Deciphering the Genomic Landscape and Virulence Mechanisms of the Wheat Powdery Mildew Pathogen Blumeria graminis f. sp. tritici Wtn1: Insights from Integrated Genome Assembly and Conidial Transcriptomics.

A high-quality genome sequence from an Indian isolate of Blumeria graminis f. sp. tritici Wtn1, a persistent threat in wheat farming, was obtained using a hybrid method. The assembly of over 9.24 million DNA-sequence reads resulted in 93 contigs, totaling a 140.61 Mb genome size, potentially encoding 8480 genes. Notably, more than 73.80% of the genome, spanning approximately 102.14 Mb, comprises retro-elements, LTR elements, and P elements, influencing evolution and adaptation significantly. The phylogenomic analysis placed B. graminis f. sp. tritici Wtn1 in a distinct monocot-infecting clade. A total of 583 tRNA anticodon sequences were identified from the whole genome of the native virulent strain B. graminis f. sp. tritici, which comprises distinct genome features with high counts of tRNA anticodons for leucine (70), cysteine (61), alanine (58), and arginine (45), with only two stop codons (Opal and Ochre) present and the absence of the Amber stop codon. Comparative InterProScan analysis unveiled "shared and unique" proteins in B. graminis f. sp. tritici Wtn1. Identified were 7707 protein-encoding genes, annotated to different categories such as 805 effectors, 156 CAZymes, 6102 orthologous proteins, and 3180 distinct protein families (PFAMs). Among the effectors, genes like Avra10, Avrk1, Bcg-7, BEC1005, CSEP0105, CSEP0162, BEC1016, BEC1040, and HopI1 closely linked to pathogenesis and virulence were recognized. Transcriptome analysis highlighted abundant proteins associated with RNA processing and modification, post-translational modification, protein turnover, chaperones, and signal transduction. Examining the Environmental Information Processing Pathways in B. graminis f. sp. tritici Wtn1 revealed 393 genes across 33 signal transduction pathways. The key pathways included yeast MAPK signaling (53 genes), mTOR signaling (38 genes), PI3K-Akt signaling (23 genes), and AMPK signaling (21 genes). Additionally, pathways like FoxO, Phosphatidylinositol, the two-component system, and Ras signaling showed significant gene representation, each with 15-16 genes, key SNPs, and Indels in specific chromosomes highlighting their relevance to environmental responses and pathotype evolution. The SNP and InDel analysis resulted in about 3.56 million variants, including 3.45 million SNPs, 5050 insertions, and 5651 deletions within the whole genome of B. graminis f. sp. tritici Wtn1. These comprehensive genome and transcriptome datasets serve as crucial resources for understanding the pathogenicity, virulence effectors, retro-elements, and evolutionary origins of B. graminis f. sp. tritici Wtn1, aiding in developing robust strategies for the effective management of wheat powdery mildew.

Rice foliar-adapted Pantoea species: Promising microbial biostimulants enhancing rice resilience against foliar pathogens, Magnaporthe oryzae and Xanthomonas oryzae pv. oryzae.

Foliar fungal blast and bacterial leaf blight have significant impacts on rice production, and their management through host resistance and agrochemicals has proven inadequate. To achieve their sustainable management, innovative approaches like leveraging the foliar microbiome, which collaborates with plants and competes against pathogens, are essential. In our study, we isolated three Pantoea strains (P. agglomerans Os-Ep-PPA-1b, P. vagans Os-Ep-PPA-3b, and P. deleyi Os-Ep-VPA-9a) from the rice phylloplane. These isolates exhibited antimicrobial action through their metabolome and volatilome, while also promoting rice growth. Our analysis, using Gas Chromatography-Mass Spectrometry (GC-MS), revealed the presence of various antimicrobial compounds such as esters and fatty acids produced by these Pantoea isolates. Inoculating rice seedlings with P. agglomerans and P. vagans led to increased root and shoot growth. Additionally, bacterized seedlings displayed enhanced immunocompetence, as evidenced by upregulated expressions of defense genes (OsEDS1, OsFLS2, OsPDF2.2, OsACO4, OsICS OsPR1a, OsNPR1.3, OsPAD4, OsCERK1.1), along with heightened activities of defense enzymes like Polyphenol Oxidase and Peroxidase. These plants also exhibited elevated levels of total phenols. In field trials, the Pantoea isolates contributed to improved plant growth, exemplified by increased flag-leaf length, panicle number, and grains per panicle, while simultaneously reducing the incidence of chaffy grains. Hypersensitivity assays performed on a model plant, tobacco, confirmed the non-pathogenic nature of these Pantoea isolates. In summary, our study underscores the potential of Pantoea bacteria in combatting rice foliar diseases. Coupled with their remarkable growth-promoting and biostimulant capabilities, these findings position Pantoea as promising agents for enhancing rice cultivation.

