bluuebunny/crossref_metadata_2025_split huggingface dataset:
Perturbations to common gardens of anaerobic co-digesters reveal relationships between functional resilience and microbial community composition
Authors: Wang Ling , Ducoste Joel J. , de los Reyes Francis L. 
Published: August 2024

ABSTRACT

We report the relationship between enrichment of adapted populations and enhancement of community functional resilience in methanogenic bioreactors. Although previous studies have shown the positive effects of acclimation, this work directly investigated the relationships between microbiome dynamics and performance of anaerobic co-digesting reactors in response to different levels of an environmental perturbation (loading of grease interceptor waste [GIW]). Using the methanogenic microbiome from a full-scale digester, we developed eight sets of microbial communities in triplicate using different feed sources. These substrate-specific microbiomes were then exposed to three independent disturbance events of low-, mid- and high-GIW loading rates. This approach allowed us to directly attribute differences in community responses to differences in community composition. Despite identical inocula, environment (digester operation, substrate loading rate, and feeding patterns) and general whole-community function (methane production and effluent quality) during the cultivation period, different substrates led to different microbial community assemblies. Lipid pre-acclimation led to enrichment of a pool of specialized populations, along with thriving of sub-dominant communities. The enrichment of these populations improved functional resilience and process performance when exposed to a low level of lipid-rich perturbation compared with less-acclimated communities. At higher levels of perturbation, the communities were not able to recover methanogenesis, indicating a loading limit to the resilience response. This study extends our current understanding of environmental perturbations, feed-specific adaptation, and functional resilience in methanogenic bioreactors.

IMPORTANCE
This study demonstrates, for the first time for GIW co-digestion, how applying similar perturbations to different microbial communities was used to directly identify the causal relationships between microbial community, function, and environment in triplicate anaerobic microbiomes. We evaluated the impact of feed-specific adaptation on methanogenic microbiomes and demonstrated how microbiomes can be influenced to improve their functional (methanogenic) resilience to GIW inhibition. These findings demonstrate how an ecological framework can help improve a biological engineering application, and more specifically, increase the potential of anaerobic co-digestion for converting wastes to energy.
A pangenomic atlas reveals eco-evolutionary dynamics that shape type VI secretion systems in plant-pathogenic
Ralstonia
Authors: Aoun Nathalie , Georgoulis Stratton J. , Avalos Jason K. , Grulla Kimberly J. , Miqueo Kasey , Tom Cloe , Lowe-Power Tiffany M. 
Published: August 2024

ABSTRACT

Soilborne
Ralstonia solanacearum
species complex (RSSC) pathogens disrupt microbial communities as they invade roots and fatally wilt plants. RSSC pathogens secrete antimicrobial toxins using a type VI secretion system (T6SS). To investigate how evolution and ecology have shaped the T6SS of these bacterial pathogens, we analyzed the T6SS gene content and architecture across the RSSC and their evolutionary relatives. Our analysis reveals that two ecologically similar Burkholderiaceae taxa, xylem-pathogenic RSSC and
Paracidovorax
, have convergently evolved to wield large arsenals of T6SS toxins. To understand the mechanisms underlying genomic enrichment of T6SS toxins, we compiled an atlas of 1,066 auxiliary T6SS toxin clusters (“
aux
” clusters) across 99 high-quality RSSC genomes. We classified 25 types of
aux
clusters with toxins that predominantly target lipids, nucleic acids, or unknown cellular substrates. The
aux
clusters were located in diverse genetic neighborhoods and had complex phylogenetic distributions, suggesting frequent horizontal gene flow. Phages and other mobile genetic elements account for most of the
aux
cluster acquisition on the chromosome but very little on the megaplasmid. Nevertheless, RSSC genomes were more enriched in
aux
clusters on the megaplasmid. Although the single, ancestral T6SS was broadly conserved in the RSSC, the T6SS has been convergently lost in atypical, non-soilborne lineages. Overall, our data suggest dynamic interplay between the lifestyle of RSSC lineages and the evolution of T6SSes with robust arsenals of toxins. This pangenomic atlas poises the RSSC as an emerging, tractable model to understand the role of the T6SS in shaping pathogen populations.

