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The suitability of F1 progeny insect larvae of the irradiated male parent, Spodoptera litura (Fabr.) for infective juveniles (IJs) of entomopathogenic nematodes (EPN), Steinernema thermophilum was assessed to comprehend the feasibility of combining EPNs with nuclear pest control tactic. As compared to the control, the IJs induced faster host mortality with reduced proliferation in F1 host larvae. IJs derived from F1 host larvae exhibited almost similar proliferation capacity on normal hosts as in control. Further, the molecular basis of EPNs induced mortality in F1 host larvae was evaluated. Dual stress of EPN infection and irradiation induced downregulation of the relative mRNA expression of antimicrobial genes and upregulated expression of antioxidative genes. A pronounced effect of EPNs in association with irradiation stress was apparent on host mortality. Radiation induced sterile F1 insect larvae of S. litura acted as a reasonably suitable host for EPNs and also provided the environment for developing viable EPNs for their potential use as biocontrol agents.

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Fusion transcripts are formed when two genes or their mRNAs fuse to produce a novel gene or chimeric transcript. Fusion genes are well-known cancer biomarkers used for cancer diagnosis and as therapeutic targets. Gene fusions are also found in normal physiology and lead to the evolution of novel genes that contribute to better survival and adaptation for an organism. Various in vitro approaches, such as FISH, PCR, RT-PCR, and chromosome banding techniques, have been used to detect gene fusion. However, all these approaches have low resolution and throughput. Due to the development of high-throughput next-generation sequencing technologies, the detection of fusion transcript becomes feasible using whole genome sequencing, RNA-Seq data, and bioinformatics tools. This chapter will overview the general computational protocol for fusion transcript detection from RNA-sequencing datasets.

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The identification of a wide variety of RNA molecules using high-throughput sequencing techniques in the transcriptome pool of living organisms has revealed hidden regulatory insights in the cell. The class of non-coding RNA fragments produced from transfer RNA, or tRFs, is one such example. They are heterogeneously sized molecules with lengths ranging between 15 and 50 nt. They have a history of being dysregulated in human malignancies and other illnesses. The detection of these molecules has been made easier by a variety of bioinformatics techniques. The various types of tRFs and how they relate to cancer are covered in this chapter. It also provides a summary of the biological significance of tRFs reported in human cancer. Additionally, it emphasizes the utilities of databases and computational tools that have been created by different research teams for the investigation of tRFs. This will further aid the exploration and analysis of tRFs in cancer research and will support future advancement and a better comprehension of these molecules.

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Liquid-liquid phase separation (LLPS) plays a crucial role in cellular organization, primarily driven by intrinsically disordered proteins (IDPs) leading to the formation of biomolecular condensates. A folded protein SUMO that post-translationally modifies cellular proteins has recently emerged as a regulator of LLPS. Given its compact structure and limited flexibility, the precise role of SUMO in condensate formation remains to be investigated. Here, we show the rapid phase separation of SUMO1 into micrometer-sized liquid-like condensates in inert crowders under physiological conditions. Subsequent time-dependent conformational changes and aggregation are probed by label-free methods (tryptophan fluorescence and Raman spectroscopy). Remarkably, experiments on a SUMO1 variant lacking the N-terminal disordered region further corroborate the role of its structured part in phase transitions. Our findings highlight the potential of folded proteins to engage in LLPS and emphasize further investigation into the influence of the SUMO tag on IDPs associated with membrane-less assemblies in cells.

