bluuebunny/crossref_metadata_2025 huggingface dataset:
Appropriation, Integration, and Nation Building: Portuguese Railways in the Second Half of the Nineteenth and Early Years of the Twentieth Century
Authors: Pereira Hugo Silveira
Published: June 2021

In 1850, after three decades of political turmoil, Portugal started investing in major public works, particularly, in the construction of a national railway network. This strategy followed closely the suggestions of the Saint-Simonian technocrats with whom Portuguese engineers had been engaging since the 1820s. Additionally, it came in response to the longtime neglect suffered by the Portuguese transportation system, which hindered communications and trade between different areas of the kingdom and with neighboring Spain. The main goal of the investment was to modernize the national transport system, attract to Portuguese harbors a large portion of the traffic between Europe, Africa, and America, and, in general terms, put the nation on the path of progress. By the end of the nineteenth century, total mileage of the Portuguese rail network exceeded 2,300 km. This article analyzes the role of railways in the improvement of communications between the Portuguese provinces, their appropriation in a unified nation-state, the degree of integration of the Portuguese economy with the Spanish and European economies, and the construction/reinvention of Portugal as a modern and technological nation. To achieve these goals, I will use three key concepts: territorial appropriation, circulation, and globalization. Sources include statistics of railway operation and previous works analyzing the impact of railways on the Portuguese transport system and economy, the outcomes of operating transnational lines, and the importance of technology for the reinvention of Portugal during the second half of the nineteenth century.
Rezension
Authors: Zegelin Angelika
Published: June 2021

Zusammenfassung. Patientenedukation ist ein weites Feld. Hier kommt ein eher ungewöhnlicher Ansatz, nämlich kindgerechte Erklärungen für verschiedene Probleme. Ich bin eher zufällig auf die Reihe gestoßen und möchte hier das obengenannte Buch vorstellen, dabei geht es um Arbeitslosigkeit der Eltern. Gleichzeitig ist mir wichtig, auf die gesamte Reihe hinzuweisen.
Seismic Noise Autocorrelations on Mars
Authors: Schimmel Martin , Stutzmann Eleonore , Lognonné Philippe , Compaire Nicolas , Davis Paul , Drilleau Melanie , Garcia Raphael , Kim Doyeon , Knapmeyer‐Endrun Brigitte , Lekic Vedran , Margerin Ludovic , Panning Mark , Schmerr Nicholas , Scholz John Robert , Spiga Aymeric , Tauzin Benoit , Banerdt Bruce
Published: June 2021

Mars is the first extraterrestrial planet with seismometers (Seismic Experiment for Interior Structure, SEIS) deployed directly on its surface in the framework of the Interior Exploration using Seismic Investigations, Geodesy and Heat Transport (InSight) mission. The lack of strong Marsquakes, however, strengthens the need of seismic noise studies to additionally constrain the Martian structure. Seismic noise autocorrelations of single‐station recordings permit the determination of the zero‐offset reflection response underneath SEIS. We present a new autocorrelation study which employs state‐of‐the‐art approaches to determine a robust reflection response by avoiding bias from aseismic signals which are recorded together with seismic waves due to unfavorable deployment and environmental conditions. Data selection and segmentation is performed in a data‐adaptive manner which takes the data root‐mean‐square amplitude variability into account. We further use the amplitude‐unbiased phase cross‐correlation and work in the 1.2–8.9 Hz frequency band. The main target are crustal scale reflections, their robustness and convergence. The strongest signal appears at 10.6 s, and, if interpreted as a P‐wave reflection, would correspond to a discontinuity at about 21 km depth. This signal is a likely candidate for a reflection from the base of the Martian crust due to its strength, polarity, and stability. Additionally we identify, among the stable signals, a signal at about 6.15 s that can be interpreted as the P‐wave reflection from the mid‐crust at about 9.5 km depth.
Extensive Remineralization of Peatland‐Derived Dissolved Organic Carbon and Ocean Acidification in the Sunda Shelf Sea, Southeast Asia
Authors: Zhou Yongli , Evans Christopher D. , Chen Yuan , Chang Kristy Y. W. , Martin Patrick
Published: June 2021

Southeast Asia is a hotspot of riverine export of terrigenous organic carbon to the ocean, accounting for ∼10% of the global land‐to‐ocean riverine flux of terrigenous dissolved organic carbon (tDOC). While anthropogenic disturbance is thought to have increased the tDOC loss from peatlands in Southeast Asia, the fate of this tDOC in the marine environment and the potential impacts of its remineralization on coastal ecosystems remain poorly understood. We collected a multi‐year biogeochemical time series in the central Sunda Shelf (Singapore Strait), where the seasonal reversal of ocean currents delivers water masses from the South China Sea first before (during Northeast Monsoon) and then after (during Southwest Monsoon) they have mixed with run‐off from peatlands on Sumatra. The concentration and stable isotope composition of DOC, and colored dissolved organic matter spectra, reveal a large input of tDOC to our site during Southwest Monsoon. Using isotope mass balance calculations, we show that 60%–70% of the original tDOC input is remineralized in the coastal waters of the Sunda Shelf, causing seasonal acidification. The persistent CO2 oversaturation drives a CO2 efflux of 2.4–4.9 mol m−2 yr−1 from the Singapore Strait, suggesting that a large proportion of the remineralized peatland tDOC is ultimately emitted to the atmosphere. However, incubation experiments show that the remaining 30%–40% tDOC exhibits surprisingly low lability to microbial and photochemical degradation, suggesting that up to 20%–30% of peatland tDOC might be relatively refractory and exported to the open ocean.
Field-emission electron gun for a MEMS electron microscope
Authors: Krysztof Michał
Published: June 2021

