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India is blessed with vast biodiversity and is a home to different native bird species. Out of all birds, domestic pigeons (Columba livia) are most commonly found in and around human localities. Various attractive types of pigeons are also being kept by humans as pets or companion. Hence, basic management practices (housing, feeding, grooming etc.) are important for general healthcare and well-being of pigeons. Diseases and disorders of pigeons are required to be explored considering their close proximity to humans and possibilities of disease transmission. Out of all diseases, ectoparasitic infestations are common in birds; however, their actual prevalence among pigeons kept in city areas is yet to be identified. A study was undertaken between September-2020 to March-2021 to assess prevalence of ectoparasites in 432 pigeons kept by different owners, sellers and at a shelter house in 05 cities of Gujarat state, India (viz., Rajkot, Patan, Ahmedabad, Bharuch and Himmatnagar). Two different lice (viz., Columbicola columbae and Menacanthus spp.), one type of fly (viz., Pseudolynchia spp.) and one type of tick (viz., Argas reflexus) could be observed on pigeons. The overall prevalence of lice infestation, fly infestation and tick infestation in pigeons (N = 432) was 46.46%, 27.55% and 11.34%, respectively. Clinical infestation by two or three different types of ectoparasites was also observed in some pigeons. The results indicate noticeable prevalence and distribution of ectoparasites among pigeons in cities of Gujarat highlighting a need to conduct wide-spread surveys to recognize their health impacts. [ABSTRACT FROM AUTHOR]

Ceramic BiFe1−xZnxO3 multiferroic samples were prepared by the solid combustion method for x = 0.1, 0.15, and 0.2. Structural, magnetic, and magnetocaloric properties of the multiferroics have been studied. For all samples, an antiferromagnetic phase transition is observed in the region of 630 K. With increase in x, the reduction in magnitude of magnetization and Neel temperature is observed. The magnetocaloric properties, entropy, relative cooling power, and heat capacity have been calculated within the framework of thermodynamic theory. It has been established that the maximum changes of magnetocaloric properties of multiferroics are observed in the region of magnetic phase transition. [ABSTRACT FROM AUTHOR]

Candida species are important pathogens of humans and the fourth most commonly isolated pathogen from nosocomial blood stream infections. Although Candida albicans is the principle causative agent of invasive candidosis, the incidence of Candida glabrata infections has rapidly grown. The reason for this increase is not fully understood, but it is clear that the species has a higher innate tolerance to commonly administered azole antifungals, in addition to being highly tolerant to stresses especially oxidative stress. Taking the approach that using the model organism, Saccharomyces cerevisiae , with its intrinsic sensitivity to oxidative stress, we hypothesized that by expressing mediators of stress resistance from C. glabrata in S. cerevisiae , it would result in induced resistance. To test this we transformed, en-masse, the C. glabrata ORFeome library into S. cerevisiae . This resulted in 1,500 stress resistant colonies and the recovered plasmids of 118 ORFs. Sequencing of these plasmids revealed a total of 16 different C. glabrata ORFs. The recovery of genes encoding known stress protectant proteins such as GPD1, GPD2 and TRX3 was predicted and validated the integrity of the screen. Through this screen we identified a C. glabrata unique ORF that confers oxidative stress resistance. We set to characterise this gene herein, examining expression in oxidative stress sensitive strains, comet assays to measure DNA damage and synthetic genetic array analysis to identify genetic interaction maps in the presence and absence of oxidative stress., (Copyright © 2020 Usher, Chaudhari, Attah, Ho and Haynes.)

