bluuebunny/crossref_metadata_2025 huggingface dataset:
Grazing Impacts on Soil Enzyme Activities Vary with Vegetation Types in the Forest-Steppe Ecotone of Northeastern China
Authors: Wang Long , Jia Zhiqing , Li Qingxue , He Lingxianzi , Tian Jiapeng , Ding Wei , Liu Tao , Gao Ya , Zhang Jiapeng , Han Dong , Tian Hui
Published: November 2023

Grazing impacts soil enzyme activities by changing soil conditions and microbial functions. Yet, the specific effects of grazing on soil enzymes in different northeastern China forest-steppe vegetation types remain poorly understood. To examine this, catalase (CA), urease (UA), and cellulase (CEA) activities were measured in different vegetation types (NS, MF, CP, GL) under both grazing and non-grazing conditions. Soil microbial biomass carbon and nitrogen (MBC and MBN) and other soil factors were also studied to gauge their impact on enzyme activities. The results indicated that enzyme activities were influenced by grazing, soil nutrient levels, mineralization, and microbial biomass carbon and nitrogen content. Grazing exerted the most significant influence on UA. CEA was predominantly affected by the content of biomass nitrogen and soil mineralization. CA, on the other hand, was primarily influenced by soil nutrient levels. Grazing influenced enzyme activities differently based on vegetation type. Under grazing, CA showed higher values in NS, MF, CP, and GL (4.09, 2.42, 3.26, and 3.90 mL 0.1 mol L−1 KMnO4 g−1 soil 20 min−1, respectively) with increases ranging from 32.52% to 505.00% (p < 0.05). Additionally, UA values were significantly higher in MF and CP (0.24 and 0.59 mg NH4+-N g−1 soil d−1, respectively) with increases of 66.67% and 156.00%, while UA and CEA were lower in GL, showing reductions of 78.79% and 166.67% (p < 0.05) (0.33 NH4+-N g−1 soil d−1 and 0.06 mg glucose g−1 soil 72 h−1, respectively) under grazing conditions. These findings underscore the importance of vegetation types in the grazing effects on soil enzymes at the forest-steppe ecotone and suggest that further efforts should be made to strengthen grassland grazing management to mitigate negative impacts on soil environmental health.
Genetic Parameters and Selection Responses for Important Breeding Traits in Liquidambar formosana Based on a Provenance–Family Trial
Authors: Dong Mingliang , Zhou Li , Yu Niu , Li Rongsheng , Wu Shijun , Yang Jinchang , Su Jianyu
Published: November 2023

Liquidambar formosana is a multipurpose tree species native to China. There has been increasing interest in L. formosana due to its leaves being rich in shikimic acid, which plays a key role in the synthesis of the antiviral drug oseltamivir phosphate. Here, shikimic acid content (SAC) and other breeding traits, including tree height (HT), diameter at breast height (DBH), height to crown base (HCB), individual tree volume (VOL), leaf color (LC) and stem straightness degree (SSD), for 387 families of 19 provenances were evaluated in a provenance–family trial of L. formosana to estimate genetic parameters and reveal geographical variation patterns and, ultimately, screen out superior provenances and families. Differences among provenances and families were significant for all tested traits, indicating a high potential for selective breeding. Broad-sense heritabilities of provenance (hp2 = 0.19–0.57) and family (hf2 = 0.16–0.31) were moderate for most traits. Moderate to strong genetic correlations were found among HT, DBH, VOL, HCB and LC (rA = 0.339–0.982), while adverse correlations (rA = −0.494 to −0.816) were observed between SAC and growth traits. All target traits, excluding SSD, exhibited clinal variation in response to latitudinal gradients, and a clustering heatmap divided the 19 provenances into three groups. For single-trait selection, SAC persistently had the highest genetic gains (85.14%–163.57%). A weighted index based on breeding values was used to concomitantly improve SAC, HT and DBH. At a selection rate of 25%, the genetic gains at the provenance and family levels for SAC were 36.42% and 73.52%, and those for core growth traits ranged from −2.29% to 3.49% and 4.05% to 4.47%, respectively. As far as we know, this is the first study in L. formosana to explore the inheritance of SAC and its correlations with other traditional breeding traits. The genetic parameter estimations contribute to a better understanding of the genetic basis of SAC, and the superior provenances and families obtained lay a material foundation for the development of new varieties rich in shikimic acid, thereby promoting the in-depth exploitation and utilization of germplasm resources of L. formosana.
Korean Pines Demonstrate Cold Resilience through Non-Structural Carbohydrate Concentrations despite Light Deprivation during the Growing Season
Authors: Li Bei , Ma Xiao , Saha Sudipta , Wu Haibo , Zhang Peng , Shen Hailong
Published: November 2023

