bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rumen
Lachnospiraceae
isolate NK3A20 exhibits metabolic flexibility in response to substrate and coculture with a methanogen
Authors: Kaminsky Rachel A. , Reid Peter M. , Altermann Eric , Kenters Nikki , Kelly William J. , Noel Samantha J. , Attwood Graeme T. , Janssen Peter H. 
Published: October 2023

ABSTRACT

Hydrogen (H
2
) is the primary electron donor for methane formation in ruminants, but the H
2
-producing organisms involved are largely uncharacterized. This work integrated studies of microbial physiology and genomics to characterize rumen bacterial isolate NK3A20 of the family
Lachnospiraceae
. Isolate NK3A20 was the first recognized isolate of the NK3A20 group, which is among the ten most abundant bacterial genera in 16S rRNA gene surveys of rumen microbiota. NK3A20 produced acetate, butyrate, H
2
, and formate from glucose. The end product ratios varied when grown with different substrates and at different H
2
partial pressures. NK3A20 produced butyrate as a major product using glucose or under high H
2
partial pressures and switched to mainly acetate in the presence of galacturonic acid (an oxidized sugar) or in coculture with a methanogen. Growth with galacturonic acid was faster at elevated H
2
concentrations, while elevated H
2
slowed growth with glucose. Genome analyses revealed the presence of multiple hydrogenases including a membrane-bound Ech hydrogenase, an electron bifurcating butyryl-CoA dehydrogenase (Bcd-Etf), and an Rnf complex that may be involved in modulating the observed metabolic pathway changes, providing insight into H
2
formation in the rumen.

IMPORTANCE
The genus-level NK3A20 group is one of the ten most abundant genera of rumen bacteria. Like most of the rumen bacteria that produce the hydrogen that is converted to methane in the rumen, it is understudied, without any previously characterized isolates. We investigated isolate NK3A20, a cultured member of this genus, and showed that it modulates hydrogen production in response to its growth substrates and the hydrogen concentration in its environment. Low-hydrogen concentrations stimulated hydrogen formation, while high concentrations inhibited its formation and shifted the fermentation to more reduced organic acid products. We found that growth on uronic acids, components of certain plant polymers, resulted in low hydrogen yields compared to glucose, which could aid in the selection of low-methane feeds. A better understanding of the major genera that produce hydrogen in the rumen is part of developing strategies to mitigate biogenic methane emitted by livestock agriculture.
Selection of mutant
Listeria
phages under food-relevant conditions can enhance application potential
Authors: Schamp Claire N. , Dhowlaghar Nitin , Hudson Lauren K. , Bryan Daniel W. , Zhong Qixin , Fozo Elizabeth M. , Gaballa Ahmed , Wiedmann Martin , Denes Thomas G. 
Published: October 2023

ABSTRACT

Bacteriophages are viruses that infect and kill bacteria. Currently, phage products are available for the control of the pathogen
Listeria monocytogenes
in food products in the United States. In this study, we explore whether experimental evolution can be used to generate phages with improved abilities to function under specific food-relevant conditions. Ultra-pasteurized oat and whole milk were chosen as test matrices as they represent different food groups, yet have similar physical traits and macronutrient composition. We showed that (i) wild-type phage LP-125 infection kinetics are different in the two matrices and (ii) LP-125 has a significantly higher burst size in oat milk. From this, we attempted to evolve LP-125 to have improved infection kinetics in whole milk. Ancestral LP-125 was passaged through 10 rounds of amplification in milk conditions. Plaque-purified DNA samples from milk-selected phages were isolated and sequenced, and mutations present in the isolated phages were identified. We found two nonsynonymous substitutions in
LP125_108
and
LP125_112
genes, which encode putative baseplate-associated glycerophosphoryl diester phosphodiesterase and baseplate protein, respectively. Protein structural modeling showed that the substituted amino acids in the mutant phages are predicted to localize to surface-exposed helices on the corresponding structures, which might affect the surface charge of proteins and their interaction with the bacterial cell. The phage containing the
LP125_112
mutation adsorbed significantly faster than the ancestral phage in both oat and whole milk. Follow-up experiments suggest that fat content may be a key factor for the expression of the phenotype of this mutation.

