bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparative Transcriptomics Reveals the microRNA-Mediated Immune Response of Large Yellow Croaker (Larimichthys crocea) to Pseudomonas plecoglossicida Infection
Authors: Chen Huazhi , Zhang Yameng , Shao Guangming , Chen You , Shen Yibo , Mu Yinnan , Chen Xinhua
Published: December 2022

Visceral white nodules disease (VWND), caused by Pseudomonas plecoglossicida, is a common disease among cage-farmed large yellow croaker (Larimichthys crocea) in China. However, comprehensive investigations of the molecular defensive mechanisms used by L. crocea in response to P. plecoglossicida infection remain relatively rare. Here, we constructed transcriptomes of the L. crocea spleen at 12 h and 24 h after P. plecoglossicida challenge. We identified 518 novel miRNAs and 823 known miRNAs in the spleen of L. crocea. Between the challenge and control groups, 32 differentially expressed miRNAs (DEmiRNAs), predicted to target 356 genes, and 1152 differentially expressed mRNAs (DEmRNAs) were identified at 12 h post-infection, while 33 DEmiRNAs, predicted to target 278 genes, and 1067 DEmRNAs were identified at 24 h post-infection. Gene ontology (GO) analysis showed that 146 and 126 GO terms were significantly enriched in the target genes at 12 h and 24 h, respectively. Twenty-eight and four immune-associated Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were significantly enriched in the target genes at 12 h and 24 h, respectively. Three immune-associated pathways were among those most enriched in the target genes: Toll-like receptor signaling, endocytosis, and C-type lectin receptor signaling. Network analysis identified 47 DEmRNA-DEmiRNA pairs. In particular, the immune-related genes TLR5S and PIGR were targeted by the miRNAs lcr-miR-7132c and dre-miR-183-5p, respectively. Dual-luciferase assays verified that lcr-miR-7132c downregulated TLR5S, suggesting that this miRNA may participate in regulating the immune response of L. crocea to P. plecoglossicida infection through the TLR5S-mediated signaling pathway. Our results help to clarify the miRNA-mediated immune response of L. crocea to P. plecoglossicida infection.
Which Fish Benefit from the Combined Influence of Eutrophication and Warming in the Dnipro River (Ukraine)?
Authors: Zymaroieva Anastasiia , Bondarev Dmytro , Kunakh Olga , Svenning Jens-Christian , Zhukov Oleksandr
Published: December 2022

The effects of climate warming and eutrophication on aquatic organisms are well established, but we lack a deep understanding of the selective mechanisms of fish communities towards eutrophication and warming in tandem. The aim of the study was to identify fish traits that were positively related to eutrophication and ongoing warming. The research was conducted for 19 years in the Dnipro River channel and floodplain water system of the “Dnipro-Orylskiy” Nature Reserve. Both categorical and continuous fish traits were considered. The study area is characterized by a more intense warming trend than the average for Europe, which reflects an increase in the maximum summer air temperature. At the same time, the concentration of chlorophyll-a had a monotonic tendency to decrease during the study period. Phytophilic, limnophilic, and freshwater fish species are increasing in abundance, while rheophilic and lithophilic fish are decreasing due to global warming. Fish species with greater vulnerability and resilience have selective advantages in terms of global warming. Pelagic fish species are the most resistant to eutrophication, while benthopelagic and phytolithophilic fish species are the most sensitive. Brackish-water demersal self-settled species of marine origin have a competitive advantage over other native freshwater species in the face of increasing symptoms of eutrophication and a warming climate.
Effect of Oil Type Used in Neapolitan Pizza TSG Topping on Its Physical, Chemical, and Sensory Properties
Authors: Piscopo Amalia , Zappia Angela , Mincione Antonio , Silletti Roccangelo , Summo Carmine , Pasqualone Antonella
Published: December 2022

Background: According to the regulations of the Neapolitan Pizza TSG, extra virgin olive oil must be exclusively used as topping ingredient, together with tomato for pizza marinara-type production. As, often deliberately, other oils are replaced by pizza makers for economical and organoleptic purposes, the present study was conducted to analyze the quality of pizza depending on the oil typology used. Methods: Chemical and sensory analyses were performed on olive oils and on pizza topping mix samples after cooking to detect changes due to the applied cooking processing. Results: The results revealed the best quality of a monovarietal olive oil (Ottobratica cv.) for their peculiar phenolic content related to the best oxidation stability after pizza’s cooking, expressed as bioactive amounts and lower presence of undesired volatile compounds. Conclusions: The use of an extra virgin monovarietal olive oil, such as Ottobratica cv., in the topping of pizza is preferable to other oils, also EVOO, because of its higher quality, which is reflected in greater health and pleasant characteristics from a sensorial point of view.
Changes in the Physicochemical Properties, Antioxidant Activity and Metabolite Analysis of Black Elephant Garlic (Allium ampeloprasum L.) during Aging Period
Authors: Nam Se-Hyun , Han Young-Sil , Sim Ki-Hyeon , Yang Seung-Ok , Kim Myung-Hyun
Published: December 2022

