bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of Soil Fauna on the Home-Field Advantage of Litter Total Phenol and Condensed Tannin Decomposition
Authors: Lei Lingyuan , Zeng Jing , Liu Quanwei , Luo Lijuan , Ma Zhiliang , Chen Yamei , Liu Yang
Published: February 2024

Soil fauna play a vital role in contributing to the home-field advantage (HFA: litter decomposes faster in its natural habitat than elsewhere) during litter decomposition. Whether the presence of soil fauna affects the HFA of the decomposition of total phenols and condensed tannins, which are important components of litter, has rarely been investigated. In this study, litterbags with different mesh sizes were transplanted reciprocally, 0.04 mm (basically excluding soil fauna) and 3 mm (basically allowing all soil fauna to enter), in Lindera megaphylla and Cryptomeria fortunei forests. The results illustrated that the loss rates of total phenols and condensed tannins reached 64.07% to 84.49% and 69.67% to 88.37%, respectively, after 2 months of decomposition. Moreover, soil fauna positively contributed to the decomposition of condensed tannins in high-quality litter. After 2 months of decomposition, a significantly positive HFA (HFA index: 10.32) was found for total phenol decomposition in the coarse mesh, while a significantly negative HFA (HFA index: −1.81) was observed for condensed tannin decomposition in the fine mesh after 10 months of decomposition. Polyphenol oxidase (PPO) and peroxidase (POD) activities were significantly influenced by litter types. The loss rates of total phenols and condensed tannins were significantly negatively correlated with the initial N content, P content, N/P ratio, and POD activity and were positively related to the initial C content, total phenol content, condensed tannin content, C/P ratio, and C/N ratio. Only the loss of condensed tannins was negatively correlated with PPO activity (after 2 months’ decomposition). However, none of these correlations were observed after 10 months of decomposition. Our study illustrated that (1) soil fauna contributed to the decomposition of total phenols and condensed tannins but were influenced by litter type for condensed tannins. (2) The soil fauna had inconsistent effects on the HFA of total phenols and condensed tannins, possibly due to the combined regulatory effects of environmental context, litter quality, and rapid decomposition rates. In sum, the results indicated that soil fauna played an important role in the decomposition of condensed tannins and total phenols in litter, and additional studies on the effects of soil faunal abundance and class on HFA of condensed tannins and total phenols are needed.
Fine Classification of Urban Tree Species Based on UAV-Based RGB Imagery and LiDAR Data
Authors: Wu Jingru , Man Qixia , Yang Xinming , Dong Pinliang , Ma Xiaotong , Liu Chunhui , Han Changyin
Published: February 2024

Rapid and accurate classification of urban tree species is crucial for the protection and management of urban ecology. However, tree species classification remains a great challenge because of the high spatial heterogeneity and biodiversity. Addressing this challenge, in this study, unmanned aerial vehicle (UAV)-based high-resolution RGB imagery and LiDAR data were utilized to extract seven types of features, including RGB spectral features, texture features, vegetation indexes, HSV spectral features, HSV texture features, height feature, and intensity feature. Seven experiments involving different feature combinations were conducted to classify 10 dominant tree species in urban areas with a Random Forest classifier. Additionally, Plurality Filling was applied to further enhance the accuracy of the results as a post-processing method. The aim was to explore the potential of UAV-based RGB imagery and LiDAR data for tree species classification in urban areas, as well as evaluate the effectiveness of the post-processing method. The results indicated that, compared to using RGB imagery alone, the integrated LiDAR and RGB data could improve the overall accuracy and the Kappa coefficient by 18.49% and 0.22, respectively. Notably, among the features based on RGB, the HSV and its texture features contribute most to the improvement of accuracy. The overall accuracy and Kappa coefficient of the optimal feature combination could achieve 73.74% and 0.70 with the Random Forest classifier, respectively. Additionally, the Plurality Filling method could increase the overall accuracy by 11.76%, which could reach 85.5%. The results of this study confirm the effectiveness of RGB imagery and LiDAR data for urban tree species classification. Consequently, these results could provide a valuable reference for the precise classification of tree species using UAV remote sensing data in urban areas.
Contrasting Altitudinal Patterns and Composition of Soil Bacterial Communities along Stand Types in Larix principis-rupprechtii Forests in Northern China
Authors: Niu Yajie , Li Xin , Wang Chuanxu , Han Youzhi , Wang Zhuo , Yang Jing
Published: February 2024

Bacterial communities inhabiting the soil of mountain ecosystems perform critical ecological functions. Although several studies have reported the altitudinal distribution patterns of bacterial communities in warm-temperate mountain forests, our understanding of typical zonal vegetation dominated by Larix principis-rupprechtii Mayr (abbreviated as larch hereafter) and the understory elevation distribution patterns of soil bacterial communities is still limited. In this study, the Illumina NovaSeq 6000 sequencing platform was used to investigate the changes of surface and subsurface soil bacterial communities along an altitudinal gradient (from 1720 m to 2250 m) in larch forests in northern China. Altitude significantly affected the relative abundance of Proteobacteria, Actinobacteria, Acidobacteria, and Chloroflexi (bacterial dominant phylum) and Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria (bacterial dominant classes). The diversity of bacterial communities showed a concomitant increase with altitude. The variations in available nitrogen and soil temperature content at different altitudes were the main factors explaining the bacterial community structures in pure stands and mixed stands, respectively. Altitude and the contents of soil organic carbon and soil organic matter were the main factors explaining the dominant phylum (taxonomy). Our results suggest that stand type has a greater effect on the structure and composition of soil bacterial communities than elevation and soil depth, and bacterial communities show divergent patterns along the altitudes, stand types, and soil profiles.
Stability and Effects of Protected Palmitic Acid on In Vitro Rumen Degradability and Fermentation in Lactating Goats
Authors: Álvarez-Torres Jenny Nathalia , Ramírez-Bribiesca Jacinto Efrén , Bautista-Martínez Yuridia , Crosby-Galván María Magdalena , Granados-Rivera Lorenzo Danilo , Ramírez-Mella Mónica , Ruiz-González Alexis
Published: February 2024

