scholarly journals Generation of a Biobank From Two Adult Thoroughbred Stallions for the Functional Annotation of Animal Genomes Initiative

2021 ◽  
Vol 12 ◽  
Author(s):  
Callum G. Donnelly ◽  
Rebecca R. Bellone ◽  
Erin N. Hales ◽  
Annee Nguyen ◽  
Scott A. Katzman ◽  
...  
Keyword(s):  
Functional Annotation ◽  
Snp Array ◽  
Dermal Fibroblasts ◽  
Specific Gene ◽  
Sample Collection ◽  
Tissue Samples ◽  
Thickness Skin ◽  
Thoracic Limb ◽  
Limb Ataxia ◽  
Pelvic Limb

Following the successful creation of a biobank from two adult Thoroughbred mares, this study aimed to recapitulate sample collection in two adult Thoroughbred stallions as part of the Functional Annotation of the Animal Genome (FAANG) initiative. Both stallions underwent thorough physical, lameness, neurologic, and ophthalmic (including electroretinography) examinations prior to humane euthanasia. Epididymal sperm was recovered from both stallions immediately postmortem and cryopreserved. Aseptically collected full thickness skin biopsies were used to isolate, culture and cryopreserve dermal fibroblasts. Serum, plasma, cerebrospinal fluid, urine, and gastrointestinal content from various locations were collected and cryopreserved. Under guidance of a board-certified veterinary anatomic pathologist, 102 representative tissue samples were collected from both horses. Whole tissue samples were flash-frozen and prioritized tissues had nuclei isolated and cryopreserved. Spatially contemporaneous samples of each tissue were submitted for histologic examination. Antemortem and gross pathologic examination revealed mild abnormalities in both stallions. One stallion (ECA_UCD_AH3) had unilateral thoracic limb lameness and bilateral chorioretinal scars. The second stallion (ECA_UCD_AH4) had subtle symmetrical pelvic limb ataxia, symmetrical prostatomegally, and moderate gastrointestinal nematodiasis. DNA from each was whole-genome sequenced and genotyped using the GGP Equine 70K SNP array. The genomic resources and banked biological samples from these animals augments the existing resource available to the equine genomics community. Importantly we may now improve the resolution of tissue-specific gene regulation as affected by sex, as well as add sex-specific tissues and gametes.

scholarly journals Cervical spondylomyelopathy (wobbler syndrome) in the Boerboel

2003 ◽  
Vol 74 (4) ◽  
Author(s):  
M.J. Gray ◽  
R.M. Kirberger ◽  
T.C. Spotswood
Keyword(s):  
South African ◽  
Clinical Signs ◽  
Acute Onset ◽  
Thoracic Vertebrae ◽  
Wobbler Syndrome ◽  
Thoracic Limb ◽  
Limb Ataxia ◽  
Dorsal Laminectomy ◽  
Pelvic Limb ◽  
Synovial Cysts

The Boerboel is a South African large-breed dog resembling a Bullmastiff. The records of Onderstepoort Veterinary Academic Hospital were searched for dogs that had presented, between 1998 and 2003, with symptoms indicative of wobbler syndrome and had undergone survey radiographic and myelographic studies. Ten cases fitted the inclusion criteria. Dogs presented within the first 2 years of life, often with acute onset of symptoms. All presented with pelvic limb and 6 with concomitant thoracic limb ataxia or paresis. Treatment varied and included none (4), prednisolone (2), and dorsal laminectomy (2). Two dogs were euthanased at the time of diagnosis. The breed appears to be affected with a form of spondylomyelopathy that comprises bony malformation of cervical and/or thoracic vertebrae. In 8 dogs, malformations were evident on survey radiographs and were characterised by enlarged, irregular articular facets and associated medial deviation of the pedicles. These changes resulted in axial compression of the spinal cord best seen on ventrodorsal or dorsoventral myelographic studies. Multiple vertebrae were affected in some dogs and lesions were not confined to the caudal area of the cervical spine. Three dogs were alive and without symptoms at follow-up. Four were euthanased as a result of the disease and 1 died as a result of post-operative complications. Two additional dogs presenting with wobbler clinical signs are also described. One had medial deviation of the T5 and T6 caudal pedicles and 1 dog suffered from multiple cervical articular facet synovial cysts.

