Vulnerability to semantic and phonological interference in normal aging and amnestic mild cognitive impairment (aMCI).

OBJECTIVE: To determine whether the increased vulnerability to semantic interference previously observed in amnestic mild cognitive impairment (aMCI) is specifically associated with semantic material or if it also affects other types of material, suggesting generalized executive and inhibitory impairment. METHOD: Seventy-two participants divided into two groups (33 aMCI, 39 normal control [NC]) matched for age and education were included. They completed a comprehensive neuropsychological examination, the French version of the Loewenstein Acevedo Scale for Semantic Interference and Learning (LASSI-L; semantic interference test), and a homologous experimental phonological test, the phonological interference and learning test. Independent sample t tests, mixed analysis of variance (ANOVA), and analysis of covariance (ANCOVA) on memory and interference scores were conducted to compare memory and interference in both conditions for both groups. RESULTS: For memory scores, results revealed significant main effects of group (NC > aMCI) and condition (semantic > phonological) and significant interactions (poorer performance in the semantic condition for aMCI). aMCI committed more phonological false recognition errors, were disproportionately more vulnerable to retroactive semantic interference, and showed a higher percentage of intrusion errors associated with proactive semantic interference than NC. CONCLUSIONS: To our knowledge, this is the first study to compare vulnerability to interference in aMCI and normal aging with two similarly designed semantic and phonological word list learning tasks. Taken together, our results suggest that aMCI present with broad difficulties in source memory and inhibition, but that impaired deep semantic processing results in additional semantic intrusion errors during proactive interference and impacts their ability to show good recall after an interference list (greater semantic retroactive interference). Results are discussed according to the level-of-processing and activation/monitoring theories. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

Attitudes and barriers to breastfeeding among women at high-risk for not breastfeeding: a prospective observational study.

BACKGROUND: Rates of breastfeeding are lower among minority and underserved populations in the United States. Our study objective was to assess pregnant persons attitudes and barriers to breastfeeding among a cohort at high risk for not breastfeeding. METHODS: We disseminated the Iowa Infant Feeding Attitude Scale (IIFAS) to 100 pregnant persons at least 18 years of age attending a prenatal visit in a low-resource, academic practice in south-central Louisiana (Woman's Hospital). The IIFAS, as well as questions collecting information on breastfeeding experience and sociodemographic characteristics, were administered via interview. Medical records were reviewed to investigate associations between attitudes about breastfeeding in pregnancy and patient's feeding choices during the delivery hospital stay. Fisher exact tests and Wilcoxon rank-sum tests were used to assess associations between categorical and continuous variables respectively. RESULTS: Of the 98 participants who completed the study, 8% were Hispanic, 63% were Black, 95% were Medicaid eligible, and 50% were unemployed. 59% (n = 58) went on to breastfeed/combination breast-formula feed (called "Any-Breastfeeding Group") during the delivery stay. Total IIFAS score during pregnancy was significantly higher among those who went on to breastfeed during delivery hospital stay (Any-Breastfeeding Group vs. Formula-Feeding-Only Group: 58.9 ± 5.5 vs. 53.7 ± 6.2 respectively, p < 0.001). In the group that went on to only formula feed (Formula-Feeding-Only Group), only 4% agreed breastfeeding was more convenient when surveyed during pregnancy, compared to 45% of the Any-Breastfeeding Group. 60% of Formula-Feeding-Only Group agreed formula is as healthy as breast milk. CONCLUSION: The three major themes that coincided with favorability toward breastfeeding in the study, and can be addressed during prenatal counseling, are: mother-infant bonding, convenience, and health benefits. By identifying attitudes and barriers to breastfeeding for patients during pregnancy who went on to not breastfeed, directed educational opportunities can be developed to address these specific attitudes to ultimately increase breastfeeding initiation and continuation.

How Safe are Outpatient Electronic Health Records? An Evaluation of Medication-Related Decision Support using the Ambulatory Electronic Health Record Evaluation Tool.

