bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparative behavioral responses of grass carp (Ctenopharyngodon idella), bighead carp (Hypophthalmichthys nobilis), and silver carp (H. molitrix) to free amino acids in water
Authors: Wildhaber Mark L. , Beaman Zachary D. , Ditter Karlie K. , West Benjamin M.
Published: October 2024

Control and elimination of invasive fishes, like carps (Order Cypriniformes), may be possible by using chemical stimuli to congregate them for removal. To this end, we tested behavioral responses of grass (Ctenopharyngodon idella), bighead (Hypophthalmichthys nobilis), and silver carp (H. molitrix) to L‐alanine, L‐arginine, L‐glutamic acid, and L‐aspartic acid. In grass carp, the first three amino acids have been shown to be beneficial for growth, and all four produce a strong olfactory response in this species. This study used pairs of conspecific fish in a video‐recorded, sound‐insulated, clear acrylic, tube‐shaped tank; during trials, an amino acid stimulus was delivered at one end of that tank. Changes in space use, velocity, and acceleration across all amino acids differed significantly among species. Changes in space use by grass carp indicated avoidance of only two amino acids, L‐alanine and L‐aspartic acid. There was no evidence for attraction to amino acids for grass or silver carp. For bighead carp, change in spatial use on exposure to amino acids indicated attraction across the four amino acids. This attraction was enhanced by lowered velocity. Our results suggested that olfactory sensitivity does not directly translate to behavioral responses. Other sensory cues, for example tactile, visual, and/or taste, may mediate the selective foraging of grass carp. Amino acids may serve as a better olfactory attractant for bighead carp compared to grass or silver carp.
Comparative effect of traditional and collaborative watershed management approaches on flood components
Authors: Nasiri Khiavi Ali , Vafakhah Mehdi , Sadeghi Seyed Hamidreza , Jun Changhyun , Bateni Sayed M.
Published: October 2024

Identifying the critical areas of flood generation and determining the optimal measures for flood control and management (FCM) is one of the most important basics of watershed management. Therefore, the current study was carried out to prioritize sub‐watersheds (SWs) based on flood generation using physical (Ph‐MA), technical (Te‐MA), comanagerial (Com‐MA), and conjunct management approaches (Con‐MA), as well as determining the quantitative effects of the proposed FCM measures in the Cheshmeh‐Kileh Watershed, Iran. To prioritize SWs based on flood generation, geo‐environmental criteria were used in Ph‐MA, HEC‐HMS software was used in Te‐MA, and semi‐structured interviews with local stakeholders were used in Com‐MA. Finally, using the Condorcet algorithm based on game theory, SWs were prioritized in each approach. In the semi‐structured interviews, stakeholders were asked to provide suggested measures for FCM. Finally, the effect of each measure on the flood components was quantified. Based on the results, the measure of 10% improvement of forest cover in the entire watershed from the category of Con‐MA was selected as the optimal measure. In the return periods of 2, 5, 10, 20, 50, and 100 years, the effectiveness of this measure was 80.08%, 70.09%, 58.10%, 55.67%, 50.58%, and 43.62%, respectively. The influence of Con‐MA based on non‐structural and structural measures on reducing the components of peak flow and flood volume was more than other approaches. In general, it can be concluded that non‐structural measures have more effect than structural measures in FCM in the study watershed. The methods and approaches used in this study can be directly used by local executive managers, decision‐makers, and policymakers of watershed management and flood management activities.
Exploring the Association Between Oral Health Literacy and Oral Health‐Related Quality of Life Among Young Women in the Eastern Province of the Kingdom of Saudi Arabia: A Cross‐Sectional Study
Authors: Alzeer Muneera Essa , AlJameel AlBandary Hassan , Øzhayat Esben Boeskov
Published: October 2024

Objectives

One approach for improving oral health is focusing on oral health literacy (OHL). In this study, we aimed to investigate the association between OHL and oral health‐related quality of life (OHRQoL) and to identify relevant OHL intervention targets that can be used to improve oral health.

Methods

We performed a cross‐sectional questionnaire study among 1889 10th grade female students in the Eastern Province of the Kingdom of Saudi Arabia (KSA). We then assessed OHL using the Arabic version of the short version of the Health Literacy in Dentistry scale (A‐HeLD‐14). OHRQoL was assessed using the 14‐item oral health impact profile (OHIP‐14). Information on socio‐demographics and oral health‐related behaviours (e.g., toothbrushing, sugary diet consumption and dental attendance) was also collected. The relationship between OHL and OHRQoL was investigated using binary logistic regression adjusted for sociodemographic information and oral health‐related behaviours.

Results

In both the adjusted and unadjusted models, poor OHL was significantly associated with OHRQoL problems (odds ration [OR] = 2.90, p < 0.001). Having any OHL problem was significantly associated with having an OHRQoL problem (p < 0.001). The ORs were highest for the domains of financial barriers (OR = 2.49, p < 0.001) and receptivity (OR = 2.16, p < 0.001).

