bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterization of Calcium Silicate Hydrate Gels with Different Calcium to Silica Ratios and Polymer Modifications
Authors: Madadi Amirhossein , Wei Jianqiang
Published: January 2022

Calcium silicate hydrate (CSH) gels, the main binding phases of hydrated cement, are the most widely utilized synthetic materials. To understand the influences of composition and polymers on the reaction kinetics and phase formation, CSH gels with varying Ca/Si ratios and amounts of poly (acrylamide-co-acrylic acid) partial sodium salt (PAAm-co-PAA) were synthesized via a direct method. The CSH gels were characterized through isothermal calorimetry, thermogravimetric analysis (TGA), X-ray diffraction (XRD), Fourier-transform infrared spectroscopy (FTIR), and Raman spectroscopy at different ages. By increasing the Ca/Si ratio from 0.8 to 1.0, the formation of CSH was enhanced with a 5.4% lower activation energy, whereas the incorporation of PAAm-co-PAA increased the temperature sensitivity of the reactions with an 83.3% higher activation energy. In the presence of PAAm-co-PAA, the reaction rate was retarded at an early age and the negative impact faded over time. The results of an XRD analysis indicated the formation of tobermorite as the main phase of the CSH gels, while the addition of PAAm-co-PAA resulted in a postponed calcium hydroxide consumption and CSH formation, which was confirmed by the decreased FTIR intensity of the C=O bond, Si–O stretching and Si–O bonds. The increased Raman vibrations of Si–O–Si bending Q2, Ca–O bonds, O–Si–O and asymmetric bending vibrations of SiO4 tetrahedra in the presence of PAAm-co-PAA indicate the intercalation of the polymeric phase and internal deformation of CSH gels.
The Fullness of Enslaved Black Lives as Seen through Early Massachusetts Vital Records
Authors: Duclos-Orsello Elizabeth
Published: January 2022

In genealogy, tracing names and dates is often the initial goal, but, for many, desire soon turns to learning about the embodied lives of those who came before them. This type of texture is hard for any genealogist to locate, but excruciatingly hard for those seeking to trace family histories that include ancestors who were enslaved in the northern parts of the colonies that would become the United States. Often, records thin to nearly nothing and frame all lived experiences through the lens of an enslaver. This is true especially of public records, created, maintained, and curated by the state apparatus. By adhering to the proposition that even materials that do not immediately reveal much about Black life may be useful if we consider what is missing and left out, this article suggests that these types of documents might help breathe some fullness into the individual and collective lives of those Black ancestors whose humanity the state denied. Emerging from a larger project to locate stories and histories of Black residents of one of the first colonized spaces in British North America, this article focuses on the ways in which the publicly available Massachusetts pre-1850 Vital Records—which have specific “Negroes” sections—serve as an unexpected source of useful, if fragmentary, evidence of not only individual lives, but collective histories of the communities in which Black ancestors lived. Highlighting creative approaches to analyzing these particular vital records, and centering women’s lives throughout, this article demonstrates what is possible to learn about patterns of childbearing, relationships between and among enslaved persons owned by different families, the nature of religious lives or practices, relationships between enslavers and enslaved, and the movements, over time, of individuals and families. Alongside these possibilities, the violence, limitations, and challenges of the vital records are identified, including issues related to Afro-indigenous persons, the conflation of birth and baptismal records, and differential access to details of the lives of enslaved men vs. women.
Mutational Landscape of Autism Spectrum Disorder Brain Tissue
Authors: Woodbury-Smith Marc , Lamoureux Sylvia , Begum Ghausia , Nassir Nasna , Akter Hosneara , O’Rielly Darren D. , Rahman Proton , Wintle Richard F. , Scherer Stephen W. , Uddin Mohammed
Published: January 2022

Rare post-zygotic mutations in the brain are now known to contribute to several neurodevelopmental disorders, including autism spectrum disorder (ASD). However, due to the limited availability of brain tissue, most studies rely on estimates of mosaicism from peripheral samples. In this study, we undertook whole exome sequencing on brain tissue from 26 ASD brain donors from the Harvard Brain Tissue Resource Center (HBTRC) and ascertained the presence of post-zygotic and germline mutations categorized as pathological, including those impacting known ASD-implicated genes. Although quantification did not reveal enrichment for post-zygotic mutations compared with the controls (n = 15), a small number of pathogenic, potentially ASD-implicated mutations were identified, notably in TRAK1 and CLSTN3. Furthermore, germline mutations were identified in the same tissue samples in several key ASD genes, including PTEN, SC1A, CDH13, and CACNA1C. The establishment of tissue resources that are available to the scientific community will facilitate the discovery of new mutations for ASD and other neurodevelopmental disorders.
miRNA and lncRNA Expression Networks Modulate Cell Cycle and DNA Repair Inhibition in Senescent Prostate Cells
Authors: da Silveira Willian A. , Renaud Ludivine , Hazard Edward S. , Hardiman Gary
Published: January 2022

