bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiple‐frequency ultrasound for the inactivation of microorganisms on food: A review
Authors: Mustapha Abdullateef Taiye , Wahia Hafida , Ji Qunghua , Fakayode Olugbenga Abiola , Zhang Lei , Zhou Cunshan 
Published: April 2024

AbstractA multiple‐frequency ultrasound (MFU) technique is proficient in enhancing the effect of acoustic cavitation compared to a single‐frequency ultrasound. This comprehensive review delves into the complex field of MFU and its profound impact on microbial inactivation in food processing. The exploration begins with an intricate examination of the mechanism of power ultrasound, elucidating the intricate interplay of acoustic cavitation and its diverse effects. Subsequently, the mechanism of MFU was provided, which is basically the enhanced cavitation obtained during its application. Delving into the core mechanisms of MFU, the review navigates through microbial inactivation, unraveling the ways in which MFU disrupts and eliminates microorganisms. The exploration extends to the synergistic potential of combined applications, where MFU is applied with other treatment techniques to enhance microbial inactivation. Beyond its microbial inactivation prowess, the review meticulously explores the far‐reaching effects of MFU on the nutritional and quality attributes of food products. Furthermore, the diverse applications of MFU were also reviewed. In addition, limitations and adverse effects, emphasizing the importance of optimizing parameters to balance microbial safety and food quality, were also discussed. As the review unfolds, it lays the groundwork for future research, identifying avenues for further exploration and innovation in this dynamic field. In essence, this review not only consolidates the current understanding of MFU but also guides future research endeavors in the quest for more efficient, sustainable, and quality‐preserving food processing technologies.
Identification of phytoplasmas in stone fruit (Prunus sp.) and persimmon (Diospyros kaki L.) trees exhibiting leaf alterations and witches'‐broom in Jordan
Authors: Alloush Asem Habes Abu , Tedeschi Rosemarie , Alma Alberto , Bianco Piero Attilio , Quaglino Fabio 
Published: April 2024

AbstractDuring field surveys conducted in 2020 in Jordanian orchards, phytoplasma‐like symptoms (leaf yellowing/reddening and rolling, and witches'‐broom) were observed in three stone fruit species (peach, European plum, sweet cherry) and persimmon. Molecular analyses identified phytoplasma strains belonging to the species ‘Candidatus Phytoplasma solani’ (subgroup 16SrXII‐A) as largely prevalent in stone fruit and persimmon symptomatic plants. Moreover, ‘Ca. Phytoplasma omanense’ (16SrXXIX‐B) was found in few European plum symptomatic plants. In previous studies, such phytoplasma strains were identified in other important crops (almond, pomegranate, and grapevine) and in several putative insect vectors, suggesting their complex ecology in Jordan. Further studies are needed to in‐depth investigate the diffusion of phytoplasma‐associated diseases of stone fruits throughout the Country, to clarify their aetiology, and to study their epidemiological pattern(s).
Infant Faces Induce Behavioral Approach Tendencies: Evidence From a Manikin Task1,2
Authors: Yagi Yuto , Tomita Akitoshi , Nittono Hiroshi 
Published: April 2024

AbstractInfant faces are generally perceived as being cute and motivate the observer to look at them longer. This phenomenon is thought to be based on elemental features called baby schema (e.g., a round face and a large forehead). This study investigated the behavioral tendencies of observers in approaching infant faces using a manikin task in which infant and adult face images were presented as stimuli. Participants (N = 40) were instructed to identify with the manikin, discriminate a face on the screen, and respond by moving the manikin closer to the face (approach trials) or farther away from it (avoidance trials). The faces were presented either upright or inverted. The results showed that the approach–avoidance indices (the mean reaction time and error rate of avoidance trials minus those of approach trials) were larger for infant faces than for adult faces regardless of face orientation, although the difference was greater for upright faces than for inverted faces. This approach tendency toward infant faces is possibly due to elemental features rather than face‐specific holistic features.
Effect of Patellar Morphology on the Risk of Osteochondral Fracture after Patellar Dislocation: A Cross‐sectional Study
Authors: Zhou Zirui , Hua Qiang , Wen Chenghong , Qian Wenduo , Su Jide , Yang Min , Lei Mingming 
Published: April 2024

