pp 1-1 March 2013
pp 3-7 March 2013 Series
pp 9-12 March 2013 Brief communications
Continuous light could be produced from the firefly by making it inhale vapours of ethyl acetate. Here we perform such a control experiment on the Indian species of the firefly Luciola praeusta Kiesenwetter 1874 (Coleoptera : Lampyridae : Luciolinae), and analyse the light in the microsecond time scale. The amplitude of the continuous train of triangular pulses is apparently altered in accordance with the instantaneous values of a hypothetical signal, which exhibits pulse amplitude modulation (PAM). In addition to sampling in amplitude, this scheme apparently provides sampling in time, representing pulse width modulation (PWM). A Fourier transform spectrum of this waveform shows the `carrier’ frequency and the accompanying `side bands’.
pp 13-19 March 2013 Brief communications
Dormancy-breaking and seed germination studies in genus Lilium reveal that the majority of Lilium spp. studied have an underdeveloped embryo at maturity, which grows inside the seed before the radicle emerges. Additionally, the embryo, radicle or cotyledon has a physiological component of dormancy; thus, Lilium seeds have morphophysiological dormancy (MPD). A previous study suggested that seeds of Lilium polyphyllum have MPD but the study did not investigate the development of the embryo, which is one of the main criteria to determine MPD in seeds. To test this hypothesis, we investigated embryo growth and emergence of radicles and epicotyls in seeds over a range of temperatures. At maturity, seeds had underdeveloped embryos which developed fully at warm temperature within 6 weeks. Immediately after embryo growth, radicles also emerged at warm temperatures. However, epicotyls failed to emerge soon after radicle emergence. Epicotyls emerged from > 90% seeds with an emerged radicle only after they were subjected to 2 weeks of cold moist stratification. The overall temperature requirements for dormancy-breaking and seed germination indicate a non-deep simple epicotyl MPD in L. polyphyllum.
pp 21-26 March 2013 Brief communications
In India, as in other parts of the world, nonsyndromic cleft lip with or without cleft palate (NSCL±P) is a highly prevalent birth defect, its incidence in males being twice that in females. A case–control association study has been carried out with respect to homocysteine level and MTHFR C677T, A1298C and SLC19A1 (RFC1) G80A genotypes from an eastern Indian cohort to investigate whether Hcy and other Hcy-pathway genes also contribute to the risk level. While MTHFR 677T and SLC19A1 80G are individually and cumulatively risk factors, SLC19A1 80A appears to be protective against MTHFR 677T risk allele. Elevated Hcy associates with NSCL±P both in case mothers and cases. Significantly, this difference shows a gender bias: the level of elevation of Hcy in female cases is distinctly higher than in males, and more case females are hyperhomocyteinemic than the case males. It implies that compared with the males, higher level of Hcy is needed for NSCL±P to manifest in the females. We consider this as one of the possible factors why the incidence of this disorder in females is much lower than in males.
pp 27-33 March 2013 Brief communications
The long-term effects of repeated maternal separation (MS) during early postnatal life on reelin expression in the hippocampus of developing rats were investigated in the present study. MS was carried out by separating Wistar rat pups singly from their mothers for 3 h a day during postnatal days (PND) 2–14. Reelin mRNA and protein levels in the hippocampus were determined using qRT-PCR and Western blotting, at PND 22, PND 60 and PND 90. MS resulted in the loss of body weight in the developing rats, and reelin mRNA and protein levels in the hippocampus generally were down-regulated over the developing period, but the reelin mRNA and protein levels in the hippocampus of 90-day-old male rats were up-regulated. These findings suggest that the long-term effects of MS on the expression levels of hippocampal reelin mRNA and protein depends on the age at which the stressed rats’ brains were collected; reelin had important implications for the maternal-neonate interaction needed for normal brain development. In conclusion, repeated MS occurring during early postnatal life may cause the alterations of hippocampal reelin expression with the increasing age of developing rats.
pp 35-44 March 2013 Articles
Transcription of human cytomegalovirus UL/b′ region has been studied extensively for some genes. In this study, transcripts of the UL140 and UL141, two of the UL/b′ genes, were identified in late RNAs of three HCMV isolates using Northern blot hybridization, cDNA library screening and RACE-PCR. At least three transcripts with length of 2800, 2400 and 1700 nt, as well as a group of transcripts of about 1000–1300 nt, were found in this gene region with an accordant 3′ ends. Among the transcripts, two initiated upstream of the start code of the UL140 gene and contained the UL140 and UL141 open reading frame (ORF), one initiated in the middle of the UL140 gene, and could encode short ORFs upstream of the UL141 ORF. A group of transcripts initiated upstream or downstream of the start code of the UL141 gene, and could encode `nested’ ORFs, including the UL141 ORF. These `nested’ ORFs possess different initiation sites but the same termination site as that of the UL141 ORF.
