GeNLP: a web tool for NLP-based exploration and prediction of microbial gene function.

SUMMARY: GeNLP is a web application that enables exploring microbial gene "semantics" and predictions of uncharacterized gene families based on their genomic context. It utilizes a pre-trained language model to uncover gene relationships and allows users to access and utilize the data as well as make their own predictions through an interactive interface. AVAILABILITY AND IMPLEMENTATION: The web application is accessible from all browsers at: http://gnlp.bursteinlab.org/. All source codes are freely available from GitHub under the MIT license here: https://github.com/burstein-lab/genomic-nlp-server.

Physical and biophysical markers of assessment in medical training: A scoping review of the literature.

PURPOSE: Assessment in medical education has changed over time to measure the evolving skills required of current medical practice. Physical and biophysical markers of assessment attempt to use technology to gain insight into medical trainees' knowledge, skills, and attitudes. The authors conducted a scoping review to map the literature on the use of physical and biophysical markers of assessment in medical training. MATERIALS AND METHODS: The authors searched seven databases on 1 August 2022, for publications that utilized physical or biophysical markers in the assessment of medical trainees (medical students, residents, fellows, and synonymous terms used in other countries). Physical or biophysical markers included: heart rate and heart rate variability, visual tracking and attention, pupillometry, hand motion analysis, skin conductivity, salivary cortisol, functional magnetic resonance imaging (fMRI), and functional near-infrared spectroscopy (fNIRS). The authors mapped the relevant literature using Bloom's taxonomy of knowledge, skills, and attitudes and extracted additional data including study design, study environment, and novice vs. expert differentiation from February to June 2023. RESULTS: Of 6,069 unique articles, 443 met inclusion criteria. The majority of studies assessed trainees using heart rate variability (n = 160, 36%) followed by visual attention (n = 143, 32%), hand motion analysis (n = 67, 15%), salivary cortisol (n = 67, 15%), fMRI (n = 29, 7%), skin conductivity (n = 26, 6%), fNIRs (n = 19, 4%), and pupillometry (n = 16, 4%). The majority of studies (n = 167, 38%) analyzed non-technical skills, followed by studies that analyzed technical skills (n = 155, 35%), knowledge (n = 114, 26%), and attitudinal skills (n = 61, 14%). 169 studies (38%) attempted to use physical or biophysical markers to differentiate between novice and expert. CONCLUSION: This review provides a comprehensive description of the current use of physical and biophysical markers in medical education training, including the current technology and skills assessed. Additionally, while physical and biophysical markers have the potential to augment current assessment in medical education, there remains significant gaps in research surrounding reliability, validity, cost, practicality, and educational impact of implementing these markers of assessment.

Toward Efficient, Sustainable, and Scalable Methods of Treatment Characterization: An Investigation of Coding Clinical Practice from Chart Notes.

PURPOSE: Chart notes provide a low-cost data source that could help characterize what occurs in treatment with sufficient precision to improve management of care. This study assessed the interrater reliability of treatment content coded from chart notes and evaluated its concordance with content coded from transcribed treatment sessions. METHOD: Fifty randomly selected and digitally recorded treatment events were transcribed and coded for practice content. Independent coders then applied the same code system to chart notes for these same treatment events. ANALYSIS: We measured reliability and concordance of practice occurrence and extensiveness at two levels of specificity: practices (full procedures) and steps (subcomponents of those procedures). RESULTS: For chart notes, practices had moderate interrater reliability (M k = 0.50, M ICC = 0.56) and steps had moderate (M ICC = 0.74) to substantial interrater reliability (M k = 0.78). On average, 2.54 practices and 5.64 steps were coded per chart note and 4.53 practices and 13.10 steps per transcript. Across sources, ratings for 64% of practices and 41% of steps correlated significantly, with those with significant correlations generally demonstrating moderate concordance (practice M r = 0.48; step M r = 0.47). Forty one percent of practices and 34% of steps from transcripts were also identified in the corresponding chart notes. CONCLUSION: Chart notes provide an accessible data source for evaluating treatment content, with different levels of specificity posing tradeoffs for validity and reliability, which in turn may have implications for chart note interfaces, training, and new metrics to support accurate, reliable, and efficient measurement of clinical practice.

Oil-Water Separation using Synthetic Trees.