ObjectiveThe risk of osteochondral fracture (OCF) after patellar dislocation has been shown to be related to patellofemoral anatomy, but its relationship to patellar morphology remains unknown. The aim of this study was to investigate the associations between patellar morphology and the risk of OCF after patellar dislocation.MethodsA total of 140 patients with patellar dislocation between January 2018 and June 2023 were enrolled in this study and divided into two groups. Sixty‐five patellar dislocation patients with OCF were included in the OCF group, while 75 patellar dislocation patients without OCF were included in the non‐OCF group. Computed tomography was used to compare measurements of patellar morphology including Wiberg classification, patellar width and thickness, Wiberg angle, Wiberg index, facet ratio, lateral patellar facet angle, and patellar tilt angle. A logistic regression model was performed to evaluate the correlations between patellar morphology and the risk of OCF after patellar dislocation. Receiver operating characteristic curves were used to calculate the area under the curve (AUC) and determine the diagnostic values of patellar morphology for OCF after patellar dislocation. Subgroup analyses for gender and age were conducted to compare the differences in patellar morphology of PD patients.ResultsWiberg angle was significantly lower in the OCF group (p = 0.017), while Wiberg index (p = 0.002) and facet ratio (p = 0.023) were significantly higher in the OCF group. According to the results of logistic regression analysis, Wiberg angle (odds ratio [OR] = 0.96, p = 0.022) and Wiberg index (OR = 1.105, p = 0.032) were the final relevant factors for the occurrence of OCF after patellar dislocation. The AUC was 0.622 (95% confidence interval [CI]: 0.529–0.714) for Wiberg angle, 0.65 (95% CI: 0.558–0.742) for Wiberg index, and 0.702 (95% CI: 0.615–0.788) for the combination of Wiberg angle plus Wiberg index.ConclusionWiberg angle and Wiberg index were independent risk factors for the occurrence of osteochondral fracture after patellar dislocation. Moreover, Wiberg angle, Wiberg index, and the combination of Wiberg angle plus Wiberg index had good predictive diagnostic value for the occurrence of OCF after patellar dislocation.
Reactivity of anti‐SARS‐CoV‐2 antibodies in Serbian voluntary blood donors
Authors: Bezanovic Milomir Radoslav , Obradovic Zorana Budakov , Bujandric Nevenka , Kocic Neda , Milanovic Mirjana Krga , Majkic Milan , Obrovski Boris , Grujic Jasmina 
Published: April 2024

AbstractBackgroundThe COVID‐19 pandemic has major implications on the entire blood supply system worldwide. Seroepidemiological studies are certainly necessary for better understanding the global burden that the COVID‐19 pandemic represents.ObjectivesIn this study, we analysed the association between demographic factors, COVID‐19 severity, vaccination status and the reactivity of anti‐SARS‐CoV‐2 IgG antibodies in Serbian blood donors.Materials and MethodsIn a prospective study, demographic data and data related to previous SARS‐CoV‐2 infection, COVID‐19 severity and vaccination status among whole blood donors were analysed, from February 10 to August 10, 2022, at the Blood Transfusion Institute of Vojvodina, Serbia. The detection and determination of the level of anti‐SARS‐CoV‐2 IgG antibodies were performed using LIAISON® SARS‐CoV‐2 TrimericS IgG immunoassay.ResultsA total of 1190 blood donors were included, 24.5% were female and 75.5% were male while their average age was 41 years. Anti‐SARS‐CoV‐2 antibody values ranged from 2.40 to 3120 BAU/ml with a mean value of 1354.56 BAU/ml. Statistical analysis showed that COVID‐19 severity and vaccination status are linked with reactivity of anti‐SARS‐CoV‐2 antibodies, while gender and age of voluntary blood donors are not related to the values of anti‐SARS‐CoV‐2 antibodies.ConclusionThe values of anti‐SARS‐CoV‐2 antibodies in voluntary blood donors in Serbia are kept relatively high, especially in blood donors who have overcome the severe COVID‐19, as well as in donors who have been vaccinated against COVID‐19. Further SARS‐CoV‐2 seroprevalence studies in our country are certainly still necessary so global strategies to fight against COVID‐19 would be adequately evaluated.
Tetrahydrofolate levels influence 2-aminoacrylate stress in
Salmonella enterica
Authors: Shen Wangchen , Downs Diana M. 
Published: April 2024