Cellular senescence is a state of permanent growth arrest that arises once cells reach the limit of their proliferative capacity. It creates an inflammatory microenvironment favouring the initiation and progression of various age-related diseases, including prostate cancer. Non-coding RNAs (ncRNAs) have emerged as important regulators of cellular gene expression. Nonetheless, very little is known about the interplay of microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) and how deregulation of ncRNA networks promotes cellular senescence. To investigate this, human prostate epithelial cells were cultured through different passages until senescent, and their RNA was extracted and sequenced using RNA sequencing (RNAseq) and microRNA sequencing (miRNA-seq) miRNAseq. Differential expression (DE) gene analysis was performed to compare senescent and proliferating cells with Limma, miRNA-target interactions with multiMiR, lncRNA-target interactions using TCGA data and network evaluation with miRmapper. We found that miR-335-3p, miR-543 and the lncRNAs H19 and SMIM10L2A all play central roles in the regulation of cell cycle and DNA repair processes. Expression of most genes belonging to these pathways were down-regulated by senescence. Using the concept of network centrality, we determined the top 10 miRNAs and lncRNAs, with miR-335-3p and H19 identified as the biggest hubs for miRNAs and lncRNA respectively. These ncRNAs regulate key genes belonging to pathways involved in cell senescence and prostate cancer demonstrating their central role in these processes and opening the possibility for their use as biomarkers or therapeutic targets to mitigate against prostate ageing and carcinogenesis.
Identification and Validation of Pathogenic Genes in Sepsis and Associated Diseases by Integrated Bioinformatics Approach
Authors: Ahmed Mohd Murshad , Zaki Almaz , Alhazmi Alaa , Alsharif Khalaf F. , Bagabir Hala Abubaker , Haque Shafiul , Manda Kailash , Ahmad Shaniya , Ali Syed Mansoor , Ishrat Romana
Published: January 2022

Sepsis is a clinical syndrome with high mortality and morbidity rates. In sepsis, the abrupt release of cytokines by the innate immune system may cause multiorgan failure, leading to septic shock and associated complications. In the presence of a number of systemic disorders, such as sepsis, infections, diabetes, and systemic lupus erythematosus (SLE), cardiorenal syndrome (CRS) type 5 is defined by concomitant cardiac and renal dysfunctions Thus, our study suggests that certain mRNAs and unexplored pathways may pave a way to unravel critical therapeutic targets in three debilitating and interrelated illnesses, namely, sepsis, SLE, and CRS. Sepsis, SLE, and CRS are closely interrelated complex diseases likely sharing an overlapping pathogenesis caused by erroneous gene network activities. We sought to identify the shared gene networks and the key genes for sepsis, SLE, and CRS by completing an integrative analysis. Initially, 868 DEGs were identified in 16 GSE datasets. Based on degree centrality, 27 hub genes were revealed. The gProfiler webtool was used to perform functional annotations and enriched molecular pathway analyses. Finally, core hub genes (EGR1, MMP9, and CD44) were validated using RT-PCR analysis. Our comprehensive multiplex network approach to hub gene discovery is effective, as evidenced by the findings. This work provides a novel research path for a new research direction in multi-omics biological data analysis.
Marker-Assisted Backcrossing (MABc) to Improve Eating Quality with Thin Seed Coat and Aleurone Layer of Non-Glutinous Japonica Variety in Rice
Authors: Kim Me-Sun , Yu Ju-Kyung , Ko Seo-Rin , Kim Ki-Jo , Ji Hyeonso , Kang Kwon-Kyoo , Cho Yong-Gu
Published: January 2022

Brown rice is composed of rice bran, pericarp, seed coat, and aleurone layers, and the rice bran layer contains a large number of substances useful for the human body, such as dietary fiber, α-tocopherol, α-tocotrienol, and vitamins. However, more than 90% of these substances are removed when polished, and white rice has the disadvantage of losing food-related ingredients, such as umami-related amino acids, when compared to the unpolished group. In this study, we tried to develop new breeding lines with a thinner seed coat and aleurone layer to provide high eating quality with softer chewing characteristics and processability in rice grain. We detected an SNP for foreground selection for the backcross population by comparing genome sequences between Samgwang and Seolgaeng and developed high eating quality brown rice breeding lines by applying marker-assisted backcrossing (MABC) breeding programs to backcross populations between Samgwang and Seolgaeng using KASP markers. SNP markers for foreground selection were identified to improve eating and processability through SNP mapping of Samgwang and Seolgaeng with SSIIa as a target gene in this study. Line selection according to genotype of KASP markers was successful in BC1F1 and BC2F1 generations, with the recurrent parent genome recovery ratio ranging from 91.22% to 98.65%. In BC2F1 seeds of the selected lines, thickness of the aleurone layer was found to range from 13.82 to 21.67 μm, which is much thinner than the 30.91 μm of the wild type, suggesting that selection by MABc could be used as an additional breeding material for the development of highly processed rice varieties. These lines will be useful to develop new brown rice varieties with softer chewing characteristics and processability in rice grain.
Expanding the Clinical Phenotype of 19q Interstitial Deletions: A New Case with 19q13.32-q13.33 Deletion and Short Review of the Literature
Authors: Shelby Elena-Silvia , Morris Michael , Pădure Liliana , Mirea Andrada , Cocoș Relu , Cărămizaru Alexandru , Șerban-Sosoi Simona , Pîrvu Andrei , Streață Ioana
Published: January 2022

