• Issue front cover thumbnail

      Volume 39, Issue 3

      June 2014,   pages  333-541

    • Clipboard: Biodiversity only makes sense in the light of evolution

      R Geeta Lúcia G Lohmann Susana Magallón Daniel P Faith Andrew Hendry Keith Crandall Luc De Meester Campbell O Webb Anne-Hélène Prieur-Richard Makiko Mimura Elena Conti Joel Cracraft Felix Forest Carlos Jaramillo Michael Donoghue Tetsukazu Yahara

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    • Novel inhibitor of DNA ligase IV with a promising cancer therapeutic potential

      Ashwin Kotnis Rita Mulherkar

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    • Sidelights: Are any fungal genes nucleus-limited?

      Durgadas P Kasbekar

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    • What history tells us XXXIV. The complex history of the selective model of antibody formation

      Michel Morange

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    • FUMET: A fuzzy network module extraction technique for gene expression data

      Priyakshi Mahanta Hasin Afzal Ahmed Dhruba Kumar Bhattacharyya Ashish Ghosh

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      Construction of co-expression network and extraction of network modules have been an appealing area of bioinformatics research. This article presents a co-expression network construction and a biologically relevant network module extraction technique based on fuzzy set theoretic approach. The technique is able to handle both positive and negative correlations among genes. The constructed network for some benchmark gene expression datasets have been validated using topological internal and external measures. The effectiveness of network module extraction technique has been established in terms of well-known p-value, Q-value and topological statistics.

    • miRNAting control of DNA methylation

      Ashwani Jha Ravi Shankar

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      DNA methylation is a type of epigenetic modification where a methyl group is added to the cytosine or adenine residue of a given DNA sequence. It has been observed that DNA methylation is achieved by some collaborative agglomeration of certain proteins and non-coding RNAs. The assembly of IDN2 and its homologous proteins with siRNAs recruits the enzyme DRM2, which adds a methyl group at certain cytosine residues within the DNA sequence. In this study, it was found that de novo DNA methylation might be regulated by miRNAs through systematic targeting of the genes involved in DNA methylation. A comprehensive genome-wide and system-level study of miRNA targeting, transcription factors, DNA-methylation-causing genes and their target genes has provided a clear picture of an interconnected relationship of all these factors which regulate DNA methylation in Arabidopsis. The study has identified a DNA methylation system that is controlled by four different genes: IDN2, IDNl1, IDNl2 and DRM2. These four genes along with various critical transcription factors appear to be controlled by five different miRNAs. Altogether, DNA methylation appears to be a finely tuned process of opposite control systems of DNA-methylation-causing genes and certain miRNAs pitted against each other.

    • Multiple proteins of White spot syndrome virus involved in recognition of 𝛽-integrin

      Jing-Yan Zhang Qing-Hui Liu Jie Huang

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      The recognition and attachment of virus to its host cell surface is a critical step for viral infection. Recent research revealed that 𝛽-integrin was involved in White spot syndrome virus (WSSV) infection. In this study, the interaction of 𝛽-integrin with structure proteins of WSSV and motifs involved in WSSV infection was examined. The results showed that envelope proteins VP26, VP31, VP37, VP90 and nucleocapsid protein VP136 interacted with LvInt. RGD-, YGL- and LDV-related peptide functioned as motifs of WSSV proteins binding with 𝛽-integrin. The 𝛽-integrin ligand of RGDT had better blocking effect compared with that of YGL- and LDV-related peptides. In vivo assay indicated that RGD-, LDV- and YGL-related peptides could partially block WSSV infection. These data collectively indicate that multiple proteins were involved in recognition of 𝛽-integrin. Identification of proteins in WSSV that are associated with 𝛽-integrin will assist development of new agents for effective control of the white spot syndrome.

    • Identification of chikungunya virus interacting proteins in mammalian cells

      Mandar S Paingankar Vidya A Arankalle

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      Identification and characterization of virus host interactions is an essential step for the development of novel antiviral strategies. Very few studies have been targeted towards identification of chikungunya virus (CHIKV) interacting host proteins. In current study, virus overlay protein binding assay (VOPBA) and matrix-assisted laser desorption/ionization time of flight analysis (MALDI TOF/TOF) were employed for the identification of CHIKV binding proteins in mammalian cells. HSP70 and actin were identified as virus binding proteins in HEK-293T and Vero-E6 cells, whereas STAT-2 was identified as an additional protein in Vero-E6 cells. Pre-incubation with anti-HSP70 antibody and miRNA silencing of HSP70 significantly reduced the CHIKV production in HEK-293T and Vero-E6 cells at early time points. These results suggest that CHIKV exploits the housekeeping molecules such as actin, HSP70 and STAT-2 to establish infection in the mammalian cells.