Carbon is the fundamental element of plant life. Non-structural carbohydrates (NSC), synthesized using carbon dioxide through photosynthesis by plants, are essential for their growth and survival, which are also affected by light and temperature. However, few studies have investigated the effects of light conditions, season, and needle age together on field plants’ carbohydrates. We measured total carbon, glucose, sucrose, fructose, and starch concentrations in current and 1-year-old needles of Korean pine (Pinus koraiensis Sieb. et Zucc) growing under two distinct light conditions (dense canopy and full light) from early summer to cold winter. Total carbon, glucose, fructose, SS (soluble sugar, sucrose + glucose + fructose), NSC (soluble sugar + starch), starch, and SS/NSC all significantly (p < 0.05) related to the DOY (day of the year, 2021). Total carbon reached the maximum in September when the fresh needles were mature. Glucose, NSC, SS, and SS/NSC reached the maximum at the last sampling time, which provided protection for the cells in cold winter. The season showed a bigger impact on total carbon and NSC (all parameters except total carbon) than light and needle age. Two different-aged needles under two light conditions all had similar patterns of variation in total carbon and NSC, but twigs showed a more significant (p < 0.05) difference in NSC concentrations between two light conditions on 25 October (DOY 249). Needles of Korean pines stored soluble sugars (mainly glucose) and consumed starch in winter. Moreover, we found that needles had more glucose, while twigs had more sucrose, which may be a result of their different functions and may be helpful for future spring growth. Although lacking light during the growing season, understory Korean pines still had enough cold tolerance, similar to full-light ones, which indicated that low light during the growing season has little effect on cold tolerance.
Water Use Efficiency of Five Tree Species and Its Relationships with Leaf Nutrients in a Subtropical Broad-Leaf Evergreen Forest of Southern China
Authors: Huang Kang-Xiang , Xue Zi-Jing , Wu Jian-Cheng , Wang Hong , Zhou Hui-Qian , Xiao Ze-Bing , Zhou Wei , Cai Jin-Feng , Hu Long-Wei , Ren Jiu-Sheng , Zhang Yang , Xiao Sheng-Sheng , Shi Fu-Xi
Published: November 2023

Water use efficiency (WUE) is key to linking the water, carbon, and nutrient cycles in terrestrial ecosystems. However, the coupling between WUE and leaf nutrients is still poorly understood in subtropical forests. Here, the stable carbon isotope technique was employed to estimate the leaf-scale WUE of five common tree species (Castanopsis eyrei, Symplocos laurina, Machilus grijsii, Ternstroemia gymnanthera, and Rhododendron ovatum) in different habitat types (i.e., hillside, near the top of the peak, and peak) in a subtropical broad-leaf evergreen forest on the western slope of Wuyi Mountain, southern China. In addition, leaf carbon (C), nitrogen (N), and phosphorus (P) contents were also measured to assess plant nutrient utilization and its relationship with WUE. From the hillside to the peak, soil water content showed a decreasing trend, whereas the soil total C, N, and P contents showed an increasing trend. Regardless of species, the leaf δ13Cp value and WUE showed an increasing trend from the hillside to the peak, mainly due to an increase in soil water deficit and light. The leaf N and P contents showed an increasing trend from hillside to peak due to an increase in soil nutrients, while the leaf C: N ratio, C:P ratio, and N:P ratio showed a decreasing trend. The regression analysis showed that leaf-scale WUE was positively correlated with the leaf N and P contents but negatively correlated with the leaf N:P ratio, especially for the three species (C. eyrei, S. laurina, and T. gymnanthera). These results indicated that the differences in soil water availability, light, and soil development resulting from different habitats have a significant impact on leaf-scale WUE and nutrient status on Wuyi Mountain. Therefore, there may be a close relationship between WUE and leaf nutrients, which would help us to better understand the water-, carbon-, and nutrient-coupled relationships for the evergreen broad-leaved tree species in this region.
A Deformable Shape Model for Automatic and Real-Time Dendrometry
Authors: Wells Lucas A. , Chung Woodam
Published: November 2023

We present a stereo image-based algorithm for tree stem diameter measurement and form analysis. The algorithm uses planar parametric curves to represent two-dimensional projections of tree stems in stereo images. The curves evolve according to an energy formulation based on the gradients of the images and inductive priors related to biomechanics and morphology of tree stems. After energy minimization, the curves are reconstructed to three dimensions, allowing for diameter measurements at any point along the height of the stem. We describe the algorithm and report the validation test results comparing predicted diameter measurements to external observations. Our findings demonstrate that the algorithm can automatically estimate diameters for trees within 20 m of the camera with an error of 5.52%. We highlight how this method can aid product value optimization through taper analysis and sweep or crook detection. A run-time analysis shows that the algorithm can estimate dendrometric variables for ten trees simultaneously at 15 frames per second on a consumer-grade computer. Furthermore, we discuss the opportunity to produce training data for machine learning algorithms that generalize across domains and eliminate the need to manually tune parameters.
Whole-Genome Sequencing of Lactiplantibacillus plantarum YY-112 and Investigation of Its Immune-Modulating Abilities In Vivo
Authors: Luo Mengfan , Zhou Wanyi , Tao Wenyang , Xing Jianrong , Li Jingrui , Yang Ying , Guo Yuxing
Published: November 2023

