bluuebunny/crossref_metadata_2025 huggingface dataset:
Application of Hydro-Based Morphological Models for Environmental Assessment of Watersheds
Authors: Neto Silvio Luís Rafaeli , dos Santos Vanessa Jutel , Schutz Emili Louise Diconcili , de Moliner Leticia Margarete , Kloth Cristiane Gracieli , Schier Daiane Teixeira , Othman Arsalan Ahmed , Liesenberg Veraldo , Bispo Polyanna da Conceição
Published: July 2023

Hydro-based morphological models are representations of the terrain related to the flow or storage of water in the landscape. However, their application in the context of an integrated environmental assessment has been scarcely explored in the literature, despite the well-known importance of water for ecosystems and land use planning. Here, we derive the HAND and TWI models, which present solid conceptual bases based on water–landscape relationships from digital terrain models. We aim to present these models as useful representations in the environmental assessment of watersheds as they are relatively easy to generate and interpret. To this end, we applied these models in a Brazilian watershed and evaluated their spatial and reciprocal occurrence in the hydrological landscape through geographic entities and their spatial relationships with other landscape elements such as land use. We argue that HAND and TWI are simple hydrological-based models with robust premises that can reveal intrinsic relationships between relief parameters and water, providing new perspectives for the environmental assessment of small watersheds. Their outcomes have tremendous implications for land management initiatives. Our results show that geometric signatures of the TWI appeared through all the structural units of the hydrological landscape. The plateau areas were most prone to water accumulation/soil saturation, followed by floodplains, hillslopes, and ecotones. Thus, there is a tendency for the greatest geometric signatures of water accumulation/soil saturation entities to be located near the higher-order channels as well as the greatest geometric signatures of the floodplains. Agriculture and planted forests increased with distance, while the areas occupied by forest remnants tended to decrease within a range of up to 50 m from channels. However, they were also found within 50 m around the springs, whereas open fields, urban areas, and water bodies remained stable. We argue that HAND and TWI are simple hydrological-based models with robust premises that can reveal intrinsic relationships between the relief parameters and water, providing new perspectives for the environmental assessment of small watersheds whose outcomes have tremendous implications for land management initiatives.
Investigation of Inflammation in Lewy Body Dementia: A Systematic Scoping Review
Authors: Loveland Paula M. , Yu Jenny J. , Churilov Leonid , Yassi Nawaf , Watson Rosie
Published: July 2023

Inflammatory mechanisms are increasingly recognized as important contributors to the pathogenesis of neurodegenerative diseases, including Lewy body dementia (LBD). Our objectives were to, firstly, review inflammation investigation methods in LBD (dementia with Lewy bodies and Parkinson’s disease dementia) and, secondly, identify alterations in inflammatory signals in LBD compared to people without neurodegenerative disease and other neurodegenerative diseases. A systematic scoping review was performed by searching major electronic databases (MEDLINE, Embase, Web of Science, and PSYCHInfo) to identify relevant human studies. Of the 2509 results screened, 80 studies were included. Thirty-six studies analyzed postmortem brain tissue, and 44 investigated living subjects with cerebrospinal fluid, blood, and/or brain imaging assessments. Largely cross-sectional data were available, although two longitudinal clinical studies investigated prodromal Lewy body disease. Investigations were focused on inflammatory immune cell activity (microglia, astrocytes, and lymphocytes) and inflammatory molecules (cytokines, etc.). Results of the included studies identified innate and adaptive immune system contributions to inflammation associated with Lewy body pathology and clinical disease features. Different signals in early and late-stage disease, with possible late immune senescence and dystrophic glial cell populations, were identified. The strength of these associations is limited by the varying methodologies, small study sizes, and cross-sectional nature of the data. Longitudinal studies investigating associations with clinical and other biomarker outcomes are needed to improve understanding of inflammatory activity over the course of LBD. This could identify markers of disease activity and support therapeutic development.
Proteomics of Plasma and Plasma-Treated Podocytes: Application to Focal and Segmental Glomerulosclerosis
Authors: Chhuon Cerina , Herrera-Marcos Luis Vicente , Zhang Shao-Yu , Charrière-Bertrand Cécile , Jung Vincent , Lipecka Joanna , Savas Berkan , Nasser Nour , Pawlak André , Boulmerka Hocine , Audard Vincent , Sahali Dil , Guerrera Ida Chiara , Ollero Mario
Published: July 2023

Focal and segmental glomerulosclerosis (FSGS) is a severe form of idiopathic nephrotic syndrome (INS), a glomerulopathy of presumably immune origin that is attributed to extrarenal pathogenic circulating factors. The recurrence of FSGS (rFSGS) after transplant occurs in 30% to 50% of cases. The direct analysis of patient plasma proteome has scarcely been addressed to date, mainly due to the methodological difficulties associated with plasma complexity and dynamic range. In this study, first, we compared different methods of plasma preparation, second, we compared the plasma proteomes of rFSGS and controls using two preparation methods, and third, we analyzed the early proximal signaling events in podocytes subjected to patient plasma, through a combination of phosphoproteomics and lipid-raft proteomics (raftomics). By combining immunodepletion and high pH fractionation, we performed a differential proteomic analysis of soluble plasma proteins and of extracellular vesicles (EV) obtained from healthy controls, non-INS patient controls, and rFSGS patients (n = 4). In both the soluble- and the EV-protein sets from the rFSGS patients, we found a statistically significant increase in a cluster of proteins involved in neutrophil degranulation. A group of lipid-binding proteins, generally associated with lipoproteins, was found to be decreased in the soluble set from the rFSGS patients. In addition, three amino acid transporters involved in mTORC1 activation were found to be significantly increased in the EV from the rFSGS. Next, we incubated human podocytes for 30 min with 10% plasma from both groups of patients. The phosphoproteomics and raftomics of the podocytes revealed profound differences in the proteins involved in the mTOR pathway, in autophagy, and in cytoskeleton organization. We analyzed the correlation between the abundance of plasma and plasma-regulated podocyte proteins. The observed changes highlight some of the mechanisms involved in FSGS recurrence and could be used as specific early markers of circulating-factor activity in podocytes.
Developing New Diagnostic Tools Based on SERS Analysis of Filtered Salivary Samples for Oral Cancer Detection
Authors: Borșa Rareș-Mario , Toma Valentin , Onaciu Anca , Moldovan Cristian-Silviu , Mărginean Radu , Cenariu Diana , Știufiuc Gabriela-Fabiola , Dinu Cristian-Mihail , Bran Simion , Opriș Horia-Octavian , Văcăraș Sergiu , Onișor-Gligor Florin , Sentea Dorin , Băciuț Mihaela-Felicia , Iuga Cristina-Adela , Știufiuc Rareș-Ionuț
Published: July 2023

