bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fire blight QTL analysis in a multi-family apple population identifies a reduced-susceptibility allele in ‘Honeycrisp’
Authors: Kostick Sarah A. , Teh Soon Li , Norelli John L. , Vanderzande Stijn , Peace Cameron , Evans Kate M. 
Published: February 2021

AbstractBreeding apple cultivars with resistance offers a potential solution to fire blight, a damaging bacterial disease caused by Erwinia amylovora. Most resistance alleles at quantitative trait loci (QTLs) were previously characterized in diverse Malus germplasm with poor fruit quality, which reduces breeding utility. This study utilized a pedigree-based QTL analysis approach to elucidate the genetic basis of resistance/susceptibility to fire blight from multiple genetic sources in germplasm relevant to U.S. apple breeding programs. Twenty-seven important breeding parents (IBPs) were represented by 314 offspring from 32 full-sib families, with ‘Honeycrisp’ being the most highly represented IBP. Analyzing resistance/susceptibility data from a two-year replicated field inoculation study and previously curated genome-wide single nucleotide polymorphism data, QTLs were consistently mapped on chromosomes (Chrs.) 6, 7, and 15. These QTLs together explained ~28% of phenotypic variation. The Chr. 6 and Chr. 15 QTLs colocalized with previously reported QTLs, while the Chr. 7 QTL is possibly novel. ‘Honeycrisp’ inherited a rare reduced-susceptibility allele at the Chr. 6 QTL from its grandparent ‘Frostbite’. The highly resistant IBP ‘Enterprise’ had at least one putative reduced-susceptibility allele at all three QTLs. In general, lower susceptibility was observed for individuals with higher numbers of reduced-susceptibility alleles across QTLs. This study highlighted QTL mapping and allele characterization of resistance/susceptibility to fire blight in complex pedigree-connected apple breeding germplasm. Knowledge gained will enable more informed parental selection and development of trait-predictive DNA tests for pyramiding favorable alleles and selection of superior apple cultivars with resistance to fire blight.
Functional conservation of the grapevine candidate gene INNER NO OUTER for ovule development and seed formation
Authors: di Rienzo Valentina , Imanifard Zahra , Mascio Isabella , Gasser Charles S. , Skinner Debra J. , Pierri Ciro Leonardo , Marini Martina , Fanelli Valentina , Sabetta Wilma , Montemurro Cinzia , Bellin Diana 
Published: February 2021

AbstractSeedlessness represents a highly appreciated trait in table grapes. Based on an interesting case of seedless fruit production described in the crop speciesAnnona squamosa, we focused on theVitis vinifera INNER NO OUTER (INO)gene as a candidate. This gene encodes a transcription factor belonging to theYABBYfamily involved in the determination of abaxial identity in several organs. InArabidopsis thaliana, this gene was shown to be essential for the formation and asymmetric growth of the ovule outer integument and its mutation leads to a phenotypic defect of ovules and failure in seed formation. In this study, we identified in silico theV. viniferaorthologue and investigated its phylogenetic relationship toINOgenes from other species and its expression in different organs in seeded and seedless varieties. Applying cross-species complementation, we have tested its functionality in the Arabidopsisino-1 mutant. We show that theV. viniferaINO successfully rescues the ovule outer integument growth and seeds set and also partially complements the outer integument asymmetric growth in the Arabidopsis mutant, differently from orthologues from other species. These data demonstrate that VviINO retains similar activity and protein targets in grapevine as in Arabidopsis. Potential implications for grapevine breeding are discussed.
Isolation and comparative proteomic analysis of mitochondria from the pulp of ripening citrus fruit
Authors: Li Xin , Chai Yingfang , Yang Hongbin , Tian Zhen , Li Chengyang , Xu Rangwei , Shi Chunmei , Zhu Feng , Zeng Yunliu , Deng Xiuxin , Wang Pengwei , Cheng Yunjiang 
Published: February 2021