Conclusion

Interventions targeted at individuals with low OHL are crucial to improving OHRQoL in the population. The most relevant interventions concern (a) dedicating time and attention to oral health and (b) financial barriers.
Occurrence, Complete Genome Sequencing, and Development of Diagnostics for Black Pepper Virus F Infecting Black Pepper in India
Authors: Malavika P. , Greeshma M. , Bhat A. I.
Published: October 2024

The occurrence of black pepper virus F (BPVF) was identified for the first time from India, and its complete genome sequence was determined using overlapping fragments obtained through reverse transcription polymerase chain reaction (RT‐PCR). The RNA 1 and RNA 2 of the Indian isolate of BPVF (BPVF‐IND) contained 6376 and 3340 nucleotides potentially coding for proteins of 230.7 kDa and 114 kDa respectively. Comparison of the RNA 1 sequence of BPVF‐IND with that of BPVF from Brazil (BPVF‐ BR‐PA) and China (BPVF‐ ZYP‐1) revealed an identity of 95% and 90%, respectively, while RNA 2 showed an identity of 96% and 90%. The phylogenetic analysis of the Pro‐Pol region of RNA 1 and coat protein region of RNA 2 revealed close clustering of all three BPVF isolates well separated from other species of the genus, Fabavirus. Diagnostics assays based on the RT‐PCR and RT‐recombinase polymerase amplification (RT‐RPA) were developed for the sensitive detection of the virus that will help in the identification and propagation of virus‐free black pepper plants.
Dorsomedian nasopharyngeal masses with benign appearance in dogs: A retrospective medical review of 95 cases among 198 dogs (2019‐2022)
Authors: Petitpre Arthur , Deprez Pauline , Cervone Mario , Magnin Mathieu , Lamoureux Anaïs
Published: October 2024

Background

Dorsomedian nasopharyngeal masses with benign macroscopic appearance are frequently observed during retrograde nasopharyngoscopy, particularly in brachycephalic breeds, but are not well described.

Hypothesis/Objectives

To characterize these masses, assess their frequency, and identify the potential factors associated with their presence.

Animals

Dogs that underwent retrograde nasopharyngoscopy at a private hospital.

Methods

Medical records between November 2019 and October 2022 were retrospectively reviewed. Dogs were included if suitable nasopharynx images were available for review. Univariable and multivariable logistic regression analyses were performed to determine the factors associated with these masses.

Results

One‐hundred ninety‐eight dogs met the inclusion criteria of which 47.9% (95/198) had a dorsal nasopharyngeal mass. The masses measured <10%, 10%‐30%, and >30% of the nasopharyngeal height in 64.2% (61/95), 28.4% (27/95), and 7.4% (7/95) of cases, respectively. Univariable analysis identified associations between the presence of a nasopharyngeal mass and several factors: brachycephalic conformation (P < .001), sleep disturbances (P = .04), presence of laryngeal collapse (P = .01), and aberrant caudal turbinates (P = .04). However, according to the multivariable analysis, only the association between the presence of a mass and brachycephalic conformation was significant (odds ratio = 2.3 [1.1; 5.0], P = .03).

Conclusion and Clinical Importance

Dorsomedian nasopharyngeal masses were common in the studied dog population. These masses are mostly small and have the same appearance across breeds. Brachycephalic conformation appears to be associated with the presence of a mass.
Piercing the Mystery: Predator Identification Using the Perforated Tests of the Sea Urchin Brissus unicolor (Leske, 1778)
Authors: Rufino‐Navarro Andrés , Alfonso Beatriz , Nebelsick James H. , Hernández José Carlos
Published: October 2024

Drilling predation on echinoids (sea urchins) has been known to occur in marine ecosystems since the Jurassic Period; however, it has rarely been studied in existing species. Tests of the irregular sea urchin Brissus unicolor (Leske, 1778), which frequently occurs in shallow substrates of the Canary Islands, mostly show very evident perforations through their skeletons. The aim of this study was to describe the characteristics of these perforations in order to determine their possible origins as well as document their size, site selectivity, and frequency of occurrence among different sample sites. Of the 104 tests of B. unicolor that were collected from 15 locations off the island of Tenerife (Canary Islands, Spain), 94% showed a least one perforation. These boreholes exhibit a circular morphology, penetrating the sea urchin tests perpendicularly and entirely. Notably, they display a unique acid signature, diverging from those documented in the fossil record and other relevant studies. Our analysis showed size and site selectivity by the predator as the perforations were mainly located on the oral side of the test. The perforations are attributed to drilling predation. The characteristics of these boreholes on B. unicolor match published records of predation marks suggesting that they are produced by the predatory gastropod family Cassidae, with Semicassis undulata (Gmelin, 1791) considered to be the most probable predator.
Time‐based versus competency‐based medical education: Opportunities and challenges
Authors: Khachadoorian‐Elia Holly R.
Published: October 2024

Commenting on Wyatt and Vidal's dialogue about the relationship between time and culture, @hollykhach outlines opportunities and challenges of adopting competency‐based education.
The poplar SWEET1c glucose transporter plays a key role in the ectomycorrhizal symbiosis
Authors: Li Rui , Shi Wensheng , Zhang Pan , Ma Jianan , Zou Rong , Zhang Xinyin , Kohler Annegret , Martin Francis M. , Zhang Feng
Published: October 2024

The mutualistic interaction between ectomycorrhizal fungi and trees is characterized by the coordinated exchange of soil nutrients with soluble sugars. Despite the importance of this process, the precise mechanism by which sugars are transported from host roots to colonizing hyphae remains unclear.

This study aimed to identify the specific membrane transporters responsible for the unloading of sugars at the symbiotic interface, with a focus on the role of the root Sugars Will Eventually Be Exported Transporter (SWEET) uniporters.