IMPORTANCE

We explored the eco-evolutionary dynamics that shape the inter-microbial warfare mechanisms of a globally significant plant pathogen, the
Ralstonia solanacearum
species complex. We discovered that most
Ralstonia
wilt pathogens have evolved extensive and diverse repertoires of type VI secretion system-associated antimicrobial toxins. These expansive toxin arsenals potentially enhance the ability of
Ralstonia
pathogens to invade plant microbiomes, enabling them to rapidly colonize and kill their host plants. We devised a classification system to categorize the
Ralstonia
toxins. Interestingly, many of the toxin gene clusters are encoded on mobile genetic elements, including prophages, which may be mutualistic symbionts that enhance the inter-microbial competitiveness of
Ralstonia
wilt pathogens. Moreover, our findings suggest that the convergent loss of this multi-gene trait contributes to genome reduction in two vector-transmitted lineages of
Ralstonia
pathogens. Our findings demonstrate that the interplay between microbial ecology and pathogen lifestyle shapes the evolution of a genetically complex antimicrobial weapon.
Regulation of bacterial stringent response by an evolutionarily conserved ribosomal protein L11 methylation
Authors: Walukiewicz Hanna E. , Farris Yuliya , Burnet Meagan C. , Feid Sarah C. , You Youngki , Kim Hyeyoon , Bank Thomas , Christensen David , Payne Samuel H. , Wolfe Alan J. , Rao Christopher V. , Nakayasu Ernesto S. 
Published: August 2024

ABSTRACT

Lysine and arginine methylation is an important regulator of enzyme activity and transcription in eukaryotes. However, little is known about this covalent modification in bacteria. In this work, we investigated the role of methylation in bacteria. By reanalyzing a large phyloproteomics data set from 48 bacterial strains representing six phyla, we found that almost a quarter of the bacterial proteome is methylated. Many of these methylated proteins are conserved across diverse bacterial lineages, including those involved in central carbon metabolism and translation. Among the proteins with the most conserved methylation sites is ribosomal protein L11 (bL11). bL11 methylation has been a mystery for five decades, as the deletion of its methyltransferase PrmA causes no cell growth defects. Comparative proteomics analysis combined with inorganic polyphosphate and guanosine tetra/pentaphosphate assays of the
ΔprmA
mutant in
Escherichia coli
revealed that bL11 methylation is important for stringent response signaling. In the stationary phase, we found that the
ΔprmA
mutant has impaired guanosine tetra/pentaphosphate production. This leads to a reduction in inorganic polyphosphate levels, accumulation of RNA and ribosomal proteins, and an abnormal polysome profile. Overall, our investigation demonstrates that the evolutionarily conserved bL11 methylation is important for stringent response signaling and ribosomal activity regulation and turnover.

IMPORTANCE
Protein methylation in bacteria was first identified over 60 years ago. Since then, its functional role has been identified for only a few proteins. To better understand the functional role of methylation in bacteria, we analyzed a large phyloproteomics data set encompassing 48 diverse bacteria. Our analysis revealed that ribosomal proteins are often methylated at conserved residues, suggesting that methylation of these sites may have a functional role in translation. Further analysis revealed that methylation of ribosomal protein L11 is important for stringent response signaling and ribosomal homeostasis.
Malassezia responds to environmental pH signals through the conserved Rim/Pal pathway
Authors: Pianalto Kaila M. , Telzrow Calla L. , Brown Harding Hannah , Brooks Jacob T. , Granek Joshua A. , Gushiken-Ibañez Eduardo , LeibundGut-Landmann Salomé , Heitman Joseph , Ianiri Giuseppe , Alspaugh J. Andrew 
Published: August 2024

ABSTRACT

During mammalian colonization and infection, microorganisms must be able to rapidly sense and adapt to changing environmental conditions including alterations in extracellular pH. The fungus-specific Rim/Pal signaling pathway is one process that supports microbial adaptation to alkaline pH. This cascading series of interacting proteins terminates in the proteolytic activation of the highly conserved Rim101/PacC protein, a transcription factor that mediates microbial responses that favor survival in neutral/alkaline pH growth conditions, including many mammalian tissues. We identified the putative Rim pathway proteins Rim101 and Rra1 in the human skin colonizing fungus
Malassezia sympodialis
. Gene deletion by transconjugation and homologous recombination revealed that Rim101 and Rra1 are required for
M. sympodialis
growth at higher pH. In addition, comparative transcriptional analysis of the mutant strains compared to wild-type suggested mechanisms for fungal adaptation to alkaline conditions. These pH-sensing signaling proteins are required for optimal growth in a murine model of atopic dermatitis, a pathological condition associated with increased skin pH. Together, these data elucidate both conserved and phylum-specific features of microbial adaptation to extracellular stresses.