BACKGROUND: The purpose of the Ambulatory Electronic Health Record (EHR) Evaluation Tool is to provide outpatient clinics with an assessment that they can use to measure the ability of the EHR system to detect and prevent common prescriber errors. The tool consists of a medication safety test and a medication reconciliation module. OBJECTIVES: The goal of this study was to perform a broad evaluation of outpatient medication-related decision support using the Ambulatory EHR Evaluation Tool. METHODS: We performed a cross-sectional study with 10 outpatient clinics using the Ambulatory EHR Evaluation Tool. For the medication safety test, clinics were provided test patients and associated medication test orders to enter in their EHR, where they recorded any advice or information they received. Once finished, clinics received an overall percentage score of unsafe orders detected and individual order category scores. For the medication reconciliation module, clinics were asked to electronically reconcile two medication lists, where modifications were made by adding and removing medications and changing the dosage of select medications. RESULTS: For the medication safety test, the mean overall score was 57%, with the highest score being 70%, and the lowest score being 40%. Clinics performed well in the drug allergy (100%), drug dose daily (85%), and inappropriate medication combinations (74%) order categories. Order categories with the lowest performance were drug laboratory (10%) and drug monitoring (3%). Most clinics (90%) scored a 0% in at least one order category. For the medication reconciliation module, only one clinic (10%) could reconcile medication lists electronically; however, there was no clinical decision support available that checked for drug interactions. CONCLUSION: We evaluated a sample of ambulatory practices around their medication-related decision support and found that advanced capabilities within these systems have yet to be widely implemented. The tool was practical to use and identified substantial opportunities for improvement in outpatient medication safety.

Mutations in AcrR and RNA Polymerase Confer High-Level Resistance to Psoralen-UVA Irradiation.

DNA interstrand cross-links, such as those formed by psoralen-UVA irradiation, are highly toxic lesions in both humans and bacteria, with a single lesion being lethal in Escherichia coli. Despite the lack of effective repair, human cancers and bacteria can develop resistance to cross-linking treatments, although the mechanisms of resistance remain poorly defined. Here, we subjected E. coli to repeated psoralen-UVA exposure to isolate three independently derived strains that were >10,000-fold more resistant to this treatment than the parental strain. Analysis of these strains identified gain-of-function mutations in the transcriptional regulator AcrR and the alpha subunit of RNA polymerase that together could account for the resistance of these strains. Resistance conferred by the AcrR mutation is mediated at least in part through the regulation of the AcrAB-TolC efflux pump. Resistance via mutations in the alpha subunit of RNA polymerase occurs through a still-uncharacterized mechanism that has an additive effect with mutations in AcrR. Both acrR and rpoA mutations reduced cross-link formation in vivo. We discuss potential mechanisms in relation to the ability to repair and survive interstrand DNA cross-links. IMPORTANCE Psoralen DNA interstrand cross-links are highly toxic lesions with antimicrobial and anticancer properties. Despite the lack of effective mechanisms for repair, cells can become resistant to cross-linking agents through mechanisms that remain poorly defined. We derived resistant mutants and identified that two gain-of-function mutations in AcrR and the alpha subunit of RNA polymerase confer high levels of resistance to E. coli treated with psoralen-UVA. Resistance conferred by AcrR mutations occurs through regulation of the AcrAB-TolC efflux pump, has an additive effect with RNA polymerase mutations, acts by reducing the formation of cross-links in vivo, and reveals a novel mechanism by which these environmentally and clinically important agents are processed by the cell.

The Development and Piloting of the Ambulatory Electronic Health Record Evaluation Tool: Lessons Learned.

