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Biology subjects

Khan, M. R.

Publications and source records attributed to Khan, M. R..

At least 19 recordsLinked to original sources

Insights into the molecular systematics of montane voles of the Western Himalayan Mountains

Kashmir voles (Hyperacrius) are poorly studied fossorial arvicolines of the southern Himalayan slopes, with two species recognized. We sequenced Cytb from voles collected in northern Pakistan and combined these data with existing GenBank sequences, yielding 194 tips spanning nearly all arvicoline genera. We analyzed five data sets with maximum likelihood and compared external measurements among species using principal component and linear discriminant analyses. We recovered five well-supported clades of Hyperacrius separated by ~12-14% p-distance, which we treat as distinct species. We recognize clade 1 as H. wynnei, and populations referred to H. w. traubi are genetically indistinguishable from H. w. wynnei. We recognize H. zygomaticus, new rank (clade 2), and tentatively allocate clade 5 to H. brachelix. Clades 3 and 4 likely represent undescribed species. Morphometric analyses of external measurements clearly distinguish H. wynnei but not clades 3 and 4 (overall classification accuracy 70.3%). Phylogenetic analyses including nuclear genes placed Hyperacrius as sister to a clade containing Microtini, Arvicola, Lagurini, Dinaromys, and Ellobiusini, whereas mitochondrial analyses weakly allied it with Ellobiusini. Its traditional placement in Clethrionomyini is thus unsupported, although its exact position remains unresolved. Alticola is nonmonophyletic, with A. macrotis sequences nested within Clethrionomys, likely reflecting mitochondrial capture.

evolutionary biology↗

Assessment of the Genetic Architecture at Early-Stage Drought Tolerance in Wheat Using UAV-Based Multispectral Imaging

Recent advances in unmanned aerial vehicles (UAVs) and multispectral sensor technologies have transformed high-throughput phenotyping as an efficient alternative to traditional approaches. In this study, we employed UAV-based multispectral imaging to monitor early-stage drought stress in wheat. A panel of 221 historical spring wheat cultivars from Pakistan, representing over a century of breeding history, were evaluated under irrigated and drought conditions. UAV flights were conducted twice at early growth stages to capture multispectral imagery, which was processed in Pix4D mapper for image alignment and orthomosaic generation. Plot segmentation and trait extraction were performed in QGIS. Eight drought-responsive vegetative indices (VIs) were analyzed to assess genotypic variation. Significant to highly significant differences were observed among genotypes, treatments, and their interactions across all VIs. Broad-sense heritability estimates were moderate to high for most traits, with predominantly additive gene action. Vegetative indices such as NDVI, GNDVI, EVI, and SAVI showed strong correlations with each other and effectively detected early canopy stress under drought. Principal component analysis based on 23.897K SNPs indicated a mixed genetic population. Genome-wide association studies identified 115 significant QTNs linked to VIs under both conditions, corresponding to 74 loci, including 26 pleiotropic loci. Of these, 10 pleiotropic loci detected under drought were annotated and six putative candidate genes were identified which showed expression in multiple tissues based on transcriptome data. Two genes i.e., TraesCS1D01G217600.1 (HSP70) and TraesCS6D01G254000.1 (ZmMDAR3), showed differential expression pattern among control and drought treatment. These findings highlight the potential of UAV-based phenotyping for early drought detection and provide candidate genes for improving drought tolerance in wheat. Future research should focus on the functional roles of these genes under drought stress.

molecular biology↗

An estrogen-independent and IL-1-dependent pathway controls vulvovaginal candidiasis through combined IL-17/IL-22 signaling