This article presents a field-emission electron gun intended for use in a MEMS (microelectromechanical system) electron microscope. Its fabrication process follows the technology of a miniature device under development built from silicon electrodes and glass spacers. The electron gun contains a silicon cathode with a single very sharp protrusion and a bundle of disordered CNTs deposited on its end (called a sharp silicon/CNT cathode). It was tested in diode and triode configurations. For the diode configuration, a low threshold voltage <1000 V and a high emission current that reached 90 µA were obtained. After 30 min of operation at 900 V, the emission current decreased to 1.6 µA and was stable for at least 40 min, with RMS fluctuation in the anode current lower than 10%. The electron beam spot of the source was observed on the phosphor screen. In the diode configuration, the spot size was the same as the emission area (~10 µm), which is a satisfactory result. In the triode configuration, an extraction electrode (gate) control function was reported. The gate limited the emission current and elongated the lifetime of the gun when the current limit was set. Moreover, the electron beam current fluctuations at the anode could be reduced to ~1% by using a feedback loop circuit that controls the gate voltage, regulating the anode current. The developed sharp silicon/CNT cathodes were used to test the MEMS electron source demonstrator, a key component of the MEMS electron microscope, operating under atmospheric pressure conditions. Cathodoluminescence of the phosphor layer (ZnS:Ag) deposited on the thin silicon nitride membrane (anode) was observed.
IGF1-mediated HOXA13 overexpression promotes colorectal cancer metastasis through upregulating ACLY and IGF1R
Authors: Qiao Chenyang , Huang Wenjie , Chen Jie , Feng Weibo , Zhang Tongyue , Wang Yijun , Liu Danfei , Ji Xiaoyu , Xie Meng , Sun Mengyu , Fan Daiming , Wu Kaichun , Xia Limin
Published: June 2021

Metastasis is the major reason for the high mortality of colorectal cancer (CRC) patients and its molecular mechanism remains unclear. Here, we report a novel role of Homeobox A13 (HOXA13), a member of the Homeobox (HOX) family, in promoting CRC metastasis. The elevated expression of HOXA13 was positively correlated with distant metastasis, higher AJCC stage, and poor prognosis in two independent CRC cohorts. Overexpression of HOXA13 promoted CRC metastasis whereas downregulation of HOXA13 suppressed CRC metastasis. Mechanistically, HOXA13 facilitated CRC metastasis by transactivating ATP-citrate lyase (ACLY) and insulin-like growth factor 1 receptor (IGF1R). Knockdown of ACLY and IGFIR inhibited HOXA13-medicated CRC metastasis, whereas ectopic overexpression of ACLY and IGFIR rescued the decreased CRC metastasis induced by HOXA13 knockdown. Furthermore, Insulin-like growth factor 1 (IGF1), the ligand of IGF1R, upregulated HOXA13 expression through the PI3K/AKT/HIF1α pathway. Knockdown of HOXA13 decreased IGF1-mediated CRC metastasis. In addition, the combined treatment of ACLY inhibitor ETC-1002 and IGF1R inhibitor Linsitinib dramatically suppressed HOXA13-mediated CRC metastasis. In conclusion, HOXA13 is a prognostic biomarker in CRC patients. Targeting the IGF1-HOXA13-IGF1R positive feedback loop may provide a potential therapeutic strategy for the treatment of HOXA13-driven CRC metastasis.
Discovery of a cooperative mode of inhibiting RIPK1 kinase
Authors: Meng Huyan , Wu Guowei , Zhao Xinsuo , Wang Anhui , Li Dekang , Tong Yilun , Jin Taijie , Cao Ye , Shan Bing , Hu Shichen , Li Ying , Pan Lifeng , Tian Xiaoxu , Wu Ping , Peng Chao , Yuan Junying , Li Guohui , Tan Li , Wang Zhaoyin , Li Ying
Published: June 2021

RIPK1, a death domain-containing kinase, has been recognized as an important therapeutic target for inhibiting apoptosis, necroptosis, and inflammation under pathological conditions. RIPK1 kinase inhibitors have been advanced into clinical studies for the treatment of various human diseases. One of the current bottlenecks in developing RIPK1 inhibitors is to discover new approaches to inhibit this kinase as only limited chemotypes have been developed. Here we describe Necrostatin-34 (Nec-34), a small molecule that inhibits RIPK1 kinase with a mechanism distinct from known RIPK1 inhibitors such as Nec-1s. Mechanistic studies suggest that Nec-34 stabilizes RIPK1 kinase in an inactive conformation by occupying a distinct binding pocket in the kinase domain. Furthermore, we show that Nec-34 series of compounds can synergize with Nec-1s to inhibit RIPK1 in vitro and in vivo. Thus, Nec-34 defines a new strategy to target RIPK1 kinase and provides a potential option of combinatorial therapy for RIPK1-mediated diseases.
Exome reanalysis and proteomic profiling identified TRIP4 as a novel cause of cerebellar hypoplasia and spinal muscular atrophy (PCH1)
Authors: Töpf Ana , Pyle Angela , Griffin Helen , Matalonga Leslie , Schon Katherine ,   Solve-RD SNV-indel working group, Cohen Enzo , Cuesta Isabel , Danis Daniel , Denommé-Pichon Anne-Sophie , Duffourd Yannis , Gilissen Christian , Johari Mridul , Laurie Steven , Li Shuang , Nelson Isabelle , Paramonov Ida , Peters Sophia , Prasanth Sivakumar , Robinson Peter , Sablauskas Karolis , Savarese Marco , Steyaert Wouter , van der Velde Joeri K. , Vitobello Antonio ,   Solve-RD DITF-euroNMD, Baets Jonathan , Beijer Danique , Bonne Gisèle , Cossins Judith , Evangelista Teresinha , Ferlini Alessandra , Hackman Peter , Hanna Michael G. , Houlden Henry , Lau Jarred , Lochmüller Hanns , Macken William L. , Musacchia Francesco , Nascimento Andres , Natera-de Benito Daniel , Nigro Vincenzo , Piluso Giulio , Pini Veronica , Pitceathly Robert D. S. , Polavarapu Kiran , Cruz Pedro M. Rodriguez , Sarkozy Anna , Selvatici Rita , Thompson Rachel , Torella Annalaura , Udd Bjarne , Van de Vondel Liedewei , Vandrovcova Jana , Zaharieva Irina , Sickmann Albert , Schara–Schmidt Ulrike , Hentschel Andreas , Chinnery Patrick F. , Kölbel Heike , Roos Andreas , Horvath Rita
Published: June 2021

