bluuebunny/crossref_metadata_2025 huggingface dataset:
A Comparison of the Percentage of “Yes” (Agree) Responses and Importance of Attributes (Constructs) Determined Using Check-All-That-Apply and Check-All-Statements (Yes/No) Question Formats in Five Countries
Authors: Seninde Denis Richard , Chambers Edgar
Published: October 2020

Check All That Apply (CATA) has become a popular type of questionnaire response in sensory/consumer research in recent years. However, some authors have pointed out potential problems with the method. An online survey using either a Check-All-That-Apply (CATA) or Check-All-Statements (CAS) format for questions was conducted to provide a deeper understanding of the response data using the two question formats. With CATA, respondents select all terms or statements that apply from a given list, while, with CAS, respondents must respond (e.g., yes/no or agree/disagree) to each term or statement to show that it applies or does not apply. Respondents from five countries (Brazil, China, India, Spain, and the USA) were randomly assigned one of the two question formats (N = 200 per country per method). Motivations for eating items that belong to five food groups (starchy, protein, dairy, fruits, and desserts) were assessed. Results showed that CAS had higher percentages of “agree” responses than CATA. Also, the response ratio of CAS and CATA data was different, suggesting that interpretations of the data from each response type would also be different. Respondents in the USA, China, and Spain took longer to complete the CAS questionnaire, while respondents in Brazil and India had similar time durations for the two question formats. Overall, the CATA format was liked slightly more than the CAS format and fewer respondents dropped out of the survey when using the CATA response type. These findings suggest that the CATA format is quick and relatively easy for consumers to complete. However, it provokes fewer “apply” responses, which some psychologists suggest underestimates applicable terms or statements and CATA provides a different interpretation of data than the CAS format that requires consumers to respond to each term or statement. Further, CAS may overestimate the applicable terms. Consumer insights collected using CATA and CAS can lead to different decisions due to differences in data interpretation by researchers (e.g., marketers, nutritionists, product developers, and sensory scientists). More investigation is needed for the CATA and CAS question formats.
Can the Consumption of Ultra-Processed Food Be Associated with Anthropometric Indicators of Obesity and Blood Pressure in Children 7 to 10 Years Old?
Authors: Oliveira Tafnes , Ribeiro Isabella , Jurema-Santos Gabriela , Nobre Isabele , Santos Ravi , Rodrigues Camilla , Oliveira Kevin , Henrique Rafael , Ferreira-e-Silva Wylla , Araújo Alice
Published: October 2020

The consumption of ultra-processed foods plays an important role in the development of obesity and hypertension. The present study investigated the association between consumption of food according to the degree of processing and anthropometric indicators of obesity and blood pressure in children. This is a cross-sectional study with 164 children aged 7–10 years. The body mass index (BMI) for age, waist circumference (WC), and waist-to-height ratio (WHtR) was evaluated. Food consumption was analyzed by three 24-h dietary recalls, and classified as: G1—unprocessed or minimally processed; G2—culinary ingredients and processed food; and G3—ultra-processed food. Linear regression analyses were used to investigate the associations among variables. The average energy consumption was 1762.76 kcal/day, split into 45.42%, 10.88%, and 43.70%, provided by G1, G2, and G3, respectively. Adjusted linear regression analyses identified that the caloric contribution of G1 was inversely associated with DBP, showing that for each 10% increase in the energy intake of minimally processed foods, there was a reduction of 0.96 mmHg in the DBP (β:−0.10; 95% CI:−0.19 to −0.01; r2 = 0.20). There was no association between the caloric contribution of food groups and BMI, WC, WHtR, and SBP. Increasing consumption of G1 could be a strategy for the prevention and treatment of hypertension in schoolchildren.
Quantification of Process Lethality (5-Log Reduction) of Salmonella and Salt Concentration during Sodium Replacement in Biltong Marinade
Authors: Karolenko Caitlin , Muriana Peter
Published: October 2020

Salt (sodium chloride, NaCl) is commonly used in ready-to-eat (RTE) meat products such as biltong, a South African style dried beef product for flavor, enhanced moisture loss, and reduction of microbial growth. However, increased consumption of high sodium content foods is commonly associated with high blood pressure and heart disease. This study evaluated the use of alternative salts, potassium chloride (KCl) and calcium chloride (CaCl2) in the biltong marinade to achieve a ≥ 5-log reduction of Salmonella, a pathogen of concern in beef products. Beef pieces (1.9 cm × 5.1 cm × 7.6 cm) were inoculated with a five-serovar mixture of Salmonella (Salmonella Thompson 120, Salmonella Enteritidis H3527, Salmonella Typhimurium H3380, Salmonella Heidelberg F5038BG1, and Salmonella Hadar MF60404), vacuum-tumbled in a traditional biltong marinade of salt, spices, and vinegar containing either NaCl, KCl or CaCl2 (2.2% concentration) followed by an 8–10 day drying period at 23.9 °C (75 °F) and 55% relative humidity. Microbial enumeration of Salmonella was conducted following inoculation, after marination, and after 2, 4, 6, 8, and 10 days of drying in a humidity/temperature chamber. Biltong produced with CaCl2, NaCl, or KCl achieved a > 5-log reduction of Salmonella after 6, 7, and 8 days, respectively. The Salmonella reduction trends with biltong made with NaCl or CaCl2 were not significantly different (p < 0.05) while both were significantly different from that made with KCl (p > 0.05). Sodium, calcium, and potassium ion concentrations were measured using ion-specific electrode meters following biltong processing and drying. As expected, the biltong made with the corresponding salt had the most abundant ion in the sample. Regardless of the salt used in the marinade, the potassium ion levels were moderately elevated in all samples. This was determined to be from potassium levels naturally present in beef rather than from other ingredients. Sampling of several commercial brands of biltong for sodium content showed that some were significantly above the allowable level of claims made on package ingredient statements. The substitution of NaCl with KCl or CaCl2 during biltong processing can also provide a 5-log reduction of Salmonella to produce a safe product that can be marketed as a more healthy low-sodium food alternative that may appeal to consumers who need to reduce their blood pressure and are conscientious of sodium levels in their diet.
Molecular Characterization of Microbial and Fungal Communities on Dry-Aged Beef of Hanwoo Using Metagenomic Analysis
Authors: Ryu Sangdon , Shin Minhye , Cho Soohyun , Hwang Inho , Kim Younghoon , Oh Sangnam
Published: October 2020

