Simplified murine multipotent progenitor isolation scheme: Establishing a consensus approach for multipotent progenitor identification.

The mouse hematopoietic system has served as a paradigm for analysis of developmental fate decisions in tissue homeostasis and regeneration. However, multiple immunophenotypic definitions of, and sometimes divergent nomenclatures used to classify, murine multipotent progenitors (MPPs) have emerged in the field over time. This has created significant confusion and inconsistency in the hematology field. To facilitate easier comparison of murine MPP phenotypes between research laboratories, a working group of four International Society for Experimental Hematology (ISEH) members with extensive experience studying the functional activities associated with different MPP phenotypic definitions reviewed the current state of the field with the goal of developing a position statement toward a simplified and unified immunophenotypic definition of MPP populations. In November of 2020, this position statement was presented as a webinar to the ISEH community for discussion and feedback. Hence, the Simplified MPP Identification Scheme presented here is the result of curation of existing literature, consultation with leaders in the field, and crowdsourcing from the wider experimental hematology community. Adoption of a unified definition and nomenclature, while still leaving room for individual investigator customization, will benefit scientists at all levels trying to compare these populations between experimental settings.

Exploration of Energy Metabolism in the Mouse Using Indirect Calorimetry: Measurement of Daily Energy Expenditure (DEE) and Basal Metabolic Rate (BMR).

Current comprehensive mouse metabolic phenotyping involves studying energy balance in cohorts of mice via indirect calorimetry, which determines heat release from changes in respiratory air composition. Here, we describe the measurement of daily energy expenditure (DEE) and basal metabolic rate (BMR) in mice. These well-defined metabolic descriptors serve as meaningful first-line read-outs for metabolic phenotyping and should be reported when exploring energy expenditure in mice. For further guidance, the issue of appropriate sample sizes and the frequency of sampling of metabolic measurements is also discussed.

[Body mass, energy budget and leptin of mice under stochastic food restriction and refeeding].

Periods of restricted food intake that lead to lower body weight are often followed by rapid regaining of the lost weight after ad libitum refeeding, an event generally known as the "compensatory growth". To explore the physiological mechanisms underlying "compensatory growth", we evaluated a series of energetic parameters (energy intake, energy expenditure, body composition and serum leptin levels) of adult KM mice subjected to three cycles of stochastic food restriction following by ad libitum refeeding (SFR-Re). The results indicated that animals lost their body mass after stochastic food restriction and then regained to the control level after refeeding. After the final cycle, SFR-Re mice showed higher basal metabolic rate, lower nonshivering thermogenesis, and their cytochrome c oxydase activities, as well as uncoupling protein 1(UCP1) contents of brown adipose tissue all decreased compared with controls. Meanwhile, higher energy intake and digestibility, as well as heavier fat pads also were found in SFR-Re mice. But, serum leptin levels showed no difference between SFR-Re and control mice. On the whole, these findings indicated that when food is resourceful, SFR-Re mice are under rapid "compensatory growth" by increasing their food intake and energy storage efficiency, meanwhile, decreasing energy consumption in thermogenesis. Moreover, leptin may be a possible player in the regulations of energy budget and thermogenesis during "compensatory growth".

Biological response of free-living mouse Mus spretus from Doñana National Park under environmental stress based on assessment of metal-binding biomolecules by SEC-ICP-MS.

A metallomic approach based on the use of size-exclusion chromatography (Superdex-75) with inductively coupled plasma mass spectrometry (ICP-MS) detection is combined with anion or cation exchange chromatography to characterize the biological response of the free-living mouse Mus spretus. The approach has been applied to contaminated and non-contaminated areas from Doñana National Park (southwest Spain) and the surroundings. Several areas affected by differential contamination from mining, industrial, and agricultural activities have been considered. The high presence of Mn, Cu, and Zn in liver and As and Cd in kidney is remarkable, especially in contaminated areas. The size exclusion chromatograms traced by Mn in liver cytosolic extracts are more intense than in kidney; a Mn-peak matching with the standard of 32 kDa (superoxide dismutase) is present in these organs, and its intensity is correlated with the concentration of Mn in the extracts. High-intensity peaks traced by Cu, Zn, and Cd at 7 kDa (matching with metallothionein I standard) in liver extract are triggered by the presence of contaminants. Other peaks related with molecules of 32 and 67 kDa traced by Cu and Zn can also be observed, although their intensity is higher in sites with low contamination. In kidney extracts, the presence of a Cd-peak with Mr of 7 kDa (tentatively Cd-metallothionein) with high intensity under the action of contaminants was observed, but high biological responses are also proven in the protected area of the Park, which denotes a progressive increase of diffuse contamination.

Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers.

Clustering of multiple transcription factor binding sites (TFBSs) for the same transcription factor (TF) is a common feature of cis-regulatory modules in invertebrate animals, but the occurrence of such homotypic clusters of TFBSs (HCTs) in the human genome has remained largely unknown. To explore whether HCTs are also common in human and other vertebrates, we used known binding motifs for vertebrate TFs and a hidden Markov model-based approach to detect HCTs in the human, mouse, chicken, and fugu genomes, and examined their association with cis-regulatory modules. We found that evolutionarily conserved HCTs occupy nearly 2% of the human genome, with experimental evidence for individual TFs supporting their binding to predicted HCTs. More than half of the promoters of human genes contain HCTs, with a distribution around the transcription start site in agreement with the experimental data from the ENCODE project. In addition, almost half of the 487 experimentally validated developmental enhancers contain them as well--a number more than 25-fold larger than expected by chance. We also found evidence of negative selection acting on TFBSs within HCTs, as the conservation of TFBSs is stronger than the conservation of sequences separating them. The important role of HCTs as components of developmental enhancers is additionally supported by a strong correlation between HCTs and the binding of the enhancer-associated coactivator protein Ep300 (also known as p300). Experimental validation of HCT-containing elements in both zebrafish and mouse suggest that HCTs could be used to predict both the presence of enhancers and their tissue specificity, and are thus a feature that can be effectively used in deciphering the gene regulatory code. In conclusion, our results indicate that HCTs are a pervasive feature of human cis-regulatory modules and suggest that they play an important role in gene regulation in the human and other vertebrate genomes.

