Genome assembly and gene expression in the American black bear provides new insights into the renal response to hibernation

AbstractThe prevalence of chronic kidney disease (CKD) is rising worldwide and 10-15% of the global population currently suffers from CKD and its complications. Given the increasing prevalence of CKD there is an urgent need to find novel treatment options. The American black bear (Ursus americanus) copes with months of lowered kidney function and metabolism during hibernation without the devastating effects on metabolism and other consequences observed in humans. In a biomimetic approach to better understand kidney adaptations and physiology in hibernating black bears, we established a high-quality genome assembly. Subsequent RNA-Seq analysis of kidneys comparing gene expression profiles in black bears entering (late fall) and emerging (early spring) from hibernation identified 169 protein-coding genes that were differentially expressed. Of these, 101 genes were downregulated and 68 genes were upregulated after hibernation. Fold changes ranged from 1.8-fold downregulation (RTN4RL2) to 2.4-fold upregulation (CISH). Most notable was the upregulation of cytokine suppression genes (SOCS2, CISH, and SERPINC1) and the lack of increased expression of cytokines and genes involved in inflammation. The identification of these differences in gene expression in the black bear kidney may provide new insights in the prevention and treatment of CKD.

Download Full-text

Genome assembly and gene expression in the American black bear provides new insights into the renal response to hibernation

DNA Research ◽

10.1093/dnares/dsy036 ◽

2018 ◽

Vol 26 (1) ◽

pp. 37-44 ◽

Cited By ~ 8

Author(s):

Anuj Srivastava ◽

Vishal Kumar Sarsani ◽

Ian Fiddes ◽

Susan M Sheehan ◽

Rita L Seger ◽

...

Keyword(s):

Gene Expression ◽

Genome Assembly ◽

Black Bear ◽

Renal Response ◽

American Black Bear ◽

American Black

Download Full-text

Behavior in Free-Living American Black Bear Dens: Parturition, Maternal Care, and Cub Behavior

Animals ◽

10.3390/ani10071123 ◽

2020 ◽

Vol 10 (7) ◽

pp. 1123

Author(s):

Lynn L. Rogers ◽

Linda McColley ◽

Janet Dalton ◽

Jim Stroner ◽

Douglas Hajicek ◽

...

Keyword(s):

Ursus Americanus ◽

Post Partum ◽

Black Bear ◽

Geographic Region ◽

Black Bears ◽

Free Living ◽

Future Studies ◽

American Black Bear ◽

Eye Opening ◽

American Black

Denning behavior has long remained the least observed aspect of bear behavior. During 2010–2013, we used webcams, microphones, the internet, and 14,602 h of archived video to document the denning behaviors of two adult wild black bears (Ursus americanus) as they gave birth and cared for four litters through six winters in northeastern Minnesota. Observations included types of dens, labor, pre-parturient genital swelling, birthing positions, post-partum vocalizations, mothers removing amniotic tissues and warming newborn cubs in sub-freezing temperatures, frequency of nursing, cubs establishing nipple order, yearlings suckling, the ingestion of snow and icicles, the ingestion of foot pads, urination and defecation in latrine areas, toilet-licking, eye opening, reciprocal tongue-licking, play, rapid eye movement (REM) sleep and possible dreaming, and reactions to wildlife intruders. The use of this new method for observing natural bear dens allowed the identification of many behaviors undescribed for any species of wild bear in dens. We also discuss the need for future studies and how the depth and duration of black bear hibernation varies with body condition and geographic region.

Download Full-text

Temporal variation in food habits of the American Black Bear (Ursus americanus) in the boreal forest of northern Ontario

The Canadian Field-Naturalist ◽

10.22621/cfn.v127i2.1442 ◽

2013 ◽

Vol 127 (2) ◽

pp. 118 ◽

Cited By ~ 5

Author(s):

Derrick A. Romain ◽

Martyn E. Obbard ◽

James L. Atkinson

Keyword(s):

