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      Volume 37, Issue 1

      March 2012,   pages  1-197

    • Editorial: Rare Disease Day, our Roma cousins and the power of one

      Durgadas P Kasbekar

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    • Commentary: Life in (and on) the rocks

      Chakkiath Paul Antony Charles S Cockell Yogesh S Shouche

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    • What history tells us XXVII. A new life for allostery

      Michel Morange

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    • Sequence periodic pattern of HERV LTRs: A matrix simulation algorithm

      Shihua Zhang Jing Xu Chaoling Wei

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      Flanking regulatory long terminal repeats (LTRs) in Human endogenous retrovirus (HERV) is a kind of typical DNA repeat that is widespread in the human genome. Currently, many algorithms have been developed to detect the latent periodicity of a wide range of DNA repeats. However, no such attempt was made for HERV LTRs. The present study focused on the investigation of the possible sequence periodic patterns in the HERV LTRs and their regulatory mechanisms. We calculated the sequence periods of 5′, 3′ and combined LTRs in HERVs with our devised matrix simulation algorithm. It is interesting that 5′ and 3′ LTRs have the same period of 7, and combined LTRs have a period of 9. These results indicated that HERV LTRs have predominant periodic patterns. Based on the obtained sequence periodicity, we constructed periodic consensus sequences of 5′, 3′ and combined LTRs. As to 5′ and 3′ LTRs with the same period – 7, we manually scanned the nucleotide bases in the corresponding positions of their periodic consensus sequences, and found some positions have the nucleotide base unchanged, such as the 1st, 5th and 7th positions. These conservative nucleotide base positions represent critical binding sites of regulatory LTRs, and may be indicative of conserved regulatory mechanisms in LRT-participating regulatory networks.

    • Accumulation of rare earth elements by siderophore-forming Arthrobacter luteolus isolated from rare earth environment of Chavara, India

      E S Challaraj Emmanuel T Ananthi B Anandkumar S Maruthamuthu

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      In this study, Arthrobacter luteolus, isolated from rare earth environment of Chavara (Quilon district, Kerala, India), were found to produce catechol-type siderophores. The bacterial strain accumulated rare earth elements such as samarium and scandium. The siderophores may play a role in the accumulation of rare earth elements. Catecholate siderophore and low-molecular-weight organic acids were found to be present in experiments with Arthrobacter luteolus. The influence of siderophore on the accumulation of rare earth elements by bacteria has been extensively discussed.

    • TP53 codon 72 polymorphism in pigmentary phenotypes

      Kárita Antunes Costa Lidia Andreu Guillo

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      The p53 protein exerts different cellular functions, and recent findings have demonstrated its influence on the cascade of skin pigmentation during UV exposure. Among TP53 gene polymorphisms, the most studied is the G to C transversion in exon 4 at codon 72, which results in three distinct genotypes, Arg/Arg, Pro/Pro and Arg/Pro, each one encoding different p53 isoforms. Therefore, this study aimed to determine the relationship between TP53 codon 72 polymorphism and skin protection against sunburn. Genomic DNA was extracted from peripheral blood samples and genotyping was performed by PCR and confirmed by restriction enzyme digestion. The genotype frequency was 50% for Arg/Arg and 14.6% for Pro/Pro genotype. The frequency of heterozygous subjects was 35.4%. In our population, p53 genotypes were in Hardy–Weinberg (HW) equilibrium ($\chi^{2}_{\text{HM}}$ < 3.84), showing a predominance of arginine allele (total Arg allele frequency of 68%). No significant association between p53 genotype and skin colour, hair or eye colour and susceptibility to sun exposure was found. However, further analysis demonstrated a significant association between the genotype Pro/Pro and blue/green eyes among participants who presented redness (𝑃=0.016). Our findings indicate susceptibility to sun exposure when this phenotype (eye colour) occurs simultaneously with Pro/Pro genotype.

    • Mitogen-activated protein kinases mediate Mycobacterium tuberculosis–induced CD44 surface expression in monocytes

