International Journal of Biological Sciences http://www.biolsci.org International Journal of Biological Sciences RSS feed -- Volume 2 en-us Wed, 1 Oct 2008 04:00:00 GMT Wed, 1 Oct 2008 04:00:00 GMT http://www.biolsci.org/v02p0216.htm Homeostatic restitution of cell membranes. Nuclear membrane lipid biogenesis and transport of protein from cytosol to intranuclear spaces. http://www.biolsci.org/v02p0216.htm Our studies on homeostatic restitution of cellular and subcellular membranes showed that vesicular intracellular transport is engaged in systematic and coordinated replacement of lipids and proteins in the membranes of the secretory, non-dividing epithelial cells (Slomiany et al., J. Physiol. Pharmacol. 2004; 55: 837-860). In this report, we present evidence on the homeostatic restitution of lipids in the biomembranes that constitute nuclear envelopes. We investigated nuclear membranes lipid synthesis by employing purified intact nuclei (IN), the outer nuclear membrane (ONM), the inner nuclear membrane (INM) and the cell cytosol (CC). In contrast to Endoplasmic Reticulum (ER) which in the presence of CC generates new biomembrane that forms ER vesicles transporting ER products to Golgi, the IN, ONM and INM are not producing transport vesicles. Instead, the newly synthesized lipids remain in the nuclear membranes. The membranes (INM, ONM) of IN incubated with CC become enriched with newly synthesized phosphatidylcholine (PC), phosphatidylinositol (PI), phosphatidylinositol phosphates (PIPs) and phosphatidic acid (PA). The incubation of separated ONM and INM with CC also enriched the membranes with IN specific lipids identified above. Moreover, the incubation of IN or its membranes with CC afforded retention of numerous CC proteins on the nuclear membrane. Here, we concentrated on 30kDa CC protein that displayed affinity to nuclear membrane PIP2. The 30kDa CC protein bound to PIP2 of IN, INM, and ONM. With IN, initially the PIP2-30kDa CC protein complex was detected on ONM, after 30-120 min of incubation, was found on INM and in nuclear contents. At the same time when the 30 kDa protein was released from INM and found in nuclear contents, the PIP2 of INM and ONM became undetectable, while the lipid extract from the membrane displaced from IN contained labeled PI only. Since ONM is an uninterrupted continuum of ER and INM, we speculate that the synthesis of the lipids in the ER, in the region adjacent to nucleus, is defining nuclear outer and inner biomembrane composition, is responsible for transport of the cytosolic protein into the nucleus and, replenishment of ER membrane used for vesicular transport.

]]> Amalia Slomiany, Maria Grabska, Bronislaw L. Slomiany Ivyspring International Publisher 2 4 216 226 2006-8-30 Research Paper http://www.biolsci.org/v02p0208.htm Chimeric Antibody-Binding Vitreoscilla Hemoglobin (VHb) Mediates Redox-Catalysis Reaction: New Insight into the Functional Role of VHb http://www.biolsci.org/v02p0208.htm Experimentation was initiated to explore insight into the redox-catalysis reaction derived from the heme prosthetic group of chimeric Vitreoscilla hemoglobin (VHb). Two chimeric genes encoding chimeric VHbs harboring one and two consecutive sequences of Fc-binding motif (Z-domain) were successfully constructed and expressed in E. coli strain TG1. The chimeric ZVHb and ZZVHb were purified to a high purity of more than 95% using IgG-Sepharose affinity chromatography. From surface plasmon resonance, binding affinity constants of the chimeric ZVHb and ZZVHb to human IgG were 9.7 x 107 and 49.1 x 107 per molar, respectively. More importantly, the chimeric VHbs exhibited a peroxidase-like activity determined by activity staining on native PAGE and dot blotting. Effects of pH, salt, buffer system, level of peroxidase substrate and chromogen substrate were determined in order to maximize the catalytic reaction. From our findings, the chimeric VHbs displayed their maximum peroxidase-like activity at the neutral pH (~7.0) in the presence of high concentration (20-40 mM) of hydrogen peroxide. Under such conditions, the detection limit derived from the calibration curve was at 250 ng for the chimeric VHbs, which was approximately 5-fold higher than that of the horseradish peroxidase. These findings reveal the novel functional role of Vitreoscilla hemoglobin indicating a high trend of feasibility for further biotechnological and medical applications.

]]> Yaneenart Suwanwong, Malin Kvist, Chartchalerm Isarankura-Na-Ayudhya, Natta Tansila, Leif Bulow, Virapong Prachayasittikul Ivyspring International Publisher 2 4 208 215 2006-8-22 Research Paper http://www.biolsci.org/v02p0197.htm Carotenoid Biosynthesis in Cyanobacteria: Structural and Evolutionary Scenarios Based on Comparative Genomics http://www.biolsci.org/v02p0197.htm Carotenoids are widely distributed pigments in nature and their biosynthetic pathway has been extensively studied in various organisms. The recent access to the overwhelming amount genomic data of cyanobacteria has given birth to a novel approach called comparative genomics. The putative enzymes involved in the carotenoid biosynthesis among the cyanobacteria were determined by similarity-based tools. The reconstruction of biosynthetic pathway was based on the related enzymes. It is interesting to find that nearly all the cyanobacteria share quite similar pathway to synthesize β-carotene except for Gloeobacter violaceus PCC 7421. The enzymes, crtE-B-P-Qb-L, involved in the upstream pathway are more conserved than the subsequent ones (crtW-R). In addition, many carotenoid synthesis enzymes exhibit diversity in structure and function. Such examples in the families of ζ –carotene desaturase, lycopene cylases and carotene ketolases were described in this article. When we mapped these crt genes to the cyanobacterial genomes, the crt genes showed great structural variation among species. All of them are dispersed on the whole chromosome in contrast to the linear adjacent distribution of the crt gene cluster in other eubacteria. Moreover, in unicellular cyanobacteria, each step of the carotenogenic pathway is usually catalyzed by one gene product, whereas multiple ketolase genes are found in filamentous cyanobacteria. Such increased numbers of crt genes and their correlation to the ecological adaptation were carefully discussed.