IMPORTANCE

Bacteriophages are one of the tools available to control the foodborne pathogen,
Listeria monocytogenes
. Phage products must work under a broad range of food conditions to be an effective control for
L. monocytogenes
. Here, we show that the experimental evolution of phages can be used to generate new phages with phenotypes useful under specific conditions. We used this approach to select for a mutant phage that more efficiently binds to
L. monocytogenes
that is grown in whole milk and oat milk. We show that the fat content of these milks is necessary for the expression of this phenotype. Our findings show that experimental evolution can be used to select for improved phages with better performance under specific conditions. This approach has the potential to support the development of condition-specific phage-based biocontrols in the food industry.
Antigenic mapping of the hemagglutinin of the H9 subtype influenza A viruses using sera from Japanese quail (
Coturnix c. japonica
)
Authors: Carnaccini Silvia , Cáceres C. Joaquín , Gay L. Claire , Ferreri Lucas M. , Skepner Eugene , Burke David F. , Brown Ian H. , Geiger Ginger , Obadan Adebimpe , Rajao Daniela S. , Lewis Nicola S. , Perez Daniel R. 
Published: October 2023

ABSTRACT

Influenza A viruses (FLUAV) of the H9N2 subtype are zoonotic pathogens that cause significant economic damage to the poultry industry. Vaccination to prevent and control H9N2 infections in poultry is widely employed in the Middle East and Asia. We used phylogenetics and antigenic analysis to study the antigenic properties of the H9 hemagglutinin (HA) using sera produced in Japanese quail (
Coturnix c. japonica
). Consensus HA1 sequences were generated to capture antigenic diversity among isolates. We constructed chimeric H9N2 viruses containing the HA1 of each consensus sequence on a constant isogenic backbone. The resulting viruses were used to generate antisera from quail, a common and significant minor poultry species whose anti-HA response profiles remain poorly defined. Antigenic maps were generated by plotting the cross-hemagglutination inhibition (HI) data from the panel of quail sera against the chimeric constructs and 51 H9 field isolates. The chimeric antigens were divided into four different antigenic profiles (cyan, blue, orange, and red). Site-directed mutagenesis analysis showed nine amino acid positions of antigenic relevance. Substitutions at amino acid positions 149, 150, and 180 (H9 HA numbering) had relatively significant impact on HI activity using quail sera. Substitutions E180A and R131K/E180A led to the most significant antigenic change transitions. This study provides insights into the antigenic profile of H9 FLUAVs, with important implications for understanding antigenic drift and improving vaccine development for use in minor poultry species.

IMPORTANCE
Determining the relevant amino acids involved in antigenic drift on the surface protein hemagglutinin (HA) is critical to understand influenza virus evolution and efficient assessment of vaccine strains relative to current circulating strains. We used antigenic cartography to generate an antigenic map of the H9 hemagglutinin (HA) using sera produced in one of the most relevant minor poultry species, Japanese quail. Key antigenic positions were identified and tested to confirm their impact on the antigenic profile. This work provides a better understanding of the antigenic diversity of the H9 HA as it relates to reactivity to quail sera and will facilitate a rational approach for selecting more efficacious vaccines against poultry-origin H9 influenza viruses in minor poultry species.
Gain without pain: adaptation and increased virulence of Zika virus in vertebrate host without fitness cost in mosquito vector
Authors: Jaeger Anna S. , Marano Jeffrey , Riemersma Kasen K. , Castaneda David , Pritchard Elise M. , Pritchard Julia C. , Bohm Ellie K. , Baczenas John J. , O'Connor Shelby L. , Weger-Lucarelli James , Friedrich Thomas C. , Aliota Matthew T. 
Published: October 2023

