Sustainable seedling pots: Development and characterisation of banana waste and natural fibre-reinforced composites for horticultural applications.

Plastic pots used in horticultural nurseries generate substantial waste, causing environmental pollution. This study aimed to develop biodegradable composites from banana pseudo-stem reinforced with agricultural residues like pineapple leaves, taro and water hyacinth as eco-friendly substitutes. The aim of this study is to develop optimised banana biocomposite formulations with suitable reinforcements that balance mechanical durability, biodegradation, and seedling growth promotion properties to serve as viable eco-friendly alternatives to plastic seedling pots. This study was carried out by fabricating banana fibre mats through pulping, drying and hot pressing. Composite sheets were reinforced with 50 % pineapple, taro or water hyacinth fibres. The mechanical properties (tensile, yield strength, elongation, bursting strength), hydrophilicity (contact angle, water absorption), biodegradability (soil burial test), and seedling growth promotion were evaluated through appropriate testing methods. The results show that banana-taro composites exhibited suitable tensile strength (25 MPa), elongation (27 %), water uptake (41 %) and 82 % biodegradation in 60 days. It was observed that biodegradable seedling trays fabricated from banana-taro composite showed 95 % tomato seed germination and a 125 cm plant height increase in 30 days, superior to plastic trays. The finding shows that the study demonstrates the potential of banana-taro biocomposites as alternatives to plastic nursery pots, enabling healthy seedling growth while eliminating plastic waste pollution through biodegradation.

Optimization and modeling of vacuum impregnation of pineapple rings and comparison with osmotic dehydration.

The vacuum impregnation (VI) process parameters (vacuum pressure = 20-60 kPa; VI temperature = 35-55°C; concentration of the sucrose solution = 40-60 °Brix; and vacuum process time = 8-24 min) for pineapple rings were optimized based on the moisture content (MC), water loss (WL), solids gain (SG), yellowness index (YI), and total soluble solids (TSS) content of pineapple rings using response surface methodology (RSM). A relationship was developed between the process and response variables using RSM and artificial neural network (ANN) techniques. The effectiveness of VI was evaluated by comparing it with the osmotic dehydration (OD) technique. The optimum condition was found to be 31.782 kPa vacuum pressure, 50.441°C solution temperature, and 60 °Brix sucrose concentration for 20.068 min to attain maximum TSS, YI, SG, and WL, and minimum MC of pineapple rings. The R2 values of RSM models for all variables varied between 0.70 and 0.91, whereas mean square error values varied between 0.76 and 71.58 and for ANN models varied between 0.87-0.93 and 0.53-193.78, respectively. Scanning electron micrographs (SEM) revealed that parenchymal cell rupture was less in VI than in OD. The VI pineapple rings exhibited more pores and high SG, as compared to OD, due to the pressure impregnation. Spectroscopic analysis affirmed that the stretching vibrations of intermolecular and intramolecular interactions were significant in VI as against OD. The VI reduced the drying time by 35% compared to OD, with the highest overall acceptability score and lower microbial load during storage. PRACTICAL APPLICATION: Pineapple is a perishable fruit, which necessitates processing for extended shelf life. This study highlights the potential of the vacuum impregnation process as a promising alternative to conventional preservation methods such as osmotic dehydration for pineapples.

Effect of chitosan-based bio coating on mechanical, structural and physical characteristics of microfiber based paper packaging: An alternative to wood pulp/plastic packaging.

Limnocharis flava is a noxious aquatic weed that poses a threat to paddy cultivation. The high cellulose and low lignin contents in this plant make it a potential raw material for papermaking. Against this backdrop, this study was taken up to develop Limnocharis flava (LF) based sheets containing natural fibres from Banana (B), Pineapple (P), and Rice Straw (RS) as reinforcing agents. The influence of carboxymethyl cellulose (CMC) as a binder on the LF-based sheets was also studied. To enhance the mechanical and moisture resistance properties, a chitosan coating was provided to the sheets. Analytical tests for mechanical properties, water barrier properties, functional groups, structure and microstructure, thermal properties and biodegradability were performed. Among the samples, LF + B showed the highest tensile strength (34.86 Mpa) and bursting strength (13.055 kg/cm2), while LF + R had higher puncture and tearing strengths. Chitosan coating was found to enhance the sheets and improve the water barrier properties mechanically. The contact angle of LF + B increased from 91.6° to 110.65°, while the water vapour transmission rate of LF reduced from 532.18 to 404.47 on providing chitosan coating. The significant interactions of reinforcing agents were confirmed by the results of FTIR and that of the coating by the SEM micrographs. The LF-based sheets were also found to have decent thermal stability. The high value of the crystallinity index in LF + R samples supported their remarkable mechanical properties. This study proclaims the notable suitability of Limnocharis flava in manufacturing paper for packaging applications.