Vulvovaginal candidiasis (VVC) affects >75% of women, with considerable morbidity and high medical cost burden. While Type 17 cytokines (IL-17, IL-22) are critical for oral and dermal immunity to C. albicans, their role in VVC has been less clear. Th17 gene signatures are potently upregulated in VVC, yet impairment of individual Th17 components (IL-17A, IL-17R subunits, IL-22) does not worsen disease. Rather, estrogen activity is tightly linked to VVC, leading to a paradigm that hormonal pathways rather than immune defense, dominate susceptibility. Here, we reveal a previously unappreciated role for IL-1/Type 17 in VVC that operates independently of estrogenic hormones. In contrast to mice lacking IL-17A, IL-17RA, IL-22, or IL-22R individually, mice lacking IL-17RA and IL-22RA1 together (Il17raIl22ra1-/-) exhibited high fungal loads and exacerbated tissue damage and inflammation. In human vulvar epithelial cells, IL-17 and IL-22 drive synergistic signaling. IL-1R signaling but surprisingly not IL-23 wa upstream of this response. Il17raIl22ra1-/- mice expressed high IL-1{beta} yet did not control disease, indicating that IL-1 is upstream but not downstream of Type 17 responses. Unexpectedly, Type 17-dependent control occurred in the absence of exogenous estrogen administration and persisted even when estrus was prevented by progesterone treatment. Collectively, these data indicate that susceptibility to VVC is driven not only by estrogen sensitization but through combinatorial loss of IL-17 and IL-22. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=168 SRC="FIGDIR/small/671995v2_ufig1.gif" ALT="Figure 1000"> View larger version (52K): org.highwire.dtl.DTLVardef@19946e9org.highwire.dtl.DTLVardef@1feac71org.highwire.dtl.DTLVardef@eb433aorg.highwire.dtl.DTLVardef@18ab622_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

Lifestyle transition from rural to urban setting changes the gut bacterial profile in an ethnic community of northeast India

The human gut microbiome undergoes transformation due to various exogenous and endogenous influences. Lifestyle has been one of the major contributors of gut microbiome composition. Our study investigated the effect of migration on the gut microbiome of the Mishing ethnic community in India associated with urban migration from their pastural lifestyle. Gut bacterial diversity was profiled using 16S rRNA amplicon sequencing. We observed notable alterations in microbial diversity and composition, including changes in the core microbiome. While Bifidobacterium, Lactococcus and Streptococcus significantly increased (p < 0.01) among the migrant population there was depletion in bacteria such as Succinivibrio and Prevotella. This change in core microbiome was further reflected on the functional profile of the bacterial community harbored by the urban and rural dwellers. While the rural population was enriched in fatty acid biosynthesis pathways, amino acid and Vitamin B2 biosynthesis pathways were more prominent in the microbiome of the urban dwellers. We further observed increase in diversity and richness of the microbiome following migration. Co-analysis with ASVs from food samples consumed by the Mishing rural population revealed that 51 ASVs among the rural dwellers were from a widely consumed beverage, Apong which were completely absent among the migrants. Our analyses highlight the dietary preferences, particularly abstinence from specific foods and beverages, may modulate the alterations in gut microbial profiles. While the cross-sectional design and amplicon sequencing limited our ability to assess temporal and functional changes, our findings highlight a measurable impact of lifestyle and dietary transitions on the gut microbiome.

microbiology↗

The Single-Stranded DNA-Binding Factor SUB1/PC4 Alleviates Replication Stress at Telomeres and is a Vulnerability of ALT Cancer Cells

