bluuebunny/crossref_metadata_2025 huggingface dataset:
Increases and decreases in soil moisture in water‐limited plant communities cause asymmetrical responses in biomass but not in diversity
Authors: van den Brink Liesbeth , Canessa Rafaella , Liancourt Pierre , Neidhardt Harald , Cavieres Lohengrin A. , Oelmann Yvonne , Bader Maaike Y. , Tielbörger Katja
Published: August 2024

Aims

Changes in precipitation patterns, such as the predicted increases in the frequency of climatic extremes, are likely to alter plant communities, but whether responses to drought or to wetter conditions respectively cause consistent, opposite responses is debated. Here, we assessed the response in biomass production and species diversity of water‐limited plant communities to the direction (increase or decrease) and magnitude (micro‐ and macro‐climatic effects) of changes in soil moisture.

Location

We reciprocally translocated soils containing seed banks from two climates (semi‐arid and mediterranean) at a micro‐climatic (opposite slopes) and a macro‐climatic scale (between climates) in Chile.

Results

Biomass production for the soils that were translocated from wetter to drier climates was unrelated to the available soil moisture. The lowest biomass was produced in the wettest climate on the wet slope. Biomass production increased after a translocation to the drier climate (representing the largest change in climate). Nonetheless, the highest overall biomass for the wet to dry translocation was produced on the mediterranean dry slope with intermediate soil moisture. However, on the same mediterranean dry slope, biomass was almost zero for soil translocated the other way round (from drier to wetter). Diversity after 24 months was unaffected by micro‐climatic change, but soils transplanted toward the drier climate yielded a plant community with increased diversity.

Conclusion

Our results showed direction and magnitude of climate change but also the response factor that is studied matters to detect direction‐dependent responses; i.e., species richness had a linear and reversible response. However, the response of biomass depended on the origin of the transplanted material (soil and plant community), indicating history dependence (hysteresis). This emphasizes that responses to unidirectional climate manipulation experiments may not be able to capture the entire nature of the response of plant communities to climate change.
Manipulation impacts of jack mackerel meal in low fish meal diets on growth, feed availability, and biochemical composition of olive flounder (Paralichthys olivaceus) and economic analysis
Authors: Sim Yu Jin , Cho Sung Hwoan , Kim Taeho
Published: August 2024

Manipulation effects of jack mackerel meal (JMM) in the low fish meal (FM) diets substituting 50% FM with meat meal (MM) on growth performance of olive flounder and economic analysis were determined. Seven experimental diets were created. The control (Con) diet contained 60% FM. In the other diets, 50% of the FM level used for the Con diet was substituted with MM, and then graded levels (0, 10, 20, 30, 40, and 50%) of JMM were included at the expense of FM, named the MJ0, MJ10, MJ20, MJ30, MJ40, and MJ50 diets, respectively. The experimental diets were distributed to triplicate groups of fish. A total of 525 fish was divided into 21 flow‐through tanks. Fish were hand‐fed to apparent satiation for 8 weeks. Weight gain, specific growth rate (SGR), and feed consumption of fish fed the Con diet were comparable with fish fed the MJ20, MJ30, MJ40, and MJ50 diets. Weight gain, SGR, and feed consumption of fish linearly improved with JMM inclusion levels in the low FM diets replacing 50% FM with MM. The strong correlation between isoleucine and lysine content among essential amino acids in the experimental diets versus weight gain, SGR, and feed consumption of olive flounder were observed. Dietary treatments did not influence feed utilization, chemical composition, and amino acid profiles of fish. Incorporated 20%–50% JMM as an effective feed attractant and enhancer in the low FM diets replacing 50% FM with MM achieved comparable weight gain, SGR, and feed consumption to fish fed a 60% FM‐based diet. Finally, the MJ50 diet led to the highest economic profit index (EPI) for farmers.
An ultrasound multiparametric method to quantify liver fat using magnetic resonance as standard reference
Authors: De Rosa Laura , Salvati Antonio , Martini Nicola , Chiappino Dante , Cappelli Simone , Mancini Marcello , Demi Libertario , Ghiadoni Lorenzo , Bonino Ferruccio , Brunetto Maurizia R. , Faita Francesco
Published: August 2024

Background & Aims

There is an unmet need for a reliable and reproducible non‐invasive measure of fatty liver content (FLC) for monitoring steatotic liver disease in clinical practice. Sonographic FLC assessment is qualitative and operator‐dependent, and the dynamic quantification range of algorithms based on a single ultrasound (US) parameter is unsatisfactory.

This study aims to develop and validate a new multiparametric algorithm based on B‐mode images to quantify FLC using Magnetic Resonance (MR) values as standard reference.

Methods

Patients with elevated liver enzymes and/or bright liver at US (N = 195) underwent FLC evaluation by MR and by US. Five US‐derived quantitative features [attenuation rate(AR), hepatic renal‐ratio(HR), diaphragm visualization(DV), hepatic‐portal‐vein‐ratio(HPV), portal‐vein‐wall(PVW)] were combined by mixed linear/exponential regression in a multiparametric model (Steatoscore2.0). One hundred and thirty‐four subjects were used for training and 61 for independent validations; score‐computation underwent an inter‐operator reproducibility analysis.

