bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of Calcium and Ectomycorrhiza Collaboration on Nitrogen Nutrition and Rhizosphere Microbial Community of Pinus massoniana L. Container Seedlings
Authors: Pang Li , Wang Yunpeng , Qiao Zhiwei , Zhou Wenyang , Liu Chao
Published: November 2024

Calcium (Ca) is an essential plant nutrient and cell signal element, but in the cultivation of container seedlings, the regulatory effect of Ca on seedling nitrogen nutrition and its regulatory mechanism have been neglected. Ectomycorrhizal fungi (ECMF) inoculation is widely used in forest container seedling cultivation. Thus, we added a certain amount of Ca to the culture matrix to determine how the cooperation between Ca and ECMF improves the nitrogen nutrition of Pinus massoniana ectomycorrhizal (ECM) container seedlings. We found that addition Ca significantly increased the relative abundance of Actinomycetota and Bacillota in the rhizosphere of ECM seedlings. These enriched bacteria cooperated with the ECMF and significantly enhanced extracellular enzyme NAG and LAP secretion. Meanwhile, adding Ca promoted the microbial nitrogen cycle in the ECM seedlings rhizosphere, and the relative abundances of nitrogen fixation genes (nifD, nifH, nifK) and the dissimilatory nitrate reduction gene (narH) significantly increased. In addition, Ca promoted the infection of ECMF on seedlings and induced the sprouting of absorptive roots with larger diameter (0.5 mm < RD ≤ 2.0 mm), i.e., ECM seedlings adopted a dual strategy of enhancing mycorrhizal symbiosis and improving root absorption area to obtain soil nitrogen. These effects contributed to an increase in microbial biomass nitrogen (MBN) and seedling nitrogen content by 20.65% and 54.38%, respectively. The results provide an effective method and theoretical reference for improving the quality of container seedlings and increasing the ECM plantations early productivity.
Application of Fermentation Technology in Animal Nutrition
Authors: Wang Siran
Published: November 2024

Fermentation technology has been utilized in animal nutrition worldwide for an extended period, with particular focus on animal feed [...]
Improving the Synthesis of Odd-Chain Fatty Acids in the Oleaginous Yeast Yarrowia lipolytica
Authors: Tabaa Chalabi Nour , El Kantar Sally , Pires De Souza Camilla , Khelfa Anissa , Nicaud Jean-Marc , Debs Espérance , Louka Nicolas , Koubaa Mohamed
Published: November 2024

(1) Background: Odd-chain fatty acids (OCFAs) have garnered attention for their potential health benefits and unique roles in various biochemical pathways. Yarrowia lipolytica, a versatile yeast species, is increasingly studied for its capability to produce OCFAs under controlled genetic and environmental conditions. However, optimizing the synthesis of specific OCFAs, such as cis-9-heptadecenoic acid (C17:1), remains a challenge. (2) Methods: The gene coding for the Δ9 fatty acid desaturase, YlOLE1, and the gene coding the diacylglycerol O-acyltransferase 2, YlDGA2, were overexpressed in Y. lipolytica. With the engineered strain, the main goal was to fine-tune the production of OCFA-enriched lipids by optimizing the concentrations of sodium propionate and sodium acetate used as precursors for synthesizing odd- and even-chain fatty acids, respectively. (3) Results: In the strain overexpressing only YlDGA2, no significant changes in fatty acid composition or lipid content were observed compared to the control strain. However, in the strain overexpressing both genes, while no significant changes in lipid content were noted, a significant increase was observed in OCFA content. The optimal conditions for maximizing the cell density and the C17:1 content in lipids were found to be 2.23 g/L of sodium propionate and 17.48 g/L of sodium acetate. These conditions resulted in a cell density (optical density at 600 nm) of 19.5 ± 0.46 and a C17:1 content of 45.56% ± 1.29 in the culture medium after 168 h of fermentation. (4) Conclusions: By overexpressing the YlOLE1 gene and optimizing the concentrations of fatty acid precursors, it was possible to increase the content of OCFAs, mainly C17:1, in lipids synthesized by Y. lipolytica.
Identification of SNPs and Candidate Genes Associated with Growth Using GWAS and Transcriptome Analysis in Portuguese Oyster (Magallana angulata)
Authors: Xie Jingyi , Ning Yue , Han Yi , Su Caiyuan , Zhou Xiaoyan , Wu Qisheng , Guo Xiang , Qi Jianfei , Ge Hui , Ke Yizou , Cai Mingyi
Published: November 2024

Portuguese oyster (Magallana angulata) is one of the most important shellfish species worldwide. Although significant improvements in growth have been achieved through artificial selection breeding, the genetic basis underlying these traits remains unclear. Thus, this study aimed to (i) estimate variation and heritability for growth-related traits and (ii) identify SNPs and candidate genes associated with growth traits in Portuguese oyster. Five growth-related traits, including shell height (SH), shell length (SL), shell width (SW), whole weight (WW), and soft tissue weight (STW), were measured and analyzed in 114 one-year-old individuals from a cultivated population in Fujian Province, China. Through whole-genome sequencing and genotyping, we obtained 8,183,713 high-quality SNPs. Based on the genomic relationship matrix, heritability for the five traits was estimated, ranging from 0.071 to 0.695. Through genome-wide association analysis (GWAS), a total of nine SNPs were identified as significantly or suggestively associated with one of the growth-related traits, each explaining phenotypic variation ranging from 14.13% to 18.56%. Differentially expressed genes (DEGs) between individuals with extreme phenotypes were identified using comparative transcriptome analysis, ranging from 868 to 2274 for each trait. By combining GWAS and comparative transcriptome analysis, a total of seven candidate genes were identified, with biological functions related to growth inhibition, stress response, cell cycle regulation, and immune defense. The associations between the candidate genes and the growth-related traits were validated by using single-marker association analysis in other populations. Based on SNPs in these candidate genes, 16 haplotypes associated with growth-related traits were obtained. This study contributes to a deeper understanding of the genetic mechanisms of growth traits, and provides a theoretical basis and genetic markers for the breeding of fast-growing strains of the Portuguese oyster.
When Mediterranean Artisanal Fishers Protect Coastal Ecosystems
Authors: Nauen Cornelia E.
Published: November 2024