A potentially novel probiotic strain, YY-112, was previously isolated and identified as Lactiplantibacillus pentosus using 16S rDNA sequencing. The whole genome analysis showed that strain YY-112 has the potential to metabolize carbohydrates in the gastrointestinal environment and to regulate immunity. Further, comparative genomics analysis revealed that strain YY-112 was Lactiplantibacillus plantarum (L. plantarum) with more unique genes. The results of in vivo tests showed that L. plantarum YY-112 had no adverse effects and restored the damaged spleen and intestinal barrier of immunocompromised mice. L. plantarum YY-112 recovered the normal levels of lymphocytes, serum cytokines (Interferon-γ, tumor necrosis factor α, and interleukin-6), immunoglobulins (Ig) (IgA, IgM, and IgG) and lipids (albumin, cholesterol, triglyceride). Additionally, L. plantarum YY-112 might indirectly enhance the immune system by improving the intestinal microbiota structure. These results supported the potential of L. plantarum YY-112 as a probiotic to regulate the immune system of hosts.
Generation of a Culex Male Mosquito Sex-Separation RNAi Yeast Strain Using Cas-CLOVER and Super PiggyBac Engineering in Saccharomyces cerevisiae
Authors: Brizzee Corey , Mysore Keshava , Njoroge Teresia M. , McConnell Seth , Crawford Jack , Duman-Scheel Molly
Published: November 2023

Several emerging mosquito control technologies require mass releases of adult male mosquitoes. Previous studies resulted in the generation of a laboratory female-specific larvicidal yeast strain targeting the GGT gene, which facilitated the laboratory sex separation of male Culex quinquefasciatus mosquitoes. Global deployment of this yeast-based sex-separation technology requires engineering second generation yeast strains which can be used in industrial-scale fermentations to support global mosquito control programs. In this study, the RNA-guided Cas-CLOVER system was used in combination with piggyBac transposase to generate robust Saccharomyces cerevisiae strains with multiple integrated copies of the insecticidal GGT shRNA expression cassette. Top expressing Cas-CLOVER strains killed Culex quinquefasciatus female larvae which consumed the yeast, facilitating male sex separation. Scaled fermentation resulted in kilogram-scale production of the yeast, which can be heat-killed and dried for global deployment to mosquito mass-rearing facilities.
The Status of South Africa’s Freshwater Fish Fauna: A Spatial Analysis of Diversity, Threat, Invasion, and Protection
Authors: Kajee Mohammed , Dallas Helen F. , Griffiths Charles L. , Kleynhans Cornelius J. , Shelton Jeremy M.
Published: November 2023

In South Africa, freshwater habitats are among the most threatened ecosystems, and freshwater fishes are the most threatened species group. Understanding patterns in freshwater fish diversity, threat, invasion, and protection status are vital for their management. However, few studies have undertaken such analyses at ecologically and politically appropriate spatial scales, largely because of limited access to comprehensive biodiversity data sets. Access to freshwater fish data for South Africa has recently improved through the advent of the Freshwater Biodiversity Information System (FBIS). We used occurrence records downloaded from the FBIS to evaluate spatial patterns in distribution, diversity, threat, invasion, and protection status of freshwater fishes in South Africa. Results show that record density varies spatially, at both primary catchment and provincial scales. The diversity of freshwater fishes also varied spatially: native species hotspots were identified at a provincial level in the Limpopo, Mpumalanga, and KwaZulu-Natal provinces; endemic species hotspots were identified in the Western Cape; and threatened species hotspots in the Western Cape, Mpumalanga, Eastern Cape, and KwaZulu-Natal. Non-native species distributions mirrored threatened species hotspots in the Western Cape, Mpumalanga, Eastern Cape, and KwaZulu-Natal. Some 47% of threatened species records fell outside of protected areas, and 38% of non-native species records fell within protected areas. Concerningly, 58% of the distribution ranges of threatened species were invaded by non-native species.
Mitogenomic Architecture and Phylogenetic Relationship of European Barracuda, Sphyraena sphyraena (Teleostei: Sphyraenidae) from the Atlantic Ocean
Authors: Kundu Shantanu , Kim Hyun-Woo , Lee Jaebong , Chung Sangdeok , Lee Soo Rin , Gietbong Fantong Zealous , Wibowo Arif , Kang Kyoungmi
Published: November 2023

The collective understanding of global-scale evolutionary trends in barracuda mitogenomes is presently limited. This ongoing research delves into the maternal evolutionary path of Sphyraena species, with a specific focus on the complete mitogenome of Sphyraena sphyraena, sourced from the Atlantic Ocean through advanced next-generation sequencing. This mitogenome spans 16,841 base pairs and encompasses 37 genes, including 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and an AT-rich control region. Notably, the mitogenome of S. sphyraena exhibits a preference for AT-base pairs, constituting 55.06% of the composition, a trait consistent with a similar bias found in related species. Most protein-coding genes initiate with an ATG codon, with the exception of Cytochrome c oxidase I (COI), which begins with a GTG codon. Additionally, six PCGs terminate with a TAA codon, COI with AGA, while six others exhibit incomplete termination codons. In the S. sphyraena mitogenome, the majority of transfer RNAs exhibit typical cloverleaf secondary structures, except for tRNA-serine, which lacks a DHU stem. Comparative analysis of conserved blocks within the D-loop regions of six Sphyraenidae species reveals that the CSB-I block extends to 22 base pairs, surpassing other blocks and containing highly variable sites. Both maximum-likelihood and Bayesian phylogenetic analyses, using concatenated 13 mitochondrial PCGs, distinctly separate all Sphyraenidae species. The European Barracuda, S. sphyraena, demonstrates a sister relationship with the ‘Sphyraena barracuda’ group, including S. barracuda and S. jello. In conclusion, this study advances our understanding of the evolutionary relationship and genetic diversity within barracudas. Furthermore, it recommends comprehensive exploration of mitogenomes and broader genomic data for all existing Sphyraenidae fishes, providing invaluable insights into their systematics, genetic characterization, and maternal evolutionary history within marine environments.
Effect of Electrohydrodynamic Drying on Drying Characteristics and Physicochemical Properties of Carrot
Authors: Wang Yanghong , Ding Changjiang
Published: November 2023

