bluuebunny/crossref_metadata_2025_split huggingface dataset:
Signed permutohedra, delta‐matroids, and beyond
Authors: Eur Christopher , Fink Alex , Larson Matt , Spink Hunter 
Published: March 2024

AbstractWe establish a connection between the algebraic geometry of the type permutohedral toric variety and the combinatorics of delta‐matroids. Using this connection, we compute the volume and lattice point counts of type generalized permutohedra. Applying tropical Hodge theory to a new framework of “tautological classes of delta‐matroids,” modeled after certain vector bundles associated to realizable delta‐matroids, we establish the log‐concavity of a Tutte‐like invariant for a broad family of delta‐matroids that includes all realizable delta‐matroids. Our results include new log‐concavity statements for all (ordinary) matroids as special cases.
Distinct electrophysiological properties of long‐range GABAergic and glutamatergic neurons from the lateral amygdala to the auditory cortex of the mouse
Authors: Bertero Alice , Apicella Alfonso junior 
Published: March 2024

AbstractDifferentiating between auditory signals of various emotional significance plays a crucial role in an individual's ability to thrive and excel in social interactions and in survival. Multiple approaches, including anatomical studies, electrophysiological investigations, imaging techniques, optogenetics and chemogenetics, have confirmed that the auditory cortex (AC) impacts fear‐related behaviours driven by auditory stimuli by conveying auditory information to the lateral amygdala (LA) through long‐range excitatory glutamatergic and GABAergic connections. In addition, the LA provides glutamatergic projections to the AC which are important to fear memory expression and are modified by associative fear learning. Here we test the hypothesis that the LA also sends long‐range direct inhibitory inputs to the cortex. To address this fundamental question, we used anatomical and electrophysiological approaches, allowing us to directly assess the nature of GABAergic inputs from the LA to the AC in the mouse. Our findings elucidate the existence of a long‐range inhibitory pathway from the LA to the AC (LAC) via parvalbumin‐expressing (LAC‐Parv) and somatostatin‐expressing (LAC‐SOM) neurons. This research identifies distinct electrophysiological properties for genetically defined long‐range GABAergic neurons involved in the communication between the LA and the cortex (LAC‐Parv inhibitory projections → AC neurons; LAC‐Som inhibitory projections → AC neurons) within the lateral amygdala cortical network.
imageKey points
The mouse auditory cortex receives inputs from the lateral amygdala.
Retrograde viral tracing techniques allowed us to identify two previously undescribed lateral amygdala to auditory cortex (LAC) GABAergic projecting neurons.
Extensive electrophysiological, morphological and anatomical characterization of LAC neurons is provided here, demonstrating key differences in the three populations.
This study paves the way for a better understanding of the growing complexity of the cortico‐amygdala‐cortico circuit.
Murepavadin promotes the killing efficacies of aminoglycoside antibiotics against
Pseudomonas aeruginosa
by enhancing membrane potential
Authors: Wei Xiaoya , Gao Jiacong , Zhou Dandan , Xu Congjuan , Chen Ping , Chen Shuiping , Zhang Yanhong , Liu Xuehua , Li Guanxian , Zhu Guangbo , Liu Huimin , Li Jinjin , Geng Bin , Gao Linlin , Cheng Zhihui , Lamont Iain L. , Pletzer Daniel , Jin Yongxin , Jin Shouguang , Wu Weihui 
Published: March 2024

ABSTRACT

Murepavadin is a peptidomimetic that specifically targets the lipopolysaccharide transport protein LptD of
Pseudomonas aeruginosa
. Here, we found that murepavadin enhances the bactericidal efficacies of tobramycin and amikacin. We further demonstrated that murepavadin enhances bacterial respiration activity and subsequent membrane potential, which promotes intracellular uptake of aminoglycoside antibiotics. In addition, the murepavadin-amikacin combination displayed a synergistic bactericidal effect in a murine pneumonia model.
Efficacy and effect on lipid profiles of switching to ainuovirine-based regimen versus continuing efavirenz-based regimen in people with HIV-1: 24-week results from a real-world, retrospective, multi-center cohort study
Authors: Wang Chunmei , Yu Xiaoli , Ke Yingchun , Fu Yanhua , Luo Yanhe , Li Ying , Bi Yanmei , Chen Xingqiong , Li Linghua , Zhao Xiuhong , Chen Zhong 
Published: March 2024

