bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fensomea setacea, gen. & sp. nov. (Cladopyxidaceae, Dinophyceae), is neither gonyaulacoid nor peridinioid as inferred from morphological and molecular data
Authors: Gottschling Marc , Carbonell-Moore Maria Consuelo , Mertens Kenneth Neil , Kirsch Monika , Elbrächter Malte , Tillmann Urban 
Published: June 2021

AbstractDinophyte evolution is essentially inferred from the pattern of thecal plates, and two different labelling systems are used for the important subgroups Gonyaulacales and Peridiniales. The partiform hypotheca of cladopyxidoid dinophytes fits into the morphological concepts of neither group, although they are assigned to the Gonyaulacales. Here, we describe the thecate dinophyte Fensomea setacea, gen. & sp. nov., which has a cladopyxidoid tabulation. The cells displayed a Kofoidean plate formula APC, 3′, 4a, 7″, 7C, 6S, 6′′′, 2′′′′, and slender processes were randomly distributed over the echinate or baculate surface. In addition, we obtained rRNA sequences of F. setacea, gen. & sp. nov., but dinophytes that exhibit a partiform hypotheca did not show a close relationship to Gonyaulacales. Character evolution of thecate dinophytes may have progressed from the ancestral state of six postcingular plates, and two more or less symmetrically arranged antapical plates, towards patterns of only five postcingular plates (Peridiniales) or more asymmetrical configurations (Gonyaulacales). Based on our phylogenetic reconsiderations the contact between the posterior sulcal plate and the first postcingular plate, as well as the contact between an antapical plate and the distalmost postcingular plate, do not represent a rare, specialized gonyaulacoid plate configuration (i.e., the partiform hypotheca of cladopyxidoid dinophytes). Instead, these contacts correspond to the common and regular configuration of peridinioid (and other) dinophytes.
Extraordinary diversity of telomeres, telomerase RNAs and their template regions in Saccharomycetaceae
Authors: Peska Vratislav , Fajkus Petr , Bubeník Michal , Brázda Václav , Bohálová Natália , Dvořáček Vojtěch , Fajkus Jiří , Garcia Sònia 
Published: June 2021

AbstractTelomerase RNA (TR) carries the template for synthesis of telomere DNA and provides a scaffold for telomerase assembly. Fungal TRs are long and have been compared to higher eukaryotes, where they show considerable diversity within phylogenetically close groups. TRs of several Saccharomycetaceae were recently identified, however, many of these remained uncharacterised in the template region. Here we show that this is mainly due to high variability in telomere sequence. We predicted the telomere sequences using Tandem Repeats Finder and then we identified corresponding putative template regions in TR candidates. Remarkably long telomere units and the corresponding putative TRs were found in Tetrapisispora species. Notably, variable lengths of the annealing sequence of the template region (1–10 nt) were found. Consequently, species with the same telomere sequence may not harbour identical TR templates. Thus, TR sequence alone can be used to predict a template region and telomere sequence, but not to determine these exactly. A conserved feature of telomere sequences, tracts of adjacent Gs, led us to test the propensity of individual telomere sequences to form G4. The results show highly diverse values of G4-propensity, indicating the lack of ubiquitous conservation of this feature across Saccharomycetaceae.
Molecular mechanism of calcium induced trimerization of C1q-like domain of otolin-1 from human and zebrafish
Authors: Hołubowicz Rafał , Ożyhar Andrzej , Dobryszycki Piotr 
Published: June 2021