Libraries of protein-encoding sequences can be generated by identification of open reading frames (ORFs) from a genome of choice that are then assembled into collections of plasmids termed ORFeome libraries. These represent powerful resources to facilitate functional genomic characterization of genes and their encoded products. Here, we report the generation of an ORFeome for Zymoseptoria tritici , which causes the most serious disease of wheat in temperate regions of the world. We screened the genome of strain IP0323 for high confidence gene models, identifying 4,075 candidates from 10,933 predicted genes. These were amplified from genomic DNA, were cloned into the Gateway entry vector pDONR207, and were sequenced, providing a total of 3,022 quality-controlled plasmids. The ORFeome includes genes predicted to encode effectors ( n = 410) and secondary metabolite biosynthetic proteins ( n = 171) in addition to genes residing at dispensable chromosomes ( n = 122) or those that are preferentially expressed during plant infection ( n = 527). The ORFeome plasmid library is compatible with our previously developed suite of Gateway destination vectors, which have various combinations of promoters, selection markers, and epitope tags. The Z. tritici ORFeome constitutes a powerful resource for functional genomics and offers unparalleled opportunities to understand the biology of Z. tritici .[Formula: see text] Copyright © 2019 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

The advent of the genomic era has made elucidating gene function on a large scale a pressing challenge. ORFeome collections, whereby almost all ORFs of a given species are cloned and can be subsequently leveraged in multiple functional genomic approaches, represent valuable resources toward this endeavor. Here we provide novel, genome-scale tools for the study of Candida albicans, a commensal yeast that is also responsible for frequent superficial and disseminated infections in humans. We have generated an ORFeome collection composed of 5099 ORFs cloned in a Gateway™ donor vector, representing 83% of the currently annotated coding sequences of C. albicans. Sequencing data of the cloned ORFs are available in the CandidaOrfDB database at http://candidaorfeome.eu. We also engineered 49 expression vectors with a choice of promoters, tags and selection markers and demonstrated their applicability to the study of target ORFs transferred from the C. albicans ORFeome. In addition, the use of the ORFeome in the detection of protein-protein interaction was demonstrated. Mating-compatible strains as well as Gateway™-compatible two-hybrid vectors were engineered, validated and used in a proof of concept experiment. These unique and valuable resources should greatly facilitate future functional studies in C. albicans and the elucidation of mechanisms that underlie its pathogenicity.

Targeted gene deletion has been instrumental in elucidating many aspects of Zymoseptoria tritici pathogenicity. Gene over-expression is a complementary approach that is amenable to rapid strain construction and high-throughput screening, which has not been exploited to analyze Z. tritici, largely due to a lack of available techniques. Here we exploit the Gateway® cloning technology for rapid construction of over-expression vectors and improved homologous integration efficiency of a Z. tritici Δku70 strain to build a pilot over-expression library encompassing 32 genes encoding putative DNA binding proteins, GTPases or kinases. We developed a protocol using a Rotor-HDA robot for rapid and reproducible cell pinning for high-throughput in vitro screening. This screen identified an over-expression strain that demonstrated a marked reduction in hyphal production relative to the isogenic progenitor. This study provides a protocol for rapid generation of Z. tritici over-expression libraries and a technique for functional genomic screening in this important pathogen., (Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.)

The lack of techniques for rapid assembly of gene deletion vectors, paucity of selectable marker genes available for genetic manipulation and low frequency of homologous recombination are major constraints in construction of gene deletion mutants in Zymoseptoria tritici. To address these issues, we have constructed ternary vectors for Agrobacterium tumefaciens mediated transformation of Z. tritici, which enable the single step assembly of multiple fragments via yeast recombinational cloning. The sulfonylurea resistance gene, which is a mutated allele of the Magnaporthe oryzae ILV2 gene, was established as a new dominant selectable marker for Z. tritici. To increase the frequency of homologous recombination, we have constructed Z. tritici strains deficient in the non-homologous end joining pathway of DNA double stranded break repair by inactivating the KU70 and KU80 genes. Targeted gene deletion frequency increased to more than 85% in both Z. tritici ku70 and ku80 null strains, compared to ⩽10% seen in the wild type parental strain IPO323. The in vitro growth and in planta pathogenicity of the Z. tritici ku70 and ku80 null strains were comparable to strain IPO323. Together these molecular tools add significantly to the platform available for genomic analysis through targeted gene deletion or promoter replacements and will facilitate large-scale functional characterization projects in Z. tritici., (Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.)

