bluuebunny/crossref_metadata_2025_split huggingface dataset:
Altering under-represented DNA sequences elevates bacterial transformation efficiency
Authors: Hu Shuai , Giacopazzi Stefani , Modlin Ryan , Karplus Kevin , Bernick David L. , Ottemann Karen M. 
Published: October 2023

ABSTRACT

A cornerstone of bacterial molecular biology is the ability to genetically manipulate the microbe under study. Many bacteria are difficult to manipulate genetically, a phenotype due in part to robust removal of newly acquired DNA, for example, by restriction-modification (R-M) systems. Here, we report approaches that dramatically improve bacterial transformation efficiency, piloted using a microbe that is challenging to transform due to expression of many R-M systems,
Helicobacter pylori
. Initially, we identified conditions that dampened expression of several R-M systems and concomitantly enhanced transformation efficiency. We then identified an approach that would broadly protect newly acquired DNA. We computationally predicted under-represented short DNA sequences in the
H. pylori
genome, with the idea that these sequences reflect targets of sequence-based surveillance such as R-M systems. We then used this information to modify and eliminate such sites in antibiotic resistance cassettes, creating a “stealth” version. Modifying antibiotic resistance cassettes in this way resulted in significantly higher transformation efficiency compared to non-modified cassettes, a response that was genomic loci independent. Our results suggest that avoiding R-M systems, via modification of under-represented DNA sequences or transformation conditions, is a powerful method to enhance DNA transformation. Our approach to identify under-represented sequences is applicable to any microbe with a sequenced genome.

IMPORTANCE
Manipulating the genomes of bacteria is critical to many fields. Such manipulations are made by genetic engineering, which often requires new pieces of DNA to be added to the genome. Bacteria have robust systems for identifying and degrading new DNA, some of which rely on restriction enzymes. These enzymes cut DNA at specific sequences. We identified a set of DNA sequences that are missing normally from a bacterium’s genome, more than would be expected by chance. Eliminating these sequences from a new piece of DNA allowed it to be incorporated into the bacterial genome at a higher frequency than new DNA containing the sequences. Removing such sequences appears to allow the new DNA to fly under the bacterial radar in “stealth” mode. This transformation improvement approach is straightforward to apply and likely broadly applicable.
Rotavirus capping enzyme VP3 inhibits interferon expression by inducing MAVS degradation during viral replication
Authors: Dai Jin , Agbemabiese Chantal A. , Griffin Ashley N. , Patton John T. 
Published: October 2023

ABSTRACT
The binding of viral RNA to RIG-I-like receptors triggers the formation of mitochondrial antiviral signaling (MAVS) protein aggregates critical for interferon (IFN) expression. Several rotavirus strains have been shown to suppress IFN expression by inducing MAVS degradation. Relying on transient expression assays, previous studies reached different conclusions regarding the identity of the rotavirus protein responsible for MAVS degradation, suggesting it was an activity of the rotavirus capping enzyme VP3 or the interferon antagonist NSP1. Here, we have used recombinant SA11 rotaviruses to identify the endogenous viral protein responsible for MAVS degradation and to analyze how the attack on MAVS impacts IFN expression. The recombinant viruses included those expressing modified VP3 or NSP1 proteins deficient in the ability to induce the degradation of MAVS or interferon regulatory factor-3 (IRF3), or both. With these viruses, we determined that VP3 directs the proteasomal degradation of MAVS but plays no role in IRF3 degradation. Moreover, NSP1 was determined to induce IRF3 degradation but to have no impact on MAVS degradation. Analysis of rotavirus-infected cells indicated that IRF3 degradation was more efficient than MAVS degradation and that NSP1 was primarily responsible for suppressing IFN expression in infected cells. However, VP3-mediated MAVS degradation contributed to IFN suppression in cells that failed to produce functional NSP1, pointing to a subsidiary role for VP3 in the IFN antagonist activity of NSP1. Thus, VP3 is a multifunctional protein with several activities that counter anti-rotavirus innate immune responses, including capping of viral (+)RNAs, hydrolysis of the RNase L 2–5A (2′−5′ oligoadenylate) signaling molecule, and proteasomal degradation of MAVS.

