bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tibiofemoral Load Magnitude and Distribution During Load Carriage
Authors: Jones Blake W. , Willson John D. , DeVita Paul , Wedge Ryan D. 
Published: September 2023

Chronic exposure to high tibiofemoral joint (TFJ) contact forces can be detrimental to knee joint health. Load carriage increases TFJ contact forces, but it is unclear whether medial and lateral tibiofemoral compartments respond similarly to incremental load carriage. The purpose of our study was to compare TFJ contact forces when walking with 15% and 30% added body weight. Young healthy adults (n = 24) walked for 5 minutes with no load, 15% load, and 30% load on an instrumented treadmill. Total, medial, and lateral TFJ contact peak forces and impulses were calculated via an inverse dynamics informed musculoskeletal model. Results of 1-way repeated measures analyses of variance (α = .05) demonstrated total, medial, and lateral TFJ first peak contact forces and impulses increased significantly with increasing load. Orthogonal polynomial trends demonstrated that the 30% loading condition led to a curvilinear increase in total and lateral TFJ impulses, whereas medial first peak TFJ contact forces and impulses responded linearly to increasing load. The total and lateral compartment impulse increased disproportionally with load carriage, while the medial did not. The medial and lateral compartments responded differently to increasing load during walking, warranting further investigation because it may relate to risk of osteoarthritis.
Crystal structure and solution state of the C-terminal head region of the narmovirus receptor binding protein
Authors: Stelfox Alice J. , Oguntuyo Kasopefoluwa Y. , Rissanen Ilona , Harlos Karl , Rambo Robert , Lee Benhur , Bowden Thomas A. 
Published: September 2023

ABSTRACT

Increased viral surveillance has led to the isolation and identification of numerous uncharacterized paramyxoviruses, rapidly expanding our understanding of paramyxoviral diversity beyond the bounds of known genera. Despite this diversity, a key feature that unites paramyxoviruses is the presence of a receptor-binding protein (RBP), which facilitates host-cell attachment and plays a fundamental role in determining host range. Here, we study the RBP presented on the surface of rodent-borne paramyxoviruses Mossman and Nariva (MosV and NarV, respectively), viruses that constitute founding members of the recently defined
Narmovirus
genus within the
Paramyxoviridae
family. Crystallographic analysis of the C-terminal head region of the dimeric MosV and NarV RBPs demonstrates that while these glycoproteins retain the canonical six-bladed β-propeller fold found in other paramyxoviral RBPs, they lack the structural motifs associated with established paramyxovirus host-cell receptor entry pathways. Consistent with MosV-RBP and NarV-RBP undergoing a distinct entry pathway from other characterized paramyxoviruses, structure-based phylogenetic analysis demonstrates that these six-bladed β-propeller head domains form a singular structural class that is distinct from other paramyxoviral RBPs. Additionally, using an integrated crystallographic and small-angle X-ray scattering analysis, we confirm that MosV-RBP and NarV-RBP form homodimeric arrangements that are distinct from those adopted by other paramyxovirus RBPs. Altogether, this investigation provides a molecular-level blueprint of the narmovirus RBP that broadens our understanding of the structural space and functional diversity available to paramyxovirus RBPs.

IMPORTANCE

Genetically diverse paramyxoviruses are united in their presentation of a receptor-binding protein (RBP), which works in concert with the fusion protein to facilitate host-cell entry. The C-terminal head region of the paramyxoviral RBP, a primary determinant of host-cell tropism and inter-species transmission potential, forms structurally distinct classes dependent upon protein and glycan receptor specificity. Here, we reveal the architecture of the C-terminal head region of the RBPs from Nariva virus (NarV) and Mossman virus (MosV), two archetypal rodent-borne paramyxoviruses within the recently established genus
Narmovirus
, family
Paramyxoviridae
. Our analysis reveals that while narmoviruses retain the general architectural features associated with paramyxoviral RBPs, namely, a six-bladed β-propeller fold, they lack the structural motifs associated with known receptor-mediated host-cell entry pathways. This investigation indicates that the RBPs of narmoviruses exhibit pathobiological features that are distinct from those of other paramyxoviruses.
Suggested role of NosZ in preventing N
2
O inhibition of dissimilatory nitrite reduction to ammonium
Authors: Yoon Sojung , Heo Hokwan , Han Heejoo , Song Dong-Uk , Bakken Lars R. , Frostegård Åsa , Yoon Sukhwan 
Published: September 2023