AO_SCPLOWBSTRACTC_SCPLOWTo achieve replicative immortality, cancer cells must activate telomere maintenance mechanisms. In 10-15% of cancers, this is enabled by recombination-based alternative lengthening of telomeres pathways (ALT). ALT cells display several hallmarks including heterogeneous telomere length, extrachromosomal telomeric repeats and ALT-associated PML bodies. ALT cells also have high telomeric replication stress (RS) enhanced by fork-stalling structures (R-loops, G4s) and altered chromatin states. In ALT cells, telomeric RS promotes telomere elongation but above a certain threshold becomes detrimental to cell survival. Manipulating RS at telomeres has thus been proposed as a therapeutic strategy against ALT cancers. Through analysis of genome-wide CRISPR fitness screens, we identified ALT-specific vulnerabilities and describe here our characterization of the roles of SUB1, a ssDNA-binding protein, as a novel regulator of telomere stability. SUB1 depletion further increases RS at ALT telomeres, profoundly impairing ALT cell growth without impacting telomerase-positive cancer cells. During RS, SUB1 is recruited to stalled forks and ALT telomeres via its ssDNA-binding domain. This recruitment is potentiated by RPA depletion, suggesting that these factors may compete for ssDNA. The viability of ALT cells and their resilience towards RS also requires ssDNA-binding by SUB1. SUB1 depletion accelerates cell death induced by FANCM depletion, triggering unsustainable levels of telomeric damage specifically in ALT cells. Finally, combining SUB1 depletion with RS-inducing drugs rapidly induces replication catastrophe in ALT cells. Altogether, our work identifies SUB1 as a new ALT susceptibility with important roles in the mitigation of RS at ALT telomeres and suggests new therapeutic strategies for a host of still poorly managed cancers. SO_SCPLOWIGNIFICANCEC_SCPLOW SO_SCPLOWTATEMENTC_SCPLOWCurrently, there are few treatment options for ALT cancers with chemotherapy still occupying center stage despite often limited efficacy. ALT cancer cells experience high levels of replication stress at telomeres and its enhancement (e.g. via ATR inhibition) is a promising therapeutic strategy. Sensitivity to ATR inhibition varies amongst ALT cell lines/tumors warranting the development of additional ways to modulate telomeric replication stress. Here we identify SUB1, a single-stranded DNA-binding protein, as a vulnerability of ALT cells. SUB1 localizes to ALT telomeres and mitigates deleterious replication stress. SUB1 depletion synergizes with ATR inhibition and FANCM downregulation suggesting that co-targeting SUB1 with other regulators of replication stress at telomeres may kill ALT cancer cells more effectively.

cancer biology↗

Heat-killed probiotic Levilactobacillus brevis MKAK9 and its exopolysaccharide promote longevity by modulating aging hallmarks and enhancing immune responses in Caenorhabditis elegans

BackgroundProteostasis is a critical aging hallmark responsible for removing damaged or misfolded proteins and their aggregates by improving proteasomal degradation through the autophagy-lysosome pathway (ALP) and the ubiquitin-proteasome system (UPS). Research on the impact of heat-killed probiotic bacteria and their structural components on aging hallmarks and innate immune responses is scarce, yet enhancing these effects could potentially delay age- related diseases. ResultsThis study introduces a novel heat-killed Levilactobacillus brevis strain MKAK9 (HK MKAK9), along with its exopolysaccharide (EPS), demonstrating their ability to extend longevity by improving proteostasis and immune responses in wild-type Caenorhabditis elegans. We elucidate the underlying mechanisms through a comprehensive approach involving mRNA- and small RNA sequencing, proteomic analysis, lifespan assays on loss-of- function mutants, and quantitative RT-PCR. Mechanistically, HK MKAK9 and its EPS resulted in downregulation of the insulin-like signaling pathway in a DAF-16-dependent manner, enhancing protein ubiquitination and subsequent proteasomal degradation through activation of the ALP pathway, which is partially mediated by microRNA mir-243. Importantly, autophagosomes engulf ubiquitinylated proteins, as evidenced by increased expression of the autophagy receptor sqst-3, and subsequently fuse with lysosomes, facilitated by increased levels of the lysosome-associated membrane protein (LAMP) lmp-1, suggesting the formation of autolysosomes for degradation of the selected cargo. Moreover, HK MKAK9 and its EPS activated the p38 MAPK pathway and its downstream SKN-1 transcription factor, which are known to regulate genes involved in innate immune response (thn-1, ilys-1, cnc-2, spp-9, spp-21, clec-47, and clec-266) and antioxidation (sod-3 and gst-44), thereby reducing the accumulation of reactive oxygen species (ROS) at both cellular and mitochondrial levels. Notably, SOD-3 emerged as a transcriptional target of both DAF-16 and SKN-1 transcription factors. ConclusionOur research sets a benchmark for future investigations by demonstrating that heat-killed probiotic and its specific cellular component, EPS, can downregulate the insulin- signaling pathway, potentially improving the autophagy-lysosome pathway (ALP) for degrading ubiquitinylated proteins and promoting organismal longevity. Additionally, we discovered that increased expression of microRNA mir-243 regulates insulin-like signaling and its downstream ALP pathway. Our findings also indicate that postbiotic treatment may bolster antioxidative and innate immune responses, offering a promising avenue for interventions in aging-related diseases.

microbiology↗

Snake venom-inspired novel peptides protect Caenorhabditis elegans against paraquat induced Parkinson's pathology

