bluuebunny/crossref_metadata_2025 huggingface dataset:
Serum Amino Acid Profiling in Children with Autistic Spectrum Disorder: Insights from a Single-Center Study in Southern Romania
Authors: Anastasescu Cătălina Mihaela , Gheorman Veronica , Popescu Florica , Stoicănescu Eugen-Cristi , Gheorman Victor , Riza Anca-Lelia , Badea Oana , Streață Ioana , Militaru Felicia , Udriștoiu Ion
Published: September 2023

The objective of this study was to analyze the serum amino acid profile in children diagnosed with autistic spectrum disorder (ASD) in southern Romania. The analysis aimed to provide insights into the underlying metabolic dysregulations associated with ASD. ASD is a neurodevelopmental disorder characterized by impaired social interaction, communication deficits, and restricted repetitive behaviors. Although the exact cause of ASD is largely unknown, recent evidence suggests that abnormalities in amino acid metabolism may contribute to its pathogenesis. Therefore, studying the amino acid profile in children with ASD could offer valuable information for understanding the metabolic disturbances associated with this complex disorder. This single-center study examined serum samples from children diagnosed with ASD, utilizing advanced analytical techniques to quantify the levels of different amino acids, amino acid derivatives, and amino acid-like substances. The results showed a lower level of taurine and a higher level of asparagine and leucine in the ASD group versus the control group. In the ASD group, we observed significant differences in tryptophan and alpha-aminobutyric acid levels based on age, with higher tryptophan levels in children older than 7 years when compared to children younger than 7 years; however, no significant correlations were found with the ASD group older than 7 years old. Additionally, younger children with ASD exhibited higher levels of alpha-aminobutyric acid than older children with ASD. The findings from this study contribute to the growing body of knowledge on the metabolic aspects of ASD, highlighting potential biomarkers and therapeutic targets for improving the management and treatment of ASD in children.
Streptococcus zooepidemicus Meningitis in an HIV-Positive Horse Breeder Patient: A Case Study and Literature Review
Authors: Argirova Petya , Kalchev Yordan , Baltadzhiev Ivan , Stoycheva Mariyana , Murdjeva Marianna
Published: September 2023

Streptococcus equi subsp. zooepidemicus is a rare etiologic agent of bacterial meningitis in humans. The disease is a zoonotic infection and is transmitted through close contact with domestic animals, mainly horses. Only 37 cases of Streptococcus zooepidemicus meningitis have been reported in the literature until July 2023. The aim of this study is to present a rare clinical case of S. zooepidemicus-related meningitis in a human immunodeficiency virus (HIV)-positive patient and analyze the literature. We present a 23-year-old horse breeder patient with advanced immunosuppression due to acquired immunodeficiency syndrome (AIDS) and S. zooepidemicus meningitis, admitted at the Clinic of Infectious Diseases, St. George University Hospital, Plovdiv. The course of meningitis was severe since the beginning, with significant cerebral edema, disturbances in consciousness, persistent fever, and the development of complications against the background of AIDS-related conditions. S. zooepidemicus was microbiologically detected from cerebrospinal fluid culture. After prolonged treatment and a long hospital stay, the patient’s condition improved, and eventually he was discharged and recovered from the acute neuroinfection. Although extremely rare, S. zooepidemicus should be considered in patients with clinical and laboratory evidence of bacterial meningitis who have contact with animals, especially horses, other domestic animals, and their dairy products, as well as in immunocompromised patients. To the best of our knowledge, the current clinical case is the first report of S. zooepidemicus-related meningitis in a patient with HIV/AIDS.
Legionella spp. Monitoring in the Water Supply Systems of Accommodation Facilities in Sardinia, Italy: A Two-Year Retrospective Analysis
Authors: Marras Luisa , Bertolino Giacomo , Sanna Adriana , Carraro Valentina , Coroneo Valentina
Published: September 2023

Travel-associated Legionnaires’ disease is a significant public health concern worldwide. A high number of cases are reported every year among travellers who stay at guest houses, hotels, and spas. Indeed, hot water systems, showers, and air-conditioning systems can be contaminated by Legionella, which grows at 25–42 °C. Studies have shown that in Sardinia, especially during the summer months, the water circulation in the hotels’ pipes is exposed to extremely high temperatures. As a result, this study was conducted to assess the colonization of hotel water systems by Legionella in Sardinia, concerning a recent EU directive 2020/2184 for drinking water with a limit of 1000 CFU /L. Methods. A total of 112 accommodation facilities were analyzed, of which 61.3% were found to be colonized with Legionella, and out of a total of 807 samples, 32.5% were positive for Legionella presence. The results showed a higher number of positive samples in the summer season. This was also associated with the higher concentration presence of >1000 CFU/L in the samples. Consequently, this study confirms that local hotel operators should improve their water safety and prevention plans, especially in spring and summer.
Exploring Students’ Emotional Well-Being in the Ideal University Hostel Using the Qualitative Repertory Grid Technique
Authors: Jameel Fanan , Agiel Ahmed
Published: September 2023

