On the origin of life

The origin of life is a very rich field, filled with possibilities and ripe for discovery. RNA replication requires chemical energy and vesicle division is easy to do with mechanical energy. These requirements point to a surface lake, perhaps at some time following the period of concentrated cyanide chemistry that gave rise to nucleotides, amino acids and (maybe) fatty acids. A second requirement follows specifically from the nature of the RNA replication cycle, which requires generally cool to moderate temperatures for the copying chemistry, punctuated by brief periods of high temperature for strand separation. Remarkably, lakes in a geothermal active area provide just such a fluctuating temperature environment, because lakes similar to Yellowstone can be generally cool (even ice covered in winter), but they contain numerous hydrothermal vents that emit streams of hot water. Protocells in such an environment would occasionally be swept into these hot water streams, where the transient high temperature exposure would cause RNA strand separation. However, the protocells would be quickly mixed with surrounding cold water, and would therefore cool quickly, before their delicate RNA molecules could be destroyed by heat. Because of the combination of favorable chemical and physical environments, this could be the most likely scenario for the early Earth environment that nurtured the origin of life.

El origen de la vida es un campo lleno de posibilidades, listas para ser descubiertas. Basados en lo conocido sobre modelos de sistemas de membranas y sobre ARN, se comienza a deducir algunas características necesarias del entorno inicial. La replicación del ARN requiere energía química y la división de la vesícula es fácil de hacer con la energía mecánica. Estos requisitos apuntan a la superficie de un lago, en algún momento después del período en que la química del cianuro concentrado dio origen a los nucleótidos, aminoácidos y (tal vez) ácidos grasos. Un segundo requisito surge de la naturaleza del ciclo de replicación del ARN, que requiere temperaturas moderadas para la química de la copia, interrumpidas por breves períodos de alta temperatura para la separación en hebras. Solo lagos en una zona de actividad geotérmica proporcionan un ambiente de temperatura tan oscilante, lagos similares a Yellowstone pueden ser frescos (cubiertos de hielo en invierno), pero contienen numerosas fuentes hidrotermales que emiten chorros de agua caliente. Las protocélulas, en un ambiente así, de vez en cuando serían barridas en estas corrientes de alta temperatura, que podrían causar la separación transitoria de ARN de cadena. Pero las protocélulas serían mezcladas con rapidez en la zona de agua fría, y enfriarse antes de que sus delicadas moléculas de ARN fueran destruidas por el calor. La combinación de estos ambientes químicos y físicos favorables serían el escenario más probable del medio ambiente de la Tierra temprana que nutrió el origen de la vida.

Theoretical analysis of noncanonical base pairing interactions in RNA molecules.

Noncanonical base pairs in RNA have strong structural and functional implications but are currently not considered for secondary structure predictions. We present results of comparative ab initio studies of stabilities and interaction energies for the three standard and 24 selected unusual RNA base pairs reported in the literature. Hydrogen added models of isolated base pairs, with heavy atoms frozen in their 'away from equilibrium' geometries, built from coordinates extracted from NDB, were geometry optimized using HF/6-31G** basis set, both before and after unfreezing the heavy atoms. Interaction energies, including BSSE and deformation energy corrections, were calculated, compared with respective single point MP2 energies, and correlated with occurrence frequencies and with types and geometries of hydrogen bonding interactions. Systems having two or more N-H...O/N hydrogen bonds had reasonable interaction energies which correlated well with respective occurrence frequencies and highlighted the possibility of some of them playing important roles in improved secondary structure prediction methods. Several of the remaining base pairs with one N-H...O/N and/or one C-H...O/N interactions respectively, had poor interaction energies and negligible occurrences. High geometry variations on optimization of some of these were suggestive of their conformational switch like characteristics.

Optimization of RQRT-pCR protocols to measure beta-1,3-glucanase mRNA levels in infected tissues of rubber tree (Hevea brasiliensis).

