bluuebunny/crossref_metadata_2025 huggingface dataset:
Reclamation of abandoned magnesite site using amendments and plantation
Authors: Kaptanoğlu Aliye Sepken , Çömez Aydın , Yıldız Oktay
Published: December 2023

This study aimed to determine the suitable reclamation ways of post‐mining magnesite. It was hypothesized that adding amendments and planting would decrease pH, increasing the nutrient availability and enhancing the soil microbial activity. Treatments included 200 g gypsum, 2 kg goat manure, and 200 g sulfur per square meter. Cedar (Cedrus libani A. Rich.), black locust (Robinia pseudoacacia L.), black pine (Pinus nigra J.F. Arnold), and sainfoin (Onobrychis sativa L.) were planted. Before and after the treatments, samples were taken from each experimental unit and analyzed. Analysis of the data indicated that the pH had decreased by 0.6 and 0.5 units on the gypsum + sulfur‐ and gypsum + manure‐treated experimental units, respectively, compared to the other treated plots. In addition, using manure significantly increased the organic matter N, P, and K content, by 3‐fold, 2.5‐fold, 7.5‐fold, and 2.5‐fold, respectively, and enhanced microorganism activity. The sulfur + manure treatment increased microbial C and N approximately twofold. Because the manure, sulfur, and gypsum treatments improved the tailings conditions for plant growth, the use of these amendments for mine tailing reclamation was strongly recommended. Across all treatments, cedar and black pine demonstrated 83 and 77% survival rates for the first 3 years of afforestation, respectively. For the same period, the black locust survival rate was 35% lower than that of the other species. The gypsum + manure application increased seedling height growth by about 20% for all three species compared to the other treatments.
The transcription factor PtoMYB142 enhances drought tolerance in Populus tomentosa by regulating gibberellin catabolism
Authors: Song Qin , Kong Lingfei , Yang Jiarui , Lin Minghui , Zhang Yuqian , Yang Xuerui , Wang Xiaojing , Zhao Zhengjie , Zhang Meng , Pan Jiarui , Zhu Shunqin , Jiao Bo , Xu Changzheng , Luo Keming
Published: December 2023

Drought stress caused by global warming has resulted in significant tree mortality, driving the evolution of water conservation strategies in trees. Although phytohormones have been implicated in morphological adaptations to water deficits, the molecular mechanisms underlying these processes in woody plants remain unclear. Here, we report that overexpression of PtoMYB142 in Populus tomentosa results in a dwarfism phenotype with reduced leaf cell size, vessel lumen area, and vessel density in the stem xylem, leading to significantly enhanced drought resistance. We found that PtoMYB142 modulates gibberellin catabolism in response to drought stress by binding directly to the promoter of PtoGA2ox4, a GA2‐oxidase gene induced under drought stress. Conversely, knockout of PtoMYB142 by the CRISPR/Cas9 system reduced drought resistance. Our results show that the reduced leaf size and vessel area, as well as the increased vessel density, improve leaf relative water content and stem water potential under drought stress. Furthermore, exogenous GA3 application rescued GA‐deficient phenotypes in PtoMYB142‐overexpressing plants and reversed their drought resistance. By suppressing the expression of PtoGA2ox4, the manifestation of GA‐deficient characteristics, as well as the conferred resistance to drought in PtoMYB142‐overexpressing poplars, was impeded. Our study provides insights into the molecular mechanisms underlying tree drought resistance, potentially offering novel transgenic strategies to enhance tree resistance to drought.
Plant hypersensitive induced reaction protein facilitates cell death induced by secreted xylanase associated with the pathogenicity of Sclerotinia sclerotiorum
Authors: Wang Pei , Wang Yabo , Hu Yawen , Chen Ziyang , Han Lili , Zhu Wenjun , Tian Binnian , Fang Anfei , Yang Yuheng , Bi Chaowei , Yu Yang
Published: December 2023

Necrotrophic fungal plant pathogens employ cell death‐inducing proteins (CDIPs) to facilitate infection. However, the specific CDIPs and their mechanisms in pathogenic processes of Sclerotinia sclerotiorum, a necrotrophic pathogen that causes disease in many economically important crop species, have not yet been clearly defined. This study found that S. sclerotiorum secretes SsXyl2, a glycosyl hydrolase family 11 xylanase, at the late stage of hyphal infection. SsXyl2 targets the apoplast of host plants to induce cell death independent of xylanase activity. Targeted disruption of SsXyl2 leads to serious impairment of virulence, which can be recovered by a catalytically impaired SsXyl2 variant, thus supporting the critical role of cell death‐inducing activity of SsXyl2 in establishing successful colonization of S. sclerotiorum. Remarkably, infection by S. sclerotiorum induces the accumulation of Nicotiana benthamiana hypersensitive‐induced reaction protein 2 (NbHIR2). NbHIR2 interacts with SsXyl2 at the plasma membrane and promotes its localization to the cell membrane and cell death‐inducing activity. Furthermore, gene‐edited mutants of NbHIR2 displayed increased resistance to the wild‐type strain of S. sclerotiorum, but not to the SsXyl2‐deletion strain. Hence, SsXyl2 acts as a CDIP that manipulates host cell physiology by interacting with hypersensitive induced reaction protein to facilitate colonization by S. sclerotiorum. These findings provide valuable insights into the pathogenic mechanisms of CDIPs in necrotrophic pathogens and lead to a more promising approach for breeding resistant crops against S. sclerotiorum.
Eco‐physiology of maize crops under combined stresses
Authors: Cagnola Juan I. , D'Andrea Karina E. , Rotili Diego H. , Mercau Jorge L. , Ploschuk Edmundo L. , Maddonni Gustavo A. , Otegui María E. , Casal Jorge J.
Published: December 2023