ABSTRACT

Ainuovirine (ANV), a novel non-nucleoside reverse-transcriptase inhibitor (NNRTI), was approved in China in 2021. In a previous randomized phase 3 trial, ANV demonstrated non-inferior efficacy relative to efavirenz (EFV) and was associated with lower rates of dyslipidemia. In this study, we aimed to explore lipid changes in treatment-experienced people with human immunodeficiency virus (HIV)-1 (PWH) switching to ANV from EFV in real world. At week 24, 96.65% of patients in the ANV group and 93.25% in the EFV group had HIV-1 RNA levels below the limit of quantification (LOQ). Median changes from baseline in CD4 +T cell counts (37.0 vs 36.0 cells/µL,
P
= 0.886) and CD4+/CD8 +ratio (0.03 vs 0.10,
P
= 0.360) were similar between the two groups. The ANV group was superior to the EFV group in mean changes in total cholesterol (TC, −0.06 vs 0.26 mmol/L,
P
= 0.006), triglyceride (TG, −0.6 vs 0.14 mmol/L,
P
< 0.001), high-density lipoprotein cholesterol (HDL-C, 0.09 vs 0.08 mmol/L,
P
= 0.006), and low-density lipoprotein cholesterol (LDL-C, −0.18 vs 0.29 mmol/L,
P
< 0.001) at week 24. We also observed that a higher proportion of patients demonstrated improved TC (13.55% vs 4.45%,
P
= 0.015) or LDL-C (12.93% vs 6.89%,
P
= 0.017), and a lower proportion of patients showed worsened LDL-C (5.57% vs 13.52%,
P
= 0.017) with ANV than with EFV at week 24. In conclusion, we observed good efficacy and favorable changes in lipids in switching to ANV from EFV in treatment-experienced PWH in real world, indicating a promising switching option for PWH who may be more prone to metabolic or cardiovascular diseases.
Deciphering the molecular and functional basis of TMexCD1: the plasmid-encoded efflux pump of resistance-nodulation-division superfamily
Authors: Shang Yan , Zhang Ye , Wang Ruimin , Peng Yishu , Ding Bo , Liu Yuanxiang , Li Chongzhou , Feng Luhua , Liu Honglei , Yang Chunyu , Tang Yajie 
Published: March 2024

ABSTRACT

Horizontal gene transfer has been demonstrated to be an important driver for the emergency of multidrug-resistant pathogens. Recently, a transferable gene cluster
tmexCD1-toprJ1
of the resistance-nodulation-division (RND) superfamily was identified in the plasmids of animal-derived
Klebsiella pneumoniae
strains, with a higher efflux capacity for various drugs than the
Escherichia coli
AcrAB-TolC homolog system. In this study, we focused on the differences in the inner membrane pump of these two systems and identified some key residues that contribute to the robust efflux activity of the TMexCD1 system. With the aid of homologous modeling and molecular docking, eight residues from the proximal binding pocket (PBP) and nine from the distal binding pocket (DBP) were selected and subjected to site-directed mutagenesis. Several of them, such as S134, I139, D181, and A290, were shown to be important for substrate binding in the DBP region, and all residues in PBP and DBP showed certain substrate preferences. Apart from the conservative switch loop (L613–623
TMexD1
) previously identified in the
E. coli
AcrB (EcAcrB), a relatively unconservative loop (L665–675
TMexD1
) at the bottom of PBP was proposed as a critical element for the robust activity of TMexD1, due to variations at sites E669, G670, N673, and S674 compared to EcAcrAB, and the significantly altered efflux activity due to their mutations. The conservation and flexibility of these key factors can contribute to the evolution of the RND efflux pumps and thus serve as potential targets for developing inhibitors to block the widespread of the TMexCD1 system.
Pseudomonas aeruginosa
ventricular assist device infections: findings from ineffective phage therapies in five cases
Authors: Aslam Saima , Roach Dwayne , Nikolich Mikeljon P. , Biswas Biswajit , Schooley Robert T. , Lilly-Bishop Kimberley A. , Rice Gregory K. , Cer Regina Z. , Hamilton Theron , Henry Matthew , Luong Tiffany , Salabarria Ann-Charlott , Sisk-Hackworth Laura , Filippov Andrey A. , Lebreton Francois , Hall Lindsey , Nir-Paz Ran , Onallah Hadil , Livni Gilat , Shostak Eran , Wieder-Finesod Anat , Yahav Dafna , Yerushalmy Ortal , Alkalay-Oren Sivan , Braunstein Ron , Khalifa Leron , Rimon Amit , Gelman Daniel , Hazan Ronen 
Published: March 2024

