Miracle-dz/UniFAR-FTUs huggingface dataset:
The European Map Butterfly Araschnia levana as a Model to Study the Molecular Basis and Evolutionary Ecology of Seasonal Polyphenism

Simple Summary The European map butterfly looks different in spring and summer due to day length and temperature. If the butterfly’s caterpillars receive 16 h of light per day, the resulting butterfly hatches a few weeks later with blackish wings. However, if caterpillars receive less than 15.5 h of daylight, many overwinter as pupae. In the following spring, butterflies have orange wings. Overwintering and wing color are decided by hormones. If a certain hormone is released in the first days after the caterpillar has become a pupa, no overwintering takes place, and the wings are black. If this hormone is released later, overwintering occurs, and the wings are orange. Different genes are activated to make either of those two options happen. They guide what happens during overwintering and how long it lasts but also how the butterfly looks once it hatches. We do not yet fully understand how the caterpillars count the amount of light they receive and how this information leads to the differences described above. In addition, the butterfly’s whole body and its immune system are different in the two color types. Here we discuss how the butterfly probably makes these changes happen and which role the environment plays. Abstract The European map butterfly Araschnia levana is a well-known example of seasonal polyphenism. Spring and summer imagoes exhibit distinct morphological phenotypes. Key environmental factors responsible for the expression of different morphs are day length and temperature. Larval exposure to light for more than 16 h per day entails direct development and results in the adult f. prorsa summer phenotype. Less than 15.5 h per day increasingly promotes diapause and the adult f. levana spring phenotype. The phenotype depends on the timing of the release of 20-hydroxyecdysone in pupae. Release within the first days after pupation potentially inhibits the default “levana-gene-expression-profile” because pre-pupae destined for diapause or subitaneous development have unique transcriptomic programs. Moreover, multiple microRNAs and their targets are differentially regulated during the larval and pupal stages, and candidates for diapause maintenance, duration, and phenotype determination have been identified. However, the complete pathway from photoreception to timekeeping and diapause or subitaneous development remains unclear. Beside the wing polyphenism, the hormonal and epigenetic modifications of the two phenotypes also include differences in biomechanical design and immunocompetence. Here, we discuss research on the physiological and molecular basis of polyphenism in A. levana, including hormonal control, epigenetic regulation, and the effect of ecological parameters on developmental fate.
Adiponectin: Structure, Physiological Functions, Role in Diseases, and Effects of Nutrition

Adiponectin (a protein consisting of 244 amino acids and characterized by a molecular weight of 28 kDa) is a cytokine that is secreted from adipose tissues (adipokine). Available evidence suggests that adiponectin is involved in a variety of physiological functions, molecular and cellular events, including lipid metabolism, energy regulation, immune response and inflammation, and insulin sensitivity. It has a protective effect on neurons and neural stem cells. Adiponectin levels have been reported to be negatively correlated with cancer, cardiovascular disease, and diabetes, and shown to be affected (i.e., significantly increased) by proper healthy nutrition. The present review comprehensively overviews the role of adiponectin in a range of diseases, showing that it can be used as a biomarker for diagnosing these disorders as well as a target for monitoring the effectiveness of preventive and treatment interventions.
Relationships of Dietary Factors with Obesity, Hypertension, and Diabetes by Regional Type among Single-Person Households in Korea

This study aims to investigate whether dietary factors are differentially associated with metabolic abnormalities by regional type among single-person households in Korea. A total of 685,327 Korean adults aged ≥19 years who participated in the household and individual surveys of the Korea Community Health Survey 2015–2017 are included in the analysis. The regions are divided into three categories: metropolitan areas, mid-sized cities, and rural areas. Using multivariable logistic regressions, the adjusted odds ratios and 95% confidence intervals for metabolic abnormalities are estimated by regional type after adjusting for covariates. Among the total study population, 12.21% occupy single-person households, and 47.5%, 25.1%, and 27.4% of those single-person households are in rural areas, mid-sized cities, and metropolitan areas, respectively. Compared with single-person households in rural areas, those in mid-sized and metropolitan cities tend to be more familiar with and frequently refer to nutrition labels, skip breakfast, and experience food insecurity. Regional differences are found in the associations of dietary factors and behavior with obesity, hypertension, and diabetes. The use of nutritional fact labels is associated with obesity and hypertension in single-person households in rural areas, and the degree of association between food insecurity and diabetes is highest among single-person households in metropolitan areas. Our findings suggest that policies for improving unhealthy dietary factors by regional type are needed to reduce regional health disparities among single-person households in Korea.
Meta-Analysis of Quantitative Traits Loci (QTL) Identified in Drought Response in Rice (Oryza sativa L.)

