Microbial lipopeptides: their pharmaceutical and biotechnological potential, applications, and way forward.

As lead molecules, cyclic lipopeptides with antibacterial, antifungal, and antiviral properties have garnered a lot of attention in recent years. Because of their potential, cyclic lipopeptides have earned recognition as a significant class of antimicrobial compounds with applications in pharmacology and biotechnology. These lipopeptides, often with biosurfactant properties, are amphiphilic, consisting of a hydrophilic moiety, like a carboxyl group, peptide backbone, or carbohydrates, and a hydrophobic moiety, mostly a fatty acid. Besides, several lipopeptides also have cationic groups that play an important role in biological activities. Antimicrobial lipopeptides can be considered as possible substitutes for antibiotics that are conventional to address the current drug-resistant issues as pharmaceutical industries modify the parent antibiotic molecules to render them more effective against antibiotic-resistant bacteria and fungi, leading to the development of more resistant microbial strains. Bacillus species produce lipopeptides, which are secondary metabolites that are amphiphilic and are typically synthesized by non-ribosomal peptide synthetases (NRPSs). They have been identified as potential biocontrol agents as they exhibit a broad spectrum of antimicrobial activity. A further benefit of lipopeptides is that they can be produced and purified biotechnologically or biochemically in a sustainable manner using readily available, affordable, renewable sources without harming the environment. In this review, we discuss the biochemical and functional characterization of antifungal lipopeptides, as well as their various modes of action, method of production and purification (in brief), and potential applications as novel antibiotic agents.

Poly(lactic acid)/cholecalciferol based composites for active food packaging application.

Poly(lactic acid) (PLA) based sustainable composites incorporated with cholecalciferol (Vitamin D3) (CC) at different concentrations (1, 3, 5 and 10 wt%) were prepared using solvent casting method. Performance analysis of PLA/CC composite films in terms of food packaging properties like thermal, optical, oxygen barrier, mechanical, anti-bacterial as well as anti-oxidant effect is carried out. The PLA/CC-5 composite showed complete blockage of UV-B light at 320 nm, which is known to significantly induce the photo-chemical degradation of polymers. The incorporation of CC in the PLA matrix brought in improvement in mechanical and oxygen barrier properties. The PLA composite films showed effective antibacterial activity against food borne bacteria (S. aureus and E. coli), in addition to excellent antioxidant activity. All these important traits exhibited by PLA/CC composite films suggest its potential for food packaging application.

Intrinsic properties of chitosan on the characteristics of gold nanoparticles and its application as smart packaging device.

Storage temperature fluctuation is a major problem faced in food and pharmaceutical industry, apart from prevailing fraud in marketing frozen products as fresh. The present work aimed to study the effect of intrinsic properties of chitosan on synthesis and performance of gold nanoparticles as smart packaging devices. Different types of Chitosan from shrimp waste were used as reducing and capping agent in the synthesis of metal nanoparticle. Time is taken to reduce gold atom to gold nanoparticles varied with the type of reducing agent, between 6 min 40 s to 15 min 02 s. The maximum absorbance (λmax) for AuNPs was observed between 517 and 530 nm. An increase in the concentration of chitosan resulted in smaller and uniform size AuNPs with size ranging from 8.09 to 9.95 nm compared with 14.44 to 19.88 nm for lower concentration of chitosan. Visible ruby red colour of AuNPs synthesised using trisodium citrate (TSC) and lower concentration of chitosan (0.1%) changed to colourless and grey to blue, respectively upon exposure to frozen condition (-18 °C ± 1 °C). UV Visible spectra indicated distinctly different (broader) spectrum with reduced peak intensity. A visible change in colour from ruby red to bluish and colourless state indicates that irrespective of the properties of available chitosan, it can be used for synthesis of gold nanoparticles as smart packaging to distinguish packed fresh/chilled/refrigerated products from frozen ones.

Influence of corn starch based bio-active edible coating containing fumaric acid on the lipid quality and microbial shelf life of silver pomfret fish steaks stored at 4 °C.

