Biology subjects

Uddin, M. J.

Publications and source records attributed to Uddin, M. J..

18 recordsLinked to original sources

bioRxiv2026

Antibiotics promote susceptibility to C. difficile infection through a CCR5-dependent immune response

Antibiotics (ABXs) represent the current standard of care for treating Clostridioides difficile infection (CDI). Paradoxically, ABX-induced dysbiosis is the primary risk factor for CDI, as disruption of the colonic microbial ecosystem creates an opportunity for C. difficile colonization. Given that ABXs can also alter immune responses, we investigated whether ABXs prime the colonic immune milieu for CDI susceptibility. Here, we implicate ABXs in driving CDI severity through the emergence of pathogenic CCR5-reliant immune populations in the mouse colon. High-throughput immune cell profiling revealed that ABXs shift the colonic immune compartment toward a CCR5-associated type I immunity signature, marked by an expansion of CCR5+ ILC1s and CCR5+ Th1 cells. A partial genetic deletion of CCR5 reversed CDI severity, alleviating colonic inflammation and improving survival. Pharmacological inhibition of the CCL3/4/5-CCR5 circuit also recapitulated these favorable disease outcomes, which we attribute to reduced colonic CCR5+ ILC1, CCR5+ Th1, and CCR5+ CD8 T cell populations during CDI. Together, our findings extend beyond dysbiosis as the canonical CDI risk factor and establish ABX-induced immune imbalance as an underappreciated determinant of CDI susceptibility.

immunology↗

bioRxiv2026

Novel COX-2 Targeted Nanobodies for Molecular Endoscopic Imaging of Colorectal Adenomas

Colorectal cancer (CRC) is one of the leading causes of cancer-related mortality in men and women. Timely detection and diagnosis are key to management of CRC, which is under-diagnosed because colorectal aberrant crypt foci, hyperplastic polyps, and microadenomas are often missed with conventional colonoscopy. The enzyme cyclooxygenase-2 (COX-2) is overexpressed in early stages of colorectal carcinogenesis and plays an important regulatory role in the process, suggesting that it could be a valuable target for enhanced imaging of nascent disease. Thus, we have generated an alpaca-derived library of 73 COX-2-specific nanobody clones. Here, we describe one such nanobody, F9-K45Q-K77Q-ROX, in which two native lysine residues have been mutated followed by conjugation to a fluorophore at the N-terminus with retention of COX-2-selective binding. The site of fluorophore conjugation and COX-2 binding affinity of F9-K45Q-K77Q-ROX were determined by proteomic and microscale thermophoretic analyses, respectively. In cell culture studies using 1483 human head and neck squamous cell carcinoma cells, F9-K45Q-K77Q-ROX accumulated inside cells and bound to intracellular COX-2, as visualized by fluorescence microscopy. In vivo pharmacokinetic, and toxicological analyses revealed that F9-K45Q-K77Q-ROX is detectable in circulation with a plasma half-life of 17.9 min and there is no short-term toxicity associated with single injections of 10 mg/kg, 20 mg/kg, or 40 mg/kg doses at 24 h post-administration. Noninvasive in vivo fluorescence endoscopic imaging validated tumor-specific accumulation of F9-K45Q-K77Q-ROX in azoxymethane/dextran sodium sulfate-induced colorectal adenomas in mice. This work demonstrates the first COX-2-targeted nanobodies including a fluorescent derivative that offers significant promise for targeted endoscopic imaging of COX-2-expressing neoplasms. Significance StatementCurrent colorectal cancer screening procedures, such as white-light colonoscopy, chromoendoscopy, and narrow-band imaging aim to detect solid colon tumors and precursor lesions. However, these methods tend to detect only raised solid tumors and mature cancers, whereas precursor lesions, such as aberrant crypt foci, hyperplastic polyps, and small adenomas are frequently missed. To address the need for better visualization of early lesions, we developed a library of alpaca-derived nanobodies targeted to cyclooxygenase-2 (COX-2), an enzyme that is overexpressed in colorectal adenomas. COX-2-targeted nanobodies bearing a fluorescent tag accumulate and are retained in colonic adenomas, facilitating their endoscopic visualization. This novel COX-2-targeted nanobody platform may also be valuable for early detection of other neoplastic diseases in which COX-2 overexpression occurs. (Word counts 119, limit 120)

bioengineering↗

bioRxiv2026

TF-IDF k-mer-based Classical and Hybrid Machine Learning Models for SARS-CoV-2 Variant Classification under Imbalanced Genomic Data