ABSTRACT
Zika virus (ZIKV) is now in a post-pandemic period, for which the potential for re-emergence and future spread is unknown. Adding to this uncertainty is the unique capacity of ZIKV to directly transmit between humans via sexual transmission. Recently, we demonstrated that direct transmission of ZIKV between vertebrate hosts leads to rapid adaptation resulting in enhanced virulence in mice and the emergence of three amino acid substitutions (NS2A-A117V, NS2A-A117T, and NS4A-E19G) shared among all vertebrate-passaged lineages. Here, we further characterized these host-adapted viruses and found that vertebrate-passaged viruses do not lose fitness or transmission potential in mosquitoes. To understand the contribution of genetic changes to the enhanced virulence and transmission phenotype, we engineered these amino acid substitutions, singly and in combination, into a ZIKV infectious clone. We found that NS4A-E19G contributed to the enhanced virulence and mortality phenotype in mice. Further analyses revealed that NS4A-E19G results in increased viral loads and distinct transcriptional patterns for innate immune genes in the brain. None of the substitutions contributed to changes in mosquito vector competence. Together, these findings suggest that direct transmission chains could enable the emergence of more virulent ZIKV strains without compromising mosquito transmission capacity, although the underlying genetics of these adaptations are complex.

IMPORTANCE
Previously, we modeled direct transmission chains of Zika virus (ZIKV) by serially passaging ZIKV in mice and mosquitoes and found that direct mouse transmission chains selected for viruses with increased virulence in mice and the acquisition of non-synonymous amino acid substitutions. Here, we show that these same mouse-passaged viruses also maintain fitness and transmission capacity in mosquitoes. We used infectious clone-derived viruses to demonstrate that the substitution in nonstructural protein 4A contributes to increased virulence in mice.
Evolutionary and spatiotemporal analyses reveal multiple introductions and cryptic transmission of SARS-CoV-2 VOC/VOI in Malta
Authors: Trovao Nidia S. , Pan Vincent , Goel Chirag , Gallego-García Pilar , Liu Yunxi , Barbara Christopher , Borg Rebecca , Briffa Mark , Cilia Chanelle , Grech Laura , Vassallo Mario , Treangen Todd J. , Posada David , Beheshti Afshin , Borg Joseph , Zahra Graziella 
Published: October 2023

ABSTRACT
Genomic surveillance and epidemiology have shed light on the viral diversity driving coronavirus disease 2019 (COVID-19) outbreaks and are important during waves of highly transmissible and immune-escaping variants of interest or of concern (VOCs). We analyzed the epidemiological data of the understudied country of Malta and related the patterns observed with viral genetic sequences obtained through the surveillance system headed by the Mater Dei Hospital and the University of Malta. We reconstructed the evolutionary history and spatiotemporal dynamics of Maltese severe acute respiratory syndrome coronavirus 2 viruses using a phylodynamics framework. Our findings suggest that the number of cases associated with B.1.1.7/Alpha, B.1.617.2.X/Delta, and B.1.1.529.X/Omicron VOCs was nine times higher than those associated with wild-type variants. The positivity rates in Malta remained low to moderate (<10%). A combination of public health interventions appeared to have allowed Malta to mitigate the impact of COVID-19. Our phylodynamic reconstruction traced most of the 173 viral introductions inferred to countries in Northern Europe, which is consistent with flight connectivity patterns. We also observed prolonged periods of cryptic transmission (median = 102 days) until expansion into larger outbreaks. These larger outbreaks were more easily detected by the intermittent genomic surveillance in Malta, characterized by periods of sequencing hiatus. Our study demonstrates that integrating epidemiological and genomic data are crucial for uncovering the COVID-19 dynamics of understudied locations, particularly when genomic surveillance is suboptimal. Accordingly, strengthening the genomic surveillance system in Malta should help in the earlier detection of introductions and minimize viral expansion in the country while informing public health interventions.

IMPORTANCE
Our study provides insights into the evolution of the coronavirus disease 2019 (COVID-19) pandemic in Malta, a highly connected and understudied country. We combined epidemiological and phylodynamic analyses to analyze trends in the number of new cases, deaths, tests, positivity rates, and evolutionary and dispersal patterns from August 2020 to January 2022. Our reconstructions inferred 173 independent severe acute respiratory syndrome coronavirus 2 introductions into Malta from various global regions. Our study demonstrates that characterizing epidemiological trends coupled with phylodynamic modeling can inform the implementation of public health interventions to help control COVID-19 transmission in the community.
New insights into the pathogenesis and transmission of
Brucella pinnipedialis
: systemic infection in two bottlenose dolphins (
Tursiops truncatus
)
Authors: Vargas-Castro Ignacio , Crespo-Picazo José Luis , Fayos Manena , Jiménez-Martínez María de los Ángeles , Torre-Fuentes Laura , Álvarez Julio , Moura André E. , Hernández Marta , Buendía Aranzazu , Barroso-Arévalo Sandra , García-Seco Teresa , Pérez-Sancho Marta , De Miguel María Jesús , Andrés-Barranco Sara , Marco-Cabedo Vicente , Peñin-Villahoz Gaizka , Muñoz Pilar María , Domínguez Lucas , García-Párraga Daniel , Sánchez-Vizcaíno José Manuel 
Published: October 2023

