bluuebunny/crossref_metadata_2025 huggingface dataset:
Anti-Inflammatory and Anti-(Lymph)angiogenic Properties of an ABCB5+ Limbal Mesenchymal Stem Cell Population
Authors: Meshko Berbang , Volatier Thomas L. A. , Mann Johanna , Kluth Mark A. , Ganss Christoph , Frank Markus H. , Frank Natasha Y. , Ksander Bruce R. , Cursiefen Claus , Notara Maria
Published: September 2024

Corneal transparency and avascularity are essential for vision. The avascular cornea transitions into the vascularized conjunctiva at the limbus. Here, we explore a limbal stromal cell sub-population that expresses ABCB5 and has mesenchymal stem cell characteristics. Human primary corneal stromal cells were enriched for ABCB5 by using FACS sorting. ABCB5+ cells expressed the MSC markers CD90, CD73, and CD105. ABCB5+ but not ABCB5− cells from the same donor displayed evidence of pluripotency with a significantly higher colony-forming efficiency and the ability of trilineage differentiation (osteogenic, adipogenic, and chondrogenic). The ABCB5+ cell secretome demonstrated lower levels of the pro-inflammatory protein MIF (macrophage migration inhibitory factor) as well as of the pro-(lymph)angiogenic growth factors VEGFA and VEGFC, which correlated with reduced proliferation of Jurkat cells co-cultured with ABCB5+ cells and decreased proliferation of blood and lymphatic endothelial cells cultured in ABCB5+ cell-conditioned media. These data support the hypothesis that ABCB5+ limbal stromal cells are a putative MSC population with potential anti-inflammatory and anti-(lymph)angiogenic effects. The therapeutic modulation of ABCB5+ limbal stromal cells may prevent cornea neovascularization and inflammation and, if transplanted to other sites in the body, provide similar protective properties to other tissues.
The Role of Molecular and Cellular Aging Pathways on Age-Related Hearing Loss
Authors: Ege Tuba , Tao Litao , North Brian J.
Published: September 2024

Aging, a complex process marked by molecular and cellular changes, inevitably influences tissue and organ homeostasis and leads to an increased onset or progression of many chronic diseases and conditions, one of which is age-related hearing loss (ARHL). ARHL, known as presbycusis, is characterized by the gradual and irreversible decline in auditory sensitivity, accompanied by the loss of auditory sensory cells and neurons, and the decline in auditory processing abilities associated with aging. The extended human lifespan achieved by modern medicine simultaneously exposes a rising prevalence of age-related conditions, with ARHL being one of the most significant. While our understanding of the molecular basis for aging has increased over the past three decades, a further understanding of the interrelationship between the key pathways controlling the aging process and the development of ARHL is needed to identify novel targets for the treatment of AHRL. The dysregulation of molecular pathways (AMPK, mTOR, insulin/IGF-1, and sirtuins) and cellular pathways (senescence, autophagy, and oxidative stress) have been shown to contribute to ARHL. However, the mechanistic basis for these pathways in the initiation and progression of ARHL needs to be clarified. Therefore, understanding how longevity pathways are associated with ARHL will directly influence the development of therapeutic strategies to treat or prevent ARHL. This review explores our current understanding of the molecular and cellular mechanisms of aging and hearing loss and their potential to provide new approaches for early diagnosis, prevention, and treatment of ARHL.
SIRT1 Regulates Mitochondrial Damage in N2a Cells Treated with the Prion Protein Fragment 106–126 via PGC-1α-TFAM-Mediated Mitochondrial Biogenesis
Authors: Zhao Mengyang , Li Jie , Li Zhiping , Yang Dongming , Wang Dongdong , Sun Zhixin , Wen Pei , Gou Fengting , Dai Yuexin , Ji Yilan , Li Wen , Zhao Deming , Yang Lifeng
Published: September 2024

Mitochondrial damage is an early and key marker of neuronal damage in prion diseases. As a process involved in mitochondrial quality control, mitochondrial biogenesis regulates mitochondrial homeostasis in neurons and promotes neuron health by increasing the number of effective mitochondria in the cytoplasm. Sirtuin 1 (SIRT1) is a NAD+-dependent deacetylase that regulates neuronal mitochondrial biogenesis and quality control in neurodegenerative diseases via deacetylation of a variety of substrates. In a cellular model of prion diseases, we found that both SIRT1 protein levels and deacetylase activity decreased, and SIRT1 overexpression and activation significantly ameliorated mitochondrial morphological damage and dysfunction caused by the neurotoxic peptide PrP106–126. Moreover, we found that mitochondrial biogenesis was impaired, and SIRT1 overexpression and activation alleviated PrP106–126-induced impairment of mitochondrial biogenesis in N2a cells. Further studies in PrP106–126-treated N2a cells revealed that SIRT1 regulates mitochondrial biogenesis through the PGC-1α-TFAM pathway. Finally, we showed that resveratrol resolved PrP106–126-induced mitochondrial dysfunction and cell apoptosis by promoting mitochondrial biogenesis through activation of the SIRT1-dependent PGC-1α/TFAM signaling pathway in N2a cells. Taken together, our findings further describe SIRT1 regulation of mitochondrial biogenesis and improve our understanding of mitochondria-related pathogenesis in prion diseases. Our findings support further investigation of SIRT1 as a potential target for therapeutic intervention of prion diseases.
A Hypoxia–Decidual Macrophage Regulatory Axis in Normal Pregnancy and Spontaneous Miscarriage
Authors: Huang Xu , Lin Zhi , Zheng Zi-Meng , Shi Jia-Lu , Lu Ke-Yu , Wang Jia-Rui , Li Ming-Qing , Shao Jun
Published: September 2024

