bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selection for constrained peptides that bind to a single target protein
Authors: King Andrew M. , Anderson Daniel A. , Glassey Emerson , Segall-Shapiro Thomas H. , Zhang Zhengan , Niquille David L. , Embree Amanda C. , Pratt Katelin , Williams Thomas L. , Gordon D. Benjamin , Voigt Christopher A. 
Published: November 2021

AbstractPeptide secondary metabolites are common in nature and have diverse pharmacologically-relevant functions, from antibiotics to cross-kingdom signaling. Here, we present a method to design large libraries of modified peptides in Escherichia coli and screen them in vivo to identify those that bind to a single target-of-interest. Constrained peptide scaffolds were produced using modified enzymes gleaned from microbial RiPP (ribosomally synthesized and post-translationally modified peptide) pathways and diversified to build large libraries. The binding of a RiPP to a protein target leads to the intein-catalyzed release of an RNA polymerase σ factor, which drives the expression of selectable markers. As a proof-of-concept, a selection was performed for binding to the SARS-CoV-2 Spike receptor binding domain. A 1625 Da constrained peptide (AMK-1057) was found that binds with similar affinity (990 ± 5 nM) as an ACE2-derived peptide. This demonstrates a generalizable method to identify constrained peptides that adhere to a single protein target, as a step towards “molecular glues” for therapeutics and diagnostics.
A giant NLR gene confers broad-spectrum resistance to Phytophthora sojae in soybean
Authors: Wang Weidong , Chen Liyang , Fengler Kevin , Bolar Joy , Llaca Victor , Wang Xutong , Clark Chancelor B. , Fleury Tomara J. , Myrvold Jon , Oneal David , van Dyk Maria Magdalena , Hudson Ashley , Munkvold Jesse , Baumgarten Andy , Thompson Jeff , Cai Guohong , Crasta Oswald , Aggarwal Rajat , Ma Jianxin 
Published: November 2021

AbstractPhytophthora root and stem rot caused by P. sojae is a destructive soybean soil-borne disease found worldwide. Discovery of genes conferring broad-spectrum resistance to the pathogen is a need to prevent the outbreak of the disease. Here, we show that soybean Rps11 is a 27.7-kb nucleotide-binding site-leucine-rich repeat (NBS-LRR or NLR) gene conferring broad-spectrum resistance to the pathogen. Rps11 is located in a genomic region harboring a cluster of large NLR genes of a single origin in soybean, and is derived from rounds of unequal recombination. Such events result in promoter fusion and LRR expansion that may contribute to the broad resistance spectrum. The NLR gene cluster exhibits drastic structural diversification among phylogenetically representative varieties, including gene copy number variation ranging from five to 23 copies, and absence of allelic copies of Rps11 in any of the non-Rps11-donor varieties examined, exemplifying innovative evolution of NLR genes and NLR gene clusters.
Global roll-out of comprehensive policy measures may aid in bridging emissions gap
Authors: van Soest Heleen L. , Aleluia Reis Lara , Baptista Luiz Bernardo , Bertram Christoph , Després Jacques , Drouet Laurent , den Elzen Michel , Fragkos Panagiotis , Fricko Oliver , Fujimori Shinichiro , Grant Neil , Harmsen Mathijs , Iyer Gokul , Keramidas Kimon , Köberle Alexandre C. , Kriegler Elmar , Malik Aman , Mittal Shivika , Oshiro Ken , Riahi Keywan , Roelfsema Mark , van Ruijven Bas , Schaeffer Roberto , Silva Herran Diego , Tavoni Massimo , Unlu Gamze , Vandyck Toon , van Vuuren Detlef P. 
Published: November 2021