The present study aimed at assessing the impact of addition of fumaric acid (0.5%), as an active agent, in a corn starch (2%) based edible coating, on the lipid quality and microbial shelf life of silver pomfret (Pampus argenteus) fish steaks stored at 4 °C. Treating fish steaks with FA resulted in a bacteriostatic effect leading to reduced counts of total mesophilic and psychrotrophic bacteria, H2S producing bacteria and Pseudomonas spp. The total mesophilic bacterial count of uncoated control sample exceeded the permissible limit of 7 log cfu g-1 on 6th day and had the lowest microbial shelf life. FA incorporation in the CS coating improved the microbial stability of fish steaks resulting in a shelf life of 15 days. The outcomes of the study suggest that CS based coating is beneficial in delaying lipid oxidation as displayed by the lower TBA and PV values while FA is an effective agent for further increasing the preservative action of CS coating by significantly inhibiting microbial growth as well as lipid quality deterioration, which could be exploited by the seafood industry as an active packaging component.

Implementation and Validation of Anisotropic Analytical Algorithm in Eclipse Treatment Planning System for Indigenous Telecobalt Machine (Bhabhatron II).

Background: The photon dose calculation model anisotropic analytical algorithm (AAA) available with eclipse integrated treatment planning system (TPS) (Varian) supports telecobalt dose calculation from Version 13.6 onward. Formerly, pencil beam convolution (PBC) was used for modeling telecobalt machines. Eclipse TPS no longer supports PBC dose calculation algorithm in v13.6 and above. The AAA dose calculation model is a three-dimensional PBC/superposition algorithm. Its configuration is based on Monte-Carlo-determined basic physical parameters that are tailored to measured clinical beam data. Aim: The study investigated the feasibility of clinical implementation of AAA in Eclipse TPS for Bhabhatron II. Materials and Methods: The indigenous telecobalt machine, Bhabhatron II, was configured as a generic machine because an inbuilt machine model for the same was not available in Varian Eclipse TPS algorithm library. In such a scenario, it was necessary to evaluate and validate dosimetric parameters of the TPS because improper tailoring would cause errors in dose calculations. Beam data measurements of the machine were carried out which were used for configuration of the algorithm. Result: After successful configuration, a variety of plans created in TPS were executed on the machine and subsequently evaluated. Conclusion: From this study, we concluded that AAA-based dose calculation in TPS is very well suited for accurate dose calculations for telecobalt machine and can be implemented for clinical use.

MutT Homolog1 has multifaceted role in glioma and is under the apparent orchestration by Hypoxia Inducible factor1 alpha.

AIMS: The study focused on the expression and role of a recent potential cancer therapeutic target protein, MutT Homolog1 (MTH1). MTH1 gets activated in an increased reactive oxygen species (ROS) environment and removes the oxidized nucleotides from the cell. The study aimed to check the role of MTH1 in DNA damage and apoptosis, migration and angiogenesis and also to examine its regulation in glioma. MAIN METHODS: The experiments were carried out in human glioma tissue samples and brain tissues of epilepsy patients (non-tumor control). We used two human glioblastomas cell lines, U87MG and U251MG cells. In order to study the role of MTH1 in glioma and to analyze the relation of MTH1 with Hif1α, we have used MTH1 siRNA and Hif1α siRNA respectively. KEY FINDINGS: We found an increased expression of MTH1 in glioma tissues compared to the non-tumor brain tissues. Correlation analysis revealed that those samples showing reduced expression of MTH1 also had high levels of DNA damage and apoptotic markers, while diminished expression of angiogenesis regulators and levels of migration. MTH1 knockdown in vitro by siRNA in tumor cell lines corroborates the above observation. This justifies the emergence of MTH1 inhibitors as potential first-in-class drugs. Mechanistically, our observations suggest that Hif1α may modulate MTH1 expression. SIGNIFICANCE: We found elevated MTH1 expression in glioma irrespective of their grades, while its inhibition affects multiple tumor progression pathways, and that targeting Hif1α could simulate the same.

Proteomics dataset of adult Anopheles Stephensi female brain.

Mosquitoes with their ability to transmit several pathogens of human disease pose a serious threat to healthcare worldwide. Although much has been done to prevent the disease transmission by mosqitos. The rising rate of resistance in mosquitos towards conventionally used control strategies necessitates developing of novel strategies to counter disease transmission. The mosquito brain plays a key role in host-seeking, finding mates and selection of oviposition sites. However, not much is know about the underlying physiological processes in mosquito brain. The data presented in this study describes the proteins that have been identified in the brain tissue of adult female Anopheles stephensi and their associated processes. Interpretation of the data can be related to the previously published article "Integrating transcriptomics and proteomics data for accurate assembly and annotation of genomes" [1].

Integrated genomic analysis reveals mutated ELF3 as a potential gallbladder cancer vaccine candidate.