Cancer still represents one of the biggest challenges in current medical practice. Among different types of cancer, oral cancer has a huge impact on patients due to its great visibility, which is more likely to create social stigma and increased anxiety. New early diagnose methods are still needed to improve treatment efficiency and patients’ life quality. Raman/SERS (Surface Enhanced Raman Spectroscopy) spectroscopy has a unique and powerful potential for detecting specific molecules that can become priceless biomarkers in different pathologies, such as oral cancer. In this study, a batch of saliva samples obtained from a group of 17 patients with oro-maxillofacial pathologies compared with saliva samples from 18 healthy donors using the aforementioned methods were evaluated. At the same time, opiorphin, potassium thiocyanate and uric acid were evaluated as potential specific biomarkers for oro-maxillofacial pathologies using multivariate analysis. A careful examination of SERS spectra collected on saliva samples showed that the spectra are dominated by the vibrational bands of opiorphin, potassium thiocyanate and uric acid. Given the fact that all these small molecules are found in very small amounts, we filtrated all the samples to get rid of large molecules and to improve our analysis. By using solid plasmonic substrates, we were able to gain information about molecular concentration and geometry of interaction. On the other hand, the multivariate analysis of the salivary spectra contributed to developing a new detection method for oral cancer.
Structure and Dynamics of Compact Dinucleosomes: Analysis by Electron Microscopy and spFRET
Authors: Stefanova Maria E. , Volokh Olesya I. , Chertkov Oleg V. , Armeev Grigory A. , Shaytan Alexey K. , Feofanov Alexey V. , Kirpichnikov Mikhail P. , Sokolova Olga S. , Studitsky Vasily M.
Published: July 2023

Formation of compact dinucleosomes (CODIs) occurs after collision between adjacent nucleosomes at active regulatory DNA regions. Although CODIs are likely dynamic structures, their structural heterogeneity and dynamics were not systematically addressed. Here, single-particle Förster resonance energy transfer (spFRET) and electron microscopy were employed to study the structure and dynamics of CODIs. spFRET microscopy in solution and in gel revealed considerable uncoiling of nucleosomal DNA from the histone octamer in a fraction of CODIs, suggesting that at least one of the nucleosomes is destabilized in the presence of the adjacent closely positioned nucleosome. Accordingly, electron microscopy analysis suggests that up to 30 bp of nucleosomal DNA are involved in transient uncoiling/recoiling on the octamer. The more open and dynamic nucleosome structure in CODIs cannot be stabilized by histone chaperone Spt6. The data suggest that proper internucleosomal spacing is an important determinant of chromatin stability and support the possibility that CODIs could be intermediates of chromatin disruption.
Inflammatory Bowel Diseases: An Updated Overview on the Heat Shock Protein Involvement
Authors: Scalia Federica , Carini Francesco , David Sabrina , Giammanco Marco , Mazzola Margherita , Rappa Francesca , Bressan Noemi , Maida Giorgio , Tomasello Giovanni
Published: July 2023

Inflammatory bowel diseases (IBDs) represent chronic idiopathic disorders, including Crohn’s disease (CD) and ulcerative colitis (UC), in which one of the trigger factors is represented by aberrant immune interactions between the intestinal epithelium and the intestinal microbiota. The involvement of heat shock proteins (HSPs) as etiological and pathogenetic factors is becoming of increasing interest. HSPs were found to be differentially expressed in the intestinal tissues and sera of patients with CD and UC. It has been shown that HSPs can play a dual role in the disease, depending on the stage of progression. They can support the inflammatory and fibrosis process, but they can also act as protective factors during disease progression or before the onset of one of the worst complications of IBD, colorectal cancer. Furthermore, HSPs are able to mediate the interaction between the intestinal microbiota and intestinal epithelial cells. In this work, we discuss the involvement of HSPs in IBD considering their genetic, epigenetic, immune and molecular roles, referring to the most recent works present in the literature. With our review, we want to shed light on the importance of further exploring the role of HSPs, or even better, the role of the molecular chaperone system (CS), in IBD: various molecules of the CS including HSPs may have diagnostic, prognostic and therapeutic potential, promoting the creation of new drugs that could overcome the side-effects of the therapies currently used.
Distribution of Signal Peptides in Microvesicles from Activated Macrophage Cells
Authors: Ono Kenji , Sato Junpei , Suzuki Hiromi , Sawada Makoto
Published: July 2023