This study investigates the effects of electrohydrodynamic (EHD) drying technology on the drying kinetics, microstructure, quality, and nutritional components of carrots, along with conducting experiments on EHD drying under different voltage gradients. The experimental results showed that EHD drying technology could significantly increase the drying rate and the effective moisture diffusion coefficient. Within a certain range, the drying rate was directly proportional to the voltage. When the range was exceeded, the increase in voltage had a minimal effect on the drying rate. In terms of quality, the EHD drying group’s color, shrinkage rate, and rehydration performance were superior to the control group, and different voltages had no significant effect on the shrinkage rate and rehydration performance. The retention of carotenoids in the EHD drying group was 1.58 to 2 times that of the control group. EHD drying had a negative impact on the total phenolic content and vitamin A content of dried carrot slices. Based on the results of infrared spectroscopy and scanning electron microscopy (SEM), the dehydrated carrot slices showed wrinkling due to water loss, with numerous pores, a generally intact structure, and retained functional groups. EHD drying had a significant impact on the secondary structure of proteins, where an increase in voltage led to an increase in disordered structure, with a smaller proportion of disordered structure in the lower voltage group compared to the control group, and a similar proportion of disordered structure between the higher voltage group and the control group. Results from low-field nuclear magnetic resonance (NMR) showed that EHD drying could retain more bound water compared to the control group, with the best retention of cellular bound water at a voltage of 26 kV and the best retention of cellular immobilized water at a voltage of 38 kV, indicating the superiority of EHD drying in preserving cellular structure. This study provided a theoretical basis and experimental foundation for the application of electrohydrodynamic drying technology to carrot drying, and promoted the practical application of EHD drying technology.
Effects of Daily Ingestion of Two SunGold Kiwifruit for 6 Weeks on Metabolic and Inflammatory Biomarkers: A Randomized, Cross-Over, Exploratory Intervention Study
Authors: Mishra Suman , Bentley-Hewitt Kerry , McGhie Tony , Fraser Karl , Hedderley Duncan , Martell Sheridan , Dinnan Hannah , Monro John
Published: November 2023

Kiwifruit contain many components, some considered beneficial, such as vitamins, phytochemicals and dietary fibre, and others potentially harmful, such as fructose and glucose in fruit sugars. In a 6-week, randomised, crossover study aimed at exploring the net effects of daily consumption of kiwifruit, 23 healthy participants consumed two Actinidia chinensis var. chinensis ‘Zesy002’ (marketed as Zespri™ SunGold™ Kiwifruit) per day as part of their customary diet (intervention) or without kiwifruit (control) as their customary diet for 6 weeks in a cross-over study. Anthropometric data, venous blood, and urine samples were collected at the start and end of the 6-week intervention and control periods for the measurement of physical changes, plasma glucose, insulin, glycated haemoglobin, short-chain fatty acids, blood lipids, uric acid, inflammatory biomarkers, and urinary ascorbic acid. Variables were measured between the start and finish of interventions, and between intervention and control periods. Food diaries were completed on the 3 days before blood sampling to estimate dietary ascorbic acid and dietary fibre intakes. Despite urinary vitamin C and food diaries indicating compliance, and good precision in measurements, there were no appreciable changes in biomarkers during the study, either within or between intervention and control periods, that would indicate a change in health status. Thus, the sizes of any effects of kiwifruit ingestion were too small to become significant under the test conditions used, indicating a high probability that daily ingestion of two SunGold kiwifruit is safe with respect to metabolic health.
Cysteine–Silver–Polymer Systems for the Preparation of Hydrogels and Films with Potential Applications in Regenerative Medicine
Authors: Vishnevetskii Dmitry V. , Mekhtiev Arif R. , Averkin Dmitry V. , Polyakova Elizaveta E.
Published: November 2023

Herein, the problem concerning the poorer mechanical properties of gels based on low molecular weight gelators (LMWGs)—L-cysteine and silver nitrate—was solved by the addition of various polymers—polyvinyl alcohol (PVA), polyvinyl pyrrolidone (PVP) and polyethylene glycol (PEG)—to the initial cysteine–silver sol (CSS). The physicochemical methods of analysis—viscosimetry, UV spectroscopy, DLS, and SEM—identified that cysteine–silver hydrogels (CSG) based on PVA possess the best rheological properties and porous microstructure (the average pore size is 2–10 µm) compared to gels without the polymer or with PVP or PEG. Such gels are able to form cysteine–silver cryogels (CSC) and then porous cysteine–silver films (CSF) with an average pore size of 10–20 µm and good mechanical, swelling, and adhesion to skin characteristics as long as the structure of CSS particles remains stable. In vitro experiments have shown that hydrogels are non-toxic to normal human fibroblast cells. The obtained materials could potentially be applied to regenerative medicine.
Neuroimaging in Adolescents: Post-Traumatic Stress Disorder and Risk for Substance Use Disorders
Authors: Etami Yasameen , Lildharrie Christina , Manza Peter , Wang Gene-Jack , Volkow Nora D.
Published: November 2023