Gallbladder cancer (GBC) is an aggressive gastrointestinal malignancy with no approved targeted therapy. Here, we analyze exomes (n = 160), transcriptomes (n = 115), and low pass whole genomes (n = 146) from 167 gallbladder cancers (GBCs) from patients in Korea, India and Chile. In addition, we also sequence samples from 39 GBC high-risk patients and detect evidence of early cancer-related genomic lesions. Among the several significantly mutated genes not previously linked to GBC are ETS domain genes ELF3 and EHF, CTNNB1, APC, NSD1, KAT8, STK11 and NFE2L2. A majority of ELF3 alterations are frame-shift mutations that result in several cancer-specific neoantigens that activate T-cells indicating that they are cancer vaccine candidates. In addition, we identify recurrent alterations in KEAP1/NFE2L2 and WNT pathway in GBC. Taken together, these define multiple targetable therapeutic interventions opportunities for GBC treatment and management.

Medical Genetics for Practicing Obstetrician.

Medical genetics has evolved over a decade, and hence, all investigations are available for clinical practice. Many diseases are diagnosed accurately today because of new investigations. These advanced investigations are affordable, accessible and available in day-to-day practice. Hence, there is a need and it is a time for us to understand these advanced technologies. Karyotyping and rapid aneuploidy tests are basic tests, while chromosomal microarray and next-generation sequencing are advanced technologies. It is time to update the knowledge and utilize them in day-to-day practice. These tests are utilized both in prenatal diagnosis and in some clinical scenarios, which are elaborated in detail. Karyotyping is the basic tool to detect both numerical and structural abnormalities. It is advantageous in that it is accurate with error of 0.001% but has a resolution of up to 5 MB. Rapid aneuploidy detection tests are equally accurate and detect as good as 99%. They are FISH, QF-PCR and MLPA. They have high sensitivity and specificity, and results are available within 3 days of time. Hence, these tests are apt for Indian scenarios, where late detection of anomalies (18-20 weeks) is common. Chromosomal microarray is the hybridization technique which detects aneuploidy of all chromosomes. This is useful for detection of deletion and duplication in chromosomes. This is not available for prenatal diagnosis in India now, whereas this is available for prenatal diagnosis in developed countries. Whole-exome sequencing and whole-genome sequencing are advanced techniques which have been described and discussed at length.

Proteome data of female Anopheles stephensi antennae.

Antennae of female Anopheles stephensi mosquitoes were dissected and lysed with 1% SDS. Proteins were extracted using ultra sonication and analyzed on high resolution mass spectrometer. Proteomic data was analyzed using two search algorithms SEQUEST and Mascot, resulting in the identification of 22,729 peptides corresponding to 3262 proteins. These proteins were characterized using different bioinformatics tools. VectorBase resource was used to assign Gene Ontology (GO) terms. Using Biomart tool ortholog information was fetched from the VectorBase database. Raw mass spectrometric data was deposited in ProteomeXchange Consortium via PRIDE partner repository in the public dataset PXD001128. Proteins involved in insecticide resistance and odorant binding were the most abundant in the antennae. The proteins identified in this study could be targeted for developing novel vector control strategy.

Proteomics of Asrij Perturbation in Drosophila Lymph Glands for Identification of New Regulators of Hematopoiesis.

Hematopoiesis is the process of differentiation of precursor blood cells into mature blood cells that is controlled by a complex set of molecular interactions. Understanding hematopoiesis is important for the study of hematological disorders. However, a comprehensive understanding of how physiological and genetic mechanisms regulate blood cell precursor maintenance and differentiation is lacking. Owing to simplicity and ease of genetic analysis, the Drosophila melanogaster lymph gland (LG) is an excellent model to study hematopoiesis. Here, we quantitatively analyzed the LG proteome under genetic conditions that either maintain precursors or promote their differentiation in vivo, by perturbing expression of Asrij, a conserved endosomal regulator of hematopoiesis. Using iTRAQ-based quantitative proteomics, we determined the relative expression levels of proteins in Asrij-knockout and overexpressing LGs from 1500 larval dissections compared with wild type. Our data showed that at least 6.5% of the Drosophila proteome is expressed in wild type LGs. Of the 2133 proteins identified, 780 and 208 proteins were common to previously reported cardiac tube and hemolymph proteomes, respectively, resulting in the identification of 1238 proteins exclusive to the LG. Perturbation of Asrij levels led to differential expression of 619 proteins, of which 27% have human homologs implicated in various diseases. Proteins regulating metabolism, immune system, signal transduction and vesicle-mediated transport were significantly enriched. Immunostaining of representative candidates from the enriched categories and previous reports confirmed 73% of our results, indicating the validity of our LG proteome. Our study provides, for the first time, an in vivo proteomics resource for identifying novel regulators of hematopoiesis that will also be applicable to understanding vertebrate blood cell development.