    • Differential expression of speckled POZ protein, SPOP: Putative regulation by miR-145

      Chiu-Jung Huang Hsing-Yu Chen Wan-Yi Lin Kongbung Choo

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      The speckle POZ protein, SPOP, is an adaptor of the Cul3-based ubiquitination process, and has been implicated in the carcinogenesis process. Despite recent elucidation of biological functions, regulation of SPOP gene expression has not been reported. In this study, the mRNA levels of the mouse SPOP (mSPOP) gene were first shown to vary noticeably in different tissues. However, the SPOP protein was detected in high abundance only in Purkinje cells of the cerebellum and seminiferous tubule of the testis, echoing previous reports of involvement of ubiquitination in neuron cells and in spermatogenesis. In other mouse tissues and human cancer cell lines analysed, only low SPOP protein levels were detected. The 3′-untranslated regions of both the mSPOP and human SPOP transcripts harbor a conserved putative miR-145 binding site (BS). In some tissues and cell lines, miR-145 and SPOP protein levels were in an inverse relationship suggesting miR-145 regulation. Luciferase assays of deletion and point mutation constructs of the miR-145 BS, and miR-145 induction by serum starvation that resulted in reduced endogenous SPOP levels provided further evidence that miR-145 is likely involved in post-transcriptional regulation of SPOP expression in selected tissues, and possibly with the participation of other miRNA species.

    • DNA microarray analysis of genes differentially expressed in adipocyte differentiation

      Chunyan Yin Yanfeng Xiao Wei Zhang Erdi Xu Weihua Liu Xiaoqing Yi Ming Chang

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      In the present study, the human liposarcoma cell line SW872 was used to identify global changes in gene expression profiles occurring during adipogenesis. We further explored some of the genes expressed during the late phase of adipocyte differentiation. These genes may play a major role in promoting excessive proliferation and accumulation of lipid droplets, which contribute to the development of obesity. By using microarray-based technology, we examined differential gene expression in early differentiated adipocytes and late differentiated adipocytes. Validated genes exhibited a ≥ 10-fold increase in the late phase of adipocyte differentiation by polymerase chain reaction (RT-PCR). Compared with undifferentiated preadipocytes, we found that 763 genes were increased in early differentiated adipocytes, and 667 genes were increased in later differentiated adipocytes. Furthermore, 21 genes were found being expressed 10-fold higher in the late phase of adipocyte differentiation. The results were in accordance with the RT-PCR test, which validated 11 genes, namely, CIDEC, PID1, LYRM1, ADD1, PPAR𝛾2, ANGPTL4, ADIPOQ, ACOX1, FIP1L1, MAP3K2 and PEX14. Most of these genes were found being expressed in the later phase of adipocyte differentiation involved in obesity-related diseases. The findings may help to better understand the mechanism of obesity and related diseases.

    • A survey of chlortetracycline concentration in feed and its residue in chicken egg in commercial layer farms

      K Kodimalar R A Rajini S Ezhivalavan G Sarathchandra

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      The worldwide increase in the use of antibiotics as an integral part of poultry and livestock production industry has recently received increasing attention as a contributory factor in the international emergence of antibiotic-resistant bacteria in human beings. To gauge the presence of the aforementioned scenario in the Indian context, a preliminary survey was conducted to assess the use of chlortetracycline (CTC) in 12 commercial layer farms and to quantify and confirm its residue in the egg. Samples of feed and eggs were collected at day 0 (prior to CTC addition), 3rd, 5th and 7th day during treatment and on the 9th and 14th day (2nd and 7th day after withdrawal of CTC) from each of the 12 commercial poultry farms studied. Concentration of CTC in feed was significantly (𝑃 < 0.01) high on the 3rd, 5th and 7th day. On the 9th day and 14th day CTC concentration in feed was significantly (𝑃 <0.01) lower compared to the earlier 3 days studied. A highly significant difference (𝑃 <0.01) of the antibiotic residue in egg was observed in all the 5 days with high residual levels of CTC in egg. CTC in feed and its residue in egg were detected even on the 9th and 14th day respectively.