      Natarajan Palaniappan S Anbalagan Sujatha Narayanan

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      CD44, an adhesion molecule, has been reported to be a binding site for Mycobacterium tuberculosis (M. tuberculosis) in macrophages and it also mediates mycobacterial phagocytosis, macrophage recruitment and protective immunity against pulmonary tuberculosis in vivo. However, the signalling pathways that are involved in M. tuberculosis–induced CD44 surface expression in monocytic cells are currently unknown. Exposure of THP-1 human monocytes to M. tuberculosis H37Rv and H37Ra induced distinct, time-dependent, phosphorylation of mitogen-activated protein kinase kinase-1, extracellular signal regulated kinase 1/2, mitogen-activated protein kinase kinase 3/6, p38 mitogen-activated protein kinase and c-jun N-terminal kinases. The strains also differed in their usage of CD14 and human leukocyte antigen-DR (HLA-DR) receptors in mediating mitogen-activated protein kinase activation. M. tuberculosis H37Rv strain induced lower CD44 surface expression and tumour necrosis factor-alpha levels, whereas H37Ra the reverse. Using highly specific inhibitors of mitogen-activated protein kinase kinase-1, p38 mitogen-activated protein kinase and c-jun N-terminal kinase, we report that inhibition of extracellular signal regulated kinase 1/2 and c-jun N-terminal kinases increases, but that inhibition of p38 mitogen-activated protein kinase decreases M. tuberculosis–induced CD44 surface expression in THP-1 human monocytes.

    • Aged mice have increased inflammatory monocyte concentration and altered expression of cell-surface functional receptors

      Kelley Strohacker Whitney L Breslin Katie C Carpenter Brian K McFarlin

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      The expression of monocyte cell-surface receptors represents one index of immune dysfunction, which is common with aging. Although mouse models of aging are prevalent, monocyte subset assessment is rare. Our purpose was to compare cell receptor expression on classic (CD115+/Gr-1high) and non-classic (CD115+/Gr-1low) monocytes from 80- or 20-week-old CD-1 mice. Three-colour flow cytometry was used to determine the concentration of monocyte subsets and their respective cell-surface expression of TLR2, TLR4, CD80, CD86, MHC II and CD54. These receptors were selected because they have been previously associated with altered monocyte function. Data were analysed with independent 𝑡-tests; significance was set at 𝑃 < 0.05. Old mice had a greater concentration of both classic (258%, 𝑃=0.003) and non-classic (70%, 𝑃=0.026) monocytes. The classic : non-classic monocyte ratio doubled in old as compared with that in young mice (𝑃=0.006), indicating a pro-inflammatory shift. TLR4 ($\downarrow$27%, 𝑃=0.001) and CD80 ($\downarrow$37%, 𝑃=0.004) were decreased on classic monocytes from old as compared with those from young mice. TLR2 ($\uparrow$24%, 𝑃=0.002) and MHCII ($\downarrow$21%, 𝑃=0.026) were altered on non-classic monocytes from old as compared with those from young mice. The increased classic : non-classic monocyte ratio combined with changes in the cell-surface receptor expression on both monocyte subsets is indicative of immune dysfunction, which may increase age-associated disease risk.

    • High prevalence of oncogenic HPV-16 in cervical smears of asymptomatic women of eastern Uttar Pradesh, India: A population-based study

      Shikha Srivastava Sadhana Gupta Jagat Kumar Roy

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      In developing countries like India, occurrence of Human papillomavirus (HPV) in cervical cancer as well as in the asymptomatic population was observed to be very high. Studies on HPV prevalence have been conducted in different parts of the country but no data were available from the eastern region of Uttar Pradesh (UP). The present study aimed to determine the status of HPV prevalence and its association with different socio-demographic factors in this population. Prevalence of HPV was investigated in a total of 2424 cervical scrape samples of asymptomatic women. Primer sets from L1 consensus region of viral genome were used to detect the presence of HPV, and the positive samples were genotyped by sequencing. Univariate binary logistic regression analysis was used to evaluate association of socio-demographic factors with HPV. 9.9% of the clinically asymptomatic women were found to be infected with HPV comprising 26 different genotypes. Among HPV-positive women, 80.8% showed single infection, while 15.4% harboured multiple infections. HPV-16 (63.7%) was the most prevalent, followed by HPV-31 (6.7%), HPV-6 (5.4%), HPV-81 (4.6%) and HPV-33 (4.2%). Significant association of HPV with non-vegetarian diet (𝑃 < 0.05) and rural residential areas (𝑃 < 0.01) were observed. High prevalence of HPV-16 in asymptomatic women of this population, a frequency comparable to invasive cervical cancers, highlights an urgent need for a therapeutic HPV vaccine covering HPV-16 and other high-risk types to provide protection against the disease.