BACKGROUND: Substantial research has been performed about the impact of computerized physician order entry on medication safety in the inpatient setting; however, relatively little has been done in ambulatory care, where most medications are prescribed. OBJECTIVE: To outline the development and piloting process of the Ambulatory Electronic Health Record (EHR) Evaluation Tool and to report the quantitative and qualitative results from the pilot. METHODS: The Ambulatory EHR Evaluation Tool closely mirrors the inpatient version of the tool, which is administered by The Leapfrog Group. The tool was piloted with seven clinics in the United States, each using a different EHR. The tool consists of a medication safety test and a medication reconciliation module. For the medication test, clinics entered test patients and associated test orders into their EHR and recorded any decision support they received. An overall percentage score of unsafe orders detected, and order category scores were provided to clinics. For the medication reconciliation module, clinics demonstrated how their EHR electronically detected discrepancies between two medication lists. RESULTS: For the medication safety test, the clinics correctly alerted on 54.6% of unsafe medication orders. Clinics scored highest in the drug allergy (100%) and drug-drug interaction (89.3%) categories. Lower scoring categories included drug age (39.3%) and therapeutic duplication (39.3%). None of the clinics alerted for the drug laboratory or drug monitoring orders. In the medication reconciliation module, three (42.8%) clinics had an EHR-based medication reconciliation function; however, only one of those clinics could demonstrate it during the pilot. CONCLUSION: Clinics struggled in areas of advanced decision support such as drug age, drug laboratory, and drub monitoring. Most clinics did not have an EHR-based medication reconciliation function and this process was dependent on accessing patients' medication lists. Wider use of this tool could improve outpatient medication safety and can inform vendors about areas of improvement.

Nitrogen Source Governs Community Carbon Metabolism in a Model Hypersaline Benthic Phototrophic Biofilm.

Increasing anthropogenic inputs of fixed nitrogen are leading to greater eutrophication of aquatic environments, but it is unclear how this impacts the flux and fate of carbon in lacustrine and riverine systems. Here, we present evidence that the form of nitrogen governs the partitioning of carbon among members in a genome-sequenced, model phototrophic biofilm of 20 members. Consumption of NO3 - as the sole nitrogen source unexpectedly resulted in more rapid transfer of carbon to heterotrophs than when NH4 + was also provided, suggesting alterations in the form of carbon exchanged. The form of nitrogen dramatically impacted net community nitrogen, but not carbon, uptake rates. Furthermore, this alteration in nitrogen form caused very large but focused alterations to community structure, strongly impacting the abundance of only two species within the biofilm and modestly impacting a third member species. Our data suggest that nitrogen metabolism may coordinate coupled carbon-nitrogen biogeochemical cycling in benthic biofilms and, potentially, in phototroph-heterotroph consortia more broadly. It further indicates that the form of nitrogen inputs may significantly impact the contribution of these communities to carbon partitioning across the terrestrial-aquatic interface.IMPORTANCE Anthropogenic inputs of nitrogen into aquatic ecosystems, and especially those of agricultural origin, involve a mix of chemical species. Although it is well-known in general that nitrogen eutrophication markedly influences the metabolism of aquatic phototrophic communities, relatively little is known regarding whether the specific chemical form of nitrogen inputs matter. Our data suggest that the nitrogen form alters the rate of nitrogen uptake significantly, whereas corresponding alterations in carbon uptake were minor. However, differences imposed by uptake of divergent nitrogen forms may result in alterations among phototroph-heterotroph interactions that rewire community metabolism. Furthermore, our data hint that availability of other nutrients (i.e., iron) might mediate the linkage between carbon and nitrogen cycling in these communities. Taken together, our data suggest that different nitrogen forms should be examined for divergent impacts on phototrophic communities in fluvial systems and that these anthropogenic nitrogen inputs may significantly differ in their ultimate biogeochemical impacts.

Impact of Pharmacist Involvement on Telehealth Transitional Care Management (TCM) for High Medication Risk Patients.