Design consideration and modelling studies of ultrasound and ultraviolet combined approach for shelf-life enhancement of pine apple juice.

Although both ultraviolet (UV) radiation and ultrasound (US) treatment have their capabilities in microbial inactivation, applying any one method alone may require a high dose for complete inactivation, which may affect the sensory and nutritional properties of pineapple juice. Hence, this study was intended to analyse and optimise the effect of combined US and UV treatments on microbial inactivation without affecting the selected quality parameters of pineapple juice. US treatment (33 kHz) was done at three different time intervals, viz. 10 min, 20 min and 30 min., after which, juice samples were subjected to UV treatment for 10 min at three UV dosage levels, viz. 1 J/cm2, 1.3 J/cm2, and 1.6 J/cm2. The samples were evaluated for total colour difference, pH, total soluble solids (TSS), titrable acidity (TA), and ascorbic acid content; total bacterial count and total yeast count; and the standardization of process parameters was done using Response Surface Methodology and Artificial Neural Network. The results showed that the individual, as well as combined treatments, did not significantly impact the physicochemical properties while retaining the quality characteristics. It was observed that combined treatment resulted in 5 log cycle reduction in bacterial and yeast populations while the individual treatment failed. From the optimization studies, it was found that combined US and UV treatments with 22.95 min and1.577 J/cm2 ensured a microbiologically safe product while retaining organoleptic quality close to that of fresh juice.

A System-based Approach for the Evaluation of Electromechanical Properties of Brain Tumors.

We have developed a semi-automated system integrated with MEMS-based electromechanical sensors to characterize human brain tumors. The electrical impedance and elastic moduli of three types of brain tumors and six normal brain regions were evaluated using the system. The impedance and elastic modulus of glioma was found to be significantly lower than the normal region. It was also observed that the white matter tissues had higher impedance and elastic moduli compared with the grey matter of the same neuroanatomic location. There were observable differences in the electromechanical behavior of gliomas, which originate from glial cells to that of schwannoma and meningioma of different cellular origins. Clinical Relevance- The observations suggest that simultaneous electromechanical characterization of brain tumors can serve as an effective tool for tumor delineation. The developed tool can be used alongside gold standard histopathological analysis to better understand human brain tumors.

Heavy metals in coral reef sediments of Kavaratti Island, India: An integrated quality assessment using GIS and pollution indicators.

The present study aims to document the contamination levels and ecological risks of heavy metals in the sediments of Kavaratti lagoon, India. A total of 15 sediment samples were collected for the analysis of Al, Pb, Cd, Cu, Cr, Mn, Ni and Zn. The decreasing trend of heavy metals was observed in the lagoon sediment as Pb > Zn > Al > Mn > Ni > Cr > Cd > Cu. The Geo-accumulation index (Igeo) results indicate that Cu, Cr, Mn, Ni and Zn were uncontaminated, while Cd was strong to extremely contaminated and Al and Pb were moderately contaminated. The enrichment factors (EF) of Cd and Pb range from moderate to extremely high (EF > 1) indicating that they have anthropogenic origin on Kavaratti Island. The Contamination factor (Cf) indicated that Cd, Pb and Al belong to a high risk of contamination (Cf > 6). The pollution load index (PLI) value near one suggested that a moderate level of pollution occurs in the study area. The modified degree of contamination (mCd) shows that Al, Cd and Pb have an ultra- higher degree of contamination (mCd ≤ 32). The potential ecological risk (RI) index confirmed that Pb and Cd have considerable to the serious thread of ecological risk (RI > 600). Additionally, multivariate statistical analysis and pollution indexes showed that the Kavaratti lagoon is moderate to considerably polluted by heavy metals. Diesel-based power generation, activities related to shipping, untreated sewage, fishing and tourism activities are the main anthropogenic sources of heavy metal pollution on Kavaratti Island.