Accurate classification of SARS-CoV-2 genomic variants is essential for effective genomic surveillance, yet it is challenged by extreme class imbalance, limited representation of rare variants, and distribution shifts in real-world sequencing data. In this study, we employed hybrid RF-SVM framework designed for robust detection of rare SARS-CoV-2 variants. It integrates a random forest and a polynomial-kernel based support vector machine to enhance sensitivity to minority classes while maintaining overall predictive stability. We systematically compared classical machine learning models, deep learning approaches, and hybrid strategies under both standard and distribution-shifted evaluation settings. Our results show that classical models using TF-IDF-based k-mer features outperform deep learning methods on macro-averaged performance metrics. The Random Forest classifier using TF-IDF Feature achieved the best overall performance, with a macro-averaged F1-score of 0.8894 and an accuracy of 96.3%. The model also demonstrated strong generalization ability, as evidenced by stable cross-validation performance (CV accuracy = 0.9637). Hybrid RF-SVM model further improves rare variant detection under severe class imbalance. Calibration analysis indicates reliable probability estimates for common variants, although challenges persist for minority classes. Overall, this study highlights the limitations of deep learning in highly imbalanced genomic settings and demonstrates that carefully designed hybrid machine learning approaches provide an effective and interpretable solution for rare SARS-CoV-2 variant detection.

bioinformatics↗

bioRxiv2026

REGULATION OF COLONIC MACROPHAGES AND TYPE-17 AND REGULATORY T CELLS IN DSS-COLITIS BY IBD-ASSOCIATED TRANSCRIPTION FACTOR, CREM

BackgroundRecent genome wide association studies (GWAS) performed by our laboratory identified polymorphisms at the locus containing the gene, cAMP-responsive element modulator (CREM), that influence Entamoeba histolytica+ diarrheal disease susceptibility in children. CREM is a cAMP-responsive transcription factor that regulates genetic expression and epigenetic modulation in a context- and cell-specific manner. Polymorphisms at this locus have been previously associated with IBD susceptibility, suggesting CREM regulates enteric inflammation in infectious and autoimmune colitis. MethodsMice were generated with either a tamoxifen-inducible global deletion or an intestinal epithelial cell (IEC)-specific deletion of Crem. Dextran-sodium sulfate (DSS) was administered to chemically induce colitis and mice were assayed for weight loss, clinical score, spectral flow cytometry of colonic lamina propria and mesenteric lymph node white blood cells, and shallow shotgun whole genome sequencing of fecal samples. ResultsTamoxifen-inducible global deletion of Crem significantly ameliorated DSS-colitis severity as measured by clinical scoring and weight loss over the course of disease (p = 2.29 x 10-15, p = 2.24 x 10-21, respectively). Protection was not phenocopied when Crem was deleted exclusively in IECs. When sampled during acute colitis, protection seen in Crem-deleted mice was associated with a significant increase in macrophages, and ROR{gamma}t+ regulatory (pTregs) and T helper (Th17) cells in the colonic lamina propria, along with an increase of T-follicular like helper cells in the mesenteric lymph node. ConclusionsInducible global deletion of Crem reduced the severity of DSS colitis while increasing colonic macrophages, ROR{gamma}t+ regulatory (pTregs) and T helper (Th17) cells. Future work will investigate the aforementioned cell types to determine the mechanism by which CREM aggravates DSS-colitis, thereby defining the immunoregulatory role of CREM in intestinal inflammation with the goal of identifying new therapeutic targets for IBD.

immunology↗

bioRxiv2025

The hyaluronan receptor CD44 drives COVID-19 severity through its regulation of neutrophil migration

