bluuebunny/crossref_metadata_2025_split huggingface dataset:
Methanogens acquire and bioaccumulate nickel during reductive dissolution of nickelian pyrite
Authors: Spietz Rachel L. , Payne Devon , Boyd Eric S. 
Published: October 2023

ABSTRACT

Nickel (Ni) is a key component of the active site metallocofactors of numerous enzymes required for methanogenesis, including [NiFe]-hydrogenase, carbon monoxide dehydrogenase, and methyl CoM reductase, leading to a high demand for Ni among methanogens. However, methanogens often inhabit euxinic environments that favor the sequestration of nickel as metal-sulfide minerals, such as nickelian pyrite [(Ni,Fe)S
2
], that have low solubilities and that are not considered bioavailable. Recently, however, several different model methanogens (
Methanosarcina barkeri
,
Methanococcus voltae
,
Methanococcus maripaludis
) were shown to reductively dissolve pyrite (FeS
2
) and to utilize dissolution products to meet iron and sulfur biosynthetic demands. Here, using
M. barkeri
Fusaro, and laboratory-synthesized (Ni,Fe)S
2
that was physically isolated from cells using dialysis membranes, we show that trace nickel (<20 nM) abiotically solubilized from the mineral can support methanogenesis and limited growth, roughly fivefold less than the minimum concentration known to support methanogenesis. Furthermore, when provided direct contact with (Ni,Fe)S
2
,
M. barkeri
promoted the reductive dissolution of (Ni,Fe)S
2
and assimilated solubilized nickel, iron, and sulfur as its sole source of these elements. Cells that reductively dissolved (Ni,Fe)S
2
bioaccumulated approximately fourfold more nickel than those grown with soluble nickel and sulfide but had similar metabolic coupling efficiencies. While the mechanism for Ni uptake in archaeal methanogens is not known, homologs of the bacterial Nik uptake system were shown to be ubiquitous across methanogen genomes. Collectively, these observations indicate that (Ni,Fe)S
2
is bioavailable in anoxic environments and that methanogens can convert this mineral into nickel-, iron-, and sulfur-containing metalloenzymes to support methanogenesis and growth.

IMPORTANCE

Nickel is an essential metal, and its availability has changed dramatically over Earth history due to shifts in the predominant type of volcanism in the late Archean that limited its availability and an increase in euxinic conditions in the early Proterozoic that favored its precipitation as nickel sulfide minerals. Observations presented herein indicate that the methanogen,
Methanosarcina barkeri
, can acquire nickel at low concentration (<20 nM) from soluble and mineral sources. Furthermore,
M. barkeri
was shown to actively reduce nickelian pyrite; use dissolution products to meet their iron, sulfur, and nickel demands; and bioaccumulate nickel. These data help to explain how
M. barkeri
(and possibly other methanogens and anaerobes) can acquire nickel in contemporary and past anoxic or euxinic environments.
Hyperimmune bovine colostrum containing lipopolysaccharide antibodies (IMM124-E) has a nondetrimental effect on gut microbial communities in unchallenged mice
Authors: Gore Rachele , Mohsenipour Mitra , Wood Jennifer L. , Balasuriya Gayathri K. , Hill-Yardin Elisa L. , Franks Ashley E. 
Published: October 2023