The yield of maize (Zea mays L.) crops depends on their ability to intercept sunlight throughout the growing cycle, transform this energy into biomass and allocate it to the kernels. Abiotic stresses affect these eco‐physiological determinants, reducing crop grain yield below the potential of each environment. Here we analyse the impact of combined abiotic stresses, such as water restriction and nitrogen deficiency or water restriction and elevated temperatures. Crop yield depends on the product of kernel yield per plant and the number of plants per unit soil area, but increasing plant population density imposes a crowding stress that reduces yield per plant, even within the range that maximises crop yield per unit soil area. Therefore, we also analyse the impact of abiotic stresses under different plant densities. We show that the magnitude of the detrimental effects of two combined stresses on field‐grown plants can be lower, similar or higher than the sum of the individual stresses. These patterns depend on the timing and intensity of each one of the combined stresses and on the effects of one of the stresses on the status of the resource whose limitation causes the other. The analysis of the eco‐physiological determinants of crop yield is useful to guide and prioritise the rapidly progressing studies aimed at understanding the molecular mechanisms underlying plant responses to combined stresses.
Dysregulated miRNAs in a canine model of haemangiosarcoma metastatic to the brain
Authors: Sabattini Silvia , Baldassarro Vito Antonio , Zaccone Riccardo , Calzà Laura , Giardino Luciana , Vascellari Marta , Lorenzini Luca , Moretti Marzia , Marconato Laura
Published: December 2023

Haemangiosarcoma is a highly metastatic and lethal cancer of blood vessel‐forming cells that commonly spreads to the brain in both humans and dogs. Dysregulations in phosphatase and tensin (PTEN) homologue have been identified in various types of cancers, including haemangiosarcoma. MicroRNAs (miRNAs) are short noncoding single‐stranded RNA molecules that play a crucial role in regulating the gene expression. Some miRNAs can function as oncogenes or tumour suppressors, influencing important processes in cancer, such as angiogenesis. This study aimed to investigate whether miRNAs targeting PTEN were disrupted in canine haemangiosarcoma and its corresponding brain metastases (BM). The expression levels of miRNA‐10b, miRNA‐19b, miRNA‐21, miRNA‐141 and miRNA‐494 were assessed in samples of primary canine cardiac haemangiosarcomas and their matched BM. Furthermore, the miRNA profile of the tumours was compared to samples of adjacent non‐cancerous tissue and healthy control tissues. In primary cardiac haemangiosarcoma, miRNA‐10b showed a significant increase in expression, while miRNA‐494 and miRNA‐141 exhibited downregulation. Moreover, the overexpression of miRNA‐10b was retained in metastatic brain lesions. Healthy tissues demonstrated significantly different expression patterns compared to cancerous tissues. In particular, the expression of miRNA‐10b was nearly undetectable in both control brain tissue and perimetastatic cerebral tissue. These findings can provide a rationale for the development of miRNA‐based therapeutic strategies, aimed at selectively treating haemangiosarcoma.
Diascopy and histopathological evaluation of nonblanching erythematous dermatoses in dogs
Authors: Forbes Stephanie , Bettenay Sonya , Meertens Nadine M. , Wildermuth Brett E. , Wildermuth Kerstin , Mueller Ralf S.
Published: December 2023

Background

Diascopy is a point‐of‐care diagnostic test used to differentiate skin erythema due to vascular dilation from haemorrhage. In the veterinary literature, only a handful of diseases have been described to be associated with a negative (nonblanching) diascopy result, and histological investigation of haemorrhage has been inconsistent.

Objectives

Retrospective study to undertake a histopathological investigation of canine, nonblanching erythematous dermatoses for the presence or absence of haemorrhage and vascular changes.

Materials and Methods

Skin biopsies from dogs presented with moderate‐to‐severe nonblanching erythema were evaluated histologically. Additionally, clinical data about each patient were analysed.

Results

Twenty cases were identified with nonblanching erythema. Diagnoses included vasculopathy (n = 6), canine eosinophilic dermatitis (n = 3), cutaneous epitheliotropic T‐cell lymphoma (n = 2), and one case each of sterile granuloma and pyogranuloma syndrome, German shepherd dog pyoderma, multiple mast cell tumours, haemangiosarcoma, exfoliative cutaneous lupus erythematosus, canine leishmaniosis with sebaceous adenitis, sebaceous adenitis with concurrent dermatophytosis, calcinosis cutis and canine atopic dermatitis with insect‐bite reaction. One or more vascular changes were present in all 20 cases and included perivascular oedema, endothelial swelling and neutrophilic infiltration of vessel walls. Haemorrhage was identified in 17 of 20 cases (85%). Three cases without dermal haemorrhage were calcinosis cutis, sebaceous adenitis with dermatophytosis and canine atopic dermatitis with insect‐bite reaction.

