• Issue front cover thumbnail

      Volume 33, Issue 5

      December 2008,   pages  629-805

    • Clipboard: Monitoring the energy status of a living organism in real time

      Athel Cornish-Bowden

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    • Clipboard: The Indian genetic landscape and disease-related genes

      Evelyne Heyer

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    • Clipboard: Neuronal modulation of the immune response

      Dipankar Nandi Manoj Bhosale

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    • Commentary: Visual object recognition: building invariant representations over time

      Duje Tadin Raphael Pinaud

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    • Commentary: Multifactorial etiology of Kaposi's sarcoma: a hypothesis

      Harry W Haverkos

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    • Getting hooked on thyroid hormone action: A semi-autobiographical account

      Jamshed R Tata

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    • What history tells us XV. Cyril Norman Hinshelwood (1897–1967) – A chemical dynamic vision of the organic world

      Michel Morange

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    • Three novel single-nucleotide polymorphisms of the bovine LHX3 gene

      Y J Jing X Y Lan H Chen L Z Zhang C L Zhang C Y Pan M J Li G Ren T B Wei M Zhao

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      The LHX3 gene encodes LIM homeodomain class transcription factors that have important roles to play in pituitary and nervous system development. On the one hand, mutations of LHX3 are associated with deficiencies of growth hormone (GH), prolactin (PRL), luteotrophic hormone (LH), follicle-stimulating hormone (FSH) and thyroid-stimulating hormone (TSH); on the other hand, mutations of LHX3 are also associated with combined pituitary hormone deficiency (CPHD) diseases in human and animal models. To date, few polymorphisms of the bovine LHX3 gene have been reported. In this study, polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) and DNA sequencing methods were employed to screen the genetic variations within the bovine LHX3 gene in 802 Chinese indigenous cattle. The results revealed three novel single-nucleotide polymorphisms (SNPs): AY923832: g.7553G > A, 7631C > T and 7668C > G. Among them, a synonymous mutation of exon II was identified: GAG (Glu) > GAA (Glu) at position 72 aa (AY923832:g.7553G > A) of LHX3 (403aa) in the four Chinese bovine breeds. Significant statistical differences in genotypic frequencies for exon II and its flanking region of the LHX3 gene implied that the polymorphic locus was significantly associated with cattle breeds by the 𝜒2-test (𝜒2 = 68.975, df = 6, P < 0.001). Hence, the three novel SNPs not only extend the spectrum of genetic variations of the bovine LHX3 gene, but could also possibly contribute to conducting association analysis and evaluating these as genetic markers in bovine breeding and genetics, and CPHD detection.

    • Cloning and characterization of a novel cysteine protease gene (HbCP1) from Hevea brasiliensis

      Shi-Qing Peng Jia-Hong Zhu Hui-Liang Li Wei-Min Tian

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      The full-length cDNA encoding a cysteine protease, designated HbCP1, was isolated for the first time from Hevea brasiliensis by the rapid amplification of cDNA ends (RACE) method. HbCP1 contained a 1371 bp open reading frame encoding 457 amino acids. The deduced HbCP1 protein, which showed high identity to cysteine proteases of other plant species, was predicted to possess a putative repeat in toxin (RTX) domain at the N-terminal and a granulin (GRAN) domain at the C-terminal. Southern blot analysis indicated that the HbCP1 gene is present as a single copy in the rubber tree. Transcription pattern analysis revealed that HbCP1 had high transcription in laticifer, and low transcription in bark and leaf. The transcription of HbCP1 in latex was induced by ethylene and tapping. Cloning of the HbCP1 gene will enable us to further understand the molecular characterization of cysteine protease and its possible function in the rubber tree.

    • Homology modelling and bivalent single-chain Fv construction of anti-HepG2 single-chain immunoglobulin Fv fragments from a phage display library

      Ming Ni Bing Yu Y U Huang Zhenjie Tang Ping Lei Xin Shen Wei Xin Huifen Zhu Guanxin Shen

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      We prepared single-chain immunoglobulin Fv fragments (scFv) SLH10 specific for the HepG2 cell line after biopanning from a large human-naïve phage display library (Griffin. 1 Library). The three-dimensional (3D) structure of SLH10 was modelled by the Insight II molecule simulation software. The structure was refined using the molecular dynamics method. The structures with the least steric clashes and lowest energy were determined finally. The optimized structures of heavy (VH) and light (VL) variable chains of SLH10 scFv were obtained. Then SLH10 bivalent single-chain Fv (BsFv) was constructed that would be suitable for high-affinity targeting. SLH10 BsFv was generated by linking scFvs together and identified by sequencing. Its expression products were confirmed by western blot analysis. The relative molecular masses of scFv and BsFv were approximately 30 kDa and 60 kDa, respectively. Flow cytometry revealed that SLH10 BsFv bound the selected cell lines with greater signal intensity than the parental scFv. The improved antigen binding of SLH10 BsFv may be useful for immunodiagnostics or targeted gene therapy for liver cancer.