19q13 microdeletion syndrome is a very rare genetic disease characterized by pre- and postnatal growth retardation, intellectual disability, expressive language impairment, ectodermal dysplasia, and slender habitus. Since the description of the first case in 1998, less than 30 cases have been reported worldwide. This article aims to review the knowledge gathered so far on this subject and to present the case of a 10-year-old girl admitted to the National University Center for Children Neurorehabilitation “Dr. Nicolae Robanescu” in November of 2018 who presented a slender habitus, growth retardation, facial dysmorphism, skeletal abnormalities, and ectodermal dysplasia. Array-CGH analysis revealed a 1.53 Mb deletion in the 19q13.32-q13.33 region. MLPA for the FKRP gene revealed that the microdeletion was de novo. The patient’s phenotype overlapped with the clinical features of 19q13 microdeletion syndrome. To our knowledge, this is the first case of 19q13 microdeletion syndrome to ever be reported in Romania. We believe our case presents additional features that have never been previously reported in this syndrome, namely, dilatation of the third ventricle and subependymal cyst, left iris coloboma, and tracheomalacia. Moreover, unlike the other 19q13 microdeletion cases that presented with dystonia, our patient also presented dystonia but, interestingly, without having haploinsufficiency of the KMT2B gene.
C5 and SRGAP3 Polymorphisms Are Linked to Paediatric Allergic Asthma in the Italian Population
Authors: Messelodi Daria , Giuliani Cristina , Cipriani Francesca , Armuzzi Silvia , di Palmo Emanuela , Garagnani Paolo , Bertelli Luca , Astolfi Annalisa , Luiselli Donata , Ricci Giampaolo , Pession Andrea
Published: January 2022

Asthma is a complex and heterogeneous disease, caused by the interaction between genetic and environmental factors with a predominant allergic background in children. The role of specific genes in asthmatic bronchial reactivity is still not clear, probably because of the many common pathways shared with other allergic disorders. This study is focused on 11 SNPs possibly related to asthma that were previously identified in a GWAS study. The genetic variability of these SNPs has been analysed in a population of 773 Italian healthy controls, and the presence of an association between the polymorphisms and the asthma onset was evaluated performing genotyping analysis on 108 children affected with asthma compared with the controls. Moreover, a pool of 171 patients with only allergic rhinoconjunctivitis has been included in the case–control analysis. The comparison of allele frequencies in asthmatic patients versus healthy controls identified two SNPs—rs1162394 (p = 0.019) and rs25681 (p = 0.044)—associated with the asthmatic condition, which were not differentially distributed in the rhinoconjunctivitis group. The rs25681 SNP, together with three other SNPs, also resulted in not being homogenously distributed in the Italian population. The significantly higher frequency of the rs25681 and rs1162394 SNPs (located, respectively, in the C5 and SRGAP3 genes) in the asthmatic population suggests an involvement of these genes in the asthmatic context, playing a role in increasing the inflammatory condition that may influence asthma onset and clinical course.
Identification of a Novel Epithelial–Mesenchymal Transition-Related Gene Signature for Endometrial Carcinoma Prognosis
Authors: Ruan Tianyuan , Wan Jing , Song Qian , Chen Peigen , Li Xiaomao
Published: January 2022

(1) Background: Endometrial cancer is the most prevalent cause of gynecological malignant tumor worldwide. The prognosis of endometrial carcinoma patients with distant metastasis is poor. (2) Method: The RNA-Seq expression profile and corresponding clinical data were downloaded from the Cancer Genome Atlas database and the Gene Expression Omnibus databases. To predict patients’ overall survival, a 9 EMT-related genes prognosis risk model was built by machine learning algorithm and multivariate Cox regression. Expressions of nine genes were verified by RT-qPCR. Responses to immune checkpoint blockades therapy and drug sensitivity were separately evaluated in different group of patients with the risk model. (3) Endometrial carcinoma patients were assigned to the high- and low-risk groups according to the signature, and poorer overall survival and disease-free survival were showed in the high-risk group. This EMT-related gene signature was also significantly correlated with tumor purity and immune cell infiltration. In addition, eight chemical compounds, which may benefit the high-risk group, were screened out. (4) Conclusions: We identified a novel EMT-related gene signature for predicting the prognosis of EC patients. Our findings provide potential therapeutic targets and compounds for personalized treatment. This may facilitate decision making during endometrial carcinoma treatment.
Mitochondrial Genomes Yield Insights into the Basal Lineages of Ichneumonid Wasps (Hymenoptera: Ichneumonidae)
Authors: Zheng Boying , Han Yuanyuan , Yuan Ruizhong , Liu Jingxian , Tang Pu , van Achterberg Cornelis , Chen Xuexin
Published: January 2022

We obtained four mitochondrial genomes of Odontocolon sp., Xorides funiuensis, Euceros kiushuensis and Euceros serricornis, which represent the first two representatives from subfamily Eucerotinae and Xoridinae (Ichneumonidae), respectively. All of the 4 newly sequenced mitochondrial genomes contain 13 protein-coding genes (PCGs) and most 24 RNA genes. Furthermore, they all have novel tRNA rearrangement patterns comparing with published mitogenomes in Ichneumonidae. For the tRNA cluster trnI-trnQ-trnM, X. funiuensis is shuffled as trnM-trnI-trnQ with trnQ inversed, while Odontocolon sp. with a remote translocation of trnK, shuffling as trnI-trnM-trnQ. E. kiushuensis and E. serricornis shared the same cluster trnQ-trnY-trnW-trnC. Finally, we reconstructed the phylogenetic relationships among the sequenced subfamilies of Ichneumonidae based on nucleotides and amino acids sequences of 13 PCGs in mitochondrial genomes, and the results of both the maximum likelihood and Bayesian inference analyses highly support that Eucerotinae is the basal ichneumonid lineage rather than Xoridinae.
Conservation Genomics of Two Threatened Subspecies of Northern Giraffe: The West African and the Kordofan Giraffe
Authors: Coimbra Raphael T. F. , Winter Sven , Mitchell Barbara , Fennessy Julian , Janke Axel
Published: January 2022