IMPORTANCE
Rotavirus is an enteric RNA virus that causes severe dehydrating gastroenteritis in infants and young children through infection of enterocytes in the small intestine. Timely clearance of the virus demands a robust innate immune response by cells associated with the small intestine, including the expression of interferon (IFN). Previous studies have shown that some rotavirus strains suppress the production of interferon, by inducing the degradation of mitochondrial antiviral signaling (MAVS) protein and interferon regulatory factor-3 (IRF3). In this study, we have used reverse genetics to generate recombinant rotaviruses expressing compromised forms of VP3 or NSP1, or both, to explore the function of these viral proteins in the degradation of MAVS and IRF3. Our results demonstrate that VP3 is responsible for MAVS depletion in rotavirus-infected cells, and through this activity, helps to suppress IFN production. Thus, VP3 functions to support the activity of rotavirus NSP1, the major interferon antagonist of the virus.
Complete genome sequence of
Bacillus thuringiensis
strain RC340, isolated from a temperate forest soil sample in New England
Authors: Sullivan Brendan , Kitzmiller Claire E. , Tran Wyatt C. , Choudoir Mallory , Simoes Rachel , Dayarathne Nipuni , DeAngelis Kristen M. 
Published: October 2023

ABSTRACT

The complete genome sequence of
Bacillus thuringiensis
strain RC340, isolated from an environmental microbiology experiment soil sample is presented here.
B. thuringiensis
strain RC340 sequenced by GridION consists of a single genome consisting of 5.86 million bases, 8,152 predicted genes, and 0.23% contamination.
Complete genome sequences of microbacterium phages Tedro and BAjuniper
Authors: Anderson Grace M. , Anderson Olivia E. , Bosma Clayton A. , Brouwer Erin E. , DeGroot Kleyton M. , Hede Owen C. , Jonouchi Daiki , Kirkeby Dylan J. , Klinghagen Jayron T. , Kralik Kate J. , Kutz Julia S. , Lott Olivia F. , McKenney Erika J. , Pavik Victoria L. , Penner Cayli H. , Raymon Garrett , Rozeboom Leah B. , Skrien Jett L. , Slight Jessica K. , Stokes Maegan J. , Tiensvold Jonas D. , Wajer Kyra J. , Trevino Alaena L. , Noordewier Byron , Tolsma Sara S. 
Published: October 2023

ABSTRACT

We purified two novel bacteriophages from soil collected in Sioux County, Iowa: BAjuniper and Tedro. These bacteriophages were isolated from the host,
Microbacterium foliorum
. BAjuniper was assigned to cluster EB, and Tedro was assigned to cluster EF. Both phages display genomes typical of other phages in their clusters.
The novel bacteriocin romsacin from
Staphylococcus haemolyticus
inhibits Gram-positive WHO priority pathogens
Authors: Wolden Runa , Ovchinnikov Kirill V. , Venter Hermoine J. , Oftedal Thomas F. , Diep Dzung B. , Cavanagh Jorunn Pauline 
Published: October 2023

ABSTRACT

Staphylococcus haemolyticus
is an increasingly relevant nosocomial pathogen. The combination of multi-drug resistance and ability to form biofilms makes
S. haemolyticus
infections difficult to treat. Bacteriocins are ribosomally synthesized antimicrobial peptides produced by bacteria to inhibit growth of often closely related bacteria. Due to differences in the modes of action between bacteriocins and antibiotics, bacteriocins are normally equally potent against antibiotic-resistant and antibiotic-sensitive strains. To find bacteriocins able to inhibit
S. haemolyticus
and related species, clinical and commensal
S. haemolyticus
isolates (
n
= 174) were assayed for bacteriocin production. One commensal isolate produced an antimicrobial substance inhibiting
S. haemolyticus
and
Staphylococcus aureus
. The substance had physicochemical properties that are characteristic of bacteriocins. Purification, whole-genome sequencing, and mass spectrometry identified the antimicrobial as a novel two-peptide lantibiotic, hereafter named romsacin. The bacteriocin was active against a broad range of Gram-positive bacteria, such as the World Health Organization priority pathogens
S. aureus
[methicillin-resistant
S. aureus
(MRSA)] and
Enterococcus faecium
[vancomycin-resistant
E. faecium
(VRE)]. Importantly, the bacteriocin also eradicated
S. haemolyticus
,
Staphylococcus epidermidis
, MRSA, and VRE biofilms.

