bluuebunny/crossref_metadata_2025_split huggingface dataset:
Membrane lectins enhance SARS-CoV-2 infection and influence the neutralizing activity of different classes of antibodies
Authors: Lempp Florian A. , Soriaga Leah , Montiel-Ruiz Martin , Benigni Fabio , Noack Julia , Park Young-Jun , Bianchi Siro , Walls Alexandra C. , Bowen John E. , Zhou Jiayi , Kaiser Hannah , Agostini Maria , Meury Marcel , Dellota Exequiel , Jaconi Stefano , Cameroni Elisabetta , Virgin Herbert W. , Lanzavecchia Antonio , Veesler David , Purcell Lisa , Telenti Amalio , Corti Davide 
Published: April 2021

AbstractInvestigating the mechanisms of SARS-CoV-2 cellular infection is key to better understand COVID-19 immunity and pathogenesis. Infection, which involves both cell attachment and membrane fusion, relies on the ACE2 receptor that is paradoxically found at low levels in the respiratory tract, suggesting that additional mechanisms facilitating infection may exist. Here we show that C-type lectin receptors, DC-SIGN, L-SIGN and the sialic acid-binding Ig-like lectin 1 (SIGLEC1) function as auxiliary receptors by enhancing ACE2-mediated infection and modulating the neutralizing activity of different classes of spike-specific antibodies. Antibodies to the N-terminal domain (NTD) or to the conserved proteoglycan site at the base of the Receptor Binding Domain (RBD), while poorly neutralizing infection of ACE2 over-expressing cells, effectively block lectin-facilitated infection. Conversely, antibodies to the Receptor Binding Motif (RBM), while potently neutralizing infection of ACE2 over-expressing cells, poorly neutralize infection of cells expressing DC-SIGN or L-SIGN and trigger fusogenic rearrangement of the spike promoting cell-to-cell fusion. Collectively, these findings identify a lectin-dependent pathway that enhances ACE2-dependent infection by SARS-CoV-2 and reveal distinct mechanisms of neutralization by different classes of spike-specific antibodies.
Coral symbionts exhibit a polycistronic flavodiiron gene leading to functional proteins in photosynthesis
Authors: Shimakawa Ginga , Shoguchi Eiichi , Burlacot Adrien , Ifuku Kentaro , Che Yufen , Kumazawa Minoru , Tanaka Kenya , Nakanishi Shuji 
Published: April 2021

AbstractPhotosynthesis in cyanobacteria, green algae, and basal land plants is protected against excess reducing pressure on the photosynthetic chain by flavodiiron proteins (FLV) that dissipate photosynthetic electrons by reducing O2. In these organisms, the genes encoding FLV are always conserved in the form of a pair of two-type isozymes (FLVA and FLVB) that are believed to function in O2photo-reduction as a heterodimer. While coral symbionts (dinoflagellates of the family Symbiodiniaceae) are the only algae to harbor FLV in photosynthetic red plastid lineage, only one gene is found in transcriptomes and its role and activity remain unknown. Here, we characterized theFLVgenes in Symbiodiniaceae and found that its coding region is composed of tandemly repeated FLV sequences. By measuring the O2-dependent electron flow and P700 oxidation, we suggest that this atypical FLV is activein vivo. Based on the amino-acid sequence alignment and the phylogenetic analysis, we conclude that in coral symbionts, the gene pair for FLVA and FLVB have been fused to construct one coding region for a hybrid enzyme, which presumably occurred when or after both genes were inherited from basal green algae to the dinoflagellate. Immunodetection suggested the FLV polypeptide to be cleaved by a post-translational mechanism, adding it to the rare cases of polycistronic genes in eukaryotes. Our results demonstrate that FLV are active in coral symbionts with genomic arrangement that is unique to these species. The implication of these unique features on their symbiotic living environment is discussed.
Long-Term Persistence of Plasmids Targeted by CRISPR Interference in Bacterial Populations
Authors: Mamontov Viktor , Martynov Alexander , Morozova Natalia , Bukatin Anton , Staroverov Dmitry B. , Lukyanov Konstantin A. , Ispolatov Yaroslav , Semenova Ekaterina , Severinov Konstantin 
Published: April 2021

