bluuebunny/crossref_metadata_2025_split huggingface dataset:
Azotobacter vinelandii
N
2
fixation increases in co-culture with the PGPR
Bacillus subtilis
in a nitrogen concentration-dependent manner
Authors: Leroux Julie , Beauregard Pascale B. , Bellenger Jean-Philippe 
Published: November 2024

ABSTRACT

Biological nitrogen fixation (BNF) is an essential source of new nitrogen (N) for terrestrial ecosystems. The abiotic factors regulating BNF have been extensively studied in various ecosystems and laboratory settings. Despite this, our understanding of the impact of neighboring bacteria on N
2
fixer activity remains limited. Here, we explored this question using a co-culture of the two model species: the free-living diazotroph
Azotobacter vinelandii
and the non-fixing plant growth-promoting rhizobacteria
Bacillus subtilis
. We observed that the interaction between the two bacteria was modulated by N availability. Under N-replete conditions,
B. subtilis
outcompeted
A. vinelandii
in the co-culture. Under N-limiting conditions, BNF activity by
A. vinelandii
was enhanced in the presence of
B. subtilis
. Reciprocally, the presence of
A. vinelandii
repressed sporulation by
B. subtilis
and supported its growth likely through N transfer. N inputs by
A. vinelandii
were doubled in the presence of
B. subtilis
compared to the monoculture, primarily due to the retention of a robust N
2
fixation activity in the stationary phase. A proteomic analysis revealed that
A. vinelandii
N metabolism, particularly the molybdenum nitrogenase isoform protein levels (NifK and NifD), was upregulated during the stationary growth phase in the presence of
B. subtilis
. This study revealed that N stress drives bacterial interactions and activity in a two-species community, especially in the stationary phase.

IMPORTANCE

Reducing inputs of chemical N fertilizers is essential to develop a more sustainable agriculture. The stimulation of biological nitrogen fixation by N2 fixers in multispecies cultures, here the plant growth-promoting rhizobacteria
Azotobacter vinelandii
and
Bacillus subtilis
, opens opportunities for the formulation of biofertilizers consortia. While most research on N2 fixation historically focussed on the exponential growth phase of microorganisms, we observed that
Bacillus subtilis
stimulated
Azotobacter vinelandii
N2 fixation mostly during the stationary phase. This result highlights that more research on the factors controlling N2 fixation repression during the stationary growth phase, especially bacteria-bacteria interactions, is eagerly needed.
A novel LAMP-based assay for the identification of
Streptococcus pneumoniae
and
Streptococcus pseudopneumoniae
in clinical isolates
Authors: Basheer Mariam , Sasic Katarina , Carlsson Alice , Vestberg Nora , Henriques-Normark Birgitta , Blomqvist Karin , Garriss Geneviève 
Published: November 2024

ABSTRACT

The Gram-positive bacteria
Streptococcus pneumoniae
is part of the
Streptococcus mitis
group (SMG) and causes life-threatening infections, such as pneumonia, sepsis, and meningitis. The closely related
Streptococcus pseudopneumoniae
has recently been shown to cause respiratory tract infections, as well as invasive infections, especially in patients with comorbidities. Due to the genetic and phenotypic similarities of species belonging to the SMG, the identification of
S. pneumoniae
and
S. pseudopneumoniae
is difficult and unreliable using phenotypic tests, as well as matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and 16S rRNA sequencing. In this study, a loop-mediated isothermal amplification (LAMP)-based assay was developed using molecular markers specific for
S. pneumoniae
(SPN0001) and
S. pseudopneumoniae
(SPPN_RS10375). The LAMP assay was evaluated using a collection of SMG clinical isolates, concluding that the method provides a correct, reliable, and fast identification of both
S. pneumoniae
and
S. pseudopneumoniae
clinical isolates.
2018-2019 human seasonal H3N2 influenza A virus spillovers into swine with demonstrated virus transmission in pigs were not sustained in the pig population
Authors: Powell Joshua D. , Thomas Megan N. , Anderson Tavis K. , Zeller Michael A. , Gauger Phillip C. , Vincent Baker Amy L. 
Published: November 2024

