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Mycobacterium abscessus (Mab ) is a clinically significant pathogen and a highly genetically diverse species due to its large accessory genome. The functional consequence of this diversity remains unknown mainly because, to date, functional genomic studies in Mab have been primarily performed on reference strains. Given the growing public health threat of Mab infections, understanding the functional genomic differences among Mab clinical isolates can provide more insight into how its genetic diversity influences gene essentiality, clinically relevant phenotypes, and importantly, potential drug targets. To determine the functional genomic diversity among Mab strains, we conducted transposon-sequencing (TnSeq) on 21 genetically diverse clinical isolates, including 15 M . abscessus subsp. abscessus isolates and 6 M . abscessus subsp. massiliense isolates, cataloging all the essential and non-essential genes in each strain. Pan-genome analysis revealed a core set of 3,845 genes and a large accessory genome of 11,507. We identified 259 core essential genes across the 21 clinical isolates and 425 differentially required genes, representing ~10% of the Mab core genome. We also identified genes whose requirements were subspecies, lineage, and isolate-specific. Finally, by correlating TnSeq profiles, we identified 19 previously uncharacterized genetic networks in Mab . Altogether, we find that Mab clinical isolates are not only genetically diverse but functionally diverse as well., Importance: This study investigates the genetic diversity of Mycobacterium abscessus ( Mab ), a bacteria known for causing difficult-to-treat infections. Researchers performed transposon-sequencing (TnSeq) on 21 different clinical isolates of Mab to identify essential and non-essential genes in each strain. Through this analysis, they identified core genes required for growth across all strains. Interestingly, they also identified genes whose requirement for growth or "essentiality" were subspecies, lineage, and isolate-specific. This study reveals that Mab' s genetic diversity translates into significant functional differences among clinical isolates. Insights from this paper lay essential groundwork for future studies exploring the biological and clinical implications of genetic diversity in Mab clinical isolates. Understanding this diversity could guide targeted therapies and offer new insights into managing infections caused by Mab , a growing public health concern.

Mycobacterium abscessus is a pulmonary pathogen that exhibits intrinsic resistance to antibiotics, but the factors driving this resistance are incompletely understood. Insufficient intracellular drug accumulation could explain broad-spectrum resistance, but whether antibiotics fail to accumulate in M. abscessus and the mechanisms required for drug exclusion remain poorly understood. We measured antibiotic accumulation in M. abscessus using mass spectrometry and found a wide range of drug accumulation across clinically relevant antibiotics. Of these compounds, linezolid accumulates the least, suggesting that inadequate uptake impacts its efficacy. We utilized transposon mutagenesis screening to identify genes that cause linezolid resistance and found multiple transporters that promote membrane permeability or efflux, including an uncharacterized, M. abscessus -specific protein that effluxes linezolid and several chemically related antibiotics. This demonstrates that membrane permeability and drug efflux are critical mechanisms of antibiotic resistance in M. abscessus and suggests that targeting membrane transporters could potentiate the efficacy of certain antibiotics., Competing Interests: Declaration of Interests The authors declare no competing interests.

Proteolysis-targeting chimeras (PROTACs) represent a new therapeutic modality involving selectively directing disease-causing proteins for degradation through proteolytic systems. Our ability to exploit targeted protein degradation (TPD) for antibiotic development remains nascent due to our limited understanding of which bacterial proteins are amenable to a TPD strategy. Here, we use a genetic system to model chemically-induced proximity and degradation to screen essential proteins in Mycobacterium smegmatis (Msm), a model for the human pathogen M. tuberculosis (Mtb). By integrating experimental screening of 72 protein candidates and machine learning, we find that drug-induced proximity to the bacterial ClpC1P1P2 proteolytic complex leads to the degradation of many endogenous proteins, especially those with disordered termini. Additionally, TPD of essential Msm proteins inhibits bacterial growth and potentiates the effects of existing antimicrobial compounds. Together, our results provide biological principles to select and evaluate attractive targets for future Mtb PROTAC development, as both standalone antibiotics and potentiators of existing antibiotic efficacy., (© 2024. The Author(s).)

