bluuebunny/crossref_metadata_2025 huggingface dataset:
In Vitro Susceptibility of Clinical and Carrier Strains of Staphylococcus aureus to STAFAL® Phage Preparation
Authors: Straka Marek , Hubenáková Zuzana , Janošíková Lucia , Bugalová Aneta , Minich Andrej , Wawruch Martin , Liptáková Adriana , Drahovská Hana , Slobodníková Lívia
Published: December 2024

The treatment of infections caused by Staphylococcus aureus is currently complicated by the increasing number of strains resistant to antimicrobial agents. One promising way to solve this problem is phage therapy. Due to the lack of data on the effectiveness and safety of phage preparations, STAFAL® is the only registered phage preparation for the treatment of infectious diseases in the Slovak Republic and the entire European Union. The aim of this work was to determine the effectiveness of the STAFAL® phage preparation against S. aureus strains of different origins with variable sensitivity to antimicrobial substances and with different genetic backgrounds. For this purpose, 111 carrier strains, 35 clinical isolates from bloodstream infections, and 46 strains from skin and soft tissue infections were analysed. The effectiveness of STAFAL® was determined by the plaque forming method. STAFAL® was effective against 74.0% of the strains tested. Susceptibility to this phage preparation was significantly higher in strains resistant to methicillin (MRSA), erythromycin and clindamycin (p < 0.05). The high efficiency of the STAFAL® preparation was confirmed against spa types t003, t024 and t032, typical of the hospital environment. The in vitro results indicate high therapeutic potential of the STAFAL® antistaphylococcal phage preparation, especially against MRSA strains.
Dual Mechanisms of Salinity Tolerance in Wheat Germplasm Lines W4909 and W4910
Authors: Wang Richard R.-C. , Xu Steven S. , Monaco Thomas A. , Robbins Matthew D.
Published: December 2024

Soil salinity adversely affects plant growth and development, reducing the yield of most crops, including wheat. The highly salt-tolerant wheat germplasm lines W4909 and W4910 were derived from a cross between two moderately salt-tolerant lines, the Chinese Spring (CS)/Thinopyrum junceum disomic addition line AJDAj5 (AJ) and the Ph-inhibitor line (Ph-I) derived from CS/Aegilops speltoides. Molecular markers for gene introgressions in W4909 and W4910 were not reported. Four sequence-tagged site (STS) molecular markers of Ph-I were developed and tested in the above-mentioned lines and the F2 progenies of the two crosses, Anza (AZ) × 4740 (sib of W4910) and Yecora Rojo (YR) × 4728 (sib of W4909). Additionally, homogeneity was assessed in several derivatives of W4909, 4728, W4910, and 4740 using the four markers. The four STS markers are not associated with salt tolerance, but they provide an indication of the transfer of chromatin in 3B chromosome of Ae. speltoides via Ph-I. Moreover, salt tolerance and leaf sodium concentration were determined in CS, AJ, Ph-I, 7151 (progeny of W4909), 7157 (progeny of W4910), AZ, and YR under salt treatment and control. Surprisingly, AJ had the lowest leaf sodium concentration under the control and salt treatment, indicating greater sodium exclusion than that in CS, AZ, and YR. This low level of leaf sodium concentration was heritable from 4740 to its hybrid progenies. On the other hand, the higher leaf sodium concentration, indicative of the tissue tolerance to salinity in Ph-I, had been inherited by both W4909 and W4910 and then transmitted to their hybrid progenies. One offspring line each in both W4909 and W4910 (7762 and 7159, respectively) were homozygous for the three molecular markers and lacked the marker psr1205 of Su1-Ph1 gene, making them better materials than the original lines for future research on, for example, whole-genome sequencing and gene mining. The implications of these findings for the utilization of W4909 and W4910 in breeding salt-tolerant wheat cultivars are discussed.
Biophysical Characterization of a Novel Phosphopentomutase from the Hyperthermophilic Archaeon Thermococcus kodakarensis
Authors: Naz Zahra , Lubkowski Jacek , Saleem Muhammad , Aslam Mehwish , Rahman Moazur , Wlodawer Alexander , Rashid Naeem
Published: December 2024

Phosphopentomutases catalyze the isomerization of ribose 1-phosphate and ribose 5-phosphate. Thermococcus kodakarensis, a hyperthermophilic archaeon, harbors a novel enzyme (PPMTk) that exhibits high homology with phosphohexomutases but has no significant phosphohexomutase activity. Instead, PPMTk catalyzes the interconversion of ribose 1-phosphate and ribose 5-phosphate. Here, we report biophysical analysis, crystallization, and three-dimensional structure determination of PPMTk by X-ray diffraction at 2.39 Å resolution. The solved structure revealed a novel catalytic motif, unique to PPMTk, which makes this enzyme distinct from the homologous counterparts. We postulate that this novel catalytic motif may enable PPMTk to isomerize phosphopentose instead of phosphohexose. To the best of our knowledge, this is the first biophysical and structural analysis of a phosphopentomutase from hyperthermophilic archaea.
Physiological and Transcriptional Responses to Phosphorus Deficiency and Glucose-6-Phosphate Supplementation in Neopyropia yezoensis
Authors: Chen Yujiao , He Senhao , Wang Yinghao , Hu Chuanming , Cheng Weitao , Zhou Lingjie , Ji Nanjing , Chen Haihong , Shen Xin
Published: December 2024

