Meta-analysis to Unravel Core Transcriptomic Responses in Penaeus vannamei Exposed to Biotic and Abiotic Stresses

Shrimp farming, a dominant economic activity in coastal areas, is affected by different abiotic and biotic stress factors. These stressors, under poor management conditions, could affect growth and health of farmed animals. Understanding the common gene expressions in response to stress, regardless of the specific stress factor, holds significant importance in the field of functional genomics. Scope of this study is to identify the core transcriptomic responses in the shrimp species Penaeus vannamei exposed to various abiotic and biotic stress conditions and to decipher their functional importance. To achieve our objective, we gathered and analyzed multiple RNA-seq datasets related to twelve abiotic and nine biotic stress conditions. Through the in silico meta-analysis, we predicted 961 differentially expressed genes (meta-DEGs) for abiotic stress conditions and 517 meta-DEGs for biotic stress conditions, respectively. These meta-DEGs represent genes that are commonly expressed across different stress factors and are indicative of the organism's general response to stress. The annotation of nineteen core up-regulated meta-DEGs revealed their diverse functions in detoxification, cell adhesion, metal ion binding, and oxidative phosphorylation. These genes play a crucial role in stress response and immune defense. For abiotic stress, significant pathways associated with the stress response include tryptophan metabolism, starch and sucrose metabolism, fatty acid degradation, carbohydrate digestion and absorption, phenylalanine metabolism, drug metabolism-other enzymes, arachidonic acid metabolism, and fatty acid elongation. Similarly, for biotic stress, metabolism of xenobiotics by cytochrome P450, pentose and glucuronate interconversions, steroid hormone biosynthesis, and drug metabolism-cytochrome P450 were found to be significant pathway associations. In addition, the study also predicted 17 stress regulatory motifs present in the identified meta-DEGs. These motifs have significance in identifying the stress responses of the organism. The metabolic pathways and regulatory motifs associated with abiotic and biotic stress factors identified through this study could be a valuable resource for developing stress management approaches in shrimp aquaculture.

A helium-burning white dwarf binary as a supersoft X-ray source

Type Ia supernovae are cosmic distance indicators1,2, and the main source of iron in the Universe3,4, but their formation paths are still debated. Several dozen supersoft X-ray sources, in which a white dwarf accretes hydrogen-rich matter from a non-degenerate donor star, have been observed5 and suggested as Type Ia supernovae progenitors6-9. However, observational evidence for hydrogen, which is expected to be stripped off the donor star during the supernova explosion10, is lacking. Helium-accreting white dwarfs, which would circumvent this problem, have been predicted for more than 30 years (refs. 7,11,12), including their appearance as supersoft X-ray sources, but have so far escaped detection. Here we report a supersoft X-ray source with an accretion disk whose optical spectrum is completely dominated by helium, suggesting that the donor star is hydrogen-free. We interpret the luminous and supersoft X-rays as resulting from helium burning near the surface of the accreting white dwarf. The properties of our system provide evidence for extended pathways towards Chandrasekhar-mass explosions based on helium accretion, in particular for stable burning in white dwarfs at lower accretion rates than expected so far. This may allow us to recover the population of the sub-energetic so-called Type Iax supernovae, up to 30% of all Type Ia supernovae13, within this scenario.

Green Synthesis of Silver Nanoparticles of Vernonia cinerea Leaf Extract and their In vitro Cytotoxicity Activity against Neuroblastoma SHSY-5Y Cell Lines, Antimicrobial and Antioxidant Studies

BACKGROUND

Green syntheses of silver nanoparticles using plant extracts have potential anti- cancer, antimicrobial, and antioxidant properties, among other aspects. The aim of the present patent study was to synthesize silver nanoparticles (AgNPs) using Vernonia cinerea plant extract.

METHODS

The AgNPs were successfully prepared and characterized using UV-Vis Spectrophotometer, particle size, Zeta potential, Transmission electron microscopy (TEM), Energy-dispersive x-ray analysis (EDAX), X-ray diffraction (XRD), and Fourier transform infrared (FTIR) spectrometry. The in vitro cytotoxicity study was performed using neuroblastoma SHSY-5Y cell lines. Moreover, antimicrobial and antioxidant activity studies were also performed for AgNPs.

