Qualitative Changes during Storage of Different Ginger-Based Spice Sauces

Ready-to-eat sauces have become a trend in all kinds of meals. Five ginger-based sauces viz., ginger, ginger-black pepper, ginger-nutmeg, ginger-kokum and ginger-nutmeg-kokum were prepared as per standard procedures. Physical, biochemical, microbiological and rheological properties of the sauces were recorded at regular intervals for 135 days. There was no significant variation in physical properties (total soluble solids) during storage but colour value varied significantly. Variation in chemical parameters like pH, content of moisture, proteins, carbohydrates and total sugars was non-significant, but variation in titratable acidity and reducing sugars was significant. Storage period did not affect total plate count, consistency index and flow behavior index of the sauces, which remained constant during the entire storage period. Sensory score of the sauces showed that acceptability was high for ginger sauce, followed by ginger-black pepper and ginger-nutmeg sauce

Paenibacillus glucanolyticus, a promising potassium solubilizing bacterium isolated from black pepper (Piper nigrum L.) rhizosphere

A bacterium possessing high ability to solubilize potash was isolated from the rhizosphere of black pepper. On the basis of biochemical and 16S rDNA sequence analysis, the bacterium was identified as Paenibacillus glucanolyticus strain IISRBK2. The optimal medium composition and cultural conditions for the isolation of P. glucanolyticus were sucrose 5.0 g, Na2HPO4 2.0 g, MgSO4.7H2O 2.0 g, FeCl3 0.005 g, CaCO3 0.1 g and wood ash 1.0 g at pH 7.5 at 30oC. The strain was also evaluated for plant growth and potassium (K) uptake of black pepper in soil artificially treated with 0.5,1 and 1.5g K kg-1 soil in the form of wood ash. In this study, wood ash was used as a source of K which contained 53.1 g Kg-1 K of which 4.5% was in insoluble form. Inoculation with strain P. glucanolyticus was found to increase tissue dry mass (ranging from 37.0% to 68.3%) of black pepper in 1g K kg-1wood ash amended soil. In the soil treated with 0.5 -1.5 g K kg-1, K uptake in live bacterium inoculated black pepper plants increased by 125.0-184.0% compared to uninoculated control. &nbsp

Occurrence and distribution of viral diseases on vanilla (Vanilla planifolia Andrews) in India

Sixty-five vanilla (Vanilla planifolia) plantations in 28 locations of Karnataka and Kerala were surveyed for the occurrence and distribution of viral diseases. Two viral diseases namely, mosaic and stem necrosis with an average incidence ranging from 0% to 5% and 0% to 10%, respectively, in various locations were noticed. The distribution of the diseases was random and not restricted to any particular region or locality. Electron microscopy of leaf dip preparations of the diseased plants showed three kinds of flexuous particles resembling Potexvirus, Potyvirus and Closterovirus, and an isometric particle. &nbsp

Hydrogen bonding in duplex DNA probed by DNP enhanced solid-state NMR N-H bond length measurements

Numerous biological processes and mechanisms depend on details of base pairing and hydrogen bonding in DNA. Hydrogen bonds are challenging to quantify by X-ray crystallography and cryo-EM due to difficulty of visualizing hydrogen atom locations but can be probed with site specificity by NMR spectroscopy in solution and the solid state with the latter particularly suited to large, slowly tumbling DNA complexes. Recently, we showed that low-temperature dynamic nuclear polarization (DNP) enhanced solid-state NMR is a valuable tool for distinguishing Hoogsteen base pairs (bps) from canonical Watson-Crick bps in various DNA systems under native-like conditions. Here, using a model 12-mer DNA duplex containing two central adenine-thymine (A-T) bps in either Watson-Crick or Hoogsteen confirmation, we demonstrate DNP solid-state NMR measurements of thymine N3-H3 bond lengths, which are sensitive to details of N-H···N hydrogen bonding and permit hydrogen bonds for the two bp conformers to be systematically compared within the same DNA sequence context. For this DNA duplex, effectively identical TN3-H3 bond lengths of 1.055 ± 0.011 Å and 1.060 ± 0.011 Å were found for Watson-Crick A-T and Hoogsteen A (syn)-T base pairs, respectively, relative to a reference amide bond length of 1.015 ± 0.010 Å determined for N-acetyl-valine under comparable experimental conditions. Considering that prior quantum chemical calculations which account for zero-point motions predict a somewhat longer effective peptide N-H bond length of 1.041 Å, in agreement with solution and solid-state NMR studies of peptides and proteins at ambient temperature, to facilitate direct comparisons with these earlier studies TN3-H3 bond lengths for the DNA samples can be readily scaled appropriately to yield 1.083 Å and 1.087 Å for Watson-Crick A-T and Hoogsteen A (syn)-T bps, respectively, relative to the 1.041 Å reference peptide N-H bond length. Remarkably, in the context of the model DNA duplex, these results indicate that there are no significant differences in N-H···N A-T hydrogen bonds between Watson-Crick and Hoogsteen bp conformers. More generally, high precision measurements of N-H bond lengths by low-temperature DNP solid-state NMR based methods are expected to facilitate detailed comparative analysis of hydrogen bonding for a range of DNA complexes and base pairing environments