ABSTRACT

Human seasonal H3 clade 3C3a influenza A viruses (IAV) were detected four times in U.S. pigs from commercial swine farms in Michigan, Illinois, and Virginia in 2019. To evaluate the relative risk of this spillover to the pig population, whole genome sequencing and phylogenetic characterization were conducted, and the results revealed that all eight viral gene segments were closely related to 2018–2019 H3N2 human seasonal IAV. Next, a series of
in vitro
viral kinetics, receptor binding, and antigenic characterization studies were performed using a representative A/swine/Virginia/A02478738/2018(H3N2) (SW/VA/19) isolate. Viral replication kinetic studies of SW/VA/19 demonstrated less efficient replication curves than all 10 swine H3N2 viruses tested but higher than three human H3N2 strains. Serial passaging experiments of SW/VA/19 in swine cells did not increase virus replication, but changes at HA amino acid positions 9 and 159 occurred. In swine transmission studies, wild-type SW/VA/19 was shed in nasal secretions and transmitted to all indirect contact pigs, whereas the human seasonal strain A/Switzerland/9715293/2013(H3N2) from the same 3C3a clade failed to transmit. SW/VA/19 induced minimal macroscopic and microscopic lung lesions. Collectively, these findings demonstrate that these human seasonal H3N2 3C3a-like viruses did not require reassortment with endemic swine IAV gene segments for virus shedding and transmission in pigs. Limited detections in the U.S. pig population in the subsequent period of time suggest a yet-unknown restriction factor likely limiting the spread of these viruses in the U.S. pig population.

IMPORTANCE
Interspecies human-to-swine IAV transmission occurs globally and contributes to increased IAV diversity in pig populations. We present data that a swine isolate from a 2018–2019 human-to-swine transmission event was shed for multiple days in challenged and contact pigs. By characterizing this introduction through bioinformatic, molecular, and animal experimental approaches, these findings better inform animal health practices and vaccine decision-making. Since wholly human seasonal H3N2 viruses in the United States were not previously identified as being transmissible in pigs (i.e., reverse zoonosis), these findings reveal that the interspecies barriers for transmission to pigs may not require significant changes to all human seasonal H3N2, although additional changes may be required for sustained transmission in swine populations.
Genome sequence of
Trueperella pyogenes
isolates from liver abscesses in feedlot cattle
Authors: Gruninger Robert J. , Zaheer Rahat , Stuart-Edwards Matthew , Zovoilis Athanasios , McAllister Tim A. 
Published: November 2024

ABSTRACT

High-grain diets promote polymicrobial liver infections in cattle, commonly involving the bacterium
Trueperella pyogenes
. We have isolated
T. pyogenes
from the purulent material of abscesses and sequenced their genomes. These data enhance our understanding of the mechanisms underlying liver abscess development in cattle.
Nuclear pore complexes undergo Nup221 exchange during blood-stage asexual replication of
Plasmodium
parasites
Authors: Blauwkamp James , Ambekar Sushma V. , Hussain Tahir , Mair Gunnar R. , Beck Josh R. , Absalon Sabrina 
Published: November 2024

ABSTRACT

Plasmodium
parasites, the causative agents of malaria, undergo closed mitosis without breakdown of the nuclear envelope. Unlike closed mitosis in yeast,
Plasmodium berghei
parasites undergo multiple rounds of asynchronous nuclear divisions in a shared cytoplasm. This results in a multinucleated organism prior to the formation of daughter cells within an infected red blood cell. During this replication process, intact nuclear pore complexes (NPCs) and their component nucleoporins play critical roles in parasite growth, facilitating selective bi-directional nucleocytoplasmic transport and genome organization. Here, we utilize ultrastructure expansion microscopy to investigate
P. berghei
nucleoporins at the single nucleus level throughout the 24-hour blood-stage replication cycle. Our findings reveal that these nucleoporins are distributed around the nuclei and organized in a rosette structure previously undescribed around the centriolar plaque, responsible for intranuclear microtubule nucleation during mitosis. By adapting the recombination-induced tag exchange system to
P. berghei
through a single plasmid tagging system, which includes the tagging plasmid as well as the Cre recombinase, we provide evidence of NPC formation dynamics, demonstrating Nup221 turnover during parasite asexual replication. Our data shed light on the distribution of NPCs and their homeostasis during the blood-stage replication of
P. berghei
parasites.