Rice is an important grain that is the staple food for most of the world’s population. Drought is one of the major stresses that negatively affects rice yield. The nature of drought tolerance in rice is complex as it is determined by various components and has low heritability. Therefore, to ensure success in breeding programs for drought tolerant rice, QTLs (quantitative trait loci) of interest must be stable in a variety of plant genotypes and environments. This study identified stable QTLs in rice chromosomes in a variety of backgrounds and environments and conducted a meta-QTL analysis of stable QTLs that have been reported by previous research for use in breeding programs. A total of 653 QTLs for drought tolerance in rice from 27 genetic maps were recorded for analysis. The QTLs recorded were related to 13 traits in rice that respond to drought. Through the use of BioMercartor V4.2, a consensus map containing QTLs and molecular markers were generated using 27 genetic maps that were extracted from the previous 20 studies and meta-QTL analysis was conducted on the consensus map. A total of 70 MQTLs were identified and a total of 453 QTLs were mapped into the meta-QTL areas. Five meta-QTLs from chromosome 1 (MQTL 1.5 and MQTL 1.6), chromosome 2 (MQTL2.1 and MQTL 2.2) and chromosome 3 (MQTL 3.1) were selected for functional annotation as these regions have high number of QTLs and include many traits in rice that respond to drought. A number of genes in MQTL1.5 (268 genes), MQTL1.6 (640 genes), MQTL 2.1 (319 genes), MQTL 2.2 (19 genes) and MQTL 3.1 (787 genes) were annotated through Blast2GO. Few major proteins that respond to drought stress were identified in the meta-QTL areas which are Abscisic Acid-Insensitive Protein 5 (ABI5), the G-box binding factor 4 (GBF4), protein kinase PINOID (PID), histidine kinase 2 (AHK2), protein related to autophagy 18A (ATG18A), mitochondrial transcription termination factor (MTERF), aquaporin PIP 1-2, protein detoxification 48 (DTX48) and inositol-tetrakisphosphate 1-kinase 2 (ITPK2). These proteins are regulatory proteins involved in the regulation of signal transduction and gene expression that respond to drought stress. The meta-QTLs derived from this study and the genes that have been identified can be used effectively in molecular breeding and in genetic engineering for drought resistance/tolerance in rice.
Proteomic Characterization of Bacteriophage Peptides from the Mastitis Producer Staphylococcus aureus by LC-ESI-MS/MS and the Bacteriophage Phylogenomic Analysis

The present work describes LC-ESI-MS/MS MS (liquid chromatography-electrospray ionization-tandem mass spectrometry) analyses of tryptic digestion peptides from phages that infect mastitis-causing Staphylococcus aureus isolated from dairy products. A total of 1933 nonredundant peptides belonging to 1282 proteins were identified and analyzed. Among them, 79 staphylococcal peptides from phages were confirmed. These peptides belong to proteins such as phage repressors, structural phage proteins, uncharacterized phage proteins and complement inhibitors. Moreover, eighteen of the phage origin peptides found were specific to S. aureus strains. These diagnostic peptides could be useful for the identification and characterization of S. aureus strains that cause mastitis. Furthermore, a study of bacteriophage phylogeny and the relationship among the identified phage peptides and the bacteria they infect was also performed. The results show the specific peptides that are present in closely related phages and the existing links between bacteriophage phylogeny and the respective Staphylococcus spp. infected.
High Throughput Profiling of Flavonoid Abundance in Agave lechuguilla Residue-Valorizing under Explored Mexican Plant