RESULTS

The size of AgNPs determined through the dynamic light scattering (DLS) technique was 49.5 nm and the zeta potential was -36.8 mV. The synthesized AgNPs were checked using UV-Visible spectroscopy at ƛmax 439 nm. The color was changed from green to dark brown, indicating the formation of AgNPs. The TEM study revealed that the nanoparticles were spherical in shape. The XRD pattern of AgNPs produced in this experiment was apparently crystalline. The results of FTIR study revealed that the majority of the obtained peaks correspond to the polyphenols, triterpenoids, and alkaloids which were abundant in the corresponding to the V. cinerea leaf extract and support to the formation of AgNPs. The cytotoxicity effect of the V. cinerea plant extract and biosynthesized AgNPs was found to be dosedependent. From the results of antimicrobial studies, it was reported that the gram negative bacteria were found to be more susceptible compared to the gram positive bacteria. Moreover, the results of antioxidant study revealed that the AgNPs showed good antioxidant activity (77.21%) in comparison to the V. cinerea plant extract (56.13%).

CONCLUSION

Based on the results, it could be concluded that the green synthesized silver nanoparticles showed promising anticancer, antioxidant, and anti-bacterial activities as compared to the plain V. cineria plant extract.

Effect of ethanol/trisodium citrate lock on the mechanical properties of carbothane hemodialysis catheters

AIMS

The objective of this study was to investigate the effect of three locking solutions on the mechanical properties of carbothane hemodialysis catheters.

METHODS

Catheters were exposed in vitro to one of three locking solutions (heparin 5000 U/ml; 4% trisodium citrate (TSC) or 30% ethanol/4% TSC). Each solution was locked in six catheters and bathed at 37 degrees C for 9 weeks. Changes in the mechanical properties namely, force at break, elongation at break and elastic modulus of the catheters were determined by tensile testing.

RESULTS

The ethanol/TSC lock has an effect on the properties of carbothane hemodialysis catheters. The force at break was significantly lower in the ethanol/TSC group compared to the heparin and TSC groups (113.26 N, 191.97 N and 229.72 N, respectively, p < 0.01). Similarly, elongation at break was lower in the ethanol/TSC group, compared to the heparin and TSC groups (stretched 21.97, 38.29, and 42.42 times original length respectively, p < 0.01). The elastic modulus was not significantly different.

CONCLUSIONS

The effect of the ethanol/TSC lock on the catheters is unlikely to prohibit clinical use. After 9 weeks of exposure to the solution, the catheter segments could still be stretched to 22 times their length and withstand 11.5 kg (113 N) of force. Clinically produced forces during dialysis are many times smaller than the force required to break the catheters examined in this study. Therefore, the ethanol/TSC lock shows promise as a new catheter locking solution for the treatment of catheter-related infections. Further clinical studies are required.

Allele-specific suppression of the temperature sensitivity of fitA/fitB mutants of Escherichia coli by a new mutation (fitC4): isolation, characterization and its implications in transcription control

The temperature sensitive transcription defective mutant of Escherichia coli originally called fitA76 has been shown to harbour two missense mutations namely pheS5 and fit95. In order to obtain a suppressor of fitA76, possibly mapping in rpoD locus, a Ts+ derivative (JV4) was isolated from a fitA76 mutant. It was found that JV4 neither harbours the lesions present in the original fitA76 nor a suppressor that maps in or near rpoD. We show that JV4 harbours a modified form of fitA76 (designated fitA76*) together with its suppressor. The results presented here indicate that the fit95 lesion is intact in the fitA76* mutant and the modification should be at the position of pheS5. Based on the cotransduction of the suppressor mutation and/or its wild type allele with pps, aroD and zdj-3124::Tn10 kan we have mapped its location to 39.01 min on the E. coli chromosome. We tentatively designate the locus defined by this new extragenic suppressor as fitC and the suppressor allele as fitC4. While fitC4 could suppress the Ts phenotype of fitA76* present in JV4, it fails to suppress the Ts phenotype of the original fitA76 mutant (harbouring pheS5 and fit95). Also fitC4 could suppress the Ts phenotype of a strain harbouring only pheS5. Interestingly, the fitC4 Ts phenotype could also be suppressed by fit95. The pattern of decay of pulse labelled RNA in the strains harbouring fitC4 and the fitA76* resembles that of the original fitA76 mutant implying a transcription defect similar to that of fitA76 in both these mutants. The implications of these findings with special reference to transcription control by Fit factors in vivo are discussed.

