bluuebunny/crossref_metadata_2025 huggingface dataset:
Implementing a Standardized Clinical Pathway Leads to Reduced Asthma Admissions and Health Care Costs
Authors: McCoy Elisha M. , Kink Rudy J. , Harrold La Precious L. , Longjohn Mindy K. , Meredith Mark L. , Pishko Stephen D.
Published: June 2019

Introduction:

Asthma exacerbations are 1 of the leading causes of hospital admissions in children in the United States. High volumes in the emergency department can lead to delayed treatment. Several studies have shown that implementation of a standardized clinical pathway can improve adherence to evidence-based standards. The purpose of our quality improvement project was to develop a standardized pathway of care for children with asthma exacerbations to improve time to treatment and reduce admissions.

Methods:

The team used process mapping to review the current process of care for patients with asthma exacerbations presenting to the Emergency Department. After identification of several barriers, the team used plan-do-study-act cycles to develop a standardized clinical pathway of care for children based on their respiratory clinical score. Further interventions occurred after data collection and analyzation through run charts.

Results:

Implementation of a standardized clinical pathway for children with asthma presenting to the Emergency Department resulted in treatment with steroids in less than 60 minutes. Overall admissions were decreased from an average of 24% to 17% throughout the intervention period. We estimated cost savings for the institution at over $230,000 for the 2 years after implementation of the pathway.

Conclusions:

Using a multidisciplinary team approach to develop a standardized clinical pathway for a common childhood illness like asthma can result in reduced time to treatment and admissions.
CONNECT Workshops to Enhance Physician and Patient Experience: Interviews Reveal the Physician Perspective
Authors: Scott Jennifer E. , Jacob-Files Elizabeth , Baden Harris P.
Published: June 2019

Introduction:

Physicians’ relationships with patients are a critical determinant of job satisfaction, and patients who experience compassionate care have better outcomes. The CONNECT workshop at Seattle Children’s teaches communication strategies to optimize both patient and physician experience. This article describes participants’ experiences during the workshops and the impact on their subsequent behaviors and satisfaction.

Methods:

Thirteen semistructured interviews were conducted with physicians, representing 11 specialties. Researchers used a series of immersion-crystallization cycles through which they iteratively immersed themselves in the data by reviewing all transcripts and coming up with key themes. According to thematic findings, they adjusted the interview guides, adding or deleting probes. After crystallizing an initial list of key themes, they created a codebook, coded using qualitative analysis software and met after coding each transcript to discuss their codes, add, and change codes, and recode when necessary.

Results:

Researchers identified 2 thematic responses concerning workshop experience. Physicians valued colleague interaction (Theme A) and appreciated the nonprescriptive curriculum (Theme B). Likewise, 3 themes reflecting workshop impact also emerged. Physicians reported the workshop encouraged presence and self-awareness during patient encounters (Theme C). They learned to address patient-driven concerns (Theme D), and learned empathetic strategies to connect more deeply with patients (Theme E).

Conclusion:

This study offers perspectives from a diverse group of physicians concerning their experience with the communication workshop, including the opportunity for physicians to focus on self-discovery, authenticity, connect on a deeper level with colleagues, and adopt key strategies to enhance interactions with patients.
Implementation and Evaluation of a Standard Operating Procedure for Pediatric Infliximab Infusions
Authors: Kelly Maureen M. , Turner Barbara S. , Kappelman Michael D. , Lee Eun Jeong , Gulati Ajay S.
Published: June 2019

Background:

The purpose of this quality improvement project was to decrease care variation regarding infliximab delivery at a pediatric inflammatory bowel disease (IBD) center. This variation was driven by differences in provider and nurse practices within 2 distinct infliximab administration units in our center. Following the development of an infusion protocol, the primary project goal was to assess improvement in the submission and completion of a protocol-specific preinfusion safety checklist.

Methods:

The infusion protocol was developed based on the standard of care and expert physician opinion. A safety checklist was created to screen for active IBD symptoms and infection. We utilized continuous quality improvement to evaluate and guide the implementation of this preinfusion checklist. Checklist completion was assessed monthly over 15 months. We also conducted focus group interviews with infusion nurses and physicians to solicit qualitative protocol feedback.

Results:

We used standard run chart rules and identified a shift in the median completion rate for both units, with no trends or astronomical points. The baseline period was defined as the 6-month post-checklist implementation. The median baseline completion rate for 1 unit was 46%, and during the subsequent 9 months, the rate increased to 81%. In the other unit, the median baseline completion rate was 91%, and during the succeeding 9 months, the rate was 95%. Focus group feedback included themes of quality, communication, safety, and efficiency and helped improve the protocol.

Conclusions:

Feasibility was established for a standardized protocol to improve completion of a preinfusion safety checklist in children with IBD who receive infliximab. Nurse and physician focus group feedback was important for guiding protocol refinements.
A Project-based Curriculum for Driving Organization-wide Continuous Improvement
Authors: Harte Lory D. , Reddy Mamta , Marshall Lisa K. , Mroczka Kevin J. , Mann Keith J.
Published: June 2019

Background:

Creating the capacity and capability for meaningful improvement in healthcare quality is a challenge many organizations face. Before 2012, Children’s Mercy sponsored 20 leaders to obtain advanced improvement training from peer organizations. Recognizing an opportunity to build upon this momentum, we developed an organization-wide curriculum for teaching continuous improvement.