Our study used RNA sequencing and quantitative PCR to identify PtaSWEET gene expression in Populus tremula × alba–Laccaria bicolor ectomycorrhizal root tips. Our results suggest that symbiosis‐induced PtaSWEET1c is primarily responsible for transporting glucose and sucrose, as demonstrated by the yeast assays. Moreover, we used a promoter‐YFP reporter to confirm the localization of the PtaSWEET1c expression in cortical cells of ectomycorrhizal rootlets, supporting its major role in supplying glucose at the symbiotic interface. Furthermore, our observations confirmed the localization of PtaSWEET1c‐GFP in the plasma membrane. The inactivation of PtaSWEET1c reduced ectomycorrhizal root formation and 13C translocation to ectomycorrhizal roots.

Our findings highlight the crucial role of PtaSWEET1c in facilitating glucose and sucrose transport at the symbiotic interface of Populus–L. bicolor symbiosis.
Spatial, environmental and functional distances among temporal ponds attenuate synchronization, stabilizing plant richness and biomass dynamics
Authors: Sosa‐Panzera Lucía , Pinelli Verónica , Arim Matias
Published: October 2024

Synchronized dynamics reduces ecosystem stability, as local variations in biomass or richness are directly propagated to variations in metacommunity dynamics. Synchronization of biodiversity dynamics can occur due to dispersal among communities and similar responses of different communities to correlated environmental variations, the Moran effect. This congruent response of different communities to environmental dynamics depends on their similar functional composition, which is determined by the similarity in local conditions and the spatial distance between them. In a metacommunity of 51 temporary ponds that were surveyed for 14 years, we evaluated the existence of synchronized dynamics in plant richness and biomass among communities, and their association with temporal stability. A wide range of dynamics was observed, from asynchronous to synchronous rhythms. Path analysis based on Mantel tests supported the decoupling of richness dynamics by the geographic, environmental, and functional distances between pairs of communities. Only the functional distance between communities weakly affected biomass synchrony. Synchrony in both richness and biomass between communities reduced the stability of the biomass dynamic. While synchrony in richness reduced its stability, synchrony in biomass enhanced the stability in richness dynamic. The role of rare species in richness dynamics and of dominant species in biomass dynamics may explain the observed discrepancies. Consequently, the size of metacommunities (the spatial extent and number of local communities), spatial heterogeneity, and functional diversity promote ecosystem stabilization by the mechanisms evidenced here. Climate change, environmental homogenization and landscape fragmentation may drive the synchronization and destabilization of biodiversity dynamics.
Montane grassland recovery: lessons from 25 years of the Working for Water program on the northern Drakensberg Escarpment, South Africa
Authors: Chikowore Gerald , Bologo Nthambeleni , Steenhuisen Sandy‐Lynn , Martin Grant
Published: October 2024

Despite their strategic importance as biodiversity hotspots and water sources, montane ecosystems are among the most neglected conservation areas. In particular, the monitoring and management of invasive alien plants in this critical biome is limited. This study presents an analysis of long‐term invasive alien plant removal within montane grassland ecosystems, drawing on insights from 25 years of the Working for Water (WfW) program on the northern Drakensberg Escarpment. We assessed the response of vegetation communities to invasive alien plant removal in this region. Using data from the WfW program on clearance activities, expenditure, and re‐visit times, we compared plant species richness, diversity, and composition in sites managed under the WfW program to adjacent patches of pristine vegetation. Results showed minimal variation in species richness between cleared sites and unmanaged sites. However, these vegetation communities remain distinctly dissimilar across sites. These findings suggest the need for active restoration of montane vegetation communities if they are to return to their natural condition and further highlight the need to conserve the remaining habitats for critically endangered species, even in their depauperate state.
A control chart for monitoring image processes based on convolutional neural networks
Authors: Okhrin Yarema , Schmid Wolfgang , Semeniuk Ivan
Published: October 2024

In this paper, the problem of monitoring image processes with spatially correlated pixels over time is considered. An exponentially weighted moving average (EWMA) control chart for monitoring such processes based on a convolutional neural network (CNN) is proposed. A comparison of its performance with a Hotelling's control chart and with a control chart based on generalized likelihood ratio (GLR) approach is conducted through a simulation study. The new method outperforms other methods in most of the cases considered in the simulation study. A technique for mean intensity shift localization based on CNNs is proposed and evaluated.
Preferences in treating polyomavirus infection in kidney transplant recipients: A discrete choice experiment with patients, caregivers, and clinicians
Authors: Chong Chanel H. , Wong Germaine , Au Eric H. , Scholes‐Robertson Nicole , Muthuramalingam Shyamsundar , Roger Simon D. , Keung Karen , Jaure Allison , Teixeira‐Pinto Armando , Howell Martin
Published: October 2024

Background

Treatment strategies for BK polyomavirus (BKPyV) infection in kidney transplant recipients are heterogeneous among clinicians. We aimed to identify the treatment preferences of key stakeholders for BKPyV infection and measure the trade‐offs between treatment outcomes.

Methods

Adult kidney transplant recipients, caregivers, and clinicians were eligible to participate in a discrete choice experiment between February 2021 and June 2022. The five treatment‐related attributes were achieving viral clearance and optimal graft function, as well as reducing the risk of graft loss, acute rejection, and complications. Results were analyzed using multinomial logistic models.

Results

In total, 109 participants (57 kidney transplant recipients, 10 caregivers, and 42 health professionals) were included. The most important attribute was the risk of graft loss, followed by side effects and acute rejection. As the risk of graft loss increased, all participants were less inclined to accept an assigned treatment strategy. For instance, if graft loss risk was increased from 1% to 50%, the probability of uptake of a treatment strategy for BKPyV infection was reduced from 87% to 3%.