Leads to cancer control based on cancer patterns in a rural population in South India

OBJECTIVE

Cancer patterns and incidence rates for a rural population (359,674) resident in 384 villages spread over 2058 km2 in Palani and Oddanchathram taluks of Dindigul District, Tamil Nadu, in South India, are described in this paper.

METHODS

A population-based cancer registry was established in 1995 to register incident invasive and in-situ cancers. Cases were found and details abstracted by cancer registry staff visiting 26 data sources, comprising cancer hospitals, tertiary and secondary care hospitals, pathology laboratories and death registration offices. A customized version of CANREG-3 software was used for data entry and analysis.

RESULTS

During the period 1996-1998, 783 invasive cancers (310 male and 473 females) were registered, yielding an all-cancer crude incidence rate of 56.8/100,000 males and 88.5/100,000 females; the corresponding age standardized incidence rates (ASR) were 83.3 and 122.3 respectively. In males, mouth cancer (ASR 11.5) was the most frequently recorded malignancy followed by tongue (ASR 8.6), hypopharynx (ASR 7.8), esophagus (ASR 7.8) and larynx (ASR 7.8). Thus head and neck cancers accounted for half of the male cases. In females, cervical cancer (ASR 65.4) accounted for more than half of the cancers followed by breast (ASR 14.2) and mouth (ASR 10.2). Ambillikai Cancer Registry (ACR) reports the second highest incidence of cervical cancer in the world. More than four-fifths of cervical cancer cases were diagnosed in stages II B and III B; a third of these cancer patients either did not have, or did not complete, treatment.

CONCLUSIONS

The observed cancer patterns in this population establish that measures directed at prevention and early detection (linked with treatment) of cervix and head and neck cancers are of paramount importance for cancer control in this and other rural populations of India where three-fourths of the total population live.

Biochemical characterization of NfsA, the Escherichia coli major nitroreductase exhibiting a high amino acid sequence homology to Frp, a Vibrio harveyi flavin oxidoreductase

We identified the nfsA gene, encoding the major oxygen-insensitive nitroreductase in Escherichia coli, and determined its position on the E. coli map to be 19 min. We also purified its gene product, NfsA, to homogeneity. It was suggested that NfsA is a nonglobular protein with a molecular weight of 26,799 and is associated tightly with a flavin mononucleotide. Its amino acid sequence is highly similar to that of Frp, a flavin oxidoreductase from Vibrio harveyi (B. Lei, M. Liu, S. Huang, and S.-C. Tu, J. Bacteriol. 176:3552-3558, 1994), an observation supporting the notion that E. coli nitroreductase and luminescent-bacterium flavin reductase families are intimately related in evolution. Although no appreciable sequence similarity was detected between two E. coli nitroreductases, NfsA and NfsB, NfsA exhibited a low level of the flavin reductase activity and a broad electron acceptor specificity similar to those of NfsB. NfsA reduced nitrofurazone by a ping-pong Bi-Bi mechanism possibly to generate a two-electron transfer product.

Technical note: thyratron performance--dependence on mounting in a medical linear accelerator

A thyratron is an important component of a medical linear accelerator. The working life of a thyratron has been found to be dependent on its physical orientation in the accelerator. This observation is a result of maintaining accelerators for over 15 years.