In this review, we synthesise the results of studies that examine how the relationships between public urban nature spaces and wellbeing vary by ethnicity in cities of the Global North. We searched for articles that reported on the relationships between public urban nature spaces, ethnicity and wellbeing. We found 65 articles that met our inclusion criteria. From our review, we found positive and negative relationships between public urban nature spaces, ethnicity and wellbeing in four interrelated domains: integration/relationship building, therapy, safety and capabilities/competency building. The findings of this review inform park management by offering twelve wellbeing pathways to design urban nature spaces that are more inclusive to all residents., (© 2023. The Author(s).)

The impact of global warming presents an increased risk to the world's shorelines. The Intergovernmental Panel on Climate Change (IPCC) reported that the twenty-first century experienced a severe global mean sea-level rise due to human-induced climate change. Therefore, coastal planners require reasonably accurate estimates of the rate of sea-level rise and the potential impacts, including extreme sea-level changes, floods, and shoreline erosion. Also, land loss as a result of disturbance of shoreline is of interest as it damages properties and infrastructure. Using a nonlinear autoregressive network with an exogenous input (NARX) model, this study attempted to simulate (1991 to 2012) and predict (2013-2020) sea-level change along Merang kechil to Kuala Marang in Terengganu state shoreline areas. The simulation results show a rising trend with a maximum rate of 28.73 mm/year and an average of about 8.81 mm/year. In comparison, the prediction results show a rising sea level with a maximum rate of 79.26 mm/year and an average of about 25.34 mm/year. The database generated from this study can be used to inform shoreline defense strategies adapting to sea-level rise, flood, and erosion. Scientists can forecast sea-level increases beyond 2020 using simulated sea-level data up to 2020 and apply it for future research. The data also helps decision-makers choose measures for vulnerable shoreline settlements to adapt to sea-level rise. Notably, the data will provide essential information for policy development and implementation to facilitate operational decision-making processes for coastal cities., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Background: Nontuberculous mycobacteria are water-avid pathogens that are associated with nosocomial infections., Objective: To describe the analysis and mitigation of a cluster of Mycobacterium abscessus infections in cardiac surgery patients., Design: Descriptive study., Setting: Brigham and Women's Hospital, Boston, Massachusetts., Participants: Four cardiac surgery patients., Intervention: Commonalities among cases were sought, potential sources were cultured, patient and environmental specimens were sequenced, and possible sources were abated., Measurements: Description of the cluster, investigation, and mitigation., Results: Whole-genome sequencing confirmed homology among clinical isolates. Patients were admitted during different periods to different rooms but on the same floor. There were no common operating rooms, ventilators, heater-cooler devices, or dialysis machines. Environmental cultures were notable for heavy mycobacterial growth in ice and water machines on the cluster unit but little or no growth in ice and water machines in the hospital's other 2 inpatient towers or in shower and sink faucet water in any of the hospital's 3 inpatient towers. Whole-genome sequencing confirmed the presence of a genetically identical element in ice and water machine and patient specimens. Investigation of the plumbing system revealed a commercial water purifier with charcoal filters and an ultraviolet irradiation unit leading to the ice and water machines in the cluster tower but not the hospital's other inpatient towers. Chlorine was present at normal levels in municipal source water but was undetectable downstream from the purification unit. There were no further cases after high-risk patients were switched to sterile and distilled water, ice and water machine maintenance was intensified, and the commercial purification system was decommissioned., Limitation: Transmission pathways were not clearly characterized., Conclusion: Well-intentioned efforts to modify water management systems may inadvertently increase infection risk for vulnerable patients., Primary Funding Source: National Institutes of Health.

