htm Cloning, characterization, and expression analysis of goat (Capra hircus) phospholipid hydroperoxide glutathione peroxidase (PHGPx) http://www.biolsci.org/v06p0316.htm Phospholipid hydroperoxide glutathione peroxidase (PHGPx), as a ubiquitous antioxidant enzyme in the glutathione peroxidases (GPx) family, plays multiple roles in organisms. However, there is very little information on PHGPx in goats (Capra hircus). In this study, a full-length cDNA was cloned and characterized from Taihang black goat testes. The 844 bp cDNA contains an open reading frame (ORF) of 597 bp. The goat PHGPx nucleotide sequence contains a selenocysteine (sec) codon TGA244-246, two potential start codons ATG20-22 and ATG108-110, a polyadenylation signal AATAAA813-818 and selenocysteine insertion sequence (SECIS) motif AUGA688-691, UGA729-731 and AAA703-705. As a selenoprotein, the active-site motifs and GPx family signature motifs LAFPCNQF101-108 and WNFEK165-170 were also found. The order of PHGPx mRNA expression levels was: testes >> heart > brain > epididymis > kidney > liver > lung > spleen > muscle. Real-time PCR and immunohistochemistry results revealed similar expression differences in different age testes, with high expression levels during adolescence. Immunofluorescence results suggested that PHGPx mainly expressed in Leydig cells and spermatids in mature goat testes.

]]> Li-guang SHI, Wen-juan XUN, Wen-bin YUE, Chun-xiang ZHANG, You-she REN, Qian WANG, Xiao-ying WU, Lei SHI, Ru-jie YANG, Fu-lin LEI Ivyspring International Publisher 6 4 316 326 2010-6-10 Research Paper http://www.biolsci.org/v06p0303.htm Survival of Escherichia coli under lethal heat stress by L-form conversion http://www.biolsci.org/v06p0303.htm Transition of bacteria to cell wall deficient L-forms in response to stress factors has been assumed as a potential mechanism for survival of microbes under unfavorable conditions. In this article, we provide evidence of paradoxal survival through L-form conversion of E. coli high cell density population after lethal treatments (boiling or autoclaving). Light and transmission electron microscopy demonstrated conversion from classical rod to polymorphic L-form shape morphology and atypical growths of E. coli. Microcrystal formations observed at this stage were interpreted as being closely linked to the processes of L-form conversion and probably involved in the general phenomenon of protection against lethal environment. Identity of the morphologically modified L-forms as E. coli was verified by species specific DNA-based test. Our study might contribute to a better understanding of the L-form phenomenon and its importance for bacterial survival, as well as provoke reexamination of the traditional view of killing strategies against bacteria.

]]> Nadya Markova, Georgi Slavchev, Lilia Michailova, Mimi Jourdanova Ivyspring International Publisher 6 4 303 315 2010-6-9 Research Paper http://www.biolsci.org/v06p0294.htm Antiviral actions of flavanoid-derived compounds on dengue virus type-2 http://www.biolsci.org/v06p0294.htm Dengue viruses, mosquito-borne members of the Flaviviridae family, are the causative agents of dengue fever and its associated complications, dengue haemorrhagic fever and dengue shock syndrome. To date, more than 2.5 billion people in over 100 countries are at risk of infection, and approximately 20 million infections were reported annually. There is currently no treatment or vaccine available for dengue infection. This study employed a whole-cell organism model or in vitro methods to study the inhibitory property of the flavanoid-derived compounds against DENV2 activity. Results showed that at concentration not exceeding the maximum non-toxic dose (MNTD), these compounds completely prevented DENV2 infection in HepG2 cells as indicated by the absence of cytophatic effects. The in vitro antiviral activity assessed in HepG2 cells employing virus inhibition assay showed high inhibitory activity in a dose dependent manner. At concentration below MNTD, compounds exhibited inhibitory activity against DENV2 with a range of potency strengths of 72% to 100%. The plaque forming unit per ml (pfu/ml) was reduced prominently with a maximum reduction of 98% when the infected HepG2 cells were treated with the highest non-toxic dose of compounds. The highly potent activity of the compounds against DENV2 infection strongly suggests their potential as a lead antiviral agent for dengue.

