Analysis of natural structures and chemical mapping data reveals local stability compensation in RNA.

RNA molecules adopt complex structures that perform essential biological functions across all forms of life, making them promising candidates for therapeutic applications. However, our ability to design new RNA structures remains limited by an incomplete understanding of their folding principles. While global metrics such as the minimum free energy are widely used, they are at odds with naturally occurring structures and incompatible with established design rules.

Bovine milk consumption affects the transcriptome of porcine adipose stem cells: Do exosomes play any role?

The potential association of milk with childhood obesity has been widely debated and researched. Milk is known to contain many bioactive compounds as well as bovine exosomes rich in micro-RNA (miR) that can have effects on various cells, including stem cells. Among them, adipose stem cells (ASC) are particularly interesting due to their role in adipose tissue growth and, thus, obesity.

Selective Nonenzymatic Formation of Biologically Common RNA Hairpins.

The prebiotic formation of RNA building blocks is well-supported experimentally, yet the emergence of sequence- and structure-specific RNA oligomers is generally attributed to biological selection via Darwinian evolution rather than prebiotic chemical selectivity. In this study, we used deep sequencing to investigate the partitioning of randomized RNA overhangs into ligated products by either splinted ligation or loop-closing ligation. Comprehensive sequence-reactivity profiles revealed that loop-closing ligation preferentially yields hairpin structures with loop sequences UNNG, CNNG, and GNNA (where N represents A, C, G, or U) under competing conditions.

Artificial Space Weathering to Mimic Solar Wind Enhances the Toxicity of Lunar Dust Simulants in Human Lung Cells.

During NASA's Apollo missions, inhalation of dust particles from lunar regolith was identified as a potential occupational hazard for astronauts. These fine particles adhered tightly to spacesuits and were unavoidably brought into the living areas of the spacecraft. Apollo astronauts reported that exposure to the dust caused intense respiratory and ocular irritation.

Retinoschisis: a retrospective study of an uncommon retinal change in cats and dogs.

Retinoschisis is a poorly documented form of retinal degeneration characterized by cyst-like splitting that occurs between the inner nuclear and outer plexiform layers. The pathogenesis of retinoschisis is incompletely understood, but congenital, acquired and secondary aetiologies (glaucoma, inflammation, neoplasia) are described in humans. This retrospective study investigated the prevalence and associated histological and clinical features of retinoschisis in cats and dogs submitted for biopsy over a 10-year period.

Improving deep models of protein-coding potential with a Fourier-transform architecture and machine translation task.

Ribosomes are information-processing macromolecular machines that integrate complex sequence patterns in messenger RNA (mRNA) transcripts to synthesize proteins. Studies of the sequence features that distinguish mRNAs from long noncoding RNAs (lncRNAs) may yield insight into the information that directs and regulates translation. Computational methods for calculating protein-coding potential are important for distinguishing mRNAs from lncRNAs during genome annotation, but most machine learning methods for this task rely on previously known rules to define features.

Improving deep models of protein-coding potential with a Fourier-transform architecture and machine translation task.

Ribosomes are information-processing macromolecular machines that integrate complex sequence patterns in messenger RNA (mRNA) transcripts to synthesize proteins. Studies of the sequence features that distinguish mRNAs from long noncoding RNAs (lncRNAs) may yield insight into the information that directs and regulates translation. Computational methods for calculating protein-coding potential are important for distinguishing mRNAs from lncRNAs during genome annotation, but most machine learning methods for this task rely on previously known rules to define features.

Sulcus intraocular lens implantation in 17 dogs using a modified ab externo technique.

Objective: To describe a modified ab externo method of sulcus intraocular lens (IOL) fixation and report outcomes of eyes treated with this approach.

Procedures: Records of patients with lens instability or luxation that underwent a lensectomy and sulcus IOL implantation from January 2004 to December 2020 were reviewed.

Results: Nineteen eyes of 17 dogs had a sulcus IOL placed via a modified ab externo approach.

An improved assembly of the "Cascade" hop () genome uncovers signatures of molecular evolution and refines time of divergence estimates for the Cannabaceae family.

We present a chromosome-level assembly of the Cascade hop ( L. var. ) genome.

bpRNA-align: improved RNA secondary structure global alignment for comparing and clustering RNA structures.

Ribonucleic acid (RNA) is a polymeric molecule that is fundamental to biological processes, with structure being more highly conserved than primary sequence and often key to its function. Advances in RNA structure characterization have resulted in an increase in the number of accurate secondary structures. The task of uncovering common RNA structural motifs with a collective function through structural comparison, providing a level of similarity, remains challenging and could be used to improve RNA secondary structure databases and discover new RNA families.

Discovery and Visualization of Age-Dependent Patterns in the Diurnal Transcriptome of Drosophila.

Many critical life processes are regulated by input from 24-hour external light/dark cycles, such as metabolism, cellular homeostasis, and detoxification. The circadian clock, which helps coordinate the response to these diurnal light/dark cycles, remains rhythmic across lifespan; however, rhythmic transcript expression is altered during normal aging. To better understand how aging impacts diurnal expression, we present an improved Fourier-based method for detecting and visualizing rhythmicity that is based on the relative power of the 24-hour period compared to other periods (RP24).