The significance of hypoxia at the maternal–fetal interface is proven to be self-explanatory in the context of pregnancy. During the first trimester, low oxygen conditions play a crucial role in processes such as angiogenesis, trophoblast invasion and differentiation, and immune regulation. Recently, there has been increasing research on decidual macrophages, which contribute to the maintenance of immune tolerance, placental and fetal vascular development, and spiral artery remodeling, to investigate the effects of hypoxia on their biological behaviors. On these grounds, this review describes the dynamic changes in oxygen levels at the maternal–fetal interface throughout gestation, summarizing current knowledge on how the hypoxic environment sustains a successful pregnancy by regulating retention, differentiation and efferocytosis of decidual macrophages. Additionally, we explore the relationship between spontaneous miscarriages and an abnormal hypoxia–macrophage axis, shedding light on the underlying mechanisms. However, further studies are essential to elucidate these pathways in greater detail and to develop targeted interventions that could improve pregnancy outcomes.
Insights into the Pathobiology of GM1 Gangliosidosis from Single-Nucleus Transcriptomic Analysis of CNS Cells in a Mouse Model
Authors: Liu Sichi , Xie Ting , Huang Yonglan
Published: September 2024

GM1 gangliosidosis is a lysosomal storage disorder characterized by the accumulation of GM1 ganglioside, leading to severe neurodegeneration and early mortality. The disease primarily affects the central nervous system, causing progressive neurodegeneration, including widespread neuronal loss and gliosis. To gain a deeper understanding of the neuropathology associated with GM1 gangliosidosis, we employed single-nucleus RNA sequencing to analyze brain tissues from both GM1 gangliosidosis model mice and control mice. No significant changes in cell proportions were detected between the two groups of animals. Differential expression analysis revealed cell type-specific changes in gene expression in neuronal and glial cells. Functional analysis highlighted the neurodegenerative processes, oxidative phosphorylation, and neuroactive ligand–receptor interactions as the significantly affected pathways. The contribution of the impairment of neurotransmitter system disruption and neuronal circuitry disruption was more important than neuroinflammatory responses to GM1 pathology. In 16-week-old GM1 gangliosidosis mice, no microglial or astrocyte activation or increased expression of innate immunity genes was detected. This suggested that nerve degeneration did not induce the inflammatory response but rather promoted glial cell clearance. Our findings provide a crucial foundation for understanding the cellular and molecular mechanisms of GM1 gangliosidosis, potentially guiding future therapeutic strategies.
Insights into Gut Dysbiosis: Inflammatory Diseases, Obesity, and Restoration Approaches
Authors: Acevedo-Román Andy , Pagán-Zayas Natalia , Velázquez-Rivera Liz I. , Torres-Ventura Aryanne C. , Godoy-Vitorino Filipa
Published: September 2024

The gut microbiota is one of the most critical factors in human health. It involves numerous physiological processes impacting host health, mainly via immune system modulation. A balanced microbiome contributes to the gut’s barrier function, preventing the invasion of pathogens and maintaining the integrity of the gut lining. Dysbiosis, or an imbalance in the gut microbiome’s composition and function, disrupts essential processes and contributes to various diseases. This narrative review summarizes key findings related to the gut microbiota in modern multifactorial inflammatory conditions such as ulcerative colitis or Crohn’s disease. It addresses the challenges posed by antibiotic-driven dysbiosis, particularly in the context of C. difficile infections, and the development of novel therapies like fecal microbiota transplantation and biotherapeutic drugs to combat these infections. An emphasis is given to restoration of the healthy gut microbiome through dietary interventions, probiotics, prebiotics, and novel approaches for managing gut-related diseases.
Subgroup Analysis of TLR2, -3, -4 and -8 in Relation to the Severity of Clinical Manifestations of Cervical HPV Infection
Authors: Dushkin Alexander , Afanasiev Maxim , Afanasiev Stanislav , Grishacheva Tatiana , Biryukova Elena , Dushkina Irina , Karaulov Alexander
Published: September 2024

We present the findings of assessing the expression levels of extracellular TLR2 and TLR4 and intracellular TLR3 and TLR8 correlating with the severity of clinical manifestations of HPV infection. A total of 199 women took part in a single-center prospective comparative research study on TLR2, TLR3, TLR4 and TLR8 expression in HPV-related cervical lesions. TLRs’ mRNA expression was analyzed using real-time reverse transcription polymerase chain reaction (RT-PCR). Our results indicate the potential significance of TLR3, TLR4 and TLR8 in responding to HPV infection and its progression to SILs and CC, highlighting the importance of HPV polyinfection in relation to TLR4 and TLR8.
The Impact of Thyroiditis on the Immune Profile in Young Patients with Uncomplicated Type 1 Diabetes
Authors: Neubauer-Geryk Jolanta , Myśliwiec Małgorzata , Zorena Katarzyna , Bieniaszewski Leszek
Published: September 2024

Autoimmune thyroid disease (AIT) is the most frequently linked autoimmune condition to type 1 diabetes (T1D). The analysis of immune profiles could provide valuable insights into the study of these diseases. This knowledge could play a crucial role in understanding the relationship between immune profiles and microcirculation structures and functions. The present study aimed to test the hypothesis that cytokine levels in T1D patients without and those with comorbid Hashimoto’s disease differ significantly. The total study group (total T1D) consisted of 62 diabetic young patients: 43 T1D and 19 T1D + AIT matched for age, age at onset, and duration of diabetes. The control group consisted of 32 healthy young subjects. The levels of cytokines (including TNF-α, IL-35, IL-4, IL-10, IL-18, IL-12, VEGF, and angiogenin) were quantified throughout this investigation. A comparative assessment of the cytokines profiles between the control group and total T1D revealed a statistically significant elevation in the levels of IL-4, TNF-α, IL-18, VEGF, and angiogenin, accompanied by a notable decline in IL-10. However, IL-35 and IL-12 exhibited comparable levels between the two groups. A comparison of cytokine levels between T1D + AIT and T1D groups revealed that only angiogenin levels were statistically significantly higher in T1D + AIT. The results of our study indicated that the alterations in cytokine levels associated with AIT did not correspond to the observed changes in T1D-related outcomes. The sole notable observation was the elevation of angiogenin expression, an angiogenic factor.
Pyrroloquinoline Quinone Alleviates Intestinal Inflammation and Cell Apoptosis via the MKK3/6-P38 Pathway in a Piglet Model
Authors: Huang Caiyun , Yu Xuanci , Du Ziyuan , Zhu Zhihao , Shi Chenyu , Li Ang , Wang Fenglai
Published: September 2024