Methods:

A steering committee was created in 2011 to define, advise, and oversee education in improvement science. We agreed upon a framework for improvement, a program name [Continuous Quality and Practice Improvement (CQPI)], and a phased curriculum development approach, beginning with a project/experiential learning based course (Team CQPI). Course evaluation for Team CQPI consisted of a standard evaluation of objectives, pre- and post-course assessment, qualitative feedback, and serial assessment of project progress using the Team Assessment Score (TAS). The curriculum committee monitored improvement.

Results:

From 2012 to 2017, 297 people participated in the project-based course, completing a total of 83 projects. TAS improved throughout the 4-month project-based course, from an average starting score of 1 (“forming a team”) to 2.7 (“changes tested”). The average TAS at 12 months following completion of the Team CQPI course was 3.5 (“improvement”) out of 5.

Conclusions:

Development of a comprehensive curriculum for driving continuous improvement has resulted in a measurable change in TAS scores representative of local improvement efforts.
Increasing Trichomonas vaginalis testing for high-risk adolescents a pediatric emergency department
Authors: Stukus Kristin S. , Buckingham Don , Cohen Daniel M.
Published: June 2019

Background:

Trichomonas is a common sexually transmitted infection (STI) among adolescents, causing vaginal discharge, pelvic pain, and dysuria. Affected individuals have increased susceptibility to other STIs and may have pregnancy complications. A quality improvement project was developed to increase trichomonas testing among high-risk adolescent patients from 40% in July 2014 to 100% by December 31, 2014, and sustain over 6 months.

Methods:

An interdisciplinary team (providers and support staff) was assembled to address this objective. We collected 6 months of baseline data. Deploying the Institute for Healthcare Improvement Model for Improvement, we formulated an aim statement and identified key drivers. We used cause analysis to identify interventions for each problem area. Multiple Plan-Do-Study-Act cycles were undertaken, and results were monitored using control charts. Interventions included increasing awareness and education for clinical staff; changing computer order entry for the test; using order sets for STI; and adding a Licensed Professional Initiated Protocol to nurse ordering practice. These interventions were all done in conjunction with feedback to providers for individual missed cases.

Results:

Over 18 months, the trichomonas testing rate rose with each intervention: from 25% (January 2014) to 98% (December 2014), which we have sustained through June 2015.

Implications and Contributions:

This article demonstrates the successful use of quality improvement methodology to increase rates of Trichomonas vaginalis testing among at-risk adolescent patients. Increased testing results in increased detection and improved treatment and sexual health for our patients.

Conclusion:

Improving the trichomonas testing process in the pediatric emergency department results in higher screening rates among high-risk adolescent patients.
Transforming an Autism Pediatric Research Network into a Learning Health System: Lessons Learned
Authors: Murray Donna S. , S. Anixt Julia , Coury Daniel L. , Kuhlthau Karen A. , Seide Janet , Kelly Amy , Fedele Angie , Eskra Diane , Lannon Carole
Published: June 2019

Introduction:

The Autism Speaks Autism Treatment Network that serves as the Autism Intervention and Research Network on Physical Health (ATN/AIR-P) has a mission to improve the health and well-being of children with Autism Spectrum Disorder and determine the best practices that lead to improved outcomes and expedite the translation of findings to practice. To better achieve this mission, the ATN/AIR-P is engaging in a design process to transition to a Learning Network (LN), the Autism Learning Health Network. The purpose of this paper is to: (1) make the medical and patient communities aware of an Autism LN that is based on the Institute of Medicine’s definition of a Learning Health System; (2) describe how and why the ATN/AIR-P transformed to an LN; and (3) share lessons learned that might inform the transition of future existing networks surrounding other conditions.

Methods:

Design methods included: an in-person design session with various stakeholders, the development of a Key Driver Diagram and redesign of organizational processes, network governance, and data collection and analytics.

Results:

We realized many benefits in making the transition to an LN along with many lessons that can inform the design and implementation of the LN model when transforming existing networks to learning health systems.

Conclusions:

Transitioning a well-established research network requires a complex redesign of existing processes, data infrastructure, and cultural shifts compared with developing a new LN. We identified factors that may inform the transition of future established networks to expedite the process.
A Framework for Maintenance and Scaling of an Evidence-based Guideline Program
Authors: Seneski Annie , Stack Anne M.
Published: June 2019

Introduction:

Use of Evidence-based Guidelines (EBGs) has been shown to improve and standardize care. After implementation and maturation of a guideline program, next steps include incorporating new evidence, sustaining adherence, minimizing measurement burden and fostering scaling of the program. We propose a framework for maintenance and dissemination of an EBG program.

Methods:

Using a program of 28 EBGs developed for use in a pediatric emergency department (ED) in 2010, we developed: a framework for iterative review and revision, a strategy to measure ongoing use in practice and an approach for minimizing repeated measurement sufficient to evaluate outcomes. Also, we created a process to spread the EBG program to the hospital's Department of Pediatrics.

