Phase Separation and Aggregation of a Globular Folded Protein Small Ubiquitin-like Modifier 1 (SUMO1).

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.

Activity Guided Azide-methyllysine Photo-trapping for Substrate Profiling of Lysine Demethylases.

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.

Lymphoepithelial Carcinoma of the Breast.

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.

Navigation for youth mental health and addictions: protocol for a realist review and synthesis of approaches and practices (The NavMAP standards project).

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.

Targeted NGS-Based Analysis of Pneumocystis jirovecii Reveals Novel Genotypes.

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.

Mycobacterium tuberculosis Specific Protein Rv1509 Evokes Efficient Innate and Adaptive Immune Response Indicative of Protective Th1 Immune Signature.

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.

The cancer journey through the lens of a sibling: a photovoice intervention for teen siblings of children with cancer.

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.

Mycobacterium smegmatis Bacteria Expressing Mycobacterium tuberculosis-Specific Rv1954A Induce Macrophage Activation and Modulate the Immune Response.

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.

Engineering a methyllysine reader with photoactive amino acid in mammalian cells.

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.

Immunodominant Mycobacterium tuberculosis Protein Rv1507A Elicits Th1 Response and Modulates Host Macrophage Effector Functions.

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.

"This Research Is Cool": Engaging Youth Experiencing Homelessness in Research on Reproductive and Sexual Health.

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.

Close Relations Matter: The Association Between Depression and Refugee Status in the Canadian Longitudinal Study on Aging (CLSA).

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.

Engineering Methyllysine Writers and Readers for Allele-Specific Regulation of Protein-Protein Interactions.

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.

Process optimization and characterization of 'sev' (traditional Indian extruded snack) with the incorporation of mushroom powder.

Mushroom is a nutritious and palatable food with various health attributes. The mushroom powder is a rich source of vegetable protein. In the present study, efforts were made to optimize the process for making 'sev', a traditional Indian extruded snack, with the incorporation of mushroom powder (Agaricus bisporus) to the Bengal gram (Cicer arietinum L.) flour ('besan'). Response surface methodology with central composite rotary design was used to determine the optimum level of various ingredients for 'sev' which was then analyzed for various physicochemical and sensory characteristics. Storage studies of mushroom 'sev' (with and without rice starch/mashed potato) were done at 37 ± 1 °C. The product containing rice starch was found to be highly acceptable over that with mashed potato. The optimized mushroom 'sev' contains 7.93% mushroom powder, 8.91% rice flour, 75.95% Bengal gram flour and 7.2% other ingredients with high scores for different sensory attributes viz., colour (8.4), appearance (8.3), flavour (8.3), texture (8.5) and overall acceptability (8.4). The mushroom powder based 'sev' had 2.79% higher protein content than the control sample (without mushroom powder) with a storage life of at least 7 days at 37 ± 1 °C.

In vivo effect of two different dietary fiber blends on the milk calcium bioavailability.

Milk is a valuable source of dietary calcium and it becomes important to establish whether incorporation of dietary fiber (DF), a health promoting food constituent, would lead to any undesirable impact on the bioavailability of milk calcium or not. The DF fortified spray dried partly skimmed milk powder with prestandardized fiber Blend-I (psyllium husk, oat fiber, MCC, inulin) and fiber Blend-II (psyllium husk, oat bran, wheat fiber and inulin) was subjected to rat-feeding studies to examine the possible effects on the bioavailability of milk calcium. The differences for calcium absorption and retention among diets containing DF Blend-I, DF Blend-II and cellulose (control) were found to be non-significant. It was evident that the milk calcium bioavailability of the diets containing two fiber formulations tested (at the levels studied) was at par with that of control standard diet containing only cellulose as DF. Therefore, it is reasonable to incorporate these DF blends into dairy products, and thereby add value.

Allele-Specific Inhibition of Histone Demethylases.

Histone demethylases play a critical role in mammalian gene expression by removing methyl groups from lysine residues in degree- and site-specific manner. To specifically interrogate members and isoforms of this class of enzymes, we have developed demethylase variants with an expanded active site. The mutant enzymes are capable of performing lysine demethylation with wild-type proficiency, but are sensitive to inhibition by cofactor-competitive molecules embellished with a complementary steric "bump". The selected inhibitors show more than 20-fold selectivity over the wild-type demethylase, thus overcoming issues typical to pharmacological and genetic approaches. The mutant-inhibitor pairs are shown to act on a physiologically relevant full-length substrate. By engineering a conserved amino acid to achieve member-specific perturbation, this study provides a general approach for studying histone demethylases in diverse cellular processes.