This study investigates the underlying mechanism through which dietary supplementation of pyrroloquinoline quinone disodium (PQQ) alleviates intestinal inflammation and cell apoptosis in piglets challenged with lipopolysaccharide (LPS). Seventy-two barrows were divided into three groups: control (CTRL), LPS challenged (LPS), and LPS challenged with PQQ supplementation (PQQ + LPS). On d 7, 11, and 14, piglets received intraperitoneal injections of LPS or 0.9% of NaCl (80 μg/kg). After a 4 h interval following the final LPS injection on d 14, blood samples were obtained, and all piglets were euthanized for harvesting jejunal samples. The results showed that dietary supplementation of PQQ improved the damage of intestinal morphology, increased the down-regulated tight junction proteins, and reduced the increase of serum diamine oxidase activity, the intestinal fatty acid binding protein, and TNF-α levels in piglets challenged with LPS (p < 0.05). The proteomics analysis revealed a total of 141 differentially expressed proteins (DEPs), consisting of 64 up-regulated DEPs and 77 down-regulated DEPs in the PQQ + LPS group compared to the LPS group. The KEGG pathway analysis indicated enrichment of the tight junction pathway and the apoptosis pathway (p < 0.05). Compared to the LPS group, the piglets in the PQQ + LPS group had increased levels of Bcl-2 protein, reduced positive apoptosis signals, and a decrease in the abundance of MKK 3/6 and p-p38 proteins (p < 0.05). In conclusion, dietary supplementation of PQQ could alleviate jejunal inflammatory damage and cell apoptosis in piglets challenged with LPS through the MKK3/6-p38 signaling pathway.
Identification and Characterization of Shaker Potassium Channel Gene Family and Response to Salt and Chilling Stress in Rice
Authors: Tian Quanxiang , Yu Tongyuan , Dong Mengyuan , Hu Yue , Chen Xiaoguang , Xue Yuan , Fang Yunxia , Zhang Jian , Zhang Xiaoqin , Xue Dawei
Published: September 2024

Shaker potassium channel proteins are a class of voltage-gated ion channels responsible for K+ uptake and translocation, playing a crucial role in plant growth and salt tolerance. In this study, bioinformatic analysis was performed to identify the members within the Shaker gene family. Moreover, the expression patterns of rice Shaker(OsShaker) K+ channel genes were analyzed in different tissues and salt treatment by RT–qPCR. The results revealed that there were eight OsShaker K+ channel genes distributed on chromosomes 1, 2, 5, 6 and 7 in rice, and their promoters contained a variety of cis-regulatory elements, including hormone-responsive, light-responsive, and stress-responsive elements, etc. Most of the OsShaker K+ channel genes were expressed in all tissues of rice, but at different levels in different tissues. In addition, the expression of OsShaker K+ channel genes differed in the timing, organization and intensity of response to salt and chilling stress. In conclusion, our findings provide a reference for the understanding of OsShaker K+ channel genes, as well as their potential functions in response to salt and chilling stress in rice.
Efficient Solution-Phase Dipeptide Synthesis Using Titanium Tetrachloride and Microwave Heating
Authors: Cavallaro Palmira Alessia , De Santo Marzia , Marinaro Rocco , Belsito Emilia Lucia , Liguori Angelo , Leggio Antonella
Published: September 2024

Microwaves have been successfully employed in the Lewis acid titanium tetrachloride-assisted synthesis of peptide systems. Dipeptide systems with their amino function differently protected with urethane protecting groups have been synthesized in short periods of time and with high yields. The formation of the peptide bond between the two reacting amino acids was achieved in pyridine by using titanium tetrachloride as a condensing agent and heating the reaction mixture with a microwave reactor. The reaction conditions are compatible with amino acids featuring various side chains and different protecting groups on both the amino function and side chains. Additionally, the substrates retain their chiral integrity after reaction.
The 5:2 Diet Affects Markers of Insulin Secretion and Sensitivity in Subjects with and without Type 2 Diabetes—A Non-Randomized Controlled Trial
Authors: Ekberg Neda Rajamand , Hellberg Anton , Sundqvist Michaela Linn , Hirschberg Angelica Lindén , Catrina Sergiu-Bogdan , Brismar Kerstin
Published: September 2024

This non-randomized controlled trial aimed to compare the effect of the 5:2 diet on insulin levels as a primary outcome and markers of insulin secretion (connecting peptide (C-peptide) and insulin-like growth factor binding protein-1 (IGFBP-1)) and sensitivity (Homeostatic Model Assessment for Insulin Resistance (HOMA-IR)), as well as body composition as secondary outcomes in overweight/obese individuals with and without type 2 diabetes (T2D). Ninety-seven participants (62% women), 35 with T2D and 62 BMI- and waist-matched controls without T2D, followed the 5:2 diet (two days per week of fasting) for six months with a 12-month follow-up. At six months, there was no loss to follow-up in the T2D group, whereas four controls discontinued this study. Overall, 82% attended the 12-month follow-up. After the intervention, insulin levels decreased in the control group and glucose decreased in the T2D group, while C-peptide, HOMA-IR, waist circumference, BMI, trunk, and total fat% decreased in both groups. Furthermore, low IGFBP-1, indicating hyperinsulinemia, improved in the T2D group. The changes in fasting glucose and waist measurement were significantly more improved in the T2D group than in the controls. Persistent positive effects were observed at the 12-month follow-up. The 5:2 diet for six months was feasible and efficient to reduce markers of insulin secretion and resistance and therefore holds promise as management of overweight/obesity in subjects with and without T2D.
Short Communication: Novel Di- and Triselenoesters as Effective Therapeutic Agents Inhibiting Multidrug Resistance Proteins in Breast Cancer Cells
Authors: Radomska Dominika , Czarnomysy Robert , Marciniec Krzysztof , Nowakowska Justyna , Domínguez-Álvarez Enrique , Bielawski Krzysztof
Published: September 2024