]]> Chengwei Liang, Fangqing Zhao, Wei Wei, Zhangxiao Wen, Song Qin Ivyspring International Publisher 2 4 197 207 2006-8-18 Research Paper http://www.biolsci.org/v02p0194.htm Does WAVE1 contain a GoLoco/GPR motif? http://www.biolsci.org/v02p0194.htm Francis S. Willard Ivyspring International Publisher 2 4 194 196 2006-7-25 Letter To The Editor http://www.biolsci.org/v02p0188.htm P53 codon 11, 72, and 248 gene polymorphisms in endometriosis http://www.biolsci.org/v02p0188.htm Objective: Mutated p53 gene is related to the instability of cell growth and cell cycle progression. We aimed to evaluate the association between endometriosis and p53 codon 11, 72 and 248 gene polymorphisms.

Patients and methods: Women were divided into two groups: (1) moderate/severe endometriosis (n=148), and (2) non-endometriosis groups (n=150). P53 gene polymorphisms include codon11 Glu/Gln or Lys (GAG->CAG or AAG), codon 72 Arg/Pro (CGC->CCC), and codon 248 Arg/Thr (CGG->TCG). These gene polymorphisms were amplified by polymerase chain reaction and detected by electrophoresis after restriction enzyme (Taq I, BstU I, Hap II) digestions. Associations between the endometriosis and p53 polymorphisms were evaluated.

Results: The distributions of p53 codon 72 polymorphisms in both groups were significantly different. The proportions of Arg homozygotes/heterozygotes/Pro homozygotes in both groups were 9.5/66.2/24.3% and 30.7/50/19.3%. The proportions of Arg/Pro alleles were 42.6/57.4% and 56/44%. The distributions of p53 codon 11 and 248 polymorphisms in both groups were non-significantly different. All individuals appeared the wild genotypes (Glu11 and Arg248 homozygotes).

Conclusion: Association between endometriosis and p53 codon 72 polymorphism exists. P53 codon 72*Pro-related genotype and allele are related with higher susceptibility of endometriosis. P53 codon 11 and 248 polymorphisms are not related with endometriosis susceptibility.

]]> Yao-Yuan Hsieh, Chich-Sheng Lin Ivyspring International Publisher 2 4 188 193 2006-7-12 Research Paper http://www.biolsci.org/v02p0186.htm The new portrait of mammary gland stem cells http://www.biolsci.org/v02p0186.htm Rui-Hong Wang Ivyspring International Publisher 2 4 186 187 2006-6-10 Letter To The Editor http://www.biolsci.org/v02p0179.htm The Inhibition and Treatment of Breast Cancer with Poly (ADP-ribose) Polymerase (PARP-1) Inhibitors http://www.biolsci.org/v02p0179.htm BRCA1 and BRCA2 mutations are responsible for most familial breast carcinomas. Recent reports carried out in non-cancerous mouse BRCA1- or BRCA2-deficient embryonic stem (ES) cells, and hamster BRCA2-deficient cells have demonstrated that the targeted inhibition of poly(ADP-ribose) polymerase (PARP-1) kills BRCA mutant cells with high specificity. Although these studies bring hope for BRCA mutation carriers, the effectiveness of PARP-1 inhibitors for breast cancer remains elusive. Here we present the first in vivo demonstration of PARP-1 activity in BRCA1-deficient mammary tumors and describe the effects of PARP-1 inhibitors (AG14361, NU1025, and 3-aminobenzamide) on BRCA1-deficient ES cells, mouse and human breast cancer cells. AG14361 was highly selective for BRCA1-/- ES cells; however, NU1025 and 3-aminobenzamide were relatively non-selective. In allografts of naïve ES BRCA1-/- cells there was either partial or complete remission of tumors. However, in allografts of mouse, BRCA1-/- mammary tumors, there was no tumor regression or remission although a partial inhibition of tumor growth was observed in both the BRCA1-/- and BRCA1+/+ allografts. In human tumor cells, PARP-1 inhibitors showed no difference in vitro in limiting the growth of mammary tumors irrespective of their BRCA1 status. These results suggest that PARP-1 inhibitors may non-specifically inhibit the growth of mammary tumors.

]]> Joseph A. De Soto, Xianyan Wang, Yohei Tominaga, Rui-Hong Wang, Liu Cao, Wenhui Qiao, Cuiling Li, Xiaoling Xu, Amanda P. Skoumbourdis, Sheila A. Prindiville, Craig J. Thomas, Chu-Xia Deng Ivyspring International Publisher 2 4 179 185 2006-6-10 Research Paper http://www.biolsci.org/v02p0171.htm A novel nuclear-encoded mitochondrial poly(A) polymerase PAPD1 is a potential candidate gene for the extreme obesity related phenotypes in mammals http://www.biolsci.org/v02p0171.htm People with obesity, especially extreme obesity, are at risk for many health problems. However, the responsible genes remain unknown in >95% of severe obesity cases. Our previous genome-wide scan of Wagyu x Limousin F2 cattle crosses with extreme phenotypes revealed a molecular marker significantly associated with intramuscular fat deposition. Characterization of this marker showed that it is orthologous to the human gene KIAA1462 located on HSA10p11.23, where a major quantitative trait locus for morbid obesity has been reported. The newly identified mitochondrial poly(A) polymerase associated domain containing 1 (PAPD1) gene, which is located near this marker, is particularly interesting because the polymerase is required for the polyadenylation and stabilization of mammalian mitochondrial mRNAs. In the present study, both cDNA and genomic DNA sequences were annotated for the bovine PAPD1 gene and ten genetic markers were detected in the promoter and exon 1 region. Among seven markers assayed on ~ 250 Wagyu x Limousin F2 animals, two single nucleotide polymorphisms (SNPs) in the promoter region were significantly associated with intramuscular fat (P<0.05). However, there was a significant interaction (P<0.05) between a third SNP, which causes an amino acid change in coding exon 1, and each of these two promoter SNPs on intramuscular fat deposition. In particular, the differences between double heterozygous animals at two polymorphic sites and the slim genotype animals exceeded 2.3 standard deviations for the trait in both cases. Our study provides evidence for a new mechanism – the involvement of compound heterosis in extreme obesity, which warrants further examination.