Existing oil-water filtration techniques require gravity or a pump as the driving force for separation. Here, we demonstrate transpiration-powered oil-water filtration using a synthetic tree, which operates pumplessly and against gravity. From top to bottom, our synthetic tree was composed of: a nanoporous "leaf" to generate suction via evaporation, a vertical array of glass tubes serving as the tree's xylem conduits, and filters attached to the tube inlets to act as the oil-excluding roots. When placing the tree in an oil emulsion bath, filtrate samples were measured to be 97-98% pure water using gravimetry and refractometry. The spontaneous oil-water separation offered by synthetic trees could be useful for applications such as oil spill cleanup, wastewater purification, and oil extraction.

Cephalosporins for the treatment of uncomplicated pyelonephritis: A systematic review.

BACKGROUND: The 2011 Infectious Diseases Society of America and European Society of Clinical Microbiology and Infectious Diseases guidelines recommend ciprofloxacin or sulfamethoxazole-trimethoprim (SMX-TMP) as first-line agents to treat uncomplicated acute pyelonephritis (APN). OBJECTIVE: With increasing antimicrobial resistance rates and recent changes in practice patterns, the objective of this systematic review was to describe the effectiveness of cephalosporins for uncomplicated APN in more recently published literature. METHODS: Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines were used for reporting. We searched PubMed, Embase, and Scopus for publications between January 2010 and September 2022. Eligible articles detailed patients with uncomplicated APN, treated with first- to fourth-generation cephalosporins, and identified a clinical, microbiological, or health care utilization outcome. Studies with more than 30% of complicated APN patients, non-English-language studies, case reports, case series, pharmacodynamic or pharmacokinetic studies, and in vitro laboratory or animal studies were excluded. Screening, review, and extraction were performed independently by 2 researchers, plus a third for conflict resolution. Critical appraisal of studies was performed using Joanna Briggs Institute checklists. RESULTS: Eight studies met inclusion, including 5 cohort studies (62.5%), 2 randomized controlled trials (25%), and 1 nonrandomized experimental study (12.5%). Cephalosporins most used across the studies included cefazolin, cephalexin, cefuroxime, cefotaxime, cefdinir, cefditoren, and ceftriaxone. Outcomes assessed were diverse, including clinical or microbiological success and time to defervescence or symptom resolution. Cephalosporins displayed effectiveness for the treatment of acute uncomplicated APN regardless of study design or the presence of a comparison group. No trials reported inferiority of clinical treatment outcomes compared with a fluoroquinolone or SMX-TMP. CONCLUSION: Cephalosporins may be viable treatment options for the management of uncomplicated APN.

Bacterial and Fungal Gut Dysbiosis and Clostridium difficile in COVID-19: A Review.

BACKGROUND: Gastrointestinal symptoms are common in Coronavirus Disease 2019 (COVID-19), related to infection of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) of intestinal cells through the angiotensin converting enzyme 2 (ACE2) receptor in the brush border. Also, patients are treated with multiple antibiotics. Therefore, an increase in gut dysbiosis and in the prevalence of Clostridium difficile infection (CDI) is expected in patients with COVID-19. METHODS: A PubMed search was conducted using the terms "gut microbiota," "gut mycobiota," "dysbiosis" AND "COVID-19"; "Clostridium difficile," "Clostridioides difficile" AND "COVID-19"; "probiotics," "bacteriotherapy AND COVID-19." Only case series, observational and experimental studies were included. RESULTS: A total of 384 papers were retrieved and 21 fulfilled selection criteria. Later, a new paper was identified, thus 22 papers were reviewed. Main findings: (1) gut bacterial dysbiosis has been found in fecal samples of COVID-19 patients, with enrichment of opportunistic organisms and decrease of beneficial commensals such as Faecalibacterium prausnitizii. Dysbiosis is related to inflammatory markers and illness severity. (2) There is evidence for abnormal gut barrier and bacterial translocation with a negative impact in the lungs. (3) Fungal dysbiosis correlating with pulmonary mycobiota, has also been found. (4) There is controversy in the CDI rates among COVID-19 patients versus controls and pandemic versus prepandemic era. (5) There is no available evidence yet to support bacteriotherapy in COVID-19. (6) Fecal microbiota transplantation (FMT) has been proposed for COVID-19, although there is no evidence to support it. Also, FMT can be safely used during the pandemic for CDI if strict screening protocols for donors and fecal product are implemented. CONCLUSIONS: In COVID-19 there is bacterial and fungal dysbiosis that correlates with systemic and pulmonary inflammation, and illness severity. Further investigations are warranted to determine the efficacy of bacteriotherapy and FMT for modulating gut dysbiosis in COVID-19.