Results:

The framework for maintenance and spread of a program of EBGs resulted in an annual review of individual guidelines with 14 revisions warranted by new evidence, some leading to decreased medication utilization and hospitalization rates. We demonstrated adherence to key quality measures, and decreased the number of measures from 89 to 43, retiring 46 measures with stable peformance. We spread the process for program development to the hospital pediatric department resulting in 36 new EBGs.

Conclusions:

We developed a framework for maintenance and scale of a program of EBGs. Our key learning points were that regular incorporation of new evidence, assessment and feedback on performance and leadership with administrative support are necessary to maintain improvement. This framework may assure sustainability and inform other guideline programs. We offer processes to promote guideline dissemination within an academic hospital.
Design and Development of Daily Morning Surgical Rounds in ICU by Quality Function Deployment
Authors: Tripathi Sandeep , Naevor Ann J. , Henrekin LaMonica L. , Welke Karl F.
Published: June 2019

Objective:

Most healthcare quality improvement projects focus on change management rather than the design of the process. In this article, we describe the development of a new rounding model based on quality function deployment, a Design for Six Sigma tool.

Methods:

We used affinity diagram, focus groups, and Kano analysis to identify critical customer requirements. We also used Kano analysis to determine the design team’s ability to meet the requirements. We then completed a correlation matrix (House of Quality).

Results:

Fifteen quality characteristics were analyzed on a correlation matrix to meet 15 demanded qualities. Numerical values were calculated based on the interactions identified by the design team. We designed a new rounding model based on the House of Quality; this new rounding model resulted in higher provider satisfaction (median 76–80%, P = 0.06).

Conclusions:

We have described a sophisticated approach to the design of a new change strategy/intervention. This technique can be used as a starting point for other projects attempting to implement meaningful changes for complex processes of medical care.
Decreasing Time to Antibiotics for Patients with Sepsis in the Emergency Department
Authors: Emerson Beth L. , Ciaburri Rebecca , Brophy Cheryl , Kandil Sarah B.
Published: June 2019

Background:

Sepsis is a significant cause of morbidity and mortality. Patients may present in a spectrum, from nonsevere sepsis through septic shock. Literature supports improvement in patient outcomes with timely care. This project describes an effort to improve delays in antibiotic administration in patients with sepsis spectrum disease presenting to a pediatric emergency department (PED).

Objective:

This project aimed to decrease time to antibiotics for patients with sepsis in the PED from 154 to <120 minutes within 2 years.

Methods:

Following the collection of baseline data, we assembled a multidisciplinary team. Specific interventions included staff education, the institution of a best practice alert with order set and standardized huddle response, and local stocking of antibiotics. We included all patients with orders for intravenous antibiotics and blood culture.

Results:

From April 2015 to April 2017, the PED demonstrated reduction in time to antibiotics from 154 to 114 minutes. The time from emergency department (ED) arrival to antibiotic order also improved, from 87 to 59 minutes.

Conclusions:

This initiative improved prioritization and efficiency of care of sepsis, and overall time to antibiotics in this population. The results of this project demonstrate the effectiveness of a multidisciplinary team working to improve an essential time-driven process.
Hemisphere-Specific Properties of the Ventriloquism Aftereffect in Humans and Monkeys
Authors: Kopčo Norbert , Lokša Peter , Lin I-fan , Groh Jennifer , Shinn-Cunningham Barbara
Published: June 2019

Visual calibration of auditory space requires re-alignment of representations differing in 1) format (auditory hemispheric channels vs. visual maps) and 2) reference frames (head-centered vs. eye-centered). Here, a ventriloquism paradigm from Kopčo et al. (J Neurosci, 29, 13809-13814) was used to examine these processes in humans and monkeys for ventriloquism induced within one spatial hemifield. Results show that 1) the auditory representation is adapted even by aligned audio-visual stimuli, and 2) the spatial reference frame is primarily head-centered in humans but mixed in monkeys. These results support the view that the ventriloquism aftereffect is driven by multiple spatially non-uniform processes.

PACS numbers: 43.66.Pn, 43.66.Qp, 43.66.Mk
ETHYLENE RESPONSE FACTOR (ERF) genes modulate plant root exudate composition and the attraction of plant parasitic nematodes
Authors: Dyer Steven , Weir Ryan T , Cox Deborah , Cheseto Xavier , Torto Baldwyn , Dalzell Johnathan J
Published: June 2019

Plant root exudates are compositionally diverse, plastic and adaptive. Ethylene signalling influences the attraction of plant parasitic nematodes (PPNs), presumably through the modulation of root exudate composition. Understanding this pathway could lead to new sources of crop parasite resistance. Here we have used Virus-Induced Gene Silencing (VIGS) to knockdown the expression of two ETHYLENE RESPONSE FACTOR (ERF) genes, ERF-E2 and ERF-E3 in tomato. Root exudates are significantly more attractive to the PPNs Meloidogyne incognita, and Globodera pallida following knockdown of ERF-E2, which has no impact on the attraction of Meloidogyne javanica. Knockdown of ERF-E3 has no impact on the attraction of Meloidogyne or Globodera spp. GC-MS analysis revealed substantial changes in root exudate composition relative to controls. However, these changes do not alter the attraction of rhizosphere microbes Bacillus subtilis or Agrobacterium tumefaciens. This study further supports the potential of engineering plant root exudate for parasite control, through the modulation of plant genes.
Human subsystems of medial temporal lobes extend locally to amygdala nuclei and globally to an allostatic-interoceptive system
Authors: Ruiz-Rizzo Adriana L. , Beissner Florian , Finke Kathrin , Müller Hermann J. , Zimmer Claus , Pasquini Lorenzo , Sorg Christian
Published: June 2019