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Reversible post-translational modifications (PTMs) are key to establishing protein-protein and protein-nucleic acid interactions that govern a majority of the signaling pathways in cells. Sequence-specific PTMs are catalyzed by transferases, and their removal is carried out by a class of reverse-acting enzymes termed "detransferases". Currently available chemoproteomic approaches have been valuable in characterizing substrates of transferases. However, proteome-wide cataloging of the substrates of detransferases is challenging, mostly due to the loss of the epitope, rendering immunoprecipitation and activity-based methods ineffective. Herein, we develop a general chemoproteomic strategy called crosslinking-assisted substrate identification (CASI) for systematic characterization of cellular targets of detransferases and successfully apply it to lysine demethylases (KDMs) which catalyze the removal of methyl groups from lysine sidechain in histones to modulate gene transcription. By setting up a targeted azido-methylamino photo-reaction deep inside the active site of KDM4, engineered to carry p-azido phenylalanine, we reveal a novel "demethylome" that has escaped the traditional methods. The proteomic survey led to the identification of a battery of nonhistone substrates of KDM4, extending the biological footprint of KDM4 beyond its canonical functions in gene transcription. A notable finding of KDM4A-mediated demethylation of an evolutionarily conserved lysine residue in eukaryotic translational initiation factor argues for a much broader role of KDM4A in ribosomal processes. CASI, representing a substantive departure from earlier approaches by shifting focus from simple peptide-based probes to employing full-length photo-activatable demethylases, is poised to be applied to >400 human detransferases, many of which have remained poorly understood due to the lack of knowledge about their cellular targets.

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Lymphoepithelial malignancy is an extremely rare carcinoma of the breast characterized by a confusing histopathological picture resembling medullary carcinomas, lymphoma, etc. It has also been reported in other regions of the body like salivary glands, nasopharyngeal area and sometimes the lung. Due to its rare presence and difficult diagnosis, the treatment is often prolonged and delayed. Here we present a case report of a 56-year-old lady who was eventually diagnosed as lymphoepithelial carcinoma of the breast. Her journey of evaluation and treatment was fraught with pathological nuances and an elimination drill of multiple differentials before concluding this rare diagnosis. Although lymphoepithelial-like carcinoma is a rare entity, multiple cases have been reported in the literature and their review is mandated to further our clinical knowledge about the oncological treatment and expected prognosis of such cases in the future. Our patient underwent a simple mastectomy, followed by chemotherapy, radiotherapy, and is completely asymptomatic now. She has been cancer-free for the last seven years so far.

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INTRODUCTION: Mental health and/or addiction (MHA) concerns affect approximately 1.2 million children and youth in Canada, yet less than 20% receive appropriate treatment for these concerns. Youth who do not receive appropriate support may disengage from care and may experience lasting MHA issues. Families of these youth also support them in finding and accessing care. Thus, system supports are needed to help youth and their families find and equitably access appropriate care. Navigation is an innovation in MHA care, providing patient-centred support and care planning that helps individuals and families overcome barriers to care. Despite the increasing availability of navigation services for youth with MHA concerns, practices and models vary, and no single source has synthesised evidence regarding approaches and outcomes for this population into comprehensive standards. METHODS AND ANALYSIS: The proposed research will bring together evidence in youth MHA navigation, to establish this important system support as a factor that can enhance the integration and continuity of care for these youth. Our team, which includes researchers, administrators, clinical leads, an MHA navigator and youth and caregivers with lived experience, will be involved in all project stages. Realist Review and Synthesis methodology will be used, the stages of which include: defining scope, searching for evidence, appraising studies and extracting data, synthesising evidence and developing conclusions, and disseminating findings. ETHICS AND DISSEMINATION: Ethics approval is not required, as the study involves review of existing data. Dissemination plans include scientific publications and conferences and online products for stakeholders and the general public.

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Pneumocystis jirovecii is an important etiological agent of pneumonia that is underdiagnosed due to the inability to culture the organism. The 2019 PERCH study identified Pneumocystis as the top fungal cause of pneumonia in HIV-negative children using a PCR cutoff of 104 copies of Pneumocystis per mL of sample in nasopharyngeal/oropharyngeal (NP/OP) specimens. Given that Pneumocystis consists of an environmental ascus form and a trophic from (the latter is the form that attaches to the lung epithelium), it is possible that life-form-specific molecular assays may be useful for diagnosis. However, to accomplish this goal, these assays require genotypic information, as the current fungal genomic data are largely from the US and Europe. To genotype Pneumocystis across the globe, we developed an NGS-based genotyping assay focused on genes expressed in asci as well as trophs using PERCH throat swabs from Africa, Bangladesh, and Thailand, as well as North American samples. The NGS panel reliably detected 21 fungal targets in these samples and revealed unique genotypes in genes expressed in trophs, including Meu10, an ascospore assembly gene; two in mitochondrial gene ATP8, and the intergenic region between COX1 and ATP8. This assay can be used for enhanced Pneumocystis epidemiology to study outbreaks but also permits more accurate RT-CPR- or CRISPR-based assays to be performed to improve the non-bronchoscopic diagnosis of this under-reported fungal pathogen.

