bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome analysis ofPseudomonas aeruginosabiofilm infection in anex vivopig model of the cystic fibrosis lung
Authors: Harrington Niamh E. , Littler Jenny L. , Harrison Freya 
Published: July 2021

AbstractPseudomonas aeruginosais the predominant cause of chronic biofilm infections that form in the lungs of people with cystic fibrosis (CF). These infections are highly resistant to antibiotics and persist for years in the respiratory tract. One of the main research challenges is that current laboratory models do not accurately replicate key aspects of a chronicP. aeruginosabiofilm infection, highlighted by previous RNA-sequencing studies. We compared theP. aeruginosaPA14 transcriptome in anex vivopig lung (EVPL) model of CF and a well-studied synthetic cystic fibrosis sputum medium (SCFM).P. aeruginosawas grown in the EVPL model for 1, 2 and 7 days, andin vitroin SCFM for 1 and 2 days. The RNA was extracted and sequenced at each time point. Our findings demonstrate that expression of antimicrobial resistance genes was cued by growth in the EVPL model, highlighting the importance of growth environment in determining accurate resistance profiles. The EVPL model created two distinct growth environments: tissue-associated biofilm and the SCFM surrounding tissue, each of which cued a transcriptome distinct from that seen in SCFMin vitro. The expression of quorum sensing associated genes in the EVPL tissue-associated biofilm at 48 h relative toin vitroSCFM was found to be similar to CF sputum versusin vitroconditions. Hence, the EVPL model can replicate key aspects ofin vivobiofilm infection that are missing from other current models and provides a more accurateP. aeruginosagrowth environment for determining antimicrobial resistance.Significance StatementPseudomonas aeruginosalung infections that affect people with cystic fibrosis are a well-researched area, yet they continue to evade antimicrobial treatments. The lack of a laboratory model that captures all key aspects of these infections hinders not only research progression but also clinical diagnostics. We used transcriptome analysis to demonstrate how a model using pig lungs can more accurately replicate key characteristics ofP. aeruginosalung infection, including mechanisms of antibiotic resistance and infection establishment. Therefore, this model may be used in the future to further understand infection dynamics to develop novel treatments and more accurate treatment plans. This could improve clinical outcomes as well as quality of life for individuals affected by these infections.
Nano-Insecticides Against the Black Cutworm Agrotis ipsilon (Lepidoptera: Noctuidae): Toxicity, Development, Enzyme activity, and DNA Mutagenicity
Authors: Awad Mona , Ibrahim El-Desoky S. , Osman Engy I. , Elmenofy Wael H. , Mahmoud Abdel Wahab M. , Atia Mohamed A. M. , Moustafa Moataz A. M. 
Published: July 2021

AbstractHigh-frequency doses of chemical pesticides cause environmental pollution with high pesticide residues. In addition, increasing insecticide resistance in many insect pests requires novel pest control methods. Nanotechnology could be a promising field of modern agriculture, and is receiving considerable attention in the development of novel nano-agrochemicals, such as nanoinsectticides and nanofertilizers. This study assessed the effects of the lethal and sublethal concentrations of chlorantraniliprole, thiocyclam, and their nano-forms on the development, reproductive activity, oxidative stress enzyme activity, and DNA changes at the molecular level of the polyphagous species of black cutworm Agrotis ipsilon. The results revealed that A. ipsilon larvae were more susceptible to the nano-formsthan the regular forms of both nano chlorine and sulfur within the chlorantraniliprole and thiocyclam insecticides, respectively, with higher toxicities than the regular forms (ca. 3.86, and ca.2.06-fold, respectively). Significant differences in biological parameters, including developmental time and reproductive activity (fecundity and hatchability percent) were also observed. Correspondingly, increases in oxidative stress enzyme activities were observed, as were mutagenic effects on the genomic DNA of A. ipsilon after application of the LC50 of the nano-forms of both insecticides compared to the control. The positive results obtained here have led us to apply these nano-forms indifferent insect models in additional studies.
Inhibition of Mitochondrial Fission by Drp-1 Blockade by Short-Term Leptin and Mdvi-1 Treatment Improves White Adipose Tissue Abnormalities in Obesity and Diabetes
Authors: Finocchietto P , Perez H , Blanco G , Miksztowicz V , Marotte C , Morales C , Peralta J , Berg G , Poderoso C , Poderoso JJ , Carreras MC 
Published: July 2021