TRIP4 is one of the subunits of the transcriptional coregulator ASC-1, a ribonucleoprotein complex that participates in transcriptional coactivation and RNA processing events. Recessive variants in the TRIP4 gene have been associated with spinal muscular atrophy with bone fractures as well as a severe form of congenital muscular dystrophy. Here we present the diagnostic journey of a patient with cerebellar hypoplasia and spinal muscular atrophy (PCH1) and congenital bone fractures. Initial exome sequencing analysis revealed no candidate variants. Reanalysis of the exome data by inclusion in the Solve-RD project resulted in the identification of a homozygous stop-gain variant in the TRIP4 gene, previously reported as disease-causing. This highlights the importance of analysis reiteration and improved and updated bioinformatic pipelines. Proteomic profile of the patient’s fibroblasts showed altered RNA-processing and impaired exosome activity supporting the pathogenicity of the detected variant. In addition, we identified a novel genetic form of PCH1, further strengthening the link of this characteristic phenotype with altered RNA metabolism.
A high-quality genome assembly of Morinda officinalis, a famous native southern herb in the Lingnan region of southern China
Authors: Wang Jihua , Xu Shiqiang , Mei Yu , Cai Shike , Gu Yan , Sun Minyang , Liang Zhan , Xiao Yong , Zhang Muqing , Yang Shaohai
Published: June 2021

Morinda officinalis is a well-known medicinal and edible plant that is widely cultivated in the Lingnan region of southern China. Its dried roots (called bajitian in traditional Chinese medicine) are broadly used to treat various diseases, such as impotence and rheumatism. Here, we report a high-quality chromosome-scale genome assembly of M. officinalis using Nanopore single-molecule sequencing and Hi-C technology. The assembled genome size was 484.85 Mb with a scaffold N50 of 40.97 Mb, and 90.77% of the assembled sequences were anchored on eleven pseudochromosomes. The genome includes 27,698 protein-coding genes, and most of the assemblies are repetitive sequences. Genome evolution analysis revealed that M. officinalis underwent core eudicot γ genome triplication events but no recent whole-genome duplication (WGD). Likewise, comparative genomic analysis showed no large-scale structural variation after species divergence between M. officinalis and Coffea canephora. Moreover, gene family analysis indicated that gene families associated with plant–pathogen interactions and sugar metabolism were significantly expanded in M. officinalis. Furthermore, we identified many candidate genes involved in the biosynthesis of major active components such as anthraquinones, iridoids and polysaccharides. In addition, we also found that the DHQS, GGPPS, TPS-Clin, TPS04, sacA, and UGDH gene families—which include the critical genes for active component biosynthesis—were expanded in M. officinalis. This study provides a valuable resource for understanding M. officinalis genome evolution and active component biosynthesis. This work will facilitate genetic improvement and molecular breeding of this commercially important plant.
Easy domain adaptation method for filling the species gap in deep learning-based fruit detection
Authors: Zhang Wenli , Chen Kaizhen , Wang Jiaqi , Shi Yun , Guo Wei
Published: June 2021

Fruit detection and counting are essential tasks for horticulture research. With computer vision technology development, fruit detection techniques based on deep learning have been widely used in modern orchards. However, most deep learning-based fruit detection models are generated based on fully supervised approaches, which means a model trained with one domain species may not be transferred to another. There is always a need to recreate and label the relevant training dataset, but such a procedure is time-consuming and labor-intensive. This paper proposed a domain adaptation method that can transfer an existing model trained from one domain to a new domain without extra manual labeling. The method includes three main steps: transform the source fruit image (with labeled information) into the target fruit image (without labeled information) through the CycleGAN network; Automatically label the target fruit image by a pseudo-label process; Improve the labeling accuracy by a pseudo-label self-learning approach. Use a labeled orange image dataset as the source domain, unlabeled apple and tomato image dataset as the target domain, the performance of the proposed method from the perspective of fruit detection has been evaluated. Without manual labeling for target domain image, the mean average precision reached 87.5% for apple detection and 76.9% for tomato detection, which shows that the proposed method can potentially fill the species gap in deep learning-based fruit detection.
The role of the MAP kinase−kinase protein StMKK1 in potato immunity to different pathogens
Authors: Chen Xiaokang , Wang Wenbin , Cai Pingping , Wang Ziwei , Li Tingting , Du Yu
Published: June 2021