Extracellular vesicles, such as microvesicles (LEV) and exosomes (SEV), play an important role in intercellular signaling by encapsulating functional molecules and delivering them to specific cells. Recent studies showed that signal peptides (SPs), which are derived from sequences at the N-terminal of newly synthesized proteins, exhibited biological activity in the extracellular fluid. We previously reported that SPs were secreted into the extracellular fluid via SEV; however, it remains unclear whether the release of SPs occurs via LEV. In the present study, we demonstrated that SP fragments from human placental secreted alkaline phosphatase (SEAP) were present in LEV as well as SEV released from RAW-Blue cells, which stably express an NF-κB-inducible SEAP reporter. When RAW-Blue cells were treated with LPS at 0–10,000 ng/mL, SEAP SP fragments per particle were more abundant in LEV than in SEV, with fragments in LEV and SEV reaching a maximum at 1000 and 100 ng/mL, respectively. The content of SEAP SP fragments in LEV from IFNγ-stimulated RAW-Blue cells was higher than those from TNFα-stimulated cells, whereas that in SEV from TNFα-stimulated RAW-Blue cells was higher than those from IFNγ−stimulated cells. Moreover, the content of SEAP SP fragments in LEV and SEV decreased in the presence of W13, a calmodulin inhibitor. Collectively, these results indicate that the transportation of SP fragments to extracellular vesicles was changed by cellular activation, and calmodulin was involved in their transportation to LEV and SEV.
Mechanisms of Listeria monocytogenes Disinfection with Benzalkonium Chloride: From Molecular Dynamics to Kinetics of Time-Kill Curves
Authors: Pérez-Rodríguez Martín , López Cabo Marta , Balsa-Canto Eva , García Míriam R.
Published: July 2023

Unravelling the mechanisms of action of disinfectants is essential to optimise dosing regimes and minimise the emergence of antimicrobial resistance. In this work, we examined the mechanisms of action of a commonly used disinfectant—benzalkonium chloride (BAC)—over a significant pathogen—L. monocytogenes—in the food industry. For that purpose, we used modelling at multiple scales, from the cell membrane to cell population inactivation. Molecular modelling revealed that the integration of the BAC into the membrane requires three phases: (1) the approaching of BAC to the cellular membrane, (2) the absorption of BAC to its surface, and (3) the integration of the compound into the lipid bilayer, where it remains at least for several nanoseconds, probably destabilising the membrane. We hypothesised that the equilibrium of adsorption, although fast, was limiting for sufficiently large BAC concentrations, and a kinetic model was derived to describe time–kill curves of a large population of cells. The model was tested and validated with time series data of free BAC decay and time–kill curves of L. monocytogenes at different inocula and BAC dose concentrations. The knowledge gained from the molecular simulation plus the proposed kinetic model offers the means to design novel disinfection processes rationally.
Glucocorticoid Treatment in Acute Respiratory Distress Syndrome: An Overview on Mechanistic Insights and Clinical Benefit
Authors: Zhang Jinquan , Ge Peng , Liu Jie , Luo Yalan , Guo Haoya , Zhang Guixin , Xu Caiming , Chen Hailong
Published: July 2023

Acute lung injury/acute respiratory distress syndrome (ALI/ARDS), triggered by various pathogenic factors inside and outside the lungs, leads to diffuse lung injury and can result in respiratory failure and death, which are typical clinical critical emergencies. Severe acute pancreatitis (SAP), which has a poor clinical prognosis, is one of the most common diseases that induces ARDS. When SAP causes the body to produce a storm of inflammatory factors and even causes sepsis, clinicians will face a two-way choice between anti-inflammatory and anti-infection objectives while considering the damaged intestinal barrier and respiratory failure, which undoubtedly increases the difficulty of the diagnosis and treatment of SAP-ALI/ARDS. For a long time, many studies have been devoted to applying glucocorticoids (GCs) to control the inflammatory response and prevent and treat sepsis and ALI/ARDS. However, the specific mechanism is not precise, the clinical efficacy is uneven, and the corresponding side effects are endless. This review discusses the mechanism of action, current clinical application status, effectiveness assessment, and side effects of GCs in the treatment of ALI/ARDS (especially the subtype caused by SAP).
Nanoemulsions and Solid Microparticles Containing Pentyl Cinnamate to Control Aedes aegypti
Authors: Almeida Addison , Morais Waldenice , Oliveira Nicolas , Silva Wilken , Gomes Ana , Espindola Laila , Araujo Marianna , Araujo Renata , Albernaz Lorena , De Sousa Damião , Aragão Cicero , Ferreira Leandro
Published: July 2023

The Aedes aegypti mosquito is a vector of severe diseases with high morbidity and mortality rates. The most commonly used industrial larvicides have considerable toxicity for non-target organisms. This study aimed to develop and evaluate liquid and solid carrier systems to use pentyl cinnamate (PC), derived from natural sources, to control Ae. aegypti larvae. The liquid systems consisting of nanoemulsions with different lecithins systems were obtained and evaluated for stability over 30 days. Microparticles (MPs) were obtained by the spray drying of the nanoemulsions using maltodextrin as an adjuvant. Thermal, NMR and FTIR analysis indicated the presence of PC in microparticles. Indeed, the best nanoemulsion system was also the most stable and generated the highest MP yield. The PC larvicidal activity was increased in the PC nanoemulsion system. Therefore, it was possible to develop, characterize and obtain PC carrier systems active against Ae. aegypti larvae.
The Role of Alarmins in Osteoarthritis Pathogenesis: HMGB1, S100B and IL-33
Authors: Palumbo Antonino , Atzeni Fabiola , Murdaca Giuseppe , Gangemi Sebastiano
Published: July 2023