Dry aging has been widely applied for the aging of meat to produce a unique flavor and tenderness of meat. A number of microorganisms are present, forming a community with interactions that affect the meat aging process. However, their comprehensive compositions are still not well understood. In this study, we analyzed longitudinal changes in microbial and fungal communities in dry-aged beef using a metagenomic platform. 16S rRNA sequencing revealed that dry aging led to an increase in bacterial diversity, and Actinobacteria and Firmicutes, which are mostly lactic acid bacteria, were dominant on dry-aged beef. However, prolonged dry aging reduced the diversity of lactic acid bacteria. Sequencing of the internal transcribed spacer (ITS) region showed that fungal diversity was reduced by aging and that Helicostylum sp. was the most common species. These results suggest that there are various microorganisms on dry-aged beef that interrelate with each other and affect meat quality. Understanding microbial characteristics during the aging process will help to enhance beef quality and functional effects.
Pectin-Based Films with Cocoa Bean Shell Waste Extract and ZnO/Zn-NPs with Enhanced Oxygen Barrier, Ultraviolet Screen and Photocatalytic Properties
Authors: Mellinas Ana Cristina , Jiménez Alfonso , Garrigós María Carmen
Published: October 2020

In this work, pectin-based active films with a cocoa bean shell extract, obtained after waste valorisation of residues coming from the chocolate production process, and zinc oxide/zinc nanoparticles (ZnO/Zn-NPs) at different concentrations, were obtained by casting. The effect of the active additive incorporation on the thermal, barrier, structural, morphological and optical properties was investigated. Moreover, the photocatalytic properties of the obtained films based on the decomposition of methylene blue (MB) in aqueous solution at room temperature were also studied. A significant increase in thermal and oxidative stability was obtained with the incorporation of 3 wt% of ZnO/Zn-NPs compared to the control film. The addition of 5 wt% cocoa bean shell extract to pectin significantly affected the oxygen barrier properties due to a plasticizing effect. In contrast, the addition of ZnO/Zn-NPs at 1 wt% to pectin caused a decrease in oxygen transmission rate per film thickness (OTR.e) values of approximately 50% compared to the control film, resulting in an enhanced protection against oxidation for food preservation. The optical properties were highly influenced by the incorporation of the natural extract but this effect was mitigated when nanoparticles were also incorporated into pectin-based films. The addition of the extract and nanoparticles resulted in a clear improvement (by 98%) in UV barrier properties, which could be important for packaged food sensitive to UV radiation. Finally, the photocatalytic activity of the developed films containing nanoparticles was demonstrated, showing photodegradation efficiency values of nearly 90% after 60 min at 3 wt% of ZnO/Zn-NPs loading. In conclusion, the obtained pectin-based bionanocomposites with cocoa bean shell waste extract and zinc oxide/zinc nanoparticles showed great potential to be used as active packaging for food preservation.
Digestomics of Cow’s Milk: Short Digestion-Resistant Peptides of Casein Form Functional Complexes by Aggregation
Authors: Radosavljević Jelena , Apostolović Danijela , Mihailović Jelena , Atanasković-Marković Marina , Burazer Lidija , van Hage Marianne , Ćirković Veličković Tanja
Published: October 2020

The aim of this study was to identify short digestion-resistant peptides (SDRPs) released by pepsin digestion of the whole cow’s milk and examine their IgE reactivity and allergenicity. Raw milk was subjected to simulated gastric digestion. SDRPs were fractionated from the digests and identified by MS. Milk SDRPs were evaluated for aggregability, propensity to compete for IgE binding with individual milk allergens, and ability to bind IgG4 from allergic and milk-tolerant individuals. The majority of milk SDRPs originated from caseins (97% of peptides) and overlapped with the known IgE epitopes of cow’s milk allergens. SDRPs competed with milk proteins for binding to human IgE and readily formed aggregates. The average peptide length was 10.6 ± 3.5 amino acids. The ability to provoke allergenic in vivo responses was confirmed by skin-prick testing (SPT) in five milk-allergic subjects. This was attributed to the peptide ability to aggregate into non-covalent complexes. SDRPs are able to induce response in SPT, but only in 50% of the sera SDRPs were able to inhibit IgG4 binding to caseins. Hence, SDRPs corresponding to the mainly continuous epitopes of milk proteins induce allergenic in vivo responses in milk-allergic subjects due to aggregation.
Communication, Expectations, and Trust: An Experiment with Three Media
Authors: Abatayo Anna Lou , Lynham John , Sherstyuk Katerina
Published: October 2020