One of the ramifications of the COVID-19 pandemic is that it has lent urgency to ongoing discussions on mental well-being, particularly among university students. While standard techniques are available to diagnose mental health disorders such as depression, anxiety, and stress, ambiguity persists regarding the emotional aspect of well-being. Emotional well-being (EWB) is a recently developed concept that seeks to understand the contribution of emotions to one’s well-being. Interactive approaches for such investigations are recommended to understand people’s contextual experiences in the built environment. This study utilizes a qualitative approach, underpinned by personal construct theory (PCT) and the qualitative repertory grid technique (RGT), to understand how university hostel designs can contribute to students’ emotional well-being. We interviewed fifteen students from the United Arab Emirates University (UAEU) and obtained their perceptions of three built environments they experienced and an ideal place they imagined. The results unveiled design-related factors associated with students’ emotional constructs and elucidated characteristics of an ‘ideal’ hostel in response to these emotional constructs. These findings enrich our knowledge of EWB within university hostels offering insights for the future design that consider the emotional aspect of well-being for residents.
School-Level Socioeconomic Status and Nutrient Content of Outdoor Food/Beverage Advertisements
Authors: Ruggles Phoebe R. , Thomas Jacob E. , Poulos Natalie S. , Pasch Keryn E.
Published: September 2023

We examined if areas around schools with more students of lower socioeconomic status (SES) have more total food/beverage advertisements and/or more advertisements with poorer nutritional content as compared to areas around schools with fewer students with lower SES. All outdoor food/beverage advertisements within a half-mile radius of 47 middle and high schools in the United States were objectively documented in 2012 and coded for nutritional content. The total number of advertisements and the macronutrient and micronutrient contents (total calories, fat (g), protein (g), carbohydrate (g), sugar (g), and sodium (mg)) of food and beverage items depicted in the advertisements were calculated. In total, 9132 unique advertisements were recorded, with 3153 ads displaying food and beverages that could be coded for nutrient content. Schools located in areas of lower SES (≥60% students receiving free/reduced-price lunch) had significantly more advertisements displaying food and beverages that could be coded for nutrient content (z = 2.01, p = 0.04), as well as advertisements that contained more sodium (z = 2.20, p = 0.03), as compared to schools located in areas of higher SES. There were no differences in calorie, fat, protein, carbohydrate, or sugar content. Policies to reduce the prevalence of outdoor food and beverage advertising are warranted.
Novel CNN-Based Approach for Reading Urban Form Data in 2D Images: An Application for Predicting Restaurant Location in Seoul, Korea
Authors: Yang Jeyun , Kwon Youngsang
Published: September 2023

Artificial intelligence (AI) has demonstrated its ability to complete complex tasks in various fields. In urban studies, AI technology has been utilized in some limited domains, such as control of traffic and air quality. This study uses AI to better understand diverse urban studies data through a novel approach that uses a convolutional neural network (CNN). In this study, a building outline in the form of a two-dimensional image is used with its corresponding metadata to test the applicability of CNN in reading urban data. MobileNet, a high-efficiency CNN model, is trained to predict the location of restaurants in each building in Seoul, Korea. Consequently, using only 2D image data, the model satisfactorily predicts the locations of restaurants (AUC = 0.732); the model with 2D images and their metadata has higher performance but has an overfitting problem. In addition, the model using only 2D image data accurately predicts the regional distribution of restaurants and shows some typical urban forms with restaurants. The proposed model has several technical limitations but shows the potential to provide a further understanding of urban settings.
In Silico Mixed Ligand/Structure-Based Design of New CDK-1/PARP-1 Dual Inhibitors as Anti-Breast Cancer Agents
Authors: Bono Alessia , La Monica Gabriele , Alamia Federica , Mingoia Francesco , Gentile Carla , Peri Daniele , Lauria Antonino , Martorana Annamaria
Published: September 2023

CDK-1 and PARP-1 play crucial roles in breast cancer progression. Compounds acting as CDK-1 and/or PARP-1 inhibitors can induct cell death in breast cancer with a selective synthetic lethality mechanism. A mixed treatment by means of CDK-1 and PARP-1 inhibitors resulted in radical breast cancer cell growth reduction. Inhibitors with a dual target mechanism of action could arrest cancer progression by simultaneously blocking the DNA repair mechanism and cell cycle, resulting in advantageous monotherapy. To this aim, in the present work, we identified compound 645656 with a significant affinity for both CDK-1 and PARP-1 by a mixed ligand- and structure-based virtual screening protocol. The Biotarget Predictor Tool was used at first in a Multitarget mode to filter the large National Cancer Institute (NCI) database. Then, hierarchical docking studies were performed to further screen the compounds and evaluate the ligands binding mode, whose putative dual-target mechanism of action was investigated through the correlation between the antiproliferative activity data and the target proteins’ (CDK-1 and PARP-1) expression pattern. Finally, a Molecular Dynamics Simulation confirmed the high stability of the most effective selected compound 645656 in complex with both PARP-1 and CDK-1.
Plasma Neurofilament Light Chains as Blood-Based Biomarkers for Early Diagnosis of Canine Cognitive Dysfunction Syndrome
Authors: Wu Chung-Hsin , Pan Xun-Sheng , Su Li-Yu , Yang Shieh-Yueh
Published: September 2023

The number of elderly dogs is increasing significantly worldwide, and many elderly dogs develop canine cognitive dysfunction syndrome (CCDS). CCDS is the canine analog of Alzheimer’s disease (AD) in humans. It is very important to develop techniques for detecting CDDS in dogs. Thus, we used the detection of neurofilament light chains (NfL) in plasma as a blood-based biomarker for the early diagnosis of canine Alzheimer’s disease using immunomagnetic reduction (IMR) technology by immobilizing NfL antibodies on magnetic nanoparticles. According to the 50-point CCDS rating scale, we divided 36 dogs into 15 with CCDS and 21 without the disease. The results of our IMR assay showed that the plasma NfL levels of dogs with CCDS were significantly increased compared to normal dogs (p < 0.01). By plasma biochemical analysis, we further confirmed that the liver and renal dysfunction biomarkers of dogs with CCDS were significantly elevated compared to normal dogs (p < 0.01–0.05). On the basis of our preliminary study, we propose that IMR technology could be an ideal biosensor for detecting plasma NfL for the early diagnosis of CCDS.
Extracellular Vesicles from Immune Cells: A Biomedical Perspective
Authors: Moya-Guzmán María José , de Solminihac Javiera , Padilla Cristina , Rojas Carolina , Pinto Camila , Himmel Tomás , Pino-Lagos Karina
Published: September 2023