Osteoarthritis (OA) is a multifactorial disease in which genetics, aging, obesity, and trauma are well-known risk factors. It is the most prevalent joint disease and the largest disability problem worldwide. Recent findings have described the role of damage-associated molecular patterns (DAMPs) in the course of the disease. In particular, alarmins such as HMGB1, IL-33, and S100B, appear implicated in enhancing articular inflammation and favouring a catabolic switch in OA chondrocytes. The aims of this review are to clarify the molecular signalling of these three molecules in OA pathogenesis, to identify their possible use as staging biomarkers, and, most importantly, to find out whether they could be possible therapeutic targets. Osteoarthritic cartilage expresses increased levels of all three alarmins. HMGB1, in particular, is the most studied alarmin with increased levels in cartilage, synovium, and synovial fluid of OA patients. High levels of HMGB1 in synovial fluid of OA joints are positively correlated with radiological and clinical severity. Counteracting HMGB1 strategies have revealed improving results in articular cells from OA patients and in OA animal models. Therefore, drugs against this alarmin, such as anti-HMGB1 antibodies, could be new treatment possibilities that can modify the disease course since available medications only alleviate symptoms.
Evaluating the Oxidation Rate of Reduced Ferredoxin in Arabidopsis thaliana Independent of Photosynthetic Linear Electron Flow: Plausible Activity of Ferredoxin-Dependent Cyclic Electron Flow around Photosystem I
Authors: Ohnishi Miho , Maekawa Shu , Wada Shinya , Ifuku Kentaro , Miyake Chikahiro
Published: July 2023

The activity of ferredoxin (Fd)-dependent cyclic electron flow (Fd-CEF) around photosystem I (PSI) was determined in intact leaves of Arabidopsis thaliana. The oxidation rate of Fd reduced by PSI (vFd) and photosynthetic linear electron flow activity are simultaneously measured under actinic light illumination. The vFd showed a curved response to the photosynthetic linear electron flow activity. In the lower range of photosynthetic linear flow activity with plastoquinone (PQ) in a highly reduced state, vFd clearly showed a linear relationship with photosynthetic linear electron flow activity. On the other hand, vFd increased sharply when photosynthetic linear electron flow activity became saturated with oxidized PQ as the net CO2 assimilation rate increased. That is, under higher photosynthesis conditions, we observed excess vFd resulting in electron flow over photosynthetic linear electron flow. The situation in which excess vFd was observed was consistent with the previous Fd-CEF model. Thus, excess vFd could be attributed to the in vivo activity of Fd-CEF. Furthermore, the excess vFd was also observed in NAD(P)H dehydrogenase-deficient mutants localized in the thylakoid membrane. The physiological significance of the excessive vFd was discussed.
A Comprehensive Technology Platform for the Rapid Discovery of Peptide Inhibitors against SARS-CoV-2 Pseudovirus Infection
Authors: Beeg Marten , Baroni Sara , Piotti Arianna , Porta Alessia , De Luigi Ada , Cagnotto Alfredo , Gobbi Marco , Diomede Luisa , Salmona Mario
Published: July 2023

We developed and validated a technology platform for designing and testing peptides inhibiting the infectivity of SARS-CoV-2 spike protein-based pseudoviruses. This platform integrates target evaluation, in silico inhibitor design, peptide synthesis, and efficacy screening. We generated a cyclic peptide library derived from the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein and the angiotensin-converting enzyme 2 (ACE2) receptor. The cell-free validation process by ELISA competition assays and Surface Plasmon Resonance (SPR) studies revealed that the cyclic peptide c9_05, but not its linear form, binds well to ACE2. Moreover, it effectively inhibited the transduction in HEK293, stably expressing the human ACE2 receptor of pseudovirus particles displaying the SARS-CoV-2 spike in the Wuhan or UK variants. However, the inhibitory efficacy of c9_05 was negligible against the Omicron variant, and it failed to impede the entry of pseudoviruses carrying the B.1.351 (South African) spike. These variants contain three or more mutations known to increase affinity to ACE2. This suggests further refinement is needed for potential SARS-CoV-2 inhibition. Our study hints at a promising approach to develop inhibitors targeting viral infectivity receptors, including SARS-CoV-2’s. This platform also promises swift identification and evaluation of inhibitors for other emergent viruses.
Melanocortin 1 Receptor (MC1R): Pharmacological and Therapeutic Aspects
Authors: Mun Yoonwoo , Kim Woohyun , Shin Dongyun
Published: July 2023

Melanocortins play crucial roles in regulating the stress response, inflammation, and skin pigmentation. In this review, we focus on the melanocortin 1 receptor (MC1R), a G protein-coupled receptor primarily known for regulating skin pigmentation and exhibiting anti-inflammatory effects. First, we provide an overview of the structure, signaling pathways, and related diseases of MC1R. Next, we discuss the potential therapeutic use of synthetic peptides and small molecule modulators of MC1R, highlighting the development of various drugs that enhance stability through amino acid sequence modifications and small molecule drugs to overcome limitations associated with peptide characteristics. Notably, MC1R-targeted drugs have applications beyond skin pigmentation-related diseases, which predominantly affect MC1R in melanocytes. These drugs can also be useful in treating inflammatory diseases with MC1R expression present in various cells. Our review underscores the potential of MC1R-targeted drugs to treat a wide range of diseases and encourages further research in this area.
New Approach for Studying of Isoforms and High-Homology Proteins in Mammalian Cells
Authors: Soshnikova Nataliya V. , Simonov Yuriy P. , Feoktistov Alexey V. , Khamidullina Alvina I. , Yastrebova Margarita A. , Bayramova Darya O. , Tatarskiy Victor V. , Georgieva Sofia G.
Published: July 2023

