bluuebunny/crossref_metadata_2025 huggingface dataset:
Prediction of Anthocyanin Color Stability against Iron Co-Pigmentation by Surface-Enhanced Raman Spectroscopy
Authors: Dai Haochen , Forbes Adam , Guo Xin , He Lili
Published: October 2022

The color change resulting from anthocyanin and iron co-pigmentation has been a significant challenge for the food industry in the development of many iron-fortified foods. This present study aims to establish a quantitative model to predict the degree of color stability in the presence of dissolved iron using surface-enhanced Raman spectroscopic (SERS) spectra. The SERS spectra of anthocyanin extracts from seven different plant sources were measured and analyzed by principal component analysis (PCA). Discrimination among different sources of anthocyanin was observed in the PCA plot. Different stability indexes, obtained by measuring both the color intensity stability and color hue stability of each sample, were established based on UV–vis analysis of anthocyanin at pH 3 and 6 with and without ferric sulfate. Partial least square (PLS) regression models were applied to establish the correlation between SERS spectra and stability indexes. The best PLS model was built based on the stability index calculated from the bathochromic shift (UV–vis spectral range: 380–750 nm) in pH3 buffer and the SERS spectra, achieving a root mean square error of prediction (RMSEP) of 2.16 nm and a correlation coefficient value (R2) of 0.98. In conclusion, the present study developed a feasible approach to predict the stability of anthocyanin colorants against iron co-pigmentation. The developed method and models can be used for fast screenings of raw ingredients in iron-fortified food products.
Functional and Quality Profile Evaluation of Butters, Spreadable Fats, and Shortenings Available from Czech Market
Authors: Lapčíková Barbora , Lapčík Lubomír , Valenta Tomáš , Kučerová Tereza
Published: October 2022

The aim of this study was to assess the functional properties of butters, spreadable fats, and shortenings, collected from the Czech market, in correlation with their nutritional values declared by the producers. Various methods were applied to determine relevant parameters of the products. Using penetration tests, samples were characterized by specific textural attributes according to their composition and processing type, particularly for the presence of milk/vegetable fats. Using differential scanning calorimetry (DSC), thermal peaks corresponding to medium- and high-melting triacylglycerol fractions were detected in the ranges 15–16 °C and 31.5–34.5 °C, respectively. Rheological analysis revealed that the viscoelasticity of samples was related to frequency behavior of the fat structure, characterized by the dominance of elastic modulus (G′) over viscous modulus (G″) up to the frequency of 10 Hz. This indicated good emulsion stability of the products in the region of linear viscoelasticity. For spreadable fats, the structure was resistant to phase separation in the whole frequency range under study (0.1–100 Hz). The results showed that the applied techniques can be successfully used to characterize the processing and compositional quality of butters and vegetable fats.
Correlation Analysis between GlpQ-Regulated Degradation of Wall Teichoic Acid and Biofilm Formation Triggered by Lactobionic Acid in Staphylococcus aureus
Authors: Hou Wanwan , Kang Shimo , Chang Jiang , Tian Xiaorong , Shi Chunlei
Published: October 2022

Staphylococcus aureus biofilms are a serious problem in the food industry. Wall teichoic acid (WTA) is crucial in S. aureus biofilm formation. Overexpression of the WTA-hydrolyzing enzyme glycerophosphoryl diester phosphodiesterase (GlpQ), induced by lactobionic acid (LBA), may be related to biofilm formation. We investigated the relationship between the regulation on GlpQ degradation of WTA by LBA and S. aureus biofilm formation. LBA minimum inhibitory concentration for S. aureus was 12.5 mg/mL. Crystal violet staining revealed the LBA-mediated inhibition of S. aureus adhesion and biofilm formation. RT-qPCR revealed the repressed expression of adhesion-related genes by LBA. Scanning electron microscopy revealed the obvious disruption of S. aureus surface structure, confirming the repression of S. aureus adhesion and biofilm formation by LBA. Native-PAGE results suggested that the WTA content of S. aureus was reduced under the inhibition of LBA. Additionally, LBA induced the overexpression of glpQ. Combined with our previous work, these results suggest that glpQ is induced in S. aureus to function in WTA degradation with the addition of LBA, resulting in decreased WTA content and subsequent reduction of adhesion and biofilm formation. The findings provide new insight into the degradation mechanism of S. aureus WTA and indicate the potential of LBA as an anti-biofilm agent.
Effect of the Presence of Stem on Quality of Oolong Tea
Authors: Lin Jiazheng , Wang Yuwan , Chen Lin , Yang Yunfei , Tu Zheng , Ye Yang
Published: October 2022

Combined with the unique processing technology of oolong tea, oolong tea with stem processing has a better flavor compared to oolong tea without stem processing. However, there is currently no available evidence to support the contribution of stems to the taste quality of oolong tea. In this study, the electronic tongue, sensory evaluation method combined with liquid chromatography, and gas chromatography–mass spectrometry were used to explore the influence of the presence of stems on the flavor substances and aroma of oolong tea during processing. The results showed that the presence of stems significantly increased the umami taste of oolong tea (p < 0.05), and the content of seven free amino acids (p < 0.05), including theanine (53.165 μg/mL) and aspartic acid (3.190 μg/mL), two umami-related amino acids, significantly increased. Moreover, the content of nerolidol (2.598 μg/g) in aroma components was significantly increased. This study identifies the contribution of stems to oolong tea quality during processing.
Evaluation of Low-Cost Smartphone-Based Infrared Cameras to Assess the Cooling and Refrigerated Storage Temperatures of Fresh Produce
Authors: Yang Boran , Dev Kumar Govindaraj , Mis Solval Kevin
Published: October 2022

