Collection and Processing of Samples for Next-Generation Sequencing to Study the Gut Microbiome.

16S rRNA gene sequencing is commonly used for identification and quantitation of microorganisms in complex biological mixtures, such as the human gut microbiome. The 16S rRNA gene is an excellent target gene for sequencing DNA in a heterogenous sample, as it is a highly conserved part of the transcriptional machinery. Universal PCR primers are used to amplify the conserved regions of 16S.

Gut Microbiome and Lipidome Signatures in Irritable Bowel Syndrome Patients from a Low-Income, Food-Desert Area: A Pilot Study.

Irritable bowel syndrome (IBS) is a common gastroenterological disorder with triggers such as fructose. We showed that our IBS patients suffering from socioeconomic challenges have a significantly high consumption of high-fructose corn syrup (HFCS). Here, we characterize gut microbial dysbiosis and fatty acid changes, with respect to IBS, HFCS consumption, and socioeconomic factors.

A Pilot Study Exploring Temporal Development of Gut Microbiome/Metabolome in Breastfed Neonates during the First Week of Life.

Purpose: Exclusive breastfeeding promotes gut microbial compositions associated with lower rates of metabolic and autoimmune diseases. Its cessation is implicated in increased microbiome-metabolome discordance, suggesting a vulnerability to dietary changes. Formula supplementation is common within our low-income, ethnic-minority community.

Intensity-specific considerations for exercise for patients with inflammatory bowel disease.

The rising prevalence of inflammatory bowel disease (IBD) necessitates that patients be given increased access to cost-effective interventions to manage the disease. Exercise is a non-pharmacologic intervention that advantageously affects clinical aspects of IBD, including disease activity, immune competency, inflammation, quality of life, fatigue, and psychological factors. It is well established that exercise performed at low-to-moderate intensity across different modalities manifests many of these diseased-related benefits while also ensuring patient safety.

Probiotics for the Prevention of Antibiotic-Associated Diarrhea.

Several communities have started using probiotic-rich fermented foods as therapeutic options with presumed medicinal powers. We now know the importance of microbiome balance and how probiotics can restore imbalances in the microbiome. Probiotics have been tested for a number of clinical uses such as the prevention of antibiotic-associated diarrhea (AAD), the treatment of various diseases such as infection, irritable bowel disease, vaginitis, the prevention of allergies, and necrotizing enterocolitis in newborns.

Clinical Factors Implicated in Antibiotic Resistance in Patients.

is a common gastric pathogen associated with multiple clinical syndromes, including cancer. Eradication rates of remain suboptimal despite the progress made in the past few decades in improving treatment strategies. The low eradication rates are mainly driven by antibiotic resistance of .

Effects of Milkfat on the Gut Microbiome of Patients After Bariatric Surgery, a Pilot Study.

Background: The efficacy of bariatric surgery may be in part attributed to altered metabolism via new gut microbiome. Milkfat may promote the growth of microbes that are beneficial in long-term weight loss. Understanding the specific gut microbiome changes after surgery and their relationship to milkfat consumption may yield important strategies for managing obesity after bariatric procedures.

Characterization of gut microbiome and metabolome in patients in an underprivileged community in the United States.

Background: () a bacterium that infects approximately half of the world's population, is associated with various gastrointestinal diseases, including peptic ulcers, non-ulcer dyspepsia, gastric adenocarcinoma, and gastric lymphoma. As the burden of antibiotic resistance increases, the need for new adjunct therapies designed to facilitate eradication and reduce negative distal outcomes associated with infection has become more pressing. Characterization of the interactions between , the fecal microbiome, and fecal fatty acid metabolism, as well as the mechanisms underlying these interactions, may offer new therapeutic approaches.

Patient Awareness of Reported Adverse Effects Associated with Proton Pump Inhibitors in a Medically Underserved Community.

Reports of adverse effects associated with proton pump inhibitors (PPIs) are concerning because of high usage and over-the-counter availability. We sought to determine the awareness of PPI adverse effects among our patient population, which is medically underserved, low-income, and racially diverse. A 21-item survey was administered to gastroenterology-clinic outpatients.

Designing strategies for eradication of Helicobacter pylori based on prevalence patterns of infection and antibiotic resistance in a low-income, medically underserved community in the United States.

Background: Regional variation in Helicobacter pylori resistance patterns is a significant contributing factor for the ineffectiveness of traditional treatments. To improve treatment outcomes, we sought to create an individualized, susceptibility-driven therapeutic approach among our patient population, which is one of the poorest in the nation. It is medically underserved, minority-predominant and has high incidence of H pylori infection.

Comparative outcomes in different aortic valve stenosis surgeries and implications of TAVR surgery for cirrhotic patients: A retrospective cohort study.

Background: Our hospital system is committed to service to medically underserved, low-income, and minority populations. It is located in a city wherein 37% of people live in poverty. Overall cost effectiveness is part of our patient care quality improvement.

Shaping Perceptions of Basic Science Education by Utilizing Real Patient Encounters.

Background: Integrating basic science into clinical teaching has been a struggle for medical schools. However, early exposure to clinical experience has been associated with an increased understanding of the importance of basic science, positive attitudes, and developing clinical skills faster. Furthermore, early clinical exposure can help students reconnect with what drove them into medicine in the first place, especially when they are starting to feel burned out by the volume of lecture material.

Use of Real Patients and Patient-Simulation-Based Methodologies for Teaching Gastroenterology to Pre-Clinical Medical Students.