ABSTRACT

Enterotoxigenic
Escherichia coli
(ETEC) is a leading cause of bacterial diarrhea with the potential to cause long-term gastrointestinal (GI) dysfunction. Preventative treatments for ETEC-induced diarrhea exist, yet the effects of these treatments on GI commensals in healthy individuals are unclear. Whether administration of a prophylactic preventative treatment for ETEC-induced diarrhea causes specific shifts in gut microbial populations in controlled environments is also unknown. Here, we studied the effects of a hyperimmune bovine colostrum (IMM-124E) used in the manufacture of Travelan (AUST L 106709) on GI bacteria in healthy C57BL/6 mice. Using next-generation sequencing, we aimed to test the onset and magnitude of potential changes to the mouse gut microbiome in response to the antidiarrheagenic hyperimmune bovine colostrum product, rich in immunoglobulins against select ETEC strains (Travelan, Immuron Ltd). We show that in mice administered colostrum containing lipopolysaccharide (LPS) antibodies, there was an increased abundance of potentially gut-beneficial bacteria, such as
Akkermansia
and
Desulfovibrio,
without disrupting the underlying ecology of the GI tract. Compared to controls, there was no difference in overall weight gain, body or cecal weights, or small intestine length following LPS antibody colostrum supplementation. Overall, dietary supplementation with colostrum containing LPS antibodies produced subtle alterations in the gut bacterial composition of mice. Primarily, Travelan LPS antibody treatment decreased the ratio of Firmicutes/Bacteroidetes in gut microbial populations in unchallenged healthy mice. Further studies are required to examine the effect of Travelan LPS antibody treatment to engineer the microbiome in a diseased state and during recovery.
Responsible and ethical conduct of research (RECR) diagnostic survey using case scenarios from biology course-based undergraduate research experiences (CUREs)
Authors: Monthofer Elizabeth G. , Ito Jewel M. , Battaglia Samantha , Diaz-Martinez Laura A. 
Published: October 2023

ABSTRACT
Course-based undergraduate research experiences (CUREs) are increasingly becoming the first, and perhaps only, research experience for many biology students. Responsible and ethical conduct of research (RECR) is crucial for the integrity of scientific research and essential for students to have an understanding of the scientific process at any academic level. However, there is a current lack of RECR education in biology CUREs. To understand the level of RECR knowledge and skills in undergraduate students, we created a diagnostic survey that uses case scenarios designed to illustrate RECR issues in the CURE classroom. Analysis of students’ responses indicated that the overall percentage of students who are able to effectively use RECR terminology and identify the impact of RECR violations on science integrity and ultimately on society is low. Furthermore, some students equated RECR violations to academic dishonesty, indicating difficulties separating the research and academic aspects of CUREs. This diagnostic tool can aid instructors in identifying gaps in student RECR knowledge for the subsequent development of RECR educational interventions, particularly to ensure the integrity of the research performed in CURE settings.
Xylella fastidiosa
modulates exopolysaccharide polymer length and the dynamics of biofilm development with a β-1,4-endoglucanase
Authors: Castro Claudia , Ndukwe Ikenna , Heiss Christian , Black Ian , Ingel Brian M. , Guevara Matthew , Sun Yuling , Azadi Parastoo , Sun Qiang , Roper M. Caroline 
Published: October 2023

ABSTRACT

Xylella fastidiosa
is a Gram-negative bacterium that causes disease in many economically important crops. It colonizes the plant host xylem and the mouthparts of its insect vectors where it produces exopolysaccharide (EPS) and forms robust biofilms. Typically, the ability to form a biofilm enhances virulence, but
X. fastidiosa
does not fit neatly into that paradigm. Instead,
X. fastidiosa
enters into biofilms to attenuate its movement in the xylem, which, in turn, slows disease progression. In most of its over 600 known plant hosts,
X. fastidiosa
behaves as a benign commensal, but in some hosts like
Vitis vinifera
grapevines, it acts as a pathogen. Its ability to attenuate its own virulence in susceptible hosts may be a remnant of its commensal lifestyle in other hosts. Here, we demonstrate that
X. fastidiosa
utilizes a β-1,4 endoglucanase to cleave its self-produced β-1,4-glucan exopolysaccharide polymer to process it from a higher molecular weight to a lower molecular weight polymer. This processing mediates surface adherence of the cells and ultimately governs overall biofilm architecture, indicating enzymatic pruning of the EPS plays a key role in biofilm-mediated attenuation of
X. fastidiosa in planta
and, thus, is a key vestige that links its commensal behaviors to its parasitic behaviors in specific hosts.

