Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of the Feasibility, Efficiency, and Safety of Genome Editing Technologies

Recent advances in programmable nucleases including meganucleases (MNs), zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats-Cas (CRISPR-Cas) have propelled genome editing from explorative research to clinical and industrial settings. Each technology, however, features distinct modes of action that unevenly impact their applicability across the entire genome and are often tested under significantly different conditions. While CRISPR-Cas is currently leading the field due to its versatility, quick adoption, and high degree of support, it is not without limitations. Currently, no technology can be regarded as ideal or even applicable to every case as the context dictates the best approach for genetic modification within a target organism. In this review, we implement a four-pillar framework (context, feasibility, efficiency, and safety) to assess the main genome editing platforms, as a basis for rational decision-making by an expanding base of users, regulators, and consumers. Beyond carefully considering their specific use case with the assessment framework proposed here, we urge stakeholders interested in genome editing to independently validate the parameters of their chosen platform prior to commitment. Furthermore, safety across all applications, particularly in clinical settings, is a paramount consideration and comprehensive off-target detection strategies should be incorporated within workflows to address this. Often neglected aspects such as immunogenicity and the inadvertent selection of mutants deficient for DNA repair pathways must also be considered.
Comparative transcriptome provides insights into the selection adaptation between wild and farmed foxes

Abstract The silver fox and blue fox are economically important fur species and were domesticated by humans from their wild counterparts, the arctic fox and red fox, respectively. Farmed foxes show obvious differences from their wild counterparts, including differences in physiology, body size, energy metabolism, and immunity. However, the molecular mechanisms underlying these differences are presently unclear. In this study, we built transcriptome libraries from multiple pooled tissues for each species of farmed fox, used RNA‐seq to obtain a comprehensive dataset, and performed selection analysis and sequence‐level analyses of orthologous genes to identify the genes that may be influenced by human domestication. More than 153.3, 248.0, 81.6, and 65.8 million clean reads were obtained and assembled into a total of 118,577, 401,520, 79,900, and 186,988 unigenes with an average length range from 521 to 667 bp for AF, BF, RF, and SF, respectively. Selective pressure analysis showed that 11 and 14 positively selected genes were identified, respectively, in the two groups (AF vs. BF and RF vs. SF). Several of these genes were associated with natural immunity (CFI and LRRFIP1), protein synthesis (GOLGA4, CEP19 and SLC35A2), and DNA damage repair (MDC1). Further functional enrichment analyses demonstrated that two positively selected genes (ACO1 and ACAD10) were involved in metabolic process (GO:0008152, p‐value = .032), representing a significant enrichment. Sequence analysis of 117 orthologous genes shared by the two groups showed that the LEMD2, RRBP1, and IGBP1 genes might be affected by artificial selection in farmed foxes, with mutation sites located within sequences that are otherwise highly conserved across most mammals. Our results provide a valuable transcriptomic resource for future genetic studies and improvement in the assisted breeding of foxes and other farmed animals.
Neuromedin B receptor stimulation of Cav3.2 T-type Ca2+ channels in primary sensory neurons mediates peripheral pain hypersensitivity