In mammals, a large number of proteins are expressed as more than one isoform, resulting in the increased diversity of their proteome. Understanding the functions of isoforms is very important, since individual isoforms of the same protein can have oncogenic or pathogenic properties, or serve as disease markers. The high homology of isoforms with ubiquitous expression makes it difficult to study them. In this work, we propose a new approach for the study of protein isoforms in mammalian cells, which makes it possible to individually detect and investigate the functions of an individual isoform. The approach was developed to study the functions of isoforms of the PHF10 protein, a chromatin subunit of the PBAF remodeling complex. We demonstrated the possibility of induced simultaneous suppression of all endogenous PHF10 isoforms and the expression of a single recombinant FLAG-tagged isoform. For this purpose, we created constructs based on the pSLIK plasmid with a cloned cassette containing the recombinant gene of interest and miR30 with the corresponding shRNAs. The doxycycline-induced activation of the cassette allows on and off switching. Using this construct, we achieved the preferential expression of only one recombinant PHF10 isoform with a simultaneously reduced number of all endogenous isoforms. Our approach can be used to study the role of point mutations, the functions of individual domains and important sites, or to individually detect untagged isoforms with knockdown of all endogenous isoforms.
Murine Breast Cancer Radiosensitization Using Oxygen Microbubbles and Metformin: Vessels Are the Key
Authors: Drzał Agnieszka , Dziurman Gabriela , Hoła Paweł , Lechowski Jakub , Delalande Anthony , Swakoń Jan , Pichon Chantal , Elas Martyna
Published: July 2023

Radiotherapy is a cornerstone of cancer treatment, but tumor hypoxia and resistance to radiation remain significant challenges. Vascular normalization has emerged as a strategy to improve oxygenation and enhance therapeutic outcomes. In this study, we examine the radiosensitization potential of vascular normalization using metformin, a widely used anti-diabetic drug, and oxygen microbubbles (OMBs). We investigated the synergistic action of metformin and OMBs and the impact of this therapeutic combination on the vasculature, oxygenation, invasiveness, and radiosensitivity of murine 4T1 breast cancer. We employed in vivo Doppler ultrasonographic imaging for vasculature analysis, electron paramagnetic resonance oximetry, and immunohistochemical assessment of microvessels, perfusion, and invasiveness markers. Our findings demonstrate that both two-week metformin therapy and oxygen microbubble treatment normalize abnormal cancer vasculature. The combination of metformin and OMB yielded more pronounced and sustained effects than either treatment alone. The investigated therapy protocols led to nearly twice the radiosensitivity of 4T1 tumors; however, no significant differences in radiosensitivity were observed between the various treatment groups. Despite these improvements, resistance to treatment inevitably emerged, leading to the recurrence of hypoxia and an increased incidence of metastasis.
Transcriptomic and Functional Analyses of Two Cadmium Hyper-Enriched Duckweed Strains Reveal Putative Cadmium Tolerance Mechanisms
Authors: Yang Gui-Li , Huang Lei , Yang Xiao , Li Zhu , Liao Hai-Min , Mao Kang , Liu Zhao-Ju , Geng He-Yan , Cao Qin , Tan Ai-Juan
Published: July 2023

Cadmium (Cd) is one of the most toxic metals in the environment and exerts deleterious effects on plant growth and production. Duckweed has been reported as a promising candidate for Cd phytoremediation. In this study, the growth, Cd enrichment, and antioxidant enzyme activity of duckweed were investigated. We found that both high-Cd-tolerance duckweed (HCD) and low-Cd-tolerance duckweed (LCD) strains exposed to Cd were hyper-enriched with Cd. To further explore the underlying molecular mechanisms, a genome-wide transcriptome analysis was performed. The results showed that the growth rate, chlorophyll content, and antioxidant enzyme activities of duckweed were significantly affected by Cd stress and differed between the two strains. In the genome-wide transcriptome analysis, the RNA-seq library generated 544,347,670 clean reads, and 1608 and 2045 differentially expressed genes were identified between HCD and LCD, respectively. The antioxidant system was significantly expressed during ribosomal biosynthesis in HCD but not in LCD. Fatty acid metabolism and ethanol production were significantly increased in LCD. Alpha-linolenic acid metabolism likely plays an important role in Cd detoxification in duckweed. These findings contribute to the understanding of Cd tolerance mechanisms in hyperaccumulator plants and lay the foundation for future phytoremediation studies.
In Vivo Identification of H3K9me2/H3K79me3 as an Epigenetic Barrier to Carcinogenesis
Authors: Piro Maria Cristina , Gasperi Valeria , De Stefano Alessandro , Anemona Lucia , Cenciarelli Claudio Raffaele , Montanaro Manuela , Mauriello Alessandro , Catani Maria Valeria , Terrinoni Alessandro , Gambacurta Alessandra
Published: July 2023