Neopyropia yezoensis, a marine red algae species, has significant economic and ecological value. However, phosphorus (P) deficiency has emerged as a growing concern in many cultivation regions, negatively impacting its growth. To adapt to P deficiency, algae have evolved various strategies, including using dissolved organic phosphorus (DOP) sources to sustain growth. Despite its prevalence as a form of DOP, the utilization mechanism of glucose-6-phosphate (G6P) by N. yezoensis remains unclear. In this study, the physiological and transcriptional responses of N. yezoensis to P deficiency and G6P supplementation were examined. The results demonstrated that prolonged P deficiency significantly inhibited the growth of N. yezoensis and had a negative impact on physiological indicators such as photosynthetic pigments and antioxidant enzyme activity. However, G6P treatment gradually alleviated these adverse effects over time. Both P deficiency and G6P treatment were associated with increased expression of genes involved in signal transduction and P starvation responses while concurrently downregulating genes related to photosynthesis and antioxidant defenses. In contrast, the suppression of gene expression was less significant under G6P treatment. This study elucidates the adaptive strategies of N. yezoensis in response to P deficiency and clarifies the regulatory pathways involved in G6P utilization, providing novel insights into its P nutrient acquisition and metabolic regulation.
Human Keratin Matrices Suppress Matrix Metalloproteinase Activity to Support Wound Healing
Authors: Ramey-Ward Allison N. , Smith Shakesia , Walthall Howard , Barrows Thomas H.
Published: December 2024

Elevated protease activity is a hallmark of non-healing chronic wounds. Though multiple biomaterials exist that are successful in treating wounds, their roles in modulating the enzymatic environment of the wound are only beginning to be elucidated. Because keratin has long been known to be resistant to degradation by most enzymes, we studied a keratin biomaterial, the human keratin matrix (HKM), in the presence of enzymes identified to contribute to wound chronicity: neutrophil-derived elastase (NE), matrix metalloproteinase 1 (MMP-1), and MMP-9. Upon finding the suppression of MMP-9 activity in the presence of HKM without reducing enzyme protein levels, we further studied the ability of HKM to bind metal ions in the wound and showed the reduction of Zn2+ ion concentration in the presence of HKM. Finally, because of the enzyme resistance of keratin and the suppression of wound enzymes, we demonstrated that HKM was durable in the wound environment, and did not degrade in wound healing efficacy when left in place for two weeks compared to one week in a diabetic mouse model of wound non-healing. In this way, we show HKM is a unique and effective biomaterial for the treatment of chronic wounds through the modulation of wound MMP activity.
Echium amoenum and Rosmarinic Acid Suppress the Growth and Metastasis of Gastric Cancer AGS Cells by Promoting Apoptosis and Inhibiting EMT
Authors: Ahmadi Mahdieh , Kim Hong Lae , Park So Jin , Jung Hye Jin
Published: December 2024

Gastric cancer (GC) ranks as the fifth most prevalent cancer globally. Owing to the absence of early manifest symptoms, it is difficult to diagnose GC until it has metastasized to other organs. Hence, the prevention and treatment of GC have become major concerns for patients. Echium amoenum, a traditional medicinal plant from the Boraginaceae family, exhibits various biological activities. Although recent studies have reported the anticancer properties of E. amoenum, its effects and mechanisms of action on GC cells are not yet fully understood. This study examined the anticancer effects of the ethyl acetate extract of E. amoenum (EAEC) and its main active ingredient, rosmarinic acid (RA), in GC AGS cells. EAEC and RA suppressed AGS cell growth by inducing apoptosis through caspase mediation and inhibited AGS cell metastasis by influencing the expression of crucial epithelial–mesenchymal transition (EMT) biomarkers. Furthermore, the anti-growth and anti-metastatic effects of EAEC and RA on AGS cells involved inactivation of the STAT3, AKT, and ERK1/2 pathways. Additionally, RA notably inhibited the in vivo tumor growth in AGS cells. Overall, these results indicate that EAEC and RA could serve as potential anticancer and anti-metastasis agents for GC.
Targeting Oxidative Stress and Inflammation in the Eye: Insights from a New Model of Experimental Autoimmune Uveitis
Authors: Chistyakov Dmitry V. , Tiulina Veronika V. , Gancharova Olga S. , Baksheeva Viktoriia E. , Goriainov Sergei V. , Shebardina Natalia G. , Ivlev Vasily A. , Komarov Sergey V. , Shevelyova Marina P. , Tikhomirova Natalia K. , Philippov Pavel P. , Vasil’ev Vasiliy G. , Sergeeva Marina G. , Permyakov Sergei E. , Iomdina Elena N. , Tsvetkov Philipp O. , Senin Ivan I. , Zernii Evgeni Yu.
Published: December 2024

Autoimmune uveitis is a relapsing blind-causing ocular condition with complex pathogenesis that is not completely understood. There is a high demand for accurate animal models of experimental autoimmune uveitis (EAU) suitable for elucidating the molecular mechanisms of the disease and testing new therapeutic approaches. Here, we demonstrated that photoreceptor Ca2+/Zn2+-sensor protein recoverin is a uveoretinal antigen in albino rabbits provoking typical autoimmune chorioretinitis 2–4 weeks after immunization. The pathologic process in recoverin-induced EAU shared features with human disease and included lymphocytic infiltration of the retina, Dalen–Fuchs nodules and foci of subtotal or total retinal atrophy, manifested as a decrease in amplitude of the a-wave of the electroretinogram. In some cases, changes in the retinal vascular pattern and subretinal hemorrhages were also observed. These signs were accompanied by a gradual accumulation of serum antibodies against recoverin. Biochemical examination of the aqueous humor (AH) revealed typical characteristics of inflammation and oxidative stress, including increased levels of TNF-α and IL-6 and decreased levels of IL-10, as well as decreased total antioxidant activity, superoxide dismutase and glutathione peroxidase activities, and increased zinc concentration. Consistently, metabolomic and targeted lipidomic analysis of AH showed high lactate and low ascorbic acid levels in early EAU; increased levels of key pro-inflammatory signaling lipids such as PGE2, TXB2, 11-HETE and Lyso-PAF; and reduced levels of the anti-inflammatory fatty acid DHA in advanced stages of the disease. Uveitic AH became enriched with recoverin, confirming disruption of the blood–ocular barrier and photoreceptor damage. Notably, the application of mitochondria-targeted antioxidant therapy impeded EAU progression by maintaining local antioxidant activity and suppressing TNF-α, IL-6 and PGE2 signaling. Overall, our results demonstrate that recoverin-induced EAU in rabbits represents an accurate model of human autoimmune posterior uveitis and suggest new directions for its therapy that can be trialed using the developed model.
Mesenchymal Stromal Cells for Aging Cartilage Regeneration: A Review
Authors: Wu Kun-Chi , Chang Yu-Hsun , Ding Dah-Ching , Lin Shinn-Zong
Published: December 2024