This study investigated the effects of the aging period on the black elephant garlic (Allium ampeloprasum L.) manufacturing process. Black elephant garlic is a processed elephant garlic product prepared by high-temperature and high-humidity treatment for 40 days. The proximate composition (moisture, crude lipid, crude protein, carbohydrate, and ash), minerals, color values, reducing sugars, pH, total polyphenol contents, total flavonoid contents and antioxidant activities of elephant garlic and black elephant garlic were evaluated. The browning intensity of elephant garlic increased with the aging period, but the browning reaction terminated after aging for 30 days, exhibiting the same browning level. Reducing sugars increased over the aging period until 20 days, and then decreased with the aging period, in contrast to the pH, which decreased from 6.47 to 3.68 over the aging period. Antioxidant components, including the total polyphenol and total flavonoid contents of black elephant garlic, increased significantly until day 30 of aging. From the metabolite profiles determined through GC/MS analysis, it was confirmed that primary metabolites related to antioxidant components, such as lactic acid and 5-hydroxymethyl-2-furoic acid, were generated during the aging process of elephant garlic.
Potential Use of Cardunculus Biomass on Pleurotus eryngii Production: Heteroglycans Content and Nutritional Properties (Preliminary Results)
Authors: Battaglia Valerio , Sorrentino Roberto , Verrilli Giulia , del Piano Luisa , Sorrentino Maria Cristina , Petriccione Milena , Sicignano Mariarosaria , Magri Anna , Cermola Michele , Cerrato Domenico , Lahoz Ernesto
Published: December 2022

The new perspective of using waste biomass to cultivate mushrooms as a source of protein for human nutrition, in line with the circular economy principles, is receiving increasing attention in the scientific community and represents great wealth in terms of environmental sustainability. Pleurotus eryngii is a mushroom also known as cardunculus mushroom due to its ability to grow on this plant. This study explores the potential intrinsic properties of cardunculus (for example, the presence of inulin in the roots) as raw material for the growth of cardunculus mushrooms, and the influence on heteroglycan content and nutrition parameters of the fruiting bodies. Both mycelium and fruiting bodies were used to determine the heteroglycan content in the presence of inulin or cardunculus roots rich in inulin. To produce heteroglycans from P. eryngii in greater quantities and shorter times without having to wait for the formation of the fruiting bodies, the mycelium could be used. The results showed that the presence of cardunculus biomass positively influences the heteroglycan content of P. eryngii. In terms of nutritional parameters, higher contents of polyphenols, flavonoids, anthocyanins, and antioxidant activity were detected in P. eryngii grown on the cardunculus stem and root substrate. In conclusion, recycling cardunculus biomass to generate growth blocks for edible mushrooms is a winning choice due to the opportunity to use this biomass waste, which is gaining more and more attention due to the increase in cultivated areas and the use of fruiting bodies of P. eryngii as a functional food and source of molecules with potential biological activities.
Evaluation of the Potential Anti-Inflammatory Activity of Black Rice in the Framework of Celiac Disease
Authors: Piazza Stefano , Colombo Francesca , Bani Corinne , Fumagalli Marco , Vincentini Olimpia , Sangiovanni Enrico , Martinelli Giulia , Biella Simone , Silano Marco , Restani Patrizia , Dell’Agli Mario , Di Lorenzo Chiara
Published: December 2022

Inflammation and oxidative stress are two mechanisms involved in the pathogenesis of celiac disease (CD). Since the direct effect of gliadin on the intestinal epithelia is less studied, the aims of this study were the development of a specific cellular model based on the use of gliadin as a pro-inflammatory stimulus and the evaluation of the potential antioxidant and anti-inflammatory properties of extracts from different black rice in the framework of CD. The rice extracts were in vitro digested, characterized in terms of phenolic compounds and antioxidant capacity, and tested on Caco-2 cells to investigate their inhibitory effect on Reactive Oxygen Species, the NF-κB transcription and the CXC chemokines (sICAM-1, IL-8, and CXCL-10). In addition, the role of the extracts in modulating the activation of epithelial cells in CD was confirmed by applying the K562(S) agglutination test. The black rice extracts showed inhibitory effects on the production of the oxidative and the inflammatory mediators considered, with particular reference to lymphocyte-attracting CXCL-10 both before and after digestion. The presence of anthocyanins and their digestion metabolites may account for the observed anti-inflammatory activity after in vitro digestion. This work provided preliminary data supporting the use of black rice as a healthy food or ingredient of food supplements for celiacs.
Development of Food Multi-Mix Using a Linear Programming Approach to Fill the Nutrient Gap of Amino Acids and Micronutrients for Stunted Non-Wasted Children
Authors: Wirawan Nia N , Fahmida Umi , Purwestri Ratna C , Timan Ina S , Hegar Badriul
Published: December 2022