]]> Mudiana Muhamad, Lee Yean Kee, Noorsaadah Abd. Rahman, Rohana Yusof Ivyspring International Publisher 6 3 294 302 2010-5-23 Research Paper http://www.biolsci.org/v06p0282.htm Melatonin Plays a Protective Role in Postburn Rodent Gut Pathophysiology http://www.biolsci.org/v06p0282.htm Melatonin is a possible protective agent in postburn gut pathophysiological dynamics. We investigated the role of endogenously-produced versus exogenously-administered melatonin in a major thermal injury rat model with well-characterized gut inflammatory complications. Our rationale is that understanding in vivo melatonin mechanisms in control and inflamed tissues will improve our understanding of its potential as a safe anti-inflammatory/antioxidant therapeutic alternative. Towards this end, we tested the hypothesis that the gut is both a source and a target for melatonin and that mesenteric melatonin plays an anti-inflammatory role following major thermal injury in rats with 3rd degree hot water scald over 30% TBSA. Our methods for assessing the gut as a source of melatonin included plasma melatonin ELISA measurements in systemic and mesenteric circulation as well as rtPCR measurement of jejunum and terminal ileum expression of the melatonin synthesizing enzymes arylalkylamine N-acetyltransferase (AA-NAT) and 5-hydroxyindole-O-methyltransferase (HIOMT) in sham versus day-3 postburn rats. Our melatonin ELISA results revealed that mesenteric circulation has much higher melatonin than systemic circulation and that both mesenteric and systemic melatonin levels are increased three days following major thermal injury. Our rtPCR results complemented the ELISA data in showing that the melatonin synthesizing enzymes AA-NAT and HIOMT are expressed in the ileum and jejunum and that this expression is increased three days following major thermal injury. Interestingly, the rtPCR data also revealed negative feedback by melatonin as exogenous melatonin supplementation at a dose of 7.43 mg (32 μmole/kg), but not 1.86 mg/kg (8 μmole/kg) drastically suppressed AA-NAT mRNA expression. Our methods also included an assessment of the gut as a target for melatonin utilizing computerized immunohistochemical measurements to quantify the effects of exogenous melatonin supplementation on postburn gut mucosa barrier inflammatory profiles. Here, our results revealed that daily postburn intraperitoneal melatonin administration at a dose of 1.86 mg/kg (8 μmole/kg) significantly suppressed both neutrophil infiltration and tyrosine nitrosylation as revealed by Gr-1 and nitrotyrosine immunohistochemistry, respectively. In conclusion, our results provide support for high mesenteric melatonin levels and dynamic de novo gut melatonin production, both of which increase endogenously in response to major thermal injury, but appear to fall short of abrogating the excessive postburn hyper-inflammation. Moreover, supplementation by exogenous melatonin significantly suppresses gut inflammation, thus confirming that melatonin is protective against postburn inflammation.

]]> Walid M. Al-Ghoul, Steven Abu-Shaqra, Byeong Gyu Park, Nadeem Fazal Ivyspring International Publisher 6 3 282 293 2010-5-17 Research Paper http://www.biolsci.org/v06p0268.htm Notch and Wnt Signaling, Physiological Stimuli and Postnatal Myogenesis http://www.biolsci.org/v06p0268.htm Adult skeletal muscle stem cells, termed satellite cells are imperative to muscle regeneration. Much work has been performed on satellite cell identification and the subsequent activation of the myogenic response but the regulation of satellite cells including its activation is not well elucidated. The purpose of this review article is to synthesize what the literature reveals in regards to the current understanding of satellite cells including their contribution to muscle repair and growth following physiological stimuli. In addition, this review article will describe the recent findings on the roles of the classic developmental signaling pathways, Notch and Wnt, to the myogenic response in various muscle injury models. This purpose of this summary is to bring awareness of the impact that muscle contraction models have on the local and systemic environment of adult muscle stem cells which will be beneficial for comprehending and treatment development for muscle -associated ailments and other organ diseases.

]]> Susan Tsivitse Ivyspring International Publisher 6 3 268 281 2010-5-15 Review http://www.biolsci.org/v06p0252.htm NIP/DuoxA is essential for Drosophila embryonic development and regulates oxidative stress response http://www.biolsci.org/v06p0252.htm NIP/DuoxA, originally cloned as a protein capable of binding to the cell fate determinant Numb in Drosophila, was recently identified as a modulator of reactive oxygen species (ROS) production in mammalian systems. Despite biochemical and cellular studies that link NIP/DuoxA to the generation of ROS through the dual oxidase (Duox) enzyme, the in vivo function of NIP/DuoxA has not been characterized to date. Here we report a genetic and functional characterization of nip in Drosophila melanogaster. We show that nip is essential for Drosophila development as nip null mutants die at the 1st larval instar. Expression of UAS-nip, but not UAS-Duox, rescued the lethality. To understand the function of nip beyond the early larval stage, we generated GAL4 inducible UAS-RNAi transgenes. daG32-GAL4 driven, ubiquitous RNAi-mediated silencing of nip led to profound abnormality in pre-adult development, crinkled wing and markedly reduced lifespan at 29°C. Compared to wild type flies, da-GAL4 induced nip-RNAi transgenic flies exhibited significantly reduced ability to survive under oxidative stress and displayed impaired mitochondrial aconitase function. Our work provides in vivo evidence for a critical role for nip in the development and oxidative stress response in Drosophila.