Enhancing defense against rice blast disease: Unveiling the role of leaf endophytic firmicutes in antifungal antibiosis and induced systemic resistance.

Rice remains the primary staple for more than half of the world's population, yet its cultivation faces numerous challenges, including both biotic and abiotic stresses. One significant obstacle is the prevalence of rice blast disease, which substantially diminishes productivity and increases cultivation costs due to frequent fungicide applications. Consequently, the presence of fungicide residues in rice raises concerns about compliance with international maximum residue limits (MRLs). While host resistance has proven effective, it often remains vulnerable to new variants of the Magnaporthe oryzae pathogen. Therefore, there is a critical need to explore innovative management strategies that can complement or enhance existing methods. An unexplored avenue involves harnessing endophytic bacterial communities. To this end, the present study investigates the potential of eleven endophytic Bacillus spp. in suppressing Pyricularia oryzae, promoting plant growth, and eliciting a defense response through phyllobacterization. The results indicate that the secreted metabolome and volatilome of seven tested isolates demonstrate inhibitory effects against P.oryzae, ranging from a minimum of 40% to a maximum of 70%. Bacillus siamensis L34, B. amyloliquefaciens RA37, B. velezensis L12, and B. subtilis B18 produce antifungal antibiotics targeting P.oryzae. Additionally, B. subtilis S4 and B. subtilis S6 emerge as excellent inducers of systemic resistance against blast disease, as evidenced by elevated activity of biochemical defense enzymes such as peroxidase, polyphenol oxidase, and total phenol content. However, a balance between primary metabolic activity (e.g., chlorophyll content, chlorophyll fluorescence, and photosynthetic rate) and defense activity is observed. Furthermore, specific endophytic Bacillus spp. significantly stimulates defense-related genes, including OsPAD4, OsFMO1, and OsEDS1. These findings underscore the multifaceted potential of endophytic Bacillus in managing blast disease through antibiosis and induced systemic resistance. In conclusion, this study highlights the promising role of endophytic Bacillus spp. as a viable option for blast disease management. Their ability to inhibit the pathogen and induce systemic resistance makes them a valuable addition to the existing strategies. However, it is crucial to consider the trade-off between primary metabolic activity and defense response when implementing these bacteria-based approaches.

Unraveling the transcriptional network regulated by miRNAs in blast-resistant and blast-susceptible rice genotypes during Magnaporthe oryzae interaction.

The plant pathogen Magnaporthe oryzae poses a significant threat to global food security, and its management through the cultivation of resistant varieties and crop husbandry practices, including fungicidal sprays, has proven to be inadequate. To address this issue, we conducted small-RNA sequencing to identify the roles of miRNAs and their target genes in both resistant (PB1637) and susceptible (PB1) rice genotypes. We confirmed the expression of differentially expressed miRNAs using stem-loop qRT-PCR analysis and correlated them with rice patho-phenotypic and physio-biochemical responses. Our findings revealed several noteworthy differences between the resistant and susceptible genotypes. The resistant genotype exhibited reduced levels of total chlorophyll and carotenoids compared to the susceptible genotype. However, it showed increased levels of total protein, callose, H2O2, antioxidants, flavonoids, and total polyphenols. Additionally, among the defense-associated enzymes, guaiacol peroxidase and polyphenol oxidase responses were higher in the susceptible genotypes. In our comparative analysis, we identified 27 up-regulated and 43 down-regulated miRNAs in the resistant genotype, while the susceptible genotype exhibited 44 up-regulated and 62 down-regulated miRNAs. Furthermore, we discovered eight up-regulated and five down-regulated miRNAs shared between the resistant and susceptible genotypes. Notably, we also identified six novel miRNAs in the resistant genotype and eight novel miRNAs in the susceptible genotype. These novel miRNAs, namely Chr8_26996, Chr12_40110, and Chr12_41899, were found to negatively correlate with the expression of predicted target genes, including Cyt-P450 monooxygenase, serine carboxypeptidase, and zinc finger A20 domain-containing stress-associated protein, respectively. The results of our study on miRNA and transcriptional responses provide valuable insights for the development of future rice lines that are resistant to blast disease. By understanding the roles of specific miRNAs and their target genes in conferring resistance, we can enhance breeding strategies and improve crop management practices to ensure global food security.