AbstractMitochondria are crucial for the production of primary and secondary metabolites, which largely determine the quality of fruit. However, a method for isolating high-quality mitochondria is currently not available in citrus fruit, preventing high-throughput characterization of mitochondrial functions. Here, based on differential and discontinuous Percoll density gradient centrifugation, we devised a universal protocol for isolating mitochondria from the pulp of four major citrus species, including satsuma mandarin, ponkan mandarin, sweet orange, and pummelo. Western blot analysis and microscopy confirmed the high purity and intactness of the isolated mitochondria. By using this protocol coupled with a label-free proteomic approach, a total of 3353 nonredundant proteins were identified. Comparison of the four mitochondrial proteomes revealed that the proteins commonly detected in all proteomes participate in several typical metabolic pathways (such as tricarboxylic acid cycle, pyruvate metabolism, and oxidative phosphorylation) and pathways closely related to fruit quality (such as γ-aminobutyric acid (GABA) shunt, ascorbate metabolism, and biosynthesis of secondary metabolites). In addition, differentially abundant proteins (DAPs) between different types of species were also identified; these were found to be mainly involved in fatty acid and amino acid metabolism and were further confirmed to be localized to the mitochondria by subcellular localization analysis. In summary, the proposed protocol for the isolation of highly pure mitochondria from different citrus fruits may be used to obtain high-coverage mitochondrial proteomes, which can help to establish the association between mitochondrial metabolism and fruit storability or quality characteristics of different species and lay the foundation for discovering novel functions of mitochondria in plants.
Three-dimensional low shear culture of Mycobacterium bovis BCG induces biofilm formation and antimicrobial drug tolerance
Authors: Cantillon Daire , Wroblewska Justyna , Cooper Ian , Newport Melanie J. , Waddell Simon J. 
Published: February 2021

AbstractMycobacteria naturally grow as corded biofilms in liquid media without detergent. Such detergent-free biofilm phenotypes may reflect the growth pattern of bacilli in tuberculous lung lesions. New strategies are required to treat tuberculosis, which is responsible for more deaths each year than any other bacterial disease. The lengthy 6-month regimen for drug-sensitive tuberculosis is necessary to remove antimicrobial drug tolerant populations of bacilli that persist through drug therapy. The role of biofilm-like growth in the generation of these sub-populations remains poorly understood despite the hypothesised clinical significance and mounting evidence of biofilms in pathogenesis. We adapt a three-dimensional Rotary Cell Culture System to model M. bovis BCG biofilm growth in low-shear detergent-free liquid suspension. Importantly, biofilms form without attachment to artificial surfaces and without severe nutrient starvation or environmental stress. Biofilm-derived planktonic bacilli are tolerant to isoniazid and streptomycin, but not rifampicin. This phenotypic drug tolerance is lost after passage in drug-free media. Transcriptional profiling reveals induction of cell surface regulators, sigE and BCG_0559c alongside the ESX-5 secretion apparatus in these low-shear liquid-suspension biofilms. This study engineers and characterises mycobacteria grown as a suspended biofilm, illuminating new drug discovery pathways for this deadly disease.
Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes
Authors: Peng Xuefeng , Wilken St. Elmo , Lankiewicz Thomas S. , Gilmore Sean P. , Brown Jennifer L. , Henske John K. , Swift Candice L. , Salamov Asaf , Barry Kerrie , Grigoriev Igor V. , Theodorou Michael K. , Valentine David L. , O’Malley Michelle A. 
Published: February 2021

AbstractThe herbivore digestive tract is home to a complex community of anaerobic microbes that work together to break down lignocellulose. These microbiota are an untapped resource of strains, pathways and enzymes that could be applied to convert plant waste into sugar substrates for green biotechnology. We carried out more than 400 parallel enrichment experiments from goat faeces to determine how substrate and antibiotic selection influence membership, activity, stability and chemical productivity of herbivore gut communities. We assembled 719 high-quality metagenome-assembled genomes (MAGs) that are unique at the species level. More than 90% of these MAGs are from previously unidentified herbivore gut microorganisms. Microbial consortia dominated by anaerobic fungi outperformed bacterially dominated consortia in terms of both methane production and extent of cellulose degradation, which indicates that fungi have an important role in methane release. Metabolic pathway reconstructions from MAGs of 737 bacteria, archaea and fungi suggest that cross-domain partnerships between fungi and methanogens enabled production of acetate, formate and methane, whereas bacterially dominated consortia mainly produced short-chain fatty acids, including propionate and butyrate. Analyses of carbohydrate-active enzyme domains present in each anaerobic consortium suggest that anaerobic bacteria and fungi employ mostly complementary hydrolytic strategies. The division of labour among herbivore anaerobes to degrade plant biomass could be harnessed for industrial bioprocessing.
Synthesis of multi-organo-functionalized fibrous silica KCC-1 for highly efficient adsorption of acid fuchsine and acid orange II from aqueous solution
Authors: Soltani Roozbeh , Pelalak Rasool , Pishnamazi Mahboubeh , Marjani Azam , Albadarin Ahmad B. , Sarkar Shaheen M. , Shirazian Saeed 
Published: February 2021