IMPORTANCE

Malaria, caused by
Plasmodium
species, remains a critical global health challenge, with an estimated 249 million cases and over 600,000 deaths in 2022, primarily affecting children under five. Understanding the nuclear dynamics of
Plasmodium
parasites, particularly during their unique mitotic processes, is crucial for developing novel therapeutic strategies. Our study leverages advanced microscopy techniques, such as ultrastructure expansion microscopy, to reveal the organization and turnover of nuclear pore complexes (NPCs) during the parasite’s asexual replication. By elucidating these previously unknown aspects of NPC distribution and homeostasis, we provide valuable insights into the molecular mechanisms governing parasite mitosis. These findings deepen our understanding of parasite biology and may inform future research aimed at identifying new targets for anti-malarial drug development.
A comprehensive two-hybrid analysis to explore the
Legionella pneumophila
effector–effector interactome
Authors: Mount Harley O'Connor , Urbanus Malene L. , Sheykhkarimli Dayag , Coté Atina G. , Laval Florent , Coppin Georges , Kishore Nishka , Li Roujia , Spirohn-Fitzgerald Kerstin , Petersen Morgan O. , Knapp Jennifer J. , Kim Dae-Kyum , Twizere Jean-Claude , Calderwood Michael A. , Vidal Marc , Roth Frederick P. , Ensminger Alexander W. 
Published: November 2024

ABSTRACT

Legionella pneumophila
uses over 300 translocated effector proteins to rewire host cells during infection and create a replicative niche for intracellular growth. To date, several studies have identified
L. pneumophila
effectors that indirectly and directly regulate the activity of other effectors, providing an additional layer of regulatory complexity. Among these are “metaeffectors,” a special class of effectors that regulate the activity of other effectors once inside the host. A defining feature of metaeffectors is direct, physical interaction with a target effector. Metaeffector identification, to date, has depended on phenotypes in heterologous systems and experimental serendipity. Using a multiplexed, recombinant barcode-based yeast two-hybrid technology we screened for protein–protein interactions among all
L. pneumophila
effectors and 28 components of the Dot/Icm type IV secretion system (>167,000 protein combinations). Of the 52 protein interactions identified by this approach, 44 are novel protein interactions, including 10 novel effector–effector interactions (doubling the number of known effector–effector interactions).

IMPORTANCE

Secreted bacterial effector proteins are typically viewed as modulators of host activity, entering the host cytosol to physically interact with and modify the activity of one or more host proteins in support of infection. A growing body of evidence suggests that a subset of effectors primarily function to modify the activities of other effectors inside the host. These “effectors of effectors” or metaeffectors are often identified through experimental serendipity during the study of canonical effector function against the host. We previously performed the first global effector-wide genetic interaction screen for metaeffectors within the arsenal of
Legionella pneumophila
, an intracellular bacterial pathogen with over 300 effectors. Here, using a high-throughput, scalable methodology, we present the first global interaction network of physical interactions between
L. pneumophila
effectors. This data set serves as a complementary resource to identify and understand both the scope and nature of non-canonical effector activity within this important human pathogen.
Performance of UF-5000 in rapidly screening out urinary tract infection, predicting Gram-negative bacteria infection
Authors: Lu Wei , Li Zhaoxing , Zhang Tong , Li Yan , Zhu Huange , Zhao Ya , Lei Ke , Guo Zhi , Zhang Jing , Guo Juan , Zhang Lei 
Published: November 2024

ABSTRACT

Urine culture is the gold standard for identifying microorganisms in urine. However, the process is time-consuming and usually takes days to get the results, which impedes timely treatment. This study aimed to evaluate the performance of UF-5000 in excluding bacterial urinary tract infection (UTI) and detecting the presence of Gram-negative bacteria. A total of 1,522 urine specimens were subjected to routine urine analysis and culture. Bacteria, white blood cell counts, and UF-5000 bacteria information flags were compared with urine culture. Bacteria forward scatter (B_FSC), and bacteria fluorescent light intensity (B_FLH) parameters were assessed to determine the optimal angle for discriminating bacterial growth patterns, which was verified in the validation cohort. The optimal cut-off values were 42.2/µL and 100.2/µL to rule out UTI for bacteria at ≥10
4
CFU/mL and ≥10
5
CFU/mL, respectively. The agreement of UF-5000 bacterial classification and urine culture was fair (Kappa = 0.227). Regarding the discrimination of bacterial groups, “Gram Neg?” was associated with a specificity of 94.0% and a positive predictive value of 87.2% in the detection of Gram-negative bacteria. By estimating the B_FSC and B_FLH parameters, the best angle was 28° for distinguishing Gram-negative and Gram-positive bacteria. Among the 136 urine specimens with the low angle pattern (<28°) in the validation cohort, 127 specimens were confirmed to contain Gram-negative bacteria. The UF-5000 analyzer is a suitable and rapid tool to exclude negative urine specimens, and bacterial information flags for Gram-negative bacteria could be trusted by clinicians.

