bluuebunny/crossref_metadata_2025_split huggingface dataset:
A structural feature of Dda helicase which enhances displacement of streptavidin and trp repressor from DNA
Authors: Byrd Alicia K. , Malone Emory G. , Hazeslip Lindsey , Zafar Maroof Khan , Harrison David K. , Thompson Matthew D. , Gao Jun , Perumal Senthil K. , Marecki John C. , Raney Kevin D. 
Published: November 2021

AbstractHelicases are molecular motors with many activities. They use the energy from ATP hydrolysis to unwind double‐stranded nucleic acids while translocating on the single‐stranded DNA. In addition to unwinding, many helicases are able to remove proteins from nucleic acids. Bacteriophage T4 Dda is able to displace a variety of DNA binding proteins and streptavidin bound to biotinylated oligonucleotides. We have identified a subdomain of Dda that when deleted, results in a protein variant that has nearly wild type activity for unwinding double‐stranded DNA but exhibits greatly reduced streptavidin displacement activity. Interestingly, this domain has little effect on displacement of either gp32 or BamHI bound to DNA but does affect displacement of trp repressor from DNA. With this variant, we have identified residues which enhance displacement of some proteins from DNA.
Structure–activity relationship studies of allosteric inhibitors of EYA2 tyrosine phosphatase
Authors: Anantharajan Jothi , Baburajendran Nithya , Lin Grace , Loh Yong Yao , Xu Weijun , Ahmad Nur Huda Binte , Liu Shuang , Jansson Anna E. , Kuan John Wee Liang , Ng Elizabeth Yihui , Yeo Yee Khoon , Hung Alvin W. , Joy Joma , Hill Jeffrey , Ford Heide L. , Zhao Rui , Keller Thomas H. , Kang CongBao 
Published: November 2021

AbstractHuman eyes absent (EYA) proteins possess Tyr phosphatase activity, which is critical for numerous cancer and metastasis promoting activities, making it an attractive target for cancer therapy. In this work, we demonstrate that the inhibitor‐bound form of EYA2 does not favour binding to Mg2+, which is indispensable for the Tyr phosphatase activity. We further describe characterization and optimization of this class of allosteric inhibitors. A series of analogues were synthesized to improve potency of the inhibitors and to elucidate structure–activity relationships. Two co‐crystal structures confirm the binding modes of this class of inhibitors. Our medicinal chemical, structural, biochemical, and biophysical studies provide insight into the molecular interactions of EYA2 with these allosteric inhibitors. The compounds derived from this study are useful for exploring the function of the Tyr phosphatase activity of EYA2 in normal and cancerous cells and serve as reference compounds for screening or developing allosteric phosphatase inhibitors. Finally, the co‐crystal structures reported in this study will aid in structure‐based drug discovery against EYA2.
Elucidating important structural features for the binding affinity of spike ‐ SARS‐CoV‐2 neutralizing antibody complexes
Authors: Sharma Divya , Rawat Puneet , Janakiraman Vani , Gromiha M. Michael 
Published: November 2021

AbstractThe coronavirus disease 2019 (COVID‐19) has affected the lives of millions of people around the world. In an effort to develop therapeutic interventions and control the pandemic, scientists have isolated several neutralizing antibodies against SARS‐CoV‐2 from the vaccinated and convalescent individuals. These antibodies can be explored further to understand SARS‐CoV‐2 specific antigen–antibody interactions and biophysical parameters related to binding affinity, which can be utilized to engineer more potent antibodies for current and emerging SARS‐CoV‐2 variants. In the present study, we have analyzed the interface between spike protein of SARS‐CoV‐2 and neutralizing antibodies in terms of amino acid residue propensity, pair preference, and atomic interaction energy. We observed that Tyr residues containing contacts are highly preferred and energetically favorable at the interface of spike protein–antibody complexes. We have also developed a regression model to relate the experimental binding affinity for antibodies using structural features, which showed a correlation of 0.93. Moreover, several mutations at the spike protein–antibody interface were identified, which may lead to immune escape (epitope residues) and improved affinity (paratope residues) in current/emerging variants. Overall, the work provides insights into spike protein–antibody interactions, structural parameters related to binding affinity and mutational effects on binding affinity change, which can be helpful to develop better therapeutics against COVID‐19.
Topical and dietary toxicity of emamectin benzoate, chlorantraniliprole, cyantraniliprole and indoxacarb to larvae of the common armyworm Mythimna convecta (Lepidoptera: Noctuidae)
Authors: Stevens Mark M , Warren Glen N , Mo Jianhua 
Published: November 2021