Prevalence of risk behaviors and correlates of SARS-CoV-2 positivity among in-school contacts of confirmed cases in a Georgia school district in the pre-vaccine era, December 2020-January 2021.

BACKGROUND: There is a continuing risk for COVID-19 transmission in school settings while transmission is ongoing in the community, particularly among unvaccinated populations. To ensure that schools continue to operate safely and to inform implementation of prevention strategies, it is imperative to gain better understanding of the risk behaviors of staff and students. This secondary analysis describes the prevalence of COVID-19 risk behaviors in an exposed population of students and school staff in the pre-vaccine era and identifies associations between these behaviors and testing positive for SARS-CoV-2. METHODS: From December 2020-January 2021, school staff and students exposed to confirmed COVID-19 cases in a Georgia school district were tested for SARS-CoV-2 and surveyed regarding risk behaviors in and out of school. Prevalence of risk behaviors was described by age group and school level, and associations with SARS-CoV-2 positivity were identified using chi squared tests. RESULTS: Overall, 717 students and 79 school staff participated in the investigation; SARS-CoV-2 positivity was 9.2%. In the 2 weeks prior to COVID-19 exposure, 24% of participants reported unmasked indoor time at school, 40% attended social gatherings with non-household members, and 71% visited out-of-school indoor locations, including 19% who ate indoors in restaurants. Frequencies of risk behaviors increased by age. Among students, 17% participated in school sports, of whom 86% participated without a mask. SARS-CoV-2 positivity was significantly associated with school sports and unmasked time in sports. Among K-5 students, positivity was associated with exposure to a teacher index case. CONCLUSIONS: This analysis highlights the high prevalence of risk behaviors in an unvaccinated population exposed to COVID-19 in school and identifies an association between student sports participation and SARS-CoV-2 positivity. These findings illustrate the importance of school-level prevention measures to reduce SARS-CoV-2 transmission, including limiting close-contact indoor sports and promoting consistent mask use in unvaccinated individuals. Future research could explore the role of community vaccination programs as a strategy to reduce COVID-19 transmission and introductions into school settings.

A Bayesian Framework for Inferring the Influence of Sequence Context on Point Mutations.

The probability of point mutations is expected to be highly influenced by the flanking nucleotides that surround them, known as the sequence context. This phenomenon may be mainly attributed to the enzyme that modifies or mutates the genetic material, because most enzymes tend to have specific sequence contexts that dictate their activity. Here, we develop a statistical model that allows for the detection and evaluation of the effects of different sequence contexts on mutation rates from deep population sequencing data. This task is computationally challenging, as the complexity of the model increases exponentially as the context size increases. We established our novel Bayesian method based on sparse model selection methods, with the leading assumption that the number of actual sequence contexts that directly influence mutation rates is minuscule compared with the number of possible sequence contexts. We show that our method is highly accurate on simulated data using pentanucleotide contexts, even when accounting for noisy data. We next analyze empirical population sequencing data from polioviruses and HIV-1 and detect a significant enrichment in sequence contexts associated with deamination by the cellular deaminases ADAR 1/2 and APOBEC3G, respectively. In the current era, where next-generation sequencing data are highly abundant, our approach can be used on any population sequencing data to reveal context-dependent base alterations and may assist in the discovery of novel mutable sites or editing sites.

How much therapy is enough? The dose-response effect and its moderators in a psychology training clinic.

OBJECTIVE: The current study aims to sharpen the understanding of the psychotherapy dose-response effect and its moderators in a psychology training clinic. METHOD: Data were extracted from 58 client records. Weekly Patient Health Questionnaire-9 and Generalized Anxiety Disorder-7, as well as Outcomes Questionnaire-45.2, administered every fifth session, assessed whether clients achieved reliable change (RC) and clinically significant and reliable change (CSR) during treatment. Survival analyses were conducted to determine the sessions required for 50% of the sample to achieve these outcomes. Multilevel Cox frailty regressions were used to investigate client-and-therapy-based moderators. RESULTS: The median time for 50% of the sample to achieve RC was 8-10 sessions and 11 sessions to achieve initial CSR. Past treatment history was a significant moderator of time to achieve RC. CONCLUSIONS: From a population perspective, psychotherapy is most beneficial to patients early in treatment. Sharper understanding of the number of sessions required to achieve meaningful change can inform practice in training settings.