In mammals, the hippocampus, entorhinal, perirhinal, and parahippocampal cortices (i.e., core regions of the human medial temporal lobes, MTL) are locally interlaced with the adjacent amygdala nuclei at the structural and functional levels. At the global brain level, the human MTL has been described as part of the default mode network whereas amygdala nuclei as parts of the salience network, with both networks forming collectively a large-scale brain system supporting allostatic-interoceptive functions. We hypothesized (i) that intrinsic functional connectivity of slow activity fluctuations would reveal human MTL subsystems locally extending to the amygdala; and (ii) that these extended local subsystems would be globally embedded in large-scale brain systems supporting allostatic-interoceptive functions. From the resting-state fMRI data of three independent samples of cognitively healthy adults (one main and two replication samples: Ns = 101, 61, and 29, respectively), we analyzed the functional connectivity of fluctuating ongoing BOLD-activity within and outside the amygdala-MTL in a data-driven way using masked independent component and dual-regression analyses. We found that at the local level MTL subsystems extend to the amygdala and are functionally organized along the longitudinal amygdala-MTL axis. These subsystems were characterized by a consistent involvement of amygdala, hippocampus, and entorhinal cortex, but a variable participation of perirhinal and parahippocampal regions. At the global level, amygdala-MTL subsystems selectively connected to salience, thalamic-brainstem, and default mode networks – the major cortical and subcortical parts of the allostatic-interoceptive system. These results provide evidence for integrated amygdala-MTL subsystems in humans, which are embedded within a larger allostatic-interoceptive system.
Skill acquisition increases myelination and strengthens functional connectivity in the sensorimotor circuit of the adult rat
Authors: Sampaio-Baptista Cassandra , de Weijer Antoin , van der Toorn Annette , Otte Willem M. , Winkler Anderson M. , Lazari Alberto , Salvan Piergiorgio , Bannerman David M. , Dijkhuizen Rick M. , Johansen-Berg Heidi
Published: June 2019

The effects of skill acquisition on whole-brain structure and functional networks have been extensively investigated in humans but have yet to be explored in rodents. Forelimb reaching training in rodents results in well-established focal functional and structural reorganization within the motor cortex (M1) and cerebellum, indicating distributed alterations in both structure and function. However, it is unclear how local alterations in structure and function relate to distributed learning-related changes across motor networks. Here we trained adult rats in skilled reaching and used multimodal whole-brain in vivo MRI to assess both structural and functional plasticity over time.

We detected increases in a myelin-related MRI metric in white matter, cortical areas, and to a lesser extent in the cerebellum, paralleled by strengthened functional connectivity between M1 and cerebellum, possibly reflecting a decrease in cerebellum inhibition over M1. Skill learning therefore leads to myelin increases in pathways that connect sensorimotor regions, and in functional connectivity increases between areas involved in motor learning, all of which correlate with performance. These findings closely mirror previous reports of network-level changes following motor learning in humans and underlines the correspondence between human and rodent brain circuits for motor learning, despite important differences in the anatomy of physiology of movement circuits between species.
In vitro and in vivo efficacy of the combination of colistin and endolysins against clinical strains of Multi-Drug Resistant (MDR) pathogens
Authors: Blasco L. , Ambroa A. , Trastoy R. , Perez-Nadales E. , Fernández-Cuenca F. , Torre-Cisneros J. , Oteo J. , Oliver A. , Canton R. , Kidd T. , Navarro F. , Miró E. , Pascual A. , Bou G. , Martínez-Martínez L. , Tomas M. ,   GEMARA SEIMC/REIPI Bacterial Clinical Adaptation Study Group
Published: June 2019

The multidrug resistance (MDR) among pathogenic bacteria is jeopardizing the worth of antimicrobials, which had previously changed medical sciences. In this study, we used bioinformatic tools to identify the endolysins ElyA1 and ElyA2 (GH108-PG3 family) present in the genome of bacteriophages Ab1051Φ and Ab1052Φ, respectively. The muralytic activity of these endolysins over MDR clinical isolates (Acinetobacter baumannii, Pseudomonas aeruginosa and Klebsiella pneumoniae) was tested using the turbidity reduction assay. The minimal inhibitory concentrations (MICs) of endolysin, colistin and their combination were determined using the microdilution checkerboard method. The antimicrobial activity of the combinations was confirmed by time kill curves and in vivo assays in larvae of Galleria mellonella. Our results showed that ElyA1 displayed activity against all 25 strains of A. baumannii and P. aeruginosa tested and against 13 out of 17 strains of K. pneumoniae. No activity was detected when assays were done with endolysin ElyA2. The combined antimicrobial activity of colistin and endolysin ElyA1 yielded a reduction in the colistin MIC for all strains studied, except K. pneumoniae. These results were confirmed in vivo in G. mellonella survival assays. In conclusion, the combination of colistin with new endolysins such as ElyA1 could increase the bactericidal activity and reduce the MIC of the antibiotic, thus also reducing the associated toxicity.