Conclusions and Clinical Relevance

Negative diascopy was associated with haemorrhage and vascular pathological findings in the majority of cases, yet not all. Haemorrhage was identified histologically in all diseases previously reported as nonblanching as well as in a few additional diseases.
Stereotactic radiotherapy for advanced canine anal sac adenocarcinoma: an exploratory study
Authors: Faletti Claire , Van Asselt Nathaniel
Published: December 2023

For dogs with anal sac adenocarcinoma (ASAC), metastasis to intra‐abdominal and pelvic lymph nodes occurs early in the disease course. Death is usually related to locoregional progression. Surgical excision is the treatment of choice, but may not be possible in advanced cases. Dogs treated with RT in the gross disease setting showed a 38%–75% overall response rate, but side effects to organs at risk in this area (especially the colon, bladder, and spinal cord) were reported. Stereotactic radiation therapy (SRT) utilizes highly conformal treatment planning with rapid dose fall‐off and hypofractionation. SRT may help to reduce the risk of late side effects of radiation while also creating a larger biological effect on ASACs. A primary aim of this prospective, descriptive, exploratory study was to describe the safety and feasibility of an SRT protocol in a small sample of dogs with ASAC, using objective and subjective measures to monitor acute and late side effects. A secondary aim was to describe the anti‐tumor response of the SRT protocol using CT at 3‐ and 6 months posttreatment. Five dogs completed the radiation protocol. Four had follow‐up CT characteristics of complete response (1), partial response (2), and stable disease (1). Minimal acute side effects were observed. Despite some large tumor volumes, constraints for OAR were achieved in all but the spinal cord for one patient. Findings indicated that SRT is a safe and feasible treatment for dogs with ACAC. Future studies are warranted to compare patient outcomes for SRT versus other treatments.
Human keratin matrices promote wound healing by modulating skin cell expression of cytokines and growth factors
Authors: Ramey‐Ward Allison N. , Walthall Howard P. , Smith Shakesia , Barrows Thomas H.
Published: December 2023

A wide variety of biomaterials has been developed to assist in wound healing, including acellular animal and human‐derived protein matrices. However, millions of patients worldwide still suffer from non‐healing chronic wounds, demonstrating a need for further innovation in wound care. To address this need, a novel biomaterial, the human keratin matrix (HKM), was developed, characterised, and tested in vitro and in vivo. HKM was found to be degradation‐resistant, and a proteomics analysis showed it to be greater than 99% human keratin proteins. PCR revealed adult human epidermal keratinocytes (HEKa) grown in contact with HKM showed increased gene expression of keratinocyte activations markers such as Epidermal Growth Factor (EGF). Additionally, a cytokine microarray demonstrated culture on HKM increased the release of cytokines involved in wound inflammatory modulation by both HEKa cells and adult human dermal fibroblasts (HDFa). Finally, in a murine chronic wound model, full‐thickness wounds treated weekly with HKM were smaller through the healing process than those treated with human amniotic membrane (AM), bovine dermis (BD), or porcine decellularized small intestinal submucosa (SIS). HKM‐treated wounds also closed significantly faster than AM‐ and SIS‐treated wounds. These data suggest that HKM is an effective novel treatment for chronic wounds.
Power of Social Media in Political Marketing – An India Based Empirical Study
Authors: Chatterjee Joydeep , Dutta Gautam
Published: December 2023

This study aims to understand the importance of different factors of social media, along with relevant demographic variables of voters to predict a voter’s preferred political brand, in the context of the Indian Lok Sabha elections. To identify the relevant demographic variables, we have gone through previous literature. However, due to the lack of substantial India-based academic literature that could help us to identify the important factors of social media campaign, we referred to US-based academic literature and attempted to obtain the superset of social media impact variables. Thereafter, we conducted focussed group discussions to identify the most important attributes, which we’ve used in our survey study. We have chosen greater Kolkata to conduct the survey. We have used multinomial logistic regression model with voters’ preferred political brand as a dependent variable with four choices. We observed that there is no significant difference between the intercept and final (including all predictors) model and also found that no individual demographic and social media impact variables are significant predictors of voters’ preferred political brand. We also measured comparative effect on different political parties for each independent variable. That would help political marketers to target specific segments with effective communication and campaign plan.
Waring identifiability for powers of forms via degenerations
Authors: Casarotti Alex , Postinghel Elisa
Published: December 2023

We discuss an approach to the secant non‐defectivity of the varieties parametrising th powers of forms of degree . It employs a Terracini‐type argument along with certain degeneration arguments, some of which are based on toric geometry. This implies a result on the identifiability of the Waring decompositions of general forms of degree kd as a sum of th powers of degree forms, for which an upper bound on the Waring rank was proposed by Fröberg, Ottaviani and Shapiro.
Roughness Related to Cooling Performance of Channels Made Through Additive Manufacturing
Authors: Wildgoose Alexander J. , Thole Karen A. , Tuneskog Erika , Wang Lieke
Published: December 2023