IMPORTANCE
The strength of our study relied on being the first study assessing the bacteria forward scatter (B_FSC) and bacteria fluorescent light intensity (B_FLH) research parameters with a UF-5000 urine analyzer and establishing the best angle for distinguishing Gram-negative and Gram-positive bacteria. When the bacterial scatter plot angle is less than 28°, the possibility of Gram-negative bacterial infection is more than 80%. Meanwhile, we find that UF-5000 bacterial information flags have a significant advantage in detecting Gram-negative bacteria with a specificity of over 90% and a positive predictive value of over 80%.
Development of a Panel of Biomarkers for Differential Diagnosis of Multiple Sclerosis
Authors: Ovchinnikova L. A. , Dzhelad S. S. , Simaniv T. O. , Zakharova M. N. , Lomakin Y. A. , Gabibov A. G. , Illarioshkin S. N. 
Published: November 2024

Abstract
Demyelinating diseases are a group of heterogeneous pathologies that affect the nervous system and reduce the quality of life. One of such diseases is multiple sclerosis (MS), an inflammatory autoimmune neurodegenerative disease of the central nervous system (CNS). At the initial stages, MS can mimic some infectious, neoplastic, genetic, metabolic, vascular, and other pathologies. Accurate differential diagnosis of this disease is important to improve the quality of life of patients and reduce possible irreversible damage to the central nervous system. In this work, we confirmed the possibility of using our previously proposed candidate panel of MS biomarkers to distinguish MS from neuromyelitis optica spectrum disorder (NMOSD) and amyotrophic lateral sclerosis (ALS). We have shown that our proposed panel (SPTAN1601-644 + PRX451-494 + PTK6301-344 + LMP1285-330) allows us to distinguish MS from ALS (AUC = 0.796) and NMOSD (AUC = 0.779).
The Central American Seaway: do Magdalena River flocculates mimic deep water neodymium?
Authors: Montes Camilo , Bayona German 
Published: November 2024

A common assumption in the interpretation of seawater neodymium isotopes is that the signal is a mixture of distally advected waters. A review of the local palaeogeography and bedrock Nd isotopic compositions (
n
= 712) of the largest drainage basins of the Caribbean Sea shows: (1) unradiogenic sedimentary and crystalline sequences in the cratonic-derived eastern Andes, (2) very radiogenic sequences in the western Andes and Panama Isthmus and (3) intermediate values between them (Cauca River drainage basin). These local signatures can be matched to the Miocene–Pliocene record of Ocean Drilling Project sites ODP-998, 999 and 1000, dating the arrival of major inter-Andean drainages to the Caribbean Sea. The birth of the Atrato River at 15 Ma, following closure of the Central American Seaway, delivered very radiogenic Nd isotopes to the Caribbean Sea (
ε
Nd
= +5.5), while the arrival of Magdalena River waters at 11 Ma brought very unradiogenic values (
ε
Nd
≪ −8). Later excavation of the Cauca River canyon at ∼7 Ma added a moderately radiogenic source (
ε
Nd
= +1.9), modulating Magdalena River signatures to the Caribbean Sea. Flocculates forming in tropical deltas and estuarine environments carried these signals in hyperpicnal flows to slowly mixing Caribbean bottom waters, mimicking distally advected water.
Scalable Experimental Bounds for Entangled Quantum State Fidelities
Authors: Aktar Shamminuj , Bärtschi Andreas , Badawy Abdel-Hameed A. , Eidenbenz Stephan 
Published: November 2024

Estimating the state preparation fidelity of highly entangled states on noisy intermediate-scale quantum (NISQ) devices is important for benchmarking and application considerations. Unfortunately, exact fidelity measurements quickly become prohibitively expensive, as they scale exponentially as
O
(3

N

for
N
-qubit states, using full state tomography with measurements in all Pauli bases combinations. However, Somma et al.established that the complexity could be drastically reduced when looking at
fidelity lower bounds
for states that exhibit symmetries, such as Dicke states and GHZ states. These bounds must still be tight enough for larger states to provide reasonable estimations on NISQ devices.