IMPORTANCE

The development of multiresistance by pathogen bacteria increases the necessity of the development of new antimicrobial strategies. In this work, we combined the effect of the colistin with a new endolysin, ElyA1, from a bacteriophage present in the clinical strain of Acinetobacter baumannii Ab105. ElyA1 is a lysozyme-like family (GH108-GP3), whose antimicrobial activity was described for first time in this work. Also, another endolysin, ElyA2, with the same origin and family, was characterized but in this case no activity was detected. ElyA1 presented lytic activity over a broad spectrum of strains from A. baumannii, Pseudomonas aeruginosa, and Klebsiella pneumoniae. When colistin was combined with ElyA1 an increase of the antimicrobial activity was observed with a reduced concentration of colistin, and this observation was also confirmed in vivo in Galleria mellonella larvae. The combination of colistin with new endolysins as ElyA1 could increase the bactericidal activity and lowering the MIC of the antibiotic, thus also reducing the associated toxicity.
iNetModels 2.0: an interactive visualization and database of multi-omics data
Authors: Arif Muhammad , Zhang Cheng , Li Xiangyu , Güngör Cem , Çakmak Buğra , Arslantürk Metin , Tebani Abdellah , Özcan Berkay , Subaş Oğuzhan , Zhou Wenyu , Piening Brian , Turkez Hasan , Fagerberg Linn , Price Nathan , Hood Leroy , Snyder Michael , Nielsen Jens , Uhlen Mathias , Mardinoglu Adil
Published: June 2019

It is essential to reveal the associations between different omics data for a comprehensive understanding of the altered biological process in human wellness and disease. To date, very few studies have focused on collecting and exhibiting multi-omics associations in a single database. Here, we present iNetModels, an interactive database and visualization platform of Multi-Omics Biological Networks (MOBNs). This platform describes the associations between the clinical chemistry, anthropometric parameters, plasma proteomics and metabolomics as well as metagenomics for oral and gut microbiome obtained from the same individuals. Moreover, iNetModels includes tissue- and cancer-specific Gene Co-expression Networks (GCNs) for exploring the connections between the specific genes. This platform allows the user to interactively explore a single feature's association with other omics data and customize its particular context (e.g. male/female specific). The users can also register their own data for sharing and visualization of the MOBNs and GCNs. Moreover, iNetModels allows users who do not have a bioinformatics background to facilitate human wellness and diseases research. iNetModels can be accessed freely athttps://inetmodels.comwithout any limitation.
Alternative transcription cycle for bacterial RNA polymerase
Authors: Harden Timothy T. , Herlambang Karina S. , Chamberlain Mathew , Lalanne Jean-Benoît , Wells Christopher D. , Li Gene-Wei , Landick Robert , Hochschild Ann , Kondev Jane , Gelles Jeff
Published: June 2019

RNA polymerases (RNAPs) transcribe genes through a cycle of recruitment to promoter DNA, initiation, elongation, and termination. After termination, RNAP is thought to initiate the next round of transcription by detaching from DNA and rebinding a new promoter. We used single-molecule fluorescence microscopy to observe individual RNAP molecules after transcript release at a terminator. Following termination, RNAP almost always remained bound to DNA and sometimes exhibited one-dimensional sliding over thousands of basepairs. Unexpectedly, the DNA-bound RNAP often restarted transcription, usually in reverse direction, thus producing an antisense transcript. Furthermore, we report evidence of this “secondary initiation” in live cells, using genome-wide RNA sequencing. These findings reveal an alternative transcription cycle that allows RNAP to reinitiate without dissociating from DNA, which is likely to have important implications for gene regulation.
The impact of CO2/HCO3-availability on anaplerotic flux in PDHC-deficientCorynebacterium glutamicumstrains
Authors: Krüger Aileen , Wiechert Johanna , Gätgens Cornelia , Polen Tino , Mahr Regina , Frunzke Julia
Published: June 2019

The pyruvate dehydrogenase complex (PDHC) catalyzes the oxidative decarboxylation of pyruvate yielding acetyl-CoA and CO2. The PDHC-deficientCorynebacterium glutamicumstrain ΔaceEis therefore lacking an important decarboxylation step in central metabolism. Additional inactivation ofpyc, encoding pyruvate carboxylase, resulted in a >15 hour lag phase in the presence of glucose, while no growth defect was observed on gluconeogenetic substrates like acetate. Growth was successfully restored by deletion ofptsGencoding the glucose-specific permease of the PTS system, thereby linking the observed phenotype to the increased sensitivity of strain ΔaceEΔpycto glucose catabolism. In the following, strain ΔaceEΔpycwas used to systematically study the impact of perturbations of the intracellular CO2/HCO3-pool on growth and anaplerotic flux. Remarkably, all measures leading to enhanced CO2/HCO3-levels, such as external addition of HCO3-, increasing the pH, or rerouting metabolic flux via pentose phosphate pathway, at least partially eliminated the lag phase of strain ΔaceEΔpycon glucose medium. In accordance, inactivation of the urease enzyme, lowering the intracellular CO2/HCO3-pool, led to an even longer lag phase accompanied with the excretion of L-valine and L-alanine. Transcriptome analysis as well as an adaptive laboratory evolution experiment of strain ΔaceEΔpycrevealed the reduction of glucose uptake as a key adaptive measure to enhance growth on glucose/acetate mixtures. Altogether, our results highlight the significant impact of the intracellular CO2/HCO3-pool on metabolic flux distribution, which becomes especially evident in engineered strains suffering from low endogenous CO2production rates as exemplified by PDHC-deficient strains.