The complex surface morphology and multiscale surface features inherent in additively manufactured (AM) components contribute to the overall flow characteristics and heat transfer of cooling passages. As the AM process and cooling data in the literature continue to evolve, so does the need for more accurate heat transfer and pressure loss correlations for AM cooling schemes. This study improves the predictability of pressure loss and heat transfer for AM cooling passages by fabricating a range of coupons and investigating samples in the literature. Twenty-seven test coupons were manufactured using direct metal laser sintering in an assortment of build directions and build locations that produced a variety of surface morphologies. Nondestructive evaluation, computed tomography scanning, was used to quantify the surface morphology as well as capture the as-built geometric dimensions of the cooling schemes. The friction factor and bulk Nusselt number of the coupons were measured using an experimental rig. Pressure loss and heat transfer correlations in the literature were compared with the experimental results from the current coupons and datasets from the literature. Arithmetic mean roughness correlations in the literature struggled to predict the cooling performance of AM channels since the bulk roughness statistic did not capture the overall form of the surface morphology. A combination of root mean square roughness and skewness of the roughness was able to best predict pressure loss and heat transfer for the present samples and those in the literature while being independent of build location, build direction, material, machine, and laser parameters. The maximum absolute error was 25% and the average absolute error was 12% for the friction factor correlation. The maximum absolute error was 39% and the average absolute error was 8% for the Nusselt Number correlation.
Heat Transfer Coefficient and Adiabatic Effectiveness Measurements on a Nozzle Guide Vane With a Single Row of Cylindrical Holes
Authors: Galeotti S. , Bacci T. , Picchi A. , Facchini B. , Cubeda S.
Published: December 2023

Film-cooling injection significantly affects the thermal behavior of turbine vane surfaces. In addition to the beneficial effect of the film shielding the vane from the hot gas flow, alteration of the thermal boundary layer should also be taken into account. The aim of the present work is to detail the film-cooling performance in terms of adiabatic effectiveness and external heat transfer coefficient on a 2D nozzle guide vane. A single row of cylindrical holes was tested on both pressure and suction sides of a literature vane, the VKI LS89, in a linear cascade. The employed measurement technique is a transient thermal method based on infrared thermography, which was thoroughly described and validated in a previous work. The influence of inlet freestream turbulence and blowing ratio was evaluated, and two different injection angles were considered for both pressure and suction sides. Spatially resolved distributions of adiabatic effectiveness and heat transfer coefficient (HTC) on the vane surface allow us to precisely quantify the above-mentioned aspects and highlight qualitative differences between pressure side and suction side behavior. Details regarding the generated non-uniformities in the measured parameters could be also provided, to emphasize how average quantities are not always sufficient to characterize such complex phenomena. The impact of different reference conditions to scale HTC results was also investigated. Such effect was found not negligible on the overall performance of the film-cooling system, especially on the suction side where transition plays a critical role. Ultimately, the collected results constitute a wide and detailed experimental database for numerical modeling validation in a well-studied environment as the LS89 configuration.
Overview of Computational Methods to Predict Flutter in Aircraft
Authors: Antimirova Ekaterina , Jung Jiyoung , Zhang Zilan , Machuca Aaron , Gu Grace X.
Published: December 2023

Aeroelastic flutter is a dynamically complex phenomenon that has adverse and unstable effects on elastic structures. It is crucial to better predict the phenomenon of flutter within the scope of aircraft structures to improve the design of their wings. This review aims to establish fundamental guidelines for flutter analysis across subsonic, transonic, supersonic, and hypersonic flow regimes, providing a thorough overview of established analytical, numerical, and reduced-order models as applicable to each flow regime. The review will shed light on the limitations and missing components within the previous literature on these flow regimes by highlighting the challenges involved in simulating flutter. In addition, popular methods that employ the aforementioned analyses for optimizing wing structures under the effects of flutter—a subject currently garnering significant research attention—are also discussed. Our discussion offers new perspectives that encourage collaborative effort in the area of computational methods for flutter prediction and optimization.
Enhancing the robustness of ocean sound speed profile representation via interpretable deep matrix decomposition
Authors: Hua Xinyun , Zhang Chi , Zhang Chaojin , Cheng Lei , Zhang Ting , Li Jianlong
Published: December 2023

Developing an effective and robust representation model for ocean sound speed profiles (SSPs) is crucial for numerous ocean acoustic applications. However, the performance of existing sound speed profile (SSP) representation methods, such as empirical orthogonal function and K-singular value decomposition, heavily relies on the number of selected basis functions. This could lead to overfitting of noise, as these methods are unable to distinguish between signals and noise during the basis function learning process. To overcome these limitations and effectively learn a large number of basis functions with strong representation power from potentially noisy SSP data, we propose a novel algorithm called deep matrix decomposition (deep MD). This algorithm utilizes untrained deep neural networks as priors to reject noise within the interpretable matrix decomposition framework. To achieve optimal performance with deep MD, we propose a stopping strategy based on the rank estimate to determine the termination epoch. Experimental results using real-life datasets demonstrate that deep MD is robust against various types of noise and outperforms traditional SSP representation methods in terms of SSP reconstruction and characterizing the transmission loss in underwater acoustics.
A noncanonical IRAK4-IRAK1 pathway counters DNA damage–induced apoptosis independently of TLR/IL-1R signaling
Authors: Li Yuanyuan , Shah Richa B. , Sarti Samanta , Belcher Alicia L. , Lee Brian J. , Gorbatenko Andrej , Nemati Francesca , Yu Honglin , Stanley Zoe , Rahman Mahbuba , Shao Zhengping , Silva Jose M. , Zha Shan , Sidi Samuel
Published: December 2023