The sir locus of Escherichia coli: a gene involved in SOS-independent repair of mitomycin C-induced DNA damage

A Mud1 (lac Apr) insertion has been isolated in a delta (lac)recA+ lexA3(Ind-)rpoB87 gyrA87 mutant of Escherichia coli resulting in a decrease in mitomycin C tolerance and an increase in post-mitomycin C DNA degradation. The mitomycin C sensitivity of the insertion mutant is not further increased by substituting either the rpoB87 or the gyrA mutation by the respective wild-type alleles. However, when both rpoB87 and gyrA87 mutations are replaced by rpoB+ and gyrA+ the strain becomes hypersensitive to mitomycin C. Inactivation of recA in the insertion mutant has no effect on its mitomycin C sensitivity provided both rpoB87 and gyrA87 are present. When either or both of the mutations is/are replaced by the wild-type allele inactivation of recA renders the strain hypersensitive to mitomycin C. The locus of Mud1 (lac Apr) insertion, designated sir (SOS-independent repair), has been mapped between 57 and 61 min on the E. coli linkage map. Expression of the sir gene seems to be constitutive and not enhanced by mitomycin C. These results are discussed in relation to the SOS-independent repair of mitomycin C-induced DNA damage reported earlier.

Radiation, pepleomycin and hyperthermia in the therapy of locally advanced squamous cell carcinomas of the buccal mucosa

Oral squamous cell carcinoma is the commonest male (29%) and the second commonest female (18%) malignancy in South India. At first attendance 93% of the tumours are stage T3 or T4. They are essentially locoregional, remote metastases being rare (0.75%). Radiotherapy alone yields a poor survival (19% 5 year NED). Radiopotentiation by chemical sensitizers and cytotoxic drugs has been attempted since 1960, the best results being obtained by a combination of irradiation and bleomycin. There was, however, persistent failure in about 40% of cases. The present three-armed trial attempted to improve the results of radiotherapy and bleomycin by the addition of hyperthermia. A total of 101 T3 and T4 buccal squamous cancers were entered in the trial over a period of nearly three years. Entry closed in August 1987 and the last case was evaluated in October 1987, hence only response data are available. Hyperthermia did not confer any benefit.

SOS independent survival against mitomycin C induced lethality in a rifampicin-nalidixic acid-resistant mutant of Escherichia coli

A combination of specific rifampicin-resistant (rpoB87) and nalidixic acid-resistant (gyrA87) mutations results in a marked increase in the survival of Escherichia coli against mitomycin C-induced lethality in mutants defective for SOS induction and excision repair. Although the response does not seem to be obligatorily dependent upon the RecA protein, the efficiency is markedly increased in its presence, even in a conventionally inactive form. This response is not elicited against lethality due to ultraviolet radiation or N-methyl-N' -nitro-N-nitrosoguanidine exposure. The combination of rpoB87 and gyrA87 mutations also greatly alleviates post-mitomycin C degradation of DNA under SOS non-inducible conditions. It is proposed that the rpoB subunit of RNA polymerase and gyrA subunit of DNA gyrase could participate in the repair of certain types of DNA damage, such as cross-links, in a mode independent of SOS-regulated excision repair and post-replication repair.

Local RF capacitive hyperthermia: thermal profiles and tumour response

At the Cancer Institute we are using RF capacitive hyperthermia as an adjuvant to radiotherapy and/or chemotherapy in the local control of soft tissue sarcomas. We have studied the influence of bolus conductivity, electrode and phantom sizes on the rate of heating of agar phantoms. We have varied the bolus conductivity by varying the saline concentration in the bolus bags from zero to 2.0 per cent, during heating. We found that the rate of heating of phantoms increases and that of the bolus decreases with the increase in the saline concentration of bolus up to 1 per cent, irrespective of phantom and electrode sizes. However, for a given size of electrodes the rate of heating decreased with the increase in the phantom size. When the diameter and height of the phantom were equal to the diameters of electrodes the rate of heating of the phantom was nearly uniform. However, when the diameter of the phantom was larger than that of electrodes the rate of heating in the radial axis decreased with the increase in the radial distance. On the basis of this data we suggest the use of electrodes larger in size by 1.0-3.0 cm than the size of the tumour, where the size of the anatomical site to be heated is larger than the electrode size to be used. Phantom and clinical data have indicated that the presence of bone in the field of heating can lead to hot spots. Preliminary clinical results have shown that the response of sarcomas to thermo-chemo-radiotherapy was superior to that of either thermo-radiotherapy or radiotherapy alone.

