TK1 expression influences pathogenicity by cell cycle progression, cellular migration, and cellular survival in HCC 1806 breast cancer cells.

Breast cancer is the most common cancer diagnosis worldwide accounting for 1 out of every 8 cancer diagnoses. The elevated expression of Thymidine Kinase 1 (TK1) is associated with more aggressive tumor grades, including breast cancer. Recent studies indicate that TK1 may be involved in cancer pathogenesis; however, its direct involvement in breast cancer has not been identified. Here, we evaluate potential pathogenic effects of elevated TK1 expression by comparing HCC 1806 to HCC 1806 TK1-knockdown cancer cells (L133). Transcriptomic profiles of HCC 1806 and L133 cells showed cell cycle progression, apoptosis, and invasion as potential pathogenic pathways affected by TK1 expression. Subsequent in-vitro studies confirmed differences between HCC 1806 and L133 cells in cell cycle phase progression, cell survival, and cell migration. Expression comparison of several factors involved in these pathogenic pathways between HCC 1806 and L133 cells identified p21 and AKT3 transcripts were significantly affected by TK1 expression. Creation of a protein-protein interaction map of TK1 and the pathogenic factors we evaluated predict that the majority of factors evaluated either directly or indirectly interact with TK1. Our findings argue that TK1 elevation directly increases HCC 1806 cell pathogenicity and is likely occurring by p21- and AKT3-mediated mechanisms to promote cell cycle arrest, cellular migration, and cellular survival.

Case report: Long-term survival in puppies assessed with echocardiography, electrocardiography and cardiac troponin I after acute death in littermates due to parvoviral myocarditis.

Positive clinical outcomes of a group of surviving puppies from a litter affected by parvoviral myocarditis are detailed in this case report. Past reports focus on the negative outcomes of littermates of puppies who have died of parvoviral myocarditis. In this case, two puppies in a shelter setting, from a litter exposed to parvovirus, died suddenly with parvoviral myocarditis diagnosed at necropsy. The other seven puppies were screened for cardiac health with echocardiogram, electrocardiogram, and cardiac troponin I prior to adoption. All seven puppies had normal echocardiograms, electrocardiograms, and normal initial and recheck cardiac troponin I results. At recheck 2 years after the initial round of testing, two of the puppies were screened and continue to have normal cardiac diagnostics. All seven dogs are alive and thriving at 5 years old in homes with adopters who were given a complete medical history on the dogs prior to adoption. In summary, the outcomes for puppies in litters affected by parvoviral myocarditis are variable but they do not have to be grave. The use of cardiac diagnostics including echocardiogram, electrocardiogram and cardiac troponin I may serve as a prognostic basis for assessing the potential outcomes for the surviving puppies in affected litters.

nf-encyclopedia: A Cloud-Ready Pipeline for Chromatogram Library Data-Independent Acquisition Proteomics Workflows.

Data-independent acquisition (DIA) mass spectrometry methods provide systematic and comprehensive quantification of the proteome; yet, relatively few open-source tools are available to analyze DIA proteomics experiments. Fewer still are tools that can leverage gas phase fractionated (GPF) chromatogram libraries to enhance the detection and quantification of peptides in these experiments. Here, we present nf-encyclopedia, an open-source NextFlow pipeline that connects three open-source tools, MSConvert, EncyclopeDIA, and MSstats, to analyze DIA proteomics experiments with or without chromatogram libraries. We demonstrate that nf-encyclopedia is reproducible when run on either a cloud platform or a local workstation and provides robust peptide and protein quantification. Additionally, we found that MSstats enhances protein-level quantitative performance over EncyclopeDIA alone. Finally, we benchmarked the ability of nf-encyclopedia to scale to large experiments in the cloud by leveraging the parallelization of compute resources. The nf-encyclopedia pipeline is available under a permissive Apache 2.0 license; run it on your desktop, cluster, or in the cloud: https://github.com/TalusBio/nf-encyclopedia.