Three of the four species of giraffe are threatened, particularly the northern giraffe (Giraffa camelopardalis), which collectively have the smallest known wild population estimates. Among the three subspecies of the northern giraffe, the West African giraffe (Giraffa camelopardalis peralta) had declined to 49 individuals by 1996 and only recovered due to conservation efforts undertaken in the past 25 years, while the Kordofan giraffe (Giraffa camelopardalis antiquorum) remains at <2300 individuals distributed in small, isolated populations over a large geographical range in Central Africa. These combined factors could lead to genetically depauperated populations. We analyzed 119 mitochondrial sequences and 26 whole genomes of northern giraffe individuals to investigate their population structure and assess the recent demographic history and current genomic diversity of West African and Kordofan giraffe. Phylogenetic and population structure analyses separate the three subspecies of northern giraffe and suggest genetic differentiation between populations from eastern and western areas of the Kordofan giraffe’s range. Both West African and Kordofan giraffe show a gradual decline in effective population size over the last 10 ka and have moderate genome-wide heterozygosity compared to other giraffe species. Recent inbreeding levels are higher in the West African giraffe and in Kordofan giraffe from Garamba National Park, Democratic Republic of Congo. Although numbers for both West African and some populations of Kordofan giraffe have increased in recent years, the threat of habitat loss, climate change impacts, and illegal hunting persists. Thus, future conservation actions should consider close genetic monitoring of populations to detect and, where practical, counteract negative trends that might develop.
Sweet Bee Venom Triggers Multiple Cell Death Pathways or Spurs Acute Cell Rupture According to Its Concentration in THP-1 Monocytic Leukemia Cells
Authors: Ryu Jae-Min , Na Han-Heom , Park Yoon-Jong , Park Jin-Sung , Ahn Byung-Soo , Kim Keun-Cheol
Published: January 2022

Sweet bee venom (sBV) contains various pharmacologically active components of bee venom (BV), but it is modified via the removal of the harmful substances found in BV. Thus, sBV has been used for pain relief in Oriental medicine but has only recently been applied for the treatment of various diseases. In this study, we examined the pharmacological effects and immunomodulatory functions of sBV in THP-1 monocytic leukemia cells. Growth inhibition and cell death were observed according to the concentration of sBV. However, the rapid collapse of cell cycle distribution was shown at 20 μg/mL sBV treatment, indicating that sBV led to cell death or acute cell rupture according to concentration. sBV administration activated Caspase-9, PARP1, RIPK1, and RIPK3, suggesting that the pharmacological actions of sBV were associated with induction of apoptosis and necroptosis. On the other hand, sBV or LPS administration increased cytokine expression, including IL-1β, and showed synergistic cell death in combinatory treatment conditions. Moreover, combinatory administration of sBV and LPS induced severe damage or death during egg development. This result implies that sBV exhibits both pharmacological and toxic effects depending on its concentration. Therefore, sBV might be a promising therapeutic approach, but optimal concentration should be considered before treatment.
Selection of Candidate Genes Conferring Blast Resistance and Heat Tolerance in Rice through Integration of Meta-QTLs and RNA-Seq
Authors: Tian Tian , Chen Lijuan , Ai Yufang , He Huaqin
Published: January 2022

Due to global warming, high temperature is a significant environmental stress for rice production. Rice (Oryza sativa L.), one of the most crucial cereal crops, is also seriously devastated by Magnaporthe oryzae. Therefore, it is essential to breed new rice cultivars with blast and heat tolerance. Although progress had been made in QTL mapping and RNA-seq analysis in rice in response to blast and heat stresses, there are few reports on simultaneously mining blast-resistant and heat-tolerant genes. In this study, we separately conducted meta-analysis of 839 blast-resistant and 308 heat-tolerant QTLs in rice. Consequently, 7054 genes were identified in 67 blast-resistant meta-QTLs with an average interval of 1.00 Mb. Likewise, 6425 genes were obtained in 40 heat-tolerant meta-QTLs with an average interval of 1.49 Mb. Additionally, using differentially expressed genes (DEGs) in the previous research and GO enrichment analysis, 55 DEGs were co-located on the common regions of 16 blast-resistant and 14 heat-tolerant meta-QTLs. Among, OsChib3H-c, OsJAMyb, Pi-k, OsWAK1, OsMT2b, OsTPS3, OsHI-LOX, OsACLA-2 and OsGS2 were the significant candidate genes to be further investigated. These results could provide the gene resources for rice breeding with excellent resistance to these 2 stresses, and help to understand how plants response to the combination stresses of blast fungus and high temperature.
Evaluation and Genetic Analysis of Parthenocarpic Germplasms in Cucumber
Authors: Gou Chenxing , Zhu Pinyu , Meng Yongjiao , Yang Fan , Xu Yan , Xia Pengfei , Chen Jinfeng , Li Ji
Published: January 2022

