bluuebunny/crossref_metadata_2025 huggingface dataset:
Balancing the nutrient needs: Optimising growth in Malus sieversii seedlings through tailored nitrogen and phosphorus effects
Authors: Zhou Weiyi , Tao Ye , Peng Lan , Zheng Hongwei , Zhou Xiaobing , Yin Benfeng , Zhang Jing , Zhang Yuanming
Published: August 2024

The impact of nitrogen (N) and phosphorus (P) on the physiological and biochemical processes crucial for tree seedling growth is substantial. Although the study of plant hydraulic traits in response to N and P is growing, comprehensive research on their combined effects remains limited. Malus sieversii, a key ancestral species of modern apples and a dominant species in Xinjiang's Tianshan wild fruit forest, is witnessing a decline due to climate change, pests and diseases, compounded by challenges in seedling regeneration. Addressing this, a 4‐year study was conducted to determine the optimal fertilisation method for it. The experiment explored varying levels of N (N10, N20 and N40) and P (P2, P4 and P8), and their combined effects (N20Px: N20P2, N20P4, N20P8; NxP4: N10P4, N20P4 and N40P4), assessing their impact on gas exchange, hydraulic traits, and the interplay among functional traits in Tianshan Mountains' M. sieversii seedlings. Our study revealed that All N‐inclusive fertilisers slightly promoted the net photosynthetic rate. N10 significantly increasing leaf hydraulic conductivity. All P‐inclusive fertilisers adversely affected hydraulic conductivity. P8, N20P4 and N20P8 notably increased seedlings' vulnerability to embolism. Seedlings can adaptively adjust multiple functional traits in response to nutrient changes. The research suggests N10 and N20 as the most effective fertilisation treatments for M. sieversii seedlings in this region, while fertilisation involving phosphorus is less suitable. This study contributes valuable insights into the specific nutrient needs of it, vital for conservation and cultivation efforts in the Tianshan region.
Participation of the stress‐responsive CDSP32 thioredoxin in the modulation of chloroplast ATP‐synthase activity in Solanum tuberosum
Authors: Rey Pascal , Henri Patricia , Alric Jean , Blanchard Laurence , Viola Stefania
Published: August 2024

Plant thioredoxins (TRXs) are involved in numerous metabolic and signalling pathways, such as light‐dependent regulation of photosynthesis. The atypical TRX CDSP32, chloroplastic drought‐induced stress protein of 32 kDa, includes two TRX‐fold domains and participates in responses to oxidative stress as an electron donor to other thiol reductases. Here, we further characterised potato lines modified for CDSP32 expression to clarify the physiological roles of the TRX. Upon high salt treatments, modified lines displayed changes in the abundance and redox status of CDSP32 antioxidant partners, and exhibited sensitivity to combined saline‐alkaline stress. In non‐stressed plants overexpressing CDSP32, a lower abundance of photosystem II subunits and ATP‐synthase γ subunit was noticed. The CDSP32 co‐suppressed line showed altered chlorophyll a fluorescence induction and impaired regulation of the transthylakoid membrane potential during dark/light and light/dark transitions. These data, in agreement with the previously reported interaction between CDSP32 and ATP‐synthase γ subunit, suggest that CDSP32 affects the redox regulation of ATP‐synthase activity. Consistently, modelling of protein complex 3‐D structure indicates that CDSP32 could constitute a suitable partner of ATP‐synthase γ subunit. We discuss the roles of the TRX in the regulation of both photosynthetic activity and enzymatic antioxidant network in relation with environmental conditions.
Plant growth‐promoting abilities of Methylobacterium sp. 2A involve auxin‐mediated regulation of the root architecture
Authors: Grossi Cecilia E. M. , Tani Akio , Mori Izumi C. , Matsuura Takakazu , Ulloa Rita M.
Published: August 2024

Methylobacterium sp. 2A, a plant growth‐promoting rhizobacteria (PGPR) able to produce indole‐3‐acetic acid (IAA), significantly promoted the growth of Arabidopsis thaliana plants in vitro. We aimed to understand the determinants of Methylobacterium sp. 2A–A. thaliana interaction, the factors underlying plant growth‐promotion and the host range. Methylobacterium sp. 2A displayed chemotaxis to methanol and formaldehyde and was able to utilise 1‐aminocyclopropane carboxylate as a nitrogen source. Confocal microscopy confirmed that fluorescent protein‐labelled Methylobacterium sp. 2A colonises the apoplast of A. thaliana primary root cells and its inoculation increased jasmonic and salicylic acid in A. thaliana, while IAA levels remained constant. However, inoculation increased DR5 promoter activity in root tips of A. thaliana and tomato plants. Inoculation of this PGPR partially restored the agravitropic response in yucQ mutants and lateral root density was enhanced in iaa19, arf7, and arf19 mutant seedlings. Furthermore, Methylobacterium sp. 2A volatile organic compounds (VOCs) had a dose‐dependent effect on the growth of A. thaliana. This PGPR is also able to interact with monocots eliciting positive responses upon inoculation. Methylobacterium sp. 2A plant growth‐promoting effects can be achieved through the regulation of plant hormone levels and the emission of VOCs that act either locally or at a distance.
The B‐box protein BBX13/COL15 suppresses photoperiodic flowering by attenuating the action of CONSTANS in Arabidopsis
Authors: Rahul Puthan Valappil , Yadukrishnan Premachandran , Sasidharan Anagha , Datta Sourav
Published: August 2024