Relationship between Body Mass Index and Dental Caries in 13-15-Year-Old School Children of Government and Private Schools in Bengaluru City.

AIMS: The aim of the study was to assess the correlation between body mass index (BMI) and dental caries of 13-15-years-old school children in urban Bangalore and to compare the correlation between BMI and dental decay amongst government and private school children of age group 13-15 years in Bangalore city. SUBJECTS AND METHODS: A total of 660 students 13-15 years old were inducted in the study. According to these, 330 students from government schools and 330 students from private schools were examined. A specially designed structured questionnaire was used for compilation of data in the survey. BMI for age percentiles was deducted by weight in kilogram divided by height in meter square. RESULTS: Overall a positive correlation was found between Decayed, Missing, and Filled Teeth DMFT and BMI. In government schools, Overweight children had more mean DMFT (1.43) than other BMI categories while in Private schools, At risk of overweight children had more mean DMFT (1.4) than other category of BMI children. CONCLUSIONS: A positive correlation was found between DMFT and BMI. In government schools, Overweight children had more mean DMFT than other BMI category while in Private schools, At risk of overweight children had more mean DMFT than other category children.

Revealing Conformational Transitions in G-Protein-Coupled Receptor Rhodopsin upon Phosphorylation.

G-protein-coupled receptors (GPCRs) have evolved as highly specialized cellular machinery that can dictate biological outcomes in response to diverse stimuli. Specifically, they induce multiple pathway responses upon structural perturbations induced at local protein sites. GPCRs utilize a concurrent strategy involving a central transmembrane topology and biochemical modifications for precise functional implementation. However, the specific role of the latter is not known due to the lack of precise probing techniques that can characterize receptor dynamics upon biochemical modifications. Phosphorylation is known to be one of the critical biochemical modifications in GPCRs that aids in receptor desensitization via arrestin binding. Here, we carry out all-atom molecular dynamics simulations of rhodopsin in a membrane environment to study its conformational dynamics induced upon phosphorylation. Interestingly, our comparative analysis of non-phosphorylated and phosphorylated rhodopsin structure demonstrated enhanced receptor stability upon phosphorylation at the C-terminal region that leads to the opening of the extracellular part of the transmembrane helices. In addition, monitoring the distinct number of phosphorylation states showed that having fewer phosphorylated residues does not bring about appropriate conformational changes in the extracellular region. Since phosphorylation results in receptor desensitization and recycling of the ligand, our findings provide significant insights into the conformational dynamics of the mechanism of ligand exit from the receptor.

Prenatal hypoxia-ischemia decreases spatial memory and increases aggression during adolescence.

Prenatal hypoxia-ischemia (HI) is a major cause of mortality and chronic neurological diseases in newborns. HI contributes to the emergence of several neurological disorders such as cognitive and behavioral deficits due to the atypical brain development. This study aimed at assessing the effects of prenatal HI on the spatial memory and aggression of rats during adolescence. Pregnant rats were divided into treatment and control groups. The rats of the treatment groups underwent unilateral ligation of the uterine artery on pregnancy day 7, 12, or 17. The offspring of these rats were tested for spatial memory and aggression when they reached 33 days of age. It has been found that the percentages of alternations in the Y-maze and the number of crossings in the Morris water maze tests of the HI groups were lower than those of the control groups. The total offense and defense aggression scores of the HI groups were higher than those of the control groups. In conclusion, the longer the duration of HI, the more deficits it causes in the spatial memory and aggression of rats during adolescence.

Genome scale patterns of supercoiling in a bacterial chromosome.