Importance

CO2is a ubiquitous product of cellular metabolism and an essential substrate for carboxylation reactions. The pyruvate dehydrogenase complex (PDHC) catalyzes a central metabolic reaction contributing to the intracellular CO2/HCO3-pool in many organisms. In this study, we used a PDHC-deficient strain ofCorynebacterium glutamicum, which was additionally lacking pyruvate carboxylase (ΔaceEΔpyc). This strain featured a >15 h lag phase during growth on glucose-acetate mixtures. We used this strain to systematically assess the impact of alterations in the intracellular CO2/HCO3-pool on growth on glucose-containing medium. Remarkably, all measures enhancing the CO2/HCO3-levels successfully restored growth emphasizing the strong impact of the intracellular CO2/HCO3-pool on metabolic flux especially in strains suffering from low endogenous CO2production rates.
Characteristics and Evolutionary analysis of Photosynthetic Gene Clusters on Extrachromosomal Replicons: from streamlined plasmids to chromids
Authors: Liu Yanting , Zheng Qiang , Lin Wenxin , Jiao Nianzhi
Published: June 2019

Aerobic anoxygenic photoheterotrophic bacteria (AAPB) represent intermediates in the evolution from photoautotrophic to heterotrophic metabolisms. Substantial evidence indicates that highly conserved photosynthetic gene clusters (PGCs) of AAPB can be transferred between species, genera, and even phyla. Furthermore, analysis of recently discovered PGCs carried by extrachromosomal replicons (exPGCs) suggests that extrachromosomal replicons (ECRs) play an important role in the transfer of PGCs. In the present study, thirteenRoseobacterclade genomes from seven genera that harbored exPGCs were used to analyze characteristics and evolution of PGCs. The identification of plasmid-like and chromid-like ECRs from PGC-containing ECRs revealed two different functions: the spread of PGCs among strains and the maintenance of PGCs within genomes. Phylogenetic analyses indicated two independent origins of exPGCs, corresponding to PufC-containing and PufX-containing photosynthetic reaction complexes. Furthermore, the two different types of complexes were observed within different strains of the sameTateyamariaandJannaschiagenera. The two different complexes were also differentially carried by chromosomes and ECRs in the strains, respectively, which provided clear evidence for ECR-mediated PGC transfer. Multiple recombination events of exPGCs were also observed, wherein the majority of exPGCs were inserted by replication modules at the same genomic positions. However, the exPGCs of theJannaschiastrains comprised superoperons without evidence of insertion, and therefore likely represent an initial evolutionary stage where the PGC was translocated from chromosomes to ECRs without further combinations. Lastly, a scenario of PGC gain and loss is proposed that specifically focuses on ECR-mediated exPGC transfer to explain the evolution and patchy distribution of AAPB within theRoseobacterclade.

Importance

The evolution of photosynthesis was a significant event during the diversification of biological life. Aerobic anoxygenic heterotrophic bacteria (AAPB) share physiological characteristics with both photoautotrophs and heterotrophs and are therefore suggested to be evolutionary intermediates between the two lifestyles. Here, characterization and evolutionary analyses were conducted for thirteen bacterial strains that contained photosynthetic gene clusters (PGCs) carried by extrachromosomal replicons (ECRs) to shed light on the evolution of photosynthesis in bacteria. Specifically, these analyses improved the “Think Pink” scenario of PGC transfer that is mediated by ECRs inRoseobacterclade strains. This study advances our understanding of the importance of ECRs in the transfer of PGCs within marine photoheterotrophic bacteria.
The Cellular Immunity Agent Based Model (CIABM): Replicating the cellular immune response to viral respiratory infection
Authors: Becker Andrew , An Gary , Cockrell Chase
Published: June 2019

Viral respiratory infections, such as influenza, result in over 1 million deaths worldwide each year. To date, there are few therapeutic interventions able to affect the course of the disease once acquired, a deficit with stark consequences that were readily evident in the current COVID-19 pandemic. We present the Cellular Immune Agent Based Model (CIABM) as a flexible framework for modeling acute viral infection and cellular immune memory development. The mechanism/rule-based nature of the CIABM allows for interrogation of the complex dynamics of the human immune system during various types of viral infections. The CIABM is an extension of a prior agent-based model of the innate immune response, incorporating additional cellular types and mediators involved in the response to viral infection. The CIABM simulates the dynamics of viral respiratory infection in terms of epithelial invasion, immune cellular population changes and cytokine measurements. Validation of the CIABM involved effectively replicating in vivo measurements of circulating mediator levels from a clinical cohort of influenza patients. The general purpose nature of the CIABM allows for both the representation of various types of known viral infections and facilitates the exploration of hypothetical, novel viral pathogens.
Links between central CB1-receptor availability and peripheral endocannabinoids in patients with first episode psychosis
Authors: Dickens Alex M. , Borgan Faith , Laurikainen Heikki , Lamichhane Santosh , Marques Tiago , Rönkkö Tuukka , Veronese Mattia , Lindeman Tuomas ,   METSY Investigators, Hyötyläinen Tuulia , Howes Oliver , Hietala Jarmo , Orešič Matej
Published: June 2019