Trauma in childhood and adolescence has long-term negative consequences in brain development and behavior and increases the risk for psychiatric disorders. Among them, post-traumatic stress disorder (PTSD) during adolescence illustrates the connection between trauma and substance misuse, as adolescents may utilize substances to cope with PTSD. Drug misuse may in turn lead to neuroadaptations in learning processes that facilitate the consolidation of traumatic memories that perpetuate PTSD. This reflects, apart from common genetic and epigenetic modifications, overlapping neurocircuitry engagement triggered by stress and drug misuse that includes structural and functional changes in limbic brain regions and the salience, default-mode, and frontoparietal networks. Effective strategies to prevent PTSD are needed to limit the negative consequences associated with the later development of a substance use disorder (SUD). In this review, we will examine the link between PTSD and SUDs, along with the resulting effects on memory, focusing on the connection between the development of an SUD in individuals who struggled with PTSD in adolescence. Neuroimaging has emerged as a powerful tool to provide insight into the brain mechanisms underlying the connection of PTSD in adolescence and the development of SUDs.
The Pivotal Role of Noncoding RNAs in Flowering Time Regulation
Authors: Liu Yun , Zhu Qing-Feng , Li Wen-Yan , Chen Pei , Xue Jiao , Yu Yang , Feng Yan-Zhao
Published: November 2023

Noncoding RNAs constitute a substantial portion of the transcriptome and play pivotal roles in plant growth and development. Among these processes, flowering stands out as a crucial trait, ensuring reproductive success and seed set, and is meticulously controlled by genetic and environmental factors. With remarkable advancements in the identification and characterization of noncoding RNAs in plants, it has become evident that noncoding RNAs are intricately linked to the regulation of flowering time. In this article, we present an overview of the classification of plant noncoding RNAs and delve into their functions in the regulation of flowering time. Furthermore, we review their molecular mechanisms and their involvement in flowering pathways. Our comprehensive review enhances the understanding of how noncoding RNAs contribute to the regulation of flowering time and sheds light on their potential implications in crop breeding.
Plant Development in the Garden Pea as Revealed by Mutations in the Crd/PsYUC1 Gene
Authors: Gélinas-Marion Ariane , Eléouët Morgane P. , Cook Sam D. , Vander Schoor Jacqueline K. , Abel Steven A. G. , Nichols David S. , Smith Jason A. , Hofer Julie M. I. , Ross John J.
Published: November 2023

In common with other plant species, the garden pea (Pisum sativum) produces the auxin indole-3-acetic acid (IAA) from tryptophan via a single intermediate, indole-3-pyruvic acid (IPyA). IPyA is converted to IAA by PsYUC1, also known as Crispoid (Crd). Here, we extend our understanding of the developmental processes affected by the Crd gene by examining the phenotypic effects of crd gene mutations on leaves, flowers, and roots. We show that in pea, Crd/PsYUC1 is important for the initiation and identity of leaflets and tendrils, stamens, and lateral roots. We also report on aspects of auxin deactivation in pea.
Unlocking Dendritic Cell-Based Vaccine Efficacy through Genetic Modulation—How Soon Is Now?
Authors: Elwakeel Ahmed , Bridgewater Hannah , Bennett Jason
Published: November 2023

The dendritic cell (DC) vaccine anti-cancer strategy involves tumour-associated antigen loading and maturation of autologous ex vivo cultured DCs, followed by infusion into the cancer patient. This strategy stemmed from the idea that to induce a robust anti-tumour immune response, it was necessary to bypass the fundamental immunosuppressive mechanisms of the tumour microenvironment that dampen down endogenous innate immune cell activation and enable tumours to evade immune attack. Even though the feasibility and safety of DC vaccines have long been confirmed, clinical response rates remain disappointing. Hence, the full potential of DC vaccines has yet to be reached. Whether this cellular-based vaccination approach will fully realise its position in the immunotherapy arsenal is yet to be determined. Attempts to increase DC vaccine immunogenicity will depend on increasing our understanding of DC biology and the signalling pathways involved in antigen uptake, maturation, migration, and T lymphocyte priming to identify amenable molecular targets to improve DC vaccine performance. This review evaluates various genetic engineering strategies that have been employed to optimise and boost the efficacy of DC vaccines.
An Artificial Intelligence Prediction Model of Insulin Sensitivity, Insulin Resistance, and Diabetes Using Genes Obtained through Differential Expression
Authors: González-Martín Jesús María , Torres-Mata Laura B. , Cazorla-Rivero Sara , Fernández-Santana Cristina , Gómez-Bentolila Estrella , Clavo Bernardino , Rodríguez-Esparragón Francisco
Published: November 2023

Insulin is a powerful pleiotropic hormone that affects processes such as cell growth, energy expenditure, and carbohydrate, lipid, and protein metabolism. The molecular mechanisms by which insulin regulates muscle metabolism and the underlying defects that cause insulin resistance have not been fully elucidated. This study aimed to perform a microarray data analysis to find differentially expressed genes. The analysis has been based on the data of a study deposited in Gene Expression Omnibus (GEO) with the identifier “GSE22309”. The selected data contain samples from three types of patients after taking insulin treatment: patients with diabetes (DB), patients with insulin sensitivity (IS), and patients with insulin resistance (IR). Through an analysis of omics data, 20 genes were found to be differentially expressed (DEG) between the three possible comparisons obtained (DB vs. IS, DB vs. IR, and IS vs. IR); these data sets have been used to develop predictive models through machine learning (ML) techniques to classify patients with respect to the three categories mentioned previously. All the ML techniques present an accuracy superior to 80%, reaching almost 90% when unifying IR and DB categories.
Stability Analysis of a Multi-Layered Slope in an Open Pit Mine
Authors: Steiakakis Emmanouil , Xiroudakis George , Lazos Ilias , Vavadakis Dionysios , Bazdanis George
Published: November 2023