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Dissecting the function(s) of proteins present exclusively in Mycobacterium tuberculosis (M.tb) will provide important clues regarding the role of these proteins in mycobacterial pathogenesis. Using extensive computational approaches, we shortlisted ORFs/proteins unique to M.tb among 13 different species of mycobacteria and identified a hypothetical protein Rv1509 as a 'signature protein' of M.tb. This unique protein was found to be present only in M.tb and absent in all other mycobacterial species, including BCG. In silico analysis identified numerous putative T cell and B cell epitopes in Rv1509. Initial in vitro experiments using innate immune cells demonstrated Rv1509 to be immunogenic with potential to modulate innate immune responses. Macrophages treated with Rv1509 exhibited higher activation status along with substantial release of pro-inflammatory cytokines. Besides, Rv1509 protein boosts dendritic cell maturation by increasing the expression of activation markers such as CD80, HLA-DR and decreasing DC-SIGN expression and this interaction was mediated by innate immune receptor TLR2. Further, in vivo experiments in mice demonstrated that Rv1509 protein promotes the expansion of multifunctional CD4+ and CD8+T cells and induces effector memory response along with evoking a canonical Th1 type of immune response. Rv1509 also induces substantial B cell response as revealed by increased IgG reactivity in sera of immunized animals. This allowed us to demonstrate the diagnostic efficacy of this protein in sera of human TB patients compared to the healthy controls. Taken together, our results reveal that Rv1509 signature protein has immunomodulatory functions evoking immunological memory response with possible implications in serodiagnosis and TB vaccine development.

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Photovoice was employed as a clinical intervention to engage siblings of children with cancer, provide opportunity for sibling support, and elicit information about their lived experiences. Sibling support groups have been effective, however, none have utilized this intervention. Four teenagers who had a sibling diagnosed with cancer participated in a seven-week intervention group. Themes were identified to inform future clinical practice. Four main themes included: (i) support, (ii) changes, (iii) feelings, and (iv) Photovoice group experience. Photovoice, used as a clinical intervention, elicited valuable information and generated fruitful conversations, enabling siblings to relate to and learn from one another.

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Mycobacterium tuberculosis (M. tb), the intracellular pathogen causing tuberculosis, has developed mechanisms that endow infectivity and allow it to modulate host immune response for its survival. Genomic and proteomic analyses of non-pathogenic and pathogenic mycobacteria showed presence of genes and proteins that are specific to M. tb. In silico studies predicted that M.tb Rv1954A is a hypothetical secretory protein that exhibits intrinsically disordered regions and possess B cell/T cell epitopes. Treatment of macrophages with Rv1954A led to TLR4-mediated activation with concomitant increase in secretion of pro-inflammatory cytokines, IL-12 and TNF-α. In vitro studies showed that rRv1954A protein or Rv1954A knock-in M. smegmatis (Ms_Rv1954A) activates macrophages by enhancing the expression of CD80 and CD86. An upregulation in the expression of CD40 and MHC I/II was noted in the presence of Rv1954A, pointing to its role in enhancing the association of APCs with T cells and in the modulation of antigen presentation, respectively. Ms_Rv1954A showed increased infectivity, induction of ROS and RNS, and apoptosis in RAW264.7 macrophage cells. Rv1954A imparted protection against oxidative and nitrosative stress, thereby enhancing the survival of Ms_Rv1954A inside macrophages. Mice immunized with Ms_Rv1954A showed that splenomegaly and primed splenocytes restimulated with Rv1954A elicited a Th1 response. Infection of Ms_Rv1954A in mice through intratracheal instillation leads to enhanced infiltration of lymphocytes in the lungs without formation of granuloma. While Rv1954A is immunogenic, it did not cause adverse pathology. Purified Rv1954A or Rv1954A knock-in M. smegmatis (Ms_Rv1954A) elicited a nearly two-fold higher titer of IgG response in mice, and PTB patients possess a higher IgG titer against Rv1954A, also pointing to its utility as a diagnostic marker for TB. The observed modulation of innate and adaptive immunity renders Rv1954A a vital protein in the pathophysiology of this pathogen.