ABSTRACT

Left ventricular assist devices (LVAD) are increasingly used for management of heart failure; infection remains a frequent complication. Phage therapy has been successful in a variety of antibiotic refractory infections and is of interest in treating LVAD infections. We performed a retrospective review of four patients that underwent five separate courses of intravenous (IV) phage therapy with concomitant antibiotic for treatment of endovascular
Pseudomonas aeruginosa
LVAD infection. We assessed phage susceptibility, bacterial strain sequencing, serum neutralization, biofilm activity, and shelf-life of phage preparations. Five treatments of one to four wild-type virulent phage(s) were administered for 14–51 days after informed consent and regulatory approval. There was no successful outcome. Breakthrough bacteremia occurred in four of five treatments. Two patients died from the underlying infection. We noted a variable decline in phage susceptibility following three of five treatments, four of four tested developed serum neutralization, and prophage presence was confirmed in isolates of two tested patients. Two phage preparations showed an initial titer drop. Phage biofilm activity was confirmed in two. Phage susceptibility alone was not predictive of clinical efficacy in
P. aeruginosa
endovascular LVAD infection. IV phage was associated with serum neutralization in most cases though lack of clinical effect may be multifactorial including presence of multiple bacterial isolates with varying phage susceptibility, presence of prophages, decline in phage titers, and possible lack of biofilm activity. Breakthrough bacteremia occurred frequently (while the organism remained susceptible to administered phage) and is an important safety consideration.
Toward the development of a molecular toolkit for the microbial remediation of per-and polyfluoroalkyl substances
Authors: Hu Miao , Scott Colin 
Published: March 2024

ABSTRACT

Per- and polyfluoroalkyl substances (PFAS) are highly fluorinated synthetic organic compounds that have been used extensively in various industries owing to their unique properties. The PFAS family encompasses diverse classes, with only a fraction being commercially relevant. These substances are found in the environment, including in water sources, soil, and wildlife, leading to human exposure and fueling concerns about potential human health impacts. Although PFAS degradation is challenging, biodegradation offers a promising, eco-friendly solution. Biodegradation has been effective for a variety of organic contaminants but is yet to be successful for PFAS due to a paucity of identified microbial species capable of transforming these compounds. Recent studies have investigated PFAS biotransformation and fluoride release; however, the number of specific microorganisms and enzymes with demonstrable activity with PFAS remains limited. This review discusses enzymes that could be used in PFAS metabolism, including haloacid dehalogenases, reductive dehalogenases, cytochromes P450, alkane and butane monooxygenases, peroxidases, laccases, desulfonases, and the mechanisms of microbial resistance to intracellular fluoride. Finally, we emphasize the potential of enzyme and microbial engineering to advance PFAS degradation strategies and provide insights for future research in this field.
Impacts of litter microbial community on litter decomposition in the absence of soil microorganisms
Authors: Liu Jiaying , Ding Changjun , Teng Chao , Zhang Weixi , Su Xiaohua , Zhu Wenxu 
Published: March 2024

ABSTRACT

What is the effect of phyllosphere microorganisms on litter decomposition in the absence of colonization by soil microorganisms? Here, we simulated the litter standing decomposition stage in the field to study the differences in the composition and structure of the phyllosphere microbial community after the mixed decomposition of
Populus
×
canadensis
and
Pinus sylvestris
var.
mongolica
litter. After 15 months of mixed decomposition, we discovered that litters that were not in contact with soil had an antagonistic effect (the actual decomposition rate was 18.18%, which is lower than the expected decomposition rate) and the difference between the litters themselves resulted in a negative response to litter decomposition. In addition, there was no significant difference in bacterial and fungal community diversity after litter decomposition. The litter bacterial community was negatively responsive to litter properties and positively responsive to the fungal community. Importantly, we found that bacterial communities had a greater impact on litter decomposition than fungi. This study has enriched our understanding of the decomposition of litter itself and provided a theoretical basis for further exploring the “additive and non-additive effects” of litter decomposition and the mechanism of microbial drive.