Populations of pathogens may increase in fresh produce when subjected to temperature abuse. Smartphone-based infrared (SBIR) cameras are potential alternatives for temperature measurements of fresh produce during postharvest handling and storage. This study compared the performance of SBIR cameras (FLIR and Seek) against conventional temperature acquisition devices for evaluating fresh produce’s simulated hydrocooling and storage conditions. First, thermal images of fresh produce were obtained with SBIR cameras and handheld thermal imagers at ~35 °C, ~20 °C, and ~4 °C to simulate outdoor, packinghouse, and refrigerated environments, respectively. Next, fresh produce was incubated at ~42 °C for 20 h and immersed in chilled water for a hydrocooling simulation. Then, boxes containing cooled fresh produce were stored in a walk-in cooler at different heights for three days. FLIR SBIR cameras were more effective at capturing thermal images of fresh produce than Seek SBIR cameras in all evaluated conditions. More importantly, SBIR cameras accurately acquired temperature profiles of fresh produce during simulated hydrocooling and cold storage. Additionally, the accuracy and quality of thermal images obtained with FLIR cameras were better than those obtained with Seek cameras. The study demonstrated that SBIR cameras are practical, easy-to-use, and cost-effective devices to monitor fresh produce’s temperature during postharvest handling and storage.
Valorization of Common (Fagopyrum esculentum Moench.) and Tartary (Fagopyrum tataricum Gaertn.) Buckwheat in Gluten-Free Polenta Samples: Chemical-Physical and Sensory Characterization
Authors: Rabitti Noemi Sofia , Appiani Marta , Marti Alessandra , Buratti Susanna , Benedetti Simona , Chiodaroli Giulia , Proserpio Cristina , Laureati Monica
Published: October 2022

In recent years, increasing attention has been addressed to buckwheat, an interesting minor crop with an excellent nutritional profile that contributes to the sustainability and biodiversity of the agri-food system. However, the high content of rutin and quercitin present in this pseudocereal can elicit undesirable sensory properties, such as bitterness and astringency, that can limit its exploitation in food formulations. The aim of the present study was to characterize six gluten-free porridge-type formulations (called polenta) prepared using corn and buckwheat flour. Specifically, polenta samples were prepared adding common (CB) or Tartary buckwheat (TB) flour at 20% (CB20; TB20), 30% (CB30; TB30), and 40% (CB40; TB40) to corn flour. Product characterization included sensory and instrumental analyses (electronic tongue, colorimeter, and Texture Analyzer). Products containing Tartary buckwheat were darker, firmer, and characterized by a higher intensity of bitter taste and astringency than those prepared with common buckwheat. In this context, the impact of buckwheat species seems to be more important at 30% and 40% levels, suggesting that lower additions may mask the differences between the species. The gathered information could support the food industry in re-formulating products with buckwheat. Finally, findings about the relationship between instrumental and sensory data might be exploited by the food industry to decide/choose what indices to use to characterize new formulations and/or new products.
Occurrence of Listeria spp. in Soft Cheese and Ice Cream: Effect of Probiotic Bifidobacterium spp. on Survival of Listeria monocytogenes in Soft Cheese
Authors: Ewida Rania M. , Hasan Walaa S. , Elfaruk Mohamed Salem , Alayouni Raed Reshaid , Hammam Ahmed R. A. , Kamel Dalia G.
Published: October 2022

Listeria monocytogenes is one of the most important emerging foodborne pathogens. The objectives of this work were to investigate the incidence of Listeria spp. and L. monocytogenes in soft cheese and ice cream in Assiut city, Egypt, and to examine the effect of some probiotic Bifidobacterium spp. (Bifidobacterium breve, Bifidobacterium animalis, or a mixture of the two) on the viability of L. monocytogenes in soft cheese. The existence of Listeria spp. and L. monocytogenes was examined in 30 samples of soft cheese and 30 samples of ice cream. Bacteriological analyses and molecular identification (using 16S rRNA gene and hlyA gene for Listeria spp. and L. monocytogenes, respectively) were performed on those samples. Additionally, Bifidobacterium spp. were incorporated in the making of soft cheese to study their inhibitory impacts on L. monocytogenes. Out of 60 samples of soft cheese and ice cream, 25 samples showed Listeria spp., while L. monocytogenes was found in only 2 soft cheese samples. Approximately 37% of soft cheese samples (11 out of 30) had Listeria spp. with about 18.0% (2 out of 11) exhibiting L. monocytogenes. In ice cream samples, Listeria spp. was presented by 47% (14 out of 30), while L. monocytogenes was not exhibited. Moreover, the addition of B. animalis to soft cheese in a concentration of 5% or combined with B. breve with a concentration of 2.5% for each resulted in decreasing L. monocytogenes efficiently during the ripening of soft cheese for 28 d. Listeria spp. is widely found in milk products. Probiotic bacteria, such as Bifidobacterium spp., can be utilized as a natural antimicrobial to preserve food and dairy products.
The Effects of Pectin Structure on Emulsifying, Rheological, and In Vitro Digestion Properties of Emulsion
Authors: Shuai Xixiang , Chen Jun , Liu Qi , Dong Haolan , Dai Taotao , Li Zhaoying , Liu Chengmei , Wang Risi
Published: October 2022