Methanogenesis marker protein 10 (Mmp10) from Methanosarcina acetivorans is a radical S-adenosylmethionine methylase that unexpectedly requires cobalamin.

Methyl coenzyme M reductase (MCR) catalyzes the last step in the biological production of methane by methanogenic archaea, as well as the first step in the anaerobic oxidation of methane to methanol by methanotrophic archaea. MCR contains a number of unique post-translational modifications in its α subunit, including thioglycine, 1-N-methylhistidine, S-methylcysteine, 5-C-(S)-methylarginine, and 2-C-(S)-methylglutamine. Recently, genes responsible for the thioglycine and methylarginine modifications have been identified in bioinformatics studies and in vivo complementation of select mutants; however, none of these reactions has been verified in vitro Herein, we purified and biochemically characterized the radical S-adenosylmethionine (SAM) protein MaMmp10, the product of the methanogenesis marker protein 10 gene in the methane-producing archaea Methanosarcina acetivorans Using an array of approaches, including kinetic assays, LC-MS-based quantification, and MALDI TOF-TOF MS analyses, we found that MaMmp10 catalyzes the methylation of the equivalent of Arg285 in a peptide substrate surrogate, but only in the presence of cobalamin. We noted that the methyl group derives from SAM, with cobalamin acting as an intermediate carrier, and that MaMmp10 contains a C-terminal cobalamin-binding domain. Given that Mmp10 has not been annotated as a cobalamin-binding protein, these findings suggest that cobalamin-dependent radical SAM proteins are more prevalent than previously thought.

Promiscuity of methionine salvage pathway enzymes in Methanocaldococcus jannaschii.

The methionine salvage pathway (MSP) is critical for regeneration of S-adenosyl-l-methionine (SAM), a widely used cofactor involved in many essential metabolic reactions. The MSP has been completely elucidated in aerobic organisms, and found to rely on molecular oxygen. Since anaerobic organisms do not use O2, an alternative pathway(s) must be operating. We sought to evaluate whether the functions of two annotated MSP enzymes from Methanocaldococcus jannaschii, a methylthioinosine phosphorylase (MTIP) and a methylthioribose 1-phosphate isomerase (MTRI), are consistent with functioning in a modified anaerobic MSP (AnMSP). We show here that recombinant MTIP is active with six different purine nucleosides, consistent with its function as a general purine nucleoside phosphorylase for both AnMSP and purine salvage. Recombinant MTRI is active with both 5-methylthioribose 1-phosphate and 5-deoxyribose 1-phosphate as substrates, which are generated from phosphororolysis of 5'-methylthioinosine and 5'-deoxyinosine by MTIP, respectively. Together, these data suggest that MTIP and MTRI may function in a novel pathway for recycling the 5'-deoxyadenosine moiety of SAM in M. jannaschii. These enzymes may also enable biosynthesis of 6-deoxy-5-ketofructose 1-phosphate (DKFP), an essential intermediate in aromatic amino acid biosynthesis. Finally, we utilized a homocysteine auxotrophic strain of Methanosarcina acetivorans Δma1821-22Δoahs (HcyAux) to identify potential AnMSP intermediates in vivo. Growth recovery experiments of the M. acetivorans HcyAux were performed with known and proposed intermediates for the AnMSP. Only one metabolite, 2-keto-(4-methylthio)butyric acid, rescued growth of M. acetivorans HcyAux in the absence of homocysteine. This observation may indicate that AnMSP pathways substantially differ among methanogens from phylogenetically divergent genera.

TOPGEAR: A Randomized, Phase III Trial of Perioperative ECF Chemotherapy with or Without Preoperative Chemoradiation for Resectable Gastric Cancer: Interim Results from an International, Intergroup Trial of the AGITG, TROG, EORTC and CCTG.