Background: Neuromedin B (Nmb) is implicated in the regulation of nociception of sensory neurons. However, the underlying cellular and molecular mechanisms remain unknown. Methods: Using patch clamp recording, western blot analysis, immunofluorescent labelling, enzyme-linked immunosorbent assays, adenovirus-mediated shRNA knockdown and animal behaviour tests, we studied the effects of Nmb on the sensory neuronal excitability and peripheral pain sensitivity mediated by Cav3.2 T-type channels. Results: Nmb reversibly and concentration-dependently increased T-type channel currents (IT) in small-sized trigeminal ganglion (TG) neurons through the activation of neuromedin B receptor (NmbR). This NmbR-mediated IT response was Gq protein-coupled, but independent of protein kinase C activity. Either intracellular application of the QEHA peptide or shRNA-mediated knockdown of Gβ abolished the NmbR-induced IT response. Inhibition of protein kinase A (PKA) or AMP-activated protein kinase (AMPK) completely abolished the Nmb-induced IT response. Analysis of phospho-AMPK (p-AMPK) revealed that Nmb significantly activated AMPK, while AMPK inhibition prevented the Nmb-induced increase in PKA activity. In a heterologous expression system, activation of NmbR significantly enhanced the Cav3.2 channel currents, while the Cav3.1 and Cav3.3 channel currents remained unaffected. Nmb induced TG neuronal hyperexcitability and concomitantly induced mechanical and thermal hypersensitivity, both of which were attenuated by T-type channel blockade. Moreover, blockade of NmbR signalling prevented mechanical hypersensitivity in a mouse model of complete Freund's adjuvant-induced inflammatory pain, and this effect was attenuated by siRNA knockdown of Cav3.2. Conclusions: Our study reveals a novel mechanism by which NmbR stimulates Cav3.2 channels through a Gβγ-dependent AMPK/PKA pathway. In mouse models, this mechanism appears to drive the hyperexcitability of TG neurons and induce pain hypersensitivity.
Immune Markers and Tumor-Related Processes Predict Neoadjuvant Therapy Response in the WSG-ADAPT HER2-Positive/Hormone Receptor-Positive Trial in Early Breast Cancer

Simple Summary Patients with “HER2-positive” early breast cancer are treated with antibodies to the HER2 protein along with chemotherapy, regardless of whether their cancer also has hormone receptors, or of its molecular features. Because patients with HER2-positive/hormone receptor-positive disease tend to live longer than those with HER2-positive/hormone receptor-negative disease, there may be some patients who are being overtreated under current guidelines. The aim of our exploratory translational analysis of the ADAPT HER2-positive/hormone receptor-positive trial was to investigate the potential of several prognostic (outcome regardless of therapy) and predictive (effect of therapy) biomarkers as early predictors of response to treatment before surgery. Comparison of these biomarkers before and after one treatment cycle, and their effects on whether patients’ cancers were completely removed at surgery, suggest that certain patients (those with treatment-induced CD8 protein-expressing cells infiltrating the cancer; without PIK3CA mutation; those with HER2-enriched tumors) may be candidates for less intensive treatment following pre-surgical therapy. Abstract Prognostic or predictive biomarkers in HER2-positive early breast cancer (EBC) may inform treatment optimization. The ADAPT HER2-positive/hormone receptor-positive phase II trial (NCT01779206) demonstrated pathological complete response (pCR) rates of ~40% following de-escalated treatment with 12 weeks neoadjuvant ado-trastuzumab emtansine (T-DM1) ± endocrine therapy. In this exploratory analysis, we evaluated potential early predictors of response to neoadjuvant therapy. The effects of PIK3CA mutations and immune (CD8 and PD-L1) and apoptotic markers (BCL2 and MCL1) on pCR rates were assessed, along with intrinsic BC subtypes. Immune response and pCR were lower in PIK3CA-mutated tumors compared with wildtype. Increased BCL2 at baseline in all patients and at Cycle 2 in the T-DM1 arms was associated with lower pCR. In the T-DM1 arms only, the HER2-enriched subtype was associated with increased pCR rate (54% vs. 28%). These findings support further prospective pCR-driven de-escalation studies in patients with HER2-positive EBC.
Synthesis of Oxidized 3β,3′β-Disteryl Ethers and Search after High-Temperature Treatment of Sterol-Rich Samples

It was proven that sterols subjected to high-temperature treatment can be concatenated, which results in polymeric structures, e.g., 3β,3′β-disteryl ethers. However, it was also proven that due to increased temperature in oxygen-containing conditions, sterols can undergo various oxidation reactions. This study aimed to prove the existence and perform quantitative analysis of oxidized 3β,3′β-disteryl ethers, which could form during high-temperature treatment of sterol-rich samples. Samples were heated at 180, 200 and 220 °C for 0.5 to 4 h. Quantitative analyses of the oxidized 3β,3′β-disteryl ethers were performed with liquid extraction, solid-phase extraction and liquid chromatography coupled with mass spectrometry. Additionally, to perform this analysis, the appropriate standards of all oxidized 3β,3′β-disteryl ethers were prepared. Eighteen various oxidized 3β,3′β-disteryl ethers (derivatives of 3β,3′β-dicholesteryl ether, 3β,3′β-disitosteryl ether and 3β,3′β-distigmasteryl ether) were prepared. Additionally, the influence of metal compounds on the mechanism of ether formation at high temperatures was investigated.
Adaption and Degradation Strategies of Methylotrophic 1,4-Dioxane Degrading Strain Xanthobacter sp. YN2 Revealed by Transcriptome-Scale Analysis