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Methyllysine sites in proteins are recognized by an array of reader domains that mediate protein-protein interactions for controlling cellular processes. Herein, we engineer a chromodomain, an essential methyllysine reader, to carry 4-azido-l-phenylalanine (AzF) via amber suppressor mutagenesis and demonstrate its potential to bind and crosslink methylated proteins in human cells. We further develop a first-of-its kind chromodomain variant bearing two AzF units with enhanced crosslinking potential suitable for profiling the transient methyllysine interactome.

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Mycobacterium tuberculosis (M. tb) persists as latent infection in nearly a quarter of the global population and remains the leading cause of death among infectious diseases. While BCG is the only vaccine for TB, its inability to provide complete protection makes it imperative to engineer BCG such that it expresses immunodominant antigens that can enhance its protective potential. In-silico comparative genomic analysis of Mycobacterium species identified M. tb Rv1507A as a "signature protein" found exclusively in M. tb. In-vitro (cell lines) and in-vivo experiments carried out in mice, using purified recombinant Rv1507A revealed it to be a pro-inflammatory molecule, eliciting significantly high levels of IL-6, TNF-α, and IL-12. There was increased expression of activation markers CD69, CD80, CD86, antigen presentation molecules (MHC I/MHCII), and associated Th1 type of immune response. Rv1507A knocked-in M. smegmatis also induced significantly higher pro-inflammatory Th1 response and higher survivability under stress conditions, both in-vitro (macrophage RAW264.7 cells) and in-vivo (mice). Sera derived from human TB patients showed significantly enhanced B-cell response against M. tb Rv1507A. The ability of M. tb Rv1507A to induce immuno-modulatory effect, B cell response, and significant memory response, renders it a putative vaccine candidate that demands further exploration.

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Youth experiencing homelessness face myriad barriers and inequities regarding their reproductive and sexual health and rights. Moreover, homeless youth are often characterized as "disaffiliated" and depicted as difficult to engage in research. This study qualitatively explored homeless youths' attitudes, beliefs, and needs regarding reproductive and sexual health, and sought their perspectives on being involved in research on such topics, which are often thought of as "taboo" or sensitive. Youth were enthusiastic about openly discussing such issues, which they deemed as highly relevant to their daily lives. Youth identified that how they were engaged in such research, and having opportunities for longer-term contributions to such efforts, were both important and exciting to them. Future social work and public health research efforts should seek to further disrupt narratives of homeless youth as "disaffiliated" and difficult to engage, and in doing so, develop more creative, participatory, and youth-led opportunities for including this group in reproductive and sexual health research.

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This study examined the prevalence and social determinants of depression among refugee and non-refugee adults aged 45-85 in the Canadian Longitudinal Study on Aging. Bivariate analyses and multivariable binary logistic regression analyses were conducted. The prevalence of depression was higher in a sample of 272 refugees (22.1%) and 5059 non-refugee immigrants (16.6%), compared to 24,339 native-born Canadians (15.2%). The adjusted odds ratio (aOR) of depression for refugees were not attenuated when controlling factors such as, (1) socioeconomic status, (2) health conditions and behaviours, (3) social isolation and online social networking (aORs range from 1.61 to 1.70, p's < 0.05). However, when social support representing close personal relationships was included, the odds of depression for refugees were reduced to non-significance (aOR = 1.30, 95% CI 0.97-1.74, p = 0.08). Refugees' excess vulnerability to depression is mainly attributable to lower levels of affectionate social support. Targeted interventions in nurturing supportive interpersonal relationships for refugees are warranted.

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Protein-protein interactions mediated by methyllysine are ubiquitous in biological systems. Specific perturbation of such interactions has remained a challenging endeavor. Herein, we describe an allele-specific strategy toward an engineered protein-protein interface orthogonal to the human proteome. We develop a methyltransferase (writer) variant that installs aryllysine moiety on histones that can only be recognized by an engineered chromodomain (reader). We establish biochemical integrity of the engineered interface, provide structural evidence for orthogonality and validate its applicability to identify transcriptional regulators. Our approach provides an unprecedented strategy for specific manipulation of the methyllysine interactome.

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