Pectin, a complex hydrocolloid, attracts extensive attention and application stemming from its good emulsification. However, the source of emulsification remains a conundrum. In this experiment, the structures of six kinds of commercial pectin, including LM 101 AS (101), LM 104 AS (104), 121 SLOW SET (121), YM 150 H (150), LM 13 CG (13CG), and β-PECTIN (β-P) were determined, and the effects of pectin structure on emulsion emulsification, rheology and in vitro digestibility were studied. The results showed that the β-P pectin contained a higher content of protein, ferulic acid, and acetyl and had a lower interfacial tension; this pectin-stabilized emulsion exhibited a smaller droplet size and superior centrifugal and storage stability. The results showed that β-P pectin had higher contents of protein, ferulic acid, and acetyl and lower interfacial tension than other pectins, and its stabilized emulsion exhibited smaller droplet size and superior centrifugation and storage stability. Furthermore, the emulsion formed by the pectin with high molecular weight and degree of methoxylation (DM) had a higher viscosity, which can inhibit the aggregation of emulsion droplets to some extent. However, the DM of pectin affected the charge and digestion behavior of pectin emulsion to a great extent. The smaller the DM, the more negative charge the emulsion carried, and the higher the release rate of free fatty acids. The results provided a basis for the rational selection and structural design of the pectin emulsifier.
Comparative Effect of Cricket Protein Powder and Soy Protein Isolate on Gel Properties of Indian Mackerel Surimi
Authors: Somjid Panumas , Panpipat Worawan , Cheong Ling-Zhi , Chaijan Manat
Published: October 2022

This work comparatively investigated the effects of different levels (0, 1, 3, and 5%, w/w) of cricket protein powder (CP) and soy protein isolate (SPI) on the gel properties of mackerel surimi. Both SPI and CP enhanced the rheological properties of surimi pastes during heating, as indicated by the increase in G′ and G″ and the decrease in tan δ. With increasing SPI content, the proteolytic inhibition, gel properties, water-holding capacity, and textural profiles of surimi gel were markedly enhanced. Molecular driving-force results showed that SPI markedly promoted the hydrophobic interaction, while disulfide bonds were dominant in CP-added gel. However, the whiteness of surimi gels tended to decrease with the increased levels of both additives, in particular CP. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) demonstrated that SPI hindered the polymerization of myosin heavy chain while CP participated in the formation of non-disulfide covalent bonds with actin. Fourier transform infrared (FTIR) spectra indicated that CP and SPI did not influence the secondary structure of proteins in surimi. Scanning electron microscopy (SEM) demonstrated that CP or SPI induced the myofibrillar protein to form smoother and compact gel network structures. Overall acceptability of the mackerel surimi gel can be improved by the incorporation of 5% SPI while CP had a negative impact on several parameters. However, CP showed the remarkable ability to prevent the lipid oxidation of the gel after storage at 4 °C for 7 days. Overall, both SPI and CP demonstrated positive impacts on the gelling characteristics of mackerel surimi; however, SPI was more advantageous than CP in terms of the gel-strengthening effect and sensory qualities. This study offered a potential use for plant and insect proteins as functional and nutritional ingredients for the production of dark-fleshed fish surimi.
Aromatic, Sensory, and Fatty Acid Profiles of Arbequina Extra Virgin Olive Oils Produced Using Different Malaxation Conditions
Authors: Olmo-Cunillera Alexandra , Casadei Enrico , Valli Enrico , Lozano-Castellón Julián , Miliarakis Eleftherios , Domínguez-López Inés , Ninot Antònia , Romero-Aroca Agustí , Lamuela-Raventós Rosa Maria , Pérez Maria , Vallverdú-Queralt Anna , Bendini Alessandra
Published: October 2022

The demand for high-quality extra virgin olive oil (EVOO) is growing due to its unique characteristics. The aroma and flavor of EVOO depend on its content of volatile organic compounds (VOCs), whose formation is affected by the olive variety and maturity index, and the oil production process. In this study, the sensory quality and VOC and fatty acid (FA) profiles were determined in Arbequina olive oils produced by applying different malaxation parameters (20, 25, and 30 °C, and 30 and 45 min). All the olive oils were classified as EVOO by a sensory panel, regardless of the production conditions. However, cold extraction at 20 °C resulted in more positive sensory attributes (complexity). The FA concentration increased significantly with the malaxation temperature, although the percentage profile remained unaltered. Finally, an OPLS-DA model was generated to identify the discriminating variables that separated the samples according to the malaxation temperature. In conclusion, the tested range of malaxation parameters appeared not to degrade the distinctive attributes/organoleptic profile of olive oil and could be applied to obtain an EVOO of high sensory quality, especially at 20 °C.
Butterfly Pea Flower as a Novel Ingredient to Produce Antioxidant-Enriched Yellow Pea-Based Breakfast Cereals
Authors: Singh Ravinder , Yu Cheng-Chia , Chen Guan-Wei , Chen Ching-Hsueh , Sinaki Nasibeh Y. , Lin Jenshinn , Koksel Filiz
Published: October 2022