Mycobacterium abscessus is an emerging pathogen causing lung infection predominantly in patients with underlying structural abnormalities or lung disease and is resistant to most frontline antibiotics. As the pathogenic mechanisms of M. abscessus in the context of the lung are not well-understood, we developed an infection model using air-liquid interface culture and performed a transposon mutagenesis and sequencing screen to identify genes differentially required for bacterial survival in the lung. Biotin cofactor synthesis was required for M. abscessus growth due to increased intracellular biotin demand, while pharmacological inhibition of biotin synthesis prevented bacterial proliferation. Biotin was required for fatty acid remodelling, which increased cell envelope fluidity and promoted M. abscessus survival in the alkaline lung environment. Together, these results indicate that biotin-dependent fatty acid remodelling plays a critical role in pathogenic adaptation to the lung niche, suggesting that biotin synthesis and fatty acid metabolism might provide therapeutic targets for treatment of M. abscessus infection., (© 2023. The Author(s), under exclusive licence to Springer Nature Limited.)

Mycobacterium abscessus ( Mab ) is a rapidly growing non-tuberculous mycobacterium (NTM) that causes a wide range of infections. Treatment of Mab infections is difficult because the bacterium is intrinsically resistant to many classes of antibiotics. Developing new and effective treatments against Mab requires a better understanding of the unique vulnerabilities that can be targeted for future drug development. To achieve this, we identified essential genes in Mab by conducting transposon sequencing (TnSeq) on the reference Mab strain ATCC 19977. We generated ~51,000 unique transposon mutants and used this high-density library to identify 362 essential genes for in vitro growth. To investigate species-specific vulnerabilities in Mab , we further characterized MAB_3167c , a predicted penicillin-binding protein and hypothetical lipoprotein (PBP-lipo) that is essential in Mab and non-essential in Mycobacterium tuberculosis ( Mtb ). We found that PBP-lipo primarily localizes to the subpolar region and later to the septum as cells prepare to divide. Depletion of Mab PBP-lipo causes cells to elongate, develop ectopic branches, and form multiple septa. Knockdown of PBP-lipo along with PbpB, DacB1, and a carboxypeptidase, MAB_0519 lead to synergistic growth arrest. In contrast, these genetic interactions were absent in the Mtb model organism, Mycobacterium smegmatis , indicating that the PBP-lipo homologs in the two species exist in distinct genetic networks. Finally, repressing PBP-lipo sensitized the reference strain and 11 Mab clinical isolates to several classes of antibiotics, including the β-lactams, ampicillin, and amoxicillin by greater than 128-fold. Altogether, this study presents PBP-lipo as a key enzyme to study Mab -specific processes in cell wall synthesis and importantly positions PBP-lipo as an attractive drug target to treat Mab infections., Competing Interests: CA, BB, JZ, IW, SS, CD, TI, ER No competing interests declared, (© 2022, Akusobi et al.)

Although prokaryotic organisms lack traditional organelles, they must still organize cellular structures in space and time, challenges that different species solve differently. To systematically define the subcellular architecture of mycobacteria, we perform high-throughput imaging of a library of fluorescently tagged proteins expressed in Mycobacterium smegmatis and develop a customized computational pipeline, MOMIA and GEMATRIA, to analyze these data. Our results establish a spatial organization network of over 700 conserved mycobacterial proteins and reveal a coherent localization pattern for many proteins of known function, including those in translation, energy metabolism, cell growth and division, as well as proteins of unknown function. Furthermore, our pipeline exploits morphologic proxies to enable a pseudo-temporal approximation of protein localization and identifies previously uncharacterized cell-cycle-dependent dynamics of essential mycobacterial proteins. Collectively, these data provide a systems perspective on the subcellular organization of mycobacteria and provide tools for the analysis of bacteria with non-standard growth characteristics., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2021 The Author(s). Published by Elsevier Inc. All rights reserved.)