pp 45-51 March 2013 Articles
Virus encoded RNA-silencing suppressors (RSSs) are the key components evolved by the viruses to counter RNA-silencing defense of plants. Whitefly-transmitted begomoviruses infecting tomato crop code for five different proteins, ORF AC4, ORF AC2 and ORF AV2 in DNA-A component, ORF BV1 in DNA-B and ORF 𝛽C1 in satellite DNA 𝛽 which are predicted to function as silencing suppressors. In the present study suppressor function of ORF 𝛽C1 of three betasatellites Tomato leaf curl Bangalore betasatellite ToLCBB-[IN:Hess:08], Cotton leaf curl Multan betasatellite CLCuMB–[IN:Sri:02] and Luffa leaf distortion betasatellite LuLDB-[IN:Lu:04] were examined. Agroinfiltration of GFP-silenced Nicotiana tabaccum cv. Xanthi with the cells expressing 𝛽C1 protein resulted in reversal of silenced GFP expression. GFP-siRNA level was more than 50-fold lower compared to silenced plants in plants infiltrated with 𝛽C1 gene from ToLCBB. However, in the case of 35S-𝛽C1 CLCuMB and 35S-𝛽C1 LuLDB construct, although GFP was expressed, siRNA level was not reduced, indicating that the step at which 𝛽C1 interfere in RNA-silencing pathway is different.
pp 53-62 March 2013 Articles
Amitraz is formamidine pesticide widely used as insecticide and acaricide. In veterinary medicine, amitraz has important uses against ticks, mites and lice on animals. Also, amitraz is used in apiculture to control Varroa destructor. It this study, the alkaline Comet assay was used to evaluate DNA damaging effects of amitraz in human lymphocytes. Isolated human lymphocytes were incubated with varying concentrations of amitraz (0.035, 0.35, 3.5, 35 and 350 𝜇g/mL). The Comet assay demonstrated that all concentrations of amitraz caused statistically significant increase in the level of DNA damage, thus indicating that amitraz possesses genotoxic potential. The concentration of amitraz that produced the highest DNA damage (3.5 𝜇g/mL) was chosen for further analysis with the antioxidant catalase. The obtained results showed that co-treatment with antioxidant catalase (100 IU/mL or 500 IU/mL) significantly reduced the level of DNA damage, indicating the possible involvement of reactive oxygen species in DNA damaging effects of amitraz. Flow cytometric analysis revealed increase of the apoptotic index following treatment with amitraz. However, co-treatment with catalase reduced the apoptotic index, while treatment with catalase alone reduced the percentage of apoptotoc cells even in comparison with the negative control. Therefore, catalase had protective effects against ROS-mediated DNA damage and apoptosis.
pp 63-71 March 2013 Articles
The SH4 domain of Src family of nonreceptor protein tyrosine kinases represents the extreme N-terminal 1–16 amino acid region which mediates membrane association of these proteins and facilitates their functions. The SH4 domains among Src members lack well-defined sequence consensus and vary in the net charge. However, they readily anchor to the cytoplasmic face of the plasma membrane upon fatty acid acylation. Here, we report the membrane association of differentially acylated SH4 domain of Lck kinase, which has net negative charge at physiological pH. Our results suggest that despite the net negative charge, the SH4 domain of Lck associates with membranes upon fatty acid acylation. While myristoylation at the N-terminus is sufficient for providing membrane anchorage, multiple acylation determines orientation of the peptide chain with respect to the lipid bilayer. Hence, fatty acylation serves more than just a lipid anchor. It has an important role in regulating the spatial orientation of the peptide domain with respect to the lipid bilayer, which could be important for the interaction of the other domains of these kinases with their partners.