The optimal timing of transition from vegetative to floral reproductive phase is critical for plant productivity and agricultural yields. Light plays a decisive role in regulating this transition. The B‐box (BBX) family of transcription factors regulates several light‐mediated developmental processes in plants, including flowering. Here, we identify a previously uncharacterized group II BBX family member, BBX13/COL15, as a negative regulator of flowering under long‐day conditions. BBX13 is primarily expressed in the leaf vasculature, buds, and flowers, showing a similar spatial expression pattern to the major flowering time regulators CO and FT. bbx13 mutants flower early, while BBX13‐overexpressors exhibit delayed flowering under long days. Genetic analyses showed that BBX13 acts upstream to CO and FT and negatively regulates their expression. BBX13 physically interacts with CO and inhibits the CO‐mediated transcriptional activation of FT. In addition, BBX13 directly binds to the CORE2 motif on the FT promoter, where CO also binds. Chromatin immunoprecipitation data indicates that BBX13 reduces the in vivo binding of CO on the FT promoter. Through luciferase assay, we found that BBX13 inhibits the CO‐mediated transcriptional activation of FT. Together, these findings suggest that BBX13/COL15 represses flowering in Arabidopsis by attenuating the binding of CO on the FT promoter.
Initial treatment choices for long‐term remission of chronic insomnia disorder in adults: a systematic review and network meta‐analysis
Authors: Furukawa Yuki , Sakata Masatsugu , Furukawa Toshiaki A. , Efthimiou Orestis , Perlis Michael
Published: August 2024

Background

We aimed to evaluate the comparative efficacy and acceptability of cognitive behavioral therapy for insomnia (CBT‐I), pharmacotherapy, and their combination in the long and short terms among adults with chronic insomnia disorder.

Methods

We searched multiple databases to December 27, 2023. We included trials in hypnotic‐free adults with chronic insomnia comparing at least two of CBT‐I, pharmacotherapy, or their combination. We assessed the confidence in evidence using CINeMA. The primary outcome was long‐term remission. Secondary outcomes included all‐cause dropout and self‐reported sleep continuity measures in the long term, and the same outcomes in the short term. We performed frequentist random‐effects network meta‐analyses (CRD42024505519).

Findings

We identified 13 trials including 823 randomized participants (mean age, 47.8 years; 60% women). CBT‐I was more beneficial than pharmacotherapy in the long term (median duration, 24 weeks [range, 12 to 48 weeks]; remission odds ratio, 1.82 [95% confidence interval (CI), 1.15–2.87]; [certainty of evidence: high]), while there was weaker evidence of benefit of combination against pharmacotherapy (1.71 [95% CI, 0.88–3.30: moderate]) and no clear difference of CBT‐I against combination (1.07 [95% CI, 0.63–1.80: moderate]). CBT‐I was associated with fewer dropouts than pharmacotherapy. Short‐term outcomes favored CBT‐I over pharmacotherapy except total sleep time. Given the average long‐term remission rate in the pharmacotherapy‐initiating arms of 28%, CBT‐I resulted in a long‐term remission rate of 41% (95% CI, 31%–53%) and combination 40% (95% CI, 25%–56%).

Interpretation

The current study found that starting with CBT‐I for chronic insomnia leads to better outcomes than pharmacotherapy. Combination may be better than pharmacotherapy alone, but unlikely to be worth the additional burden over CBT‐I alone.
Wittgenstein and set theory
Authors: Mühlhölzer Felix
Published: August 2024

Wittgenstein was hostile towards set theory; see his remark in §22 of RFM II: ‘I believe and hope that a future generation will laugh at this hocus pocus’. At the same time, he says that what philosophy owes set theory is ‘tremendous’ and that this is something ‘deep’. I want to clarify these two statements and to reconcile them. The hocus‐pocus remark is mainly directed at the temptation to talk about an own world of sets, focussing on extensions and thereby forgetting the actual mathematical manoeuvres leading to them. Wittgenstein does not shy away from using set‐theoretical symbols and expressions, but he regularly deprives them of their genuine set‐theoretical character. When speaking of the ‘depth’ we encounter with regard to set theory, what he means is the depth explained in PI §111: It arises ‘through a misinterpretation of our forms of language’, and this is particularly so in set theory.
It's not just about the sun, it's about a living: Rural older farmers’ experience of skin cancer risk and prevention
Authors: Yu Shih‐Yin , Hirsch Anne , Zaslavsky Oleg , Cochrane Barbara B.
Published: August 2024

Objective

To understand rural older farmers’ perspectives and attitudes toward skin cancer risk and prevention.

Design and sample

This study used a grounded theory approach and semi‐structured interviews with 12 rural older farmers (farm owners, farmworkers ages 50 years or older) in Washington. Participants’ perspectives were explored relative to Health Belief Model constructs. Inductive and deductive analyses were used to generate relevant themes. COREQ guidelines were followed.

Results

The findings fit well and extended the Health Belief Model, which was used to arrange key themes identified in relation to skin cancer risk and prevention, specifically participants’ perceived barriers to accessing primary care and protection when outdoors, perceived benefits of sun‐protective behaviors, perceived hereditary susceptibility to skin cancer, perceived severity of the increased skin cancer risk, and cues to action for skin checks. A new construct of hope was identified to emphasize the importance of establishing emotional, instrumental, and informational support systems for promoting skin cancer prevention. Participants also indicated their hope of raising awareness of skin cancer prevention among all ages.