In recent years, there has been an increasing focus on the need to integrate formal knowledge with clinical experience in the pre-clinical years since the initial years of medical education play an important role in shaping the attitudes of medical students towards medicine and support the development of clinical reasoning. In this study, we describe approaches that involve real patients and patient-simulation-based methodologies to teach gastroenterology to second year medical students. Our goals were to (i) demonstrate bio-psychosocial aspects of clinical practice, (ii) demonstrate commonality of gastrointestinal ailments, and (iii) help understand complex gastroenterology concepts.

Creation and implementation of a flipped jigsaw activity to stimulate interest in biochemistry among medical students.

Learner-centered pedagogical methods that are based on clinical application of basic science concepts through active learning and problem solving are shown to be effective for improving knowledge retention. As the clinical relevance of biochemistry is not always apparent to health-profession students, effective teaching of medical biochemistry should highlight the implications of biochemical concepts in pathology, minimize memorization, and make the concepts memorable for long-term retention. Here, we report the creation and successful implementation of a flipped jigsaw activity that was developed to stimulate interest in learning biochemistry among medical students.

Irritable Bowel Syndrome: Clinical Manifestations, Dietary Influences, and Management.

Irritable bowel syndrome (IBS) is a functional gastrointestinal disorder that is characterized by symptoms of chronic abdominal pain and altered bowel habits in the absence of an overtly identifiable cause. It is the most commonly diagnosed functional gastrointestinal disorder, accounting for about one third of gastroenterology visits. It generally presents as a complex of symptoms, including psychological dysfunction.

An Interactive Session on Nutritional Pathologies for Health Professional Students.

Various studies have emphasized the need to improve the nutrition training of health professionals, which will help them to provide optimal patient care. Nutrition-based interactive sessions may serve as an efficient approach to instigate an interest in nutrition among the students. Here we report the reception and effectiveness of a nutrition-pathology based interactive activity that we designed and implemented in the gastroenterology course given to the second year students at our medical school.

Regression of solid tumors by induction of MazF, a bacterial mRNA endoribonuclease.

MazF from Escherichia coli is an endoribonuclease that specifically cleaves mRNAs at ACA sequences. Its induction in mammalian cells has been shown to cause programmed cell death. Here we explored if a bacterial MazF-MazE toxin-antitoxin system can be used for gene therapy.

An online guided e-journal exercise in pre-clerkship years: oxidative phosphorylation in brown adipose tissue.

The rationale for this mandatory, guided online e-journal exercise is to foster the ability of students to independently read medical and scientific literature in a critical manner and to integrate journal reading with their basic science knowledge. After a lecture on oxidative phosphorylation, students were assigned to read an article on brown adipose tissue published in New England Journal of Medicine and were guided to analyze the article by answering online questions. After two iterations, student surveys about the project, its key pedagogical features, and ways to improve it suggest that the students perceived these exercises as active learning, which is clinically relevant and built on their course material.

Over the counter drugs (and dietary supplement) exercise: a team-based introduction to biochemistry for health professional students.

For successful delivery of basic science topics for health-professional students, it is critical to reduce apprehension and illustrate relevance to clinical settings and everyday life. At the beginning of the Biochemistry course for Physician Assistants, a team-based assignment was designed to develop an understanding of the mechanism of action, effectiveness, and toxicity of five common over the counter (OTC) drugs and dietary supplements, and place these familiar medicines in a political and historical context. The objectives of this exercise were to stimulate interest in biochemistry; to provide basic information on enzymes and enzyme inhibitors related to these drugs to be expanded upon later in the course; and to encourage active and interactive learning.

Escherichia coli cold-shock gene profiles in response to over-expression/deletion of CsdA, RNase R and PNPase and relevance to low-temperature RNA metabolism.

Cold-shock response is elicited by the transfer of exponentially growing cells from their optimum temperature to a significantly lower growth temperature and is characterized by the induction of several cold-shock proteins. These proteins, which presumably possess a variety of different activities, are critical for survival and continued growth at low temperature. One of the main consequences of cold shock is stabilization of the secondary structures in nucleic acids leading to hindrance of RNA degradation.

Identification of two DNA helicases UvrD and DinG as suppressors for lethality caused by mutant cspA mRNAs.

CspA is a major cold shock-inducible protein (70 aa), and its major role in the cold shock response was shown to be as an RNA chaperone destabilizing secondary structure of mRNAs at low temperature. Previously, we showed that the overexpression of mutant cspA containing premature non-sense codons at various positions led to stalled ribosomes on mutant cspA transcripts, ultimately leading to cell death. This lethality is primarily due to the highly translatable cspA 5'-UTR that recruits most of the ribosomes from other mRNAs, which are then stalled at the abnormal stop codon.

Unwinding activity of cold shock proteins and RNA metabolism.

Temperature downshift from 37 °C to 15 °C results in the exertion of cold shock response in Escherichia coli, which induces cold shock proteins, such as CsdA. Previously, we showed that the helicase activity of CsdA is critical for its function in the cold acclimation of cells and its primary role is mRNA degradation. Only RhlE (helicase), CspA (RNA chaperone) and RNase R (exoribonuclease) were found to complement the cold shock function of CsdA.

RNA remodeling and gene regulation by cold shock proteins.

One of the many important consequences that temperature down-shift has on cells is stabilization of secondary structures of RNAs. This stabilization has wide-spread effects, such as inhibition of expression of several genes due to termination of their transcription and inefficient RNA degradation that adversely affect cell growth at low temperature. Several cold shock proteins are produced to counteract these effects and thus allow cold acclimatization of the cell.