We studied how communication media affect trust game play. Three popular media were considered: traditional face-to-face, Facebook groups, and anonymous online chat. We considered post-communication changes in players’ expectations and preferences, and further analyzed the contents of group communications to understand the channels though which communication appears to improve trust and trustworthiness. For senders, the social, emotional, and game-relevant contents of communication all matter, significantly influencing both their expectations of fair return and preferences towards receivers. Receivers increased trustworthiness is mostly explained by their adherence to the norm of sending back a fair share of the amount received. These results do not qualitatively differ among the three communication media; while face-to-face had the largest volume of messages, all three media proved equally effective in enhancing trust and trustworthiness.
Asteroseismic Analysis of δ Scuti Components of Binary Systems: The Case of KIC 8504570
Authors: Liakos Alexios , Niarchos Panagiotis
Published: October 2020

The present work concerns the Asteroseismology of the Kepler-detached eclipsing binary KIC 8504570. Particularly, it focuses on the pulsational behaviour of the oscillating component of this system and the estimation of its physical parameters in order to enrich the so far poor sample of systems of this kind. Using spectroscopic observations, the spectral type of the primary component was determined and used to create accurate light curve models and estimate its absolute parameters. The light curve residuals were subsequently analysed using Fourier transformation techniques to obtain the pulsation models. Theoretical models of δ Scuti stars were employed to identify the oscillation modes of the six detected independent frequencies of the pulsator. In addition, more than 385 combination frequencies were also detected. The absolute and the pulsational properties of the δ Scuti star of this system are discussed and compared with all the currently known similar cases. Moreover, using a recent(empirical) luminosity–pulsation period relationship for δ Scuti stars, the distance of the system was estimated.
Expression of Genes Encoding Manganese Peroxidase and Laccase of Ganoderma boninense in Response to Nitrogen Sources, Hydrogen Peroxide and Phytohormones
Authors: Ho Pei-Yin , Namasivayam Parameswari , Sundram Shamala , Ho Chai-Ling
Published: October 2020

Ganoderma produces lignolytic enzymes that can degrade the lignin component of plant cell walls, causing basal stem rot to oil palms. Nitrogen sources may affect plant tolerance to root pathogens while hydrogen peroxide (H2O2), salicylic acid (SA) and jasmonic acid (JA) play important roles in plant defense against pathogens. In this study, we examined the expression of genes encoding manganese peroxidase (MnP) and laccase (Lac) in Ganoderma boninense treated with different nitrogen sources (ammonium nitrate, ammonium sulphate, sodium nitrate and potassium nitrate), JA, SA and H2O2. Transcripts encoding MnP and Lac were cloned from G. boninense. Of the three GbMnP genes, GbMnP_U6011 was up-regulated by all nitrogen sources examined and H2O2 but was down-regulated by JA. The expression of GbMnP_U87 was only up-regulated by JA while GbMnP_35959 was up-regulated by ammonium nitrate but suppressed by sodium nitrate and down-regulated by H2O2. Among the three GbLac genes examined, GbLac_U90667 was up-regulated by ammonium nitrate, JA, SA and H2O2; GbLac_U36023 was up-regulated by JA and H2O2 while GbLac_U30636 was up-regulated by SA but suppressed by ammonium sulphate, sodium nitrate, JA and H2O2. Differential expression of these genes may be required by their different functional roles in G. boninense.
Improvement of Stable Restorer Lines for Blast Resistance through Functional Marker in Rice (Oryza sativa L.)
Authors: Ramalingam Jegadeesan , Palanisamy Savitha , Alagarasan Ganesh , Renganathan Vellaichamy Gandhimeyyan , Ramanathan Ayyasamy , Saraswathi Ramasamy
Published: October 2020

Two popular stable restorer lines, CB 87 R and CB 174 R, were improved for blast resistance through marker-assisted back-cross breeding (MABB). The hybrid rice development program in South India extensively depends on these two restorer lines. However, these restorer lines are highly susceptible to blast disease. To improve the restorer lines for resistance against blasts, we introgressed the broad-spectrum dominant gene Pi54 into these elite restorer lines through two independent crosses. Foreground selection for Pi54 was done by using gene-specific functional marker, Pi54 MAS, at each back-cross generation. Back-crossing was continued until BC3 and background analysis with seventy polymorphic SSRs covering all the twelve chromosomes to recover the maximum recurrent parent genome was done. At BC3F2, closely linked gene-specific/SSR markers, DRRM-RF3-10, DRCG-RF4-8, and RM 6100, were used for the identification of fertility restoration genes, Rf3 and Rf4, along with target gene (Pi54), respectively, in the segregating population. Subsequently, at BC3F3, plants, homozygous for the Pi54 and fertility restorer genes (Rf3 and Rf4), were evaluated for blast disease resistance under uniform blast nursery (UBN) and pollen fertility status. Stringent phenotypic selection resulted in the identification of nine near-isogenic lines in CB 87 R × B 95 and thirteen in CB 174 R × B 95 as the promising restorer lines possessing blast disease resistance along with restoration ability. The improved lines also showed significant improvement in agronomic traits compared to the recurrent parents. The improved restorer lines developed through the present study are now being utilized in our hybrid development program.
Heavy Metal Transporters-Associated Proteins in Solanum tuberosum: Genome-Wide Identification, Comprehensive Gene Feature, Evolution and Expression Analysis
Authors: He Guandi , Qin Lijun , Tian Weijun , Meng Lulu , He Tengbing , Zhao Degang
Published: October 2020