AbstractMulti-functionalized fibrous silica KCC-1 (MF-KCC-1) bearing amine, tetrasulfide, and thiol groups was synthesized via a post-functionalization method and fully characterized by several methods such as FTIR, FESEM, EDX-Mapping, TEM, and N2 adsorption–desorption techniques. Due to abundant surface functional groups, accessible active adsorption sites, high surface area (572 m2 g−1), large pore volume (0.98 cm3 g−1), and unique fibrous structure, mesoporous MF-KCC-1 was used as a potential adsorbent for the uptake of acid fuchsine (AF) and acid orange II (AO) from water. Different adsorption factors such as pH of the dye solution, the amount of adsorbent, initial dye concentration, and contact time, affecting the uptake process were optimized and isotherm and kinetic studies were conducted to find the possible mechanism involved in the process. For both AF and AO dyes, the Langmuir isotherm model and the PFO kinetic model show the most agreement with the experimental data. According to the Langmuir isotherm, the calculated maximum adsorption capacity for AF and AO were found to be 574.5 mg g−1 and 605.9 mg g−1, respectively, surpassing most adsorption capacities reported until now which is indicative of the high potential of mesoporous MF-KCC-1 as an adsorbent for removal applications.
Context-dependent extinction learning emerging from raw sensory inputs: a reinforcement learning approach
Authors: Walther Thomas , Diekmann Nicolas , Vijayabaskaran Sandhiya , Donoso José R. , Manahan-Vaughan Denise , Wiskott Laurenz , Cheng Sen 
Published: February 2021

AbstractThe context-dependence of extinction learning has been well studied and requires the hippocampus. However, the underlying neural mechanisms are still poorly understood. Using memory-driven reinforcement learning and deep neural networks, we developed a model that learns to navigate autonomously in biologically realistic virtual reality environments based on raw camera inputs alone. Neither is context represented explicitly in our model, nor is context change signaled. We find that memory-intact agents learn distinct context representations, and develop ABA renewal, whereas memory-impaired agents do not. These findings reproduce the behavior of control and hippocampal animals, respectively. We therefore propose that the role of the hippocampus in the context-dependence of extinction learning might stem from its function in episodic-like memory and not in context-representation per se. We conclude that context-dependence can emerge from raw visual inputs.
Genetic variants of small airways and interstitial pulmonary disease in children
Authors: Alsamri Mohammed T. , Alabdouli Amnah , Alkalbani Alia M. , Iram Durdana , Tawil Mohamed I. , Antony Priya , Vijayan Ranjit , Souid Abdul-Kader 
Published: February 2021

AbstractGenetic variants of small airways and interstitial pulmonary disease have not been comprehensively studied. This cluster of respiratory disorders usually manifests from early infancy (‘lung disease in utero’). In this study, 24 variants linked to these entities are described. The variants involved two genes associated with surfactant metabolism dysfunction (ABCA3 and CSF2RB), two with pulmonary fibrosis (MUC5B and SFTP), one with bronchiectasis (SCNN1B), and one with alpha-1-antitrypsin deficiency (SERPINA1). A nonsense variant, MUC5B:c.16861G > T, p.Glu5621*, was found in homozygous state in two siblings with severe respiratory disease from birth. One of the siblings also had heterozygous SFTPA1:c.675C > G, p.Asn225Lys, which resulted in a more severe respiratory disease. The sibling with only the homozygous MUC5B variant had lung biopsy, which showed alveolar simplification, interstitial fibrosis, intra-alveolar lipid-laden macrophages, and foci of foreign body giant cell reaction in distal airspaces. Two missense variants, MUC5B:c.14936 T > C, p.Ile4979Thr (rs201287218) and MUC5B:c.16738G > A, p.Gly5580Arg (rs776709402), were also found in compound heterozygous state in two siblings with severe respiratory disease from birth. Overall, the results emphasize the need for genetic studies for patients with complex respiratory problems. Identifying pathogenic variants, such as those presented here, assists in effective family counseling aimed at genetic prevention. In addition, results of genetic studies improve the clinical care and provide opportunities for participating in clinical trials, such as those involving molecularly-targeted therapies.
Regenerative tissue filler for breast conserving surgery and other soft tissue restoration and reconstruction needs
Authors: Puls Theodore J. , Fisher Carla S. , Cox Abigail , Plantenga Jeannie M. , McBride Emma L. , Anderson Jennifer L. , Goergen Craig J. , Bible Melissa , Moller Tracy , Voytik-Harbin Sherry L. 
Published: February 2021