ABSTRACT

The emergence of
Brucella
infections in marine mammals is a growing concern. The present study reports two cases of systemic
Brucella pinnipedialis
infection detected in bottlenose dolphins (
Tursiops truncatus
) pair stranded together in the Cantabrian coast of Spain. Both animals showed systemic lesions associated with the
Brucella
infection, more severe in the younger dolphin, considered the likely offspring of the other individual. Real-time PCR, bacterial culture, and whole-genome sequencing were used to detect and characterize the
Brucella
strains involved in both dolphins. The phylogenetic analysis performed on the
Brucella
genomes retrieved revealed that the species involved was
B. pinnipedialis
(ST25). Both animals resulted seropositive in a commercial multispecies blocking ELISA but tested negative in the standard Rose Bengal test. To the best of our knowledge, this is the first report of a systemic infection resulting in various lesions associated with
Brucella pinnipedialis
(ST25) in two bottlenose dolphins. It is also the initial isolation of
Brucella
in the milk of a non-pregnant or non-aborting female cetacean likely stranded with its offspring. These findings provide new insights into the epidemiology and clinical impact of
B. pinnipedialis
infection in cetaceans and underscore the importance of continued diagnostic surveillance to gain better understanding of brucellosis effects and transmission in marine mammal populations.

IMPORTANCE

Brucella
spp. are zoonotic pathogens that can affect both terrestrial and marine mammals.
Brucella ceti
has been identified in various cetacean species, but only one sequence type (ST27) has been reported in humans. However, it is important to conduct surveillance studies to better understand the impact of marine
Brucella
species on marine mammals, a typically understudied host group. Here, we describe a systemic infection by two related strains of
Brucella pinnipedialis
(ST25) in a couple of live-stranded bottlenose dolphins, with more severe lesions in the younger animal. Furthermore,
B. pinnipedialis
was first detected in milk from a female cetacean that stranded with its offspring. Our study reveals novel insights into the epidemiology and pathological consequences of
B. pinnipedialis
infections in cetaceans, emphasizing the crucial importance of ongoing surveillance and accurate diagnosis to understand the impact of this pathogen on marine mammal populations.
Another tick bites the dust: exploring the association of microbial composition with a broad transmission competence of tick vector species
Authors: Mota Tiago F. , Fukutani Eduardo R. , Martins Kelsilandia A. , Salgado Vanessa R. , Andrade Bruno B. , Fraga Deborah B. M. , Queiroz Artur T. L. 
Published: October 2023

ABSTRACT

Ticks harbor and transmit many different pathogens. While some species are competent vectors of a single pathogen, mono-competent vectors (MCV), other species are proven to be competent vectors of several pathogens, pluri-competent vectors (PCV). Such a difference in vector competence might be related to the microbiome. To better comprehend its influence on the vector competence of ticks for one or several pathogens, a data-driven approach using publicly available databases was applied on bacterial 16S rRNA from MCV and PCV tick species. Alpha and beta diversity, co-occurrence networks, and functional profiles were analyzed. A differential analysis was performed to identify bacterial genera associated with PCV ticks. These tick species presented higher richness, and the bacterial composition showed a significant difference between MCV and PCV ticks. The bacteria genera of PCV ticks demonstrated fewer correlations within each other in comparison with MCV ticks. The differential analysis revealed 14 bacteria genera related to PCV tick species, such as
Rickettsia
,
Staphylococcus
, and
Corynebacterium
. Using 24 differently abundant genera, tick samples from another data set could be classified into either PCV or MCV with high accuracy and concordance. Moreover, pathway regulation related to reactive oxygen species detoxification, β-Lactam resistance, and dTDP-L-rhamnose biosynthesis could be participating in the competence of PCV ticks for several tick-borne pathogens. These findings enlighten our understanding of the bacteria community’s role on some tick species’ broad vector competence.

