Large-scale, high-throughput screening for coagulation and hematologic phenotypes in mice*

The Mouse Phenome Project is an international effort to systematically gather phenotypic data for a defined set of inbred mouse strains. For such large-scale projects the development of high-throughput screening protocols that allow multiple tests to be performed on a single mouse is essential. Here we report hematologic and coagulation data for more than 30 inbred strains. Complete blood counts were performed using an Advia 120 analyzer. For coagulation testing, we successfully adapted the Dade Behring BCS automated coagulation analyzer for use in mice by lowering sample and reagent volume requirements. Seven automated assay procedures were developed. Small sample volume requirements make it possible to perform multiple tests on a single animal without euthanasia, while reductions in reagent volume requirements reduce costs. The data show that considerable variation in many basic hematological and coagulation parameters exists among the inbred strains. These data, freely available on the World Wide Web, allow investigators to knowledgeably select the most appropriate strain(s) to meet their individual study designs and goals.

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High Throughput Computational Mouse Genetic Analysis

10.1101/2020.09.01.278465 ◽

2020 ◽

Cited By ~ 1

Author(s):

Ahmed Arslan ◽

Yuan Guan ◽

Xinyu Chen ◽

Robin Donaldson ◽

Wan Zhu ◽

...

Keyword(s):

Genetic Factors ◽

Inbred Mouse ◽

Inbred Strains ◽

Mouse Strains ◽

Inbred Mouse Strains ◽

Mitochondrial Targeting ◽

Phenotypic Data ◽

Factors Affecting ◽

Wide Range ◽

Allelic Differences

AbstractBackgroundGenetic factors affecting multiple biomedical traits in mice have been identified when GWAS data, which measured responses in panels of inbred mouse strains, was analyzed using haplotype-based computational genetic mapping (HBCGM). Although this method was previously used to analyze one dataset at a time; but now, a vast amount of mouse phenotypic data is now publicly available, which could enable many more genetic discoveries.ResultsHBCGM and a whole genome SNP map covering 43 inbred strains was used to analyze 8300 publicly available datasets of biomedical responses (1.52M individual datapoints) measured in panels of inbred mouse strains. As proof of concept, causative genetic factors affecting susceptibility for eye, metabolic and infectious diseases were identified when structured automated methods were used to analyze the output. One analysis identified a novel genetic effector mechanism; allelic differences within the mitochondrial targeting sequence affected the subcellular localization of a protein. We also found allelic differences within the mitochondrial targeting sequences of many murine and human proteins, and these could affect a wide range of biomedical phenotypes.ImplicationsThese initial results indicate that genetic factors affecting biomedical responses could be identified through analysis of very large datasets, and they provide an early indication of how this type of ‘augmented intelligence’ can facilitate genetic discovery.

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Rat Phenome Project: The untapped potential of existing rat strains

Journal of Applied Physiology ◽

10.1152/japplphysiol.01006.2004 ◽

2005 ◽

Vol 98 (1) ◽

pp. 371-379 ◽

Cited By ~ 35

Author(s):

Tomoji Mashimo ◽

Birger Voigt ◽

Takashi Kuramoto ◽

Tadao Serikawa

Keyword(s):

High Throughput Screening ◽

Large Scale ◽

Inbred Strains ◽

Human Diseases ◽

Renal Diseases ◽

Sequence Length ◽

Rat Strains ◽

Phenotypic Data ◽

Hematological Disorders ◽

Specific Pathogen

The National Bio Resource Project for the Rat in Japan collects, preserves, and distributes rat strains. More than 250 inbred strains have been deposited thus far into the National Bio Resource Project for the Rat and are maintained as specific pathogen-free rats or cryopreserved embryos. We are now comprehensively characterizing deposited strains as part of the Rat Phenome Project to reevaluate their value as models of human diseases. Phenotypic data are being collected for 7 categories and 109 parameters: functional observational battery (neurobehavior), behavior studies, blood pressure, biochemical blood tests, hematology, urology, and anatomy. Furthermore, genotypes are being determined for 370 simple sequence-length polymorphism markers distributed through the whole rat genome. Here, we report these large-scale, high-throughput screening data that have already been collected for 54 rat strains. This comprehensive, original phenotypic data can be systematically viewed by “strain ranking” for each parameter. This allows investigators to explore the relationship between several rat strains, to identify new rat models, and to select the most suitable strains for specific experiments. The discovery of several potential models for human diseases, such as hypertension, hypotension, renal diseases, hyperlipemia, hematological disorders, and neurological disorders, illustrates the potential of many existing rat strains. All deposited strains and obtained data are freely available for any interested researcher worldwide at http://www.anim.med.kyoto-u.ac.jp/nbr .