    • Cytotoxic effects of the novel isoflavone, phenoxodiol, on prostate cancer cell lines

      Simon Mahoney Frank Arfuso Pierra Rogers Susan Hisheh David Brown Michael Millward Arun Dharmarajan

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      Phenoxodiol is an isoflavone derivative that has been shown to elicit cytotoxic effects against a broad range of human cancers. We examined the effect of phenoxodiol on cell death pathways on the prostate cell lines LNCaP, DU145 and PC3, representative of different stages of prostate cancer, and its effects on cell death pathways in these cell lines. Cell proliferation assays demonstrated a significant reduction in the rate of cell proliferation after 48 h exposure to phenoxodiol (10 and 30 𝜇M). FACS analysis and 3′-end labelling indicated that all three prostate cancer cell lines underwent substantial levels of cell death 48 h after treatment. Mitochondrial membrane depolarization, indicative of early-stage cell death signalling, using JC-1 detection, was also apparent in all cell lines after exposure to phenoxodiol in the absence of caspase-3 activation. Caspase inhibition assays indicated that phenoxodiol operates through a caspase-independent cell death pathway. These data demonstrate that phenoxodiol elicits anti-cancer effects in prostate cancer cell lines representative of early and later stages of development through an as-yet-unknown cell death mechanism. These data warrant the further investigation of phenoxodiol as a potential treatment for prostate cancer.

    • Differential expression of ZFX gene in gastric cancer

      Parvaneh Nikpour Modjtaba Emadi-Baygi Faezeh Mohammad-Hashem Mohamad Reza Maracy Shaghayegh Haghjooy-Javanmard

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      Gastric cancer accounts for 8% of the total cancer cases and 10% of total cancer deaths worldwide. In Iran, gastric cancer is the leading cause of national cancer-related mortality. Most human cancers show substantial heterogeneity. The cancer stem cell (CSC) hypothesis has been proposed to reconcile this heterogeneity. ZFX encodes a member of the krueppel C2H2-type zinc-finger protein family that is required as a transcriptional regulator for self-renewal of stem cells. A total of 30 paired tissue gastric samples were examined for ZFX gene expression by quantitative real-time RT-PCR. Although the relative expression of the gene was significantly high in 47% of the examined tumour tissues, its expression was low in the others (53%). There was a statistically significant association between the ZFX gene expression and different tumour types and grades. This is the first report that shows ZFX was differentially expressed in gastric cancer. Of note, it was overexpressed in diffused-type and grade III gastric tumoural tissues. Due to this, ZFX may have the potential to be used as a target for therapeutic interventions.

    • Leptin regulates proliferation and apoptosis of colorectal carcinoma through PI3K/Akt/mTOR signalling pathway

      Di Wang Jian Chen Hui Chen Zhi Duan Qimei Xu Meiyan Wei Lianghua Wang Meizuo Zhong

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      Epidemiological studies have indicated that obesity is associated with colorectal cancer. The obesity hormone leptin is considered as a key mediator for cancer development and progression. The present study aims to investigate regulatory effects of leptin on colorectal carcinoma. The expression of leptin and its receptor Ob-R was examined by immunohistochemistry in 108 Chinese patients with colorectal carcinoma. The results showed that leptin/Ob-R expression was significantly associated with T stage, TNM stage, lymph node metastasis, distant metastasis, differentiation and expression of p-mTOR, p-70S6 kinase, and p-Akt. Furthermore, the effects of leptin on proliferation and apoptosis of HCT-116 colon carcinoma cells were determined. The results showed that leptin could stimulate the proliferation and inhibit the apoptosis of HCT-116 colon cells through the PI3K/Akt/mTOR pathway. Ly294002 (a PI3K inhibitor) and rapamycin (an mTOR inhibitor) could prevent the regulatory effects of leptin on the proliferation and apoptosis of HCT-116 cells via abrogating leptin-mediated PI3K/Akt/mTOR pathway. All these results indicated that leptin could regulate proliferation and apoptosis of colorectal carcinoma through the PI3K/Akt/mTOR signalling pathway.

    • Expression, purification and characterization of the interferon-inducible, antiviral and tumour-suppressor protein, human RNase L

      Ankush Gupta Pramod C Rath

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      The interferon (IFN)-inducible, 2′,5′-oligoadenylate (2-5A)-dependent ribonuclease L (RNase L) plays key role in antiviral defense of mammalian cells. Induction by IFN and activation by double-stranded RNA lead to 2-5A cofactor synthesis, which activates RNase L by causing its dimerization. Active RNase L degrades single-stranded viral as well as cellular RNAs causing apoptosis of virus-infected cells. Earlier, we had reported that expression of recombinant human RNase L caused RNA-degradation and cell-growth inhibition in E. coli without the need for exogenous 2-5A. Expression of human RNase L in E. coli usually leads to problems of leaky expression, low yield and degradation of the recombinant protein, which demands number of chromatographic steps for its subsequent purification thereby, compromising its biochemical activity. Here, we report a convenient protocol for expression of full-length, soluble and biochemically active recombinant human RNase L as GST-R Nase L fusion protein from E. coli utilizing a single-step affinity purification with an appreciable yield of the highly purified protein. Recombinant R Nase L was characterized by SDS-PAGE, immunoblotting and MALDI-TOF analysis. A semi-quantitative agarose-gel-based ribonuclease assay was developed for measuring its 2-5A-dependent R Nase L activity against cellular large rRNAs as substrates. The optimized expression conditions minimized degradation of the protein, making it a convenient method for purification of R Nase L, which can be utilized to study effects of various agents on the R Nase L activity and its protein–protein interactions.