This pilot study sought to evaluate the impact of pharmacist involvement in the preexisting telehealth transitional care management (TCM) program at Atrium Health on the quality and safety of the medication discharge process for high medication risk patients. Eligible participants were those 18 years of age or older with moderate-to-high risk for hospital readmission who were contacted by a TCM Nurse, identified as high medication risk patients, and referred to the TCM Pharmacist from September 2018 through February 2019. The TCM Pharmacist contacted patients by phone, completed a comprehensive medication review, identified medication list discrepancies (MLDs) and medication-related problems (MRPs), and made interventions or recommendations to primary care providers. Primary endpoints included the number and types of MLDs identified, number and types of MRPs identified, and the rate of unplanned 30-day hospital readmissions. Seventy-six patients were enrolled, and 78 MLDs and 108 MRPs were identified. Of the identified MRPs, 74.1% were resolved. A relative risk reduction of 36.8% was achieved for 30-day hospital readmissions for those with high medication risk contacted by the TCM Pharmacist compared to those only contacted by the TCM Nurse. Overall, TCM Pharmacists identified and resolved 80 medication-related problems, improved access to medication therapy, provided comprehensive medication counseling, and bridged gaps in care following hospital discharge.

Limited Capacity or Involvement of Excision Repair, Double-Strand Breaks, or Translesion Synthesis for Psoralen Cross-Link Repair in Escherichia coli.

DNA interstrand cross-links are complex lesions that covalently bind complementary strands of DNA and whose mechanism of repair remains poorly understood. In Escherichia coli, several gene products have been proposed to be involved in cross-link repair based on the hypersensitivity of mutants to cross-linking agents. However, cross-linking agents induce several forms of DNA damage, making it challenging to attribute mutant hypersensitivity specifically to interstrand cross-links. To address this, we compared the survival of UVA-irradiated repair mutants in the presence of 8-methoxypsoralen-which forms interstrand cross-links and monoadducts-to that of angelicin-a congener forming only monoadducts. We show that incision by nucleotide excision repair is not required for resistance to interstrand cross-links. In addition, neither RecN nor DNA polymerases II, IV, or V is required for interstrand cross-link survival, arguing against models that involve critical roles for double-strand break repair or translesion synthesis in the repair process. Finally, estimates based on Southern analysis of DNA fragments in alkali agarose gels indicate that lethality occurs in wild-type cells at doses producing as few as one to two interstrand cross-links per genome. These observations suggest that E. coli may lack an efficient repair mechanism for this form of damage.

Bridging the Expertise Gap: Developing and Utilizing a Radiological Advisory Committee for New York City.

From the Field is a semi-regular column that explores what it means to be a local health professional on the front lines of an emergency. Typically, National Association of County and City Health Officials (NACCHO) members share their stories of preparing for and responding to disasters, epidemics, and other major health issues. This month's column features a submission from the New York City health department that describes their experience in setting up a radiological advisory committee. Through exploring the analysis of the challenges faced and the solutions developed, readers can learn how these public health champions keep their communities safe even in extreme situations. Readers may submit topics of interest to the column's editor, Meghan McGinty, PhD, MPH, MBA, at mmcginty@naccho.org . A significant radiological emergency response in New York City would require scientific expertise beyond the routine capability of the New York City Department of Health and Mental Hygiene (DOHMH) and its partner agencies. Health physicists (radiological safety specialists) are chronically in short supply in the United States, which translates into a limited supply available to local health departments facing a radiological crisis. These professionals support medicine, industry, and the military in routine, nonemergency situations. In order to prearrange the availability of this expertise, a radiological advisory committee (RAC) was formed. The committee engages leading experts in the fields of radiation medicine and environmental radiation science in anticipation of the technical questions that arise from the clinical aspects of internalized radioactivity and the mitigation of the urban environment following a terrorist attack using radioactive materials. The creation of the RAC and its application in a nonemergency public policy forum is described, as are the problems foreseen in operationalizing the RAC during an emergency. Some conclusions are drawn about the effort and cost of maintaining the RAC and the benefits obtained by maintaining it. This information may be useful for other jurisdictions seeking to form a similar expert committee.