Conclusion

Graft loss is the predominant concern for patients, caregivers, and health professionals when deciding on the treatment for BKPyV infection, and should be included in intervention trials of BKPyV infection.

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Geometry of symplectic flux and Lagrangian torus fibrations
Authors: Shelukhin Egor , Tonkonog Dmitry , Vianna Renato
Published: October 2024

Symplectic flux measures the areas of cylinders swept in the process of a Lagrangian isotopy. We study flux via a numerical invariant of a Lagrangian submanifold that we define using its Fukaya algebra. The main geometric feature of the invariant is its concavity over isotopies with linear flux. We derive constraints on flux, Weinstein neighbourhood embeddings and holomorphic disk potentials for Gelfand–Cetlin fibres of Fano varieties in terms of their polytopes. We also describe the space of fibres of almost toric fibrations on the complex projective plane up to Hamiltonian isotopy, and provide other applications.
Enhancing Production in Robot-Enabled Manufacturing Systems: A Dynamic Model and Moving Horizon Control Strategy for Mobile Robot Assignment
Authors: Bhatta Kshitij , Chang Qing
Published: October 2024

This article presents a dynamic mathematical model for a robot-enabled manufacturing system, where mobile robots independently manage workstation tasks. Each robot possesses one or multiple skills, enabling collaborative work at workstations. A real-time robot assignment problem is formulated to maximize production of the system, and a novel control strategy is developed to address this problem. Leveraging system properties derived from the model and moving window downtime prediction, the problem of maximizing system production is transformed into a more tractable control problem focused on identifying and achieving ideal clean configurations. The proposed solution significantly outperforms various benchmarks, including a pure reinforcement learning-based strategy, underscoring the importance of system understanding and its crucial role in enhancing flexibility and productivity in manufacturing systems.
Synthesis of group-IV ternary and binary semiconductors using epitaxy of GeH3Cl and SnH4
Authors: Zhang Aixin , Ringwala Dhruve A. , Mircovich Matthew A. , Roldan Manuel A. , Kouvetakis John , Menéndez José
Published: October 2024

Ge1−x−ySixSny alloys were grown on Ge buffers via reactions of SnH4 and GeH3Cl. The latter is a new CVD source designed for epitaxial development of group-IV semiconductors under low thermal budgets and CMOS-compatible conditions. The Ge1−x−ySixSny films were produced at very low temperatures between 160 and 200 °C with 3%–5% Si and ∼5%–11% Sn. The films were characterized using an array of structural probes that include Rutherford backscattering, x-ray photoelectron spectroscopy, high-resolution x-ray diffraction, scanning transmission electron microscopy, and atomic force microscopy. These studies indicate that the films are strained to Ge and exhibit defect-free microstructures, flat surfaces, homogeneous compositions, and sharp interfaces. Raman was used to determine the compositional dependence of the vibrational modes indicating atomic distributions indistinguishable from those obtained when using high-order Ge hydrides. For a better understanding of the growth mechanisms, a parallel study was conducted to investigate the GeH3Cl applicability for synthesis of binary Ge1−ySny films. These grew strained to Ge, but with reduced Sn compositions and lower thicknesses relative to Ge1−x−ySixSny. Bypassing the Ge buffers led to Ge1−ySny-on-Si films with compositions and thicknesses comparable to Ge1−ySny-on-Ge; but their strains were mostly relaxed. Efforts to increase the concentration and thickness of Ge1−ySny-on-Si resulted in multiphase materials containing large amounts of interstitial Sn. These outcomes suggest that the incorporation of even small Si amounts in Ge1−x−ySixSny might compensate for the large Ge–Sn mismatch by lowering bond strains. Such an effect reduces strain energy, enhances stability, promotes higher Sn incorporation, and increases critical thickness.
Scalable fabrication approach and fill factor optimization for single pixel microlens arrays
Authors: Bonitz Jens , Helke Christian , Dittmar Nils , Schermer Sebastian , Haase Micha , Hofmann Lutz , Reuter Danny
Published: October 2024

Microlenses are a suitable approach to improve the performance of optical systems. An important optical efficiency determining parameter is the fill factor, which describes the relation of the lens area to the total optical active area. In this work, an optimization of the fill factor by optimizing the fabrication process steps is presented. The approach here is the use of i-line waferstepper lithography in combination with thermal reflow of photoresist and subsequent 1:1 pattern transfer in the lens material by reactive ion etching. For this method, the fill factor is determined by the minimum lens gap and, thus, the optical efficiency is strongly limited by the resolution limit of the i-line waferstepper lithography (350 nm). The goal of this investigation is to achieve the lowest possible lens gap even below the stepper-based resolution limit by optimizing each single process step without developing a new approach. The final result of the optimization was a fill factor improvement of 15%.
A high-resolution method for direction of arrival estimation based on an improved self-attention module
Authors: Fu Xiaoying , Sun Dajun , Teng Tingting
Published: October 2024