Conclusions

Findings highlighted the importance of integrating skin cancer prevention services for rural older farmers and across the lifespan. Public health approaches are needed to enhance the awareness of and access to preventive care in these underserved populations.
Nitrate transporters and mechanisms of nitrate signal transduction in Arabidopsis and rice
Authors: Zhang Xiaojia , Zhang Qian , Gao Na , Liu Mingchao , Zhang Chang , Luo Jiajun , Sun Yibo , Feng Yulong
Published: August 2024

Nitrate (NO3−) is a significant inorganic nitrogen source in soil, playing a crucial role in influencing crop productivity. As sessile organisms, plants have evolved complex mechanisms for nitrate uptake and response to varying soil levels. Recent advancements have enhanced our understanding of nitrate uptake and signaling pathways. This mini‐review offers a comparative analysis of nitrate uptake mechanisms in Arabidopsis and rice. It also examines nitrate signal transduction, highlighting the roles of AtNRT1.1 and AtNLP7 as nitrate receptors and elucidating the OsNRT1.1B‐OsSPX4‐OsNLP3 cascade. Additionally, it investigates nuclear transcriptional networks that regulate nitrate‐responsive genes, controlled by various transcription factors (TFs) crucial for plant development. By integrating these findings, we highlight mechanisms that may help to enhance crop nitrogen utilization.
The Contemporary Presidency: The (vice) presidential pivot? Examining Kamala Harris's messaging before and after the 2022 midterms
Authors: Meeks Lindsey
Published: August 2024

Aspirational vice presidents need to continuously support the president yet still make a name for themselves for future elections. To understand how US VP Kamala Harris attempted to communicatively enact this balance, this study content‐analyzed Harris's official VP and personal Twitter/X accounts leading up to and following the 2022 midterms to determine how she shifted her message emphases before and after the elections and across officeholder and personal accounts. Results indicate she played her “party role” pre‐midterms and “executive branch role” post‐midterms, championed Joe Biden and Democrats but not herself, and used her personal account for campaigning.
Hepatitis B vaccine responders show higher frequencies of CD8+ effector memory and central memory T cells compared to non‐responders
Authors: Vakili Mahsa Eshkevar , Mashhadi Niloofar , Ataollahi Mohammad Reza , Meri Seppo , Kabelitz Dieter , Kalantar Kurosh
Published: August 2024

Hepatitis B (HB) infection is a major global health problem. There is limited knowledge about HB vaccination‐induced immune memory responses. We compared the frequency of CD8+ memory T cell subsets between responders (RSs) and non‐responders (NRs) to HB vaccination. Blood samples were collected from RSs and NRs. PBMCs were cultured in the presence of Hepatitis B surface antigens (HBsAg) and PHA for 48 h to restimulate CD8+ memory T cells and T cell memory subsets were detected by flow cytometry using memory cell markers. The frequency of TEM, TCM, and TCMhi was significantly higher in responders compared to non‐responders (p = 0.024, 0.022, and 0.047, respectively). Additionally, we report a positive correlation between the frequency of TEM cells in RSs with age and anti‐HBsAb level (p = 0.03 and rs = 0.5; p = 0.01 and rs = 0.06). Responders display a higher level of CD8+ T cell‐mediated immunity. Therefore, we suggest a possible defect in the formation of immunological CD8+ memory T cells in NRs and it may reduce antibody production compared to the RSs, although more experiments are needed.
Identification of the novel HLA‐B*51:360 allele in a Chinese individual
Authors: Dong Lina , Li Qi , Wang Fang , Zhang Wei , Zhu Faming
Published: August 2024

HLA‐B*51:360 differs from HLA‐B*51:01:01:01 by a single nucleotide substitution at position 955 G > A in exon 5.
Characterisation of the novel HLA‐DQB1*06:02:62 allele using short‐ and long‐read sequencing technologies
Authors: Oliveira Victoria , Pinto Jonathan , Vianna Romulo , Porto Luís Cristóvão , Secco Danielle
Published: August 2024

The novel HLA‐DQB1*06:02:62 allele, first described in an individual from Brazil.
Validating Silent Gesture Lab Studies in a Naturally Emerging Sign Language: How Order is Used to Describe Intensional Versus Extensional Events in Nicaraguan Sign Language
Authors: Flaherty Molly , Schouwstra Marieke
Published: August 2024

Languages are neither designed in classrooms nor drawn from dictionaries—they are products of human minds and human interactions. However, it is challenging to understand how structure grows in these circumstances because generations of use and transmission shape and reshape the structure of the languages themselves. Laboratory studies on language emergence investigate the origins of language structure by requiring participants, prevented from using their own natural language(s), to create a novel communication system and then transmit it to others. Because the participants in these lab studies are already speakers of a language, it is easy to question the relevance of lab‐based findings to the creation of natural language systems. Here, we take the findings from a lab‐based language emergence paradigm and test whether the same pattern is also found in a new natural language: Nicaraguan Sign Language. We find evidence that signers of Nicaraguan Sign Language may show the same biases seen in lab‐based language emergence studies: (1) they appear to condition word order based on the semantic dimension of intensionality and extensionality, and (2) they adjust this conditioning to satisfy language‐internal order constraints. Our study adds to the small, but growing literature testing the relevance of lab‐based studies to natural language birth, and provides convincing evidence that the biases seen in the lab play a role in shaping a brand new language.
Distributions of exotic herbaceous species along a roadside on Chichijima, the Ogasawara Islands, and their relationship with human disturbance
Authors: Eguchi Aoi , Hata Kenji , Numata Shinya
Published: August 2024