The design of slopes in open pit mines requires an in-depth understanding of the ground behavior to predict the potential failure mechanism and to better determine the stabilization measures. This study compares the critical slip surface defined by the limit equilibrium method (LEM), the limit analysis (LA), and the finite elements method (FEM) for the stability analysis to better approach the stability on a multi-layered slope. The safety factor, the size, and the location of the critical slip surface obtained from the applied methods are considered in the comparisons. This study highlights some features that affect the slope stability and presents a procedure for addressing the evaluation challenges in a multi-layered formation. Moreover, it presents some aspects of the upper-bound computation on the safety factor of a layered slope subjected to the effects of pore water pressures. Based on the obtained results, the critical slip surface defined by the limit equilibrium method compares well with the slip mechanism suggested by the limit analysis and the finite element approach. In view of the differences in the shape and location of the critical slip surface, as well as the values obtained for the safety factor, it is recommended that an engineer should analyze critical slopes using the finite element method in combination with the limit equilibrium or limit analysis method as a cross reference. The authors propose that in defining the potential failure mass, consideration must be given to the conducted field research and monitoring.
User Walking Speed and Standing Posture Influence Head/Neck Flexion and Viewing Behavior While Using a Smartphone
Authors: Chen Yi-Lang , Nguyen Hong-Tam
Published: November 2023

The habit of using smartphones while walking has become widespread among modern individuals, particularly when pedestrians are in a hurry. However, there has been little exploration into the differences between standing and walking at various speeds in terms of smartphone use. In this study, we examined 60 young participants (30 men and 30 women) who engaged in smartphone tasks such as one-handed browsing or two-handed texting while standing, walking slowly, and walking normally. The measured variables included neck flexion (NF), head flexion (HF), gaze angle (GA), and viewing distance (VD). The study findings indicate that using smartphones while walking may cause a more pronounced kyphotic curve in the cervical spine compared to when standing, leading to increased strain in the neck region. The heightened neck load can be attributed to the concurrent dynamic nature of both walking and smartphone usage. Moreover, two-handed texting had a more detrimental impact on NF, HF, and GA when contrasted with one-handed browsing. The interplay among hand operation, posture, and maintaining arm position displayed an uncertain correlation with VD. While women typically exhibited smaller NF, HF, and GA than men, it is important to explore whether their shorter VD might contribute to increased eyestrain.
Hard to Reach and Hidden: Improving the Identification of Young Dementia Carers
Authors: Masterson-Algar Patricia , Egan Kieren , Flynn Greg , Hughes Gwenllian , Spector Aimee , Stott Joshua , Windle Gill
Published: November 2023

Young dementia carers (YDCs) rarely receive appropriate training and support. Their visibility and identification remain dangerously low, and, consequently, support initiatives being developed are failing to reach them. This study explored the success (or failure) of YDC identification pathways as well as the barriers and enablers to their implementation. An explorative qualitative approach was followed, drawing on the experiences of parents of YDCs, dementia researchers, professionals in the field of dementia/young carers, and young adult carers. Data collection involved semi-structured interviews (n = 17) and a participatory 2-h workshop to discuss and critique preliminary themes as well as explore strategies to increase the visibility and identification of YDCs. Five themes were identified: a “whole-family approach” (as a pathway to identification), “not a carer” (self/family identification), a postcode lottery (high variability of support services), tailored support that is “fit for purpose”, and the “power” of peer support. Recommendations on potential initiatives and actions that can help raise awareness and increase the identification success of YDCs are proposed. Our findings support the need for a broad and holistic approach to the identification of YDCs that runs alongside the development of support initiatives that are accessible and relatable. The support itself will play a role in improving subsequent identification or hindering it if not “fit for purpose”.
BRACNAC: A BRCA1 and BRCA2 Copy Number Alteration Caller from Next-Generation Sequencing Data
Authors: Kechin Andrey , Boyarskikh Ulyana , Borobova Viktoriya , Khrapov Evgeniy , Subbotin Sergey , Filipenko Maxim
Published: November 2023