The high-resolution direction of arrival (DOA) estimation is a prominent research issue in underwater acoustics. The existing high-resolution methods include subspace methods and sparse representation methods. However, the performance of subspace methods suffers from low signal-to-noise ratio (SNR) and limited snapshots conditions, and the computational complexity of sparse representation methods is too high. The neural network methods are emerging high-resolution methods. However, insufficient support for big data is frequently observed in underwater acoustics, and conventional network structures present challenges in further enhancing performance. To address the aforementioned problems, we propose a neural network method based on an improved self-attention module to achieve high accuracy and robust DOA estimation. First, we design a multi-head self-attention module with large-scale convolutional kernels and residual structures to improve the estimated accuracy. Second, we propose an improved input feature to enhance the robustness to non-uniform noise and unequal-intensity targets. The simulations demonstrate that the proposed method exhibits superior angle resolution compared to sparse representation methods under the same simulation conditions. The proposed method demonstrates exceptional accuracy and robustness in DOA estimation under challenging conditions of low SNR, limited snapshots, and unequal-intensity targets. The experimental results further prove the effectiveness of the proposed method.
Enhancing ultrasonic attenuation images through multi-frequency coupling with total nuclear variation
Authors: Miranda Edmundo A. , Basarab Adrian , Lavarello Roberto
Published: October 2024

Quantitative ultrasound is a non-invasive image modality that numerically characterizes tissues for medical diagnosis using acoustical parameters, such as the attenuation coefficient slope. A previous study introduced the total variation spectral log difference (TVSLD) method, which denoises spectral log ratios on a single-channel basis without inter-channel coupling. Therefore, this work proposes a multi-frequency joint framework by coupling information across frequency channels exploiting structural similarities among the spectral ratios to increase the quality of the attenuation images. A modification based on the total nuclear variation (TNV) was considered. Metrics were compared to the TVSLD method with simulated and experimental phantoms and two samples of fibroadenoma in vivo breast tissue. The TNV demonstrated superior performance, yielding enhanced attenuation coefficient slope maps with fewer artifacts at boundaries and a stable error. In terms of the contrast-to-noise ratio enhancement, the TNV approach obtained an average percentage improvement of 34% in simulation, 38% in the experimental phantom, and 89% in two in vivo breast tissue samples compared to TVSLD, showing potential to enhance visual clarity and depiction of attenuation images.
Differential expression of the
yfj
operon in a
Bacillus subtilis
biofilm
Authors: Finn James P. , Luzinski Cora , Burton Briana M.
Published: October 2024

Type VII protein secretion systems play an important role in the survival and virulence of pathogens and in the competition among some microbes. Potential polymorphic toxin substrates of the type VII secretion system (T7SS) in
Bacillus subtilis
are important for competition in the context of biofilm communities. Within a biofilm, there is significant physiological heterogeneity as cells within the population take on differential cell fates. Which cells express and deploy the various T7SS substrates is still unknown. To identify which cells express at least one of the T7SS substrates, we investigated the
yfj
operon. The
yfjABCDEF
operon encodes at least one predicted T7SS substrate. Starting with an
in silico
analysis of the
yfj
operon promoter region, we identified potential regulatory sequences. Using a
yfj
promoter-reporter fusion, we then identified several regulators that impact expression of the operon, including a regulator of biofilm formation, DegU. In a
degU
deletion mutant,
yfj
expression is completely abolished. Mutation of predicted DegU binding sites also results in a significant reduction in
yfj
reporter levels. Further analysis of
yfj
regulation reveals that deletion of
spo0A
has the opposite effect of the
degU
deletion. Following the
yfj
reporter by microscopy of cells harvested from biofilms, we find that the
yfj
operon is expressed specifically in the subset of cells undergoing sporulation. Together, our results define cells entering sporulation as the subpopulation most likely to express products of the
yfj
operon in
B. subtilis
.

IMPORTANCE

Differential expression of genes in a bacterial community allows for the division of labor among cells in the community. The toxin substrates of the type VII secretions system (T7SS) are known to be active in
Bacillus subtilis
biofilm communities. This work describes the expression of one of the T7SS-associated operons, the
yfj
operon, which encodes the YFJ toxin, in the sporulating subpopulation within a biofilm. The evidence that the YFJ toxin may be deployed specifically in cells at the early stages of sporulation provides a potential role for deployment of T7SS in community-associated activities, such as cannibalism.
Near-atomic structures of RHDV reveal insights into capsid assembly and different conformations between mature virion and VLP
Authors: Ruan Zhiyang , Shao Qianqian , Song Yanhua , Hu Bo , Fan Zhiyu , Wei Houjun , Liu Yunshu , Wang Fang , Fang Qianglin
Published: October 2024

Rabbit hemorrhagic disease virus (RHDV) poses a significant threat to rabbits, causing substantial economic losses in rabbit farming. The virus also endangers wild populations of rabbit species and the predatory animals that rely on rabbits as a food source, thereby disturbing the ecological balance. However, the structural understanding of RHDV has been limited due to the lack of high-resolution structures. Here, we present the first high-resolution cryo-EM structures of the mature virion and virus-like particles (VLPs) derived from both full-length and N-terminal arm (NTA)-truncated VP60. These structures reveal intricate structural details of the icosahedral capsid and crucial NTA-mediated interactions essential for capsid assembly. In addition, dramatic conformational differences are unexpectedly observed between the mature virion and VLP. The protruding spikes of the A-B dimers adopt a “raised” state in the mature virion and a “resting” state in the VLP. These findings enhance our understanding of the structure, assembly, and conformational dynamics of the RHDV capsid, laying the essential groundwork for further virological research and therapeutic advancements.