Parthenocarpy is an important agronomic trait in cucumber (Cucumis sativus L.) production. However, the systematic identification of parthenocarpic germplasms from national gene banks for cucumber improvement remains an international challenge. In this study, 201 cucumber lines were investigated, including different ecotypes. The percentages of parthenocarpic fruit set (PFS) and parthenocarpic fruit expansion (PFE) were evaluated in three experiments. In natural populations, the PFS rates fit a normal distribution, while PFE rates showed a skewed distribution, suggesting that both PFS and PFE rates are typical quantitative traits. Genetic analysis showed that parthenocarpy in different ecotypes was inherited in a similar incompletely dominant manner. A total of 5324 single nucleotide polymorphisms (SNPs) associated with parthenocarpy were detected in a Genome-wide association study (GWAS) of parthenocarpy in the 31 cucumber lines, from which six parthenocarpic loci, including two novel loci (Pfs1.1 and Pfs4.1), were identified. Consequently, fifteen of the elite lines that were screened presented relatively stronger parthenocarpy ability (PFS > 90%, PFE > 50%), among which six cucumber lines (18007s, 18008s, 18022s, 18076s, 18099s, and 18127s) exhibited weak first-fruit inhibition. Three lines (18011s, 18018s, and 18019s) were screened for super ovary parthenocarpy, which showed more attractive performance. Four low-temperature-enhanced parthenocarpy lines (18018s, 18022s, 18029s, and 18012s) were identified, which were suited for breeding for counter-season production. Our approaches could help increase efficiency and lead to parthenocarpy improvements for modern cucumber cultivars.
MIF rs755622 and IL6 rs1800795 Are Implied in Genetic Susceptibility to End-Stage Renal Disease (ESRD)
Authors: Guarneri Marco , Scola Letizia , Giarratana Rosa Maria , Bova Manuela , Carollo Caterina , Vaccarino Loredana , Calandra Leonardo , Lio Domenico , Balistreri Carmela Rita , Cottone Santina
Published: January 2022

Chronic kidney disease (CKD) is characterized by an increased risk of kidney failure and end-stage renal disease (ESRD). Aging and comorbidities as cardiovascular diseases, metabolic disorders, infectious diseases, or tumors, might increase the risk of dialysis. In addition, genetic susceptibility factors might modulate kidney damage evolution. We have analyzed, in a group of ESRD patients and matched controls, a set of SNPs of genes (Klotho rs577912, rs564481, rs9536314; FGF23 rs7955866; IGF1 rs35767; TNFA rs1800629; IL6 rs1800795; MIF rs755622, rs1007888) chosen in relation to their possible involvement with renal disease and concomitant pathologies. Analysis of the raw data did indicate that IL6 rs180795 and MIF rs755622 SNPs might be markers of genetic susceptibility to ESRD. In particular, the C positive genotypes of MIF rs755622, (dominant model) seem to be an independent risk factor for ESDR patients (data adjusted for age, gender, and associated pathologies). Stratifying results according to age MIF rs755622 C positive genotype frequencies are increased in both the two age classes considered (<59 and ≥59-year-old subjects). Analyses of data according to gender allowed us to observe that ESRD women shoved a significantly reduced frequency of genotypes bearing IL6 rs180795 C allele. In addition, MIF rs755622 might interact with diabetes or hypercholesterolemia in increasing susceptibility to ESRD. In conclusion, our data indicate that some polymorphisms involved in the regulation of both renal function and inflammatory response can influence the evolution of chronic kidney disease and suggest that the modulation of the activities of these and other genes should also be considered as therapeutic targets on to intervene with innovative therapies.
The Role of the MYC/miR-150/MYB/ZDHHC11 Network in Hodgkin Lymphoma and Diffuse Large B-Cell Lymphoma
Authors: Ziel-Swier Lotteke J. Y. M. , Liu Yichen , Seitz Annika , de Jong Debora , Koerts Jasper , Rutgers Bea , Veenstra Rianne , Razak Fazlyn R. Abdul , Dzikiewicz-Krawczyk Agnieszka , van den Berg Anke , Kluiver Joost
Published: January 2022

We previously described involvement of the MYC/miR-150/MYB/ZDHHC11 network in the growth of Burkitt lymphoma (BL) cells. Here we studied the relevance of this network in the two other B-cell lymphomas: Hodgkin lymphoma (HL) and diffuse large B-cell lymphoma (DLBCL). Expression levels of the network components were assessed at the RNA and protein level. The effect of modulating levels of the network components on cell growth was determined through GFP competition assay. AGO2-RNA immunoprecipitation was performed to validate targeting by miR-150. Expression levels of MYC, MYB and ZDHHC11 were increased, while miR-150 levels were decreased similar to the pattern observed in BL. The knockdown of MYC, MYB and ZDHHC11 decreased the growth of HL and DLBCL cells. In contrast, overexpression of miR-150 did not induce clear phenotypes in HL, and limited the effects in DLBCL. This could not be explained by the differences in overexpression levels. Furthermore, we showed that in HL, ZDHHC11 and MYB are efficiently targeted by miR-150. To conclude, MYC, MYB and ZDHHC11 are critical for the growth of HL and DLBCL cells consistent with the role observed in BL cells, while low endogenous miR-150 levels appeared to be less critical for the growth of HL and DLBCL cells despite the effective targeting of ZDHHC11 and MYB.
Y-Chromosomal Insights into Breeding History and Sire Line Genealogies of Arabian Horses
Authors: Remer Viktoria , Bozlak Elif , Felkel Sabine , Radovic Lara , Rigler Doris , Grilz-Seger Gertrud , Stefaniuk-Szmukier Monika , Bugno-Poniewierska Monika , Brooks Samantha , Miller Donald C. , Antczak Douglas F. , Sadeghi Raheleh , Cothran Gus , Juras Rytis , Khanshour Anas M. , Rieder Stefan , Penedo Maria C. , Waiditschka Gudrun , Kalinkova Liliya , Kalashnikov Valery V. , Zaitsev Alexander M. , Almarzook Saria , Reißmann Monika , Brockmann Gudrun A. , Brem Gottfried , Wallner Barbara
Published: January 2022