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Invited Review: Identifying new mouse models of cardiovascular disease: a review of high-throughput screens of mutagenized and inbred strains

Journal of Applied Physiology ◽

10.1152/japplphysiol.01029.2003 ◽

2003 ◽

Vol 94 (4) ◽

pp. 1650-1659 ◽

Cited By ~ 49

Author(s):

Karen L. Svenson ◽

Molly A. Bogue ◽

Luanne L. Peters

Keyword(s):

Cardiovascular Disease ◽

Mouse Models ◽

High Throughput ◽

Human Disease ◽

Early Stage ◽

Inbred Mouse ◽

Inbred Strains ◽

Mouse Strains ◽

Complex Disorders ◽

Lung Dysfunction

The mouse is a proven model for studying human disease. Many strains exist that exhibit either natural or engineered genetic variation and thereby enable the elucidation of pathways involved in the development of cardiovascular disease. Although those mouse models have been fundamental to advancing our knowledge base, we are still at an early stage in understanding how genes contribute to complex disorders. There remains a need for new animal models that closely represent human disease. To expedite their development, we have established the Center for New Mouse Models of Heart, Lung, Blood, and Sleep Disorders at The Jackson Laboratory. We are using a phenotype-driven approach to identify mutations leading to atherosclerosis, hypertension, obesity, blood disorders, lung dysfunction, thrombosis, and disordered sleep. Our high-throughput, comprehensive phenotyping draws from two sources for new models: 1) the natural variation among over 40 inbred mouse strains and 2) chemically induced, whole-genome mutagenized mice. Here, we review our cardiovascular screens and present some hypertensive, obese, and cardiovascular models identified with this approach.

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Skin Grafting and The Homogeneity of Inbred Mouse Strains

Laboratory Animals ◽

10.1258/002367767781035585 ◽

1967 ◽

Vol 1 (2) ◽

pp. 81-90 ◽

Cited By ~ 2

Author(s):

Annie M. Brown ◽

Marjorie Dinsley

Keyword(s):

Breeding System ◽

Large Scale ◽

Common Ancestor ◽

Inbred Mouse ◽

Skin Grafting ◽

Inbred Strains ◽

Mouse Strains ◽

Inbred Mouse Strains ◽

Two Generations ◽

Line Breeding

Summary The results of the routine skin grafting on mice from fifteen inbred strains have been collated and examined. It has been shown that when strains are maintained on a modification of the single line breeding system there is an overall frequency of only two per cent of graft rejections with at least six generations between donor and recipient mice. Successful grafts are usually obtained even when donor and recipient mice are separated by as many as fourteen generations. It is suggested that mice not more than two generations from their common ancestor should be used for large scale skin grafting experiments because of the unsuccessful skin transfer between some mice more distantly related. With some mouse strains difficulty of graft healing is apparent, and it has been shown that these results point to a valid difference between the C57 and A strains.

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Accelerated Discovery of High-Refractive-Index Polyimides via First-Principles Molecular Modeling, Virtual High-Throughput Screening, and Data Mining

10.26434/chemrxiv.7670903.v1 ◽

2019 ◽

Author(s):

Mohammad Atif Faiz Afzal ◽

Mojtaba Haghighatlari ◽

Sai Prasad Ganesh ◽

Chong Cheng ◽

Johannes Hachmann

Keyword(s):

Data Mining ◽

Refractive Index ◽

High Throughput ◽

First Principles ◽

High Throughput Screening ◽

Large Scale ◽

Computational Study ◽

High Refractive Index ◽

Structural Features ◽

Learning Program

<div>We present a high-throughput computational study to identify novel polyimides (PIs) with exceptional refractive index (RI) values for use as optic or optoelectronic materials. Our study utilizes an RI prediction protocol based on a combination of first-principles and data modeling developed in previous work, which we employ on a large-scale PI candidate library generated with the ChemLG code. We deploy the virtual screening software ChemHTPS to automate the assessment of this extensive pool of PI structures in order to determine the performance potential of each candidate. This rapid and efficient approach yields a number of highly promising leads compounds. Using the data mining and machine learning program package ChemML, we analyze the top candidates with respect to prevalent structural features and feature combinations that distinguish them from less promising ones. In particular, we explore the utility of various strategies that introduce highly polarizable moieties into the PI backbone to increase its RI yield. The derived insights provide a foundation for rational and targeted design that goes beyond traditional trial-and-error searches.</div>

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Large-scale High-throughput Screening Revealed 5'-(carbonylamino)-2,3'- bithiophene-4'-carboxylate as Novel Template for Antibacterial Agents

Current Drug Discovery Technologies ◽

10.2174/1570163816666190603095521 ◽

2020 ◽

Vol 17 (5) ◽

pp. 716-724

Author(s):

Yan A. Ivanenkov ◽

Renat S. Yamidanov ◽

Ilya A. Osterman ◽

Petr V. Sergiev ◽

Vladimir A. Aladinskiy ◽

...