AbstractClosing the emissions gap between Nationally Determined Contributions (NDCs) and the global emissions levels needed to achieve the Paris Agreement’s climate goals will require a comprehensive package of policy measures. National and sectoral policies can help fill the gap, but success stories in one country cannot be automatically replicated in other countries. They need to be adapted to the local context. Here, we develop a new Bridge scenario based on nationally relevant, short-term measures informed by interactions with country experts. These good practice policies are rolled out globally between now and 2030 and combined with carbon pricing thereafter. We implement this scenario with an ensemble of global integrated assessment models. We show that the Bridge scenario closes two-thirds of the emissions gap between NDC and 2 °C scenarios by 2030 and enables a pathway in line with the 2 °C goal when combined with the necessary long-term changes, i.e. more comprehensive pricing measures after 2030. The Bridge scenario leads to a scale-up of renewable energy (reaching 52%–88% of global electricity supply by 2050), electrification of end-uses, efficiency improvements in energy demand sectors, and enhanced afforestation and reforestation. Our analysis suggests that early action via good-practice policies is less costly than a delay in global climate cooperation.
Crosstalk between CST and RPA regulates RAD51 activity during replication stress
Authors: Lei Kai-Hang , Yang Han-Lin , Chang Hao-Yen , Yeh Hsin-Yi , Nguyen Dinh Duc , Lee Tzu-Yu , Lyu Xinxing , Chastain Megan , Chai Weihang , Li Hung-Wen , Chi Peter 
Published: November 2021

AbstractReplication stress causes replication fork stalling, resulting in an accumulation of single-stranded DNA (ssDNA). Replication protein A (RPA) and CTC1-STN1-TEN1 (CST) complex bind ssDNA and are found at stalled forks, where they regulate RAD51 recruitment and foci formation in vivo. Here, we investigate crosstalk between RPA, CST, and RAD51. We show that CST and RPA localize in close proximity in cells. Although CST stably binds to ssDNA with a high affinity at low ionic strength, the interaction becomes more dynamic and enables facilitated dissociation at high ionic strength. CST can coexist with RPA on the same ssDNA and target RAD51 to RPA-coated ssDNA. Notably, whereas RPA-coated ssDNA inhibits RAD51 activity, RAD51 can assemble a functional filament and exhibit strand-exchange activity on CST-coated ssDNA at high ionic strength. Our findings provide mechanistic insights into how CST targets and tethers RAD51 to RPA-coated ssDNA in response to replication stress.
Progenitor translatome changes coordinated by Tsc1 increase perception of Wnt signals to end nephrogenesis
Authors: Jarmas Alison E. , Brunskill Eric W. , Chaturvedi Praneet , Salomonis Nathan , Kopan Raphael 
Published: November 2021

AbstractMammalian nephron endowment is determined by the coordinated cessation of nephrogenesis in independent niches. Here we report that translatome analysis in Tsc1+/− nephron progenitor cells from mice with elevated nephron numbers reveals how differential translation of Wnt antagonists over agonists tips the balance between self-renewal and differentiation. Wnt agonists are poorly translated in young niches, resulting in an environment with low R-spondin and high Fgf20 promoting self-renewal. In older niches we find increased translation of Wnt agonists, including R-spondin and the signalosome-promoting Tmem59, and low Fgf20, promoting differentiation. This suggests that the tipping point for nephron progenitor exit from the niche is controlled by the gradual increase in stability and possibly clustering of Wnt/Fzd complexes in individual cells, enhancing the response to ureteric bud-derived Wnt9b inputs and driving synchronized differentiation. As predicted by these findings, removing one Rspo3 allele in nephron progenitors delays cessation and increases nephron numbers in vivo.
Underwater CAM photosynthesis elucidated by Isoetes genome
Authors: Wickell David , Kuo Li-Yaung , Yang Hsiao-Pei , Dhabalia Ashok Amra , Irisarri Iker , Dadras Armin , de Vries Sophie , de Vries Jan , Huang Yao-Moan , Li Zheng , Barker Michael S. , Hartwick Nolan T. , Michael Todd P. , Li Fay-Wei 
Published: November 2021

AbstractTo conserve water in arid environments, numerous plant lineages have independently evolved Crassulacean Acid Metabolism (CAM). Interestingly, Isoetes, an aquatic lycophyte, can also perform CAM as an adaptation to low CO2 availability underwater. However, little is known about the evolution of CAM in aquatic plants and the lack of genomic data has hindered comparison between aquatic and terrestrial CAM. Here, we investigate underwater CAM in Isoetes taiwanensis by generating a high-quality genome assembly and RNA-seq time course. Despite broad similarities between CAM in Isoetes and terrestrial angiosperms, we identify several key differences. Notably, Isoetes may have recruited the lesser-known ‘bacterial-type’ PEPC, along with the ‘plant-type’ exclusively used in other CAM and C4 plants for carboxylation of PEP. Furthermore, we find that circadian control of key CAM pathway genes has diverged considerably in Isoetes relative to flowering plants. This suggests the existence of more evolutionary paths to CAM than previously recognized.
The Tharsis mantle source of depleted shergottites revealed by 90 million impact craters
Authors: Lagain A. , Benedix G. K. , Servis K. , Baratoux D. , Doucet L. S. , Rajšic A. , Devillepoix H. A. R. , Bland P. A. , Towner M. C. , Sansom E. K. , Miljković K. 
Published: November 2021