Effect of biocontrol agents on production of rooted back pepper cutting in serpentine method

Availability of disease free quality planting material is a major limiting factor in black pepper cultivation. In order to meet the increasing demand and also to create awareness on good agricultural practices for healthy disease free planting material production to farmers, a nursery experiment was started with improved varieties of black pepper by adopting a non-chemical bio-intensive management strategy. Here solarization of potting mixture was the main concern followed my amending the solarized potting mixture with potential bioagents. The experiment was designed in a two factor CRD with four improved varieties and five treatments. Each treatment contains a combination of two bioagents with antifungal and nematicidal properties respectively. The common recommended fungicide Metalaxyl-Mancozeb (0.125%) and nematicide carbsosulfan (0.1%) was used as control. The treatments were incorporated individually into solarized potting mixture and planted with improved varieties used viz., IISR Girimunda, Malabar Excel, Shakti and Thevam, The plants in each treatment were kept for multiplication by serpentine method with proper irrigation and phytosanitation. The results of plant growth and establishment in different treatments, showed that  fortification of solarized potting mixture with Trichoderma harzianum + Pochonia chlamydosporia combination or combination of Streptomyces  strains  (Act 2+9) are significantly superior (35.46% and 21% respectively) for the production of healthy rooted planting material. IISR Malabar Excel and IISR Thevam produced the maximum  number of plants from a single node cutting in treatment with T. harzianum + P. chlamydosporia (T1) (59 nos. and 51 nos. respectively) followed by Malabar Excel with Act 2+9 and Act 5+9 (45 nos. each). So an average of 6-7 plants/month/cutting was produced in the potential treatment while it was only 3-4 plants in control. The advantage of the method is that, after solarization and fortification with respective bioagents, there is no need for further application of any fungicides, insecticides or any other nutrient spray as usually done. Thus the method of soil solarization followed by fortification of either T. harzianum+ P. chlamydosporia  or combination of Streptomyces strains viz., Ketasatospora setae (Act 2) and S. tauricus (Act9) is found suitable for the production of healthy quality planting material of high yielding varieties to meet the increasing demand of planting material with a C:B ratio of 1:2

Mitigating Phytophthora foot rot and slow decline diseases of black pepper through the deployment of bacterial antagonists

