bluuebunny/crossref_metadata_2025_split huggingface dataset:
Minor alleles are associated with white rust (Albugo occidentalis) susceptibility in spinach (Spinacia oleracea)
Authors: Awika Henry O. , Marconi Thiago G. , Bedre Renesh , Mandadi Kranthi K. , Avila Carlos A. 
Published: December 2019

AbstractMinor alleles (MA) have been associated with disease incidence in human studies, enabling the identification of diagnostic risk factors for various diseases. However, allelic mapping has rarely been performed in plant systems. The goal of this study was to determine whether a difference in MA prevalence is a strong enough risk factor to indicate a likely significant difference in disease resistance against white rust (WR;Albugo occidentalis) in spinach (Spinacia oleracea). We used WR disease severity ratings (WR-DSRs) in a diversity panel of 267 spinach accessions to define resistant- and susceptibility-associated groups within the distribution scores and then tested the single-nucleotide polymorphism (SNP) variants to interrogate the MA prevalence in the most susceptible (MS) vs. most resistant (MR) individuals using permutation-based allelic association tests. A total of 448 minor alleles associated with WR severity were identified in the comparison between the 25% MS and the 25% MR accessions, while the MA were generally similar between the two halves of the interquartile range. The minor alleles in the MS group were distributed across all six chromosomes and made up ~71% of the markers that were also strongly associated with WR in parallel performed genome-wide association study. These results indicate that susceptibility may be highly determined by the disproportionate overrepresentation of minor alleles, which could be used to select for resistant plants. Furthermore, by focusing on the distribution tails, allelic mapping could be used to identify plant markers associated with quantitative traits on the most informative segments of the phenotypic distribution.
Global analysis of lysine succinylation in patchouli plant leaves
Authors: Wang Xiaobing , Chen Xiuzhen , Li Junren , Zhou Xuanxuan , Liu Yanting , Zhong Liting , Tang Yun , Zheng Hai , Liu Jiyun , Zhan Ruoting , Chen Likai 
Published: December 2019

AbstractLysine succinylation is a novel, naturally occurring posttranslational modification (PTM) in living organisms. Global lysine succinylation identification has been performed at the proteomic level in various species; however, the study of lysine succinylation in plant species is relatively limited. Patchouli plant (P. cablin (Blanco) Benth., Lamiaceae) is a globally important industrial plant and medicinal herb. In the present study, lysine succinylome analysis was carried out in patchouli plants to determine the potential regulatory role of lysine succinylation in patchouli growth, development, and physiology. The global succinylation sites and proteins in patchouli plants were screened with an immunoprecipitation affinity enrichment technique and advanced mass spectrometry-based proteomics. Several bioinformatic analyses, such as function classification and enrichment, subcellular location predication, metabolic pathway enrichment and protein−protein interaction networking, were conducted to characterize the functions of the identified sites and proteins. In total, 1097 succinylation sites in 493 proteins were detected in patchouli plants, among which 466 succinylation sites in 241 proteins were repeatedly identified within three independent experiments. The functional characterization of these proteins indicated that the tricarboxylic acid (TCA) cycle, oxidative phosphorylation, photosynthesis processes, and amino acid biosynthesis may be regulated by lysine succinylation. In addition, these succinylated proteins showed a wide subcellular location distribution, although the chloroplast and cytoplasm were the top two preferred cellular components. Our study suggested the important role of lysine succinylation in patchouli plant physiology and biology and could serve as a useful reference for succinylation studies in other medicinal plants.
A detached petal disc assay and virus-induced gene silencing facilitate the study of Botrytis cinerea resistance in rose flowers
Authors: Cao Xiaoqian , Yan Huijun , Liu Xintong , Li Dandan , Sui Mengjie , Wu Jie , Yu Hongqiang , Zhang Zhao 
Published: December 2019