BACKGROUND: Postoperative chemoradiation and perioperative chemotherapy using epirubicin/cisplatin/5-fluorouracil (ECF) represent two standards of care for resectable gastric cancer. In the TOPGEAR (Trial Of Preoperative therapy for Gastric and Esophagogastric junction AdenocaRcinoma) trial, we hypothesized that adding preoperative chemoradiation to perioperative ECF will improve survival; however, the safety and feasibility of preoperative chemoradiation have yet to be determined. METHODS: TOPGEAR is an international phase III trial in which patients with adenocarcinoma of the stomach were randomized to perioperative ECF alone or with preoperative chemoradiation. The ECF-alone group received three preoperative cycles of ECF, while the chemoradiation group received two cycles of preoperative ECF followed by chemoradiation. Both groups received three postoperative cycles of ECF. A planned interim analysis of the first 120 patients was conducted, and was reviewed by the Independent Data Safety Monitoring Committee to assess treatment compliance, toxicity/safety, and response rates. RESULTS: The proportion of patients who received all cycles of preoperative chemotherapy was 93% (ECF group) and 98% (chemoradiation group), while 65 and 53%, respectively, received all cycles of postoperative chemotherapy. Overall, 92% of patients allocated to preoperative chemoradiation received this treatment. The proportion of patients proceeding to surgery was 90% (ECF group) and 85% (chemoradiation group). Grade 3 or higher surgical complications occurred in 22% of patients in both groups. Furthermore, grade 3 or higher gastrointestinal toxicity occurred in 32% (ECF group) and 30% (chemoradiation group) of patients, while hematologic toxicity occurred in 50 and 52% of patients. CONCLUSIONS: These results demonstrate that preoperative chemoradiation can be safely delivered to the vast majority of patients without a significant increase in treatment toxicity or surgical morbidity.

Contributions of polygenic risk for obesity to PTSD-related metabolic syndrome and cortical thickness.

BACKGROUND: Research suggests that posttraumatic stress disorder (PTSD) is associated with metabolic syndrome (MetS) and that PTSD-associated MetS is related to decreased cortical thickness. However, the role of genetic factors in these associations is unclear. This study evaluated contributions of polygenic obesity risk and PTSD to MetS and of MetS and polygenic obesity risk to cortical thickness. METHODS: 196 white, non-Hispanic veterans of the wars in Iraq and Afghanistan underwent clinical diagnostic interviews, physiological assessments, and genome-wide genotyping; 168 also completed magnetic resonance imaging scans. Polygenic risk scores (PRSs) for obesity were calculated from results of a prior genome-wide association study (Speliotes et al., 2010) and PTSD and MetS severity factor scores were obtained. RESULTS: Obesity PRS (ß=0.15, p=0.009) and PTSD (ß=0.17, p=0.005) predicted MetS and interacted such that the association between PTSD and MetS was stronger in individuals with greater polygenic obesity risk (ß=0.13, p=0.02). Whole-brain vertex-wise analyses suggested that obesity PRS interacted with MetS to predict decreased cortical thickness in left rostral middle frontal gyrus (ß=-0.40, p<0.001). CONCLUSIONS: Results suggest that PTSD, genetic variability, and MetS are related in a transactional fashion wherein obesity genetic risk increases stress-related metabolic pathology, and compounds the ill health effects of MetS on the brain. Genetic proclivity towards MetS should be considered in PTSD patients when prescribing psychotropic medications with adverse metabolic profiles. Results are consistent with a growing literature suggestive of PTSD-related accelerated aging.

Posttraumatic stress disorder symptom severity is associated with reduced default mode network connectivity in individuals with elevated genetic risk for psychopathology.

BACKGROUND: Accumulating evidence suggests that posttraumatic stress disorder (PTSD) is associated with disrupted default mode network (DMN) connectivity, but findings across studies have not been uniform. Individual differences in relevant genes may account for some of the reported variability in the relationship between DMN connectivity and PTSD. In this study, we investigated this possibility using genome-wide association study (GWAS) derived polygenic risk scores (PRSs) for relevant psychiatric traits. We hypothesized that the association between PTSD and DMN connectivity would be moderated by genetic risk for one or more psychiatric traits such that individuals with elevated polygenic risk for psychopathology and severe PTSD would exhibit disrupted DMN connectivity. METHODS: Participants were 156 white, non-Hispanic veterans of the wars in Iraq and Afghanistan who were genotyped and underwent resting state functional magnetic resonance imaging and clinical assessment. PRSs for neuroticism, anxiety, major depressive disorder, and cross-disorder risk (based on five psychiatric disorders) were calculated using summary statistics from published large-scale consortia-based GWASs. RESULTS: Cross-disorder polygenic risk influenced the relationship between DMN connectivity and PTSD symptom severity such that individuals at greater genetic risk showed a significant negative association between PTSD symptom severity and connectivity between the posterior cingulate cortex and right middle temporal gyrus. Polygenic risk for neuroticism, anxiety, and major depressive disorder did not influence DMN connectivity directly or through an interaction with PTSD. CONCLUSIONS: Findings illustrate the potential power of genome-wide PRSs to advance understanding of the relationship between PTSD and DMN connectivity, a putative neural endophenotype of the disorder.