Dataset on fat body proteome of Anopheles stephensi Liston.

Fat body from Anopheles stephensi female mosquitoes were dissected and processed for proteomic analysis. Both SDS-PAGE and basic Reverse Phase Liquid Chromatography-based fractionation strategies were used to achieve a broad coverage of protein identification. The fractionated peptides were then analyzed on a high-resolution mass spectrometer. Searching the raw data against the protein database of An. stephensi resulted in identification of 4535 proteins, which is, to our knowledge, the largest catalog of fat body proteome in any mosquito vector species reported so far. Bioinformatics analysis on these fat body proteins suggested the enrichment of biological processes including carbon and lipid metabolism, amino acid metabolism, signal peptide processing and oxidation-reduction. In addition, using proteogenomic approaches, 43 novel proteins were identified, which were not listed in the annotated gene annotations of An. stephensi. The data used in the analysis are related to the article 'Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes' (Prasad et al., 2017).

Quantitative proteome of midgut, Malpighian tubules, ovaries and fat body from sugar-fed adult An. stephensi mosquitoes.

The data presented in this article is associated with the quantitative proteomic analysis of four mosquito tissues - midgut, Malpighian tubules, ovaries and fat body from female Anopheles stephensi mosquitoes. To identify the proteins that were expressed in a tissue-specific manner, the four mosquito tissues were labelled with iTRAQ labels and analyzed using a high-resolution mass spectrometer. Database searches of the 1,10,616 raw spectra from 23 peptide fractions resulted in the identification of 84,733 peptide spectrum matches corresponding to 16,278 peptides and 3372 proteins. Of these, 959 proteins were found to be differentially expressed across the tissues. Gene ontology-based bioinformatic analysis of the differentially expressed proteins are also provided in the article. The data in this article has been deposited in the (ProteomeXchange) Consortium via the PRIDE repository and can be accessed through the accession ID, PXD001128.

Proteome data of Anopheles stephensi ovary using high-resolution mass spectrometry.

This article contains data on the proteins expressed in the ovaries of Anopheles stephensi, a major vector of malaria in India. Data acquisition was performed using a high-resolution Orbitrap-Velos mass spectrometer. The acquired MS/MS data was searched against An. stephensi protein database comprising of 11,789 sequences. Overall, 4407 proteins were identified, functional analysis was performed for the identified proteins and a protein-protein interaction map predicted. The data provided here is also related to a published article - "Integrating transcriptomics and proteomics data for accurate assembly and annotation of genomes" (Prasad et al., 2017) [1].

A Next-Generation Sequencing-Based Molecular Approach to Characterize a Tick Vector in Lyme Disease.

Next-generation sequencing approaches have revolutionized genomic medicine and enabled rapid diagnosis for several diseases. These approaches are widely used for pathogen detection in several infectious diseases. Lyme disease is a tick-borne infectious disease, which affects multiple organs. The causative organism is a spirochete, Borrelia burgdorferi, which is transmitted by ticks. Lyme disease can be treated easily if detected early, but its diagnosis is often delayed or is incorrect leading to a chronic debilitating condition. Current confirmatory diagnostic tests for Lyme disease rely on detection of antigens derived from B. burgdorferi, which are prone to both false positives and false negatives. Instead of focusing only on the human host for the diagnosis of Lyme disease, one could also attempt to identify the vector (tick) and the causative organism carried by the tick. Since all ticks do not transmit Lyme disease, it can be informative to accurately identify the tick from the site of bite, which is often observed by the patient and discarded. However, identifying ticks based on morphology alone requires a trained operator and can still be incorrect. Thus, we decided to take a molecular approach by sequencing DNA and RNA from a tick collected from an individual bitten by the tick. Using next-generation sequencing, we confirmed the identity of the tick as a dog tick, Dermacentor variabilis, and did not identify any pathogenic bacterial sequences, including Borrelia species. Despite the limited availability of nucleotide sequences for many types of ticks, our approach correctly identified the tick species. This proof-of-principle study demonstrates the potential of next-generation sequencing in the diagnosis of tick-borne infections, which can also be extended to other zoonotic diseases.

Proteome data of Anopheles stephensi hemolymph using high resolution mass spectrometry.