Few studies have evaluated the impact of a lipid-rich diet with palmitic acid (PA) in ruminal fermentation. The objective was to evaluate the in vitro bath culture of the protected PA on the ruminal fermentative variables. Four diets were used: (a) without protected PA (nPA) and (b) inclusion of protected PA at three levels: PA3 = 3%, PA6 = 6%, and PA9 = 9% dry matter (DM). The maximum gas production occurred without including protected PA and the low gas production given with the inclusion of protected PA9 (p ≤ 0.05). Meanwhile, the inclusion with 3 and 6% of protected PA showed a higher level of gas production kinetics than the other treatments (p ≤ 0.05). DM and organic matter degradation after 72 h of incubation linearly decreased (p ≤ 0.05) with a high level of protected PA. The level of C16:0 in the protected AP increased with the higher level of supplemented AP (p ≤ 0.05). The best efficiency in propionic acid, decrease in methane, and increase in biohydrogenation (79%) occurred with the inclusion of protected PA3 (p ≤ 0.05). In conclusion, supplements with protected PA at 3 and 6% increased PA availability. The results indicate good benefits of protected PA on fermentative variables, and these doses seem ideal for future research in lactating goats.
Effect of Different Salt Additions on the Flavor Profile of Fermented Ciba Pepper
Authors: Xiong Yiling , Zhu Chenglin , Wu Baozhu , Wang Tianyang , Yang Lian , Guan Ju , Yi Yuwen , Deng Jing , Wu Huachang
Published: February 2024

Salt is a key ingredient that can both enhance the taste and extend the shelf life of fermented vegetables. However, it is important to note that excessive salt levels can have adverse effects on consumer health. This study aimed to investigate the impact of various salt additions (2%, 4%, 6%, 8%, and 10% wt/wt) on the flavor profile of fermented ciba pepper, a traditional Chinese fermented chili sauce, using gas chromatography–ion mobility spectrometry (GC-IMS) in combination with an electronic nose (E-nose). Fermented ciba pepper samples were prepared with different salt additions: 2% (LJA), 4% (LJB), 6% (LJC), 8% (LJD), and 10% (LJE) (wt/wt). The physicochemical and sensory properties of the fermented ciba pepper samples were evaluated. Sensory evaluation indicated that LJC and LJD received higher scores compared to the other groups. The total acid and amino acid nitrogen contents displayed contrasting trends with the salt additions (p < 0.05). The E-nose analysis successfully differentiated the flavor profiles of the ciba pepper samples fermented with varying salt additions. Additionally, the GC-IMS analysis identified a total of 72 volatile compounds, including 14 alcohols, 21 esters, nine aldehydes, four acids, eight ketones, three terpenes, and eight other substances. Notably, the ciba pepper samples with lower salt additions exhibited higher levels of alcohols, aldehydes, and esters. In conclusion, the addition of salt during the fermentation process significantly influenced the formation of flavor compounds in ciba pepper. This study provides valuable insights into ciba pepper fermentation with different salt additions and offers prospects for the development of low-salt fermented ciba pepper products.
The Potential Use of Pseudomonas stutzeri as a Biocatalyst for the Removal of Heavy Metals and the Generation of Bioelectricity
Authors: Segundo Rojas-Flores , De La Cruz-Noriega Magaly , Cabanillas-Chirinos Luis , Otiniano Nélida , Soto-Deza Nancy , Rojas-Villacorta Walter , De La Cruz-Cerquin Mayra
Published: February 2024

Currently, industry in all its forms is vital for the human population because it provides the services and goods necessary to live. However, this process also pollutes soils and rivers. This research provides an environmentally friendly solution for the generation of electrical energy and the bioremediation of heavy metals such as arsenic, iron, and copper present in river waters used to irrigate farmers’ crops. This research used single-chamber microbial fuel cells with activated carbon and zinc electrodes as anodes and cathodes, respectively, and farmers’ irrigation water contaminated with mining waste as substrate. Pseudomonas stutzeri was used as a biocatalyst due to its ability to proliferate at temperatures between 4 and 44 °C—at which the waters that feed irrigated rivers pass on their way to the sea—managing to generate peaks of electric current and voltage of 4.35 mA and 0.91 V on the sixth day, which operated with an electrical conductivity of 222 mS/cm and a pH of 6.74. Likewise, the parameters of nitrogen, total organic carbon, carbon lost on the ignition, dissolved organic carbon, and chemical oxygen demand were reduced by 51.19%, 79.92%, 64.95%, 79.89%, 79.93%, and 86.46%. At the same time, iron, copper, and arsenic values decreased by 84.625, 14.533, and 90.831%, respectively. The internal resistance values shown were 26.355 ± 4.528 Ω with a power density of 422.054 mW/cm2 with a current density of 5.766 A/cm2. This research gives society, governments, and private companies an economical and easily scalable prototype capable of simultaneously generating electrical energy and removing heavy metals.
Synergistic Effects of Essential Oil Blends and Fumaric Acid on Ruminal Fermentation, Volatile Fatty Acid Production and Greenhouse Gas Emissions Using the Rumen Simulation Technique (RUSITEC)
Authors: Alabi Joel O. , Dele Peter A. , Okedoyin Deborah O. , Wuaku Michael , Anotaenwere Chika C. , Adelusi Oludotun O. , Gray DeAndrea , Ike Kelechi A. , Oderinwale Olatunde A. , Subedi Kiran , Anele Uchenna Y.
Published: February 2024