    • Comparative docking studies of CYP1b1 and its PCG-associated mutant forms

      Malkaram Sridhar Achary Hampapathalu Adimurthy Nagarajaram

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      Molecular docking has been used to compare and contrast the binding modes of oestradiol with the wild-type and some disease-associated mutant forms of the human CYP1b1 protein. The receptor structures used for docking were derived from molecular dynamics simulations of homology-modelled structures. Earlier studies involving molecular dynamics and principal component analysis indicated that mutations could have a disruptive effect on function, by destabilizing the native properties of the functionally important regions, especially those of the haem-binding and substrate-binding regions, which constitute the site of catalytic activity of the enzyme. In order to gain more insights into the possible differences in substrate-binding and catalysis between the wild-type and mutant proteins, molecular docking studies were carried out. Mutants showed altered protein–ligand interactions compared with the wild-type as a consequence of changes in the geometry of the substrate-binding region and in the position of haem relative to the active site. An important difference in ligand–protein interactions between the wild-type and mutants is the presence of stacking interaction with phenyl residues in the wild-type, which is either completely absent or considerably weaker in mutants. The present study revealed essential differences in the interactions between ligand and protein in wild-type and disease mutants, and helped in understanding the deleterious nature of disease mutations at the level of molecular function.

    • Proteomic analysis of cervical cancer cells treated with suberonylanilide hydroxamic acid

      Jianxiong He Canhua Huang Aiping Tong Bin Chen Zhi Zeng Peng Zhang Chunting Wang Yuquan Wei

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      Suberonylanilide hydroxamic acid (SAHA) is an orally administered histone deacetylase inhibitor (HDACI) that has shown significant antitumour activity in a variety of tumour cells. To identify proteins involved in its antitumour activity, we utilized a proteomic approach to reveal protein expression changes in the human cervical cancer cell line HeLa following SAHA treatment. Protein expression profiles were analysed by 2-dimensional polyacrylamide gel electrophoresis (2-DE) and protein identification was performed on a MALDI-Q-TOF MS/MS instrument. As a result, a total of nine differentially expressed proteins were visualized by 2-DE and Coomassie brilliant blue (CBB) staining. Further, all the changed proteins were positively identified via mass spectrometry (MS)/MS analysis. Of these, PGAM1 was significantly downregulated in HeLa cells after treatment with SAHA. Moreover, PGAM1 has been proven to be downregulated in another cervical cancer cell line (CaSki) by western blot analysis. Together, using proteomic tools, we identified several differentially expressed proteins that underwent SAHA-induced apoptosis. These changed proteins may provide some clues to a better understanding of the molecular mechanisms underlying SAHA-induced apoptosis in cervical cancer.

    • Redifferentiation of human hepatoma cells (SMMC-7721) induced by two new highly oxygenated bisabolane-type sesquiterpenes

      Ruidong Miao Juan Wei Q I Zhang Venkateswara Sajja Jinbo Yang Qin Wang

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      Bisabolane-type sesquiterpenes are a class of biologically active compounds that has antitumour, antifungal, antibacterial, antioxidant and antivenom properties. We investigated the effect of two new highly oxygenated bisabolane-type sesquiterpenes (HOBS) isolated from Cremanthodium discoideum (C. discoideum) on tumour cells. Our results showed that HOBS induced morphological differentiation and reduced microvilli formation on the cell surface in SMMC-7721 cells. Flow cytometry analysis demonstrated that HOBS could induce cell-cycle arrest in the G1 phase. Moreover, HOBS was able to increase tyrosine-𝛼-ketoglutarate transaminase activity, decrease 𝛼-foetoprotein level and 𝛾-glutamyl transferase activity. In addition, we found that HOBS inhibited the anchorage-independent growth of SMMC-7721 cells in a dose-dependent manner. Taken together, all the above observations indicate that HOBS might be able to normalize malignant SMMC-7721 cells by inhibiting cell proliferation and inducing redifferentiation.