Results

The model is based on a mixed linear/exponential combination of 3 US parameters (AR, HR, DV), modelled by 2 equations according to AR values. The computation of FLC by Steatoscore2.0 (mean ± std, 7.91% ± 8.69) and MR (mean ± std, 8.10% ± 10.31) is highly correlated with a low root mean square error in both training/validation cohorts, respectively (R = 0.92/0.86 and RMSE = 5.15/4.62, p < .001). Steatoscore2.0 identified patients with MR‐FLC≥5%/≥10% with sensitivity = 93.2%/89.4%, specificity = 86.1%/95.8%, AUROC = 0.958/0.975, respectively and correlated with MR (R = 0.92) significantly (p < .001) better than CAP (R = 0.73).

Conclusions

Multiparametric Steatoscore2.0 measures FLC providing values highly comparable with MR. It is reliable, inexpensive, easy to use with any US equipment and qualifies to be tested in larger, prospective studies as new tool for the non‐invasive screening and monitoring of FLC.
Disentangling effects of dispersal, environment and anthropogenic barriers on functional connectivity in aquatic systems
Authors: Day Casey C. , Alò Dominique , Simmons Ryan K. , Cotey Stacy R. , Zarn Katherine E. , Gazeley Ian F. , Small Maureen , Fortin Marie‐Josee , Bearlin Andrew R. , Smith Seth R. , Landguth Erin L.
Published: August 2024

Disentangling the roles of structural landscape factors and animal movement behaviour can present challenges for practitioners managing landscapes to maintain functional connectivity and achieve conservation goals. We used a landscape genetics approach to combine robust demographic, behavioural and genetic datasets with spatially explicit simulations to evaluate the effects of anthropogenic barriers (dams, culverts) and natural landscape resistance (gradient, elevation) affecting dispersal behaviour, genetic connectivity and genetic structure in a resident population of Westslope Cutthroat Trout (Oncorhynchus clarkii lewisi). Analyses based on 10 years of sampling effort revealed a pattern of restricted dispersal, and population genetics identified discrete population clusters between distal tributaries and the mainstem stream and no structure within the mainstem stream. Demogenetic simulations demonstrated that, for this population, the effects of existing anthropogenic barriers on population structure are redundant with effects of restricted dispersal associated with the underlying environmental resistance. Our approach provides an example of how extensive field sampling combined with landscape genetics can be incorporated into spatially explicit simulation modelling to explore how, together, movement ecology and landscape resistance can be used to inform decisions around restoration and connectivity.
The epigenetic mechanism of metabolic risk in bipolar disorder
Authors: Huang Kexin , Li Sujuan , Yang Min , Teng Ziwei , Xu Baoyan , Wang Bolun , Chen Jindong , Zhao Liping , Wu Haishan
Published: August 2024

Bipolar disorder (BD) is a complex and severe mental illness that causes significant suffering to patients. In addition to the burden of depressive and manic symptoms, patients with BD are at an increased risk for metabolic syndrome (MetS). MetS includes factors associated with an increased risk of atherosclerotic cardiovascular disease (CVD) and type 2 diabetes mellitus (T2DM), which may increase the mortality rate of patients with BD. Several studies have suggested a link between BD and MetS, which may be explained at an epigenetic level. We have focused on epigenetic mechanisms to review the causes of metabolic risk in BD.
Euler‐angle norms for tooth rotation, torque and tip
Authors: Steinvorth Benjamin , Troiani Stefano , Weir Tony , Meade Maurice J.
Published: August 2024

Intro

The aim of the current study was to develop and describe a new measuring system for the orientation of a tooth in a digitalized cast of a jaw and provide new angular values for the rotation, torque and tip of maxillary and mandibular teeth.

Methods

This retrospective cross‐sectional study involved the utilization of a sub‐group of extrinsic Euler‐angles to derive optimal norm values per tooth in three different planes of orientation (‘rotation’, ‘torque’ and ‘tip’) by evaluating the digital representations of the teeth derived from a database containing over 17,500 patients. The process involved the entry of the .stl files of the jaw pairs into a fully automated software system (Smyl:Ai, Ulm, Germany) whereupon jaw alignment, teeth segmentation, landmark identification and visual validation of input files was conducted prior to calculation of the norm values for the three different planes of orientation.

Results

The digital scans in stereolithography (.STL)‐file format of the upper and lower dentitions of 1914 individuals with optimal occlusion were chosen and evaluated. New mean (standard deviation) angular values were determined for the rotation, torque and tip of maxillary and mandibular teeth.

Conclusion

The findings facilitate the reappraisal of rotation, torque and tip values currently acceptable as ideal. They will inform anthropologists and dental researchers about occlusion and alignment in orthodontic and non‐orthodontic patients and provide baseline data for future studies. The methodology will also enable the evaluation of large numbers of data in relatively short timeframes.
miR1432 negatively regulates cold tolerance by targeting OsACAs
Authors: Dai Yan , Feng Xiujing , Liu Zheming , Wang Meng , Zhou Yun , Cui Lie , Wei Xiaoli , Zhu Zhen
Published: August 2024