Detecting copy number variations (CNVs) and alterations (CNAs) in the BRCA1 and BRCA2 genes is essential for testing patients for targeted therapy applicability. However, the available bioinformatics tools were initially designed for identifying CNVs/CNAs in whole-genome or -exome (WES) NGS data or targeted NGS data without adaptation to the BRCA1/2 genes. Most of these tools were tested on sample cohorts of limited size, with their use restricted to specific library preparation kits or sequencing platforms. We developed BRACNAC, a new tool for detecting CNVs and CNAs in the BRCA1 and BRCA2 genes in NGS data of different origin. The underlying mechanism of this tool involves various coverage normalization steps complemented by CNV probability evaluation. We estimated the sensitivity and specificity of our tool to be 100% and 94%, respectively, with an area under the curve (AUC) of 94%. The estimation was performed using the NGS data obtained from 213 ovarian and prostate cancer samples tested with in-house and commercially available library preparation kits and additionally using multiplex ligation-dependent probe amplification (MLPA) (12 CNV-positive samples). Using freely available WES and targeted NGS data from other research groups, we demonstrated that BRACNAC could also be used for these two types of data, with an AUC of up to 99.9%. In addition, we determined the limitations of the tool in terms of the minimum number of samples per NGS run (≥20 samples) and the minimum expected percentage of CNV-negative samples (≥80%). We expect that our findings will improve the efficacy of BRCA1/2 diagnostics. BRACNAC is freely available at the GitHub server.
Novel COX11 Mutations Associated with Mitochondrial Disorder: Functional Characterization in Patient Fibroblasts and Saccharomyces cerevisiae
Authors: Caron-Godon Chenelle A. , Della Vecchia Stefania , Romano Alessandro , Doccini Stefano , Dal Canto Flavio , Pasquariello Rosa , Rubegni Anna , Battini Roberta , Santorelli Filippo Maria , Glerum D. Moira , Nesti Claudia
Published: November 2023

Genetic defects in the nuclear encoded subunits and assembly factors of cytochrome c oxidase (mitochondrial complex IV) are very rare and are associated with a wide variety of phenotypes. Biallelic pathogenic variants in the COX11 protein were previously identified in two unrelated children with infantile-onset mitochondrial encephalopathies. Through comprehensive clinical, genetic and functional analyses, here we report on a new patient harboring novel heterozygous variants in COX11, presenting with Leigh-like features, and provide additional experimental evidence for a direct correlation between COX11 protein expression and sensitivity to oxidative stress. To sort out the contribution of the single mutations to the phenotype, we employed a multi-faceted approach using Saccharomyces cerevisiae as a genetically manipulable system, and in silico structure-based analysis of human COX11. Our results reveal differential effects of the two novel COX11 mutations on yeast growth, respiration, and cellular redox status, as well as their potential impact on human protein stability and function. Strikingly, the functional deficits observed in patient fibroblasts are recapitulated in yeast models, validating the conservation of COX11’s role in mitochondrial integrity across evolutionarily distant organisms. This study not only expands the mutational landscape of COX11-associated mitochondrial disorders but also underscores the continued translational relevance of yeast models in dissecting complex molecular pathways.
A New Drug Discovery Platform: Application to DNA Polymerase Eta and Apurinic/Apyrimidinic Endonuclease 1
Authors: Das Debanu , Duncton Matthew A. J. , Georgiadis Taxiarchis M. , Pellicena Patricia , Clark Jennifer , Sobol Robert W. , Georgiadis Millie M. , King-Underwood John , Jobes David V. , Chang Caleb , Gao Yang , Deacon Ashley M. , Wilson David M.
Published: November 2023

The ability to quickly discover reliable hits from screening and rapidly convert them into lead compounds, which can be verified in functional assays, is central to drug discovery. The expedited validation of novel targets and the identification of modulators to advance to preclinical studies can significantly increase drug development success. Our SaXPyTM (“SAR by X-ray Poses Quickly”) platform, which is applicable to any X-ray crystallography-enabled drug target, couples the established methods of protein X-ray crystallography and fragment-based drug discovery (FBDD) with advanced computational and medicinal chemistry to deliver small molecule modulators or targeted protein degradation ligands in a short timeframe. Our approach, especially for elusive or “undruggable” targets, allows for (i) hit generation; (ii) the mapping of protein–ligand interactions; (iii) the assessment of target ligandability; (iv) the discovery of novel and potential allosteric binding sites; and (v) hit-to-lead execution. These advances inform chemical tractability and downstream biology and generate novel intellectual property. We describe here the application of SaXPy in the discovery and development of DNA damage response inhibitors against DNA polymerase eta (Pol η or POLH) and apurinic/apyrimidinic endonuclease 1 (APE1 or APEX1). Notably, our SaXPy platform allowed us to solve the first crystal structures of these proteins bound to small molecules and to discover novel binding sites for each target.
The Blinking of Small-Angle X-ray Scattering Reveals the Degradation Process of Protein Crystals at Microsecond Timescale
Authors: Arai Tatsuya , Mio Kazuhiro , Onoda Hiroki , Chavas Leonard M. G. , Umena Yasufumi , Sasaki Yuji C.
Published: November 2023

X-ray crystallography has revolutionized our understanding of biological macromolecules by elucidating their three-dimensional structures. However, the use of X-rays in this technique raises concerns about potential damage to the protein crystals, which results in a quality degradation of the diffraction data even at very low temperatures. Since such damage can occur on the micro- to millisecond timescale, a development in its real-time measurement has been expected. Here, we introduce diffracted X-ray blinking (DXB), which was originally proposed as a method to analyze the intensity fluctuations of diffraction of crystalline particles, to small-angle X-ray scattering (SAXS) of a lysozyme single-crystal. This novel technique, called the small-angle X-ray blinking (SAXB) method, analyzes the fluctuation in SAXS intensity reflecting the domain fluctuation in the protein crystal caused by the X-ray irradiation, which could be correlated with the X-ray-induced damage on the crystal. There was no change in the protein crystal’s domain dynamics between the first and second X-ray exposures at 95K, each of which lasted 0.7 s. On the other hand, its dynamics at 295K increased remarkably. The SAXB method further showed a dramatic increase in domain fluctuations with an increasing dose of X-ray radiation, indicating the significance of this method.
Genome-Wide and Transcriptome Analysis of Jacalin-Related Lectin Genes in Barley and the Functional Characterization of HvHorcH in Low-Nitrogen Tolerance in Arabidopsis
Authors: Quan Xiaoyan , Meng Chen , Xie Chunjuan , Sun Huifang , Xu Boyang , Santos Bermudez Ramon , He Wenxing
Published: November 2023

