Mechanisms for gut microbiome dysbiosis following stroke

"Over 795,000 people in the US suffer a stroke every year. Survivors are often left with severe cognitive, functional, and emotional impairments. Gut dysbiosis and increased gut permeability have been shown to occur following stroke, leading to a systemic flood of neuro- and immuno-modulatory substances. Evidence from animal model studies suggests that gut microbes modulate the bidirectional gut brain axis. It is unknown how post-stroke dysbiosis correlates with gut permeability."--Introduction

Gut microbiome dysbiosis in at-risk versus low-risk stroke adults

"Healthy brain aging has been a significant focus in older adults. Lifestyle changes such as diet and exercise have been implemented by adults to avoid brain related disease processes such stroke and Alzheimer’s disease. Stroke risk factors such as high BMI, hypertension, diabetes, and the presence of ApoE4 gene have been explored in hopes to find interventions targeted to promote more healthy brain aging. Currently there is a knowledge gap on how interventions can promote healthy brain aging. Targeting the bidirectional gut-brain axis by manipulating the gut microbiome can be a possible intervention to promote brain health."--Introduction

Age Drives Distortion of Brain Metabolic, Vascular and Cognitive Functions, and the Gut Microbiome

Advancing age is the top risk factor for the development of neurodegenerative disorders, including Alzheimer’s disease (AD). However, the contribution of aging processes to AD etiology remains unclear. Emerging evidence shows that reduced brain metabolic and vascular functions occur decades before the onset of cognitive impairments, and these reductions are highly associated with low-grade, chronic inflammation developed in the brain over time. Interestingly, recent findings suggest that the gut microbiota may also play a critical role in modulating immune responses in the brain via the brain-gut axis. In this study, our goal was to identify associations between deleterious changes in brain metabolism, cerebral blood flow (CBF), gut microbiome and cognition in aging, and potential implications for AD development. We conducted our study with a group of young mice (5–6 months of age) and compared those to old mice (18–20 months of age) by utilizing metabolic profiling, neuroimaging, gut microbiome analysis, behavioral assessments and biochemical assays. We found that compared to young mice, old mice had significantly increased levels of numerous amino acids and fatty acids that are highly associated with inflammation and AD biomarkers. In the gut microbiome analyses, we found that old mice had increased Firmicutes/Bacteroidetes ratio and alpha diversity. We also found impaired blood-brain barrier (BBB) function and reduced CBF as well as compromised learning and memory and increased anxiety, clinical symptoms often seen in AD patients, in old mice. Our study suggests that the aging process involves deleterious changes in brain metabolic, vascular and cognitive functions, and gut microbiome structure and diversity, all which may lead to inflammation and thus increase the risk for AD. Future studies conducting comprehensive and integrative characterization of brain aging, including crosstalk with peripheral systems and factors, will be necessary to define the mechanisms underlying the shift from normal aging to pathological processes in the etiology of AD

Ketogenic Diet Enhances Neurovascular Function with Altered Gut Microbiome in Young Healthy Mice

Neurovascular integrity, including cerebral blood flow (CBF) and blood-brain barrier (BBB) function, plays a major role in determining cognitive capability. Recent studies suggest that neurovascular integrity could be regulated by the gut microbiome. The purpose of the study was to identify if ketogenic diet (KD) intervention would alter gut microbiome and enhance neurovascular functions, and thus reduce risk for neurodegeneration in young healthy mice (12–14 weeks old). Here we show that with 16 weeks of KD, mice had significant increases in CBF and P-glycoprotein transports on BBB to facilitate clearance of amyloid-beta, a hallmark of Alzheimer’s disease (AD). These neurovascular enhancements were associated with reduced mechanistic target of rapamycin (mTOR) and increased endothelial nitric oxide synthase (eNOS) protein expressions. KD also increased the relative abundance of putatively beneficial gut microbiota (Akkermansia muciniphila and Lactobacillus), and reduced that of putatively pro-inflammatory taxa (Desulfovibrio and Turicibacter). We also observed that KD reduced blood glucose levels and body weight, and increased blood ketone levels, which might be associated with gut microbiome alteration. Our findings suggest that KD intervention started in the early stage may enhance brain vascular function, increase beneficial gut microbiota, improve metabolic profile, and reduce risk for AD

Apolipoprotein E Genotype-Dependent Nutrigenetic Effects to Prebiotic Inulin for Modulating Systemic Metabolism and Neuroprotection in Mice via Gut-Brain Axis

OBJECTIVE: The goal of the study was to identify the potential nutrigenetic effects to inulin, a prebiotic fiber, in mice with different human apolipoprotein E (APOE) genetic variants. Specifically, we compared responses to inulin for the potential modulation of the systemic metabolism and neuroprotection via gut-brain axis in mice with human APOE ϵ3 and ϵ4 alleles. METHOD: We performed experiments with young mice expressing the human APOE3 (E3FAD mice and APOE4 gene (E4FAD mice). We fed mice with either inulin or control diet for 16 weeks starting from 3 months of age. We determined gut microbiome diversity and composition using16s rRNA sequencing, systemic metabolism using in vivo MRI and metabolomics, and blood–brain barrier (BBB) tight junction expression using Western blot. RESULTS: In both E3FAD and E4FAD mice, inulin altered the alpha and beta diversity of the gut microbiome, increased beneficial taxa of bacteria and elevated cecal short chain fatty acid and hippocampal scyllo-inositol. E3FAD mice had altered metabolism related to tryptophan and tyrosine, while E4FAD mice had changes in the tricarboxylic acid cycle, pentose phosphate pathway, and bile acids. Differences were found in levels of brain metabolites related to oxidative stress, and levels of Claudin-1 and Claudin-5 BBB tight junction expression. DISCUSSION: We found that inulin had many similar beneficial effects in the gut and brain for both E3FAD and E4FAD mice, which may be protective for brain functions and reduce risk for neurodegeneration. . E3FAD and E4FAD mice also had distinct responses in several metabolic pathways, suggesting an APOE-dependent nutrigenetic effects in modulating systemic metabolism and neuroprotection