miRNAs function as negative regulators that significantly influence plant growth and stress responses. Within rice and other monocotyledonous plants, miR1432 plays a conserved role in seed development and disease resistance. However, its involvement in the response to abiotic stresses remains unclear. Our study aimed to elucidate this mechanism by predicting the targeting of the rice P‐type IIB Ca2+ ATPase gene OsACAs by miR1432 and identifying its cleavage sites via 5′RACE. We observed induced expression of miR1432 and its target gene, OsACA6, under abiotic stresses. Overexpression (OX) of miR1432 and suppression of OsACA6 resulted in reduced cold, salt, and drought tolerance, while OsACA6 suppression/knockout and OX had opposite effects on cold tolerance. Additionally, miR1432 may target other OsACA6 homologs. RNA‐sequencing data highlighted the differential expression of stress‐related genes in miR1432‐overexpressing rice. Furthermore, miR1432‐overexpressing rice exhibited weakened vigor, dwarfism, yellowing leaves and reduced fertility. Collectively, our results strongly suggest that miR1432 not only negatively modulates abiotic stress tolerance by suppressing Ca2+ ATPase gene(s) but also influences plant growth and development.
Comparative transcriptome profiling of resistant and susceptible groundnut (Arachis hypogaea) genotypes in response to stem rot infection caused by Sclerotium rolfsii
Authors: Tatmiya Ritisha N. , Padhiyar Shital M. , Chandramohan Sangh , Bera Sandip K. , Bhatt Shradda B. , Iquebal Mir Asif , Ambalam Padma S. , Tomar Rukam S.
Published: August 2024

This study aimed to explore transcriptomic distinctions between resistant (CS‐319) and susceptible (JAL‐42) groundnut (Arachis hypogaea) genotypes exposed to Sclerotium rolfsii infection across different developmental stages. Employing a de novo assembly‐based approach, we analysed the transcriptomic response in these groundnut plants under control and infected conditions at 24, 72 and 120 hours post‐inoculation (hpi). Our RNA‐Seq data yielded a total of 133,900,261 reads, revealing 7796 differentially expressed genes (DEGs). We constructed a gene regulatory network with 59 hub genes, identified 6783 transcription factors and uncovered 88,424 putative markers, including 17,236 simple‐sequence repeats (SSRs), 10,099 single‐nucleotide polymorphisms (SNPs) and 78,332 indels. Notably, the majority of DEGs were upregulated at 24 hpi in the resistant genotype, encompassing diverse functional categories such as pathogenesis‐related genes, defence‐related (R) genes, genes involved in plant–fungus interactions, oxidation–reduction‐related genes, transport, metabolism and proteolysis genes, along with transcription factors (FAR1, B3, GATA, NAC, WRKY, MYBC1 and bHLH), secondary metabolic pathway‐related genes and photosynthesis‐related genes. The up‐regulation of WRKY transcripts, associated with the activation of the jasmonic acid defence signalling pathway, potentially induced systemic acquired resistance (SAR). Conversely, these DEGs exhibited down‐regulation in the susceptible genotype. Furthermore, a total of 17,236 expressed sequence tag (EST)‐SSRs were identified from the unigenes, holding significant potential for advancing plant breeding through marker‐assisted methods, facilitating quantitative trait locus (QTL) mapping and evaluating genetic diversity among genotypes. This study's approach contributes to a more profound understanding of the molecular‐level defence mechanisms involved in the interaction between groundnuts and S. rolfsii.
The scientific journey to eradicate smuts on the prairies
Authors: Aboukhaddour Reem , McCallum Brent D. , Menzies Jim , Hiebert Colin
Published: August 2024

The cultivation of wheat in North America represents a relatively recent endeavour, spanning a mere 150 years. This relatively brief period of its recent cultivation has allowed the opportunity to document the threats and diseases farmers had to face from the start. In this minireview, our primary objective is to provide a detailed exploration of the historical context on how we end up effectively managing what was once among the most destructive and hard to manage diseases affecting wheat, namely, common bunt (covered smut). This review delves into the early research efforts dedicated to understanding the biology of the causal pathogens and developing effective management approaches. These efforts encompass a wide spectrum of potential methods, ranging from seed treatments to cropping practices, and the development of genetic resistance. Throughout this exploration, we will also spotlight the remarkable scientific success story that has unfolded within the Canadian context. In essence, this review aims to provide a scientific examination of the history, challenges and innovative approaches associated with mitigating the impact of bunt pathogens on wheat cultivation in North America, and future challenges.
Spider mite infestation triggers coordinated hormonal trade‐offs enabling plant survival with a fitness cost
Authors: Garcia Alejandro , Talavera‐Mateo Lucia , Petrik Ivan , Oklestkova Jana , Novak Ondrej , Santamaria M. Estrella
Published: August 2024

Tetranychus urticae is an important pest that causes severe damage to a wide variety of plants and crops, leading to a substantial productivity loss. Previous research has been focused on plant defence response to T. urticae to improve plant resistance. However, plant growth, development and reproduction throughout the infestation process have not been previously studied. Through physiological, biochemical, transcriptomic and hormonomic evaluation, we uncover the molecular mechanisms directing the defence‐growth trade‐off established in Arabidopsis upon T. urticae infestation. Upon mite attack, plants suffer an adaptation process characterized by a temporal separation between the defence and growth responses. Jasmonic and salicylic acids regulate the main defence responses in combination with auxin and abscisic acid. However, while the reduction of both auxin signalling and gibberellin, cytokinin and brassinosteroid biosynthesis lead to initial growth arrest, increasing levels of growth hormones at later stages enables growth restart. These alterations lead to a plant developmental delay that impacts both seed production and longevity. We demonstrate that coordinated trade‐offs determine plant adaptation and survival, revealing mite infestation has a long‐lasting effect negatively impacting seed viability. This study provides additional tools to design pest management strategies that improve resistance without penalty in plant fitness.
N‐Acetylcysteine Supplementation Improves Testicular Haemodynamics, Testosterone Levels, Seminal Antioxidant Capacity and Semen Quality in Heat‐Stressed Goat Bucks
Authors: Adel Ola , El‐Sherbiny Hossam R. , M. Shahat Abdallah , Ismail Sayed Taha
Published: August 2024