    • Hypoxia influences expression profile of Pleckstrin homology-like domain, family A, member 2 in Indian catfish, Clarias batrachus (Linnaeus, 1758): A new candidate gene for hypoxia tolerance in fish

      Vindhya Mohindra Ratnesh K Tripathi Prabhaker Yadav Rajeev K Singh Kuldeep K Lal

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      Several physiologically important genes were found to be regulated by hypoxia at the transcriptional level. The Pleckstrin homology-like domain, family A, member 2 (PHLDA2) gene was previously identified as an imprinted gene. The present study was aimed to determine the structure of complete cDNA and the deduced protein of PHLDA2 along with analysing the changes in its mRNA expression in Clarias batrachus tissues under hypoxic conditions. The complete cDNA of CbPHLDA2 gene consisted of 1009 nucleotides with an open reading frame of 417 nucleotides. The deduced CbPHLDA2 protein of 139 amino acids shared high homology with PHLD2A of other fishes as well as that of vertebrates. Importantly, a single amino acid (asparagine/lysine) insertion was identified in the PH domain of CbPHLDA2 and other fishes, which was absent in other vertebrates studied. Furthermore, under normoxic conditions, CbPHLDA2 was constitutively expressed with varying levels in analysed tissues. Short- and long-term hypoxia exposure resulted in significant changes in the expression of CbPHLDA2 in liver, spleen, head kidney, brain and muscle in a time-dependent manner. The results suggested that CbPHLDA2 might play an important role for adaptive significance under hypoxia.

    • Evaluation of antibody response in mice against avian influenza A (H5N1) strain neuraminidase expressed in yeast Pichia pastoris

      Murugan Subathra Ponsekaran Santhakumar Mangamoori Lakshmi Narasu Syed Sultan Beevi Sunil K Lal

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      Avian influenza has raised many apprehension in the recent years because of its potential transmitability to humans. With the increasing emergence of drug-resistant avian influenza strains, development of potential vaccines are imperative to manage this disease. Two structural antigens, haemagglutinin and neuraminidase, have been the target candidates for the development of subunit vaccine against influenza. In an effort to develop a faster and economically beneficial vaccine, the neuraminidase gene of a highly pathogenic avian influenza isolate was cloned and expressed in the methylotrophic yeast Pichia pastoris. The recombinant neuraminidase (rNA) antigen was purified, and its bioactivity was analysed. The rNA was found to be functional, as determined by the neuraminidase assay. Four groups of mice were immunized with different concentrations of purified rNA antigen, which were adjuvanted with aluminium hydroxide. The immune response against rNA was analysed by enzyme-linked immunosorbent assay (ELISA) and neuraminidase inhibition assay. The mice groups immunized with 25 𝜇g and 10 𝜇g of antigen had a significant immune response against rNA. This method can be utilized for faster and cost-effective development of vaccines for a circulating and newer strain of avian influenza, and would aid in combating the disease in a pandemic situation, in which production time matters greatly.

    • Molecular screening of Chinese medicinal plants for progestogenic and anti-progestogenic activity

      H M Manir Ahmed Jan-Ying Yeh Yi-Chia Tang Winston Teng-Kuei Cheng Bor-Rung Ou

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      Estrogen and progestins have adverse effects, and many of these adverse effects are caused by progestins. Due to this, many women choose to use botanical alternatives for hormone replacement therapy, which does not trigger steroidogenic properties. Therefore, it is necessary to screen these herbs for progestogenic and anti-progestogenic properties. Extract of 13 Chinese medicinal plants were analysed for progestogenic and anti-progestogenic activities by using progesterone response element-driven luciferase reporter gene bioassay. MTT assay was carried out to investigate the cytotoxic effect of herb extract on PAE cells. Among the 13 herbs, Dipsacus asperoides extract exhibited progestogenic activity, and 10 species – Cortex eucommiae, Folium artemisiae argyi, Glycyrrhiza uralensis, Angelica sinensis, Atractylodes macrocephala koidz, Scutellaria baicalensis, Cuscuta chinensis, Euscaphis japonica, Ailanthus altissima, and Dioscorea opposita – were recognized to have anti-progestogenic like activities. Extract of Dipsacus asperoides demonstrated dose-dependent progestogenic activity, and the progestogenic activity of 100 𝜇g/mL extracts was equivalent to 31.45 ng/mL progesterone activity. Herbs extracts that exhibited anti-progestogenic-like activity also inhibited the 314.46 ng/mL progesterone activity in a dose-response manner. None of the herb extracts shown significant toxic effect on PAE cells at 40–100 𝜇g/mL compared to control. This discovery will aid selection of suitable herbs for hormone replacement therapy.