The highly dynamic nature of chromatin’s structure, due to the epigenetic alterations of histones and DNA, controls cellular plasticity and allows the rewiring of the epigenetic landscape required for either cell differentiation or cell (re)programming. To dissect the epigenetic switch enabling the programming of a cancer cell, we carried out wide genome analysis of Histone 3 (H3) modifications during osteogenic differentiation of SH-SY5Y neuroblastoma cells. The most significant modifications concerned H3K27me2/3, H3K9me2, H3K79me1/2, and H3K4me1 that specify the process of healthy adult stem cell differentiation. Next, we translated these findings in vivo, assessing H3K27, H3K9, and H3K79 methylation states in biopsies derived from patients affected by basalioma, head and neck carcinoma, and bladder tumors. Interestingly, we found a drastic decrease in H3K9me2 and H3K79me3 in cancer specimens with respect to their healthy counterparts and also a positive correlation between these two epigenetic flags in all three tumors. Therefore, we suggest that elevated global levels of H3K9me2 and H3K79me3, present in normal differentiated cells but lost in malignancy, may reflect an important epigenetic barrier to tumorigenesis. This suggestion is further corroborated, at least in part, by the deranged expression of the most relevant H3 modifier enzymes, as revealed by bioinformatic analysis. Overall, our study indicates that the simultaneous occurrence of H3K9me2 and H3K79me3 is fundamental to ensure the integrity of differentiated tissues and, thus, their combined evaluation may represent a novel diagnostic marker and potential therapeutic target.
Genomic Regions Associated with Resistance to Three Rusts in CIMMYT Wheat Line “Mokue#1”
Authors: Qureshi Naeela , Singh Ravi Prakash , Gonzalez Blanca Minerva , Velazquez-Miranda Hedilberto , Bhavani Sridhar
Published: July 2023

Understanding the genetic basis of rust resistance in elite CIMMYT wheat germplasm enhances breeding and deployment of durable resistance globally. “Mokue#1”, released in 2023 in Pakistan as TARNAB Gandum-1, has exhibited high levels of resistance to stripe rust, leaf rust, and stem rust pathotypes present at multiple environments in Mexico and Kenya at different times. To determine the genetic basis of resistance, a F5 recombinant inbred line (RIL) mapping population consisting of 261 lines was developed and phenotyped for multiple years at field sites in Mexico and Kenya under the conditions of artificially created rust epidemics. DArTSeq genotyping was performed, and a linkage map was constructed using 7892 informative polymorphic markers. Composite interval mapping identified three significant and consistent loci contributed by Mokue: QLrYr.cim-1BL and QLrYr.cim-2AS on chromosome 1BL and 2AS, respectively associated with stripe rust and leaf rust resistance, and QLrSr.cim-2DS on chromosome 2DS for leaf rust and stem rust resistance. The QTL on 1BL was confirmed to be the Lr46/Yr29 locus, whereas the QTL on 2AS represented the Yr17/Lr37 region on the 2NS/2AS translocation. The QTL on 2DS was a unique locus conferring leaf rust resistance in Mexico and stem rust resistance in Kenya. In addition to these pleiotropic loci, four minor QTLs were also identified on chromosomes 2DL and 6BS associated with stripe rust, and 3AL and 6AS for stem rust, respectively, using the Kenya disease severity data. Significant decreases in disease severities were also demonstrated due to additive effects of QTLs when present in combinations.
Predicted Membrane-Associated Domains in Proteins Encoded by Novel Monopartite Plant RNA Viruses Related to Members of the Family Benyviridae
Authors: Morozov Sergey Y. , Lezzhov Alexander A. , Solovyev Andrey G.
Published: July 2023

As a continuation of our previous work, in this paper, we examine in greater detail the genome organization and some protein properties of the members of a potential group named Reclovirids and belonging to Benyviridae-related viruses. It can be proposed that the single-component Reclovirid genomes encode previously undiscovered transport genes. Indeed, analysis of the coding potential of these novel viral genomes reveals one or more cistrons ranging in size from 40 to 80 to about 600 codons, located in the 3′-terminal region of the genomic RNA, encoding proteins with predicted hydrophobic segments that are structurally diverse among Reclovirids and have no analogues in other plant RNA viruses. Additionally, in many cases, the possible methyltransferase domain of Reclovirid replicases is preceded by membrane-embedded protein segments that are not present in annotated members of the Benyviridae family. These observations suggest a general association of most Reclovirid proteins with cell membranes.
Nanostructured Aluminum Oxyhydroxide—A Prospective Support for Functional Porphyrin-Based Materials
Authors: Korobkov Stepan M. , Birin Kirill P. , Khodan Anatole N. , Grafov Oleg Yu. , Gorbunova Yulia G. , Tsivadze Aslan Yu.
Published: July 2023

A method for the grafting of unsymmetrical A2BC-type 5,15-bis(4-butoxyphenyl)-10-(4-carboxyphenyl)-20-(phenanthrenoimidazolyl)-porphyrin onto the surface of nanostructured aluminum oxyhydroxide modified with a single SiO2 layer (NAOM) was successfully developed. A straightforward procedure towards surface modification of NAOM allowed us to prepare a new porphyrin-containing hybrid material. The obtained 3D heterostructure was extensively characterized using XPS, TEM and diffuse reflectance spectroscopy. Structural and morphological peculiarities of the inorganic support before and after the immobilization procedure were studied and discussed in detail. The stability of the material against leaching and the porphyrin immobilization ratio ca. 14% by weight were also revealed.
The Characteristic Function of Blood-Derived Exosomes and Exosomal circRNAs Isolated from Dairy Cattle during the Dry Period and Mid-Lactation
Authors: Shi Yiru , Zhao Zhengjiang , He Xiao , Luo Junyi , Chen Ting , Xi Qianyun , Zhang Yongliang , Sun Jiajie
Published: July 2023