AbstractThe C1q superfamily includes proteins involved in innate immunity, insulin sensitivity, biomineralization and more. Among these proteins is otolin-1, which is a collagen-like protein that forms a scaffold for the biomineralization of inner ear stones in vertebrates. The globular C1q-like domain (gC1q), which is the most conserved part of otolin-1, binds Ca2+ and stabilizes its collagen-like triple helix. The molecular details of the assembly of gC1q otolin-1 trimers are not known. Here, we substituted putative Ca2+-binding acidic residues of gC1q otolin-1 with alanine to analyse how alanine influences the formation of gC1q trimers. We used human and zebrafish gC1q otolin-1 to assess how evolutionary changes affected the function of the protein. Surprisingly, the mutated forms of gC1q otolin-1 trimerized even in the absence of Ca2+, although they were less stable than native proteins saturated with Ca2+. We also found that the zebrafish gC1q domain was less stable than the human homologue under all tested conditions and became stabilized at higher concentrations of Ca2+, which showed that specific interactions leading to the neutralization of the negative charge at the axis of a gC1q trimer by Ca2+ are required for the trimers to form. Moreover, human gC1q otolin-1 seems to be optimized to function at lower concentrations of Ca2+, which is consistent with reported Ca2+ concentrations in the endolymphs of fish and mammals. Our results allow us to explain the molecular mechanism of assembly of proteins from the C1q superfamily, the modulating role of Ca2+ and expand the knowledge of biomineralization of vertebrate inner ear stones: otoliths and otoconia.
Russian forest sequesters substantially more carbon than previously reported
Authors: Schepaschenko Dmitry , Moltchanova Elena , Fedorov Stanislav , Karminov Victor , Ontikov Petr , Santoro Maurizio , See Linda , Kositsyn Vladimir , Shvidenko Anatoly , Romanovskaya Anna , Korotkov Vladimir , Lesiv Myroslava , Bartalev Sergey , Fritz Steffen , Shchepashchenko Maria , Kraxner Florian 
Published: June 2021

AbstractSince the collapse of the Soviet Union and transition to a new forest inventory system, Russia has reported almost no change in growing stock (+ 1.8%) and biomass (+ 0.6%). Yet remote sensing products indicate increased vegetation productivity, tree cover and above-ground biomass. Here, we challenge these statistics with a combination of recent National Forest Inventory and remote sensing data to provide an alternative estimate of the growing stock of Russian forests and to assess the relative changes in post-Soviet Russia. Our estimate for the year 2014 is 111 ± 1.3 × 109 m3, or 39% higher than the value in the State Forest Register. Using the last Soviet Union report as a reference, Russian forests have accumulated 1163 × 106 m3 yr-1 of growing stock between 1988–2014, which balances the net forest stock losses in tropical countries. Our estimate of the growing stock of managed forests is 94.2 × 109 m3, which corresponds to sequestration of 354 Tg C yr-1 in live biomass over 1988–2014, or 47% higher than reported in the National Greenhouse Gases Inventory.
The effect of cane vigour on the kiwifruit (Actinidia chinensis) and kiwiberry (Actinidia arguta) quality
Authors: Medic Aljaz , Hudina Metka , Veberic Robert 
Published: June 2021

AbstractKiwifruit has not been studied as much as other well-known fruits especially when it comes to studies about plant vigour and training systems. The aim of the study was to determine the importance of cane vigour of Actinidia chinensis var. deliciosa ‘Hayward’ and Actinidia arguta ‘Issai’ in order to develop the proper pruning technique that results in the best fruit quality. In addition, the effect of storage parameters such as weight, firmness and quality of the fruit was also studied. The study showed that the fruit size and weight are lower in low vigour canes in A. arguta, in contrast to A. chinensis, where the fruit size and weight are smaller on high-vigorous canes. For A. arguta, it is recommended to choose high-vigour canes as the optimal fruit wood during pruning. In this way, the fruits will ripen more evenly. The other possibility is to perform the harvest two to three times per season to achieve a more uniform fruit quality. In the case of A. chinensis the fruit are less variable between different cane vigour, so harvesting can be done in a single picking. In A. chinensis the less vigorous canes tend to show a slightly better fruit quality.
Exploring nine simultaneously occurring transients on April 12th 1950
Authors: Villarroel Beatriz , Marcy Geoffrey W. , Geier Stefan , Streblyanska Alina , Solano Enrique , Andruk Vitaly N. , Shultz Matthew E. , Gupta Alok C. , Mattsson Lars 
Published: June 2021

