bluuebunny/crossref_metadata_2025_split huggingface dataset:
Curing genetic skin disease through altered replication stress response
Authors: Miyauchi Toshinari , Suzuki Shotaro , Takeda Masae , Peh Jin Teng , Aiba Masayuki , Natsuga Ken , Fujita Yasuyuki , Takeichi Takuya , Sakamoto Taiko , Akiyama Masashi , Shimizu Hiroshi , Nomura Toshifumi 
Published: August 2020

SummaryRevertant mosaicism, or ‘natural gene therapy’, refers to the spontaneousin vivoreversion of an inherited mutation in a somatic cell1. Only ∼50 human genetic disorders exhibit revertant mosaicism, implicating a distinctive role played by mutant proteins in somatic correction of a pathogenic germline mutation2. However, the process by which mutant proteins induce somatic genetic reversion in these diseases remains unknown. Here we show that heterozygous pathogenicCARD14mutations causing autoinflammatory skin diseases, including psoriasis and pityriasis rubra pilaris, are repaired mainly via homologous recombination. Rather than altering the DNA damage response to exogenous stimuli such as X-irradiation or etoposide treatment, mutant CARD14 increased DNA double-strand breaks under conditions of replication stress. Furthermore, mutant CARD14 suppressed new origin firings without promoting crossover events in the replication stress state. Together, these results suggest that mutant CARD14 alters the replication stress response and preferentially drives break-induced replication (BIR), which is generally suppressed in eukaryotes3. Our results highlight the involvement of BIR in reversion events, thus revealing a previously undescribed role of BIR that could potentially be exploited to develop therapeutics for currently intractable genetic diseases.
Engineered Terpenoid Production inSynechocystissp. PCC 6803 Under Different Growth Conditions
Authors: Herold Ryan A. , Bryan Samantha J. 
Published: August 2020

ABSTRACTTerpenoids are the largest class of natural products and have applications in a wide variety of industries. Many terpenoids can be chemically synthesized or extracted from plants, but this is often uneconomical or unsustainable. An alternative production method relies on the heterologous expression of terpene synthase enzymes in cyanobacteria, producing the desired compounds directly from carbon dioxide. In this work, a patchoulol synthase enzyme fromPogostemon cablin(patchouli) was expressed in the cyanobacteriumSynechocystissp. PCC 6803 under four different growth conditions. Final yields of patchoulol from each growth condition were as follows: 249 μg L−1, photoautotrophic growth; 6.5 μg L−1, mixotrophic growth; 27.6 μg L−1, bicarbonate low light; 31.7 μg L−1, bicarbonate high light. By comparing patchoulol production across growth conditions, we identified a significant positive correlation between the production of photopigments (chlorophyll and carotenoids) and the production of patchoulol. Importantly, this relationship was found to be stronger than the correlation between cell density and patchoulol production across growth conditions, which was not statistically significant. The relationship between photopigments and patchoulol should be generalizable to the production of other terpenoids that rely on expression of the endogenous methylerythritol phosphate (MEP) pathway in cyanobacteria. Based on the results of this work, we propose a strategy for maximizing terpenoid production in cyanobacteria by optimizing growth conditions for photopigment production, resulting in increased flux through the MEP pathway. This strategy has the advantage of facile photopigment quantification using simple spectroscopic methods, and optimized growth conditions can be utilized in partnership with conventional terpenoid production strategies to further improve yields.
Identification of Cis-Regulatory Sequences Controlling Pollen-Specific Expression of Hydroxyproline-Rich Glycoprotein Genes inArabidopsis thaliana
Authors: Li Yichao , Mullin Maxwell , Zhang Yingnan , Drews Frank , Welch Lonnie , Showalter Allan 
Published: August 2020