    • Modelling the transition from simple to complex Ca2+ oscillations in pancreatic acinar cells

      Neeraj Manhas James Sneyd K R Pardasani

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      A mathematical model is proposed which systematically investigates complex calcium oscillations in pancreatic acinar cells. This model is based on calcium-induced calcium release via inositol trisphosphate receptors (IPR) and ryanodine receptors (RyR) and includes calcium modulation of inositol (1,4,5) trisphosphate (IP3) levels through feedback regulation of degradation and production. In our model, the apical and the basal regions are separated by a region containing mitochondria, which is capable of restricting Ca2+ responses to the apical region. We were able to reproduce the observed oscillatory patterns, from baseline spikes to sinusoidal oscillations. The model predicts that calcium-dependent production and degradation of IP3 is a key mechanism for complex calcium oscillations in pancreatic acinar cells. A partial bifurcation analysis is performed which explores the dynamic behaviour of the model in both apical and basal regions.

    • Life at a different pace: Annual itineraries are conserved in seasonal songbirds

      S Malik S Singh S Rani V Kumar

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      The duration of life history state (LHS) reflects the adaptive strategy a species has evolved to cope with a changing environment. Inhabitants at different latitudes may thus have significant differences in the rates of metabolic and physiological processes underlying LHSs. Birds, in order to maximize their fitness in the environment in which they live, seasonally switch from one LHS to another during the year. The present study investigated whether an annual itinerary of a species would determine its rate of reaction to inductive long days. We compared the photoinduced cycles of changes in body mass and testes, as indices of migratory and reproductive LHSs, between two long day breeding species, the migratory redheaded bunting and non-migratory Indian weaverbird. Changes in body mass and testis size were measured in photosensitive buntings and weaverbirds (𝑛 = 7 each) on short days (LD 8:16) subjected first to 0.5 h weekly light increments until the light period was 13 h per day, and then maintained on LD 13:11 for another 32 weeks. A similar observation was recorded on a group of buntings (𝑛 = 14) and weaverbirds (𝑛 = 9) maintained on increasing natural day lengths (NDL; Lucknow, 26°55′ N, 80°59′ E) for 47 weeks. As predicted, the rates of induction of seasonal cycles under an identical inductive photoperiod were significantly faster in temperate buntings with five annual LHSs than in the subtropical weaverbirds with three annual LHSs. This suggests that annual itineraries of songbirds with which they may have evolved with at their breeding latitudes, determine their response to the external photoperiodic environment.

    • The evolutionary strata of DARPP-32 tail implicates hierarchical functional expansion in higher vertebrates

      Choong Yong Ung Teow Chong Teoh

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      DARPP-32 (dopamine and adenosine 3′,5′-monophosphate-regulated phosphoprotein of 32 kDa), which belongs to PPP1R1 gene family, is known to act as an important integrator in dopamine-mediated neurotransmission via the inhibition of protein phosphatase-1 (PP1). Besides its neuronal roles, this protein also behaves as a key player in pathological and pharmacological aspects. Use of bioinformatics and phylogenetics approaches to further characterize the molecular features of DARPP-32 can guide future works. Predicted phosphorylation sites on DARPP-32 show conservation across vertebrates. Phylogenetics analysis indicates evolutionary strata of phosphorylation site acquisition at the C-terminus, suggesting functional expansion of DARPP-32, where more diverse signalling cues may involve in regulating DARPP-32 in inhibiting PP1 activity. Moreover, both phylogenetics and synteny analyses suggest de novo origination of PPP1R1 gene family via chromosomal rearrangement and exonization.

    • The rare intracellular RET mutation p.S891A in a Chinese Han family with familial medullary thyroid carcinoma

      Xiao-Ping Qi Rong-Xin Zhang Jin-Lin Cao Zhen-Guang Chen Hang-Yang Jin Ren-Rong Yang