According to EuroStat data, the recorded landings of fisheries products from European waters were estimated at about 6 million tons in 2001, down to 3.2 million tons in 2022. This gradual decline slowed after the entering into force of the reform of the European Common Fisheries Policy (CFP) at the end of 2013, but was followed by a steeper decline after 2018. This is reflected in the last assessment of the Scientific Technical and Economic Committee for Fisheries (STEPF), noting that despite progress in the NE Atlantic management, 41% of the assessed stocks in 2022 were outside safe biological limits, down from 80% in 2003. Improvements in the Mediterranean are significantly slower. A warming ocean provokes the measurable poleward migration of species and adds stress to predator–prey relations in all European seas. Within this general picture, the broad-brush landscape is influenced by policy applications more in favour of industrial exploitation and regulatory and market environments, making it very hard for many small-scale fishers (SSFs) to remain in business, let alone attract younger successors for generational transition. In crowded marine spaces, it is a challenge to allocate access rights fairly between fisheries, exclusion zones for resource and habitat protection and much-needed ecosystem recovery, platforms for fossil exploitation, wind farms, underwater cables and recreational uses. Two examples of local initiatives with faunal recovery potential in the Mediterranean are briefly presented as a bottom-up complement to more top-down management approaches. They are spearheaded by artisanal fishers, who seek to restore spawning grounds and other coastal habitats as a way to procure enough fish and other complementary activities to secure their livelihoods in the future. They are supported by local scientists and nature conservation organisations. While promising, this is still rather the exception. Here, it is argued that trust-building between artisanal fishers, conservationists and scientists, and greater systemic support to SSFs by governments, increase chances for the urgently needed structural shifts that deliver the reversal in the ongoing decline in biodiversity and ocean productivity that all aspire to, to ensure sustained social and economic benefits.
Correlation Between Sensory Characteristics and Physicochemical Properties of Wild and Farmed Frozen Southern Bluefin Tuna (Thunnus maccoyii)
Authors: Kashikura Hiroki , Yagi Masafumi , Nakamura Yusa , Sakai Akira , Takahashi Kigen , Hiratsuka Seiichi , Goto Keiichi
Published: November 2024

In this study, to investigate the quality of wild and farmed frozen southern bluefin tuna, physicochemical analyses and sensory evaluations were conducted. Principal component analysis was then performed using the results obtained to examine the correlation between the bluefin tuna’s taste characteristics and physicochemical properties. The sensory evaluation suggested differences in texture and acidity between wild and farmed fish, whereas the principal component analysis indicated differences in fatty acid and amino acid composition. Wild fish contained higher levels of docosahexaenoic acid and monounsaturated fatty acids, while farmed fish had higher levels of saturated fatty acids. Regarding free amino acids and dipeptides, wild fish had higher levels of anserine and alanine, whereas farmed fish showed higher levels of glutamine and histidine, and acidity was observed in farmed fish. Furthermore, based on the results of the principal component analysis, it was inferred that the content of inosinic acid, which is considered an umami component in fish, may have a low impact on palatability. These factors were suggested to influence the differences between wild and farmed tuna.
Effects of Transport Stress (Duration and Density) on the Physiological Conditions of Marbled Rockfish (Sebastiscus marmoratus, Cuvier 1829) Juveniles and Water Quality
Authors: Wang Jiahao , Xu Kaida , Chen Xinyi , Wang Haoxue , Li Zhe
Published: November 2024

Live transportation is a critical component of fish farming and hatchery release. To optimize hatchery-release techniques and improve the survival rate of marbled rockfish (Sebastiscus marmoratus, Cuvier 1829) juveniles, the effects of varying transport durations (2, 4, 6, and 8 h) and densities (60, 90, 120, and 150 kg m−3) on the physiological indicators of the fish and water quality were investigated under controlled laboratory conditions. We found that as transport duration and density increased, water quality significantly deteriorated, with ammonia nitrogen levels rising and dissolved oxygen content and pH levels decreasing. Physiological indicators including levels of lactate, cortisol, and malondialdehyde and activities of superoxide dismutase, alkaline phosphatase, and glutamate oxaloacetate transaminase notably increased, indicating that the fish experienced heightened stress during transport. Additionally, the mortality rate of juveniles increased significantly with increasing density and transport duration. The high mortality rate might be associated with sustained elevated cortisol levels and liver damage. Our results are helpful for determining the optimal transport conditions for S. marmoratus juveniles and also provide valuable insights for improving transport techniques for other aquatic animal species.
Numerical Analysis of Knudsen Number of Helium Flow Through Gas-Focused Liquid Sheet Micro-Nozzle
Authors: Kovačič Krištof , Bajt Saša , Šarler Božidar
Published: November 2024