Neuroimaging of deployment-associated traumatic brain injury (TBI) with a focus on mild TBI (mTBI) since 2009.

OBJECTIVES: A substantial body of recent research has aimed to better understand the clinical sequelae of military trauma through the application of advanced brain imaging procedures in Veteran populations. The primary objective of this review was to highlight a portion of these recent studies to demonstrate how imaging tools can be used to understand military-associated brain injury. METHODS: We focus here on the phenomenon of mild traumatic brain injury (mTBI) given its high prevalence in the Veteran population and current recognition of the need to better understand the clinical implications of this trauma. This is intended to provide readers with an initial exposure to the field of neuroimaging of mTBI with a brief introduction to the concept of traumatic brain injury, followed by a summary of the major imaging techniques that have been applied to the study of mTBI. RESULTS: Taken together, the collection of studies reviewed demonstrates a clear role for neuroimaging towards understanding the various neural consequences of mTBI as well as the clinical complications of such brain changes. CONCLUSIONS: This information must be considered in the larger context of research into mTBI, including the potentially unique nature of blast exposure and the long-term consequences of mTBI.

SLC44A2 single nucleotide polymorphisms, isoforms, and expression: Association with severity of Meniere's disease?

SLC44A2 was discovered as the target of an antibody that causes hearing loss. Knockout mice develop age related hearing loss, loss of sensory cells and spiral ganglion neurons. SLC44A2 has polymorphic sites implicated in human disease. Transfusion related acute lung injury (TRALI) is linked to rs2288904 and genome wide association studies link rs2288904 and rs9797861 to venous thromboembolism (VTE), coronary artery disease and stroke. Here we report linkage disequilibrium of rs2288904 with rs3087969 and the association of these SLC44A2 SNPs with Meniere's disease severity. Tissue-specific isoform expression differences suggest that the N-terminal domain is linked to different functions in different cell types. Heterozygosity at rs2288904 CGA/CAA and rs3087969 GAT/GAC showed a trend for association with intractable Meniere's disease compared to less severe disease and to controls. The association of SLC44A2 SNPs with VTE suggests that thrombi affecting cochlear vessels could be a factor in Meniere's disease.

Purine salvage in Methanocaldococcus jannaschii: Elucidating the role of a conserved cysteine in adenine deaminase.

Adenine deaminases (Ade) and hypoxanthine/guanine phosphoribosyltransferases (Hpt) are widely distributed enzymes involved in purine salvage. Characterization of the previously uncharacterized Ade (MJ1459 gene product) and Hpt (MJ1655 gene product) are discussed here and provide insight into purine salvage in Methanocaldococcus jannaschii. Ade was demonstrated to use either Fe(II) and/or Mn(II) as the catalytic metal. Hpt demonstrated no detectable activity with adenine, but was equally specific for hypoxanthine and guanine with a kcat /KM of 3.2 × 10(7) and 3.0 × 10(7) s(- 1) M(- 1) , respectively. These results demonstrate that hypoxanthine and IMP are the central metabolites in purine salvage in M. jannaschii for AMP and GMP production. A conserved cysteine (C127, M. jannaschii numbering) was examined due to its high conservation in bacterial and archaeal homologues. To assess the role of this highly conserved cysteine in M. jannaschii Ade, site-directed mutagenesis was performed. It was determined that mutation to serine (C127S) completely abolished Ade activity and mutation to alanine (C127A) exhibited 10-fold decrease in kcat over the wild type Ade. To further investigate the role of C127, detailed molecular docking and dynamics studies were performed and revealed adenine was unable to properly orient in the active site in the C127A and C127S Ade model structures due to distinct differences in active site conformation and rotation of D261. Together this work illuminates purine salvage in M. jannaschii and the critical role of a cysteine residue in maintaining active site conformation of Ade. Proteins 2016; 84:828-840. © 2016 Wiley Periodicals, Inc.