AbstractFresh-cut roses (Rosa hybrida) are one of the most important ornamental crops worldwide, with annual trade in the billions of dollars. Gray mold disease caused by the pathogen Botrytis cinerea is the most serious fungal threat to cut roses, causing extensive postharvest losses. In this study, we optimized a detached petal disc assay (DPDA) for artificial B. cinerea inoculation and quantification of disease symptoms in rose petals. Furthermore, as the identification of rose genes involved in B. cinerea resistance could provide useful genetic and genomic resources, we devised a virus-induced gene silencing (VIGS) procedure for the functional analysis of B. cinerea resistance genes in rose petals. We used RhPR10.1 as a reporter of silencing efficiency and found that the rose cultivar ‘Samantha’ showed the greatest decrease in RhPR10.1 expression among the cultivars tested. To determine whether jasmonic acid and ethylene are required for B. cinerea resistance in rose petals, we used VIGS to silence the expression of RhLOX5 and RhEIN3 (encoding a jasmonic acid biosynthesis pathway protein and an ethylene regulatory protein, respectively) and found that petal susceptibility to B. cinerea was affected. Finally, a VIGS screen of B. cinerea-induced rose transcription factors demonstrated the potential benefits of this method for the high-throughput identification of gene function in B. cinerea resistance. Collectively, our data show that the combination of the DPDA and VIGS is a reliable and high-throughput method for studying B. cinerea resistance in rose.
PbGA2ox8 induces vascular-related anthocyanin accumulation and contributes to red stripe formation on pear fruit
Authors: Zhai Rui , Wang Zhigang , Yang Chengquan , Lin-Wang Kui , Espley Richard , Liu Jianlong , Li Xieyu , Wu Zhongying , Li Pengmin , Guan Qingmei , Ma Fengwang , Xu Lingfei 
Published: December 2019

AbstractFruit with stripes, which are generally longitudinal, can occur naturally, but the bioprocesses underlying this phenomenon are unclear. Previously, we observed an atypical anthocyanin distribution that caused red-striped fruit on the spontaneous pear bud sport “Red Zaosu” (Pyrus bretschneideri Rehd.). In this study, comparative transcriptome analysis of the sport and wild-type “Zaosu” revealed that this atypical anthocyanin accumulation was tightly correlated with abnormal overexpression of the gene-encoding gibberellin (GA) 2-beta-dioxygenase 8, PbGA2ox8. Consistently, decreased methylation was also observed in the promoter region of PbGA2ox8 from “Red Zaosu” compared with “Zaosu”. Moreover, the GA levels in “Red Zaosu” seedlings were lower than those in “Zaosu” seedlings, and the application of exogenous GA4 reduced abnormal anthocyanin accumulation in “Red Zaosu”. Transient overexpression of PbGA2ox8 reduced the GA4 level and caused anthocyanin accumulation in pear fruit skin. Moreover, the presence of red stripes indicated anthocyanin accumulation in the hypanthial epidermal layer near vascular branches (VBs) in “Red Zaosu”. Transient overexpression of PbGA2ox8 resulting from vacuum infiltration induced anthocyanin accumulation preferentially in calcium-enriched areas near the vascular bundles in pear leaves. We propose a fruit-striping mechanism, in which the abnormal overexpression of PbGA2ox8 in “Red Zaosu” induces the formation of a longitudinal array of anthocyanin stripes near vascular bundles in fruit.
Photoresponsive spiro-polymers generated in situ by C–H-activated polyspiroannulation
Authors: Han Ting , Yao Zhanshi , Qiu Zijie , Zhao Zheng , Wu Kaiyi , Wang Jianguo , Poon Andrew W. , Lam Jacky W. Y. , Tang Ben Zhong 
Published: December 2019

AbstractThe development of facile and efficient polymerizations toward functional polymers with unique structures and attractive properties is of great academic and industrial significance. Here we develop a straightforward C–H-activated polyspiroannulation route to in situ generate photoresponsive spiro-polymers with complex structures. The palladium(II)-catalyzed stepwise polyspiroannulations of free naphthols and internal diynes proceed efficiently in dimethylsulfoxide at 120 °C without the constraint of apparent stoichiometric balance in monomers. A series of functional polymers with multisubstituted spiro-segments and absolute molecular weights of up to 39,000 are produced in high yields (up to 99%). The obtained spiro-polymers can be readily fabricated into different well-resolved fluorescent photopatterns with both turn-off and turn-on modes based on their photoinduced fluorescence change. Taking advantage of their photoresponsive refractive index, we successfully apply the polymer thin films in integrated silicon photonics techniques and achieve the permanent modification of resonance wavelengths of microring resonators by UV irradiation.
Genome-wide CRISPR screen identifies ELP5 as a determinant of gemcitabine sensitivity in gallbladder cancer
Authors: Xu Sunwang , Zhan Ming , Jiang Cen , He Min , Yang Linhua , Shen Hui , Huang Shuai , Huang Xince , Lin Ruirong , Shi Yongheng , Liu Qiang , Chen Wei , Mohan Man , Wang Jian 
Published: December 2019