Plants have evolved a number of defense and adaptation responses to protect themselves against challenging environmental stresses. Genes containing a heavy metal associated (HMA) domain are required for the spatiotemporal transportation of metal ions that bind with various enzymes and co-factors within the cell. To uncover the underlying mechanisms mediated by StHMA genes, we identified 36 gene members in the StHMA family and divided them into six subfamilies by phylogenetic analysis. The StHMAs had high collinearity and were segmentally duplicated. Structurally, most StHMAs had one HMA domain, StHIPPc and StRNA1 subfamilies had two, and 13 StHMAs may be genetically variable. The StHMA gene structures and motifs varied considerably among the various classifications, this suggests the StHMA family is diverse in genetic functions. The promoter analysis showed that the StHMAs had six main cis-acting elements with abiotic stress. An expression pattern analysis revealed that the StHMAs were expressed tissue specifically, and a variety of abiotic stresses may induce the expression of StHMA family genes. The HMA transporter family may be regulated and expressed by a series of complex signal networks under abiotic stress. The results of this study may help to establish a theoretical foundation for further research investigating the functions of HMA genes in Solanum tuberosum to elucidate their regulatory role in the mechanism governing the response of plants to abiotic stress.
Multi-Trait Genomic Prediction of Yield-Related Traits in US Soft Wheat under Variable Water Regimes
Authors: Guo Jia , Khan Jahangir , Pradhan Sumit , Shahi Dipendra , Khan Naeem , Avci Muhsin , Mcbreen Jordan , Harrison Stephen , Brown-Guedira Gina , Murphy Joseph Paul , Johnson Jerry , Mergoum Mohamed , Esten Mason Richanrd , Ibrahim Amir M. H. , Sutton Russel , Griffey Carl , Babar Md Ali
Published: October 2020

The performance of genomic prediction (GP) on genetically correlated traits can be improved through an interdependence multi-trait model under a multi-environment context. In this study, a panel of 237 soft facultative wheat (Triticum aestivum L.) lines was evaluated to compare single- and multi-trait models for predicting grain yield (GY), harvest index (HI), spike fertility (SF), and thousand grain weight (TGW). The panel was phenotyped in two locations and two years in Florida under drought and moderately drought stress conditions, while the genotyping was performed using 27,957 genotyping-by-sequencing (GBS) single nucleotide polymorphism (SNP) makers. Five predictive models including Multi-environment Genomic Best Linear Unbiased Predictor (MGBLUP), Bayesian Multi-trait Multi-environment (BMTME), Bayesian Multi-output Regressor Stacking (BMORS), Single-trait Multi-environment Deep Learning (SMDL), and Multi-trait Multi-environment Deep Learning (MMDL) were compared. Across environments, the multi-trait statistical model (BMTME) was superior to the multi-trait DL model for prediction accuracy in most scenarios, but the DL models were comparable to the statistical models for response to selection. The multi-trait model also showed 5 to 22% more genetic gain compared to the single-trait model across environment reflected by the response to selection. Overall, these results suggest that multi-trait genomic prediction can be an efficient strategy for economically important yield component related traits in soft wheat.
Slc4 Gene Family in Spotted Sea Bass (Lateolabrax maculatus): Structure, Evolution, and Expression Profiling in Response to Alkalinity Stress and Salinity Changes
Authors: Wang Ling-Yu , Tian Yuan , Wen Hai-Shen , Yu Peng , Liu Yang , Qi Xin , Gao Zhi-Chao , Zhang Kai-Qiang , Li Yun
Published: October 2020

The solute carrier 4 (SLC4) family is a class of cell membranes transporters involved in base transport that plays crucial roles in diverse physiological processes. In our study, 15 slc4 genes were identified and annotated in spotted sea bass, including five members of Cl−/HCO3− exchangers, eight genes coding Na+-dependent HCO3− transporters, and two copies of Na+-coupled borate transporters. The gene sequence and structure, chromosomal and syntenic arrangement, phylogenetic and evolution profiles were analyzed. Results showed that the slc4 gene in teleosts obviously expanded compared with higher vertebrates, arising from teleost-specific whole genome duplication event. Most gene sites of slc4 in spotted sea bass were under strong purifying selection during evolution, while positive selection sites were only detected in slc4a1b, slc4a8, and slc4a10b. Additionally, qRT-PCR results showed that different slc4 genes exhibited distinct branchial expression patterns after alkalinity and salinity stresses, of which the strongly responsive members may play essential roles during these physiological processes. Our study provides the systemic overview of the slc4 gene family in spotted sea bass and enables a better understanding for the evolution of this family and further deciphering the biological roles in maintaining ion and acid–base homeostasis in teleosts.
Genome-Wide Association Study of Metamizole-Induced Agranulocytosis in European Populations
Authors: Cismaru Anca , Rudin Deborah , Ibañez Luisa , Liakoni Evangelia , Bonadies Nicolas , Kreutz Reinhold , Carvajal Alfonso , Lucena Maria , Martin Javier , Sancho Ponce Esther , Molokhia Mariam , Eriksson Niclas ,   EuDAC collaborators, Krähenbühl Stephan , Largiadèr Carlo , Haschke Manuel , Hallberg Pär , Wadelius Mia , Amstutz Ursula
Published: October 2020