A formally verified compiler back-end

This article describes the development and formal verification (proof of semantic preservation) of a compiler back-end from Cminor (a simple imperative intermediate language) to PowerPC assembly code, using the Coq proof assistant both for programming the compiler and for proving its correctness. Such a verified compiler is useful in the context of formal methods applied to the certification of critical software: the verification of the compiler guarantees that the safety properties proved on the source code hold for the executable compiled code as well

Gut microbiome association with brain imaging markers, APOE genotype, calcium and vegetable intakes, and obesity in healthy aging adults

IntroductionAdvanced age is a significant factor in changes to brain physiology and cognitive functions. Recent research has highlighted the critical role of the gut microbiome in modulating brain functions during aging, which can be influenced by various factors such as apolipoprotein E (APOE) genetic variance, body mass index (BMI), diabetes, and dietary intake. However, the associations between the gut microbiome and these factors, as well as brain structural, vascular, and metabolic imaging markers, have not been well explored.MethodsWe recruited 30 community dwelling older adults between age 55-85 in Kentucky. We collected the medical history from the electronic health record as well as the Dietary Screener Questionnaire. We performed APOE genotyping with an oral swab, gut microbiome analysis using metagenomics sequencing, and brain structural, vascular, and metabolic imaging using MRI.ResultsIndividuals with APOE e2 and APOE e4 genotypes had distinct microbiota composition, and higher level of pro-inflammatory microbiota were associated higher BMI and diabetes. In contrast, calcium- and vegetable-rich diets were associated with microbiota that produced short chain fatty acids leading to an anti-inflammatory state. We also found that important gut microbial butyrate producers were correlated with the volume of the thalamus and corpus callosum, which are regions of the brain responsible for relaying and processing information. Additionally, putative proinflammatory species were negatively correlated with GABA production, an inhibitory neurotransmitter. Furthermore, we observed that the relative abundance of bacteria from the family Eggerthellaceae, equol producers, was correlated with white matter integrity in tracts connecting the brain regions related to language, memory, and learning.DiscussionThese findings highlight the importance of gut microbiome association with brain health in aging population and could have important implications aimed at optimizing healthy brain aging through precision prebiotic, probiotic or dietary interventions

Cooperative Integration of an Interactive Proof Assistant and an Automated Prover Abstract

We propose a mechanism for semi-automated proving of theorems, using a tactic for the Coq proof assistant that consults a proof-generating Nelson-Oppen-style automated prover. Instead of simply proving or failing to prove a goal, our tactic decides on relevant case splits using theory-specific axioms, proves some of the resulting cases, and returns the remainder to the Coq user as subgoals. These subgoals can then be proved using inductions and lemma instantiations that are beyond the capabilities of the automated prover. We show that the Coq tactic language provides an excellent way to script this process to an extent not supported by current Nelson-Oppen provers. Like with any Coq proof, a separately checkable proof term in a core calculus is produced at the end of any successful proving session where our method is used, and we take advantage of the “proof by reflection ” technique to translate the specialized first-order proofs of the automated prover into compact Coq representations

A framework for certified program analysis and its applications to mobile-code safety

Abstract. A certified program analysis is an analysis whose implementation is accompanied by a checkable proof of soundness. We present a framework whose purpose is to simplify the development of certified program analyses without compromising the run-time efficiency of the analyses. At the core of the framework is a novel technique for automatically extracting Coq proof-assistant specifications from ML implementations of program analyses, while preserving to a large extent the structure of the implementation. We show that this framework allows developers of mobile code to provide to the code receivers untrusted code verifiers in the form of certified program analyses. We demonstrate efficient implementations in this framework of bytecode verification, typed assembly language, and proof-carrying code.

The Open Verifier framework for foundational verifiers

We present the Open Verifier approach for verifying untrusted code using customized verifiers. This approach can be viewed as an instance of foundational proof-carrying code where an untrusted program can be checked using the verifier most natural for it instead of using a single generic type system. In this paper we focus on a specialized architecture designed to reduce the burden of expressing both type-based and Hoare-style verifiers. A new verifier is created by providing an untrusted executable extension module, which can incorporate directly pre-existing non-foundational verifiers based on dataflow analysis or type checking. The extensions control virtually all aspects of the verification by carrying on a dialogue with the Open Verifier using a language designed both to correspond closely to common verification actions and to carry simple adequacy proofs for those actions. We describe the design of the trusted core of the Open Verifier, along with our experience implementing proof-carrying code, typed assembly language, and dataflow or abstract interpretation based verifiers in this unified setting