Oceanic islands are a major tourist destination, and the invasion of exotic plants on oceanic islands is a serious problem. To discuss how exotic herbaceous plant invasion is driven by human disturbance on an oceanic island, we assessed the distribution patterns of exotic herbaceous species along a metropolitan road, including parking lots, on the island of Chichijima in the Ogasawara Islands of Japan in the North Pacific Ocean. We observed 16 exotic herbaceous species representing seven families, and all the species have also been recorded in surveys 25 years ago. Species richness (number of species per plot) ranged from 0 to 9 with an average of 2.49. Distance from a parking lot was significantly negatively related to the distribution patterns of seven species and positively related to three species, pointing to parking lots being critical nodes along the dispersal pathways of exotic herbaceous species in Chichijima. Although roads are well known to play an important role as corridors for the invasion and seed dispersal of exotic plants, our results suggest that it would also be important to consider the location of parking lots to understand the distribution of exotic herbaceous species in road networks. We suggest that intensive weed management near parking lots and car wash protocols on Chichijima may be effective in halting exotic species spread.
Modeling of Metal Matrix Concentrated Solar Receivers for Supercritical Carbon Dioxide Power Blocks
Authors: Duggirala Vyas , Hegde Venkatanarasimha , Kumar Pramod , Reddy Venkateswara
Published: August 2024

Supercritical carbon dioxide (sCO2) power blocks for concentrating solar power (CSP) with novel metal matrix solar receivers have the potential to reduce operating expenses while improving overall system efficiencies. These concentrated solar receivers integrated with a metal matrix-based phase change material (PCM) thermal storage medium provide the compounding effect of an efficient heat exchanger while also integrating thermal storage within the receiver. Detailed numerical modeling of such devices with enthalpy–porosity-based formulation for phase change and turbulent convective heat transfer for the sCO2 microchannels is described in the current work. With sCO2 power blocks operating at temperatures and pressures beyond 800 °C and 200 bar, different high-temperature PCMs are studied. Steady-state charging and discharging cycles in addition to transient charging are simulated to analyze the thermal performance of the device. Energy storage density of the PCM is evaluated by tracking the movement of the melt-pool interface along the streamwise direction in a highly corrugated wavy microchannel. A detailed scaling analysis carried out to estimate the order of magnitude of the heat transfer coefficients is found to agree well with the numerical predictions. The outcomes from the current work can be utilized for sizing and detailed design of integrated solar receivers for high temperature sCO2 power block applications.
Experimental Study of the Dynamics of Lean Premixed Hydrogen Flames in a Multi Jet Combustor
Authors: Beuth Jan Paul , Reumschüssel Johann Moritz , von Saldern Jakob G. R. , Ćosić Bernhard , Paschereit Christian Oliver , Oberleithner Kilian
Published: August 2024

In this study, the flame dynamics of lean premixed hydrogen jet flames are experimentally investigated. Acoustic and optical measurement devices are used to capture the response of a bundle of jet flames to acoustic forcing. Using helium as a fuel surrogate, we simulate the change in acoustic properties in the burner during the determination of cold burner transfer matrix (BTM) measurements in order to avoid dangerous experiments. We investigate the influence of the equivalence ratio and the addition of methane as well as the interaction of the individual flames to evaluate the scalability of the results to systems with more flames. It is shown that the changes in the dynamic flame response can primarily be explained by the flame length, which changes both with the methane share and with the equivalence ratio. It can be observed that with small changes in the equivalence ratio, the flame length and the flame transfer function (FTF) change in the same way as with a small change in the gas composition. To assess the scalability of these results, we deactivate some of the jet flames and analyze how the overall response to acoustic forcing changes. We find that the FTF phase is not affected by the number of active flames. Analyzing the respective gain values, significantly stronger responses are measured for a few flames, but only small difference can be measured above a certain number of neighboring flames so that the lab scale results can also be expected to be valid for industrial configurations with a high number of flames.
Centrifugal Compressor Surge in Closed-Loop Systems: Initial Modeling and Comparison With Experiments
Authors: Purushothaman Sreenath , Niccolini Marmont Du Haut Champ Carlo Alberto , Reggio Federico , Silvestri Paolo , Traverso Alberto , Halbe Chaitanya
Published: August 2024