IMPORTANCE

It is well established that exopolysaccharide (EPS) is an integral structural component of bacterial biofilms necessary for assembly and maintenance of the three-dimensional architecture of the biofilm. However, the process and role of EPS turnover within a developing biofilm is not fully understood. Here, we demonstrated that
Xylella fastidiosa
uses a self-produced endoglucanase to enzymatically process its own EPS to modulate EPS polymer length. This enzymatic processing of EPS dictates the early stages of
X. fastidiosa
’s biofilm development, which, in turn, affects its behavior
in planta
. A deletion mutant that cannot produce the endoglucanase was hypervirulent, thereby linking enzymatic processing of EPS to attenuation of virulence in symptomatic hosts, which may be a vestige of
X. fastidiosa
’s commensal behavior in many of its other non-symptomatic hosts.
The cystic fibrosis treatment Trikafta affects the growth, viability, and cell wall of
Aspergillus fumigatus
biofilms
Authors: Jones Jane T. , Morelli Kaesi A. , Vesely Elisa M. , Puerner Charles T. S. , Pavuluri Chetan K. , Ross Brandon S. , van Rhijn Norman , Bromley Michael J. , Cramer Robert A. 
Published: October 2023

ABSTRACT

People with cystic fibrosis (pwCF) commonly test positive for the pathogenic fungus
Aspergillus fumigatus
, which is associated with a decline in lung function. Trikafta is a recently approved therapy for pwCF that improves quantity and function of the CFTR protein; however, it is not known how Trikafta affects microbial communities in the lung. Therefore, the aim of this study was to determine whether Trikafta directly affects
A. fumigatus
growth and biology. While Trikafta did not impact the viability of
A. fumigatus
conidia, treatment of
A. fumigatus
biofilms with Trikafta reduced overall biofilm biomass. This finding was associated with increased membrane permeability, decreased viability, and reduced metabolic activity following long-term treatment of biofilms. Trikafta-induced membrane permeability, and biomass reduction was partially blocked with the calcium channel inhibitor verapamil and fully blocked by the mammalian CFTR inhibitor GlyH-101. Trikafta-induced biomass reduction and metabolic activity was shown to be regulated by the high-osmolarity glycerol pathway gene
sakA
. Trikafta treatment also induced resistance to the cell wall stressor calcofluor white, susceptibility to the anti-fungal drug caspofungin, and decreased inflammatory responses from murine bone marrow cells. Collectively, these results reveal that Trikafta affects infection-relevant
A. fumigatus
biology and host-microbial interactions.

IMPORTANCE

PwCF commonly test positive for pathogenic fungi, and more than 90% of the cystic fibrosis patient population is approved for the modulator treatment, Trikafta. Therefore, it is critical to understand how fungal communities, specifically
A. fumigatus
, respond to Trikafta exposure. Therefore, we sought to determine whether Trikafta impacted the biology of
A. fumigatus
biofilms. Our data demonstrate that Trikafta reduces biomass in several laboratory strains as well as clinical strains isolated from the expectorated sputum of pwCF. Furthermore, Trikafta reduces fungal viability and the capacity of biofilms to recover following treatment. Of particular importance, Trikafta affects how
A. fumigatus
biofilms respond to cell wall stressors, suggesting that Trikafta modulates components of the cell wall. Since the cell wall directly affects how a host immune system will respond to and effectively neutralize pathogens, our work, demonstrating that Trikafta impacts the
A. fumigatus
cell wall, is potentially highly relevant to fungal-induced disease pathogenesis.
Epstein-Barr virus infectious particles initiate B cell transformation and modulate cytokine response
Authors: Baccianti Francesco , Masson Charlène , Delecluse Susanne , Li Zhe , Poirey Remy , Delecluse Henri-Jacques 
Published: October 2023

ABSTRACT
The Epstein-Barr virus (EBV) efficiently transforms primary B cells. Here, we show that this process starts immediately after cellular exposure to infectious viral particles. Virus binding to B cells led to the activation of intracytoplasmic tyrosine kinases and STAT3. Tegument proteins within the virion in turn activated the p38-MK2 pathway upon cell entry, independently of the viral DNA. Engagement of STAT3 and p38/MK2, two pro-inflammatory pathways, was essential for expression of the key EBV transforming gene EBNA2 but also facilitated IL-6 and TNFα release. However, these pathways simultaneously activated ZFP36L1, a stress response protein that targets transcripts with an AU-rich 3′UTR, to reduce IL-6 and TNFα transcription in infected cells. Expression of viral latent proteins after infection amplified the viral effects on p38 and MK2, but also on ZFP36L1, altogether resulting in a transitory and limited increase in IL-6 and TNFα transcription and release. Thus, EBV virions are not merely vehicles that allow injection of the viral DNA into the nucleus but manipulate cellular pathways to initiate transformation while limiting cytokine release.