AbstractNine point sources appeared within half an hour on a region within $$\sim $$
∼
10 arcmin of a red-sensitive photographic plate taken in April 1950 as part of the historic Palomar Sky Survey. All nine sources are absent on both previous and later photographic images, and absent in modern surveys with CCD detectors which go several magnitudes deeper. We present deep CCD images with the 10.4-m Gran Telescopio Canarias, reaching brightness $$r \sim 26$$

r
∼
26

mag, that reveal possible optical counterparts, although these counterparts could equally well be just chance projections. The incidence of transients in the investigated photographic plate is far higher than expected from known detection rates of optical counterparts to e.g. flaring dwarf stars, Fast Radio Bursts, Gamma Ray Bursts or microlensing events. One possible explanation is that the plates have been subjected to an unknown type of contamination producing mainly point sources with of varying intensities along with some mechanism of concentration within a radius of $$\sim $$
∼
10 arcmin on the plate. If contamination as an explanation can be fully excluded, another possibility is fast (t $$<0.5$$

<
0.5

s) solar reflections from objects near geosynchronous orbits. An alternative route to confirm the latter scenario is by looking for images from the First Palomar Sky Survey where multiple transients follow a line.
Increased duration of pollen and mold exposure are linked to climate change
Authors: Paudel Bibek , Chu Theodore , Chen Meng , Sampath Vanitha , Prunicki Mary , Nadeau Kari C. 
Published: June 2021

AbstractPollen and molds are environmental allergens that are affected by climate change. As pollen and molds exhibit geographical variations, we sought to understand the impact of climate change (temperature, carbon dioxide (CO2), precipitation, smoke exposure) on common pollen and molds in the San Francisco Bay Area, one of the largest urban areas in the United States. When using time-series regression models between 2002 and 2019, the annual average number of weeks with pollen concentrations higher than zero increased over time. For tree pollens, the average increase in this duration was 0.47 weeks and 0.51 weeks for mold spores. Associations between mold, pollen and meteorological data (e.g., precipitation, temperature, atmospheric CO2, and area covered by wildfire smoke) were analyzed using the autoregressive integrated moving average model. We found that peak concentrations of weed and tree pollens were positively associated with temperature (p < 0.05 at lag 0–1, 0–4, and 0–12 weeks) and precipitation (p < 0.05 at lag 0–4, 0–12, and 0–24 weeks) changes, respectively. We did not find clear associations between pollen concentrations and CO2levels or wildfire smoke exposure. This study’s findings suggest that spore and pollen activities are related to changes in observed climate change variables.
Correlative Microscopy: a tool for understanding soil weathering in modern analogues of early terrestrial biospheres
Authors: Mitchell R. L. , Davies P. , Kenrick P. , Volkenandt T. , Pleydell-Pearce C. , Johnston R. 
Published: June 2021

AbstractCorrelative imaging provides a method of investigating complex systems by combining analytical (chemistry) and imaging (tomography) information across dimensions (2D-3D) and scales (centimetres-nanometres). We studied weathering processes in a modern cryptogamic ground cover from Iceland, containing early colonizing, and evolutionary ancient, communities of mosses, lichens, fungi, and bacteria. Targeted multi-scale X-ray Microscopy of a grain in-situ within a soil core revealed networks of surficial and internal features (tunnels) originating from organic-rich surface holes. Further targeted 2D grain characterisation by optical microscopy (OM), scanning electron microscopy (SEM), and energy dispersive X-ray spectroscopy (SEM–EDS), following an intermediate manual correlative preparation step, revealed Fe-rich nodules within the tunnels. Finally, nanotomographic imaging by focussed ion beam microscopy (FIB-SEM) revealed coccoid and filamentous-like structures within subsurface tunnels, as well as accumulations of Fe and S in grain surface crusts, which may represent a biological rock varnish/glaze. We attribute these features to biological processes. This work highlights the advantages and novelty of the correlative imaging approach, across scales, dimensions, and modes, to investigate biological weathering processes. Further, we demonstrate correlative microscopy as a means of identifying fingerprints of biological communities, which could be used in the geologic rock record and on extra-terrestrial bodies.
Isolation and characterization of a new cold-active protease from psychrotrophic bacteria of Western Himalayan glacial soil
Authors: Farooq Saleem , Nazir Ruqeya , Ganai Shabir Ahmad , Ganai Bashir Ahmad 
Published: June 2021

