Native RNA sequencing in fission yeast reveals frequent alternative splicing isoforms.

The unicellular yeast (fission yeast) retains many of the splicing features observed in humans and is thus an excellent model to study the basic mechanisms of splicing. Nearly half the genes contain introns, but the impact of alternative splicing in gene regulation and proteome diversification remains largely unexplored. Here we leverage Oxford Nanopore Technologies native RNA sequencing (dRNA), as well as ribosome profiling data, to uncover the full range of polyadenylated transcripts and translated open reading frames.

Identification of Taxonomically Restricted Transcripts from Illumina RNA Sequencing Data.

In order to perform a well-balanced comparative transcriptomic analysis, the reference genome and annotations for all species included in the comparison must be of a similar quality and completeness. Frequently, comparative transcriptomic analyses include non-model organisms whose annotations are not as well curated; this inequality can lead to biases.To avoid potential biases stemming from incomplete annotations, a comparative transcriptomic analysis can incorporate de novo transcriptome assemblies for each species, which reduces this disparity.

Uncovering de novo gene birth in yeast using deep transcriptomics.

De novo gene origination has been recently established as an important mechanism for the formation of new genes. In organisms with a large genome, intergenic and intronic regions provide plenty of raw material for new transcriptional events to occur, but little is know about how de novo transcripts originate in more densely-packed genomes. Here, we identify 213 de novo originated transcripts in Saccharomyces cerevisiae using deep transcriptomics and genomic synteny information from multiple yeast species grown in two different conditions.

Extensive post-transcriptional buffering of gene expression in the response to severe oxidative stress in baker's yeast.

Cells responds to diverse stimuli by changing the levels of specific effector proteins. These changes are usually examined using high throughput RNA sequencing data (RNA-Seq); transcriptional regulation is generally assumed to directly influence protein abundances. However, the correlation between RNA-Seq and proteomics data is in general quite limited owing to differences in protein stability and translational regulation.

Transcriptomics data of 11 species of yeast identically grown in rich media and oxidative stress conditions.

Objective: The objective of this experiment was to identify transcripts in baker's yeast (Saccharomyces cerevisiae) that could have originated from previously non-coding genomic regions, or de novo. We generated this data to be able to compare the transcriptomes of different species of Ascomycota.

Data Description: We generated high-depth RNA sequencing data for 11 species of yeast: Saccharomyces cerevisiae, Saccharomyces paradoxus, Saccharomyces mikatae, Saccharomyces kudriavzevii, Saccharomyces bayanus, Naumovia castelii, Kluyveromyces lactis, Lachancea waltii, Lachancea thermotolerans, Lachancea kluyveri, and Schizosaccharomyces pombe.

Chronic desmitis and enthesiophytosis of the radio-ulnar interosseous ligament in a dog.

A 10-year-old golden retriever dog was presented for chronic right forelimb lameness associated with a painful swelling at the lateral aspect of the proximal ulna. Proximal ulnar ostectomy and stabilization resulted in a good clinical outcome. The proposed diagnosis is chronic desmitis and enthesiophytosis of the radio-ulnar interosseous ligament.

Slow-growing cells within isogenic populations have increased RNA polymerase error rates and DNA damage.

Isogenic cells show a large degree of variability in growth rate, even when cultured in the same environment. Such cell-to-cell variability in growth can alter sensitivity to antibiotics, chemotherapy and environmental stress. To characterize transcriptional differences associated with this variability, we have developed a method--FitFlow--that enables the sorting of subpopulations by growth rate.

Minimally invasive colopexy for pediatric Chilaiditi syndrome.

Chilaiditi syndrome is a rare disorder characterized by abdominal pain, respiratory distress, constipation, and vomiting in association with Chilaiditi's sign. Chilaiditi's sign is the finding on plain roentgenogram of colonic interposition between the liver and diaphragm and is usually asymptomatic. Surgery is typically reserved for cases of catastrophic colonic volvulus or perforation because of the syndrome.

Endovascular management of critical limb ischemia.

Endovascular management of critical limb ischemia has advanced significantly in the recent past, especially the ability to treat tibial artery lesions with reasonable results. The indications, results, and technical aspects or endovascular management of CLI is reviewed herein. An algorithm for clinical management of CLI in patients with tibial occlusive disease is also presented.

Bilateral iliopsoas muscle contracture and spinous process impingement in a German Shepherd dog.

Objective: To report diagnosis and treatment of bilateral iliopsoas muscle contracture in a dog with spinous process impingement.