Biodegradation of 1,4-dioxane (dioxane) contamination has gained much attention for decades. In our previous work, we isolated a highly efficient dioxane degrader, Xanthobacter sp. YN2, but the underlying mechanisms of its extraordinary degradation performance remained unresolved. In this study, we performed a comparative transcriptome analysis of YN2 grown on dioxane and citrate to elucidate its genetic degradation mechanism and investigated the transcriptomes of different dioxane degradation stages (T0, T24, T48). We also analyzed the transcriptional response of YN2 over time during which the carbon source switched from citrate to dioxane. The results indicate that strain YN2 was a methylotroph, which provides YN2 a major advantage as a pollutant degrader. A large number of genes involved in dioxane metabolism were constitutively expressed prior to dioxane exposure. Multiple genes related to the catabolism of each intermediate were upregulated by treatment in response to dioxane. Glyoxylate metabolism was essential during dioxane degradation by YN2, and the key intermediate glyoxylate was metabolized through three routes: glyoxylate carboligase pathway, malate synthase pathway, and anaplerotic ethylmalonyl–CoA pathway. Genes related to quorum sensing and transporters were significantly upregulated during the early stages of degradation (T0, T24) prior to dioxane depletion, while the expression of genes encoding two-component systems was significantly increased at late degradation stages (T48) when total organic carbon in the culture was exhausted. This study is the first to report the participation of genes encoding glyoxalase, as well as methylotrophic genes xoxF and mox, in dioxane metabolism. The present study reveals multiple genetic and transcriptional strategies used by YN2 to rapidly increase biomass during growth on dioxane, achieve high degradation efficiency and tolerance, and adapt to dioxane exposure quickly, which provides useful information regarding the molecular basis for efficient dioxane biodegradation.
Biomonitoring of Mercury Contamination in Poland Based on Its Concentration in Scots Pine (Pinus sylvestris L.) Foliage

This work evaluates current mercury (Hg) contamination in Poland, represented by the Hg concentrations in Scots pine foliage. Samples were collected over 295 investigation plots in monitoring grids throughout Poland, from pines aged between 12 and 147 years. Analyses were conducted with consideration of bioclimatic factors and soil properties. Concentrations in the pine foliage did not exceed the values characteristic of an ecosystem unaffected by industrial pollution, ranging from 0.0032 to 0.0252 mg kg−1 dry mass. However, pine stands located in western and central Poland, and in the northwest near the Baltic Sea, exhibited higher Hg concentrations in foliage than in eastern regions. Hg content in foliage depends on the mean temperature of the driest quarter, as well as on Hg content in soils. This indicates that the periods of drought observed in recent years in Poland may affect Hg concentrations in pine foliage.
Pesticide Use, Perceived Health Risks and Management in Ethiopia and in Hungary: A Comparative Analysis

Pesticides play a very important role for ensuring food security and economic growth but their use can cause harmful effects to human health and to the environment. The study aimed to investigate the level of knowledge, health risk perceptions, and experiences on the practice of pesticide use and management among extension officers in Ethiopia and plant doctors in Hungary. A questionnaire survey among 326 officers was conducted in the two study areas and data were analyzed by ordinal logistic regression. According to the findings, Hungarian officers had much better knowledge of pesticide products (92%), and less frequently experienced pesticide poisoning among applicators (7%) than the Ethiopians (66% and 41%, respectively). Hungarian officers perceived less health risk of pesticide use (AOR = 0.46, 95%, Cl: 0.27–0.80), were ten times more likely to deem the pesticide management system effective (AOR = 10.23, 95%, Cl: 5.68–18.46) and were nine times more likely to report that applicators used personal protective equipment (AOR = 8.95, 95%, Cl: 4.94–16.28). A significant proportion of officers from both countries reported inappropriate methods of pesticide residue disposal. These observations point out that the situation of pesticide use and knowledge and management of pesticide products is definitely better in Hungary; nevertheless, the issue continues to need more attention in both settings.
Mechanical Properties of Crumb Rubber Mortar Containing Nano-Silica Using Response Surface Methodology