Cartilage degeneration is a key feature of aging and osteoarthritis, characterized by the progressive deterioration of joint function, pain, and limited mobility. Current treatments focus on symptom relief, not cartilage regeneration. Mesenchymal stromal cells (MSCs) offer a promising therapeutic option due to their capability to differentiate into chondrocytes, modulate inflammation, and promote tissue regeneration. This review explores the potential of MSCs for cartilage regeneration, examining their biological properties, action mechanisms, and applications in preclinical and clinical settings. MSCs derived from bone marrow, adipose tissue, and other sources can self-renew and differentiate into multiple cell types. In aging cartilage, they aid in tissue regeneration by secreting growth factors and cytokines that enhance repair and modulate immune responses. Recent preclinical studies show that MSCs can restore cartilage integrity, reduce inflammation, and improve joint function, although clinical translation remains challenging due to limitations such as cell viability, scalability, and regulatory concerns. Advancements in MSC delivery, including scaffold-based approaches and engineered exosomes, may improve therapeutic effectiveness. Potential risks, such as tumorigenicity and immune rejection, are also discussed, emphasizing the need for optimized treatment protocols and large-scale clinical trials to develop effective, minimally invasive therapies for cartilage regeneration.
5-PC as a Lipid Probe Molecule and as a Second Phospholipid in Binary Phospholipid Mixtures: Saturation Recovery EPR Studies
Authors: Subczynski Witold K. , Widomska Justyna
Published: December 2024

Mixtures of two phospholipids (PLs) with different main phase transition temperatures were investigated. Host PLs (HPLs) were represented by DMPC, DPPC, DSPC, and DMPE. The admixed PL was the spin-labeled phosphatidylcholine 5-PC(1-palmitoyl-2-(5-doxylstearoyl)phosphatidylcholine), with a unique opportunity to monitor the properties and the local environments of all admixed PL molecules using saturation recovery EPR methods. Below the HPL phase transition temperatures, 5-PC mixes with HPL to form two distinct pools with different rotational diffusion rates. The fluidity of the local environment in these two pools is very different, being more fluid for molecules with greater rotational diffusion rates. Above the HPL phase transition temperature, 5-PC mixes with HPL uniformly. This is independent of the HPL, observed for 5-PC concentrations from 0.25 mol% up to 20 mol% and for the wide temperature range. Assuminga very low concentration of 5-PC is an ideal probe molecule, we can conclude that small fluid phase domains made of HPL molecules are formed below the phase transition temperature of the HPL bilayers. In binary mixtures of HPLs with 5-PC, below the phase transition of HPL bilayers, fluid phase domains are created within the bulk gel phase of HPL lipids by the admixed second PL, namely 5-PC.
Spectroscopic Analysis of Tryptophan as a Potential Optical Biomarker for Estimating the Time of Death
Authors: Gruszczyńska Emilia , Lewkowicz Aneta , Czarnomska Martyna , Koczur Joanna , Walczewska-Szewc Katarzyna , Kaliszan Michał , Balwicki Łukasz , Bojarski Piotr
Published: December 2024

The estimation of the time of death represents a highly complex and challenging task within the field of forensic medicine and science. It is essential to approach this matter with the utmost respect for human rights while acknowledging the inherent limitations of the current methods, which require continuous refinement and expansion. Forensic science recognizes the necessity to improve existing techniques and develop new, more accurate, and non-invasive procedures, such as physicochemical approaches, to enhance the precision and reliability of time of death determinations. This article proposes a novel, non-invasive method for estimating the time of death using a spectroscopic analysis of tryptophan. The initial phase of the study concerns the presentation of the spectroscopic properties of tryptophan at varying pH levels, with consideration given to the pH fluctuations that occur during the decomposition of cadavers. The findings confirm the stability of the spectroscopic properties at different environmental pH levels. Subsequently, preliminary trials were conducted on 15 healthy human volunteers, which demonstrated that tryptophan concentrations in fingerprint samples were within the detection limits using molecular spectroscopy techniques. The final objective was to ascertain whether the composition of the substance present on the skin surface of a deceased individual up to 48 h postmortem is comparable to that of the sweat–fatty substance in living individuals. This was confirmed by the absorption and emission spectral profiles, which showed overlapping patterns with those obtained from living volunteers. The most significant outcome at this stage was the demonstration of a considerable increase in emission intensity in the spectra for samples obtained approximately 48 h after death in comparison to that obtained from a sample taken approximately 24 h after death. This indicates a rise in the concentration of tryptophan on the skin surface as the postmortem interval (PMI) increases, which could serve as a basis for developing a tool to estimate the time of death.
Role of Blood P-Tau Isoforms (181, 217, 231) in Predicting Conversion from MCI to Dementia Due to Alzheimer’s Disease: A Review and Meta-Analysis
Authors: Lombardi Gemma , Pancani Silvia , Manca Riccardo , Mitolo Micaela , Baiardi Simone , Massa Federico , Coppola Luigi , Franzese Monica , Nicolai Emanuele , Guerini Franca Rosa , Mancuso Roberta , Agliardi Cristina , Agostini Simone , Pardini Matteo , Virgili Gianni , Sorbi Sandro , Parchi Piero , Nacmias Benedetta , Venneri Annalena
Published: December 2024