AbstractBACKGROUNDThe common armyworm Mythimna convecta is an important pest of pastures and graminaceous crops in Australia, but materials currently registered for its control are limited to broad‐spectrum compounds incompatible with integrated pest management (IPM) systems. In this study we assessed the response of M. convecta larvae to four alternative compounds using topical and dietary bioassays.RESULTSEmamectin benzoate [LC50 (lethal concentration for 50% of insects tested) values 2.69 μg mL−1 topical, 0.017 μg active ingredient (AI) g−1 dietary] and chlorantraniliprole (LC50 values 4.87 μg mL−1 topical, 0.080 μg AI g−1 dietary) were significantly more active than either indoxacarb or cyantraniliprole. Our results showed strong parallels with data on the more extensively studied Australian strains of Helicoverpa armigera, with the most notable differences being the higher contact toxicity of emamectin benzoate to M. convecta and the lower acute dietary activity of formulated cyantraniliprole to this species, which was linked to feeding deterrence. Cyantraniliprole at dietary concentrations of ≥0.02 μg AI g−1 significantly reduced the weight of surviving larvae and frass production (an indirect measure of food consumption) over the seven‐day exposure period. There was also some evidence of chlorantraniliprole deterring larval feeding, although to a much more limited extent.CONCLUSIONSBoth emamectin benzoate and chlorantraniliprole are suitable for use against M. convecta. The decision as to which of these compounds should be prioritized for further development should be based on their potential effects on beneficial species once their optimal field rates have been determined.
Hydrologic connectivity and land cover affect floodplain lake water quality, fish abundance, and fish diversity in floodplain lakes of the Wabash‐White River basin
Authors: Carlson Mazur Martha L. , Smith Bradley , Bird Broxton , McMillan Sara , Pyron Mark , Hauswald Cassie 
Published: November 2021

AbstractFloodplain lakes are important aquatic resources for supporting ecosystem services, such as organismal habitat, biodiversity, and the retention of nutrients and sediment. Due to geomorphic alteration of river channels and land‐cover change, degradation to floodplain lakes in the Ohio River basin is occurring at a rate that will escalate as climate change causes increased flood intensity and the seasonal redistribution of rainfall. A better understanding of the local drivers that affect oxbow lakes is needed for targeted floodplain restoration efforts designed to slow degradation. We examined the effects of land cover, topography, and hydrologic connectivity on water quality and fish diversity and abundance in nine floodplain lakes with potentially high remnant ecological function in the Wabash‐White watershed (Indiana, Ohio, and Illinois). Data collection included water‐quality parameters; stable water isotopes; total phosphorus, total nitrogen, and chlorophyll‐a; and fish community diversity and abundance. Results indicate that hay/pasture land cover and decreased topographic relief in the local oxbow watersheds, along with reduced river hydrologic connectivity, were related to an increase in total phosphorus, total nitrogen, and chlorophyll‐a. Greater biodiversity and abundance in fish assemblages were evident in oxbow lakes that were more disconnected from the main channel. The results of this study suggest that hydrologic connectivity of oxbow lakes with the contributing drainage area and the main channel influence nutrients and fish communities. Knowing the influencing factors can help ecosystem managers better protect these valuable floodplain lake ecosystems and prioritize restoration efforts amidst increasing stressors due to climate and land‐use changes.
On‐field test campaign performance of VDE‐SAT Link ID 20 over Norsat‐2 LEO satellite
Authors: Andreotti Riccardo , Nanna Leonardo , Andrenacci Marco , Isca Agostino , Haugli Hans‐Christian , Alagha Nader 
Published: November 2021