Functional characterization of bacterial proteins lags far behind the identification of new protein families. This is especially true for bacterial species that are more difficult to grow and genetically manipulate than model systems such as Escherichia coli and Bacillus subtilis To facilitate functional characterization of mycobacterial proteins, we have established a Mycobacterial Systems Resource (MSR) using the model organism Mycobacterium smegmatis This resource focuses specifically on 1,153 highly conserved core genes that are common to many mycobacterial species, including Mycobacterium tuberculosis , in order to provide the most relevant information and resources for the mycobacterial research community. The MSR includes both biological and bioinformatic resources. The biological resource includes (i) an expression plasmid library of 1,116 genes fused to a fluorescent protein for determining protein localization; (ii) a library of 569 precise deletions of nonessential genes; and (iii) a set of 843 CRISPR-interference (CRISPRi) plasmids specifically targeted to silence expression of essential core genes and genes for which a precise deletion was not obtained. The bioinformatic resource includes information about individual genes and a detailed assessment of protein localization. We anticipate that integration of these initial functional analyses and the availability of the biological resource will facilitate studies of these core proteins in many Mycobacterium species, including the less experimentally tractable pathogens M. abscessus , M. avium , M. kansasii , M. leprae , M. marinum , M. tuberculosis , and M. ulcerans IMPORTANCE Diseases caused by mycobacterial species result in millions of deaths per year globally, and present a substantial health and economic burden, especially in immunocompromised patients. Difficulties inherent in working with mycobacterial pathogens have hampered the development and application of high-throughput genetics that can inform genome annotations and subsequent functional assays. To facilitate mycobacterial research, we have created a biological and bioinformatic resource (https://msrdb.org/) using Mycobacterium smegmatis as a model organism. The resource focuses specifically on 1,153 proteins that are highly conserved across the mycobacterial genus and, therefore, likely perform conserved mycobacterial core functions. Thus, functional insights from the MSR will apply to all mycobacterial species. We believe that the availability of this mycobacterial systems resource will accelerate research throughout the mycobacterial research community., (Copyright © 2021 Judd et al.)

The recalcitrance of mycobacteria to antibiotic therapy is in part due to its ability to build proteins into a multi-layer cell wall. Proper synthesis of both cell wall constituents and associated proteins is crucial to maintaining cell integrity, and intimately tied to antibiotic susceptibility. How mycobacteria properly synthesize the membrane-associated proteome, however, remains poorly understood. Recently, we found that loss of lepA in Mycobacterium smegmatis (Msm) altered tolerance to rifampin, a drug that targets a non-ribosomal cellular process. LepA is a ribosome-associated GTPase found in bacteria, mitochondria, and chloroplasts, yet its physiological contribution to cellular processes is not clear. To uncover the determinants of LepA-mediated drug tolerance, we characterized the whole-cell proteomes and transcriptomes of a lepA deletion mutant relative to strains with lepA We find that LepA is important for the steady-state abundance of a number of membrane-associated proteins, including an outer membrane porin, MspA, which is integral to nutrient uptake and drug susceptibility. Loss of LepA leads to a decreased amount of porin in the membrane which leads to the drug tolerance phenotype of the lepA mutant. In mycobacteria, the translation factor LepA modulates mycobacterial membrane homeostasis, which in turn affects antibiotic tolerance. Importance The mycobacterial cell wall is a promising target for new antibiotics due to the abundance of important membrane-associated proteins. Defining mechanisms of synthesis of the membrane proteome will be critical to uncovering and validating drug targets. We found that LepA, a universally conserved translation factor, controls the synthesis of a number of major membrane proteins in M. smegmatis LepA primarily controls synthesis of the major porin MspA. Loss of LepA results in decreased permeability through the loss of this porin, including permeability to antibiotics like rifampin and vancomycin. In mycobacteria, regulation from the ribosome is critical for the maintenance of membrane homeostasis and, importantly, antibiotic susceptibility., (Copyright © 2020 American Society for Microbiology.)