The in vivo protective mechanisms of two low molecular mass ([~]1.4 kDa) novel custom peptides (CPs) against paraquat (PT)-induced neurodegenerative dysfunction in the Caenorhabditis elegans model were deciphered. CPs prevent the PT binding to the nerve ring adjacent to the pharynx in C. elegans (N2 strain) by stable and high-affinity binding to the tyrosine-protein kinase receptor CAM-1, resulting in significant inhibition of PT-induced toxicity by reducing enhanced reactive oxygen species production, mitochondrial membrane depolarization, and chemosensory dysfunction. The CPs inhibited PT-induced dopaminergic (DAergic) neuron degeneration and alpha-synuclein aggregation, the hallmarks of Parkinsons Disease, in transgenic BZ555 and NL5901 strains of C. elegans. The transcriptomic, functional proteomics, and quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analyses show that CPs prevented the increased expression of the genes involved in the skn-1 downstream pathway, thereby restoring PT-mediated oxidative stress, apoptosis, and neuronal damage in C. elegans. The CPs ability to repair PT-induced damage was demonstrated by a network of gene expression profiles illustrating the molecular relationships between the regulatory proteins. Further, CPs (10 mg/kg, parental route) did not show toxicity or induce inflammatory mediators in the mouse model.

neuroscience↗

HEMATO-CHEMICAL VARIATIONS- A DIAGNOSTIC TOOL FOR BABESIA, THEILERIA AND ANAPLASMA INFECTIONS IN CAPTIVE HOG DEER (AXIS PORCINUS)

Hog deer are an essential component of Pakistans biodiversity. Their conservation helps maintain integrity of local ecosystems, contributing to overall stability and balance of regions wildlife populations. In Pakistan, they are classified as an endangered species according to IUCN. Theileria, babesia and anaplasma are among most prevalent blood parasites in ruminants which require diagnosis at early stages of the infection so that treatment protocols can be followed and more severe pathological alterations can be prevented. The changes in hemato-chemical parameters caused by Theileria, babesia and anaplasma were recorded individually and then compared with healthy group of hog deer respectively. Alterations in hemato-chemical parameters produced by these parasite-infected hog deer were assessed as potential diagnostic tools for distinguishing between individual blood parasites. Total leukocyte count, monocytes and eosinophils were observed to be higher than normal in babesia infected hog deer while level was lower than normal hog deer in anaplasma and theileria infected hog deer. The main objective of this study is to promote early diagnosis of parasitic infections in hog deer to facilitate prompt treatment, pathological prevention and allocate resources for further research on hemato-chemical parameters as diagnostic tools, enhancing understanding and management of blood parasite infections in hog deer.

pathology↗

Exploring the probiotic potential, antioxidant capacity, and healthy aging based on whole genome analysis of Lactiplantibacillus plantarum LPJBC5 isolated from fermented milk product

AbstractLactiplantibacillus plantarum is a beneficial bacterium commonly found in fermented foods, including fermented milk products. In the present study, we reported the whole genome sequence of L. plantarum LPJBC5. The complete genome sequence of LPJBC5 was 3.23Mb, and the average GC% was found to be 44.55% encoding a total of 3016 genes. A comprehensive analysis of the LPJBC5 genome detected major carbohydrate-active enzymes, exopolysaccharide synthesis genes (eps), and the presence of genes related to stress response and antioxidant activity. Longevity regulating genes including katE, CAT (chloramphenicol acetyltransferase), catB and their regulating pathways (MAPK signaling pathway) were detected in the LPJBC5 genome. The genome was found to contain plantaracin (pln) operon for the production of antimicrobial bacteriocin and various regions of secondary metabolite biosynthetic gene clusters, including the type III polyketide synthases (T3PKS), Ribosomally synthesized and post- translationally modified peptide product (Ripp-Like), which exhibit specific antimicrobial activity. A comparative pangenome analysis was performed to further evaluate the metabolic framework of L. plantarum JBC5, including the complete L. plantarum genome (N=30) retrieved from publicly available repositories. The core/soft-core genome was found to harbor probiotic associated marker genes. Functional analysis revealed the presence of genes majorly enriched in cell wall/membrane/envelop biogenesis, carbohydrate metabolism and transport, amino acid metabolism and transport, translational mechanism, and transcription processes. Identification of probiotic and longevity associated genes suggests that LPJBC5 holds potential as a probiotic candidate with multifaceted applications in the food industries. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=92 SRC="FIGDIR/small/584937v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@1a0299dorg.highwire.dtl.DTLVardef@c347dorg.highwire.dtl.DTLVardef@14a28baorg.highwire.dtl.DTLVardef@1b7f81b_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