Agranulocytosis is a rare yet severe idiosyncratic adverse drug reaction to metamizole, an analgesic widely used in countries such as Switzerland and Germany. Notably, an underlying mechanism has not yet been fully elucidated and no predictive factors are known to identify at-risk patients. With the aim to identify genetic susceptibility variants to metamizole-induced agranulocytosis (MIA) and neutropenia (MIN), we conducted a retrospective multi-center collaboration including cases and controls from three European populations. Association analyses were performed using genome-wide genotyping data from a Swiss cohort (45 cases, 191 controls) followed by replication in two independent European cohorts (41 cases, 273 controls) and a joint discovery meta-analysis. No genome-wide significant associations (p < 1 × 10−7) were observed in the Swiss cohort or in the joint meta-analysis, and no candidate genes suggesting an immune-mediated mechanism were identified. In the joint meta-analysis of MIA cases across all cohorts, two candidate loci on chromosome 9 were identified, rs55898176 (OR = 4.01, 95%CI: 2.41–6.68, p = 1.01 × 10−7) and rs4427239 (OR = 5.47, 95%CI: 2.81–10.65, p = 5.75 × 10−7), of which the latter is located in the SVEP1 gene previously implicated in hematopoiesis. This first genome-wide association study for MIA identified suggestive associations with biological plausibility that may be used as a stepping-stone for post-GWAS analyses to gain further insight into the mechanism underlying MIA.
Revealing Prognosis-Related Pathways at the Individual Level by a Comprehensive Analysis of Different Cancer Transcription Data
Authors: Fang Jingya , Pian Cong , Xu Mingmin , Kong Lingpeng , Li Zutan , Ji Jinwen , Chen Yuanyuan , Zhang Liangyun
Published: October 2020

Identifying perturbed pathways at an individual level is important to discover the causes of cancer and develop individualized custom therapeutic strategies. Though prognostic gene lists have had success in prognosis prediction, using single genes that are related to the relevant system or specific network cannot fully reveal the process of tumorigenesis. We hypothesize that in individual samples, the disruption of transcription homeostasis can influence the occurrence, development, and metastasis of tumors and has implications for patient survival outcomes. Here, we introduced the individual-level pathway score, which can measure the correlation perturbation of the pathways in a single sample well. We applied this method to the expression data of 16 different cancer types from The Cancer Genome Atlas (TCGA) database. Our results indicate that different cancer types as well as their tumor-adjacent tissues can be clearly distinguished by the individual-level pathway score. Additionally, we found that there was strong heterogeneity among different cancer types and the percentage of perturbed pathways as well as the perturbation proportions of tumor samples in each pathway were significantly different. Finally, the prognosis-related pathways of different cancer types were obtained by survival analysis. We demonstrated that the individual-level pathway score (iPS) is capable of classifying cancer types and identifying some key prognosis-related pathways.
Strong Correlation between HLA and Clinical Course of Subacute Thyroiditis—A Report of the Three Siblings
Authors: Stasiak Magdalena , Lewiński Andrzej
Published: October 2020

Subacute thyroiditis (SAT) is a thyroid inflammatory disease with susceptibility associated with the presence of human leukocyte antigen (HLA)-B*35, -B*18:01, -DRB1*01 and -C*04:01. Previous viral infection is considered as a triggering factor in genetically predisposed individuals. The influence of HLA on the SAT course was previously suggested. We aim to present the three siblings—female twins and their brother—with very close onset but different clinical courses of SAT, which appeared to be HLA-dependent. The HLA profile in the reported three siblings is strongly correlated with both SAT and Graves’ disease (GD), however the coexistence of particular sets of high risk and protective alleles seems to be crucial for the GD development and the SAT course. The co-occurrence of HLA-DRB1*15:01 and/or -B*07:02, possibly together with the lack of HLA-A*01:01 and -B*41:01 seems to be key factors protecting against the development of GD with high TRAb levels, as well as against the recurrent SAT course and steroid dependence.
Next-Generation Sequencing in the Diagnosis of Patients with Bardet–Biedl Syndrome—New Variants and Relationship with Hyperglycemia and Insulin Resistance
Authors: Jeziorny Krzysztof , Antosik Karolina , Jakiel Paulina , Młynarski Wojciech , Borowiec Maciej , Zmysłowska Agnieszka
Published: October 2020

Bardet-Biedl syndrome (BBS) is a rare autosomal recessively inherited disease with major clinical symptoms such as: obesity, retinal degeneration, polydactyly and renal abnormalities. The aim of the study was to assess the spectrum of gene variants among patients with BBS, identified on the basis of nationwide genetic studies of monogenic diabetes in Polish population. Out of 575 patients enrolled for genetic testing from February 2017 to July 2019, 25 patients with a clinical suspicion of BBS were selected. The identification of pathogenic variants was performed by using targeted next-generation sequencing (NGS) on Illumina NextSeq 550 platform involving the SureSelect assay (Agilent, Santa Clara, CA, USA). BBS was genetically confirmed in 10 of 25 suspected patients. In patients, 14 different variants were found in six genes, mainly in BBS9 and BBS10 gene, including two novel variants. A strong association between hyperglycemia and insulin resistance in patients and the presence of variants in BBS9 gene was observed. Identification of 14 variants, including two new mutations using the NGS method, is the first molecular characteristic of Polish patients with Bardet–Biedl syndrome. It gives hope for earlier proper diagnosis of BBS in future patients selected from children with early childhood obesity and their medical multidisciplinary care.
The Transcriptional Network in the Arabidopsis Circadian Clock System
Authors: Nakamichi Norihito
Published: October 2020