Genomic dissection of antibiotic resistance in bacterial pathogens has largely focused on genetic changes conferring growth above a single critical concentration of drug. However, reduced susceptibility to antibiotics-even below this breakpoint-is associated with poor treatment outcomes in the clinic, including in tuberculosis. Clinical strains of Mycobacterium tuberculosis exhibit extensive quantitative variation in antibiotic susceptibility but the genetic basis behind this spectrum of drug susceptibility remains ill-defined. Through a genome wide association study, we show that non-synonymous mutations in dnaA, which encodes an essential and highly conserved regulator of DNA replication, are associated with drug resistance in clinical M. tuberculosis strains. We demonstrate that these dnaA mutations specifically enhance M. tuberculosis survival during isoniazid treatment via reduced expression of katG, the activator of isoniazid. To identify DnaA interactors relevant to this phenotype, we perform the first genome-wide biochemical mapping of DnaA binding sites in mycobacteria which reveals a DnaA interaction site that is the target of recurrent mutation in clinical strains. Reconstructing clinically prevalent mutations in this DnaA interaction site reproduces the phenotypes of dnaA mutants, suggesting that clinical strains of M. tuberculosis have evolved mutations in a previously uncharacterized DnaA pathway that quantitatively increases resistance to the key first-line antibiotic isoniazid. Discovering genetic mechanisms that reduce drug susceptibility and support the evolution of high-level drug resistance will guide development of biomarkers capable of prospectively identifying patients at risk of treatment failure in the clinic., Competing Interests: The authors have declared that no competing interests exist.

Vegetation communities along recreational tracks may suffer from substantial edge-effects through the impacts of trampling, modified environmental conditions and competition with species that benefit from disturbance. We assessed impacts on trackside vegetation by comparing high and low usage tourism sites at a 1-10 m distance from recreational tracks in a popular arid-lands tourism destination in South Australia. The central aim was quantification of the strengths and spatial extent of tourism impacts along recreational tracks with a qualitative comparison of roads and trails. Track-distance gradients were most prevalent at high usage sites. There, species community composition was altered, total plant cover decreased, non-native species cover increased, plant diversity increased or decreased (depending on the distance) and soil compaction increased towards recreational tracks. Roadside effects were greater and more pervasive than trailside effects. Further, plant diversity did not continuously increase towards the road verge as it did along trails but dropped sharply in the immediate road shoulder which indicated high disturbance conditions that few species were able to tolerate. To our knowledge, we are the first to demonstrate that the access mode to a recreation site influences the potential of certain impacts, such as the increase of non-native species, to self-perpetuate from their points of introduction to disjointed sites with a predisposition to disturbance. Due to this propulsion of impacts, the overall spatial extent of roadside impacts was far greater than initially apparent from assessments at the road verge. We discuss possible means of mitigating these impacts., (Copyright © 2014 Elsevier Ltd. All rights reserved.)

Bird communities inhabiting ecosystems adjacent to recreational tracks may be adversely affected by disturbance from passing tourism traffic, vehicle-related mortality, habitat alteration and modified biotic relationships such as the increase of strong competitors. This study investigated the effects of tourist usage of roads vs. hiking trails on bird communities in gorges of the Flinders Ranges, a popular South Australian tourist destination in the arid-lands. High tourist usage along roads decreased the individual abundance and species richness of birds relative to low usage trails. The decrease in species richness, though less pronounced, also occurred at high-usage sites along trails. Changes in the species response to recreational disturbance/impacts varied depending on the ecology of the species. Bigger, more competitive birds with a generalist diet were overrepresented at high-usage sites along roads and trails. Species using microhabitats in lower vegetation layers were more sensitive. However, structural and floristic complexity of vegetation was a more important factor influencing bird abundance than tourist usage. Sites with a better developed shrub and tree layer sustained higher species abundance and richer communities. Importantly, vegetation qualities moderated the negative effect of high usage on the individual abundance of birds along roads, to the extent that such an effect was absent at sites with the best developed shrub and tree layer. To protect avifauna along recreational tracks in arid-lands gorges, we recommend the closure of some gorges or sections for vehicle or any access. Further, open space particularly for camping needs to be minimized as it creates areas of high tourist usage with modified habitat that provides birds with little buffer from disturbance., (Copyright © 2013 Elsevier Ltd. All rights reserved.)