This study investigated the combined impact of essential oil blends (EOBs) and fumaric acid (FA) on ruminal fermentation in dairy cows using the rumen simulation technique (RUSITEC) system. Three rumen-cannulated, non-lactating Holstein Friesian cows served as inoculum donors. The substrate, a total mixed ration (TMR), comprised corn silage, alfalfa hay, and a concentrate mix in a 3:1:1 ratio. The four treatments evaluated were Control (TMR without additives), EFA1 (TMR + EOB1 + FA), EFA2 (TMR + EOB2 + FA), and EFA3 (TMR + EOB3 + FA). Sixteen fermentation chambers were randomly assigned to the treatments, each with four replicates, following a completely randomized design during a 9-day experimental period. EOBs and FA were added at 10 µL/g feed and 3% of TMR, respectively. After a 4-day adaptation, samples were collected for 5 days. Results revealed that EFA1 significantly reduced (p = 0.0351) CH4 emissions by 60.2% without negatively impacting dry matter disappearance, fiber fraction digestibility, pH, or gas volume. All EFAs increased (p < 0.001) the propionate molar proportion and decreased (p < 0.001) the acetate-to-propionate ratio. EFA2 decreased (p < 0.05) the acetate proportion by 3.3% compared to the control. In conclusion, EFA1 is recommended as an effective nutritional intervention to mitigate CH4 emissions and optimize ruminal fermentation in dairy cows.
Reasoning on Pore Terminology in 3D Bioprinting
Authors: Trifonov Alexander , Shehzad Ahmer , Mukasheva Fariza , Moazzam Muhammad , Akilbekova Dana
Published: February 2024

Terminology is pivotal for facilitating clear communication and minimizing ambiguity, especially in specialized fields such as chemistry. In materials science, a subset of chemistry, the term “pore” is traditionally linked to the International Union of Pure and Applied Chemistry (IUPAC) nomenclature, which categorizes pores into “micro”, “meso”, and “macro” based on size. However, applying this terminology in closely-related areas, such as 3D bioprinting, often leads to confusion owing to the lack of consensus on specific definitions and classifications tailored to each field. This review article critically examines the current use of pore terminology in the context of 3D bioprinting, highlighting the need for reassessment to avoid potential misunderstandings. We propose an alternative classification that aligns more closely with the specific requirements of bioprinting, suggesting a tentative size-based division of interconnected pores into ‘parvo’-(d < 25 µm), ‘medio’-(25 < d < 100 µm), and ‘magno’-(d > 100 µm) pores, relying on the current understanding of the pore size role in tissue formation. The introduction of field-specific terminology for pore sizes in 3D bioprinting is essential to enhance the clarity and precision of research communication. This represents a step toward a more cohesive and specialized lexicon that aligns with the unique aspects of bioprinting and tissue engineering.
Family in Medieval Society: A Bioarchaeological Perspective
Authors: Gomes Cláudia , Curto Ana
Published: February 2024

One of the periods with the greatest social, cultural, and religious changes was, without a doubt, the European medieval period. The concept of “Family” was one of the fields that gradually evolved, from individuals who shared the same biological lineage, to members of the same “House”. One of the ways to study the concept of “Family” in ancient periods is through a bioarchaeological perspective, where both anthropology and genetics have proven to be essential disciplines for studying “Families”. Through burial rituals, observing whether the graves were single or multiple, as is carried out in the study of human remains, we discuss the profound contribution of anthropology to the “Family” investigation, through mobility studies, the investigation of biological sex, observing certain congenital anomalies or, even, the study of certain ancient infectious diseases. Concerning genetics, the study of bones or teeth allows us to determine whether individuals were from the same close family or if they belonged to the same lineage through the maternal and paternal sides, being one of the only scientific ways of proposing social relationships between individuals, such as that created through adoption.
De Novo Genome Assembly of the Whitespot Parrotfish (Scarus forsteni): A Valuable Scaridae Genomic Resource
Authors: Liang Yu , Xian Lin , Pan Jinmin , Zhu Kecheng , Guo Huayang , Liu Baosuo , Zhang Nan , Ou-Yang Yan , Zhang Qin , Zhang Dianchang
Published: February 2024