scholarly journals Clinical, pathological and epidemiological aspects of outbreaks of bluetongue disease in sheep in the central region of Rio Grande do Sul

2017 ◽  
Vol 37 (12) ◽  
pp. 1443-1452
Author(s):  
Ronaldo M. Bianchi ◽  
Welden Panziera ◽  
Tatiane C. Faccin ◽  
Gisane L. de Almeida ◽  
Juliana F. Cargnelutti ◽  
...  
Keyword(s):  
Central Region ◽  
Striated Muscle ◽  
Clinical Signs ◽  
Rio Grande ◽  
Nasal Discharge ◽  
Rio Grande Do Sul ◽  
Sample Collection ◽  
Area At Risk ◽  
Tissue Samples ◽  
Facial Swelling

ABSTRACT: This article describes the clinical, pathological and epidemiological aspects of 17 outbreaks of bluetongue (BT) disease in sheep occurring between December 2014 and July 2015 in the central region of Rio Grande do Sul state (RS), southern Brazil. Affected farms were visited for clinical examination, necropsy, sample collection and epidemiological investigation. The outbreaks were seasonal and occurred during the summer and autumn. A total of 180 sheep (20.4%) out of 884 in 17 small herds were affected. All ages of Texel and mixed breed sheep were affected. However, lambs (younger than one year) had higher morbidity than adult sheep. The most frequent clinical signs were anorexia, lethargy, loss of body condition, facial swelling mainly involving the lips, and greenish seromucous or mucous nasal discharge. Pulmonary lesions characterized by edema were the most prevalent findings; however, erosive and ulcerative lesions in the upper gastrointestinal tract, as well as cardiac, skeletal muscle and esophageal striated muscle necrosis, and hemorrhage in the pulmonary artery were also frequent. The bluetongue virus (BTV) genome was detected by RT-PCR in blood and tissue samples (spleen and lungs) of 21 animals from 17 outbreaks. The virus involved in the outbreak 3 was subsequently isolated and shown to belong to serotype 17, for the first time reported in Brazil. In summary, our data support the BTV genotype 17 as the etiological agent of the outbreaks and indicate that the central region of RS is an area at risk for BT in sheep, a disease previously not recognized in the region.

A Modified Western Blot Protocol for Enhanced Sensitivity in the Detection of a Tissue Protein

2020 ◽  
pp. 35-43
Keyword(s):  
Amino Acid Residues ◽  
Data Generation ◽  
Sample Collection ◽  
Nylon Membrane ◽  
Western Blots ◽  
Tissue Samples ◽  
Protein Levels ◽  
Enhanced Sensitivity ◽  
Present Book ◽  
Control Procedures

Western blots (WB) are designed to investigate protein levels and their patterns of modification in homogenized tissue samples. Although, Western blots are quantifiable, unlike immunohistochemistry, cellular integrity is lost. The availability of antibodies against the protein and their patterns of modification of interest form the basis of both Western blots and Immunohistochemistry. Antibodies can also be directed not only against proteins but against chemical modifications of the proteins too, such as phosphorylation and glycosylation of specific amino acid residues. In Western blotting, the proteins in the sample are denatured, size-separated on a denaturing acrylamide gel, and transferred to a nylon membrane. Antibody paratopes can then bind to the antigenic epitope in the protein present on the nylon membrane. Thus, with the help of a chemiluminescent assay system that darkens X-ray films, the resulting antibody-antigen complex can be visualized. Because of the ubiquitous and relatively inexpensive availability of WB equipment, the quality of WB in publications and following analysis and investigation of the data can be variable, possibly resulting in forged conclusions. This may be because of the poor laboratory technique and/or lack of understanding of the significant steps involved in WB and what quality control procedures should be followed to ensure effective data generation. The present book chapter focuses on providing a detailed description and critique of WB procedures and technicalities, from sample collection through preparation, blotting, and detection, to examination of the data collected. We aim to provide the reader with the improved expertise to decisively carry out, assess, and troubleshoot the WB process, in order to produce reproducible and reliable blots.

scholarly journals Addressing cellular heterogeneity in tumor and circulation for refined prognostication