    • Corticoadrenal activity in rat regulates betaine-homocysteine S-methyltransferase expression with opposite effects in liver and kidney

      Osvaldo Fridman Analía V Morales Laura E Bortoni Paula C Turk-Noceto Elio A Prieto

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      Betaine-homocysteine 𝑆-methyltransferase (BHMT) is an enzyme that converts homocysteine (Hcy) to methionine using betaine as a methyl donor. Betaine also acts as osmolyte in kidney medulla, protecting cells from high extracellular osmolarity. Hepatic BHMT expression is regulated by salt intake. Hormones, particularly corticosteroids, also regulate BHMT expression in rat liver. We investigated to know whether the corticoadrenal activity plays a role in kidney BHMT expression. BHMT activity in rat kidneys is several orders of magnitude lower than in rat livers and only restricted to the renal cortex. This study confirms that corticosteroids stimulate BHMT activity in the liver and, for the first time in an animal model, also up-regulate the BHMT gene expression. Besides, unlike the liver, corticosteroids in rat kidney down-regulate BHMT expression and activity. Given that the classical effect of adrenocortical activity on the kidney is associated with sodium and water re-absorption by the distal tubule leading to volume expansion, by promoting lesser use of betaine as a methyl donor, corticosteroids would preserve betaine for its other role as osmoprotectant against changes in the extracellular osmotic conditions. We conclude that corticosteroids are, at least in part, responsible for the inhibition of BHMT expression and activity in rat kidneys.

    • Transient expression of Human papillomavirus type 16 L2 epitope fused to N- and C-terminus of coat protein of Potato virus X in plants

      Noemi Cerovska Hana Hoffmeisterova Tomas Moravec Helena Plchova Jitka Folwarczna Helena Synkova Helena Ryslava Viera Ludvikova Michal Smahel

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      Transient expression of foreign genes based on plant viral vectors is a suitable system for the production of relevant immunogens that can be used for the development of a new generation of vaccines against a variety of infectious diseases. In the present study the epitope derived from HPV-16 L2 minor capsid protein (amino acids 108–120) was expressed from Potato virus X (PVX)-based vector pGR106 as N- or C-terminal fusion with the PVX coat protein (PVX CP) in transgenic Nicotiana benthamiana plants. The fusion protein L2108-120-PVX CP was successfully expressed in plants at a level of 170 mg/kg of fresh leaf tissue. The C-terminal fusion protein PVX CP- L2108-120 was expressed using mutated vector sequence to avoid homologous recombination at a level of 8 mg/kg of fresh leaf tissue. Immunogenicity of L2108-120-PVX CP virus-like particles was tested after immunization of mice by subcutaneous injection or tattoo administration. In animal sera the antibodies against the PVX CP and the L2108-120 epitope were found after both methods of vaccine delivery.

    • Development of transgenic finger millet (Eleusine coracana (L.) Gaertn.) resistant to leaf blast disease

      S Ignacimuthu S Antony Ceasar

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      Finger millet plants conferring resistance to leaf blast disease have been developed by inserting a rice chitinase (chi11) gene through Agrobacterium-mediated transformation. Plasmid pHyg-Chi.11 harbouring the rice chitinase gene under the control of maize ubiquitin promoter was introduced into finger millet using Agrobacterium strain LBA4404 (pSB1). Transformed plants were selected and regenerated on hygromycin-supplemented medium. Transient expression of transgene was confirmed by GUS histochemical staining. The incorporation of rice chitinase gene in R0 and R1 progenies was confirmed by PCR and Southern blot analyses. Expression of chitinase gene in finger millet was confirmed by Western blot analysis with a barley chitinase antibody. A leaf blast assay was also performed by challenging the transgenic plants with spores of Pyricularia grisea. The frequency of transient expression was 16.3% to 19.3%. Stable frequency was 3.5% to 3.9%. Southern blot analysis confirmed the integration of 3.1 kb chitinase gene. Western blot analysis detected the presence of 35 kDa chitinase enzyme. Chitinase activity ranged from 19.4 to 24.8. In segregation analysis, the transgenic R1 lines produced three resistant and one sensitive for hygromycin, confirming the normal Mendelian pattern of transgene segregation. Transgenic plants showed high level of resistance to leaf blast disease compared to control plants. This is the first study reporting the introduction of rice chitinase gene into finger millet for leaf blast resistance.