AbstractAs an approach to the exploration of cold-active enzymes, in this study, we isolated a cold-active protease produced by psychrotrophic bacteria from glacial soils of Thajwas Glacier, Himalayas. The isolated strain BO1, identified as Bacillus pumilus, grew well within a temperature range of 4–30 °C. After its qualitative and quantitative screening, the cold-active protease (Apr-BO1) was purified. The Apr-BO1 had a molecular mass of 38 kDa and showed maximum (37.02 U/mg) specific activity at 20 °C, with casein as substrate. It was stable and active between the temperature range of 5–35 °C and pH 6.0–12.0, with an optimum temperature of 20 °C at pH 9.0. The Apr-BO1 had low Km value of 1.0 mg/ml and Vmax 10.0 µmol/ml/min. Moreover, it displayed better tolerance to organic solvents, surfactants, metal ions and reducing agents than most alkaline proteases. The results exhibited that it effectively removed the stains even in a cold wash and could be considered a decent detergent additive. Furthermore, through protein modelling, the structure of this protease was generated from template, subtilisin E of Bacillus subtilis (PDB ID: 3WHI), and different methods checked its quality. For the first time, this study reported the protein sequence for psychrotrophic Apr-BO1 and brought forth its novelty among other cold-active proteases.
Remodeling of bronchial epithelium caused by asthmatic inflammation affects its response to rhinovirus infection
Authors: Jakiela Bogdan , Rebane Ana , Soja Jerzy , Bazan-Socha Stanislawa , Laanesoo Anet , Plutecka Hanna , Surmiak Marcin , Sanak Marek , Sladek Krzysztof , Bochenek Grazyna 
Published: June 2021

AbstractHuman rhinoviruses (HRV) are frequent cause of asthma exacerbations, however the influence of airway inflammation on the severity of viral infection is poorly understood. Here, we investigated how cytokine-induced remodeling of airway epithelium modulates antiviral response. We analyzed gene expression response in in vitro differentiated bronchial epithelium exposed to cytokines and next infected with HRV16. IL-13-induced mucous cell metaplasia (MCM) was associated with impaired ciliogenesis and induction of antiviral genes, resulting in lower susceptibility to HRV. Epithelial-mesenchymal transition caused by TGF-β was associated with increased virus replication and boosted innate response. Moreover, HRV infection per se caused transient upregulation of MCM markers and growth factors, followed by low-level virus replication and shedding. Our data suggest that the outcome of HRV infection depends on the type of lower airway inflammation and the extent of epithelial damage. Type-2 inflammation (eosinophilic asthma) may induce antiviral state of epithelium and decrease virus sensitivity, while growth factor exposure during epithelial repair may facilitate virus replication and inflammatory response. Additionally, responses to HRV were similar in cells obtained from asthma patients and control subjects, which implicates that antiviral mechanisms are not intrinsically impaired in asthma, but may develop in the presence of uncontrolled airway inflammation.
Inhibitory and facilitatory effects of phonological and orthographic similarity on L2 word recognition across modalities in bilinguals
Authors: Frances Candice , Navarra-Barindelli Eugenia , Martin Clara D. 
Published: June 2021

AbstractLanguage perception studies on bilinguals often show that words that share form and meaning across languages (cognates) are easier to process than words that share only meaning. This facilitatory phenomenon is known as the cognate effect. Most previous studies have shown this effect visually, whereas the auditory modality as well as the interplay between type of similarity and modality remain largely unexplored. In this study, highly proficient late Spanish–English bilinguals carried out a lexical decision task in their second language, both visually and auditorily. Words had high or low phonological and orthographic similarity, fully crossed. We also included orthographically identical words (perfect cognates). Our results suggest that similarity in the same modality (i.e., orthographic similarity in the visual modality and phonological similarity in the auditory modality) leads to improved signal detection, whereas similarity across modalities hinders it. We provide support for the idea that perfect cognates are a special category within cognates. Results suggest a need for a conceptual and practical separation between types of similarity in cognate studies. The theoretical implication is that the representations of items are active in both modalities of the non-target language during language processing, which needs to be incorporated to our current processing models.
GLT1 gene delivery based on bone marrow-derived cells ameliorates motor function and survival in a mouse model of ALS
Authors: Ohashi Natsuko , Terashima Tomoya , Katagi Miwako , Nakae Yuki , Okano Junko , Suzuki Yoshihisa , Kojima Hideto 
Published: June 2021