Scarus forsteni, a whitespot parrotfish from the Scaridae family, is a herbivorous fish inhabiting coral reef ecosystems. The deterioration of coral reefs has highly affected the habitats of the parrotfish. The decline in genetic diversity of parrotfish emphasizes the critical importance of conserving their genetic variability to ensure the resilience and sustainability of marine ecosystems for future generations. In this study, a genome of S. forsteni was assembled de novo through using Illumina and Nanopore sequencing. The 1.71-Gb genome of S. forsteni, was assembled into 544 contigs (assembly level: contig). It exhibited an N50 length of 17.97 Mb and a GC content percentage of 39.32%. Our BUSCO analysis revealed that the complete protein of the S. forsteni genome had 98.10% integrity. Combined with structure annotation data, 34,140 (74.81%) genes were functionally annotated out of 45,638 predicted protein-coding genes. Upon comparing the genome size and TE content of teleost fishes, a roughly linear relationship was observed between these two parameters. However, TE content is not a decisive factor in determining the genome size of S. forsteni. Population history analysis results indicate that S. forsteni experienced two major population expansions, both of which occurred before the last interglacial period. In addition, through a comparative genomic analysis of the evolutionary relationship of other species, it was found that S. forsteni had the closest relationship with Cheilinus undulatus, another member of the Labridae family. Our expansion and contraction analysis of the gene family showed that the expansion genes were mainly associated with immune diseases, organismal systems, and cellular processes. At the same time, cell transcription and translation, sex hormone regulation, and other related pathways were also more prominent in the positive selection genes. The genomic sequence of S. forsteni offers valuable resources for future investigations on the conservation, evolution, and behavior of fish species.
Allelic Variations in Vernalization (Vrn) Genes in Triticum spp.
Authors: Afshari-Behbahanizadeh Sanaz , Puglisi Damiano , Esposito Salvatore , De Vita Pasquale
Published: February 2024

Rapid climate changes, with higher warming rates during winter and spring seasons, dramatically affect the vernalization requirements, one of the most critical processes for the induction of wheat reproductive growth, with severe consequences on flowering time, grain filling, and grain yield. Specifically, the Vrn genes play a major role in the transition from vegetative to reproductive growth in wheat. Recent advances in wheat genomics have significantly improved the understanding of the molecular mechanisms of Vrn genes (Vrn-1, Vrn-2, Vrn-3, and Vrn-4), unveiling a diverse array of natural allelic variations. In this review, we have examined the current knowledge of Vrn genes from a functional and structural point of view, considering the studies conducted on Vrn alleles at different ploidy levels (diploid, tetraploid, and hexaploid). The molecular characterization of Vrn-1 alleles has been a focal point, revealing a diverse array of allelic forms with implications for flowering time. We have highlighted the structural complexity of the different allelic forms and the problems linked to the different nomenclature of some Vrn alleles. Addressing these issues will be crucial for harmonizing research efforts and enhancing our understanding of Vrn gene function and evolution. The increasing availability of genome and transcriptome sequences, along with the improvements in bioinformatics and computational biology, offers a versatile range of possibilities for enriching genomic regions surrounding the target sites of Vrn genes, paving the way for innovative approaches to manipulate flowering time and improve wheat productivity.
The First Complete Mitochondrial Genome of the Genus Litostrophus: Insights into the Rearrangement and Evolution of Mitochondrial Genomes in Diplopoda
Authors: Zhang Gaoji , Gao Ming , Chen Yukun , Wang Yinuo , Gan Tianyi , Zhu Fuyuan , Liu Hongyi
Published: February 2024

This study presents the complete mitochondrial genome (mitogenome) of Litostrophus scaber, which is the first mitogenome of the genus Litostrophus. The mitogenome is a circular molecule with a length of 15,081 bp. The proportion of adenine and thymine (A + T) was 69.25%. The gene ND4L used TGA as the initiation codon, while the other PCGs utilized ATN (A, T, G, C) as the initiation codons. More than half of the PCGs used T as an incomplete termination codon. The transcription direction of the L. scaber mitogenome matched Spirobolus bungii, in contrast to most millipedes. Novel rearrangements were found in the L. scaber mitogenome: trnQ -trnC and trnL1- trnP underwent short-distance translocations and the gene block rrnS-rrnL-ND1 moved to a position between ND4 and ND5, resulting in the formation of a novel gene order. The phylogenetic analysis showed that L. scaber is most closely related to S. bungii, followed by Narceus magnum. These findings enhance our understanding of the rearrangement and evolution of Diplopoda mitogenomes.
Effects of Ozone Treatment on Postharvest Mucor Rot of Codonopsis pilosula Caused by Actinomucor elegans
Authors: Zhang Dan , Chen Jiangyang , Liu Zhiguang , Shang Suqin , Xue Huali
Published: February 2024

Fresh Codonopsis pilosula is highly susceptible to fungus contamination during post-harvest storage, which not only compromises the quality of C. pilosula but also contributes mycotoxin contamination, posing a significant threat to human health. Studies have indicated that ozone treatment can inhibit post-harvest diseases in fruits and vegetables. The impact of ozone treatment on the disease incidence, disease severity index, and weight loss rate of the fresh C. pilosula infected with Actinomucor elegans was investigated through the spray inoculation of A. elegans on C. pilosula tissues. Changes in the main active ingredients of C. pilosula after ozone treatment were analyzed, and the effects of ozone treatment on the integrity of cell membranes in C. pilosula tissue and reactive oxygen species (ROS) metabolism were studied. The results showed that ozone treatment had a significant inhibitory effect on the A. elegans-induced mucor rot in C. pilosula, significantly reducing the incidence of the disease. Compared with the control group, the ozone-treated group maintained the effective components of C. pilosula well. Furthermore, ozone treatment reduced the cell membrane permeability and Malondialdehyde (MDA) content in C. pilosula, significantly increased the activity of antioxidant enzymes in the ROS metabolism pathway, prevented oxidative stress caused by the accumulation of ROS in C. pilosula tissues, and maintained the integrity of cell membranes.
Pathogenetic Contributions and Therapeutic Implications of Transglutaminase 2 in Neurodegenerative Diseases
Authors: Liu Jun , Mouradian M. Maral
Published: February 2024