This work aims to verify whether the continuum mechanics assumption holds for the numerical simulation of a typical sample delivery system in serial femtosecond crystallography (SFX). Knudsen numbers were calculated based on the numerical simulation results of helium flow through the gas-focused liquid sheet nozzle into the vacuum chamber, representing the upper limit of Knudsen number for such systems. The analysed flow is considered steady, compressible, and laminar. The numerical results are mesh-independent, with a Grid Convergence Index significantly lower than 1% for global and local analysis. This study is based on an improved definition of the numerical Knudsen number: a combination of the cell Knudsen number and the physical Knudsen number. In the analysis, no-slip boundary and low-pressure boundary slip conditions are compared. No significant differences are observed. This study justifies using computational fluid dynamics (CFD) analysis for SFX sample delivery systems based on the assumption of continuum mechanics.
Effect of Dual-Modified Tapioca Starch/Chitosan/SiO2 Coating Loaded with Clove Essential Oil Nanoemulsion on Postharvest Quality of Green Grapes
Authors: Chang Hui , Li Kaimian , Ye Jianqiu , Chen Jian , Zhang Jie
Published: November 2024

As consumer awareness regarding health and nutrition continues to increase, there is a growing demand for fresh, nutritious fruits such as green grapes. However, the short storage life and susceptibility of these fruits to spoilage lead to significant commercial losses. Currently, the plastic wrap method is commonly used to keep green grapes fresh, but this packaging effect is limited and not environmentally friendly. Therefore, there is an urgent need to explore sustainable and effective preservation methods. In this study, a high-pressure microfluidization technique was employed to prepare an essential oil nanoemulsion with a ratio of Tween 80 to clove essential oil of 1:1, and a biopolymer-based film solution was prepared using dual-modified tapioca starch and chitosan loaded with clove essential oil nanoemulsion. The dual-modified tapioca starch/chitosan/SiO2/1.25 wt % clove essential oil (DM/Ceo-1.25) solution coating was successfully applied for the packaging and preservation of fresh green grapes. Compared with the CK and polyethylene wrap (PE) groups, the DM/Ceo-1.25 coating significantly improved the quality of the green grapes, increasing the storage period of the green grapes from 4 to 8 days at room temperature. On the 10th day of storage, the coated grapes retained significantly better quality, with a hardness of 4.01 N, a titratable acidity of 1.625%, an anthocyanin content of 1.013 mg/kg, and a polyphenol content of 21.32 μg/mL. These results indicate that the DM/Ceo-1.25 solution coating developed in this study can be used as a new active material for fruit preservation and provides ideas for the development of safer and more sustainable food packaging.
Correlations Between the Bacterial and Fungal Flora and Amino Acid Composition of the Zhuangzu Acid Congee Produced Around the Zuojiang River Basin, Guangxi
Authors: Huang Ao , Zhang Qin-Ren , Xiao De-Qiang , Xu Wei-Sheng , Bi Zu-Lian , Deng Xiu-Die , Huang Xiu-Lian , Song Jia-Le , Li Quan-Yang
Published: November 2024

In this study, the bacterial, fungal, and amino acid compositions of the Zhuangzu acid congee (ZAC) along the Zuojiang River of Guangxi were analyzed. A total of 14 samples of ZAC were collected in four regions: Fusui (F), Ningming (N), Xiashi (X), and Suxu (S). The predominant bacterial phyla of the four groups were Firmicutes and Proteobacteria. The dominant bacterial genera were Lactobacillus, Bacillus, Schleiferitobacillus, and Acetobacter. The fungal alpha diversity in Group S was significantly lower than that in Groups F, X, and N. PCoA clearly distinguished Group S from Groups F, X, and N. The dominant fungal phylum in Group S was Ascomycota (89.12%), whereas those in Groups F, X, and N were Basidiomycota (38.07%), Ascomycota (30.65%), and Fungi (17.39%). The dominant fungal genera in Group S were Saccharomyces (42.36%) and Pichia (31.66%), whereas those in Groups F, X, and N were Mortierella (17.23%) and Russula (13.34%). The proportions of the six flavor amino acids were relatively high, and all four groups of samples were above 30.00%. PLS-DA of amino acids demonstrated that all four groups of samples could be significantly distinguished. Additionally, the concentrations of taurine, serine, leucine, phosphoserine, asparagine, 1-methylhistidine, and 3-methylhistidine in Group S were significantly greater than those in Groups F, X, and N. Correlation analysis revealed that 6 bacterial and 15 fungal genera were significantly correlated with amino acids, particularly Leuconostoc and Schleiferlactobacillus, among bacteria, as well as Saccharomyces and Russula, among fungi. In conclusion, compared with the disparity in the bacterial community, the disparity in the fungal community was more strongly correlated with the amino acid composition of ZAC. This result indicated that the difference in the fungal community might cause the variation in the amino acid composition of ZAC.
Classification of Chicken Carcass Breast Blood-Related Defects Using Hyperspectral Imaging Combined with Convolutional Neural Networks
Authors: Duan Liukui , Bao Juanfang , Yang Hao , Gao Liuqian , Zhang Xu , Li Shengjie , Wang Huihui
Published: November 2024