]]> Xiaojun Xie, Jack Hu, Xiping Liu, Hanjuan Qin, Anthony Percival-Smith, Yong Rao, Shawn S.C. Li Ivyspring International Publisher 6 3 252 267 2010-5-11 Research Paper http://www.biolsci.org/v06p0228.htm Natural and artificial mutants as valuable resources for functional genomics and molecular breeding http://www.biolsci.org/v06p0228.htm With the completion of rice genome sequencing, large collection of expression data and the great efforts in annotating rice genomes, the next challenge is to systematically assign functions to all predicted genes in the genome. The generations and collections of mutants at the genome-wide level form technological platform of functional genomics. In this study, we have reviewed currently employed tools to generate such mutant populations. These tools include natural, physical, chemical, tissue culture, T-DNA, transposon or gene silencing based mutagenesis. We also reviewed how these tools were used to generate a large collection of mutants and how these mutants can be screened and detected for functional analysis of a gene. The data suggested that the current population of mutants might be large enough to tag all predicted genes. However, the collection of flanking sequencing tags (FSTs) is limited due to the relatively higher cost. Thus, we have proposed a new strategy to generate gene-silencing mutants at the genome-wide level. Due to the large collection of insertion mutants, the next step to rice functional genomics should be focusing on functional characterization of tagged genes by detailed survey of corresponding mutants. Additionally, we also evaluated the utilization of these mutants as valuable resources for molecular breeding.

]]> Shu-Ye Jiang, Srinivasan Ramachandran Ivyspring International Publisher 6 3 228 251 2010-4-28 Review http://www.biolsci.org/v06p0225.htm Leukocyte infiltration as a surrogate marker for diagnosis of invasion http://www.biolsci.org/v06p0225.htm Dr. YG Man's hypothesis that breast tumor invasion is triggered by the aberrant leukocyte infiltration induced by degeneration of myoepithelial cells holds a lot of truth in our clinical practice, and leukocyte infiltration may be regarded as a surrogate marker for diagnosis of invasion.

]]> Aijun Liu, Lixin Wei Ivyspring International Publisher 6 3 225 227 2010-4-28 Letter http://www.biolsci.org/v06p0213.htm Analysis of differentially expressed mitochondrial proteins in chromophobe renal cell carcinomas and renal oncocytomas by 2-D gel electrophoresis http://www.biolsci.org/v06p0213.htm Renal oncocytomas (RO) and chromophobe renal cell carcinomas (RCC) display morphological and functional alterations of the mitochondria. Previous studies showed that accumulation of mitochondria in ROs is associated with somatic mutations of mitochondrial DNA (mtDNA) resulting in decreased activity of the respiratory chain complex I, whereas in chromophobe RCC only heteroplasmic mtDNA mutations were found. To identify proteins associated with these changes, for the first time we have compared the mitochondrial proteomes of mitochondria isolated from ROs and chromophobe RCCs as well as from normal kidney tissues by two-dimensional polyacrylamide gel electrophoresis. The proteome profiles were reproducible within the same group of tissues in subsequent experiments. The expression patterns within each group of samples were compared and 81 in-gel digested spots were subjected to nanoLC-MS/MS-based identification of proteins. Although the list of mitochondrial proteins identified in this study is incomplete, we identified the downregulation of NDUFS3 from complex I of the respiratory chain and upregulation of COX5A, COX5B, and ATP5H from complex IV and V in ROs. In chromophobe RCCs downregulation of ATP5A1, the alpha subunit of complex V, has been observed, but no changes in expression of other complexes of the respiratory chain were detected. To confirm the role of respiratory chain complex alterations in the morphological and/or functional changes in chromophobe RCCs and ROs, further studies will be necessary.

]]> Maria V. Yusenko, Thomas Ruppert, Gyula Kovacs Ivyspring International Publisher 6 3 213 224 2010-4-23 Research Paper http://www.biolsci.org/v06p0199.htm Uncoupling oxidative/energy metabolism with low sub chronic doses of 3-nitropropionic acid or iodoacetate in vivo produces striatal cell damage http://www.biolsci.org/v06p0199.htm A variety of evidence suggests that the failure of cellular metabolism is one of the underlying causes of neurodegenerative diseases. For example, the inhibition of mitochondrial function produces a pattern of cellular pathology in the striatum that resembles that seen in Huntington's disease. However, neurons can also generate ATP through the glycolytic pathway. Recent work has suggested a direct interaction between mutated huntingtin and a key enzyme in the glycolytic pathway, glyceraldehyde-3-phosphate dehydrogenase (GAPDH). Yet little work has been gone into examination of the cellular pathology that results from the inhibition of this alternative energy source. Therefore, the aim of the present study is to characterize the cellular pathology that results in the striatum of mice after treatment with a toxin (iodoacete, IOA) that compromises anaerobic metabolism. This striatal pathology is compared to that produced by a widely studied blocker of mitochondrial function (3-nitropropionic acid, 3-NP).