New Insights on Endophytic Microbacterium-Assisted Blast Disease Suppression and Growth Promotion in Rice: Revelation by Polyphasic Functional Characterization and Transcriptomics.

Plant growth-promoting endophytic microbes have drawn the attention of researchers owing to their ability to confer fitness benefits in many plant species. Here, we report agriculturally beneficial traits of rice-leaf-adapted endophytic Microbacterium testaceum. Our polyphasic taxonomic investigations revealed its identity as M. testaceum. The bacterium displayed typical endophytism in rice leaves, indicated by the green fluorescence of GFP-tagged M. testaceum in confocal laser scanning microscopy. Furthermore, the bacterium showed mineral solubilization and production of IAA, ammonia, and hydrolytic enzymes. Tobacco leaf infiltration assay confirmed its non-pathogenic nature on plants. The bacterium showed antifungal activity on Magnaporthe oryzae, as exemplified by secreted and volatile organic metabolome-mediated mycelial growth inhibition. GC-MS analysis of the volatilome of M. testaceum indicated the abundance of antimicrobial compounds. Bacterization of rice seedlings showed phenotypic traits of MAMP-triggered immunity (MTI), over-expression of OsNPR1 and OsCERK, and the consequent blast suppressive activity. Strikingly, M. testaceum induced the transcriptional tradeoff between physiological growth and host defense pathways as indicated by up- and downregulated DEGs. Coupled with its plant probiotic features and the defense elicitation activity, the present study paves the way for developing Microbacterium testaceum-mediated bioformulation for sustainably managing rice blast disease.

FastSS: Fast and smooth segmentation of JPEG compressed printed text documents using DC and AC signal analysis.

With the surge of COVID-19 pandemic, the world is moving towards digitization and automation more than it was presumed. The Internet is becoming one of the popular mediums for communication, and multimedia (image, audio, and video) combined with data compression techniques play a pivotal role in handling a huge volume of data that is being generated on a daily basis. Developing novel algorithms for automatic analysis of compressed data without decompression is the need of the present hour. JPEG is a popular compression algorithm supported in the digital electronics world that achieves compression by dividing the whole image into non-overlapping blocks of 8 × 8 pixels, and subsequently transforming each block using Discrete Cosine Transform (DCT). This research paper proposes to carry out Fast and Smooth Segmentation (FastSS) directly in JPEG compressed printed text document images at text-line and word-level using DC and AC signals. From each 8 × 8 block, DC and AC signals are analyzed for accomplishing Fast and Smooth segmentation, and subsequently, two Faster segmentation (MFastSS) algorithms are also devised using low resolution-images generated by mapping the DC signal (DC Reduced Image) and encoded DCT (ECM Image) coefficients separately. Proposed models are tested on various JPEG compressed printed text document images created with varied space and fonts. The experimental results have demonstrated that the direct analysis of compressed streams is computationally efficient, and has achieved speed gain more than 90% when compared to uncompressed domains.

Recurrent upper extremity arterial thrombosis preceding a diagnosis of COVID-19.

Arterial thrombosis occurs when there is endothelial damage in the setting of hypercoagulability and arterial blood stasis. COVID-19 has been theorized to cause both endothelial damage and promote hypercoagulability by causing an imbalance of clotting factors. In many studies, there have been a large proportion of COVID-19 patients that suffered a thromboembolic event, in both the venous and arterial systems. Our patient, who did not have a significant past medical history, presented with a recurrent brachial artery occlusion despite medical and surgical management, and subsequently tested positive for COVID-19 late in his admission. In conclusion, there is high suspicion that there is a relationship between COVID-19 infection and recurrent arterial thrombosis.