    • Drosophila-based in vivo assay for the validation of inhibitors of the epidermal growth factor receptor/Ras pathway

      Anuradha Aritakula Annadurai Ramasamy

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      Overexpression of epidermal growth factor receptor (EGFR) is a common phenomenon observed in most cancers. Clinical treatment of such cancer involves the use of chemotherapeutic agents such as gefitinib and erlotinib which are inhibitors of tyrosine kinase (TK). These small molecules bind to the ATP-binding sites of the TK domain of EGFR. Our in silico analysis suggests that the TK domains of Drosophila and human EGFR are highly conserved. We therefore employed the Drosophila system to validate the in silico observations made with two important anticancer drugs. Since a large number of mutant flies are available, it was possible to investigate the various components of the EGFR/Ras/Raf/ MAPK pathways and the phosphorylation status of diphosphorylated extracellular signal-regulated kinase (dp-ERK1/2). These studies confirm the binding of the anilinoquinazolines to the Drosophila EGFR protein and modulation of its activity. Thus, Drosophila appears to be a robust and simple model system for screening newer anticancer drugs that act as TK inhibitors (TKIs).

    • Numerical exploration of the influence of neural noise on the psychometric function at low stimulation intensity levels

      C M Gómez

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      The relationship between stimulus intensity and the probability of detecting the presence of the stimulus is described by the psychometrical function. The probabilistic nature of this relationship is based on the stochastic behaviour of sensory neural channels and sensory networks involved in perceptual processing (Kiang 1968). This study tries to establish a continuum of variability across different levels of integration in the central nervous system. Once the opening and closing times of ionic channels was simulated, a threshold to the collective behaviour of voltage-gated ionic channels was imposed in order to generate the spike train of a single neuron. Afterwards, the trains of spikes of different neurons were added up, simulating the activity of a sensory nerve. By adding the activity due to the stimulus to the spontaneous neural behaviour, the psychometric function was simulated using a thresholding approach. The results can replicate the stochastic resonance phenomenon, but also open up the possibility that attentional phenomena can be mediated not only by increasing neural activity (bursting or oscillatory), but also by increasing noise at the neural level.

    • Inherent rhythmcity and interstitial cells of Cajal in a frog vein

      Dipanwita Ghose Lingu Jose S Manjunatha Muddanna S Rao J Prakasa Rao

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      Interstitial cells of Cajal are responsible for rhythmic contractions of the musculature of the gastrointestinal tract and blood vessels. The existence of these cells and spontaneous rhythmicity were noticed in amphibian vein and the findings are reported in this paper. The postcaval vein was identified in the frog, Rana tigrina and was perfused with amphibian Ringer solution after isolation. Contractile activity was recorded through a tension transducer connected to a polygraph. The isolated postcaval vein showed spontaneous rhythmic activity. Addition of cold Ringer solution decreased, while warm Ringer increased, the rate of contraction. Adrenaline caused inhibition of rhythmic activity at a dosage that increased the rate of isolated sinus venosus. Sections of the postcaval vein, when stained supravitally with methylene blue, showed the presence of interstitial cells of Cajal. Photic stimulation of the vein in the presence of methylene blue led to a significant decrease in the rate of spontaneous beating of the vein. These findings indicate that the postcaval vein of frog is capable of inherent rhythmcity, which is dependent on the interstitial cells of Cajal but is independent of the sinus venosus.

    • Primate numts and reticulate evolution of capped and golden leaf monkeys (Primates: Colobinae)

      K Praveen Karanth

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      A recent phylogenetic study of langurs and leaf monkeys of South Asia suggested a reticulate evolution of capped and golden leaf monkeys through ancient hybridization between Semnopithecus and Trachypithecus. To test this hybridization scenario, I analysed nuclear copies of the mitochondrial cytochrome 𝑏 gene (numts) from capped, golden and Phayre’s leaf monkeys. These numts were aligned with mitochondrial cytochrome 𝑏 sequences of various species belonging to the genera Semnopithecus and Trachypithecus. In the phylogenetic tree derived from this alignment, the numts fell into three distinct clades (A, B and C) suggesting three independent integration events. Clade A was basal to Semnopithecus, and clades B and C were basal to Trachypithecus. Among the numts in clades A and C were sequences derived from species not represented in their respective sister mitochondrial groups. This unusual placement of certain numts is taken as additional support for the hybridization scenario. Based on the molecular dating of these integration events, hybridization is estimated to have occurred around 7.1 to 3.4 million years ago. Capped and golden leaf monkeys might have to be assigned to a new genus to reconcile their unique evolutionary history. Additionally, northeast India appears to be a ‘hot spot’ for lineages that might have evolved through reticulate evolution.