We found that low doses of either toxin resulted in significant pathology in the mouse striatum. Signs of apoptosis were observed in both experimental groups, although apoptosis triggered by IOA treatment was independent from caspase-3 activation. Importantly, each toxin appears to produce cellular damage through distinct mechanisms; only 3-NP generated clear evidence of oxidative stress as well as inhibition of endogenous antioxidants. Understanding the distinct pathological fingerprints of cell loss produced by blockade of oxidative and anaerobic metabolisms may give us insights into neurodegenerative diseases.

]]> E Rodríguez, I Rivera, S Astorga, E Mendoza, F García, E Hernández-Echeagaray Ivyspring International Publisher 6 3 199 212 2010-4-22 Research Paper http://www.biolsci.org/v06p0192.htm Studies on the Developmental Potentiality of Cultured Cell Nuclei of Fish http://www.biolsci.org/v06p0192.htm By means of the serial nuclear transplantation technique, the authors obtained a nuclear transplant fish from subcultured cell originated from the blastula cells of the crucian carp (Carassius auratus Linnaeus). This nuclear transplant fish survived for three years, but its sexual glands were undifferentiated. The authors have also obtained a sexually mature adult fish from short-term cultured kidney cell nucleus of an adult crucian carp.

Results of the experiment implied that the subcultured cell nuclei of fish blastula cells and the specialized somatic cell nuclei of adult fish still retained their developmental totipotency, and thus, it indicated that there is a possibility of fish somatic cell breeding through the use of nuclear transplantation.

]]> Hongxi Chen, Yonglan Yi, Minrong Chen, Xingqi Yang Ivyspring International Publisher 6 2 192 198 2010-4-21 Research Paper http://www.biolsci.org/v06p0190.htm An Unknown Piece of Early Work of Nuclear Reprogramming in Fish Eggs http://www.biolsci.org/v06p0190.htm Chuxia Deng, Hanqin Liu Ivyspring International Publisher 6 2 190 191 2010-4-21 Editorial http://www.biolsci.org/v06p0187.htm Rab5(Q79L) interacts with the carboxyl terminus of RUFY3 http://www.biolsci.org/v06p0187.htm Hitomi Yoshida, Naoko Okumura, Yasuko Kitagishi, Naoki Shirafuji, Satoru Matsuda Ivyspring International Publisher 6 2 187 189 2010-4-4 Letter To The Editor http://www.biolsci.org/v06p0172.htm The complete mitochondrial genome of the fall webworm, Hyphantria cunea (Lepidoptera: Arctiidae) http://www.biolsci.org/v06p0172.htm The complete mitochondrial genome (mitogenome) of the fall webworm, Hyphantria cunea (Lepidoptera: Arctiidae) was determined. The genome is a circular molecule 15 481 bp long. It presents a typical gene organization and order for completely sequenced lepidopteran mitogenomes, but differs from the insect ancestral type for the placement of tRNAMet. The nucleotide composition of the genome is also highly A + T biased, accounting for 80.38%, with a slightly positive AT skewness (0.010), indicating the occurrence of more As than Ts, as found in the Noctuoidea species. All protein-coding genes (PCGs) are initiated by ATN codons, except for COI, which is tentatively designated by the CGA codon as observed in other lepidopterans. Four of 13 PCGs harbor the incomplete termination codon, T or TA. All tRNAs have a typical clover-leaf structure of mitochondrial tRNAs, except for tRNASer(AGN), the DHU arm of which could not form a stable stem-loop structure. The intergenic spacer sequence between tRNASer(AGN) and ND1 also contains the ATACTAA motif, which is conserved across the Lepidoptera order. The H. cunea A+T-rich region of 357 bp is comprised of non-repetitive sequences, but harbors several features common to the Lepidoptera insects, including the motif ATAGA followed by an 18 bp poly-T stretch, a microsatellite-like (AT)8 element preceded by the ATTTA motif, an 11 bp poly-A present immediately upstream tRNAMet. The phylogenetic analyses support the view that the H. cunea is closerly related to the Lymantria dispar than Ochrogaster lunifer, and support the hypothesis that Noctuoidea (H. cunea, L. dispar, and O. lunifer) and Geometroidea (Phthonandria atrilineata) are monophyletic. However, in the phylogenetic trees based on mitogenome sequences among the lepidopteran superfamilies, Papillonoidea (Artogeia melete, Acraea issoria, and Coreana raphaelis) joined basally within the monophyly of Lepidoptera, which is different to the traditional classification.