Heat pumps are expected to play a primary role in electrification of thermal users in the residential and industrial sectors. Dynamic compressors are widely used in large size heat pumps, thanks to their industrial replicability, compact size, affordable costs, and good performance in terms of efficiency and low acoustic emissions. The instability, which may occur in a compressor installed in closed-loop cycle such as in a heat pump, is quite different from the classic open loop configuration involving dynamic compressors. This is mainly due to the complexity of the compressor instability mechanism coupled to a vapor compression system connected with two-phase heat exchangers, having different thermal and fluid dynamic capacitance properties, under a physical feedback loop. The aim of this paper is to investigate the behavior of a dynamic compressor installed in an innovative heat pump prototype, of laboratory scale, under stable and unstable conditions. A preliminary simple dynamic model of the compression system consisting of a radial compressor, condenser, and evaporator is developed to represent the heat pump compression system, aiming at its time-dependent representation during compressor instable behavior. The evaporator and condenser are modeled using empirical correlations representing the heat exchange and phase change phenomena and including the thermal capacitances due to refrigerant mass and heat exchanger pipes. The preliminary validation of the dynamic model results is done through a dedicated experimental campaign, under different operating conditions. Results show the complexity of the interaction between the centrifugal compressor and the heat pump loop, discerning the different contributions to the time-dependent response of the system. Future steps will encompass a more detailed modeling of the heat pump loop and the use of updated field measurements, including liquid-level meters in the heat exchangers.
Raffinocyclicin is a novel plasmid-encoded circular bacteriocin produced by
Lactococcus raffinolactis
with broad-spectrum activity against many gram-positive food pathogens
Authors: Miceli de Farias Felipe , O'Connor Paula M. , Buttimer Colin , Kamilari Eleni , Soria Maria Cecilia , Johnson Crystal Nicole , Deliephan Aiswariya , Hill Daragh , Fursenko Oxana , Wiese Jonathan , Draper Lorraine A. , Stanton Catherine , Hill Colin , Ross R. Paul
Published: August 2024

This study describes the discovery and characterization of raffinocyclicin, a novel plasmid-encoded circular bacteriocin, produced by the raw milk isolate
Lactococcus raffinolactis
APC 3967. This bacteriocin has a molecular mass of 6,092 Da and contains 61 amino acids with a three-amino acid leader peptide. It shows the highest identity to the circular bacteriocins bacicyclicin XIN-1 (42.62%), aureocyclicin 4185 (42.62%), and garvicin ML (41.53%). A broad inhibitory spectrum includes strains from
Staphylococcus
,
Enterococcus
,
Streptococcus
,
Micrococcus
,
Lactobacillus
,
Leuconostoc,
and
Listeria
, in addition to a pronounced inhibitory effect against
Lactococcus
and
Clostridium
. It displays low sensitivity to trypsin, most likely as a result of its circular nature. The raffinocyclicin gene cluster is composed of 10 genes: 6 core genes, genes encoding an accessory three-component ABC transporter (
rafCDE
), and a putative transcriptional regulator related to the MutR family. A lack of inhibitory activity in the cell-free supernatant combined with the pronounced activity of cell extracts suggests that the majority of raffinocyclicin is associated with the cell rather than being released to the extracellular environment. This is the first report of a bacteriocin produced by the
L. raffinolactis
species.

IMPORTANCE

The present study aimed to characterize raffinocyclicin, a novel circular bacteriocin produced by the lactic acid bacteria
Lactococcus raffinolactis
APC 3967. Bacteriocins are generally cationic and hydrophobic peptides with antimicrobial activity, which present diverse biotechnological properties of interest for the food industry. Raffinocyclicin inhibits a wide range of bacteria, including foodborne pathogens, and is stable against different treatments which suggest its potential as a natural biopreservative. Whole-genome sequencing and the genetic analysis of the raffinocyclicin gene cluster showed that it is encoded by plasmid that could be used in the future to transfer the ability to produce the bacteriocin to other lactic acid bacteria for industrial applications. These results together highlight the potential of this novel antimicrobial as a biopreservative to be used by the food industry.
Serosurveillance of
Coxiella burnetii
in feral swine populations of Hawaiʻi and Texas identifies overlap with human Q fever incidence
Authors: McMillan Ian A. , Norris Michael H. , Golon Samuel J. , Franckowiak Gregory A. , Grinolds James M. , Goldstein Samuel M. , Phelps Darrin M. , Bodenchuk Michael J. , Leland Bruce R. , Bowen Richard A. , Brown Vienna R. , Borlee Bradley R.
Published: August 2024

Feral swine are invasive in the United States and a reservoir for infectious diseases. The increase in feral swine population and the geographic range are a concern for the spread of zoonotic diseases to humans and livestock. Feral swine could contribute to the spread of
Coxiella burnetii,
the causative agent of human Q fever. In this study, we characterized the seroprevalence of
C. burnetii
in feral swine populations of Hawaiʻi and Texas, which have low and high rates of human Q fever, respectively. Seropositivity rates were as high as 0.19% and 6.03% in Hawaiʻi and Texas, respectively, indicating that feral swine cannot be ruled out as a potential reservoir for disease transmission and spread. In Texas, we identified the overlap between seropositivity of feral swine and human Q fever incidence. These results indicate that there is a potentially low but detectable risk of
C. burnetii
exposure associated with feral swine populations in Hawaiʻi and Texas.
Advanced biology students’ individual conceptions of scientific researchers after participating in biomedically relevant CRE
Authors: Waring-Sparks Ashley L. , Waring-Sparks Rachel A. , Darner Rebekka , Mortimer Nathan T.
Published: August 2024

While undergraduate research has been shown to be a high-impact educational practice, it is logistically impossible for all undergraduate biology majors to have long-term faculty-mentored research experience. Therefore, biology educators and researchers must devise opportunities to engage more students in undergraduate research outside of working directly in their labs. Course-Based Research Experiences (CREs), structured as authentic research experiences, are one such opportunity. In this work, we describe the effects of a CRE with biomedical relevance on students’ research skills, attitudes toward science, and perceptions of scientific research and scientific researchers. Results demonstrate that students gained experience in independent research skills including designing their own research project, being accountable for part of a project, and writing a research proposal. Students’ perceptions of scientific research and researchers, assessed by the Draw-A-Researcher Task, did not show changes among the whole group, but individual analysis yielded meaningful results related to students’ personal changes in how they perceived research and researchers, including their perception of themselves as researchers. This work demonstrates the substantial impact of CREs on upper-level biology undergraduate and graduate students.
Algal exudates promote conjugation in marine Roseobacters
Authors: Duchin Rapp Yemima , Lipsman Valeria , Yuda Lilach , Kublanov Ilya V. , Matsliyah Dor , Segev Einat
Published: August 2024