ABSTRACTHydroxyproline-rich glycoproteins (HRGPs) are a superfamily of plant cell wall structural proteins that function in various aspects of plant growth and development, including pollen tube growth. We have previously characterized HRGP superfamily into three family members: the hyperglycosylated arabinogalactan-proteins, the moderately glycosylated extensins, and the lightly glycosylated proline-rich proteins. However, the mechanism of pollen-specific HRGP expression remains untouched. To this end, we developed an integrative analysis pipeline combining RNA-seq gene expression and promoter sequences that identified 15 transcriptional cis-regulatory motifs responsible for pollen-specific expression of HRGP inArabidopsis Thaliana. Specifically, we mined the public RNA-seq datasets and identified 13 pollen-specific HRGP genes. Ensemble motif discovery with various filters identified 15 conserved promoter elements betweenThalianaandLyrata. Known motif analysis revealed pollen related transcription factors of GATA12 and brassinosteroid (BR) signaling pathway regulator BZR1. Lastly, we performed a machine learning regression analysis and demonstrated that the identified 15 motifs well captured the HRGP gene expression in pollen (R=0.61). In conclusion, we performed the integrative analysis as the first-of-its-kind study to identify cis-regulatory motifs in pollen-specific HRGP genes and shed light on its transcriptional regulation in pollen.
Brassica napusL. dwarfing gene: Determining candidate intervals of dwarfing genes by BSA and SNP typing
Authors: Jing Luo , Chao Li , Ruimao Zhang , Zhineng Chen , Xianqiang Zhang , Zhihong Gao , Lei Lei , Pan Li 
Published: August 2020

AbstractThe plant height of rapeseed is one of the important factors that affects the production of rapeseed. If the plant height of rapeseed is too high, on the one hand, it will cause rapeseed to lodge and affect the yield, on the other hand, it will also affect the mechanized harvesting of rapeseed. In this research, the high-stalked line (YY50) and the dwarfed line (DW871) are crossed to obtain an F2 rapeseed population which was used to build pools, and then we used this to mine the main dwarfing genes. In the pools composed of tall and short stalks, we obtained 192.80Mb clean reads, which can be used for BSA (bulked segregant analysis). Preliminary positioning around the candidate section identified 23 SNP markers. Then 17 polymorphic SNP markers were obtained through polymorphism screening. Further we narrowed the candidate interval, and finally determined between 15.51-16.60Mb of ChrA10. Through identifying 231 genes from the above interval, it’s predicted that the production of dwarf traits may be related to lignin synthesis and limited inflorescence. It provides a basis for further mapping and cloning of the dwarfing gene DW871.
Aquaporin-3 regulates endosome-to-cytosol transfer via lipid peroxidation for cross presentation
Authors: Nalle Sam C. , da Silva Rosa Barreira , Zhang Hua , Decker Markus , Chalouni Cecile , Xu Min , Posthuma George , de Mazière Ann , Klumperman Judith , Baz Morelli Adriana , Fleire Sebastian J. , Verkman Alan S. , Trombetta E. Sergio , Albert Matthew L. , Mellman Ira 
Published: August 2020

ABSTRACTAntigen cross presentation, whereby exogenous antigens are presented by MHC class I molecules to CD8+ T cells, is essential for generating adaptive immunity to pathogens and tumor cells (1). Following endocytosis, it is widely understood that protein antigens must be transferred from endosomes to the cytosol where they are subject to ubiquitination and proteasome degradation prior to being translocated into the endoplasmic reticulum (ER), or possibly endosomes, via the TAP1/TAP2 complex (2, 3). Revealing how antigens egress from endocytic organelles (endosome-to-cytosol transfer, ECT), however, has proved vexing. Here, we used two independent screens to identify the hydrogen peroxide-transporting channel aquaporin-3 (AQP3) as a regulator of ECT. AQP3 overexpression increased ECT, whereas AQP3 knockout or knockdown decreased ECT. Mechanistically, AQP3 appears to be important for hydrogen peroxide entry into the endosomal lumen where it affects lipid peroxidation and subsequent antigen release. AQP3-mediated regulation of ECT was functionally significant, as AQP3 modulation had a direct impact on the efficiency of antigen cross presentationin vitro. Finally,AQP3-/-mice exhibited a reduced ability to mount an anti-viral response and cross present exogenous extended peptide. Together, these results indicate that the AQP3-mediated transport of hydrogen peroxide can regulate endosomal lipid peroxidation and suggest that compromised membrane integrity and coordinated release of endosomal cargo is a likely mechanism for ECT.
MicroRNA-1 promotes the development of and prolongs engorgement time inHyalomma anatolicum anatolicum(Acari: Ixodidae) ticks
Authors: Luo Jin , Ren Qiaoyun , Liu Wenge , Qiu Xiaofei , Zhang Gaofeng , Tan Yangchun , Cao Runlai , Yin Hong , Luo Jianxun , Li Xiangrui , Liu Guangyuan 
Published: August 2020