RQRT-PCR technique was evaluated for its validity as an alternative to Northern blotting for quantification of plant gene expression in diseased tissues of Hevea. Reliable RT-PCR results could be obtained by co-amplification of housekeeping actin gene as the internal control along with the gene of interest. The product of interest was quantified relative to that of the internal control by measuring net intensity of bands. Expression levels of defense-related beta-1,3-glucanase gene was studied in the pathogen infected tissues of rubber. The beta-1,3-glucanase gene was found to be induced in infected leaf tissues and reached a peak at 48 h after inoculation. The beta-1,3-glucanase gene expression during pathogen infection was determined through Northern blot hybridization also, using 18S RNA as the internal control. RQRT-PCR and Northern hybridization showed almost similar results, thereby validating the use of this technique to study the gene expression in rubber.

Effect of estradiol on expression of cytoskeletal proteins during spermatogenesis in testis of sexually mature rats.

Earlier studies had shown that long term treatment with estradiol arrests spermatogenesis in adult male rats, at a dose of 0.1 mg/kg/day. The present study was therefore undertaken to ascertain the causes underlying the reduction in sperm counts by administering estradiol for a short term, at the dose of 0.1 mg/kg/day. Estradiol valerate was injected at a dose of 0.1 mg/kg/day, for a period of 10 days to one group of adult male rats, which were administered saline for 12 days prior to estradiol injection, and sacrificed after 22 days. The control group was administered saline for 22 days. The sera were analyzed for testosterone and FSH levels. One testis of each male was immersion fixed for histology, and for immunohistochemistry of two testicular cytoskeletal proteins, vimentin and vinculin. The contralateral testes were used for analysis of vimentin and vinculin gene expression by reverse transcriptase polymerase chain reaction (RTPCR) and western blotting. Another group exposed to estradiol for 10 days was injected with bromodeoxyuridine (BrdU), at a dose of 100 mg/kg/day, to ascertain the effect on germ cell proliferation, and sacrificed 12 days later, while estradiol treatment was continued till sacrifice. BrdU, at a dose of 100 mg/kg/day was injected i.p. to a group of control rats treated with saline for 10 days, and sacrificed 12 days later. The testes from both groups were immersion fixed for immunohistochemical detection of BrdU. Histology of estradiol treated testis showed predominance of tubules with round spermatids with accumulation of lipid droplets in Sertoli cell cytoplasm and decreased cell height, whereas controls showed elongating spermatids. BrdU immunolocalization in the testis, irrespective of treatment, indicated its incorporation in deoxyribonucleic acid (DNA) suggesting that estradiol sustained germ cell proliferation. Both vimentin and vinculin could be immunolocalized to the testis. The testicular levels of vimentin and vinculin, quantified after western blotting, were unaffected. The testicular expression of vimentin and vinculin seen by RTPCR was also unaffected. The study suggested that estradiol induced reduction in sperm counts was not due to adverse effects on proliferation. The observed predominance of seminiferous tubules showing round spermatids, accumulation of lipid droplets as compared to controls suggested that reduction in elongated spermatids occurred through reduced spermiation and phagocytosis. The study also suggested that reduction in Sertoli cell height after short-term estradiol treatment was not due to reduced expression of vimentin and vinculin, which could be maintained by estradiol. However, reduction in Sertoli cell height could have been due to suppression of FSH and testosterone, implicated in the polymerization of vimentin and organization of vinculin, two cytoskeletal proteins involved in inter-Sertoli or Sertoli-germ cell junctions. The study suggested that disorganization of Sertoli cell cytoskeleton and reduction in the volume of Sertoli cells could be an important factor for reduced efficiency of spermatogenesis after exposure to estrogenic molecules.

When proteome meets genome: the alpha helix and the beta strand of proteins are eschewed by mRNA splice junctions and may define the minimal indivisible modules of protein architecture.

The significance of the intron-exon structure of genes is a mystery. As eukaryotic proteins are made up of modular functional domains, each exon was suspected to encode some form of module; however, the definition of a module remained vague. Comparison of pre-mRNA splice junctions with the three-dimensional architecture of its protein product from different eukaryotes revealed that the junctions were far less likely to occur inside the alpha-helices and beta-strands of proteins than within the more flexible linker regions ('turns' and 'loops') connecting them. The splice junctions were equally distributed in the different types of linkers and throughout the linker sequence, although a slight preference for the central region of the linker was observed. The avoidance of the alpha-helix and the beta-strand by splice junctions suggests the existence of a selection pressure against their disruption, perhaps underscoring the investment made by nature in building these intricate secondary structures. A corollary is that the helix and the strand are the smallest integral architectural units of a protein and represent the minimal modules in the evolution of protein structure. These results should find use in comparative genomics, designing of cloning strategies, and in the mutual verification of genome sequences with protein structures.