Food-based approaches using locally available food escalates the feasibility and the sustainability of nutrition intervention. A complementary feeding recommendation (CFR) integrated with the food multi-mix (FMM) formulation was targeted to fulfill micronutrient and amino acid requirements for stunted non-wasted (SNW) children aged 12–23 months living in agricultural areas. A seven-day estimated food record (EFR) of 87 children was used to design the CFR and 4 identified underutilized foods were integrated as the FMM. A linear programming approach using Optifood was applied to optimize the CFR and FMM. CFR alone successfully fulfills the vitamin C, riboflavin, iron, and zinc, but it cannot fulfill calcium, thiamin, niacin, vitamin B6, folate, vitamin B12, and histidine. With the incorporation of the selected underutilized cowpea, buncis batik, wader fish, and cows’ milk in the FMM development, the nutrients that are challenging in CFR development, can be fulfilled. Therefore, these findings present evidence that food multi-mix developed based on locally available nutrient-dense food sources can help to meet the nutrient gaps, which often remained even after a complementary feeding diet is optimized. Efficacy study using the developed CFR and FMM is recommended to assess effect in improving intake of micronutrients and amino acids and improving the linear growth of stunted, non-wasted children.
Drying Kinetic of Jaboticaba Berries and Natural Fermentation for Anthocyanin-Rich Fruit Vinegar
Authors: Chua Lee , Abd Wahab Nurul
Published: December 2022

This study aimed to determine the drying kinetic of jaboticaba berries that were then used for the fermentation of natural fruit vinegar. The drying behavior was fitted well to the thin-layer kinetic model of Midilli et al. in a vacuum oven at 40 °C. Moisture diffusion was the dominant mechanism because two falling rate periods were observed. The effective moisture diffusivity was decreased (2.52 × 10−10 m2/s) after being pretreated with 70% sugar (1.84 × 10−10 m2/s) and 10% salt (6.73 × 10−11 m2/s) solutions. Fresh berry vinegar was found to have higher flavonoids, including anthocyanins, to exhibit higher antiradical and anti-pathogenic microorganism activities. However, the phenolic content in dried berries vinegar was higher, mainly from the bond breaking of tannins and lignins from fruit peel. Some extent of oxidation occurred because of the change in the color index of vinegar samples. The acidity of both vinegars was 3% acetic acid. Headspace GC-MS also detected acetic acid as the major compound (>60%) in the vapor of vinegar samples. A wide range of non-volatile compounds composed of alkaloids, terpenoids, flavonoids, organic acids, and sugar derivatives was detected by UHPLC-TWIMS-QTOFMS. The peak intensity of anthocyanins was reduced by 28–77% in dried berry vinegar. Therefore, it is better to prepare natural fruit vinegar using fresh berries, preserving anthocyanins for high antioxidant capacity.
Integrated Processes Turning Pepper Sauce Waste into Valuable By-Products
Authors: Shu Jicheng , Yin Yongqin , Liu Zhijun
Published: December 2022

Background: Safe and efficient disposal of millions of tons of pepper sauce waste (PSW) can be a challenge to pepper sauce manufacturers that are concerned about creating environmental hazards from the processing (e.g., preservative salt and vinegar) and intrinsic (e.g., the pungent capsaicins) ingredients. It will be immensely beneficial to process these waste materials before they go to disposal. This work presents integrated approaches for a complete utilization of waste materials by removing and recovering valuable by-products and/or ingredients while succeeding to minimal to zero hazards. Methods: Laboratory- and pilot-scale extraction processes were used to demonstrate the recovery of intrinsic compounds from PSW to pungent pepper oil. Flash chromatography was then applied to isolate the pungent capsaicins out of the pepper oil, thus generating a no-heat pepper oil. Results: By processing the waste materials, a number of valuable by-products with various yield percentages were produced. They included (1) hot red pepper oil (RPO, 8.0% v/w), (2) no-heat pepper residue (NHPR, 25.3% w/w), (3) no-heat red pepper oil (NHRPO, 4.0% v/w), (4) capsaicinoids (0.8% w/w), and (5) capsaicin (0.4% w/w). The optimum processing conditions for products 1, 2, and 3 include extracting the waste materials with 95% ethanol twice, each lasting three hours. The optimal isolation conditions of flash column chromatography to obtain products 4 and 5 include the use of the pre-packed chromatography column 130 g Redisep C18, preparing the sample concentration to 100 mg/mL, eluting with aqueous ethanol, and detecting capsaicins at a wavelength of 228 nm. Conclusions: An integrated approach is offered for the complete utilization of PSW. It not only turns organic food waste into numerous new commodities but also significantly reduces the volume and degree of potential environmental hazard to the disposal sites.
On the Absorbing Problems for Wiener, Ornstein–Uhlenbeck, and Feller Diffusion Processes: Similarities and Differences
Authors: Giorno Virginia , Nobile Amelia G.
Published: December 2022

For the Wiener, Ornstein–Uhlenbeck, and Feller processes, we study the transition probability density functions with an absorbing boundary in the zero state. Particular attention is paid to the proportional cases and to the time-homogeneous cases, by obtaining the first-passage time densities through the zero state. A detailed study of the asymptotic average of local time in the presence of an absorbing boundary is carried out for the time-homogeneous cases. Some relationships between the transition probability density functions in the presence of an absorbing boundary in the zero state and between the first-passage time densities through zero for Wiener, Ornstein–Uhlenbeck, and Feller processes are proven. Moreover, some asymptotic results between the first-passage time densities through zero state are derived. Various numerical computations are performed to illustrate the role played by parameters.
On Implicit Coupled Hadamard Fractional Differential Equations with Generalized Hadamard Fractional Integro-Differential Boundary Conditions
Authors: Guo Limin , Riaz Usman , Zada Akbar , Alam Mehboob
Published: December 2022