DEVELOPMENT AND EVALUATION OF COATED RICOTTA CHEESE WITH WHEY PROTEIN AND CLOVE OIL

Cheese, oldest dairy product which is used to preserve the nutrients of milk for long time. It is available in different shapes, sizes, flavors and textures. Ricotta is fresh soft cheese, is prepared through coagulating the whey proteins. It is a value-added product manufactured from cheese whey. Microbial spoiling occurs as a result of unmanaged conditions, resulting in the unfavorable changes in odor, flavor, and texture. That leads to food poisoning when infected food is consumed. Natural preservatives are preferred by consumers over synthetic preservatives since they are safer and extend the shelf life of food goods. Synthetic preservatives are poisonous and have negative health consequences. Edible coatings are biodegradable, natural films that can improve the products safety, quality, and nutritional content until it is consumed. This research was carried out to analyse the effect of whey protein and clove essential oil on the shelf life of ricotta cheese due to their excellent gas barrier properties, antioxidant and antimicrobial properties. Different concentrations of clove oil (0.1, 0.2, 0.3 %) are incorporated in whey protein coating solution (2.5,5,7.5%). The overall findings for all groups showed that there was gradual decrease in acidity and moisture content. Therefore, sample TRC3 treated with 0.75 % whey protein and 0.3% clove oil showed significant results (P<0.05). They showed less microbial count, increased fat and protein value. But it also had great impact on sensory analysis such as on color, texture, aroma while it showed significant overall acceptability due to high clove oil and whey protein concentrations. Hence, this study showed significant effect on shelf life of ricotta cheese and its shelf life increased from 7 to 21 days.

microbiology↗

Disulfiram reduces atherosclerosis and enhances efferocytosis, autophagy, and atheroprotective gut microbiota in hyperlipidemic mice.

Pyroptosis executor Gasdermin (GsdmD) promotes atherosclerosis in mice and humans. Disulfiram (DSF) was recently shown to potently inhibit GsdmD, but the in-vivo efficacy and mechanism of DSFs anti-atherosclerotic activity is yet to be explored. We used human/mouse macrophages and a hyperlipidemic mouse model of atherosclerosis to determine DSF anti-atherosclerotic efficacy and mechanism. DSF-fed hyperlipidemic apoE-/- mice showed significantly reduced IL-1{beta} release upon in-vivo Nlrp3 inflammasome assembly and showed smaller atherosclerotic lesions ([~]27% and 29% reduction in males and females, respectively). The necrotic core area was also smaller ([~]50% and 46% reduction in DSF-fed males and females, respectively). DSF induced autophagy in macrophages, hepatocytes/liver, and in atherosclerotic plaques. DSF modulated other atheroprotective pathways such as efferocytosis, phagocytosis, and gut microbiota. DSF-treated macrophages showed enhanced phagocytosis/efferocytosis, with a mechanism being a marked increase in cell-surface expression of efferocytic receptor MerTK. Atomic-force microscopy analysis revealed altered biophysical membrane properties of DSF treated macrophages, showing increased ordered-state of the plasma membrane and increased adhesion strength. Furthermore, the 16sRNA sequencing of DSF-fed hyperlipidemic mice showed highly significant enrichment in atheroprotective gut microbiota Akkermansia and a reduction in atherogenic Romboutsia species. Taken together, our data shows that DSF can simultaneously modulate multiple atheroprotective pathways, and thus may serve as novel adjuvant therapeutic to treat atherosclerosis.

cell biology↗

Contrasting patterns of presence-absence variation of NLRS within S. chilense are mainly shaped by past demographic history