AbstractCRISPR-Cas systems provide prokaryotes with an RNA-guided defense against foreign mobile genetic elements (MGEs) such as plasmids and viruses. A common mechanism by which MGEs avoid interference by CRISPR consists of acquisition of escape mutations in regions targeted by CRISPR. Here, using microbiological, live microscopy, and microfluidics analyses we demonstrated that plasmids can persist inEscherichia colicells at conditions of continuous targeting by the type I-E CRISPR-Cas system without acquiring any genetic alterations. We used mathematical modeling to show how plasmid persistence in a subpopulation of cells mounting CRISPR interference is achieved due to the stochastic nature of CRISPR interference and plasmid replication events. We hypothesize that the observed complex dynamics provides bacterial populations with long-term benefits due to the presence of mobile genetic elements in some cells, leading to diversification of phenotypes in the entire community and allowing rapid changes in the population structure to meet the demands of a changing environment.
Integrative physiological, biochemical and transcriptomic analysis of hexaploid wheat roots and shoots provides new insights into the molecular regulatory network during Fe & Zn starvation
Authors: Gupta Om Prakash , Pandey Vanita , Saini Ritu , Khandale Tushar , Singh Ajeet , Malik Vipin Kumar , Narwal Sneh , Ram Sewa , Singh Gyanendra Pratap 
Published: April 2021

AbstractIn plants, iron (Fe) & zinc (Zn) uptake and transportation from the rhizosphere to the grain is a critical process regulated by complex transcriptional regulatory networks. However, understanding the combined effect of Fe & Zn starvation on their uptake and transportation and the molecular regulatory networks that control them lack in wheat. Here, we performed a comprehensive physiological, biochemical and transcriptome analysis in two bread wheat genotypes,i.e.Narmada 195 and PBW 502, differing in inherent Fe & Zn content to understand the mechanism of Fe & Zn homeostasis. Compared to PBW 502, Narmada 195 exhibited increased tolerance to Fe & Zn withdrawal by an increased level of antioxidant enzymes and DPPH radical scavenging activity along with less malondialdehyde (MDA), H2O2level, increased PS accumulation and lower reduction of root and shoot Fe & Zn content and length, leaf chlorosis, and leaf area. By integrating physiological and biochemical data along with co-expression & functional genome annotation and gene expression analysis, we identified 25 core genes associated with four key pathways,i.e.Met cycle (10), PS biosynthesis (4), antioxidant (3) and transport system (8) that were significantly modulated by Fe & Zn withdrawal in both the genotypes. Genes of these four pathways were more considerably up-regulated in Narmada 195, allowing better tolerance to Fe & Zn withdrawal and efficient uptake and transportation of Fe & Zn. Chromosomal distribution and sub-genome wise mapping of these genes showed a contribution from all the chromosomes except group 5 chromosomes with the highest number of genes mapped to chromosome 4 (24%) and sub-genome D (40%). Besides, we also identified 26 miRNAs targeting 14 core genes across the four pathways. Together, our work provides a crucial angle for an in-depth understanding of regulatory cross-talk among physiological, biochemical and transcriptional reprogramming underlying Fe & Zn withdrawal in wheat. Core genes identified can serve as valuable resources for further functional research for genetic improvement of Fe & Zn content in wheat grain.HighlightOur work provides a crucial angle for a comprehensive understanding of the regulatory mechanism underlying Fe & Zn withdrawal associated with physiological, biochemical and transcriptional reprogramming in wheat.
Real-time lens-free visualization of strong light scattering by biogenic guanine platelets
Authors: Iwasaka Masakazu 
Published: April 2021

AbstractMicroscopic observation system without lens has a potential to realize ubiquitous sensing network detecting micro/nano biological hazards to modern society because the lens-free imaging device can provide an extremely compact microscope. In addition toin slicomicro-mirrors, liquid injectable organic micro-mirrors should be found and utilized for achieving the ideal imaging device for micro/nano objects. This study demonstrates a high contrast lens-free image of the projection from a biogenic guanine platelet floating in water. The fish guanine platelet generated intense and high directional diffraction as well as regular reflection of incident light. The light projection from guanine platelet individually formed an intense platelet-shaped image in real-time on CMOS image sensor arrays. A dynamic projection movie of the guanine platelet, the size of which was approximately 20 ∼ 40 μm × 5 ∼ 10 μm × 100 nm in thickness, was obtained in a small aqueous droplet whose height was less than 2 mm. The developed new lens-free technology using biogenic tiny platelet has an ability to portably visualize movements of the micro/nano objects interacting with the platelet. The compact lens-free inspection can contribute to keep our society in safe.
Cell layer-specific expression of the homeotic MADS-box transcription factor PhDEF contributes to modular petunia petal morphogenesis
Authors: Chopy M. , Cavallini-Speisser Q. , Chambrier P. , Morel P. , Just J. , Hugouvieux V. , Rodrigues Bento S. , Zubieta C. , Vandenbussche M. , Monniaux M. 
Published: April 2021