Agave lechuguilla waste biomass (guishe) is an undervalued abundant plant material with natural active compounds such as flavonoids. Hence, the search and conservation of flavonoids through the different productive areas have to be studied to promote the use of this agro-residue for industrial purposes. In this work, we compared the proportion of total flavonoid content (TFC) among the total polyphenolics (TPC) and described the variation of specific flavonoid profiles (HPLC-UV-MS/MS) of guishe from three locations. Descriptive environmental analysis, using remote sensing, was used to understand the phytochemical variability among the productive regions. Furthermore, the effect of extractive solvent (ethanol and methanol) and storage conditions on specific flavonoid recovery were evaluated. The highest TPC (16.46 ± 1.09 GAE/g) was observed in the guishe from region 1, which also had a lower normalized difference water index (NDWI) and lower normalized difference vegetation index (NDVI). In contrast, the TFC was similar in the agro-residue from the three studied areas, suggesting that TFC is not affected by the studied environmental features. The highest TFC was found in the ethanolic extracts (6.32 ± 1.66 QE/g) compared to the methanolic extracts (3.81 ± 1.14 QE/g). Additionally, the highest diversity in flavonoids was found in the ethanolic extract of guishe from region 3, which presented an intermedia NDWI and a lower NDVI. Despite the geo-climatic induced variations of the phytochemical profiles, the results confirm that guishe is a valuable raw material in terms of its flavonoid-enriched bioactive extracts. Additionally, the bioactive flavonoids remain stable when the conditioned agro-residue was hermetically stored at room temperature in the dark for nine months. Finally, the results enabled the establishment of both agro-ecological and biotechnological implications.
Biofilm and Spore Formation of Clostridium perfringens and Its Resistance to Disinfectant and Oxidative Stress

Clostridium perfringens is a major human pathogen that causes gastroenteritis via enterotoxin production and has the ability to form spores and biofilms for environmental persistence and disease transmission. This study aimed to compare the disinfectant and environmental resistance properties of C. perfringens vegetative cells and spores in planktonic and sessile conditions, and to examine the nucleotide polymorphisms and transcription under sessile conditions in C. perfringens strains isolated from meat. The sporulation rate of sessile C. perfringens TYJAM-D-66 (cpe+) was approximately 19% at day 5, while those of CMM-C-80 (cpe−) and SDE-B-202 (cpe+) were only 0.26% and 0.67%, respectively, at day 7. When exposed to aerobic conditions for 36 h, TYJAM-D-66, CMM-C-80, and SDE-B-202 vegetative cells showed 1.70 log, 5.36 log, and 5.67 log reductions, respectively. After treatment with sodium hypochlorite, the survival rates of TYJAM-D-66 vegetative cells (53.6%) and spores (82.3%) in biofilms were higher than those of planktonic cells (9.23%). Biofilm- and spore-related genes showed different expression within TYJAM-D-66 (–4.66~113.5), CMM-C-80 (–3.02~2.49), and SDE-B-202 (–5.07~2.73). Our results indicate the resistance of sessile cells and spores of C. perfringens upon exposure to stress conditions after biofilm formation.
Hearing Loss Caused by HCMV Infection through Regulating the Wnt and Notch Signaling Pathways

Hearing loss is one of the most prevalent sensory disabilities worldwide with huge social and economic burdens. The leading cause of sensorineural hearing loss (SNHL) in children is congenital cytomegalovirus (CMV) infection. Though the implementation of universal screening and early intervention such as antiviral or anti-inflammatory ameliorate the severity of CMV-associated diseases, direct and targeted therapeutics is still seriously lacking. The major hurdle for it is that the mechanism of CMV induced SNHL has not yet been well understood. In this review, we focus on the impact of CMV infection on the key players in inner ear development including the Wnt and Notch signaling pathways. Investigations on these interactions may gain new insights into viral pathogenesis and reveal novel targets for therapy.
Quantitative Control of Early Flowering in White Lupin (Lupinus albus L.)

White lupin (Lupinus albus L.) is a pulse annual plant cultivated from the tropics to temperate regions for its high-protein grain as well as a cover crop or green manure. Wild populations are typically late flowering and have high vernalization requirements. Nevertheless, some early flowering and thermoneutral accessions were found in the Mediterranean basin. Recently, quantitative trait loci (QTLs) explaining flowering time variance were identified in bi-parental population mapping, however, phenotypic and genotypic diversity in the world collection has not been addressed yet. In this study, a diverse set of white lupin accessions (n = 160) was phenotyped for time to flowering in a controlled environment and genotyped with PCR-based markers (n = 50) tagging major QTLs and selected homologs of photoperiod and vernalization pathway genes. This survey highlighted quantitative control of flowering time in white lupin, providing statistically significant associations for all major QTLs and numerous regulatory genes, including white lupin homologs of CONSTANS, FLOWERING LOCUS T, FY, MOTHER OF FT AND TFL1, PHYTOCHROME INTERACTING FACTOR 4, SKI-INTERACTING PROTEIN 1, and VERNALIZATION INDEPENDENCE 3. This revealed the complexity of flowering control in white lupin, dispersed among numerous loci localized on several chromosomes, provided economic justification for future genome-wide association studies or genomic selection rather than relying on simple marker-assisted selection.
Elimination of Intravenous Di-2-Ethylhexyl Phthalate Exposure Abrogates Most Neonatal Hypertension in Premature Infants with Bronchopulmonary Dysplasia