Corrigendum: Saliniramus fredricksonii gen. nov., sp. nov., a heterotrophic halophile isolated from Hot Lake, Washington, a member of a novel lineage (Salinarimonadaceae fam. nov.) within the order Rhizobiales, and reclassification of the genus Salinarimonas Liu et al. 2010 into Salinarimonadaceae.

There was an error in the proposed genus name in the published article, in that the genus 'Salinivirga' was effectively published while this article was in review. Therefore, the genus 'Salinivirga' should be replaced with 'Saliniramus'. For the convenience of future readers, we have included the complete corrected article below, in which all occurrences of the incorrect genus name have been amended: A halophilic bacterial strain, HL-109T, was isolated from the unicyanobacterial consortium UCC-O, which was obtained from the photosynthetic mat of Hot Lake (Washington, USA). A polyphasic approach using phenotypic, genotypic and chemotaxonomic data was used to classify the strain within the order Rhizobiales. The organism stained Gram-negative and was a moderate thermophile with a growth optimum of 45 °C. It was obligately aerobic, heterotrophic and halophilic, growing in both NaCl and MgSO4 brines. The novel isolate had a polymorphic cellular morphology of short rods with occasional branching, and cells were monotrichous. The major fatty acids detected were C18 : 1, C18 : 0, C16 : 0 and C18 : cyc. Phylogenetic analysis of the 16S rRNA gene placed the strain in the order Rhizobiales and it shared 94 % identity with the type strain of its nearest relative, Salinarimonas ramus. Morphological, chemotaxonomic and phylogenetic results did not affiliate the novel organism with any of the families in the Rhizobiales; therefore, HL-109T is representative of a new lineage, for which the name Saliniramus fredricksonii gen. nov., sp. nov. is proposed, with the type strain HL-109T (=JCM 31876T=DSM 102886T). In addition, examination of the phylogenetics of strain HL-109T and its nearest relatives, Salinarimonas ramus and Salinarimonasrosea, demonstrates that these halophiles form a clade distinct from the described families of the Rhizobiales. We further propose the establishment of a new family, Salinarimonadaceae fam. nov., to accommodate the genera Saliniramus and Salinarimonas (the type genus of the family).

Salinivirga fredricksonii gen. nov., sp. nov., a heterotrophic halophile isolated from a photosynthetic mat, a member of a novel lineage (Salinarimonadaceae fam. nov.) within the order Rhizobiales, and reclassification of the genus Salinarimonas Liu et al. 2010 into Salinarimonadaceae.

A halophilic bacterial strain, HL-109T, was isolated from the unicyanobacterial consortium UCC-O, which was obtained from the photosynthetic mat of Hot Lake (Washington, USA). A polyphasic approach using phenotypic, genotypic and chemotaxonomic data was used to classify the strain within the order Rhizobiales. The organism stained Gram-negative and was a moderate thermophile with a growth optimum of 45 °C. It was obligately aerobic, heterotrophic and halophilic, growing in both NaCl and MgSO4 brines. The novel isolate had a polymorphic cellular morphology of short rods with occasional branching, and cells were monotrichous. The major fatty acids detected were C18 : 1, C18 : 0, C16 : 0 and C18 : cyc. Phylogenetic analysis of the 16S rRNA gene placed the strain in the order Rhizobiales and it shared 94 % identity with the type strain of its nearest relative, Salinarimonas ramus. Morphological, chemotaxonomic and phylogenetic results did not affiliate the novel organism with any of the families in the Rhizobiales; therefore, HL-109T is representative of a new lineage, for which the name Salinivirga fredricksonii gen. nov., sp. nov. is proposed, with the type strain HL-109T (=JCM 31876T=DSM 102886T). In addition, examination of the phylogenetics of strain HL-109T and its nearest relatives, Salinarimonas ramus and Salinarimonasrosea, demonstrates that these halophiles form a clade distinct from the described families of the Rhizobiales. We further propose the establishment of a new family, Salinarimonadaceae fam. nov., to accommodate the genera Salinivirga and Salinarimonas (the type genus of the family).