IMPORTANCE

RHDV is a pathogen with significant economic and ecological impact. By presenting the first high-resolution cryo-EM structures of RHDV, we have uncovered detailed interactions among neighboring VP60 subunits of the icosahedral capsid. The NTA of VP60 is uniquely clustered around the threefold axis of the capsid, probably play a critical role in dragging the six VP60 dimers around the threefold axis during capsid assembly. Additionally, we observed dramatic conformational differences between the mature virion and VLPs. VLPs are commonly used for vaccine development, under the assumption that their structure closely resembles that of the mature virion. Our findings significantly advance the understanding of the RHDV capsid structure, which may be used for developing potential therapeutic strategies against RHDV.
Complete genome sequence of
Borrelia miyamotoi
strain MN18-0001, an Am-East-2 strain type isolate derived from an
Ixodes scapularis
tick (Minnesota)
Authors: Kneubehl Alexander R. , Osikowicz Lynn M. , Parise Christina M. , Van Gundy Taylor J. , Replogle Adam J. , Lopez Job E. , Eisen Rebecca J. , Hojgaard Andrias
Published: October 2024

We report the genomic sequence of the hard tick relapsing fever spirochete
Borrelia miyamotoi
strain MN18-0001.
B. miyamotoi
causes human illness and is geographically widespread in
Ixodes
spp. (Acari: Ixodidae) ticks. This is a chromosome- and plasmid-resolved genome assembly of an Am-East-2 strain type isolate from the midwestern United States.
Metagenome-assembled genomes of
Macrocystis
-associated bacteria
Authors: Aguirre Emily G. , Schwartzman Julia A.
Published: October 2024

Microbes are important for the development of kelp, but little is understood about the functions encoded by these microbes. Here, we assembled 1,794 metagenome-associated genomes (MAGs) from bacteria that colonize gametophytes of the giant kelp
Macrocystis pyrifera
. MAGs were grouped into 149 dereplicated strains. Functional annotation is also presented.
The draft genome sequence of a carbapenem-resistant
Klebsiella pneumoniae
strain belonging to sequence type 11 and capsular type 62
Authors: Zhang Linwan , Feng Yu , Yang Yongqiang , He Yanling , Zong Zhiyong
Published: October 2024

Carbapenem-resistant
Klebsiella pneumoniae
(CRKP) of sequence type 11 (ST11) and capsular type KL47 or KL64 are dominant in China. We report the draft genome sequence of an ST11
bla
KPC-2
-carrying CRKP strain belonging to uncommon capsular type KL62. This strain carries virulence factors encoding multiple iron acquisition systems and mucoid regulators.
Genetic insight into the relationship between inflammatory bowel disease and
Clostridioides difficile
infection
Authors: Cushing-Damm Kelly C. , Chen Yanhua , Du Xiaomeng , Kuppa Annapurna , Raut Chinmay , Oliveri Antonino , Chen Vincent L. , Vanderwerff Brett , Zawistowski Matt , Rao Krishna , Higgins Peter , Speliotes Elizabeth K.
Published: October 2024

Patients with inflammatory bowel disease (IBD) are at increased risk of
Clostridioides difficile
infection (CDI). Herein, we aimed to determine if genetic risk contributes to this observed association. We carried out a genome-wide association study (GWAS) analysis in the Michigan Genomics Initiative and the United Kingdom Biobank for CDI based on ICD codes and meta-analyzed these results with similar publicly accessible GWAS summary statistics from Finngen. Conditional and joint multi-SNP analyses were used to identify independent associations. Imputation of the human leukocyte antigen (HLA) region with fine mapping was used to try to identify causal HLA allele groups. Two-sample bidirectional Mendelian randomization (MR) was implemented to determine causal relationships between IBD and CDI. A total of 3,500 cases of CDI and 674,323 controls were meta-analyzed, revealing one genome-wide significant variant for CDI,
HLA-C;LINC02571
-rs3134745-C (
P
= 4.27E−08), which annotated to the major histocompatibility complex on chromosome 6. While fine mapping did not identify a statistically significant HLA allele group, there was a suggestive signal for
HLA-B
*35:01 (
P
= 4.74e−04). Using two-sample MR, genetically predicted IBD was associated with increased risk of CDI (MR Egger [odds ratio {OR} 1.16, 95% confidence interval {CI} 1.02–1.31]). Subset analysis revealed that risk was primarily driven by genetically predicted ulcerative colitis (MR Egger [OR 1.22, 95% CI 1.05–1.41]). These results highlight the importance of the host immune response in CDI pathogenesis, help explain the observed relationship between IBD and CDI, and open new avenues for targeted treatment of CDI in IBD.

IMPORTANCE

Data from this paper (i) provide reproducible evidence that susceptibility CDI is genetically mediated, (ii) highlight genetic risk as a mechanism for the increased risk of CDI in patients with inflammatory bowel disease, and (iii) point toward anti-interleukin-23 therapy as a common therapeutic strategy.
Alterations in purine and pyrimidine metabolism associated with latent tuberculosis infection: insights from gut microbiome and metabolomics analyses
Authors: Yang Boyi , Guo Xiaojing , Shi Chongyu , Liu Gang , Qin Xiaoling , Chen Shiyi , Gan Li , Liang Dongxu , Shao Kai , Xu Ruolan , Zhong Jieqing , Mo Yujie , Li Hai , Luo Dan
Published: October 2024