ABSTRACT

In
Salmonella enterica,
the absence of the RidA deaminase results in the accumulation of the reactive enamine 2-aminoacrylate (2AA). The resulting 2AA stress impacts metabolism and prevents growth in some conditions by inactivating a specific target pyridoxal 5′-phosphate (PLP)-dependent enzyme(s). The detrimental effects of 2AA stress can be overcome by changing the sensitivity of a critical target enzyme or modifying flux in one or more nodes in the metabolic network. The catabolic L-alanine racemase DadX is a target of 2AA, which explains the inability of an
alr ridA
strain to use L-alanine as the sole nitrogen source. Spontaneous mutations that suppressed the growth defect of the
alr ridA
strain were identified as lesions in
folE,
which encodes GTP cyclohydrolase and catalyzes the first step of tetrahydrofolate (THF) synthesis. The data here show that THF limitation resulting from a
folE
lesion, or inhibition of dihydrofolate reductase (FolA) by trimethoprim, decreases the 2AA generated from endogenous serine. The data are consistent with an increased level of threonine, resulting from low folate levels, decreasing 2AA stress.

IMPORTANCE
RidA is an enamine deaminase that has been characterized as preventing the 2-aminoacrylate (2AA) stress. In the absence of RidA, 2AA accumulates and damages various cellular enzymes. Much of the work describing the 2AA stress system has depended on the exogenous addition of serine to increase the production of the enamine stressor. The work herein focuses on understanding the effect of 2AA stress generated from endogenous serine pools. As such, this work describes the consequences of a subtle level of stress that nonetheless compromises growth in at least two conditions. Describing mechanisms that alter the physiological consequences of 2AA stress increases our understanding of endogenous metabolic stress and how the robustness of the metabolic network allows perturbations to be modulated.
Draft genome sequences of five
Stenotrophomonas indicatrix
strains isolated from soil
Authors: Żur-Pińska Joanna , Sharma Vrinda , Hay Anthony G. 
Published: April 2024

ABSTRACT

Here, we present genome sequences of five
Stenotrophomonas indicatrix
strains, isolated from agricultural soil.
Stenotrophomonas
strains are commonly associated with the rhizosphere and are well-known for their ability to degrade xenobiotics. Yet, to date, knowledge about
S. indicatrix
is limited.
MYST regulates DNA repair and forms a NuA4-like complex in the malaria parasite
Plasmodium falciparum
Authors: Kalamuddin Mohammad , Shakri Ahmad Rushdi , Wang Chengqi , Min Hui , Li Xiaolian , Cui Liwang , Miao Jun 
Published: April 2024

ABSTRACT

Histone lysine acetyltransferase MYST-associated NuA4 complex is conserved from yeast to humans and plays key roles in cell cycle regulation, gene transcription, and DNA replication/repair. Here, we identified a
Plasmodium falciparum
MYST-associated complex, PfNuA4, which contains 11 of the 13 conserved NuA4 subunits. Reciprocal pulldowns using PfEAF2, a shared component between the NuA4 and SWR1 complexes, not only confirmed the PfNuA4 complex but also identified the PfSWR1 complex, a histone remodeling complex, although their identities are low compared to the homologs in yeast or humans. Notably, both H2A.Z/H2B.Z were associated with the PfSWR1 complex, indicating that this complex is involved in the deposition of H2A.Z/H2B.Z, the variant histone pair that is enriched in the activated promoters. Overexpression of PfMYST resulted in earlier expression of genes involved in cell cycle regulation, DNA replication, and merozoite invasion, and upregulation of the genes related to antigenic variation and DNA repair. Consistently, PfMYST overexpression led to high basal phosphorylated PfH2A (γ-PfH2A), the mark of DNA double-strand breaks, and conferred protection against genotoxic agent methyl methanesulfonate (MMS), X-rays, and artemisinin, the first-line antimalarial drug. In contrast, the knockdown of PfMYST caused a delayed parasite recovery upon MMS treatment. MMS induced the gradual disappearance of PfMYST in the cytoplasm and concomitant accumulation of PfMYST in the nucleus, suggesting cytoplasm-nucleus shuttling of PfMYST. Meanwhile, PfMYST colocalized with the γ-PfH2A, indicating PfMYST was recruited to the DNA damage sites. Collectively, PfMYST plays critical roles in cell cycle regulation, gene transcription, and DNA replication/DNA repair in this low-branching parasitic protist.