The Y chromosome is a valuable genetic marker for studying the origin and influence of paternal lineages in populations. In this study, we conducted Y-chromosomal lineage-tracing in Arabian horses. First, we resolved a Y haplotype phylogeny based on the next generation sequencing data of 157 males from several breeds. Y-chromosomal haplotypes specific for Arabian horses were inferred by genotyping a collection of 145 males representing most Arabian sire lines that are active around the globe. These lines formed three discrete haplogroups, and the same haplogroups were detected in Arabian populations native to the Middle East. The Arabian haplotypes were clearly distinct from the ones detected in Akhal Tekes, Turkoman horses, and the progeny of two Thoroughbred foundation sires. However, a haplotype introduced into the English Thoroughbred by the stallion Byerley Turk (1680), was shared among Arabians, Turkomans, and Akhal Tekes, which opens a discussion about the historic connections between Oriental horse types. Furthermore, we genetically traced Arabian sire line breeding in the Western World over the past 200 years. This confirmed a strong selection for relatively few male lineages and uncovered incongruences to written pedigree records. Overall, we demonstrate how fine-scaled Y-analysis contributes to a better understanding of the historical development of horse breeds.
The Ecology and Evolution of the Baker’s Yeast Saccharomyces cerevisiae
Authors: Bai Feng-Yan , Han Da-Yong , Duan Shou-Fu , Wang Qi-Ming
Published: January 2022

The baker’s yeast Saccharomyces cerevisiae has become a powerful model in ecology and evolutionary biology. A global effort on field survey and population genetics and genomics of S. cerevisiae in past decades has shown that the yeast distributes ubiquitously in nature with clearly structured populations. The global genetic diversity of S. cerevisiae is mainly contributed by strains from Far East Asia, and the ancient basal lineages of the species have been found only in China, supporting an ‘out-of-China’ origin hypothesis. The wild and domesticated populations are clearly separated in phylogeny and exhibit hallmark differences in sexuality, heterozygosity, gene copy number variation (CNV), horizontal gene transfer (HGT) and introgression events, and maltose utilization ability. The domesticated strains from different niches generally form distinct lineages and harbor lineage-specific CNVs, HGTs and introgressions, which contribute to their adaptations to specific fermentation environments. However, whether the domesticated lineages originated from a single, or multiple domestication events is still hotly debated and the mechanism causing the diversification of the wild lineages remains to be illuminated. Further worldwide investigations on both wild and domesticated S. cerevisiae, especially in Africa and West Asia, will be helpful for a better understanding of the natural and domestication histories and evolution of S. cerevisiae.
miRNome Profiling Detects miR-101-3p and miR-142-5p as Putative Blood Biomarkers of Frailty Syndrome
Authors: Carini Giulia , Mingardi Jessica , Bolzetta Francesco , Cester Alberto , Bolner Andrea , Nordera Giampietro , La Via Luca , Ieraci Alessandro , Russo Isabella , Maggi Stefania , Calza Stefano , Popoli Maurizio , Veronese Nicola , Musazzi Laura , Barbon Alessandro
Published: January 2022

Frailty is an aging-related pathology, defined as a state of increased vulnerability to stressors, leading to a limited capacity to meet homeostatic demands. Extracellular microRNAs (miRNAs) were proposed as potential biomarkers of various disease conditions, including age-related pathologies. The primary objective of this study was to identify blood miRNAs that could serve as potential biomarkers and candidate mechanisms of frailty. Using the Fried index, we enrolled 22 robust and 19 frail subjects. Blood and urine samples were analysed for several biochemical parameters. We observed that sTNF-R was robustly upregulated in the frail group, indicating the presence of an inflammatory state. Further, by RNA-seq, we profiled 2654 mature miRNAs in the whole blood of the two groups. Expression levels of selected differentially expressed miRNAs were validated by qPCR, and target prediction analyses were performed for the dysregulated miRNAs. We identified 2 miRNAs able to significantly differentiate frail patients from robust subjects. Both miR-101-3p and miR-142-5p were found to be downregulated in the frail vs. robust group. Finally, using bioinformatics targets prediction tools, we explored the potential molecular mechanisms and cellular pathways regulated by the two miRNAs and potentially involved in frailty.
Towards the Genetic Architecture of Complex Gene Expression Traits: Challenges and Prospects for eQTL Mapping in Humans
Authors: Lee Chaeyoung
Published: January 2022

The discovery of expression quantitative trait loci (eQTLs) and their target genes (eGenes) has not only compensated for the limitations of genome-wide association studies for complex phenotypes but has also provided a basis for predicting gene expression. Efforts have been made to develop analytical methods in statistical genetics, a key discipline in eQTL analysis. In particular, mixed model– and deep learning–based analytical methods have been extremely beneficial in mapping eQTLs and predicting gene expression. Nevertheless, we still face many challenges associated with eQTL discovery. Here, we discuss two key aspects of these challenges: 1, the complexity of eTraits with various factors such as polygenicity and epistasis and 2, the voluminous work required for various types of eQTL profiles. The properties and prospects of statistical methods, including the mixed model method, Bayesian inference, the deep learning method, and the integration method, are presented as future directions for eQTL discovery. This review will help expedite the design and use of efficient methods for eQTL discovery and eTrait prediction.
The Österplana Fossil Meteorites and… What Else? Terrestrial Cr-Spinels and Zircons in the Ordovician Limestones of the Thorsberg Quarry (Sweden)
Authors: Lenaz Davide , Velicogna Matteo , Petrelli Maurizio , Schmitz Birger
Published: January 2022