Interleukin-1 receptor (IL-1R)–associated kinases (IRAKs) are core effectors of Toll-like receptors (TLRs) and IL-1R in innate immunity. Here, we found that IRAK4 and IRAK1 together inhibited DNA damage–induced cell death independently of TLR or IL-1R signaling. In human cancer cells, IRAK4 was activated downstream of ATR kinase in response to double-strand breaks (DSBs) induced by ionizing radiation (IR). Activated IRAK4 then formed a complex with and activated IRAK1. The formation of this complex required the E3 ubiquitin ligase Pellino1, acting structurally but not catalytically, and the activation of IRAK1 occurred independently of extracellular signaling, intracellular TLRs, and the TLR/IL-1R signaling adaptor MyD88. Activated IRAK1 translocated to the nucleus in a Pellino2-dependent manner. In the nucleus, IRAK1 bound to the PIDD1 subunit of the proapoptotic PIDDosome and interfered with platform assembly, thus supporting cell survival. This noncanonical IRAK signaling pathway was also activated in response to other DSB-inducing agents. The loss of IRAK4, of IRAK4 kinase activity, of either Pellino protein, or of the nuclear localization sequence in IRAK1 sensitized p53-mutant zebrafish to radiation. Thus, the findings may lead to strategies for overcoming tumor resistance to conventional cancer treatments.
RHOA drivers take alternate routes in gastric cancer
Authors: Benton Dorothy , Chernoff Jonathan
Published: December 2023

Oncogenic small guanosine triphosphatases (GTPases) are often characterized by a limited set of activating mutations that affect their intrinsic biochemical function, but RHOA—which is frequently mutated in gastric cancer—appears not to have read the instruction manual. Having previously characterized the Y42C RHOA mutation in gastric cancer, in this issue of
Science Signaling
, Schaefer
et al.
take on the slightly less common L57V mutation and find that individual RHOA mutations can have different and unpredictable signaling outcomes.
A rumen virosphere with implications of contribution to fermentation and methane production, and endemism in cattle breeds and individuals
Authors: Sato Yoshiaki , Takebe Hiroaki , Tominaga Kento , Yasuda Jumpei , Kumagai Hajime , Hirooka Hiroyuki , Yoshida Takashi
Published: December 2023

Viruses have a potential to modify the ruminal digestion via infection and cell lysis of prokaryotes, suggesting that viruses are related to animal performance and methane production. This study aimed to elucidate the genome-based diversity of rumen viral communities and the differences in virus structure between individuals and cattle breeds and to understand how viruses influence on the rumen. To these ends, a metagenomic sequencing of virus-like particles in the rumen of 22 Japanese cattle, including Japanese Black (JB,
n
= 8), Japanese Shorthorn (
n
= 2), and Japanese Black sires × Holstein dams crossbred steers (F1,
n
= 12) was conducted. Additionally, the rumen viromes of six JB and six F1 that were fed identical diets and kept in a single barn were compared. A total of 8,232 non-redundant viral genomes (≥5-kb length and ≥50% completeness), including 982 complete genomes, were constructed, and rumen virome exhibited lysogenic signatures. Furthermore, putative hosts of 1,223 viral genomes were predicted using tRNA and clustered regularly interspaced short palindromic repeat (CRISPR)-spacer matching. The genomes included 1 and 10 putative novel complete genomes associated with
Fibrobacter
and
Ruminococcus
, respectively
,
which are the main rumen cellulose-degrading bacteria. Additionally, the hosts of 22 viral genomes, including 2 complete genomes, were predicted as methanogens, such as
Methanobrevibacter
and
Methanomethylophilus
. Most rumen viruses were highly rumen and individual specific and related to rumen-specific prokaryotes. Furthermore, the rumen viral community structure was significantly different between JB and F1 steers, indicating that cattle breed is one of the factors influencing the rumen virome composition.

IMPORTANCE

Here, we investigated the individual and breed differences of the rumen viral community in Japanese cattle. In the process, we reconstructed putative novel complete viral genomes related to rumen fiber-degrading bacteria and methanogen. The finding strongly suggests that rumen viruses contribute to cellulose and hemicellulose digestion and methanogenesis. Notably, this study also found that rumen viruses are highly rumen and individual specific, suggesting that rumen viruses may not be transmitted through environmental exposure. More importantly, we revealed differences of viral communities between JB and F1 cattle, indicating that cattle breed is a factor that influences the establishment of rumen virome. These results suggest the possibility of rumen virus transmission from mother to offspring and its potential to influence beef production traits. These rumen viral genomes and findings provide new insights into the characterizations of the rumen viruses.
Selected cachaça yeast strains share a genomic profile related to traits relevant to industrial fermentation processes
Authors: Campos Anna Clara Silva , Araújo Thalita Macedo , Moraes Lauro , Corrêa dos Santos Renato Augusto , Goldman Gustavo Henrique , Riano-Pachon Diego Maurício , Oliveira Juliana Velasco de Castro , Squina Fabio Marcio , Castro Ieso de Miranda , Trópia Maria José Magalhães , da Cunha Aureliano Claret , Rosse Izinara C. , Brandão Rogelio Lopes
Published: December 2023