Breast cancer has the highest incidence rate among all malignancies worldwide. Its high mortality is mainly related to the occurrence of multidrug resistance, which significantly limits therapeutic options. In this regard, there is an urgent need to develop compounds that would overcome this phenomenon. There are few reports in the literature that selenium compounds can modulate the activity of P-glycoprotein (MDR1). Therefore, we performed in silico studies and evaluated the effects of the novel selenoesters EDAG-1 and EDAG-8 on BCRP, MDR1, and MRP1 resistance proteins in MCF-7 and MDA-MB-231 breast cancer cells. The cytometric analysis showed that the tested compounds (especially EDAG-8) are inhibitors of BCRP, MDR1, and MRP1 efflux pumps (more potent than the reference compounds—novobiocin, verapamil, and MK-571). An in silico study correlates with these results, suggesting that the compound with the lowest binding energy to these transporters (EDAG-8) has a more favorable spatial structure affecting its anticancer activity, making it a promising candidate in the development of a novel anticancer agent for future breast cancer therapy.
Safety and Efficacy of Bispecific Antibodies in Adults with Large B-Cell Lymphomas: A Systematic Review of Clinical Trial Data
Authors: Bayly-McCredie Elena , Treisman Maxine , Fiorenza Salvatore
Published: September 2024

Bispecific antibodies (bsAbs) are an emerging therapy in the treatment of large B-cell lymphomas (LBCLs). There is a gap in the research on the safety and efficacy of bsAbs in adults with LBCL, with current research focusing on the wider non-Hodgkin’s lymphoma population. To address this research gap, we conducted a systematic review aiming to evaluate the safety and efficacy outcomes of bsAbs in adults with LBCL. A systematized search was conducted in PubMed, EMBASE, and CENTRAL on 10 April 2024. Interventional clinical trials were eligible for inclusion. Observational studies, reviews, and meta-analyses were excluded. According to the Revised Risk of Bias Assessment Tool for Nonrandomized Studies, the included studies were largely of a high quality for safety outcome reporting, but of mixed quality for efficacy outcome reporting. Due to the heterogeneity of the included studies, the results were discussed as a narrative synthesis. Nineteen early phase studies were evaluated in the final analysis, with a pooled sample size of 1332 patients. Nine bsAbs were investigated across the studies as monotherapy (nine studies) or in combination regimes (10 studies). The rates of cytokine release syndrome were variable, with any grade events ranging from 0 to 72.2%. Infection rates were consistently high across the reporting studies (38–60%). Cytopenias were found to be common, in particular, anemia (4.4–62%), thrombocytopenia (3.3–69%), and neutropenia (4.4–70%). Immune effector cell-associated neurotoxicity syndrome (ICANS) and grade ≥3 adverse events were not commonly reported. Promising efficacy outcomes were reported, with median overall response rates of 95–100% in the front-line and 36–91% in terms of relapsed/refractory disease. The results of this systematic review demonstrate that bsAbs are generally well-tolerated and effective in adults with LBCL. BsAbs appear to have superior tolerability, but inferior efficacy to CAR T-cell therapies in adults with LBCL. Future research on safety and efficacy should focus on evaluating adverse event timing and management, the impact on the patient’s quality of life, the burden on the healthcare system, and overall survival outcomes.
The Immunosuppressive Receptor CD32b Regulation of Macrophage Polarization and Its Implications in Tumor Progression
Authors: Chuang Hong-Jing , Chen Ying-Yin , Chung Yi-Da , Huang Evelyn , Huang Cadence Yoshang , Lung Jrhau , Chen Chung-Yu , Liao Hui-Fen
Published: September 2024

Macrophages, pivotal components of the immune system, orchestrate host defense mechanisms in humans and mammals. Their polarization into classically activated macrophages (CAMs or M1) and alternatively activated macrophages (AAMs or M2) dictates distinct functional roles in immunity and tissue homeostasis. While the negative regulatory role of CD32b within the FC gamma receptor (FCγR) family is recognized across various immune cell types, its influence on macrophage polarization remains elusive. This study aimed to elucidate the regulatory role of CD32b in macrophage polarization and discern the differential expression markers between the M1 and M2 phenotypes following CD32b siRNA transfection. The results revealed a decrease in the CD32b levels in lipopolysaccharide (LPS)-treated M1 and an increase in interleukin-4 (IL-4)-treated M2 macrophages, as observed in macrophage Raw264.7 cells. Furthermore, CD32b siRNA transfection significantly downregulated the M2 markers (IL-10, VEGF, Arg-1, and STAT6), while upregulating the M1 markers (IL-6, NF-κB, NOS2, and STAT1) in the Raw264.7 cells. Similar findings were recapitulated in macrophage-rich adherent cells isolated from mouse spleens. Additionally, the cytopathological analysis of pleural effusions and ascitic fluids from patients with cancer revealed a positive correlation between advanced tumor stages, metastasis, and elevated CD32b levels. In conclusion, this study highlights the regulatory influence of CD32b in suppressing M1 expression and promoting M2 polarization. Moreover, heightened M2 activation and CD32b levels appear to correlate with tumor progression. A targeted CD32b blockade may serve as a novel therapeutic strategy to inhibit M2 macrophage polarization and is promising for anti-tumor intervention.
Gene Therapy for Achromatopsia
Authors: Baxter Megan F. , Borchert Grace A.
Published: September 2024

