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

Economic viability of large-scale production of the biocontrol agent Trichoderma harzianum Rifai

The economic viability of large scale production of the biocontrol agent Trichoderma harzianumeffective against the soil-borne disease Phytophthora foot rot (caused by  P. capsici)  of blackpepper (Piper nigrum) was studied.  The enterprise was highly profitable for the entrepreneurwith a benefit:cost ratio of 1.84. The investment returned a net present worth of Rs. 2,42,618@ 11% interest rate for 10 years period with an internal rate of return of 121%. &nbsp

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

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