Blood-based biomarkers are minimally invasive tools to detect the pathological changes of Alzheimer’s Disease (AD). This meta-analysis aims to investigate the use of blood-derived p-tau isoforms (181, 217, 231) to predict conversion from mild cognitive impairment (MCI) to AD dementia (ADD). Studies involving MCI patients with data on blood p-tau isoforms at baseline and clinical diagnosis at follow-up (≥1 year) were included. Twelve studies on p-tau 181 (4340 MCI, conversion rate 20.6%), four on p-tau 217 (913 MCI, conversion rate 33.4%), and one on p-tau 231 (135 MCI, conversion rate 33%) were included. For p-tau 181, the pooled area under the receiver operating characteristic curve (AUC) was 0.73 (95% CI = 0.68–0.78), and for p-tau 217 was 0.85 (95% CI = 0.75–0.91). Plasma levels of p-tau 181 had good discriminatory power to identify MCI patients who will convert to ADD. Although only four studies on p-tau 217 have been included in the meta-analysis, in the last year the predictive power of p-tau 217 is emerging as superior to that of other isoforms. However, given the high heterogeneity detected in the p-tau 217 studies included in this meta-analysis, additional supportive evidence is needed. Insufficient results were available for p-tau 231. These findings support the prognostic utility of p-tau 181 and p-tau 217 measured in blood to predict progression to ADD in MCI and encourage its future implementation in clinical practice.
HOXA11-As Promotes Lymph Node Metastasis Through Regulation of IFNL and HMGB Family Genes in Pancreatic Cancer
Authors: Nishiyama Hayato , Niinuma Takeshi , Kitajima Hiroshi , Ishiguro Kazuya , Yamamoto Eiichiro , Sudo Gota , Sasaki Hajime , Yorozu Akira , Aoki Hironori , Toyota Mutsumi , Kai Masahiro , Suzuki Hiromu
Published: December 2024

Recent studies have shown that long noncoding RNAs (lncRNAs) play pivotal roles in the development and progression of cancer. In the present study, we aimed to identify lncRNAs associated with lymph node metastasis in pancreatic ductal adenocarcinoma (PDAC). We analyzed data from The Cancer Genome Atlas (TCGA) database to screen for genes overexpressed in primary PDAC tumors with lymph node metastasis. Our screen revealed 740 genes potentially associated with lymph node metastasis, among which were multiple lncRNA genes located in the HOXA locus, including HOXA11-AS. Elevated expression of HOXA11-AS was associated with more advanced tumor stages and shorter overall survival in PDAC patients. HOXA11-AS knockdown suppressed proliferation and migration of PDAC cells. RNA-sequencing analysis revealed that HOXA11-AS knockdown upregulated interferon lambda (IFNL) family genes and downregulated high-mobility group box (HMGB) family genes in PDAC cells. Moreover, HMGB3 knockdown suppressed proliferation and migration by PDAC cells. These results suggest that HOXA11-AS contributes to PDAC progression, at least in part, through regulation of IFNL and HMGB family genes and that HOXA11 AS is a potential therapeutic target in PDAC.
Mechanism, Kinetics and Modelling of Phenol Carboxylation Reactions with CO2
Authors: Kojčinović Aleksa , Likozar Blaž , Grilc Miha
Published: December 2024

Combining carboxylation reactions using carbon dioxide (CO2) as a reactant with phenol results in creation of new C-C bonds, and represents one of the most promising routes in sustainable utilization of ubiquitous and readily available resources for production of highly valuable products. This study provides a detailed and well-structured investigation of the effect of various reaction conditions (reactant loading, reaction duration, temperature, CO2 pressure) on the carboxylation of phenol. Sodium phenoxide carboxylation showed well-resolved trends with variation of temperature and time, and resulted in production of salicylic acid (SA) in the range of 11.4 to 47.8%, 4-hydoxybenzoic acid (4HBA) in the range of 2.0 to 8.2%, while the dicarboxylated 4-hydroxyisophthalic acid (4HiPh) was only detected in trace amounts. The effect of the variation of reactant content was shown to be significantly influenced by the reactor size, solid/vessel and gas/solid contact area, as well as the efficiency of the stirring. CO2 pressure was shown to be a crucial element, where reactions carried out below 2 MPa CO2 did not show any activity. While investigating the reaction mechanism, it was shown that the salt analogues of potential products could be acidified in situ by the moisture present, and immediately degraded back to phenol, thus lowering yields of potentially obtained products. The experimental results were successfully used to compose a kinetic model, which very well describes the experimentally obtained results. As such, this study provides a valuable dataset for valorization of lignocellulosic aromatic compounds as well as highly abundant and environmentally detrimental carbon dioxide into industrially valuable mono- and dicarboxylic acids.
Gene and Its Promoter Cloning, and Functional Validation of JmSOC1 Revealed Its Role in Promoting Early Flowering and the Interaction with the JmSVP Protein
Authors: Dong Tianyi , Zhang Mengmeng , Wu Jingwen , Li Jingze , Liu Chunping , Zhang Lijie
Published: December 2024

