Publications by authors named "John R Kirby"

The soil-dwelling delta-proteobacterium is a model organism to study predation and competition. preys on a broad range of bacteria mediated by lytic enzymes, exopolysaccharides, Type-IV pilus-based motility, and specialized metabolites. Competition between and prey bacterial strains with various specialized metabolite profiles indicates a range of fitness, suggesting that specialized metabolites contribute to prey survival.

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The Triangle Model of Reading proposes that phonology, orthography, and semantics are crucial to understand word reading and reading disability (RD). Morphology has been added as a binding agent to this model. However, it is unclear how these variables relate to word reading in children with attention deficit/hyperactivity disorder (ADHD) or comorbid ADHD and RD (ADHD+RD).

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Introduction: Roux-en-Y gastric bypass (RYGB) significantly alters the gut microbiome and may be a mechanism for post-operative cardiovascular disease improvement. We have previously found an association between the class of peri-operative, intravenous antibiotic administered at the time of RYGB and the resolution rate of hypertension suggesting the gut microbiome as a mechanism. In this study, we performed a prospective study of RYGB to determine if a single intravenous antibiotic could alter the gastrointestinal microbial composition.

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writing is an important tactic for learning from text and the summaries provide information on students' comprehension and learning processes. We investigated the nature of the summaries produced by bilingual adolescents, and whether their summaries were related to their reading abilities in their first and second languages. In each language, we examined the performance of students identified as typically developing, poor decoders, or poor comprehenders.

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Cardiovascular disease represents the leading cause of death in the United States, and metabolic diseases such as obesity represent the primary impediment to improving cardiovascular health. Rodent (mouse and rat) models are widely used to model cardiometabolic disease, and as a result, there is increasing interest in the development of accurate and precise methodologies with sufficiently high resolution to dissect mechanisms controlling cardiometabolic physiology in these small organisms. Further, there is great utility in the development of centralized core facilities furnished with high-throughput equipment configurations and staffed with professional content experts to guide investigators and ensure the rigor and reproducibility of experimental endeavors.

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The gut microbiome plays an essential role in host energy homeostasis and influences the development of obesity and related conditions. Studies demonstrate that nicotinamide riboside (NR) supplementation for diet-induced obesity (DIO) reduces weight gain and increases energy expenditure in mice. NR is a vitamin B derivative and an NAD precursor with potential for treating human diseases arising from mitochondrial degeneration, including obesity and type 2 diabetes.

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This study examined (a) the identification of various reading groups across languages in Chinese (L1) adolescents learning English as a second language (ESL), in terms of their word-reading and reading comprehension skills, (b) overlap in reading group membership across languages, and (c) the performance of the various reading groups on reading-related language comprehension measures in English. The participants were 246 eighth-grade students from an English-immersion program in a middle school in China. Latent profile analysis identified three reading groups in each language: (a) a typically developing reader group with average or above-average word-reading and reading comprehension, (b) a group with poor decoding/word-reading skills and weak reading comprehension, and (c) a group with poor reading comprehension in the absence of poor decoding/word reading.

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Evidence supports various roles for microbial metabolites in the control of multiple aspects of host energy flux including feeding behaviors, digestive efficiency, and energy expenditure, but few studies have quantified the energy utilization of the biomass of the gut microbiota itself. Because gut microbiota exist in an anoxic environment, energy flux is expected to be anaerobic; unfortunately, commonly utilized O/CO respirometry-based approaches are unable to detect anaerobic energy flux. To quantify the contribution of the gut microbial biomass to whole-animal energy flux, we examined the effect of surgical reduction of gut biomass in C57BL/6J mice via cecectomy and assessed energy expenditure using methods sensitive to anaerobic flux, including bomb and direct calorimetry.

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Aim: Our previous studies have demonstrated the importance of dietary factors in the determination of hypertension in Dahl salt-sensitive (SS) rats. Since the gut microbiota has been implicated in chronic diseases like hypertension, we hypothesized that dietary alterations shift the microbiota to mediate the development of salt-sensitive hypertension and renal disease.

Methods: This study utilized SS rats from the Medical College of Wisconsin (SS/MCW) maintained on a purified, casein-based diet (0.

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Studying the typical development of reading is key to understanding the precise deficits that underlie reading disabilities. An important correlate of efficient reading is the speed of naming arrays of simple stimuli such as letters and pictures. In this cross-sectional study, we examined developmental changes in visual processing that occurs during letter and object naming from childhood to early adulthood in terms of behavioral task efficiency, associated articulation and eye movement parameters, and the coordination between them, as measured by eye-voice span in both the spatial and temporal domains.