This study is devoted to studying the existence and uniqueness of solutions for Hadamard implicit fractional differential equations with generalized Hadamard fractional integro-differential boundary conditions by utilizing the contraction principle of the Banach and Leray–Schauder fixed point theorems. Moreover, with two different approaches, the Hyers–Ulam stabilities are also discussed. Different ordinary differential equations of the third order with different boundary conditions (e.g., initial, anti periodic and integro-differential) can be obtained as a special case for our proposed model. Finally, for verification, an example is presented, and some graphs for the particular variables and particular functions are drawn using MATLAB.
Estimation Method of Ideal Fractal Parameters for Multi-Scale Measurement of Polished Surface Topography
Authors: Li Hongju , Liu Ying , Wang Yuechang , Liao Haoran
Published: December 2022

A surface topography characterization parameter system based on fractal parameters has been established, and several estimation methods for these fractal parameters have been suggested accordingly. Since scale dependence exists in these conventional methods, it is necessary to find an estimation method for characterization parameters with uniqueness. An estimation method for ideal fractal parameters for multi-scale measurement of polished surface topography is proposed in this study. Polished surfaces of two materials, WC-Ni and 9Cr18Mo, are measured under multi-scale for frequency component analysis. This study proposes an estimation method for ideal fractal parameters based on a modified determination method for the scale-free region and the decomposition of frequency components into three classifications. The reasonable results verify the existence of ideal fractal parameters: for the WC-Ni surface, ideal fractal dimension D = 1.3 and scale coefficient G = 2.23×1020 μm; for the 9Cr18Mo surface, ideal fractal dimension D = 1.2 and scale coefficient G = 3.33×1033 μm. Additionally, it is revealed that the scale-dependent components conform to the same regulation on the same instrument by comparing the results of two materials. The conclusions of this study are expected to support tribology research and mechanical engineering related to surface topography.
High-Tracking-Precision Sensorless Control of PMSM System Based on Fractional Order Model Reference Adaptation
Authors: Niu Hongjie , Liu Ling , Jin Dongsong , Liu Siyuan
Published: December 2022

In order to solve parameter fluctuations and disturbances, a novel fractional order model reference adaptive speed observer that estimates the rotor position and the angular velocity from the stator currents is proposed for sensorless control of permanent-magnet synchronous motors (PMSM). Firstly, a novel fractional order model reference adaptive controller (FOMRAC) for adaptive identification is designed to achieve fast response and high precise identification of load torque in the full speed range when the motor is running at variable-speed or variable-load. Additionally, an appropriate adjustable matrix P is chosen to make the convergence of the adaptive law meet the requirements. Next, an improved model reference adaptive observer (MRAO) is proposed to suppress the serious chattering and compensate rotor position error, which can stabilize the system. The validity of the proposed fractional order model reference adaptive sensorless control strategy for PMSM is demonstrated with simulations.
Driving Behaviour and Usability: Should In-Vehicle Speed Limit Warnings Be Paired with Overhead Gantry?
Authors: Payre William , Diels Cyriel
Published: December 2022

Variable speed limits (VSL) aim at improving safety and traffic fluidity by increasing drivers’ awareness. In the present simulator study, VSL displayed on overhead gantries on a motorway were also displayed on a mobile phone, fixed on the vehicle’s centre console, with distance-based triggers (250 m vs. 500 m from the overhead gantry). Results showed drivers (N = 20) complied with the in-vehicle information, which was congruent with the upcoming gantry. The sooner the in-vehicle VSL, the faster the speed when speed limits increased. Similarly, the sooner the in-vehicle VSL, the slower the speed when speed limits decreased. Later in-vehicle VSL resulted in lower speed homogeneity, which is a safety concern. Speed homogeneity was greater when no in-vehicle VSL were displayed. Finally, the 70 mph VSL were affecting driving behaviour differently. These results suggested that there might be traffic disruption and more erratic longitudinal vehicle control on real roads.
The Effect of Branched Alkyl Chain Length on the Properties of Supramolecular Organogels from Mono-N-Alkylated Primary Oxalamides
Authors: Azyat Khalid , Makeiff Darren , Smith Bradley , Wiebe Mickie , Launspach Steve , Wagner Ashley , Kulka Marianna , Godbert Nicolas
Published: December 2022

Mono-N-alkylated primary oxalamide derivatives with different sized branched alkyl tail-groups were excellent low molecular weight gelators for a variety of different organic solvents with different polarities and hydrogen-bonding abilities. Solvent-gelator interactions were analyzed using Hansen solubility parameters, while 1H NMR and FTIR spectroscopy were used to probe the driving forces for the supramolecular gelation. The molecular structures of the twin tail-groups did not significantly affect the supramolecular gelation behavior in different solvents. However, for select solvents, the molecular structures of the tail-groups did have a significant effect on gel properties such as the critical gelator concentration, thermal stability, gel stiffness, gel strength, network morphology, and molecular packing. Finally, metabolic activity studies showed that the primary alkyl oxalamide gelators had no effect on the metabolic activity of mouse immune cells, which suggests that the compounds are not cytotoxic and are suitable for use in biomedical applications.
Chlorella vulgaris Extract-Decorated Gold Nanoparticle Hybridized Antimicrobial Hydrogel as a Potential Dressing
Authors: He Ruiying , Zhou Dong , Xiao Lan , Li Yulin
Published: December 2022