]]> Fang Liao, Lin Wang, Song Wu, Yu-Ping Li, Lei Zhao, Guo-Ming Huang, Chun-Jing Niu, Yan-Qun Liu, Ming-Gang Li Ivyspring International Publisher 6 2 172 186 2010-3-29 Research Paper http://www.biolsci.org/v06p0163.htm The ulcerative colitis marker protein WAFL interacts with accessory proteins in endocytosis http://www.biolsci.org/v06p0163.htm Ulcerative colitis (UC) is one of the major forms of inflammatory bowel disease with unknown cause. A molecular marker, WAFL, has recently been found to be up-regulated in the inflamed colonic mucosa of UC patients. Towards understanding biological function of WAFL, we analyzed proteins interacting with WAFL in HEK-293 cells by immunoprecipitation and mass spectrometry. Among four proteins found to specifically interact with WAFL, both KIAA0196 and KIAA1033 bind to α-appendage of the adaptor protein complex 2 (AP2), which acts as an interaction hub for accessory proteins in endocytosis mediated by clathrin-coated vesicle (CCV). The specific interaction between WAFL and KIAA0196 was also confirmed in human colorectal carcinoma HCT-116 cells by co-immunoprecipitation with specific antibodies. Meta-analyses of the databases of expressed genes suggest that the three genes are co-expressed in many tissues and cell types, and that their molecular function may be classified in the category of 'membrane traffic protein'. Therefore, these results suggest that WAFL may play an important role in endocytosis and subsequent membrane trafficking by interacting with AP2 through KIAA0196 and KIAA1033.

]]> You Fu Pan, Ing-Marie Viklund, Heng Hang Tsai, Sven Pettersson, Ichiro N. Maruyama Ivyspring International Publisher 6 2 163 171 2010-3-29 Research Paper http://www.biolsci.org/v06p0151.htm Tumors Induced in Mice by Direct Inoculation of Plasmid DNA Expressing Both Activated H-ras and c-myc http://www.biolsci.org/v06p0151.htm Vaccines contain residual DNA derived from the cells used to produce them. As part of our investigation to assess the risk of this cellular DNA, we are developing a quantitative in vivo assay to assess the oncogenicity of DNA. In an earlier study, we had generated expression plasmids for two oncogenes - human activated T24-H-ras and murine c-myc - and had shown that these two plasmids, pMSV-T24-H-ras and pMSV-c-myc, could act in concert to induce tumors in mice, although the efficiency was low. In this study, we took two approaches to increase the oncogenic efficiency: 1) both oncogene-expression cassettes were placed on the same plasmid; 2) transfection facilitators, which increase DNA uptake and expression in vitro, were tested. The dual-expression plasmid, pMSV-T24-H-ras/MSV-c-myc, is about 20-fold more efficient at tumor induction in newborn NIH Swiss mice than the separate expression plasmids, with tumors being induced with 1 µg of the dual-expression plasmid DNA. However, none of the transfection facilitators tested increased the efficiency of tumor induction. Based on these data, the dual-expression plasmid pMSV-T24-H-ras/MSV-c-myc will be used as the positive control to develop a sensitive and quantitative animal assay that can be used to assess the oncogenic activity of DNA.

]]> Li Sheng-Fowler, Fang Cai, Haiqing Fu, Yong Zhu, Brian Orrison, Gideon Foseh, Don G. Blair, Stephen H. Hughes, John M. Coffin, Andrew M. Lewis Jr, Keith Peden Ivyspring International Publisher 6 2 151 162 2010-3-29 Research Paper http://www.biolsci.org/v06p0133.htm Does the difference between physically active and couch potato lie in the dopamine system? http://www.biolsci.org/v06p0133.htm Obesity and other inactivity related diseases are increasing at an alarming rate especially in Western societies. Because of this, it is important to understand the regulating mechanisms involved in physical activity behavior. Much research has been done in regard to the psychological determinants of physical activity behavior; however, little is known about the underlying genetic and biological factors that may contribute to regulation of this complex trait. It is true that a significant portion of any trait is regulated by genetic and biological factors. In the case of voluntary physical activity behavior, these regulating mechanisms appear to be concentrated in the central nervous system. In particular, the dopamine system has been shown to regulate motor movement, as well as motivation and reward behavior. The pattern of regulation of voluntary physical activity by the dopamine system is yet to be fully elucidated. This review will summarize what is known about the dopamine system and regulation of physical activity, and will present a hypothesis of how this signaling pathway is mechanistically involved in regulating voluntary physical activity behavior. Future research in this area will aid in developing personalized strategies to prevent inactivity related diseases.