There is an established, albeit poorly-understood link between psychosis and metabolic abnormalities such as altered glucose metabolism and dyslipidemia, which often precede the initiation of antipsychotic treatment. It is known that obesity-associated metabolic disorders are promoted by peripheral activation of the endocannabinoid system (ECS). Our recent data suggest that ECS dysregulation may also play a role in psychosis. With the aim of characterizing the involvement of the central and peripheral ECSs and their mutual associations, here we performed a combined neuroimaging and metabolomic study in patients with first-episode psychosis (FEP) and healthy controls (HC). Regional brain cannabinoid receptor type 1 (CB1R) availability was quantified in two, independent samples of patients with FEP (n=20 and n=8) and HC (n=20 and n=10), by applying 3D positron emission tomography (PET), using two radiotracers, [11C]MePPEP and [18F]FMPEP-d2. Ten endogenous endocannabinoids or related metabolites were quantified in serum, drawn from these individuals during the same imaging session. Circulating levels of arachidonic acid and oleyl ethanolamide were reduced in FEP individuals, but not in those who were predominantly medication-free. In HC, there was an inverse association between levels of circulating arachidonoyl glycerol, anandamide, oleyl ethanolamide and palmitoyl ethanolamide, and CB1R availability in the posterior cingulate cortex. This phenomenon was, however, not observed in FEP patients. Our data thus provide evidence of cross-talk and dysregulation between peripheral endocannabinoids and central CB1R availability in FEP.
Nanopore device-based fingerprinting of RNA oligos and microRNAs enhanced with an Osmium tag
Authors: Sultan Madiha , Kanavarioti Anastassia
Published: June 2019

Nanopores, both protein and solid-state, are explored as single molecule analytical tools, but using an experimental platform is challenging. Here we show that a commercially available nanopore device, MinION from Oxford Nanopore Technologies (ONT), successfully accomplishes a task challenging for a conventional analytical tool. Specifically the MinION discriminates among 31 nucleotide (nt) long oligoriboadenylates with a single pyrimidine (Py) substitution, when this pyrimidine is tagged/labeled with a bulky group (Osmium tetroxide 2,2’-bipyridine or OsBp). This platform also discriminates between an osmylated Py (Py-OsBp) followed by a purine (Pu) and a Py-OsBp followed by a second Py-OsBp, leading to the conjecture that the bulky tag enables sensing of a two-nucleotide sequence. Two-nucleotide sensing could greatly improve base-calling accuracy in motor enzyme-assisted nanopore sequencing.

We attribute the observed discrimination neither to the specific pore protein nor to OsBp, but to the tag’s bulkiness, that leads to markedly slower translocation and “touching” proximity at the pore’s constriction zone, that forces desolvation and reorganization, and enables strong interactions among the nanopore, the tagged pyrimidine, and the adjacent nucleobase. These results constitute proof-of-principle that size-suitable nanopores may be superior to traditional analytical tools, for the characterization of RNA oligos and microRNAs enhanced by selective labelling.
Magainin 2 and PGLa in Bacterial Membrane Mimics I: Peptide-Peptide and Lipid-Peptide Interactions
Authors: Pachler Michael , Kabelka Ivo , Appavou Marie-Sousai , Lohner Karl , Vácha Robert , Pabst Georg
Published: June 2019

We addressed the onset of synergistic activity of the two well-studied antimicrobial peptides magainin 2 (MG2a) and PGLa using lipid-only mimics of Gram-negative cytoplasmic membranes. Specifically, we coupled a joint analysis of small-angle X-ray and neutron scattering experiments on fully hydrated lipid vesicles in the presence of MG2a and L18W-PGLa to all-atom and coarse-grained molecular dynamics simulations. In agreement with previous studies both peptides, as well as their equimolar mixture, were found to remain in a surface-aligned topology upon membrane insertion and to induce significant membrane perturbation as evidenced by membrane thinning and hydrocarbon order parameter changes in the vicinity of the inserted peptide. These effects were particularly pronounced for the so called synergistic mixture of 1:1 (mol/mol) L18W-PGLa/MG2a and cannot be accounted for by a linear combination of the membrane perturbations of two peptides individually. Our data are consistent with parallel heterodimers forming at much lower concentrations than previously considered, but which do not induce a synergistic leakage of dyes. Our simulations further show that the heterodimers interact via salt bridges and hydrophobic forces, which apparently makes them more stable than putatively formed antiparallel L18W-PGLa and MG2a homodimers. Moreover, dimerization of L18W-PGLa and MG2a leads to a relocation of the peptides within the lipid headgroup regime as compared to the individual peptides. The early onset of dimerization of L18W-PGLa and MG2a at low peptide concentrations consequently appears to be key to their synergistic dye-releasing activity from lipid vesicles at high concentrations.