Hierarchical Nanoflowers of MgFe2O4, Bentonite and B-,P- Co-Doped Graphene Oxide as Adsorbent and Photocatalyst: Optimization of Parameters by Box-Behnken Methodology.

In the present study, nanocomposites having hierarchical nanoflowers (HNFs) -like morphology were synthesized by ultra-sonication approach. HNFs were ternary composite of MgFe2O4 and bentonite with boron-, phosphorous- co-doped graphene oxide (BPGO). The HNFs were fully characterized using different analytical tools viz. X-ray photoelectron spectroscopy, scanning electron microscopy, energy dispersion spectroscopy, transmission electron microscopy, X-ray diffraction, vibrating sample magnetometry and Mössbauer analysis. Transmission electron micrographs showed that chiffon-like BPGO nanosheets were wrapped on the MgFe2O4-bentonite surface, resulting in a porous flower-like morphology. The red-shift in XPS binding energies of HNFs as compared to MgFe2O4-bentoniteand BPGO revealed the presence of strong interactions between the two materials. Box-Behnken statistical methodology was employed to optimize adsorptive and photocatalytic parameters using Pb(II) and malathion as model pollutants, respectively. HNFs exhibited excellent adsorption ability for Pb(II) ions, with the Langmuir adsorption capacity of 654 mg g-1 at optimized pH 6.0 and 96% photocatalytic degradation of malathion at pH 9.0 as compared to MgFe2O4-bentonite and BPGO. Results obtained in this study clearly indicate that HNFs are promising nanocomposite for the removal of inorganic and organic contaminants from the aqueous solutions.

Comparison of various delignification/desilication pre-treatments and indigenous fungal cellulase for improved hydrolysis of paddy straw.

The efficient removal of lignin and silica from paddy straw is essential for its volarization into biofuels and other value-added products. In this work, different chemical pre-treatments viz. acid/alkali, organosolv and deep eutectic solvents were carried out to assess the extent of delignification and desilication of paddy straw. Maximum lignin and silica removal of 96.08 and 95.51% was observed with two step acid (0.5% sulphuric acid) followed by alkali (4% sodium hydroxide) pre-treatment with significantly low total lignin (2.30%) and silica content (0.80%) of the treated straw residue. The treated straw residue contained significantly high holocellulose (91.65%), cellulose (75.01%) and hemicellulose content (16.64%). Among the four indigenous fungal isolates, Penicillium mallochii (JS17) cellulase showed better accessibility for the treated straw residue with maximum release of 504.18 mg g-1 of reducing sugars and saccharification efficiency of 56.90%. The two-step acid/alkali pre-treatment of paddy straw was highly effective for removing lignin and silica from paddy straw, thereby, resulting in enhanced enzymatic accessibility of the substrate and more efficient hydrolysis of cellulose into fermentable sugars.

Evaluation of polyphenols enriched dairy products developed by incorporating black carrot (Daucus carota L.) concentrate.

BACKGROUND: Dairy products like ice cream, yogurt and buttermilk are consumed widely due to their rich taste but these products lack anthocyanins, which are polyphenol and exhibit great antioxidant activity in both in vivo and in vitro studies. Therefore, adding a natural source of these antioxidants to the commonly consumed dairy product will be beneficial to the masses. Among all the sources, black carrots are the extraordinary and cheapest source of anthocyanins, which are commonly consumed as a natural fermented drink. In this study, an attempt has been made to examine the feasibility of black carrot concentrate as an ingredient into dairy products. METHODOLOGY: Ice cream, yogurt and buttermilk were prepared by incorporating black carrot concentrate at 2.5, 5.0, 7.5 and 10% level and were subjected to sensory analysis. The most acceptable products with 7.5% black carrot concentrate were analyzed for minerals, polyphenols and antioxidant activity. Effects of storage on physicochemical, microbial and sensory attributes of black carrot concentrate incorporated dairy products were further analyzed. RESULTS: Sensory analysis revealed that black carrot concentrate could be used up to 7.5% as an ingredient into dairy product with high acceptability. Significant improvement in mineral content (Mg and Fe), polyphenols and antioxidant activity were reported in black carrot concentrate added dairy products. Developed dairy products exhibited an excellent amount of 24.52-113.27 mg/100g anthocyanins. Flavonoids increased by 14.52-34.62 times and Folin-Ciocalteu reducing capacity increased by 26.39-35.87 times in experimental dairy products. The storage study revealed that ice cream could be stored for more than 60 days, yogurt up to 5 days and buttermilk up to 10 days with excellent stability attributes. CONCLUSION: Incorporation of black carrot concentrate at the level of 7.5% resulted in high acceptability and exceptional nutraceutical property of dairy products. Incorporation of black carrot concentrate into dairy products would enhance the nutraceutical properties and mineral content of food, which could be highly significant in preventing hidden hunger and oxidative stress-induced disorders in developing countries.