This study reports a novel design of a moisturizing and antimicrobial hydrogel with injectable properties, using a green solvent (glycerol) as a cross-linking agent and gold nanoparticle reduced by Chlorella extract as an antimicrobial approach. We have synthesized gold nanoparticles (AuNPs) with environmentally friendly and bio-safe properties using Chlorella aqueous extracts (AuNPs@Chlorella). Characterization of the nanoparticles by ultraviolet-visible spectroscopy (UV-Vis), Fourier transform infrared spectroscopy (FTIR), Raman spectrum, and transmission electron microscope (TEM) confirmed that spherical AuNPs with the particle size of 10–20 nm were successfully synthesized. An analysis of the enhancement of the stability of gelatin hydrogels by the addition of glycerol and AuNPs was performed by rheometry. In addition, we also used Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli) to confirm the good antibacterial activity. Therefore, the as-prepared gelatin–glycerol hydrogels containing AuNPs@Chlorella are most likely promising alternatives for wound healing dressings.
Predictors of Smoking in Older Adults and an Epigenetic Validation of Self-Report
Authors: Long Jeffrey D. , Gehlsen Michael P. , Moody Joanna , Weeks Gracie , Philibert Robert
Published: December 2022

There are several established predictors of smoking, but it is unknown if these predictors operate similarly for young and old smokers. We examined clinical data from the National Lung Screening Trial (NLST) to determine the predictive ability of gender, body mass index (BMI), marital status, and race on smoking behavior, with emphasis on gender interactions. In addition, we validated the self-report of smoking behaviors for a subgroup that had available epigenetic data in the form of cg05575921 methylation. Participants were N=9572 current or former smokers from the NLST biofluids database, age 55–74, minimum of 30 pack years, and mostly White. A subgroup of N=3084 who had DNA were used for the self-report validation analysis. The predictor analysis was based on the larger group and used penalized logistic regression to predict the self-report of being a former or current smoker at baseline. Cg05575921 methylation showed a moderate ability to discriminate among former and current smokers, AUC = 0.85 (95% confidence interval = [0.83, 0.86]). The final selected variables for the prediction model were BMI, gender, BMI by gender, age, divorced (vs. married), education, and race. The gender by BMI interaction was such that males had a higher probability of current smoking for lower BMI, but this switched to females having higher current smoking for overweight to obese. There is evidence that the self-reported smoking behavior in NLST is moderately accurate. The results of the primary analysis are consistent with the general smoking literature, and our results provide additional specificity regarding the gender by BMI interaction. Body weight issues might play a role in smoking cessation for older established smokers in a similar manner as younger smokers. It could be that women have less success with cessation when their BMI increases.
Comparative Gene Enrichment Analysis for Drought Tolerance in Contrasting Maize Genotype
Authors: Gillani Syed Faheem Anjum , Rasheed Adnan , Abbasi Asim , Majeed Yasir , Abbas Musawer , Hassan Muhammad Umair , Qari Sameer H. , Binothman Najat , Al Kashgry Najla Amin T. , Tahir Majid Mahmood , Peng Yunling
Published: December 2022

Drought stress is a significant abiotic factor influencing maize growth and development. Understanding the molecular mechanism of drought tolerance is critical to develop the drought tolerant genotype. The identification of the stress responsive gene is the first step to developing a drought tolerant genotype. The aim of the current research was to pinpoint the genes that are essential for conserved samples in maize drought tolerance. In the current study, inbred lines of maize, 478 and H21, a drought-tolerant and susceptible line, were cultivated in the field and various treatments were applied. The circumstances during the vegetative stage (severe drought, moderate drought and well-watered environments) and RNA sequencing were used to look into their origins. In 478, 68%, 48% and 32% of drought-responsive genes (DRGs) were found, with 63% of DRGs in moderate drought and severe drought conditions in H21, respectively. Gene ontology (GO) keywords were explicitly enriched in the DRGs of H21, which were considerably over-represented in the two lines. According to the results of the GSEA, “phenylpropanoid biosynthesis” was exclusively enriched in H21, but “starch and sucrose metabolism” and “plant hormone signal transduction” were enhanced in both of the two lines. Further investigation found that the various expression patterns of genes linked to the trehalose biosynthesis pathway, reactive oxygen scavenging, and transcription factors, may have a role in maize’s ability to withstand drought. Our findings illuminate the molecular ways that respond to lack and offer gene resources for maize drought resistance. Similarly, SNP and correlation analysis gave us noticeable results that urged us to do the same kind of analysis on other crops. Additionally, we isolated particular transcription factors that could control the expression of genes associated to photosynthesis and leaf senescence. According to our findings, a key factor in tolerance is the equilibrium between the induction of leaf senescence and the preservation of photosynthesis under drought.
Analysis of Genetic Diversity and Phylogenetic Relationships of Wheat (Triticum aestivum L.) Genotypes Using Phenological, Molecular and DNA Barcoding Markers
Authors: El-Esawi Mohamed A. , Elashtokhy Mohamed M. A. , Shamseldin Sahar A. M. , El-Ballat Enas M. , Zayed Ehab M. , Heikal Yasmin M.
Published: December 2022