Neurodegenerative diseases encompass a heterogeneous group of disorders that afflict millions of people worldwide. Characteristic protein aggregates are histopathological hallmark features of these disorders, including Amyloid β (Aβ)-containing plaques and tau-containing neurofibrillary tangles in Alzheimer’s disease, α-Synuclein (α-Syn)-containing Lewy bodies and Lewy neurites in Parkinson’s disease and dementia with Lewy bodies, and mutant huntingtin (mHTT) in nuclear inclusions in Huntington’s disease. These various aggregates are found in specific brain regions that are impacted by neurodegeneration and associated with clinical manifestations. Transglutaminase (TG2) (also known as tissue transglutaminase) is the most ubiquitously expressed member of the transglutaminase family with protein crosslinking activity. To date, Aβ, tau, α-Syn, and mHTT have been determined to be substrates of TG2, leading to their aggregation and implicating the involvement of TG2 in several pathophysiological events in neurodegenerative disorders. In this review, we summarize the biochemistry and physiologic functions of TG2 and describe recent advances in the pathogenetic role of TG2 in these diseases. We also review TG2 inhibitors tested in clinical trials and discuss recent TG2-targeting approaches, which offer new perspectives for the design of future highly potent and selective drugs with improved brain delivery as a disease-modifying treatment for neurodegenerative disorders.
Future-Proofing Agriculture: De Novo Domestication for Sustainable and Resilient Crops
Authors: Rogo Ugo , Simoni Samuel , Fambrini Marco , Giordani Tommaso , Pugliesi Claudio , Mascagni Flavia
Published: February 2024

The worldwide agricultural system confronts a significant challenge represented by the increasing demand for food in the face of a growing global population. This challenge is exacerbated by a reduction in cultivable land and the adverse effects of climate change on crop yield quantity and quality. Breeders actively embrace cutting-edge omics technologies to pursue resilient genotypes in response to these pressing issues. In this global context, new breeding techniques (NBTs) are emerging as the future of agriculture, offering a solution to introduce resilient crops that can ensure food security, particularly against challenging climate events. Indeed, the search for domestication genes as well as the genetic modification of these loci in wild species using genome editing tools are crucial steps in carrying out de novo domestication of wild plants without compromising their genetic background. Current knowledge allows us to take different paths from those taken by early Neolithic farmers, where crop domestication has opposed natural selection. In this process traits and alleles negatively correlated with high resource environment performance are probably eradicated through artificial selection, while others may have been lost randomly due to domestication and genetic bottlenecks. Thus, domestication led to highly productive plants with little genetic diversity, owing to the loss of valuable alleles that had evolved to tolerate biotic and abiotic stresses. Recent technological advances have increased the feasibility of de novo domestication of wild plants as a promising approach for crafting optimal crops while ensuring food security and using a more sustainable, low-input agriculture. Here, we explore what crucial domestication genes are, coupled with the advancement of technologies enabling the precise manipulation of target sequences, pointing out de novo domestication as a promising application for future crop development.
Alterations in Genome Organization in Lymphoma Cell Nuclei due to the Presence of the t(14;18) Translocation
Authors: Garimberti Elisa , Federico Concetta , Ragusa Denise , Bruno Francesca , Saccone Salvatore , Bridger Joanna Mary , Tosi Sabrina
Published: February 2024

Chromosomal rearrangements have been shown to alter genome organization, consequently having an impact on gene expression. Studies on certain types of leukemia have shown that gene expression can be exacerbated by the altered nuclear positioning of fusion genes arising from chromosomal translocations. However, studies on lymphoma have been, so far, very limited. The scope of this study was to explore genome organization in lymphoma cells carrying the t(14;18)(q32;q21) rearrangement known to results in over-expression of the BCL2 gene. In order to achieve this aim, we used fluorescence in situ hybridization to carefully map the positioning of whole chromosome territories and individual genes involved in translocation in the lymphoma-derived cell line Pfeiffer. Our data show that, although there is no obvious alteration in the positioning of the whole chromosome territories, the translocated genes may take the nuclear positioning of either of the wild-type genes. Furthermore, the BCL2 gene was looping out in a proportion of nuclei with the t(14;18) translocation but not in control nuclei without the translocation, indicating that chromosome looping may be an essential mechanism for BCL2 expression in lymphoma cells.
A New Generation of Gene Therapies as the Future of Wet AMD Treatment
Authors: Blasiak Janusz , Pawlowska Elzbieta , Ciupińska Justyna , Derwich Marcin , Szczepanska Joanna , Kaarniranta Kai
Published: February 2024

Age-related macular degeneration (AMD) is an eye disease and the most common cause of vision loss in the Western World. In its advanced stage, AMD occurs in two clinically distinguished forms, dry and wet, but only wet AMD is treatable. However, the treatment based on repeated injections with vascular endothelial growth factor A (VEGFA) antagonists may at best stop the disease progression and prevent or delay vision loss but without an improvement of visual dysfunction. Moreover, it is a serious mental and financial burden for patients and may be linked with some complications. The recent first success of intravitreal gene therapy with ADVM-022, which transformed retinal cells to continuous production of aflibercept, a VEGF antagonist, after a single injection, has opened a revolutionary perspective in wet AMD treatment. Promising results obtained so far in other ongoing clinical trials support this perspective. In this narrative/hypothesis review, we present basic information on wet AMD pathogenesis and treatment, the concept of gene therapy in retinal diseases, update evidence on completed and ongoing clinical trials with gene therapy for wet AMD, and perspectives on the progress to the clinic of “one and done” therapy for wet AMD to replace a lifetime of injections. Gene editing targeting the VEGFA gene is also presented as another gene therapy strategy to improve wet AMD management.
The Auto-Regulation of ATL2 E3 Ubiquitin Ligase Plays an Important Role in the Immune Response against Alternaria brassicicola in Arabidopsis thaliana
Authors: Kim Daewon , Jeon Su Jeong , Hong Jeum Kyu , Kim Min Gab , Kim Sang Hee , Kadam Ulhas S. , Kim Woe-Yeon , Chung Woo Sik , Stacey Gary , Hong Jong Chan
Published: February 2024