AbstractGemcitabine is the first-line treatment for locally advanced and metastatic gallbladder cancer (GBC), but poor gemcitabine response is universal. Here, we utilize a genome-wide CRISPR screen to identify that loss of ELP5 reduces the gemcitabine-induced apoptosis in GBC cells in a P53-dependent manner through the Elongator complex and other uridine 34 (U34) tRNA-modifying enzymes. Mechanistically, loss of ELP5 impairs the integrity and stability of the Elongator complex to abrogate wobble U34 tRNA modification, and directly impedes the wobble U34 modification-dependent translation of hnRNPQ mRNA, a validated P53 internal ribosomal entry site (IRES) trans-acting factor. Downregulated hnRNPQ is unable to drive P53 IRES-dependent translation, but rescuing a U34 modification-independent hnRNPQ mutant could restore P53 translation and gemcitabine sensitivity in ELP5-depleted GBC cells. GBC patients with lower ELP5, hnRNPQ, or P53 expression have poor survival outcomes after gemcitabine chemotherapy. These results indicate that the Elongator/hnRNPQ/P53 axis controls gemcitabine sensitivity in GBC cells.
Magnetic field-tuned Fermi liquid in a Kondo insulator
Authors: Kushwaha Satya K. , Chan Mun K. , Park Joonbum , Thomas S. M. , Bauer Eric D. , Thompson J. D. , Ronning F. , Rosa Priscila F. S. , Harrison Neil 
Published: December 2019

AbstractKondo insulators are expected to transform into metals under a sufficiently strong magnetic field. The closure of the insulating gap stems from the coupling of a magnetic field to the electron spin, yet the required strength of the magnetic field–typically of order 100 T–means that very little is known about this insulator-metal transition. Here we show that Ce$${}_{3}$$

3

Bi$${}_{4}$$

4

Pd$${}_{3}$$

3

, owing to its fortuitously small gap, provides an ideal Kondo insulator for this investigation. A metallic Fermi liquid state is established above a critical magnetic field of only $${B}_{{\rm{c}}}\approx$$

B

c

≈
11 T. A peak in the strength of electronic correlations near $${B}_{{\rm{c}}}$$

B

c

, which is evident in transport and susceptibility measurements, suggests that Ce$${}_{3}$$

3

Bi$${}_{4}$$

4

Pd$${}_{3}$$

3

may exhibit quantum criticality analogous to that reported in Kondo insulators under pressure. Metamagnetism and the breakdown of the Kondo coupling are also discussed.
Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea
Authors: Zhu Qiyun , Mai Uyen , Pfeiffer Wayne , Janssen Stefan , Asnicar Francesco , Sanders Jon G. , Belda-Ferre Pedro , Al-Ghalith Gabriel A. , Kopylova Evguenia , McDonald Daniel , Kosciolek Tomasz , Yin John B. , Huang Shi , Salam Nimaichand , Jiao Jian-Yu , Wu Zijun , Xu Zhenjiang Z. , Cantrell Kalen , Yang Yimeng , Sayyari Erfan , Rabiee Maryam , Morton James T. , Podell Sheila , Knights Dan , Li Wen-Jun , Huttenhower Curtis , Segata Nicola , Smarr Larry , Mirarab Siavash , Knight Rob 
Published: December 2019

AbstractRapid growth of genome data provides opportunities for updating microbial evolutionary relationships, but this is challenged by the discordant evolution of individual genes. Here we build a reference phylogeny of 10,575 evenly-sampled bacterial and archaeal genomes, based on a comprehensive set of 381 markers, using multiple strategies. Our trees indicate remarkably closer evolutionary proximity between Archaea and Bacteria than previous estimates that were limited to fewer “core” genes, such as the ribosomal proteins. The robustness of the results was tested with respect to several variables, including taxon and site sampling, amino acid substitution heterogeneity and saturation, non-vertical evolution, and the impact of exclusion of candidate phyla radiation (CPR) taxa. Our results provide an updated view of domain-level relationships.
Sustainable polycarbonate adhesives for dry and aqueous conditions with thermoresponsive properties
Authors: Beharaj Anjeza , McCaslin Ethan Z. , Blessing William A. , Grinstaff Mark W. 
Published: December 2019