Prolonged persistence of canine distemper virus RNA, and virus isolation in naturally infected shelter dogs.

Canine distemper virus remains an important source of morbidity and mortality in animal shelters. RT-PCR is commonly used to aid diagnosis and has been used to monitor dogs testing positive over time to gauge the end of infectious potential. Many dogs excrete viral RNA for prolonged periods which has complicated disease management. The goal of this retrospective study was to describe the duration and characteristics of viral RNA excretion in shelter dogs with naturally occurring CDV and investigate the relationship between that viral RNA excretion and infectious potential using virus isolation data. Records from 98 different humane organizations with suspect CDV were reviewed. A total of 5,920 dogs were tested with 1,393; 4,452; and 75 found to be positive, negative, or suspect on RT-PCR respectively. The median duration of a positive test was 34 days (n = 325), and 25% (82/325) of the dogs still excreting viral RNA after 62 days of monitoring. Virus isolation was performed in six dogs who were RT-PCR positive for > 60 days. Infectious virus was isolated only within the first two weeks of monitoring at or around the peak viral RNA excretion (as detected by the lowest cycle threshold) reported for each dog. Our findings suggest that peak viral RNA excretion and the days surrounding it might be used as a functional marker to gauge the end of infectious risk. Clarifying the earliest point in time when dogs testing positive for canine distemper by RT-PCR can be considered non-contagious will improve welfare and lifesaving potential of shelters by enabling recovered dogs to be cleared more quickly for live release outcomes.

Identification of Rodent Husbandry Refinement Opportunities through Benchmarking and Collaboration.

Expanding the use of methods that refine, reduce, and replace (3Rs) the use of animals in research is fundamental for both ethical and scientific reasons. The mission of the 3Rs Translational and Predictive Sciences Leadership Group (3Rs TPS LG) of the International Consortium for Innovation and Quality in Pharmaceutical Development (IQ Consortium) is to promote sharing and integration of science and technology to advance the 3Rs in the discovery and development of new medicines, vaccines, medical devices, and health care products for humans and animals. The 3Rs TPS LG is dedicated to identifying opportunities for member companies to share practices, enhance learning, promote discussions, and advance the 3Rs across the industry. One such opportunity was a benchmarking survey, conducted by the Contract Research Organization (CRO) Outreach Working Group, designed to share practices in rodent husbandry for drug safety research and to identify potential opportunities for refinement. IQ member companies and CROs in Asia, North America, and Europe were surveyed. Areas identified for potential alignment included provision of corncob bedding and wire-grid flooring, management of the nest at cage change, approaches to social housing for male mice, evidence-based enrichment strategies, and evaluating the effects of the timing of studies in relation to the animals' circadian rhythm and light-cycle, with consideration for how such extrinsic factors influence animal welfare and scientific outcomes. This manuscript presents the results of the benchmarking survey, including general trends in mouse and rat husbandry practices in toxicology studies, considerations for social housing, enrichment selection, and potential effects of bedding substrate, emphasizing opportunities for collaboration that can help to identify refinements to rodent husbandry practices.

Prss29 Cre recombinase mice are useful to study adult uterine gland function.

All mammalian uteri contain glands in their endometrium that develop only or primarily after birth. In mice, those endometrial glands govern post implantation pregnancy establishment via regulation of blastocyst implantation, stromal cell decidualization, and placental development. Here, we describe a new uterine glandular epithelium (GE) specific Cre recombinase mouse line that is useful for the study of uterine gland function during pregnancy. Utilizing CRISPR-Cas9 genome editing, Cre recombinase was inserted into the endogenous serine protease 29 precursor (Prss29) gene. Both Prss29 mRNA and Cre recombinase activity was specific to the GE of the mouse uterus following implantation, but was absent from other areas of the female reproductive tract. Next, Prss29-Cre mice were crossed with floxed forkhead box A2 (Foxa2) mice to conditionally delete Foxa2 specifically in the endometrial glands. Foxa2 was absent in the glands of the post-implantation uterus, and Foxa2 deleted mice exhibited complete infertility after their first pregnancy. These results establish that Prss29-Cre mice are a valuable resource to elucidate and explore the functions of glands in the adult uterus.