Heat stress (HS) disrupts testicular homeostasis because of oxidative stress. N‐acetylcysteine (NAC) is a thiol compound with antioxidants, anti‐inflammatory and anti‐apoptotic properties. As a sequel, this research aimed to assess the ameliorative effects of NAC supplementation on the reproductive performance of goat bucks kept under environmental HS. Primarily, Doppler examination as well as semen collection and evaluation were conducted on 12 mature bucks for 2 weeks (W) as pre‐heat stress control (W1 and W2) during winter (February 2023). The temperature–humidity index (THI) was 63.4–64.3 (winter season). Then during summer HS conditions (from the beginning of July till the end of August 2023) bucks were assessed before NAC supplementation (W0), afterwards they were arbitrarily assigned into two groups. The control group (CON; n = 6) received the basal diet while the NAC group (n = 6) received the basal diet in addition to oral NAC daily for 7 weeks (W1–W7). The THI was 78.1–81.6 (summer season). Testicular blood flow parameters, serum concentration of nitric oxide (NO) and testosterone were measured. Additionally, total antioxidant capacity (TAC) and malondialdehyde (MDA) content in seminal plasma and semen quality parameters were evaluated. There were marked reductions (p < 0.05) in the resistive index (RI; W1, W4 and W5), pulsatility index (PI; W2 and W4–W7), and systolic/diastolic ratio (S/D; W4–W7) in the NAC group compared to the CON group. Furthermore, testosterone and NO levels were higher (p < 0.01 and p < 0.05, respectively) in the NAC group (W2, W3, W5 and W3–W5, respectively). Seminal plasma TAC increased (p < 0.05) and MDA decreased (p < 0.05) in the NAC group (W2, W4 and W5) compared to the CON group. Moreover, there were marked improvements (p < 0.05) in semen quality parameters (mass motility, total motility, viability and normal morphology) in the NAC group. In conclusion, oral NAC supplementation could be used to enhance the reproductive performance of goat bucks during HS conditions which is supported by remarkable enhancement in testicular haemodynamics, NO, testosterone levels and semen quality parameters.
Are profiles of job insecurity associated with health‐related indicators among faculty in Swedish academia?
Authors: Tanimoto Anna S. , Richter Anne , Bujacz Aleksandra , Lindfors Petra
Published: August 2024

Job insecurity is a work stressor associated with various health‐related impairments. As concerns about the ubiquity of job insecurity in academia have become increasingly prominent, the potential implications of job insecurity for the health and well‐being of faculty require attention. Specifically, these implications may vary between groups within academia, yet little is known about such variations, particularly with respect to different indicators of health and well‐being. This study aims to identify and examine profiles of job insecurity (including quantitative and qualitative dimensions) in relation to exhaustion, depressive symptoms, well‐being, and work–family conflict among faculty in Sweden. Self‐reports in questionnaires were collected in 2021 from a representative sample of faculty, with a doctoral degree, working in Swedish public higher education institutions (N = 2,729 respondents; 48% women; average age: 50 years; 82% born in Sweden). Latent profile analysis was conducted to identify profiles of job insecurity, followed by statistical comparisons on demographic covariates and health‐related indicators across profiles. The latent profile analysis revealed five job insecurity profiles: the moderately insecure (n = 215), the secure (n = 1777), the secure; quality‐concerned (n = 406), the insecure; employment‐concerned (n = 177), and the insecure (n = 154). Twelve percent of the sample was identified as vulnerable, particularly the insecure profile, where these individuals may be most at a risk for exhaustion disorder and depression. Among faculty in Sweden, quantitative and qualitative dimensions of job insecurity appear to be closely connected, with the qualitative dimension seemingly more informative for health‐related indicators.
CORRIGENDUM
Authors: David Allen Paul , Daud Suzairi , Sulaiman Abdul Hadi , Ahmad Zain Muhammad Ilham , Abd Aziz Muhammad Safwan , Ahmad Noorden Ahmad Fakhrurrazi
Published: August 2024

This article corrects the following:
First published: 29 August 2024 | https://doi.org/10.11113/mjfas.v20n4.3813
S. Daud, M. I. A. Zaini, M. S. A. Aziz, and A. F. A. Noorden, "Generation of multiwavelength fibre laser based on erbium-doped fibre amplifier with Lyot filter," Malaysian Journal of Fundamental and Applied Sciences, vol. 20, pp. 378-384, 2024.https://doi.org/10.11113/mjfas.v20n2.3091
CORRIGENDUM:
After thorough discussions with the editor and following an official correspondence, it was decided to make the following correction in the article. The name of the author has been corrected to accurately reflect the contributions, and the acknowledgments section has been updated to properly recognize the individuals and institutions that provided support.
Allen Paul Davida, Suzairi Daudb,c,*, Abdul Hadi Sulaimana, Muhammad Ilham Ahmad Zainib, Muhammad Safwan Abd Azizb,c and Ahmad Fakhrurrazi Ahmad Noordend, "Generation of multiwavelength fibre laser based on erbium-doped fibre amplifier with Lyot filter," Malaysian Journal of Fundamental and Applied Sciences, vol. 20, pp. 378-384, 2024.
a    Institute of Power Engineering, Universiti Tenaga Nasional, Jalam IKRAM-UNITEN, 43000 Kajang, Selangor, Malaysiab    Department of Physics, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Johor Bahru, Johor, Malaysiac     Laser Center, Ibnu Sina Institute for Scientific & Industrial Research, Universiti Teknologi Malaysia, 81310 UTM Johor Bahru, Johor, Malaysiad    Department of Physics, Kulliyah of Science, International Islamic University Malaysia, Bandar Indera Mahkota, 25200 Kuantan, Pahang, Malaysia
The acknowledgment for this published paper should be as follows:
This work was supported by Universiti Tenaga Nasional through the BOLD Refresh Postdoctoral Fellowships under the project code of J510050002-IC-6 BOLD REFRESH 2025 and Universiti Teknologi Malaysia by UTM Encouragement Grant Vote No. Q.J130000.3854.31J54.
The authors apologize for this error.
Evaluating the consistency of lenition measures: Neural networks' posterior probability, intensity velocity, and duration
Authors: Tang Kevin , Wayland Ratree , Wang Fenqi , Vellozzi Sophia , Sengupta Rahul
Published: August 2024