Keyword(s):

Antibacterial Activity ◽

High Throughput ◽

High Throughput Screening ◽

Large Scale ◽

Antibacterial Agents ◽

Sos Response ◽

Luciferase Assay ◽

Translational Machinery ◽

E Coli ◽

New Class

Background: The key issue in the development of novel antimicrobials is a rapid expansion of new bacterial strains resistant to current antibiotics. Indeed, World Health Organization has reported that bacteria commonly causing infections in hospitals and in the community, e.g. E. Coli, K. pneumoniae and S. aureus, have high resistance vs the last generations of cephalosporins, carbapenems and fluoroquinolones. During the past decades, only few successful efforts to develop and launch new antibacterial medications have been performed. This study aims to identify new class of antibacterial agents using novel high-throughput screening technique. Methods: We have designed library containing 125K compounds not similar in structure (Tanimoto coeff.< 0.7) to that published previously as antibiotics. The HTS platform based on double reporter system pDualrep2 was used to distinguish between molecules able to block translational machinery or induce SOS-response in a model E. coli system. MICs for most active chemicals in LB and M9 medium were determined using broth microdilution assay. Results: In an attempt to discover novel classes of antibacterials, we performed HTS of a large-scale small molecule library using our unique screening platform. This approach permitted us to quickly and robustly evaluate a lot of compounds as well as to determine the mechanism of action in the case of compounds being either translational machinery inhibitors or DNA-damaging agents/replication blockers. HTS has resulted in several new structural classes of molecules exhibiting an attractive antibacterial activity. Herein, we report as promising antibacterials. Two most active compounds from this series showed MIC value of 1.2 (5) and 1.8 μg/mL (6) and good selectivity index. Compound 6 caused RFP induction and low SOS response. In vitro luciferase assay has revealed that it is able to slightly inhibit protein biosynthesis. Compound 5 was tested on several archival strains and exhibited slight activity against gram-negative bacteria and outstanding activity against S. aureus. The key structural requirements for antibacterial potency were also explored. We found, that the unsubstituted carboxylic group is crucial for antibacterial activity as well as the presence of bulky hydrophobic substituents at phenyl fragment. Conclusion: The obtained results provide a solid background for further characterization of the 5'- (carbonylamino)-2,3'-bithiophene-4'-carboxylate derivatives discussed herein as new class of antibacterials and their optimization campaign.

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Identification of a juvenile-hormone signaling inhibitor via high-throughput screening of a chemical library

Scientific Reports ◽

10.1038/s41598-020-75386-x ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Takumi Kayukawa ◽

Kenjiro Furuta ◽

Keisuke Nagamine ◽

Tetsuro Shinoda ◽

Kiyoaki Yonesu ◽

...

Keyword(s):

Juvenile Hormone ◽

Cell Line ◽

Signaling Pathway ◽

High Throughput ◽

High Throughput Screening ◽

Large Scale ◽

Ex Vivo ◽

Agricultural Field ◽

Chemical Library ◽

Field Development

Abstract Insecticide resistance has recently become a serious problem in the agricultural field. Development of insecticides with new mechanisms of action is essential to overcome this limitation. Juvenile hormone (JH) is an insect-specific hormone that plays key roles in maintaining the larval stage of insects. Hence, JH signaling pathway is considered a suitable target in the development of novel insecticides; however, only a few JH signaling inhibitors (JHSIs) have been reported, and no practical JHSIs have been developed. Here, we established a high-throughput screening (HTS) system for exploration of novel JHSIs using a Bombyx mori cell line (BmN_JF&AR cells) and carried out a large-scale screening in this cell line using a chemical library. The four-step HTS yielded 69 compounds as candidate JHSIs. Topical application of JHSI48 to B. mori larvae caused precocious metamorphosis. In ex vivo culture of the epidermis, JHSI48 suppressed the expression of the Krüppel homolog 1 gene, which is directly activated by JH-liganded receptor. Moreover, JHSI48 caused a parallel rightward shift in the JH response curve, suggesting that JHSI48 possesses a competitive antagonist-like activity. Thus, large-scale HTS using chemical libraries may have applications in development of future insecticides targeting the JH signaling pathway.