SbcC-SbcD and ExoI process convergent forks to complete chromosome replication.

SbcC-SbcD are the bacterial orthologs of Mre11-Rad50, a nuclease complex essential for genome stability, normal development, and viability in mammals. In vitro, these enzymes degrade long DNA palindromic structures. When inactivated along with ExoI in Escherichia coli, or Sae2 in eukaryotes, palindromic amplifications arise and propagate in cells. However, long DNA palindromes are not normally found in bacterial or human genomes, leaving the cellular substrates and function of these enzymes unknown. Here, we show that during the completion of DNA replication, convergent replication forks form a palindrome-like structural intermediate that requires nucleolytic processing by SbcC-SbcD and ExoI before chromosome replication can be completed. Inactivation of these nucleases prevents completion from occurring, and under these conditions, cells maintain viability by shunting the reaction through an aberrant recombinational pathway that leads to amplifications and instability in this region. The results identify replication completion as an event critical to maintain genome integrity and cell viability, demonstrate SbcC-SbcD-ExoI acts before RecBCD and is required to initiate the completion reaction, and reveal how defects in completion result in genomic instability.

Rolling Circle Mutagenesis of GST-mCherry to Understand Mutation, Gene Expression, and Regulation.

Undergraduates are often familiar with textbook examples of human mutations that affect coding regions and the subsequent disorders, but they may struggle with understanding the implications of mutations in the regulatory regions of genes. We have designed a laboratory sequence that will allow students to explore the effect random mutagenesis can have on protein function, expression, and ultimately phenotype. Students design and perform a safe and time-efficient random mutagenesis experiment using error-prone rolling circular amplification of a plasmid expressing the inducible fusion protein glutathione S-transferase (GST)-mCherry. Mutagenized and wild-type control plasmid DNA, respectively, are then purified and transformed into bacteria to assess phenotypic changes. While bacteria transformed with the wild type control should be pink, some bacterial colonies transformed with mutagenized plasmids will exhibit a different color. Students attempt to identify their mutations by isolating plasmid from these mutant colonies, sequencing, and comparing their mutant sequence to the wild-type sequence. Additionally, students evaluate the potential effects of mutations on protein production by inducing GST-mCherry expression in cultures, generating cell lysates, and analyzing them using SDS-PAGE. Students who have a phenotypic difference but do not obtain a coding region mutation will be able to think critically about plasmid structure and regulation outside of the gene sequence. Students who do not obtain bacterial transformants have the chance to contemplate how mutation of antibiotic resistance genes or replication origins may have contributed to their results. Overall, this series of laboratories exposes students to basic genetic techniques and helps them conceptualize mutation beyond coding regions.

Predicting Species-Resolved Macronutrient Acquisition during Succession in a Model Phototrophic Biofilm Using an Integrated 'Omics Approach.

The principles governing acquisition and interspecies exchange of nutrients in microbial communities and how those exchanges impact community productivity are poorly understood. Here, we examine energy and macronutrient acquisition in unicyanobacterial consortia for which species-resolved genome information exists for all members, allowing us to use multi-omic approaches to predict species' abilities to acquire resources and examine expression of resource-acquisition genes during succession. Metabolic reconstruction indicated that a majority of heterotrophic community members lacked the genes required to directly acquire the inorganic nutrients provided in culture medium, suggesting high metabolic interdependency. The sole primary producer in consortium UCC-O, cyanobacterium Phormidium sp. OSCR, displayed declining expression of energy harvest, carbon fixation, and nitrate and sulfate reduction proteins but sharply increasing phosphate transporter expression over 28 days. Most heterotrophic members likewise exhibited signs of phosphorus starvation during succession. Though similar in their responses to phosphorus limitation, heterotrophs displayed species-specific expression of nitrogen acquisition genes. These results suggest niche partitioning around nitrogen sources may structure the community when organisms directly compete for limited phosphate. Such niche complementarity around nitrogen sources may increase community diversity and productivity in phosphate-limited phototrophic communities.