IMPORTANCE

Bacteria produce bacteriocins to inhibit growth of other bacterial species. We have studied the antimicrobial activity of a new bacteriocin produced by the skin bacterium
S. haemolyticus
. The bacteriocin is effective against several types of Gram-positive bacteria, including highly virulent and antibiotic-resistant strains such as
Staphylococcus aureus
and
Enterococcus faecium
. Effective antimicrobials are important for the treatment of infections and the success of major surgery and chemotherapy. Bacteriocins can be part of the solution to the global concern of antimicrobial resistance.
Machine learning to predict ceftriaxone resistance using single nucleotide polymorphisms within a global database of
Neisseria gonorrhoeae
genomes
Authors: Ha Sung Min , Lin Eric Y. , Klausner Jeffrey D. , Adamson Paul C. 
Published: October 2023

ABSTRACT

Antimicrobial resistance (AMR) in
Neisseria gonorrhoeae
is an urgent global health issue. Machine learning (ML) is a powerful tool that can aid in identifying mutations and predicting their impact on AMR. The study aimed to use ML models to predict ceftriaxone susceptibility and decreased susceptibility (S/DS). A public database of
N. gonorrhoeae
genomes with minimum inhibitory concentration (MIC) data was used to evaluate seven ML models using 97 single nucleotide polymorphisms (SNPs) known to be associated with ceftriaxone resistance. Ceftriaxone MICs ≤ 0.064 mg/L were classified as susceptible, and ceftriaxoneMICs > 0.064 mg/L were classified as DS. The contributions of individual SNPs to predict S/DS were calculated using SHapley Additive exPlanation (SHAP) values. An ML model was retrained using different combinations of SNPs with the highest SHAP values. The performance of ML models was assessed using different metrics including area under the curve (AUC) and balanced accuracy (bAcc). The ML analyses included 9,540
N
.
gonorrhoeae
genomes; 368 (0.04%) were classified as DS. Of the models evaluated, the model trained with a random forest classifier had the highest performance (AUC 0.965; bAcc 0.926). A model retrained the top five SNPs, according to SHAP values, demonstrated a similar performance (AUC 0.916; bAcc 0.879) as the model with 97 SNPs. An ML approach using mutations in
N. gonorrhoeae
can be used to predict S/DS to ceftriaxone. The results highlight a practical application of ML to identify mutations most associated with S/DS to ceftriaxone, which can aid in the development of assays to predict AMR.

IMPORTANCE

Antimicrobial resistance in
Neisseria gonorrhoeae
is an urgent global health issue. The objectives of the study were to use a global collection of 12,936
N
.
gonorrhoeae
genomes from the PathogenWatch database to evaluate different machine learning models to predict ceftriaxone susceptibility/decreased susceptibility using 97 mutations known to be associated with ceftriaxone resistance. We found the random forest classifier model had the highest performance. The analysis also reported the relative contributions of different mutations within the ML model predictions, allowing for the identification of the mutations with the highest importance for ceftriaxone resistance. A machine learning model retrained with the top five mutations performed similarly to the model using all 97 mutations. These results could aid in the development of molecular tests to detect resistance to ceftriaxone in
N. gonorrhoeae
. Moreover, this approach could be applied to building and evaluating machine learning models for predicting antimicrobial resistance in other pathogens.
Can earlier biomarker measurements explain a treatment effect on diabetes incidence? A robust comparison of five surrogate markers
Authors: Parast Layla , Tian Lu , Cai Tianxi , Palaniappan Latha P 
Published: October 2023