In the Ordovician limestone of the Thorsberg quarry (South Sweden), about 130 meteorites have been found. Among the extraterrestrial material, several terrestrial Cr-spinels and zircons have been found too. In particular, in the interval 416–447 cm above the Arkeologen bed, terrestrial Cr-spinels, compositionally different from previous studied Cr-spinels of the same sequence, are present. Previous studies on zircon provided depositional ages that range from 464.22 ± 0.37 Ma to 465.01 ± 0.26 Ma. The trace element content of zircons suggests different possible source rocks. In fact, zircons from the oldest ash layer resemble those from dolerite, while those in the youngest layers are similar to zircons commonly found in granitoids, with more than 65% wt. SiO2. The chemistry of Cr-spinels suggests a strong alteration, so that it is difficult to assign them to a specific area, however they recall the chemistry of altered spinels from ophiolitic occurrences (among other possibilities). The geological setting of the Laurentia and Baltica areas, including the description of basalts to rhyolite association and the presence of ophiolitic slices, makes us confident about the derivation of these zircons and Cr-spinels from those areas.
Assessment of Geological Heritage Sites and Their Significance for Geotouristic Exploitation: The Case of Lefkas, Meganisi, Kefalonia and Ithaki Islands, Ionian Sea, Greece
Authors: Spyrou Evangelos , Triantaphyllou Maria V. , Tsourou Theodora , Vassilakis Emmanuel , Asimakopoulos Christos , Konsolaki Aliki , Markakis Dimitris , Marketou-Galari Dimitra , Skentos Athanasios
Published: January 2022

Geological heritage or geoheritage refers to the total of geosites, i.e., areas of high geological interest in a given area. Geosites have a high potential of attracting geotourists, thus contributing to the development of the local economy. Assessing sites of geological interest can contribute to their promotion, as well as their preservation and protection. Greece’s geotectonic position in the convergent zone between the African and Eurasian plates has contributed to the existence of a considerable wealth of geosites, with the particularly active geotectonic region of the Ionian Sea characterized as a geoheritage hotspot. The purpose of this study is the selection of several such sites from the islands of Lefkas, Meganisi, Kefalonia and Ithaki and their assessment regarding their scientific, environmental, cultural, economic and aesthetic value. The most representative sites for the individual disciplines of geology (e.g., geomorphology, tectonics, stratigraphy and palaeontology) have been chosen, mapped and assessed, while indicative georoutes are proposed, which could aid the island’s geotouristic promotion to geologist and non-geologist future visitors.
Vestiges of the Pre-Caledonian Passive Margin of Baltica in the Scandinavian Caledonides: Overview, Revisions and Control on the Structure of the Mountain Belt
Authors: Andersen Torgeir B. , Jakob Johannes , Kjøll Hans Jørgen , Tegner Christian
Published: January 2022

The Pre-Caledonian margin of Baltica has been outlined as a tapering wedge with increasing magmatism towards the ocean–continent transition. It is, however, well known that margins are complex, with different and diachronous evolution along and across strike. Baltica’s vestiges in the Scandes have complexities akin to modern margins. It included a microcontinent and magma-poor hyperextended and magma-rich segments. It was probably up to 1500 km wide before distal parts were affected by plate convergence. Characteristic features are exhumed mantle peridotites and their detrital equivalents, some exposed to the seafloor by the pre-orogenic hyperextension. A major change in the architecture of the mountain belt occurred across the NW–SE trending Sveconorwegian front in the Baltican basement. This coincided with the NE termination of the Jotun-Lindås-Dalsfjord basement nappes, the remains of the Jotun Microcontinent (JMC) formed by hyperextension prior to the orogeny. Mantle with ophicalcite breccias exhumed by hyperextension are covered by deep-marine sediments and local conglomerates. Baltican basement slivers are common in the transitional crust basins. Outboard the JMC, the margin was magma-rich. The main break-up magmatism at 605 ± 10 Ma was part of the vast Central Iapetus Magmatic Province. The along-strike heterogeneity of the margin controlled diachronous and contrasting tectonic evolution during the later Caledonian plate convergence and collision.
Ground Penetrating Radar Survey of the UNESCO Painted Churches in the Troodos Region (Cyprus)
Authors: Mitchell William L. , Abate Dante , Colls Kevin S. , Faka Marina , Sturdy Colls Caroline , Bakirtzis Nikolas
Published: January 2022

In the framework of the IH-AT (Invisible Heritage Analysis and Technology) project, a cluster of churches ranging from the 11th to the 16th centuries, located in the Troodos Mountain range of Cyprus, designated by UNESCO as World Heritage monuments, were investigated using Non-Destructive-Techniques (NDT) (geophysical and topographic survey), 3D modelling and visualisation methods, contextualised and interpreted by art-historical and archaeological research. A geophysical survey, performed using a Ground Penetrating Radar (GPR), specifically aimed to confirm the presence or absence of buried features of archaeological interest at each of these sites, in particular, evidence of monastic complexes and buildings that used to surround preserved churches. This paper describes the preliminary results of this survey and some initial interpretations concerning what new information can be discerned about the now lost monastery complexes, in advance of future excavation.
The Power of Combining MA-XRF, Infrared Reflectography and Digital Microscopy to Unveil the Production of the 16th Century Illuminated Charter of Évora: What May Be Hidden under a Painted Surface?
Authors: Miguel Catarina , Bottura-Scardina Silvia , Bottaini Carlo , Valadas Sara , Candeias Antonio , Bilou Francisco
Published: January 2022