Research on the role of extracellular vesicles (sEV) in physiology has demonstrated their undoubted importance in processes such as the transportation of molecules with significance for cell metabolism, cell communication, and the regulation of mechanisms such as cell differentiation, inflammation, and immunity. Although the role of EVs in the immune response is actively investigated, there is little literature revising, in a comprehensive manner, the role of small EVs produced by immune cells. Here, we present a review of studies reporting the release of sEV by different types of leukocytes and the implications of such observations on cellular homeostasis. We also discuss the function of immune cell-derived sEV and their relationship with pathological states, highlighting their potential application in the biomedical field.
Citri Reticulatae Pericarpium Limits TLR-4-Triggered Inflammatory Response in Raw264.7 Macrophages by Activating RasGRP3
Authors: Lee Ji Hye , Kim Yon-Suk , Leem Kang Hyun
Published: September 2023

Inflammation is an important immune response to pathogen invasion, but excessive inflammation leads to tissue injury and even cytokine storm. Therefore, proper response is needed depending on the intensity of the infection. Ras guanine nucleotide releasing protein 3 (RasGRP3) is a regulator of the TLR-mediated response. In low-intensity inflammation, it negatively regulates production of pro-inflammatory cytokines, especially IL-6. Citri Reticulatae Pericarpium, the peel of Citrus reticulata Blanco, is a major medicinal herb in Korean medicine. The present study aims to investigate whether the Citri Reticulatae Pericarpium extract (CRE) has immunomodulatory activity using the Raw264.7 macrophage. Also, we investigated the effect of CRE on RasGRP3 expression. In the present study, CRE reduced IL-6 production in the low-LPS environment (1 ng/mL) and did not in the high-LPS environment (100 ng/mL). The suppression of IL-6 production in the low-LPS environment (1 ng/mL) was abolished after the pretreatment of RasGRP3 siRNA. The reduced RasGRP3 protein content by 100 ng/mL LPS treatment was increased by CRE treatment. Additionally, nobiletin, a major component of CRE showed a suppressive effect on IL-6 production in the low-LPS environment (1 ng/mL). The present results suggest that CRE alleviates inflammatory response via activating RasGRP3 expression in low-intensity inflammation.
Oral Iron Absorption of Ferric Citrate Hydrate and Hepcidin-25 in Hemodialysis Patients: A Prospective, Multicenter, Observational Riona-Oral Iron Absorption Trial
Authors: Tomosugi Naohisa , Koshino Yoshitaka , Ogawa Chie , Maeda Kunimi , Shimada Noriaki , Tomita Kimio , Daimon Shoichiro , Shikano Tsutomu , Ryu Kazuyuki , Takatani Toru , Sakamoto Kazuya , Ueyama Satonori , Nagasaku Daisuke , Nakamura Masato , Ra Shibun , Nishimura Masataka , Takagi Chieko , Ishii Yoji , Kudo Noritoshi , Takechi Shinsuke , Ishizu Takashi , Yanagawa Takamoto , Fukuda Masamichi , Nitta Yutaka , Yamaoka Takayuki , Saito Taku , Imayoshi Suzuko , Omata Momoyo , Oshima Joji , Onozaki Akira , Ichihashi Hiroaki , Matsushima Yasuhisa , Takae Hisahito , Nakazawa Ryoichi , Ikeda Koichi , Tsuboi Masato , Konishi Keiko , Kato Shouzaburo , Ooura Maki , Koyama Masaki , Naganuma Tsukasa , Ogi Makoto , Katayama Shigeyuki , Okumura Toshiaki , Kameda Shigemi , Shirai Sayuri
Published: September 2023

Oral ferric citrate hydrate (FCH) is effective for iron deficiencies in hemodialysis patients; however, how iron balance in the body affects iron absorption in the intestinal tract remains unclear. This prospective observational study (Riona-Oral Iron Absorption Trial, R-OIAT, UMIN 000031406) was conducted at 42 hemodialysis centers in Japan, wherein 268 hemodialysis patients without inflammation were enrolled and treated with a fixed amount of FCH for 6 months. We assessed the predictive value of hepcidin-25 for iron absorption and iron shift between ferritin (FTN) and red blood cells (RBCs) following FCH therapy. Serum iron changes at 2 h (ΔFe2h) after FCH ingestion were evaluated as iron absorption. The primary outcome was the quantitative delineation of iron variables with respect to ΔFe2h, and the secondary outcome was the description of the predictors of the body’s iron balance. Generalized estimating equations (GEEs) were used to identify the determinants of iron absorption during each phase of FCH treatment. ΔFe2h increased when hepcidin-25 and TSAT decreased (−0.459, −0.643 to −0.276, p = 0.000; −0.648, −1.099 to −0.197, p = 0.005, respectively) in GEEs. FTN increased when RBCs decreased (−1.392, −1.749 to −1.035, p = 0.000) and hepcidin-25 increased (0.297, 0.239 to 0.355, p = 0.000). Limiting erythropoiesis to maintain hemoglobin levels induces RBC reduction in hemodialysis patients, resulting in increased hepcidin-25 and FTN levels. Hepcidin-25 production may prompt an iron shift from RBC iron to FTN iron, inhibiting iron absorption even with continued FCH intake.
Role of Rho/MRTF in Aggressive Vemurafenib-Resistant Murine Melanomas and Immune Checkpoint Upregulation
Authors: Foda Bardees M. , Neubig Richard R.
Published: September 2023