For chicken carcass breast blood-related defects (CBDs), which occur with high frequency, the visual features are approximated in terms of the similarity of the composition of these defects, making it challenging to classify them, either manually or automatically, using conventional machine vision. The aim of this paper was to introduce a method of CBD classification based on hyperspectral imaging combined with Convolutional Neural Networks (CNNs). To process hyperspectral data, the Improved Firefly Band Selection Algorithm was constructed with the 1-D CNN CBD classification model as the objective function, achieving a reduction in the dimensionality of hyperspectral data. The multidimensional data CBD classification models were developed based on YOLOv4 and Faster R-CNN, incorporating the 1-D CNN CBD classification model and the feature fusion layer. The combination of hyperspectral data and CNN can effectively accomplish the classification of CBDs, although different model architectures emphasize classification speed and accuracy differently. The multidimensional data YOLOv4 CBD classification model achieves an mAP of 0.916 with an inference time of 41.8 ms, while the multidimensional data Faster R-CNN CBD classification model, despite having a longer inference time of 58.2 ms, reaches a higher mAP of 0.990. In practical production scenarios, the appropriate classification model can be selected based on specific needs.
Valorizing Astringent ‘Rojo Brillante’ Persimmon Through the Development of Persimmon-Based Bars
Authors: Hosseininejad Sepideh , Moraga Gemma , Hernando Isabel
Published: November 2024

This study developed a new energy bar using the astringent ‘Rojo Brillante’ variety of persimmons to address postharvest losses. The bar was formulated with dehydrated persimmons, walnuts, hazelnuts, and chia seeds to enhance their nutritional profile. The proximate composition was evaluated and the mechanical and optical properties, soluble tannins, carotenoids, and antioxidant activities were monitored during storage. In addition, in vitro gastrointestinal digestion was performed to determine the recovery index of the bioactive compounds. The results showed that the formulated energy bar contained higher levels of healthy fats, proteins, and fibers than other fruit energy bars. The mechanical properties of dehydrated persimmon effectively supported the consistency of the bar, eliminating the need for hydrocolloids or syrups. During storage, soluble tannin content decreased, mitigating astringency issues commonly found in persimmon products, whereas carotenoid levels and antioxidant activity remained stable. In vitro digestion analysis revealed a higher recovery index for soluble tannins (180.08%) than carotenoids (9.87%). This persimmon-based energy bar offers a sustainable and nutritious option for the snack industry, catering to consumer preferences for natural products while contributing to the reduction of agricultural waste.
Effect of Adding Konjac Glucomannan on the Physicochemical Properties of Indica Rice Flour and the Quality of Its Product of Instant Dry Rice Noodles
Authors: Lu Chunmiao , Yang Ying , Zhao Xin , Liu Zhiyu , Liao Xiaoyan , Zhang Yingying , Wu Dailin , Li Jing , Li Jiangtao
Published: November 2024

Instant dry rice noodles have a broad market prospect due to their advantages of long shelf life, convenient transportation, and convenient eating, but there are still quality problems such as long rehydration times and poor eating quality. In order to improve the quality of instant dry rice noodles, the effects of konjac glucomannan (KGM) on the gelatinization characteristics, pasting properties, and rheological properties of Indica rice flour and the structure, food quality, and starch digestibility of instant dry rice noodles made of Indica rice flour were studied. The results showed that the starch gelatinization conclusion temperature and endothermic enthalpy of Indica rice flour were reduced by adding ≤ 3% KGM, the peak viscosity, valley viscosity, final viscosity, and setback value of Indica rice flour in the pasting process decreased with the increase in the KGM addition amount, and the pseudoplasticity, viscosity, and elasticity of Indica rice flour paste were reduced by adding > 1% KGM. When the KGM addition amount was 2%, the endothermic enthalpy, final viscosity, and setback value of Indica rice flour were 2.74 J/g, 2379.5 cp, and 961.5 cp, respectively. The instant dry rice noodles made of Indica rice flour had a looser microstructure after adding KGM, and its short-range ordered structure and double helix content were reduced by adding 1~3% KGM. When the KGM addition amount was 2%, the rehydration time of instant dry rice noodles was 290 s, which was shortened by 14.7%, while the texture and sensory quality remained unchanged, and the SDS content was reduced by 16.4% while the RS content was increased by 28.8%. Therefore, the physicochemical properties of Indica rice flour and the quality of its instant dry rice noodles can be improved by adding an appropriate amount of KGM. This study can promote the application of KGM in improving the quality of rice products.
Environmentally Friendly Nanoporous Polymeric Gels for Sustainable Wastewater Treatment
Authors: Madkour Tarek M. , Elsayed Rasha E. , Azzam Rasha A.
Published: November 2024

Environmentally friendly nanoporous gels are tailor-designed and employed in the adsorption of toxic organic pollutants in wastewater. To ensure the maximum adsorption of the contaminant molecules by the gels, molecular modeling techniques were used to evaluate the binding affinity between the toxic organic contaminants such as methylene blue (MB) and Congo red (CR) and various biopolymers. To generate nanopores in the matrix of the polymeric gels, salt crystals were used as porogen. The pores were then used to accommodate catalytic nickel (Ni0) nanoparticles. Under UV irradiation, the nanoparticles demonstrated the effective adsorption and photocatalytic degradation of both the methylene blue and Congo red dyes, achieving removal efficiencies of up to 90% for MB and 80% for CR. The thermodynamic analysis suggested a spontaneous endothermic dissociative adsorption mechanism, which implies the oxidative catalytic degradation of the dyes. The kinetic modeling suggested a pseudo-second-order model, while the model for intra-particle diffusion revealed that Congo red diffuses faster than methylene blue. MB adsorption followed a Langmuir isotherm, while CR adsorption followed a linear isotherm. The results confirm that dye molecules initially undergo physisorption and subsequent dissociative adsorption. The products of the catalytic degradation of methylene blue continue to be absorbed on the surface of the nanoparticles, while those of Congo red switch to preferential desorption.
Genomic Regions Associated with Spontaneous Abortion in Holstein Heifers
Authors: Suarez Emaly M. , Kelson Victoria C. , Kiser Jennifer N. , Davenport Kimberly M. , Murdoch Brenda M. , Neibergs Holly L.
Published: November 2024