Mitogen-activated protein kinase (MAPK) cascades play important roles in plant immunity. Previously, we reported that the potato StMKK1 protein negatively regulates Nicotiana benthamiana resistance to Phytophthora infestans. However, the functions of StMKK1 in potato immunity are unknown. To investigate the roles of StMKK1 in potato resistance to different pathogens, such as the potato late-blight pathogen P. infestans, the bacterial wilt pathogen Ralstonia solanacearum, and the gray-mold fungal pathogen Botrytis cinerea, we generated StMKK1 transgenic lines and investigated the response of potato transformants to destructive oomycete, bacterial, and fungal pathogens. The results showed that overexpression and silencing of StMKK1 do not alter plant growth and development. Interestingly, we found that StMKK1 negatively regulated potato resistance to the hemibiotrophic/biotrophic pathogens P. infestans and R. solanacearum, while it positively regulated potato resistance to the necrotrophic pathogen B. cinerea. Further investigation showed that overexpression of StMKK1 suppressed potato pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and salicylic acid (SA)-related responses, while silencing of StMKK1 enhanced PTI and SA-related immune responses. Taken together, our results showed that StMKK1 plays dual roles in potato defense against different plant pathogens via negative regulation of PTI and SA-related signaling pathways.
The chromosome-level reference genome of Coptis chinensis provides insights into genomic evolution and berberine biosynthesis
Authors: Chen Da-xia , Pan Yuan , Wang Yu , Cui Yan-Ze , Zhang Ying-Jun , Mo Rang-yu , Wu Xiao-li , Tan Jun , Zhang Jian , Guo Lian-an , Zhao Xiao , Jiang Wenkai , Sun Tian-lin , Hu Xiao-Di , Li Long-yun
Published: June 2021

Coptis chinensis Franch, a perennial herb, is mainly distributed in southeastern China. The rhizome of C. chinensis has been used as a traditional medicine for more than 2000 years in China and many other Asian countries. The pharmacological activities of C. chinensis have been validated by research. Here, we present a de novo high-quality genome of C. chinensis with a chromosome-level genome of ~958.20 Mb, a contig N50 of 1.58 Mb, and a scaffold N50 of 4.53 Mb. We found that the relatively large genome size of C. chinensis was caused by the amplification of long terminal repeat (LTR) retrotransposons. In addition, a whole-genome duplication event in ancestral Ranunculales was discovered. Comparative genomic analysis revealed that the tyrosine decarboxylase (TYDC) and (S)-norcoclaurine synthase (NCS) genes were expanded and that the aspartate aminotransferase gene (ASP5) was positively selected in the berberine metabolic pathway. Expression level and HPLC analyses showed that the berberine content was highest in the roots of C. chinensis in the third and fourth years. The chromosome-level reference genome of C. chinensis provides important genomic data for molecular-assisted breeding and active ingredient biosynthesis.
Comprehensive analysis of SSRs and database construction using all complete gene-coding sequences in major horticultural and representative plants
Authors: Song Xiaoming , Yang Qihang , Bai Yun , Gong Ke , Wu Tong , Yu Tong , Pei Qiaoying , Duan Weike , Huang Zhinan , Wang Zhiyuan , Liu Zhuo , Kang Xi , Zhao Wei , Ma Xiao
Published: June 2021

Simple sequence repeats (SSRs) are one of the most important genetic markers and widely exist in most species. Here, we identified 249,822 SSRs from 3,951,919 genes in 112 plants. Then, we conducted a comprehensive analysis of these SSRs and constructed a plant SSR database (PSSRD). Interestingly, more SSRs were found in lower plants than in higher plants, showing that lower plants needed to adapt to early extreme environments. Four specific enriched functional terms in the lower plantChlamydomonas reinhardtiiwere detected when it was compared with seven other higher plants. In addition, Guanylate_cyc existed in more genes of lower plants than of higher plants. In our PSSRD, we constructed an interactive plotting function in the chart interface, and users can easily view the detailed information of SSRs. All SSR information, including sequences, primers, and annotations, can be downloaded from our database. Moreover, we developed Web SSR Finder and Batch SSR Finder tools, which can be easily used for identifying SSRs. Our database was developed using PHP, HTML, JavaScript, and MySQL, which are freely available athttp://www.pssrd.info/. We conducted an analysis of the Myb gene families and flowering genes as two applications of the PSSRD. Further analysis indicated that whole-genome duplication and whole-genome triplication played a major role in the expansion of the Myb gene families. These SSR markers in our database will greatly facilitate comparative genomics and functional genomics studies in the future.
Transcriptome and physiological analyses provide insights into the leaf epicuticular wax accumulation mechanism in yellowhorn
Authors: Zhao Yang , Liu Xiaojuan , Wang Mengke , Bi Quanxin , Cui Yifan , Wang Libing
Published: June 2021

Plantations and production of yellowhorn, one of the most important woody oil and urban greening trees widely cultivated in northern China, have gradually become limited by drought stress. The epicuticular wax layer plays a key role in the protection of yellowhorn trees from drought and other stresses. However, there is no research on the mechanism of wax loading in yellowhorn trees. In this study, we investigated the anatomical and physiological characteristics of leaves from different germplasm resources and different parts of the same tree and compared their cuticle properties. In addition, the different expression patterns of genes involved in wax accumulation were analyzed, and a coexpression network was built based on transcriptome sequencing data. Morphological and physiological comparisons found that the sun leaves from the outer part of the crown had thicker epicuticular wax, which altered the permeability and improved the drought resistance of leaves, than did shade leaves. Based on transcriptome data, a total of 3008 and 1324 differentially expressed genes (DEGs) were identified between the sun leaves and shade leaves in glossy- and non-glossy-type germplasm resources, respectively. We identified 138 DEGs involved in wax biosynthesis and transport, including structural genes (such as LACS8, ECH1, and ns-LTP) and transcription factors (such as MYB, WRKY, and bHLH transcription factor family proteins). The coexpression network showed a strong correlation between these DEGs. The differences in gene expression patterns between G- and NG-type germplasm resources under different light conditions were very clear. These results not only provide a theoretical basis for screening and developing drought-resistant yellowhorn germplasm resources but also provide a data platform to reveal the wax accumulation process of yellowhorn leaves.
The chromosome-level Stevia genome provides insights into steviol glycoside biosynthesis
Authors: Xu Xiaoyang , Yuan Haiyan , Yu Xiaqing , Huang Suzhen , Sun Yuming , Zhang Ting , Liu Qingquan , Tong Haiying , Zhang Yongxia , Wang Yinjie , Liu Chunxiao , Wu Lei , Hou Menglan , Yang Yongheng
Published: June 2021