pp 73-83 March 2013 Articles
Vacuolar protein sorting 1 (Vps1), the yeast homolog to human dynamin, is a GTP hydrolyzing protein, which plays an important role in protein sorting and targeting between the Golgi and late endosomal compartments. In this study, we assessed the functional significance of Vps1 in the membrane traffic towards the vacuole. We show here that vps1𝛥 cells accumulated FM4-64 to a greater extent than wild-type (WT) cells, suggesting slower endocytic degradation traffic toward the vacuole. In addition, we observed that two endosome-to-vacuole traffic markers, DsRed-FYVE and Ste2-GFP, were highly accumulated in Vps1-deficient cells, further supporting Vps1’s implication in efficient trafficking of endocytosed materials to the vacuole. Noteworthy, a simultaneous imaging analysis in conjunction with FM4-64 pulse-chase experiment further revealed that Vps1 plays a role in late endosome to the vacuole transport. Consistently, our subcellular localization analysis showed that Vps1 is present at the late endosome. The hyperaccumulation of endosomal intermediates in the vps1 mutant cells appears to be caused by the disruption of integrity of HOPS tethering complexes, manifested by mislocalization of Vps39 to the cytoplasm. Finally, we postulate that Vps1 functions together with the Endosomal Sorting Complex Required for Transport (ESCRT) complex at the late endosomal compartments, based on the observation that the double mutants, in which VPS1 along with singular ESCRT I, II and III genes have been disrupted, exhibited synthetic lethality. Together, we propose that Vps1 is required for correct and efficient trafficking from the late endosomal compartments to the vacuole.
pp 85-92 March 2013 Articles
The Y-chromosome-encoded gene RBMY (RNA-binding motif on Y) is a male germline RNA-binding protein and is postulated to be a RNA-splicing regulator. In order to understand the roles of RBMY in different stages of male gamete maturation, the present study aimed at determining its cellular expression during spermatogenesis, spermeogenesis and in mature spermatozoa. In the spermatogonia (cKIT-positive cells), RBMY immunolocalized as two distinct foci, one in the nucleolus and the other in the subnuclear region; in the spermatocytes (cKIT-negative cells), the nucleus had punctuate staining with a subnuclear foci; in the pachytene cells, the protein was localized as a punctuate pattern in the nucleus spread along the elongating chromosomes. In the round and the elongating spermatids, the protein expression was polarized and restricted to the cytoplasm and in the developing mid-piece. In testicular and ejaculated sperm, RBMY was localized to the mid-piece region and weakly in the tail. Incubation of spermatozoa with the RBMY antibody reduced its motility. The spatial differences in expression of RBMY in the germ cells and the presences of this protein in post-meiotic cells and in transcriptionally inert spermatozoa suggest its involvement in multiple functions beyond RNA splicing. One such possible function of RBMY could be its involvement in sperm motility.
pp 93-103 March 2013 Articles
Traumatic brain injury (TBI) causes significant mortality in most developing countries worldwide. At present, it is imperative to identify a treatment to address the devastating post-TBI consequences. Therefore, the present study has been performed to assess the specific effect of immediate exposure to normabaric hyperoxia (NBO) after fluid percussion injury FPI) in the striatum of mice. To execute FPI, mice were anesthetised and sorted into
a TBI group,
a sham group without injury and
a TBI group treated with immediate exposure to NBO for 3 h.
Afterwards, brains were harvested for morphological assessment. The results revealed no changes in morphological and neuronal damage in the sham group as compared to the TBI group. Conversely, the TBI group showed severe morphological changes as well as neuronal damage as compared to the TBI group exposed to NBO for 3 h. Interestingly, our findings also suggested that NBO treatment could diminish the neuronal damage in the striatum of mice after FPI. Neuronal damage was evaluated at different points of injury and the neighbouring areas using morphology, neuronal apoptotic cell death and pan-neuronal markers to determine the complete neuronal structure. In conclusion, immediate exposure to NBO following FPI could be a potential therapeutic approach to reduce neuronal damage in the TBI model.
pp 105-112 March 2013 Articles
Mammalian SFMBTs have been considered to be polycomb group repressors. However, molecular mechanisms underlying mammalian SFMBTs-mediated gene regulation and their biological function have not been characterized. In the present study, we identified YY1 and methylated histones as interacting proteins of human SFMBT2. We also found that human SFMBT2 binds preferentially to methylated histone H3 and H4 that are associated with transcriptional repression. Using DU145 prostate cancer cells as a model, we showed that SFMBT2 has a transcriptional repression activity on HOXB13 gene expression. In addition, occupancy of SFMBT2 coincided with enrichment of diand tri-methylated H3K9 and H4K20 as well as tri-methylated H3K27 at the HOXB13 gene promoter. When SFMBT2 was depleted by siRNA in DU145 prostate cancer cells, significant up-regulation of HOXB13 gene expression and decreased cell growth were observed. Collectively, our findings indicate that human SFMBT2 may regulate cell growth via epigenetic regulation of HOXB13 gene expression in DU145 prostate cancer cells.