Background/Objectives: The dairy industry relies on reproductive efficiency to maintain efficient milk production. Spontaneous abortion (SA), defined as pregnancy loss between gestation days 42 and 260, occurred in 4.5% of the artificially inseminated (AI) Holstein heifers and 31.6% of the embryo transfer (ET) recipient Holstein heifers that received in vitro-produced frozen embryos on a single dairy farm in Idaho. Methods: A genome-wide association analysis (GWAA) was performed to identify the associations (FDR p < 0.05) with SA in heifers that were bred by AI (1351 controls that delivered at term and 63 cases that aborted) that conceived following the first insemination, as well as in 59 controls and 273 cases of ET recipient heifers pregnant from the first ET. Results: There were 216 loci and 413 positional candidate genes associated (FDR p < 0.05) with SA in the heifers bred by AI in a recessive model and no loci associated with SA in the ET recipients. Conclusions: The identification of loci associated with SA in the heifers bred by AI may be used to reduce fetal loss through genomic selection.
Targeted Transcriptome Analysis of Beef Cattle Persistently Infected with Bovine Viral Diarrhea Virus
Authors: Adkins Morgan , Moisa Sonia , Beever Jon , Lear Andrea
Published: November 2024

Background: Bovine viral diarrhea virus (BVDV) is an endemic virus of North American cattle populations with significant economic and animal health impacts. While BVDV infection has a myriad of clinical manifestations, a unique and problematic outcome is the establishment of a persistently infected (PI) animal following in utero viral infection. While it is well established that PI animals serve as a constant reservoir of BVDV, the mechanism for the maintained infection remains unknown despite multiple theories. Objective: The purpose of this study was to use transcriptome analysis to investigate the long-term immune status of adult PI cattle and offer insight into the potential mechanistic establishment of persistent BVDV infection. Methods: Peripheral blood mononuclear cells were collected from PI beef cattle (N = 6) and controls (N = 6) for targeted RNAseq analysis using 54 immune-related genes followed by pathway enrichment analysis. Results: Analysis revealed 29 differentially expressed genes (FDR < 0.05, fold change ≥ 2), representing 14 significant KEGG pathways between groups (FDR < 0.05). Transcriptome changes indicated chronic upregulation of interferon-gamma (IFNG) with an unexpected expression of related genes. Conclusions: These results provide novel insight into understanding the adult PI immune system and indicate maintained stimulation resulting from virus-mediated dysregulation.
Genetic Polymorphism of Y-Chromosome in Turkmen Population from Turkmenistan
Authors: Zhabagin Maxat , Tashkarayeva Assel , Bukayev Alizhan , Zhunussova Aigul , Ponomarev Georgy , Tayshanova Saltanat , Maxutova Albina , Adamov Dmitry , Balanovska Elena , Sabitov Zhaxylyk
Published: November 2024

This study investigates the Y-chromosome genetic diversity of the Turkmen population in Turkmenistan, analyzing 23 Y-STR loci for the first time in a sample of 100 individuals. Combined with comparative data from Turkmen populations in Afghanistan, Iran, Iraq, Russia, and Uzbekistan, this analysis offers insights into the genetic structure and relationships among Turkmen populations across regions across Central Asia and the Near East. High haplotype diversity in the Turkmen of Turkmenistan is shaped by founder effects (lineage expansions) from distinct haplogroups, with haplogroups Q and R1a predominating. Subhaplogroups Q1a and Q1b identified in Turkmenistan trace back to ancient Y-chromosome lineages from the Bronze Age. Comparative analyses, including genetic distance (RST), median-joining network, and multidimensional scaling (MDS), highlight the genetic proximity of the Turkmen in Turkmenistan to those in Afghanistan and Iran, while Iraqi Turkmen display unique characteristics, aligning with Near Eastern populations. This study underscores the Central Asian genetic affinity across most Turkmen populations. It demonstrates the value of deep-sequencing Y-chromosome data in tracing the patrilineal history of Central Asia for future studies. These findings contribute to a more comprehensive understanding of Turkmen genetic ancestry and add new data to the ongoing study of Central Asian population genetics.
Dermatology-Related Emergency Department Visits in Tertiary Care Center in Riyadh, Saudi Arabia: A Descriptive Study
Authors: Alshibani Abdullah , Alagha Saif Osama , Alshammari Abdulmohsen Jameel , Alshammari Khaled Jameel , Alghamdi Abdulelah Saeed , Nagshabandi Khalid Nabil
Published: November 2024