DNA in bacterial cells primarily exists in a negatively supercoiled state. The extent of supercoiling differs between regions of the chromosome, changes in response to external conditions and regulates gene expression. Here we report the use of trimethylpsoralen intercalation to map the extent of supercoiling across the Escherichia coli chromosome during exponential and stationary growth phases. We find that stationary phase E. coli cells display a gradient of negative supercoiling, with the terminus being more negatively supercoiled than the origin of replication, and that such a gradient is absent in exponentially growing cells. This stationary phase pattern is correlated with the binding of the nucleoid-associated protein HU, and we show that it is lost in an HU deletion strain. We suggest that HU establishes higher supercoiling near the terminus of the chromosome during stationary phase, whereas during exponential growth DNA gyrase and/or transcription equalizes supercoiling across the chromosome.

Restriction modification systems as engines of diversity.

Restriction modification (RM) systems provide protection against a broad spectrum of phages. However, the likelihood of a phage permanently bypassing this can be as high as 0.1 per infection (Korona et al., 1993) which makes for a relatively weak defense. Here we argue that, apart from providing such transient defenses, RM systems can facilitate long-term coexistence of many bacterial strains. We show that this diversity can be as large as the burst size of the phage but no larger-a curious correspondence between a number at the level of species and another number at the level of individuals. Such a highly diverse and stably coexisting ecosystem is robust to substantial variation in both bacterial growth rates and strength of their RM systems, which might be one reason why quite weak RM systems exist in the wild.

Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription.

DNA cytosine methylation regulates gene expression in mammals. In bacteria, its role in gene expression and genome architecture is less understood. Here we perform high-throughput sequencing of bisulfite-treated genomic DNA from Escherichia coli K12 to describe, for the first time, the extent of cytosine methylation of bacterial DNA at single-base resolution. Whereas most target sites (C(m)CWGG) are fully methylated in stationary phase cells, many sites with an extended CC(m)CWGG motif are only partially methylated in exponentially growing cells. We speculate that these partially methylated sites may be selected, as these are slightly correlated with the risk of spontaneous, non-synonymous conversion of methylated cytosines to thymines. Microarray analysis in a cytosine methylation-deficient mutant of E. coli shows increased expression of the stress response sigma factor RpoS and many of its targets in stationary phase. Thus, DNA cytosine methylation is a regulator of stationary phase gene expression in E. coli.

Evidence of non-random mutation rates suggests an evolutionary risk management strategy.

A central tenet in evolutionary theory is that mutations occur randomly with respect to their value to an organism; selection then governs whether they are fixed in a population. This principle has been challenged by long-standing theoretical models predicting that selection could modulate the rate of mutation itself. However, our understanding of how the mutation rate varies between different sites within a genome has been hindered by technical difficulties in measuring it. Here we present a study that overcomes previous limitations by combining phylogenetic and population genetic techniques. Upon comparing 34 Escherichia coli genomes, we observe that the neutral mutation rate varies by more than an order of magnitude across 2,659 genes, with mutational hot and cold spots spanning several kilobases. Importantly, the variation is not random: we detect a lower rate in highly expressed genes and in those undergoing stronger purifying selection. Our observations suggest that the mutation rate has been evolutionarily optimized to reduce the risk of deleterious mutations. Current knowledge of factors influencing the mutation rate­including transcription-coupled repair and context-dependent mutagenesis­do not explain these observations, indicating that additional mechanisms must be involved. The findings have important implications for our understanding of evolution and the control of mutations.

Genomic analysis of DNA binding and gene regulation by homologous nucleoid-associated proteins IHF and HU in Escherichia coli K12.

IHF and HU are two heterodimeric nucleoid-associated proteins (NAP) that belong to the same protein family but interact differently with the DNA. IHF is a sequence-specific DNA-binding protein that bends the DNA by over 160°. HU is the most conserved NAP, which binds non-specifically to duplex DNA with a particular preference for targeting nicked and bent DNA. Despite their importance, the in vivo interactions of the two proteins to the DNA remain to be described at a high resolution and on a genome-wide scale. Further, the effects of these proteins on gene expression on a global scale remain contentious. Finally, the contrast between the functions of the homo- and heterodimeric forms of proteins deserves the attention of further study. Here we present a genome-scale study of HU- and IHF binding to the Escherichia coli K12 chromosome using ChIP-seq. We also perform microarray analysis of gene expression in single- and double-deletion mutants of each protein to identify their regulons. The sequence-specific binding profile of IHF encompasses ∼30% of all operons, though the expression of <10% of these is affected by its deletion suggesting combinatorial control or a molecular backup. The binding profile for HU is reflective of relatively non-specific binding to the chromosome, however, with a preference for A/T-rich DNA. The HU regulon comprises highly conserved genes including those that are essential and possibly supercoiling sensitive. Finally, by performing ChIP-seq experiments, where possible, of each subunit of IHF and HU in the absence of the other subunit, we define genome-wide maps of DNA binding of the proteins in their hetero- and homodimeric forms.

Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli.

Nucleoid-associated proteins (NAPs) are global regulators of gene expression in Escherichia coli, which affect DNA conformation by bending, wrapping and bridging the DNA. Two of these--H-NS and Fis--bind to specific DNA sequences and structures. Because of their importance to global gene expression, the binding of these NAPs to the DNA was previously investigated on a genome-wide scale using ChIP-chip. However, variation in their binding profiles across the growth phase and the genome-scale nature of their impact on gene expression remain poorly understood. Here, we present a genome-scale investigation of H-NS and Fis binding to the E. coli chromosome using chromatin immunoprecipitation combined with high-throughput sequencing (ChIP-seq). By performing our experiments under multiple time-points during growth in rich media, we show that the binding regions of the two proteins are mutually exclusive under our experimental conditions. H-NS binds to significantly longer tracts of DNA than Fis, consistent with the linear spread of H-NS binding from high- to surrounding lower-affinity sites; the length of binding regions is associated with the degree of transcriptional repression imposed by H-NS. For Fis, a majority of binding events do not lead to differential expression of the proximal gene; however, it has a significant indirect effect on gene expression partly through its effects on the expression of other transcription factors. We propose that direct transcriptional regulation by Fis is associated with the interaction of tandem arrays of Fis molecules to the DNA and possible DNA bending, particularly at operon-upstream regions. Our study serves as a proof-of-principle for the use of ChIP-seq for global DNA-binding proteins in bacteria, which should become significantly more economical and feasible with the development of multiplexing techniques.

Comparative genomics of cyclic-di-GMP signalling in bacteria: post-translational regulation and catalytic activity.

Cyclic-di-GMP is a bacterial second messenger that controls the switch between motile and sessile states. It is synthesized by proteins containing the enzymatic GGDEF domain and degraded by the EAL domain. Many bacterial genomes encode several copies of proteins containing these domains, raising questions on how the activities of parallel c-di-GMP signalling systems are segregated to avoid potentially deleterious cross-talk. Moreover, many 'hybrid' proteins contain both GGDEF and EAL domains; the relationship between the two apparently opposing enzymatic activities has been termed a 'biochemical conundrum'. Here, we present a computational analysis of 11 248 GGDEF- and EAL-containing proteins in 867 prokaryotic genomes to address these two outstanding questions. Over half of these proteins contain a signal for cell-surface localization, and a majority accommodate a signal-sensing partner domain; these indicate widespread prevalence of post-translational regulation that may segregate the activities of proteins that are co-expressed. By examining the conservation of amino acid residues in the GGDEF and EAL catalytic sites, we show that there are predominantly two types of hybrid proteins. In the first, both sites are intact; an additional regulatory partner domain, present in most of these proteins, might determine the balance between the two enzymatic activities. In the second type, only the EAL catalytic site is intact; these--unlike EAL-only proteins--generally contain a signal-sensing partner domain, suggesting distinct modes of regulation for EAL activity under different sequence contexts. Finally, we discuss the role of proteins that have lost GGDEF and EAL catalytic sites as potential c-di-GMP-binding effectors. Our findings will serve as a genomic framework for interpreting ongoing molecular investigations of these proteins.

Principles of transcriptional regulation and evolution of the metabolic system in E. coli.