The novel respiratory disease COVID-19 caused by the coronavirus SARS-CoV-2 continues to be a public health emergency worldwide, and there is a need for more effective therapy for patients. The relationship between the extracellular matrix and the host immune response to infection is severely understudied. Deposition of the polysaccharide hyaluronan (HA) into the lungs is associated with more severe COVID-19 disease outcomes. HA is a major component of the extracellular matrix in connective tissues and is abundant in many parts of the body, including cartilage, skin, brain, and vitreous body. CD44 is the primary receptor for HA and is found on almost all immune cells in the lung. Known functions of CD44 include mediation of immune cell migration, activation, and differentiation. We hypothesized that increased HA deposition during COVID-19 increases CD44-mediated immune cell infiltration into lungs and results in more severe pathology. Here, we report that in mice infected with a mouse-adapted strain of SARS-CoV-2, treatment with a combination of two anti-CD44 monoclonal antibodies confers a significant survival benefit and reduces weight loss and clinical score of the mice on Day 4 post infection. We show that anti-CD44 treatment decreases many key cytokines and chemokines in the bronchoalveolar lavage fluid on Day 4. With flow cytometry, we show that anti-CD44 reduces the numbers of neutrophils in infected lungs. We also show through immunofluorescence that treatment with anti-CD44 antibodies reduces colocalization of HA and CD45 in lung sections, indicating that HAs interaction with immune cells contributes to pathology. Our findings demonstrate that disruption of HA-receptor interactions is a way to prevent inflammatory pathology in pulmonary infection.

immunology↗

bioRxiv2025

Using The Cancer Genome Atlas from cBioPortal to Develop Genomic Datasets for Machine Learning Assisted Cancer Treatment

Predicting the impact of genetic mutations is crucial for understanding diseases like cancer. Polymorphism Phenotyping (PolyPhen) and Sorting Intolerant From Tolerant (SIFT) are key tools for assessing how amino acid substitutions affect protein function and mutation pathogenicity. To our knowledge, no ready-to-use genomic dataset exists for prediction models to identify potentially harmful mutations, which could support research and clinical decisions. This study develops genomic and non-genomic datasets using The Cancer Genome Atlas (TCGA) from cBioPortal and applies machine learning models to predict PolyPhen and SIFT scores. We explore three classification models: Random Forest (RF), Extreme Gradient Boosting (XGBoost), and an ensemble RF-XGBoost model. Experimental results show that genomic data yields more accurate predictions than non-genomic data. The ensemble RF-XGBoost model performs best on genomic data, achieving average accuracies of 88.43% for PolyPhen and 95.13% for SIFT, highlighting the potential of artificial intelligence in genetic mutation analysis for disease treatment.

genomics↗

bioRxiv2024

IL-33 protects from recurrent C. difficile infection by restoration of humoral immunity

Clostridioides difficile infection (CDI) recurs in one of five patients. Monoclonal antibodies targeting the virulence factor TcdB reduce disease recurrence, suggesting that an inadequate anti-TcdB response to CDI leads to recurrence. In patients with CDI, we discovered that IL-33 measured at diagnosis predicts future recurrence, leading us to test the role of IL-33 signaling in the induction of humoral immunity during CDI. Using a mouse recurrence model, IL-33 was demonstrated to be integral for anti-TcdB antibody production. IL-33 acted via ST2+ ILC2 cells, facilitating germinal center T follicular helper (GC-Tfh) cell generation of antibodies. IL-33 protection from reinfection was antibody-dependent, as MT KO mice and mice treated with anti-CD20 mAb were not protected. These findings demonstrate the critical role of IL-33 in generating humoral immunity to prevent recurrent CDI. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=176 SRC="FIGDIR/small/623943v1_ufig1.gif" ALT="Figure 1"> View larger version (60K): org.highwire.dtl.DTLVardef@9ec4aeorg.highwire.dtl.DTLVardef@1827bd3org.highwire.dtl.DTLVardef@18f761dorg.highwire.dtl.DTLVardef@19396d4_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract:C_FLOATNO IL-33 restoration induces toxin-B-specific antibody production via the ILC2-TFH axis. In the left panel, IL-33 remediation increases ILC2s, subsequently inducing TFH directly or indirectly. TFH cell induction is pivotal for the production of antibodies. IL-33 also downregulates type 1 and type 3 immunity, favoring type 2 immunity to enhance host survival and reduce morbidity. The middle panel illustrates antibiotic-induced dysbiosis, resulting in decreased IL-33 levels and reduced antibody production. The right panel demonstrates the protective effect in reinfection, attributed to toxin-specific antibodie generated by IL-33 remediation. C_FIG