Cutaneous melanoma is the deadliest skin cancer. Most have Ras-MAPK pathway (BRAFV600E or NRAS) mutations and highly effective targeted therapies exist; however, they and immune therapies are limited by resistance, in part driven by small GTPase (Rho and Rac) activation. To facilitate preclinical studies of combination therapies to provide durable responses, we describe the first mouse melanoma lines resistant to BRAF inhibitors. Treatment of mouse lines, YUMM1.7 and YUMMER, with vemurafenib (Vem), the BRAFV600E-selective inhibitor, resulted in high-level resistance (IC50 shifts 20–30-fold). Resistant cells showed enhanced activation of Rho and the downstream transcriptional coactivator, myocardin-related transcription factor (MRTF). Resistant cells exhibited increased stress fibers, nuclear translocation of MRTF-A, and an increased MRTF-A gene signature. Pharmacological inhibition of the Rho/MRTF pathway using CCG-257081 reduced viability of resistant lines and enhanced sensitivity to Vem. Remarkably, co-treatment of parental lines with Vem and CCG-257081 eliminated resistant colony development. Resistant cells grew more slowly in vitro, but they developed highly aggressive tumors with a shortened survival of tumor-bearing mice. Increased expression of immune checkpoint inhibitor proteins (ICIs) in resistant lines may contribute to aggressive in vivo behavior. Here, we introduce the first drug-resistant mouse melanoma models for assessing combinations of targeted and immune therapies.
European Real-World Assessment of the Clinical Validity of a CE-IVD Panel for Ultra-Fast Next-Generation Sequencing in Solid Tumors
Authors: Normanno Nicola , Machado José Carlos , Pescarmona Edoardo , Buglioni Simonetta , Navarro Lara , Esposito Abate Riziero , Ferro Anabela , Mensink Rob , Lambiase Matilde , Lespinet-Fabre Virginie , Calgua Byron , Jermann Philip M. , Ilié Marius , Hofman Paul
Published: September 2023

Molecular profiling of solid tumors facilitates personalized, targeted therapeutic interventions. The ability to perform next-generation sequencing (NGS), especially from small tissue samples, in a short turnaround time (TAT) is essential to providing results that enable rapid clinical decisions. This multicenter study evaluated the performance of a CE in vitro diagnostic (IVD) assay, the Oncomine Dx Express Test, on the Ion Torrent Genexus System for detecting DNA and RNA variants in solid tumors. Eighty-two archived formalin-fixed paraffin embedded (FFPE) tissue samples from lung, colorectal, central nervous system, melanoma, breast, gastric, thyroid, and soft tissue cancers were used to assess the presence of single nucleotide variants (SNVs), insertions and deletions (indels), copy number variations (CNVs), gene fusions, and splice variants. These clinical samples were previously characterized at the various academic centers using orthogonal methods. The Oncomine Dx Express Test showed high performance with 100% concordance with previous characterization for SNVs, indels, CNVs, gene fusions, and splice variants. SNVs and indels with allele frequencies as low as 5% were correctly identified. The test detected all the expected ALK, RET, NTRK1, and ROS1 fusion isoforms and MET exon 14-skipping splice variants. The average TAT from extracted nucleic acids to the final variant report was 18.3 h. The Oncomine Dx Express Test in combination with the Ion Torrent Genexus System is a CE-IVD-compliant, performant, and multicenter reproducible method for NGS detection of actionable biomarkers from a range of tumor samples, providing results in a short TAT that could support timely decision- making for targeted therapeutic interventions.
New Approaches for Pb(II) Removal from Aqueous Media Using Nanopowder Sodium Titanosilicate: Kinetics Study and Thermodynamic Behavior
Authors: Popovici Ionela Carazeanu , Dobrinaș Simona , Soceanu Alina , Popescu Viorica , Prodan Gabriel , Omer Ichinur
Published: September 2023

Microporous sodium titanosilicate, Na2TiSiO5, has been successfully prepared using the sol–gel method. The structural and morphological characterization of synthesized product has been made via thermal analyses (TG-DTG), X-ray diffraction (XRD), and electron microscopy (SEM and TEM). Adsorption properties of the synthesized Na2TiSiO5 nanopowder for Pb(II) removal of aqueous media was investigated in different experimental conditions such as the contact time, the initial metal concentration, the pH, and the temperature. The Pb(II) adsorption on Na2TiSiO5 was discussed according to the kinetics and thermodynamics models. The adsorption kinetics of Pb(II) have been better described by the PS-order kinetic model which has the highest fitting correlation coefficients (R2: 0.996–0.999) out of all the other models. The adsorption results have been successfully fitted with the Langmuir and Redlich–Paterson models (R2: 0.9936–0.9996). The calculated thermodynamic parameters indicate that the Pb(II) adsorption is an endothermic process, with increased entropy, having a spontaneous reaction. The results have revealed a maximum adsorption capacity of 155.71 mg/g at 298 K and a very high adsorption rate at the beginning, more than 85% of the total amount of Pb(II) being removed within the first 120 min, depending on the initial concentration.
Effects of Biological Nitrogen Metabolism on Glufosinate-Susceptible and -Resistant Goosegrass (Eleusine indica L.)
Authors: Luo Qiyu , Fu Hao , Hu Fang , Li Shiguo , Chen Qiqi , Peng Shangming , Yang Cunyi , Liu Yaoguang , Chen Yong
Published: September 2023