Evaluating Decision-Making: Validation and Regression-Based Normative Data of the Judgment Assessment Tool.

OBJECTIVE: This study presents the results of the development and validation of the Judgment Assessment Tool (JAT). The JAT measures two core aspects of judgment, namely generation of solutions (G) and assessment of options (A), the two first stages of decision-making process. METHOD: During the test development phase (study 1), a preliminary version of the JAT was evaluated by 14 experts and tested on 30 healthy controls (HC). One hundred and twenty HC (20-84 years old) and 24 participants with mild Alzheimer's disease (AD) were subsequently tested on the final version of the JAT (study 2). HC participants aged 60 and over and AD participants underwent a neuropsychological evaluation. RESULTS: The internal consistency of the final version of the JAT assessed by Cronbach's a was 0.71 for the HC group and 0.85 for the AD group. Performance on the JAT was normally distributed both in the HC and AD groups. The test correlated with abstract reasoning, verbal fluency, and working memory. Results revealed adequate test-retest reliability and excellent interrater reliability (k coefficient was 0.92 for the G section and 0.93 for the A section). Demographically adjusted normative data were generated based on a regression analysis and results showed that AD participants performed worse than HC with a large effect size (Cohen's d = 1.79). CONCLUSION: Overall, these results provide evidence of the reliability and strong construct validity of the JAT to evaluate judgment.

Quantifying element incorporation in multispecies biofilms using nanoscale secondary ion mass spectrometry image analysis.

Elucidating nutrient exchange in microbial communities is an important step in understanding the relationships between microbial systems and global biogeochemical cycles, but these communities are complex and the interspecies interactions that occur within them are not well understood. Phototrophic consortia are useful and relevant experimental systems to investigate such interactions as they are not only prevalent in the environment, but some are cultivable in vitro and amenable to controlled scientific experimentation. Nanoscale secondary ion mass spectrometry (NanoSIMS) is a powerful, high spatial resolution tool capable of visualizing the metabolic activities of single cells within a biofilm, but quantitative analysis of the resulting data has typically been a manual process, resulting in a task that is both laborious and susceptible to human error. Here, the authors describe the creation and application of a semiautomated image-processing pipeline that can analyze NanoSIMS-generated data, applied to phototrophic biofilms as an example. The tool employs an image analysis process, which includes both elemental and morphological segmentation, producing a final segmented image that allows for discrimination between autotrophic and heterotrophic biomass, the detection of individual cyanobacterial filaments and heterotrophic cells, the quantification of isotopic incorporation of individual heterotrophic cells, and calculation of relevant population statistics. The authors demonstrate the functionality of the tool by using it to analyze the uptake of (15)N provided as either nitrate or ammonium through the unicyanobacterial consortium UCC-O and imaged via NanoSIMS. The authors found that the degree of (15)N incorporation by individual cells was highly variable when labeled with (15)NH4 (+), but much more even when biofilms were labeled with (15)NO3 (-). In the (15)NH4 (+)-amended biofilms, the heterotrophic distribution of (15)N incorporation was highly skewed, with a large population showing moderate (15)N incorporation and a small number of organisms displaying very high (15)N uptake. The results showed that analysis of NanoSIMS data can be performed in a way that allows for quantitation of the elemental uptake of individual cells, a technique necessary for advancing research into the metabolic networks that exist within biofilms with statistical analyses that are supported by automated, user-friendly processes.

High-Quality Draft Genome Sequence of Kallotenue papyrolyticum JKG1T Reveals Broad Heterotrophic Capacity Focused on Carbohydrate and Amino Acid Metabolism.