immunology↗

bioRxiv2024

Synthesis and characterization of chloroquine-modified albumin-binding siRNA-lipid conjugates for improved intracellular delivery and gene silencing in cancer cells

siRNA therapeutics have considerable potential as molecularly-targeted therapeutics in malignant disease, but identification of effective delivery strategies that mediate rapid intracellular delivery while minimizing toxicity has been challenging. Our group recently developed and optimized an siRNA conjugate platform termed "siRNA-L2," which harnesses non-covalent association with endogenous circulating albumin to extend circulation half-life and achieve tumor-selective delivery without the use of traditional cationic lipids or polymers for transfection. To improve intracellular delivery and particularly the endosomal escape properties of siRNA-L2 towards more efficient gene silencing, we report synthesis of siRNA-CQ-L2 conjugates, in which chloroquine (CQ), an endosomolytic quinoline alkaloid, is covalently incorporated into the branching lipid tail structure. We accomplished this via synthesis of a novel CQ phosphoramidite, which can be incorporated into a modular siRNA-L2 backbone using on-column solid-phase synthesis through use of asymmetric branchers with levulinyl-protected hydroxide groups that allow covalent addition of pendant CQ repeats. We demonstrate that siRNA-CQ-L2 maintains the ability to non-covalently bind albumin, and with multiple copies of CQ, siRNA-CQ-L2 mediates higher endosomal disruption, cellular uptake/retention, and reporter gene knockdown in cancer cells. Further, in mice, the addition of CQ did not significantly affect circulation kinetics nor organ biodistribution and did not produce hematologic or organ-level toxicity. Thus, controlled, multivalent conjugation of albumin-binding siRNA-L2 to endosomolytic small molecule compounds holds promise in improving siRNA-L2 knockdown potency while maintaining albumin-binding properties and overall safety.

bioengineering↗

bioRxiv2024

Polymeric Micellar Nanoparticles Enable Image-guided Drug Delivery in Solid Tumors

We report the development of a nanotechnology to co-deliver chemocoxib A with a reactive oxygen species (ROS)-activatable and COX-2 targeted pro-fluorescent probe, fluorocoxib Q (FQ) enabling real time visualization of COX-2 and CA drug delivery into solid cancers, using a di-block PPS135-b-POEGA17 copolymer, selected for its intrinsic responsiveness to elevated reactive oxygen species (ROS), a key trait of the tumor microenvironment. FQ and CA were synthesized independently, then co-encapsulated within micellar PPS135-b-POEGA17 co-polymeric nanoparticles (FQ-CA-NPs), and were assessed for cargo concentration, hydrodynamic diameter, zeta potential, and ROS-dependent cargo release. The uptake of FQ-CA-NPs in mouse mammary cancer cells and cargo release was assessed by fluorescence microscopy. Intravenous delivery of FQ-CA-NPs to mice harboring orthotopic mammary tumors, followed by vital optimal imaging, was used to assess delivery to tumors in vivo. The CA-FQ-NPs exhibited a hydrodynamic diameter of 109.2 {+/-} 4.1 nm and a zeta potential ({zeta}) of -1.59 {+/-} 0.3 mV. Fluorescence microscopy showed ROS-dependent cargo release by FQ-CA-NPs in 4T1 cells, decreasing growth of 4T1 breast cancer cells, but not affecting growth of primary human mammary epithelial cells (HMECs). NP-derived fluorescence was detected in mammary tumors, but not in healthy organs. Tumor LC-MS/MS analysis identified both CA (2.38 nmol/g tumor tissue) and FQ (0.115 nmol/g tumor tissue), confirming the FQ-mediated image guidance of CA delivery in solid tumors. Thus, co-encapsulation of FQ and CA into micellar nanoparticles (FQ-CA-NPs) enabled ROS-sensitive drug release and COX-2-targeted visualization of solid tumors.

bioengineering↗

bioRxiv2024

Activity-Based Protein Profiling Identifies Klebsiella pneumoniae Serine Hydrolases with Potential Roles in Host-Pathogen Interactions

