Robust linear DNA degradation supports replication-initiation-defective mutants in Escherichia coli.

RecBCD helicase/nuclease supports replication fork progress via recombinational repair or linear DNA degradation, explaining recBC mutant synthetic lethality with replication elongation defects. Since replication initiation defects leave chromosomes without replication forks, these should be insensitive to the recBCD status. Surprisingly, we found that both Escherichia coli dnaA46(Ts) and dnaC2(Ts) initiation mutants at semi-permissive temperatures are also recBC-colethal. Interestingly, dnaA46 recBC lethality suppressors suggest underinitiation as the problem, while dnaC2 recBC suppressors signal overintiation. Using genetic and physical approaches, we studied the dnaA46 recBC synthetic lethality, for the possibility that RecBCD participates in replication initiation. Overproduced DnaA46 mutant protein interferes with growth of dnaA+ cells, while the residual viability of the dnaA46 recBC mutant depends on the auxiliary replicative helicase Rep, suggesting replication fork inhibition by the DnaA46 mutant protein. The dnaA46 mutant depends on linear DNA degradation by RecBCD, rather than on recombinational repair. At the same time, the dnaA46 defect also interacts with Holliday junction-moving defects, suggesting reversal of inhibited forks. However, in contrast to all known recBC-colethals, which fragment their chromosomes, the dnaA46 recBC mutant develops no chromosome fragmentation, indicating that its inhibited replication forks are stable. Physical measurements confirm replication inhibition in the dnaA46 mutant shifted to semi-permissive temperatures, both at the level of elongation and initiation, while RecBCD gradually restores elongation and then initiation. We propose that RecBCD-catalyzed resetting of inhibited replication forks allows replication to displace the "sticky" DnaA46(Ts) protein from the chromosomal DNA, mustering enough DnaA for new initiations.

Oxidative Damage Blocks Thymineless Death and Trimethoprim Poisoning in Escherichia coli.

Cells that cannot synthesize one of the DNA precursors, dTTP, due to thyA mutation or metabolic poisoning, undergo thymineless death (TLD), a chromosome-based phenomenon of unclear mechanisms. In Escherichia coli, thymineless death is caused either by denying thyA mutants thymidine supplementation or by treating wild-type cells with trimethoprim. Two recent reports promised a potential breakthrough in TLD understanding, suggesting significant oxidative damage during thymine starvation. Oxidative damage in vivo comes from Fenton's reaction when hydrogen peroxide meets ferrous iron to produce hydroxyl radical. Therefore, TLD could kill via irreparable double-strand breaks behind replication forks when starvation-caused single-strand DNA gaps are attacked by hydroxyl radicals. We tested the proposed Fenton-TLD connection in both thyA mutants denied thymidine, as well as in trimethoprim-treated wild-type (WT) cells, under the following three conditions: (i) intracellular iron chelation, (ii) mutational inactivation of hydrogen peroxide (HP) scavenging, and (iii) acute treatment with sublethal HP concentrations. We found that TLD kinetics are affected by neither iron chelation nor HP stabilization in cultures, indicating no induction of oxidative damage during thymine starvation. Moreover, acute exogenous HP treatments completely block TLD, apparently by blocking cell division, which may be a novel TLD prerequisite. Separately, the acute trimethoprim sensitivity of the rffC and recBCD mutants demonstrates how bactericidal power of this antibiotic could be amplified by inhibiting the corresponding enzymes. IMPORTANCE Mysterious thymineless death strikes cells that are starved for thymine and therefore replicating their chromosomal DNA without dTTP. After 67 years of experiments testing various obvious and not so obvious explanations, thymineless death is still without a mechanism. Recently, oxidative damage via in vivo Fenton's reaction was proposed as a critical contributor to the irreparable chromosome damage during thymine starvation. We have tested this idea by either blocking in vivo Fenton's reaction (expecting no thymineless death) or by amplifying oxidative damage (expecting hyperthymineless death). Instead, we found that blocking Fenton's reaction has no influence on thymineless death, while amplifying oxidative damage prevents thymineless death altogether. Thus, oxidative damage does not contribute to thymineless death, while the latter remains enigmatic.