IMPORTANCE

The ability to adapt to host pH has been previously associated with microbial virulence in several pathogenic fungal species. Here we demonstrate that a fungal-specific alkaline response pathway is conserved in the human skin commensal fungus
Malassezia sympodialis
(
Ms
). This pathway is characterized by the pH-dependent activation of the Rim101/PacC transcription factor that controls cell surface adaptations to changing environmental conditions. By disrupting genes encoding two predicted components of this pathway, we demonstrated that the Rim/Pal pathway is conserved in this fungal species as a facilitator of alkaline pH growth. Moreover, targeted gene mutation and comparative transcriptional analysis support the role of the
Ms
Rra1 protein as a cell surface pH sensor conserved within the basidiomycete fungi, a group including plant and human pathogens. Using an animal model of atopic dermatitis, we demonstrate the importance of
Ms
Rim/Pal signaling in this common inflammatory condition characterized by increased skin pH.
Draft genome sequence of the fungal biocontrol agent,
Bacillus velezensis
Kos
Authors: Clarke Joy , Kosanovic Dejana , Kavanagh Kevin , Grogan Helen , Fitzpatrick David A. 
Published: August 2024

ABSTRACT

Here, we report the draft genome sequence of
Bacillus velezensis
strain Kos, isolated from casing soil used during
Agaricus bisporus
cultivation in Dublin, Ireland.
B. velezensis
Kos exhibits a suppressive ability toward
Cladobotryum mycophilum
,
Trichoderma aggressivum
, and
Lecanicillium fungicola
, which are common threats to
A. bisporus
production, cultivation, and quality.
Gut microbiota metabolically mediate intestinal helminth infection in zebrafish
Authors: Hammer Austin J. , Gaulke Christopher A. , Garcia-Jaramillo Manuel , Leong Connor , Morre Jeffrey , Sieler Jr. Michael J. , Stevens Jan F. , Jiang Yuan , Maier Claudia S. , Kent Michael L. , Sharpton Thomas J. 
Published: August 2024

ABSTRACT

Intestinal helminth parasite (IHP) infection induces alterations in the composition of microbial communities across vertebrates, although how gut microbiota may facilitate or hinder parasite infection remains poorly defined. In this work, we utilized a zebrafish model to investigate the relationship between gut microbiota, gut metabolites, and IHP infection. We found that extreme disparity in zebrafish parasite infection burden is linked to the composition of the gut microbiome and that changes in the gut microbiome are associated with variation in a class of endogenously produced signaling compounds, N-acylethanolamines, that are known to be involved in parasite infection. Using a statistical mediation analysis, we uncovered a set of gut microbes whose relative abundance explains the association between gut metabolites and infection outcomes. Experimental investigation of one of the compounds in this analysis reveals salicylaldehyde, which is putatively produced by the gut microbe
Pelomonas
, as a potent anthelmintic with activity against
Pseudocapillaria tomentosa
egg hatching, both
in vitro
and
in vivo
. Collectively, our findings underscore the importance of the gut microbiome as a mediating agent in parasitic infection and highlight specific gut metabolites as tools for the advancement of novel therapeutic interventions against IHP infection.

IMPORTANCE
Intestinal helminth parasites (IHPs) impact human health globally and interfere with animal health and agricultural productivity. While anthelmintics are critical to controlling parasite infections, their efficacy is increasingly compromised by drug resistance. Recent investigations suggest the gut microbiome might mediate helminth infection dynamics. So, identifying how gut microbes interact with parasites could yield new therapeutic targets for infection prevention and management. We conducted a study using a zebrafish model of parasitic infection to identify routes by which gut microbes might impact helminth infection outcomes. Our research linked the gut microbiome to both parasite infection and to metabolites in the gut to understand how microbes could alter parasite infection. We identified a metabolite in the gut, salicylaldehyde, that is putatively produced by a gut microbe and that inhibits parasitic egg growth. Our results also point to a class of compounds, N-acyl-ethanolamines, which are affected by changes in the gut microbiome and are linked to parasite infection. Collectively, our results indicate the gut microbiome may be a source of novel anthelmintics that can be harnessed to control IHPs.
Repeated radiological procedures in the last 6 months of life in old age: a retrospective study
Authors: Hawkins Joseph , Beardsmore-Rust Sam , Adra Myra , Halford Zoe 
Published: August 2024