Klebsiella pneumoniae is a normal resident of the human gastro-intestinal tract and an opportunistic, critical priority pathogen that can cause a variety of severe systemic infections. Due to emerging multi-drug resistance of this pathogen, the discovery and validation of novel targets for the development of new treatment options is an urgent priority. Here, we explored the family of serine hydrolases, a highly druggable and functionally diverse enzyme family which is uncharacterized in K. pneumoniae. Using functionalized covalent fluorophosphonate inhibitors as activity-based probes we identified 10 serine hydrolases by mass spectrometry-based activity-based protein profiling, 7 of which were previously uncharacterized. Functional validation using transposon mutants deficient in either of the putative lysophospholipase PldB, esterase YjfP and patatin-like phospholipase YchK revealed severe growth defects in human colonic organoid co-culture models and reduced virulence during Galleria mellonella infection. Mutants deficient in the PldB and YjfP, but not YchK show increased susceptibility to killing by complement and the antimicrobial peptide antibiotic polymyxin B, suggesting a role in maintaining cell envelope integrity. Biochemical characterization and structural analysis of recombinant YjfP suggest this protein is a deacetylase. This study gives important insights into the molecular mechanisms underlying virulence and cell physiology of K. pneumoniae at the host-pathogen interface and it positions PldB, YjfP and YchK as potential antimicrobial or anti-virulence target candidates, inhibition of which might synergize with existing antibiotics and human immune defenses.

microbiology↗

bioRxiv2024

Machine Learning Approaches for Skin Neoplasm Diagnosis

Approaches for skin neoplasm diagnosis include physical exam, skin biopsy, lab tests of biopsy samples, and image analyses. These approaches often involve error-prone and time-consuming processes. Recent studies show that machine learning has promises to effectively classify skin images into different classes such as melanoma and melanocytic nevi. In this work, we investigate machine learning approaches to enhance the performance of computer-aided diagnosis (CADx) systems to diagnose skin diseases. In the proposed CADx system, generative adversarial network (GAN) is used to identify (and remove) fake images. Exploratory data analysis (EDA) is applied to normalize the original dataset for preventing model overfitting. Synthetic minority over-sampling technique (SMOTE) is employed to rectify class imbalances in the original dataset. To accurately classify skin images, the following four machine learning models are utilized: linear discriminant analysis (LDA), support vector machine (SVM), convolutional neural network (CNN), and an ensemble CNN-SVM. Experimental results using the HAM10000 dataset demonstrate the ability of the machine learning models to improve CADx performance in treating skin neoplasm. Initially, the LDA, SVM, CNN, and ensemble CNN-SVM show 49%, 72%, 77%, and 79% accuracy, respectively. After applying GAN, EDA, and SMOTE, the LDA, SVM, CNN, and ensemble CNN-SVM show 76%, 83%, 87%, and 94% accuracy, respectively. We plan to explore other machine learning models and datasets in our next endeavor.

bioengineering↗

bioRxiv2023

Neuronal SNCA transcription during Lewy body formation

BackgroundMisfolded -synuclein (-syn) is believed to contribute to neurodegeneration in Lewy body disease (LBD) based on considerable evidence including a gene-dosage effect observed in relation to point mutations and multiplication of SNCA in familial Parkinsons disease. A contradictory concept proposes early loss of the physiological -syn as the major driver of neurodegeneration. There is a paucity of data on SNCA transcripts in various -syn immunoreactive cytopathologies. MethodsSNCA transcripts in neurons without and with various -syn immunoreactive cytopathologies in the substantia nigra and amygdala in LBD (n = 5) were evaluated using RNAscope combined with immunofluorescence for disease-associated -syn. Single-nucleus RNA sequencing was performed to elucidate cell-type specific SNCA expression in non-diseased frontal cortex (n = 3). ResultsSNCA transcripts in neurons with punctate -syn immunoreactivity were preserved both in the substantia nigra and amygdala but were reduced in neurons with compact -syn inclusions. Only single SNCA transcripts were detected in astrocytes with or without -syn immunoreactivity in the amygdala. Single-nucleus RNA sequencing revealed that excitatory and inhibitory neurons, oligodendrocyte progenitor cells, oligodendrocytes, and homeostatic microglia expressed SNCA transcripts, while expression was largely absent in astrocytes and microglia. ConclusionsThe preserved cellular SNCA expression in the more abundant non-Lewy body type -syn cytopathologies provides a pool for local protein production that can aggregate and serve as a seed for misfolded -syn. Successful segregation of disease-associated -syn is associated with the exhaustion of SNCA production in the terminal cytopathology, the Lewy body. Our observations support a therapeutic strategy incorporating a finely tuned dual approach targeting the elimination of misfolded -syn along with the reduction of the SNCA transcription to avoid feeding of pathological -syn seeding.