Horizontal gene transfer (HGT) is a pivotal mechanism driving bacterial evolution, conferring adaptability within dynamic marine ecosystems. Among HGT mechanisms, conjugation mediated by type IV secretion systems (T4SSs) plays a central role in the ecological success of marine bacteria. However, the conditions promoting conjugation events in the marine environment are not well-understood. Roseobacters, abundant marine bacteria commonly associated with algae, possess a multitude of T4SSs. Many Roseobacters are heterotrophic bacteria that rely on algal secreted compounds to support their growth. These compounds attract bacteria, facilitating colonization and attachment to algal cells. Algae and their metabolites bring bacteria into close proximity, potentially promoting bacterial HGT. Investigation across various Roseobacters revealed that algal exudates indeed enhance plasmid transfer through conjugation. While algal exudates do not influence the transcription of bacterial conjugative machinery genes, they promote bacterial attachment, potentially stabilizing proximity and facilitating HGT. Notably, under conditions where attachment is less advantageous, the impact of algal exudates on conjugation is reduced. These findings suggest that algae enhance bacterial conjugation primarily by fostering attachment and highlight the importance of studying bacterial HGT within the context of algal–bacterial interactions.

IMPORTANCE

This study explores how algal–bacterial interactions influence horizontal gene transfer (HGT) among marine bacteria. HGT, a key driver of bacterial evolution, is facilitated by conjugation mediated by type IV secretion systems (T4SSs). Through investigating Roseobacters, abundant marine bacteria often found to be associated with algae, the study reveals that algal exudates enhance plasmid transfer via conjugation. This enhancement is attributed to the promotion of bacterial attachment by algal compounds, emphasizing the role of algal–bacterial interactions in shaping genetic exchange within dynamic marine ecosystems. Understanding these mechanisms is crucial for elucidating bacterial adaptability and evolution in the marine environment.
Physiological role and complex regulation of O
2
-reducing enzymes in the obligate anaerobe
Clostridioides difficile
Authors: Caulat Léo C. , Lotoux Aurélie , Martins Maria C. , Kint Nicolas , Anjou Cyril , Teixeira Miguel , Folgosa Filipe , Morvan Claire , Martin-Verstraete Isabelle
Published: August 2024

Clostridioides difficile
, the major cause of antibiotic-associated diarrhea, is a strict anaerobic, sporulating Firmicutes. However, during its infectious cycle, this anaerobe is exposed to low oxygen (O
2
) tensions, with a longitudinal decreasing gradient along the gastrointestinal tract and a second lateral gradient with higher O
2
tensions in the vicinity of the cells. A plethora of enzymes involved in oxidative stress detoxication has been identified in
C. difficile
, including four O
2
-reducing enzymes: two flavodiiron proteins (FdpA and FdpF) and two reverse rubrerythrins (revRbr1 and revRbr2). Here, we investigated the role of the four O
2
-reducing enzymes in the tolerance to increasing physiological O
2
tensions and air. The four enzymes have different, yet overlapping, spectra of activity. revRbr2 is specific to low O
2
tensions (<0.4%), FdpA to low and intermediate O
2
tensions (0.4%–1%), revRbr1 has a wider spectrum of activity (0.1%–4%), and finally FdpF is more specific to tensions > 4% and air. These different O
2
ranges of action partly arise from differences in regulation of expression of the genes encoding those enzymes. Indeed, we showed that
revrbr2
is under the dual control of σ
A
and σ
B
. We also identified a regulator of the Spx family that plays a role in the induction of
fdp
and
revrbr
genes upon O
2
exposure. Finally,
fdpF
is regulated by Rex, a regulator sensing the NADH/NAD
+
ratio. Our results demonstrate that the multiplicity of O
2
-reducing enzymes of
C. difficile
is associated with different roles depending on the environmental conditions, stemming from a complex multi-leveled network of regulation.

IMPORTANCE

The gastrointestinal tract is a hypoxic environment, with the existence of two gradients of O
2
along the gut, one longitudinal anteroposterior decreasing gradient and one proximodistal increasing from the lumen to the epithelial cells. O
2
is a major source of stress for an obligate anaerobe such as the enteropathogen
C. difficile
. This bacterium possesses a plethora of enzymes capable of scavenging O
2
and reducing it to H
2
O. In this work, we identified the role of the four O
2
-reducing enzymes in the tolerance to the physiological O
2
tensions faced by
C. difficile
during its infectious cycle. These four enzymes have different spectra of action and protect the vegetative cells over a large range of O
2
tensions. These differences are associated with a distinct regulation of each gene encoding those enzymes. The complex network of regulation is crucial for
C. difficile
to adapt to the various O
2
tensions encountered during infection.
ResMAP—a saturation mutagenesis platform enabling parallel profiling of target-specific resistance-conferring mutations in
Plasmodium
Authors: Wall Richard J. , MacGowan Stuart A. , Hallyburton Irene , Syed Aisha J. , Ajay Castro Sowmya , Dey Gourav , Milne Rachel , Patterson Stephen , Phelan Jody , Wiedemar Natalie , Wyllie Susan
Published: August 2024