(1) Background: The incidence of hypertension in very low birthweight (VLBW) infants in a single neonatal intensive care unit (NICU) dropped markedly during a 2-year period when the IV fluid (IVF) in both the antenatal unit and the NICU temporarily changed to a di-2-ethylhexyl phthalate (DEHP)-free formulation. The objective of the current report is to document this observation and demonstrate the changes in incidence of hypertension were not associated with the variation in risk factors for hypertension; (2) Methods: The charts of all VLBW infants born in a single NICU during a 7-year span were reviewed. This time includes 32 months of baseline, 20 months of DEHP-free IVF, 20 months of IVF DEHP re-exposure, and two 4-month washout intervals. The group of interest was limited to VLBW infants with bronchopulmonary dysplasia (BPD). Chi-square analysis was used to compare incidence of hypertension among periods. Vermont Oxford NICU Registry data were examined for variation in maternal and neonatal risk factors for hypertension; Results: Incidence of hypertension in VLBW infants with BPD decreased from 7.7% (baseline) to 1.4% when IVF was DEHP-free, rising back to 10.1% when DEHP-containing IVF returned to use. Risk factors for neonatal hypertension were stable across the 3 study periods in the NICU’s group of VLBW infants; (3) Conclusions: Serendipitous removal of IVF containing DEHP resulted in near elimination of hypertension in one NICU—an effect entirely reversed after the same brand of DEHP-containing IVF returned to clinical use. These results suggest that DEHP exposure from IVF plays a major role in neonatal hypertension.
Binding and Action of Triphenylphosphonium Analog of Chloramphenicol upon the Bacterial Ribosome

Chloramphenicol (CHL) is a ribosome-targeting antibiotic that binds to the peptidyl transferase center (PTC) of the bacterial ribosome and inhibits peptide bond formation. As an approach for modifying and potentially improving the properties of this inhibitor, we explored ribosome binding and inhibitory properties of a semi-synthetic triphenylphosphonium analog of CHL—CAM-C4-TPP. Our data demonstrate that this compound exhibits a ~5-fold stronger affinity for the bacterial ribosome and higher potency as an in vitro protein synthesis inhibitor compared to CHL. The X-ray crystal structure of the Thermus thermophilus 70S ribosome in complex with CAM-C4-TPP reveals that, while its amphenicol moiety binds at the PTC in a fashion identical to CHL, the C4-TPP tail adopts an extended propeller-like conformation within the ribosome exit tunnel where it establishes multiple hydrophobic Van der Waals interactions with the rRNA. The synthesized compound represents a promising chemical scaffold for further development by medicinal chemists because it simultaneously targets the two key functional centers of the bacterial ribosome—PTC and peptide exit tunnel.
Nuclear Medicine Imaging in Neuroblastoma: Current Status and New Developments

Neuroblastoma is the most common extracranial solid malignancy in children. At diagnosis, approximately 50% of patients present with metastatic disease. These patients are at high risk for refractory or recurrent disease, which conveys a very poor prognosis. During the past decades, nuclear medicine has been essential for the staging and response assessment of neuroblastoma. Currently, the standard nuclear imaging technique is meta-[123I]iodobenzylguanidine ([123I]mIBG) whole-body scintigraphy, usually combined with single-photon emission computed tomography with computed tomography (SPECT-CT). Nevertheless, 10% of neuroblastomas are mIBG non-avid and [123I]mIBG imaging has relatively low spatial resolution, resulting in limited sensitivity for smaller lesions. More accurate methods to assess full disease extent are needed in order to optimize treatment strategies. Advances in nuclear medicine have led to the introduction of radiotracers compatible for positron emission tomography (PET) imaging in neuroblastoma, such as [124I]mIBG, [18F]mFBG, [18F]FDG, [68Ga]Ga-DOTA peptides, [18F]F-DOPA, and [11C]mHED. PET has multiple advantages over SPECT, including a superior resolution and whole-body tomographic range. This article reviews the use, characteristics, diagnostic accuracy, advantages, and limitations of current and new tracers for nuclear medicine imaging in neuroblastoma.
Detection of Carrageenan in Meat Products Using Lectin Histochemistry