pp 113-122 March 2013 Articles
Telomere shortening is emerging as a biological indicator of accelerated aging and aging-related diseases including type 2 diabetes. While telomere length measurements were largely done in white blood cells, there is lack of studies on telomere length in relation to oxidative stress in target tissues affected in diabetes. Therefore, the aim of this study is to induct oxidative stress in adipocytes and to test whether these adipocytes exhibit shortened telomeres, senescence and functional impairment. 3T3-L1 adipocytes were subjected to oxidative stress and senescence induction by a variety of means for 2 weeks (exogenous application of H2O2, glucose oxidase, asymmetric dimethylarginine (ADMA) and glucose oscillations). Cells were probed for reactive oxygen species generation (ROS), DNA damage, mRNA and protein expression of senescent and pro-inflammatory markers, telomere length and glucose uptake. Compared to untreated cells, both ROS generation and DNA damage were significantly higher in cells subjected to oxidative stress and senescence. Adipocytes subjected to oxidative stress also showed shortened telomeres and increased mRNA and protein expression of p53, p21, TNF𝛼 and IL-6. Senescent cells were also characterized by decreased levels of adiponectin and impaired glucose uptake. Briefly, adipocytes under oxidative stress exhibited increased ROS generation, DNA damage, shortened telomeres and switched to senescent/pro-inflammatory phenotype with impaired glucose uptake.
pp 123-134 March 2013 Articles
Millions of people world over suffer visual disability due to retinal dystrophies which can be age-related or a genetic disorder resulting in gradual degeneration of the retinal pigmented epithelial (RPE) cells and photoreceptors. Therefore, cell replacement therapy offers a great promise in treating such diseases. Since the adult retina does not harbour any stem cells, alternative stem cell sources like the embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) offer a great promise for generating different cell types of the retina. Here, we report the derivation of four iPSC lines from mouse embryonic fibroblasts (MEFs) using a cocktail of recombinant retroviruses carrying the genes for Oct4, Sox2, Klf4 and cMyc. The iPS clone MEF-4F3 was further characterized for stemness marker expression and stable reprogramming by immunocytochemistry, FACS and RT-PCR analysis. Methylation analysis of the nanog promoter confirmed the reprogrammed epigenetic state. Pluripotency was confirmed by embryoid body (EB) formation and lineage-specific marker expression. Also, upon retinal differentiation, patches of pigmented cells with typical cobble-stone phenotype similar to RPE cells are generated within 6 weeks and they expressed ZO-1 (tight junction protein), RPE65 and bestrophin (mature RPE markers) and showed phagocytic activity by the uptake of fluorescent latex beads.
pp 135-147 March 2013 Articles
The aim of this study was to investigate the effects of Raloxifene (Ral) on degeneration-related changes in osteoarthritis (OA)-like chondrocytes using two- and three-dimensional models. Five-azacytidine (Aza-C) was used to induce OA-like alterations in rat articular chondrocytes and the model was verified at molecular and macrolevels. Chondrocytes were treated with Ral (1, 5 and 10 𝜇M) for 10 days. Caspase-3 activity, gene expressions of aggrecan, collagen II, alkaline phosphatase (ALP), collagen X, matrix metalloproteinases (MMP-13, MMP-3 and MMP-2), and MMP-13, MMP-3 and MMP-2 protein expressions were studied in two-dimensional model. Matrix deposition and mechanical properties of agarose-chondrocyte discs were evaluated in three-dimensional model. One 𝜇M Ral reduced expression of OA-related genes, decreased apoptosis, and MMP-13 and MMP-3 protein expressions. It also increased aggrecan and collagen II gene expressions relative to untreated OA-like chondrocytes. In three-dimensional model, 1 𝜇M Ral treatment resulted in increased collagen deposition and improved mechanical properties, although a significant increase for sGAG was not observed. In summation, 1 𝜇M Ral improved matrix-related activities, whereas dose increment reversed these effects except ALP gene expression and sGAG deposition. These results provide evidence that low-dose Ral has the potential to cease or reduce the matrix degeneration in OA.