An Efficient Method for Coronavirus Detection Through X-rays Using Deep Neural Network.

BACKGROUND: Coronavirus (COVID-19) is a group of infectious diseases caused by related viruses called coronaviruses. In humans, the seriousness of infection caused by a coronavirus in the respiratory tract can vary from mild to lethal. A serious illness can be developed in old people and those with underlying medical problems like diabetes, cardiovascular disease, cancer, and chronic respiratory disease. For the diagnosis of coronavirus disease, due to the growing number of cases, a limited number of test kits for COVID-19 are available in the hospitals. Hence, it is important to implement an automated system as an immediate alternative diagnostic option to pause the spread of COVID-19 in the population. OBJECTIVE: This paper proposes a deep learning model for the classification of coronavirus infected patient detection using chest X-ray radiographs. METHODS: A fully connected convolutional neural network model is developed to classify healthy and diseased X-ray radiographs. The proposed neural network model consists of seven convolutional layers with the rectified linear unit, softmax (last layer) activation functions, and max-pooling layers which were trained using the publicly available COVID-19 dataset. RESULTS AND CONCLUSION: For validation of the proposed model, the publicly available chest X-ray radiograph dataset consisting of COVID-19 and normal patient's images were used. Considering the performance of the results that are evaluated based on various evaluation metrics such as precision, recall, MSE, RMSE and accuracy, it is seen that the accuracy of the proposed CNN model is 98.07%.

Electron Microscopy Reveals Unexpected Cytoplasm and Envelope Changes during Thymineless Death in Escherichia coli.

Bacterial rod-shaped cells experiencing irreparable chromosome damage should filament without other morphological changes. Thymineless death (TLD) strikes thymidine auxotrophs denied external thymine/thymidine (T) supplementation. Such T-starved cells cannot produce the DNA precursor dTTP and therefore stop DNA replication. Stalled replication forks in T-starved cells were always assumed to experience mysterious chromosome lesions, but TLD was recently found to happen even without origin-dependent DNA replication, with the chromosome still remaining the main TLD target. T starvation also induces morphological changes, as if thymidine prevents cell envelope or cytoplasm problems that otherwise translate into chromosome damage. Here, we used transmission electron microscopy (TEM) to examine cytoplasm and envelope changes in T-starved Escherichia coli cells, using treatment with a DNA gyrase inhibitor as a control for "pure" chromosome death. Besides the expected cell filamentation in response to both treatments, we see the following morphological changes specific for T starvation and which might lead to chromosome damage: (i) significant cell widening, (ii) nucleoid diffusion, (iii) cell pole damage, and (iv) formation of numerous cytoplasmic bubbles. We conclude that T starvation does impact both the cytoplasm and the cell envelope in ways that could potentially affect the chromosome. IMPORTANCE Thymineless death is a dramatic and medically important phenomenon, the mechanisms of which remain a mystery. Unlike most other auxotrophs in the absence of the required supplement, thymidine-requiring E. coli mutants not only go static in the absence of thymidine, but rapidly die of chromosomal damage of unclear nature. Since this chromosomal damage is independent of replication, we examined fine morphological changes in cells undergoing thymineless death in order to identify what could potentially affect the chromosome. Here, we report several cytoplasm and cell envelope changes that develop in thymidine-starved cells but not in gyrase inhibitor-treated cells (negative control) that could be linked to subsequent irreparable chromosome damage. This is the first electron microscopy study of cells undergoing "genetic death" due to irreparable chromosome lesions.

Exopolysaccharide defects cause hyper-thymineless death in Escherichia coli via massive loss of chromosomal DNA and cell lysis.