A critical assessment of Mus musculus gene function prediction using integrated genomic evidence.

BACKGROUND: Several years after sequencing the human genome and the mouse genome, much remains to be discovered about the functions of most human and mouse genes. Computational prediction of gene function promises to help focus limited experimental resources on the most likely hypotheses. Several algorithms using diverse genomic data have been applied to this task in model organisms; however, the performance of such approaches in mammals has not yet been evaluated. RESULTS: In this study, a standardized collection of mouse functional genomic data was assembled; nine bioinformatics teams used this data set to independently train classifiers and generate predictions of function, as defined by Gene Ontology (GO) terms, for 21,603 mouse genes; and the best performing submissions were combined in a single set of predictions. We identified strengths and weaknesses of current functional genomic data sets and compared the performance of function prediction algorithms. This analysis inferred functions for 76% of mouse genes, including 5,000 currently uncharacterized genes. At a recall rate of 20%, a unified set of predictions averaged 41% precision, with 26% of GO terms achieving a precision better than 90%. CONCLUSION: We performed a systematic evaluation of diverse, independently developed computational approaches for predicting gene function from heterogeneous data sources in mammals. The results show that currently available data for mammals allows predictions with both breadth and accuracy. Importantly, many highly novel predictions emerge for the 38% of mouse genes that remain uncharacterized.

Assessment of dermal wound repair after collagen implantation with optical coherence tomography.

We present an animal study to examine the utility and potential limitations of optical coherence tomography (OCT) for noninvasive evaluation of biomaterial scaffold-assisted wound healing. The transverse and axial resolutions of the OCT system at the wavelength of 1.3 microm were 12 and 10 microm, respectively. A murine full-thickness transcutaneous wound model was employed, in which a phi 10 mm full-thickness wound was created on the back of each male Balb/cJ mouse and a porous collagen scaffold was implanted in the wound bed followed by coverage with a Tegaderm film. Sequential cross-sectional OCT scans were performed at different time points postsurgical intervention to track morphological changes during wound recovery, and the captured OCT images were validated by their corresponding histological specimens. The results indicated that with removal of the high-scattering skin, OCT was capable of imaging to a depth of over 1.5 mm into the wound bed and differentiating various features evolved during wound healing at a high resolution approaching histopathology. OCT was able to not only delineate the epidermis and dermis of normal mouse skin, but also differentiate collagen implant from the underlying subcutaneous tissue; besides, it could track the wound size changes in both lateral and vertical directions. More importantly, OCT was able to detect inflammation, early re-epithelialization, and resorption of the collagen scaffold. These findings suggested the potential of OCT for noninvasive and high-resolution monitoring of assisted wound healing in vivo, longitudinally, and instantaneously.

A risk assessment approach to DDE exposure based on the case of the eastern screech-owl (Megascops asio) in apple orchards of southern Quebec,Canada.

As part of a larger study assessing exposure of the Eastern screech-owl to pesticides in apple orchards from consumption of contaminated small-mammal prey, we evaluated the potential for owls in orchards of southern Quebec to be exposed to persistent contaminants with emphasis on DDE. Levels were highest in short-tailed shrews (0.94 to 26.29 microg/g wet wt). Based on a worst-case scenario, it is possible that consumption of small-mammal prey in orchards of the study area may result in exposure to DDE at a level associated with significant eggshell thinning; however, consumption of other prey, (e.g., robins) may represent a more important threat. Other organochlorines and persistent contaminants such as trace metals and PCBs, reported elsewhere, were found at negligible levels only. Based on an evaluation of the data used, we identify critical information required to enhance the proposed risk assessment.

Costs of immune response in cold-stressed laboratory mice selected for high and low basal metabolism rates.

To study whether mounting an immune response is energetically costly, mice from two lines divergently selected for high (H-BMR) and low (L-BMR) basal metabolic rate (BMR) were immunized with sheep red blood cells. Their energy budgets were then additionally burdened by sudden transfer from an ambient temperature of 23 degrees C to 5 degrees C. We found that the immune response of H-BMR mice was lower than that of L-BMR mice. However, the interaction between line affiliation and ambient temperature was not significant and cold exposure did not result in immunosuppression in either line. At 23 degrees C the animals of both lines seemed to cover the costs of immune response by increasing food consumption and digestive efficiency. This was not observed at 5 degrees C, so these costs must have been covered at the expense of other components of the energy budget. Cold exposure itself elicited a considerable increase in food intake and the mass of internal organs, which were also heavier in H-BMR than in L-BMR mice. However, irrespective of the temperature or line affiliation, immunized mice had smaller intestines, while cold-exposed immunized mice had smaller hearts. Furthermore, the observed larger mass of the liver and kidneys in immunized mice of both lines kept at 23 degrees C was not observed at 5 degrees C. Hence, immunization compromised upregulation of the function of metabolically active internal organs, essential for meeting the energetic demands of cold. We conclude that the difficulties with a straightforward demonstration of the energetic costs of immune responses in these animals stem from the extreme flexibility of their energy budgets.