Wheat (Triticum aestivum L.) is a key food crop, accounting for approximately 765 million tons produced worldwide. The present study evaluated 16 wheat genotypes using 19 morphological and phenological traits, 16 molecular markers (Inter Simple Sequence Repeats and Start Codon Targeted; ISSR and SCoT) and rbcL and matK plastid gene barcoding. The 16 wheat genotypes showed significant genetic variation using the markers assayed. Cell plot of phenological parameters revealed significant differences among the 16-day-old seedlings of wheat genotypes at Z1.1 growth stage. Collectively, W2 genotype had the lowest shoot length (SL), length of first internodes (LFI) and leaf area (LA) values, while W8 genotype had the highest diameter of first internode (DFI) and LA values. Furthermore, W7 genotype had the maximum plant biomass (PB) and leaf width (LW) values. Geometric models grouped wheat kernels into “rounded” and “nearly elongated”. Estimates of heritability (H2) for these morphological characters ranged from 4.93 to 100%. The highest H2 values were recorded for root number (RN) (100%) followed by SL (88.72%), LFI (88.30%), LA (87.76%) and Feret diameter (86.68%), while the lowest H2 value was recorded for DFI (4.93%). Furthermore, highly significant genotypic and phenotypic correlations were also observed among those traits. Reproducible fingerprinting profiles and high levels of polymorphism (PPB%) of SCoT (95.46%) and ISSR (82.41%) were recorded, indicating that they are effective tools for detecting genetic variation levels among wheat genotypes. The informativeness of markers were measured through estimation of polymorphic information content (PIC), resolving power (RP) and marker index (MI). The RP and PPB% of SCoT were significantly higher compared to those of ISSR. Comparatively, the two molecular markers were effective for studying genetic diversity among wheat genotypes, but SCoT markers were more informative. Moreover, based on the two chloroplast DNA regions (rbcL and matK), MatK was found to be more reliable for differentiating among T. aestivum genotypes. Taken together, using all the studied attributes, a clear taxonomic relationship can be used to identify T. aestivum species and improve their pragmatic production and development.
Lasp1 Expression Is Implicated in Embryonic Development of Zebrafish
Authors: Grossi Ilaria , Schiavone Marco , Cannone Elena , Grejdan Oana Andreea , Tobia Chiara , Bonomini Francesca , Rezzani Rita , Salvi Alessandro , De Petro Giuseppina
Published: December 2022

The LIM and SH3 domain protein 1 (LASP1) was originally identified in metastatic breast cancer and mainly characterized as a cytoskeleton protein overexpressed in various cancer types. At present, little is known about LASP1 expression in physiological conditions, and its function during embryonic development has not been elucidated. Here, we focused on Lasp1 and embryonic development, choosing zebrafish as a vertebrate model. For the first time, we identified and determined the expression of Lasp1 protein at various stages of development, at 48 and 72 h post-fertilization (hpf), at 6 days pf and in different organs of zebrafish adults by Western blotting, 3D light-sheet microscopy and fluorescent immunohistochemistry. Further, we showed that specific lasp1 morpholino (MO) led to (i) abnormal morphants with alterations in several organs, (ii) effective knockdown of endogenous Lasp1 protein and (iii) an increase in lasp1 mRNA, as detected by ddPCR. The co-injection of lasp1 mRNA with lasp1 MO partially rescued morphant phenotypes, thus confirming the specificity of the MO oligonucleotide-induced defects. We also detected an increase in apoptosis following lasp1 MO treatment. Our results suggest a significant role for Lasp1 in embryonic development, highlighting zebrafish as a vertebrate model suitable for studying Lasp1 function in developmental biology and organogenesis.
Antimicrobial Resistance and Genomic Epidemiology of tet(X4)-Bearing Bacteria of Pork Origin in Jiangsu, China
Authors: Li Yuhan , Li Yan , Bu Kefan , Wang Mianzhi , Wang Zhiqiang , Li Ruichao
Published: December 2022

The emergence of tigecycline-resistant bacteria in agri-food chains poses a public health concern. Recently, plasmid-mediated tet(X4) was found to be resistant to tigecycline. However, genome differences between tet(X4)-positive Escherichia coli of human and pork origins are still under-investigated. In this study, 53 pork samples were collected from markets in Jiangsu, China, and 23 tet(X4)-positive isolates were identified and shown to confer resistance to multiple antibiotics, including tigecycline. tet(X4)-positive isolates were mainly distributed in E. coli (n = 22), followed by Klebsiella pneumoniae (n = 1). More than half of the tet(X4) genes were able to be successfully transferred into E. coli C600. We downloaded all tet(X4)-positive E. coli isolates from humans and pork found in China from the NCBI database. A total of 42 known STs were identified, of which ST10 was the dominant ST. The number of ARGs and plasmid replicons carried by E. coli of human origin were not significantly different from those carried by E. coli of pork origin. However, the numbers of insertion sequences and virulence genes carried by E. coli of human origin were significantly higher than those carried by E. coli of pork origin. In addition to E. coli, we analyzed all 23 tet(X4)-positive K. pneumoniae strains currently reported. We found that these tet(X4)-positive K. pneumoniae were mainly distributed in China and had no dominant STs. This study systematically investigated the tet(X4)-positive isolates, emphasizing the importance of the continuous surveillance of tet(X4) in pork.
Evaluating DNA Mixtures with Contributors from Different Populations Using Probabilistic Genotyping
Authors: Kruijver Maarten , Kelly Hannah , Bright Jo-Anne , Buckleton John
Published: December 2022