Background/Objectives: Dermatological complaints are commonly seen in the emergency department (ED) setting and may be attributed to infectious, inflammatory, allergic, hypersensitivity, or traumatic processes, yet few studies have been carried out in Saudi Arabia addressing this topic. This study, therefore, aimed to explore this issue by investigating the most common dermatology-related ED encounters in a large tertiary care center in Riyadh, Saudi Arabia, and estimating the incidence of these encounters. Methods: This was a retrospective cohort study conducted in the ED of King Abdulaziz Medical City, a tertiary care center in Riyadh, Saudi Arabia. Data included all patients with dermatology-related ED visits during the period of 2022–2023. Demographic information including, for example, age and sex was collected. The International Classification of Diseases, 10th Revision (ICD-10) was used for the classification of diagnoses. Results: A total of 11,443 patients were included in the study, with male patients making up the majority (54.9%). The mean age upon diagnosis was 22.4 ± 23.2 years. More than half of the patients (55.3%) were diagnosed during childhood (<18), while proportions of older ages declined gradually. Average monthly presentations ranged from 400 to 560. Rash and non-specific skin eruptions (16%), cellulitis (13.6%), and urticaria (12.2%) were the most frequent dermatological emergencies. Conclusions: This study examined the dermatological conditions commonly seen in the emergency department. The findings highlighted a range of dermatology diseases that are typically seen in the ED. Addressing these prevalent disorders in the future will enhance ER physicians’ understanding and management of such common dermatological problems.
Biophysical, Spatial, Functional, and Constructive Analysis of the Pre-Hispanic Terraces of the Ancient City of Pisaq, Cusco, Peru, 2024
Authors: Huaman Francis , Esenarro Doris , Prado Meza Jesus , Vilchez Cairo Jesica , Vargas Beltran Carlos , Alfaro Aucca Crayla , Arriola Cecilia , Peña Calle Valeria
Published: November 2024

The aim of the research is to examine the biophysical, spatial, functional, and structural components of the pre-Hispanic terracing systems located in the ancient city of Pisaq, considering the impacts of tourism, geological instability, and cultural loss on the ecological and economic value of the terracing system. The methodology includes site analysis, climatology, and an examination of local flora and fauna, supported by digital tools such as QGIS 3.34, Google Earth Pro 2024, and Sun-Path. The results were primarily supported by the use of software tools such as QGIS, AutoCAD 2023, SketchUp 2022, 3D Sun-Path, D5 Render 2024, and Photoshop 2021. The findings include a biophysical analysis related to ecological and economic zoning (EEZ), which determines variables for preservation and reforestation; a spatial analysis measuring the cultivation terraces, with areas ranging from 4.89 ha to 110.20 ha; a functional analysis examining geophysical aspects such as seismic resistance and microclimate effects due to the greenhouse effect; and a constructive analysis that characterizes terrace typologies from an architectural perspective. In conclusion, this analysis evaluates the terracing system of the archaeological park to ensure its preservation and effective management. It also highlights that Inca culture has left a legacy of sustainable architecture, which aligns with the current Sustainable Development Goals (SDGs) (6, 11, 13, 15).
Design and Ventilation Optimization of a Mechanized Corridor in a Solar Greenhouse Cluster
Authors: He Ming , Jiang Xinxia , Wan Xiuchao , Li Yiming , Fan Qinglu , Liu Xingan
Published: November 2024

Corridors play an important role in the mechanized production of fruits and vegetables in solar greenhouse clusters. A corridor structure that is suitable for the automated production of solar greenhouse clusters is designed in this paper. To increase the corridor’s ventilation efficiency and enhance the temperature environment, the computational fluid dynamics method is applied to analyze the effects of corridor structure, ventilation mode, wind speed, and direction on internal temperature and humidity. Studies have indicated that an erroneous layout of the corridor structure may result in the formation of accumulated temperature and heat concentration inside, and ventilation within the corridor is essential. The corridor’s ideal dimensions are 3.2 m high by 5 m wide, and it has an internal wind speed and cooling rate that are superior to other structural factors. The ventilation method adopts a combination of top and bottom ventilation, and when the bottom window opening is 70%, there is a good ventilation effect inside the corridor. The corridor has an excellent ventilation effect when the wind speed is 2 m/s and the wind direction is east or west. This study supports the intensive and sustainable growth of greenhouse vegetable production by providing guidance for the planning and corridor design of solar greenhouse clusters.
Impact of Missense Mutations on AFB1 Metabolism in Bovine Cytochrome P4503A Isoforms: A Computational Mutagenesis and Molecular Docking Analysis
Authors: Montanucci Ludovica , Iori Silvia , Lahtela-Kakkonen Maija , Pauletto Marianna , Giantin Mery , Dacasto Mauro
Published: November 2024

Cytochrome P450 3A (CYP3A) enzymes catalyze the metabolism of a wide range of endogenous and exogenous compounds. Genetic variations in the 3 CYP3A isoforms (CYP3A28, CYP3A74, and CYP3A76) may influence their expression and activity, leading to inter-individual differences in xenobiotic metabolism. In domestic cattle, understanding how genetic variations modulate CYP3A activity is crucial for both its therapeutic implications (clinical efficacy and adverse drug effects) and food safety (residues in foodstuff). Here, we updated the variant calling of CYP3As in 300 previously sequenced Piedmontese beef cattle, using the most recent reference genome, which contains an updated, longer sequence for CYP3A28. All but one previously identified missense variants were confirmed and a new variant, R105W in CYP3A28, was discovered. Through computational mutagenesis and molecular docking, we computationally predicted the impact of all identified CYP3A variant enzymes on protein stability and their affinity for aflatoxin B1 (AFB1), a potent carcinogen and food contaminant. For CYP3A28, we also computationally predicted its affinity for the probe substrate nifedipine (NIF). We found that CYP3A28 with R105W variant cannot accommodate NIF nor AFB1 in the binding pocket, thus affecting their metabolism. Our work provides computational foundation and prioritized ranking of CYP3A variants for future experimental validations.
Genome-Wide Analysis of CSL Family Genes Involved in Petiole Elongation, Floral Petalization, and Response to Salinity Stress in Nelumbo nucifera
Authors: Yang Jie , Wang Juan , Yang Dongmei , Xia Wennian , Wang Li , Wang Sha , Zhao Hanqian , Chen Longqing , Hu Huizhen
Published: November 2024