Achromatopsia is the most common cone dysfunction syndrome, affecting 1 in 30,000 people. It is an autosomal recessive disorder with a heterogeneous genetic background with variants reported in CNGA3, CNGB3, GNAT2, PDE6C, PDE6H, and ATF6. Up to 90% of achromatopsia patients harbour mutations in CNGA3 or CNB3, which encode for the alpha and beta subunits of the cone cyclic nucleotide-gated (CNG) channel in cone-specific phototransduction. The condition presents at birth or early infancy with poor visual acuity, nystagmus, photophobia, and colour vision loss in all axes. Multimodal retinal imaging has provided insightful information to characterise achromatopsia patients based on their genotype. There is no FDA-approved treatment for achromatopsia; however, studies have reported several preclinical gene therapies with anatomical and functional improvements reported in vivo. There are currently five gene therapy clinical trials registered for human patients at the phase I/II stage and for CNGA3 or CNGB3 causing achromatopsia. This review aims to discuss the genetics of achromatopsia, genotypic and phenotypic correlations in multimodal retinal imaging, and the developments and challenges in gene therapy clinical trials.
DNA Methylation and Subgenome Dominance Reveal the Role of Lipid Metabolism in Jinhu Grouper Heterosis
Authors: Liu Yang , Wang Linna , Li Zhentong , Li Linlin , Chen Shuai , Duan Pengfei , Wang Xinyi , Qiu Yishu , Ding Xiaoyu , Su Jinzhi , Deng Yuan , Tian Yongsheng
Published: September 2024

Heterosis of growth traits in economic fish has benefited the production of aquaculture for many years, yet its genetic and molecular basis has remained obscure. Nowadays, a new germplasm of hybrid Jinhu grouper (Epinephelus fuscoguttatus ♀ × E. tukula ♂), abbreviated as EFT, exhibiting paternal-biased growth heterosis, has provided an excellent model for investigating the potential regulatory mechanisms of heterosis. We integrated transcriptome and methylome to unravel the changes of gene expression, epigenetic modification, and subgenome dominance in EFT compared with maternal E. fuscoguttatus. Integration analyses showed that the heterotic hybrids showed lower genomic DNA methylation levels than the purebred parent, and the up-regulated genes were mostly DNA hypomethylation. Furthermore, allele-specific expression (ASE) detected paternal subgenome dominance-regulated paternal-biased heterosis, and paternal bias differentially expressed genes (DEGs) were wholly up-regulated in the muscle. Multi-omics results highlighted the role of lipid metabolism, particularly “Fatty acid synthesis”, “EPA biosynthesis”, and “Signaling lipids”, in EFT heterosis formation. Coherently, our studies have proved that the eicosapentaenoic acid (EPA) of EFT was greater than that of maternal E. fuscoguttatus (8.46% vs. 7.46%). Finally, we constructed a potential regulatory network for control of the heterosis formation in EFT. Among them, fasn, pparg, dgat1, igf1, pomca, fgf8a, and fgfr4 were identified as key genes. Our results provide new and valuable clues for understanding paternal-biased growth heterosis in EFT, taking a significant step towards the molecular basis of heterosis.
Metabolic Engineering of Escherichia coli for Production of a Bioactive Metabolite of Bilirubin
Authors: Chen Huaxin , Xiong Peng , Guo Ning , Liu Zhe
Published: September 2024

Bilirubin (BR) is an important ingredient of a valuable Chinese medicine, Calculus bovis. Over recent decades, increasing evidence has confirmed that BR offers health benefits in cardiovascular health, stroke, diabetes, and metabolic syndrome. However, BR is mainly produced by extraction from pig bile. In this study, we assembled an efficient pathway for BR production by metabolic engineering of Escherichia coli. First, heme oxygenase (HO1) and biliverdin reductase were co-expressed in E. coli. HPLC and LC–MS confirmed the accumulation of BR in the recombinant E. coli cells. To improve BR production, the catalytic abilities of HO1 from different species were investigated. In addition, the outermembrane-bound heme receptor (ChuA) and the enzymes involved in heme biosynthesis were overexpressed among which ChuA, 5-aminolevulinic acid dehydratase (HemB), protoporphyrin oxidase (HemG), and ferrochelatase (HemH) were found to enhance BR accumulation in E. coli. In addition, expression of ferredoxin (Fd) was shown to contribute to efficient conversion of heme to BR in E. coli. To increase supply of NADPH, isocitrate dehydrogenase (IDH), NAD kinase (nadK), NADP-specific glutamate dehydrogenase (gdhA), and glucose-6-phosphate 1-dehydrogenase (ZWF) were overexpressed and were found to enhance BR accumulation when these proteins were expressed with a low-copy plasmid pACYCduet-1. Modular optimization of the committed genes led to a titer of 17.2 mg/L in strain M1BHG. Finally, fed-batch fermentation was performed for the strains M1BHG and M1, resulting in accumulation of 75.5 mg/L and 25.8 mg/L of BR, respectively. This is the first report on biosynthesis of BR through metabolic engineering in a heterologous host.
Role of CD44-Positive Extracellular Vesicles Derived from Highly Metastatic Mouse Mammary Carcinoma Cells in Pre-Metastatic Niche Formation
Authors: Ikari Ayana , Ito Yuko , Taniguchi Kohei , Shibata Masa-Aki , Kimura Kosei , Iwamoto Mitsuhiko , Lee Sang-Woong
Published: September 2024