IMPORTANCE
Some tick species are competent to transmit more than one pathogen while other species are, until now, known to be competent to transmit only one single or any pathogen. Such a difference in vector competence for one or more pathogens might be related to the microbiome, and understanding what differentiates these two groups of ticks could help us control several diseases aiming at the bacteria groups that contribute to such a broad vector competence. Using 16S rRNA from tick species that could be classified into these groups, genera such as Rickettsia and Staphylococcus seemed to be associated with such a broad vector competence. Our results highlight differences in tick species when they are divided based on the number of pathogens they are competent to transmit. These findings are the first step into understanding the relationship between one single tick species and the pathogens it transmits.
Air Composition over the Russian Arctic: 1—Methane
Authors: Antokhina O. Yu. , Antokhin P. N. , Arshinova V. G. , Arshinov M. Yu. , Belan B. D. , Belan S. B. , Guruleva E. V. , Davydov D. K. , Ivlev G. A. , Kozlov A. V. , Law K. , Rasskazchikova T. M. , Paris J.-D. , Savkin D. E. , Simonenkov D. V. , Sklyadneva T. K. , Tolmachev G. N. , Fofonov A. V. 
Published: October 2023

Abstract
In the Arctic, global warming is 2–3 times faster than over other regions of the globe. As a result, noticeable changes are already being recorded in all areas of the environment. However, there is very little data on such changes in the Russian Arctic. Therefore, to fill the gap in the data on the vertical distribution of the gas and aerosol composition of air in this region, an experiment was carried out on the Tu-134 Optik flying laboratory in September 2020 to sound the atmosphere and water surface over the water areas of all seas in the Russian Arctic. This paper analyzes the spatial distribution of methane. It is shown that during the experiment its concentration was the highest over the Kara Sea (2090 ppb) and the lowest over the Chukchi Sea (2005 ppb). The East Siberian and Bering Seas were slightly different from the Chukchi Sea in terms of the methane concentration. Average values of CH4 are characteristic of the Barents (2030 ppb) and the Laptev Seas (2040 ppb). The difference between the concentrations at an altitude of 200 meters and in the free troposphere attained 150 ppb over the Kara Sea, decreased to 91 and 94 ppb over the Barents and Laptev Seas, and further decreased over the East Siberian, Chukchi, and Bering Seas to 66, 63, and 74 ppb, respectively. Horizontal heterogeneity in the distribution of methane over the Arctic seas is the greatest over the Laptev Sea, where it attained 73 ppb. It is two times higher than over the Barents and Kara Seas, and 5–7 times higher than over the East Siberian and Bering Seas.
Deeply virtual compton scattering at future electron-ion colliders
Authors: Xie Gang , Kou Wei , Fu Qiang , Ye Zhenyu , Chen Xurong 
Published: October 2023

AbstractThe study of hadronic structure has been carried out for many years. Generalized parton distribution functions (GPDs) provide broad information on the internal structure of hadrons. Combining GPDs and high-energy scattering experiments, we expect yielding three-dimensional physical quantities from experiments. The Deeply Virtual Compton Scattering (DVCS) process is a powerful tool for studying GPDs. It is one of the important experiments of Electron Ion Collider (EIC) and Electron ion collider at China (EicC) in the future. In the initial stage, the proposed EicC will have polarized electrons with energies of $$3 \sim 5$$

3
∼
5

GeV colliding with polarized protons with energies of $$12 \sim 25$$

12
∼
25

GeV, with luminosity up to $$1 \sim 2 \times 10^{33}$$

1
∼
2
×

10
33

cm$$^{-2}$$

-
2

s$$^{-1}$$

-
1

. EIC, which will be constructed in the coming years, will cover center-of-mass energies ranging from 30 to 50 GeV, with a luminosity of about $$10^{33} \sim 10^{34}$$

10
33

∼

10
34

cm$$^{-2}$$

-
2

s$$^{-1}$$

-
1

. In this work, we present a detailed simulation of DVCS to study the feasibility of experiments at EicC and EIC. Referring the method used by HERMES Collaboration, and comparing the model calculations with pseudo data of asymmetries attributed to the DVCS, we obtained a model-dependent constraint on the total angular momentum of up and down quarks in the proton.