Organisms must adapt to make optimal use of the metabolic system in response to environmental changes. In the long-term, this involves evolution of the genomic repertoire of enzymes; in the short-term, transcriptional control ensures that appropriate enzymes are expressed in response to transitory extracellular conditions. Unicellular organisms are particularly susceptible to environmental changes; however, genome-scale impact of these modulatory effects has not been explored so far in bacteria. Here, we integrate genome-scale data to investigate the evolutionary trends and transcriptional control of metabolism in Escherichia coli K12. Globally, the regulatory system is organized in a clear hierarchy of general and specific transcription factors (TFs) that control differing ranges of metabolic functions. Further, catabolic, anabolic, and central metabolic pathways are targeted by distinct combinations of these TFs. Locally, enzymes catalyzing sequential reactions in a metabolic pathway are co-regulated by the same TFs. Regulation is more complex at junctions: General TFs control the overall activity of all connecting reactions, whereas specific TFs control individual enzymes. Divergent junctions play a special role in delineating metabolic pathways and decouple the regulation of incoming and outgoing reactions. We find little evidence for differential usage of isozymes, which are generally co-expressed in similar conditions, and thus are likely to reinforce the metabolic system through redundancy. Finally, we show that enzymes controlled by the same TFs have a strong tendency to co-evolve, suggesting a significant constraint to maintain similar regulatory regimes during evolution. Catabolic, anabolic, and central energy pathways evolve differently, emphasizing the role of the environment in shaping the metabolic system. Many of the observations also occur in yeast, and our findings may apply across large evolutionary distances.

Complete genome sequence of uropathogenic Proteus mirabilis, a master of both adherence and motility.

The gram-negative enteric bacterium Proteus mirabilis is a frequent cause of urinary tract infections in individuals with long-term indwelling catheters or with complicated urinary tracts (e.g., due to spinal cord injury or anatomic abnormality). P. mirabilis bacteriuria may lead to acute pyelonephritis, fever, and bacteremia. Most notoriously, this pathogen uses urease to catalyze the formation of kidney and bladder stones or to encrust or obstruct indwelling urinary catheters. Here we report the complete genome sequence of P. mirabilis HI4320, a representative strain cultured in our laboratory from the urine of a nursing home patient with a long-term (> or =30 days) indwelling urinary catheter. The genome is 4.063 Mb long and has a G+C content of 38.88%. There is a single plasmid consisting of 36,289 nucleotides. Annotation of the genome identified 3,685 coding sequences and seven rRNA loci. Analysis of the sequence confirmed the presence of previously identified virulence determinants, as well as a contiguous 54-kb flagellar regulon and 17 types of fimbriae. Genes encoding a potential type III secretion system were identified on a low-G+C-content genomic island containing 24 intact genes that appear to encode all components necessary to assemble a type III secretion system needle complex. In addition, the P. mirabilis HI4320 genome possesses four tandem copies of the zapE metalloprotease gene, genes encoding six putative autotransporters, an extension of the atf fimbrial operon to six genes, including an mrpJ homolog, and genes encoding at least five iron uptake mechanisms, two potential type IV secretion systems, and 16 two-component regulators.

Transcriptomics and adaptive genomics of the asymptomatic bacteriuria Escherichia coli strain 83972.

Escherichia coli strains are the major cause of urinary tract infections in humans. Such strains can be divided into virulent, UPEC strains causing symptomatic infections, and asymptomatic, commensal-like strains causing asymptomatic bacteriuria, ABU. The best-characterized ABU strain is strain 83972. Global gene expression profiling of strain 83972 has been carried out under seven different sets of environmental conditions ranging from laboratory minimal medium to human bladders. The data reveal highly specific gene expression responses to different conditions. A number of potential fitness factors for the human urinary tract could be identified. Also, presence/ absence data of the gene expression was used as an adaptive genomics tool to model the gene pool of 83972 using primarily UPEC strain CFT073 as a scaffold. In our analysis, 96% of the transcripts filtered present in strain 83972 can be found in CFT073, and genes on six of the seven pathogenicity islands were expressed in 83972. Despite the very different patient symptom profiles, the two strains seem to be very similar. Genes expressed in CFT073 but not in 83972 were identified and can be considered as virulence factor candidates. Strain 83972 is a deconstructed pathogen rather than a commensal strain that has acquired fitness properties.