It is common practice to evaluate DNA profiling evidence with likelihood ratios using allele frequency estimates from a relevant population. When multiple populations may be relevant, a choice has to be made. For two-person mixtures without dropout, it has been reported that conservative estimates can be obtained by using the Person of Interest’s population with a θ value of 3%. More accurate estimates can be obtained by explicitly modelling different populations. One option is to present a minimum likelihood ratio across populations; another is to present a stratified likelihood ratio that incorporates a weighted average of likelihoods across multiple populations. For high template single source profiles, any difference between the methods is immaterial as far as conclusions are concerned. We revisit this issue in the context of potentially low-level and mixed samples where the contributors may originate from different populations and study likelihood ratio behaviour. We first present a method for evaluating DNA profiling evidence using probabilistic genotyping when the contributors may originate from different ethnic groups. In this method, likelihoods are weighted across a prior distribution that assigns sample donors to ethnic groups. The prior distribution can be constrained such that all sample donors are from the same ethnic group, or all permutations can be considered. A simulation study is used to determine the effect of either assumption on the likelihood ratio. The likelihood ratios are also compared to the minimum likelihood ratio across populations. We demonstrate that the common practise of taking a minimum likelihood ratio across populations is not always conservative when FST=0. Population stratification methods may also be non-conservative in some cases. When FST>0 is used in the likelihood ratio calculations, as is recommended, all compared approaches become conservative on average to varying degrees.
Distinct Gut Microbiome Induced by Different Feeding Regimes in Weaned Piglets
Authors: Zhang Jie , Long Xi , Liao Qinfeng , Chai Jie , Zhang Tinghuan , Chen Li , He Hang , Yuan Yancong , Wan Kun , Wang Jinyong , Liu Anfang
Published: December 2022

It is well accepted that the gut microbiota of breast-fed (BF) and formula-fed (FF) infants are significantly different. However, there is still a limited number of studies comparing the gut microbiota of BF and FF piglets, despite increasing numbers of FF piglets in the modern pig industry. The present study identified the differences in gut microbiota composition between BF- and FF-weaned Rongchang piglets at 30 days old, using pair-end sequencing on the Illumina HiSeq 2500 platform. The BF piglets had lower microbiota diversities than FF piglets (p < 0.05), and the community structures were well clustered as a result of each feeding pattern. Firmicutes and Bacteroidetes represented the most dominant phyla, and Ruminococcus, Prevotella, and Gemmiger were prominent genera in all piglets. Ruminococcus, Prevotella, Oscillospira, Eubacterium, Gemmiger, Dorea, and Lactobacillus populations were significantly higher, while Treponema and Coprococcus were significantly lower in BF piglets compared to FF piglets (p < 0.05). The metabolism pathways in the BF piglets were significantly different from FF piglets, which included carbohydrate and amino acid metabolism (p < 0.05). In addition, the top 10 abundance of microbiota were more or less significantly associated with the two phenotypes (p < 0.05). Collectively, these findings provide probable explanations for the importance of BF in neonates and support a theoretical basis for feeding regimes in indigenous Chinese piglets.
Genetic Research and Plant Breeding
Authors: Kang Kwon-Kyoo , Cho Yong-Gu
Published: December 2022

In the past 20 years, plant genetics and breeding research using molecular biology has been greatly improved via the functional analysis of genes, species identification and transformation techniques [...]
Association of Early Childhood Caries with Bitter Taste Receptors: A Meta-Analysis of Genome-Wide Association Studies and Transcriptome-Wide Association Study
Authors: Orlova Ekaterina , Dudding Tom , Chernus Jonathan M. , Alotaibi Rasha N. , Haworth Simon , Crout Richard J. , Lee Myoung Keun , Mukhopadhyay Nandita , Feingold Eleanor , Levy Steven M. , McNeil Daniel W. , Foxman Betsy , Weyant Robert J. , Timpson Nicholas J. , Marazita Mary L. , Shaffer John R.
Published: December 2022