Study Design: Case report.

Animals: German Shepherd dog.

Osteocartilaginous metaplasia in the right atrial myocardium of healthy adult sheep.

Among 172 hearts from clinically normal adult sheep aged 1.5 to 7 years evaluated for the presence of cartilage and/or bone in the right atrial myocardium, 3.49% (6/172) had palpable evidence of osteocartilaginous foci.

Syndactyly in a litter of cats.

In this case report, we describe the clinical and radiographic features of a litter of kittens affected with complex syndactyly. We also provide guidelines for the diagnosis, possible treatment and prevention of propagation of this condition. This is the first report of syndactyly in a litter of kittens and syndactyly affecting both the pectoral and pelvic limbs.

The use of prognostic indicators in the development of a statistical model predictive for adrenal insufficiency in trauma patients.

We performed a retrospective chart review of trauma patients admitted to Palmetto Richland Memorial Hospital and identified 63 cases of adrenal insufficiency along with 65 trauma patient controls. Two statistical models, a neural network and a multiple logistic regression, were developed to predict patients with increased risk of developing adrenal insufficiency. Each model had 11 selected independent variables, along with patient demographic data, to make a probabilistic prediction of patient outcome.

Morphological and functional evaluation of a dog with dimelia.

Weight bearing patterns were investigated on a young Cocker Spaniel with dimelia (mirror hand) of the left forelimb, using a pressure sensing walkway (PS walkway). The dog had two left forelimb paws, both originating from the carpus, with symmetrical duplication of metacarpal bones and phalanges. In addition, the left radial head was subluxated and asynchronous growth of the left radius and ulna was noted.

Spontaneous retrograde movement of ureteroliths in two dogs and five cats.

Case Description: 2 dogs and 5 cats were evaluated for treatment of ureteroliths.

Clinical Findings: Spontaneous retrograde movement of 1 or more ureteroliths was detected by radiography, ultrasonography, fluoroscopy, and a combination of fluoroscopy and ultrasonography. The ureteroliths moved retrograde up to 4 centimeters.

Extraskeletal osteosarcoma associated with retained surgical sponge in a dog.

Retained surgical sponges are usually discovered in the abdominal cavity, sometimes years after the surgical procedure, and the typical reaction is formation of a foreign-body granuloma, often called gossypiboma or textiloma. In this instance, an extraskeletal osteosarcoma, associated with the granulomatous reaction to a retained surgical sponge adjacent to the stifle, was diagnosed in an 11-year-old Labrador Retriever 9 years after repair of a ruptured cranial cruciate ligament. Radiographic detection of linear foreign material in the soft tissue mass was the basis for a diagnosis of gossypiboma.

Arthrodesis of the talocalcaneal joint for the treatment of two horses with talocalcaneal osteoarthritis.

Two horses with lameness due to tolocalcaneal osteoarthritis that failed to respond to conservative management were treated by tolocalcaneal arthrodesis using cortex screws placed in lag fashion. The affected joint of one horse was arthrodesed by compressing and stabilizing the medial facet of the joint with three screws. In the second horse, the medial and lateral facets of the affected tolocalcaneal joint were each compressed and stabilized with two screws.

Songbirds tune their vocal tract to the fundamental frequency of their song.

In human speech, the sound generated by the larynx is modified by articulatory movements of the upper vocal tract, which acts as a variable resonant filter concentrating energy near particular frequencies, or formants, essential in speech recognition. Despite its potential importance in vocal communication, little is known about the presence of tunable vocal tract filters in other vertebrates. The tonal quality of much birdsong, in which upper harmonics have relatively little energy, depends on filtering of the vocal source, but the nature of this filter is controversial.

Secretion of sex hormones in dogs with adrenal dysfunction.

Objective: To evaluate adrenal sex hormone concentrations in response to ACTH stimulation in healthy dogs, dogs with adrenal tumors, and dogs with pituitary-dependent hyperadrenocorticism (PDH).

Design: Prospective study.

Animals: 11 healthy control dogs, 9 dogs with adrenal-dependent hyperadrenocorticism (adenocarcinoma [ACA] or other tumor); 11 dogs with PDH, and 6 dogs with noncortisol-secreting adrenal tumors (ATs).

Treatment of tracheal collapse with an intraluminal stent in a miniature horse.

A 7-month-old miniature horse was referred for respiratory distress. Tracheal collapse at the level of the thoracic inlet was diagnosed. An intraluminal nitinol stent was placed with endoscopic guidance.