]]> Qianjun Xiao, Xiao-Lin Wu, Jennifer J. Michal, Jerry J. Reeves, Jan R. Busboom, Gary H. Thorgaard, Zhihua Jiang Ivyspring International Publisher 2 4 171 178 2006-5-18 Research Paper http://www.biolsci.org/v02p0161.htm Murine Wee1 Plays a Critical Role in Cell Cycle Regulation and Pre-Implantation Stages of Embryonic Development http://www.biolsci.org/v02p0161.htm Wee1 kinase regulates the G2/M cell cycle checkpoint by phosphorylating and inactivating the mitotic cyclin-dependent kinase 1 (Cdk1). Loss of Wee1 in many systems, including yeast and drosophila, leads to premature mitotic entry. However, the developmental role of Wee1 in mammals remains unclear. In this study, we established Wee1 knockout mice by gene targeting. We found that Wee-/- embryos were defective in the G2/M cell cycle checkpoint induced by γ-irradiation and died of apoptosis before embryonic (E) day 3.5. To study the function of Wee1 further, we have developed MEF cells in which Wee1 is disrupted by a tamoxifen inducible Cre-LoxP approach. We found that acute deletion of Wee1 resulted in profound growth defects and cell death. Wee1 deficient cells displayed chromosome aneuploidy and DNA damage as revealed by γ-H2AX foci formation and Chk2 activation. Further studies revealed a conserved mechanism of Wee1 in regulating mitotic entry and the G2/M checkpoint compared with other lower organisms. These data provide in vivo evidence that mammalian Wee1 plays a critical role in maintaining genome integrity and is essential for embryonic survival at the pre-implantation stage of mouse development.

]]> Yohei Tominaga, Cuiling Li, Rui-Hong Wang, Chu-Xia Deng Ivyspring International Publisher 2 4 161 170 2006-5-18 Short Research Communication http://www.biolsci.org/v02p0149.htm A gene catalogue of the amphioxus nervous system http://www.biolsci.org/v02p0149.htm The elaboration of extremely complex nervous systems is a major success of evolution. However, at the dawn of the post-genomic era, few data have helped yet to unravel how a nervous system develops and evolves to complexity. On the evolutionary road to vertebrates, amphioxus occupies a key position to tackle this exciting issue. Its “simple” nervous system basically consists of a dorsal nerve cord and a diffuse net of peripheral neurons, which contrasts greatly with the complexity of vertebrate nervous systems. Notwithstanding, increasing data on gene expression has faced up this simplicity by revealing a mounting level of cryptic complexity, with unexpected levels of neuronal diversity, organisation and regionalisation of the central and peripheral nervous systems. Furthermore, recent gene expression data also point to the high neurogenic potential of the epidermis of amphioxus, suggestive of a skin-brain track for the evolution of the vertebrate nervous system. Here I attempt to catalogue and synthesise current gene expression data in the amphioxus nervous system. From this global point of view, I suggest scenarios for the evolutionary origin of complex features in the vertebrate nervous system, with special emphasis on the evolutionary origin of placodes and neural crest, and postulate a pre-patterned migratory pathway of cells, which, in the epidermis, may represent an intermediate state towards the deployment of one of the most striking innovative features of vertebrates: the neural crest and its derivatives.

]]> Èlia Benito-Gutiérrez Ivyspring International Publisher 2 3 149 160 2006-5-22 Review http://www.biolsci.org/v02p0142.htm Exploring developmental, functional, and evolutionary aspects of amphioxus sensory cells http://www.biolsci.org/v02p0142.htm Amphioxus has neither elaborated brains nor definitive sensory organs, so that the two may have evolved in a mutually affecting manner and given rise to the forms seen in extant vertebrates. Clarifying the developmental and functional aspects of the amphioxus sensory system is thus pivotal for inferring the early evolution of vertebrates. Morphological studies have identified and classified amphioxus sensory cells; however, it is completely unknown whether the morphological classification makes sense in functional and evolutionary terms. Molecular markers, such as gene expression, are therefore indispensable for investigating the developmental and functional aspects of amphioxus sensory cells. This article reviews recent molecular studies on amphioxus sensory cells. Increasing evidence shows that the non-neural ectoderm of amphioxus can be subdivided into molecularly distinct subdomains by the combinatorial code of developmental cues involving the RA-dependent Hox code, suggesting that amphioxus epithelial sensory cells developed along positional information. This study focuses particularly on research involving the molecular phylogeny and expression of the seven-transmembrane, G protein-coupled receptor (GPCR) genes and discusses the usefulness of this information for characterizing the sensory cells of amphioxus.

]]> Gouki Satoh Ivyspring International Publisher 2 3 142 148 2006-5-17 Review http://www.biolsci.org/v02p0133.htm Genome duplications of early vertebrates as a possible chronicle of the evolutionary history of the neural crest http://www.biolsci.org/v02p0133.htm It is now accepted that ancestral vertebrates underwent two rounds of genome duplication. Here we test the possible utility of these genome duplication events as a reference time for the evolutionary history of vertebrates, by tracing the molecular evolutionary history of the genes involved in vertebrate neural crest development. For most transcription factors that are involved in neural crest specification, more than two paralogs are involved in that process. These were likely involved in the specification of the neural crest before the genome duplications occurred in ancestral vertebrates, although FoxD3 may have acquired that role after the genome duplications. By contrast, the epithelial-mesenchymal transition of neural crest cells is controlled by genes that evolved after the genome duplications, such as cadherin6, cadherin7, cadherin11, and rhoB. This suggests that primitive neural crest cells control their delamination by using a small or distinct set of cell adhesion molecules. Alternatively, these observations suggest that delamination of the neural crest evolved after the genome duplications. In that case, the neural crest might have evolved in sequential steps; the specification of the neural crest occurred before the genome duplications, and the neural crest acquired a new cell migration property after the genome duplications.