]]> Amy M. Knab, J Timothy Lightfoot Ivyspring International Publisher 6 2 133 150 2010-3-9 Review http://www.biolsci.org/v06p0129.htm Aberrant leukocyte infiltration: a direct trigger for breast tumor invasion and metastasis http://www.biolsci.org/v06p0129.htm Our previous studies revealed that leukocyte infiltration could trigger breast and prostate tumor invasion through physical disruption of tumor capsules. Our current study, involving multiple types of human tumors, further suggests that leukocyte infiltration also triggers metastasis through the following pathways : 1) the physical movement into the epithelium disrupts inter-cellular junctions and surface adhesion molecules, which cause the disassociation of tumor cells from tumor cores, 2) some of these tumor cells subsequently form tight junctions with the plasma membranes of leukocytes creating tumor cell-leukocyte chimeras (TLCs), and 3) the leukocytes of TLCs impart migratory capacity to associated tumor cell partners. Our findings suggest a novel pathway for tumor cell dissemination from primary sites and journey to new sites.

]]> Yan-gao Man Ivyspring International Publisher 6 2 129 132 2010-3-9 Short Research Communication http://www.biolsci.org/v06p0116.htm E2F-1 has dual roles depending on the cell cycle http://www.biolsci.org/v06p0116.htm The E2F family of transcription factors play a critical role in the control of cell proliferation. E2F-1 is the major cellular target of pRB and is regulated by pRB during cell proliferation. E2F-1-mediated activation and repression of target genes occurs in different settings. The role of E2F-1 and E2F-1/pRB complexes in regulation of different target genes, and in cycling versus quiescent cells, is unclear. In this study, effects of free E2F-1 (doesn't complex with pRb) and E2F-1/pRb complex, on E2F-1 target gene expression were compared in different cell growth conditions. Findings suggest that E2F-1 acts in different ways, not only depending on the target gene but also depending on different stages of the cell cycle. For example, E2F-1 acts as part of the repression complex with pRB in the expression of DHFR, b-myb, TK and cdc2 in asynchronously growing cells; on the other hand, E2F-1 acts as an activator in the expression of the same genes in cells that are re-entering the cycle.

]]> Fikret Sahin, Todd L. Sladek Ivyspring International Publisher 6 2 116 128 2010-3-3 Research Paper http://www.biolsci.org/v06p0107.htm High prevalence of multiple paternity in the invasive crayfish species, Procambarus clarkii http://www.biolsci.org/v06p0107.htm Reproductive strategy is a central feature of the ecology of invasive species as it determines the potential for population increase and range expansion. The red swamp crayfish, Procambarus clarkii, has invaded many countries and caused serious problems in freshwater ecosystems. However, little is known about the effects of environmental conditions on crayfish paternity and offspring traits in the wild. We studied these reproductive characteristics of P. clarkii in wild populations from two different habitats (ponds and ditches) in three locations with different environmental conditions in China. Genotyping of 1,436 offspring and 30 mothers of 30 broods was conducted by using four microsatellites. An analysis of genotyping results revealed that gravid females were the exclusive mother of the progeny they tended. Twenty-nine of 30 mothers had mated with multiple (2-4) males, each of which contributed differently to the number of offspring in a brood. The average number of fathers per brood and the number of offspring per brood were similar (P > 0.05) among six sampling sites, indicating that in P. clarkii multiple paternity and offspring number per brood are independent of environmental conditions studied. Indirect benefits from increasing the genetic diversity of broods, male and sperm competition, and cryptic female choice are a possible explanation for the high level multiple paternity and different contribution of fathers to offspring in this species.

]]> Gen Hua Yue, Jia Le Li, Chun Ming Wang, Jun Hong Xia, Gen Lin Wang, Jian Bing Feng Ivyspring International Publisher 6 1 107 115 2010-2-17 Research Paper http://www.biolsci.org/v06p0096.htm Overexpression of bacterial ethylene-forming enzyme gene in Trichoderma reesei enhanced the production of ethylene http://www.biolsci.org/v06p0096.htm In order to efficiently utilize natural cellulose materials to produce ethylene, three expression vectors containing the ethylene-forming enzyme (efe) gene from Pseudomonas syringae pv. glycinea were constructed. The target gene was respectively controlled by different promoters: cbh I promoter from Trichoderma reesei cellobiohydrolases I gene, gpd promoter from Aspergillus nidulans glyceraldehyde-3-phosphate dehydrogenase gene and pgk I promoter from T. reesei 3-phosphoglycerate kinase I gene. After transforming into T. reesei QM9414, 43 stable transformants were obtained by PCR amplification and ethylene determination. Southern blot analysis of 14 transformants demonstrated that the efe gene was integrated into chromosomal DNA with copy numbers from 1 to 4. Reverse transcription polymerase chain reaction (RT-PCR) analysis of 6 transformants showed that the heterologous gene was transcribed. By using wheat straw as a carbon source, the ethylene production rates of aforementioned 14 transformants were measured. Transformant C30-3 with pgk I promoter had the highest ethylene production (4,012 nl h-1 l-1). This indicates that agricultural wastes could be used to produce ethylene in recombinant filamentous fungus T. reesei.