Malignant breast cancers pose a notable challenge when it comes to treatment options. Recently, research has implicated extracellular vesicles (EVs) secreted by cancer cells in the formation of a pre-metastatic niche. Small clumps of CD44-positive breast cancer cells are efficiently transferred through CD44–CD44 protein homophilic interaction. This study aims to examine the function of CD44-positive EVs in pre-metastatic niche formation in vitro and to suggest a more efficacious EV formulation. We used mouse mammary carcinoma cells, BJMC3879 Luc2 (Luc2 cells) as the source of CD44-positive EVs and mouse endothelial cells (UV2 cells) as the recipient cells in the niche. Luc2 cells exhibited an enhanced secretion of EVs expressing CD44 and endothelial growth factors (VEGF-A, -C) under 20% O2 (representative of the early stage of tumorigenesis) compared to its expression under 1% O2 (in solid tumor), indicating that pre-metastatic niche formation occurs in the early stage. Furthermore, UV2 endothelial cells expressing CD44 demonstrated a high level of engulfment of EVs that had been supplemented with hyaluronan, and the proliferation of UV2 cells occurred following the engulfment of EVs. These results suggest that anti-VEGF-A and -C encapsulated, CD44-expressing, and hyaluronan-coated EVs are more effective for tumor metastasis.
Identification of SNPs and Candidate Genes Associated with Monocyte/Lymphocyte Ratio and Neutrophil/Lymphocyte Ratio in Duroc × Erhualian F2 Population
Authors: Qiao Jiakun , Xu Minghang , Xu Fangjun , Che Zhaoxuan , Han Pingping , Dai Xiangyu , Miao Na , Zhu Mengjin
Published: September 2024

Understanding the pig immune function is crucial for disease-resistant breeding and potentially for human health research due to shared immune system features. Immune cell ratios, like monocyte/lymphocyte ratio (MLR) and neutrophil/lymphocyte ratio (NLR), offer a more comprehensive view of immune status compared to individual cell counts. However, research on pig immune cell ratios remains limited. This study investigated MLR and NLR in a Duroc × Erhualian F2 resource population. Heritability analysis revealed high values (0.649 and 0.688 for MLR and NLR, respectively), suggesting a strong genetic component. Furthermore, we employed an ensemble-like GWAS (E-GWAS) strategy and functional annotation analysis to identify 11 MLR-associated and 6 NLR-associated candidate genes. These genes were significantly enriched in immune-related biological processes. These findings provide novel genetic markers and candidate genes associated with porcine immunity, thereby providing valuable insights for addressing biosecurity and animal welfare concerns in the pig industry.
The Role of the Endometrium in Implantation: A Modern View
Authors: Deryabin Pavel I. , Borodkina Aleksandra V.
Published: September 2024

According to the current data, the endometrium acts as a “sensor” of embryo quality, which promotes the implantation of euploid embryos and prevents the implantation and/or subsequent development of genetically abnormal embryos. The present review addresses the nature of the “sensory function” of the endometrium and highlights the necessity for assessing its functional status. The first section examines the evolutionary origin of the “sensory” ability of the endometrium as a consequence of spontaneous decidualization that occurred in placental animals. The second section details the mechanisms for implementing this function at the cellular level. In particular, the recent findings of the appearance of different cell subpopulations during decidualization are described, and their role in implantation is discussed. The pathological consequences of an imbalance among these subpopulations are also discussed. Finally, the third section summarizes information on currently available clinical tools to assess endometrial functional status. The advantages and disadvantages of the approaches are emphasized, and possible options for developing more advanced technologies for assessing the “sensory” function of the endometrium are proposed.
Key Disease-Related Genes and Immune Cell Infiltration Landscape in Inflammatory Bowel Disease: A Bioinformatics Investigation
Authors: Alghamdi Kawthar S. , Kassar Rahaf H. , Farrash Wesam F. , Obaid Ahmad A. , Idris Shakir , Siddig Alaa , Shakoori Afnan M. , Alshehre Sallwa M. , Minshawi Faisal , Mujalli Abdulrahman
Published: September 2024

Inflammatory Bowel Diseases (IBD), which encompass ulcerative colitis (UC) and Crohn’s disease (CD), are characterized by chronic inflammation and tissue damage of the gastrointestinal tract. This study aimed to uncover novel disease-gene signatures, dysregulated pathways, and the immune cell infiltration landscape of inflamed tissues. Eight publicly available transcriptomic datasets, including inflamed and non-inflamed tissues from CD and UC patients were analyzed. Common differentially expressed genes (DEGs) were identified through meta-analysis, revealing 180 DEGs. DEGs were implicated in leukocyte transendothelial migration, PI3K-Akt, chemokine, NOD-like receptors, TNF signaling pathways, and pathways in cancer. Protein–protein interaction network and cluster analysis identified 14 central IBD players, which were validated using eight external datasets. Disease module construction using the NeDRex platform identified nine out of 14 disease-associated genes (CYBB, RAC2, GNAI2, ITGA4, CYBA, NCF4, CPT1A, NCF2, and PCK1). Immune infiltration profile assessment revealed a significantly higher degree of infiltration of neutrophils, activated dendritic cells, plasma cells, mast cells (resting/activated), B cells (memory/naïve), regulatory T cells, and M0 and M1 macrophages in inflamed IBD tissue. Collectively, this study identified the immune infiltration profile and nine disease-associated genes as potential modulators of IBD pathogenesis, offering insights into disease molecular mechanisms, and highlighting potential disease modulators and immune cell dynamics.
Identification of SYNJ1 in a Complex Case of Juvenile Parkinsonism Using a Multiomics Approach
Authors: Leno-Durán Ester , Arrabal Luisa , Roldán Susana , Medina Inmaculada , Alcántara-Domínguez Clara , García-Cabrera Victor , Saiz Jorge , Barbas Coral , Sánchez Maria José , Entrala-Bernal Carmen , Fernández-Rosado Francisco , Lorente Jose Antonio , Gutierrez-Ríos Purificacion , Martínez-Gonzalez Luis Javier
Published: September 2024