pp 149-156 March 2013 Articles
Seeding dispersal is an active detachment exhibit in aging Pseudomonas aeruginosa biofilm. Yet, effect factors of this process in the biofilm of clinical isolated mucoid P. aeruginosa strain remain to be better characterized. In our previous work, one mucoid P. earuginosa strain PA17 was isolated from a patient with recurrent pulmonary infection. In this study, confocal scanning laser microscope combined with LIVE/DEAD viability staining revealed that PA17 biofilm exhibited earlier seeding dispersal than non-mucoid PAO1. We further compared the motility and the expression of motility-associated gene during biofilm development between PA17 and PAO1. PA17 was found to be impaired in all three kinds of motility compared to PAO1. Moreover, we investigated the expression of rhamnolipid-associated genes in PA17 and PAO1 biofilm. The expression of these genes was in accordance with the process of seeding dispersal. Our results indicated that rhamnolipid but not motility is associated with the initiation of seeding dispersal of PA17 biofilm.
pp 157-166 March 2013 Articles
Seagrass ecosystems provide unique coastal habitats critical to the life cycle of many species. Seagrasses are a major store of organic carbon. While seagrasses are globally threatened and in decline, in Cairns Harbour, Queensland, on the tropical east coast of Australia, they have flourished. We assessed seagrass distribution in Cairns Harbour between 1953 and 2012 from historical aerial photographs, Google map satellite images, existing reports and our own surveys of their distribution. Seasonal seagrass physiology was assessed through gross primary production, respiration and photosynthetic characteristics of three seagrass species, Cymodocea serrulata, Thalassia hemprichii and Zostera muelleri. At the higher water temperatures of summer, respiration rates increased in all three species, as did their maximum rates of photosynthesis. All three seagrasses achieved maximum rates of photosynthesis at low tide and when they were exposed. For nearly six decades there was little change in seagrass distribution in Cairns Harbour. This was most likely because the seagrasses were able to achieve sufficient light for growth during intertidal and low tide periods. With historical data of seagrass distribution and measures of species production and respiration, could seagrass survival in a changing climate be predicted? Based on physiology, our results predicted the continued maintenance of the Cairns Harbour seagrasses, although one species was more susceptible to thermal disturbance. However, in 2011 an unforeseen episodic disturbance – Tropical Cyclone Yasi – and associated floods lead to the complete and catastrophic loss of all the seagrasses in Cairns Harbour.
pp 167-172 March 2013 Articles
Genomic DNA isolation in cotton is complicated because of the presence of secondary metabolites that are inhibitory to PCR amplification. We report here that radicle tips, but not other parts of cotton seedlings, yield high-quality DNA that is readily amenable for PCR. The radicle-tip-excised seedlings retain viability because of the formation of adventitious roots. We demonstrate the utility of this method in distinguishing homozygotes from heterozygotes in a cotton breeding population and in hybrid seed purity testing.
pp 173-177 March 2013 Articles
A palindrome is a set of characters that reads the same forwards and backwards. Since the discovery of palindromic peptide sequences two decades ago, little effort has been made to understand its structural, functional and evolutionary significance. Therefore, in view of this, an algorithm has been developed to identify all perfect palindromes (excluding the palindromic subset and tandem repeats) in a single protein sequence. The proposed algorithm does not impose any restriction on the number of residues to be given in the input sequence. This avant-garde algorithm will aid in the identification of palindromic peptide sequences of varying lengths in a single protein sequence.
pp 179-179 March 2013 Erratum
A tissue-specific cDNA library was constructed using polyA+ RNA from pituitary glands of the Indian catfish Heteropneustes fossilis (Bloch) and a cDNA clone encoding growth hormone (GH) was isolated. Using polymerase chain reaction (PCR) primers representing the conserved regions of fish GH sequences the 3′ region of catfish GH cDNA (540 bp) was cloned by random amplification of cDNA ends and the clone was used as a probe to isolate recombinant phages carrying the full-length cDNA sequence. The full-length cDNA clone is 1132 bp in length, coding for an open reading frame (ORF) of 603 bp; the reading frame encodes a putative polypeptide of 200 amino acids including the signal sequence of 22 amino acids. The 5′ and 3′ untranslated regions of the cDNA are 58 bp and 456 bp long, respectively. The predicted amino acid sequence of H. fossils GH shared 98% homology with other catfishes. Mature GH protein was efficiently expressed in bacterial and zebrafish systems using appropriate expression vectors. The successful expression of the cloned GH cDNA of catfish confirms the functional viability of the clone.
Volume 45, 2020
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