IMPORTANCE
The study of litter decomposition mechanism plays an important role in the material circulation of the global ecosystem. However, previous studies have often looked at contact with soil as the starting point for decomposition. But actually, standing litter is very common in forest ecosystems. Therefore, we used field simulation experiments to simulate the decomposition of litters without contact with soil for 15 months, to explore the combined and non-added benefits of the decomposition of mixed litters, and to study the influence of microbial community composition on the decomposition rate while comparing the differences of microbial communities.
Pyoluteorin regulates the biosynthesis of 2,4-DAPG through the TetR family transcription factor PhlH in
Pseudomonas protegens
Pf-5
Authors: Luo Li-Ming , Xu Hang , Zhang Nannan , Ge Honghua , Xiang Yun , Yang Hao , He Yong-Xing 
Published: March 2024

ABSTRACT

Soil and rhizosphere bacteria act as a rich source of secondary metabolites, effectively fighting against a diverse array of pathogens. Certain
Pseudomonas
species harbor biosynthetic gene clusters for producing both pyoluteorin and 2,4-diacetylphloroglucinol (2,4-DAPG), which are polyketides that exhibit highly similar antimicrobial spectrum against bacteria and fungi or oomycete. A complex cross talk exists between pyoluteorin and 2,4-DAPG biosynthesis, and production of 2,4-DAPG was strongly repressed by pyoluteorin, yet the underlying mechanism is still elusive. In this study, we find that the TetR family transcription factor PhlH is involved in the cross talk between pyoluteorin and 2,4-DAPG biosynthesis. PhlH binds to a palindromic sequence within the promoter of
phlG
(PphlG), which encodes a C-C bond hydrolase responsible for degrading 2,4-DAPG. As a signaling molecule, pyoluteorin disrupts the PhlH-PphlG complex by binding to PhlH, leading to decreased levels of 2,4-DAPG. Proteomics data suggest that pyoluteorin regulates multiple physiological processes including fatty acid biosynthesis and transportation of taurine, siderophore, and amino acids. Our work not only reveals a novel mechanism of cross talk between pyoluteorin and 2,4-DAPG biosynthesis, but also highlights pyoluteorin’s role as a messenger in the complex communication network of
Pseudomonas
.

IMPORTANCE

Antibiosis serves as a crucial defense mechanism for microbes against invasive bacteria and resource competition. These bacteria typically orchestrate the production of multiple antibiotics in a coordinated fashion, wherein the synthesis of one antibiotic inhibits the generation of another. This strategic coordination allows the bacterium to focus its resources on producing the most advantageous antibiotic under specific circumstances. However, the underlying mechanisms of distinct antibiotic production in bacterial cells remain largely elusive. In this study, we reveal that the TetR family transcription factor PhlH detects the secondary metabolite pyoluteorin and mediates the cross talk between pyoluteorin and 2,4-DAPG biosynthesis in the biocontrol strain
Pseudomonas protegens
Pf-5. These findings hold promise for future research, potentially informing the manipulation of these systems to enhance the effectiveness of biocontrol agents.
Comparison of the performance of multiple whole-genome sequence-based tools for the identification of
Bacillus cereus sensu stricto
biovar
Thuringiensis
Authors: Chung Taejung , Salazar Abimel , Harm Grant , Johler Sophia , Carroll Laura M. , Kovac Jasna 
Published: March 2024