For the first time and more than 15 years after the theoretical introduction, we report meaningful lower bounds for the state preparation fidelity of all Dicke states up to
N
=10 and all GHZ states up to
N
=20 on Quantinuum H1 ion-trap systems using efficient implementations of recently proposed scalable circuits for these states. Our achieved lower bounds match or exceed previously reported exact fidelities on superconducting systems for much smaller states. Furthermore, we provide evidence that for large Dicke states

\(\left|\smash{D_{N/2}^{N}} \right\rangle\)

, we may resort to a GHZ-based approximate state preparation to achieve better fidelity. This work provides a path forward to benchmarking entanglement as NISQ devices improve in size and quality.
Genetically Predicted Immune Cells Mediate the Association Between Gut Microbiota and Gastroesophageal Reflux Disease
Authors: Wang Jia , Fei Bojian , Wang Chao 
Published: November 2024

Background: Recent evidence increasingly acknowledges the close interrelationship between immunity and gut microbiota (GM) in humans. Furthermore, previous studies have demonstrated a strong correlation between GM and gastroesophageal reflux disease (GERD). However, the specific impact of GM on immune factors in GERD remains largely unexplored. Therefore, we conducted the Mendelian randomization (MR) analysis to investigate the precise causal relationships and underlying mechanisms linking GM, immunity, and GERD.Method: We employed the mediation MR utilizing summary statistics derived from Genome‐Wide Association Study (GWAS) data to investigate the causal effects of 207 taxa and 205 bacterial pathways on GERD. The analysis concentrated on 731 immune cell traits as potential mediators. The inverse variance weighted (IVW) approach was the primary analytical method. To ensure robustness, we employed additional MR methods, including Bayesian weighted MR (BWMR), MR‐Egger, Weighted Median, Weighted Mode, and Simple Mode. Furthermore, a series of sensitivity analyses, such as the Cochran’s Q test, leave‐one‐out test, MR‐Egger intercept analysis, and MR‐PRESSO test, were conducted to ensure the reliability and consistency of the findings.Results: The study identified three taxa and eight bacterial pathways that exhibited a negative correlation with GERD. Mediation MR analyses indicated that four bacterial pathways influence GERD through four immune cell types acting as mediators. For instance, the “arginine, ornithine, and proline interconversion” pathway was implicated in reducing the risk of GERD via “PDL‐1 on CD14‐ CD16+ monocyte” cells, with a total effect of −0.0484 and a mediation effect of −0.0093. Sensitivity analyses provided additional validation for the reliability of the MR findings.Conclusion: Our study contributes evidence to the close causal relationship between the GM and GERD, emphasizing the possible role of immune cells as mediators. Future research should focus on developing microbiome‐oriented therapeutic approaches for managing GERD.
Gastric Cancer Risk among Immigrants and Socioeconomic Groups in the Netherlands
Authors: Mülder Duco T. , van de Schootbrugge - Vandermeer Hilliene J. , O’Mahony James F. , Sun Dianqin , Han Weiran , Verhoeven Rob H.A. , van Loo Marlon , van de Veerdonk Wessel , Spaander Manon C.W. , Lansdorp-Vogelaar Iris 
Published: November 2024

Abstract

Background:
Identification of groups at a high risk of gastric cancer could facilitate targeted screening in countries with a low gastric cancer incidence. Our aim was to identify such high-risk groups based on individual-level population data on migration history and socioeconomic status (SES) in the Netherlands.

Methods:
In this retrospective cohort study, patient data from the Netherlands Cancer Registry were linked to demographic data of Statistics Netherlands in the period 2010 to 2022. Gastric cancer incidence rates in the 14 largest immigrant populations were compared with those born in the Netherlands. Odds ratios (OR) were computed per birthplace and controlled for age, sex, and SES. Additionally, we investigated gastric cancer risk among second-generation immigrants and by SES.

Results:
Immigrant populations at a significantly higher gastric cancer risk compared with the general population were identified. Specifically, foreign-born first-generation immigrants from Bosnia–Herzegovina (OR, 2.42), Turkey (OR, 2.22), and China (OR, 1.92) showed elevated risk. Whereas low SES increased the odds of developing gastric cancer, first-generation immigrants remained at higher risk even after controlling for SES. Second-generation immigrants did not have a significantly higher risk of developing gastric cancer.

Conclusions:
Certain first-generation immigrants remain at an elevated risk for gastric cancer despite migration to a low-risk region. Identification of these high-risk groups should be used to facilitate targeted gastric cancer prevention.

Impact:
Potential benefits of targeted Helicobacter pylori test-and-treat policy in immigrant populations should be explored in clinical and modeling studies. Primary care physicians should be cognizant of high-risk groups, facilitating the early detection of cancer within these populations.