Juglans mandshurica, a notable woody oil tree species, possesses both fruit and timber value. However, the complete heterodichogamous flowering mechanism in this species remains elusive. SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) is a crucial regulator of flower bud development in Arabidopsis thaliana. In this study, we cloned the coding DNA sequence (CDS) of the JmSOC1 gene, revealing a 705 base pair (bp) sequence that encodes a protein of 234 amino acids. The JmSOC1 protein contains a highly conserved MADS-box domain, indicating its role as a transcription factor, and is predominantly localized in the nucleus. The JmSOC1 gene expressed the highest in flower buds. The peak expression level of JmSOC1 during the physiological differentiation phase occurred earlier in male flower buds of protandry (MPD) on April 10th compared to female flower buds of protandry (FPD) on April 14th; similarly, the peak expression in female flower buds of protogyny (FPG) on April 2nd preceded that in male flower buds of protogyny (MPG) on April 14th. This may be the primary reason for the earlier differentiation of the male flowers in protandry individuals and the female flowers in protogyny individuals. Overexpression of JmSOC1 in wild-type A. thaliana resulted in earlier flowering, accompanied by an upregulation of key flowering-related genes such as LEAFY (LFY), APETALA1 (AP1), and FLOWERING LOCUS T (FT). To further explore the function of JmSOC1, a 782 bp promoter sequence of JmSOC1 gene was cloned, which has been verified to have promoter activity by GUS staining. Furthermore, the interaction between the JmSOC1 gene promoter and its upstream regulatory protein JmSVP was verified using a yeast one-hybrid. These results offer valuable insights into the molecular mechanisms underpinning the promotion of early flowering in J. mandshurica and hold promise for laying a theoretical foundation for the flowering regulation network of this species.
Establishment and Validation of an Efficient Agrobacterium Tumefaciens-Mediated Transient Transformation System for Salix Psammophila
Authors: Yang Yanfei , Chen Zhicheng , Zhao Jinna , Zheng Guangshun , Wang Fei , Li Shaofeng , Ren Xingrong , Li Jianbo
Published: December 2024

Salix psammophila, C. Wang & Chang Y. Yang, a desert-adapted shrub, is recognized for its exceptional drought tolerance and plays a vital role in ecosystem maintenance. However, research on S. psammophila has been limited due to the lack of an efficient and reliable genetic transformation method, including gene functional studies. The Agrobacterium-mediated transient overexpression assay is a rapid and powerful tool for analyzing gene function in plant vivo. In this study, tissue culture seedlings of S. psammophila were utilized as the recipient materials, and the plant expression vector pCAMBIA1301, containing the GUS reporter gene, was transferred into the seedlings via an Agrobacterium-mediated method. To enhance the efficiency of the system, the effects of secondary culture time, Agrobacterium concentration, infection time, and co-culture duration on the transient transformation efficiency of S. psammophila were explored. The optimal combination for the instantaneous transformation of S. psammophila tissue culture seedlings mediated by Agrobacterium was determined as follows: a secondary culture time of 30 d, a value of OD600 of 0.8, an infection time of 3 h, and a co-culture duration of 48 h. Subsequently, the effectiveness of the transformation system was validated using the S. psammophila drought response gene SpPP2C80. To further confirm the accuracy of the system, SpPP2C80-overexpressing Arabidopsis was constructed and drought resistance analysis was performed. The results were consistent with the transient overexpression of SpPP2C80 in S. psammophila tissue culture seedlings, indicating that this system can be effectively employed for studying gene function in S. psammophila. These findings provide essential information for investigating gene function in non-model plants and pave the way for advancements in molecular biology research in S. psammophila.
A Single-Cell Atlas of Porcine Skeletal Muscle Reveals Mechanisms That Regulate Intramuscular Adipogenesis
Authors: Xu Zhong , Wu Junjing , Li Yujie , Zhou Jiawei , Zhang Yu , Qiao Mu , Feng Yue , Sun Hua , Li Zipeng , Li Lianghua , Oyelami Favour Oluwapelumi , Peng Xianwen , Mei Shuqi
Published: December 2024

Porcine skeletal muscle development is closely linked to meat production efficiency and quality. The accumulation of porcine intramuscular fat is influenced by the hyperplasia and hypertrophy of adipocytes within the muscle. However, the cellular profiles corresponding to the two stages of muscle development remain undetermined. Single-nucleus RNA sequencing (snRNA-seq) can elucidate cell subsets in tissues, capture gene expression at the individual cell level, and provide innovative perspectives for studying muscle and intramuscular fat formation. In this study, a total of 78,302 nuclei and 9 clusters of cells, which included fibro/adipogenic progenitor (FAP), myonuclei, adipocytes, and other cell types, of Xidu black pigs, were identified on Day 1 and Day 180. The pattern of cell clustering varied between the two developmental stages. Notably, the percentage of adipocytes in the Day 180 group was higher than in the Day 1 group (0.51% vs. 0.15%). Pseudo-time sequence analysis indicated that FAPs could differentiate into adipocytes and myonuclei cells, respectively. The THRSP gene was identified as a biomarker for swine intramuscular fat cells, and its down-regulation resulted in significant reduction in lipid droplet formation in porcine preadipocytes. Our research provides new insights into the cellular characteristics of intramuscular fat formation, which may facilitate the development of novel strategies to enhance intramuscular fat deposition and improve pork quality.
Comprehensive Genome-Wide Identification and Expression Profiling of bHLH Transcription Factors in Areca catechu Under Abiotic Stress
Authors: Ali Akhtar , Khan Noor Muhammad , Jiang Yiqi , Zhou Guangzhen , Wan Yinglang
Published: December 2024