Transient suppression of F-plasmid incompatibility in a strain of Escherichia coli

The incompatibility between F plasmids is transiently suppressed in Escherichia coli strain CSH54. As a result this strain is able to maintain two F' factors or an F' factor and a mini-F plasmid for considerably longer periods than normal strains. When selective pressure for two markers carried by two separate F's (or an F' and mini-F) is imposed on normal strains, the two plasmids tend to form a cointegrate structure which can be detected genetically by the joint transfer of both the markers upon mating. This does not happen in CSH54; instead, the two plasmids are maintained and transferred independently. Physical evidence for the maintenance of an F' and a mini-F plasmid is provided by agarose gel electrophoresis.

Intragenic suppression of the temperature-sensitivity caused by a mutation in a gene controlling transcription (fit) in Escherichia coli

Starting from a transcription-defective strain harbouring a temperature-sensitive mutation in the fit gene, a rifampicin-resistant, temperature-insensitive derivative has been isolated. Genetic analysis of this derivative demonstrated the presence of a second temperature-sensitive mutation in the same gene. The two mutations mutually suppress each other's phenotype. From cotransduction experiments, the fit gene has been mapped 0.32 min and 0.16 min clockwise from the aroD and pps loci, respectively, at 37.5 min on the linkage map. The mutants harbouring either or both of the fit mutations are defective in RNA synthesis at the non-permissive temperature. The fit gene product is suggested to function as an accessory transcription factor.

Inhibitors of nitrofuran reduction in Escherichia coli: evidence for their existence, partial purification, binding of nitrofurantoin in vitro, and implications for nitrofuran resistance

Nitrofurantoin (NF)-resistant mutants of Escherichia coli were isolated as described previously (18). One of the mutants (SSJ-2) was found to possess NF reductase activity equal to that of its parent (E. coli KL16). Two NF-resistant transductional derivatives, SSJ-2A and SSJ-2B, were isolated using SSJ-2 as the donor. SSJ-2 was found to be a double mutant carrying two mutations, nfnA and nfnB, while SSJ-2A (nfnA) and SSJ-2B (nfnB) carried these mutations individually. Heated extracts from SSJ-2A and SSJ-2B were found to inhibit the reduction of NF by unheated extracts of the NF-sensitive strain E. coli KL16 in vitro. Unheated extracts of these mutants reduced NF poorly relative to E. coli KL16. The poor reduction of NF by unheated extracts of SSJ-2A and SSJ-2B was greatly stimulated by heated extracts of SSJ-2B and SSJ-2A, respectively, and also by heated extracts of E. coli KL16. When heated extracts of SSJ-2A and SSJ-2B were mixed in a particular ratio and added to unheated extracts of E. coli KL16 they lost their inhibitory activity. Two proteins, designated inhibitor A and inhibitor B, have been partially purified from heated extracts of SSJ-2B and SSJ-2A, respectively. Their respective molecular weights, as determined by gel chromatography, were 37,000 and 20,500. The two inhibitors bound nitrofurantoin in vitro, and the NF-binding ability was lost when mixed in the molar ration of 3/1 (B/A). These observations were rationalized in terms of a hypothesis which explains (i) maximal NF reduction in wild-type cells, (ii) maximal NF reduction of nfnA-nfnB- double mutant, and (iii) poor NF reduction in nfnA- or nfnB- single mutants. The possible role of these inhibitors in nitrofurantoin resistance is also discussed.

Nitrofurantoin-resistant mutants of Escherichia coli: isolation and mapping

Mutants of Escherichia coli resistant to nitrofurantoin have been isolated. The mutations, designated nfnA and nfnB were introduced individually into a multiply auxotrophic E. coli F- strain and mapped by conjugation and transduction. nfnA is located at 79.8 min and nfnB at 13.0 min on the E. coli chromosome.

Mapping of two transcription mutations (tlnI and tlnII) conferring thiolutin resistance, adjacent to dnaZ and rho in Escherichia coli

Two mutations in Escherichia coli conferring resistance to the transcription initiation inhibitor, thiolutin, have been mapped. One of these mutations (tln-I)( maps at 10.2 min on the genetic map and is cotransducible with dnaZ at a frequency of approximately 50%. The other mutation (tln-II) maps between metE and ilvD, probably close to rho, and is cotransducible with ilvD at a frequency of approximately 65%. The presence of both the mutations in the same cell confers resistance to thiolutin in minimal medium. Either one of them alone renders the cell 'conditionally auxotrophic' in the presence of the drug. The implications of these findings are discussed in relation to the mode of action of the thiolutin sensitive factors in transcription.

