A deep learning algorithm for 3D cell detection in whole mouse brain image datasets

Understanding the function of the nervous system necessitates mapping the spatial distributions of its constituent cells defined by function, anatomy or gene expression. Recently, developments in tissue preparation and microscopy allow cellular populations to be imaged throughout the entire rodent brain. However, mapping these neurons manually is prone to bias and is often impractically time consuming. Here we present an open-source algorithm for fully automated 3D detection of neuronal somata in mouse whole-brain microscopy images using standard desktop computer hardware. We demonstrate the applicability and power of our approach by mapping the brain-wide locations of large populations of cells labeled with cytoplasmic fluorescent proteins expressed via retrograde trans-synaptic viral infection.     

A class of gyrase mutants of Salmonella typhimurium show quinolone-like lethality and require Rec functions for viability

We have identified a new class of DNA gyrase mutants of Salmonella typhimurium that show chronic derepression of the SOS regulon. Thus, these mutants mimic the response of wild-type cells to gyrase inhibitors of the quinolone family. SOS induction by conditional lethal mutations gyrA208 or gyrB652, like that mediated by quinolones, is completely dependent on the function of the recB gene product. Introduction of recA or recB null mutations into these strains exacerbates their temperature-sensitive phenotype and prevents growth at the otherwise permissive temperature of 37°C. Selection of suppressors that concomitantly restore growth at 37°C and SOS induction in a recB^? background yielded mutations that relieve the RecB requirement for homologous recombination; namely, sbcB mutations as well as mutations at a new locus that was named sbcE. Such mutations also restore SOS induction in quinolone-treated gyr⁺recB^? strains. These findings indicate that Rec functions are needed for growth of the gyrase mutants at 37°C and suggest that recombinational repair intermediates constitute the SOS-inducing signal in the mutants as well as in quinolone-treated wild-type bacteria. Unlike quinolones, however, the gyr mutations described in this study do not cause detectable accumulation of ‘cleavable’ gyrase–DNA complexes in plasmid or chromosomal DNA. Yet gyrA208 (the only allele tested) was found to trigger RecB-mediated reckless degradation of chromosomal DNA in recA^? cells at restrictive temperatures. Indirect evidence suggests that double-stranded DNA ends, entry sites for the RecBCD enzyme, are generated in the gyr mutants by the breakage of DNA-replication forks. We discuss how this could occur and how recombinational rescue of collapsed replication forks could account for cell survival (and SOS induction) in the gyr mutants as well as in quinolone-treated bacteria.     

Interpreting the Dependence of Mutation Rates on Age and Time

Mutations can originate from the chance misincorporation of nucleotides during DNA replication or from DNA lesions that arise between replication cycles and are not repaired correctly. We introduce a model that relates the source of mutations to their accumulation with cell divisions, providing a framework for understanding how mutation rates depend on sex, age, and cell division rate. We show that the accrual of mutations should track cell divisions not only when mutations are replicative in origin but also when they are non-replicative and repaired efficiently. One implication is that observations from diverse fields that to date have been interpreted as pointing to a replicative origin of most mutations could instead reflect the accumulation of mutations arising from endogenous reactions or exogenous mutagens. We further find that only mutations that arise from inefficiently repaired lesions will accrue according to absolute time; thus, unless life history traits co-vary, the phylogenetic “molecular clock” should not be expected to run steadily across species.     

Environmental Effects of Steam Explosion Pretreatment on Biogas from Maize—Case Study of a 500-kW Austrian Biogas Facility

Potential environmental impacts of biogas electricity from agricultural residues (maize stover) with steam explosion (SE) pretreatment were compared to a typical Austrian biogas system (maize silage) using the method of life cycle assessment. Besides the biogas plant, the system includes substrate production, a combined heat-and-power (CHP) unit, digestate management, and transportation. The stover scenario (including construction and operation of the SE unit) results in lower total climate change impacts than those of the typical biogas system (239 g CO₂-eq/kWh electricity vs. 287 g CO₂-eq/kWh electricity; 100-year global warming potential (GWP)), and this holds also for the other impact categories (e.g., cumulative energy demand, acidification, eutrophication). While uncertainties in other areas could change the results, based on the uncertainty information considered, the overall results for the two scenarios were significantly different. Methane slip emissions from the CHP exhaust account for the largest GWP share in both scenarios. Other large GWP contributions are from substrate production and grid electricity for plant operations. The findings were robust against worst-case assumptions about the energy requirements of the SE pretreatment.     