The basic helix-loop-helix (bHLH) transcription factor (TF) family, the second-largest among eukaryotes, is known for its evolutionary and functional diversity across plant species. However, bHLH genes have not yet been characterized in Areca catechu. In this study, we identified 76 AcbHLH genes, which exhibit a variety of physicochemical properties. Phylogenetic analysis revealed evolutionary relationships between Arabidopsis thaliana bHLH genes (AtbHLH) and their counterparts in A. catechu (AcbHLH). These analyses also highlighted conserved amino acid motifs (S, R, K, P, L, A, G, and D), conserved domains, and evolutionary changes, such as insertions, deletions, and exon gains or losses. Promoter analysis of AcbHLH genes revealed 76 cis-elements related to growth, phytohormones, light, and stress. Gene duplication analysis revealed four tandem duplications and twenty-three segmental duplications, while AcbHLH63 in the Areca genome exhibited significant synteny with bHLH genes from A. thaliana, Vitis vinifera, Solanum lycopersicum, Brachypodium distachyon, Oryza sativa, and Zea mays. Furthermore, relative expression analysis showed that under drought stress (DS), AcbHLH22, AcbHLH39, AcbHLH45, and AcbHLH58 showed distinct upregulation in leaves at specific time points, while all nine AcbHLH genes were upregulated in roots. Under salt stress (SS), AcbHLH22, AcbHLH39, AcbHLH45, and AcbHLH58 were upregulated in leaves, and AcbHLH22, AcbHLH34, and AcbHLH39 exhibited differential expression in roots at various time points. This study provides valuable insights into the bHLH superfamily in A. catechu, offering a solid foundation for further investigation into its role in responding to abiotic stresses.
Genome-Wide Identification of NLP Gene Families and Haplotype Analysis of SiNLP2 in Foxtail Millet (Setaria italica)
Authors: Bai Yanming , Wang Juncheng , Tang Wensi , Sun Daizhen , Wang Shuguang , Chen Kai , Zhou Yongbin , Wang Chunxiao , Chen Jun , Xu Zhaoshi , Chen Ming , Wang Huajun , Ma Youzhi
Published: December 2024

Nitrogen is a critical factor in plant growth, development, and crop yield. NODULE-INCEPTION-like proteins (NLPs), which are plant-specific transcription factors, function as nitrate sensors and play a vital role in the nitrogen response of plants. However, the genome-wide identification of the NLP gene family, the elucidation of the underlying molecular mechanism governing nitrogen response, and haplotype mining remain elusive in millet. In this study, we identified seven members of the NLP gene family in the millet genome and systematically analyzed their physicochemical properties. Evolutionary tree analysis indicated that SiNLP members can be classified into three subgroups, with NLP members from the same species preferentially grouped together within each subgroup. Analysis of gene structure characteristics revealed that all SiNLP members contained 10 conserved motifs, as well as the RWP-RK and PB1 domains, indicating that these motifs and domains have been relatively conserved throughout evolution. Additionally, we identified a significant abundance of response elements related to hormones, stress, growth, and development within the promoter regions of SiNLP members, suggesting that these members are involved in regulating diverse physiological processes in millet. Transcriptome data under low-nitrogen conditions showed significant differences in the expression profiles of SiNLP2 and SiNLP4 compared to the other members. RNA-seq and qRT-PCR results demonstrated that SiNLP2 significantly responds to low-nitrogen stress. Notably, we found that SiNLP2 is involved in nitrogen pathways by regulating the expression of the SiNAR2.1A, SiNAR2.1B, SiNRT1.1, and SiNR2 genes. More importantly, we identified an elite haplotype, Hap2, of SiNLP2, which is gradually being utilized in the breeding process. Our study established a foundation for a comprehensive understanding of the SiNLP gene family and provided gene resources for variety improvement and marker-assisted selection breeding.
Pharmacological Nephroprotection in Chronic Kidney Disease Patients with Type 2 Diabetes Mellitus—Clinical Practice Position Statement of the Polish Society of Nephrology
Authors: Adamczak Marcin , Kurnatowska Ilona , Naumnik Beata , Stompór Tomasz , Tylicki Leszek , Krajewska Magdalena
Published: December 2024

Both chronic kidney disease (CKD) and type 2 diabetes (T2D) are modern epidemics worldwide and have become a severe public health problem. Chronic kidney disease progression in T2D patients is linked to the need for dialysis or kidney transplantation and represents the risk factor predisposing to serious cardiovascular complications. In recent years, important progress has occurred in nephroprotective pharmacotherapy in CKD patients with T2D. In the current position paper, we described a nephroprotective approach in CKD patients with T2D based on the five following pillars: effective antihyperglycemic treatment, SGLT2 inhibitor or semaglutide, antihypertensive therapy, use of RASi (ARB or ACEi), and in selected patients, finerenone, as well as sodium bicarbonate in patients with metabolic acidosis. We thought that the current statement is comprehensive and up-to-date and addresses multiple pathways of nephroprotection in patients with CKD and T2D.
The Oxidative Stress in Epilepsy—Focus on Melatonin
Authors: Kamieniak Maciej , Kośmider Kamil , Miziak Barbara , Czuczwar Stanisław J.
Published: December 2024