Genetic mapping of a putative temperature-sensitive transcription mutation in Escherichia coli K12

A putative temperature-sensitive transcription mutant described earlier (Jabbar and Jayaraman, 1976) has been genetically mapped. The locus maps at 38 min to the left of aroD. The mutation is recessive to the wild type and it affects a gene probably other than the genes coding for the alpha and beta subunits of phenylalanine tRNA synthetase and protein synthesis initiation factor IF-3 which also map in the same region.

Thiolutin resistant mutants of Escherichia coli are they RNA chain initiation mutants?

Four mutants of Escherichia coli KL16 resistant to the antibiotic Thiolutin have been isolated. This drug was earlier reported to be an inhibitor of RNA chain elongation. The first mutant, TLrI, is resistant only in rich or partially rich media: it can, however, grow in minimal medium containing the drug with a very long doubling time. The other mutants TLrII, TLrIIIa and TLrIIIb are resistant in rich as well as minimal media. beta-galactosidase could not be induced in TLrI and TLrII in the presence of thiolutin whereas the enzyme is constitutively synthesised in TLrIIIa and TLrIIIb irrespective of the drug. The mutants do not support the development of phage T4 in presence of the drug, if the drug is added along with the phage, but "escape" the inhibition if phage development is allowed to proceed for some time before the addition of the drug. The time of this escape is characteristic of the mutant. Even in a sensitive strain, T7 growth escapes inhibition very soon after infection, around the time the phage-specific RNA polymerase is synthesized. In the parent strain the kinetics of inhibition of beta-galactosidase induction resembles more the inhibition caused by rifampicin than by streptolydigin. It is proposed that thiolutin could be an inhibitor of RNA chain initiation and resistance might be due to mutation in the subunit(s)/factor(s) involved in initiation.

Transcription of bacteriophage T4 genome in vitro. Heterogeneity of RNA polymerase in crude extracts of normal and T4-infected Escherichia coli B

In order to obtain RNA polymerase preparations carrying the necessary specificity determinants to transcribe the delayed-early genes of bacteriophage T4, crude extracts of uninfected and T4-infected Escherichia coli were fractionated in glycerol gradients of low ionic strength. In contrast to the reported sedimentation behavior of the purified enzyme, the RNA polymerase activity in crude extracts of normal and infected cells sedimented heterogeneously over a wide range of sedimentation coefficients. When the "heavy" (24-33 S) and "light" (14-20 S) regions of the gradient were precipitated with ammonium sulfate and recentrifuged, the former split into two subfractions, one again sedimenting heavy and the other sedimenting light. The latter did not split under the same conditions. The resulting subfractions from uninfected cell extracts had different thermal thermal stabilities at 50 degrees (half-lives ranging from 2-3 to 25 min) while those from T4-infected cell extracts were very thermolabile (half-life of 1-2 min). All the subfractions were more active on T4 DNA than on calf-thymus DNA. They also formed rifampicin-resistant, RNA chain initiation complexes with T4 DNA. Based on the kinetics of heat inactivation with T4 and calf thymus DNAs as templates and preferential transcription of T4 DNA, it is proposed that the T4-infected cell enzymes prepared as described here harbor heat-labile initiation factor(s). During infection the heavy sedimenting RNA polymerase activity disappears after 2.5 min at 37 degrees. This appears to require phage-specific protein synthesis because (a) it does not happen in the presence of chloramphenicol and (b) it does not happen in T4 ghost-infected cells.

A genetic assay for mRNA's of phage T4

A method has been developed by which many gene-specific mRNA's in T4-infected cells can be quantitatively assayed. The method involves separation of complementary strands of phage T4 DNA, hybridization of the strands with RNA, digestion of nonhybridized regions of DNA with an endonuclease specific for single-stranded DNA, and assay of protected genetic markers by transformation. It has been shown that the gene gammaIIB is transcribed early from the light strand and that the gene 21 is transcribed late from the heavy strand.