IMPORTANCE
The Epstein-Barr virus efficiently infects and transforms B lymphocytes. During this process, infectious viral particles transport the viral genome to the nucleus of target cells. We show here that these complex viral structures serve additional crucial roles by activating transcription of the transforming genes encoded by the virus. We show that components of the infectious particle sequentially activate proinflammatory B lymphocyte signaling pathways that, in turn, activate viral gene expression but also cause cytokine release. However, virus infection activates expression of ZFP36L1, an RNA-binding stress protein that limits the length and the intensity of the cytokine response. Thus, the infectious particles can activate viral gene expression and initiate cellular transformation at the price of a limited immune response.
Thioflavin-T does not report on electrochemical potential and memory of dormant or germinating bacterial spores
Authors: Li Yong-qing , He Lin , Aryal Makunda , Wicander James , Korza George , Setlow Peter 
Published: October 2023

ABSTRACT

Bacterial spores are metabolically dormant, resistant to microbicides, and vectors of food spoilage and diseases, while germinated spores are easy to kill. Consequently, understanding germination mechanisms may facilitate the development of “germinate-to-eradicate” strategies. Spores germinate in response to many compounds (called germinants). They can also retain the memory of a germinant exposure, such that a second exposure triggers more efficient germination, but how is not clear. A recent high-profile paper [Science (2022) 378:43] suggested that increasing spore electrochemical potential is how memory is “stored” based on measurements of
Bacillus subtilis
spores’ accumulation of the dye thioflavin-T after germinant exposure. Indeed, we found that wild-type spores of three
Bacillus
and one
Clostridioides
species all exhibited this early thioflavin-T accumulation during nutrient pulses. However, our data indicate that inferring spores’ electrochemical potential from thioflavin-T accumulation is problematic. We found that
B. subtilis
spores lacking their proteinaceous coat exhibited memory but did not accumulate thioflavin-T prior to germinant addition or during nutrient pulses. Furthermore, wild-type
Bacillus
spores germinating with dodecylamine, which also elicits memory, showed no thioflavin-T accumulation. Finally, we found that thioflavin-T accumulation by a germinating spore is outside the spore core at early stages but inside the spore core as germination proceeds. These findings suggest that thioflavin-T accumulation during the early stages of germination is due to its binding to one or more protein in the spore coat rather than to changes in spores’ electrochemical potential; thus, thioflavin-T is not a potentiometric dye for the study of spore memory of germinant pulses.

IMPORTANCE

Bacillus
and
Clostridium
spores cause food spoilage and disease because of spores’ dormancy and resistance to microbicides. However, when spores “come back to life” in germination, their resistance properties are lost. Thus, understanding the mechanisms of spore germination could facilitate the development of “germinate to eradicate” strategies. One germination feature is the memory of a pulsed germinant stimulus leading to greater germination following a second pulse. Recent observations of increases in spore binding of the potentiometric dye thioflavin-T early in their germination of spores led to the suggestion that increasing electrochemical potential is how spores “remember” germinant pulses. However, new work finds no increased thioflavin-T binding in the physiological germination of Coatless spores or of intact spores germinating with dodecylamine, even though spore memory is seen in both cases. Thus, using thioflavin-T uptake by germinating spores to assess the involvement of electrochemical potential in memory of germinant exposure, as suggested recently, is questionable.
Genomic, transcriptomic, and phenotypic differences among archetype
Shigella flexneri
strains of serotypes 2a, 3a, and 6
Authors: Gabor Caitlin E. , Hazen Tracy H. , Delaine-Elias BreOnna C. , Rasko David A. , Barry Eileen M. 
Published: October 2023