Stevia (Stevia rebaudianaBertoni) is well known for its very sweet steviol glycosides (SGs) consisting of a common tetracyclic diterpenoid steviol backbone and a variable glycone. Steviol glycosides are 150–300 times sweeter than sucrose and are used as natural zero-calorie sweeteners. However, the most promising compounds are biosynthesized in small amounts. Based on Illumina, PacBio, and Hi-C sequencing, we constructed a chromosome-level assembly of Stevia covering 1416 Mb with a contig N50 value of 616.85 kb and a scaffold N50 value of 106.55 Mb. More than four-fifths of the Stevia genome consisted of repetitive elements. We annotated 44,143 high-confidence protein-coding genes in the high-quality genome. Genome evolution analysis suggested that Stevia and sunflower diverged ~29.4 million years ago (Mya), shortly after the whole-genome duplication (WGD) event (WGD-2, ~32.1 Mya) that occurred in their common ancestor. Comparative genomic analysis revealed that the expanded genes in Stevia were mainly enriched for biosynthesis of specialized metabolites, especially biosynthesis of terpenoid backbones, and for further oxidation and glycosylation of these compounds. We further identified all candidate genes involved in SG biosynthesis. Collectively, our current findings on the Stevia reference genome will be very helpful for dissecting the evolutionary history of Stevia and for discovering novel genes contributing to SG biosynthesis and other important agronomic traits in future breeding programs.
Identification of the PmWEEP locus controlling weeping traits in Prunus mume through an integrated genome-wide association study and quantitative trait locus mapping
Authors: Zhuo Xiaokang , Zheng Tangchun , Li Suzhen , Zhang Zhiyong , Zhang Man , Zhang Yichi , Ahmad Sagheer , Sun Lidan , Wang Jia , Cheng Tangren , Zhang Qixiang
Published: June 2021

WeepingPrunus mume(mei) has long been cultivated in East Asia for its specific ornamental value. However, little is known about the regulatory mechanism of the weeping trait in mei, which limits molecular breeding for the improvement of weeping-type cultivars. Here, we quantified the weeping trait in mei using nested phenotyping of 214 accessions and 342 F1hybrids. Two major associated loci were identified from the genome-wide association study (GWAS), which was conducted using 3,014,409 single nucleotide polymorphisms (SNPs) derived from resequencing, and 8 QTLs and 55 epistatic loci were identified from QTL mapping using 7,545 specific lengths amplified fragment (SLAF) markers. Notably, an overlappingPmWEEPmajor QTL was fine mapped within a 0.29 Mb region on chromosome 7 (Pa7), and a core SNP locus closely associated with the weeping trait was screened and validated. Furthermore, a total of 22 genes in thePmWEEPQTL region were expressed in weeping or upright mei based on RNA-seq analysis. Among them, only a novel gene (Pm024213) containing a thioredoxin (Trx) domain was found to be close to the core SNP and specifically expressed in buds and branches of weeping mei. Co-expression analysis ofPm024213showed that most of the related genes were involved in auxin and lignin biosynthesis. These findings provide insights into the regulatory mechanism of the weeping trait and effective molecular markers for molecular-assisted breeding inPrunus mume.
Abnormal brain cholesterol homeostasis in Alzheimer’s disease—a targeted metabolomic and transcriptomic study
Authors: Varma Vijay R. , Büşra Lüleci H. , Oommen Anup M. , Varma Sudhir , Blackshear Chad T. , Griswold Michael E. , An Yang , Roberts Jackson A. , O’Brien Richard , Pletnikova Olga , Troncoso Juan C. , Bennett David A. , Çakır Tunahan , Legido-Quigley Cristina , Thambisetty Madhav
Published: June 2021

The role of brain cholesterol metabolism in Alzheimer’s disease (AD) remains unclear. Peripheral and brain cholesterol levels are largely independent due to the impermeability of the blood brain barrier (BBB), highlighting the importance of studying the role of brain cholesterol homeostasis in AD. We first tested whether metabolite markers of brain cholesterol biosynthesis and catabolism were altered in AD and associated with AD pathology using linear mixed-effects models in two brain autopsy samples from the Baltimore Longitudinal Study of Aging (BLSA) and the Religious Orders Study (ROS). We next tested whether genetic regulators of brain cholesterol biosynthesis and catabolism were altered in AD using the ANOVA test in publicly available brain tissue transcriptomic datasets. Finally, using regional brain transcriptomic data, we performed genome-scale metabolic network modeling to assess alterations in cholesterol biosynthesis and catabolism reactions in AD. We show that AD is associated with pervasive abnormalities in cholesterol biosynthesis and catabolism. Using transcriptomic data from Parkinson’s disease (PD) brain tissue samples, we found that gene expression alterations identified in AD were not observed in PD, suggesting that these changes may be specific to AD. Our results suggest that reduced de novo cholesterol biosynthesis may occur in response to impaired enzymatic cholesterol catabolism and efflux to maintain brain cholesterol levels in AD. This is accompanied by the accumulation of nonenzymatically generated cytotoxic oxysterols. Our results set the stage for experimental studies to address whether abnormalities in cholesterol metabolism are plausible therapeutic targets in AD.
Modeling transcriptomic age using knowledge-primed artificial neural networks
Authors: Holzscheck Nicholas , Falckenhayn Cassandra , Söhle Jörn , Kristof Boris , Siegner Ralf , Werner André , Schössow Janka , Jürgens Clemens , Völzke Henry , Wenck Horst , Winnefeld Marc , Grönniger Elke , Kaderali Lars
Published: June 2021