]]> Hiroshi Wada, Kaz Makabe Ivyspring International Publisher 2 3 133 141 2006-5-23 Review http://www.biolsci.org/v02p0125.htm Phylogenetic analysis of Amphioxus genes of the proprotein convertase family, including aPC6C, a marker of epithelial fusions during embryology http://www.biolsci.org/v02p0125.htm The proprotein convertases (PCs) comprise a family of subtilisin-like endoproteases that activate precursor proteins (including, prohormones, growth factors, and adhesion molecules) during their transit through secretory pathways or at the cell surface. To explore the evolution of the PC gene family in chordates, we made a phylogenetic analysis of PC genes found in databases, with special attention to three PC genes of the cephalochordate amphioxus, the closest living invertebrate relative to the vertebrates. Since some vertebrate PC genes are essential for early development, we investigated the expression pattern of the C isoform of the amphioxus PC6 gene (aPC6C). In amphioxus embryos and larvae, aPC6C is expressed at places where epithelia fuse. Several kinds of fusions occur: ectoderm-to-ectoderm during neurulation; mesoderm-to-ectoderm during formation of the preoral ciliated pit; and endoderm-to-ectoderm during formation of the mouth, pharyngeal slits, anus, and external opening of the club-shaped gland. Presumably, at all these sites, aPC6C is activating proteins favoring association between previously disjunct cell populations.

]]> Stéphanie Bertrand, Alain Camasses, Mathilde Paris, Nicholas D. Holland, Hector Escriva Ivyspring International Publisher 2 3 125 132 2006-5-6 Research Paper http://www.biolsci.org/v02p0117.htm S-nitrosogluthathione reductase activity of amphioxus ADH3: insights into the nitric oxide metabolism http://www.biolsci.org/v02p0117.htm Nitric oxide (NO) is a signalling molecule involved in many physiological functions. An important via of NO action is through the S-nitrosylation of proteins, a post-translational modification that regulates the activity of enzymes, protein-protein interactions and signal transduction pathways. Alcohol dehydrogenase class III (ADH3) recognises S-nitrosoglutathione (GSNO), the main reservoir of non-protein S-nitrosothiol, and functions as an effective GSNO reductase (GSNOR) and as a safeguard against nitrosative stress. To investigate the evolutionary conservation of this metabolic role, we have produced recombinant Branchiostoma floridae ADH3. Pure preparations of ADH3 showed 2-fold higher activity as GSNOR than as formaldehyde dehydrogenase, the previously assumed main role for ADH3. To correlate ADH3 expression in the gut with areas of NO production, we analysed the tissue distribution of the nitric oxide synthase (NOS) enzyme in amphioxus larvae. Immunostaining of the NOS enzyme revealed expression in the gut and in the dorsal region of the club-shaped gland. Co-localization in the gut supports the ADH3 and NOS joint contribution to the NO/SNO homeostasis.

]]> Laura Godoy, Roser Gonzàlez-Duarte, Ricard Albalat Ivyspring International Publisher 2 3 117 124 2006-5-5 Research Paper http://www.biolsci.org/v02p0110.htm An amphioxus LIM-homeobox gene, AmphiLim1/5, expressed early in the invaginating organizer region and later in differentiating cells of the kidney and central nervous system http://www.biolsci.org/v02p0110.htm A LIM-homeobox gene, AmphiLim1/5, from the Florida amphioxus (Branchiostoma floridae) encodes a protein that phylogenetic analysis positions at the base of a clade comprising vertebrate Lim1 and Lim5. Amphioxus AmphiLim1/5 is expressed in domains that are a composite of those of vertebrate Lim1 and Lim5, which evidently underwent subfunctionalization after duplication of an ancestral protochordate Lim1/5. During amphioxus development, transcription is first detected in the ectoderm of the blastula. Then, in the gastrula, a second expression domain appears in the mesendoderm just within the dorsal lip of the blastopore, a region known to have organizer properties in amphioxus. This mesendodermal expression corresponds to Lim1 expression in the Spemann organizer of vertebrates. At least one of the functions of vertebrate Lim1 in the organizer is to control the transcription of genes involved in cell and tissue movements during gastrulation, and a comparable early function seems likely for AmphiLim1/5 during gastrular invagination of amphioxus. Later embryos and larvae of amphioxus express AmphiLim1/5 in clusters of cells, probably motoneurons, in the anterior part of the central nervous system, in the hindgut, in Hatschek's right diverticulum (a rudiment of the rostral coelom), and in the wall of the first somite on the left side (a precursor of Hatschek's nephridium). In the early larva, expression continues in neural cells, in Hatschek's nephridium, in the wall of the rostral coelom, in the epidermis of the upper lip, and in mesoderm cells near the opening of the second gill slit. The developmental expression in Hatschek's nephridium is especially interesting because it helps support the homology between this amphioxus organ and the vertebrate pronephros.