IMPORTANCE

Understanding gene regulation and DNA repair in malaria parasites is critical for identifying targets for antimalarials. This study found PfNuA4, a PfMYST-associated, histone modifier complex, and PfSWR1, a chromatin remodeling complex in malaria parasite
Plasmodium falciparum
. These complexes are divergent due to the low identities compared to their homologs from yeast and humans. Furthermore, overexpression of PfMYST resulted in substantial transcriptomic changes, indicating that PfMYST is involved in regulating the cell cycle, antigenic variation, and DNA replication/repair. Consistently, PfMYST was found to protect against DNA damage caused by the genotoxic agent methyl methanesulfonate, X-rays, and artemisinin, the first-line antimalarial drug. Additionally, DNA damage led to the relocation of cytoplasmic PfMYST to the nucleus and colocalization of PfMYST with γ-PfH2A, the mark of DNA damage. In summary, this study demonstrated that the PfMYST complex has critical functions in regulating cell cycle, antigenic variation, and DNA replication/DNA repair in
P. falciparum
.
Interactions between
Epichloë
endophyte and the plant microbiome impact nitrogen responses in host
Achnatherum inebrians
plants
Authors: Jin Yuanyuan , Chen Zhenjiang , White James F. , Malik Kamran , Li Chunjie 
Published: April 2024

ABSTRACT

The clavicipitaceous fungus
Epichloë gansuensis
forms symbiotic associations with drunken horse grass (
Achnatherum inebrians
), providing biotic and abiotic stress protection to its host. However, it is unclear how
E. gansuensis
affects the assembly of host plant-associated bacterial communities after ammonium nitrogen (NH
4
+
-N) treatment. We examined the shoot- and root-associated bacterial microbiota and root metabolites of
A. inebrians
when infected (I) or uninfected (F) with
E. gansuensis
endophyte. The results showed more pronounced NH
4
+
-N-induced microbial and metabolic changes in the endophyte-infected plants compared to the endophyte-free plants.
E. gansuensis
significantly altered bacterial community composition and β-diversity in shoots and roots and increased bacterial α-diversity under NH
4
+
-N treatment. The relative abundance of 117 and 157 root metabolites significantly changed with
E. gansuensis
infection under water and NH
4
+
-N treatment compared to endophyte-free plants. Root bacterial community composition was significantly related to the abundance of the top 30 metabolites [variable importance in the projection (VIP) > 2 and VIP > 3] contributing to differences between I and F plants, especially alkaloids. The correlation network between root microbiome and metabolites was complex. Microorganisms in the Proteobacteria and Firmicutes phyla were significantly associated with the R00693 metabolic reaction of cysteine and methionine metabolism. Co-metabolism network analysis revealed common metabolites between host plants and microorganisms.

IMPORTANCE
Our results suggest that the effect of endophyte infection is sensitive to nitrogen availability. Endophyte symbiosis altered the composition of shoot and root bacterial communities, increasing bacterial diversity. There was also a change in the class and relative abundance of metabolites. We found a complex co-occurrence network between root microorganisms and metabolites, with some metabolites shared between the host plant and its microbiome. The precise ecological function of the metabolites produced in response to endophyte infection remains unknown. However, some of these compounds may facilitate plant-microbe symbiosis by increasing the uptake of beneficial soil bacteria into plant tissues. Overall, these findings advance our understanding of the interactions between the microbiome, metabolome, and endophyte symbiosis in grasses. The results provide critical insight into the mechanisms by which the plant microbiome responds to nutrient stress in the presence of fungal endophytes.
Complete sequence of carbapenem-resistant
Ralstonia mannitolilytica
clinical isolate co-producing novel class D β-lactamase OXA-1176 and OXA-1177 in Japan
Authors: Hayashi Wataru , Kaiju Hiroyuki , Kayama Shizuo , Yu Liansheng , Zuo Hui , Sugawara Yo , Azuma Kaoru , Takahashi Akemi , Hata Yuka , Sugai Motoyuki 
Published: April 2024