Oxidative stress develops when there is an excess of oxidants leading to molecular and cellular damage. Seizure activity leads to oxidative stress and the resulting increased lipid peroxidation. Generally, antiseizure medications reduce oxidative stress, although the data on levetiracetam are ambiguous. Exogenous antioxidants (vitamin E, resveratrol, hesperidin, and curcumin) have been documented to exert an anticonvulsant effect in animal models of seizures and some recent clinical data point to curcumin as an affective adjuvant for the therapy of pediatric intractable epilepsy. Melatonin is an antioxidant with an ability to attenuate seizure activity induced by various convulsants in rodents. Its clinical effectiveness has been also confirmed in a number of clinical studies. Experimental studies point to a possibility that endogenous melatonin may possess proconvulsive activity. Moreover, some scarce clinical data seem to express this view; however, a limited number of patients were included. The anticonvulsant activity of exogenous melatonin may involve GABA-mediated inhibition, while endogenous melatonin may act as a proconvulsant due to a decrease in the brain dopaminergic transmission. Antioxidants, including melatonin, may be considered as adjuvants in the therapy of epilepsy and melatonin, in addition, in patients with epilepsy suffering from sleep disorders.
Advanced PROTAC and Quantitative Proteomics Strategy Reveals Bax Inhibitor-1 as a Critical Target of Icaritin in Burkitt Lymphoma
Authors: Zhang Peixi , Zhang Ziqing , Li Jie , Xu Meng , Lu Weiming , Chen Ming , Shi Jiaqi , Wang Qiaolai , Zhang Hengyuan , Huang Shi , Lian Chenlei , Liu Jia , Ma Junjie , Liu Jieqing
Published: December 2024

Understanding the molecular targets of natural products is crucial for elucidating their mechanisms of action, mitigating toxicity, and uncovering potential therapeutic pathways. Icaritin (ICT), a bioactive flavonoid, demonstrates significant anti-tumor activity but lacks defined molecular targets. This study employs an advanced strategy integrating proteolysis targeting chimera (PROTAC) technology with quantitative proteomics to identify ICT’s key targets. A library of 22 ICT-based PROTAC derivatives were synthesized, among which LJ-41 exhibited a superior IC50 of 5.52 μM against Burkitt lymphoma (CA-46) cells. Then, differential proteomic analysis identified Bax inhibitor-1 (BI-1) as a potential target. Target validation techniques, including cellular thermal shift assay (CETSA), drug affinity responsive target stability (DARTS) assay, surface plasmon resonance (SPR) assay, and molecular docking, confirmed LJ-41’s high specificity for BI-1. Mechanistic investigations revealed that LJ-41 induces apoptosis through BI-1 degradation, triggering endoplasmic reticulum stress and activating inositol-requiring enzyme 1 α (IRE1α), activating transcription factor 6 (ATF6), and nuclear factor erythroid 2-related factor transcription factor heme oxygenase 1 (NRF2-HO-1) signaling pathways. This study establishes a refined methodological framework for natural product target discovery and highlights ICT-PROTAC derivatives’ potential for clinical application in Burkitt lymphoma treatment.
Aberrant Positions of the Chemosensory Neurons in the Neurotransmitter-Release Mutant unc-13
Authors: Bokman Eduard , Kalij Ido Padro , Zaslaver Alon
Published: December 2024

Secretion of neurotransmitter- and neuropeptide-containing vesicles is a regulated process orchestrated by multiple proteins. Of these, mutants, defective in the unc-13 and unc-31 genes, responsible for neurotransmitter and neuropeptide release, respectively, are routinely used to elucidate neural and circuitry functions. While these mutants result in severe functional deficits, their neuroanatomy is assumed to be intact. Here, using C. elegans as the model animal system, we find that the head sensory neurons show aberrant positional layout in neurotransmitter (unc-13), but not in neuropeptide (unc-31), release mutants. This finding suggests that synaptic activity may be important for proper cell migration during neurodevelopment and warrants considering possible anatomical defects when using unc-13 neurotransmitter release mutants.
Association of Inflammasome Gene Expression Levels with Pathogenesis of Familial Mediterranean Fever in Armenians
Authors: Hayrapetyan Varduhi , Karapetyan Lana , Ghukasyan Lilit , Atshemyan Sofi , Ghazaryan Hovsep , Vardanyan Valentina , Mukuchyan Vahan , Arakelyan Arsen , Zakharyan Roksana
Published: December 2024

Familial Mediterranean fever (FMF) is a genetically determined autoinflammatory disease transmitted mostly by an autosomal recessive mechanism and caused by point mutations of the MEFV (Mediterranean FeVer) gene. The aim of this study was to evaluate the expression of inflammasome genes (p65, Casp1, MEFV, and NLRP3) in patients with FMF compared to controls to understand the changes playing a key role in disease development. We found altered expression levels of the full-length MEFV isoform as well as Casp1 and p65 in FMF patients versus controls. This, once again, highlighted the significance of inflammasome genes in terms of FMF.
Ubiquitin Ligase U-Box51 Positively Regulates Drought Stress in Potato (Solanum tuberosum L.)
Authors: Wei Meng , Ghimire Shantwana , Rijal Anuja , Wang Kaitong , Zhang Huanhuan , Si Huaijun , Tang Xun
Published: December 2024