AbstractComplete removal of cancerous tissue and preservation of breast cosmesis with a single breast conserving surgery (BCS) is essential for surgeons. New and better options would allow them to more consistently achieve this goal and expand the number of women that receive this preferred therapy, while minimizing the need for re-excision and revision procedures or more aggressive surgical approaches (i.e., mastectomy). We have developed and evaluated a regenerative tissue filler that is applied as a liquid to defects during BCS prior to transitioning to a fibrillar collagen scaffold with soft tissue consistency. Using a porcine simulated BCS model, the collagen filler was shown to induce a regenerative healing response, characterized by rapid cellularization, vascularization, and progressive breast tissue neogenesis, including adipose tissue and mammary glands and ducts. Unlike conventional biomaterials, no foreign body response or inflammatory-mediated “active” biodegradation was observed. The collagen filler also did not compromise simulated surgical re-excision, radiography, or ultrasonography procedures, features that are important for clinical translation. When post-BCS radiation was applied, the collagen filler and its associated tissue response were largely similar to non-irradiated conditions; however, as expected, healing was modestly slower. This in situ scaffold-forming collagen is easy to apply, conforms to patient-specific defects, and regenerates complex soft tissues in the absence of inflammation. It has significant translational potential as the first regenerative tissue filler for BCS as well as other soft tissue restoration and reconstruction needs.
Label-free spectral imaging to study drug distribution and metabolism in single living cells
Authors: Alshammari Qamar A. , Pala Rajasekharreddy , Katzir Nir , Nauli Surya M. 
Published: February 2021

AbstractDuring drug development, evaluation of drug and its metabolite is an essential process to understand drug activity, stability, toxicity and distribution. Liquid chromatography (LC) coupled with mass spectrometry (MS) has become the standard analytical tool for screening and identifying drug metabolites. Unlike LC/MS approach requiring liquifying the biological samples, we showed that spectral imaging (or spectral microscopy) could provide high-resolution images of doxorubicin (dox) and its metabolite doxorubicinol (dox’ol) in single living cells. Using this new method, we performed measurements without destroying the biological samples. We calculated the rate constant of dox translocating from extracellular moiety into the cell and the metabolism rate of dox to dox’ol in living cells. The translocation rate of dox into a single cell for spectral microscopy and LC/MS approaches was similar (~ 1.5 pM min−1 cell−1). When compared to spectral microscopy, the metabolism rate of dox was underestimated for about every 500 cells using LC/MS. The microscopy approach further showed that dox and dox’ol translocated to the nucleus at different rates of 0.8 and 0.3 pM min−1, respectively. LC/MS is not a practical approach to determine drug translocation from cytosol to nucleus. Using various methods, we confirmed that when combined with a high-resolution imaging, spectral characteristics of a molecule could be used as a powerful approach to analyze drug metabolism. We propose that spectral microscopy is a new method to study drug localization, translocation, transformation and identification with a resolution at a single cell level, while LC/MS is more appropriate for drug screening at an organ or tissue level.
Using 3PG to assess climate change impacts on management plan optimization of Eucalyptus plantations. A case study in Southern Brazil
Authors: HN Palma João , Hakamada Rodrigo , Moreira Gabriela Gonçalves , Nobre Silvana , Rodriguez Luiz Carlos Estraviz 
Published: February 2021