ABSTRACT

Climate change and nutrient pollution are among the most urgent environmental issues. Enhancing the abundance and/or the activity of beneficial organisms is an attractive strategy to counteract these problems. Dissimilatory nitrate reduction to ammonium (DNRA), which theoretically improves nitrogen retention in soils, has been suggested as a microbial process that may be harnessed, especially since many DNRA-catalyzing organisms have been found to possess
nosZ
genes and the ability to respire N
2
O. However, the selective advantage that may favor these
nosZ
-harboring DNRA-catalyzing organisms is not well understood. Here, the effect of N
2
O on Nrf-mediated DNRA was examined in a soil isolate,
Bacillus
sp. DNRA2, possessing both
nrfA
and
nosZ
genes. The DNRA metabolism of this bacterium was observed in the presence of C
2
H
2,
a NosZ inhibitor, with or without N
2
O, and the results were compared with C
2
H
2
-free controls. Cultures were also exposed to repeated oxic-anoxic transitions in the sustained presence of N
2
O. The NO
2
−
-to-NH
4
+
reduction following oxic-to-anoxic transition was significantly delayed in NosZ-inhibited C
2
H
2
-amended cultures, and the inhibition was more pronounced with repeated oxic-anoxic transitions. The possibility of C
2
H
2
involvement was dismissed since the cultures continuously flushed with C
2
H
2
/N
2
mixed gas after initial oxic incubation did not exhibit a similar delay in DNRA progression as that observed in the culture flushed with N
2
O-containing gas. The findings suggest a possibility that the oft-observed
nosZ
presence in DNRA-catalyzing microorganisms secures an early transcription of their DNRA genes by scavenging N
2
O, thus enhancing their capacity to compete with denitrifiers at oxic-anoxic interfaces.

IMPORTANCE

Dissimilatory nitrate/nitrite reduction to ammonium (DNRA) is a microbial energy-conserving process that reduces NO
3
−
and/or NO
2
−
to NH
4
+
. Interestingly, DNRA-catalyzing microorganisms possessing
nrfA
genes are occasionally found harboring
nosZ
genes encoding nitrous oxide reductases, i.e., the only group of enzymes capable of removing the potent greenhouse gas N
2
O. Here, through a series of physiological experiments examining DNRA metabolism in one of such microorganisms,
Bacillus
sp. DNRA2, we have discovered that N
2
O may delay the transition to DNRA upon an oxic-to-anoxic transition, unless timely removed by the nitrous oxide reductases. These observations suggest a novel explanation as to why some
nrfA
-possessing microorganisms have retained
nosZ
genes: to remove N
2
O that may otherwise interfere with the transition from O
2
respiration to DNRA.
Human GBP1 facilitates the rupture of the
Legionella-
containing vacuole and inflammasome activation
Authors: Bass Antonia R. , Egan Marisa S. , Alexander-Floyd Jasmine , Lopes Fischer Natasha , Doerner Jessica , Shin Sunny 
Published: September 2023