Butterfly pea flower (BP) is a rich source of bioactive components and can potentially be utilized to produce appealing, wholesome foods. Antioxidant and dietary fiber-enriched breakfast cereals were produced by extrusion cooking using blends of BP and yellow pea flour (YP). BP was added to YP at 0%, 5% and 10% levels (w/w), respectively, and extruded at two temperature profiles with die temperatures of 130 and 150 °C. Incorporation of BP significantly (p < 0.05) improved the total phenolics content, antioxidant properties, and insoluble and total dietary fiber content of the extrudates, with 10% BP extrudates showing the highest values. At a die temperature of 150 °C, the extrudates had a higher expansion ratio, a lower dry hardness, and a higher dry crispiness as compared to those at 130 °C. The color of BP-incorporated extrudates was darker and bluer as compared to the no-BP extrudates. The 10% BP extrudates retained relatively more of their hardness, crispiness, and crunchiness after soaking, indicating a better bowl-life and, therefore, better suitability of this blend formula for breakfast cereal production. Overall, this research shows that healthier breakfast cereals with appealing color and relatively longer bowl-life can be produced using BP, making BP a potential novel ingredient for extrusion formulations.
Screening and Enzymatic Evaluation of Saccharomyces cerevisiae Populations from Spontaneous Fermentation of Organic Verdejo Wines
Authors: López-Enríquez Lorena , Vila-Crespo Josefina , Rodríguez-Nogales José Manuel , Fernández-Fernández Encarnación , Ruipérez Violeta
Published: October 2022

Microbial populations in spontaneous winemaking contribute to the distinctiveness and quality of the wines. In this study, molecular methods were applied to 484 isolated yeasts to survey the diversity of the Saccharomyces cerevisiae population in spontaneous fermentations of organic Verdejo grapes. Identification was carried out at strain level for samples from different vineyards correct.and stages of the winemaking process over the course of two vintages, establishing 54 different strains. The number of isolates belonging to each strain was not homogeneous, as two predominant strains represented more than half of the isolates independent of vineyard or vintage. Regarding the richness and abundance, differences among the stages of fermentation were confirmed, finding the highest diversity values in racked must and in the end of fermentation stages. Dissimilarity in S. cerevisiae communities was found among vineyards and vintages, distinguishing representative groups of isolates for each of the populations analysed. These results highlight the effect of vineyard and vintage on yeast communities as well as the presence of singular strains in populations of yeasts. Oenologically relevant enzymatic activities, β-lyase, protease and β-glucanase, were detected in 83.9%, 96.8% and 38.7% of the isolates, respectively, which may be of interest for potential future studies.
Has EU Accession Boosted Patent Performance in the EU-13? A Critical Evaluation Using Causal Impact Analysis with Bayesian Structural Time-Series Models
Authors: Kleszcz Agnieszka , Rusek Krzysztof
Published: October 2022

This paper provides new insights into the causal effects of the enlargement of the European Union (EU) on patent performance. The study focuses on the new EU member states (EU-13) and accession is considered as an intervention whose causal effect is estimated by the causal impact method using a Bayesian structural time-series model (proposed by Google). The empirical results based on data collected from the OECD database from 1985–2017 point towards a conclusion that joining the EU has had a significant impact on patent performance in Romania, Estonia, Poland, the Czech Republic, Croatia and Lithuania, although in the latter two countries, the impact was negative. For the rest of the EU-13 countries, there is no significant effect on patent performance. Whether the EU accession effect is significant or not, the EU-13 are far behind the EU-15 (countries which entered the EU before 2004) in terms of patent performance. The majority of patents (98.66%) are assigned to the EU-15, with just 1.34% of assignees belonging to the EU-13.
Analysis of a Hidden-Memory Variably Distributed-Order Time-Fractional Diffusion Equation
Authors: Jia Jinhong
Published: October 2022

We analyze the well-posedness and regularity of a variably distributed-order time-fractional diffusion equation (tFDE) with a hidden-memory fractional derivative, which provide a competitive means to describe the anomalously diffusive transport of particles in heterogeneous media. We prove that the solution of a variably distributed-order tFDE has weak singularity at the initial time t=0 which depends on the upper bound of a distributed order α¯(0).
Rational Play in Extensive-Form Games
Authors: Bonanno Giacomo
Published: October 2022

We argue in favor of a departure from the equilibrium approach in game theory towards the less ambitious goal of describing only the actual behavior of rational players. The notions of Nash equilibrium and its refinements require a specification of the players’ choices and beliefs not only along the equilibrium play but also at counterfactual histories. We discuss an alternative—counterfactual-free—approach that focuses on choices and beliefs along the actual play, while being silent on choices and beliefs at unreached histories. Such an approach was introduced in an earlier paper that considered only perfect-information games. Here we extend the analysis to general extensive-form games (allowing for imperfect information) and put forward a behavioral notion of self-confirming play, which is close in spirit to the literature on self-confirming equilibrium. We also extend, to general extensive-form games, the characterization of rational play that is compatible with pure-strategy Nash equilibrium.
Properties of Grass Carp (Ctenopharyngodon idella) Collagen and Gel for Application in Biomaterials
Authors: Shen Zhiyuan , Zhang Qi , Li Li , Li Dapeng , Takagi Yasuaki , Zhang Xi
Published: October 2022

The biochemical properties of collagens and gels from grass carp (Ctenopharyngodon idella) were studied to explore the feasibility of their application in biomaterials. The yields of skin collagen (SC) and swim bladder collagen (SBC) extracted from grass carp were 10.41 ± 0.67% and 6.11 ± 0.12% on a wet basis, respectively. Both collagens were characterized as type I collagen. Denaturation temperatures of SC and SBC were 37.41 ± 0.02 °C and 39.82 ± 0.06 °C, respectively. SC and SBC had high fibril formation ability in vitro, and higher values of salinity (NaCl, 0–280 mM) and pH (6–8) in formation solution were found to result in faster self-assembly of SC and SBC fibrils as well as thicker fibrils. Further tests of SC gels with regular morphology revealed that their texture properties and water content were affected by pH and NaCl concentration. The hardness, springiness, and cohesiveness of SC gels increased and the chewiness and water content decreased as pH increased from 7 to 8 and NaCl concentration increased from 140 to 280 mM. These properties suggest that collagens from grass carp may be useful in biomaterial applications in the future.
Enhanced Delivery of Insulin through Acrylamide-Modified Chitosan Containing Smart Carrier System
Authors: Dahan Wasmia Mohammed , Mohammad Faruq , Ezzat AbdelRahman O. , Atta Ayman M. , Al-Tilasi Hissah Hamad , Al-Lohedan Hamad A.
Published: October 2022