AbstractMicroRNAs act as mRNA posttranscriptional regulators, playing important roles in cell differentiation, transcriptional regulation, growth and development. In this study, microRNA expression profiles ofHyalomma anatolicum anatolicumticks at different developmental stages were detected by high-throughput sequencing and functionally assessed. In total, 2,585,169, 1,252,678, 1,558,217 and 1,155,283 unique reads were obtained from eggs, larvae, nymphs and adults, respectively, with 42, 46, 45 and 41 conserved microRNAs in these stages, respectively. Using eggs as a control, 48, 43 and 39 microRNAs were upregulated and 3, 10 and 9 downregulated in larvae, nymphs and adults, respectively. microRNA-1 (miR-1) was expressed in high abundance throughoutHa. anatolicumdevelopment, with an average of nearly one million transcripts, and it is highly conserved among tick species. Quantitative real-time PCR (qPCR) showed that miR-1 expression gradually increased with tick development, reaching the highest level at engorgement. Differential tissue expression was detected, with significantly higher levels in the salivary glands and epidermis than in the midgut. Inhibition assays showed no significant change in body weight or spawning time or amount between experimental and control groups, but there was a significant difference (p<0.01) in engorgement time. With miR-1 inhibition, ticks displayed obvious deformities during later development. To more fully explain the microRNA mechanism of action, the miR-1 family was analyzed regarding target gene; members acting on Hsp60 include miR-5, miR-994, miR-969, and miR-1011, which jointly play a role. Therefore, microRNAs are critical for normal tick development, and the primary structure of the mature sequence of miR-1 is highly conserved. Nonetheless, different developmental stages and tissues show different expression patterns, with a certain role in prolonging feeding. miR-1, together with other family members, regulates mRNA function and may be used as a molecular marker for species origin and evolution analysis and internal reference gene selection.
Poliovirus-nonsusceptible Vero cell line for the World Health Organization global action plan
Authors: Okemoto-Nakamura Yuko , Someya Kenji , Yamaji Toshiyuki , Saito Kyoko , Takeda Makoto , Hanada Kentaro 
Published: August 2020

AbstractPolio or poliomyelitis is a disabling and life-threatening disease caused by poliovirus (PV). As a consequence of global polio vaccination efforts, wild PV serotype 2 has been eradicated, and wild PV serotypes 1- and 3-transmitted cases have been largely eliminated except for in limited regions around the world. However, vaccine-derived PV, pathogenically reverted live PV vaccine strains in vaccinated humans, has become a serious issue. For the global eradication of polio, the World Health Organization is conducting the third edition of the Global Action Plan, which is requesting stringent control of potentially PV-infected materials. To facilitate the mission, we generated a PV-nonsusceptible Vero cell subline, which may serve as an ideal replacement of standard Vero cells to isolate emerging/re-emerging viruses without the risk of generating PV-infected materials.
Vascular control of the CO2/H+dependent drive to breathe
Authors: Cleary CM , Moreira TS , Takakura AC , Nelson MT , Longden TA , Mulkey DK 
Published: August 2020

AbstractRespiratory chemoreceptors regulate breathing in response to changes in tissue CO2/H+. Blood flow is a fundamental determinant of tissue CO2/H+, yet little is known regarding how regulation of vascular tone in chemoreceptor regions contributes to respiratory behavior. Previously, we showed in rat that CO2/H+-vasoconstriction in the retrotrapezoid nucleus (RTN) supports chemoreception by a purinergic-dependent mechanism (Hawkins et al. 2017). Here, we show in mice that CO2/H+dilates arterioles in other chemoreceptor regions, thus demonstrating CO2/H+vascular reactivity in the RTN is unique. We also identify P2Y2receptors in RTN smooth muscle cells as the substrate responsible for this response. Specifically, pharmacological blockade or genetic deletion of P2Y2from smooth muscle cells blunted the ventilatory response to CO2, and re-expression of P2Y2receptors only in RTN smooth muscle cells fully rescued the CO2/H+chemoreflex. These results identify P2Y2receptors in RTN smooth muscle cells as requisite determinants of respiratory chemoreception.Significance StatementDisruption of vascular control as occurs in cardiovascular disease leads to compromised chemoreceptor function and unstable breathing. Despite this, virtually nothing is known regarding how regulation of vascular tone in chemoreceptor regions contributes to respiratory behavior. Here, we identify P2Y2receptors in RTN vascular smooth muscle cells as a novel vascular element of respiratory chemoreception. Identification of this mechanism may facilitate development of treatments for breathing problems including those associated with cardiovascular disease.
The Response of Bacterial Flagellar Motor to Stepwise Increase in NaCl Concentration
Authors: Soman V. , Kumari S. , Nath S. , Elangovan R. 
Published: August 2020