Predictions of gradient degree of lenition of voiceless and voiced stops in a corpus of Argentine Spanish are evaluated using three acoustic measures (minimum and maximum intensity velocity and duration) and two recurrent neural network (Phonet) measures (posterior probabilities of sonorant and continuant phonological features). While mixed and inconsistent predictions were obtained across the acoustic metrics, sonorant and continuant probability values were consistently in the direction predicted by known factors of a stop's lenition with respect to its voicing, place of articulation, and surrounding contexts. The results suggest the effectiveness of Phonet as an additional or alternative method of lenition measurement. Furthermore, this study has enhanced the accessibility of Phonet by releasing the trained Spanish Phonet model used in this study and a pipeline with step-by-step instructions for training and inferencing new models.
Change-of-Direction Performance and Its Deficits in Relation to Countermovement-Jump Height and Phase-Specific Performance Among Female Athletes
Authors: Yamashita Naoyuki , Sato Daisuke , Mishima Takaaki
Published: August 2024

Purpose: Jump and linear sprint performances both correlate with pro-agility performance. However, correlation does not imply causation, and potential confounders may affect the correlation. Therefore, this study aimed to determine the relationship between change-of-direction (COD) performance and COD deficits (COD-D) in linear-sprint and countermovement-jump (CMJ) -related performance using multiple stepwise linear-regression models. Methods: The study included 42 female national-level intercollegiate athletes. The 10- and 20-m linear-sprint and pro-agility times, COD-D, CMJ height, and phase-specific force production and rate of force development during eccentric unloading, eccentric braking, and the concentric phases of CMJ were measured. Stepwise linear-regression analyses were used to predict the factors related to COD and COD-D. Results: CMJ height was the sole predictor in the 10-m pro-agility model (adjusted R2 = .234, P = .001). Modified Reactive Strength Index (standardized coefficient, −.710) and the lowest center-of-mass depth during the CMJ (standardized coefficient, .323) were predictors in the 20-m pro-agility model (adjusted R2 = .330, P < .001). For the 10- and 20-m COD-D models, the rate of force development at 30 and 60 milliseconds, respectively, during the concentric phase was the only predictor of performance (adjusted R2 = .183, P = .003 and .237, P = .001, respectively). Conclusions: These results suggest that athletes should concentrate on improving their CMJ height, increasing their ability to lower their center of mass more deeply, and increasing their instantaneous force-production abilities immediately after the eccentric braking phase of CMJ to improve their COD performance.
Adenovirus infections: new insights for the clinical laboratory
Authors: Kajon Adriana E.
Published: August 2024

Since their discovery in 1953, research on human adenoviruses (HAdVs) has had diverse foci, resulted in groundbreaking discoveries, such as gene splicing, and generated powerful oncolytic constructs and expression vectors for vaccine development and gene therapy. In contrast, virologists working in this field have made relatively little progress toward the prevention and treatment of the wide spectrum of HAdV-associated diseases. The understanding of species-specific features of viral pathogenesis, or of the mechanisms underlying the establishment of latency and reactivation, is still limited. This group of viruses currently comprises 7 species, 51 serotypes, and 116 unique genotypes. This complexity manifests with a challenging pathophenotypic diversity. Some types are highly virulent, and others do not seem to cause disease in immunocompetent hosts. The assessment of viral load in blood and respiratory specimens has well-acknowledged clinical utility, but the lack of virus typing capabilities easily implementable in clinical laboratories represents a lingering major limitation to the interpretation of positive tests. Some HAdV infections do have severe consequences for both immunocompetent and immunocompromised patients, and the understanding of why this is the case will require more research. Clinical isolates and collections of positive specimens can provide unique resources to investigate the molecular bases of viral virulence and fitness and also help gather information of spatial–temporal patterns of viral circulation in susceptible communities, but they are extremely scarce. Clinical laboratories are underutilized interfaces between patients and academic scientists and have, therefore, a high potential to become valuable collaborators in research moving forward.
From local bacterial communities to energy: application of microbial fuel cells in laboratory experimentation
Authors: Pazmiño-Arias Esteban , Montero-Calderon Abigail , Perez-Cárdenas Mariela , Gudiño Gomezjurado Marco Esteban
Published: August 2024