2019 ◽  
Vol 116 (36) ◽  
pp. 17957-17962 ◽  
Author(s):  
Su Bin Lim ◽  
Trifanny Yeo ◽  
Wen Di Lee ◽  
Ali Asgar S. Bhagat ◽  
Swee Jin Tan ◽  
...  
Keyword(s):  
Risk Model ◽  
Expression Profiles ◽  
Metastatic Potential ◽  
Cellular Heterogeneity ◽  
Intratumor Heterogeneity ◽  
Specific Gene ◽  
Label Free ◽  
Tissue Samples ◽  
Inertial Focusing ◽  
Gene Signatures

Despite pronounced genomic and transcriptomic heterogeneity in non–small-cell lung cancer (NSCLC) not only between tumors, but also within a tumor, validation of clinically relevant gene signatures for prognostication has relied upon single-tissue samples, including 2 commercially available multigene tests (MGTs). Here we report an unanticipated impact of intratumor heterogeneity (ITH) on risk prediction of recurrence in NSCLC, underscoring the need for a better genomic strategy to refine prognostication. By leveraging label-free, inertial-focusing microfluidic approaches in retrieving circulating tumor cells (CTCs) at single-cell resolution, we further identified specific gene signatures with distinct expression profiles in CTCs from patients with differing metastatic potential. Notably, a refined prognostic risk model that reconciles the level of ITH and CTC-derived gene expression data outperformed the initial classifier in predicting recurrence-free survival (RFS). We propose tailored approaches to providing reliable risk estimates while accounting for ITH-driven variance in NSCLC.

EFFECTS OF SEX, GENOTYPE AND NUTRITION ON THE RELATIVE GROWTH OF MUSCLES IN THE PIG

1982 ◽  
Vol 62 (2) ◽  
pp. 587-596 ◽  
Author(s):  
R. J. RICHMOND ◽  
R. T. BERG
Keyword(s):  
Muscle Development ◽  
Muscle Growth ◽  
Abdominal Muscles ◽  
Relative Growth ◽  
Feeding Level ◽  
Thoracic Limb ◽  
Breed Differences ◽  
Limb Muscles ◽  
Pelvic Limb ◽  
Muscle Groups

The effects of liveweight, breed, sex, diet and feeding level on muscle distribution were studied by comparing nine anatomical muscle groups dissected from the half carcasses of pigs from two studies. The first study consisted of 109 pigs representing barrows and gilts of three breed groups, fed two diets differing in energy and protein. The second study consisted of 72 barrows and gilts from two breed groups fed a low-energy diet at one of three feed levels. Animals were slaughtered at 23, 68, 91 or 114 kg liveweight. The results were compared with data from one other study. In pigs, major differentiation in muscle development appears to take place prior to 23 kg liveweight. Muscle differentiation appeared to follow functional demands. Muscles associated with mobility immediately after birth such as the distal limb muscles, developed early while those associated with greater locomotion and propulsion, such as the proximal pelvic limb muscles, developed later in life. Sex had little influence on muscle distribution between 23 and 114 kg liveweight. Proportion of abdominal muscles had apparently increased markedly prior to 23 kg liveweight and continued to be influenced by the level of feeding throughout. Breed differences in muscle distribution were observed for spinal, abdominal and distal thoracic limb muscles. Key words: Swine, muscle growth, muscle distribution

scholarly journals Neuromuscular development of Felis catus

1980 ◽  
Vol 14 (3) ◽  
pp. 197-198 ◽  
Author(s):  
Bonnie V. Beaver
Keyword(s):  
Felis Catus ◽  
Muscle Control ◽  
Thoracic Limb ◽  
Pelvic Limb ◽  
Neuromuscular Development

Neuromuscular development was studied for 12 weeks in 22 kittens. Vertebral extensor, flexor and combined dominance was recorded in several phases. Thoracic limb support began between days 1 and 10, while the initiation of pelvic limb support ranged up to day 25. Crossed extensor and Landau reflexes were present in most kittens at various times up to day 19, although the Magnus response was not seen. Auricular muscle control developed at 1·5 weeks, about the same time as claw control.