Although genetics affects early childhood caries (ECC) risk, few studies have focused on finding its specific genetic determinants. Here, we performed genome-wide association studies (GWAS) in five cohorts of children (aged up to 5 years, total N = 2974, cohorts: Center for Oral Health Research in Appalachia cohorts one and two [COHRA1, COHRA2], Iowa Fluoride Study, Iowa Head Start, Avon Longitudinal Study of Parents and Children [ALSPAC]) aiming to identify genes with potential roles in ECC biology. We meta-analyzed the GWASs testing ~3.9 million genetic variants and found suggestive evidence for association at genetic regions previously associated with caries in primary and permanent dentition, including the β-defensin anti-microbial proteins. We then integrated the meta-analysis results with gene expression data in a transcriptome-wide association study (TWAS). This approach identified four genes whose genetically predicted expression was associated with ECC (p-values < 3.09 × 10−6; CDH17, TAS2R43, SMIM10L1, TAS2R14). Some of the strongest associations were with genes encoding members of the bitter taste receptor family (TAS2R); other members of this family have previously been associated with caries. Of note, we identified the receptor encoded by TAS2R14, which stimulates innate immunity and anti-microbial defense in response to molecules released by the cariogenic bacteria, Streptococcus mutans and Staphylococcus aureus. These findings provide insight into ECC genetic architecture, underscore the importance of host-microbial interaction in caries risk, and identify novel risk genes.
Exome Array Analysis of 9721 Ischemic Stroke Cases from the SiGN Consortium
Authors: Xu Huichun , Nguyen Kevin , Gaynor Brady J. , Ling Hua , Zhao Wei , McArdle Patrick F. , O’Connor Timothy D. , Stine O. Colin , Ryan Kathleen A. , Lynch Megan , Smith Jennifer A. , Faul Jessica D. , Hu Yao , Haessler Jeffrey W. , Fornage Myriam , Kooperberg Charles ,   on behalf of the Trans-Omics for Precision Medicine (TOPMed) Stroke Working Group, Perry James A. , Hong Charles C. , Cole John W. , Pugh Elizabeth , Doheny Kimberly , Kardia Sharon L. R. , Weir David R. , Kittner Steven J. , Mitchell Braxton D.
Published: December 2022

Recent genome wide association studies have identified 89 common genetic variants robustly associated with ischemic stroke and primarily located in non-coding regions. To evaluate the contribution of coding variants, which are mostly rare, we performed an exome array analysis on 106,101 SNPs for 9721 ischemic stroke cases from the SiGN Consortium, and 12,345 subjects with no history of stroke from the Health Retirement Study and SiGN consortium. We identified 15 coding variants significantly associated with all ischemic stroke at array-wide threshold (i.e., p < 4.7 × 10−7), including two common SNPs in ABO that have previously been associated with stroke. Twelve of the remaining 13 variants were extremely rare in European Caucasians (MAF < 0.1%) and the associations were driven by African American samples. There was no evidence for replication of these associations in either TOPMed Stroke samples (n = 5613 cases) or UK Biobank (n = 5874 stroke cases), although power to replicate was very low given the low allele frequencies of the associated variants and a shortage of samples from diverse ancestries. Our study highlights the need for acquiring large, well-powered diverse cohorts to study rare variants, and the technical challenges using array-based genotyping technologies for rare variant genotyping.
Are the Organellar Genomes Useful for Fine Scale Population Structure Analysis of Endangered Plants?—A Case Study of Pulsatilla patens (L.) Mill
Authors: Szandar Kamil , Jakub Sawicki , Paukszto Łukasz , Krawczyk Katarzyna , Szczecińska Monika
Published: December 2022

Pulsatilla patens is a rare and endangered species in Europe and its population resources have significantly decreased over the past decades. Previous genetic studies of this species made it possible to estimate the genetic diversity of the European population and to describe the structure of chloroplast and mitochondrial genomes. The main aim of these studies was to characterize the variability of chloroplast and mitochondrial genomes in more detail at the intra-population and inter-population levels. Our study presents new organelle genome reference sequences that allow the design of novel markers that can be the starting point for testing hypotheses, past and modern biogeography of rare and endangered species P. patens, and adaptive responses of this species to changing environments. The study included sixteen individuals from five populations located in Northeastern Poland. Comparative analysis of 16 P. patens plastomes from 5 populations enabled us to identify 160 point mutations, including 64 substitutions and 96 InDels. The most numerous detected SNPs and Indels (75%) were accumulated in three intergenic spacers: ndhD—ccsA, rps4—rps16, and trnL(UAG)—ndhF. The mitogenome dataset, which was more than twice as large as the plastome (331 kbp vs. 151 kbp), revealed eight times fewer SNPs (8 vs. 64) and six times fewer InDels (16 vs. 96). Both chloroplast and mitochondrial genome identified the same number of haplotypes—11 out of 16 individuals, but both organellar genomes slightly differ in haplotype clustering. Despite the much lower variation, mitogenomic data provide additional resolution in the haplotype detection of P. patens, enabling molecular identification of individuals, which were unrecognizable based on the plastome dataset.
Sway and Acceleration Changes of the Center of Mass during Walking Stance Phase before and after Total Knee Arthroplasty
Authors: Fukaya Takashi , Mutsuzaki Hirotaka , Mori Koichi
Published: December 2022

Elucidating the sway and changes in the acceleration of center of mass (COM) during walking is important for effective gait training and rehabilitation. The objective of this study was to verify the improvement in gait before and after total knee arthroplasty (TKA) from COM sway and the changes in the acceleration of COM during the stance phase of walking. This study included 13 patients (1 male and 12 females) with medial knee osteoarthritis who were hospitalized for TKA. The COM sway during the stance phase of walking was evaluated using root mean square (RMS) normalized by walking speed, and the changes in acceleration were further verified. Lateral and vertical RMS showed significant differences between preoperative and postoperative states and demonstrated low values after TKA. The lateral acceleration at the latter part of the early stance phase demonstrated a significant difference between preoperative and postoperative states. A significant difference was also observed in the lateral acceleration in the late stance phase between the two groups. Improvement in pain and alignment after TKA reduced the lateral sway of COM and the changes in acceleration during the gait stance phase, which is speculated to lead to improvement in gait and prevention of falls.