Evaluation of mature miR398 family, expression analysis and the post-transcriptional regulation evidence in gamma-irradiated and nitrogen-stressed Medicago sativa seedlings.

BACKGROUND: The miR398 (microRNA398) posttranscriptionally regulates the superoxide dismutase (Cu/Zn-SOD). MATERIALS AND METHODS: The miR398 level was quantitated in gamma-irradiated (20Gy and 200Gy) and nitrogen-stressed seedlings by stem-loop RT-PCR (Real Time-Polymerase chain reaction). The positional preference of nucleotide (nt) for miR398 families and new targets was done. The SOD enzyme was assayed in native PAGE (Polyacrylamide gel electrophoresis). RESULTS: A relative increase in miR398-3p expression in the roots, and reduction in shoots for gamma-irradiated tissue and downregulation in miR398-5p in shoots is noted. The nitrogen stress shows upregulation of miR398-3p in roots and shoots, whereas the expression of miR398-5p is upregulated in roots and downregulated in shoots. Positional preference in miR398-3p for 1-14 nt is 90% conserved unlike miR398-5p where no nucleotide positional preference is seen. Targets obtained were functionally characterized. CONCLUSIONS: The mature miR398-5p and miR398-3p levels estimated in gamma-irradiated (20 and 200Gy) and nitrogen-stressed Medicago sativa seedlings show differential levels in roots and shoots. Native PAGE of Cu/Zn-SOD suggests its negative correlation with miR398 in shoots of irradiated and nitrogen-stressed samples. The nucleotide preferences for the nucleotide for a given position and functional characterization of targets are reported herein.

Position Based Nucleotide Analysis of miR168 Family in Higher Plants and its Targets in Mammalian Transcripts.

BACKGROUND: miRNA are the post transcriptional regulator of the genes. The conserved miR168 family is evaluated for position based nucleotide preference in higher plants. Low density lipoprotein receptor adaptor protein 1 (LDLRAP1) target validated for miR168a obtained from rice origin is reported. METHODS: The mature miRNA sequences include miR168-5p and miR168-3p, were obtained from miRBase (v21, June 2014) for 15 families (28 plants). The preferred position based nucleotide sequences were obtained using Data Analysis in Molecular Biology and Evolution software. The miR168-5p was subjected to cross kingdom analysis using psRNATarget. Target expression and functional annotation was analyzed by using Human Protein Atlas database WEB-based Gene SeTAnaLysis Toolkit. RESULTS: miR168-5p shows same nucleotides at positions 1-6, 8-9, 11-12, 15-17 and 19. Also, miR168-3p is present in 3 families (10 plants) shows the same nucleotide at position 1-11, 13-15 and 17-21. The 123 targets in human transcriptome were identified showing 58% cleavage and 41% translation repression. Low density lipoprotein receptor adaptor protein 1 (LDLRAP1) target validated for miR168a obtained from rice origin, could also be targeted from miR168 from any other plant sources. The randomly selected 10 targets include some important genes likeRPL34, ATXN1, AKAPI3 and ALS2 and is involved in transcription, cell trafficking, cell metabolism and neurodegenerative disorder. CONCLUSION: Our work suggests that miR168 family has conserved sequence in higher plants. The seed region position 2-8 shows 70-95% pairing with human targets. Cleavage site at position 10-14 and these were analysed for the base preference with the targets showed 80-96% Watson Crick pairing.

Nutritional profiles of urban and rural men of Punjab with regard to dietary fat intake.