The isolation and selection of yeast strains to improve the quality of the
cachaça
—Brazilian Spirit—have been studied in our research group. Our strategy considers
Saccharomyces cerevisiae
as the predominant species involved in sugarcane juice fermentation and the presence of different stressors (osmolarity, temperature, ethanol content, and competition with other microorganisms). It also considers producing balanced concentrations of volatile compounds (higher alcohols and acetate and/or ethyl esters), flocculation capacity, and ethanol production. Since the genetic bases behind these traits of interest are not fully established, the whole genome sequencing of 11 different
Saccharomyces cerevisiae
strains isolated and selected from different places was analyzed to identify the presence of a specific genetic variation common to cachaça yeast strains. We have identified 20,128 single-nucleotide variants shared by all genomes. Of these shared variants, 37 were new variants (being six missenses), and 4,451 were identified as missenses. We performed a detailed functional annotation (using enrichment analysis, protein–protein interaction network analysis, and database and in-depth literature searches) of these new and missense variants. Many genes carrying these variations were involved in the phenotypes of flocculation, tolerance to fermentative stresses, and production of volatile compounds and ethanol. These results demonstrate the existence of a genetic profile shared by the 11 strains under study that could be associated with the applied selective strategy. Thus, this study points out genes and variants that may be used as molecular markers for selecting strains well suited to the fermentation process, including genetic improvement by genome editing, ultimately producing high-quality beverages and adding value.

IMPORTANCE

This work demonstrates the existence of new genetic markers related to different phenotypes used to select yeast strains and mutations in genes directly involved in producing flavoring compounds and ethanol, and others related to flocculation and stress resistance.
First Canadian report of transmission of fluconazole-resistant
Candida parapsilosis
within two hospital networks confirmed by genomic analysis
Authors: McTaggart Lisa R. , Eshaghi AliReza , Hota Susy , Poutanen Susan M. , Johnstone Jennie , De Luca Domenica G. , Bharat Amrita , Patel Samir N. , Kus Julianne V.
Published: December 2023

Candida parapsilosis
is a common cause of non
-
albicans candidemia. It can be transmitted in healthcare settings resulting in serious healthcare-associated infections and can develop drug resistance to commonly used antifungal agents. Following a significant increase in the percentage of fluconazole (FLU)-nonsusceptible isolates from sterile site specimens of patients in two Ontario acute care hospital networks, we used whole genome sequence (WGS) analysis to retrospectively investigate the genetic relatedness of isolates and to assess potential in-hospital spread. Phylogenomic analysis was conducted on all 19 FLU-resistant and seven susceptible-dose dependent (SDD) isolates from the two hospital networks, as well as 13 FLU susceptible
C. parapsilosis
isolates from the same facilities and 20 isolates from patients not related to the investigation. Twenty-five of 26 FLU-nonsusceptible isolates (resistant or SDD) and two susceptible isolates from the two hospital networks formed a phylogenomic cluster that was highly similar genetically and distinct from other isolates. The results suggest the presence of a persistent strain of FLU-nonsusceptible
C. parapsilosis
causing infections over a 5.5-year period. Results from WGS were largely comparable to microsatellite typing. Twenty-seven of 28 cluster isolates had a K143R substitution in lanosterol 14-α-demethylase (ERG11) associated with azole resistance. As the first report of a healthcare-associated outbreak of FLU-nonsusceptible
C. parapsilosis
in Canada, this study underscores the importance of monitoring local antimicrobial resistance trends and demonstrates the value of WGS analysis to detect and characterize clusters and outbreaks. Timely access to genomic epidemiological information can inform targeted infection control measures.
Single-tube protocol for culture-independent spoligotyping of
Mycobacterium tuberculosis
based on MeltArray
Authors: Xia Zihan , Su Biyi , Tu Chunxia , Sun Siyang , Tan Yaoju , Xu Ye , Li Qingge
Published: December 2023

Spacer oligonucleotide typing (spoligotyping), the first-line genotyping assay for
Mycobacterium tuberculosis
(MTB), plays a fundamental role in the investigation of its epidemiology and evolution. However, the traditional spoligotyping protocol was established by using the reverse dot blot hybridization technique, which is characterized by a complex procedure, long turnaround time, and subjectivity in result interpretation, thus hindering its widespread use in low- and middle-income countries (LMICs) with a high tuberculosis burden. In this study, we established a single-tube spoligotyping assay using MeltArray, a highly multiplex polymerase chain reaction (PCR) approach that runs on a real-time PCR thermocycler. The MeltArray protocol included an internal positive control,
gyrB
, to indicate the abundance of MTB via the quantification cycle (Cq) and 43 spacers to identify the spoligotype via melting curve analysis. The entire protocol was completed in a single step within 2.5 hours. The lowest detectable copy number for the tested strains was 20 copies/reaction. In a blind evaluation of 318 MTB isolates, the MeltArray assay yielded 98.1% (312/318) concordance with the traditional approach and 100.0% with Sanger sequencing. Further evaluation of 151 liquid culture-matched sputum samples showed that all qualified (Cq <35) sputum samples (80.8%, 122/151) yielded results consistent with those of the liquid culture samples, including 97.5% (119/122) single spoligotypes and 2.5% (3/122) mixed spoligotypes. We conclude that MeltArray-based spoligotyping could be used immediately in LMICs, given its easy access, improved throughput, and potential applicability to clinical samples.