New and improved drugs are required for the treatment and ultimate eradication of malaria. The efficacy of front-line therapies is now threatened by emerging drug resistance; thus, new tools to support the development of drugs with a lower propensity for resistance are needed. Here, we describe the development of a RESistance Mapping And Profiling (ResMAP) platform for the identification of resistance-conferring mutations in
Plasmodium
drug targets. Proof-of-concept studies focused on interrogating the antimalarial drug target,
Plasmodium falciparum
lysyl tRNA synthetase (
Pf
KRS). Saturation mutagenesis was used to construct a plasmid library encoding all conceivable mutations within a 20-residue span at the base of the
Pf
KRS ATP-binding pocket. The superior transfection efficiency of
Plasmodium knowlesi
was exploited to generate a high coverage parasite library expressing
Pf
KRS bearing all possible amino acid changes within this region of the enzyme. The selection of the library with
Pf
KRS inhibitors, cladosporin and DDD01510706, successfully identified multiple resistance-conferring substitutions. Genetic validation of a subset of these mutations confirmed their direct role in resistance, with computational modeling used to dissect the structural basis of resistance. The application of ResMAP to inform the development of resistance-resilient antimalarials of the future is discussed.

IMPORTANCE

An increase in treatment failures for malaria highlights an urgent need for new tools to understand and minimize the spread of drug resistance. We describe the development of a RESistance Mapping And Profiling (ResMAP) platform for the identification of resistance-conferring mutations in
Plasmodium
spp, the causative agent of malaria. Saturation mutagenesis was used to generate a mutation library containing all conceivable mutations for a region of the antimalarial-binding site of a promising drug target,
Plasmodium falciparum
lysyl tRNA synthetase (
Pf
KRS). Screening of this high-coverage library with characterized
Pf
KRS inhibitors revealed multiple resistance-conferring substitutions including several clinically relevant mutations. Genetic validation of these mutations confirmed resistance of up to 100-fold and computational modeling dissected their role in drug resistance. We discuss potential applications of this data including the potential to design compounds that can bypass the most serious resistance mutations and future resistance surveillance.
A group B streptococcal type VII-secreted LXG toxin mediates interbacterial competition and colonization of the murine female genital tract
Authors: Job Alyx M. , Doran Kelly S. , Spencer Brady L.
Published: August 2024

Group B
Streptococcus
(GBS) asymptomatically colonizes the vagina but can opportunistically ascend to the uterus and be transmitted vertically during pregnancy, resulting in neonatal pneumonia, bacteremia, and meningitis. GBS is a leading etiologic agent of neonatal infection and understanding the mechanisms by which GBS persists within the polymicrobial female genital mucosa has the potential to mitigate subsequent transmission and disease. Type VIIb secretion systems (T7SSb) are encoded by Bacillota and often mediate interbacterial competition using LXG toxins that contain conserved N-termini important for secretion and variable C-terminal toxin domains that confer diverse biochemical activities. Our recent work characterized a role for the GBS T7SSb in vaginal colonization and ascending infection but the mechanisms by which the T7SSb promotes GBS persistence in this polymicrobial niche remain unknown. Herein, we investigate the GBS T7SS in interbacterial competition and GBS niche establishment in the female genital tract. We demonstrate GBS T7SS-dependent inhibition of mucosal pathobiont
Enterococcus faecalis
both
in vitro
using predator-prey assays and
in vivo
in the murine genital tract and found that a GBS LXG protein encoded within the T7SS locus (herein named group
B
streptococcal
L
XG
T
oxin
A
) contributes to these phenotypes. We identify BltA as a T7SS substrate that is toxic to
E. coli
and
S. aureus
upon induction of intracellular expression along with associated chaperones. Finally, we show that BltA and its chaperones contribute to GBS vaginal colonization. Altogether, these data reveal a role for a novel T7b-secreted toxin in GBS mucosal persistence and competition.

IMPORTANCE

Competition between neighboring, non-kin bacteria is essential for microbial niche establishment in mucosal environments. Gram-positive bacteria encoding T7SSb have been shown to engage in competition through the export of LXG-motif-containing toxins, but these have not been characterized in group B
Streptococcus
(GBS), an opportunistic colonizer of the polymicrobial female genital tract. Here, we show a role for GBS T7SS in competition with mucosal pathobiont
Enterococcus faecalis
, both
in vitro
and
in vivo
. We further find that a GBS LXG protein contributing to this antagonism is exported by the T7SS and is intracellularly toxic to other bacteria; therefore, we have named this protein group
B
streptococcal
L
XG
T
oxin
A
(BltA). Finally, we show that BltA and its associated chaperones promote persistence within female genital tract tissues,
in vivo
. These data reveal previously unrecognized mechanisms by which GBS may compete with other mucosal opportunistic pathogens to persist within the female genital tract.
Draft genome of an anaerobic nitrate-reducing, benzene-degrading member of the order
Thermincolales
Authors: Xiao Johnny Z. , Nesbø Camilla L. , Molenda Olivia , Toth Courtney R. A. , Edwards Elizabeth A.
Published: August 2024