Thymidine kinase 1 through the ages: a comprehensive review.

Proliferation markers, such as proliferating cell nuclear antigen (PCNA), Ki-67, and thymidine kinase 1 (TK1), have potential as diagnostic tools and as prognostic factors in assessing cancer treatment and disease progression. TK1 is involved in cellular proliferation through the recovery of the nucleotide thymidine in the DNA salvage pathway. TK1 upregulation has been found to be an early event in cancer development. In addition, serum levels of TK1 have been shown to be tied to cancer stage, so that higher levels of TK1 indicate a more serious prognosis. As a result of these findings and others, TK1 is not only a potentially viable biomarker for cancer recurrence, treatment monitoring, and survival, but is potentially more advantageous than current biomarkers. Compared to other proliferation markers, TK1 levels during S phase more accurately determine the rate of DNA synthesis in actively dividing tumors. Several reviews of TK1 elaborate on various assays that have been developed to measure levels in the serum of cancer patients in clinical settings. In this review, we include a brief history of important TK1 discoveries and findings, a comprehensive overview of TK1 regulation at DNA to protein levels, and recent findings that indicate TK1's potential role in cancer pathogenesis and its growing potential as a tumor biomarker and therapeutic target.

Intracellular calcium leak as a therapeutic target for RYR1-related myopathies.

RYR1 encodes the type 1 ryanodine receptor, an intracellular calcium release channel (RyR1) on the skeletal muscle sarcoplasmic reticulum (SR). Pathogenic RYR1 variations can destabilize RyR1 leading to calcium leak causing oxidative overload and myopathy. However, the effect of RyR1 leak has not been established in individuals with RYR1-related myopathies (RYR1-RM), a broad spectrum of rare neuromuscular disorders. We sought to determine whether RYR1-RM affected individuals exhibit pathologic, leaky RyR1 and whether variant location in the channel structure can predict pathogenicity. Skeletal muscle biopsies were obtained from 17 individuals with RYR1-RM. Mutant RyR1 from these individuals exhibited pathologic SR calcium leak and increased activity of calcium-activated proteases. The increased calcium leak and protease activity were normalized by ex-vivo treatment with S107, a RyR stabilizing Rycal molecule. Using the cryo-EM structure of RyR1 and a new dataset of > 2200 suspected RYR1-RM affected individuals we developed a method for assigning pathogenicity probabilities to RYR1 variants based on 3D co-localization of known pathogenic variants. This study provides the rationale for a clinical trial testing Rycals in RYR1-RM affected individuals and introduces a predictive tool for investigating the pathogenicity of RYR1 variants of uncertain significance.

Randomized controlled trial of N-acetylcysteine therapy for RYR1-related myopathies.

OBJECTIVE: To investigate the efficacy of N-acetylcysteine (NAC) for decreasing elevated oxidative stress and increasing physical endurance in individuals with ryanodine receptor 1-related myopathies (RYR1-RM). METHODS: In this 6-month natural history assessment (n = 37) followed by a randomized, double-blinded, placebo-controlled trial, 33 eligible participants were block-randomized (1:1) to receive NAC (n = 16) or placebo (n = 17), orally for 6 months (adult dose 2,700 mg/d; pediatric dose 30 mg/kg/d). The primary endpoint was urine 15-F2t isoprostane concentration and the clinically meaningful co-primary endpoint was 6-minute walk test (6MWT) distance. RESULTS: When compared to the general population, participants had elevated baseline 15-F2t isoprostane concentrations and most had a decreased 6MWT distance (mean ± SD 3.2 ± 1.5 vs 1.1 ± 1.7 ng/mg creatinine and 468 ± 134 vs 600 ± 58 m, respectively, both p < 0.001). 15-F2t isoprostane concentration and 6MWT distance did not change over the 6-month natural history assessment (p = 0.98 and p = 0.61, respectively). NAC treatment did not improve 15-F2t isoprostane concentration (least squares means difference 0.1 [95% confidence interval [CI] -1.4 to 1.6] ng/mg creatinine, p = 0.88) or 6MWT distance (least squares means difference 24 [95% CI -5.5 to 53.4] m, p = 0.11). NAC was safe and well-tolerated at the doses administered in this study. CONCLUSION: In ambulatory RYR1-RM-affected individuals, we observed stable disease course, and corroborated preclinical reports of elevated oxidative stress and decreased physical endurance. NAC treatment did not decrease elevated oxidative stress, as measured by 15-F2t isoprostane. CLASSIFICATION OF EVIDENCE: This study provides Class I evidence that, for people with RYR1-RM, treatment with oral NAC does not decrease oxidative stress as measured by 15-F2t isoprostane. CLINICALTRIALSGOV IDENTIFIER: NCT02362425.