ABSTRACT

In 2020, the
Ralstonia mannitolilytica
strain JARB-RN-0044 was isolated from a midstream urine sample of an elderly hospitalized patient in Japan and was highly resistant to carbapenem (i.e., imipenem, meropenem, and doripenem). Whole-genome sequencing revealed that the complete genome consists of two replicons, a 3.5-Mb chromosome and a 1.5-Mb large non-chromosomal replicon which has not been reported in
R. mannitolilytica,
and referred to as the “megaplasmid” in this study based on Cluster of Orthologous Group of proteins functional analysis. The strain JARB-RN-0044 harbored two novel OXA-60 and OXA-22 family class D β-lactamase genes
bla
OXA-1176
and
bla
OXA-1177
on the megaplasmid. Cloning experiments indicated that
Escherichia coli
recombinant clone expressing
bla
OXA-1176
gene showed increased minimum inhibitory concentrations (MICs) of imipenem, meropenem, and doripenem, indicating that
bla
OXA-1176
gene encodes carbapenemase. In contrast,
E. coli
recombinant clone expressing
bla
OXA-1177
gene showed increased MICs of piperacillin and cefazolin, but not of carbapenem. Interestingly, the 44.6 kb putative prophage region containing genes encoding phage integrase, terminase, head and tail protein was identified in the downstream region of
bla
OXA-1176
gene, and comparative analysis with some previously reported
R. mannitolilytica
isolates revealed that the prophage region was unique to strain JARB-RN-0044. The existence of a highly carbapenem-resistant
R. mannitolilytica
isolate may raise human health concerns in Japan, where the population is rapidly aging.

IMPORTANCE

Ralstonia mannitolilytica
is an aerobic non-fermenting Gram-negative rod commonly found in aquatic environments and soil. The bacteria can occasionally cause severe hospital-acquired bloodstream infections in immunocompromised patients and it has been recently recognized as an emerging opportunistic human pathogen. Furthermore, some
R. mannitolilytica
isolates are resistant to various antimicrobial agents, including β-lactams and aminoglycosides, making antimicrobial therapy challenging and clinically problematic. However, clinical awareness of this pathogen is limited. To our knowledge, in Japan, there has been only one report of a carbapenem-resistant
R. mannitolilytica
clinical isolate from urine by Suzuki et al. in 2015. In this study, whole-genome sequencing analysis revealed the presence and genetic context of novel
bla
OXA-1176
and
bla
OXA-1177
genes on the 1.5 Mb megaplasmid from highly carbapenem-resistant
R. mannitolilytica
isolate and characterized the overall distribution of functional genes in the chromosome and megaplasmid. Our findings highlight the importance of further attention to
R. mannitolilytica
isolate in clinical settings.
Experimental and analytical pipeline for sub-genomic RNA landscape of coronavirus by Nanopore sequencer
Authors: Chen Bo-Jia , Lin Ching-Hung , Wu Hung-Yi , Cai James J. , Chao Day-Yu 
Published: April 2024

ABSTRACT

Coronaviruses (CoVs), including severe acute respiratory syndrome coronavirus 2, can infect a variety of mammalian and avian hosts with significant medical and economic consequences. During the life cycle of CoV, a coordinated series of subgenomic RNAs, including canonical subgenomic messenger RNA and non-canonical defective viral genomes (DVGs), are generated with different biological implications. Studies that adopted the Nanopore sequencer (ONT) to investigate the landscape and dynamics of viral RNA subgenomic transcriptomes applied arbitrary bioinformatics parameters without justification or experimental validation. The current study used bovine coronavirus (BCoV), which can be performed under biosafety level 2 for library construction and experimental validation using traditional colony polymerase chain reaction and Sanger sequencing. Four different ONT protocols, including RNA direct and cDNA direct sequencing with or without exonuclease treatment, were used to generate RNA transcriptomic libraries from BCoV-infected cell lysates. Through rigorously examining the k-mer, gap size, segment size, and bin size, the optimal cutoffs for the bioinformatic pipeline were determined to remove the sequence noise while keeping the informative DVG reads. The sensitivity and specificity of identifying DVG reads using the proposed pipeline can reach 82.6% and 99.6% under the k-mer size cutoff of 15. Exonuclease treatment reduced the abundance of RNA transcripts; however, it was not necessary for future library preparation. Additional recovery of clipped BCoV nucleotide sequences with experimental validation expands the landscape of the CoV discontinuous RNA transcriptome, whose biological function requires future investigation. The results of this study provide the benchmarks for library construction and bioinformatic parameters for studying the discontinuous CoV RNA transcriptome.

IMPORTANCE

Functional defective viral genomic RNA, containing all the
cis
-acting elements required for translation or replication, may play different roles in triggering cell innate immune signaling, interfering with the canonical subgenomic messenger RNA transcription/translation or assisting in establishing persistence infection. This study does not only provide benchmarks for library construction and bioinformatic parameters for studying the discontinuous coronavirus RNA transcriptome but also reveals the complexity of the bovine coronavirus transcriptome, whose functional assays will be critical in future studies.