The present study develops on insulin-release studies from the chitosan-amide-modified stimuli-responsive polymers formed from various fatty acids including stearic acid, oleic acid, linoleic acid, and linolenic acid. This is the continuation of an earlier reported study that investigates the insulin-release profiles of chitosan-modified fatty acid amides (without stimuli responsive polymers). Following the synthesis and characterization of many different fatty acid amides with a varying amount of unsaturation, the insulin drug loading and release effects were compared among N-isopropylacrylamide (NIPAm), a thermo-responsive polymer, and 2-acrylamide-2-methylpropane sulfonic acid (AMPS), a pH-responsive polymer-modified hydrogel that is expected to enhance environmental response and the controllability of release. Finally, drug release effects were studied to investigate the drug release mechanisms with the help of five different pharmacokinetic models including the zero-order, first-order, Higuchi, Korsmeyers–Peppas, and Hixson models. The results indicate that the Higuchi and Hixson models are valid in terms of the operation of the NIPAm and AMPS matrices during the delivery of insulin.
Metal Oxide Hydrogel Composites for Remediation of Dye-Contaminated Wastewater: Principal Component Analysis
Authors: Murshid Nimer , Mouhtady Omar , Abu-samha Mahmoud , Obeid Emil , Kharboutly Yahya , Chaouk Hamdi , Halwani Jalal , Younes Khaled
Published: October 2022

Water pollution is caused by multiple factors, such as industrial dye wastewater. Dye-contaminated water can be treated using hydrogels as adsorbent materials. Recently, composite hydrogels containing metal oxide nanoparticles (MONPs) have been used extensively in wastewater remediation. In this study, we use a statistical and artificial intelligence method, based on principal component analysis (PCA) with different applied parameters, to evaluate the adsorption efficiency of 27 different MONP composite hydrogels for wastewater dye treatment. PCA showed that the hydrogel composites CTS@Fe3O4, PAAm/TiO2, and PEGDMA-rGO/Fe3O4@cellulose should be used in situations involving high pH, time to reach equilibrium, and adsorption capacity. However, as the composites PAAm-co-AAc/TiO2, PVPA/Fe3O4@SiO2, PMOA/ATP/Fe3O4, and PVPA/Fe3O4@SiO2, are preferred when all physical and chemical properties investigated have low magnitudes. To conclude, PCA is a strong method for highlighting the essential factors affecting hydrogel composite selection for dye-contaminated water treatment.
Spectrum of Skeletal Imaging Features in Osteopetrosis: Inheritance Pattern and Radiological Associations
Authors: Spinnato Paolo , Pedrini Elena , Petrera Miriana Rosaria , Zarantonello Paola , Trisolino Giovanni , Sangiorgi Luca , Carpenzano Maria , Crombé Amandine , Tetta Cecilia
Published: October 2022

Osteopetrosis (from the Greek “osteo”: bone; “petrosis”: stone) is a clinically and genetically heterogeneous group of rare diseases of the skeleton, sharing the same main characteristic of an abnormally increased bone density. Dense bones in radiological studies are considered the hallmark of these diseases, and the reason for the common term used: “Marble bone disease”. Interestingly, a radiologist, Dr. Albers-Schonberg, described this disease for the first time in Germany in 1904. Indeed, radiology has a key role in the clinical diagnosis of osteopetrosis and is fundamental in assessing the disease severity and complications, as well as in follow-up controls and the evaluation of the response to treatment. Osteopetrosis includes a broad spectrum of genetic mutations with very different clinical symptoms, age onset, and prognosis (from mild to severe). This diversity translates into different imaging patterns related to specific mutations, and different disease severity. The main recognized types of osteopetrosis are the infantile malignant forms with autosomal recessive transmission (ARO—including the rarer X-linked recessive form); the intermediate autosomal recessive form (IAO); and the autosomal dominant ones ADO, type I, and type II, the latter being called ‘Albers-Schonberg’ disease. Imaging features may change among those distinct types with different patterns, severities, skeletal segment involvement, and speeds of progression. There are several classical and well-recognized radiological features related to osteopetrosis: increased bone density (all types with different degrees of severity assuming a ‘Marble Bone Appearance’ especially in the ARO type), different metaphyseal alterations/enlargement including the so-called ‘Erlenmeyer flask deformity’ (particularly of femoral bones, more frequent in ADO type 2, and less frequent in ARO and IAO), ‘bone in bone’ appearance (more frequent in ADO type 2, less frequent in ARO and IAO), and ‘rugger-jersey spine’ appearance (typical of ADO type 2). After conducting an overview of the epidemiological and clinical characteristic of the disease, this review article aims at summarizing the main radiological features found in different forms of osteopetrosis together with their inheritance pattern.
Membrane Clustering of Coronavirus Variants Using Document Similarity
Authors: Lehotay-Kéry Péter , Kiss Attila
Published: October 2022