Exosomes are key mediators of intercellular communication. They are secreted by most cells and contain a cargo of protein-coding genes, long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs), which modulate recipient cell behavior. Herein, we collected blood samples from Holstein cows at days 30 (mid-lactation) and 250 (dry period) of pregnancy. Prolactin, follicle-stimulating hormone, luteinizing hormone, estrogen, and progesterone levels showed an obvious increase during D250. We then extracted exosomes from bovine blood samples and found that their sizes generally ranged from 100 to 200 nm. Further, Western blotting validated that they contained CD9, CD63, and TSG101, but not calnexin. Blood-derived exosomes significantly promoted the proliferation of mammary epithelial cells, particularly from D250. This change was accompanied by increased expression levels of proliferation marker proteins PCNA, cyclin D, and cyclin E, as detected by EdU assay, cell counting kit-8 assay, and flow cytometric cell cycle analysis. Moreover, we treated mammary epithelial cells with blood-derived exosomes that were isolated from the D30 and D250 periods. And RNA-seq of two groups of cells led to the identification of 839 differentially expressed genes that were significantly enriched in KEGG signaling pathways associated with apoptosis, cell cycle and proliferation. In bovine blood-derived exosomes, we found 12,747 protein-coding genes, 31,181 lncRNAs, 9374 transcripts of uncertain coding potential (TUCP) candidates, and 460 circRNAs, and 32 protein-coding genes, 806 lncRNAs, 515 TUCP candidates, and 45 circRNAs that were differentially expressed between the D30 and D250 groups. We selected six highly expressed and four differentially expressed circRNAs to verify their head-to-tail splicing using PCR and Sanger sequencing. To summarize, our findings improve our understanding of the key roles of blood-derived exosomes and the characterization of exosomal circRNAs in mammary gland development.
Phytochemicals and Vitamin D for a Healthy Life and Prevention of Diseases
Authors: Santa Kazuki , Watanabe Kenji , Kumazawa Yoshio , Nagaoka Isao
Published: July 2023

A variety of phytocompounds contained in medical plants have been used as medication, including Kampo (traditional Japanese) medicine. Phytochemicals are one category of the chemical compounds mainly known as antioxidants, and recently, their anti-inflammatory effects in preventing chronic inflammation have received much attention. Here, we present a narrative review of the health-promotion and disease-prevention effects of phytochemicals, including polyphenols, the latter of which are abundant in onions, oranges, tea, soybeans, turmeric, cacao, and grapes, along with the synergetic effects of vitamin D. A phenomenon currently gaining popularity in Japan is finding non-disease conditions, so-called ME-BYO (mibyou) and treating them before they develop into illnesses. In addition to lifestyle-related diseases such as metabolic syndrome and obesity, dementia and frailty, commonly found in the elderly, are included as underlying conditions. These conditions are typically induced by chronic inflammation and might result in multiple organ failure or cancer if left untreated. Maintaining gut microbiota is important for suppressing (recently increasing) intestinal disorders and for upregulating immunity. During the COVID-19 pandemic, the interest in phytochemicals and vitamin D for disease prevention increased, as viral and bacterial infection to the lung causes fatal inflammation, and chronic inflammation induces pulmonary fibrosis. Furthermore, sepsis is a disorder inducing severe organ failure by the infection of microbes, with a high mortality ratio in non-coronary ICUs. However, antimicrobial peptides (AMPs) working using natural immunity suppress sepsis at the early stage. The intake of phytochemicals and vitamin D enhances anti-inflammatory effects, upregulates immunity, and reduces the risk of chronic disorders by means of keeping healthy gut microbiota. Evidence acquired during the COVID-19 pandemic revealed that daily improvement and prevention of underlying conditions, in terms of lifestyle-related diseases, is very important because they increase the risk of infectious diseases. This narrative review discusses the importance of the intake of phytochemicals and vitamin D for a healthy lifestyle and the prevention of ME-BYO, non-disease conditions.
Phosphatidylethanol (PEth) in Blood as a Marker of Unhealthy Alcohol Use: A Systematic Review with Novel Molecular Insights
Authors: Perilli Matteo , Toselli Federico , Franceschetto Lisa , Cinquetti Alessandro , Ceretta Arianna , Cecchetto Giovanni , Viel Guido
Published: July 2023

The Alcohol Use Disorders Identification Test (AUDIT) and its short form, the AUDIT-C, the main clinical instruments used to identify unhealthy drinking behaviors, are influenced by memory bias and under-reporting. In recent years, phosphatidylethanol (PEth) in blood has emerged as a marker of unhealthy alcohol use. This systematic review aims to investigate the molecular characteristics of PEth and summarize the last ten years of published literature and its use compared to structured questionnaires. A systematic search was performed, adhering to PRISMA guidelines, through “MeSH” and “free-text” protocols in the databases PubMed, SCOPUS, and Web of Science. The inclusion criteria were as follows: PEth was used for detecting unhealthy alcohol consumption in the general population and quantified in blood through liquid chromatography coupled to mass spectrometry, with full texts in the English language. Quality assessment was performed using the JBI critical appraisal checklist. Twelve papers were included (0.79% of total retrieved records), comprising nine cross-sectional studies and three cohort studies. All studies stratified alcohol exposure and quantified PEth 16:0/18:1 through liquid chromatography coupled to mass spectrometry (LC-MS) in liquid blood or dried blood spots (DBS) with lower limits of quantitation (LLOQ) ranging from 1.7 ng/mL to 20 ng/mL. A correlation between blood PEth level and the amount of alcohol ingested in the previous two weeks was generally observed. PEth interpretative cut-offs varied greatly among the included records, ranging from 4.2 ng/mL to 250 ng/mL, with sensitivity and specificity in the ranges of 58–100% and 64–100%, respectively. Although the biomarker seems promising, further research elucidating the variability in PEth formation and degradation, as well as the molecular mechanisms behind that variability, are necessary.
Electron Scattering from 1-Methyl-5-Nitroimidazole: Cross-Sections for Modeling Electron Transport through Potential Radiosensitizers
Authors: Lozano Ana I. , Álvarez Lidia , García-Abenza Adrián , Guerra Carlos , Kossoski Fábris , Rosado Jaime , Blanco Francisco , Oller Juan Carlos , Hasan Mahmudul , Centurion Martin , Weber Thorsten , Slaughter Daniel S. , Mootheril Deepthy M. , Dorn Alexander , Kumar Sarvesh , Limão-Vieira Paulo , Colmenares Rafael , García Gustavo
Published: July 2023