AbstractBackgroundObesity and type 2 diabetes are chronic diseases characterized by insulin resistance, mitochondrial dysfunction and morphology abnormalities.ObjectiveHerein, we investigated if dysregulation of mitochondrial dynamics and biogenesis is involved in an animal model of obesity and diabetes.MethodsThe effect of short-term leptin and mdivi-1 –a selective inhibitor of Drp-1 fission-protein– treatment on mitochondrial dynamics and biogenesis was evaluated in epididymal white adipose tissue (WAT) from male ob/ob mice.ResultsAn increase in Drp-1 protein levels and a decrease in Mfn2 and OPA-1 protein expression were observed with enhanced and sustained mitochondrial fragmentation in ob/ob mice compared to wt C57BL/6 animals (p<0.05). The content of mitochondrial DNA and mRNA expression of PGC-1α –both parameters of mitochondrial biogenesis– were reduced in ob/ob mice (p<0.05). Leptin and mdivi-1 treatment significantly increased mitochondrial biogenesis, improved fusion-to-fission balance and attenuated mitochondrial dysfunction, thus inducing white-to-beige adipocyte transdifferentiation. Measurements of glucose and lipid oxidation in adipocytes revealed that both leptin and mdivi-1 increase substrates oxidation while in vivo determination of blood glucose concentration showed decreased levels by 50% in ob/ob mice, almost to the wt level.ConclusionsPharmacological targeting of Drp-1 fission protein may be a potential novel therapeutic tool for obesity and type 2 diabetes.
US Dog Importations during the COVID-19 Pandemic: Do we have an erupting problem?
Authors: Pieracci Emily G , Williams Cara , Wallace Ryan M , Kalapura Cheryl , Brown Clive M 
Published: July 2021

AbstractDog importation data from 2018-2020 were evaluated to ascertain whether the dog importation patterns in the United States changed during the COVID-19 pandemic, specifically with regard to denial of entry. Dog denial of entry reports from January 1, 2018, to December 31, 2020, stored within the Centers for Disease Control and Prevention (CDC) Quarantine Activity Reporting System, were reviewed. Basic descriptive statistics were used to analyze the data. Reason for denial, country of origin, and month of importation were all examined to determine which countries of origin resulted in the largest number of denials, and whether there was a seasonal change in importations during the COVID-19 pandemic (2020), compared to previous years (2018 and 2019). During 2020, CDC denied entry to 458 dogs. This represents a 52% increase in dogs denied entry compared to the averages in 2018 and 2019. Dogs were primarily denied entry for falsified rabies vaccination certificates (56%). Three countries exported 74% of all dogs denied entry into the United States, suggesting that targeted interventions may be needed for certain countries. Increased attempts to import inadequately vaccinated dogs from countries with canine rabies in 2020 may have been due to the increased demand for domestic pets during the COVID-19 pandemic. Educational messaging should highlight the risk of rabies and the importance of making informed pet purchases from foreign entities to protect pet owners, their families, and the public.
Automated identification of piglet brain tissue from MRI images using Region-based Convolutional Neural Networks
Authors: Stanke Kayla L. , Larsen Ryan J. , Rund Laurie , Leyshon Brian J. , Louie Allison Y. , Steelman Andrew J. 
Published: July 2021

AbstractMagnetic Resonance Imaging is an important tool for characterizing volumetric changes of the piglet brain during development. Typically, an early step of an imaging analysis pipeline is brain extraction, or skull stripping. Brain extractions are usually performed manually; however, this approach is time-intensive and can lead to variation between brain extractions when multiple raters are used. Automated brain extractions are important for reducing the time required for analyses and improving the uniformity of the extractions. Here we demonstrate the use of Mask R-CNN, a Region-based Convolutional Neural Network (R-CNN), for automated brain extractions of piglet brains. We validate our approach using Nested Cross-Validation on six sets of training/validation data drawn from 32 pigs. Visual inspection of the extractions shows acceptable accuracy, Dice coefficients are in the range of 0.95-0.97, and Hausdorff Distance values in the range of 4.1-8.3 voxels. These results demonstrate that R-CNNs provide a viable tool for skull stripping of piglet brains.
TELSAM polymers accelerate crystallization of fused target proteins by stabilizing minimal crystal contacts and in the absence of direct inter-TELSAM contacts
Authors: Sarath Nawarathnage Supeshala D. , Soleimani Sara , Mathis Moriah H. , Bezzant Braydan D. , Ramírez Diana T , Gajjar Parag , Bunn Derick , Stewart Cameron , Smith Tobin , Pedroza Romo Maria J , Brown Seth , Doukov Tzanko , Moody James D. 
Published: July 2021