AbstractAmyotrophic lateral sclerosis (ALS) is an intractable neurodegenerative disease. CD68-positive bone marrow (BM)-derived cells (BMDCs) accumulate in the pathological lesion in the SOD1(G93A) ALS mouse model after BM transplantation (BMT). Therefore, we investigated whether BMDCs can be applied as gene carriers for cell-based gene therapy by employing the accumulation of BMDCs. In ALS mice, YFP reporter signals were observed in 12–14% of white blood cells (WBCs) and in the spinal cord via transplantation of BM after lentiviral vector (LV) infection. After confirmation of gene transduction by LV with the CD68 promoter in 4–7% of WBCs and in the spinal cord of ALS mice, BM cells were infected with LVs expressing glutamate transporter (GLT) 1 that protects neurons from glutamate toxicity, driven by the CD68 promoter, which were transplanted into ALS mice. The treated mice showed improvement of motor behaviors and prolonged survival. Additionally, interleukin (IL)-1β was significantly suppressed, and IL-4, arginase 1, and FIZZ were significantly increased in the mice. These results suggested that GLT1 expression by BMDCs improved the spinal cord environment. Therefore, our gene therapy strategy may be applied to treat neurodegenerative diseases such as ALS in which BMDCs accumulate in the pathological lesion by BMT.
ELV-N32 and RvD6 isomer decrease pro-inflammatory cytokines, senescence programming, ACE2 and SARS-CoV-2-spike protein RBD binding in injured cornea
Authors: Pham Thang L. , He Jiucheng , Kakazu Azucena H. , Calandria Jorgelina , Do Khanh V. , Nshimiyimana Robert , Lam Ting F. , Petasis Nicos A. , Bazan Haydee E. P. , Bazan Nicolas G. 
Published: June 2021

AbstractThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection that causes coronavirus disease 2019 (COVID-19) has resulted in a pandemic affecting the most vulnerable in society, triggering a public health crisis and economic collapse around the world. Effective treatments to mitigate this viral infection are needed. Since the eye is a route of virus entrance, we use an in vivo rat model of corneal inflammation as well as human corneal epithelial cells (HCEC) in culture challenged with IFNγ as models of the eye surface to study this issue. We explore ways to block the receptor-binding domain (RBD) of SARS-CoV-2 Spike (S) protein to angiotensin-converting enzyme 2 (ACE2). We found that the lipid mediators, elovanoid (ELV)-N32 or Resolvin D6-isomer (RvD6i) decreased the expression of the ACE2 receptor, furin, and integrins in damaged corneas or IFNγ-stimulated HCEC. There was also a concomitant decrease in the binding of Spike RBD with the lipid treatments. Using RNA-seq analysis, we uncovered that the lipid mediators also attenuated the expression of pro-inflammatoy cytokines participating in hyper-inflammation and senescence programming. Thus, the bioactivity of these lipid mediators will contribute to open therapeutic avenues to counteract virus attachment and entrance to the body.
X-chromosomal STR based genetic polymorphisms and demographic history of Sri Lankan ethnicities and their relationship with global populations
Authors: Perera Nandika , Galhena Gayani , Ranawaka Gaya 
Published: June 2021

AbstractA new 16 X-short tandem repeat (STR) multiplex PCR system has recently been developed for Sr Lankans, though its applicability in evolutionary genetics and forensic investigations has not been thoroughly assessed. In this study, 838 unrelated individuals covering all four major ethnic groups (Sinhalese, Sri Lankan Tamils, Indian Tamils and Moors) in Sri Lanka were successfully genotyped using this new multiplex system. The results indicated a high forensic efficiency for the tested loci in all four ethnicities confirming its suitability for forensic applications of Sri Lankans. Allele frequency distribution of Indian Tamils showed subtle but statistically significant differences from those of Sinhalese and Moors, in contrast to frequency distributions previously reported for autosomal STR alleles. This suggest a sex biased demographic history among Sri Lankans requiring a separate X-STR allele frequency database for Indian Tamils. Substantial differences observed in the patterns of LD among the four groups demand the use of a separate haplotype frequency databases for each individual ethnicity. When analysed together with other 14 world populations, all Sri Lankan ethnicities except Indian Tamils clustered closely with populations from Indian Bhil tribe, Bangladesh and Europe reflecting their shared Indo-Aryan ancestry.