AbstractPressure sensitive adhesives are ubiquitous in commodity products such as tapes, bandages, labels, packaging, and insulation. With single use plastics comprising almost half of yearly plastic production, it is essential that the design, synthesis, and decomposition products of future materials, including polymer adhesives, are within the context of a healthy ecosystem along with comparable or superior performance to conventional materials. Here we show a series of sustainable polymeric adhesives, with an eco-design, that perform in both dry and wet environments. The terpolymerization of propylene oxide, glycidyl butyrate, and CO2, catalyzed by a cobalt salen complex bearing a quaternary ammonium salt, yields the poly(propylene-co-glycidyl butyrate carbonate)s (PPGBC)s. This polymeric adhesive system, composed of environmentally benign building blocks, implements carbon dioxide sequestration techniques, poses minimal environmental hazards, exhibits varied peel strengths from scotch tape to hot-melt wood-glue, and adheres to metal, glass, wood, and Teflon® surfaces.
Weyl-like points from band inversions of spin-polarised surface states in NbGeSb
Authors: Marković I. , Hooley C. A. , Clark O. J. , Mazzola F. , Watson M. D. , Riley J. M. , Volckaert K. , Underwood K. , Dyer M. S. , Murgatroyd P. A. E. , Murphy K. J. , Fèvre P. Le , Bertran F. , Fujii J. , Vobornik I. , Wu S. , Okuda T. , Alaria J. , King P. D. C. 
Published: December 2019

AbstractBand inversions are key to stabilising a variety of novel electronic states in solids, from topological surface states to the formation of symmetry-protected three-dimensional Dirac and Weyl points and nodal-line semimetals. Here, we create a band inversion not of bulk states, but rather between manifolds of surface states. We realise this by aliovalent substitution of Nb for Zr and Sb for S in the ZrSiS family of nonsymmorphic semimetals. Using angle-resolved photoemission and density-functional theory, we show how two pairs of surface states, known from ZrSiS, are driven to intersect each other near the Fermi level in NbGeSb, and to develop pronounced spin splittings. We demonstrate how mirror symmetry leads to protected crossing points in the resulting spin-orbital entangled surface band structure, thereby stabilising surface state analogues of three-dimensional Weyl points. More generally, our observations suggest new opportunities for engineering topologically and symmetry-protected states via band inversions of surface states.
Seawater softening of suture zones inhibits fracture propagation in Antarctic ice shelves
Authors: Kulessa Bernd , Booth Adam D. , O’Leary Martin , McGrath Daniel , King Edward C. , Luckman Adrian J. , Holland Paul R. , Jansen Daniela , Bevan Suzanne L. , Thompson Sarah S. , Hubbard Bryn 
Published: December 2019

AbstractSuture zones are abundant on Antarctic ice shelves and widely observed to impede fracture propagation, greatly enhancing ice-shelf stability. Using seismic and radar observations on the Larsen C Ice Shelf of the Antarctic Peninsula, we confirm that such zones are highly heterogeneous, consisting of multiple meteoric and marine ice bodies of diverse provenance fused together. Here we demonstrate that fracture detainment is predominantly controlled by enhanced seawater content in suture zones, rather than by enhanced temperature as previously thought. We show that interstitial seawater can reduce fracture-driving stress by orders of magnitude, promoting both viscous relaxation and the development of micro cracks, the incidence of which scales inversely with stress intensity. We show how simple analysis of viscous buckles in ice-penetrating radar data can quantify the seawater content of suture zones and their modification of the ice-shelf’s stress regime. By limiting fracture, enhancing stability and restraining continental ice discharge into the ocean, suture zones act as vital regulators of Antarctic mass balance.
Re-annotation of 191 developmental and epileptic encephalopathy-associated genes unmasks de novo variants in SCN1A
Authors: Steward Charles A. , Roovers Jolien , Suner Marie-Marthe , Gonzalez Jose M. , Uszczynska-Ratajczak Barbara , Pervouchine Dmitri , Fitzgerald Stephen , Viola Margarida , Stamberger Hannah , Hamdan Fadi F. , Ceulemans Berten , Leroy Patricia , Nava Caroline , Lepine Anne , Tapanari Electra , Keiller Don , Abbs Stephen , Sanchis-Juan Alba , Grozeva Detelina , Rogers Anthony S. , Diekhans Mark , Guigó Roderic , Petryszak Robert , Minassian Berge A. , Cavalleri Gianpiero , Vitsios Dimitrios , Petrovski Slavé , Harrow Jennifer , Flicek Paul , Lucy Raymond F. , Lench Nicholas J. , Jonghe Peter De , Mudge Jonathan M. , Weckhuysen Sarah , Sisodiya Sanjay M. , Frankish Adam 
Published: December 2019