It is well known that bacterial communities are an essential component to maintain the balance of terrestrial ecosystems due to the functions and services performed by microorganisms in the environment. The research seeking on alternative energy sources has shown that bacterial communities can bioconvert the chemical energy of an organic substrate into electrical energy, within devices known as microbial fuel cells. For this reason, this class project allows students of Biotechnology, Environmental Science, and Microbiology to apply the appropriate methodology to develop a class project throughout an environmental bacterial community capable of generating electrical energy.
Draft genome sequence of
Paraclostridium benzoelyticum
strain YGCA10, isolated from sediment of the Etoliko lagoon in Greece
Authors: Galiatsatos Ioannis , Asimakis Elias , Stathopoulou Panagiota , Tsiamis George
Published: August 2024

Paraclostridium benzoelyticum
is a Gram-positive, heterotrophic, and obligately anaerobic bacterial species. This report describes the draft genome sequence of
P. benzoelyticum
strain YGCA10, isolated from lagoon sediment under anaerobic culture conditions.
Food-breastmilk combinations alter the colonic microbiome of weaning infants: an
in silico
study
Authors: da Silva Vitor G. , Smith Nick W. , Mullaney Jane A. , Wall Clare , Roy Nicole C. , McNabb Warren C.
Published: August 2024

The introduction of solid foods to infants, also known as weaning, is a critical point for the development of the complex microbial community inhabiting the human colon, impacting host physiology in infancy and later in life. This research investigated
in silico
the impact of food-breastmilk combinations on growth and metabolite production by colonic microbes of New Zealand weaning infants using the metagenome-scale metabolic model named Microbial Community. Eighty-nine foods were individually combined with breastmilk, and the 12 combinations with the strongest influence on the microbial production of short-chain fatty acids (SCFAs) and branched-chain fatty acids (BCFAs) were identified. Fiber-rich and polyphenol-rich foods, like pumpkin and blackcurrant, resulted in the greatest increase in predicted fluxes of total SCFAs and individual fluxes of propionate and acetate when combined, respectively, with breastmilk. Identified foods were further combined with other foods and breastmilk, resulting in 66 multiple food-breastmilk combinations. These combinations altered
in silico
the impact of individual foods on the microbial production of SCFAs and BCFAs, suggesting that the interaction between the dietary compounds composing a meal is the key factor influencing colonic microbes. Blackcurrant combined with other foods and breastmilk promoted the greatest increase in the production of acetate and total SCFAs, while pork combined with other foods and breastmilk decreased the production of total BCFAs.

IMPORTANCE

Little is known about the influence of complementary foods on the colonic microbiome of weaning infants. Traditional
in vitro
and
in vivo
microbiome methods are limited by their resource-consuming concerns. Modeling approaches represent a promising complementary tool to provide insights into the behavior of microbial communities. This study evaluated how foods combined with other foods and human milk affect the production of short-chain fatty acids and branched-chain fatty acids by colonic microbes of weaning infants using a rapid and inexpensive
in silico
approach. Foods and food combinations identified here are candidates for future experimental investigations, helping to fill a crucial knowledge gap in infant nutrition.
Randomized control trial of moderate dose vitamin D alters microbiota stability and metabolite networks in healthy adults
Authors: Wyatt Madhur , Choudhury Ankan , Von Dohlen Gabriella , Heileson Jeffery L. , Forsse Jeffrey S. , Rajakaruna Sumudu , Zec Manja , Tfaily Malak M. , Greathouse Leigh
Published: August 2024

Evidence indicates that both vitamin D and the gut microbiome are involved in the process of colon carcinogenesis. However, it is unclear what effects supplemental vitamin D
3
has on the gut microbiome and its metabolites in healthy adults. We conducted a double-blind, randomized, placebo-controlled trial to identify the acute and long-term microbiota structural and metabolite changes that occur in response to a moderate dose (4,000 IU) of vitamin D
3
for 12 weeks in healthy adults. Our results demonstrated a significant increase in serum 25-hydroxy-vitamin D (25(OH)D) in the treatment group compared to placebo (
P
< 0.0001). Vitamin D
3
significantly increased compositional similarity (
P
< 0.0001) in the treatment group, and enriched members of the Bifidobacteriaceae family. We also identified a significant inverse relationship between the percent change in serum 25(OH)D and microbial stability in the treatment group (
R
= −0.52,
P
< 0.019). Furthermore, vitamin D
3
supplementation resulted in notable metabolic shifts, in addition to resulting in a drastic rewiring of key gut microbial-metabolic associations. In conclusion, we show that a moderate dose of vitamin D
3
among healthy adults has unique acute and persistent effects on the fecal microbiota, and suggest novel mechanisms by which vitamin D may affect the host-microbiota relationship.

IMPORTANCE

Preventative measures to reduce the rise in early-onset colorectal cancer are of critical need. Both vitamin D, dietary and serum levels, and the gut microbiome are implicated in the etiology of colorectal cancer. By understanding the intimate relationship between vitamin D, the gut microbiome, and its metabolites, we may be able to identify key mechanisms that can be targeted for intervention, including inflammation and metabolic dysfunction. Furthermore, the similarity of vitamin D to cholesterol, which is metabolized by the gut microbiome, gives precedence to its ability to produce metabolites that can be further studied and leveraged for controlling colorectal cancer incidence and mortality.
Reversion of KPC-114 to KPC-2 in ceftazidime-avibactam- resistant/meropenem-susceptible
Klebsiella pneumoniae
ST11 is related to low mutation rates
Authors: Pariona Jesus G. M. , Vásquez-Ponce Felipe , Becerra Johana , Martins-Gonçalves Thais , Pariona Eva M. M. , Madueño Fabio T. , Esposito Fernanda , V. de Lima Aline , Mello Sampaio Jorge L. , Galhardo Rodrigo S. , Lincopan Nilton
Published: August 2024