ABSTRACT

The inflammasome is essential for host defense against intracellular bacterial pathogens, including
Legionella pneumophila
, the causative agent of the severe pneumonia Legionnaires’ disease. Inflammasomes recruit and activate caspases, which promote IL-1 family cytokine release and pyroptosis to restrict infection. In mice, interferon (IFN) signaling promotes inflammasome responses against
L. pneumophila
and other bacteria
,
in part, through inducing a family of IFN-inducible GTPases known as guanylate-binding proteins (GBPs). Within murine macrophages, IFN promotes the rupture of the
L. pneumophila
-containing vacuole (LCV), while GBPs are dispensable for vacuole rupture. Instead, GBPs facilitate the lysis of cytosol-exposed
L. pneumophila
. In contrast, the functions of IFN-γ and GBPs in human inflammasome responses to
L. pneumophila
are poorly understood. Here, we show that IFN-γ enhances caspase-1- and caspase-4-dependent inflammasome responses to
L. pneumophila
in human macrophages. We find that human GBP1 is required for these IFN-γ-driven inflammasome responses. Furthermore, we find that GBP1 co-localizes with
L. pneumophila
and/or LCVs in a type IV secretion system (T4SS)-dependent manner and facilitates damage to the LCV, resulting in increased bacterial access to the host cell cytosol. Our findings reveal species- and pathogen-specific differences in how GBPs function during infection.

Importance

Inflammasomes are essential for host defense against intracellular bacterial pathogens like
Legionella
, as they activate caspases, which promote cytokine release and cell death to control infection. In mice, interferon (IFN) signaling promotes inflammasome responses against bacteria by inducing a family of IFN-inducible GTPases known as guanylate-binding proteins (GBPs). Within murine macrophages, IFN promotes the rupture of the
Legionella
-containing vacuole (LCV), while GBPs are dispensable for this process. Instead, GBPs facilitate the lysis of cytosol-exposed
Legionella
. In contrast, the functions of IFN and GBPs in human inflammasome responses to
Legionella
are poorly understood. We show that IFN-γ enhances inflammasome responses to
Legionella
in human macrophages. Human GBP1 is required for these IFN-γ-driven inflammasome responses. Furthermore, GBP1 co-localizes with
Legionella
and/or LCVs in a type IV secretion system (T4SS)-dependent manner and promotes damage to the LCV, which leads to increased exposure of the bacteria to the host cell cytosol. Thus, our findings reveal species- and pathogen-specific differences in how GBPs function to promote inflammasome responses.
Conformational variability of cyanobacterial ChlI, the AAA+ motor of magnesium chelatase involved in chlorophyll biosynthesis
Authors: Shvarev Dmitry , Scholz Alischa Ira , Moeller Arne 
Published: September 2023

ABSTRACT
Magnesium chelatase is a conserved enzyme complex responsible for the first committed step of chlorophyll biosynthesis in photosynthetic organisms, which is the addition of magnesium to the chlorophyll precursor, protoporphyrin IX. The complex is composed of the catalytic subunit ChlH, the bridging subunit ChlD, and the subunit ChlI, which serves as the motor that drives the entire complex. Although the enzyme is well-characterized functionally, high-resolution structures are available only for individual subunits. Hence, the full assembly and molecular mechanism of the enzyme complex remain unknown. Here, we used cryogenic electron microscopy, supported by biochemical analysis and mass photometry, to determine the structures of the ChlI motor subunit of magnesium chelatase under turnover conditions in the presence of ATP. Our data reveal the molecular details of ChlI oligomerization and conformational dynamics upon ATP binding and hydrolysis. These findings provide new insights into the mechanistic function of ChlI and its implications for the entire magnesium chelatase complex machinery.

Importance
Photosynthesis is an essential life process that relies on chlorophyll. In photosynthetic organisms, chlorophyll synthesis involves multiple steps and depends on magnesium chelatase. This enzyme complex is responsible for inserting magnesium into the chlorophyll precursor, but the molecular mechanism of this process is not fully understood. By using cryogenic electron microscopy and conducting functional analyses, we have discovered that the motor subunit ChlI of magnesium chelatase undergoes conformational changes in the presence of ATP. Our findings offer new insights into how energy is transferred from ChlI to the other components of magnesium chelatase. This information significantly contributes to our understanding of the initial step in chlorophyll biosynthesis and lays the foundation for future studies on the entire process of chlorophyll production.
Ultrastructure and 3D reconstruction of a diplonemid protist (Diplonemea) and its novel membranous organelle
Authors: Tashyreva Daria , Týč Jiří , Horák Aleš , Lukeš Julius 
Published: September 2023