Glufosinate is a broad-spectrum herbicide used to control most weeds in agriculture worldwide. Goosegrass (Eleusine indica L.) is one of the top ten malignant weeds across the world, showing high tolerance to glufosinate via different mechanisms that are not yet fully understood. This study revealed that nitrogen metabolism could be a target-resistant site, providing clues to finally clarify the mechanism of glufosinate resistance in resistant goosegrass populations. Compared to susceptible goosegrass (NX), the resistant goosegrass (AUS and CS) regarding the stress of glufosinate showed stronger resistance with lower ammonia contents, higher target enzyme GS (glutamine synthetase) activity, and lower GOGAT (glutamine 2-oxoglutarate aminotransferase) activity. The GDH (glutamate dehydrogenase) activity of another pathway increased, but its gene expression was downregulated in resistant goosegrass (AUS). Analyzing the transcriptome and proteome data of goosegrass under glufosinate stress at 36 h showed that the KEGG pathway of the nitrogen metabolism was enriched in glufosinate-susceptible goosegrass (NX), but not in glufosinate-resistant goosegrass (CS and AUS). Several putative target genes involved in glufosinate stress countermeasures were identified. This study provides specific insights into the nitrogen metabolism of resistant goosegrass, and gives a basis for future functional verification of glufosinate-tolerance genes in plants.
Unraveling the Impact of Acetylation Patterns in Chitosan Oligomers on Cu2+ Ion Binding: Insights from DFT Calculations
Authors: Singh Ratna , Smiatek Jens , Moerschbacher Bruno M.
Published: September 2023

Chitosans are partially acetylated polymers of glucosamine, structurally characterized by their degree of polymerization as well as their fraction and pattern of acetylation. These parameters strongly influence the physico-chemical properties and biological activities of chitosans, but structure-function relationships are only poorly understood. As an example, we here investigated the influence of acetylation on chitosan-copper complexation using density functional theory. We investigated the electronic structures of completely deacetylated and partially acetylated chitosan oligomers and their copper-bound complexes. Frontier molecular orbital theory revealed bonding orbitals for electrophiles and antibonding orbitals for nucleophiles in fully deacetylated glucosamine oligomers, while partially acetylated oligomers displayed bonding orbitals for both electrophiles and nucleophiles. Our calculations showed that the presence of an acetylated subunit in a chitosan oligomer affects the structural and the electronic properties of the oligomer by generating new intramolecular interactions with the free amino group of neighboring deacetylated subunits, thereby influencing its polarity. Furthermore, the band gap energy calculated from the fully and partially deacetylated oligomers indicates that the mobility of electrons in partially acetylated chitosan oligomers is higher than in fully deacetylated oligomers. In addition, fully deacetylated oligomers form more stable complexes with higher bond dissociation energies with copper than partially acetylated ones. Interestingly, in partially acetylated oligomers, the strength of copper binding was found to be dependent on the pattern of acetylation. Our study provides first insight into the influence of patterns of acetylation on the electronic and ion binding properties of chitosans. Depending on the intended application, the obtained results can serve as a guide for the selection of the optimal chitosan for a specific purpose.
The Dual Role of Autophagy in Postischemic Brain Neurodegeneration of Alzheimer’s Disease Proteinopathy
Authors: Pluta Ryszard
Published: September 2023

Autophagy is a self-defense and self-degrading intracellular system involved in the recycling and elimination of the payload of cytoplasmic redundant components, aggregated or misfolded proteins and intracellular pathogens to maintain cell homeostasis and physiological function. Autophagy is activated in response to metabolic stress or starvation to maintain homeostasis in cells by updating organelles and dysfunctional proteins. In neurodegenerative diseases, such as cerebral ischemia, autophagy is disturbed, e.g., as a result of the pathological accumulation of proteins associated with Alzheimer’s disease and their structural changes. Postischemic brain neurodegeneration, such as Alzheimer’s disease, is characterized by the accumulation of amyloid and tau protein. After cerebral ischemia, autophagy was found to be activated in neuronal, glial and vascular cells. Some studies have shown the protective properties of autophagy in postischemic brain, while other studies have shown completely opposite properties. Thus, autophagy is now presented as a double-edged sword with possible therapeutic potential in brain ischemia. The exact role and regulatory pathways of autophagy that are involved in cerebral ischemia have not been conclusively elucidated. This review aims to provide a comprehensive look at the advances in the study of autophagy behavior in neuronal, glial and vascular cells for ischemic brain injury. In addition, the importance of autophagy in neurodegeneration after cerebral ischemia has been highlighted. The review also presents the possibility of modulating the autophagy machinery through various compounds on the development of neurodegeneration after cerebral ischemia.
Measuring Up: A Comparison of TapeStation 4200 and Bioanalyzer 2100 as Measurement Tools for RNA Quality in Postmortem Human Brain Samples
Authors: Walker Jessica E. , Oliver Javon C. , Stewart Analisa M. , Beh Suet Theng , Arce Richard A. , Glass Michael J. , Vargas Daisy E. , Qiji Sanaria H. , Intorcia Anthony J. , Borja Claryssa I. , Cline Madison P. , Hemmingsen Spencer J. , Krupp Addison N. , McHattie Rylee D. , Mariner Monica R. , Lorenzini Ileana , Aslam Sidra , Tremblay Cecilia , Beach Thomas G. , Serrano Geidy E.
Published: September 2023