ABSTRACT

The
Bacillus cereus sensu stricto
(
s.s
.) species comprises strains of biovar
Thuringiensis
(
Bt
) known for their bioinsecticidal activity, as well as strains with foodborne pathogenic potential.
Bt
strains are identified (i) based on the production of insecticidal crystal proteins, also known as Bt toxins, or (ii) based on the presence of
cry
,
cyt
, and
vip
genes, which encode Bt toxins. Multiple bioinformatics tools have been developed for the detection of crystal protein-encoding genes based on whole-genome sequencing (WGS) data. However, the performance of these tools is yet to be evaluated using phenotypic data. Thus, the goal of this study was to assess the performance of four bioinformatics tools for the detection of crystal protein-encoding genes. The accuracy of sequence-based identification of
Bt
was determined in reference to phenotypic microscope-based screening for the production of crystal proteins. A total of 58 diverse
B. cereus sensu lato
strains isolated from clinical, food, environmental, and commercial biopesticide products underwent WGS. Isolates were examined for crystal protein production using phase contrast microscopy. Crystal protein-encoding genes were detected using BtToxin_Digger, BTyper3, IDOPS (identification of pesticidal sequences), and Cry_processor. Out of 58 isolates, the phenotypic production of crystal proteins was confirmed for 18 isolates. Specificity and sensitivity of
Bt
identification based on sequences were 0.85 and 0.94 for BtToxin_Digger, 0.97 and 0.89 for BTyper3, 0.95 and 0.94 for IDOPS, and 0.88 and 1.00 for Cry_processor, respectively. Cry_processor predicted crystal protein production with the highest specificity, and BtToxin_Digger and IDOPS predicted crystal protein production with the highest sensitivity. Three out of four tested bioinformatics tools performed well overall, with IDOPS achieving high sensitivity and specificity (>0.90).

IMPORTANCE

Strains of
Bacillus cereus sensu stricto
(
s.s
.) biovar
Thuringiensis
(
Bt
) are used as organic biopesticides
. Bt
is differentiated from the foodborne pathogen
Bacillus cereus s.s
. by the production of insecticidal crystal proteins. Thus, reliable genomic identification of biovar
Thuringiensis
is necessary to ensure food safety and facilitate risk assessment. This study assessed the accuracy of whole-genome sequencing (WGS)-based identification of
Bt
compared to phenotypic microscopy-based screening for crystal protein production. Multiple bioinformatics tools were compared to assess their performance in predicting crystal protein production. Among them, identification of pesticidal sequences performed best overall at WGS-based
Bt
identification.
Queen bee gut microbiota extends honeybee lifespan by inhibiting insulin signaling
Authors: Wang Hongfang , Chen Wenfeng , Lei Li , Zhang Wei , Liu Zhenguo , Wang Ying , Xu Baohua 
Published: March 2024

ABSTRACT

Queen and worker bees are natural models for aging research, as their lifespans vary considerably independent of genetic variation. Investigating the reasons why queens live longer than workers is of great significance for research on the universal processes of aging in animals. The gut microbiome has received attention as a vital regulator of host health, while its precise role in honeybee aging needs further investigation. The effects and mechanisms behind the relationship between gut microbiota and worker lifespan were measured by transplanting queen bee gut bacteria (QG) and worker bee gut bacteria (WG) into microbiota-free (MF) workers. The transplantation of QG to MF bees significantly extended the workers’ lifespans compared with MF and WG bees. Untargeted metabolomics identified 49 lifespan-related differential metabolites, and Kyoto Encyclopedia of Genes and Genomes analysis of these revealed three lifespan-related metabolic pathways: insulin/insulin-like growth factor signaling, immune, and ketone body metabolism pathways. Further verification showed that QG inhibited the expression of insulin-like peptides (ILPs), and the expression of ILPs was lower in natural queens than in natural workers. QG transplantation also stimulated the expression of antioxidant genes and lowered oxidative damage products in natural queen bees. However, gut microbiota transplantation failed to mimic the immune properties and ketone body metabolism profiles of natural queens and workers. Concisely, QG could increase the antioxidant capacity to extend lifespan by inhibiting insulin signaling. These findings may help determine the mechanisms behind queen longevity and provide further insights into the role of gut symbionts.

IMPORTANCE
Queen and worker bees share the same genetic background but have vastly different lifespans. The gut microbiome regulates host health, suggesting that differences in lifespan between queen and worker bees could be related to gut bacteria. Herein, we used an innovative method to transplant gut microbiota from adult queen or worker bees to microbiota-free bees. The transplantation of queen gut microbiota to microbiota-free bees extended their lifespan. Insulin/insulin-like growth factor signaling, a highly conserved metabolic pathway related to lifespan, displayed identical expression profiles in natural queen bees and microbiota-free bees transplanted with queen microbiota. This finding significantly expands our understanding of the relationships between intestinal bacteria, host health, and the biology of aging.