The jacalin-related lectins (JRLs) are widely distributed in plants and are involved in plant development and multiple stress responses. However, the characteristics of the HvJRL gene family at the genome-wide level and the roles of JRLs in barley’s response to low-nitrogen (LN) stress have been rarely reported. In this study, 32 HvJRL genes were identified and unevenly distributed at both ends of the seven chromosomes in barley. HvJRL proteins generally exhibited low sequence similarity but shared conserved jacalin domains by multiple sequence analysis. These proteins were classified into seven subfamilies based on phylogenetic analysis, with a similar gene structure and conserved motifs in the same subfamily. The HvJRL promoters contained a large number of diverse cis-elements associated with hormonal response and stress regulation. Based on the phylogenetic relationships and functionally known JRL homologs, it was predicted that some HvJRLs have the potential to serve functions in multiple stress responses but not nutrition deficiency stress. Subsequently, nine differentially expressed genes (DEGs) encoding eight HvJRL proteins were identified in two barley genotypes with different LN tolerance by transcriptome analysis. Furthermore, 35S:HvHorcH transgenic Arabidopsis seedlings did enhance LN tolerance, which indicated that HvHorcH may be an important regulator of LN stress response (LNSR). The HvJRL DEGs identified herein could provide new candidate genes for LN tolerance studies.
Controlling Gut Microbiota by Twendee X® May Contribute to Dementia Prevention
Authors: You Fukka , Harakawa Yoshiaki , Yoshikawa Toshikazu , Inufusa Haruhiko
Published: November 2023

The human gut microbiota (GM) is a complex and dynamic ecosystem that hosts trillions of commensal and potentially pathogenic microorganisms. It is crucial in protecting humans from pathogens and in maintaining immune and metabolic homeostasis. Numerous studies have demonstrated that GM has a significant impact on health and disease, including Alzheimer’s disease (AD). AD is a progressive neurodegenerative disorder characterized by impaired short-term memory and cognitive deficits. Patients with AD have been reported to exhibit abnormalities in GM density and species composition. Oxidative stress (OS) has been implicated in the onset and progression of AD; however, the relationship between OS and gut microbiota in AD onset and progression is not clear. Twendee X® (TwX), an oral supplement consisting of eight active ingredients, has been shown to prevent dementia in mild cognitive impairment (MCI) in humans and substantially improve cognitive impairment in mouse models of AD. This positive effect is achieved through the potency of the combined antioxidants that regulate OS; therefore, similar results cannot be achieved by a single antioxidant ingredient. To examine the impact of long-term OS elevation, as seen in AD on the body and GM, we examined GM alterations during the initial OS elevation using a two-week OS loading rat model, and examined the effects of TwX on OS and GM. Furthermore, using a questionnaire survey and fecal samples, we analyzed the impact of TwX on healthy individuals’ gut bacteria and the associated effect on their quality of life (QOL). TwX was found to increase the number of bacteria species and their diversity in GM, as well as butyrate-producing bacteria, which tend to be reduced in AD patients. Additionally, TwX improved defecation condition and QOL. The gut bacteria function as part of the homeostatic function during OS elevation, and the prophylactic administration of TwX strengthened this function. The results suggest that the preventative effect of TwX on dementia may involve the GM, in addition to the other previously demonstrated effects.
The Association between BZIP Transcription Factors and Flower Development in Litsea cubeba
Authors: Wang Siqi , Zhao Yunxiao , Chen Yicun , Gao Ming , Wang Yangdong
Published: November 2023

The basic leucine zipper (bZIP) family is one of the largest families of transcription factors among eukaryotic organisms. Members of the bZIP family play various roles in regulating the intricate process of flower development in plants. Litsea cubeba (Lour.) (family: Lauraceae) is an aromatic, dioecious plant used in China for a wide range of applications. However, no study to date has undertaken a comprehensive analysis of the bZIP gene family in L. cubeba. In this work, we identified 68 members of the bZIP gene family in L. cubeba and classified them into 12 subfamilies based on previous studies on Arabidopsis thaliana. Transcriptome data analysis revealed that multiple LcbZIP genes exhibit significantly high expression levels in the flowers of L. cubeba, while some also demonstrate distinct temporal specificity during L. cubeba flower development. In particular, some LcbZIP genes displayed specific and high expression levels during the stamen and pistil degradation process. Using differential gene expression analysis, weighted gene co-expression network analysis, and Gene Ontology enrichment analysis, we identified six candidate LcbZIP genes that potentially regulate stamen or pistil degradation during flower development. In summary, our findings provide a framework for future functional analysis of the LcbZIP gene family in L. cubeba and offer novel insights for investigating the mechanism underlying pistil and stamen degeneration in this plant.