Diel vertical migration (DVM) of herbivorous zooplankton is a widespread behavioural phenomenon in freshwater ecosystems. So far only little attention has been paid to the impact of DVM on the phytoplankton community in the epilimnion. Some theoretical models predict that algal population growth in the epilimnion should depend on the herbivores' migration and grazing patterns: even if migrating zooplankton consume the same total amount of algae per day in the epilimnion as non-migrating zooplankton, nocturnal grazing should result in enhanced algal growth and favour algal species with high intrinsic growth rates over species with lower intrinsic growth rates. To test these hypotheses we performed experiments in which several algal species were confronted with different feeding regimes of Daphnia. In the experiments algal growth did not only depend on the absolute time of grazing but was comparatively higher when grazing took place only during the night, even when the grazing pressure was the same. Furthermore, algal species with higher intrinsic growth rates had higher advantages when being grazed upon only discontinuously during the night than algal species with a smaller intrinsic growth rate. The grazing pattern itself was an important factor for relative algal performance.

In order to investigate whether cholesterol intake influences the hepatic copper content of rabbits, we compared the hepatic copper content of two rabbit inbred strains after feeding the animals a control or a cholesterol-rich diet. One strain was not reactive to dietary cholesterol (IIIVO/JU), whereas the other strain was reactive to dietary cholesterol (AX/JU). The coefficient of inbreeding (F) >0.95 for both strains. Dietary cholesterol-reactive rabbits when compared with their non-reactive counterparts had a higher hepatic copper content. The consumption of a hypercholesterolemic diet decreased liver copper concentration (expressed in micro g/g dry weight) in both strains of rabbits, which was (in part) due to dietary-induced hepatomegaly. A decrease in the absolute hepatic copper content was found only in the dietary cholesterol-reactive inbred strain. It is discussed that differences in glucocorticoid levels may be responsible for the strain difference in liver copper content. The cholesterol effect on the hepatic copper content in the reactive strain might be caused by an increased bilirubin secretion.

Significant differences in liver copper content have been observed between rat inbred strains. To define loci controlling this trait, the offspring (n = 190) from an (LEW/OlaHsd x BC/CpbU) F(2)-intercross was genetically analyzed. From each F(2) animal, liver copper content was determined and genomic DNA was screened with polymorphic DNA markers. We found a major quantitative trait locus (QTL) for liver copper content in females on chromosome 2 and in males on chromosome 10. Both QTLs accounted for approximately 20% of the genetic variance. In addition, suggestive linkage for liver copper content was found on rat chromosomes 1, 8, 10, 12, 14, and 19. The regions on these chromosomes contain genes that are responsible for 9.0-15.5% of the genetic variance of liver copper content.

Thirty recombinant inbred (RI) strains derived from the spontaneous hypertensive rat (SHR/OlaIpcv) and the Brown Norway (BN-Lx/Cub) progenitors were used to search for quantitative trait loci (QTLs) that are responsible for differences in liver copper between these two strains. The heritability of liver copper concentration (expressed as microg/g liver wet wt and microg/g liver dry wt) and liver copper store (microg/whole liver) was estimated to be 57, 57, and 46%, respectively. In a total genome scan of the RI strains, involving over 600 genetic markers, suggestive association was found between liver copper store (microg/whole liver) and the D16Wox9 marker on chromosome 16 (lod score = 2.8), and between liver copper concentration (microg/g dry wt) and the D10Cebrp1016s2 marker on chromosome 10 (lod score = 3.0). These putative QTLs are responsible for nearly 34 and 40% of the additive genetic variability for liver copper store and concentration, respectively.

A systematic approach to analyzing food preservation - food preparation recipes for potential hazards is presented. The method is based on the Hazard Analysis Critical Control Point (HACCP) concept developed by the food processing industry for identifying potential hazards in processing. The Recipe Hazard Analysis System (RHAS) is used to identify potential hazards in several recipes. Worksheets and the method of analysis are given.