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We examined the naming speed performance of 18 typically achieving and 16 dyslexic adults while simultaneously recording eye movements, articulations and fMRI data. Naming speed tasks, which require participants to name a list of letters or objects, have been proposed as a proxy for reading and are thought to recruit similar reading networks in the left hemisphere of the brain as more complex reading tasks. We employed letter and object naming speed tasks, with task manipulations to make the stimuli more or less phonologically and/or visually similar.

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is increasingly recognized as a colonizer of cystic fibrosis (CF) patients, but the role that plays in pathology remains unknown. This knowledge gap is largely due to the lack of model systems available to study the toxic potential of this bacterium. Recently, a phospholipase A (PLA) encoded by a majority of genomes, termed AxoU, was identified.

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The distinctive features of the Arabic language and orthography offer opportunities to investigate multiple word characteristics at the item level. The aim of this paper was to model differences in word reading at the item level among 3rd grade native Arabic-speaking children (n = 303) using cross-classified generalized random-effects (CCGRE) analysis. The participants read 80 vowelized words that varied in multiple elements that may contribute to their decodability: number of letters, number of syllables, number of morphemes, ligaturing (connectivity), semantics (concrete vs.

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infections can lead to diseases that range from localized skin abscess to life-threatening toxic shock syndrome. The SrrAB two-component system (TCS) is a global regulator of virulence and critical for survival under environmental conditions such as hypoxic, oxidative, and nitrosative stress found at sites of infection. Despite the critical role of SrrAB in pathogenicity, the mechanism by which the SrrAB TCS senses and responds to these environmental signals remains unknown.

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We combined fMRI with eye tracking and speech recording to examine the neural and cognitive mechanisms that underlie reading. To simplify the study of the complex processes involved during reading, we used naming speed (NS) tasks (also known as rapid automatized naming or RAN) as a focus for this study, in which average reading right-handed adults named sets of stimuli (letters or objects) as quickly and accurately as possible. Due to the possibility of spoken output during fMRI studies creating motion artifacts, we employed both an overt session and a covert session.

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Purpose We investigated the cognitive and linguistic processes that underlie reading in Arabic in relation to a well-defined theoretical framework of reading and the factors that underlie reading. Method The sample was 201 (101 boys, 100 girls) 3rd-grade Arabic-speaking children. Children were administered measures of Vocabulary, Phonological Awareness (PA), Naming Speed, Orthographic Processing, Morphological Awareness (MA), Memory, Nonverbal Ability, and 5 reading outcomes.

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Two-component signaling systems (TCS) regulate bacterial responses to environmental signals through the process of protein phosphorylation. Specifically, sensor histidine kinases (SK) recognize signals and propagate the response via phosphorylation of a cognate response regulator (RR) that functions to initiate transcription of specific genes. Signaling within a single TCS is remarkably specific and cross-talk between TCS is limited.

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Lysine acetylation is a common protein post-translational modification in bacteria and eukaryotes. Unlike phosphorylation, whose functional role in signaling has been established, it is unclear what regulatory mechanism acetylation plays and whether it is conserved across evolution. By performing a proteomic analysis of 48 phylogenetically distant bacteria, we discovered conserved acetylation sites on catalytically essential lysine residues that are invariant throughout evolution.

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Purpose Of Review: The influence of gut bacteria upon host physiology is increasingly recognized, but mechanistic links are lacking. Diseases of energetic imbalance such as obesity and diabetes represent major risk factors for cardiovascular diseases such as hypertension. Thus, here, we review current mechanistic contributions of the gut microbiota to host energetics.

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Unlabelled: The vector-borne disease leishmaniasis, caused by Leishmania species protozoa, is transmitted to humans by phlebotomine sand flies. Development of Leishmania to infective metacyclic promastigotes in the insect gut, a process termed metacyclogenesis, is an essential prerequisite for transmission. Based on the hypothesis that vector gut microbiota influence the development of virulent parasites, we sequenced midgut microbiomes in the sand fly Lutzomyia longipalpis with or without Leishmania infantum infection.

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Unlabelled: Soil bacteria engage each other in competitive and cooperative ways to determine their microenvironments. In this study, we report the identification of a large number of genes required for Myxococcus xanthus to engage Bacillus subtilis in a predator-prey relationship. We generated and tested over 6,000 individual transposon insertion mutants of M.

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Myxococcus xanthus is an environmental bacterium that displays a complex life cycle that includes motility, predation, multicellular fruiting body development, and sporulation. Given the elaborate fruiting body development of this bacterial species, M. xanthus has served as a model organism for the study of multicellular development of bacteria, and a remarkable number of genes have been identified that contribute to the regulation of this highly dynamic process.

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Myxococcus xanthus is an environmental bacterium with two forms of motility. One type, known as social motility, is dependent on extension and retraction of Type-IV pili (T4P) and production of extracellular polysaccharides (EPS). Several signaling systems have been linked to regulation of T4P-dependent motility.

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