Currently, as an effect of the COVID-19 pandemic, bioinformatics, genomics, and biological computations are gaining increased attention. Genomes of viruses can be represented by character strings based on their nucleobases. Document similarity metrics can be applied to these strings to measure their similarities. Clustering algorithms can be applied to the results of their document similarities to cluster them. P systems or membrane systems are computation models inspired by the flow of information in the membrane cells. These can be used for various purposes, one of them being data clustering. This paper studies a novel and versatile clustering method for genomes and the utilization of such membrane clustering models using document similarity metrics, which is not yet a well-studied use of membrane clustering models.
Genomic Signatures Reveal Breeding Effects of Lulai Pigs
Authors: Cao Rui , Feng Jian , Xu Yuejin , Fang Yifei , Zhao Wei , Zhang Zhenyang , Zhang Zhe , Li Meng , Wang Qishan , Pan Yuchun
Published: October 2022

In Chinese pig populations in which crossbreeding is used, these animals show a level of weakness compared with their original purebred ancestors. For instance, in the Lulai pig, a newly developed Chinese breed that is raised on the basis of the Laiwu pig (a Chinese indigenous breed with exceptionally high intramuscular fat content) and the Yorkshire pig using a method of systematic crossbreeding, both their market acceptance and performance are inferior. To reveal the practical role of these admixed breeds and traditional systematic crossbreeding methods at the genomic level, we explored population structure, genetic signatures, and introgression. We conducted this study based on the SNP chip data of 381 Lulai pigs, 182 Laiwu pigs, and 127 Yorkshires, which showed deficient genome coverage during our study. Therefore, we further selected the Genotyping by Genome Reducing and Sequencing (GGRS) method, which has a high density and suitable genome coverage as a supplement. We applied the GGRS data of 38 Lulai pigs, 75 Laiwu pigs, and 75 Yorkshires. In terms of the SNP chip data, by Fst analysis, we detected 782 significantly different genes between Lulai pigs and Yorkshires, including 3 major genes associated with growth (LEPR) and meat quality (SCD and TBC1D1), and we detected 426 significantly different genes between Lulai pigs and Laiwu pigs. With rIBD, we detected 12 genomic regions that included 182 genes that Yorkshires introgressed to Lulai pigs, and we detected 27 genomic regions that included 229 genes with a major gene (SCD) that Laiwu pigs introgressed to Lulai pigs. Regarding the GGRS data, we detected 601 significantly different genes between Lulai pigs and Yorkshires by Fst analysis, including 3 major genes associated with growth and fat deposits (IGF2 and FTO) and with hair color (KIT), and we detected 634 significantly different genes between Lulai pigs and Laiwu pigs, including 3 major genes related to their body composition (MYPN), hair color (KIT), and ear size (PPARD). By rIBD, we detected 94 deep sections that included 363 genes that Yorkshires introgressed to Lulai pigs, and we detected 149 deep sections that included 727 genes with a major gene (ESR1) that Laiwu pigs introgressed to Lulai pigs. Altogether, this study provides both insight into the molecular background of synthesized breeds of Lulai pigs and a reference for the evaluation of systematic crossbreeding in China.
Molecular Characteristics and Promoter Analysis of Porcine COL1A1
Authors: Xiang Guangming , Huang Lei , Zhang Xiuling , Wang Nan , Wang Hui , Mu Yulian , Li Kui , Liu Zhiguo
Published: October 2022

COL1A1 encodes the type I collagen α1 chain, which shows the highest abundance among members of the collagen family and is widely expressed in different mammalian cells and tissues. However, its molecular characteristics are not completely elucidated. In this study, the molecular profiles of COL1A1 and characteristics of the COL1A1 protein were investigated using a promoter activity assay and multiple bioinformatics tools. The results showed that the 5′ flanking region of porcine COL1A1 contained two CpG islands, five core promoter sequences, and twenty-six transcription factor-binding sites. In the luciferase assay, the upstream 294 bp region of the initiation codon of COL1A1 showed the highest activity, confirming that this section is the core region of the porcine COL1A1 promoter. Bioinformatic analysis revealed that COL1A1 is a negatively charged, hydrophilic secreted protein. It does not contain a transmembrane domain and is highly conserved in humans, mice, sheep, and pigs. Protein interaction analysis demonstrated that the interaction coefficient of COL1A1 with COL1A2, COL3A1, ITGB1, and ITGA2 was greater than 0.9, suggesting that this protein plays a crucial role in collagen structure formation and cell adhesion. These results provide a theoretical basis for further investigation of the functions of porcine COL1A1.
Reclassification of DMD Duplications as Benign: Recommendations for Cautious Interpretation of Variants Identified in Prenatal Screening
Authors: He Wenbin , Meng Guiquan , Hu Xiao , Dai Jing , Liu Jiyang , Li Xiurong , Hu Hao , Tan Yueqiu , Zhang Qianjun , Lu Guangxiu , Lin Ge , Du Juan
Published: October 2022

Duplications are the main type of dystrophin gene (DMD) variants, which typically cause dystrophinopathies such as Duchenne muscular dystrophy and Becker muscular dystrophy. Maternally inherited exon duplication in DMD in fetuses is a relatively common finding of genetic screening in clinical practice. However, there is no standard strategy for interpretation of the pathogenicity of DMD duplications during prenatal screening, especially for male fetuses, in which maternally inherited pathogenic DMD variants more frequently cause dystrophinopathies. Here, we report three non-contiguous DMD duplications identified in a woman and her male fetus during prenatal screening. Multiplex ligation probe amplification and long-read sequencing were performed on the woman and her family members to verify the presence of DMD duplications. Structural rearrangements in the DMD gene were mapped by long-read sequencing, and the breakpoint junction sequences were validated using Sanger sequencing. The woman and her father carried three non-contiguous DMD duplications. Long-read and Sanger sequencing revealed that the woman’s father carried an intact DMD copy and a complex structural rearrangement of the DMD gene. Therefore, we reclassified these three non-contiguous DMD duplications, one of which is listed as pathogenic, as benign. We postulate that breakpoint analysis should be performed on identified DMD duplication variants, and the pathogenicity of the duplications found during prenatal screening should be interpreted cautiously for clinical prediction and genetic/reproductive counseling.
Regulation of Proliferation and Apoptosis of Hair Follicle Stem Cells by miR-145-5p in Yangtze River Delta White Goats
Authors: Wu Xi , Wang Jian , Kang Yan , Wang Qiang , Qu Jingwen , Sun Xiaomei , Ji Dejun , Li Yongjun
Published: October 2022