The development of ‘age clocks’, machine learning models predicting age from biological data, has been a major milestone in the search for reliable markers of biological age and has since become an invaluable tool in aging research. However, beyond their unquestionable utility, current clocks offer little insight into the molecular biological processes driving aging, and their inner workings often remain non-transparent. Here we propose a new type of age clock, one that couples predictivity with interpretability of the underlying biology, achieved through the incorporation of prior knowledge into the model design. The clock, an artificial neural network constructed according to well-described biological pathways, allows the prediction of age from gene expression data of skin tissue with high accuracy, while at the same time capturing and revealing aging states of the pathways driving the prediction. The model recapitulates known associations of aging gene knockdowns in simulation experiments and demonstrates its utility in deciphering the main pathways by which accelerated aging conditions such as Hutchinson–Gilford progeria syndrome, as well as pro-longevity interventions like caloric restriction, exert their effects.
Whole-exome sequencing identifies somatic mutations and intratumor heterogeneity in inflammatory breast cancer
Authors: Luo Rui , Chong Weelic , Wei Qiang , Zhang Zhenchao , Wang Chun , Ye Zhong , Abu-Khalaf Maysa M. , Silver Daniel P. , Stapp Robert T. , Jiang Wei , Myers Ronald E. , Li Bingshan , Cristofanilli Massimo , Yang Hushan
Published: June 2021

Inflammatory breast cancer (IBC) is the most aggressive form of breast cancer. Although it is a rare subtype, IBC is responsible for roughly 10% of breast cancer deaths. In order to obtain a better understanding of the genomic landscape and intratumor heterogeneity (ITH) in IBC, we conducted whole-exome sequencing of 16 tissue samples (12 tumor and four normal samples) from six hormone-receptor-positive IBC patients, analyzed somatic mutations and copy number aberrations, and inferred subclonal structures to demonstrate ITH. Our results showed that KMT2C was the most frequently mutated gene (42%, 5/12 samples), followed by HECTD1, LAMA3, FLG2, UGT2B4, STK33, BRCA2, ACP4, PIK3CA, and DNAH8 (all nine genes tied at 33% frequency, 4/12 samples). Our data indicated that PTEN and FBXW7 mutations may be considered driver gene mutations for IBC. We identified various subclonal structures and different levels of ITH between IBC patients, and mutations in the genes EIF4G3, IL12RB2, and PDE4B may potentially generate ITH in IBC.
Risk of primary lung cancer after adjuvant radiotherapy in breast cancer—a large population-based study
Authors: Wennstig Anna-Karin , Wadsten Charlotta , Garmo Hans , Johansson Mikael , Fredriksson Irma , Blomqvist Carl , Holmberg Lars , Nilsson Greger , Sund Malin
Published: June 2021

Adjuvant radiotherapy (RT) for breast cancer (BC) has been associated with an increased risk of later radiation-induced lung cancer (LC). We examined the risk of primary LC in a population-based cohort of 52300 women treated for BC during 1992 to 2012, and 253796 age-matched women without BC. Cumulative incidence of LC was calculated by the Kaplan–Meier method, and the risk of LC after BC treatment was estimated by Cox proportional hazards regression analyses. Women with BC receiving RT had a higher cumulative incidence of LC compared to women with BC not receiving RT and women without BC. This became apparent 5 years after RT and increased with longer follow-up. Women with BC receiving RT had a Hazard ratio of 1.59 (95% confidence interval 1.37–1.84) for LC compared to women without BC. RT techniques that lower the incidental lung doses, e.g breathing adaption techniques, may lower this risk.
Bone health in spacefaring rodents and primates: systematic review and meta-analysis
Authors: Fu Jingyan , Goldsmith Matthew , Crooks Sequoia D. , Condon Sean F. , Morris Martin , Komarova Svetlana V.
Published: June 2021

Animals in space exploration studies serve both as a model for human physiology and as a means to understand the physiological effects of microgravity. To quantify the microgravity-induced changes to bone health in animals, we systematically searched Medline, Embase, Web of Science, BIOSIS, and NASA Technical reports. We selected 40 papers focusing on the bone health of 95 rats, 61 mice, and 9 rhesus monkeys from 22 space missions. The percentage difference from ground control in rodents was –24.1% [Confidence interval: −43.4, −4.9] for trabecular bone volume fraction and –5.9% [−8.0, −3.8] for the cortical area. In primates, trabecular bone volume fraction was lower by –25.2% [−35.6, −14.7] in spaceflight animals compared to GC. Bone formation indices in rodent trabecular and cortical bone were significantly lower in microgravity. In contrast, osteoclast numbers were not affected in rats and were variably affected in mice. Thus, microgravity induces bone deficits in rodents and primates likely through the suppression of bone formation.
3D cell culture using a clinostat reproduces microgravity-induced skin changes
Authors: Choi Dong Hyun , Jeon Byoungjun , Lim Min Hyuk , Lee Dong Hun , Ye Sang-Kyu , Jeong Seung-Yong , Kim Sungwan
Published: June 2021