ABSTRACT

Although diplonemid protists (Diplonemea, Euglenozoa) are among the most species-rich microeukaryotes in the ocean, many ultrastructural features of this lineage remain to be clarified. Using serial block-face scanning and transmission electron microscopy, we provide the whole-cell three-dimensional model of a previously undescribed diplonemid
Lacrimia vacuolata
sp. nov. For the first time, we were able to reconstruct a diplonemid cell in detail, including all its organelles and the flagellar and feeding apparatuses. By analyzing various stages of the cell cycle, we provide the first description of a diplonemid cell division, which is characterized by the disassembly of flagellar axonemes and the feeding apparatus and their further construction in the daughter cells. Moreover, we have identified a novel, ultrastructurally complex organelle, herein named the colv (
C
enter for
O
rganization of
L
ayered
V
esicles). We suggest that the colv is involved in food processing and membrane trafficking, and describe its close association with other components of the cellular digestive system.

IMPORTANCE
The knowledge of cell biology of a eukaryotic group is essential for correct interpretation of ecological and molecular data. Although diplonemid protists are one of the most species-rich lineages of marine eukaryotes, only very fragmentary information is available about the cellular architecture of this taxonomically diverse group. Here, a large serial block-face scanning electron microscopy data set complemented with light and fluorescence microscopy allowed the first detailed three-dimensional reconstruction of a diplonemid species. We describe numerous previously unknown peculiarities of the cellular architecture and cell division characteristic for diplonemid flagellates, and illustrate the obtained results with multiple three-dimensional models, comprehensible for non-specialists in protist ultrastructure.
Draft genome sequence of
Acinetobacter
sp. AYS6, a potential plant growth-promoting endophyte
Authors: Fadiji Ayomide Emmanuel , Ayangbenro Ayansina Segun , Akanmu Akinlolu Olalekan , Babalola Olubukola Oluranti 
Published: September 2023

ABSTRACT

Here, we report the draft genome sequence of
Acinetobacter sp
. AYS6, an endophyte isolated from the roots of maize plant in Mafikeng, South Africa. The genome was 7,072,605 bp and exhibited a GC content of 45.6% and 3,654 genes with 3,539 coding sequences, 64 rRNA, 60 tRNAs, and 2 CRISPR.
The resistomes of rural and urban pigs and poultry in Ghana
Authors: Jensen Emilie Egholm Bruun , Sedor Victoria , Eshun Emmanuel , Njage Patrick , Otani Saria , Aarestrup Frank M. 
Published: September 2023

ABSTRACT

There is limited knowledge on the bacteriome and resistome in livestock in Africa and the potential influence of the animal husbandry practices and scale has also been scantly explored. We quantified and characterized the antimicrobial resistance gene (ARG) pools (resistomes) and bacteriome in 30 pigs and 60 poultry samples (free-range: rural and urban, and industrialized) across Ghana using Resfinder and Silva databases and compared them to similar data from pigs and poultry from nine European countries. The pig and poultry were very different in ARG and bacterial abundance and composition. The bacterial communities in the Ghanaian samples also differed substantially from the European samples, especially driven by a much higher abundance of
Subdoligranulum
in both animals. We found lower ARG loads in Ghanaian pigs compared to European counterparts. Among poultry, urban free-range samples exhibited lower ARG abundances compared to the lowest European levels, while rural free-range samples were comparable to the European average, and industrialized samples showed higher ARG abundances. Despite major differences in abundance, the resistome composition of Ghanaian urban, rural, and industrialized poultry samples was similar. Contrasts with European samples were mainly driven by increased abundances of different tetracycline resistance genes in Ghanaian samples, and increased abundances of ARGs encoding resistance to macrolides, beta-lactams, and trimethoprim in Europe. Among pig samples, the main differences were caused by ARGs encoding resistance to nitroimidazoles, beta-lactams, and macrolides in European samples. This study is, to the best of our knowledge, the first report on the resistome measured using metagenomics in livestock from Sub-Saharan Africa.