Feeding modes, duration, and diarrhea in infancy: Continued evidence of the protective effects of breastfeeding.

OBJECTIVES: To evaluate the effect of early breastfeeding cessation on incidence of diarrhea in a cohort of U.S. infants. DESIGN, SAMPLE, AND MEASUREMENTS: A secondary data analysis was conducted using data from 2,340 mother-infant dyads participating in the Infant Feeding Practices Study II. We examined associations between duration of feeding type (e.g., exclusive breastfeeding [EBF], any breastfeeding [BF], formula feeding) and incidence of diarrhea before one year. RESULTS: The sample included mother-infant dyads that were 86.2% White, 3% Black, and 5% Hispanic. Interruption of EBF before 3 months was significantly associated with higher odds of having diarrhea at 6 months (OR = 1.80, p value ≤ 0.01) and between 6 and 12 months (OR = 1.45, p ≤ .01). Breastfeeding interruption before 6 months was associated with higher odds of having diarrhea at 6 months (OR = 3.19, p ≤ .01). Formula feeding for ≥3 months was associated with higher odds of diarrhea between 6 and 12 months. CONCLUSIONS: Exclusive breastfeeding for 3 months accompanied by any breastfeeding for 6 months provided the most protective effect against diarrhea. Public health interventions should address disparities in breastfeeding practices and provide support across clinical, workplace and community settings. Research should include more diverse population groups.

Correlation of phenotype with genotype and protein structure in RYR1-related disorders.

Variants in the skeletal muscle ryanodine receptor 1 gene (RYR1) result in a spectrum of RYR1-related disorders. Presentation during infancy is typical and ranges from delayed motor milestones and proximal muscle weakness to severe respiratory impairment and ophthalmoplegia. We aimed to elucidate correlations between genotype, protein structure and clinical phenotype in this rare disease population. Genetic and clinical data from 47 affected individuals were analyzed and variants mapped to the cryo-EM RyR1 structure. Comparisons of clinical severity, motor and respiratory function and symptomatology were made according to the mode of inheritance and affected RyR1 structural domain(s). Overall, 49 RYR1 variants were identified in 47 cases (dominant/de novo, n = 35; recessive, n = 12). Three variants were previously unreported. In recessive cases, facial weakness, neonatal hypotonia, ophthalmoplegia/paresis, ptosis, and scapular winging were more frequently observed than in dominant/de novo cases (all, p < 0.05). Both dominant/de novo and recessive cases exhibited core myopathy histopathology. Clinically severe cases were typically recessive or had variants localized to the RyR1 cytosolic shell domain. Motor deficits were most apparent in the MFM-32 standing and transfers dimension, [median (IQR) 85.4 (18.8)% of maximum score] and recessive cases exhibited significantly greater overall motor function impairment compared to dominant/de novo cases [79.7 (18.8)% vs. 87.5 (17.7)% of maximum score, p = 0.03]. Variant mapping revealed patterns of clinical severity across RyR1 domains, including a structural plane of interest within the RyR1 cytosolic shell, in which 84% of variants affected the bridging solenoid. We have corroborated genotype-phenotype correlations and identified RyR1 regions that may be especially sensitive to structural modification.