Exposure to microgravity affects human physiology in various ways, and astronauts frequently report skin-related problems. Skin rash and irritation are frequent complaints during space missions, and skin thinning has also been reported after returning to Earth. However, spaceflight missions for studying the physiological changes in microgravity are impractical. Thus, we used a previously developed 3D clinostat to simulate a microgravity environment and investigate whether physiological changes of the skin can be reproduced in a 3D in vitro setting. Our results showed that under time-averaged simulated microgravity (taSMG), the thickness of the endothelial cell arrangement increased by up to 59.75%, indicating skin irritation due to vasodilation, and that the diameter of keratinocytes and fibroblast co-cultured spheroids decreased by 6.66%, representing skin thinning. The α1 chain of type I collagen was upregulated, while the connective tissue growth factor was downregulated under taSMG. Cytokeratin-10 expression was significantly increased in the taSMG environment. The clinostat-based 3D culture system can reproduce physiological changes in the skin similar to those under microgravity, providing insight for understanding the effects of microgravity on human health before space exploration.
Phenotype and management of chronic obstructive pulmonary disease patients in general population in China: a nationally cross-sectional study
Authors: Bao Heling , Jia Guohua , Cong Shu , Sun Wanlu , Fan Jing , Wang Ning , Feng Yajing , Wang Baohua , Curtis Jeffrey L. , Wang Linhong , Fang Liwen , Chen Yahong
Published: June 2021

This study aims to investigate the characteristics of the phenotype and management of chronic obstructive pulmonary disease (COPD) patients in the general population in China. We analyzed spirometry-confirmed COPD patients who were identified from a population-based, nationally representative sample in China. All participants were measured with airflow limitation severity based on post-bronchodilator FEV1 percent predicted, bronchodilator responsiveness, exacerbation history, and respiratory symptoms. Among a total of 9134 COPD patients, 90.3% were non-exacerbators, 2.9% were frequent exacerbators without chronic bronchitis, 2.0% were frequent exacerbators with chronic bronchitis, and 4.8% were asthma-COPD overlap. Less than 5% of non-exacerbators ever had pulmonary function testing performed. The utilization rate of inhaled medication in non-exacerbators, exacerbators without chronic bronchitis, exacerbators with chronic bronchitis, and asthma-COPD overlap was 1.4, 23.5, 29.5, and 19.4%, respectively. A comprehensive strategy for the management of COPD patients based on phenotype in primary care is urgently needed.
Next generation of heart regenerative therapies: progress and promise of cardiac tissue engineering
Authors: Tenreiro Miguel F. , Louro Ana F. , Alves Paula M. , Serra Margarida
Published: June 2021

The adult heart is a vital and highly specialized organ of the human body, with limited capability of self-repair and regeneration in case of injury or disease. Engineering biomimetic cardiac tissue to regenerate the heart has been an ambition in the field of tissue engineering, tracing back to the 1990s. Increased understanding of human stem cell biology and advances in process engineering have provided an unlimited source of cells, particularly cardiomyocytes, for the development of functional cardiac muscle, even though pluripotent stem cell-derived cardiomyocytes poorly resemble those of the adult heart. This review outlines key biology-inspired strategies reported to improve cardiomyocyte maturation features and current biofabrication approaches developed to engineer clinically relevant cardiac tissues. It also highlights the potential use of this technology in drug discovery science and disease modeling as well as the current efforts to translate it into effective therapies that improve heart function and promote regeneration.
Engineering aligned human cardiac muscle using developmentally inspired fibronectin micropatterns
Authors: Batalov Ivan , Jallerat Quentin , Kim Sean , Bliley Jacqueline , Feinberg Adam W.
Published: June 2021

Cardiac two-dimensional tissues were engineered using biomimetic micropatterns based on the fibronectin-rich extracellular matrix (ECM) of the embryonic heart. The goal of this developmentally-inspired, in vitro approach was to identify cell–cell and cell-ECM interactions in the microenvironment of the early 4-chambered vertebrate heart that drive cardiomyocyte organization and alignment. To test this, biomimetic micropatterns based on confocal imaging of fibronectin in embryonic chick myocardium were created and compared to control micropatterns designed with 2 or 20 µm wide fibronectin lines. Results show that embryonic chick cardiomyocytes have a unique density-dependent alignment on the biomimetic micropattern that is mediated in part by N-cadherin, suggesting that both cell–cell and cell-ECM interactions play an important role in the formation of aligned myocardium. Human induced pluripotent stem cell-derived cardiomyocytes also showed density-dependent alignment on the biomimetic micropattern but were overall less well organized. Interestingly, the addition of human adult cardiac fibroblasts and conditioning with T3 hormone were both shown to increase human cardiomyocyte alignment. In total, these results show that cardiomyocyte maturation state, cardiomyocyte-cardiomyocyte and cardiomyocyte-fibroblast interactions, and cardiomyocyte-ECM interactions can all play a role when engineering anisotropic cardiac tissues in vitro and provides insight as to how these factors may influence cardiogenesis in vivo.
Drug screening with zebrafish visual behavior identifies carvedilol as a potential treatment for an autosomal dominant form of retinitis pigmentosa
Authors: Ganzen Logan , Ko Mee Jung , Zhang Mengrui , Xie Rui , Chen Yongkai , Zhang Liyun , James Rebecca , Mumm Jeff , van Rijn Richard M. , Zhong Wenxuan , Pang Chi Pui , Zhang Mingzhi , Tsujikawa Motokazu , Leung Yuk Fai
Published: June 2021