The ubiquitin/26S proteasome system is a crucial regulatory mechanism that governs various cellular processes in plants, including signal transduction, transcriptional regulation, and responses to biotic and abiotic stressors. Our study shows that the RING-H2-type E3 ubiquitin ligase, Arabidopsis Tóxicos en Levadura 2 (ATL2), is involved in response to fungal pathogen infection. Under normal growth conditions, the expression of the ATL2 gene is low, but it is rapidly and significantly induced by exogenous chitin. Additionally, ATL2 protein stability is markedly increased via chitin treatment, and its degradation is prolonged when 26S proteasomal function is inhibited. We found that an atl2 null mutant exhibited higher susceptibility to Alternaria brassicicola, while plants overexpressing ATL2 displayed increased resistance. We also observed that the hyphae of A. brassicicola were strongly stained with trypan blue staining, and the expression of A. brassicicola Cutinase A (AbCutA) was dramatically increased in atl2. In contrast, the hyphae were weakly stained, and AbCutA expression was significantly reduced in ATL2-overexpressing plants. Using bioinformatics, live-cell confocal imaging, and cell fractionation analysis, we revealed that ATL2 is localized to the plasma membrane. Further, it is demonstrated that the ATL2 protein possesses E3 ubiquitin ligase activity and found that cysteine 138 residue is critical for its function. Moreover, ATL2 is necessary to successfully defend against the A. brassicicola fungal pathogen. Altogether, our data suggest that ATL2 is a plasma membrane-integrated protein with RING-H2-type E3 ubiquitin ligase activity and is essential for the defense response against fungal pathogens in Arabidopsis.
Changes in Cells Associated with Insulin Resistance
Authors: Szablewski Leszek
Published: February 2024

Insulin is a polypeptide hormone synthesized and secreted by pancreatic β-cells. It plays an important role as a metabolic hormone. Insulin influences the metabolism of glucose, regulating plasma glucose levels and stimulating glucose storage in organs such as the liver, muscles and adipose tissue. It is involved in fat metabolism, increasing the storage of triglycerides and decreasing lipolysis. Ketone body metabolism also depends on insulin action, as insulin reduces ketone body concentrations and influences protein metabolism. It increases nitrogen retention, facilitates the transport of amino acids into cells and increases the synthesis of proteins. Insulin also inhibits protein breakdown and is involved in cellular growth and proliferation. On the other hand, defects in the intracellular signaling pathways of insulin may cause several disturbances in human metabolism, resulting in several chronic diseases. Insulin resistance, also known as impaired insulin sensitivity, is due to the decreased reaction of insulin signaling for glucose levels, seen when glucose use in response to an adequate concentration of insulin is impaired. Insulin resistance may cause, for example, increased plasma insulin levels. That state, called hyperinsulinemia, impairs metabolic processes and is observed in patients with type 2 diabetes mellitus and obesity. Hyperinsulinemia may increase the risk of initiation, progression and metastasis of several cancers and may cause poor cancer outcomes. Insulin resistance is a health problem worldwide; therefore, mechanisms of insulin resistance, causes and types of insulin resistance and strategies against insulin resistance are described in this review. Attention is also paid to factors that are associated with the development of insulin resistance, the main and characteristic symptoms of particular syndromes, plus other aspects of severe insulin resistance. This review mainly focuses on the description and analysis of changes in cells due to insulin resistance.
The Structure of the Cardiac Mitochondria Respirasome Is Adapted for the β-Oxidation of Fatty Acids
Authors: Panov Alexander V.
Published: February 2024

It is well known that in the heart and kidney mitochondria, more than 95% of ATP production is supported by the β-oxidation of long-chain fatty acids. However, the β-oxidation of fatty acids by mitochondria has been studied much less than the substrates formed during the catabolism of carbohydrates and amino acids. In the last few decades, several discoveries have been made that are directly related to fatty acid oxidation. In this review, we made an attempt to re-evaluate the β-oxidation of long-chain fatty acids from the perspectives of new discoveries. The single set of electron transporters of the cardiac mitochondrial respiratory chain is organized into three supercomplexes. Two of them contain complex I, a dimer of complex III, and two dimers of complex IV. The third, smaller supercomplex contains a dimer of complex III and two dimers of complex IV. We also considered other important discoveries. First, the enzymes of the β-oxidation of fatty acids are physically associated with the respirasome. Second, the β-oxidation of fatty acids creates the highest level of QH2 and reverses the flow of electrons from QH2 through complex II, reducing fumarate to succinate. Third, β-oxidation is greatly stimulated in the presence of succinate. We argue that the respirasome is uniquely adapted for the β-oxidation of fatty acids. The acyl-CoA dehydrogenase complex reduces the membrane’s pool of ubiquinone to QH2, which is instantly oxidized by the smaller supercomplex, generating a high energization of mitochondria and reversing the electron flow through complex II, which reverses the electron flow through complex I, increasing the NADH/NAD+ ratio in the matrix. The mitochondrial nicotinamide nucleotide transhydrogenase catalyzes a hydride (H-, a proton plus two electrons) transfer across the inner mitochondrial membrane, reducing the cytosolic pool of NADP(H), thus providing the heart with ATP for muscle contraction and energy and reducing equivalents for the housekeeping processes.
Chitosan-Based Beads Incorporating Inorganic–Organic Composites for Copper Ion Retention in Aqueous Solutions
Authors: Miron Andreea , Iordache Tanta-Verona , Valente Artur J. M. , Durães Luisa Maria Rocha , Sarbu Andrei , Ivan Georgeta Ramona , Zaharia Anamaria , Sandu Teodor , Iovu Horia , Chiriac Anita-Laura
Published: February 2024