pathology↗

bioRxiv2023

Identification of Therapeutic Leads from Ficus hispida Fruit Phytochemicals against Prostate Cancer Using Pharmacoinformatic and Molecular Dynamics Simulation Approach

Prostate cancer is one of the leading causes of death and the most common cancer type in men. In this study, potential leads from the phytochemicals of Ficus hispida fruit were screened using in silico tools against androgen receptor (AR), a known target for prostate cancer. PASS online and ADMET tools were used to screen specific phytochemicals that are relevant to prostate cancer treatment and have drug-like properties. Of 13, a total of 10 phytochemicals passed PASS online and ADMET screening. Next, a total of three phytochemicals, including nodakenetin (CID: 26305), isowigtheone hydrate (CID: 66728267), and 7-hydroxycoumarin (CID: 5281426) were selected based on their docking scores (-9.946 to -7.653 kcal/mol) and relevance to selective bioactivity. The MD simulation further confirmed the binding stability of these three phytochemicals with their target AR protein and determined that the main amino acid residues mainly responsible for this stability including RMSD, RMSF, and post simulation binding free energies. These findings suggest that these three phytochemicals of Ficus hispida fruit can further be developed as prospective therapeutics against prostate cancer.

bioinformatics↗

bioRxiv2021

Clostridioides difficile binary toxin binding component (CDTb) increases virulence in a hamster model

Clostridioides difficile is the leading cause of hospital-acquired gastrointestinal infection, in part due to the existence of binary toxin (CDT)-expressing hypervirulent strains. We have previously shown that CDT interacts with the TLR2/6 heterodimer to induce inflammation, and in this study we further explore this interaction as well as the contribution of the separate components of CDT, CDTa and CDTb. We found that the binding component, CDTb, is capable of inducing inflammation. Additionally, complementation of a CDT-deficient C. difficile strain with CDTb alone restored virulence in a hamster model of C. difficile infection. Overall, this study demonstrates that the binding component of C. difficile binary toxin contributes to virulence during infection.

microbiology↗

bioRxiv2021

The IL-33-ILC2 pathway protects from amebic colitis

Entamoeba histolytica is a pathogenic protozoan parasite that causes intestinal colitis, diarrhea, and in some cases, liver abscess. Through transcriptomics analysis, we observed that E. histolytica infection was associated with increased expression of IL-33 mRNA in both the human and murine colon. IL-33, the IL-1 family cytokine, is released after cell injury to alert the immune system of tissue damage during infection. Treatment with recombinant IL-33 protected mice from amebic infection and colonic tissue damage; moreover, blocking IL-33 signaling made mice more susceptible to infection and weight loss. IL-33 limited the recruitment of inflammatory immune cells and decreased the pro-inflammatory cytokine IL-6 in the colon. Type 2 immune responses, which are known to be involved in tissue repair, were upregulated by IL-33 treatment during amebic infection. Interestingly, administration of IL-33 protected RAG2-/- mice but not RAG2-/-{gamma}c-/- mice, demonstrating that IL-33 mediated protection occurred in the absence of T or B cells but required the presence of innate lymphoid cells (ILCs). IL-33 induced recruitment of ILC2 but not ILC1 and ILC3 in RAG2-/- mice. Adoptive transfer of ILC2s to RAG2-/-{gamma}c-/- mice restored IL-33 mediated protection. These data reveal that the IL-33-ILC2 pathway is an important host defense mechanism against amebic colitis.