IMPORTANCE

Spacer oligonucleotide typing (spoligotyping), the first-line genotyping assay for
Mycobacterium tuberculosis
(MTB), plays a fundamental role in the investigation of its epidemiology and evolution. In this study, we established a single-tube spoligotyping assay using MeltArray, a highly multiplex polymerase chain reaction (PCR) approach that runs on a real-time PCR thermocycler. The MeltArray protocol included an internal positive control,
gyrB
, to indicate the abundance of MTB via the quantification cycle and 43 spacers to identify the spoligotype via melting curve analysis. The entire protocol was completed in a single step within 2.5 hours. The lowest detectable copy number for the tested strains was 20 copies/reaction and thus sufficient for analyzing both culture and sputum samples. We conclude that MeltArray-based spoligotyping could be used immediately in low- and middle-income countries with a high tuberculosis burden, given its easy access, improved throughput, and potential applicability to clinical samples.
The complete genome of two
Lactiplantibacillus plantarum
isolates from the traditional Mexican fermented pulque beverage assembled with a combination of PacBio and Illumina platforms
Authors: Gutiérrez Rodríguez Elisa Karen , Astudillo-Melgar Fernando , Larios Violeta , Bolívar Francisco , Escalante Adelfo , Giles-Gómez Martha
Published: December 2023

We report the sequence of the complete genome and associated plasmids of two
Lactiplantibacillus plantarum
isolates from the traditional Mexican pulque beverage assembled with a combination of PacBio and Illumina data. The resulting complete genome for strain LB1_P46 is 3,287,706 bp; for strain LB2_P47, the complete genome is 3,289,072 bp.
The complete genome sequence of
Kineothrix
sp. MB12-C1, isolated from the feces of black soldier fly larvae
Authors: Guo Wenjie , Qiu Wanling , Zhu Junyu , Shih Chao-Jen , Wu Yen-Chi , Lai Shu-Jung , Zhou Jiahui , Zhu Zetao , You Yi-Ting , Li Yin , Chen Sheng-Chung
Published: December 2023

Here, we present the complete genome sequence of
Kineothrix
sp. MB12-C1 (= BCRC 81406), isolated from the feces of black soldier fly (
Hermetia illucens
) larvae. The genome of strain MB12-C1 was chosen for further species classification and comparative genomic analysis.
Genome sequence of an
Acinetobacter pittii
strain obtained from a red
-
lored parrot with pneumonia
Authors: Bello-López E. , Escobedo-Muñoz A. S. , Hernández-Castro R. , Cevallos M. A.
Published: December 2023

Acinetobacter pittii
978-A_19 was obtained from a parrot with pneumonia. It is resistant to ampicillin, carbenicillin, cephalosporins, clindamycin, and trimethoprim + sulfamethoxazole. The genome encodes a new
bla
ADC allele, a
bla
OXA-502 gene, possesses several virulence genes related to adherence and biofilm formation, and has types I, II, and IV secretion systems.
Distinct epigenetic signatures of classical and hypervirulent
Klebsiella pneumoniae
Authors: Ghosh Dipannita , Pal Arijit , Mohapatra Sarita , Raj Stephen , Vivekanandan Perumal
Published: December 2023

Emergence and spread of the hypervirulent pathotype of
Klebsiella pneumoniae
have significantly increased infection rates in community as well as healthcare settings. There is an increasing interest to identify discriminating features between classical
K. pneumoniae
(cKp) and hypervirulent
K. pneumoniae
(hvKp) to facilitate our understanding of the rapid emergence and dissemination of the hypervirulent pathotype. Here, we sought to identify unique epigenetic signatures of hvKp pathotype that differ from its classical counterpart using single-base resolution methylome analysis of native DNA sequencing on the Oxford Nanopore Technologies platform. The overall global adenine methylation in GATC motifs (i.e., Dam methylation motif) and cytosine methylation in CCWGG motifs (i.e., Dcm methylation motif) were significantly higher in hvKp isolates compared to that in cKp isolates, irrespective of their position in chromosomes or putative extra-chromosomal genetic elements. Notably, we observed significant enrichment of hypermethylated GATC and CCWGG motifs in the virulome of hvKp compared to hvKp genes not directly associated with virulence. We also observed increased methylation of GATC and CCWGG motifs in the capsule synthesis locus of hvKp isolates compared to cKp isolates. Furthermore, we identified several differentially methylated genes (DMGs) between the two pathotypes; interestingly, these DMGs include metal ion transporters, multidrug efflux pumps, transcriptional regulators of stress response, and genes associated with biofilm formation. Our results highlight hypermethylation of GATC and CCWGG motifs as unique epigenetic signatures of hvKp isolates.

IMPORTANCE

Hypervirulent
Klebsiella pneumoniae
(hvKp) is a more virulent and rapidly evolving hypermucoviscous pathotype of classical
K. pneumoniae
(cKp). The hypervirulent pathotype is a major public health concern and is associated with high infection rates in community as well as hospital settings. With the recent emergence of multidrug-resistant hvKp, it has become imperative to investigate non-classical mechanisms such as epigenetics in addition to canonical biochemical and genetic mechanisms that delineate and differentiate the hypervirulent pathotype from its classical counterpart. Here, we identify genome-wide differences in adenine and cytosine methylation marks at well-characterized motifs between the two pathotypes. Overall, significantly higher levels of methylation were observed across chromosomal DNA and extrachromosomal elements in hvKp compared to cKp. Among hvKp isolates, the genes associated with virulence are particularly enriched for methylation marks. Our findings shed light on how epigenetic signatures may help distinguish the pathogenic potential of bacteria.
Synergistic horizontal transfer of antibiotic resistance genes and transposons in the infant gut microbial genome
Authors: Ding Yanwen , Jiang Xin , Wu Jiacheng , Wang Yihui , Zhao Lanlan , Pan Yingmiao , Xi Yaxuan , Zhao Guoping , Li Ziyun , Zhang Lei
Published: December 2023