In this study, we present a complete set of electron scattering cross-sections from 1-Methyl-5-Nitroimidazole (1M5NI) molecules for impact energies ranging from 0.1 to 1000 eV. This information is relevant to evaluate the potential role of 1M5NI as a molecular radiosensitizers. The total electron scattering cross-sections (TCS) that we previously measured with a magnetically confined electron transmission apparatus were considered as the reference values for the present analysis. Elastic scattering cross-sections were calculated by means of two different schemes: The Schwinger multichannel (SMC) method for the lower energies (below 15 eV) and the independent atom model-based screening-corrected additivity rule with interferences (IAM-SCARI) for higher energies (above 15 eV). The latter was also applied to calculate the total ionization cross-sections, which were complemented with experimental values of the induced cationic fragmentation by electron impact. Double differential ionization cross-sections were measured with a reaction microscope multi-particle coincidence spectrometer. Using a momentum imaging spectrometer, direct measurements of the anion fragment yields and kinetic energies by the dissociative electron attachment are also presented. Cross-sections for the other inelastic channels were derived with a self-consistent procedure by sampling their values at a given energy to ensure that the sum of the cross-sections of all the scattering processes available at that energy coincides with the corresponding TCS. This cross-section data set is ready to be used for modelling electron-induced radiation damage at the molecular level to biologically relevant media containing 1M5NI as a potential radiosensitizer. Nonetheless, a proper evaluation of its radiosensitizing effects would require further radiobiological experiments.
Combination of Bisphenol A and Its Emergent Substitute Molecules Is Related to Heart Disease and Exerts a Differential Effect on Vascular Endothelium
Authors: Moreno-Gómez-Toledano Rafael , Delgado-Marín María , Sánchez-Esteban Sandra , Cook-Calvete Alberto , Ortiz Sara , Bosch Ricardo J. , Saura Marta
Published: July 2023

Plastic production, disposal, and recycling systems represent one of the higher challenges for the planet’s health. Its direct consequence is the release of endocrine disruptors, such as bisphenol A (BPA), and its emerging substitute molecules, bisphenol F and S (BPF and BPS), into the environment. Consequently, bisphenols are usually present in human biological fluids. Since BPA, BPS, and BPF have structural analogies and similar hormonal activity, their combined study is urgently needed. The present manuscript studied the effect of the mixture of bisphenols (BPmix) in one of the world’s largest human cohorts (NHANES cohort). Descriptive and comparative statistics, binomial and multinomial logistic regression, weighted quantile sum regression, quantile g-computation, and Bayesian kernel machine regression analysis determined a positive association between BPmix and heart disease, including confounders age, gender, BMI, ethnicity, Poverty/Income Ratio, and serum cotinine. Endothelial dysfunction is a hallmark of cardiovascular disease; thus, the average ratio of bisphenols found in humans was used to conduct murine aortic endothelial cell studies. The first results showed that BPmix had a higher effect on cell viability than BPA, enhancing its deleterious biological action. However, the flow cytometry, Western blot, and immunofluorescence assays demonstrated that BPmix induces a differential effect on cell death. While BPA exposure induces necroptosis, its combination with the proportion determined in the NHANES cohort induces apoptosis. In conclusion, the evidence suggests the need to reassess research methodologies to study endocrine disruptors more realistically.
Surveillance of Human Rotaviruses in Wuhan, China (2019–2022): Whole-Genome Analysis of Emerging DS-1-like G8P[8] Rotavirus
Authors: Zhou Xuan , Wang Yuanhong , Chen Nan , Pang Beibei , Liu Manqing , Cai Kun , Kobayashi Nobumichi
Published: July 2023

Group A rotaviruses (RVAs) are major etiologic agents of gastroenteritis in infants and young children worldwide. To study the prevalence and genetic characteristics of RVAs, a hospital-based surveillance study was conducted in Wuhan, China from June 2019 through May 2022. The detection rates of RVAs were 19.40% (142/732) and 3.51% (8/228) in children and adults, respectively. G9P[8] was the predominant genotype, followed by G8P[8] and G3P[8]. G8P[8] emerged and was dominant in the 2021–2022 epidemic season. The genome constellation of six G8P[8] strains was assigned to G8-P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2. Phylogenetic analysis revealed that the VP7, VP4, VP2, VP3, NSP1, NSP2, NSP3, and NSP5 genes of these G8P[8] strains clustered closely with those of the G8P[8] strains in Asia and were distant from those of the P[8] and G2P[4] strains simultaneously detected in Wuhan. In contrast, the VP1, VP6, and NSP4 genes were closely related to the typical G2P[4] rotavirus, including those of G2P[4] strains simultaneously detected in Wuhan. The detection rate of RVAs decreased in the COVID-19 pandemic era. It was deduced that the G8P[8] rotaviruses that emerged in China may be reassortants, carrying the VP6, VP1, and NSP4 genes derived from the G2P[4] rotavirus in the backbone of the neighboring DS-1-like G8P[8] strains represented by CAU17L-103.