Thymineless death in Escherichia coli thyA mutants growing in the absence of thymidine (dT) is preceded by a substantial resistance phase, during which the culture titer remains static, as if the chromosome has to accumulate damage before ultimately failing. Significant chromosomal replication and fragmentation during the resistance phase could provide appropriate sources of this damage. Alternatively, the initial chromosomal replication in thymine (T)-starved cells could reflect a considerable endogenous dT source, making the resistance phase a delay of acute starvation, rather than an integral part of thymineless death. Here we identify such a low-molecular-weight (LMW)-dT source as mostly dTDP-glucose and its derivatives, used to synthesize enterobacterial common antigen (ECA). The thyA mutant, in which dTDP-glucose production is blocked by the rfbA rffH mutations, lacks a LMW-dT pool, the initial DNA synthesis during T-starvation and the resistance phase. Remarkably, the thyA mutant that makes dTDP-glucose and initiates ECA synthesis normally yet cannot complete it due to the rffC defect, maintains a regular LMW-dT pool, but cannot recover dTTP from it, and thus suffers T-hyperstarvation, dying precipitously, completely losing chromosomal DNA and eventually lysing, even without chromosomal replication. At the same time, its ECA+thyA parent does not lyse during T-starvation, while both the dramatic killing and chromosomal DNA loss in the ECA-deficient thyA mutants precede cell lysis. We conclude that: 1) the significant pool of dTDP-hexoses delays acute T-starvation; 2) T-starvation destabilizes even nonreplicating chromosomes, while T-hyperstarvation destroys them; and 3) beyond the chromosome, T-hyperstarvation also destabilizes the cell envelope.

Sources of thymidine and analogs fueling futile damage-repair cycles and ss-gap accumulation during thymine starvation in Escherichia coli.

Thymine deprivation in thyA mutant E. coli causes thymineless death (TLD) and is the mode of action of popular antibacterial and anticancer drugs, yet the mechanisms of TLD are still unclear. TLD comprises three defined phases: resistance, rapid exponential death (RED) and survival, with the nature of the resistance phase and of the transition to the RED phase holding key to TLD pathology. We propose that a limited source of endogenous thymine maintains replication forks through the resistance phase. When this source ends, forks undergo futile break-repair cycle during the RED phase, eventually rendering the chromosome non-functional. Two obvious sources of the endogenous thymine are degradation of broken chromosomal DNA and recruitment of thymine from stable RNA. However, mutants that cannot degrade broken chromosomal DNA or lack ribo-thymine, instead of shortening the resistance phase, deepen the RED phase, meaning that only a small fraction of T-starved cells tap into these sources. Interestingly, the substantial chromosomal DNA accumulation during the resistance phase is negated during the RED phase, suggesting futile cycle of incorporation and excision of wrong nucleotides. We tested incorporation of dU or rU, finding some evidence for both, but DNA-dU incorporation accelerates TLD only when intracellular [dUTP] is increased by the dut mutation. In the dut ung mutant, with increased DNA-dU incorporation and no DNA-dU excision, replication is in fact rescued even without dT, but TLD still occurs, suggesting different mechanisms. Finally, we found that continuous DNA synthesis during thymine starvation makes chromosomal DNA increasingly single-stranded, and even the dut ung defect does not completely block this ss-gap accumulation. We propose that instability of single-strand gaps underlies the pathology of thymine starvation.

Improvement of post-harvest quality of pear fruit with optimized composite edible coating formulations.