The draft genome of Kallotenue papyrolyticum JKG1(T), a member of the order Kallotenuales, class Chloroflexia, consists of 4,475,263 bp in 4 contigs and encodes 4,010 predicted genes, 49 tRNA-encoding genes, and 3 rRNA operons. The genome is consistent with a heterotrophic lifestyle including catabolism of polysaccharides and amino acids.

Phototrophic biofilm assembly in microbial-mat-derived unicyanobacterial consortia: model systems for the study of autotroph-heterotroph interactions.

Microbial autotroph-heterotroph interactions influence biogeochemical cycles on a global scale, but the diversity and complexity of natural systems and their intractability to in situ manipulation make it challenging to elucidate the principles governing these interactions. The study of assembling phototrophic biofilm communities provides a robust means to identify such interactions and evaluate their contributions to the recruitment and maintenance of phylogenetic and functional diversity over time. To examine primary succession in phototrophic communities, we isolated two unicyanobacterial consortia from the microbial mat in Hot Lake, Washington, characterizing the membership and metabolic function of each consortium. We then analyzed the spatial structures and quantified the community compositions of their assembling biofilms. The consortia retained the same suite of heterotrophic species, identified as abundant members of the mat and assigned to Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes. Autotroph growth rates dominated early in assembly, yielding to increasing heterotroph growth rates late in succession. The two consortia exhibited similar assembly patterns, with increasing relative abundances of members from Bacteroidetes and Alphaproteobacteria concurrent with decreasing relative abundances of those from Gammaproteobacteria. Despite these similarities at higher taxonomic levels, the relative abundances of individual heterotrophic species were substantially different in the developing consortial biofilms. This suggests that, although similar niches are created by the cyanobacterial metabolisms, the resulting webs of autotroph-heterotroph and heterotroph-heterotroph interactions are specific to each primary producer. The relative simplicity and tractability of the Hot Lake unicyanobacterial consortia make them useful model systems for deciphering interspecies interactions and assembly principles relevant to natural microbial communities.

Thermoflexus hugenholtzii gen. nov., sp. nov., a thermophilic, microaerophilic, filamentous bacterium representing a novel class in the Chloroflexi, Thermoflexia classis nov., and description of Thermoflexaceae fam. nov. and Thermoflexales ord. nov.

A thermophilic, filamentous, heterotrophic bacterium, designated strain JAD2(T), a member of an as-yet uncultivated lineage that is present and sometimes abundant in some hot springs worldwide, was isolated from sediment of Great Boiling Spring in Nevada, USA. Cells had a mean diameter of 0.3 µm and length of 4.0 µm, and formed filaments that typically ranged in length from 20 to 200 µm. Filaments were negative for the Gram stain reaction, spores were not formed and motility was not observed. The optimum temperature for growth was 72.5-75 °C, with a range of 67.5-75 °C, and the optimum pH for growth was 6.75, with a range of pH 6.5-7.75. Peptone, tryptone or yeast extract were able to support growth when supplemented with vitamins, but no growth was observed using a variety of defined organic substrates. Strain JAD2(T) was microaerophilic and facultatively anaerobic, with optimal growth at 1% (v/v) O2 and an upper limit of 8% O2. The major cellular fatty acids (>5%) were C(16 : 0), C(19 : 0), C(18 : 0), C(20 : 0) and C(19 : 1). The genomic DNA G+C content was 69.3 mol%. Phylogenetic and phylogenomic analyses using sequences of the 16S rRNA gene and other conserved genes placed JAD2(T) within the phylum Chloroflexi, but not within any existing class in this phylum. These results indicate that strain JAD2(T) is the first cultivated representative of a novel lineage within the phylum Chloroflexi, for which we propose the name Thermoflexus hugenholtzii gen. nov., sp. nov., within Thermoflexia classis nov., Thermoflexales ord. nov. and Thermoflexaceae fam. nov. The type strain of Thermoflexus hugenholtzii is JAD2(T) ( = JCM 19131(T) = CCTCC AB-2014030(T)).