ObjectivesThis novel study looks at the use of radiological procedures in an elderly cohort of patients in their last 6 months of life. Radiological imaging plays a central part of clinical investigations, but too many may override the judgement of benefits, risks and resources. There is little information on the burden of radiological procedures performed towards the end of life in patients of old age.MethodsData from every fourth patient aged 80 years and over who died between 4 July 2021 and 30 December 2021 in a National Health Service (NHS) hospital were collected. All radiological procedures performed within the last 6 months of the patients’ life were recorded from clinical documentation and related to their age.Results96 patients were studied with a total of 699 radiological procedures performed. When scaled up, costs of CT and MRI scans alone are conservatively estimated as £312 000/annum in patients aged ≥80 years in their last 6 months of life for a single medium-sized NHS hospital.ConclusionsA very large number of radiological procedures were performed towards the end of life among patients of old age. This is consistent with the national trend of increased medicalisation and poor recognition of dying.
The impact of tobacco tax increases on cost-minimising behaviours and subsequent smoking cessation in Australia: an analysis of the International Tobacco Control Policy Evaluation Project
Authors: Cho Ara , Scollo Michelle , Chan Gary , Driezen Pete , Hyland Andrew , Shang Ce , Gartner Coral E 
Published: August 2024

ObjectiveWe examined the relationship in Australia from 2007 to 2020 between tobacco tax increases and use of cost-minimising behaviours (CMBs) when purchasing tobacco and: (1) tobacco expenditure and (2) smoking cessation attempts and quit success.MethodsWe used data collected from adults who smoked factory-made and/or roll-your-own (RYO) cigarettes in nine waves (2007–2020) of the International Tobacco Control Policy Evaluation Project Australia Survey (Nsample=4975, Nobservations=10 474). CMBs included buying RYO tobacco, cartons, large-sized packs, economy packs, or tax avoidance/evasion, smoking reduction and e-cigarette use. Logistic regression, fit using generalised estimating equations, estimated the CMB-outcome association for quit attempts and quit success at the next wave follow-up (Nsubsample=2984, Nobservations=6843).ResultsOver half of respondents used a CMB for tobacco purchase (P-CMB) at baseline (57.1% in 2007–2008), increasing to 76.8% (2018) post-tax increases. Participating in any P-CMB was associated with having higher weekly tobacco expenditure. Engaging in any P-CMB was negatively associated with attempting to quit (aOR=0.82, 95% CI 0.69–0.98). Purchasing RYO tobacco or cartons was associated with making no quit attempts (aOR=0.66, 95% CI 0.52–0.83; aOR=0.72, 95% CI 0.59–0.89, respectively). Among respondents smoking cigarettes who made quit attempts, there were no significant associations between all P-CMBs and quit success. Neither smoking reduction nor vaping were significantly associated with quit attempts.ConclusionP-CMBs are associated with reduced smoking cessation. Reducing opportunities for industry to promote purchasing-related CMB options, such as by standardising pack sizes and reducing the price differential between RYO and manufactured cigarettes could increase the effectiveness of tax increases.
Burrow nests fall below critical temperatures of threatened seabirds but offer thermal refuge during extreme cold events
Authors: Richards Cerren , Collins Sydney M. , Fisher Kayla , Blackmore Robert J. , Fifield David A. , Bates Amanda E. 
Published: August 2024