AbstractThe only martian rock samples on Earth are meteorites ejected from the surface of Mars by asteroid impacts. The locations and geological contexts of the launch sites are currently unknown. Determining the impact locations is essential to unravel the relations between the evolution of the martian interior and its surface. Here we adapt a Crater Detection Algorithm that compile a database of 90 million impact craters, allowing to determine the potential launch position of these meteorites through the observation of secondary crater fields. We show that Tooting and 09-000015 craters, both located in the Tharsis volcanic province, are the most likely source of the depleted shergottites ejected 1.1 million year ago. This implies that a major thermal anomaly deeply rooted in the mantle under Tharsis was active over most of the geological history of the planet, and has sampled a depleted mantle, that has retained until recently geochemical signatures of Mars’ early history.
Laser nano-filament explosion for enabling open-grating sensing in optical fibre
Authors: Mahmoud Aghdami Keivan , Rahnama Abdullah , Ertorer Erden , Herman Peter R. 
Published: November 2021

AbstractEmbedding strong photonic stopbands into traditional optical fibre that can directly access and sense the outside environment is challenging, relying on tedious nano-processing steps that result in fragile thinned fibre. Ultrashort-pulsed laser filaments have recently provided a non-contact means of opening high-aspect ratio nano-holes inside of bulk transparent glasses. This method has been extended here to optical fibre, resulting in high density arrays of laser filamented holes penetrating transversely through the silica cladding and guiding core to provide high refractive index contrast Bragg gratings in the telecommunication band. The point‐by‐point fabrication was combined with post-chemical etching to engineer strong photonic stopbands directly inside of the compact and flexible fibre. Fibre Bragg gratings with sharply resolved π-shifts are presented for high resolution refractive index sensing from $${n}_{{{{{{\rm{H}}}}}}}$$

n

H

= 1 to 1.67 as the nano-holes were readily wetted and filled with various solvents and oils through an intact fibre cladding.
The EMT activator ZEB1 accelerates endosomal trafficking to establish a polarity axis in lung adenocarcinoma cells
Authors: Banerjee Priyam , Xiao Guan-Yu , Tan Xiaochao , Zheng Veronica J. , Shi Lei , Rabassedas Maria Neus Bota , Guo Hou-fu , Liu Xin , Yu Jiang , Diao Lixia , Wang Jing , Russell William K. , Roszik Jason , Creighton Chad J. , Kurie Jonathan M. 
Published: November 2021

AbstractEpithelial-to-mesenchymal transition (EMT) is a transcriptionally governed process by which cancer cells establish a front-rear polarity axis that facilitates motility and invasion. Dynamic assembly of focal adhesions and other actin-based cytoskeletal structures on the leading edge of motile cells requires precise spatial and temporal control of protein trafficking. Yet, the way in which EMT-activating transcriptional programs interface with vesicular trafficking networks that effect cell polarity change remains unclear. Here, by utilizing multiple approaches to assess vesicular transport dynamics through endocytic recycling and retrograde trafficking pathways in lung adenocarcinoma cells at distinct positions on the EMT spectrum, we find that the EMT-activating transcription factor ZEB1 accelerates endocytosis and intracellular trafficking of plasma membrane-bound proteins. ZEB1 drives turnover of the MET receptor tyrosine kinase by hastening receptor endocytosis and transport to the lysosomal compartment for degradation. ZEB1 relieves a plus-end-directed microtubule-dependent kinesin motor protein (KIF13A) and a clathrin-associated adaptor protein complex subunit (AP1S2) from microRNA-dependent silencing, thereby accelerating cargo transport through the endocytic recycling and retrograde vesicular pathways, respectively. Depletion of KIF13A or AP1S2 mitigates ZEB1-dependent focal adhesion dynamics, front-rear axis polarization, and cancer cell motility. Thus, ZEB1-dependent transcriptional networks govern vesicular trafficking dynamics to effect cell polarity change.
Marcus inverted region of charge transfer from low-dimensional semiconductor materials
Authors: Wang Junhui , Ding Tao , Gao Kaimin , Wang Lifeng , Zhou Panwang , Wu Kaifeng 
Published: November 2021