The ubiquitin-proteasome system (UPS) is a key protein degradation pathway in eukaryotes, in which E3 ubiquitin ligases mediate protein ubiquitination, directly or indirectly targeting substrate proteins to regulate various biological processes, including plant growth, hormone signaling, immune responses, and adaptation to abiotic stress. In this study, we identified plant U-box protein 51 in Solanum tuberosum (StPUB51) as an E3 ubiquitin ligase through transcriptomic analysis, and used it as a candidate gene for gene-function analysis. Quantitative real-time PCR (qRT-PCR) was used to examine StPUB51 expression across different tissues, and its expression patterns under simulated drought stress induced by polyethylene glycol (PEG 6000) were assessed. Transgenic plants overexpressing StPUB51 and plants with down-regulated StPUB51 expression were generated to evaluate drought tolerance. The activities of key antioxidant enzymes-superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) as well as malondialdehyde (MDA) content in transgenic plants’ leaves were measured under drought conditions. Protein–protein interactions involving StPUB51 were explored via yeast two-hybrid (Y2H) screening, with interaction verification by bimolecular fluorescence complementation (BiFC). StPUB51 was predominantly expressed in stems, with lower expression observed in tubers, and its expression was significantly upregulated in response to 20% PEG-6000 simulated drought. Subcellular localization assays revealed nuclear localization of the StPUB51 protein. Under drought stress, StPUB51-overexpressing plants exhibited enhanced SOD, POD, and CAT activities and reduced MDA levels, in contrast to plants with suppressed StPUB51 expression. Y2H and BiFC analyses identified two interacting proteins, StSKP2A and StGATA1, which may be functionally linked to StPUB51. Collectively, these findings suggest that StPUB51 plays a positive regulatory role in drought tolerance, enhancing resilience in potato growth and stress adaptation.
5-Aminolevulinic Acid (5-ALA)-Induced Drought Resistance in Maize Seedling Root at Physiological and Transcriptomic Levels
Authors: Shi Yaqiong , Jin Zihao , Wang Jingyi , Zhou Guangkuo , Wang Fang , Peng Yunling
Published: December 2024

Drought stress seriously affects the growth, development, yield, and quality of maize. This study aimed to investigate the effects of exogenous 5-ALA on root morphology and physiological changes in maize seedlings and to detect its regulatory network. The results showed that adding 25 mg/L 5-ALA accelerated root morphogenesis (root average diameter, main root length, total root length, and root surface area) and promoted dry matter accumulation and free radical removal. Transcriptome analysis showed that after applying exogenous 5-ALA, differently expressed genes (DEGs) were mainly involved in histidine metabolism, amino acid biosynthesis, plasma membrane components, secondary active sulfate transmembrane transporter activity, and anion reverse transporter activity. Two inbred lines specifically responded to organelle and structural molecular activity, and 5-ALA may regulate maize roots to achieve drought tolerance through these two pathways. In addition, candidate genes that may regulate maize root growth were screened by weighted gene co-expression network analysis (WGCNA). These genes may play important roles in alleviating drought stress through lignin synthesis, heat shock proteins, iron storage and transport, calcium binding proteins, and plasma membrane regulation of exogenous regulator 5-ALA. Our results may provide a theoretical basis for clarifying the response of maize seedling roots to drought and the mechanism of exogenous hormones in alleviating drought.
Soil Salinity Differentiates Winter Triticale Genotypes in Physiological and Biochemical Characteristics of Seedlings and Consequently Their Yield
Authors: Golebiowska-Paluch Gabriela , Stawoska Iwona , Jelonek-Kozioł Małgorzata , Wesełucha-Birczyńska Aleksandra , Kornaś Andrzej
Published: December 2024

The aim of this study was to test the hypothesis that both the winter triticale genotype and salinity treatment influence the photosynthesis efficiency and content of metabolites and proteins, including antioxidant enzymes, under field conditions, as well as that these parameters are correlated with yielding capacity. The research material involved four genotypes differing in their tolerance to stress in previous tests. Chlorophyll a fluorescence parameters and antioxidant activity were assessed in the seedlings. Specific antibodies were then used to verify the involvement of selected proteins. Simultaneously, Raman spectroscopy was employed to detect chlorophyll, carotenoids, phenolic compounds, and protein levels. The findings suggest that improved PSII performance, reduced catalase activity, increased pigment levels, and higher thioredoxin reductase abundance in the seedlings were associated with better yield potential in triticale genotypes grown under salt stress conditions. The Raman analysis revealed that salinity caused changes in the photosynthetic pigments, particularly carotenoids. The carbon isotope ratios indicate that the salinization generated different physiological stresses in the availability of water.
In-Hole Measurements of Flow Inside Fan-Shaped Film Cooling Holes and Downstream Effects
Authors: Issakhanian Emin
Published: December 2024

The study of low-speed jets into crossflow is critical to the performance of gas turbines. Film cooling is a method to maintain manageable blade temperatures in turbine sections while increasing turbine inlet temperatures and turbine efficiencies. Initially, cooling holes were cylindrical. Film cooling jets from these discrete round holes were found to be very susceptible to jet liftoff, which reduces surface effectiveness. Shaped holes have become prominent for improved coolant coverage. Fan-shaped holes are the most common design and have shown good improvement over round holes. However, fan-shaped holes introduce additional parameters to the already complex task of modeling cooling effectiveness. Studies of these flows range in hole lengths from those found in actual turbine blades to very long holes with fully developed flow. The flow within the holes themselves is difficult to study as there is limited optical access. However, the flow within the holes has a strong effect on the resulting properties of the jet. This study presents velocity and vorticity fields measured using high-resolution magnetic resonance velocimetry (MRV) to study three different fan-shaped hole geometries at two blowing ratios. Because MRV does not require line of sight, it provides otherwise hard-to-obtain experimental data of the flow within the film cooling hole in addition to the mainflow measurements. By allowing measurement within the cooling hole, MRV shows how a poor choice of diffuser start point and angle can be detrimental to film cooling if overall hole length and cooling flow velocity are not properly accounted for in the design. The downstream effect of these choices on the jet height and counter-rotating vortex pair is also observed.