]]> James A. Langeland, Linda Z. Holland, Roger A. Chastain, Nicholas D. Holland Ivyspring International Publisher 2 3 110 116 2006-5-5 Research Paper http://www.biolsci.org/v02p0104.htm Prospective protochordate homologs of vertebrate midbrain and MHB, with some thoughts on MHB origins http://www.biolsci.org/v02p0104.htm The MHB (midbrain-hindbrain boundary) is a key organizing center in the vertebrate brain characterized by highly conserved patterns of gene expression. The evidence for an MHB homolog in protochordates is equivocal, the "neck" region immediately caudal to the sensory vesicle in ascidian larvae being the best accepted candidate. It is argued here that similarities in expression patterns between the MHB and the ascidian neck region are more likely due to the latter being the principal source of neurons in the adult brain, and hence where all the genes involved in patterning the latter will necessarily be expressed. The contrast with amphioxus is exemplified by pax2/5/8, expressed in the neck region in ascidian larvae, but more caudally, along much of the nerve cord in amphioxus. The zone of expression in each case corresponds with that part of the nerve cord ultimately responsible for innervating the adult body, which suggests the spatially restricted MHB-like expression pattern in ascidians is secondarily reduced from a condition more like that in amphioxus. Patterns resembling those of the vertebrate MHB are nevertheless found elsewhere among metazoans. This suggests that, irrespective of its modern function, the MHB marks the site of an organizing center of considerable antiquity. Any explanation for how such a center became incorporated into the chordate brain must take account of the dorsoventral inversion chordates have experienced relative to other metazoans. Especially relevant here is a concept developed by Claus Nielsen, in which the brain is derived from a neural center located behind the ancestral mouth. While this is somewhat counterintuitive, it accords well with emerging molecular data.

]]> Thurston C. Lacalli Ivyspring International Publisher 2 3 104 109 2006-5-5 Review/essay http://www.biolsci.org/v02p0095.htm Hox genes are not always Colinear http://www.biolsci.org/v02p0095.htm The deuterostomes are the clade of animals for which we have the most detailed understanding of Hox cluster organisation. With the Hox cluster of amphioxus (Branchiostoma floridae) we have the best prototypical, least derived Hox cluster for the group, whilst the urochordates present us with some of the most highly derived and disintegrated clusters. Combined with the detailed mechanistic understanding of vertebrate Hox regulation, the deuterostomes provide much of the most useful data for understanding Hox cluster evolution. Considering both the prototypical and derived deuterostome Hox clusters leads us to hypothesize that Temporal Colinearity is the main constraining force on Hox cluster organisation, but until we have a much deeper understanding of the mechanistic basis for this phenomenon, and know how widespread across the Bilateria the mechanism(s) is/are, then we cannot know how the Hox cluster of the last common bilaterian operated and what have been the major evolutionary forces operating upon the Hox gene cluster.

]]> Ana Sara Monteiro, David E.K. Ferrier Ivyspring International Publisher 2 3 95 103 2006-5-5 Review http://www.biolsci.org/v02p0093.htm Amphioxus: a peaceful anchovy fillet to illuminate Chordate Evolution (II) http://www.biolsci.org/v02p0093.htm The genome of the amphioxus is on the horizon. With Linda Holland and Jeremy Gibson-Brown at the forefront, with all the amphioxus community behind, and with the Joint Genome Institute, the amphioxus genome will see the light this year, 2006. Hope that it will reflect the “prototypical” preduplicative genome of vertebrates. It may answer definitively what the human genome did not: Are we vertebrates octaploid? Will it shed light on the novelties that helped non-chordates to be chordates? And more, will amphioxus, with a simpler genome, be developed to a senior “experimental model system”, allowing the testing of molecular functions in a non-duplicated genome background and allowing genetic modification to “recapitulate” evolution? Thanks to an outstanding collaboration between labs, the laboratory culture of amphioxus is underway after years of hard work in the field. 2007 looks promising for amphioxus research.

]]> Jordi Garcia-Fernàndez Ivyspring International Publisher 2 3 93 94 2006-5-22 Editorial http://www.biolsci.org/v02p0087.htm Free amino acids in the nervous system of the amphioxus Branchiostoma lanceolatum. A comparative study http://www.biolsci.org/v02p0087.htm The cephalochordate amphioxus is the closest invertebrate relative to vertebrates. In this study, using HPLC technique, free L-amino acids (L-AAs) and D-aspartic acid (D-Asp) have been detected in the nervous system of the amphioxus Branchiostoma lanceolatum. Among other amino acids glutamate, aspartate, glycine, alanine and serine are the amino acids found at the greatest concentrations. As it occurs in the nervous system of other animal phyla, glutamate (L-Glu) and aspartate (L-Asp) are present at very high concentrations in the amphioxus nervous system compared to other amino acids, whereas the concentration of taurine and γ-aminobutyric acid (GABA) is very low. Interestingly, as it is the case in vertebrates, D-aspartic acid is present as an endogenous compound in amphioxus nervous tissues. The physiological function of excitatory amino acids, and D-aspartate in particular, are discussed in terms of evolution of the nervous system under an Evo-fun (Evolution of function) perspective.

]]> Juan Pascual-Anaya, Salvatore D'Aniello Ivyspring International Publisher 2 2 87 92 2006-4-10 Research Paper http://www.biolsci.org/v02p0079.htm Expression of AmphiNaC, a new member of the amiloride-sensitive sodium channel related to degenerins and epithelial sodium channels in amphioxus http://www.biolsci.org/v02p0079.htm Degenerins and amiloride-sensitive Na+ channels form a new family of cationic ion channels (DEG/NaC). DEG/NaC family emerged as common denominator within a metazoan mechanosensory apparatus. In this study, we characterized a new member of such family in amphioxus, Branchiostoma floridae. The AmphiNaC cDNA sequence encodes a protein showing amino acid residues characteristic of DEG/NaC family, such as two hydrophobic domains surrounding a large extracellular loop that includes cystein-rich domains; nevertheless its predicted sequence is quite divergent from other family members. AmphiNaC is expressed at early larval stage in some putative sensory epidermal cells in the middle of the body and in neurons of the posterior cerebral vesicle, as well as in some ventrolateral and mediolateral neurons of the neural tube. In late larvae, AmphiNaC expression is maintained in some neurons of the neural tube, and it is expressed in putative sensory epidermal cells of rostrum and mouth. The analysis of AmphiNaC gene expression pattern suggests that it might be involved in neurotransmission and sensory modulation.