We present a metagenome assembled genome (MAG) of an anaerobic bacterium from a nitrate-reducing, benzene-degrading enrichment culture (NRBC). The draft
Thermincolales
genome consists of 20 contigs with a total length of 4.09 Mbp and includes putative carboxylase genes likely involved in benzene activation.
Genomic sequences and annotations of two
Pseudomonas
species isolated from marine and terrestrial habitats
Authors: Manirakiza Eric , Chaumier Timothée , Tirichine Leïla
Published: August 2024

Here, we present the complete genome sequences and annotations of two species of the
Pseudomonas
genus isolated from marine and terrestrial environments. Both genomes and their annotations are available on BacBrowse (
https://BacBrowse.univ-nantes.fr
). This study will contribute to a better understanding of the diversity present within the
Pseudomonas
genus.
Role of glycogen metabolism in
Clostridioides difficile
virulence
Authors: Hasan Md Kamrul , Pizzarro-Guajardo Marjorie , Sanchez Javier , Govind Revathi
Published: August 2024

Glycogen plays a vital role as an energy reserve in various bacterial and fungal species.
Clostridioides difficile
possesses a glycogen metabolism operon that contains genes for both glycogen synthesis and utilization. In our investigation, we focused on understanding the significance of glycogen metabolism in the physiology and pathogenesis of
C. difficile
. To explore this, we engineered a
C. difficile
JIR8094 strain lacking glycogen synthesis capability by introducing a group II intron into the
glgC
gene, the operon’s first component. Quantification of intracellular glycogen levels validated the impact of this modification. Interestingly, the mutant strain exhibited a 1.5-fold increase in toxin production compared with the parental strain, without significant changes in the sporulation rate. Our analysis also revealed that wild-type
C. difficile
spores contained glycogen, whereas spores from the mutant strain lacking stored glycogen showed increased sensitivity to physical and chemical treatments and had a shorter storage life. By suppressing
glgP
expression, the gene coding for glycogen-phosphorylase, via CRISPRi, we demonstrated that glycogen accumulation but not the utilization is needed for spore resilience in
C. difficile
. Transmission electron microscopy analysis revealed a significantly lower core/cortex ratio in
glgC
mutant strain spores. In hamster challenge experiments, both the parental and
glgC
mutant strains colonized hosts similarly; however, the mutant strain failed to induce infection relapse after antibiotic treatment cessation. These findings highlight the importance of glycogen metabolism in
C. difficile
spore resilience and suggest its role in disease relapse.

IMPORTANCE

This study on the role of glycogen metabolism in
Clostridioides difficile
highlights its critical involvement in the pathogen’s energy management, its pathogenicity, and its resilience. Our results also revealed that glycogen presence in spores is pivotal for their structural integrity and resistance to adverse conditions, which is essential for their longevity and infectivity. Importantly, the inability of the mutant strain to cause infection relapse in hamsters post-antibiotic treatment pinpoints a potential target for therapeutic interventions, highlighting the importance of glycogen in disease dynamics. This research thus significantly advances our understanding of
C. difficile
physiology and pathogenesis, offering new avenues for combating its persistence and recurrence.
Overexpression of native carbonic anhydrases increases carbon conversion efficiency in the methanotrophic biocatalyst
Methylococcus capsulatus
Bath
Authors: Lee Spencer A. , Henard Jessica M. , Alba Robyn A. C. , Benedict Chance A. , Mayes Tyler A. , Henard Calvin A.
Published: August 2024

Methanotrophic bacteria play a vital role in the biogeochemical carbon cycle due to their unique ability to use CH
4
as a carbon and energy source. Evidence suggests that some methanotrophs, including
Methylococcus capsulatus
, can also use CO
2
as a carbon source, making these bacteria promising candidates for developing biotechnologies targeting greenhouse gas capture and mitigation. However, a deeper understanding of the dual CH
4
and CO
2
metabolism is needed to guide methanotroph strain improvements and realize their industrial utility. In this study, we show that
M. capsulatus
expresses five carbonic anhydrase (CA) isoforms, one α-CA, one γ-CA, and three β-CAs, that play a role in its inorganic carbon metabolism and CO
2
-dependent growth. The CA isoforms are differentially expressed, and transcription of all isoform genes is induced in response to CO
2
limitation. CA null mutant strains exhibited markedly impaired growth compared to an isogenic wild-type control, suggesting that the CA isoforms have independent, non-redundant roles in
M. capsulatus
metabolism and physiology. Overexpression of some, but not all, CA isoforms improved bacterial growth kinetics and decreased CO
2
evolution from CH
4
-consuming cultures. Notably, we developed an engineered methanotrophic biocatalyst overexpressing the native α-CA and β-CA with a 2.5-fold improvement in the conversion of CH
4
to biomass. Given that product yield is a significant cost driver of methanotroph-based bioprocesses, the engineered strain developed here could improve the economics of CH
4
biocatalysis, including the production of single-cell protein from natural gas or anaerobic digestion-derived biogas.

IMPORTANCE

Methanotrophs transform CH
4
into CO
2
and multi-carbon compounds, so they play a critical role in the global carbon cycle and are of interest for biotechnology applications. Some methanotrophs, including
Methylococcus capsulatus
, can also use CO
2
as a carbon source, but this dual one-carbon metabolism is incompletely understood. In this study, we show that
M. capsulatus
carbonic anhydrases are critical for this bacterium to optimally utilize CO
2
. We developed an engineered strain with improved CO
2
utilization capacity that increased the overall carbon conversion to cell biomass. The improvements to methanotroph-based product yields observed here are expected to reduce costs associated with CH
4
conversion bioprocesses.