SummaryThe latest technical recommendation by the International Telecommunication Union (ITU) for a data exchange system in the VHF maritime mobile band defines a random access channel (RAC) for communications on the uplink channel between vessels and satellites. The physical layer frame for random uplink channel is designed to allow for a more efficient use of the power amplifiers and includes features to assist the satellite receivers to resolve overlapping reception of multiple messages. This paper presents the performance results of an over‐the‐air test campaign carried out exploiting the NorSat‐2 Low Earth orbit (LEO) satellite. After a review of the VDE‐SAT RAC and Link ID 20 burst, a possible demodulator implementation is shown. Then, the VDE‐SAT transmitter platform, located in Pisa, Italy, emulating a population of vessels transmitting to the NorSat‐2 LEO satellite is introduced, and the test cases are described. Afterward, the analysis of the recorded signals is provided. The post‐analysis first focuses on the demodulation performance in terms of probability of successful demodulation of the interfering bursts. Further investigation has also been carried out to better understand the interference environment in this frequency band for satellite signal reception. Tests indicate promising results of successfully detecting and demodulating up to 22 overlapping RAC messages, confirming the robustness of the protocol. Finally, capitalizing on the above analysis, conclusions suggest possible improvements.
First occurrence of Nyssa endocarps and associated fungi in the Oligocene of South China: palaeogeographical and palaeoecological significance
Authors: Xu Sheng‐Lan , Kodrul Tatiana M. , Maslova Natalia P. , Song Han‐Zhang , Tobias Anna V. , Wu Xin‐Kai , Quan Cheng , Jin Jian‐Hua 
Published: November 2021

AbstractCo‐evolutionary relationships of plants and fungi are of great importance for the phylogeny of both groups. Nyssa was widely distributed in the northern hemisphere during the Cenozoic. Extant species of Nyssa exhibit a disjunct distribution between eastern North America, Central America and East Asia. Here, a new species, Nyssa nanningensis Xu & Jin, is described based on fruit endocarps from the upper Oligocene Yongning Formation of the Nanning Basin, South China. This new fossil record of Nyssa expands the known palaeogeographical distribution of the genus to the low latitudes of East Asia. Associated fossil fungal fruiting bodies on Nyssa endocarps are assigned to the new fossil genus and species, Yongnicta nyssae Tobias & Maslova. This new genus is similar to some members of extant wood destructor taxa Coronophorales and Amphisphaeriales (Sordariomycetes, Ascomycota). About 3% of the Nyssa endocarps studied were affected by Yongnicta nyssae. Low frequency of fruit damage indicates that endocarps could be released from mesocarps by animals eating fleshy parts of fruits, making them potentially available to wood‐destroying fungi.
IKEA Wien Westbahnhof – Eine nachhaltige Oase im Großstadtdschungel
Authors: Mühl Bernd , Salzer Christian 
Published: November 2021

AbstractAm Wiener Westbahnhof entstand ein innovatives und einladendes Einrichtungshaus. Mit seinen begrünten Fassaden und viel Raum für die Menschen – von ansprechender Gastronomie bis zur allgemein zugänglichen begrünten Dachterrasse – ist es so viel mehr als nur ein Einrichtungshaus. Insgesamt umfasst das Gebäude 25.000 m2 auf sieben Geschossen. Der Möbelriese selbst nutzt fünf der Geschosse – in den beiden obersten Etagen befindet sich ein Hotel mit 345 Betten, das Konzept ist besonders auf junge Geschäftsreisende ausgerichtet. Als besonderer Kontrapunkt zu historisch massiven Fassaden stellt „das Hus“, wie es liebevoll von IKEA genannt wird, mit seiner umhüllenden und frei sichtbaren Stahlkonstruktion eine Besonderheit im städtischen Raum dar. Sein offenes, transparentes Regalsystem spendet Schatten, reduziert die sommerliche Überhitzung der Fassaden und beeinflusst durch die umfangreiche Bepflanzung das Mikroklima der Umgebung nachweislich. In der Dachzone trägt die Stahl‐Pergola eine 800 m2 große Photovoltaikanlage. Das Gebäude ist ein Vorreiter in Sachen Nachhaltigkeit und wurde deshalb mit dem Greenpass‐Platinum‐Zertifikat ausgezeichnet. Das nachhaltige Einrichtungshaus am Wiener Westbahnhof ist auf Fußgänger, U‐ und Straßenbahnfahrer sowie Radfahrer ausgerichtet – für Autos gibt es dort keinen Platz. Sperrgut wird frei Haus geliefert, den Rest nimmt man in der bekannten blauen Tasche mit. Zusammenfassend gibt es viel Erlebnis, Gastronomie, Raum zum Bummeln bzw. Schauen und mehr Grün, als es ein ebener Park auf dieser Fläche bieten könnte, denn auf allen Etagen sind Freiflächen mit Grünpflanzen, begrünte Fassadenelemente, Vogelnester, Bienenstöcke und lichtdurchflutete Bereiche.
Fabrication of Oleic Acid Grafted Starch‐based Hybrid Carriers forl‐Asparaginase Encapsulation
Authors: Hafızosmanoğlu Gülşah , Ulu Ahmet , Köytepe Süleyman , Ateş Burhan 
Published: November 2021