In recent decades, many works have been devoted to the study of materials and painting techniques used to produce illuminated manuscripts. If the analyses were once largely invasive, the approach has become increasingly more in situ and non-invasive over the years. This work presents the results of the analysis of the Portuguese Charter of Évora, an illuminated manuscript that dates back to 1501, combining an elemental mapping technique (MA-XRF) with the non-invasive imaging techniques of infrared reflectography and digital microscopy. Remarkably, this approach allowed us to obtain unexpected results regarding the chronology of production of the illumination of the view of the City of Évora and of the Charter of Évora itself, posing new questions for art history on the political, social and artistic context of the early 16th century City of Évora.
Advances in Breeding, Bioprospecting, and In Vitro Culture of Laelia Orchid Species
Authors: Mayo-Mosqueda Alberto , García-Hernández Eleazar , Noguera-Savelli Eliana , Cetzal-Ix William , Alatorre-Cobos Fulgencio
Published: January 2022

Orchids (Orchidaceae) are plants that are highly appreciated by their beautiful flowers worldwide. Moreover, they represent a source of metabolites with applications in medicine and biotechnology. Within the Orchidaceae family, the Laelia genus is a group of orchid species from the Neotropics and is probably one of the most representative genera of America. Laelia orchids are cultivated by their splendid flowers and are widely used in orchid breeding. Here, we revise the use of the Laelia genus in orchid breeding and metabolite bioprospecting. We also analyze the use of plant tissue culture (PTC) as an alternative to conventional propagation and as a strategy for the recovery of those Laelia species threatened with extinction. We summarize and discuss the recent advances in the application of different PTC techniques for mass multiplication based on asymbiotic germination, organogenesis, protocorm-like bodies development, and somatic embryogenesis, and the advances of in vitro conservation by cryoconservation and the use of slow-growth promoting hormones. Finally, we suggest future directions and venues in research for Laelia species.
Fruiting, Morphology, and Architecture of ‘Arbequina’ and ‘Calatina’ Olive Branches
Authors: Carella Alessandro , Massenti Roberto , Milazzo Giuseppe , Caruso Tiziano , Lo Bianco Riccardo
Published: January 2022

Two different olive cultivars grown under a high-density hedgerow system were studied to compare their fruiting and branch architecture features and to determine the possibility to use ‘Calatina’ olive trees for intensive plantings, as a local alternative to the international reference ‘Arbequina’. Weights of two-year-old branches, fruits and leaves were recorded to estimate the growth partitioning. Growth and architectural parameters, such as shoot length, vector and diameter, branching angle, branch total length, height, width, area, and branching frequency, were determined by digital image analysis. Digital images of the fruits were also used to estimate fruit maturation by peel color analysis. Whole branch and fruit crop weights were similar in the ‘Arbequina’ and ‘Calatina’, while the latter had a greater fruit/leaf ratio, showing a higher production efficiency than ‘Arbequina’. Fruits were fewer but bigger in ‘Calatina’ than in ‘Arbequina’, suggesting an advantage for both trunk-shaking and straddle machine harvesting in the Sicilian cultivar. Leaf/wood ratio, branching frequency and branching angle were similar in the two cultivars. ‘Calatina’ shoots exhibited a greater bending degree than those of ‘Arbequina’ and this trait particularly favors straddle harvesting. In addition to many similarities between the two cultivars, the present study indicates that ‘Calatina’ is more efficient in terms of yield and harvesting than ‘Arbequina’. This qualifies ‘Calatina’ as a superior, yield-efficient olive cultivar suitable for intensive hedgerow plantings to be harvested with straddle or side-by-side trunk shaker machines.
“60 Years on”—Effects of Climatic Change on Tree Phenology—A Case Study Using Pome Fruit
Authors: Kunz Achim , Blanke Michael
Published: January 2022

Phenological records of apple and pear trees, including flowering, harvest and leaf drop, and concomitant weather records at Klein-Altendorf (50° N) near Bonn, Germany were correlated using two approaches: (a) linear curve fitting and (b) comparison of mean values of the first 30 years (1956–1988) versus the recent 30 years of climate change (1989–2017). The annual air temperature increased by 1.7 °C from 8.6 °C in 1958 to 10.3 °C in 2017 over the last 60 years and similarly in the vegetation period (1 April–30 October) from 13.7 °C in 1958 to 15.2 °C in 2017 by 1.5 °C. The combination of stronger increase in winter temperatures (by +1.2 °C) than in the summer (air +1.0 °C) with advanced bud break and −0.3 °C lower minimum temperatures in April during flowering resulted a continued risk of a late frost, as experienced in 2017. The strongest climate change effect, i.e., 11–14 days advanced flowering (in apple and pear) highly correlated (R2 −0.7) with the March/April temperature. Fruit ontogeny was 4 days shorter in cv. ‘Lucas’ pear, but 5 days longer in cv. ‘Cox’ and 10 days longer in cv. ‘Boskoop’, but remained unchanged in cv. ‘Golden Delicious’, irrespective of early or late ripening variety and contradictory climate effects, fruit matured 4–12 days earlier indicating its sole dependency on variety. Climate data and (earlier) harvest date closely correlated (R2: 0.6–0.7). The lowest correlation was between canopy duration (bloom to leaf fall), which was consistently extended by 6–10 days and the leaf drop stage beginning 2–4 days earlier. The correlations indicated that the Meckenheim fruit growing region is strongly affected by climate change and the comparison between two equally-balanced 30-year phases gave more realistic results than linear curve fitting.