immunology↗

bioRxiv2021

Targeting Diacylglycerol Lipase to Reduce AlcoholConsumption

Alcohol use disorder (AUD) is associated with substantial morbidity, mortality, and societal cost, and pharmacological treatment options for AUD are limited. The endogenous cannabinoid (eCB) signaling system is critically involved in reward processing and alcohol intake is positively correlated with release of the eCB ligand 2-Arachidonoylglycerol (2-AG) within reward neurocircuitry. Here we show that genetic and pharmacological inhibition of diacylglycerol lipase (DAGL), the rate limiting enzyme in the synthesis of 2-AG, reduces alcohol consumption in a variety of preclinical models ranging from a voluntary free-access model to aversion resistant-drinking, and dependence-like drinking induced via chronic intermittent ethanol vapor exposure in mice. DAGL inhibition also prevented ethanol-induced suppression of GABAergic transmission onto midbrain dopamine neurons, providing mechanistic insight into how DAGL inhibition could affect alcohol reward. Lastly, DAGL inhibition during either chronic alcohol consumption or protracted withdrawal was devoid of anxiogenic and depressive-like behavioral effects. These data suggest reducing 2-AG signaling via inhibition of DAGL could represent a novel approach to reduce alcohol consumption across the spectrum of AUD severity.

neuroscience↗

bioRxiv2020

Megasphaera in the stool microbiota is negatively associated with diarrheal cryptosporidiosis

BackgroundThe protozoan parasites in the Cryptosporidium genus cause both acute diarrheal disease and subclinical (i.e. non-diarrheal) disease. It is unclear if the microbiota can influence the manifestation of diarrhea during a Cryptosporidium infection. MethodsTo characterize the role of the gut microbiota in diarrheal cryptosporidiosis, the microbiome composition of both diarrheal and surveillance Cryptosporidium-positive fecal samples was evaluated using 16S rRNA gene sequencing. Additionally, the microbiome composition prior to infection was examined to test whether a preexisting microbiome profile could influence the Cryptosporidium infection phenotype. ResultsFecal microbiome composition was associated with diarrheal symptoms at two timepoints. Megasphaera was significantly less abundant in diarrheal samples when compared to subclinical samples at the time of Cryptosporidium detection (log2(fold change) = -4.3, p=10-10) and prior to infection (log2(fold change) = -2.0, p=10-4). Random forest classification also identified Megasphaera abundance in the pre- and post-exposure microbiota.as predictive of a subclinical infection. ConclusionsMicrobiome composition broadly, and specifically low Megasphaera abundance, was associated with diarrheal symptoms prior to and at the time of Cryptosporidium detection. This observation suggests that the gut microenvironment may play a role in determining the severity of a Cryptosporidium infection. SummaryMegasphaera abundance in the stool of Bangladeshi infants is associated with the development of diarrhea upon infection with the Cryptosporidium parasite.

microbiology↗

bioRxiv2018

Gut microbiome communication with bone marrow regulates susceptibility to amebiasis

The gut microbiome provides resistance to infection. However, the mechanisms for this are poorly understood. Colonization with the intestinal bacterium Clostridium scindens provided protection from the parasite Entamoeba histolytica via innate immunity. Introduction of C. scindens into the gut microbiota epigenetically altered and expanded bone marrow granulocyte-monocyte-progenitors (GMPs) and provided neutrophil-mediated protection against subsequent challenge with E. histolytica. Adoptive transfer of bone-marrow from C. scindens colonized-mice into naive-mice protected against ameba infection and increased intestinal neutrophils. Because of the known ability of C. scindens to metabolize the bile salt cholate, we measured deoxycholate and discovered that it was increased in the sera of C. scindens colonized mice, as well as in children protected from amebiasis. Administration of deoxycholate alone (in the absence of C. scindens) increased the epigenetic mediator JMJD3 and GMPs and provided protection from amebiasis. In conclusion the microbiota was shown to communicate to the bone marrow via microbially-metabolized bile salts to train innate immune memory to provide antigen-nonspecific protection from subsequent infection. This represents a novel mechanism by which the microbiome protects from disease.\n\nOne Sentence SummaryIntroduction of the human commensal bacteria Clostridium scindens into the intestinal microbiota epigenetically alters bone marrow and protects from future parasite infection.

microbiology↗