Novel Variants in Individuals with RYR1-Related Congenital Myopathies: Genetic, Laboratory, and Clinical Findings.

The ryanodine receptor 1-related congenital myopathies (RYR1-RM) comprise a spectrum of slow, rare neuromuscular diseases. Affected individuals present with a mild-to-severe symptomatology ranging from proximal muscle weakness, hypotonia and joint contractures to scoliosis, ophthalmoplegia, and respiratory involvement. Although there is currently no FDA-approved treatment for RYR1-RM, our group recently conducted the first clinical trial in this patient population (NCT02362425). This study aimed to characterize novel RYR1 variants with regard to genetic, laboratory, muscle magnetic resonance imaging (MRI), and clinical findings. Genetic and histopathology reports were obtained from participant's medical records. Alamut Visual Software was used to determine if participant's variants had been previously reported and to assess predicted pathogenicity. Physical exams, pulmonary function tests, T1-weighted muscle MRI scans, and blood measures were completed during the abovementioned clinical trial. Six novel variants (two de novo, three dominant, and one recessive) were identified in individuals with RYR1-RM. Consistent with established RYR1-RM histopathology, cores were observed in all biopsies, except Case 6 who exhibited fiber-type disproportion. Muscle atrophy and impaired mobility with Trendelenburg gait were the most common clinical symptoms and were identified in all cases. Muscle MRI revealed substantial inter-individual variation in fatty infiltration corroborating the heterogeneity of the disease. Two individuals with dominant RYR1 variants exhibited respiratory insufficiency: a clinical symptom more commonly associated with recessive RYR1-RM cases. This study demonstrates that a genetics-led approach is suitable for the diagnosis of suspected RYR1-RM which can be corroborated through histopathology, muscle MRI and clinical examination.

Transthoracic needle aspiration in solitary pulmonary nodule.

With improved awareness of public health and the recent advances in various imaging technologies, the detection rate of solitary pulmonary nodules (SPN) is continuously increasing. Transthoracic needle aspiration (TTNA) has represented a major approach for the diagnosis and differential diagnosis of pulmonary masses, owing to its simplicity and minimal invasiveness. This paper demonstrates the role of TTNA in SPN.

Pictorial essay of radiological features of benign intrathoracic masses.

With increased exposure of patients to routine imaging, incidental benign intrathoracic masses are frequently recognized. Most have classical imaging features, which are pathognomonic for their benignity. The aim of this pictorial review is to educate the reader of radiological features of several types of intrathoracic masses. The masses are categorized based on their location/origin and are grouped into parenchymal, pleural, mediastinal, or bronchial. Thoracic wall masses that invade the thorax such as neurofibromas and lipomas are included as they may mimic intrathoracic masses. All examples are illustrated and include pulmonary hamartoma, pleural fibroma, sarcoidosis, bronchial carcinoid, and bronchoceles together with a variety of mediastinal cysts on plain radiographs, computed tomography (CT) and magnetic resonance imaging (MRI). Sometimes a multimodality approach would be needed to confirm the diagnosis in atypical cases. The study would include the incorporation of radionuclide studies and relevant discussion in a multidisciplinary setting.

Pictorial review of intrathoracic manifestations of progressive systemic sclerosis.

Intra-thoracic manifestations of progressive systemic sclerosis (PSS) are not well known particularly the imaging features, which forms the basis of accurate and timely diagnosis. The aim of this study is to familiarize the physicians and radiologists with these features. The diagnosis can remain elusive because of the non-specific nature of symptoms which mimic many common conditions. Thus, the diagnosis of PSS can be missed leading to continuous morbidity if the correct imaging is not pursued. The authors examined the records of rheumatology patient referrals of over a 5 year period. A hundred and seventy patients with systemic sclerosis and mixed connective tissue disorders were chosen for detailed study of the imaging available, which form the basis of this review. The images included conventional chest radiographs, digital radiographs computed radiography (CT) and high resolution computed tomography (HRCT). Where applicable computed pulmonary angiography (CTPA) and radionuclide scans were also interrogated.