ABSTRACTFloral homeotic MADS-box transcription factors ensure the correct morphogenesis of floral organs, which are organized in different cell layers deriving from the meristematic L1, L2 and L3 layers. How cells from these distinct layers acquire their respective identity and coordinate their growth to ensure normal floral organ morphogenesis is unresolved. Here, we study petunia petals that form a limb and tube through congenital fusion, a complex morphology that coevolved with pollinators. We have identified petunia mutants expressing the B-class MADS-box genePhDEFin the epidermis or in the mesophyll of the petal only, called wico and star respectively. Strikingly, wico flowers form a strongly reduced tube while their limbs are almost normal, while star flowers form a normal tube but very reduced and unpigmented limbs, showing that petunia petal morphogenesis is highly modular. Comparative transcriptome analysis of star, wico and wild-type petals revealed a strong down-regulation of the anthocyanin production pathway in star petals including its major regulatorANTHOCYANIN2 (AN2).We found that PhDEF directly binds toAN2regulatory sequencein vitroby gel shift assay, andin vivoby chromatin immunoprecipitation, suggesting that PhDEF directly activates the petal pigmentation pathway by activatingAN2. Altogether, we show that cell-layer specific homeotic activity in petunia petals differently impacts tube and limb development, revealing the relative importance of the different cell layers in the modular architecture of petunia petals.
Comparison of the Drug Entrapment Efficiency of Almond Gum (Badam Pisin) to Span-60 Niosomes by Folin-Ciocalteu Assay
Authors: Hari Krishnan R 
Published: April 2021

AbstractAlmond gum (Badam Gum/ Badam Pisin) is a natural polymer composed of mainly carbohydrates (>90%) which makes it a potential candidate in targeted drug delivery. It contains 46% L-arabinose which is known to have fluid entrapment capacity. Various methods of drug targeting against tumor have been developed but due to poor solubility in body fluids, the bioavailability of the drug is reduced and so is its effectiveness. Almond gum is known to be water-soluble so the required bioavailability will be achieved and the drug dosage will also be minimal. Since it is of natural origin side effects will be less compared to that of artificially prepared drugs. Studies show that almond gum is known to have various health benefits including increasing immunity and acting as a coolant.Terminalia catappa(Indian almond), the source of almond gum is abundant in the Indian subcontinent hence making it more economical than chemical surfactants. The objective of this study is to determine whether Almond gum has a higher drug entrapment efficiency than that of Niosomes.
A global map of human pressures on tropical coral reefs
Authors: Andrello Marco , Darling Emily , Wenger Amelia , Suárez-Castro Andrés F. , Gelfand Sharla , Ahmadia Gabby N. 
Published: April 2021

AbstractAs human activities on the world’s oceans intensify, mapping human pressures is essential to develop appropriate conservation strategies and prioritize investments with limited resources. Here, we map non-climatic pressures on coral reefs using the latest quantitative data layers on fishing, nitrogen and sediment pollution, coastal and industrial development, and tourism. Across 54,596 coral reef pixels worldwide, we identify the top-ranked local pressure and estimate a cumulative pressure index mapped at 0.05-degree (∼5 km) resolution. Fishing was the most common top-ranked pressure followed by water pollution (nutrients and sediments), although there is substantial variation by regions. We also find that local pressures are similar inside and outside a proposed global portfolio of coral reef climate refugia. We provide the best available information to inform critical conservation strategies and ensure local pressures are effectively managed to increase the likelihood of the persistence of coral reefs to climate change.
Decisions in an Innate Behavioral Sequence
Authors: Cury Kevin M. , Axel Richard 
Published: April 2021