Individuals with latent tuberculosis infection (LTBI) account for almost 30% of the population worldwide and have the potential to develop active tuberculosis (ATB). Despite this, the current understanding of the pathogenesis of LTBI is limited. The gut microbiome can be altered in tuberculosis patients, and an understanding of the changes associated with the progression from good health to LTBI to ATB can provide novel perspectives for understanding the pathogenesis of LTBI by identifying microbial and molecular biomarkers associated therewith. In this study, fecal samples from healthy controls (HC), individuals with LTBI and ATB patients were collected for gut microbiome and metabolomics analyses. Compared to HC and LTBI subjects, participants with ATB showed a significant decrease in gut bacterial α-diversity. Additionally, there were significant differences in gut microbial communities and metabolism among the HC, LTBI, and ATB groups. PICRUSt2 analysis revealed that microbiota metabolic pathways involving the degradation of purine and pyrimidine metabolites were upregulated in LTBI and ATB individuals relative to HCs. Metabolomic profiling similarly revealed that purine and pyrimidine metabolite levels were decreased in LTBI and ATB samples relative to those from HCs. Further correlation analyses revealed that the levels of purine and pyrimidine metabolites were negatively correlated with those of gut microbial genera represented by
Ruminococcus_gnavus_group
(
R. gnavus
), and the levels of
R. gnavus
were also positively correlated with adenosine nucleotide degradation II, which is a purine degradation pathway. Moreover, a combined signature including hypoxanthine and xanthine was found to effectively distinguish between LTBI and HC samples (area under the curve [AUC] of training set = 0.796; AUC of testing set = 0.924). Therefore, through gut microbiome and metabolomic analyses, these findings provide valuable clues regarding how alterations in gut purine and pyrimidine metabolism are linked to the pathogenesis of LTBI.

IMPORTANCE

This study provides valuable insight into alterations in the gut microbiome and metabolomic profiles in a cohort of adults with LTBI and ATB. Perturbed gut purine and pyrimidine metabolism in LTBI was associated with the compositional alterations of gut microbiota, which may be an impetus for developing novel diagnostic strategies and interventions targeting LTBI.
Histone deacetylase 2 and 3 of
Sarcoptes scabiei
: characterization of a potential drug target
Authors: He Ran , Xu Luyang , Guo Maochuan , Cheng Kai , Song Ziyi , Xie Yue , Wang Hui , Zhou Xuan , Gu Xiaobin , Xu Jing , Deng Huidan , Yang Guangyou
Published: October 2024

Scabies is a contagious zoonotic parasitic disease that causes a substantial risk to both human and animal health and results in significant financial losses. No vaccine is available for scabies, and drug resistance to the conventional treatment for the disease has increased. Histone deacetylase (HDAC) modifies proteins by removing acetyl moieties from histones, regulates transcription, and is crucial for the immune system and apoptotic processes. This study aimed to clone, express, and determine the immunoreactivity of HDAC-2 and HDAC-3 of scabies mites to investigate their potential as scabies drug targets. The effects of inhibitors on recombinant
Sarcoptes scabiei
HDAC-2 (rSsHDAC-2) and rSsHDAC-3, as well as on the survival rate and ultrastructure of scabies mites
in vitro
, were also verified. The findings showed that the inhibitors reduced the acetylase activity of rSsHDAC-2 and rSsHDAC-3. Additionally, these inhibitors could significantly reduce the survival rate of scabies mites, making structural alterations in the mites such as mitochondrial pyknosis and cytoplasmic vacuoles and reaching a fatality rate of 76.7% after 24 h of action. In conclusion, HDAC-2 and HDAC-3 were critical to the survival of scabies mites and might be targeted by medications. Furthermore, the effect of inhibitors on the survival rate and structure of isolated scabies mites provides a new direction for developing therapeutic drugs for scabies.

IMPORTANCE

In this study, we successfully cloned and expressed recombinant SsHDAC-2 and SsHDAC-3 in a prokaryotic system and confirmed their acetylation-deacetylase activities. These results provide a solid experimental foundation for subsequent research on SsHDAC-2 and SsHDAC-3. Furthermore, we report for the first time the use of SsHDAC-2 and SsHDAC-3 as drug targets. We demonstrated that the inhibition of these HDACs by pharmacological agents can lead to structural damage in the parasite, thereby impacting the survival activity of the scabies mite. This finding opens up a novel therapeutic avenue for the treatment of scabies.
Dynamics of microbial-induced oil degradation at the microscale
Authors: Zhang Hong , Zhang Wenchao , Zong Yiwu , Kong Dongyang , Ma Luyan , Wu Xiao-Lei , Zhao Kun
Published: October 2024

Microbial-induced oil degradation (MIOD) has a wide range of applications, such as microbial enhanced oil recovery and bioremediation of oil pollution. However, our understanding of MIOD is still far from complete. Particularly, how is the dynamics of degradation process at the microscale level with a single-cell resolution remains to be disclosed. In this work, using hexadecane droplets in water as a model system, we have studied the dynamics of hexadecane degradation by different strains, including
Pseudomonas aeruginosa
PAO1, IMP68, O-2-2, and
Dietzia
sp. DQ12-45-1b, at the microscale. Based on visualization of MIOD, the dynamics of MIOD can be characterized by a three-stage process, including adhesion, adaptation, and degradation stages. Although different strains showed similar three-stage dynamics of MIOD, the effective degradation rate varied and followed an order of PAO1 > O-2-2 > IMP68 > DQ12-45-1b under aerobic conditions. Different oxygen conditions were also tested, and the dynamics of MIOD was slowed down under anaerobic conditions in comparison to under aerobic conditions. Further investigations at the degradation stage revealed that biofilms formed at the oil-water interface enhanced oil degradation, but a prerequisite for such enhanced degradation is proper stimulation of biofilm cells in the course of biofilm formation. The findings in this work provided a detailed picture on the dynamics of MIOD at the microscale and would be beneficial for better applications of MIOD.