Understanding the evolution of pathogen resistance genes (nucleotide-binding site-leucine-rich repeats, also known as NLRs) within a species requires a comprehensive examination of factors that affect gene loss and gain. We present a new reference genome of Solanum chilense, that leads to an increased number and more accurate annotation of NLRs. Next, using a target-capture approach, we quantify the presence-absence variation (PAV) of NLR loci across 20 populations from different habitats. We build a rigorous pipeline to validate the identification of PAV of NLRs, then show that PAV is larger within populations than between populations, suggesting that maintenance of NLR diversity is linked to population dynamics. Furthermore, the amount of PAV is not correlated with the NLR presence in gene clusters in the genome, but rather with the past demographic history of the species, with loss of NLRs in diverging populations at the distribution edges and smaller population sizes. Finally, using a redundancy analysis, we find limited evidence of PAV being linked to environmental gradients. Our results contradict the classic assumptions of the important selective role of PAV for NLRs, and suggest that NLRs PAV is driven by random processes (and weak selection) in an outcrossing plant with high nucleotide diversity.

evolutionary biology↗

A single dietary factor, daily consumption of a fermented beverage, can modulate the gut microbiome within the same ethnic community

In this study, the impact of traditional rice-based fermented alcoholic beverages (Apong) on the gut microbiome and health of the Mishing community in India was examined. Two groups that consumed one of these beverages were compared to a control group that did not consume either beverage. Gut microbial composition was analyzed by sequencing 16S rRNA of fecal metagenomes and analyzing untargeted fecal metabolites, and short-chain fatty acids (SCFAs). We also collected data on anthropometric measures and serum biochemical markers. Our results showed that Apong drinkers had higher blood pressure, but lower blood glucose and total protein levels than other non-drinkers. Also, gut microbiome composition was found to be affected by the choice of Apong, with Apong drinkers having a more diverse and distinct microbiome compared to non-drinkers. Apong drink type or being a non-drinker explained even a higher variation of fecal metabolome composition than microbiome composition and Apong drinkers had lower levels of the SCFA isovaleric acid than non-drinkers. Overall, this study shows that a single dietary factor can significantly impact the gut microbiome of a community and highlights the potential role of traditional fermented beverages in maintaining gut health.

microbiology↗

MRI-to-Synthetic 3D Gel Brain: Proof-of-Concept Fabrication For Intra-Parenchymal Diffusion Studies

Bioprinting technologies utilize hydrogel-based biomaterials to more accurately depict in vivo physical conditions within in vitro studies, yet, manufacturing the human brain from soft, poroelastic hydrogels remains a fundamental challenge. Conventional manufacturing routes to fabricate hydrogel brain models using techniques, i.e., 3D printing, seems challenging. This study aims to demonstrate an inverse replica molding fabrication technique that can overcome these challenges while maintaining the complex shape of an individual subjects brain in a miniaturized model--allowing for a more robust hydrogel model that can capture the interactions between diffusing molecules and brain boundaries. This is done by taking a subjects magnetic resonance imaging (MRI) scan and reconstructing the outer pial surface into a mesh surface. The mesh was then converted to an STL and printed out using an extrusion printer. A silicon mold was made from this print into which agarose was gelled. Once fully gelated, the synthetic gel brain was then carefully removed. Two infusion trials were run in the gel brain, each using a different infusion site. Then a diffusion profile was established and compared to a simple gel infusion model. The result shows different diffusion profiles at each location and between the simple and complex models. This model can better represent the interference the complex shape of the brain has on particle movement compared to simple gel models.

bioengineering↗

In Silico, Brain Mesh Platform for Computing Topographic Dependent Internal Facets

Individualized and anatomically correct computational models of the brain can be leveraged to improve knowledge of drug dispersal following simulation of drug delivery. Using a patients magnetic resonance image (MRI) scans, we were able to reconstruct the pial surface of the brain of the left hemisphere with strong anatomic accuracy. We then established the major internal features, including the lateral ventricle, a tumor, and drug delivery catheters. These were able to include relevant tissue characteristics such as porosity and permeability in the Multiphysics platform COMSOL to create a platform for brain modeling. To test the performance of this platform, we simulated direct drug infusion in both a healthy patient brain and a diseased patient model, focusing on glioblastoma (GBM). Using this platform, we simulated perturbed convection enhanced delivery of a cancer medication (similar to temozolomide (TMZ) but modeled using methylene blue) to the tumor. Consequently, with our patient derived model, we are able to simulate solute dispersal and fluid flow representative of in vivo conditions.