AbstractWe extend investigation into the usefulness of genetic fusion to TELSAM polymers as an effective protein crystallization strategy. We tested various numbers of the target protein fused per turn of the TELSAM helical polymer and various TELSAM–target connection strategies. We provide definitive evidence that: 1. A TELSAM–target protein fusion can crystallize more rapidly than the same target protein alone, 2. TELSAM–target protein fusions can form well-ordered, diffracting crystals using either flexible or rigid TELSAM–target linkers, 3. Well-ordered crystals can be obtained when either 2 or 6 copies of the target protein are presented per turn of the TELSAM helical polymer, 4. The TELSAM polymers themselves need not directly contact one another in the crystal lattice, and 5. Fusion to TELSAM polymer confers immense avidity to stabilize exquisitely weak inter-target protein crystal contacts. We report features of TELSAM-target protein crystals and outline future work needed to define the requirements for reliably obtaining optimal crystals of TELSAM–target protein fusions.
Selection of reference genes for quantitative analysis of microRNA expression in three cancers
Authors: Veryaskina Yuliya A. , Titov Sergei E. , Ivanov Mikhail K. , Ruzankin Pavel S. , Tarasenko Anton S. , Shevchenko Sergei P. , Kovynev Igor B. , Stupak Evgenij V. , Pospelova Tatiana I. , Zhimulev Igor F. 
Published: July 2021

AbstractMicroRNAs (miRNAs) are promising biomarkers in cancer research. Quantitative PCR (qPCR), also known as real-time PCR, is the most frequently used technique for measuring miRNA expression levels. The use of this technique, however, requires that expression data be normalized against reference genes. The problem is that a universal internal control for quantitative analysis of miRNA expression by qPCR has yet to be known. The aim of this work was to find the miRNAs with stable expression in the thyroid gland, brain and bone marrow according to NanoString nCounter miRNA quantification data. As a results, the most stably expressed miRNAs were as follows: miR-361-3p, -151a-3p and -29b-3p in the thyroid gland; miR-15a-5p, -194-5p and -532-5p in the brain; miR-140-5p, -148b-3p and -362-5p in bone marrow; and miR-423-5p, -28-5p and -532-5p, no matter what tissue type. These miRNAs represent promising reference genes for miRNA quantification by qPCR.
Expression of Spred2 in the urothelial tumorigenesis of the urinary bladder
Authors: Oda Shinsuke , Fujisawa Masayoshi , Chunning Li , Ito Toshihiro , Yamaguchi Takahiro , Yoshimura Teizo , Matsukawa Akihiro 
Published: July 2021

AbstractAberrant activation of the Ras/Raf/ERK (extracellular-signal-regulated kinase)-MAPK (mitogen-activated protein kinase) pathway is involved in the progression of cancer, including urothelial carcinoma; but the negative regulation remains unclear. In the present study, we investigated pathological expression of Spred2 (Sprouty-related EVH1 domain-containing protein 2), a negative regulator of the Ras/Raf/ERK-MAPK pathway, and the relation to ERK activation and Ki67 index in various categories of 275 urothelial tumors obtained from clinical patients. In situ hybridization demonstrated that Spred2 mRNA was highly expressed in high-grade non-invasive papillary urothelial carcinoma (HGPUC), and the expression was decreased in carcinoma in situ (CIS) and infiltrating urothelial carcinoma (IUC). Immunohistochemically, membranous Spred2 expression, important to interact with Ras/Raf, was preferentially found in HGPUC. Interestingly, membranous Spred2 expression was decreased in CIS and IUC relative to HGPUC, while ERK activation and the expression of the cell proliferation marker Ki67 index were increased. HGPUC with membranous Spred2 expression correlated significantly with lower levels of ERK activation and Ki67 index as compared to those with negative Spred2 expression. Thus, our pathological findings suggest that Spred2 negatively regulates cancer progression in non-invasive papillary carcinoma possibly through inhibiting the Ras/Raf/ERK-MAPK pathway, but this regulatory mechanism is lost in cancers with high malignancy. Spred2 appears to be a key regulator in the progression of non-invasive bladder carcinoma.
CardiOvascular examination in awake Orangutans (Pongo pygmaeus pygmaeus): Low-stress Echocardiography including Speckle Tracking imaging (the COOLEST method)
Authors: Chetboul Valérie , Concordet Didier , Tissier Renaud , Vonfeld Irène , Poissonnier Camille , Alvarado Maria Paz , Passavin Peggy , Gluntz Mathilde , Lefort Solène , Bourgeois Aude , Duby Dylan , Hano Christelle , Chai Norin 
Published: July 2021