]]> Simona Candiani, Diana Oliveri, Manuela Parodi, Mario Pestarino Ivyspring International Publisher 2 2 79 86 2006-4-10 Research Paper http://www.biolsci.org/v02p0073.htm Immunohistochemical study of cytoskeletal and extracellular matrix components in the notochord and notochordal sheath of amphioxus http://www.biolsci.org/v02p0073.htm A major cytoskeletal and extracellular matrix proteins of the amphioxus notochordal cells and sheath were detected by immunohistochemical techniques. The three-layered amphioxus notochordal sheath strongly expressed fish collagen type I in its outer and middle layers, while in the innermost layer expression did not occur. The amphioxus notochordal sheath was reactive to applied anti-human antibodies for intermediate filament proteins such as cytokeratins, desmin and vimentin, as well as to microtubule components (ß-tubulin), particularly in the area close to the epipharyngeal groove. Alpha-smooth muscle actin was expressed in some notochordal cells and in the area of the notochordal attachment to the sheath. Thus muscular nature of notochordal cells was shown by immunohistochemistry in tissue section. Our results confirm that genes encoding intermediate filament proteins, microtubules and microfilaments are highly conserved during evolution. Collagen type I was proven to be the key extracellular matrix protein that forms the amphioxus notochordal sheath.

]]> Ivana Bočina, Mirna Saraga-Babić Ivyspring International Publisher 2 2 73 78 2006-4-10 Research Paper http://www.biolsci.org/v02p0066.htm Evolutionary genomics of the recently duplicated amphioxus Hairy genes http://www.biolsci.org/v02p0066.htm Amphioxus Hairy genes have gone through a number of lineage-specific duplications, resulting in eight members, some of which are differentially expressed in the embryo. In order to gain insights into the evolution and function of this gene family we have compared their genomic structure and searched for conserved non-coding sequence elements. We have found that introns have been lost independently from these genes at least twice and after the duplication events. By carrying out phylogenetic footprinting between paralogues expressed in the embryo, we have found a differential distribution of conserved elements that could explain the limited overlap in expression patterns of Hairy genes in the amphioxus embryo. Furthermore, clustering of RBP-Jk binding sites in these conserved elements suggests that amphioxus Hairy genes are downstream targets of the Notch signaling pathway, as occurs in vertebrates. All of this evidence suggests that amphioxus Hairy genes have gone through a process of subfunctionalization shortly after their duplication, representing an extreme and rapid case of the duplication-degeneration-complementation model.

]]> Senda Jiménez-Delgado, Miguel Crespo, Jon Permanyer, Jordi Garcia-Fernàndez, Miguel Manzanares Ivyspring International Publisher 2 2 66 72 2006-4-10 Research Paper http://www.biolsci.org/v02p0061.htm A SINE in the genome of the cephalochordate amphioxus is an Alu element http://www.biolsci.org/v02p0061.htm Transposable elements of about 300 bp, termed “short interspersed nucleotide elements or SINEs are common in eukaryotes. However, Alu elements, SINEs containing restriction sites for the AluI enzyme, have been known only from primates. Here I report the first SINE found in the genome of the cephalochordate, amphioxus. It is an Alu element of 375 bp that does not share substantial identity with any genomic sequences in vertebrates. It was identified because it was located in the FoxD regulatory region in a cosmid derived from one individual, but absent from the two FoxD alleles of BACs from a second individual. However, searches of sequences of BACs and genomic traces from this second individual gave an estimate of 50-100 copies in the amphioxus genome. The finding of an Alu element in amphioxus raises the question of whether Alu elements in amphioxus and primates arose by convergent evolution or by inheritance from a common ancestor. Genome-wide analyses of transposable elements in amphioxus and other chordates such as tunicates, agnathans and cartilaginous fishes could well provide the answer.

]]> Linda Z. Holland Ivyspring International Publisher 2 2 61 65 2006-4-10 Research Paper http://www.biolsci.org/v02p0054.htm Identification and Characterisation of five novel Miniature Inverted-repeat Transposable Elements (MITEs) in amphioxus (Branchiostoma floridae) http://www.biolsci.org/v02p0054.htm As the sister group to vertebrates, amphioxus is consistently used as a model of genome evolution for understanding the invertebrate/vertebrate transition. The amphioxus genome has not undergone massive duplications like those in the vertebrates or disruptive rearrangements like in the genome of Ciona, a urochordate, making it an ideal evolutionary model. Transposable elements have been linked to many genomic evolutionary changes including increased genome size, modified gene expression, massive gene rearrangements, and possibly intron evolution. Despite their importance in genome evolution, few previous examples of transposable elements have been identified in amphioxus. We report five novel Miniature Inverted-repeat Transposable Elements (MITEs) identified by an analysis of amphioxus DNA sequence, which we have named LanceleTn-1, LanceleTn-2, LanceleTn-3a, LanceleTn-3b and LanceleTn-4. Several of the LanceleTn elements were identified in the amphioxus ParaHox cluster, and we suggest these have had important implications for the evolution of this highly conserved gene cluster. The estimated high copy numbers of these elements implies that MITEs are probably the most abundant type of mobile element in amphioxus, and are thus likely to have been of fundamental importance in shaping the evolution of the amphioxus genome.

]]> PW. Osborne, GN. Luke, PWH. Holland, DEK. Ferrier Ivyspring International Publisher 2 2 54 60 2006-4-10 Research Paper http://www.biolsci.org/v02p0048.htm Getting closer to a pre-vertebrate genome: the non-LTR retrotransposons of Branchiostoma floridae http://www.biolsci.org/v02p0048.htm Non-LTR retrotransposons are common in vertebrate genomes and although present in invertebrates they appear at a much lower frequency. The cephalochordate amphioxus is the closest living relative to vertebrates and has been considered a good model for comparative analyses of genome expansions during vertebrate evolution. With the aim to assess the involvement of transposable elements in these events, we have analysed the non-LTR retrotransposons of Branchiostoma floridae. In silico searches have allowed to reconstruct non-LTR elements of six different clades (CR1, I, L1, L2, NeSL and RTE) and assess their structural features. According to the estimated copy number of these elements they account for less than 1% of the haploid genome, which reminds of the low abundance also encountered in the urochordate Ciona intestinalis. Amphioxus (B. floridae) and Ciona share a pre-vertebrate-like organization for the non-LTR retrotransposons (<150 copies, < 1% of the genome) versus the complexity associated to higher vertebrates (Homo sapiens >1.3·106 copies, > 20% of the genome).