Application of edible coatings is a suitable method to maintain the quality and reduce post-harvest losses in fresh vegetables and fruits. Pear fruits being climacteric have a short shelf life, and coating is considered as one of the most popular techniques to prolong its shelf life.The present study evaluates the effect of optimized edible coatings containing soy protein isolate (SPI) in combination with additives like hydroxypropyl methylcellulose (HPMC) and olive oil on 'Babughosha' Pears (Pyrus communis L.) stored at ambient temperature (28 ± 5 °C and 60 ± 10% RH). Four different coatings optimized by response surface methodology study were used in the present experiment. The results of the present study shows that the optimized edible coatings help retain the firmness of fruits and lowered the moisture loss. The tested combination of coating could also withhold the levels of ascorbic acid, chlorophyll and sugar contents in the treated fruits. Activities of enzymes associated with fruit softening (ß-galactosidase, polygalacturonase, pectin methyl esterase) showed delayed peaks. Amongst all treatments, T1 (SPI 5.0%, HPMC 0.40%, Olive oil 1%, Potassium sorbate 0.22%) and T2 (SPI 5.0%, HPMC 0.40%, Olive oil 0.98% Potassium sorbate 0.20%) were found to have pronounced effect on retention of nutritional quality in pears. Observations of shelf-life extension established that T2 (SPI 5.0%, HPMC 0.40%, Olive oil 0.98% Potassium sorbate 0.20%) was successful in extending shelf-life of pear fruits up to 15 days, as compared to 8 days for untreated pear fruits.

Optimization of edible coating formulations for improving postharvest quality and shelf life of pear fruit using response surface methodology.

The effect of composite edible films containing soy protein isolate (SPI) in combination with additives like hydroxypropyl methylcellulose (HPMC) and olive oil on 'Babughosha' pear (Pyrus communis L.) stored at ambient temperature (28 ± 5 °C and 60 ± 10% RH) was evaluated using Response surface methodology (RSM). A total of 30 edible coating formulations comprising of SPI (2-6%, w/v), olive oil (0.7-1.1%, v/v), HPMC (0.1-0.5%, w/v) and potassium sorbate (0-0.4% w/v) were evaluated for optimizing the most suitable combination. Quality parameters like weight loss%, TSS, pH and titrable acidity of the stored pears were selected as response variables for optimization. The optimization procedure was carried out using RSM. It was observed that the response variables were mainly effected by concentration of SPI and olive oil in the formulation. Edible coating comprising of SPI 5%, HPMC 0.40%, olive oil 1% and potassium sorbate 0.22% was found to be most suitable combination for pear fruit with predicted values of response variables indicated as weight loss% 3.50, pH 3.41, TSS 11.13 and TA% 0.513.

Composite coating of alginate-olive oil enriched with antioxidants enhances postharvest quality and shelf life of Ber fruit (Ziziphus mauritiana Lamk. Var. Gola).

The present study has been carried out to evaluate the effect of a composite edible coating of 2 % Sodium alginate and 0.2 % Olive oil with combination of 1 % ascorbic acid and 1 % citric acid on the post harvest nutritional quality and shelf life of Ber fruit stored at 25 ± 2 °C and 65 % R.H. The coatings reduced the decay occurrence, weight loss, accumulation of total soluble solids (TSS) and total sugars in Ber fruit and enhanced the level of antioxidants. The delayed activity of polygalacturonase (PG), Pectate lyase (PL) and Pectin methyl esterase (PME) was noticed in coated fruits than that of the control fruit indicating the reduced softening and ripening process. These findings suggest that the composite edible coating tested under the current study has the potential to control decaying incidence of Ber fruit, extends its storage life and also improves its valuable nutritional characteristics.

Investigations on Substrate Temperature-Induced Growth Modes of Organic Semiconductors at Dielectric/semiconductor Interface and Their Correlation with Threshold Voltage Stability in Organic Field-Effect Transistors.

Influence of substrate temperature on growth modes of copper phthalocyanine (CuPc) thin films at the dielectric/semiconductor interface in organic field effect transistors (OFETs) is investigated. Atomic force microscopy (AFM) imaging at the interface reveals a change from 'layer+island' to "island" growth mode with increasing substrate temperatures, further confirmed by probing the buried interfaces using X-ray reflectivity (XRR) and positron annihilation spectroscopic (PAS) techniques. PAS depth profiling provides insight into the details of molecular ordering while positron lifetime measurements reveal the difference in packing modes of CuPc molecules at the interface. XRR measurements show systematic increase in interface width and electron density correlating well with the change from layer + island to coalesced huge 3D islands at higher substrate temperatures. Study demonstrates the usefulness of XRR and PAS techniques to study growth modes at buried interfaces and reveals the influence of growth modes of semiconductor at the interface on hole and electron trap concentrations individually, thereby affecting hysteresis and threshold voltage stability. Minimum hole trapping is correlated to near layer by layer formation close to the interface at 100 °C and maximum to the island formation with large voids between the grains at 225 °C.