AbstractMany species of bacteria use flagella to navigate in its environment. The flagellum is a 7-10 μm long helical filament with a rotary motor at its base embedded in the cell membrane and almost a dozen stator complexes. Proton motive force across the cell membrane powers the flagellar motors ofE.coliandSalmonella. The motor stochastically switches between clockwise and counter-clockwise direction. A chemotaxis system causes the motor to change its direction, but the process is more complex as the switch is sensitive to load and proton motive force as well. NaCl is significant with regard to the flagellar motor as it affects the stator dynamics, proton motive force, and osmotaxis at higher concentration. Chemotaxis helps the bacteria for its growth and survival.E.coli’s natural habitat has high osmolarity and the organism uses use various mechanisms for osmoregulation. However, the role of flagellar motor to adapt to the changes in osmolarity, or osmotaxis, is not well studied. In this work, we dissipated the membrane potential of bacteria in pH 7 using step-wise increase in concentration of NaCl in motility buffer and studied the output of E.coli’s flagellar motor using tethered bead assay and swimming Salmonella enteritidis cells. We observed decrease in motor speed and switching rates with stepwise increase in NaCl concentration in the motility buffer. The mean speed of the motors decreased with NaCl concentration. The population of swimming cells tumbled more with increase in concentration of NaCl. At the single motor level, the motors biased to CCW rotation with decrease in membrane potential. In this study, we present our observations of the flagellar motor in high NaCl concentration, and explore how NaCl can be used to study various aspects of the bacterial flagellar motor.Statement of significanceSodium ion has been significant in the both the cellular energetics and the function of bacterial flagellar motor. Growing evidence show that the effect of sodium ions was not what hitherto thought it would be. It is involved in the sodium energetics, dissipate membrane potential, affect the flagellar stator dynamics of bacteria. Being an osmolyte, it influences the osmotaxis of bacteria. In this work, we studied the effect of NaCl on the response of the single bacterial flagellar motor ofE.coliand swimming cells ofSalmonella enteritidis. We observed that the effect of NaCl on the output of the flagellar motor was significant and it may affect the cells in various ways.
Collaboration of multiple pathways in making a compound leaf
Authors: Israeli Alon , Ben-Herzel Ori , Burko Yogev , Shwartz Ido , Ben-Gera Hadas , Harpaz-Saad Smadar , Bar Maya , Efroni Idan , Ori Naomi 
Published: August 2020

SummaryThe variability in leaf form in nature is immense. Leaf patterning occurs by differential growth that occurs during a limited window of morphogenetic activity at the leaf marginal meristem. While many regulators have been implicated in the designation of the morphogenetic window and in leaf patterning, how these effectors interact to generate a particular form is still not well understood.We addressed the interaction among different effectors of tomato compound leaf development, using genetic and molecular analyses.Mutations in the tomato auxin response factor SlARF5/SlMP, which promotes leaflet formation, suppressed the increased leaf complexity of mutants with extended morphogenetic window. Impaired activity of the NAC/CUC transcription factor GOBLET (GOB), which specifies leaflet boundaries, also reduced leaf complexity in these backgrounds. Analysis of genetic interactions showed that the patterning factors SlMP, GOBand the MYB transcription factor LYRATE (LYR) act in parallel to promote leaflet formation.This work places an array of developmental regulators in a morphogenetic context. It reveals how organ-level differentiation rate and local growth are coordinated to sculpture an organ. These concepts and findings are applicable to other plant species and developmental processes that are regulated by patterning and differentiation.
What evolutionary processes maintain MHCIIβ diversity within and among populations of stickleback?
Authors: Peng Foen , Ballare Kimberly M. , Woodard S. Hollis , den Haan Stijn , Bolnick Daniel I. 
Published: August 2020