Carrageenan is a polysaccharide that is widely used in the food industry. Due to its water holding capacity, there is a higher risk of adulteration for economic reasons related to it. A verifiable method for detecting carrageenan is still missing in the food inspection sector. The detection of carrageenan in meat products is not well described. Our study describes lectin histochemistry as a novel approach for carrageenan detection. Within this study, the detection of carrageenan in meat products by lectin histochemistry is validated. Lectins of Arachis hypogaea (PNA) and Bandeiraea simlicifolia (BSA), specific for galactose units of carrageenan, were used. The samples included model meat products (ground chicken-meat products) and meat products from retail markets (chicken and pork hams, sausages, salami, and dried sausages). The limit of determination (LoD) of this method was set at 0.01 g kg−1. The method sensitivity for lectin PNA reached 1, and, for lectin BSA, it reached 0.96. Method specificity for lectin PNA was 1, and, for lectin BSA, it was 1.33. Cross-reactivity with other hydrocolloids tested was not confirmed. The results confirm that lectin histochemistry is suitable for detecting carrageenan in meat products.
Green Design of Novel Starch-Based Packaging Materials Sustaining Human and Environmental Health

A critical overview of current approaches to the development of starch-containing packaging, integrating the principles of green chemistry (GC), green technology (GT) and green nanotechnology (GN) with those of green packaging (GP) to produce materials important for both us and the planet is given. First, as a relationship between GP and GC, the benefits of natural bioactive compounds are analyzed and the state-of-the-art is updated in terms of the starch packaging incorporating green chemicals that normally help us to maintain health, are environmentally friendly and are obtained via GC. Newer approaches are identified, such as the incorporation of vitamins or minerals into films and coatings. Second, the relationship between GP and GT is assessed by analyzing the influence on starch films of green physical treatments such as UV, electron beam or gamma irradiation, and plasma; emerging research areas are proposed, such as the use of cold atmospheric plasma for the production of films. Thirdly, the approaches on how GN can be used successfully to improve the mechanical properties and bioactivity of packaging are summarized; current trends are identified, such as a green synthesis of bionanocomposites containing phytosynthesized metal nanoparticles. Last but not least, bioinspiration ideas for the design of the future green packaging containing starch are presented.
Mevalonate Kinase-Associated Diseases: Hunting for Phenotype–Genotype Correlation

Mevalonate kinase-associated diseases (MKAD) are caused by pathogenic mutations in the mevalonate kinase gene (MVK) and encompass several phenotypically different rare and hereditary autoinflammatory conditions. The most serious is a recessive systemic metabolic disease called mevalonic aciduria, and the most recently recognized is disseminated superficial actinic porokeratosis, a dominant disease limited to the skin. To evaluate a possible correlation between genotypes and (1) the different MKAD clinical subtypes or (2) the occurrence of severe manifestations, data were reviewed for all patients with MVK variants described in the literature (N = 346), as well as those referred to our center (N = 51). The genotypes including p.(Val377Ile) (homozygous or compound heterozygous) were more frequent in mild systemic forms but were also sometimes encountered with severe disease. We confirmed that amyloidosis was more prevalent in patients compound heterozygous for p.(Ile268Thr) and p.(Val377Ile) than in others and revealed new associations. Patients homozygous for p.(Leu264Phe), p.(Ala334Thr) or compound heterozygous for p.(His20Pro) and p.(Ala334Thr) had increased risk of severe neurological or ocular symptoms. All patients homozygous for p.(Leu264Phe) had a cataract. The variants associated with porokeratosis were relatively specific and more frequently caused a frameshift than in patients with other clinical forms (26% vs. 6%). We provide practical recommendations focusing on phenotype–genotype correlation in MKAD that could be helpful for prophylactic management.