Biomarker analysis from completely resected NSCLC patients enrolled in an adjuvant erlotinib clinical trial (RADIANT)

2009 ◽  
Vol 27 (15_suppl) ◽  
pp. 7520-7520 ◽  
Author(s):  
F. Richardson ◽  
K. Richardson ◽  
G. Sennello ◽  
D. Young ◽  
S. Orlov ◽  
...  
Keyword(s):  
Tumor Tissue ◽  
Early Stage ◽  
Tumor Stage ◽  
Phase Iii ◽  
Sample Collection ◽  
Kras Mutations ◽  
Tissue Samples ◽  
Resected Nsclc ◽  
Biomarker Analysis ◽  
Nsclc Patients

7520 Background: RADIANT is a phase III trial comparing erlotinib 150 mg daily vs. placebo (2:1) in stage IB-IIIA NSCLC patients with EGFR-positive tumors (IHC and/or FISH), following complete surgical resection. Planned accrual is 945 patients. Correlative biomarker studies on primary tumor tissue, whole blood, and serum are key components of the study. Methods: Tumor tissue was evaluated by IHC for protein expression of EGFR (PharmDx Kit, Dako with + ≥ 1% positive tumor cells), by FISH for gene expression of EGFR (Vysis, Abbott), and by Wave HS for EGFR and Kras mutations. Results: Among 655 tissue samples analyzed, 96% were EGFR IHC+ and 74% EGFR FISH+. Of the 476 tissue samples analyzed to date for mutations (mut), 12% had activating EGFR and 19% had Kras mut. Preliminary comparisons suggest that EGFR mut rate increased while Kras mut rate decreased with tumor stage. EGFR mut occurred in 29/178 (16%) females (F) vs. 23/271 (8%) males (M), 19/57 (33%) Asians (A) vs. 33/392 (8%) non-Asians (NA), and 29/66 (44%) never smokers (NS) vs. 23/383 (6%) current or former smokers (S). The differences between A vs. NA and NS vs. S were significantly different (P <0.0001) for all comparisons made. Kras mut occurred in 40/180 (22%) F vs. 48/280 (17%) M, 4/57 (7%) A vs. 84/403 (21%) NA, and 3/68 (4%) NS vs. 85/392 (22%) S. The difference between A vs. NA and NS vs. S were significantly different (P ≤0.0389) for all comparisons made. In adenoca, 51/254 (20%) had EGFR and 79/261 (30%) had Kras mut, and in SCC, 0/157 (0%) had EGFR and 3/162 (2%) had Kras mut. One tumor sample demonstrated both an activating EGFR and Kras mut. Conclusions: Ongoing comprehensive biomarker assessment in the RADIANT population indicates successful sample collection and analysis. FISH positivity rates are greater than observed in late-stage tumors. Remaining results in this early-stage population are consistent with those observed in advanced-stage disease. Once complete, this study will provide a robust biomarker dataset on which to evaluate predictive and prognostic response markers, which may help determine who may benefit from treatment with erlotinib in the adjuvant setting. [Table: see text]

scholarly journals Gene expression in the human mammary epithelium during lactation: the milk fat globule transcriptome

2009 ◽  
Vol 37 (1) ◽  
pp. 12-22 ◽  
Author(s):  
Patricia D. Maningat ◽  
Partha Sen ◽  
Monique Rijnkels ◽  
Agneta L. Sunehag ◽  
Darryl L. Hadsell ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Milk Fat ◽  
Mammary Epithelium ◽  
Specific Gene ◽  
Molecular Physiology ◽  
Tissue Samples ◽  
Milk Fat Globule ◽  
Fat Globule

The molecular physiology underlying human milk production is largely unknown because of limitations in obtaining tissue samples. Determining gene expression in normal lactating women would be a potential step toward understanding why some women struggle with or fail at breastfeeding their infants. Recently, we demonstrated the utility of RNA obtained from breast milk fat globule (MFG) to detect mammary epithelial cell (MEC)-specific gene expression. We used MFG RNA to determine the gene expression profile of human MEC during lactation. Microarray studies were performed using Human Ref-8 BeadChip arrays (Illumina). MFG RNA was collected every 3 h for 24 h from five healthy, exclusively breastfeeding women. We determined that 14,070 transcripts were expressed and represented the MFG transcriptome. According to GeneSpring GX 9, 156 ontology terms were enriched (corrected P < 0.05), which include cellular ( n = 3,379 genes) and metabolic ( n = 2,656) processes as the most significantly enriched biological process terms. The top networks and pathways were associated primarily with cellular activities most likely involved with milk synthesis. Multiple sampling over 24 h enabled us to demonstrate core circadian clock gene expression and the periodicity of 1,029 genes (7%) enriched for molecular functions involved in cell development, growth, proliferation, and cell morphology. In addition, we found that the MFG transcriptome was comparable to the metabolic gene expression profile described for the lactating mouse mammary gland. This paper is the first to describe the MFG transcriptome in sequential human samples over a 24 h period, providing valuable insights into gene expression in the human MEC.