    • Branch-point stoichiometry can generate weak links in metabolism: the case of glycine biosynthesis

      Enrique Meléndez-Hevia Patricia D E Paz-Lugo

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      Although the metabolic network permits conversion between almost any pair of metabolites, this versatility fails at certain sites because of chemical constraints (kinetic, thermodynamic and stoichiometric) that seriously restrict particular conversions. We call these sites weak links in metabolism, as they can interfere harmfully with management of matter and energy if the network as a whole does not include adequate safeguards. A critical weak link is created in glycine biosynthesis by the stoichiometry of the reaction catalyzed by glycine hydroxymethyltransferase (EC, which converts serine into glycine plus one C1 unit: this produces an absolute dependence of the glycine production flux on the utilization of C1 units for other metabolic pathways that do not work coordinately with glycine use. It may not be possible, therefore, to ensure that glycine is always synthesized in sufficient quantities to meet optimal metabolic requirements.

    • The neural crest and neural crest cells: discovery and significance for theories of embryonic organization

      Brian K Hall

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      The neural crest has long fascinated developmental biologists, and, increasingly over the past decades, evolutionary and evolutionary developmental biologists. The neural crest is the name given to the fold of ectoderm at the junction between neural and epidermal ectoderm in neurula-stage vertebrate embryos. In this sense, the neural crest is a morphological term akin to head fold or limb bud. This region of the dorsal neural tube consists of neural crest cells, a special population(s) of cell, that give rise to an astonishing number of cell types and to an equally astonishing number of tissues and organs. Neural crest cell contributions may be direct — providing cells — or indirect — providing a necessary, often inductive, environment in which other cells develop. The enormous range of cell types produced provides an important source of evidence of the neural crest as a germ layer, bringing the number of germ layers to four — ectoderm, endoderm, mesoderm, and neural crest. In this paper I provide a brief overview of the major phases of investigation into the neural crest and the major players involved, discuss how the origin of the neural crest relates to the origin of the nervous system in vertebrate embryos, discuss the impact on the germ-layer theory of the discovery of the neural crest and of secondary neurulation, and present evidence of the neural crest as the fourth germ layer. A companion paper (Hall, Evol. Biol. 2008) deals with the evolutionary origins of the neural crest and neural crest cells.

    • Bacterial persistence: some new insights into an old phenomenon

      R Jayaraman

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      Bigger discovered more than 60 years ago, at the very beginning of the antibiotic era, that populations of antibiotic-sensitive bacteria contained a very small fraction (approximately 10–6) of antibiotic-tolerant cells (persisters). Persisters are different from antibiotic-resistant mutants in that their antibiotic tolerance is non-heritable and reversible. In spite of its importance as an interesting biological phenomenon and in the treatment of infectious diseases, persistence did not attract the attention of the scientific community for more than four decades since its discovery. The main reason for this lack of interest was the difficulty in isolating sufficient numbers of persister cells for experimentation, since the proportion of persisters in a population of wild-type cells is extremely small. However, with the discovery of high-persister (hip) mutants of Escherichia coli by Moyed and his group in the early 1980s, the phenomenon attracted the attention of many groups and significant progress has occurred since then. It is now believed that persistence is the end result of a stochastic switch in the expression of some toxin–antitoxin (TA) modules (of which the hipA and hipB genes could be examples), creating an imbalance in their intracellular levels. There are also models invoking the involvement of the alarmone (p) ppGpp in the generation of persisters. However, the precise mechanisms are still unknown. Bacterial persistence is part of a wider gamut of phenomena variously called as bistability, multistability, phenotypic heterogeneity, stochastic switching processes, etc. It has attracted the attention of not only microbiologists but also a diverse band of researchers such as biofilm researchers, evolutionary biologists, sociobiologists, etc. In this article, I attempt to present a broad overview of bacterial persistence to illustrate its significance and the need for further exploration.

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