Assessment of suitability of two serotype A candidate vaccine strains for inclusion in FMD vaccine in India.

The recent type A foot and mouth disease virus field isolates recovered in India are shown to be antigenically quite divergent from the in-use vaccine strain (IND 17/82), warranting the selection of a suitable vaccine strain which can cover this diversity in antigenic spectrum. In earlier studies employing neutralization test with anti-146S rabbit sera raised against eight candidate vaccine strains, IND 81/00 and IND 40/00 belonging to genotype VII were found to offer the best antigenic coverage. In order to assess the credibility of IND 81/00 and IND 40/00 as vaccine strains, 17 recent isolates received during 2005-2006 and representative isolates from older genotypes were subjected to two-dimensional micro-neutralization assay using bovine convalescent serum (against IND 81/00 and IND 40/00) and bovine vaccinate serum (against IND 40/00). From the results it is evident that both the isolates IND 81/00 (antigenic relationship 'r-value' >0.40 with 86% of isolates) and IND 40/00 ('r-value' >0.40 with 78% of isolates) show nearly equal antigenic relatedness with the recent field viruses and hence both of these are effective vaccine candidates in present context. Though very limited in its extent, these useful data obtained with antisera raised in homologous host system are logical extension of the on going quest for the appropriate vaccine strain and circumvents species disparities in the immune recognition of epitopes.

Prevalence and distribution of cardiovascular risk factors in an urban industrial population in south India: a cross-sectional study.

BACKGROUND: Cardiovascular diseases (CVD) are leading cause of death in developing countries including India. The huge burden of CVD in Indian subcontinent is the consequence of the large population and high prevalence of cardiovascular risk factors. This study was done to determine the prevalence of cardiovascular risk factors in two industrial units in Chennai, India. METHODS: Survey of behavioural risk factors using structured questionnaires and anthropometric measurements were done for the study population. Blood samples were collected for the fasting plasma glucose and serum cholesterol. Trend chi-square was employed to test the linear trend. RESULTS: The total study population included 2262 male subjects. Blood samples were collected for 2148 (95.0%) subjects. Age range was 18-69 years. Prevalence of major cardiovascular risk factors was: current smokers 462 (20.2%), body mass index > or = 23 kg/m2 1510 (66.8%), central obesity 1589 (70.2%), hypertension 615 (27.2%), diabetes mellitus 350(16.3%) and total cholesterol > or = 200mg/dl in 650(30.3%). CONCLUSIONS: The study results indicated high prevalence of behavioural risk factors, central obesity, hypertension and diabetes in a select group of middle and high-income young urban males. The long-term follow-up in such settings will provide an opportunity to understand the influence of risk factors on cardiovascular disease outcomes.

Congenital fiber-type disproportion myopathy with type I fiber predominance and type II fiber smallness and atrophy--a sterological analysis.

Congenital myopathy with fiber-type disproportion is an established disorder, where type I fibers predominate with smallness of the same type. We report a family with three siblings (12-year-old boy, 9-year-old girl, and 6-year-old boy) with clinical features of congenital myopathy, where muscle biopsy in the eldest sib showed fiber-type disproportion. Type I fibers predominated with small and atrophic type II fibers which is unusual, especially when the child did not have any other clinical or biochemical abnormality to account for this type of variation. Further, a stereological analysis highlighted the differences with regards to number, size and even volume of the fiber types. A 3-dimensional concept is proposed for this morphological abnormality.

Effect of pyridoxine (Vitamin-B(6)) supplementation on calciuria and oxaluria levels of some normal healthy persons and urinary stone patients.