AbstractA key process underlying the application of low-dimensional, quantum-confined semiconductors in energy conversion is charge transfer from these materials, which, however, has not been fully understood yet. Extensive studies of charge transfer from colloidal quantum dots reported rates increasing monotonically with driving forces, never displaying an inverted region predicted by the Marcus theory. The inverted region is likely bypassed by an Auger-like process whereby the excessive driving force is used to excite another Coulomb-coupled charge. Herein, instead of measuring charge transfer from excitonic states (coupled electron-hole pairs), we build a unique model system using zero-dimensional quantum dots or two-dimensional nanoplatelets and surface-adsorbed molecules that allows for measuring charge transfer from transiently-populated, single-charge states. The Marcus inverted region is clearly revealed in these systems. Thus, charge transfer from excitonic and single-charge states follows the Auger-assisted and conventional Marcus charge transfer models, respectively. This knowledge should enable rational design of energetics for efficient charge extraction from low-dimensional semiconductor materials as well as suppression of the associated energy-wasting charge recombination.
Full-color enhanced second harmonic generation using rainbow trapping in ultrathin hyperbolic metamaterials
Authors: Li Junhao , Hu Guangwei , Shi Lina , He Nan , Li Daqian , Shang Qiuyu , Zhang Qing , Fu Huange , Zhou Linlin , Xiong Wei , Guan Jianguo , Wang Jian , He Sailing , Chen Lin 
Published: November 2021

AbstractMetasurfaces have provided a promising approach to enhance the nonlinearity at subwavelength scale, but usually suffer from a narrow bandwidth as imposed by sharp resonant features. Here, we counterintuitively report a broadband, enhanced second-harmonic generation, in nanopatterned hyperbolic metamaterials. The nanopatterning allows the direct access of the mode with large momentum, rendering the rainbow light trapping, i.e. slow light in a broad frequency, and thus enhancing the local field intensity for boosted nonlinear light-matter interactions. For a proof-of-concept demonstration, we fabricated a nanostructured Au/ZnO multilayer, and enhanced second harmonic generation can be observed within the visible wavelength range (400-650 nm). The enhancement factor is over 50 within the wavelength range of 470-650 nm, and a maximum conversion efficiency of 1.13×10−6 is obtained with a pump power of only 8.80 mW. Our results herein offer an effective and robust approach towards the broadband metasurface-based nonlinear devices for various important technologies.
Equivalent method for obtaining concrete age on the basis of electrical resistivity
Authors: Lu Xiaochun , Tong Fuguo , Zha Xinyuan , Liu Gang 
Published: November 2021

AbstractConcrete age is the time since the moment water is added to the cement, and the age of concrete comprehensively reflects the physical properties of the concrete when curing under standard conditions. For concrete under nonstandard conditions, its physical properties are directly related to both its age and temperature history. The equivalent age of concrete is the time at which concrete under nonstandard conditions reaches the same state as concrete under standard conditions. Most equivalent methods, such as the Nurse-Saul function and the Arrhenius function, are based on a maturity index. However, the accuracy of these methods breaks down when the curing temperature range is wide. In this paper, the electrical resistivity of concrete is used as the index to determine the equivalent age of concrete. This method is based on the assumption that concrete with the same mixture proportions has the same electrical resistivity when the maturity of the concrete is the same, regardless of the curing history. The proposed method is advantageous because it can be performed in real time and is nondestructive. To constantly measure the electrical resistivity of concrete, an automatic data acquisition system is developed to monitor the electrical resistivity of concrete and reduce the error caused by polarization as much as possible. Then, a model for predicting the electrical resistivity of concrete under different curing temperatures is proposed to conveniently calculate the equivalent coefficient. Finally, the results calculated by the proposed equivalent method are compared with those of the standard method (Nurse-Saul equation), and the results of the proposed model are found to be more reasonable.
Assessing the origin, genetic structure and demographic history of the common pheasant (Phasianus colchicus) in the introduced European range
Authors: Ashrafzadeh Mohammad Reza , Khosravi Rasoul , Fernandes Carlos , Aguayo Cecilia , Bagi Zoltán , Lavadinović Vukan M. , Szendrei László , Beuković Dejan , Mihalik Bendegúz , Kusza Szilvia 
Published: November 2021