AbstractIntroductionCardiovascular diseases have been identified as a major cause of mortality and morbidity in Borneo orangutans (Pongo pygmaeus pygmaeus). Transthoracic echocardiography is usually performed under anesthesia in great apes, which may be stressful and risky in cardiac animals. The aim of the present pilot study was hence to develop a quick and non-stressful echocardiographic method (i.e., the COOLEST method) in awake Borneo orangutans (CardiOvascular examination in awake Orangutans: Low-stress Echocardiography including Speckle Tracking imaging) and assess the variability of corresponding variables.Materials and MethodsFour adult Borneo orangutans trained to present their chest to the trainers were involved. A total of 96 TTE examinations were performed on 4 different days by a trained observer examining each orangutans 6 times per day. Each examination included four two-dimensional views, with offline assessment of 28 variables (i.e., two-dimensional (n=12), M-mode and anatomic M-mode (n=6), Doppler (n=7), and speckle tracking imaging (n=3)), representing a total of 2,688 measurements. A general linear model was used to determine the within-day and between-day coefficients of variation.ResultsMean±SD (minimum-maximum) images acquisition duration was 3.8±1.6 minutes (1.3-6.3). All within-day and between-day coefficients of variation but one (n=55/56, 98%) were <15%, and most (51/56, 91%) were <10% including those of speckle tracking systolic strain variables (2.7% to 5.4%).DiscussionHeart morphology as well as global and regional myocardial function can be assessed in awake orangutans with good to excellent repeatability and reproducibility.ConclusionsThis non-stressful method may be used for longitudinal cardiac follow-up in awake orangutans.
Long-term changes in populations of rainforest birds in the Australia Wet Tropics bioregion: a climate-driven biodiversity emergency
Authors: Williams Stephen E. , de la Fuente Alejandro 
Published: July 2021

AbstractMany authors have suggested that the vulnerability of montane biodiversity to climate change worldwide is significantly higher than in most other ecosystems. Despite the extensive variety of studies predicting severe impacts of climate change globally, few studies have empirically validated the predicted changes in distribution and population density. Here, we used 17 years of bird monitoring across latitudinal/elevational gradients in the rainforest of the Australian Wet Tropics World Heritage Area to assess changes in local abundance and distribution. We used relative abundance in 1977 surveys across 114 sites ranging from 0-1500m above sea level and utilised a trend analysis approach (TRIM) to investigate elevational shifts in abundance of 42 species between 2000 – 2016. The local abundance of most mid and high elevation species has declined at the lower edges of their distribution by >40% while lowland species increased by up to 190% into higher elevation areas. Upland-specialised species and regional endemics have undergone dramatic population declines of almost 50%. The “Outstanding Universal Value” of the Australian Wet Tropics World Heritage Area, one of the most irreplaceable biodiversity hotspots on Earth, is rapidly degrading. These observed impacts are likely to be similar in many tropical montane ecosystems globally.
Comparative analysis of transcriptomic profiles among ascidians, zebrafish, and mice: insights from tissue-specific gene expression
Authors: Matsubara Shin , Osugi Tomohiro , Shiraishi Akira , Wada Azumi , Satake Honoo 
Published: July 2021