AbstractThe developmental and epileptic encephalopathies (DEE) are a group of rare, severe neurodevelopmental disorders, where even the most thorough sequencing studies leave 60–65% of patients without a molecular diagnosis. Here, we explore the incompleteness of transcript models used for exome and genome analysis as one potential explanation for a lack of current diagnoses. Therefore, we have updated the GENCODE gene annotation for 191 epilepsy-associated genes, using human brain-derived transcriptomic libraries and other data to build 3,550 putative transcript models. Our annotations increase the transcriptional ‘footprint’ of these genes by over 674 kb. Using SCN1A as a case study, due to its close phenotype/genotype correlation with Dravet syndrome, we screened 122 people with Dravet syndrome or a similar phenotype with a panel of exon sequences representing eight established genes and identified two de novo SCN1A variants that now - through improved gene annotation - are ascribed to residing among our exons. These two (from 122 screened people, 1.6%) molecular diagnoses carry significant clinical implications. Furthermore, we identified a previously classified SCN1A intronic Dravet syndrome-associated variant that now lies within a deeply conserved exon. Our findings illustrate the potential gains of thorough gene annotation in improving diagnostic yields for genetic disorders.
Pembrolizumab microgravity crystallization experimentation
Authors: Reichert Paul , Prosise Winifred , Fischmann Thierry O. , Scapin Giovanna , Narasimhan Chakravarthy , Spinale April , Polniak Ray , Yang Xiaoyu , Walsh Erika , Patel Daya , Benjamin Wendy , Welch Johnathan , Simmons Denarra , Strickland Corey 
Published: December 2019

AbstractCrystallization processes have been widely used in the pharmaceutical industry for the manufacture, storage, and delivery of small-molecule and small protein therapeutics. However, the identification of crystallization processes for biologics, particularly monoclonal antibodies, has been prohibitive due to the size and the flexibility of their overall structure. There remains a challenge and an opportunity to utilize the benefits of crystallization of biologics. The research laboratories of Merck Sharp & Dome Corp. (MSD) in collaboration with the International Space Station (ISS) National Laboratory performed crystallization experiments with pembrolizumab (Keytruda®) on the SpaceX-Commercial Resupply Services-10 mission to the ISS. By leveraging microgravity effects such as reduced sedimentation and minimal convection currents, conditions producing crystalline suspensions of homogeneous monomodal particle size distribution (39 μm) in high yield were identified. In contrast, the control ground experiments produced crystalline suspensions with a heterogeneous bimodal distribution of 13 and 102 μm particles. In addition, the flight crystalline suspensions were less viscous and sedimented more uniformly than the comparable ground-based crystalline suspensions. These results have been applied to the production of crystalline suspensions on earth, using rotational mixers to reduce sedimentation and temperature gradients to induce and control crystallization. Using these techniques, we have been able to produce uniform crystalline suspensions (1–5 μm) with acceptable viscosity (<12 cP), rheological, and syringeability properties suitable for the preparation of an injectable formulation. The results of these studies may help widen the drug delivery options to improve the safety, adherence, and quality of life for patients and caregivers.
Mesenchymal stem cell perspective: cell biology to clinical progress
Authors: Pittenger Mark F. , Discher Dennis E. , Péault Bruno M. , Phinney Donald G. , Hare Joshua M. , Caplan Arnold I. 
Published: December 2019

AbstractThe terms MSC and MSCs have become the preferred acronym to describe a cell and a cell population of multipotential stem/progenitor cells commonly referred to as mesenchymal stem cells, multipotential stromal cells, mesenchymal stromal cells, and mesenchymal progenitor cells. The MSCs can differentiate to important lineages under defined conditions in vitro and in limited situations after implantation in vivo. MSCs were isolated and described about 30 years ago and now there are over 55,000 publications on MSCs readily available. Here, we have focused on human MSCs whenever possible. The MSCs have broad anti-inflammatory and immune-modulatory properties. At present, these provide the greatest focus of human MSCs in clinical testing; however, the properties of cultured MSCs in vitro suggest they can have broader applications. The medical utility of MSCs continues to be investigated in over 950 clinical trials. There has been much progress in understanding MSCs over the years, and there is a strong foundation for future scientific research and clinical applications, but also some important questions remain to be answered. Developing further methods to understand and unlock MSC potential through intracellular and intercellular signaling, biomedical engineering, delivery methods and patient selection should all provide substantial advancements in the coming years and greater clinical opportunities. The expansive and growing field of MSC research is teaching us basic human cell biology as well as how to use this type of cell for cellular therapy in a variety of clinical settings, and while much promise is evident, careful new work is still needed.