Chronic blue light leads to accelerated aging in Drosophila by impairing energy metabolism and neurotransmitter levels.

Blue light (BL) is becoming increasingly prevalent in artificial illumination, raising concerns about its potential health hazard to humans. In fact, there is evidence suggesting that acute BL exposure may lead to oxidative stress and death of retinal cells specialized for photoreception. On the other hand, recent studies in demonstrated that chronic BL exposure across lifespan leads to accelerated aging manifested in reduced lifespan and brain neurodegeneration even in flies with genetically ablated eyes, suggesting that BL can damage cells and tissues not specialized for light perception.

Age-dependent effects of blue light exposure on lifespan, neurodegeneration, and mitochondria physiology in Drosophila melanogaster.

Blue light is a predominant component of light emitting devices (LEDs), which are increasingly present in our environment. There is already accumulating evidence that blue light exposure causes damage to retinal cells in vitro and in vivo; however, much less is known about potential effects of blue light on non-retinal cells. That blue light may be detrimental at the organismal level independent from retinal effect was recently shown by findings that it reduces lifespan in worms and also in flies with genetically ablated retinas.

Pathology in Practice.

In collaboration with the American College of Veterinary Pathologists.

Predicting Drosha and Dicer Cleavage Sites with DeepMirCut.

MicroRNAs are a class of small RNAs involved in post-transcriptional gene silencing with roles in disease and development. Many computational tools have been developed to identify novel microRNAs. However, there have been no attempts to predict cleavage sites for Drosha from primary sequence, or to identify cleavage sites using deep neural networks.

Ocular findings in cats with blastomycosis: 19 cases (1978-2019).

Objective: To document ocular findings in cats with blastomycosis.

Animals: 35 cats with blastomycosis.

Procedures: Medical records from 1978 through 2019 were reviewed to identify cats with confirmed Blastomyces infection.

Olivine Dissolution in Simulated Lung and Gastric Fluid as an Analog to the Behavior of Lunar Particulate Matter Inside the Human Respiratory and Gastrointestinal Systems.

With the Artemis III mission scheduled to land humans on the Moon in 2025, work must be done to understand the hazards lunar dust inhalation would pose to humans. In this study, San Carlos olivine was used as an analog of lunar olivine, a common component of lunar dust. Olivine was dissolved in a flow-through apparatus in both simulated lung fluid and 0.

Comparison of antimicrobial resistance patterns in dogs with bacterial keratitis presented to a veterinary teaching hospital over two multi-year time periods (1993-2003 and 2013-2019) in the Southeastern United States.

Objective: To report clinical characteristics of dogs with bacterial keratitis, identify the most common bacterial isolates within this population, characterize the bacterial isolates' antimicrobial resistance patterns, and compare those resistance patterns to previously reported resistance patterns.

Animal Studied: Dogs diagnosed with bacterial keratitis between 2013 and 2019.

Procedures: Data pertaining to breed; Schirmer tear test I results; use of cyclosporine, tacrolimus, or corticosteroids at time of ulcer diagnosis; bacterial genus or species isolated; and resistance to selected antimicrobials as measured by Kirby-Bauer disk diffusion were collected.

A draft phased assembly of the diploid Cascade hop (Humulus lupulus) genome.

Hop (Humulus lupulus L. var Lupulus) is a diploid, dioecious plant with a history of cultivation spanning more than one thousand years. Hop cones are valued for their use in brewing and contain compounds of therapeutic interest including xanthohumol.

Nanoengineered Light-Activatable Polybubbles for On-Demand Therapeutic Delivery.

Vaccine coverage is severely limited in developing countries due to inefficient protection of vaccine functionality as well as lack of patient compliance to receive the additional booster doses. Thus, there is an urgent need to design a thermostable vaccine delivery platform that also enables release of the bolus after predetermined time. Here, the formation of injectable and light-activatable polybubbles for vaccine delivery is reported.

Retrobulbar and Tongue Base Pyogranulomatous Myositis Resulting in Strabismus in a Dog: Case Report.

A seven-year-old female spayed Australian Shepherd was presented for a 3-day history of left eye ventromedial strabismus, episcleral injection, protrusion of the third eyelid, miosis, and enophthalmia. Magnetic Resonance Imaging (MRI) identified lesions in the left medial pterygoid muscle and left tongue base. Cytology and histopathology revealed pyogranulomatous inflammation with rod-shaped bacteria and pyogranulomatous myositis, respectively.

Tear film concentrations of topically applied 0.5% oxytetracycline ointment in normal canine eyes.

Objective: To determine the tear film levels of oxytetracycline in normal canine eyes after application of the ophthalmic ointment, Terramycin™ (0.5% oxytetracycline, polymyxin B sulfate), to guide appropriate treatment frequency.

Animals Studied: Ten research beagles.