The circadian clock is the biological timekeeping system that governs the approximately 24-h rhythms of genetic, metabolic, physiological and behavioral processes in most organisms. This oscillation allows organisms to anticipate and adapt to day–night changes in the environment. Molecular studies have indicated that a transcription–translation feedback loop (TTFL), consisting of transcriptional repressors and activators, is essential for clock function in Arabidopsis thaliana (Arabidopsis). Omics studies using next-generation sequencers have further revealed that transcription factors in the TTFL directly regulate key genes implicated in clock-output pathways. In this review, the target genes of the Arabidopsis clock-associated transcription factors are summarized. The Arabidopsis clock transcriptional network is partly conserved among angiosperms. In addition, the clock-dependent transcriptional network structure is discussed in the context of plant behaviors for adapting to day–night cycles.
Overexpression of Two CCCH-type Zinc-Finger Protein Genes Leads to Pollen Abortion in Brassica campestris ssp. chinensis
Authors: Xu Liai , Liu Tingting , Xiong Xingpeng , Liu Weimiao , Yu Youjian , Cao Jiashu
Published: October 2020

The pollen grains produced by flowering plants are vital for sexual reproduction. Previous studies have shown that two CCCH-type zinc-finger protein genes in Brassica campestris, BcMF30a and BcMF30c, are involved in pollen development. Due to their possible functional redundancy, gain-of-function analysis is helpful to reveal their respective biological functions. Here, we found that the phenotypes of BcMF30a and BcMF30c overexpression transgenic plants driven by their native promoters were similar, suggesting their functional redundancy. The results showed that the vegetative growth was not affected in both transgenic plants, but male fertility was reduced. Further analysis found that the abortion of transgenic pollen was caused by the degradation of pollen contents from the late uninucleate microspore stage. Subcellular localization analysis demonstrated that BcMF30a and BcMF30c could localize in cytoplasmic foci. Combined with the studies of other CCCH-type genes, we speculated that the overexpression of these genes can induce the continuous assembly of abnormal cytoplasmic foci, thus resulting in defective plant growth and development, which, in this study, led to pollen abortion. Both the overexpression and knockout of BcMF30a and BcMF30c lead to abnormal pollen development, indicating that the appropriate expression levels of these two genes are critical for the maintenance of normal pollen development.
Transcriptome Analysis Reveals Functional Diversity in Salivary Glands of Plant Virus Vector, Graminella nigrifrons
Authors: Rajarapu Swapna Priya , Bansal Raman , Mittapelly Priyanka , Michel Andrew
Published: October 2020

Insect salivary glands play an important role for host feeding, specifically by secreting salivary proteins for digestion and potentially modulating host defenses. Compared to other hemipterans, the significance of salivary glands is less studied in the black-faced leafhopper, Graminella nigrifrons, a crop pest that vectors several agronomically important plant viruses. To identify functionally important genes in the salivary glands of the black-faced leafhopper, we compared transcriptomes between adult salivary glands (SG) and the remaining carcasses. We identified 14,297 salivary gland-enriched transcripts and 195 predicted secretory peptides (i.e., with a signal peptide and extracellular localization characteristics). Overall, the SG transcriptome included functions such as ‘oxidoreduction’, ‘membrane transport’, and ‘ATP-binding’, which might be important for the fundamental physiology of this tissue. We further evaluated transcripts with potential contributions in host feeding using RT-qPCR. Two SG-enriched transcripts (log2 fold change > 5), GnP19 and GnE63 (a putative calcium binding protein), were significantly upregulated in maize-fed adults relative to starved adults, validating their importance in feeding. The SG-enriched transcripts of the black-faced leafhopper could play a potential role for interacting with maize and could be targets of interest for further functional studies and improve pest control and disease transmission.
Transcriptional Analysis of Carotenoids Accumulation and Metabolism in a Pink-Fleshed Lemon Mutant
Authors: Lana Giuseppe , Zacarias-Garcia Jaime , Distefano Gaetano , Gentile Alessandra , Rodrigo María J. , Zacarias Lorenzo
Published: October 2020

Pink lemon is a spontaneous bud mutation of lemon (Citrus limon, L. Burm. f) characterized by the production of pink-fleshed fruits due to an unusual accumulation of lycopene. To elucidate the genetic determinism of the altered pigmentation, comparative carotenoid profiling and transcriptional analysis of both the genes involved in carotenoid precursors and metabolism, and the proteins related to carotenoid-sequestering structures were performed in pink-fleshed lemon and its wild-type. The carotenoid profile of pink lemon pulp is characterized by an increased accumulation of linear carotenoids, such as lycopene, phytoene and phytofluene, from the early stages of development, reaching their maximum in mature green fruits. The distinctive phenotype of pink lemon is associated with an up-regulation and down-regulation of the genes upstream and downstream the lycopene cyclase, respectively. In particular, 9-cis epoxycarotenoid dioxygenase genes were overexpressed in pink lemon compared with the wild-type, suggesting an altered regulation of abscisic acid biosynthesis. Similarly, during early development of the fruits, genes of the carotenoid-associated proteins heat shock protein 21, fibrillin 1 and 2 and orange gene were overexpressed in the pulp of the pink-fleshed lemon compared to the wild-type, indicating its increased capacity for sequestration, stabilization or accumulation of carotenes. Altogether, the results highlighted significant differences at the transcriptomic level between the pink-fleshed lemon and its wild-type, in terms of carotenoid metabolism and the capacity of stabilization in storage structures between the two accessions. Such changes may be either responsible for the altered carotenoid accumulation or in contrast, a metabolic consequence.
NSDHL Frameshift Deletion in a Mixed Breed Dog with Progressive Epidermal Nevi
Authors: Christen Matthias , Austel Michaela , Banovic Frane , Jagannathan Vidhya , Leeb Tosso
Published: October 2020