AbstractTissue/organ-specific genes (TSGs) are important not only for understanding organ development and function, but also for investigating the evolutionary lineages of organs in animals. Here, we investigate the TSGs of 9 adult tissues of an ascidian, Ciona intestinalis Type A (Ciona robusta), which lies in the important position of being the sister group of vertebrates. RNA-seq and qRT-PCR identified the Ciona TSGs in each tissue, and BLAST searches identified their homologs in zebrafish and mice. Tissue distributions of the vertebrate homologs were analyzed and clustered using public RNA-seq data for 12 zebrafish and 30 mouse tissues. Among the vertebrate homologs of the Ciona TSGs in the neural complex, 48% and 63% showed high expression in the zebrafish and mouse brain, respectively, suggesting that the central nervous system is evolutionarily conserved in chordates. In contrast, vertebrate homologs of Ciona TSGs in the ovary, pharynx, and intestine were not consistently highly expressed in the corresponding tissues of vertebrates, suggesting that these organs have evolved in Ciona-specific lineages. Intriguingly, more TSG homologs of the Ciona stomach were highly expressed in the vertebrate liver (17-29%) and intestine (22-33%) than in the mouse stomach (5%). Expression profiles for these gene suggest that the biological roles of the Ciona stomach are distinct from those of their vertebrate counterparts. Collectively, Ciona tissues were categorized into 3 groups: i) high similarity to the corresponding vertebrate tissues (neural complex and heart), ii) low similarity to the corresponding vertebrate tissues (ovary, pharynx, and intestine), and iii) low similarity to the corresponding vertebrate tissues, but high similarity to other vertebrate tissues (stomach, endostyle, and siphons). The present study provides transcriptomic catalogs of adult ascidian tissues and significant insights into the evolutionary lineages of the brain, heart, and digestive tract of chordates.
Improving RT-LAMP Detection of SARS-CoV-2 RNA through Primer Set Selection and Combination
Authors: Zhang Yinhua , Tanner Nathan A. 
Published: July 2021

AbstractReverse transcription loop-mediated isothermal amplification (RT-LAMP) has emerged as a viable molecular diagnostic method to expand the breadth and reach of nucleic acid testing, particularly for SARS-CoV-2 detection and surveillance. While rapidly growing in prominence, RT-LAMP remains a relatively new method compared to the standard RT-qPCR, and contribution to our body of knowledge on designing LAMP primer sets and assays can have significant impact on its utility and adoption. Here we evaluate 18 LAMP primer sets for SARS-CoV-2, comparing speed and sensitivity with different LAMP formulations and conditions across more than 5,000 RT-LAMP reactions and identifying several primer sets with similar high sensitivity for different SARS-CoV-2 gene targets. Significantly we observe a consistent sensitivity enhancement by combining primer sets for different targets, confirming and building on earlier work to create a simple, general approach to building better and more sensitive RT-LAMP assays.
Fine-tuned method to extract high purified proteins from the seagrass Halophila stipulacea to be used for proteome analyses
Authors: Piro Amalia , Anagnostopoulou Vasileia , Apostolaki Eugenia T. , Mazzuca Silvia 
Published: July 2021

AbstractThe non-indigenous to the Mediterranean tropical seagrass Halophila stipulacea has the possibility to become more prevalent in the Mediterranean basin, exacerbated by the rapid increase of water temperature. Molecular profiling appears a promising tool to study the traits that render H. stipulacea tolerant and resilient and facilitate its rapid and vast geographical spread. Taking advantage from recent seagrass genomes sequencing, proteomics specialty has been applied to several seagrasses giving new insight on the biology and physiology of this group of angiosperms. Thus, it could be of interest to apply proteomics to H. stipulacea that it could be considered as a possible plant model species to study marine biological invasion. The first step to achieve this goal is to obtain high quality proteins from plant tissue. Tissue fixation and protein extraction protocol are the most challenging steps in proteomics. Here we report a fine-tuned procedure obtained by comparing protein yield from H. stipulacea plants frozen in liquid nitrogen or preserved in RNAlater and processed following two different extraction protocols. Higher protein yield have been extracted from the procedure that use the RNAlater preserved plants, extracted with trichloroacetic acid in water followed by trichloroacetic acid in acetone, compared to those obtained from all other procedures. Protein purity of these samples have been tested by the separation in SDS-PAGE comfirming a better resolved profile of peptide bands suitable for a gel-based proteomics. Then, to assess the quality of proteins the mHPLC-ESI-MS/MS mass spectrometry analyses and bioinformatics have been performed. Hundreds proteins have been identified against several seagrass genomic resources available at UniProt, NCBI, SeagrassDB and transcriptomic datasets, which were merged to form the first customized dataset useful for H. stipulacea proteomic investigations.