This study aimed to elucidate the genetic causes underlying the juvenile parkinsonism (JP) diagnosed in a girl with several family members diagnosed with spinocerebellar ataxia type 2 (SCA2). To achieve this, whole-exome sequencing, analysis of CAG repeats, RNA sequencing analysis on fibroblasts, and metabolite identification were performed. As a result, a homozygous missense mutation SNP T>C (rs2254562) in synaptojamin 1 (SYNJ1), which has been implicated in the regulation of membrane trafficking in the synaptic vesicles, was identified. Additionally, we observed overexpression of L1 cell adhesion molecule (L1CAM), Cdc37, GPX1, and GPX4 and lower expression of ceruloplasmin in the patient compared to the control. We also found changes in sphingolipid, inositol, and inositol phosphate metabolism. These findings help to clarify the mechanisms of JP and suggest that the etiology of JP in the patient may be multifactorial. This is the first report of the rs2254562 mutation in the SYNJ gene identified in a JP patient with seizures and cognitive impairment.
Analysis of the Mechanism of Wood Vinegar and Butyrolactone Promoting Rapeseed Growth and Improving Low-Temperature Stress Resistance Based on Transcriptome and Metabolomics
Authors: Zhu Kunmiao , Liu Jun , Lyu Ang , Luo Tao , Chen Xin , Peng Lijun , Hu Liyong
Published: September 2024

Rapeseed is an important oil crop in the world. Wood vinegar could increase the yield and abiotic resistance of rapeseed. However, little is known about the underlying mechanisms of wood vinegar or its valid chemical components on rapeseed. In the present study, wood vinegar and butyrolactone (γ-Butyrolactone, one of the main components of wood vinegar) were applied to rapeseed at the seedling stage, and the molecular mechanisms of wood vinegar that affect rapeseed were studied by combining transcriptome and metabolomic analyses. The results show that applying wood vinegar and butyrolactone increases the biomass of rapeseed by increasing the leaf area and the number of pods per plant, and enhances the tolerance of rapeseed under low temperature by reducing membrane lipid oxidation and improving the content of chlorophyll, proline, soluble sugar, and antioxidant enzymes. Compared to the control, 681 and 700 differentially expressed genes were in the transcriptional group treated with wood vinegar and butyrolactone, respectively, and 76 and 90 differentially expressed metabolites were in the metabolic group. The combination of transcriptome and metabolomic analyses revealed the key gene-metabolic networks related to various pathways. Our research shows that after wood vinegar and butyrolactone treatment, the amino acid biosynthesis pathway of rapeseed may be involved in mediating the increase in rapeseed biomass, the proline metabolism pathway of wood vinegar treatment may be involved in mediating rapeseed’s resistance to low-temperature stress, and the sphingolipid metabolism pathway of butyrolactone treatment may be involved in mediating rapeseed’s resistance to low-temperature stress. It is suggested that the use of wood vinegar or butyrolactone are new approaches to increasing rapeseed yield and low-temperature resistance.
What Is Your Favorite Gender, MLM? Gender Bias Evaluation in Multilingual Masked Language Models
Authors: Yu Jeongrok , Kim Seong Ug , Choi Jacob , Choi Jinho D.
Published: September 2024

Bias is a disproportionate prejudice in favor of one side against another. Due to the success of transformer-based masked language models (MLMs) and their impact on many NLP tasks, a systematic evaluation of bias in these models is now needed more than ever. While many studies have evaluated gender bias in English MLMs, only a few have explored gender bias in other languages. This paper proposes a multilingual approach to estimating gender bias in MLMs from five languages: Chinese, English, German, Portuguese, and Spanish. Unlike previous work, our approach does not depend on parallel corpora coupled with English to detect gender bias in other languages using multilingual lexicons. Moreover, a novel model-based method is presented to generate sentence pairs for a more robust analysis of gender bias. For each language, lexicon-based and model-based methods are applied to create two datasets, which are used to evaluate gender bias in an MLM specifically trained for that language using one existing and three new scoring metrics. Our results show that the previous approach is data-sensitive and unstable, suggesting that gender bias should be assessed on a large dataset using multiple evaluation metrics for best practice.
Assessing Heterogeneity Among Cyclists Towards Importance of Bicycle Infrastructural Elements in Urban Areas
Authors: Ahmed Tufail , Pirdavani Ali , Wets Geert , Janssens Davy
Published: September 2024

Promoting bicycling and making it attractive requires appropriate infrastructure. Sociodemographic characteristics, frequency and experiences of bike use, and purpose of bicycle trips can affect preferences towards bicycle infrastructure facilities in urban areas. Hence, this study aims to explore the heterogeneity in the perceived importance of bicycle infrastructure facility attributes in various cyclist groups based on gender, age, weekly biking frequency, daily cycling distance, cycling experience, and bicycle trip purpose. Data were collected from bicycle users through a questionnaire disseminated via social media platforms and QR code brochures distributed in Hasselt, Belgium. A 5-point Likert-type ordinal scale was used to collect data on the perceived importance of bicycle infrastructure facility indicators. The Technique for Order Preference by Similarity to Ideal Solution (TOPSIS) was used to rank the indicators. At the same time, Mann–Whitney U and Kruskal–Wallis tests were utilized to verify the heterogeneity among the groups. The findings reveal that bicycle infrastructure, i.e., bicycle lanes or paths, is the most critical variable, while the slope was considered the least important. No heterogeneity was found regarding the importance of bicycle infrastructure indicators based on gender. However, heterogeneity was observed based on age, daily bicycle use, cycling experience, weekly bicycle use, and bicycle trip purpose. The findings of this research help urban and transport planners develop improvement strategies for the city’s existing bicycling facilities and prioritize future developments by considering various cyclist groups’ preferences.
Dynamics of Bactrocera dorsalis Resistance to Seven Insecticides in South China
Authors: Li Xinlian , Li Peizheng , Li Doudou , Cai Xinyan , Gu Shiwei , Zeng Ling , Cheng Daifeng , Lu Yongyue
Published: September 2024