This study was undertaken to determine the quantity and type of fat consumed by urban and rural men in relation to BMI. Researchers surveyed 200 Punjabi men from rural and urban areas of Ludhiana District; total fat intake (74 g/day) by urban men was significantly more than that of men in rural areas. The energy percentage from total fat was positively and significantly (p ≤ .05) associated with BMI, accounting for 3.1%, 4.2%, and 2.9% of variation in the rural, urban, and total sample, respectively. Fatty-acid ratios were closer to recommendations for urban men than for men from rural areas.

A site for direct integrin αvß6·uPAR interaction from structural modelling and docking.

Integrin αvß6 is an epithelially-restricted heterodimeric transmembrane glycoprotein, known to interact with the urokinase plasminogen activating receptor (uPAR), playing a critical role in cancer progression. While the X-ray crystallographic structures of segments of other integrin heterodimers are known, there is no structural information for the complete αvß6 integrin to assess its direct interaction with uPAR. We have performed structural analysis of αvß6·uPAR interactions using model data with docking simulations to pinpoint their interface, in accord with earlier reports of the ß-propeller region of integrin α-chain interacting with uPAR. Interaction of αvß6·uPAR was demonstrated by our previous study using immunoprecipitation coupled with proteomic analysis by mass spectrometry. Recently this interaction was validated with proximity ligation assays and peptide arrays. The data suggested that two potential peptide regions from domain II and one peptide region from domain III of uPAR, interact with αvß6 integrin. Only the peptide region from domain III is consistent with the three-dimensional interaction site proposed in this study. The molecular basis of integrin αvß6·uPAR binding using structural data is discussed for its implications as a potential therapeutic target in cancer management.

Combined carbon dioxide laser with photodynamic therapy for nodular and superficial basal cell carcinoma.

BACKGROUND: Basal cell carcinomas (BCCs) are often seen by general practitioners, plastic surgeons, and dermatologists in the outpatient setting. Photodynamic therapy (PDT) and CO2 laser when used as monotherapy have been successfully used to treat small BCC, with greatest success in the superficial histological subtype but have limitations compared to surgical excision due to a limited depth of penetration of PDT (2 mm absorption) limiting efficacy. We describe our experience of dual-modality treatment improving efficacy, cosmetic outcomes, and minimizing recurrence. METHODS: One hundred ten patients with a total of 177 lesions mainly on the head and neck were treated with combined therapy using an UltraPulse CO2 laser and PDT using methyl aminolevulinate (METVIX) at the same sitting, with repeat PDT 1 week later. We evaluated recurrences, cosmetic outcomes, patient satisfaction, and costs. RESULTS: The mean age of patients was 67 years. The mean follow-up period was 32.2 months, with a range of 7.7 to 68.5 months. Eighty six lesions were followed up for more than 3 years. A total of 177 lesions were diagnosed and treated. Only biopsy-proven BCCs were included in this study. Histologically, 34 (19.2%) were superficial subtype, 50 (28.2%) nodular, 9 (5.08%) infiltrative, 7 (3.95%) morpheic, 3 (1.69%) mixed, and in 74 (41.8%) diagnosis was simply BCC. All lesions responded to treatment as assessed by clinical evaluation with regular follow-up. The total recurrence-free rate was 97.1%. In 88.1% lesions, a single cycle of treatment was required; 9.03% had 2 cycles and 0.56% underwent 3 cycles. In 3 of the patients, no data were available. Recurrences were noted in 5 (2.82%) cases. All recurrences were treated successfully, all but one using repeat laser-PDT. One patient underwent surgical excision. No significant complications were encountered, although mild hypopigmentation was occasionally seen and some discomfort is experienced with PDT. CONCLUSIONS: Combined CO2 laser and PDT have equivalent cure rates to surgery for BCCs--notably of the nodular subtype--these modalities acting synergistically. This strategy provides cure often with scarless outcomes as illustrated. Laser with PDT is most appropriate for patients who value excellent cosmetic outcomes and where avoidance of an invasive procedure is an important factor. In addition, this modality comes into its own for specific groups of patients, such as those on Warfarin or those with diffuse or multiple lesions.

Unlocking the puzzling biology of the black Périgord truffle Tuber melanosporum.