AbstractIn this study, artificial red blood cells (RBCs) for immobilization ofl‐asparaginase are developed. The artificial red blood cells are prepared via a self‐assembly method and characterized by various methods. The prepared material shows a small hydrodynamic size of nearly 120 nm and a zeta potential of ‐7.2 ± 0.2 mV. Afterl‐asparaginase encapsulation, the particle size is nearly 295 nm and the zeta potential value is ‐9.8 ± 0.1. As expected, the immobilized enzyme shows better pH stability and thermal stability than the free enzyme. For instance, at 60 °C, the immobilized enzyme maintains 63.5% of the original activity, while the free enzyme retains only 27.6% of the original activity. Furthermore, the immobilized enzyme exhibits excellent reusability and storage stability, retaining 46.1% of its initial activity after 15 reuses. Overall, the developed artificial RBCs can potentially be applied as a novel support for immobilization ofl‐asparaginase.
Chemical Induction of Neurogenic Properties in Mammalian Müller Glia
Authors: Xia Xiaohuan , Teotia Pooja , Patel Hiren , Van Hook Matthew J. , Ahmad Iqbal 
Published: November 2021

Abstract
Müller glia (MG), cells that maintain homeostasis in the retina, are dormant stem cells that can regenerate neurons upon injury. However, the regenerative property of MG, which is reproducibly displayed in the lower vertebrates, is not readily observed in the mammals even upon forced expression of regulatory genes or exposure to growth factors. Here, we demonstrate a reproducible unmasking of the neurogenic properties of enriched rodent MG by serial exposure to different combinations of small molecules. The enriched MG, in response to changing culture conditions, silenced glia-specific genes and acquired transcriptional signature of neurons, accompanied by upregulation of genes known to regulate neuronal potential of MG. The MG-derived neurons expressed immunoreactivities corresponding to neuronal proteins and displayed electrophysiological features of immature neurons. Our study presents a proof of principle of pharmacological activation of neurogenic properties of mammalian MG, which may be utilized for therapeutic regeneration.
Radiotherapy and the immune system: More than just immune suppression
Authors: Rückert Michael , Flohr Ann-Sophie , Hecht Markus , Gaipl Udo S. 
Published: November 2021

AbstractRadiotherapy (RT) is still one of the standard cancer therapies, with up to two third of all cancer patients with solid tumors being irradiated in the course of their disease. The aim of using ionizing radiation in fractionated treatment schedules was always to achieve local tumor control by inducing DNA damage which can be repaired by surrounding normal tissue but leads to cell death in tumor cells. Meanwhile, it is known that RT also has immunological effects reshaping the tumor microenvironment. Nevertheless, RT alone often fails to elicit potent antitumor immune responses as these effects can be immunostimulatory as well as immunosuppressive. Here, we discuss how immunotherapies can be exploited in combined therapies to boost RT-induced antitumor immune responses or to counteract preexisting and RT-mediated immunosuppression to improve local and systemic tumor control. Furthermore, we highlight some parameters of radioimmunotherapies (RITs) which are under investigation for potential optimizations and how RIT approaches are tested in first phases II and III trials. Finally, we discuss how RT might affect normal and cancer stem cells.
Zbtb46-Dependent Altered Developmental Program in Embryonic Stem Cell-Derived Blood Cell Progenitors
Authors: Boto Pal , Gerzsenyi Timea Beatrix , Lengyel Adel , Szunyog Balint , Szatmari Istvan 
Published: November 2021