The article provides insights into the protein expression in Anopheles stephensi hemolymph. We carried out data acquisition using a high-resolution LTQ-Orbitrap Velos mass spectrometer to identify the hemolymph proteins of An. stephensi. Experimentally derived mass spectrometry data was analyzed using Proteome Discoverer 2.1 software using two different search algorithms SEQUEST and MASCOT. A total of 1091 proteins were identified from the hemolymph. The identified proteins were categorized for their role in biological processes and molecular functions. The interactions between these proteins were predicted using STRING online tool. Relation can be drawn between the data provided in this study to the already published article "Integrating transcriptomics and proteomics data for accurate assembly and annotation of genomes" (Prasad et al., 2017) [1].

Mapping Anopheles stephensi midgut proteome using high-resolution mass spectrometry.

Anopheles stephensi Liston is one of the major vectors of malaria in urban areas of India. Midgut plays a central role in the vector life cycle and transmission of malaria. Because gene expression of An. stephensi midgut has not been investigated at protein level, an unbiased mass spectrometry-based proteomic analysis of midgut tissue was carried out. Midgut tissue proteins from female An. stephensi mosquitoes were extracted using 0.5% SDS and digested with trypsin using two complementary approaches, in-gel and in-solution digestion. Fractions were analysed on high-resolution mass spectrometer, which resulted in acquisition of 494,960 MS/MS spectra. The MS/MS spectra were searched against protein database comprising of known and predicted proteins reported in An. stephensi using Sequest and Mascot software. In all, 47,438 peptides were identified corresponding to 5,709 An. stephensi proteins. The identified proteins were functionally categorized based on their cellular localization, biological processes and molecular functions using Gene Ontology (GO) annotation. Several proteins identified in this data are known to mediate the interaction of the Plasmodium with vector midgut and also regulate parasite maturation inside the vector host. This study provides information about the protein composition in midgut tissue of female An. stephensi, which would be useful in understanding vector parasite interaction at molecular level and besides being useful in devising malaria transmission blocking strategies. The data of this study is related to the research article "Integrating transcriptomics and proteomics data for accurate assembly and annotation of genomes".

Rhegmatogenous retinal detachment in paediatric patients after pars plana vitrectomy and sutured scleral-fixated intraocular lenses.

PurposeTo report the incidence rate, management, and surgical outcomes of rhegmatogenous retinal detachment (RRD) in children who underwent pars plana vitrectomy (PPV) with sutured scleral-fixated intraocular lens implantation (SSFIOL).Patients and methodsOf the 279 eyes of 230 children who underwent PPV with SSFIOL at a tertiary eye care centre, 16 eyes of 15 children developed RRD. Retrospective analysis of the surgical details of RRD, the structural and functional outcomes was done.ResultsOf the 279 eyes of 230 children who underwent PPV with SSFIOL, RRD was seen in 5.7% of the eyes. Average age was 10.7 years (range 4-15 years). Indication for SSFIOL implantation was congenital subluxation of lens (8 eyes) and traumatic aphakia or lens subluxation (4 eyes each). PPV was done in 15 of the 16 eyes, and 1 patient underwent scleral buckling. Retina was attached at the last follow-up visit in 87.5% of the eyes with median number of surgeries being 1. BCVA at the time of retinal detachment, multiple surgeries, and PVR at presentation were associated with poor visual outcome.ConclusionSurgery for SSFIOL in our series of paediatric eyes was complicated by vision-threatening RRD in 5.7% of cases. Surgical outcome in eyes with RRD without PVR was better (100%) than that in those, where PVR had already set in (75%). Need for regular follow-up and self-monitoring of vision should be emphasized and discussed with the parents before surgical intervention.

Proteome data of Anopheles stephensi salivary glands using high-resolution mass spectrometry analysis.

The data article reports data of the proteins expressed in female Anopheles stephensi salivary glands. Proteomic data were acquired using high-resolution mass spectrometers - Orbitrap-Velos and Orbitrap-Elite. Samples derived from adult female A. stephensi salivary glands led to the identification of 4390 proteins. Mass spectrometry data were analyzed on Proteome Discoverer (Version 2.1) platform with Sequest and Mascot search engines. The identified proteins were analyzed for their Gene Ontology annotation, interaction network and their possible roles in vector-parasite interaction. The data provided here are related to our published article "Integrating transcriptomics and proteomics data for accurate assembly and annotation of genomes" (Prasad et al., 2017) [1].