IMPORTANCE

Microbial-induced oil degradation is environmental friendly and economic and has become a promising technique in the fields of enhanced oil recovery and remediation of crude oil-polluted environments. For better applications of microbial-induced oil degradation, understanding the degradation dynamics particularly at the microscale is crucial. In this study, we investigated the degradation dynamics of hexadecane oil droplets incubated with different strains, including
Pseudomonas aeruginosa
PAO1, O-2-2, IMP68, and
Dietzia
sp. DQ12-45-1b at the microscale by employing microdroplet-based methods and bacterial tracking techniques. The findings in this study provided a detailed picture on the dynamics of microbial-induced oil degradation at the microscale, which will deepen our understandings on the biodegradation mechanisms of alkanes and shed insights for developing more effective biodegradation techniques.
Characteristics of methicillin-resistant
Staphylococcus aureus
isolates from bovine mastitis milk in South Korea: molecular characteristics, biofilm, virulence, and antimicrobial resistance
Authors: Kang Hye Jeong , You Ju-Yeon , Kim Seung Hoe , Moon Jin-San , Kim Ha-Young , Kim Jae-Myeong , Lee Young Ju , Kang Hyun-Mi
Published: October 2024

Methicillin-resistant
Staphylococcus aureus
(MRSA) is a drug-resistant pathogen causing subclinical and clinical bovine mastitis. This study examined the molecular properties, biofilm formation, virulence genes, and antimicrobial susceptibility of MRSA isolates from mastitis-infected dairy cow milk in South Korea. Whole-genome sequencing of an ST22-SCC
mec
IV MRSA strain positive for Panton–Valentine leukocidin (PVL) and toxic shock syndrome toxin-1 (TSST-1) was also performed. Of the 488
S
.
aureus
isolates, 30 (6.1%) were identified as MRSA, harboring the
mecA
gene. MRSA exhibited the highest resistance to kanamycin (66.7%) among non-beta-lactam antibiotics. Multidrug resistance was observed in 83.3% of MRSA isolates. All MRSA strains had the capacity to form biofilm and harbored biofilm-related genes. The primary virulence genes included
hla
,
hlb
,
lukED
,
seg
,
sei
,
sem
,
sen
, and
seo
. The ST72-t324-SCC
mec
IV genotype was the most prevalent. Of note, three ST22-SCC
mec
IV isolates were positive for PVL and TSST-1. Our findings suggest that the majority of MRSA isolates from milk obtained from dairy cows with mastitis are multidrug-resistant, capable of forming robust biofilms, and harbor multiple virulence genes. The presence of PVL- and TSST-1-positive ST22-SCC
mec
IV isolates in mastitis-infected bovine milk highlights the need for persistent monitoring to mitigate possible public health risks.

IMPORTANCE

This study reports on the presence and characteristics of methicillin-resistant
Staphylococcus aureus
strains in milk from mastitis-infected cows. To our knowledge, this is the first report of a Panton–Valentine leukocidin- and toxic shock syndrome toxin-1-positive ST22-SCC
mec
IV strain in South Korea.
The host cells suppress the proliferation of pseudorabies virus by regulating the PI3K/Akt/mTOR pathway
Authors: Xu Lei , Tao Qian , Zhang Yang , Lee Feng-qin , Xu Tong , Deng Li-shuang , Jian Zhi-jie , Zhao Jun , Lai Si-yuan , Zhou Yuan-cheng , Zhu Ling , Xu Zhi-wen
Published: October 2024

Pseudorabies virus (PRV), a member of the alpha-herpesviruses, can infect both the nervous and reproductive systems of pigs, causing neonatal mortality and reproductive failure in sows, which incurs substantial economic losses. Neurotropism is a common characteristic of various viruses, allowing them to cross the blood-brain barrier and access the central nervous system. However, the precise mechanisms by which PRV affects the blood-brain barrier are not well understood. To investigate the mechanism of PRV’s interaction with the blood-brain barrier and its engagement with the PI3K/Akt signaling pathway during infection, an
in vitro
monolayer cell model of the blood-brain barrier was established. Our research found that PRV activates Matrix metallopeptidase 2 (MMP2), which degrades Zonula occludens-1 (ZO-1) and consequently enhances the permeability of the blood-brain barrier. PRV infection elevated the transcriptional levels of tissue inhibitor of metalloproteinases 1 (TIMP1) and inhibited its degradation through the ubiquitin-proteasome pathway, leading to higher intracellular concentrations of TIMP1 protein. TIMP1 regulates apoptosis and inhibits PRV replication in mouse brain microvascular endothelial cells through the PI3K/Akt/mTOR signaling pathway. In summary, our study delineates the mechanism through which PRV compromises the blood-brain barrier and provides insights into the host’s antiviral defense mechanisms post-infection.

IMPORTANCE

PRV, known for its neurotropic properties, is capable of inducing severe neuronal damage. Our study discovered that following PRV infection, the expression of MMP2 was upregulated, leading to the degradation of ZO-1. Furthermore, upon PRV infection in the host, the promoter of TIMP1 is significantly activated, resulting in a significant increase in TIMP1 protein levels. This upregulation of TIMP1 inhibits the proliferation of PRV through the PI3K/Akt signaling pathway. This study elucidated the mechanism through which PRV, including the PRV XJ delgE/gI/TK strains, compromises the blood-brain barrier and identifies the antiviral response characterized by the activation of the PI3K/Akt signaling pathway within infected host cells. These findings provide potential therapeutic targets for the clinical management and treatment of PRV.