In recent years, there has been a challenging interest in developing low-cost biopolymeric materials for wastewater treatment. In the present work, new adsorbents, based on different types of chitosan (commercial, commercial chitin-derived chitosan and chitosan synthesized from shrimp shell waste) and inorganic–organic composites have been evaluated for copper ions removal. The efficacy of the synthesis of chitosan-based composite beads has been determined by studying various characteristics using several techniques, including FTIR spectroscopy, X-ray diffraction, porosimetry (N2 adsorption), and scanning electron microscopy (SEM). Adsorption kinetics was performed using different adsorption models to determine the adsorption behavior of the materials in the aqueous media. For all composite beads, regardless of the type of chitosan used, good capacity to remove copper ions from simulated waters was observed (up to 17 mg/g), which proves that the new materials hold potential for heavy metal retention. However, the adsorption efficiency was influenced by the type of chitosan used. Thus, for the series where commercial chitosan (CC) was used, the removal efficiency was approximately 29%; for the series with chitosan obtained from commercial chitin (SC), the removal efficiency was approximately 34%; for the series with chitosan enriched with CaCO3 (SH), the removal efficiency was approximately 52%.
Novel Immortalized Human Multipotent Mesenchymal Stromal Cell Line for Studying Hormonal Signaling
Authors: Primak Alexandra , Kalinina Natalia , Skryabina Mariya , Usachev Vladimir , Chechekhin Vadim , Vigovskiy Maksim , Chechekhina Elizaveta , Voloshin Nikita , Kulebyakin Konstantin , Kulebyakina Maria , Grigorieva Olga , Tyurin-Kuzmin Pyotr , Basalova Nataliya , Efimenko Anastasia , Dzhauari Stalik , Antropova Yulia , Plyushchii Ivan , Akopyan Zhanna , Sysoeva Veronika , Tkachuk Vsevolod , Karagyaur Maxim
Published: February 2024

Multipotent mesenchymal stromal cells (MSCs) integrate hormone and neuromediator signaling to coordinate tissue homeostasis, tissue renewal and regeneration. To facilitate the investigation of MSC biology, stable immortalized cell lines are created (e.g., commercially available ASC52telo). However, the ASC52telo cell line has an impaired adipogenic ability and a depressed response to hormones, including 5-HT, GABA, glutamate, noradrenaline, PTH and insulin compared to primary cells. This markedly reduces the potential of the ASC52telo cell line in studying the mechanisms of hormonal control of MSC’s physiology. Here, we have established a novel immortalized culture of adipose tissue-derived MSCs via forced telomerase expression after lentiviral transduction. These immortalized cell cultures demonstrate high proliferative potential (up to 40 passages), delayed senescence, as well as preserved primary culture-like functional activity (sensitivity to hormones, ability to hormonal sensitization and differentiation) and immunophenotype up to 17–26 passages. Meanwhile, primary adipose tissue-derived MSCs usually irreversibly lose their properties by 8–10 passages. Observed characteristics of reported immortalized human MSC cultures make them a feasible model for studying molecular mechanisms, which regulate the functional activities of these cells, especially when primary cultures or commercially available cell lines are not appropriate.
From the Friend to the Foe—Enterococcus faecalis Diverse Impact on the Human Immune System
Authors: Daca Agnieszka , Jarzembowski Tomasz
Published: February 2024

Enterococcus faecalis is a bacterium which accompanies us from the first days of our life. As a commensal it produces vitamins, metabolizes nutrients, and maintains intestinal pH. All of that happens in exchange for a niche to inhabit. It is not surprising then, that the bacterium was and is used as an element of many probiotics and its positive impact on the human immune system and the body in general is hard to ignore. This bacterium has also a dark side though. The plasticity and relative ease with which one acquires virulence traits, and the ability to hide from or even deceive and use the immune system to spread throughout the body make E. faecalis a more and more dangerous opponent. The statistics clearly show its increasing role, especially in the case of nosocomial infections. Here we present the summarization of current knowledge about E. faecalis, especially in the context of its relations with the human immune system.
An Integrated Comprehensive Peptidomics and In Silico Analysis of Bioactive Peptide-Rich Milk Fermented by Three Autochthonous Cocci Strains
Authors: Banić Martina , Butorac Katarina , Čuljak Nina , Butorac Ana , Novak Jasna , Pavunc Andreja Leboš , Rušanac Anamarija , Stanečić Željka , Lovrić Marija , Šušković Jagoda , Kos Blaženka
Published: February 2024