IntroductionWe measured and compared five individual surrogate markers—change from baseline to 1 year after randomization in hemoglobin A1c (HbA1c), fasting glucose, 2-hour postchallenge glucose, triglyceride–glucose index (TyG) index, and homeostatic model assessment of insulin resistance (HOMA-IR)—in terms of their ability to explain a treatment effect on reducing the risk of type 2 diabetes mellitus at 2, 3, and 4 years after treatment initiation.Research design and methodsStudy participants were from the Diabetes Prevention Program study, randomly assigned to either a lifestyle intervention (n=1023) or placebo (n=1030). The surrogate markers were measured at baseline and 1 year, and diabetes incidence was examined at 2, 3, and 4 years postrandomization. Surrogacy was evaluated using a robust model-free estimate of the proportion of treatment effect explained (PTE) by the surrogate marker.ResultsAcross all time points, change in fasting glucose and HOMA-IR explained higher proportions of the treatment effect than 2-hour glucose, TyG index, or HbA1c. For example, at 2 years, glucose explained the highest (80.1%) proportion of the treatment effect, followed by HOMA-IR (77.7%), 2-hour glucose (76.2%), and HbA1c (74.6%); the TyG index explained the smallest (70.3%) proportion.ConclusionsThese data suggest that, of the five examined surrogate markers, glucose and HOMA-IR were the superior surrogate markers in terms of PTE, compared with 2-hour glucose, HbA1c, and TyG index.
Exercise testing to guide safe discharge from hospital in COVID-19: a scoping review to identify candidate tests
Authors: Rhys Gwenllian Haf , Wakeling Tara , Moore Jonathan P , Subbe Christian Peter 
Published: October 2023

ObjectivesWe aimed to identify exercise tests that have been validated to support a safe discharge to home in patients with or without COVID-19.Study designScoping review, using PRISMA-ScR reporting standards. Medline, PubMed, AMED, Embase, CINAHL and LitCovid databases were searched between 16 and 22 February 2021, with studies included from any publication date up to and including the search date.InterventionShort exercise tests.Primary outcome measuresSafe discharge from hospital, readmission rate, length of hospital stay, mortality. Secondary outcomes measures: safety, feasibility and reliability.ResultsOf 1612 original records screened, 19 studies were included in the analysis. These used a variety of exercise tests in patients with chronic obstructive pulmonary disease, suspected pulmonary embolism and pneumocystis carinii pneumonia, heart failure or critical illness. Only six studies had examined patients with COVID-19, of these two were still recruiting to evaluate the 1 min sit-to-stand test and the 40-steps test. There was heterogeneity in patient populations, tests used and outcome measures. Few exercise tests have been validated to support discharge decisions. There is currently no support for short exercise tests for triage of care in patients with COVID-19.ConclusionsFurther research is needed to aid clinical decision-making at discharge from hospital.
What happens when pharmacist independent prescribers lead on medicine management in older people’s care homes: a qualitative study
Authors: Birt Linda , Dalgarno Lindsay , Poland Fiona , Wright David , Bond Christine 
Published: October 2023

ObjectiveOlder people in care homes frequently experience polypharmacy, increasing the likelihood of medicine-related burden. Pharmacists working within multidisciplinary primary care teams are ideally placed to lead on medication reviews. A randomised controlled trial placed pharmacists, with independent prescribing rights (PIPs), into older people care homes. In the intervention service, PIPs worked with general practitioners (GPs) and care home staff for 6 months, to optimise medicine management at individual resident and care home level. PIP activity included stopping medicines that were no longer needed or where potential harms outweighed benefits. This analysis of qualitative data examines health and social care stakeholders’ perceptions of how the service impacted on care home medicine procedures and resident well-being.DesignPragmatic research design with secondary analysis of interviews.SettingPrimary care pharmacist intervention in older people care homes in England, Scotland and Northern Ireland.ParticipantsRecruited from intervention arm of the trial: PIPs (n=14), GPs (n=8), care home managers (n=9) and care home staff (n=6).ResultsThere were resonances between different participant groups about potential benefits to care home residents of a medicine service provided by PIPs. There were small differences in perceptions about changes related to communication between professionals. Results are reported through three themes (1) ‘It’s a natural fit’—pharmacists undertaking medication review in care homes fitted within multidisciplinary care; (2) ‘The resident is cared for’—there were subjective improvements in residents’ well-being; (3) ‘Moving from “firefighting” to effective systems’—there was evidence of changes to care home medicine procedures.ConclusionThis study suggests that pharmacist independent prescribers in primary care working within the multidisciplinary team can manage care home residents’ medicines leading to subjective improvements in residents’ well-being and medicine management procedures. Care home staff appreciated contact with a dedicated person in the GP practice.Trial registrationISRCTN 17847169
Adolescent’s anhedonia and association with childhood trauma among Chinese adolescents: a cross-sectional study
Authors: Han Jing , Zhang Liu-hong , Zhang Cai-yi , Bi Liuna , Wang Lin-lin , Cai Yan-xiu 
Published: October 2023