Temporal Variation ◽

Food Habits ◽

Ursus Americanus ◽

Late Summer ◽

Black Bear ◽

Black Bears ◽

Northern Ontario ◽

American Black Bear ◽

American Black ◽

American Black Bears

We used scat analysis to investigate temporal variation in the food habits of American Black Bears (Ursus americanus) in the boreal forest of northern Ontario. Specifically, we examined whether there was a seasonal shift in foraging over three years (1990–1992) and which foods, if any, varied in occurrence among years. American Black Bears ate foods ranging from green vegetation in the spring to ants in mid-summer and berries and nuts in late summer and fall. Late summer berry forage, especially blueberries (Vaccinium spp.), varied greatly among years. American Black Bears in northern Ontario consumed a variety of foods opportunistically. Understanding how American Black Bears in northern Ontario exploit food resources and how these food items vary among years can provide insights into demographic processes and help wildlife managers better anticipate changes in the structure of the harvest of American Black Bears and in human–bear conflict levels. In northern Ontario, forest management practices that increase the availability of early successional species would be beneficial to American Black Bear populations.

Download Full-text

Gene Expression Profiles from Needle Biopsies Provide Useful Signatures of Non-Small Cell Lung Carcinomas

Biomarker Insights ◽

10.1177/117727190700200031 ◽

2007 ◽

Vol 2 ◽

pp. 117727190700200

Author(s):

Douglas E. Paull ◽

Kevin Kelley ◽

Jazbieh Moezzi ◽

Madhavi Kadakia ◽

Steven J. Berberich

Keyword(s):

Gene Expression ◽

Dna Microarrays ◽

Expression Profiles ◽

Treatment Options ◽

Gene Expression Profiles ◽

Small Cell ◽

Small Cell Lung ◽

Lung Carcinomas ◽

Fine Needle Aspirates ◽

Resected Tumor

Gene expression profiles from DNA microarrays can provide molecular signatures that improve tumor classification, prognosis, and treatment options. While much of this work has focused on isolation of RNA from the resected tumor, fewer studies have utilized RNA from fine needle aspirates (FNA). In this pilot study we examined whether the gene signatures obtained from FNA samples would correlate with signatures taken from the resected tumor. Based on NSCLC gene expression profiles obtained from eleven sets of FNA and tumor samples we obtained a high concordance of FNA profiles matching their matched tumor sample. These results suggest that FNA samples may provide informative gene expression signatures regarding the potential aggressiveness of non-small-cell lung carcinomas.

Download Full-text

Individual identification via remote video verified by DNA analysis: a case study of the American black bear

Wildlife Research ◽

10.1071/wr18049 ◽

2019 ◽

Vol 46 (4) ◽

pp. 326

Author(s):

Alan B. Ramsey ◽

Michael A. Sawaya ◽

Lorinda S. Bullington ◽

Philip W. Ramsey

Keyword(s):

Habitat Use ◽

Dna Analysis ◽

Black Bear ◽

Black Bears ◽

Individual Identification ◽

Video Cameras ◽

American Black Bear ◽

Open Population ◽

Other Information ◽

American Black

Context Researchers and managers often use DNA analysis and remote photography to identify cryptic animals and estimate abundance. Remote video cameras are used less often but offer an increased ability to distinguish similar-looking individuals as well as to observe behavioural patterns that cannot be adequately captured with still photography. However, the use of this approach in species with minimally distinguishing marks has not been tested. Aims To determine the utility and accuracy of distinguishing characteristics of American black bears, Ursus americanus, observed on remote video for identifying individuals in an open population. Methods We compared individuals identified on video with individuals and their sex identified by DNA analysis of hairs collected from hair traps visited by the bears. Key results We found that remote video could be used to determine the number of male and female black bears sampled by the video cameras. Specifically, we matched 13 individual bear genotypes with 13 video identifications, one genotype for each individual. We correctly matched ~82% of video identifications with all 38 genotypes collected from hair traps. Conclusions We demonstrated that distinguishing characteristics of a cryptic animal in remote video can be used to accurately identify individuals. Remote video complements genetic analysis by providing information about habitat use and behaviour. Implications When remote video cameras can be used to identify individuals, a wealth of other information will subsequently be obtained. Multi-year video-based studies can show sex ratios, and relative physical condition; shed light on fine-scale habitat use, such as when and where animals feed and what they eat; and display social interactions and rare behaviours.