Lotus (Nelumbo nucifera), a perennial aquatic plant, endures various environmental stresses. Its diverse ornamental traits make it an ideal model for studying multigene family functional differentiation and abiotic stress responses. The cellulose synthase-like (CSL) gene family includes multiple subfamilies and holds potentially pivotal roles in plant growth, development, and stress responses. Thus, understanding this family is essential for uncovering the attributes of ancient dicotyledonous lotus species and offering new genetic resources for targeted genetic improvement. Herein, we conducted a genome-wide NnCSL gene identification study, integrating tissue-specific expression analysis, RNA-seq, and qRT-PCR validation. We identified candidate NnCSL genes linked to petiole elongation, floral petalization, salinity stress responses, and potential co-expressed TFs. 22 NnCSL genes were categorized into six subfamilies: NnCSLA, NnCSLB, NnCSLC, NnCSLD, NnCSLE, and NnCSLG. Promoter regions contain numerous cis-acting elements related to growth, development, stress responses, and hormone regulation. Nineteen NnCSL genes showed specific differential expression in LPA (large plant architecture) versus SPA (small plant architecture): petioles, petalized carpels (CP) and normal carpels (C), and petalized stamens (SP) and normal stamens (S). Notably, most NnCSLC, NnCSLA, and NnCSLB subfamily genes play diverse roles in various aspects of lotus growth and development, while NnCSLE and NnCSLG are specifically involved in carpel petalization and petiole elongation, respectively. Additionally, 11 candidate NnCSL genes responsive to salinity stress were identified, generally exhibiting antagonistic effects on growth and developmental processes. These findings provide an important theoretical foundation and novel insights for the functional study of NnCSL genes in growth, development, and stress resistance in lotus.
Enhancing Crop Resilience: The Role of Plant Genetics, Transcription Factors, and Next-Generation Sequencing in Addressing Salt Stress
Authors: Singh Akhilesh Kumar , Pal Priti , Sahoo Uttam Kumar , Sharma Laxuman , Pandey Brijesh , Prakash Anand , Sarangi Prakash Kumar , Prus Piotr , Pașcalău Raul , Imbrea Florin
Published: November 2024

Salt stress is a major abiotic stressor that limits plant growth, development, and agricultural productivity, especially in regions with high soil salinity. With the increasing salinization of soils due to climate change, developing salt-tolerant crops has become essential for ensuring food security. This review consolidates recent advances in plant genetics, transcription factors (TFs), and next-generation sequencing (NGS) technologies that are pivotal for enhancing salt stress tolerance in crops. It highlights critical genes involved in ion homeostasis, osmotic adjustment, and stress signaling pathways, which contribute to plant resilience under saline conditions. Additionally, specific TF families, such as DREB, NAC (NAM, ATAF, and CUC), and WRKY, are explored for their roles in activating salt-responsive gene networks. By leveraging NGS technologies—including genome-wide association studies (GWASs) and RNA sequencing (RNA-seq)—this review provides insights into the complex genetic basis of salt tolerance, identifying novel genes and regulatory networks that underpin adaptive responses. Emphasizing the integration of genetic tools, TF research, and NGS, this review presents a comprehensive framework for accelerating the development of salt-tolerant crops, contributing to sustainable agriculture in saline-prone areas.
Molecular Mechanism of Action of Endocrine-Disrupting Chemicals on the Respiratory System
Authors: Molinari Francesco , Franco Gianluca Antonio , Tranchida Nicla , Di Paola Rosanna , Cordaro Marika
Published: November 2024

Endocrine-disrupting chemicals (EDCs) are a growing health hazard for humankind and respiratory health in particular. Such chemical compounds are present in the environment and food and may interfere with physiological processes through interference with functions of the endocrine system, making humans more susceptible to various types of diseases. This review aims to discuss the effects of EDCs on the respiratory system. Exposure to EDCs during fetal development and adulthood increases susceptibility to respiratory diseases such as asthma, COPD, and pulmonary fibrosis. EDCs are both multiple and complex in the ways they can act. Indeed, these chemicals may induce oxidative stress, modify cell proliferation and differentiation, interfere with tissue repair, and modulate the inflammatory response. Moreover, EDCs may also break the integrity of the blood–air barrier, allowing noxious substances to penetrate into the lung and thus enhancing the opportunity for infection. In conclusion, the scientific evidence available tends to indicate that EDCs exposure is strongly linked to the initiation of respiratory disease. Further research will be important in discovering the underlying molecular mechanisms and devising preventive and therapeutic measures.
Comprehensive Clinical Genetics, Molecular and Pathological Evaluation Efficiently Assist Diagnostics and Therapy Selection in Breast Cancer Patients with Hereditary Genetic Background
Authors: Nagy Petra , Papp János , Grolmusz Vince Kornél , Bozsik Anikó , Pócza Tímea , Oláh Edit , Patócs Attila , Butz Henriett
Published: November 2024