Klebsiella pneumoniae
strains that produce
Klebsiella pneumoniae
Carbapenemase (KPC) variants displaying resistance to ceftazidime-avibactam (CZA) often remain susceptible to meropenem (MEM), suggesting a potential therapeutic use of this carbapenem antibiotic. However,
in vitro
studies indicate that these sorts of strains can mutate becoming MEM-resistant, raising concerns about the effectiveness of carbapenems as treatment option. We have studied mutation rates occurring from the reversion of MEM-susceptible KPC-114 to MEM-resistant KPC-2, in CZA-resistant
K. pneumoniae
belonging to ST11. Two-step fluctuation assays (FAs) were conducted. In brief, initial cultures of KPC-114-producing
K. pneumoniae
showing 1 µg/mL MEM MIC were spread on Mueller–Hinton agar plates containing 2–8 µg/mL MEM. A second step of FA, at 4–16 µg/mL MEM was performed from a mutant colony obtained at 2 µg/mL MEM. Mutation rates were calculated using maximum likelihood estimation. Parental and mutant strains were sequenced by Illumina NextSeq, and mutations were predicted by variant-calling analysis. At 8 µg/mL MEM, mutants derived from parental CZA-resistant (MIC ≥ 64 µg/mL)/MEM-susceptible (MIC = 1 µg/mL) KPC-114-positive
K. pneumoniae
exhibited an accumulative mutation rate of 3.05 × 10
−19
mutations/cell/generation, whereas at 16 µg/mL MEM an accumulative mutation rate of 1.33 × 10
−19
mutations/cell/generation resulted in the reversion of KPC-114 (S181_P182 deletion) to KPC-2. These findings highlight that the reversion of MEM-susceptible KPC-114 to MEM-resistant KPC-2, in CZA-resistant
K. pneumoniae
ST11 is related to low mutation rates suggesting a low risk of therapeutic failure.
In vivo
investigations are necessary to confirm the clinical potential of MEM against CZA-resistant KPC variants.

IMPORTANCE

The emergence of ceftazidime-avibactam (CZA) resistance among carbapenem-resistant
Klebsiella pneumoniae
is a major concern due to the limited therapeutic options. Strikingly, KPC mutations mediating CZA resistance are generally associated with meropenem susceptibility, suggesting a potential therapeutic use of this carbapenem antibiotic. However, the reversion of meropenem-susceptible to meropenem-resistant could be expected. Therefore, knowing the mutation rate related to this genetic event is essential to estimate the potential use of meropenem against CZA-resistant KPC-producing
K. pneumoniae
. In this study, we demonstrate,
in vitro
, that under high concentrations of meropenem, reversion of KPC-114 to KPC-2 in CZA-resistant/meropenem-susceptible
K. pneumoniae
belonging to the global high-risk ST11 is related to low mutation rates.
Testing the sequence of successional processes in miniature ecosystems
Authors: Hanusch Maximilian , He Xie , Böll Laura , Junker Robert R.
Published: August 2024

Dispersal, environmental filtering, and biotic interactions define the species inventory of local communities. Along successional gradients, these assembly processes are predicted to sequentially vary in their relative importance with dispersal as the dominating process early in succession, followed by environmental filtering and biotic interactions at later stages. While observational data from field studies supported this prediction, controlled experiments confirming a sequence of successional processes are still lacking. We designed miniature ecosystems to explicitly test these assumptions under controlled laboratory conditions. Our “Ecosystems on a Plate” (EsoaP) are 3D-printed customized microplates with 24 connected wells allowing us to track dispersal, niche filtering, and biotic interactions among bacteria and plants in time and space. Within EsoaPs, we created heterogeneous habitat landscapes by well-specific nutrient levels or by providing plant seedlings as mutualistic partners in a checkerboard pattern. Bacteria of a single strain were released in one well and subsequently distributed themselves within the plates. We measured the spatial distribution of bacterial abundances at two time points as a function of abiotic or biotic heterogeneity. Bacterial abundance distribution confirmed a shift from initial dispersal-dominated processes to later niche filtering and biotic interactions as more important processes. Our approach follows the principles of
open science
as the affordable availability of 3D printers as well as shared STL files makes EsoaPs disseminatable and accessible to all levels of society, facilitating future experimental research.

IMPORTANCE

Hypotheses regarding the underlying processes of ecological successions have primarily emerged from and have been tested in observational studies, lacking substantial support through controlled experiments. The design of such experiments should focus on testing contemporary ecological theories at the intersection of community assembly and successional research. To achieve this, we developed and employed 3D-printed “Ecosystems on a Plate” (EsoaP) within controlled laboratory settings. EsoaPs surmount several limitations of nanoscale instruments that had hindered their application in ecologically meaningful research. By sharing 3D printing designs, experimental protocols, and data openly, we facilitate reproducibility of our experiments by researchers across diverse ecological disciplines. Moreover, our approach facilitates cost-effective replication of experiments, democratizing access to tools for ecological research, and thus holds the potential to serve as a model for future studies and educational purposes.
Enhanced salt tolerance in
Glycyrrhiza uralensis
Fisch. via
Bacillus subtilis
inoculation alters microbial community
Authors: Xiao Jiancai , Xiao Jing , Gao Pengchao , Zhang You , Yan Binbin , Wu Hongli , Zhang Yan
Published: August 2024