Transposons, plasmids, bacteriophages, and other mobile genetic elements facilitate horizontal gene transfer in the gut microbiota, allowing some pathogenic bacteria to acquire antibiotic resistance genes (ARGs). Currently, the relationship between specific ARGs and specific transposons in the comprehensive infant gut microbiome has not been elucidated. In this study, ARGs and transposons were annotated from the Unified Human Gastrointestinal Genome (UHGG) and the Early-Life Gut Genomes (ELGG). Association rules mining was used to explore the association between specific ARGs and specific transposons in UHGG, and the robustness of the association rules was validated using the external database in ELGG. Our results suggested that ARGs and transposons were more likely to be relevant in infant gut microbiota compared to adult gut microbiota, and nine robust association rules were identified, among which
Klebsiella pneumoniae
,
Enterobacter hormaechei_A
, and
Escherichia coli_D
played important roles in this association phenomenon. The emphasis of this study is to investigate the synergistic transfer of specific ARGs and specific transposons in the infant gut microbiota, which can contribute to the study of microbial pathogenesis and the ARG dissemination dynamics.

IMPORTANCE

The transfer of transposons carrying antibiotic resistance genes (ARGs) among microorganisms accelerates antibiotic resistance dissemination among infant gut microbiota. Nonetheless, it is unclear what the relationship between specific ARGs and specific transposons within the infant gut microbiota.
K. pneumoniae
,
E. hormaechei_A
, and
E. coli_D
were identified as key players in the nine robust association rules we discovered. Meanwhile, we found that infant gut microorganisms were more susceptible to horizontal gene transfer events about specific ARGs and specific transposons than adult gut microorganisms. These discoveries could enhance the understanding of microbial pathogenesis and the ARG dissemination dynamics within the infant gut microbiota.
Supplemental Material: Material and mechanical properties of young basalt in drill cores from the oceanic island of Surtsey, Iceland
Authors: Jackson M.D. , et al.
Published: December 2023

Supplemental Text S1–S6, Supplemental Data S1 (physical property measurements), and Supplemental Data S2 (QPA-XRPD results).
5-Fluorouracil-associated severe hypertriglyceridaemia with positive rechallenge
Authors: Giacomuzzi Moore Bianca , Durigova Anna , Lamine Faiza , Chtioui Haithem , Salati Emanuela
Published: December 2023

Chemotherapy-induced hypertriglyceridaemia (HTG) is a potential serious adverse event. Severe HTG with triglycerides (TG) >11.3 mmol/L (1000 mg/dL) can cause acute pancreatitis in addition to cardiovascular diseases such as coronary artery disease. While the association of capecitabine (5-fluorouracil (5-FU) prodrug) with clinically relevant HTG is a well-known adverse reaction, 5-FU is not typically associated with HTG. We here report the case of a patient who developed 5-FU-associated grade 4 HTG with TG level raising up to 37.1 mmol/L (3286 mg/dL) occurring after the ninth cycle of adjuvant FOLFOX (Fluorouracil and Oxaliplatin) chemotherapy. Fenofibrate treatment and diet were started. Chemotherapy was postponed and then resumed for two additional cycles. However, severe HTG recurred shortly after. Chemotherapy was therefore permanently stopped. Approximately 8 weeks after chemotherapy discontinuation, TG fell back to range at 2.1 mmol/L (189 mg/dL) allowing interruption of fenofibrate without HTG recurrence at 3 months.
Study protocol for Care cOORDInatioN And sympTom managEment (COORDINATE) programme: a feasibility study
Authors: Koirala Binu , Badawi Sarah , Frost Steven , Ferguson Caleb , Hager David N , Street Lara , Perrin Nancy , Dennison Himmelfarb Cheryl , Davidson Patricia
Published: December 2023

Introduction

Sustainable approaches to support care coordination and symptom management needs of critically ill adults living with multimorbidity are needed to combat the challenges and complexity that multimorbidity presents. The study aims to test the feasibility of the Care cOORDInatioN And sympTom managEment (COORDINATE) intervention to improve health outcomes of adults living with multimorbidity.

Methods and analysis

A multicomponent nurse-driven intervention was developed using experience-based co-design and human-centred design. Inclusion criteria include (1) age 55 years and older, (2) admitted to an intermediate care unit, (3) presence of two or more chronic health conditions and (4) signed informed consent. Data collection will occur at baseline (time of recruitment predischarge) and 6 weeks and 3 months following hospital discharge. Outcome of interest from this feasibility study is to evaluate the financial, technical and logistic feasibility of a full-scale study including data collection and protocol adherence. Additionally, Cohen’s d effect sizes for the change in outcomes over time will be computed to establish power calculations required for a full-scale study. The protocol was prepared in accordance with Standard Protocol Items: Recommendations for Interventional Trials (SPIRIT) checklist.

Ethics and dissemination

The study has been reviewed and approved by the Institutional Review Board of Johns Hopkins Medical Institutions. Given the success of this feasibility study, the potential for the COORDINATE intervention to decrease the symptom burden and improve participant quality of life among critically ill people with multimorbidity will be tested in a full-scale study, and findings will be actively disseminated.

Trial registration number

NCT05985044.