Evidence that the fully assembled capsid of Leishmania RNA virus 1-4 possesses catalytically active endoribonuclease activity

In this study, Leishmania RNA virus 1-4 (LRV1-4) particles purified from host Leishmania guyanensis promastigotes were examined for capsid endoribonuclease. Temperature optimum for the endoribonulease activity was found to be at 37degrees C to 42degrees C and the activity was specifically inhibited by the aminoglycoside antibiotics, neomycin, kanamycin, and hygromycin and by 100 mM levels of NaCl or KCl. To determine the catalytic domain of the capsid endoribonuclease activity, three point-mutation at cysteine residues at C47S (P1), C128/ 133S (P2), and C194R (P3) were prepared and each gene was constructed into baculoviruses and expressed in Sf9 insect cells. LRV1-4 capsid N- terminus (N2 and N3) and C-terminus (C1 and C2) deletion mutants (Cadd et al., 1994) were also examined by in vitro RNA cleavage assay. The results showed that the capsid mutants; C1, C2, N3, P1, and P2 were capable of forming proper virus-like particles (VLPs) and they all possessed the specific endoribonuclease activity. However, two assembly-defective capsid mutants, N2 (N- terminus 24-amino acids deletion) and P3 mutants, did not retain the specific endoribonuclease activity. Taken together, the results suggest that at least 24 amino acids from the N-terminal region and C194 residue in LRV1-4 capsid protein are functionally important for LRV1-4 viral assembly and the capsid endoribonuclease activity may be dependent upon the properly assembled LRV1-4 virus particles.

Exposure to genistein does not adversely affect the reproductive system in adult male mice adapted to a soy-based commercial diet

Genistein, a soybean-originated isoflavone, is widely consumed by humans for putative beneficial health effects but its estrogenic activity may affect adversely the development of male reproductive system. Five-week-old ICR mice were purchased and fed with a soybean-based Purina Chow diet until 6 months of age. The animals were exposed by gavage to genistein (2.5 mg/kg/day) or 17beta-estradiol (7.5 microgram/kg/day) for five weeks. Corn oil was used for the negative control. The animals were fed the caseinbased AIN-76A diet throughout the experimental periods. There were no significant differences in body and organ weights of mice among experimental groups. No significant differences in sperm counts and sperm motile characteristics were found between the control and the genistein groups. Treatment of 17beta-estradiol caused a significant decrease in epididymal sperm counts compared to the control (p<0.05). The level of phospholipid hydroxide glutathione peroxidase in the epididymis of mice exposed to genistein was significantly higher than that of the control mice (p<0.05). 17beta-estradiol treatment caused a reduction of germ cells in the testis and hyperplasia of mucosal fold region in the prostate of mice. Genistein treatment did not cause any lesion in the testis, epididymis, and prostate. These results suggest that dietary uptake of genistein at adult stage of life may not affect male reproductive system and functions.

An improved method for constructing a full-length enriched cDNA library using small amounts of total RNA as a starting material

We have developed an improved method for constructing a full-length cDNA library using small quantity of material by modifying the original oligo-capping method. In our devised method, total RNAs are used in sequential oligo-capping steps directly without preliminary mRNA purification. Using this method, we constructed full- length cDNA libraries from 100 microg of total RNA. These libraries contained 8x10(5) to 8x10(6) independent clones with average insert sizes of 2.0 kb. Moreover, the number of full-length cDNAs containing the translation initiation codon ATG in the constructed libraries was estimated to 60-70%. In addition, 54% of the known cDNAs had a longer 5' end than the corresponding genes in the public database. Our results show that the method can be effectively used to construct full-length enriched cDNA libraries, especially, if starting material is limited.