AbstractMajor Histocompatibility Complex (MHC) genes encode for proteins that recognize foreign protein antigens to initiate T-cell mediated adaptive immune responses. They are often the most polymorphic genes in vertebrate genomes. How evolution maintains this diversity is still an unsettled issue. Three main hypotheses seek to explain the maintenance of MHC diversity by invoking pathogen-mediated selection: heterozygote advantage, frequency-dependent selection, and fluctuating selection across landscapes or through time. Here, we use a large-scale field parasite survey in a stickleback metapopulation to test predictions derived from each of these hypotheses. We identify over a thousand MHCIIβ alleles and find that many of them covary positively or negatively with parasite load, suggesting that these genes contribute to resistance or susceptibility. However, despite our large sample-size, we find no evidence for the widely-cited stabilizing selection on MHC heterozygosity, in which individuals with an intermediate number of MHC alleles have the lowest parasite burden. Nor do we observe a rare-allele advantage, or widespread fluctuating selection across populations. In contrast, we find that MHC diversity is best predicted by neutral genome-wide heterozygosity and between-population genomic divergence, suggesting neutral processes are important in shaping the pattern of metapopulation MHC diversity. Thus, although MHCIIβ is highly diverse and relevant to the type and intensity of macroparasite infection in these populations of stickleback, the main models of MHC evolution still provide little explanatory power in this system.
Is there any incremental benefit to conducting neuroimaging and neurocognitive assessments in the diagnosis of ADHD in young children? A machine learning investigation
Authors: Öztekin Ilke , Finlayson Mark A. , Graziano Paulo A. , Dick Anthony S. 
Published: August 2020

ABSTRACTGiven the negative trajectories of early behavior problems associated with Attention-Deficit/Hyperactivity Disorder (ADHD), early diagnosis of ADHD is considered critical to enable early intervention and treatment. To this end, the current investigation employed machine learning to evaluate the relative predictive value of parent/teacher ratings, as well as behavioral and neural measures of executive function in predicting ADHD diagnostic category in a sample consisting of 162 young children (53.7% ADHD, ages 4 to 7, mean age 5.55, 67.9% male, 82.6% Hispanic/Latino). Among all the target measures assessed in the study, teacher ratings of executive function were identified as by far the most important measure in predicting ADHD diagnostic category. While a more extensive evaluation of neural measures, such as diffusion-weighted imaging, may provide more information as they relate to the underlying cognitive deficits associated with ADHD, the current study indicates that commonly used structural imaging measures of cortical thickness, as well as widely used cognitive measures of executive function, have little incremental value in differentiating typically developing children from those diagnosed with ADHD. Future research evaluating the importance of such measures in predicting children’s functional impairment in academic and social areas would provide additional insight into their contributing role in ADHD.
Inferring protein sequence-function relationships with large-scale positive-unlabeled learning
Authors: Song Hyebin , Bremer Bennett J. , Hinds Emily C. , Raskutti Garvesh , Romero Philip A. 
Published: August 2020

SummaryMachine learning can infer how protein sequence maps to function without requiring a detailed understanding of the underlying physical or biological mechanisms. It’s challenging to apply existing supervised learning frameworks to large-scale experimental data generated by deep mutational scanning (DMS) and related methods. DMS data often contain high dimensional and correlated sequence variables, experimental sampling error and bias, and the presence of missing data. Importantly, most DMS data do not contain examples of negative sequences, making it challenging to directly estimate how sequence affects function. Here, we develop a positive-unlabeled (PU) learning framework to infer sequence-function relationships from large-scale DMS data. Our PU learning method displays excellent predictive performance across ten large-scale sequence-function data sets, representing proteins of different folds, functions, and library types. The estimated parameters pinpoint key residues that dictate protein structure and function. Finally, we apply our statistical sequence-function model to design highly stabilized enzymes.