Yangtze River Delta white goats are the sole goat breed producing brush hair of high quality. The gene DUSP6 has been extensively studied in tumor cells but rarely in hair follicle stem cells (HFSCs). Per the previous sequencing data, it was determined that DUSP6 expression was up-regulated in superior-quality brush hair tissues, confirming it as a candidate gene associated with this trait. The targeting relationship of miR-145-5p with DUSP6 was determined based on online database prediction and was authenticated using a dual-luciferase gene reporter assay and quantitative reverse-transcription PCR (RT-qPCR). The regulatory effect of miR-145-5p on the growth of HFSCs was determined by targeting DUSP6 with RT-qPCR, 5-ethynyl-2′-deoxyuridine assays, Western blotting, and flow cytometry. The proliferation of HFSCs was inhibited and their apoptosis capacity was enhanced due to the presence of miR-145-5p. Therefore, it was proposed that this may have occurred through a repression effect of DUSP6 on the MAPK signaling pathway. The regulatory network of the HFSCs can be further understood using the theoretical basis established by the findings derived from this study.
CircRNAs Related to Breast Muscle Development and Their Interaction Regulatory Network in Gushi Chicken
Authors: Yuan Pengtao , Zhao Yinli , Li Hongtai , Li Shuaihao , Fan Shengxin , Zhai Bin , Li Yuanfang , Han Ruili , Liu Xiaojun , Tian Yadong , Kang Xiangtao , Zhang Yanhua , Li Guoxi
Published: October 2022

Circular RNAs (circRNAs) play a significant regulatory role during skeletal muscle development. To identify circRNAs during postnatal skeletal muscle development in chickens, we constructed 12 cDNA libraries from breast muscle tissues of Chinese Gushi chickens at 6, 14, 22, and 30 weeks and performed RNA sequencing. In total, 2112 circRNAs were identified, and among them 79.92% were derived from exons. CircRNAs are distributed on all chromosomes of chickens, especially chromosomes 1–9 and Z. Bioinformatics analysis showed that each circRNA had an average of 38 miRNA binding sites, 61.32% of which have internal ribosomal entry site (IRES) elements. Furthermore, in total 543 differentially expressed circRNAs (DE-circRNAs) were identified. Functional enrichment analysis revealed that DE-circRNAs source genes are engaged in biological processes and muscle development-related pathways; for example, cell differentiation, sarcomere, and myofibril formation, mTOR signaling pathway, and TGF-β signaling pathway, etc. We also established a competitive endogenous RNA (ceRNA) regulatory network associated with skeletal muscle development. The results in this report indicate that circRNAs can mediate the development of chicken skeletal muscle by means of a complex ceRNA network among circRNAs, miRNAs, genes, and pathways. The findings of this study might help increase the number of known circRNAs in skeletal muscle tissue and offer a worthwhile resource to further investigate the function of circRNAs in chicken skeletal muscle development.
Tumor Microenvironment Characterization in Breast Cancer Identifies Prognostic Pathway Signatures
Authors: Li Ji , Qiu Jiayue , Han Junwei , Li Xiangmei , Jiang Ying
Published: October 2022

Breast cancer is one of the most common female malignancies worldwide. Due to its early metastases formation and a high degree of malignancy, the 10 year-survival rate of metastatic breast cancer does not exceed 30%. Thus, more precise biomarkers are urgently needed. In our study, we first estimated the tumor microenvironment (TME) infiltration using the xCell algorithm. Based on TME infiltration, the three main TME clusters were identified using consensus clustering. Our results showed that the three main TME clusters cause significant differences in survival rates and TME infiltration patterns (log-rank test, p = 0.006). Then, multiple machine learning algorithms were used to develop a nine-pathway-based TME-related risk model to predict the prognosis of breast cancer (BRCA) patients (the immune-related pathway-based risk score, defined as IPRS). Based on the IPRS, BRCA patients were divided into two subgroups, and patients in the IPRS-low group presented significantly better overall survival (OS) rates than the IPRS-high group (log-rank test, p < 0.0001). Correlation analysis revealed that the IPRS-low group was characterized by increases in immune-related scores (cytolytic activity (CYT), major histocompatibility complex (MHC), T cell-inflamed immune gene expression profile (GEP), ESTIMATE, immune, and stromal scores) while exhibiting decreases in tumor purity, suggesting IPRS-low patients may have a strong immune response. Additionally, the gene-set enrichment analysis (GSEA) result confirmed that the IPRS-low patients were significantly enriched in several immune-associated signaling pathways. Furthermore, multivariate Cox analysis revealed that the IPRS was an independent prognostic biomarker after adjustment by clinicopathologic characteristics. The prognostic value of the IPRS model was further validated in three external validation cohorts. Altogether, our findings demonstrated that the IPRS was a powerful predictor to screen out certain populations with better prognosis in breast cancer and may serve as a potential biomarker guiding clinical treatment decisions.
The Complex Dynamic of Phase I Drug Metabolism in the Early Stages of Doxorubicin Resistance in Breast Cancer Cells
Authors: Barata Isabel S. , Gomes Bruno C. , Rodrigues António S. , Rueff José , Kranendonk Michel , Esteves Francisco
Published: October 2022