ABSTRACT

Shigella
is one of the leading causes of diarrheal disease in low-to-middle income countries, where it accounts for significant disease burden in children under the age of five.
Shigella flexneri
, one of four
Shigella
species, is composed of 15 serotypes and caused 65.9% of all shigellosis cases within the Global Enteric Multicenter Study.
S. flexneri
serotypes 2a, 3a, and 6 are the three leading serotypes implicated in clinical disease, yet there are limited studies examining the variation of pathogenesis and virulence between serotypes. Our data revealed through
in silico
and
in vitro
analysis that several serotype-pecific differences exist between archetype strains 2457T (
S. flexneri
serotype 2a [
Sf
2a]), J17B (
S. flexneri
serotype 3a [
Sf
3a), and CCH060 (
S. flexneri
serotype 6 [
Sf6
]). Comparative genomics of these archetype strains demonstrated that CCH060 contains the greatest amount of unique genomic content compared to the
Sf
3a and
Sf
2a archetype strains, as well as lacks several previously identified
Shigella
virulence genes. The pINV virulence plasmid contains a highly conserved core genome irrespective of the archetype reference strain with the greatest strain-specific genomic features. The transcriptional responses of each archetype strain to bile salt stimulus were unique in a strain-dependent manner. Phenotypic analysis revealed that while archetype strains adhere at similar levels to cultured HT-29 intestinal cells, there are differences in the production and secretion of IpaB, IpaC, and IpaD, as well as reduced invasion by CCH060 compared to 2457T and J17B. Our results identify strain-specific features that support further large-scale analysis to identify unique serotype-specific host-pathogen interactions.

IMPORTANCE

Given the genomic diversity between
S. flexneri
serotypes and the paucity of data to support serotype-specific phenotypic differences, we applied
in silico
and
in vitro
functional analyses of archetype strains of 2457T (
Sf
2a), J17B (
Sf
3a), and CH060 (
Sf
6). These archetype strains represent the three leading
S. flexneri
serotypes recommended for inclusion in multivalent vaccines. Characterizing the genomic and phenotypic variation among these clinically prevalent serotypes is an important step toward understanding serotype-specific host-pathogen interactions to optimize the efficacy of multivalent vaccines and therapeutics. This study underpins the importance for further large-scale serotype-targeted analyses.
Serine protease CrKP43 interacts with MAPK and regulates fungal development and mycoparasitism in
Clonostachys chloroleuca
Authors: Lv Binna , Zhao Xue , Guo Yan , Li Shidong , Sun Manhong 
Published: October 2023

ABSTRACT

Serine proteases are a group of important hydrolytic enzymes that play vital roles in various cellular processes in fungi. In this study, the S8 serine protease-encoding gene
CrKP43
was identified in the highly efficient
Clonostachys chloroleuca
67–1 (formerly
C. rosea
67–1) strain, which was markedly upregulated when parasitizing
Sclerotinia sclerotiorum
. The function of
CrKP43
was investigated using gene deletion and complementation, and the results indicated that the lack of
CrKP43
resulted in deformed fungal hyphae and cell morphology, inhibition of conidiation, and decreased antagonistic activity toward the pathogenic fungus
Fusarium oxysporum
f. sp.
cucumerinum
. Moreover, the mutants displayed much weaker mycoparasitic ability to
S. sclerotiorum
sclerotia and lower control efficiency against soybean
Sclerotinia
rot compared with the wild-type strain. All biological characteristics and biocontrol activities were recovered when the
CrKP43
gene was reinserted into the fungus. Using qRT-PCR analysis and protein-protein interaction assays, it was further proved that the CrKP43 protein interacted with the mitogen-activated protein kinase (MAPK) Crmapk, suggesting serine proteases might be involved in the mycoparasitism of
C. chloroleuca
with the regulation of Crmapk. The findings improve our knowledge of serine proteases and their regulation in mycoparasites and help to illuminate the mechanisms underlying mycoparasitism of
C. chloroleuca
.

IMPORTANCE

Mycoparasites play important roles in the biocontrol of plant fungal diseases, during which they secret multiple hydrolases such as serine proteases to degrade their fungal hosts. In this study, we demonstrated that the serine protease CrKP43 was involved in
C. chloroleuca
development and mycoparasitism with the regulation of Crmapk. To the best of our knowledge, it is the first report on the functions and regulatory mechanisms of serine proteases in
C. chloroleuca
. Our findings will provide new insight into the regulatory mechanisms of serine proteases in mycoparasites and contribute to clarifying the mechanisms underlying mycoparasitism of
C. chloroleuca
, which will facilitate the development of highly efficient fungal biocontrol agents as well.