The black Périgord truffle (Tuber melanosporum Vittad.) is a highly prized food today, with its unique scent (i.e., perfume) and texture. Despite these attributes, it remains relatively poorly studied, lacking "omics" information to characterize its biology and biochemistry, especially changes associated with freshness and the proteins/metabolites responsible for its organoleptic properties. In this study, we have functionally annotated the truffle proteome from the 2010 T. melanosporum genome comprising 12,771 putative nonredundant proteins. Using sequential BLAST search strategies, we identified homologues for 2587 proteins with 2486 (96.0%) fungal homologues (available from http://biolinfo.org/protannotator/blacktruffle.php). A combined 1D PAGE and high-accuracy LC-MS/MS proteomic study was employed to validate the results of the functional annotation and identified 836 (6.5%) proteins, of which 47.5% (i.e., 397) were present in our bioinformatics studies. Our study, functionally annotating 6487 black Périgord truffle proteins and confirming 836 by proteomic experiments, is by far the most comprehensive study to date contributing significantly to the scientific community. This study has resulted in the functional characterization of novel proteins to increase our biological understanding of this organism and to uncover potential biomarkers of authenticity, freshness, and perfume maturation.

Molecular prevalence of Babesia bigemina and Trypanosoma evansi in dairy animals from Punjab, India, by duplex PCR: a step forward to the detection and management of concurrent latent infections.

Specific duplex polymerase chain reaction (PCR) was employed on 411 (386 cattle and 25 buffaloes) blood samples of dairy animals from 9 districts of Punjab, India, for simultaneous detection of Babesia bigemina and Trypanosoma evansi. The results were compared and correlated with conventional Giemsa stained thin blood smear (GSTBS) examination and haematological alterations to know the clinical status and pathogenicity of infections. The Bg3/Bg4 and TR3/TR4 primers were used in duplex PCR for B. bigemina and T. evansi amplified products of 689 bp and 257 bp, respectively. The overall prevalence by duplex PCR was found to be 36.49, 2.43, and 3.41% for T. evansi, B. bigemina, and dual infection, respectively. A more significant difference was observed for dual infection status (P ≤ 0.005) as compared to T. evansi (P ≤ 0.05) and B. bigemina (P ≤ 0.01) among various districts under study. A very low prevalence of T. evansi (0.73%) and B. bigemina (0.48%) was seen by GSTBS. The highly sensitive, specific, and cost-effective duplex PCR was able to detect latent T. evansi and B. bigemina infection in cattle and buffaloes. Haematological evaluation revealed marked pathology in B. bigemina infected group and in dual infected group in contrast to that infected with T. evansi alone.

Understanding TR binding to pMHC complexes: how does a TR scan many pMHC complexes yet preferentially bind to one.

Understanding the basis of the binding of a T cell receptor (TR) to the peptide-MHC (pMHC) complex is essential due to the vital role it plays in adaptive immune response. We describe the use of computed binding (free) energy (BE), TR paratope, pMHC epitope, molecular surface electrostatic potential (MSEP) and calculated TR docking angle (θ) to analyse 61 TR/pMHC crystallographic structures to comprehend TR/pMHC interaction. In doing so, we have successfully demonstrated a novel/rational approach for θ calculation, obtained a linear correlation between BE and θ without any "codon" or amino acid preference, provided an explanation for TR ability to scan many pMHC ligands yet specifically bind one, proposed a mechanism for pMHC recognition by TR leading to T cell activation and illustrated the importance of the peptide in determining TR specificity, challenging the "germline bias" theory.

MPID-T2: a database for sequence-structure-function analyses of pMHC and TR/pMHC structures.

UNLABELLED: Sequence-structure-function information is critical in understanding the mechanism of pMHC and TR/pMHC binding and recognition. A database for sequence-structure-function information on pMHC and TR/pMHC interactions, MHC-Peptide Interaction Database-TR version 2 (MPID-T2), is now available augmented with the latest PDB and IMGT/3Dstructure-DB data, advanced features and new parameters for the analysis of pMHC and TR/pMHC structures. AVAILABILITY: http://biolinfo.org/mpid-t2. CONTACT: shoba.ranganathan@mq.edu.au SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.