Download Full-text

Computational Drug-repositioning Approach Identifying Sirolimus as a Potential Therapeutic Option for Inflammatory Dilated Cardiomyopathy

Drug Research ◽

10.1055/a-0950-9608 ◽

2019 ◽

Vol 69 (10) ◽

pp. 565-571 ◽

Cited By ~ 1

Author(s):

Kyoko Shibata ◽

Toshinori Endo ◽

Yoshikazu Kuribayashi

Keyword(s):

Gene Expression ◽

Dilated Cardiomyopathy ◽

Drug Repositioning ◽

Expression Profiles ◽

Therapeutic Option ◽

Treatment Options ◽

Antiviral Drug ◽

Specific Treatment ◽

Gene Expression Profiles ◽

Connectivity Map

Abstract Objective The aim of this study was to determine promising treatment options for human inflammatory dilated cardiomyopathy using a computational drug-repositioning approach (repurposing established drug compounds for new therapeutic indications). Background If the myocardial tissue is detected to be infiltrated with inflammatory cells, primarily of lymphocytes, and if the virus is confirmed using genetic examination (PCR) or immunostaining, the infection is suspected. However, there is no specific treatment (i. e., an antiviral drug) even if the virus is identified; therefore, we used Connectivity Map to identify compounds showing inverse drug–disease signatures, indicating activity against inflammatory dilated cardiomyopathy. Results Potential drug-repositioning candidates for the treatment of inflammatory dilated cardiomyopathy were explored through a systematic comparison of the gene expression profiles induced by drugs using Gene Expression Omnibus and Connectivity Map databases. Conclusion Using a computational drug-repositioning approach based on the integration of publicly available gene expression signatures of drugs and diseases, sirolimus was suggested as a novel therapeutic option for inflammatory dilated cardiomyopathy.

Download Full-text

MLL-Rearranged ALL Cells Are Highly Dependent On the Expression of EP300-Interacting Inhibitor of Differentiation 1 (EID1)

Blood ◽

10.1182/blood.v120.21.1462.1462 ◽

2012 ◽

Vol 120 (21) ◽

pp. 1462-1462

Author(s):

Marieke Hendrika van der Linden ◽

Pauline Schneider ◽

Rob Pieters ◽

Ronald Stam

Keyword(s):

Gene Expression ◽

Conflicts Of Interest ◽

Expression Profiles ◽

Lymphoblastic Leukemia ◽

Treatment Options ◽

Gene Expression Profiles ◽

Pcr Analysis ◽

Rapid Reduction ◽

Adequate Treatment ◽

Inhibitor Of Differentiation 1

Abstract Abstract 1462 MLL-rearranged acute lymphoblastic leukemia (ALL) remains a difficult to treat type of leukemia, for which alternative and more adequate treatment options are still urgently needed. Various genome-wide transcriptome studies, including ours, have shown that MLL-rearranged ALL patients display highly unique gene expression profiles. In search of new and valid therapeutic targets to which more adequate treatments could be developed, we constantly screen our gene expression profiling data for potential candidates. In the present study we set out to investigate EID1 (EP300-interacting inhibitor of differentiation 1), which we found highly and specifically expressed in MLL-rearranged ALL cells. Validating this observation, quantitative RT-PCR analysis confirmed that EID1 expression was significantly higher in MLL-rearranged ALL cells as compared with other ALL subtypes or healthy bone marrow samples. Next, we performed shRNA-mediated knockdown of EID1 in MLL-rearranged ALL cells, which resulted in a dramatic reduction of viable cells. Subsequently, flow cytometry analyses demonstrated that this rapid reduction of cell viability was due to massive induction of apoptosis as well as an abrupt cell cycle arrest. Consequently, it appeared difficult to study the actual function of EID1 over-expression in MLL-rearranged ALL cells. On the other hand, these features make EID1 an attractive target for therapeutic intervention in MLL-rearranged ALL. Hence, further studies on the function of EID1 in MLL-rearranged ALL and exploring the possibilities to inhibit it are warranted. Disclosures: No relevant conflicts of interest to declare.

Download Full-text