How does adaptation sweep through the genome? Insights from long-term selection experiments

A major goal in evolutionary biology is to understand the origins and fates of adaptive mutations. Natural selection may act to increase the frequency of de novo beneficial mutations, or those already present in the population as standing genetic variation. These beneficial mutations may ultimately reach fixation in a population, or they may stop increasing in frequency once a particular phenotypic state has been achieved. It is not yet well understood how different features of population biology, and/or different environmental circumstances affect these adaptive processes. Experimental evolution is a promising technique for studying the dynamics of beneficial alleles, as populations evolving in the laboratory experience natural selection in a replicated, controlled manner. Whole-genome sequencing, regularly obtained over the course of sustained laboratory selection, could potentially reveal insights into the mutational dynamics that most likely occur in natural populations under similar circumstances. To date, only a few evolution experiments for which whole-genome data are available exist. This review describes results from these resequenced laboratory-selected populations, in systems with and without sexual recombination. In asexual systems, adaptation from new mutations can be studied, and results to date suggest that the complete, unimpeded fixation of these mutations is not always observed. In sexual systems, adaptation from standing genetic variation can be studied, and in the admittedly few examples we have, the complete fixation of standing variants is not always observed. To date, the relative frequency of adaptation from new mutations versus standing variation has not been tested using a single experimental system, but recent studies using Caenorhabditis elegans and Saccharomyces cerevisiae suggest that this a realistic future goal.     

Effect of Mitochondrial Inhibitors On Metaphase-Telophase Progression and Nuclear Membrane Formation In Chinese Hamster Cells

Chinese hamster Don cells in log-phase were exposed to Colcemid during the G₂ period with and without a combination of divalent cation chelators and mitochondrial inhibitors. Isolated metaphase cells were incubated as follows: (i) without Colcemid but with other agents and the progression was monitored from metaphase (M) to telophase (Tel) and to cell division; (ii) with Colcemid and other agents and the rate of micronuclei formation in the absence of anaphase was studied. Both EDTA and EGTA accelerated the progression from M to Tel, but did not affect the overall rate of cell division. Chloramphenicol (CAP), an inhibitor of mitochondrial protein synthesis, blocked the effect of the chelators and also retarded the progression. an inhibitor of mitochondrial respiration, Antimycin A (AA), also retarded the progression in the absence of the chelators and prevented the promoting effect of the chelators. A stimulator of ATPase for ATP breakdown. 2,4-dinitrophenol (DNP), accelerated the M to Tel progression. Chloramphenicol (CAP) and AA, as well as DNP, appeared to have little effect on the formation of micronuclei in the presence of Colcemid. EGTA, which affects cell surface Ca²⁺, stimulated the formation of micronuclei. This study indicates that Ca²⁺ ions and mitochondrial function are involved in the regulation of a certain segment of mitosis beyond metaphase, with Ca²⁺ sequestration in the mitochondria and chelation of Ca²⁺ by EGTA as dominant factors.     

The Causes and Consequences of Color Vision

The ability to see colors is not universal in the animal kingdom. Those animals that can detect differences in the wavelengths of the electromagnetic spectrum glean valuable sensory information about their environment. They use color vision to forage, avoid predators, and find high-quality mates. In the past, the colors that humans could see clouded scientists’ study of animals’ color perception. Leaving that bias behind has led to new insights about how and why the color vision of animals evolved. This paper provides a brief introduction to color vision, the genetics of color vision in humans, what colors other animals see, and how scientists study color vision. We examine the consequences of having color vision, including speciation, loss of olfactory capabilities, and sexual selection.     

Microvascular characteristics of the acoustic fats: Novel data suggesting taxonomic differences between deep and shallow‐diving odontocetes

Odontocetes have specialized mandibular fats, the extramandibular (EMFB) and intramandibular fat bodies (IMFB), which function as acoustic organs, receiving and channeling sound to the ear during hearing and echolocation. Recent strandings of beaked whales suggest that these fat bodies are susceptible to nitrogen (N₂) gas embolism and empirical evidence has shown that the N₂ solubility of these fat bodies is higher than that of blubber. Since N₂ gas will diffuse from blood into tissue at any blood/tissue interface and potentially form gas bubbles upon decompression, it is imperative to understand the extent of microvascularity in these specialized acoustic fats so that risk of embolism formation when diving can be estimated. Microvascular density was determined in the EMFB, IMFB, and blubber from 11 species representing three odontocete families. In all cases, the acoustic tissues had less (typically 1/3 to 1/2) microvasculature than did blubber, suggesting that capillary density in the acoustic tissues may be more constrained than in the blubber. However, even within these constraints there were clear phylogenetic differences. Ziphiid (Mesoplodon and Ziphius, 0.9 ± 0.4% and 0.7 ± 0.3% for EMFB and IMFB, respectively) and Kogiid families (1.2 ± 0.2% and 1.0 ± 0.01% for EMFB and IMFB, respectively) had significantly lower mean microvascular densities in the acoustic fats compared to the Delphinid species (Tursiops, Grampus, Stenella, and Globicephala, 1.3 ± 0.3% and 1.3 ± 0.3% for EMFB and IMFB, respectively). Overall, deep‐diving beaked whales had less microvascularity in both mandibular fats and blubber compared to the shallow‐diving Delphinids, which might suggest that there are differences in the N₂ dynamics associated with diving regime, phylogeny, and tissue type. These novel data should be incorporated into diving physiology models to further understand potential functional disruption of the acoustic tissues due to changes in normal diving behavior.