Field trial was conducted at ICAR-IISR Experimental Farm, Peruvannamuzhi, Kozhikode district, Kerala, during 2008-2013 using IPM modules. Planting materials of black pepper were produced by raising two node runners cuttings treated with chemicals and bioagents. A plot having non-living standards in 3 x 2 m spacing was selected. Pits of 50 cm3 were made and buffered with lime and cow dung. Planting was done with three month old rooted plants where roots were primed with respective bacterium/chemical. The experiment was in RCBD with eight treatments viz., Pseudomonas aeruginosa (Bp 35) + Phorate, P. putida (Bp 25) + Phorate, P. fluorescence (IISR 6)  (later identified as P.aeruginosa) + Phorate, Bacillus megaterium (Bp 17) + Metalaxyl Mz, Curtobacterium luteum (TC10) + Metalaxyl Mz, P. aeruginosa (IISR 853) + Metalaxyl Mz and Phorate + Metalaxyl Mz (chemical check) and an absolute control having no treatments.  The differential treatments were imposed at planting in May and subsequent application in September and thereafter every year. Initial two years, plants were maintained weed free by plastic mulching. Commonly, shade and irrigation were provided during summer in the first two years and thereafter only mulching and irrigation were continued. All the plants were sprayed with ZnSO4 (0.25%), DAP (0.5%) and MgSO4 (0.25%) during May and September from second year onwards. For controlling ‘Pollu’ beetle (Longitarsus nigripennis) and anthracnose (Colletotrichum gloeosporioides), quinalphos (0.075%) + Bordeaux mixture (1%) was sprayed twice during September and November. Soil biological properties and pathogen population were monitored regularly. No foot rot incidence due to Phytophthora spp. could be noticed in any of the treatments till the end of the experimental period. However, nematode infection, manifested as yellowing of the vines, as well as nematode population showed a gradual increase. Among the treatments, C. luteum (TC 10) with Metalaxyl- Mz showed significant reduction in nematode population and also showed better performance in growth and yield

Clinical Utility of a Unique Genome-Wide DNA Methylation Signature for KMT2A-Related Syndrome

Wiedemann\u2013Steiner syndrome (WDSTS) is a Mendelian syndromic intellectual disability (ID) condition associated with hypertrichosis cubiti, short stature, and characteristic facies caused by pathogenic variants in the KMT2A gene. Clinical features can be inconclusive in mild and unusual WDSTS presentations with variable ID (mild to severe), facies (typical or not) and other associated malformations (bone, cerebral, renal, cardiac and ophthalmological anomalies). Interpretation and classification of rare KMT2A variants can be challenging. A genome-wide DNA methylation episignature for KMT2A-related syndrome could allow functional classification of variants and provide insights into the pathophysiology of WDSTS. Therefore, we assessed genome-wide DNA methylation profiles in a cohort of 60 patients with clinical diagnosis for WDSTS or Kabuki and identified a unique highly sensitive and specific DNA methylation episignature as a molecular biomarker of WDSTS. WDSTS episignature enabled classification of variants of uncertain significance in the KMT2A gene as well as confirmation of diagnosis in patients with clinical presentation of WDSTS without known genetic variants. The changes in the methylation profile resulting from KMT2A mutations involve global reduction in methylation in various genes, including homeobox gene promoters. These findings provide novel insights into the molecular etiology of WDSTS and explain the broad phenotypic spectrum of the disease

Ensembl Genomes 2022: an expanding genome resource for non-vertebrates

Ensembl Genomes (https://www.ensemblgenomes.org) provides access to non-vertebrate genomes and analysis complementing vertebrate resources developed by the Ensembl project (https://www.ensembl.org). The two resources collectively present genome annotation through a consistent set of interfaces spanning the tree of life presenting genome sequence, annotation, variation, transcriptomic data and comparative analysis. Here we present our largest increase in plant, metazoan and fungal genomes since the project’s inception creating one of the world’s most comprehensive genomic resources and describe our efforts to reduce genome redundancy in our Bacteria portal. We also detail our new efforts in gene annotation, our emerging support for pangenome analysis and efforts to accelerate data dissemination through the Ensembl Rapid Release resource. We also present our new AlphaFold visualisation. Finally, we present details of our future plans including updates on our integration with Ensembl, and how we plan to improve our support for the microbial research community. Software and data are made available without restriction via our website, online tools platform and programmatic interfaces (available under an Apache 2.0 license). Data updates are synchronised with Ensembl’s release cycle

Pneumococcal lineages associated with serotype replacement and antibiotic resistance in childhood invasive pneumococcal disease in the post-PCV13 era: an international whole-genome sequencing study