Using multigene panel testing for the diagnostic evaluation of patients with hereditary breast and ovarian cancer (HBOC) syndrome often identifies clinically actionable variants in genes with varying levels of penetrance. High-penetrance genes (BRCA1, BRCA2, CDH1, PALB2, PTEN, STK11, TP53) inform specific clinical surveillance and therapeutic decisions, while recommendations for moderate-penetrance genes (ATM, BARD1, BRIP1, CHEK2, MLH1, MSH2, MSH6, PMS2, EPCAM, NF1, RAD51C, RAD51D) are more limited. A detailed disease history, including pedigree data, helps formulate the most appropriate and personalised management strategies. In this study, we evaluated the clinical benefits of comprehensive hereditary cancer gene panel testing and a pre-sent questionnaire in Hungarian patients with suspected HBOC syndrome. We prospectively enrolled 513 patients referred for HBOC testing. Of these, 463 met the genetic testing criteria, while 50 did not but were tested due to potential therapeutic indications. Additionally, a retrospective cohort of 47 patients who met the testing criteria but had previously only been tested for BRCA1/2 was also analysed. Among the 463 patients in the prospective cohort, 96 (20.7%) harboured pathogenic/likely pathogenic (P/LP) variants—67 in high-penetrance genes and 29 in moderate-penetrance genes. This ratio was similar in the retrospective cohort (6/47; 12.7%). In patients who did not meet the testing criteria, no mutations in high-penetrance genes were found, and only 3 of 50 (6%) harboured P/LP variants in moderate-penetrance genes. Secondary findings (P/LP variants in non-HBOC-associated genes) were identified in two patients. In the prospective cohort, P/LP variants in BRCA1 and BRCA2 were the most prevalent (56/96; 58.3%), and the extended testing doubled the P/LP detection ratio. Among moderate-penetrance genes, five cases (three in the prospective and two in the retrospective cohorts) had P/LP variants in Lynch syndrome-associated genes. Further immunohistochemistry analysis of breast tumour tissues helped clarify the causative role of these variants. Comprehensive clinical and molecular genetic evaluation is beneficial for the diagnosis and management of patients with P/LP variants in hereditary tumour-predisposing genes and can serve as a basis for effective therapy selection, such as PARP inhibitors or immunotherapy.
Plasmalogens Improve Lymphatic Clearance of Amyloid Beta from Mouse Brain and Cognitive Functions
Authors: Shirokov Alexander , Zlatogosrkaya Daria , Adushkina Viktoria , Vodovozova Elena , Kardashevskaya Kristina , Sultanov Ruslan , Kasyanov Sergey , Blokhina Inna , Terskov Andrey , Tzoy Maria , Evsyukova Arina , Dubrovsky Alexander , Tuzhilkin Matvey , Elezarova Inna , Dmitrenko Alexander , Manzhaeva Maria , Krupnova Valeria , Semiachkina-Glushkovskaia Anastasiia , Ilyukov Egor , Myagkov Dmitry , Tuktarov Dmitry , Popov Sergey , Inozemzev Tymophey , Navolokin Nikita , Fedosov Ivan , Semyachkina-Glushkovskaya Oxana
Published: November 2024

Amyloid beta (Aβ) is a neuronal metabolic product that plays an important role in maintaining brain homeostasis. Normally, intensive brain Aβ formation is accompanied by its effective lymphatic removal. However, the excessive accumulation of brain Aβ is observed with age and during the development of Alzheimer’s disease (AD) leading to cognitive impairment and memory deficits. There is emerging evidence that plasmalogens (Pls), as one of the key brain lipids, may be beneficial for AD and cognitive aging. Here, we studied the effects of Pls on cognitive functions and the lymphatic clearance of Aβ from the brain of AD mice and mice of different ages. The results showed that Pls effectively reduce brain Aβ levels and facilitate learning in aged but not old mice. In AD mice, Pls improve the lymphatic clearance of Aβ that is accompanied by an increase in general motor activity and an improvement of the emotional status and learning ability. Thus, these findings suggest that Pls could be a promising candidate for the alternative or concomitant therapy of AD and age-related brain diseases to enhance the lymphatic clearance of Aβ from the brain and cognitive functions.
Effect of Long-Term Cisplatin Exposure on the Proliferative Potential of Immortalized Renal Progenitor Cells
Authors: Ighofose Eloho , Garrett Scott H. , Al-Marsoummi Sarmad , Mehus Aaron A. , Sens Donald A. , Singhal Sandeep K. , Singhal Sonalika , Somji Seema
Published: November 2024

Cisplatin (CisPt) is a widely used chemotherapeutic agent. However, its nephrotoxic effects pose significant risks, particularly for the development of acute kidney injury (AKI) and potential progression to chronic kidney disease (CKD). The present study investigates the impact of non-lethal exposure of CisPt to immortalized human renal epithelial precursor TERT cells (HRTPT cells) that co-express PROM1 and CD24, markers characteristic of renal progenitor cells. Over eight serial passages, HRTPT cells were exposed to 1.5 µM CisPt, leading to an initial growth arrest, followed by a gradual recovery of proliferative capacity. Despite maintaining intracellular platinum (Pt) levels, the cells exhibited normal morphology by passage eight (P8), with elevated expression of renal stress and damage markers. However, the ability to form domes was not restored. RNA-seq analysis revealed 516 differentially expressed genes between CisPt-exposed and control cells, with significant correlations to cell cycle and adaptive processes, as determined by the Reactome, DAVID, and Panther analysis programs. The progenitor cells treated with CisPt displayed no identity, or close identity, with cells of the normal human nephron. Additionally, several upregulated genes in P8 cells were linked to cancer cell lines, suggesting a complex interaction between CisPt exposure and cellular repair mechanisms. In conclusion, our study demonstrates that renal progenitor cells can recover from CisPt exposure and regain proliferative potential in the continued presence of both extracellular CisPt and intracellular Pt.