    • Molecular cytogenetic identification of a novel dwarf wheat line with introgressed Thinopyrum ponticum chromatin

      Guiling Chen Q I Zheng Yinguang Bao Shubing Liu Honggang Wang Xingfeng Li

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      Novel dwarfing germplasms and dwarfing genes are valuable for the wheat breeding. A novel semi-dwarf line, 31505-1, with reduced height compared with its common wheat parent, was derived from a cross between common wheat and Thinopyrum ponticum. Cytological studies demonstrated that 31505-1 contained 42 chromosomes and formed 21 bivalents at meiotic metaphase I. Genomic in situ hybridization (GISH) analysis showed that 31505-1 had no large Th. ponticum chromosome fragments. Fluorescence in situ hybridization (FISH) results revealed the absence of a pAs1 hybridization band on 2DL chromosome of 31505-1. Two SSR markers (Xwmc41 and Xcfd168) and two STS markers (Xmag4059 and Xmag3596), which were located on 2D chromosome, amplified unique bands of Th. Ponticum in 31505-1. These revealed presence of an introgressed Th. ponticum segment in 2DL chromosome of dwarf line 31505-1, although the alien segment could not be detected by GISH.

    • Autophagy: A double-edged sword in Alzheimer's disease

      Ying-Tsen Tung Bo-Jeng Wang Ming-Kuan Hu Wen-Ming Hsu Hsinyu Lee Wei-Pang Huang Yung-Feng Liao

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      Autophagy is a major protein degradation pathway that is essential for stress-induced and constitutive protein turnover. Accumulated evidence has demonstrated that amyloid-𝛽 (A𝛽) protein can be generated in autophagic vacuoles, promoting its extracellular deposition in neuritic plaques as the pathological hallmark of Alzheimer’s disease (AD). The molecular machinery for A𝛽 generation, including APP, APP-C99 and 𝛽-/𝛾-secretases, are all enriched in autophagic vacuoles. The induction of autophagy can be vividly observed in the brain at early stages of sporadic AD and in an AD transgenic mouse model. Accumulated evidence has also demonstrated a neuroprotective role of autophagy in mediating the degradation of aggregated proteins that are causative of various neurodegenerative diseases. Autophagy is thus widely regarded as an intracellular hub for the removal of the detrimental A𝛽 peptides and Tau aggregates. Nonetheless, compelling data also reveal an unfavorable function of autophagy in facilitating the production of intracellular A𝛽. The two faces of autophagy on the homeostasis of A𝛽 place it in a very unique and intriguing position in ADpathogenesis. This article briefly summarizes seminal discoveries that are shedding new light on the critical and unique roles of autophagy in AD and potential therapeutic approaches against autophagy-elicited AD.

    • Recent advances in development of marker-free transgenic plants: Regulation and biosafety concern

      Narendra Tuteja Shiv Verma Ranjan Kumar Sahoo Sebastian Raveendar In Bheema Lingeshwara Reddy

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      During the efficient genetic transformation of plants with the gene of interest, some selectable marker genes are also used in order to identify the transgenic plant cells or tissues. Usually, antibiotic- or herbicide-selective agents and their corresponding resistance genes are used to introduce economically valuable genes into crop plants. From the biosafety authority and consumer viewpoints, the presence of selectable marker genes in released transgenic crops may be transferred to weeds or pathogenic microorganisms in the gastrointestinal tract or soil, making them resistant to treatment with herbicides or antibiotics, respectively. Sexual crossing also raises the problem of transgene expression because redundancy of transgenes in the genome may trigger homology-dependent gene silencing. The future potential of transgenic technologies for crop improvement depends greatly on our abilities to engineer stable expression of multiple transgenic traits in a predictable fashion and to prevent the transfer of undesirable transgenic material to non-transgenic crops and related species. Therefore, it is now essential to develop an efficient marker-free transgenic system. These considerations underline the development of various approaches designed to facilitate timely elimination of transgenes when their function is no longer needed. Due to the limiting number of available selectable marker genes, in future the stacking of transgenes will be increasingly desirable. The production of marker-free transgenic plants is now a critical requisite for their commercial deployment and also for engineering multiple and complex trait. Here we describe the current technologies to eliminate the selectablemarker genes (SMG) in order to develop marker-free transgenic plants and also discuss the regulation and biosafety concern of genetically modified (GM) crops.

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