scholarly journals Impact of Hemolysis on Multi-OMIC Pancreatic Biomarker Discovery: Derisking Precision Medicine Biomarker Development

2021 ◽  
Author(s):  
Richard Searfoss ◽  
Punit Shah ◽  
Kennedy Ofori-Mensa ◽  
Valerie Bussberg ◽  
Vladimir Tolstikov ◽  
...  
Keyword(s):  
Biomarker Discovery ◽  
Hemoglobin Concentration ◽  
Cancer Biomarker ◽  
Buffy Coat ◽  
Sample Collection ◽  
Serum Samples ◽  
Tissue Samples ◽  
Analyte Detection ◽  
Study Participants ◽  
The Impact

Abstract Cancer biomarker discovery is critically dependent on the integrity of biofluid, and tissue samples acquired from study participants. Multi-omic profiling of candidate protein, lipid, and metabolite biomarkers is confounded by timing and fasting status of sample collection, participant demographics and treatment exposures of the study population. Contamination by hemoglobin, whether caused by hemolysis during sample preparation or underlying red cell fragility, contributes 0 – 10 g/L of extraneous protein to plasma, serum, and Buffy coat samples and may interfere with biomarker detection and validation. We analyzed 617 plasma, 701 serum, and 657 buffy coat samples from a 7 year longitudinal multi-omic biomarker discovery program evaluating 400+ participants with or at risk for pancreatic cancer, known as Project Survival™. Hemolysis was undetectable in 93.1% of plasma and 95.0% of serum samples, whereas only 37.1% of Buffy coat samples were free of contamination by hemoglobin. Regression analysis of multi-omic data demonstrated a statistically significant correlation between hemoglobin concentration and the resulting pattern of analyte detection and concentration. Although hemolysis had the greatest impact on identification and quantitation of the proteome, distinct differentials in metabolomics and lipidomics were also observed and correlated with severity. We conclude that quality control is vital to accurate detection of informative molecular differentials using OMIC technologies and that caution must be exercised to minimize the impact of hemolysis as a factor driving false discovery in large cancer biomarker studies.

scholarly journals Post-Mortem Brain Donations vs Pre-Mortem Surgical Resections for Glioblastoma Research: Viewing the Matter as a Whole

2021 ◽  
Author(s):  
Cassandra P Griffin ◽  
Christine L Paul ◽  
Kimberley L Alexander ◽  
Marjorie M Walker ◽  
Hubert Hondermarck ◽  
...  
Keyword(s):  
Treatment Resistance ◽  
Biological Research ◽  
Histopathological Diagnosis ◽  
Post Mortem ◽  
Sample Collection ◽  
Surgical Biopsy ◽  
Tissue Samples ◽  
Post Mortem Brain ◽  
Stage Disease ◽  
End Stage

Abstract There have been limited improvements in diagnosis, treatment and outcomes of primary brain cancers, including glioblastoma, over the past 10 years. This is largely attributable to persistent deficits in understanding brain tumour biology and pathogenesis due to a lack of high-quality biological research specimens. Traditional, pre-mortem, surgical biopsy samples do not allow full characterisation of the spatial and temporal heterogeneity of glioblastoma, nor capture end-stage disease to allow full evaluation of the evolutionary and mutational processes that lead to treatment resistance and recurrence. Furthermore, the necessity of ensuring sufficient viable tissue is available for histopathological diagnosis, while minimising surgically induced functional deficit, leaves minimal tissue for research purposes and results in formalin fixation of most surgical specimens. Post-mortem brain donation programs are rapidly gaining support due to their unique ability to address the limitations associated with surgical tissue sampling. Collecting, processing, and preserving tissue samples intended solely for research provides both a spatial and temporal view of tumour heterogeneity as well as the opportunity to fully characterise end-stage disease from histological and molecular standpoints. This review explores the limitations of traditional sample collection and the opportunities afforded by post-mortem brain donations for future neurobiological cancer research.

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