Retinitis Pigmentosa (RP) is a mostly incurable inherited retinal degeneration affecting approximately 1 in 4000 individuals globally. The goal of this work was to identify drugs that can help patients suffering from the disease. To accomplish this, we screened drugs on a zebrafish autosomal dominant RP model. This model expresses a truncated human rhodopsin transgene (Q344X) causing significant rod degeneration by 7 days post-fertilization (dpf). Consequently, the larvae displayed a deficit in visual motor response (VMR) under scotopic condition. The diminished VMR was leveraged to screen an ENZO SCREEN-WELL REDOX library since oxidative stress is postulated to play a role in RP progression. Our screening identified a beta-blocker, carvedilol, that ameliorated the deficient VMR of the RP larvae and increased their rod number. Carvedilol may directly on rods as it affected the adrenergic pathway in the photoreceptor-like human Y79 cell line. Since carvedilol is an FDA-approved drug, our findings suggest that carvedilol can potentially be repurposed to treat autosomal dominant RP patients.
Monitoring of transfer and internalization of Escherichia coli from inoculated knives to fresh cut cucumbers (Cucumis sativus L.) using bioluminescence imaging
Authors: Sun Yeting , Zhao Xiaoyan , Xu Xiulan , Ma Yue , Guan Hongyang , Liang Hao , Wang Dan
Published: June 2021

Slicing may cause the risk of cross-contamination in cucumber. In this study, knife inoculated with Escherichia coli (E. coli) was used to cut cucumbers, bioluminescence imaging (BLI) was used to visualize the possible distribution and internalization of E. coli during cutting and storage. Results showed that the initial two slices resulted in greater bacterial transfer. The bacterial transfer exhibited a fluctuating decay trend, E. coli was most distributed at the initial cutting site. The contaminated area on the surface of cucumber slices decreased during the storage period, which can be attributed to the death and internalization of E. coli. The maximum internalization distance of E. coli was about 2–3 mm, and did not further spread after 30 min from inoculation. Hence, our results provide useful information for risk management in both home and industrial environment.
Comparative transcriptome analysis reveals key genes associated with pigmentation in radish (Raphanus sativus L.) skin and flesh
Authors: Zhang Jifang , Zhao Jian , Tan Qunyun , Qiu Xiaojun , Mei Shiyong
Published: June 2021

Radish (Raphanus sativus) is an important vegetable worldwide that exhibits different flesh and skin colors. The anthocyanins responsible for the red and purple coloring in radishes possess nutritional value and pharmaceutical potential. To explore the structural and regulatory networks related to anthocyanin biosynthesis and identify key genes, we performed comparative transcriptome analyses of the skin and flesh of six colored radish accessions. The transcript profiles showed that each accession had a species-specific transcript profile. For radish pigmentation accumulation, the expression levels of anthocyanin biosynthetic genes (RsTT4, RsC4H, RsTT7, RsCCOAMT, RsDFR, and RsLDOX) were significantly upregulated in the red- and purple-colored accessions, but were downregulated or absent in the white and black accessions. The correlation test, combined with metabolome (PCC > 0.95), revealed five structural genes (RsTT4, RsDFR, RsCCOAMT, RsF3H, and RsBG8L) and three transcription factors (RsTT8-1, RsTT8-2, and RsPAR1) to be significantly correlated with flavonoids in the skin of the taproot. Four structural genes (RsBG8L, RsDFR, RsCCOAMT, and RsLDOX) and nine transcription factors (RsTT8-1, RsTT8-2, RsMYB24L, RsbHLH57, RsPAR2L, RsbHLH113L, RsOGR3L, RsMYB24, and RsMYB34L) were found to be significantly correlated with metabolites in the flesh of the taproot. This study provides a foundation for future studies on the gene functions and genetic diversity of radish pigmentation and should aid in the cultivation of new valuable radish varieties.
Comprehensive machine learning based study of the chemical space of herbicides
Authors: Oršolić Davor , Pehar Vesna , Šmuc Tomislav , Stepanić Višnja
Published: June 2021

Widespread use of herbicides results in the global increase in weed resistance. The rotational use of herbicides according to their modes of action (MoAs) and discovery of novel phytotoxic molecules are the two strategies used against the weed resistance. Herein, Random Forest modeling was used to build predictive models and establish comprehensive characterization of structure–activity relationships underlying herbicide classifications according to their MoAs and weed selectivity. By combining the predictive models with herbicide-likeness rules defined by selected molecular features (numbers of H-bond acceptors and donors, logP, topological and relative polar surface area, and net charge), the virtual stepwise screening platform is proposed for characterization of small weight molecules for their phytotoxic properties. The screening cascade was applied on the data set of phytotoxic natural products. The obtained results may be valuable for refinement of herbicide rotational program as well as for discovery of novel herbicides primarily among natural products as a source for molecules of novel structures and novel modes of action and translocation profiles as compared with the synthetic compounds.
Directional changes in Levallois core technologies between Eastern Africa, Arabia, and the Levant during MIS 5
Authors: Blinkhorn James , Groucutt Huw S. , Scerri Eleanor M. L. , Petraglia Michael D. , Blockley Simon
Published: June 2021

Marine Isotope Stage (MIS) 5, ~ 130 to 71 thousand years ago, was a key period for the geographic expansion of Homo sapiens, including engagement with new landscapes within Africa and dispersal into Asia. Occupation of the Levant by Homo sapiens in MIS 5 is well established, while recent research has documented complementary evidence in Arabia. Here, we undertake the first detailed comparison of Levallois core technology from eastern Africa, Arabia, and the Levant during MIS 5, including multiple sites associated with Homo sapiens fossils. We employ quantitative comparisons of individual artefacts that provides a detailed appraisal of Levallois reduction activity in MIS 5, thereby enabling assessment of intra- and inter-assemblage variability for the first time. Our results demonstrate a pattern of geographically structured variability embedded within a shared focus on centripetal Levallois reduction schemes and overlapping core morphologies. We reveal directional changes in core shaping and flake production from eastern Africa to Arabia and the Levant that are independent of differences in geographic or environmental parameters. These results are consistent with a common cultural inheritance between these regions, potentially stemming from a shared late Middle Pleistocene source in eastern Africa.