]]> Jon Permanyer, Ricard Albalat, Roser Gonzàlez-Duarte Ivyspring International Publisher 2 2 48 53 2006-4-10 Research Paper http://www.biolsci.org/v02p0038.htm Retinoic acid signaling and the evolution of chordates http://www.biolsci.org/v02p0038.htm In chordates, which comprise urochordates, cephalochordates and vertebrates, the vitamin A-derived morphogen retinoic acid (RA) has a pivotal role during development. Altering levels of endogenous RA signaling during early embryology leads to severe malformations, mainly due to incorrect positional codes specifying the embryonic anteroposterior body axis. In this review, we present our current understanding of the RA signaling pathway and its roles during chordate development. In particular, we focus on the conserved roles of RA and its downstream mediators, the Hox genes, in conveying positional patterning information to different embryonic tissues, such as the endoderm and the central nervous system. We find that some of the control mechanisms governing RA-mediated patterning are well conserved between vertebrates and invertebrate chordates, such as the cephalochordate amphioxus. In contrast, outside the chordates, evidence for roles of RA signaling is scarce and the evolutionary origin of the RA pathway itself thus remains elusive. In sum, to fully understand the evolutionary history of the RA pathway, future research should focus on identification and study of components of the RA signaling cascade in non-chordate deuterostomes (such as hemichordates and echinoderms) and other invertebrates, such as insects, mollusks and cnidarians.

]]> Ferdinand Marlétaz, Linda Z. Holland, Vincent Laudet, Michael Schubert Ivyspring International Publisher 2 2 38 47 2006-4-10 Review http://www.biolsci.org/v02p0032.htm Metaphylogeny of 82 gene families sheds a new light on chordate evolution http://www.biolsci.org/v02p0032.htm Achieving a better comprehension of the evolution of species has always been an important matter for evolutionary biologists. The deuterostome phylogeny has been described for many years, and three phyla are distinguishable: Echinodermata (including sea stars, sea urchins, etc…), Hemichordata (including acorn worms and pterobranchs), and Chordata (including urochordates, cephalochordates and extant vertebrates). Inside the Chordata phylum, the position of vertebrate species is quite unanimously accepted. Nonetheless, the position of urochordates in regard with vertebrates is still the subject of debate, and has even been suggested by some authors to be a separate phylum from cephalochordates and vertebrates. It was also the case for agnathans species –myxines and hagfish– for which phylogenetic evidence was recently given for a controversial monophyly. This raises the following question: which one of the cephalochordata or urochordata is the sister group of vertebrates and what are their relationships? In the present work, we analyzed 82 protein families presenting homologs between urochordata and other deuterostomes and focused on two points: 1) testing accurately the position of urochordata and cephalochordata phyla in regard with vertebrates as well as chordates monophyly, 2) performing an estimation of the rate of gene loss in the Ciona intestinalis genome. We showed that the urochordate phyla is the vertebrate sister group and that gene loss played a major role in structuring the urochordate genome.

]]> Alexandre Vienne, Pierre Pontarotti Ivyspring International Publisher 2 2 32 37 2006-4-10 Research Paper http://www.biolsci.org/v02p0030.htm Amphioxus: a peaceful anchovy fillet to illuminate Chordate Evolution (I) http://www.biolsci.org/v02p0030.htm The cephalochordate amphioxus occupies a central place in evolutionary thoughts to the origin of Vertebrates. With a prototypical vertebrate-like body plan and a preduplicative genome, the friendly lancelet seems to be in morphological and genetic motionless since its separation from the major branch of evolution that eventually ended up in our corner in the Animal Kingdom. This makes it an ideal model system with which, with the current development of genomic and experimental tools, an Evo-Devo approach to the understanding of the origin of vertebrates looks proper, reliable, and excitingly promising.

]]> Jordi Garcia-Fernàndez Ivyspring International Publisher 2 2 30 31 2006-4-10 Editorial http://www.biolsci.org/v02p0023.htm Seminal malondialdehyde concentration but not glutathione peroxidase activity is negatively correlated with seminal concentration and motility http://www.biolsci.org/v02p0023.htm Objectives: Reactive oxygen species (ROS) induced lipid peroxidation is associated with sperm function. Malondialdehyde (MDA) concentration and glutathione peroxidase (GPx) activity represent the lipid peroxidation and spermicidal antioxidant, respectively. We aimed to evaluate the relationship of MDA and GPx levels with sperm parameters.

Patients and methods: Specimens were divided into two groups: group 1. normospermia (n=20); group 2. oligoasthenospermia (n=31). Seminal MDA concentration was measured by thiobarbituric acid reaction method. Seminal GPx activity was measured by oxidation of reduced nicotinamide-adenine dinucleotide. Seminal MDA levels and GPx activities in both groups were compared.

Results: MDA concentrations in both groups were significantly different (1.52 ± 0.75 vs. 2.25 ± 0.88 nM, p = 0.0021). GPx activities in both groups were non-significantly different (0.48 ± 0.11 vs. 0.47 ± 0.12 U/ml). MDA levels were negatively correlated with the sperm motility (MDA = -0.014 x motility + 2.62, p =0.017) and concentration (MDA = -0.0045 x concentration + 2.23, p = 0.0166). GPx activities were positively but non-significantly correlated with the sperm concentration and sperm motility.

Conclusions: Seminal MDA concentrations are negatively correlated with sperm concentration and motility, which might provide a simple and useful tool in predicting sperm parameters. GPx activity is non-significantly correlated with the seminal quality. Roles of seminal MDA upon spermatogenesis merits further surveys.