AbstractEucalyptus plantations around the world have been largely used by the paper industry. Optimizing the management of resources is a common practice in this highly competitive industry and new forest growth models may help to understand the impact of climate change on the decisions of the optimization processes. Current optimized management plans use empirical equations to predict future forest stands growth, and it is currently impractical to replace these empirical equations with physiological models due to data input requirements. In this paper, we present a different approach, by first carrying out a preliminary assessment with the process-based physiological model 3PG to evaluate the growth of Eucalyptus stands under climate change predictions. The information supplied by 3PG was then injected as a modifier in the projected yield that feeds the management plan optimizer allowing the interpretation of climate change impacts on the management plan. Modelling results show that although a general increase of rain with climate change is predicted, the distribution throughout the year will not favor the tree growth. On the contrary, rain will increase when it is less needed (summer) and decrease when it is most needed (winter), decreasing forest stand productivity between 3 and 5%, depending on the region and soil. Evaluation of the current optimized plan that kept constant the relation between wood price/cellulose ton shows a variation in different strategic management options and an overall increase of costs in owned areas between 2 and 4%, and a decrease of cumulated net present value, initially at 15% with later stabilization at 6–8%. This is a basic comparison to observe climate change effects; nevertheless, it provides insights into how the entire decision-making process may change due to a reduction in biomass production under future climate scenarios. This work demonstrates the use of physiological models to extract information that could be merged with existing and already implemented empirical models. The methodology may also be considered a preliminary alternative to the complete replacement of empirical models by physiological models. Our approach allows some insight into forest responses to different future climate conditions, something which empirical models are not designed for.
Defining priority areas for blue whale conservation and investigating overlap with vessel traffic in Chilean Patagonia, using a fast-fitting movement model
Authors: Bedriñana-Romano Luis , Hucke-Gaete Rodrigo , Viddi Francisco A. , Johnson Devin , Zerbini Alexandre N. , Morales Juan , Mate Bruce , Palacios Daniel M. 
Published: February 2021

AbstractDefining priority areas and risk evaluation is of utmost relevance for endangered species` conservation. For the blue whale (Balaenoptera musculus), we aim to assess environmental habitat selection drivers, priority areas for conservation and overlap with vessel traffic off northern Chilean Patagonia (NCP). For this, we implemented a single-step continuous-time correlated-random-walk model which accommodates observational error and movement parameters variation in relation to oceanographic variables. Spatially explicit predictions of whales’ behavioral responses were combined with density predictions from previous species distribution models (SDM) and vessel tracking data to estimate the relative probability of vessels encountering whales and identifying areas where interaction is likely to occur. These estimations were conducted independently for the aquaculture, transport, artisanal fishery, and industrial fishery fleets operating in NCP. Blue whale movement patterns strongly agreed with SDM results, reinforcing our knowledge regarding oceanographic habitat selection drivers. By combining movement and density modeling approaches we provide a stronger support for purported priority areas for blue whale conservation and how they overlap with the main vessel traffic corridor in the NCP. The aquaculture fleet was one order of magnitude larger than any other fleet, indicating it could play a decisive role in modulating potential negative vessel-whale interactions within NCP.
SAR image wave spectra to retrieve the thickness of grease-pancake sea ice using viscous wave propagation models
Authors: De Carolis Giacomo , Olla Piero , De Santi Francesca 
Published: February 2021

AbstractYoung sea ice composed of grease and pancake ice (GPI), as well as thin floes, considered to be the most common form of sea ice fringing Antarctica, is now becoming the “new normal” also in the Arctic. A study of the rheological properties of GPI is carried out by comparing the predictions of two viscous wave propagation models: the Keller model and the close-packing (CP) model, with the observed wave attenuation obtained by SAR image techniques. In order to fit observations, it is shown that describing GPI as a viscous medium requires the adoption of an ice viscosity which increases with the ice thickness. The consequences regarding the possibility of ice thickness retrieval from remote sensing data of wave attenuation are discussed. We provide examples of GPI thickness retrievals from a Sentinel-1 C band SAR image taken in the Beaufort Sea on 1 November 2015, and three CosmoSkyMed X band SAR images taken in the Weddell Sea on March 2019. The estimated GPI thicknesses are consistent with concurrent SMOS measurements and available local samplings.