Loss-of-function variants in the NSDHL gene have been associated with epidermal nevi in humans with congenital hemidysplasia, ichthyosiform nevi, and limb defects (CHILD) syndrome and in companion animals. The NSDHL gene codes for the NAD(P)-dependent steroid dehydrogenase-like protein, which is involved in cholesterol biosynthesis. In this study, a female Chihuahua cross with a clinical and histological phenotype consistent with progressive epidermal nevi is presented. All exons of the NSDHL candidate gene were amplified by PCR and analyzed by Sanger sequencing. A heterozygous frameshift variant, c.718_722delGAACA, was identified in the affected dog. In lesional skin, the vast majority of NSDHL transcripts lacked the five deleted bases. The variant is predicted to produce a premature stop codon truncating 34% of the encoded protein, p.Glu240Profs*17. The mutant allele was absent from 22 additionally genotyped Chihuahuas, as well as from 647 control dogs of diverse breeds and eight wolves. The available experimental data together with current knowledge about NSDHL variants and their functional impact in humans, dogs, and other species prompted us to classify this variant as pathogenic according to the ACMG guidelines that were previously established for human sequence variants. Therefore, we propose the c.718_722delGAACA variant as causative variant for the observed skin lesions in this dog.
Advancement of the Acetylene Inhibition Technique Using Time Series Analysis on Air-Dried Floodplain Soils to Quantify Denitrification Potential
Authors: Kaden Ute Susanne , Fuchs Elmar , Hecht Christian , Hein Thomas , Rupp Holger , Scholz Mathias , Schulz-Zunkel Christiane
Published: October 2020

Denitrification in floodplain soils is one key process that determines the buffering capacity of riparian zones in terms of diffuse nitrate pollution. One widely used approach to measure the denitrification potential is the acetylene inhibition technique that requires fresh soil samples. We conducted experiments with air-dried soils using a time series analysis to determine the optimal rewetting period. Thus, air-dried soil samples from six different floodplain areas in Germany were rewetted for 1 to 13days to 100% water-filled pore space. We analyzed nitrogen accumulated as N2O in the top of anaerobic flasks with and without acetylene by gas chromatography after four hours of incubation. We observed an overall optimal rewetting of at least seven days for complete denitrification. We also saw the strong influence of pH and field capacity on the denitrification product ratio; in soils with pH < 7, we hardly assumed complete denitrification, whereas the treatments with pH > 7 achieved stable values after seven days of rewetting. This advanced method provides the opportunity to carry out campaigns with large soil sample sizes on the landscape scale, as samples can be stored dry until measurements are taken.
Femicide Fatal Risk Factors: A Last Decade Comparison between Italian Victims of Femicide by Age Groups
Authors: Sorrentino Anna , Guida Chiara , Cinquegrana Vincenza , Baldry Anna Costanza
Published: October 2020

Femicide is a wide-spread lethal form of violence against women. Despite its diffusion, to date, very few studies analyzed possible victims’ age differences in regard to fatal risk factors for femicide. To this aim, we carried out archive research on Italian femicide cases in the last decade, by comparing prior types of violence suffered and motives for femicide, which are considered crucial fatal risk factors for femicide, across adolescent/young (15–24 years), adults (25–64 years) and older women (65–93 years). From 2010 to 2019 we found 1207 female victims. Characteristics of victims, perpetrators, and their relationship were consistent with those found by international studies and underlined that the majority of femicides were perpetrated by an intimate partner. The results regarding fatal risk factors comparisons across age groups showed the existence of significant differences regarding both types of violence suffered prior to femicide and motives for femicide. The results are discussed in terms of policy implication and intervention.
Accuracy of Self-Reported Items for the Screening of Depression in the General Population
Authors: Arias-de la Torre Jorge , Vilagut Gemma , Serrano-Blanco Antoni , Martín Vicente , Molina Antonio José , Valderas Jose M , Alonso Jordi
Published: October 2020

Introduction: Though self-reported items (SRD, self-reported depression) are commonly used in health surveys and cohort studies, their metric properties as a depression indicator remain unclear. The aims were to evaluate the measurement properties of SRD using the Patient Health Questionnaire-8 (PHQ-8) as reference and to identify factors related to the agreement between both indicators. Methods: Data from the European Health Interview Survey in Spain in 2014/2015 (n = 22,065) were analyzed. Two indicators of depression were considered: SRD based on two items yes/no (positive: both yes), and the PHQ-8 (positive ≥ 10). Socioeconomic factors and use of health services were considered as independent variables. The prevalence of depression, sensitivity, specificity, global agreement, and positive and negative predictive values (PPV and NPV) of SRDs were evaluated using the PHQ-8 as a reference. Logistic regression models were fitted to determine factors associated with the agreement between indicators. Results: The prevalence of depression was lower when assessed with PHQ-8 (5.9%) than with SRD (7.7%). SRD sensitivity and PPV were moderate–low (52.9% and 40.4%, respectively) whereas global agreement, specificity, and NPV were high (92.7%, 95.1%, and 97.0%, respectively). Positive agreement was associated with marital status, country of birth, employment status, and social class. Negative agreement was related to all independent variables except country of birth. Conclusions: SRD items tend to overestimate the current prevalence of depression. While its use in health surveys and cohorts may be appropriate as a quick assessment of possible depression, due to their low sensitivity, its use in clinical contexts is questionable.
Involvement of DAT1 Gene on Internet Addiction: Cross-Correlations of Methylation Levels in 5′-UTR and 3’-UTR Genotypes, Interact with Impulsivity and Attachment-Driven Quality of Relationships
Authors: De Nardi Laura , Carpentieri Valentina , Pascale Esterina , Pucci Mariangela , D'Addario Claudio , Cerniglia Luca , Adriani Walter , Cimino Silvia
Published: October 2020