AbstractThe common pheasant, a game species widely introduced throughout the world, can be considered as an ideal model to study the effects of introduction events on local adaptations, biogeographic patterns, and genetic divergence processes. We aimed to assess the origin, spatial patterns of genetic variation, and demographic history of the introduced populations in the contact zone of Central and Southeast Europe, using mitochondrial DNA control region sequences and microsatellite loci. Both types of molecular markers indicated relatively low to moderate levels of genetic variation. The mtDNA analyses revealed that common pheasants across the study area are divided into two distinct clades: B (mongolicus group) and F (colchicus group). Analyses of the microsatellite data consistently suggested a differentiation between Hungary and Serbia, with the pheasant population in Hungary being much more genetically homogeneous, while that of Serbia has much more genetic mixture and admixture. This cryptic differentiation was not detected using a non-spatial Bayesian clustering model. The analyses also provided strong evidence for a recent population expansion. This fundamental information is essential for adequate and effective conservation management of populations of a game species of great economic and ecological importance in the studied geographical region.
Molecular strategies for antibody binding and escape of SARS-CoV-2 and its mutations
Authors: Hendy Mohamed , Kaufman Samuel , Ponga Mauricio 
Published: November 2021

AbstractThe COVID19 pandemic, caused by SARS-CoV-2, has infected more than 200 million people worldwide. Due to the rapid spreading of SARS-CoV-2 and its impact, it is paramount to find effective treatments against it. Human neutralizing antibodies are an effective method to fight viral infection. However, the recent discovery of new strains that substantially change the S-protein sequence has raised concern about vaccines and antibodies’ effectiveness. Here, using molecular simulations, we investigated the binding mechanisms between the S-protein and several antibodies. Multiple mutations were included to understand the strategies for antibody escape in new variants. We found that the combination of mutations K417N, E484K, L452R, and T478K produced higher binding energy to ACE2 than the wild type, suggesting higher efficiency to enter host cells. The mutations’ effect depends on the antibody class. While Class I enhances the binding avidity in the presence of N501Y mutation, class II antibodies showed a sharp decline in the binding affinity. Our simulations suggest that Class I antibodies will remain effective against the new strains. In contrast, Class II antibodies will have less affinity to the S-protein, potentially affecting these antibodies’ efficiency.
Different prognostic impact of glucose uptake in visceral adipose tissue according to sex in patients with colorectal cancer
Authors: Lee Jae-Hoon , Kim Soyoung , Lee Hye Sun , Park Eun Jung , Baik Seung Hyuk , Jeon Tae Joo , Lee Kang Young , Ryu Young Hoon , Kang Jeonghyun 
Published: November 2021

AbstractThe purpose of this study was to investigate whether sex differences in visceral fat volume and glucose uptake measured by positron emission tomography/computed tomography (PET/CT) in abdominal visceral fat can stratify overall survival (OS) in patients with colorectal cancer (CRC). We retrospectively enrolled 293 patients diagnosed with CRC who underwent PET/CT before surgical resection. Fluorodeoxyglucose uptake of visceral adipose tissue (VAT-SUV) and subcutaneous adiposity tissue (SAT-SUV) were measured using PET/CT. The relative VAT (rVAT) was defined as the visceral fat volume normalized to the total volume of fat (VAT plus SAT). We defined sex-specific cutoff values for VAT-SUV, SAT-SUV, and rVAT. Univariate and multivariate analyses using Cox proportional hazard regression analysis were performed to identify the independent prognostic factors. The study population comprised 181 men and 112 women. The rVAT (0.40 vs. 0.29, p < 0.001) and VAT-SUV (0.55 vs. 0.48, p = 0.007) were significantly greater in men than in women. High rVAT (than low rVAT) and high VAT-SUV (than low VAT-SUV) showed a worse prognosis in male and female patients, respectively. Multivariate analysis indicated that the combination of rVAT and VAT-SUV was an independent prognostic factor for predicting OS in both male and female patients. The combination of rVAT and VAT-SUV could differentiate the patients with the best survival outcome from the other three individual groups in female patients, but not in males. Glucose uptake and relative volume of visceral fat may provide a new risk stratification for patients with CRC, especially female patients.