Bioactive peptides (BPs) are molecules of paramount importance with great potential for the development of functional foods, nutraceuticals or therapeutics for the prevention or treatment of various diseases. A functional BP-rich dairy product was produced by lyophilisation of bovine milk fermented by the autochthonous strains Lactococcus lactis subsp. lactis ZGBP5-51, Enterococcus faecium ZGBP5-52 and Enterococcus faecalis ZGBP5-53 isolated from the same artisanal fresh cheese. The efficiency of the proteolytic system of the implemented strains in the production of BPs was confirmed by a combined high-throughput mass spectrometry (MS)-based peptidome profiling and an in silico approach. First, peptides released by microbial fermentation were identified via a non-targeted peptide analysis (NTA) comprising reversed-phase nano-liquid chromatography (RP nano-LC) coupled with matrix-assisted laser desorption/ionisation-time-of-flight/time-of-flight (MALDI-TOF/TOF) MS, and then quantified by targeted peptide analysis (TA) involving RP ultrahigh-performance LC (RP-UHPLC) coupled with triple-quadrupole MS (QQQ-MS). A combined database and literature search revealed that 10 of the 25 peptides identified in this work have bioactive properties described in the literature. Finally, by combining the output of MS-based peptidome profiling with in silico bioactivity prediction tools, three peptides (75QFLPYPYYAKPA86, 40VAPFPEVFGK49, 117ARHPHPHLSF126), whose bioactive properties have not been previously reported in the literature, were identified as potential BP candidates.
Immunoinformatic Identification of Multiple Epitopes of gp120 Protein of HIV-1 to Enhance the Immune Response against HIV-1 Infection
Authors: Habib Arslan , Liang Yulai , Xu Xinyi , Zhu Naishuo , Xie Jun
Published: February 2024

Acquired Immunodeficiency Syndrome is caused by the Human Immunodeficiency Virus (HIV), and a significant number of fatalities occur annually. There is a dire need to develop an effective vaccine against HIV-1. Understanding the structural proteins of viruses helps in designing a vaccine based on immunogenic peptides. In the current experiment, we identified gp120 epitopes using bioinformatic epitope prediction tools, molecular docking, and MD simulations. The Gb-1 peptide was considered an adjuvant. Consecutive sequences of GTG, GSG, GGTGG, and GGGGS linkers were used to bind the B cell, Cytotoxic T Lymphocytes (CTL), and Helper T Lymphocytes (HTL) epitopes. The final vaccine construct consisted of 315 amino acids and is expected to be a recombinant protein of approximately 35.49 kDa. Based on docking experiments, molecular dynamics simulations, and tertiary structure validation, the analysis of the modeled protein indicates that it possesses a stable structure and can interact with Toll-like receptors. The analysis demonstrates that the proposed vaccine can provoke an immunological response by activating T and B cells, as well as stimulating the release of IgA and IgG antibodies. This vaccine shows potential for HIV-1 prophylaxis. The in-silico design suggests that multiple-epitope constructs can be used as potentially effective immunogens for HIV-1 vaccine development.
The Pathophysiology and Treatment of Pyoderma Gangrenosum—Current Options and New Perspectives
Authors: Łyko Magdalena , Ryguła Anna , Kowalski Michał , Karska Julia , Jankowska-Konsur Alina
Published: February 2024

Pyoderma gangrenosum (PG) is an uncommon inflammatory dermatological disorder characterized by painful ulcers that quickly spread peripherally. The pathophysiology of PG is not fully understood; however, it is most commonly considered a disease in the spectrum of neutrophilic dermatoses. The treatment of PG remains challenging due to the lack of generally accepted therapeutic guidelines. Existing therapeutic methods focus on limiting inflammation through the use of immunosuppressive and immunomodulatory therapies. Recently, several reports have indicated the successful use of biologic drugs and small molecules administered for coexisting diseases, resulting in ulcer healing. In this review, we summarize the discoveries regarding the pathophysiology of PG and present treatment options to raise awareness and improve the management of this rare entity.
Myconoside and Calceolarioside E Restrain UV-Induced Skin Photoaging by Activating NRF2-Mediated Defense Mechanisms
Authors: Stoykova Iva D. , Koycheva Ivanka K. , Binev Biser K. , Mihaylova Liliya V. , Benina Maria Y. , Alipieva Kalina I. , Georgiev Milen I.
Published: February 2024

Chronic and excessive ultraviolet (UVA/UVB) irradiation exposure is known as a major contributor to premature skin aging, which leads to excessive reactive oxygen species generation, disturbed extracellular matrix homeostasis, DNA damage, and chronic inflammation. Sunscreen products are the major preventive option against UVR-induced photodamage, mostly counteracting the acute skin effects and only mildly counteracting accelerated aging. Therefore, novel anti-photoaging and photopreventive compounds are a subject of increased scientific interest. Our previous investigations revealed that the endemic plant Haberlea rhodopensis Friv. (HRE) activates the antioxidant defense through an NRF2-mediated mechanism in neutrophiles. In the present study, we aimed to investigate the photoprotective potential of HRE and two of its specialized compounds—the phenylethanoid glycosides myconoside (MYC) and calceolarioside E (CAL)—in UVA/UVB-stimulated human keratinocytes in an in vitro model of photoaging. The obtained data demonstrated that the application of HRE, MYC, and CAL significantly reduced intracellular ROS formation in UVR-exposed HaCaT cells. The NRF2/PGC-1α and TGF-1β/Smad/Wnt signaling pathways were pointed out as having a critical role in the observed CAL- and MYC-induced photoprotective effect. Collectively, CAL is worth further evaluation as a potent natural NRF2 activator and a promising photoprotective agent that leads to the prevention of UVA/UVB-induced premature skin aging.