SUMMARYInnate behaviors are comprised of ordered sequences of component actions that progress to satisfy drives. We have characterized the structure of egg-laying behavior inDrosophilain detail and observed that the sequence is not merely comprised of motor acts but also acts of sensory exploration that govern the transitions between component actions. We have identified a cluster of internal sensory neurons that provide information about the progression of the egg during ovipositor burrowing, a behavior necessary for the subterraneous deposition of the egg. These neurons impart sensory feedback that allows burrowing to continue to egg deposition or to abort in favor of further exploration. Diminished activity of these neurons upon completed egg expulsion may initiate the transition to the final phase of egg-laying, allowing the cycle to repeat. Sensory feedback therefore plays a critical role at decision points between transitions affording innate behaviors with an adaptive flexibility.
The global ocean size-spectrum from bacteria to whales
Authors: Hatton Ian A. , Heneghan Ryan F. , Bar-On Yinon M. , Galbraith Eric D. 
Published: April 2021

AbstractIt has long been hypothesized that aquatic biomass is evenly distributed among logarithmic body mass size-classes. Although this community structure has been observed locally among plankton groups, its generality has never been formally tested across all marine life, nor have its impacts by humans been broadly assessed. Here, we bring together data at the global scale to test the hypothesis from bacteria to whales. We find that biomass within most order of magnitude size-classes is indeed remarkably constant, near 1 Gt wet weight (1015grams), but that bacteria and whales are markedly above and below this value, respectively. Furthermore, human impacts have significantly truncated the upper one-third of the spectrum. Size-spectrum theory has yet to provide an explanation for what is possibly life’s largest scale regularity.One Sentence SummaryHuman activities have fundamentally altered one of life’s largest scale patterns; a global power law size distribution spanning bacteria to whales.
A daily-updated database and tools for comprehensive SARS-CoV-2 mutation-annotated trees
Authors: McBroome Jakob , Thornlow Bryan , Hinrichs Angie S. , De Maio Nicola , Goldman Nick , Haussler David , Corbett-Detig Russell , Turakhia Yatish 
Published: April 2021

AbstractThe vast scale of SARS-CoV-2 sequencing data has made it increasingly challenging to comprehensively analyze all available data using existing tools and file formats. To address this, we present a database of SARS-CoV-2 phylogenetic trees inferred with unrestricted public sequences, which we update daily to incorporate new sequences. Our database uses the recently-proposed mutation-annotated tree (MAT) format to efficiently encode the tree with branches labeled with parsimony-inferred mutations as well as Nextstrain clade and Pango lineage labels at clade roots. As of June 9, 2021, our SARS-CoV-2 MAT consists of 834,521 sequences and provides a comprehensive view of the virus’ evolutionary history using public data. We also present matUtils – a command-line utility for rapidly querying, interpreting and manipulating the MATs. Our daily-updated SARS-CoV-2 MAT database and matUtils software are available at http://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/UShER_SARS-CoV-2/ and https://github.com/yatisht/usher, respectively.
Integrative RNA-Seq analysis ofCapsicum annuum L.-Phytophthora capsici L.pathosystem reveals molecular cross-talk and activation of host defence response
Authors: Rabuma Tilahun , Gupta Om Prakash , Yadav Manju , Chhokar Vinod 
Published: April 2021

AbstractBackgroundChili pepper (Capsicum annuumL.) being one of an important member of the Solanaceae family, and its productivity is highly affected by the fungal pathogenPhytophthora capsiciL. Other to CM-344, the unavailability of resistant landraces to all possible strains ofP. capsiciimposes a serious threat to its global production. This is because of our current understanding of the molecular mechanisms associated with the defence response inC. annuum-P. capsicipathosystem is limited. Therefore, the current study used RNA-seq technology to dissect the genes associated with defence response againstP. capsiciinfection in two contrasting landraces,i.e.GojamMecha_9086 (Resistant) and Dabat_80045 (susceptible) exposed toP. capsiciinfection.ResultsThe transcriptomes from 4 leaf samples (RC, RI, SC and SI) of chili pepper resulted in a total of 1,18, 879 assembled transcripts (with a mean TL of 813.23bp and N50 of 1,277bp) along with 52,384 pooled unigenes with (mean UL of 1029.36 bp and N50 of 1,403bp). The enrichment analysis of the transcripts indicated 23 different KEGG pathways under five main categories. Further, 774 and 484 differentially expressed genes (DEGs) were obtained from RC vs. RI and SC vs. SI leaf samples, respectively. Of these, 57 DEGs were found to be associated with defence responses againstP. capsiciinfection. The defence-related genes, such asLTPL, defensin J1-2-like, peroxidase 5-like, UGT, and GRP proteins-like, were more significantly upregulated in RC vs. RI. Furthermore, RT-qPCR analysis of six randomly selected genes validated the results of Illumina NextSeq500 sequencing results. Furthermore, a total of 58 TF families (bHLH most abundant) and 2,095 protein families (Protein kinase, PF00069, most abundant) were observed across all the samples with maximum hits in RI and SI samples.ConclusionsRNA-Seq analysis of chili pepper’s duringP.capsiciinfection revealed differential regulation of genes associated with defence and signaling response with shared coordination of molecular function, cellular component and biological processing. The results presented here would enhance our present understanding of the defence response in chili pepper againstP. capsiciinfection, which could be utilized by the molecular breeders to develop resistant chili genotypes.
Deuterium Magnetic Resonance Spectroscopy of Early Treatment-Induced Changes in Tumour Lactatein vitro
Authors: Tan Josephine L , Djayakarsana Daniel , Wang Hanzhi , Chan Rachel W , Bailey Colleen , Lau Angus Z 
Published: April 2021