Background: Invasive pneumococcal disease remains an important health priority owing to increasing disease incidence caused by pneumococci expressing non-vaccine serotypes. We previously defined 621 Global Pneumococcal Sequence Clusters (GPSCs) by analysing 20 027 pneumococcal isolates collected worldwide and from previously published genomic data. In this study, we aimed to investigate the pneumococcal lineages behind the predominant serotypes, the mechanism of serotype replacement in disease, as well as the major pneumococcal lineages contributing to invasive pneumococcal disease in the post-vaccine era and their antibiotic resistant traits. / Methods: We whole-genome sequenced 3233 invasive pneumococcal disease isolates from laboratory-based surveillance programmes in Hong Kong (n=78), Israel (n=701), Malawi (n=226), South Africa (n=1351), The Gambia (n=203), and the USA (n=674). The genomes represented pneumococci from before and after pneumococcal conjugate vaccine (PCV) introductions and were from children younger than 3 years. We identified predominant serotypes by prevalence and their major contributing lineages in each country, and assessed any serotype replacement by comparing the incidence rate between the pre-PCV and PCV periods for Israel, South Africa, and the USA. We defined the status of a lineage as vaccine-type GPSC (≥50% 13-valent PCV [PCV13] serotypes) or non-vaccine-type GPSC (>50% non-PCV13 serotypes) on the basis of its initial serotype composition detected in the earliest vaccine period to measure their individual contribution toward serotype replacement in each country. Major pneumococcal lineages in the PCV period were identified by pooled incidence rate using a random effects model. / Findings: The five most prevalent serotypes in the PCV13 period varied between countries, with only serotypes 5, 12F, 15B/C, 19A, 33F, and 35B/D common to two or more countries. The five most prevalent serotypes in the PCV13 period varied between countries, with only serotypes 5, 12F, 15B/C, 19A, 33F, and 35B/D common to two or more countries. These serotypes were associated with more than one lineage, except for serotype 5 (GPSC8). Serotype replacement was mainly mediated by expansion of non-vaccine serotypes within vaccine-type GPSCs and, to a lesser extent, by increases in non-vaccine-type GPSCs. A globally spreading lineage, GPSC3, expressing invasive serotypes 8 in South Africa and 33F in the USA and Israel, was the most common lineage causing non-vaccine serotype invasive pneumococcal disease in the PCV13 period. We observed that same prevalent non-vaccine serotypes could be associated with distinctive lineages in different countries, which exhibited dissimilar antibiotic resistance profiles. In non-vaccine serotype isolates, we detected significant increases in the prevalence of resistance to penicillin (52 [21%] of 249 vs 169 [29%] of 575, p=0·0016) and erythromycin (three [1%] of 249 vs 65 [11%] of 575, p=0·0031) in the PCV13 period compared with the pre-PCV period. / Interpretation: Globally spreading lineages expressing invasive serotypes have an important role in serotype replacement, and emerging non-vaccine serotypes associated with different pneumococcal lineages in different countries might be explained by local antibiotic-selective pressures. Continued genomic surveillance of the dynamics of the pneumococcal population with increased geographical representation in the post-vaccine period will generate further knowledge for optimising future vaccine design. / Funding: Bill & Melinda Gates Foundation, Wellcome Sanger Institute, and the US Centers for Disease Control

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Not AvailableMethanol, a by-product associated with plant metabolism, is a substrate for pink pigmented facultative methylotrophs (PPFMs) of phyllosphere. The symbiotic interaction of PPFMs has many desirable effects on plant growth and disease resistance. The present study investigated the potential of native PPFMs for mitigating biotic stress and plant growth promotion in ginger. PPFMs were isolated from ginger phyllosphere by leaf imprint technique and screened against major fungal phytopathogens of ginger viz. Macrophomina phaseolina, Sclerotium rolfsii, Pythium myriotylum, Colletotrichum gloeosporioides and Fusarium oxysporum. Among the 60 PPFMs, IISRGPPFM13 was selected for its highly inhibitory activity against the target pathogens. The isolate was useful for mineral solubility, production of IAA, siderophores and hydrolytic enzymes like cellulase, pectinase, lipase, amylase and chitinase. On in planta experiments revealed that IISRGPPFM13 considerably increased plant growth parameters when the bacterium was applied as soil drenching cum foliar spraying. Methanol utilization potential of the isolate was confirmed by mxaF gene analysis where the sequence showing 95.51% identity towards Methylobacterium platani and M. iners. Further, 16S rRNA gene sequence showing 98.73% identity with M. komagatae 002-079 T (AB252201). This is the first report of its kind that a genus of Methylobacterium with biostimulant potential isolated from the phyllosphere of ginger.Not Availabl