Abstract
Zbtb46 is a recently identified dendritic cell (DC)-specific transcription factor with poorly defined biology. Although Zbtb46 is highly expressed in conventional DCs, evidence also points to its presence in erythroid progenitors and endothelial cells suggesting that this factor might influence the early hematopoietic development. Here, we probe the effect of this transcription factor in embryonic stem cell (ESC)-derived blood cell progenitors using chemically inducible mouse cell lines. Unexpectedly, forced expression of this protein elicited a broad repressive effect at the early stage of ESC differentiation. Ectopic expression of Zbtb46 interfered with the mesoderm formation and cell proliferation was also negatively impacted. More importantly, reduced number of CD11b+ myeloid blood cells were generated from ESC-derived Flk1+ mesoderm cells in the presence of Zbtb46. Consistent with this finding, our gene expression profiling revealed that numerous myeloid and immune response related genes, including Irf8, exhibited lower expression in the Zbtb46-primed cells. Despite these repressive effects, however, Zbtb46 overexpression was associated with enhanced formation of erythroid blood cell colonies and increased adult hemoglobin (Hbb-b1) expression at the early phase of ESC differentiation. Moreover, elevated percent of CD105 (Endoglin) positive cells were detected in the Zbtb46-primed samples. In summary, our results support that Zbtb46 suppresses the ESC-derived myeloid development and diverts mesoderm cells toward erythroid developmental pathway. Moreover, our transcriptomic data provide a resource for exploration of the Zbtb46 regulatory network in ESC-derived progenitors.
Mitochondria in Neurogenesis: Implications for Mitochondrial Diseases
Authors: Brunetti Dario , Dykstra Werner , Le Stephanie , Zink Annika , Prigione Alessandro 
Published: November 2021

Abstract
Mitochondria are organelles with recognized key roles in cellular homeostasis, including bioenergetics, redox, calcium signaling, and cell death. Mitochondria are essential for neuronal function, given the high energy demands of the human brain. Consequently, mitochondrial diseases affecting oxidative phosphorylation (OXPHOS) commonly exhibit neurological impairment. Emerging evidence suggests that mitochondria are important not only for mature postmitotic neurons but also for the regulation of neural progenitor cells (NPCs) during the process of neurogenesis. These recent findings put mitochondria as central regulator of cell fate decisions during brain development. OXPHOS mutations may disrupt the function of NPCs and thereby impair the metabolic programming required for neural fate commitment. Promoting the mitochondrial function of NPCs could therefore represent a novel interventional approach against incurable mitochondrial diseases.
DUSP5 Promotes Osteogenic Differentiation Through SCP1/2-Dependent Phosphorylation of SMAD1
Authors: Liu Xuejiao , Liu Xuenan , Du Yangge , Hu Menglong , Tian Yueming , Li Zheng , Lv Longwei , Zhang Xiao , Liu Yunsong , Zhou Yongsheng , Zhang Ping 
Published: November 2021

Abstract
Dual-specificity phosphatases (DUSPs) are defined by their capability to dephosphorylate both phosphoserine/phosphothreonine (pSer/pThr) and phosphotyrosine (pTyr). DUSP5, a member of DUSPs superfamily, is located in the nucleus and plays crucially regulatory roles in the signaling pathway transduction. In our present study, we discover that DUSP5 significantly promotes osteogenic differentiation of mesenchymal stromal cells (MSCs) by activating SMAD1 signaling pathway. Mechanistically, DUSP5 physically interacts with the phosphatase domain of small C-terminal phosphatase 1/2 (SCP1/2, SMAD1 phosphatases) by the linker region. In addition, we further confirm that DUSP5 activates SMAD1 signaling through a SCP1/2-dependent manner. Specifically, DUSP5 attenuates the SCP1/2-SMAD1 interaction by competitively binding to SCP1/2, which is responsible for the SMAD1 dephosphorylation, and thus results in the activation of SMAD1 signaling. Importantly, DUSP5 expression in mouse bone marrow MSCs is significantly reduced in ovariectomized (OVX) mice in which osteogenesis is highly passive, and overexpression of Dusp5 via tail vein injection reverses the bone loss of OVX mice efficiently. Collectively, this work demonstrates that the linker region of DUSP5 maybe a novel chemically modifiable target for controlling MSCs fate choices and for osteoporosis treatment.