Crumb rubber (CR) from scrap tires is used as a partial replacement of fine aggregates in cement paste. This promotes the sustainable development of the environment, economy, and society, as waste tires are non-biodegradable and flammable. They occupy large landfill areas and are breeding grounds for mosquitoes and rodents. Inclusion of CR in mortar leads to several improvements on the mixture properties such as ductility, toughness, and impact resistance. However, it exhibits lower strengths and Modulus of Elasticity (ME). Therefore, to promote the use of mortar containing CR, it is vital to improve its mechanical strength. Past studies proved that nano-silica (NS) improves the strength of concrete due to the physico-chemical effects of NS. This study aims to examine the mechanical properties of crumb rubber mortar containing nano-silica (NS-CRM) and to develop models to predict these properties using Response Surface Methodology (RSM). Two variables were considered, CR as partial replacement to sand by volume (0%, 7.5%, 15%), and NS as partial replacement to cement by weight (0%, 2.5%, 5%). The results demonstrated a significant improvement in the mechanical properties of CRM when incorporating NS, and the models developed using RSM were acceptable with a 2% to 3% variation.
CGRP Inhibitors and Oxidative Stress Biomarkers in Resistant Migraine: A Real-Life Study with Erenumab, Fremanezumab, and Galcanezumab

Patients with high-frequency resistant migraine and medication-overuse headache are still the main clinical challenge in tertiary headache centers. The approval of targeted antibodies against the calcitonin gene-related peptide (CGRP) and its receptor represents a powerful instrument. In this study, we observed how biological and clinical features of resistant migraineurs responded to erenumab, fremanezumab, or galcanezumab. We found a reduction in advanced oxidation protein products (AOPP) as a biomarker of improved redox state after six months of treatment. We also found that treatment efficacy was precocious and maintained with high individual responder rates. In particular, seven out of ten patients achieved a reduction of 50% from the baseline at three months, which was maintained at six months, while about one out of our patients experienced a 75% reduction in headache frequency from the first month of treatment. The migraine disability assessment (MIDAS) and the associated fatigue, anxiety, and sleep quality also significantly improved. The allodynia symptom dropped from moderate/severe to mild/absent as a sign of central sensitization reduction. Our study confirmed the safety and efficacy of CGRP inhibition in real-life, high-challenging patients. Additional evidence is needed to understand the role of oxidative stress as a migraine biomarker.
Melatonin-Activated Receptor Signaling Pathways Mediate Protective Effects on Surfactant-Induced Increase in Jejunal Mucosal Permeability in Rats

A well-functional intestinal mucosal barrier can be compromised as a result of various diseases, chemotherapy, radiation, and chemical exposures including surfactants. Currently, there are no approved drugs targeting a dysfunctional intestinal barrier, which emphasizes a significant medical need. One candidate drug reported to regulate intestinal mucosal permeability is melatonin. However, it is still unclear if its effect is primarily receptor mediated or antioxidative, and if it is associated with enteric neural pathways. The aim of this rat intestinal perfusion study was to investigate the mechanisms of melatonin and nicotinic acetylcholine receptors on the increase in intestinal mucosal clearance of 51Cr-labeled ethylenediaminetetraacetate induced by 15 min luminal exposure to the anionic surfactant, sodium dodecyl sulfate. Our results show that melatonin abolished the surfactant-induced increase in intestinal permeability and that this effect was inhibited by luzindole, a melatonin receptor antagonist. In addition, mecamylamine, an antagonist of nicotinic acetylcholine receptors, reduced the surfactant-induced increase in mucosal permeability, using a signaling pathway not influenced by melatonin receptor activation. In conclusion, our results support melatonin as a potentially potent candidate for the oral treatment of a compromised intestinal mucosal barrier, and that its protective effect is primarily receptor-mediated.
Caregiver Willingness to Vaccinate Their Children against COVID-19 after Adult Vaccine Approval