The widespread prevalence of saline environments poses a significant global environmental challenge. Salt stress, induced by saline soils, disrupts soil microecology and affects the plant-microbe-soil cycling process. Utilizing microbial fungicides stands as a primary strategy to mitigate salt stress-induced damage to plants and soils. This study investigated the influence of
Bacillus subtilis
(Bs) inoculation on the microbial community, assembly processes, and functional changes in bacteria and fungi in
Glycyrrhiza uralensis
Fisch. (licorice) seedlings under varying salt stress levels, primarily employing microbiomics techniques. Soil enzyme activities displayed a declining trend with increasing salt stress, which was mitigated by Bs inoculation. Microbiome analysis revealed a significant increase in bacterial and fungal operational taxonomic units, particularly in Ascomycetes and Nitrogen-fixing Bacteria, thereby enhancing soil denitrification. The abundance of Proteobacteria, Actinobacteriota, Bacteroidota, and Firmicutes in bacteria, as well as Ascomycota in fungi, increased with higher salt stress levels, a process facilitated by Bs inoculation. However, functional predictions indicated a reduction in the relative abundance of Dung Saprotrophs with Bs inoculation. Salt stress disrupted soil assembly processes, showcasing a continuous decline in diffusion limitation with increased salt concentration, where Bs inoculation reached a peak under moderate stress. In summary, this research elucidates the communication mechanism of Bs in enhancing salt tolerance in licorice from a microbiome perspective, contributing to a comprehensive understanding of abiotic and biotic factors.

IMPORTANCE

Licorice is a herb that grows in deserts or saline soils. Enhancing the salt tolerance of licorice is necessary to maintain the quality of cultivated licorice and to ensure the supply of medicinal herbs. In the past, we have demonstrated the effectiveness of inoculation with
Bacillus subtilis
(Bs) to enhance the salt tolerance of licorice and revealed the key metabolic pathways for the development of salt tolerance through multi-omics. In this study, we used the microbiomics approach to reveal the plant-microbe-soil interactions at the level of inoculation of Bs affecting the dynamics of soil microbial communities from bacterial and fungal perspectives, thus bridging the interactions between biotic and abiotic factors.
The relationship between youth’s exposure to unhealthy digital food marketing and their dietary intake in Canada
Authors: Vergeer Laura , Soto Carolina , Bagnato Mariangela , Pauzé Elise , Amson Ashley , Ramsay Tim , Olstad Dana Lee , Welch Vivian , Potvin Kent Monique
Published: August 2024

There is limited evidence on how exposure to digital marketing of unhealthy foods affects youth’s dietary behaviours. This study therefore aimed to examine the association between youth’s self-reported digital food marketing exposure and dietary intakes, and explore predictors of frequent unhealthy food consumption. A survey was conducted among 1075 youth in Canada (aged 10–17 years) in April 2023. Proportional odds models examined associations between frequency of exposure to digital marketing of unhealthy foods and frequency of consumption of those foods, adjusted for sociodemographic characteristics and digital device usage. Compared with participants reporting no exposure to digital fast-food marketing in the past week, those exposed ≥4 times per week were more likely to consume fast food more frequently. Youth exposed to digital marketing of sugary drinks and salty/savoury snacks ≥1 time(s) in the previous week were more likely to consume these foods on a greater number of days, compared with those reporting no exposure to this marketing in the past week. Reporting exposure to digital marketing of desserts/sweet treats every day or more than once a day was associated with more frequent consumption of desserts/sweet treats. Province of residence (Ontario/Quebec) and total daily time spent online predicted more frequent consumption of fast food, sugary drinks, salty/savoury snacks, and desserts/sweet treats. Overall, more frequent self-reported exposure to digital marketing of unhealthy foods is associated with more frequent consumption of these foods by Canadian youth. Regulations are needed to help protect youth from digital food marketing, which may help reduce their unhealthy food consumption.
Assessing the effects of high-carvacrol oregano oil on rumen microbial fermentation, gas production, and methane production in vitro
Authors: Benchaar Chaouki , Hassanat Fadi
Published: August 2024

The objective of this in vitro study was to assess the effects of high-carvacrol oregano oil (ORE; 50 g/kg oregano oil, 800–802 g/kg carvacrol), on microbial fermentation and CH4 production. In the experiment (a complete randomized block design), treatments included a negative control (CTL, no additive), a positive control (monensin, MON, 10 mg/L of culture fluid), and ORE (20, 40, 80, 120, 200, 160, and 1000 mg/L of culture fluid). Compared with CTL, MON shifted ( p < 0.05) volatile fatty acid (VFA) profile from acetate and butyrate to propionate production, thereby reducing ( p < 0.05) CH4 production (−26%). Monensin decreased ( p < 0.05) NH3 and branched-chain VFA concentrations. Of the doses evaluated, only the highest dose (1000 mg/L) affected ruminal microbial fermentation and CH4 production. At this dose, ORE reduced ( p < 0.05) gas production, total VFA, acetate, propionate and NH3 concentrations, and CH4 production (−22%). The reduced gas production and total VFA is an indication of feed digestion inhibition. These results suggest that ORE may decrease CH4 production and improve ruminal N utilization. However, these findings need to be validated in vivo to determine the optimal dose to benefit from the positive effects while avoiding the negative impact of ORE on feed digestion.