ObjectivesTo estimate the level of anhedonia among adolescents and explore the association between anhedonia and childhood trauma (CT).DesignA stratified random cluster sample of adolescents participated in a survey, which included three questionnaires: Snaith-Pamilton Pleasure Scale, Childhood Trauma Questionnaire and Patient Health Questionnaire-9.SettingThe study was conducted in 60 classes in 10 primary, middle and high schools in five economically developed cities along the Southeast Coast of China from April to October 2022.ParticipantsOne thousand seven hundred and forty-five adolescents with ages ranging from 9 to 18 years participated in the study.Primary and secondary outcomesThe primary outcome was the level of anhedonia, CT and depression among adolescents. The association between anhedonia and CT was determined.ResultsThe mean scores of anhedonia, CT and depression were 24.88 (6.18), 36.75 (8.87) and 4.46 (5.36), respectively. Anhedonia scores of boys (24.24±6.12) and girls (25.62±6.16) were different (t=−4.69, p<0.01). After controlling for sex, age, the presence of siblings and depression, CT was associated with adolescent anhedonia. Emotional abuse (β=0.14), emotional neglect (β=0.15) and physical neglect (β=0.10) positively predicted adolescent anhedonia (p<0.01), whereas physical abuse negatively predicted adolescent anhedonia (β=−0.07, p<0.01). Sex had a moderating effect on the relationship between adolescent anhedonia and emotional neglect during childhood, and the negative effect of emotional neglect on adolescent anhedonia in girls was greater than in boys.ConclusionsCT, including emotional abuse, physical abuse, emotional neglect, and physical neglect, was an independent predictor of adolescents’ ability to experience pleasure in daily life. Therefore, awareness of CT should be promoted. Emotional neglect had a more severe effect on anhedonia among girls than among boys, suggesting that emotional neglect should be paid much attention among girls
Estimation of non-health gross domestic product (NHGDP) loss due to COVID-19 deaths in West Bengal, India
Authors: Bhattacharya Paramita , John Denny , Mukherjee Nirmalaya , MS Narassima , Menon Jaideep , Banerjee Amitava 
Published: October 2023

ObjectivesThe state of West Bengal witnessed a significant surge of COVID-19 in all three waves. However, there is a gap in understanding the economic loss associated with COVID-19. This study estimates future non-health gross domestic product (NHGDP) losses associated with COVID-19 deaths in West Bengal, India.SettingVarious open domains were used to gather data on COVID-19 deaths in West Bengal and the aforementioned estimates.Primary and secondary outcome measuresThe NHGDP losses were evaluated using the cost-of-illness approach. Future NHGDP losses were discounted at 3%. Excess death estimates by the WHO and Global Burden of Disease (GBD) were used. Sensitivity analysis was carried out by varying discount rates and average age of death (AAD).Results21 532 deaths in West Bengal from 17 March 2020 to 31 December 2022 decreased the future NHGDP by $0.92 billion. Nearly 90% of loss was due to deaths occurring in the age group of 30 years and above. Majority of the NHGDP loss was borne by the 46–60 years age group. NHGDP loss/death was $55,171; however, the average loss/death declined with rise in age. Based on the GBD and WHO excess death estimates, the NHGDP loss increased to $9.38 billion and $9.42 billion, respectively. When the lower age interval is considered as AAD, the NHGDP loss increased to $1.3 billion. At 5% and 10% discount rates, the losses reduced to $0.767 billion and $0.549 billion, respectively.ConclusionsResults from the study suggest that COVID-19 contributed to a major economic loss in West Bengal. The mortality and morbidity caused by COVID-19, the substantial economic costs at individual and population levels in West Bengal, and probably across India and other countries, is another economic argument for better infection control strategies across the globe to minimise the impact of COVID-19.