Bactrocera dorsalis is a highly invasive and destructive pest distributed worldwide. Chemical insecticides remain the primary measure for their control; however, this species has already developed resistance to several insecticides. In recent years, there have been several reports of monitoring B. dorsalis resistance in China, but continuous monitoring results are lacking and do not even span a decade. In this study, we monitored the dynamics of resistance to seven insecticides among 11 geographically distinct Chinese populations of B. dorsalis (2010–2013; follow-up in 2023). The 11 populations were found to adapt rapidly to antibiotic insecticides (spinosad, emamectin benzoate, and avermectin), reaching high levels of insecticide resistance in several areas. Overall, a decreasing trend in resistance to organophosphorus insecticides (chlorpyrifos and trichlorfon) was observed, whereas pyrethroid (beta-cypermethrin and cyhalothrin) resistance trends were observed to both increase and decrease. The monitoring of field resistance among different B. dorsalis populations over the duration of this study is important for improving the efficiency and sustainability of agricultural pest management, and the results provide a scientific basis for the development of more effective resistance management strategies.
Novel Computed Tomography Angiography Parameter Is Associated with Low Cardiac Index in Patients with Chronic Thromboembolic Pulmonary Hypertension: A Retrospective Analysis
Authors: Oliveros Estefania , Ibrahim Michel , Romero Carlos Manuel , Navo Paul , Otero Valdes Patricia , Brailovsky Yevgeniy , Darki Amir , Bashir Riyaz , Vaidya Anjali , Forfia Paul , Dass Chandra
Published: September 2024

Chronic thromboembolic pulmonary hypertension (CTEPH) is a complication of incomplete resolution of acute pulmonary embolism. We hypothesize changes in CT Hounsfield Unit gradient (HU-Δ) created by the dispersion of IV contrast through the downstream blood pool correlate with cardiac index (CI). We sought to compare HU-Δ with invasively obtained CI. Methods: We completed a retrospective analysis of CTEPH patients in which individuals with low CI (<2.2-L/min/m2) were identified. Both absolute and fractional HU-Δ were derived from pulmonary CTA by subtracting the HU value of the left atrium (LA) and left ventricle (LV) from the main pulmonary artery (MPA) (absolute) and expressing them as a percentage of MPA-HU (fractional) on static axial images. These were compared between low and normal CI. Results: Of the 237 patients, 50.2% were female, 53.2% were White, 36.7% were Black. Hemodynamics were mean pulmonary artery (PA) pressure = 45.4 ± 11.2-mmHg, pulmonary vascular resistance = 9.2 ± 4.4-WU, CI = 2.05 ± 0.48-L/min/m2. There was a higher mean MPA-HU = 391.1 ± 113.6 than LA-HU = 251.6 ± 81. In patients with low CI, the HU-Δ was higher, HU-ΔMPA-LA was 148.9 ± 78.4 vs. 124.5 ± 77.2 (p = 0.02), and HU-ΔMPA-LV was 170.7 ± 87 vs. 140 ± 82 (p = 0.009). A HU-ΔMPA-LA = 118 had a sensitivity of 75.6% and specificity of 77% to detect low CI, AUC 0.61, p = 0.003. A HU-ΔPA-LV = 156 had a sensitivity of 77% and specificity of 53% to detect low CI, AUC = 0.62, p = 0.001. A fractional reduction HU-ΔMPA-LA of 35% had a sensitivity and specificity of 79% and 53%, respectively, to detect low CI (AUC 0.65, p < 0.001). A fractional reduction of the HU-ΔMPA-LV of 40% had a sensitivity and specificity of 80% and 55%, respectively, to detect low CI (AUC 0.65, p < 0.001). HU Δ were highly reproducible (Kappa = 0.9, p < 0.001, 95% CI 0.86–0.95). Conclusions: High HU Δ between MPA-LA and MPA-LV were associated with low CI in patients with CTEPH.
The Effect of Upright Posture on Left Atrial Strain in Competitive Athletes
Authors: Kandels Joscha , Stöbe Stephan , Marshall Robert Percy , Hagendorff Andreas , Metze Michael
Published: September 2024

Background: Left atrial strain (LAS) assessment by speckle tracking echocardiography (STE) has been shown to be a remarkable means of quantifying LA function as an early marker of LV pathology. As exercise testing is also performed on a treadmill, the aim of this study was to investigate the effect of upright posture on LAS in healthy athletes. Methods: Fifty male athletes (mean age 25.7 ± 7.3 years) underwent transthoracic echocardiography (TTE) in the upright and left lateral positions. In addition to the conventional echocardiographic parameters, in all athletes, LA conduction strain (LAScd), contraction strain (LASct), reservoir strain (LASr), and maximum LA volume (LAVmax) were assessed by STE in both positions. Results: Comparing upright posture and the left lateral position, LAScd (−14.0 ± 5.9% vs. −27.4 ± 7.1%; p < 0.001), LASct (−4.6 ± 3.5% vs. −11.3 ± 4.1%; p < 0.001), LASr (18.7 ± 7.6% vs. 38.7 ± 8.0%; p < 0.001), and LAVmax (24.4 ± 8.8% vs. 50.0 ± 14.2%) differed significantly. Conclusions: Upright posture has a significant effect on LA deformation, with decreased LAScd, LASct, and LASr. The results of this study contribute to the understanding of athletes’ hearts and must be considered when performing echocardiography in healthy athletes on a treadmill.