]]> Xi Chen, Yong Liang, Jing Hua, Li Tao, Wensheng Qin, Sanfeng Chen Ivyspring International Publisher 6 1 96 106 2010-2-6 Research Paper http://www.biolsci.org/v06p0089.htm Comparative study of the binding pockets of mammalian proprotein convertases and its implications for the design of specific small molecule inhibitors http://www.biolsci.org/v06p0089.htm Proprotein convertases are enzymes that proteolytically cleave protein precursors in the secretory pathway to yield functional proteins. Seven mammalian subtilisin/Kex2p-like proprotein convertases have been identified: furin, PC1, PC2, PC4, PACE4, PC5 and PC7. The binding pockets of all seven proprotein convertases are evolutionarily conserved and highly similar. Among the seven proprotein convertases, the furin cleavage site motif has recently been characterized as a 20-residue motif that includes one core region P6-P2´ inside the furin binding pocket. This study extended this information by examining the 3D structural environment of the furin binding pocket surrounding the core region P6-P2´ of furin substrates. The physical properties of mutations in the binding pockets of the other six mammalian proprotein convertases were compared. The results suggest that: 1) mutations at two positions, Glu230 and Glu257, change the overall density of the negative charge of the binding pockets, and govern the substrate specificities of mammalian proprotein convertases; 2) two proprotein convertases (PC1 and PC2) may have reduced sensitivity for positively charged residues at substrate position P5 or P6, whereas the substrate specificities of three proprotein convertases (furin, PACE4, and PC5) are similar to each other. This finding led to a novel design of a short peptide pattern for small molecule inhibitors: [K/R]-X-V-X-K-R. Compared with the widely used small molecule dec-RVKR-cmk that inhibits all seven proprotein convertases, a finely-tuned derivative of the short peptide pattern [K/R]-X-V-X-K-R may have the potential to more effectively inhibit five of the proprotein convertases (furin, PC4, PACE4, PC5 and PC7) compared to the remaining two (PC1 and PC2). The results not only provide insights into the molecular evolution of enzyme function in the proprotein convertase family, but will also aid the study of the functional redundancy of proprotein convertases and the development of therapeutic applications.

]]> Sun Tian, Wu Jianhua Ivyspring International Publisher 6 1 89 95 2010-2-3 Research Paper http://www.biolsci.org/v06p0080.htm Cellular and molecular comparison of redifferentiation of intramuscular- and visceral-adipocyte derived progeny cells http://www.biolsci.org/v06p0080.htm In the present study, mature adipocytes from pig-derived visceral and intramuscular adipose depots were isolated, purified, and allowed to undergo dedifferentiation and redifferentiation in vitro. During the redifferentiation process at days 1, 2, 4, 6, and 8, we observed that both visceral- and intramuscular adipose-derived progeny cells possessed a similar capacity to accumulate lipid. However, at days 10, 12, 14, and 16, the latter progeny cells accumulated lipid much faster--the content almost doubled at day 16 (P < 0.05). Such faster potential of lipid accumulation in the intramuscular adipose-derived progeny cells was then supported by higher expressions of CCAAT/enhancer binding protein-α (CEBP-α) and peroxisome proliferator-activated receptor-γ (PPAR-γ) at all these nine time points, and diacylglycerol O-acyltransferase homolog 1 (DGAT1), fatty acid binding protein 4 (FABP4) and fatty acid synthase (FASN) at some time points (P < 0.05). These preliminary data suggest that adipose depot differences exist with respect to ability of purified cells of the adipose lineage to redifferentiate and form viable lipid-assimilating cells in vitro. Therefore, our present study might provide a foundation to develop tools for biomedical and agricultural applications, as well as to determine the regulation of depot-specific cells of the adipose lineage. Further studies with more animals will validate and expand our results.

]]> Jie Chen, Michael V. Dodson, Zhihua Jiang Ivyspring International Publisher 6 1 80 88 2010-1-21 Short Research Communication http://www.biolsci.org/v06p0068.htm Keratin promoter based gene manipulation in the murine conducting airway http://www.biolsci.org/v06p0068.htm Systems capable of targeting genetic manipulations to keratin-positive airway basal cells are more poorly developed than systems targeting other airway epithelial cell populations and this has likely hindered development of animal models of diseases such as lung squamous cell carcinoma. Although keratin promoter driven-Cre recombinase constructs are potentially useful for targeting these cells, these constructs have substantially higher activity in the skin and oral epithelium than in the airways. We developed a method for delivering RU486, the conditional activator of Cre recombinase progesterone receptor (CrePR) fusion proteins to the lung and then examined the activity of three keratin-driven CrePR constructs in the conducting airways. We also developed a technique for survival bronchioalveolar lavage on non-ventilated animals to examine the effects of the acetone/oil vehicle required to deliver RU486 to the lung. K5CrePR1 and K14CrePR1 constructs differ only in the keratin promoter used to target CrePR1 expression while K5Cre*PR contains a truncated progesterone receptor designed to reduce RU486-independent Cre activity. While all three constructs demonstrate RU486-inducible Cre activity in the conducting airways, both construct activity and tightness of regulation vary considerably. K5Cre*PR is the most tightly regulated Cre driver making it ideal for targeting somatic mutations to the airway epithelia while K5CrePR1 and K14CrePR1 may be better suited to studying diseases of the conducting airways where gene targeting of keratin expressing cells and their derivatives is desired.