White matter abnormalities are associated with chronic postconcussion symptoms in blast-related mild traumatic brain injury.

Blast-related mild traumatic brain injury (mTBI) is a common injury among Iraq and Afghanistan military veterans due to the frequent use of improvised explosive devices. A significant minority of individuals with mTBI report chronic postconcussion symptoms (PCS), which include physical, emotional, and cognitive complaints. However, chronic PCS are nonspecific and are also associated with mental health disorders such as posttraumatic stress disorder (PTSD). Identifying the mechanisms that contribute to chronic PCS is particularly challenging in blast-related mTBI, where the incidence of comorbid PTSD is high. In this study, we examined whether blast-related mTBI is associated with diffuse white matter changes, and whether these neural changes are associated with chronic PCS. Ninety Operation Enduring Freedom/Operation Iraqi Freedom (OEF/OIF) veterans were assigned to one of three groups including a blast-exposed no--TBI group, a blast-related mTBI without loss of consciousness (LOC) group (mTBI--LOC), and a blast-related mTBI with LOC group (mTBI + LOC). PCS were measured with the Rivermead Postconcussion Questionnaire. Results showed that participants in the mTBI + LOC group had more spatially heterogeneous white matter abnormalities than those in the no--TBI group. These white matter abnormalities were significantly associated with physical PCS severity even after accounting for PTSD symptoms, but not with cognitive or emotional PCS severity. A mediation analysis revealed that mTBI + LOC significantly influenced physical PCS severity through its effect on white matter integrity. These results suggest that white matter abnormalities are associated with chronic PCS independent of PTSD symptom severity and that these abnormalities are an important mechanism explaining the relationship between mTBI and chronic physical PCS.

S-Inosyl-L-Homocysteine Hydrolase, a Novel Enzyme Involved in S-Adenosyl-L-Methionine Recycling.

UNLABELLED: S-Adenosyl-L-homocysteine, the product of S-adenosyl-L-methionine (SAM) methyltransferases, is known to be a strong feedback inhibitor of these enzymes. A hydrolase specific for S-adenosyl-L-homocysteine produces L-homocysteine, which is remethylated to methionine and can be used to regenerate SAM. Here, we show that the annotated S-adenosyl-L-homocysteine hydrolase in Methanocaldococcus jannaschii is specific for the hydrolysis and synthesis of S-inosyl-L-homocysteine, not S-adenosyl-L-homocysteine. This is the first report of an enzyme specific for S-inosyl-L-homocysteine. As with S-adenosyl-L-homocysteine hydrolase, which shares greater than 45% sequence identity with the M. jannaschii homologue, the M. jannaschii enzyme was found to copurify with bound NAD(+) and has Km values of 0.64 ± 0.4 mM, 0.0054 ± 0.006 mM, and 0.22 ± 0.11 mM for inosine, L-homocysteine, and S-inosyl-L-homocysteine, respectively. No enzymatic activity was detected with S-adenosyl-L-homocysteine as the substrate in either the synthesis or hydrolysis direction. These results prompted us to redesignate the M. jannaschii enzyme an S-inosyl-L-homocysteine hydrolase (SIHH). Identification of SIHH demonstrates a modified pathway in this methanogen for the regeneration of SAM from S-adenosyl-L-homocysteine that uses the deamination of S-adenosyl-L-homocysteine to form S-inosyl-L-homocysteine. IMPORTANCE: In strictly anaerobic methanogenic archaea, such as Methanocaldococcus jannaschii, canonical metabolic pathways are often not present, and instead, unique pathways that are deeply rooted on the phylogenetic tree are utilized by the organisms. Here, we discuss the recycling pathway for S-adenosyl-L-homocysteine, produced from S-adenosyl-L-methionine (SAM)-dependent methylation reactions, which uses a hydrolase specific for S-inosyl-L-homocysteine, an uncommon metabolite. Identification of the pathways and the enzymes involved in the unique pathways in the methanogens will provide insight into the biochemical reactions that were occurring when life originated.