bioengineering↗

Convection-enhanced diffusion and directed withdrawal of methylene blue in agarose hydrogel using finite element analyses

Precision drug delivery for optimized therapeutic targeting requires knowledge of momentum transport and molecular diffusion of molecules within the patients interstitial tissue, especially for tumor treatment within the brain. Dispersion in the interstitial space is impacted by delivery method, tissue material properties, individual-specific fluid flow, and particle size of the input solute. Knowledge of a drugs dispersion allows for optimizing solute delivery, concentration, and flow rates to maximize drug distribution and biomarker recovery. For delivering drugs, increased knowledge of drug location after delivery can improve therapeutic treatment by optimizing the dosing of healthy and unhealthy tissue. Finite element methods (FEM) tools, such as COMSOL Multiphysics, can simulate molecular distribution inside-individual specific shapes and porous material properties. Furthermore, an additional unmet need is delivery methods that can be adjusted to manipulate diffusion regions through tissue via techniques such as directed flow. This would be especially valuable in targeted drug delivery within tumors to increase the cancerous surface area covered while limiting damage to surrounding tissues. In this project, the directed flow was induced by perfusing the injected solution at an input probe while withdrawing fluid at an output probe, enabling targeted flow through the desired region. FEM computation faithfully replicated these conditions and could be used to determine the effective concentrations perfused over the region of interest. We leveraged COMSOL Multiphysics to perform a computational study simulating convection-enhanced delivery (CED) with an output probe pulling the concentration profile over the region of interest. This simulation system can be applied to therapeutics targeting, vaccine subcutaneous injection, and waste and media diffusion in tissue engineering.

bioengineering↗

Functional characterization of a PHF8 processed pseudogene in the mouse genome

The majority of pseudogenes are generated when an RNA transcript is reverse-transcribed and integrated into the genome at a new location. Pseudogenes are often considered as an imperfect and silent copy of a functional gene because of the accumulation of numerous mutations in their sequence. Here we report the presence of PHF8-ps, a PHF8 retrotransposed pseudogene in the mouse genome, which has no disruptions in its coding sequence. We showed that this pseudogene was specifically transcribed in testis and can produce a Phf8-ps protein in vivo. As Phf8-ps protein has a well-conserved JmjC domain, we characterized its enzymatic activity and showed that Phf8-ps did not have the intrinsic capability to demethylate H3K9me2 in vitro compared to the parental Phf8 protein. Surprisingly, Phf8-ps did not localize in the nucleus like Phf8 but rather was mostly located at the cytoplasm. Finally, our proteomic analysis of Phf8-ps associated proteins revealed that Phf8-ps interacted with mitochondrial proteins but also with prefoldin subunits (PFDN proteins) that deliver unfolded proteins to the cytosolic chaperonin complex implicated the folding of cytosolic proteins. Together, our findings highlighted Phf8-ps as a new pseudogene-derived protein with distinct molecular functions from Phf8.

biochemistry↗

Enhanced mTORC1 signaling and Protein Synthesis in Parkinson Disease Pathogenesis

Pathologic -syn destabilizes the TSC 1 and 2 complex leading to mTORC1 activation, enhanced protein translation and neurodegeneration in PD. AbstractPathological -synuclein (-syn) plays an important role in the pathogenesis of -synucleinopathies such as Parkinsons disease (PD). Disruption of protein homeostasis is thought be central to PD pathogenesis, however the molecular mechanism of this deregulation is poorly understood. Here we report that pathologic -syn binds to tuberous sclerosis protein (TSC) 2 and destabilizes the TSC1-TSC2 complex leading to activation of the mechanistic target of rapamycin (mTOR) complex 1 (mTORC1) and enhanced mRNA translation. Dopamine neuron loss, behavioral deficits and aberrant biochemical signaling in the -syn preformed fibril (PFF) and Drosophila -syn transgenic models of pathologic -syn induced degeneration were attenuated by genetic and pharmacologic inhibition of mTOR and protein translation. Our findings establish a potential molecular mechanism by which pathologic -syn activates mTORC1 leading to enhanced protein translation and concomitant neurodegeneration in PD.

neuroscience↗