Atypical radiological manifestations of thoracic sarcoidosis: A review and pictorial essay.

Thoracic sarcoidosis is a common disease, with well-described and recognizable radiographic features. Nevertheless, most physicians are not familiar with the rare atypical often-confusing manifestations of thoracic sarcoid. Although these findings have been previously reviewed, but more recent advances in imaging and laboratory science, need to be incorporated. We present a review of literature and illustrate the review with unpublished data, intended to provide a more recent single comprehensive reference to assist with the diagnosis when atypical radiographic findings of thoracic sarcoidosis are encountered. Thoracic involvement accounts for most of morbidity and mortality associated with sarcoidosis. An accurate timely identification is required to minimize morbidity and mortality. It is essential to recognize atypical imaging findings and relate these to clinical manifestations and histology.

Genetics and preterm birth.

Although the etiology of preterm birth is incompletely understood, phenotype classifications combined with recent technologies such as genome-wide association studies and next-generation sequencing could lead to discovering genotypes associated with preterm birth. Identifying genetic contributions will allow for genetic screening tests to predict or detect pregnancies with potential for preterm birth. In this article we discuss current knowledge regarding phenotype classifications, genotypes, and their associations with preterm birth.

Effects of fertility on gene expression and function of the bovine endometrium.

Infertility and subfertility are important and pervasive reproductive problems in both domestic animals and humans. The majority of embryonic loss occurs during the first three weeks of pregnancy in cattle and women due, in part, to inadequate endometrial receptivity for support of embryo implantation. To identify heifers of contrasting fertility, serial rounds of artificial insemination (AI) were conducted in 201 synchronized crossbred beef heifers. The heifers were then fertility classified based on number of pregnancies detected on day 35 in four AI opportunities. Heifers, classified as having high fertility, subfertility or infertility, were selected for further study. The fertility-classified heifers were superovulated and flushed, and the recovered embryos were graded and then transferred to synchronized recipients. Quantity of embryos recovered per flush, embryo quality, and subsequent recipient pregnancy rates did not differ by fertility classification. Two in vivo-produced bovine embryos (stage 4 or 5, grade 1 or 2) were then transferred into each heifer on day 7 post-estrus. Pregnancy rates were greater in high fertility than lower fertility heifers when heifers were used as embryo recipients. The reproductive tracts of the classified heifers were obtained on day 14 of the estrous cycle. No obvious morphological differences in reproductive tract structures and histology of the uterus were observed in the heifers. Microarray analysis revealed differences in the endometrial transcriptome based on fertility classification. A genome-wide association study, based on SNP genotyping, detected 7 moderate associations with fertility across 6 different chromosomes. Collectively, these studies support the idea that innate differences in uterine function underlie fertility and early pregnancy loss in ruminants. Cattle with defined early pregnancy success or loss is useful to elucidate the complex biological and genetic mechanisms governing endometrial receptivity and uterine competency for pregnancy.

Imaging review of procedural and periprocedural complications of central venous lines, percutaneous intrathoracic drains, and nasogastric tubes.

Placements of central venous lines (CVC), percutaneous intrathoracic drains (ITDs), and nasogastric tubes (NGTs) are some of the most common interventional procedures performed on patients that are unconscious and in almost all intensive care/high dependency patients in one form or the other. These are standard procedures within the remit of physicians, and other trained health professionals. Procedural complications may occur in 7%-15% of patients depending upon the intervention and experience of the operator. Most complications are minor, but other serious complications may add significantly to morbidity and even mortality of already compromised patients. Imaging findings are the key to the detection of misplaced lines, and tubes and their prompt recognition are vital to avoid harm to the patient. It is, therefore, pertinent that healthcare professionals who perform these procedures are familiar with imaging complications of these procedures. Here, we present the imaging characteristics of procedural complications.