The determination of RNA integrity is a critical quality assessment tool for gene expression studies where the experiment’s success is highly dependent on the sample quality. Since its introduction in 1999, the gold standard in the scientific community has been the Agilent 2100 Bioanalyzer’s RNA integrity number (RIN), which uses a 1–10 value system, from 1 being the most degraded, to 10 being the most intact. In 2015, Agilent launched 4200 TapeStation’s RIN equivalent, and reported a strong correlation of r2 of 0.936 and a median error < ±0.4 RIN units. To evaluate this claim, we compared the Agilent 4200 TapeStation’s RIN equivalent (RINe) and DV200 to the Agilent 2100 Bioanalyzer’s RIN for 183 parallel RNA samples. In our study, using RNA from a total of 183 human postmortem brain samples, we found that the RIN and RINe values only weakly correlate, with an r2 of 0.393 and an average difference of 3.2 RIN units. DV200 also only weakly correlated with RIN (r2 of 0.182) and RINe (r2 of 0.347). Finally, when applying a cut-off value of 6.5 for both metrics, we found that 95.6% of samples passed with RIN, while only 23.5% passed with RINe. Our results suggest that even though RIN (Bioanalyzer) and RINe (TapeStation) use the same 1–10 value system, they should not be used interchangeably, and cut-off values should be calculated independently.
Survival Bias, Non-Lineal Behavioral and Cortico-Limbic Neuropathological Signatures in 3xTg-AD Mice for Alzheimer’s Disease from Premorbid to Advanced Stages and Compared to Normal Aging
Authors: Muntsant Aida , Castillo-Ruiz Maria del Mar , Giménez-Llort Lydia
Published: September 2023

Pre-clinical research in aging is hampered by the scarcity of studies modeling its heterogeneity and complexity forged by pathophysiological conditions throughout the life cycle and under the sex perspective. In the case of Alzheimer’s disease, the leading cause of dementia in older adults, we recently described in female wildtype and APP23 mice a survival bias and non-linear chronology of behavioral signatures from middle age to long life. Here, we present a comprehensive and multidimensional (physical, cognitive, and neuropsychiatric-like symptoms) screening and underlying neuropathological signatures in male and female 3xTg-AD mice at 2, 4, 6, 12, and 16 months of age and compared to their non-transgenic counterparts with gold-standard C57BL/6J background. Most variables studied detected age-related differences, whereas the genotype factor was specific to horizontal and vertical activities, thigmotaxis, coping with stress strategies, working memory, and frailty index. A sex effect was predominantly observed in classical emotional variables and physical status. Sixteen-month-old mice exhibited non-linear age- and genotype-dependent behavioral signatures, with higher heterogeneity in females, and worsened in naturalistically isolated males, suggesting distinct compensatory mechanisms and survival bias. The underlying temporal and spatial progression of Aβ and tau pathologies pointed to a relevant cortico-limbic substrate roadmap: premorbid intracellular Aβ immunoreactivity and pSer202/pThr205 tau phosphorylation in the amygdala and ventral hippocampus, and the entorhinal cortex and ventral hippocampus as the areas most affected by Aβ plaques. Therefore, depicting phenotypic signatures and neuropathological correlates can be critical to unveiling preventive/therapeutic research and intervention windows and studying adaptative behaviors and maladaptive responses relevant to psychopathology.
Plant Aquaporin Gating Is Reversed by Phosphorylation on Intracellular Loop D—Evidence from Molecular Dynamics Simulations
Authors: Mom Robin , Réty Stéphane , Mocquet Vincent , Auguin Daniel
Published: September 2023

Aquaporins (AQPs) constitute a wide and ancient protein family of transmembrane channels dedicated to the regulation of water exchange across biological membranes. In plants, higher numbers of AQP homologues have been conserved compared to other kingdoms of life such as in animals or in bacteria. As an illustration of this plant-specific functional diversity, plasma membrane intrinsic proteins (PIPs, i.e., a subfamily of plant AQPs) possess a long intracellular loop D, which can gate the channel by changing conformation as a function of the cellular environment. However, even though the closure of the AQP by loop D conformational changes is well described, the opening of the channel, on the other hand, is still misunderstood. Several studies have pointed to phosphorylation events as the trigger for the transition from closed- to open-channel states. Nonetheless, no clear answer has been obtained yet. Hence, in order to gain a more complete grasp of plant AQP regulation through this intracellular loop D gating, we investigated the opening of the channel in silico through molecular dynamics simulations of the crystallographic structure of Spinacia oleracea PIP2;1 (SoPIP2;1). Through this technique, we addressed the mechanistic details of these conformational changes, which eventually allowed us to propose a molecular mechanism for PIP functional regulation by loop D phosphorylation. More precisely, our results highlight the phosphorylation of loop D serine 188 as a trigger of SoPIP2;1 water channel opening. Finally, we discuss the significance of this result for the study of plant AQP functional diversity.
Genome-Wide Analysis of the Amino Acid Permeases Gene Family in Wheat and TaAAP1 Enhanced Salt Tolerance by Accumulating Ethylene
Authors: Wang Kai , Zhai Mingjuan , Cui Dezhou , Han Ran , Wang Xiaolu , Xu Wenjing , Qi Guang , Zeng Xiaoxue , Zhuang Yamei , Liu Cheng
Published: September 2023