Effect of pyridoxine (Vitamin-B(6)) supplementation on calciuria and oxaluria levels of 20 normal healthy persons and 17 urinary stone patients has been studied. Mean 24 hr urinary calcium and oxalate levels of controls (healthy persons) and stone patients were estimated in presupplementation period and at every 20 days interval during supplementation. Stone patients were divided into two groups viz., mild hyperoxaluriacs and moderate hyperoxaluriacs, based on their pre-supplementation (base line) oxaluria levels. 60 days of pyridoxine supplementation, at the rate of 10 mg/day, resulted in a significant decrease (p<0.01 for mild hyperoxaluriacs and p<0.001 for moderate hyperoxaluriacs) in mean 24 hr urinary oxalate levels of urinary stone patients. The corresponding decrement in mean oxaluria level of controls was, however, only mild. The decrease of mean calciuria level of controls as well as stone patients, upon pyridoxine supplementation, were also found to be only mild and not significant. Utility of pyridoxine therapy in oxalate urolithiasis has been discussed in the light of results.

In situ UV-vis-NIR diffuse reflectance and Raman spectroscopy and catalytic activity studies of propane oxidative dehydrogenation over supported CrO3/ZrO2 catalysts.

The molecular structures, oxidation states, and reactivity of 3 and 6% CrO3/ZrO2 catalysts prepared by incipient wetness impregnation were examined under different conditions. The in situ Raman spectroscopic studies under dehydrated conditions reveal that the 3 and 6% CrO3/ZrO2 catalysts possess equal amounts of monochromate and polychromate species. Consequently, monolayer coverage on this ZrO2 support is about 3% CrO3. The 6% CrO3/ZrO2 possesses an additional Raman band due to Cr2O3 crystals corresponding to the remaining 3% CrO3. Furthermore, during reaction conditions the polychromate species is preferentially reduced, the monochromate species are slightly affected, and the Cr2O3 crystals are not affected. The in situ UV-vis-NIR diffuse reflectance spectroscopy results reveal that under steady-state reaction conditions the extent of reduction and edge energy position of surface Cr6+ cations increase with an increase in reduction environment for the 3 and 6% CrO3/ZrO2 samples. Propane oxidative dehydrogenation (ODH) studies reveal that the catalytic activity expressed in moles of propane converted per gram catalyst per second is similar for the two catalysts, which is consistent with equal amounts of molecularly dispersed chromia present. The turnover frequency for the 6% CrO3/ZrO2 catalyst is, however, smaller than that for the 3% CrO3/ZrO2 sample due to the presence of Cr2O3 crystals, which are relatively inactive for propane ODH. For this catalytic system and for the experimental conditions used, propene, CO, and CO2 are primary products. Furthermore, the 33-39% propene selectivity is not affected by the C3H8/O2 ratio for both catalysts. Structure-reactivity studies suggest that the molecularly dispersed species are present in equal amounts in the 3 and 6% CrO3/ZrO2 samples as Cr6+ monochromate and polychromate species are the most effective catalytic active sites taking part in the propane ODH reaction.

The microstructures of biomineralized surfaces: a spectroscopic study on the exoskeletons of fresh water (Apple) snail, Pila globosa.

In view of the importance in understanding biomineralization processes in different molluskan species, the common fresh water apple snail Pila globosa in Indian origin was taken to explore its mineralized exoskeleton structures. The detailed structural studies of the exoskeletons of P. globosa have been undertaken. The isolated layers present in these shells were studied by electron paramagnetic resonance (EPR), optical absorption, and infrared spectral techniques. The EPR spectra of the organic protein layer periostracum show the characteristic signals corresponding to Fe(3+) ions at g = 4.1 and 2.0. The EPR spectra of the ostracum (middle) layer at room temperature gives a complicated spectrum consisting of a number of Mn(2+) signals of at least three sets due to the aragonite nature of the material. The results indicate the presence of the multivalent manganese ions, which undergo the redox mechanisms. The thermal variation of the EPR spectra show marked effect on these samples both in g-values and the basic spectral pattern.