]]> Stephen P. Malkoski, Timothy G. Cleaver, Shi-Long Lu, Jessyka G. Lighthall, Xiao-Jing Wang Ivyspring International Publisher 6 1 68 79 2010-1-20 Research Paper http://www.biolsci.org/v06p0051.htm A manually curated network of the PML nuclear body interactome reveals an important role for PML-NBs in SUMOylation dynamics http://www.biolsci.org/v06p0051.htm Promyelocytic Leukaemia Protein nuclear bodies (PML-NBs) are dynamic nuclear protein aggregates. To gain insight in PML-NB function, reductionist and high throughput techniques have been employed to identify PML-NB proteins. Here we present a manually curated network of the PML-NB interactome based on extensive literature review including database information. By compiling 'the PML-ome', we highlighted the presence of interactors in the Small Ubiquitin Like Modifier (SUMO) conjugation pathway. Additionally, we show an enrichment of SUMOylatable proteins in the PML-NBs through an in-house prediction algorithm. Therefore, based on the PML network, we hypothesize that PML-NBs may function as a nuclear SUMOylation hotspot.

]]> Ellen Van Damme, Kris Laukens, Thanh Hai Dang, Xaveer Van Ostade Ivyspring International Publisher 6 1 51 67 2010-1-12 Review http://www.biolsci.org/v06p0009.htm An Overview of Stress Response and Hypometabolic Strategies in Caenorhabditis elegans: Conserved and Contrasting Signals with the Mammalian System http://www.biolsci.org/v06p0009.htm Studies of the molecular mechanisms that are involved in stress responses (environmental or physiological) have long been used to make links to disease states in humans. The nematode model organism, Caenorhabditis elegans, undergoes a state of hypometabolism called the 'dauer' stage. This period of developmental arrest is characterized by a significant reduction in metabolic rate, triggered by ambient temperature increase and restricted oxygen/ nutrients. C. elegans employs a number of signal transduction cascades in order to adapt to these unfavourable conditions and survive for long times with severely reduced energy production. The suppression of cellular metabolism, providing energetic homeostasis, is critical to the survival of nematodes through the dauer period. This transition displays molecular mechanisms that are fundamental to control of hypometabolism across the animal kingdom. In general, mammalian systems are highly inelastic to environmental stresses (such as extreme temperatures and low oxygen), however, there is a great deal of conservation between the signal transduction pathways of nematodes and mammals. Along with conserving many of the protein targets in the stress response, many of the critical regulatory mechanisms are maintained, and often differ only in their level of expression. Hence, the C. elegans model outlines a framework of critical molecular mechanisms that may be employed in the future as therapeutic targets for addressing disease states.

]]> Benjamin Lant, Kenneth B. Storey Ivyspring International Publisher 6 1 9 50 2010-1-7 Review http://www.biolsci.org/v06p0001.htm Smad4-mediated TGF-β signaling in tumorigenesis http://www.biolsci.org/v06p0001.htm Transforming growth factor-β (TGF-β) family members exert their function via specific type I and type II serine/threonine kinase receptors and intracellular Smad transcription factors, including the common mediator Smad4. The dual effects of TGF-β signaling on tumor initiation and progression are cell-specific and yet to be determined under distinct contexts. A number of genetically manipulated mouse models with alterations in the TGF-β pathway genes, particularly the pivotal Smad4, revealed that these genes play crucial functions in maintaining tissue homeostasis and suppressing tumorigenesis. Loss of Smad4 plays a causal role in initiating squamous cell carcinomas of skin and upper digestive tract as well as adenocarcinomas of gastrointestinal tract. However, for some cancers like pancreatic and cholangiocellular carcinomas, Smad4 deficiency does not initiate the tumorigenesis but acts as a promoter to accelerate or synergize the development and progression of cancers that are started by other oncogenic pathways. Intriguingly, emerging evidences from mouse models have highlighted the important roles of non-cell autonomous effects of Smad4-mediated TGF-β signaling in the inhibition of oncogenesis. All these data have greatly deepened our understanding of molecular mechanisms of cell-autonomous and non-cell autonomous effect of Smad4-mediated TGF-β signaling in suppressing carcinogenesis, which may facilitate the development of successful therapies targeting TGF-β signaling for the treatment of human cancers.

]]> Guan Yang, Xiao Yang Ivyspring International Publisher 6 1 1 8 2010-1-1 Review