Phenotype of peroxisome proliferator-activated receptor-alpha(PPARalpha)deficient mice on mixed background fed high fat diet

Considerable controversy exists in determining the role of peroxisome proliferator-activated receptor-alpha(PPARalpha) on obesity. Previous reports demonstrated that PPARalpha is a critical modulator of lipid homeostasis, but the overt, obese phenotypic characterization in the strain of PPAR deficient (PPARalpha-/-) mice is influenced by other factors, including diet and genetics. Therefore, it is necessary to establish the phenotypic characterization of PPARalpha-/- mice prior to the obesity-related study. In this study, we observed phenotype of PPARalpha-/- mice on mixed genetic background (C57BL/6Nx129/Sv) fed a high fat diet for 16 weeks. PPARalpha-/- mice, regardless of sex, raised body growth rate significantly comparing with wild type and showed male-specific fatty change in the liver. They were shown to lack hepatic induction of PPARalpha target genes encoding enzymes for fatty acid beta-oxidation.

Effects of Benzoapyrene, 2-Bromopropane, Phenol and 2,3,7,8-Tetrachlorodibenzo-p-Dioxin on Proinflammatory Cytokines Gene Expression by Mice Spleen Cells

The detrimental effects of environmental pollutants on the health of the individual are generally accepted, although the mechanisms of these effects remain to be incompletely understood. In the present study, we examined the effects of B[a]P, 2-BP, phenol and TCDD on proinflammatory cytokine gene expression in mice spleen cells which were stimulated with anti-CD3. 10-9M TCDD increased IFN gammar and TNF alpha gene expression, but suppressed IL-1 gene expression. 10-6M phenol inhibited IL-1, IL-6 and TNF alpha gene expression, and 10-6M of 2-BP downregulated TNF alpha gene expression. However, 10-6M of B[a]P did not influence on IL-1, IL-6, IFN gammar and TNF alpha gene expression. These findings suggest that TCDD may impair the immune functions of mice by enhancing proinflammatory cytokines production, whereas phenol and 2-BP may impair the functions by inhibiting the production of these cytokines.

RNA and DNA aptamers as potential tools to prevent cell adhesion in disease

Recent research has shown that receptor-ligand interactions between surfaces of communicating cells are necessary prerequisites for cell proliferation, cell differentiation and immune defense. Cell-adhesion events have also been proposed for pathological conditions such as cancer growth, metastasis, and host-cell invasion by parasites such as Trypanosoma cruzi. RNA and DNA aptamers (aptus = Latin, fit) that have been selected from combinatorial nucleic acid libraries are capable of binding to cell-adhesion receptors leading to a halt in cellular processes induced by outside signals as a consequence of blockage of receptor-ligand interactions. We outline here a novel approach using RNA aptamers that bind to T. cruzi receptors and interrupt host-cell invasion in analogy to existing procedures of blocking selectin adhesion and function in vitro and in vivo

Quantitative structure activity relationship (QSAR) studies of some substituted benzenesulphonyl glutamines as tumour suppressors.

As a part of a composite programme of rational drug design (RDD), we had synthesized some substituted benzenesulphonyl glutamines and evaluated their inhibitory activities against Ehrlich Ascites Carcinoma (EAC) cell line in Swiss albino mice. Quantitative structure activity relationship (QSAR) studies of these inhibitory activities using Fujita-Ban model as well as Modified Hansch-Fujita model gave excellent correlations (correlation coefficient r = 0.89 and 0.82 respectively). These results could be useful in designing 'lead' compound with potent inhibitory activity on DNA and RNA synthesis and tumour development.

Three-stranded (triplex) DNAs (RNAs): do they have a role in biology?

The first triplexes were homopolymer mixtures, e.g. dTn.dAn.dTn. More complex triplexes could be made on the basis that the base triads [symbol: see text] and [symbol: see text] containing Watson-Crick and Hoogsteen base pairs are isomorphous and so could be expected to give regular triple helices. It follows that such triplexes can only be formed from asymmetric DNAs with pyrimidines (Yn) in one strand and purines (Rn) in the complementary strand. Such triplexes Yn.Rn.Yn are formed with the above rules for pairing of triads with the Hoogsteen C protonated, [symbol: see text]. There are also triplexes built on the theme Yn.Rn.Rn (with triads T:A:A and [symbol: see text]). Here the triads are nearly isomorphous. Recently other triplexes without isomorphous triads at all have been obtained. Also RecA protein can promote triplex formation between a duplex DNA of any sequence and an homologous single-stranded DNA. The latter triplex is evidently important in recombination. The other possible roles for triplexes include transcriptional control, and roles in origins of replication and DNA condensation.