AbstractElevated production of lactate is a key characteristic of aberrant tumour cell metabolism and can be non-invasively measured as an early marker of tumour response using deuterium (2H) magnetic resonance spectroscopy (MRS). Following treatment, changes in the2H-labeled lactate signal could identify tumour cell death or impaired metabolic function, which precede morphological changes conventionally used to assess tumour response. In this work, the association between apoptotic cell death, extracellular lactate concentration, and early treatment-induced changes in the2H-labeled lactate signal was established in anin vitrotumour model. Experiments were conducted at 7 T on acute myeloid leukemia cells which had been treated with 10 µg/mL of the chemotherapeutic agent cisplatin. At 24 and 48 hours after cisplatin treatment, the cells were injected with 20 mM of [6,6’-2H2]glucose and scanned over two hours using a two-dimensional2H MR spectroscopic imaging sequence. The resulting signals from2H-labeled glucose, lactate, and water were quantified using a spectral fitting algorithm implemented on the OXford Spectroscopy Analysis (OXSA) MATLAB toolbox. After scanning, the cells were processed for histological stains (TUNEL [terminal deoxynucleotidyl transferase UTP nick end labeling] and H&E [hematoxylin and eosin]) to assess apoptotic area fraction and cell morphology respectively, while a colorimetric assay was used to measure extracellular lactate concentrations in the supernatant. Significantly lower levels of2H-labeled lactate were observed in the 48-hour treated cells compared to the untreated and 24-hour treated cells, and these changes were significantly correlated with an increase in apoptotic fraction and a decrease in extracellular lactate. By establishing the biological processes associated with treatment-induced changes in the2H-labeled lactate signal, these findings suggest that2H MRS of lactate may be valuable in evaluating early tumour response.
Differential Effects of endogenous and exogenous attention on sensory tuning
Authors: Fernández Antonio , Okun Sara , Carrasco Marisa 
Published: April 2021

AbstractCovert spatial attention (without concurrent eye movements) improves performance in many visual tasks (e.g., orientation discrimination and visual search). However, both covert attention systems, endogenous (voluntary) and exogenous (involuntary), exhibit differential effects on performance in tasks mediated by spatial and temporal resolution suggesting an underlying mechanistic difference. We investigated whether these differences manifest in sensory tuning by assessing whether and how endogenous and exogenous attention differentially alter the representation of two basic visual dimensions: orientation and spatial frequency (SF). The same human observers detected a vertical grating embedded in noise in two separate experiments (with cues to elicit either endogenous or exogenous attention) and reverse correlation was used to infer the underlying neural representation from behavioral responses. Both endogenous and exogenous attention similarly improved performance at the attended location by enhancing the gain of all orientations without changing tuning width. In the SF dimension, endogenous attention enhanced the gain of SFs above and below the target SF, whereas exogenous attention only enhanced those above. Additionally, exogenous attention shifted peak sensitivity to SFs above the target SF, whereas endogenous attention did not. Both covert attention systems modulated sensory tuning via the same computation (gain changes). However, there were differences in the strength of the gain. Compared to endogenous attention, exogenous attention had a stronger orientation gain enhancement but a weaker overall SF gain enhancement. These differences in sensory tuning may underlie differential effects of endogenous and exogenous attention on performance.