Internet influences our communication, social and work interactions, entertainment, and many other aspects of life. Even if the original purpose was to simplify our lives, an excessive and/or maladaptive use of it may have negative consequences. The dopamine transporter (DAT1) gene was studied in relation to addictions, including excessive use of the Internet. The crucial role of DAT1 was previously underlined in modulating emotional aspects, such as affiliative behaviors. The present research follows a new approach based on cross-correlation between (de)methylation levels in couples of CpG loci, as previously shown. We investigated the possible relationships between Internet addiction, impulsivity, quality of attachment, DAT1 genotypes (from the 3′-untranslated region (UTR) variable number of tandem repeats (VNTR) poly-morphism), and the dynamics of methylation within the 5’-UTR of the DAT1 gene. From a normative sample of 79 youths, we extrapolated three subgroups a posteriori, i.e., one “vulnerable” with high Internet Addiction Test (IAT) scores (and high Barrat Impulsivity Scale (BIS) scores; n = 9) and two “controls’’ with low BIS scores and 10/10 vs. 9/x genotype (n = 12 each). Controls also had a “secure” attachment pattern, while genotypes and attachment styles were undistinguished in the vulnerable subgroup (none showed overt Internet addiction). We found a strongly positive correlation in all groups between CpG2 and CpG3. An unsuspected relationship between the 3’-UTR genotype and a 5’-UTR intra-motif link was revealed by CpG5–CpG6 comparison. The negative correlation between the CpG3–CpG5 positions was quite significant in the control groups (both with genotype 10/10 and with genotype 9/x), whereas a tendency toward positive correlation emerged within the high IAT group. In conclusion, future attention shall be focused on the intra- and inter-motif interactions of methylation on the CpG island at the 5′-UTR of DAT1.
The Unexpected Holiday Souvenir: The Public Health Risk to UK Travellers from Ticks Acquired Overseas
Authors: Gillingham Emma L. , Cull Benjamin , Pietzsch Maaike E. , Phipps L. Paul , Medlock Jolyon M. , Hansford Kayleigh
Published: October 2020

Overseas travel to regions where ticks are found can increase travellers’ exposure to ticks and pathogens that may be unfamiliar to medical professionals in their home countries. Previous studies have detailed non-native tick species removed from recently returned travellers, occasionally leading to travel-associated human cases of exotic tick-borne disease. There are 20 species of tick endemic to the UK, yet UK travellers can be exposed to many other non-native species whilst overseas. Here, we report ticks received by Public Health England’s Tick Surveillance Scheme from humans with recent travel history between January 2006 and December 2018. Altogether, 16 tick species were received from people who had recently travelled overseas. Confirmed imports (acquired outside of the UK) were received from people who recently travelled to 22 countries. Possible imports (acquired abroad or within the UK) were received from people who had recently travelled to eight European countries. Species-specific literature reviews highlighted nine of the sixteen tick species are known to vector at least one tick-borne pathogen to humans in the country of acquisition, suggesting travellers exposed to ticks may be at risk of being bitten by a species that is a known vector, with implications for novel tick-borne disease transmission to travellers.
Health Impact of Air Pollution from Shipping in the Baltic Sea: Effects of Different Spatial Resolutions in Sweden
Authors: Mwase Nandi S. , Ekström Alicia , Jonson Jan Eiof , Svensson Erik , Jalkanen Jukka-Pekka , Wichmann Janine , Molnár Peter , Stockfelt Leo
Published: October 2020

In 2015, stricter regulations to reduce sulfur dioxide emissions and particulate air pollution from shipping were implemented in the Baltic Sea. We investigated the effects on population exposure to particles <2.5 µm (PM2.5) from shipping and estimated related morbidity and mortality in Sweden’s 21 counties at different spatial resolutions. We used a regional model to estimate exposure in Sweden and a city-scale model for Gothenburg. Effects of PM2.5 exposure on total mortality, ischemic heart disease, and stroke were estimated using exposure–response functions from the literature and combining them into disability-adjusted life years (DALYS). PM2.5 exposure from shipping in Gothenburg decreased by 7% (1.6 to 1.5 µg/m3) using the city-scale model, and 35% (0.5 to 0.3 µg/m3) using the regional model. Different population resolutions had no effects on population exposures. In the city-scale model, annual premature deaths due to shipping PM2.5 dropped from 97 with the high-sulfur scenario to 90 in the low-sulfur scenario, and in the regional model from 32 to 21. In Sweden, DALYs lost due to PM2.5 from Baltic Sea shipping decreased from approximately 5700 to 4200. In conclusion, sulfur emission restrictions for shipping had positive effects on health, but the model resolution affects estimations.