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Genetic Control of Mammalian Meiotic Recombination. I. Variation in Exchange Frequencies Among Males From Inbred Mouse Strains

Genetics ◽

10.1093/genetics/162.1.297 ◽

2002 ◽

Vol 162 (1) ◽

pp. 297-306 ◽

Cited By ~ 13

Author(s):

Kara E Koehler ◽

Jonathan P Cherry ◽

Audrey Lynn ◽

Patricia A Hunt ◽

Terry J Hassold

Keyword(s):

Meiotic Recombination ◽

Inbred Mouse ◽

Inbred Strains ◽

Male Meiosis ◽

Mouse Strains ◽

Recombination Rates ◽

The Mean ◽

Genetic Background Effects ◽

Exchange Patterns ◽

Positive Interference

AbstractGenetic background effects on the frequency of meiotic recombination have long been suspected in mice but never demonstrated in a systematic manner, especially in inbred strains. We used a recently described immunostaining technique to assess meiotic exchange patterns in male mice. We found that among four different inbred strains—CAST/Ei, A/J, C57BL/6, and SPRET/Ei—the mean number of meiotic exchanges per cell and, thus, the recombination rates in these genetic backgrounds were significantly different. These frequencies ranged from a low of 21.5 exchanges in CAST/Ei to a high of 24.9 in SPRET/Ei. We also found that, as expected, these crossover events were nonrandomly distributed and displayed positive interference. However, we found no evidence for significant differences in the patterns of crossover positioning between strains with different exchange frequencies. From our observations of >10,000 autosomal synaptonemal complexes, we conclude that achiasmate bivalents arise in the male mouse at a frequency of 0.1%. Thus, special mechanisms that segregate achiasmate chromosomes are unlikely to be an important component of mammalian male meiosis.

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EVIDENCE THAT TWO LOCI PREDOMINANTLY DETERMINE THE DIFFERENCE IN SUSCEPTIBILITY TO THE HIGH PRESSURE NEUROLOGIC SYNDROME TYPE I SEIZURE IN MICE

Genetics ◽

10.1093/genetics/99.2.285 ◽

1981 ◽

Vol 99 (2) ◽

pp. 285-307

Author(s):

R D McCall ◽

D Frierson

Keyword(s):

High Pressure ◽

Inbred Mouse ◽

Inbred Strains ◽

Chromosome 17 ◽

Seizure Threshold ◽

Mouse Strains ◽

Compression Rate ◽

Type I ◽

Major Locus ◽

The Difference

ABSTRACT Most mammals tested, when exposed to increasing pressure in helium/oxygen atmospheres, exhibit progressive motor disturbances culminating in two, usually successive, well-differentiated convulsive seizures. The seizures are highly reproducible components of the constellation of events that collectively constitute the High Pressure Neurologic Syndrome (HPNS). In the present study, we present evidence that the mean difference in seizure threshold pressures of the first seizure to occur (HPNS Type I) between inbred mouse strains DBA/2J and C57BL/6J is predominantly determined (> 60%) by the expression of a major locus—possibly linked to the H-2 locus on chromosome 17—and a minor locus, probably unlinked. This outcome is derived from applications of the maximum likelihood modeling procedure of Elston and Stewart (1973) and Stewart and Elston (1973) to eleven models of genetic determinacy and tests (including breeding tests) of "preferred" models so derived using BXD recombinant inbred strains that show the following: The major locus exhibits conditional dominance characteristics depending upon compression rate and minor locus genotype. At a constant mean compression rate of 100 atm hr-1, the major locus manifests strong, though incomplete, dominance apparently independent of minor locus genotype. Its expression is, however, highly sensitive to compression rate, losing its dominance altogether at a linear rate of 1,000 atm hr-1. The major locus interacts with the weakly dominant and relatively compression-rate-insensitive minor locus to retain dominance at fast compression only when the dominant alleles of both loci are present. A principal finding of this study is that employing two compression rates permits fuller genetic characterization of murine high-pressure seizure susceptibility differences than could be achieved by use of a single compression rate.

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High-Throughput Phenotyping Methods for Breeding Drought-Tolerant Crops

International Journal of Molecular Sciences ◽

10.3390/ijms22158266 ◽

2021 ◽

Vol 22 (15) ◽

pp. 8266

Author(s):

Minsu Kim ◽

Chaewon Lee ◽

Subin Hong ◽

Song Lim Kim ◽

Jeong-Ho Baek ◽

...

Keyword(s):

Drought Stress ◽

High Throughput ◽

Large Scale ◽

Crop Yields ◽

Plant Traits ◽

Rapid Development ◽

Plant Responses ◽

Phenotypic Data ◽

Agricultural Technologies ◽

High Throughput Phenotyping

Drought is a main factor limiting crop yields. Modern agricultural technologies such as irrigation systems, ground mulching, and rainwater storage can prevent drought, but these are only temporary solutions. Understanding the physiological, biochemical, and molecular reactions of plants to drought stress is therefore urgent. The recent rapid development of genomics tools has led to an increasing interest in phenomics, i.e., the study of phenotypic plant traits. Among phenomic strategies, high-throughput phenotyping (HTP) is attracting increasing attention as a way to address the bottlenecks of genomic and phenomic studies. HTP provides researchers a non-destructive and non-invasive method yet accurate in analyzing large-scale phenotypic data. This review describes plant responses to drought stress and introduces HTP methods that can detect changes in plant phenotypes in response to drought.

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