Amino acid permeases (AAPs) are proteins of the integral membrane that play important roles in plant growth, development, and responses to various stresses. The molecular functions of several AAPs were characterized in Arabidopsis and rice, but there is still limited information on wheat. Here, we identified 51 AAP genes (TaAAPs) in the wheat genome, classified into six groups based on phylogenetic and protein structures. The chromosome location and gene duplication analysis showed that gene duplication events played a crucial role in the expansion of the TaAAPs gene family. Collinearity relationship analysis revealed several orthologous AAPs between wheat and other species. Moreover, cis-element analysis of promoter regions and transcriptome data suggested that the TaAAPs can respond to salt stress. A TaAAP1 gene was selected and transformed in wheat. Overexpressing TaAAP1 enhanced salt tolerance by increasing the expression of ethylene synthesis genes (TaACS6/TaACS7/TaACS8) and accumulating more ethylene. The present study provides an overview of the AAP family in the wheat genome as well as information on systematics, phylogenetics, and gene duplication, and shows that overexpressing TaAAP1 enhances salt tolerance by regulating ethylene production. These results serve as a theoretical foundation for further functional studies on TaAAPs in the future.
A Case Study from the Past: “The RGC-5 vs. the 661W Cell Line: Similarities, Differences and Contradictions—Are They Really the Same?”
Authors: Hurst José , Attrodt Gesine , Bartz-Schmidt Karl-Ulrich , Mau-Holzmann Ulrike Angelika , Spitzer Martin Stephan , Schnichels Sven
Published: September 2023

In the pursuit of identifying the underlying pathways of ocular diseases, the use of cell lines such as (retinal ganglion cell-5) RGC-5 and 661W became a valuable tool, including pathologies like retinal degeneration and glaucoma. In 2001, the establishment of the RGC-5 cell line marked a significant breakthrough in glaucoma research. Over time, however, concerns arose about the true nature of RGC-5 cells, with conflicting findings in the literature regarding their identity as retinal ganglion cells or photoreceptor-like cells. This study aimed to address the controversy surrounding the RGC-5 cell line’s origin and properties by comparing it with the 661W cell line, a known cone photoreceptor model. Both cell lines were differentiated according to two prior published redifferentiation protocols under the same conditions using 500 nM of trichostatin A (TSA) and investigated for their morphological and neuronal marker properties. The results demonstrated that both cell lines are murine, and they exhibited distinct morphological and neuronal marker properties. Notably, the RGC-5 cells showed higher expression of the neuronal marker β-III tubulin and increased Thy-1-mRNA compared with the 661W cells, providing evidence of their different properties. The findings emphasize the importance of verifying the authenticity of cell lines used in ocular research and highlight the risks of contamination and altered cell properties.
Current Status of Next-Generation Sequencing in Bone Genetic Diseases
Authors: Aida Natsuko , Saito Akiko , Azuma Toshifumi
Published: September 2023

The development of next-generation sequencing (NGS) has dramatically increased the speed and volume of genetic analysis. Furthermore, the range of applications of NGS is rapidly expanding to include genome, epigenome (such as DNA methylation), metagenome, and transcriptome analyses (such as RNA sequencing and single-cell RNA sequencing). NGS enables genetic research by offering various sequencing methods as well as combinations of methods. Bone tissue is the most important unit supporting the body and is a reservoir of calcium and phosphate ions, which are important for physical activity. Many genetic diseases affect bone tissues, possibly because metabolic mechanisms in bone tissue are complex. For instance, the presence of specialized immune cells called osteoclasts in the bone tissue, which absorb bone tissue and interact with osteoblasts in complex ways to support normal vital functions. Moreover, the many cell types in bones exhibit cell-specific proteins for their respective activities. Mutations in the genes encoding these proteins cause a variety of genetic disorders. The relationship between age-related bone tissue fragility (also called frailty) and genetic factors has recently attracted attention. Herein, we discuss the use of genomic, epigenomic, transcriptomic, and metagenomic analyses in bone genetic disorders.
Fucoxanthin Ameliorates Sepsis via Modulating Microbiota by Targeting IRF3 Activation
Authors: Su Jingqian , Guan Biyun , Su Qiaofen , Hu Shan , Wu Shun , Tong Zhiyong , Zhou Fen
Published: September 2023

To improve patient survival in sepsis, it is necessary to curtail exaggerated inflammatory responses. Fucoxanthin (FX), a carotenoid derived from brown algae, efficiently suppresses pro-inflammatory cytokine expression via IRF3 activation, thereby reducing mortality in a mouse model of sepsis. However, the effects of FX-targeted IRF3 on the bacterial flora (which is disrupted in sepsis) and the mechanisms by which it impacts sepsis development remain unclear. This study aims to elucidate how FX-targeted IRF3 modulates intestinal microbiota compositions, influencing sepsis development. FX significantly reduced the bacterial load in the abdominal cavity of mice with cecal ligation and puncture (CLP)-induced sepsis via IRF3 activation and increased short-chain fatty acids, like acetic and propionic acids, with respect to their intestines. FX also altered the structure of the intestinal flora, notably elevating beneficial Verrucomicrobiota and Akkermansia spp. while reducing harmful Morganella spp. Investigating the inflammation–flora link, we found positive correlations between the abundances of Morganella spp., Proteus spp., Escherichia spp., and Klebsiella spp. and pro-inflammatory cytokines (IL-6, IL-1β, and TNF-α) induced by CLP. These bacteria were negatively correlated with acetic and propionic acid production. FX alters microbial diversity and promotes short-chain fatty acid production in mice with CLP-induced sepsis, reshaping gut homeostasis. These findings support the value of FX for the treatment of sepsis.
The Properties of Linezolid, Rifampicin, and Vancomycin, as Well as the Mechanism of Action of Pentamidine, Determine Their Synergy against Gram-Negative Bacteria
Authors: Tang Miran , Zhao Deyi , Liu Sichen , Zhang Xiaotuan , Yao Zhuocheng , Chen Hule , Zhou Cui , Zhou Tieli , Xu Chunquan
Published: September 2023