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      We report intracellular RET mutation in a Han Chinese pedigree with familial medullary thyroid carcinoma (FMTC). Direct sequencing of RET proto-oncogene identified a missense c.2671T > G (p.S891A) mutation in 6 of 14 family members. The single nucleotide polymorphisms c. 135A > G (p.A45A), IVS4+48A >G, c. 1296A > G (p.A432A), c. 2071G > A (p.G691S), c. 2307T > G (p.L769L) and a variant c. 833C > A (p.T278N) were also found in 6 carriers. Among 5 of the 6 carriers presented medullary thyroid carcinoma (MTC) as an isolated clinical phenotype, with elevated basal serum calcitonin (Ct). Two underwent non-normative thyroidectomy either two or four times without physician awareness or diagnosis of this disease at initial treatment, but with elevated Ct. One with elevated pre-Ct accepted total thyroidectomy (TT) with modified bilateral neck dissection (MBiND), and whose seventh posterior rib MTC metastases was confirmed 5 months after surgery. Moreover, results of two affected individuals with elevated Ct were reduced to normal after TT with MBiND or prophylactic VI compartmental dissection. However, only another carrier with the variant p.T278N had slightly elevated Ct rejected surgery and was strictly monitored. Given these case results, we suggest that screening of RET and pre-surgical Ct levels in the management of MTC patients is essential for earlier diagnosis and more normative initial treatment, that FMTC patients with cervical lymph nodes metastases may be cured by TT with MBiND, and that prophylactic VI compartmental dissection should be avoided when Ct levels are low.

    • Phylogenetic diversity of Mesorhizobium in chickpea

      Dong Hyun Kim Mayank Kaashyap Abhishek Rathore Roma R Das Swathi Parupalli Hari D Upadhyaya S Gopalakrishnan Pooran M Gaur Sarvjeet Singh Jagmeet Kaur Mohammad Yasin Rajeev K Varshney

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      Crop domestication, in general, has reduced genetic diversity in cultivated gene pool of chickpea (Cicer arietinum) as compared with wild species (C. reticulatum, C. bijugum). To explore impact of domestication on symbiosis, 10 accessions of chickpeas, including 4 accessions of C. arietinum, and 3 accessions of each of C. reticulatum and C. bijugum species, were selected and DNAs were extracted from their nodules. To distinguish chickpea symbiont, preliminary sequences analysis was attempted with 9 genes (16S rRNA, atpD, dnaJ, glnA, gyrB, nifH, nifK, nodD and recA) of which 3 genes (gyrB, nifK and nodD) were selected based on sufficient sequence diversity for further phylogenetic analysis. Phylogenetic analysis and sequence diversity for 3 genes demonstrated that sequences from C. reticulatum were more diverse. Nodule occupancy by dominant symbiont also indicated that C. reticulatum (60%) could have more various symbionts than cultivated chickpea (80%). The study demonstrated that wild chickpeas (C. reticulatum) could be used for selecting more diverse symbionts in the field conditions and it implies that chickpea domestication affected symbiosis negatively in addition to reducing genetic diversity.

    • MicroRNAs as regulators of cutaneous wound healing

      Wing-Fu Lai Parco M Siu

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      MicroRNAs (miRNAs) have emerged as key post-transcriptional regulators of gene expression, and have displayed important roles in areas spanning from embryonic development to skin physiology. Despite this, till now little is known about the significance of miRNAs in cutaneous wound healing. In this mini-review, we discuss the existing evidence on the roles of miRNAs in physiological processes relevant to cutaneous wound healing, followed by a highlight of the prospects and challenges of future development of miRNA-based wound therapies. With existing technologies of nucleic acid transfer and miRNA modulation, it is anticipated that once the roles of miRNAs in wound healing have been clarified, there will be a vast new vista of opportunities brought up for development of miRNA-targeted therapies for wound care.

    • Conservation of PHO pathway in ascomycetes and the role of Pho84

      Parul Tomar Sinha Sinha

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      In budding yeast, Saccharomyces cerevisiae, the phosphate signalling and response pathway, known as PHO pathway, monitors phosphate cytoplasmic levels by controlling genes involved in scavenging, uptake and utilization of phosphate. Recent attempts to understand the phosphate starvation response in other ascomycetes have suggested the existence of both common and novel components of the budding yeast PHO pathway in these ascomycetes. In this review, we discuss the components of PHO pathway, their roles in maintaining phosphate homeostasis in yeast and their conservation across ascomycetes. The role of high-affinity transporter, Pho84, in sensing and signalling of phosphate has also been discussed.

    • Gene therapy in India: A focus

      Sarvani Chodisetty Everette Jacob Remington Nelson

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      Gene therapy refers to the treatment of genetic diseases using normal copies of the defective genes. It has the potential to cure any genetic disease with long-lasting therapeutic benefits. It remained an enigma for a long period of time, which was followed by a series of setbacks in the late 1990s. Gene therapy has re-emerged as a therapeutic option with reports of success from recent clinical studies. The United States and Europe has been pioneers in this field for over two decades. Recently, reports of gene therapy have started coming in from Asian countries like China, Japan and Korea. This review focuses on the current status of gene therapy in India.

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