STATEMENT OF SIGNIFICANCE

We demonstrate that specific interactions of the antimicrobial peptides MG2a and PGLa with each other in POPE/POPG bilayers lead to the formation of surface-aligned parallel dimers, which provide already at low peptide concentrations the nucleus for the peptides’ well-known synergistic activity.
Differential turnover of Nup188 controls its levels at centrosomes and role in centriole duplication
Authors: Vishnoi Nidhi , Dhanasekeran Karthigeyan , Chalfant Madeleine , Surovstev Ivan , Khokha Mustafa K. , Lusk C. Patrick
Published: June 2019

NUP188 encodes a scaffold component of the nuclear pore complex (NPC) and has been implicated as a congenital heart disease gene through an ill-defined function at centrioles. Here, we explore the mechanisms that physically and functionally segregate Nup188 between the pericentriolar material (PCM) and NPCs throughout the cell cycle. Pulse-chase fluorescent labeling approaches indicate that Nup188 populates centrosomes with newly synthesized protein that does not exchange with NPCs even after mitotic NPC breakdown. In addition, the steady-state level of Nup188 at centrosomes is controlled by the sensitivity of the PCM pool, but not the NPC pool, to proteasomal degradation. Proximity-labeling and super-resolution microscopy supports that Nup188 interacts with components of PCM including Cep192 and the centriolar satellite component, PCM1. Consistent with this, Nup188 plays a role in centriole duplication at or upstream of Sas6 loading. Together, our data establish Nup188 as a functional component of PCM and potentially provides insight into the pathogenesis of congenital heart disease.
A robust benchmark for germline structural variant detection
Authors: Zook Justin M. , Hansen Nancy F. , Olson Nathan D. , Chapman Lesley M. , Mullikin James C. , Xiao Chunlin , Sherry Stephen , Koren Sergey , Phillippy Adam M. , Boutros Paul C. , Sahraeian Sayed Mohammad E. , Huang Vincent , Rouette Alexandre , Alexander Noah , Mason Christopher E. , Hajirasouliha Iman , Ricketts Camir , Lee Joyce , Tearle Rick , Fiddes Ian T. , Barrio Alvaro Martinez , Wala Jeremiah , Carroll Andrew , Ghaffari Noushin , Rodriguez Oscar L. , Bashir Ali , Jackman Shaun , Farrell John J , Wenger Aaron M , Alkan Can , Soylev Arda , Schatz Michael C. , Garg Shilpa , Church George , Marschall Tobias , Chen Ken , Fan Xian , English Adam C. , Rosenfeld Jeffrey A. , Zhou Weichen , Mills Ryan E. , Sage Jay M. , Davis Jennifer R. , Kaiser Michael D. , Oliver John S. , Catalano Anthony P. , Chaisson Mark JP , Spies Noah , Sedlazeck Fritz J. , Salit Marc ,   the Genome in a Bottle Consortium
Published: June 2019

New technologies and analysis methods are enabling genomic structural variants (SVs) to be detected with ever-increasing accuracy, resolution, and comprehensiveness. Translating these methods to routine research and clinical practice requires robust benchmark sets. We developed the first benchmark set for identification of both false negative and false positive germline SVs, which complements recent efforts emphasizing increasingly comprehensive characterization of SVs. To create this benchmark for a broadly consented son in a Personal Genome Project trio with broadly available cells and DNA, the Genome in a Bottle (GIAB) Consortium integrated 19 sequence-resolved variant calling methods, both alignment- and de novo assembly-based, from short-, linked-, and long-read sequencing, as well as optical and electronic mapping. The final benchmark set contains 12745 isolated, sequence-resolved insertion and deletion calls ≥50 base pairs (bp) discovered by at least 2 technologies or 5 callsets, genotyped as heterozygous or homozygous variants by long reads. The Tier 1 benchmark regions, for which any extra calls are putative false positives, cover 2.66 Gbp and 9641 SVs supported by at least one diploid assembly. Support for SVs was assessed using svviz with short-, linked-, and long-read sequence data. In general, there was strong support from multiple technologies for the benchmark SVs, with 90 % of the Tier 1 SVs having support in reads from more than one technology. The Mendelian genotype error rate was 0.3 %, and genotype concordance with manual curation was >98.7 %. We demonstrate the utility of the benchmark set by showing it reliably identifies both false negatives and false positives in high-quality SV callsets from short-, linked-, and long-read sequencing and optical mapping.
Modeling microbial metabolic trade-offs in a chemostat
Authors: Li Zhiyuan , Liu Bo , Li Sophia Hsin-Jung , King Christopher G. , Gitai Zemer , Wingreen Ned S.
Published: June 2019

Microbes face intense competition in the natural world, and so need to wisely allocate their resources to multiple functions, in particular to metabolism. Understanding competition among metabolic strategies that are subject to trade-offs is therefore crucial for deeper insight into the competition, cooperation, and community assembly of microorganisms. In this work, we evaluate competing metabolic strategies within an ecological context by considering not only how the environment influences cell growth, but also how microbes shape their chemical environment. Utilizing chemostat-based resource-competition models, we exhibit a set of intuitive and general procedures for assessing metabolic strategies. Using this framework, we are able to relate and unify multiple metabolic models, and to demonstrate how the fitness landscape of strategies becomes intrinsically dynamic due to species-environment feedback. Such dynamic fitness landscapes produce rich behaviors, and prove to be crucial for ecological and evolutionary stable coexistence in all the models we examined.