The altered activity of drug metabolism enzymes (DMEs) is a hallmark of chemotherapy resistance. Cytochrome P450s (CYPs), mainly CYP3A4, and several oxidoreductases are responsible for Phase I metabolism of doxorubicin (DOX), an anthracycline widely used in breast cancer (BC) treatment. This study aimed to investigate the role of Phase I DMEs involved in the first stages of acquisition of DOX-resistance in BC cells. For this purpose, the expression of 92 DME genes and specific CYP-complex enzymes activities were assessed in either sensitive (MCF-7 parental cells; MCF-7/DOXS) or DOX-resistant (MCF-7/DOXR) cells. The DMEs genes detected to be significantly differentially expressed in MCF-7/DOXR cells (12 CYPs and eight oxidoreductases) were indicated previously to be involved in tumor progression and/or chemotherapy response. The analysis of CYP-mediated activities suggests a putative enhanced CYP3A4-dependent metabolism in MCF-7/DOXR cells. A discrepancy was observed between CYP-enzyme activities and their corresponding levels of mRNA transcripts. This is indicative that the phenotype of DMEs is not linearly correlated with transcription induction responses, confirming the multifactorial complexity of this mechanism. Our results pinpoint the potential role of specific CYPs and oxidoreductases involved in the metabolism of drugs, retinoic and arachidonic acids, in the mechanisms of chemo-resistance to DOX and carcinogenesis of BC.
A Comparative Phylogenetic Analysis on the Chloroplast Genome in Different Reynoutria japonica Populations
Authors: Chen Jianhui , Huang Tiran , Fan Haili , Lin Fan , Ma Hongping , Cao Jie , Chai Tuanyao , Ma Lanqing , Wang Hong
Published: October 2022

Reynoutria japonica Houtt., a traditional medicine herb of the Polygonaceae family, has been used since ancient times in China due to its various pharmacological effects. Chloroplast genomes are conservative and play an essential role in population diversity analysis. However, there are few studies on the chloroplast genome of R. japonica. In this study, the complete chloroplast genomes of three R. japonica from different regions were performed by next-generation sequencing technology. The results revealed that the lengths of the three chloroplast genomes are between 163,371~163,372 bp, and they have a highly conserved structure with a pair of inverted repeat (IR) regions (31,121 bp), a large single-copy (LSC) region (87,571~87,572 bp), and a small single-copy (SSC) region (13,558 bp). In total, 132 genes were annotated, including 8 rRNA genes, 37 tRNA genes, and 87 protein-coding genes. The phylogenetic analysis strongly revealed that 13 populations of R. japonica form a monophyly, and Fallopia multiflora (Polygonaceae) is its closest species. The two species diverged at ~20.47 million years ago, and R. japonica in China could be further divided into two major groups based on genetic structure analysis. In addition, several potential loci with suitable polymorphism were identified as molecular markers. Our study provides important genetic resources for further development and utilization of R. japonica germplasm, as well as some new insights into the evolutionary characteristics of this medicinal plant.
Estimation of Nuclear DNA Content in Some Aegilops Species: Best Analyzed Using Flow Cytometry
Authors: Najafi Solmaz , Ulker Mehmet , Oral Erol , Tuncturk Ruveyde , Tuncturk Murat , Sayyed R. Z. , Perveen Kahkashan , Poczai Peter , Cseh Andras
Published: October 2022

The genera Triticum and Aegilops have been considered as the main gene pool of wheat due to their features, such as tolerance of all types of abiotic and biotic stresses. This study was conducted to evaluate the cytogenetic analyses in 115 native and wild populations from eleven Aegilops species using their nuclear DNA quantification. Mean 2C nuclear DNA contents of different ploidy levels in the wild wheat of Turkey and Iran were measured using the flow cytometry technique. The obtained results showed that the mean nuclear DNA content in diploid species varied from 10.09 pg/2C (Ae. umbellulata) to 10.95 pg/2C (Ae. speltoides var. ligustica) in Turkey. In Iranian diploids, the mean nuclear DNA content varied from 10.20 pg/2C (Ae. taushii) to 11.56 pg/2C (Ae. speltoides var. ligustica). This index in the tetraploid species of Turkey varied from 18.09 pg/2C (Ae. cylindrica) to 21.65 pg/2C (Ae. triaristata), and in Iranian species, it was from 18.61 pg/2C (Ae. cylindrica) to 21.75 pg/2C (Ae. columnaris). On the other hand, in the hexaploid species of Turkey, this index varied from 31.59 pg/2C (Ae. crassa) to 31.81 pg/2C (Ae. cylindrica); in the Iranian species, it varied from 32.58 pg/2C (Ae. cylindrica) to 33.97 pg/2C (Ae. crassa). There was a significant difference in the DNA content of Turkey and Iran diploid as well as tetraploid species; however, in hexaploid species, the difference was not significant. It was concluded that the variation in intraspecific genome size was very low in diploid and tetraploid populations; this means that the low variation is not dependent on geographic and climatic parameters. On the other hand, the interspecific variation is significant at the diploid and tetraploid populations. It is generally very difficult to distinguish Aegilops species from each other in natural conditions; meanwhile, in this study, all species could be, easily, quickly and unambiguously, distinguished and separated using the FCM technique.