Climate change is altering the severity and intensity of extreme weather events. Occupying microhabitats that buffer extreme weather may help species avoid harsh environmental conditions. We describe the thermal microclimate of Atlantic Puffin ( Fratercula arctica) and Leach’s Storm-petrel ( Hydrobates leucorhous) burrows and quantify whether burrows are thermal refuges during extreme cold weather events. We further test for the effect of weather conditions and burrow characteristics on nest microclimate and buffering capacity during extreme cold weather. We find that both species actively breed in burrow microclimates that are below their lower critical temperatures, which may impose significant thermoregulatory costs. However, burrows do act as thermal refuges because nests are kept 7.4–8.0 °C warmer than ambient temperatures during extreme cold weather events. Overall, external temperature and wind speed were strong drivers of burrow temperature, but burrow and habitat characteristics did not explain the variability in burrow buffering capacity during extreme cold weather. Our results suggest that burrows may provide a direct line of defence for seabird chicks against cold events. Given the complex responses of burrow microclimates to extreme events, quantifying how changes in environmental conditions will impact burrow-nesting seabirds in the future is key.
The exact relativistic scalar quasibound states of the dyonic Kerr–Sen black hole: quantized energy, and Hawking radiation
Authors: Senjaya David , Burikham Piyabut , Harko Tiberiu 
Published: August 2024

AbstractWe consider Klein–Gordon equation in the Dyonic Kerr–Sen black hole background, which is the charged rotating axially symmetric solution of the Einstein–Maxwell–Dilaton–Axion theory of gravity. The black hole incorporates electric, magnetic, dilatonic and axionic charges and is constructed in 3+1 dimensional spacetime. We begin our investigations with the construction of the scalar field’s governing equation, i.e., the covariant Klein–Gordon equation. With the help of the ansatz of separation of variables, we successfully separate the polar part, and find the exact solution in terms of Spheroidal Harmonics, while the radial exact solution is obtained in terms of the Confluent Heun function. The quantization of the quasibound state is done by applying the polynomial condition of the Confluent Heun function that gives rise to discrete complex-valued energy levels for massive scalar fields. The real part is the scalar field relativistic quantized energy, while the imaginary part represents the quasibound states’s decay. We present all of the sixteen possible exact energy solutions for both massive and massless scalars. We also present the investigation the Hawking radiation of the Dyonic Kerr–Sen black hole’s apparent horizon, via the Sigurd–Sannan method by making use of the obtained exact scalar wave functions. The radiation distribution function, and the Hawking temperature are also obtained.
Gaussian quantum steering for continuous variables sharing in an expanding universe
Authors: Wu Hengyu , Gong Xiaolong , Liu Tonghua , Wu Shu-Min 
Published: August 2024

AbstractRealistic quantum systems are affected by the expanding universe in their preparation and quantum information processing. In this paper, we study the relationship between the Gaussian quantum steering distribution and the parameters of the expanding universe. The expansion process of the universe can be described as a channel acting on a two-mode squeezed Gaussian state, with the evolution of quantum steering from the asymptotic past to the asymptotic future resulting in new distributions parameterized by cosmic parameters. We find that Gaussian quantum steering is more sensitive to the volume change of the expanding universe than the expansion rate, and the Gaussian quantum steering generated by particles with suitable mass and small momentum is more affected by the expanding universe.
Postoperative Radiographic Outcomes Following Abduction–Extension Metacarpal Osteotomy: A Comparison between Early and Advanced Carpometacarpal Arthritis
Authors: SHIRAKAWA Ken 
Published: August 2024

Background: This study aimed to investigate the effect of thumb metacarpal osteotomy on dorsal subluxation of the carpometacarpal (CMC) joint and compare the effects of early and advanced osteoarthritis (OA). Methods: We retrospectively reviewed 42 thumbs of 37 patients who underwent metacarpal osteotomy with a postoperative extension angle of 90° or more between January 2018 and October 2021 and were followed up for more than 2 years. The thumbs were classified into two groups: early OA (Eaton stage I or II) and advanced OA (Eaton stage III). We measured the reduction ratio, which was defined as the ratio of improvement in dorsal subluxation, at 3 months and 1 year postoperatively, and at the latest follow-up. We statistically compared the reduction ratio between the two groups and investigated the factors affecting the reduction ratio using correlation analysis. Results: The reduction ratio was significantly higher in the early OA group than in the advanced OA group at 3 months after surgery, whereas no significant difference was found between the two groups at 1 year after surgery and at the latest follow-up. A significant positive correlation was detected between the reduction ratio and the postoperative extension angle. Conclusions: First metacarpal osteotomy reduces dorsal subluxation in both early- and advanced-stage CMC OA. This procedure yields immediate marked reduction in early-stage OA, while improvement of the subluxation progressed gradually in advanced-stage OA. Level of Evidence: Level IV (Therapeutic)