]]> Yao-Yuan Hsieh, Chi-Chen Chang, Chich-Sheng Lin Ivyspring International Publisher 2 1 23 29 2006-3-27 Short Research Communication http://www.biolsci.org/v02p0017.htm The effects of sympathectomy and dexamethasone in rats ingesting sucrose http://www.biolsci.org/v02p0017.htm Both high-sucrose diet and dexamethasone (D) treatment increase plasma insulin and glucose levels and induce insulin resistance. We showed in a previous work (Franco-Colin, et al. Metabolism 2000; 49:1289-1294) that combining both protocols for 7 weeks induced less body weight gain in treated rats without affecting mean daily food intake. Since such an effect may be explained by an increase in caloric expenditure, possibly due to activation of the sympathetic nervous system by sucrose ingestion, in this work, and using 10% sucrose in the drinking water, male Wistar rats were divided into 4 groups. Two groups were sympathectomized using guanethidine (Gu) treatment for 3 weeks. One of these groups of rats received D in the drinking water. Of the 2 groups not receiving Gu, one was the control (C) and the other received D. After 8 weeks a glucose tolerance test was done. The rats were sacrificed and liver triglyceride (TG), perifemoral muscle lipid, and norepinephrine (NE) levels in the liver spleen, pancreas, and heart were determined. Gu-treated rats (Gu and Gu+D groups) showed less than 10% NE concentration compared to C and D rats, less daily caloric intake and body-weight gain, more sucrose intake, and better glucose tolerance. The area under the curve after glucose administration correlated significantly with the mean body weight gain of the rats, except for D group. Groups D (D and Gu+D) also showed less caloric intake and body-weight gain but higher liver weight and TG concentration and lower peripheral muscle mass. The combination of Gu+D treatments showed some peculiar results: negative body weight gain, a fatty liver, and low muscle mass. Though the glucose tolerance test had the worst results for the D group, it showed the best results in the Gu+D group. There were significant interactions for Guan X Dex by two-way ANOVA test for the area under the curve in the glucose tolerance test, muscle mass, and muscle lipids. The results suggest that dexamethasone catabolic effect is not caused by sympathetic activation.

]]> Margarita Franco-Colín, Iván Villanueva, Manuel Piñón, Radu Racotta Ivyspring International Publisher 2 1 17 22 2006-3-4 Research Paper http://www.biolsci.org/v02p0010.htm NAD(H) recycling activity of an engineered bifunctional enzyme galactose dehydrogenase/lactate dehydrogenase http://www.biolsci.org/v02p0010.htm A chimeric bifunctional enzyme composing of galactose dehydrogenase (galDH; from Pseudomonas fluorescens) and lactate dehydrogenase (LDH; from Bacillus stearothermophilus) was successfully constructed. The chimeric galDH/LDH possessed dual characteristics of both galactose dehydrogenase and lactate dehydrogenase activities while exhibiting hexameric rearrangement with a molecular weight of approximately 400 kDa. In vitro observations showed that the chimeric enzyme was able to recycle NAD with a continuous production of lactate without any externally added NADH. Two fold higher recycling rate (0.3 mM/h) than that of the native enzyme was observed at pH values above 8.5. Proximity effects became especially pronounced during the recycling assay when diffusion hindrance was induced by polyethylene glycol. All these findings open up a high feasibility to apply the NAD(H) recycling system for metabolic engineering purposes e.g. as a model to gain a better understanding on the molecular proximity process and as the routes for synthesizing of numerous high-value-added compounds.

]]> Virapong Prachayasittikul, Sarah Ljung, Chartchalerm Isarankura-Na-Ayudhya, Leif Bülow Ivyspring International Publisher 2 1 10 16 2006-3-1 Research Paper http://www.biolsci.org/v02p0001.htm Dephosphorylation specificities of protein phosphatase for cardiac troponin I, troponin T, and sites within troponin T http://www.biolsci.org/v02p0001.htm Protein dephosphorylation by protein phosphatase 1 (PP1), acting in concert with protein kinase C (PKC) and protein kinase A (PKA), is a pivotal regulatory mechanism of protein phosphorylation. Isolated rat cardiac myofibrils phosphorylated by PKC/PKA and dephosphorylated by PP1 were used in determining dephosphorylation specificities, Ca2+-stimulated Mg2+ATPase activities, and Ca2+ sensitivities. In reconstituted troponin (Tn) complex, PP1 displayed distinct substrate specificity in dephosphorylation of TnT preferentially to TnI, in vitro. In situ phosphorylation of cardiomyocytes with calyculin A, a protein phosphatase inhibitor, resulted in an increase in the phosphorylation stiochiometry of TnT (0.3 to 0.5 (67%)), TnI (2.6 to 3.6 (38%)), and MLC2 (0.4 to 1.7 (325%)). These results further confirmed that though MLC2 is the preferred target substrate for protein phosphatase in the thick filament, the Tn complex (TnI and TnT) from thin filament and C-protein in the thick filament are also protein phosphatase substrates. Our in vitro dephosphorylation experiments revealed that while PP1 differentially dephosphorylated within TnT at multiple sites, TnI was uniformly dephosphorylated. Phosphopeptide maps from the in vitro experiments show that TnT phosphopeptides at spots 4A and 4B are much more resistant to PP1 dephosphorylation than other TnT phosphopeptides. Mg2+ATPase assays of myofibrils phosphorylated by PKC/PKA and dephosphorylated by PP1 delineated that while PKC and PKA phosphorylation decreased the Ca2+-stimulated Mg2+ATPase activities, dephosphorylation antagonistically restored it. PKC and PKA phosphorylation decreased Ca2+ sensitivity to 3.6 µM and 5.0 µM respectively. However, dephosphorylation restored the Mg2+ATPase activity of PKC (99%) and PKA (95%), along with the Ca2+ sensitivities (3.3 µM and 3.0 µM, respectively).

]]> Nathan M. Jideama, Brian H. Crawford, AKM A. Hussain, Robert L. Raynor Ivyspring International Publisher 2 1 1 9 2006-3-1 Research Paper