Combining pentamidine with Gram-positive-targeting antibiotics has been proven to be a promising strategy for treating infections from Gram-negative bacteria (GNB). However, which antibiotics pentamidine can and cannot synergize with and the reasons for the differences are unclear. This study aimed to identify the possible mechanisms for the differences in the synergy of pentamidine with rifampicin, linezolid, tetracycline, erythromycin, and vancomycin against GNB. Checkerboard assays were used to detect the synergy of pentamidine and the different antibiotics. To determine the mechanism of pentamidine, fluorescent labeling assays were used to measure membrane permeability, membrane potential, efflux pump activity, and reactive oxygen species (ROS); the LPS neutralization assay was used to evaluate the target site; and quantitative PCR was used to measure changes in efflux pump gene expression. Our results revealed that pentamidine strongly synergized with rifampicin, linezolid, and tetracycline and moderately synergized with erythromycin, but did not synergize with vancomycin against E. coli, K. pneumoniae, E. cloacae, and A. baumannii. Pentamidine increased the outer membrane permeability but did not demolish the outer and inner membranes, which exclusively permits the passage of hydrophobic, small-molecule antibiotics while hindering the entry of hydrophilic, large-molecule vancomycin. It dissipated the membrane proton motive force and inactivated the efflux pump, allowing the intracellular accumulation of antimicrobials that function as substrates of the efflux pump, such as linezolid. These processes resulted in metabolic perturbation and ROS production which ultimately was able to destroy the bacteria. These mechanisms of action of pentamidine on GNB indicate that it is prone to potentiating hydrophobic, small-molecule antibiotics, such as rifampicin, linezolid, and tetracycline, but not hydrophilic, large-molecule antibiotics like vancomycin against GNB. Collectively, our results highlight the importance of the physicochemical properties of antibiotics and the specific mechanisms of action of pentamidine for the synergy of pentamidine–antibiotic combinations. Pentamidine engages in various pathways in its interactions with GNB, but these mechanisms determine its specific synergistic effects with certain antibiotics against GNB. Pentamidine is a promising adjuvant, and we can optimize drug compatibility by considering its functional mechanisms.
Discrepancy Analysis between Histology and Molecular Diagnoses in Kidney Allograft Biopsies: A Single-Center Experience
Authors: Suo Liye , Murillo Martha Caicedo , Gallay Brian , Hod-Dvorai Reut
Published: September 2023

Histology diagnosis is essential for the monitoring and management of kidney transplant patients. Nowadays, the accuracy and reproducibility of histology have been criticized when compared with molecular microscopy diagnostic system (MMDx). Our cohort included 95 renal allograft biopsies with both histology and molecular diagnoses. Discrepancies between histology and molecular diagnosis were assessed for each biopsy. Among the 95 kidney allograft biopsies, a total of 6 cases (6%) showed clear (n = 4) or borderline (n = 2) discrepancies between histology and molecular diagnoses. Four out of the six (67%) were cases with pathologically and clinically confirmed active infections that were diagnosed as mild to moderate T-cell-mediated rejection (TCMR) with MMDx. Two cases showed pathological changes that were not sufficient to make a definitive diagnosis of active rejection via histology, while MMDx results showed antibody-mediated rejection (ABMR). In addition, there were six cases with recurrent or de novo glomerular diseases diagnosed only via histology. All other biopsy results were in an agreement. Our results indicate that histology diagnosis of kidney allograft biopsy is superior to molecular diagnosis in the setting of infections and glomerular diseases; however, MMDx can provide helpful information to confirm the diagnosis of active ABMR.
New Copper Complexes with Antibacterial and Cytotoxic Activity
Authors: Hangan Adriana Corina , Lucaciu Roxana Liana , Turza Alexandru , Dican Lucia , Sevastre Bogdan , Páll Emöke , Oprean Luminița Simona , Borodi Gheorghe
Published: September 2023

The discovery of a new non-toxic metal complex with biological activity represents a very active area of research. Two Cu+2 complexes, [Cu4(L1)4(OH)4(DMF)2(H2O)] (C1) (HL1 = N-(5-ethyl-[1,3,4]–thiadiazole–2-yl)-benzenesulfonamide) and [Cu(L2)2(phen)(H2O)] (C2) (HL2 = N-(5-(4-methylphenyl)-[1,3,4]–thiadiazole–2-yl)-naphtalenesulfonamide), with two new ligands were synthesized. The X-ray crystal structures of the complexes were determined. In both complexes, Cu+2 is five-coordinated, forming a CuN2O3 and CuN4O chromophore, respectively. The ligands act as monodentate, coordinating the metal ion through a single Nthiadiazole atom; for the two complexes, the molecules from the reaction medium (phenantroline, dimethylformamide and water) are also involved in the coordination of Cu+2. The complexes have a distorted square pyramidal square-planar geometry. The compounds were characterized by FT-IR and UV-Vis spectroscopy. Using the microdilution method, the antibacterial activity of the complexes was determined against four Gram-positive and two Gram-negative bacteria, with Gentamicin as the positive control. Cytotoxicity studies were carried out on two tumor cell lines (HeLa, DLD-1) and on a normal cell line (HFL1) using the MTT method and Cisplatin as a positive control. Flow cytometric assessment of apoptosis induced by the complexes on the three cell lines was also performed. Both complexes present in vitro biological activities but complex C2 is more active.