IMPORTANCE
To the best of our knowledge, this is the first report on the resistomes that are measured using metagenomics in livestock from Sub-Saharan Africa. We find notable differences in the microbiomes between both pigs and poultry, and those also varied markedly compared to similar samples from Europe. However, for both animal species, the same bacterial taxa drove such differences. In pigs and urban free-range poultry, we find a very low abundance of antimicrobial resistance genes (ARGs), whereas rural free-range poultry displayed similarity to the European average, and industrialized poultry exhibited higher levels. These findings show how different African livestock bacterial communities and resistomes are from their European counterparts. They also underscore the importance of continued surveillance and investigation into antimicrobial resistance across diverse ecosystems, contributing significantly to global efforts toward combating the threat of antibiotic resistance.
Tonsils are major sites of persistence of SARS-CoV-2 in children
Authors: Lima Thais Melquiades de , Martins Ronaldo Bragança , Miura Carolina Sponchiado , Souza Maria Vitória Oliveira , Cassiano Murilo Henrique Anzolini , Rodrigues Tamara Silva , Veras Flávio Protásio , Sousa Josane de Freitas , Gomes Rogério , Almeida Glaucia Maria de , Melo Stella Rezende , Silva Gabriela Condé da , Dias Matheus , Capato Carlos Fabiano , Silva Maria Lúcia , Luiz Veridiana Ester Dias de Barros , Carenzi Lucas Rodrigues , Zamboni Dario Simões , Jorge Daniel Macedo de Melo , Cunha Fernando de Queiroz , Tamashiro Edwin , Anselmo-Lima Wilma Terezinha , Valera Fabiana Cardoso Pereira , Arruda Eurico 
Published: September 2023

ABSTRACT

In the present study, we show that SARS-CoV-2 can infect palatine tonsils, adenoids, and secretions in children without symptoms of COVID-19, with no history of recent upper airway infection. We studied 48 children undergoing tonsillectomy due to snoring/OSA or recurrent tonsillitis between October 2020 and September 2021. Nasal cytobrushes, nasal washes, and tonsillar tissue fragments obtained at surgery were tested by RT-qPCR, immunohistochemistry (IHC), flow cytometry, and neutralization assay. We detected the presence of SARS-CoV-2 in at least one specimen tested in 27% of patients. IHC revealed the presence of the viral nucleoprotein in epithelial surface and in lymphoid cells in both extrafollicular and follicular regions, in adenoids and palatine tonsils. Also, IHC for the SARS-CoV-2 non-structural protein NSP-16 indicated the presence of viral replication in 53.8% of the SARS-CoV-2-infected tissues. Flow cytometry showed that CD20
+
B lymphocytes were the most infected phenotypes, followed by CD4+ lymphocytes and CD123 dendritic cells, CD8+ T lymphocytes, and CD14+ macrophages. Additionally, IF indicated that infected tonsillar tissues had increased expression of ACE2 and TMPRSS2. NGS sequencing demonstrated the presence of different SARS-CoV-2 variants in tonsils from different tissues. SARS-CoV-2 antigen detection was not restricted to tonsils but was also detected in nasal cells from the olfactory region. Palatine tonsils and adenoids are sites of prolonged RNA presence by SARS-CoV-2 in children, even without COVID-19 symptoms.

IMPORTANCE
This study shows that SRS-CoV-2 of different lineages can infect tonsils and adenoids in one quarter of children undergoing tonsillectomy. These findings bring advancement to the area of SARS-CoV-2 pathogenesis, by showing that tonsils may be sites of prolonged infection, even without evidence of recent COVID-19 symptoms. SARS-CoV-2 infection of B and T lymphocytes, macrophages, and dendritic cells may interfere with the mounting of immune responses in these secondary lymphoid organs. Moreover, the shedding of SARS-CoV-2 RNA in respiratory secretions from silently infected children raises concern about possible diagnostic confusion in the presence of symptoms of acute respiratory infections caused by other etiologies.