Vaccines against COVID-19 are likely to be approved for children under 12 years in the near future. Understanding vaccine hesitancy in parents is essential for reaching herd immunity. A cross-sectional survey of caregivers in 12 emergency departments (ED) was undertaken in the U.S., Canada, and Israel. We compared reported willingness to vaccinate children against COVID-19 with an initial survey and post-adult COVID-19 vaccine approval. Multivariable logistic regression models were performed for all children and for those <12 years. A total of 1728 and 1041 surveys were completed in phases 1 and 2, respectively. Fewer caregivers planned to vaccinate against COVID-19 in phase 2 (64.5% and 59.7%, respectively; p = 0.002). The most significant positive predictor of willingness to vaccinate against COVID-19 was if the child was vaccinated per recommended local schedules. Fewer caregivers plan to vaccinate their children against COVID-19, despite vaccine approval for adults, compared to what was reported at the peak of the pandemic. Older caregivers who fully vaccinated their children were more likely to adopt vaccinating children. This study can inform target strategy design to implement adherence to a vaccination campaign.
Computational Screening of Natural Compounds for Identification of Potential Anti-Cancer Agents Targeting MCM7 Protein

Minichromosome maintenance complex component 7 (MCM7) is involved in replicative licensing and the synthesis of DNA, and its overexpression is a fascinating biomarker for various cancer types. There is currently no effective agent that can prevent the development of cancer caused by the MCM7 protein. However, on the molecular level, inhibiting MCM7 lowers cancer-related cellular growth. With this purpose, this study screened 452 biogenic compounds extracted from the UEFS Natural Products dataset against MCM protein by using the in silico art of technique. The hit compounds UEFS99, UEFS137, and UEFS428 showed good binding with the MCM7 protein with binding energy values of −9.95, −8.92, and −8.71 kcal/mol, which was comparatively higher than that of the control compound ciprofloxacin (−6.50). The hit (UEFS99) with the minimum binding energy was picked for molecular dynamics (MD) simulation investigation, and it demonstrated stability at 30 ns. Computational prediction of physicochemical property evaluation revealed that these hits are non-toxic and have good drug-likeness features. It is suggested that hit compounds UEFS99, UEFS137, and UEFS428 pave the way for further bench work validation in novel inhibitor development against MCM7 to fight the cancers.
Role of HSP90 in Cancer

HSP90 is a vital chaperone protein conserved across all organisms. As a chaperone protein, it correctly folds client proteins. Structurally, this protein is a dimer with monomer subunits that consist of three main conserved domains known as the N-terminal domain, middle domain, and the C-terminal domain. Multiple isoforms of HSP90 exist, and these isoforms share high homology. These isoforms are present both within the cell and outside the cell. Isoforms HSP90α and HSP90β are present in the cytoplasm; TRAP1 is present in the mitochondria; and GRP94 is present in the endoplasmic reticulum and is likely secreted due to post-translational modifications (PTM). HSP90 is also secreted into an extracellular environment via an exosome pathway that differs from the classic secretion pathway. Various co-chaperones are necessary for HSP90 to function. Elevated levels of HSP90 have been observed in patients with cancer. Despite this observation, the possible role of HSP90 in cancer was overlooked because the chaperone was also present in extreme amounts in normal cells and was vital to normal cell function, as observed when the drastic adverse effects resulting from gene knockout inhibited the production of this protein. Differences between normal HSP90 and HSP90 of the tumor phenotype have been better understood and have aided in making the chaperone protein a target for cancer drugs. One difference is in the conformation: HSP90 of the tumor phenotype is more susceptible to inhibitors. Since overexpression of HSP90 is a factor in tumorigenesis, HSP90 inhibitors have been studied to combat the adverse effects of HSP90 overexpression. Monotherapies using HSP90 inhibitors have shown some success; however, combination therapies have shown better results and are thus being studied for a more effective cancer treatment.