Gene overexpression is a widely used functional genomics approach in fungal biology. However, to date it has not been established in Zymoseptoria tritici which is an important pathogen of wheat (Triticum species). Here we report a suite of Gateway® recombination compatible ternary expression vectors for Agrobacterium tumefaciens mediated transformation of Z. tritici. The suite of 32 vectors is based on a combination of four resistance markers for positive selection against glufosinate ammonium, geneticin, hygromycin and sulfonylurea; three constitutive Z. tritici promoters (pZtATUB, pZtGAPDH and pZtTEF) and a nitrogen responsive promoter (pZtNIA1) for controlled expression of the open reading frames. Half of the vectors facilitate expression of proteins tagged with C-terminal EGFP. All 32 vectors allow high frequency targeting of the overexpression cassette into the Ku70 locus and complement the Ku70 gene when transformed into a Z. tritici ku70 null strain, thus circumventing additional phenotypes that can arise from random integration. This suite of ternary expression vectors will be a useful tool for functional analysis through gene overexpression in Z. tritici., (Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.)

This work demonstrates the efficacy of a support matrix prepared by plasma process for trypsin immobilization without any surface activator. Plasma polymerization cum sputtering process is used to prepare the nanocomposite support matrix. Plasma sputtered silver nanoparticles (AgNPs) are uniformly embedded into plasma polymerized aniline (PPAni) film. Various characterization tools are employed to study the surface morphology, microstructure and chemical composition of the support matrices. Trypsin is immobilized onto the support matrix via the formation of covalent bond between them. Plasma generated free radicals on composite films activate the support matrix and make it efficient for increasing the tertiary enzyme stability via multipoint covalent attachment. Trypsin immobilized onto Ag/PPAni matrix has more hydrolyzing capacity of bovine serum albumin (BSA) than free trypsin as well as trypsin immobilized onto PPAni films., (Copyright © 2014 Elsevier B.V. All rights reserved.)

Over-expression is a valid functional genomics approach to characterise genes of unknown function on a genome-wide scale. Strains are engineered to over-express a specific gene and the resulting gain-of-function phenotype assessed. Here, we describe the strategy we are adopting to synthesise a Candida albicans ORFeome collection and the options available to create over-expressing strains from this collection.

Position-sensitive avalanche photodiodes (PSAPDs) are gaining widespread acceptance in modern PET scanner designs, and owing to their relative insensitivity to magnetic fields, especially in those that are MRI-compatible. Flood histograms in PET scanners are used to determine the crystal of annihilation photon interaction and hence, for detector characterization and routine quality control. For PET detectors that use PSAPDs, flood histograms show a characteristic pincushion distortion when Anger logic is used for event positioning. A small rotation in the flood histogram is also observed when the detectors are placed in a magnetic field. We first present a general purpose automatic method for spatial distortion correction for flood histograms of PSAPD-based PET detectors when placed both inside and outside a MRI scanner. Analytical formulae derived for this scheme are based on a hybrid approach that combines desirable properties from two existing event positioning schemes. The rotation of the flood histogram due to the magnetic field is determined iteratively and is accounted for in the scheme. We then provide implementation details of a method for crystal identification we have previously proposed and evaluate it for cases when the PET detectors are both outside and in a magnetic field. In this scheme, Fourier analysis is used to generate a lower-order spatial approximation of the distortion-corrected PSAPD flood histogram, which we call the 'template'. The template is then registered to the flood histogram using a diffeomorphic iterative intensity-based warping scheme. The calculated deformation field is then applied to the segmentation of the template to obtain a segmentation of the flood histogram. A manual correction tool is also developed for exceptional cases. We present a quantitative assessment of the proposed distortion correction scheme and crystal identification method against conventional methods. Our results indicate that our proposed methods lead to a large reduction in manual labor and indeed can routinely be used for calibration and characterization studies in MRI-compatible PET scanners based on PSAPDs.