Characteristics of melanomacrophage centers in the liver and spleen of the roach Rutilus rutilus (Cypriniformes: Cyprinidae) in Lake Kotokel during the Haff disease outbreak

Characteristics of morphology and number of melanomacrophage centers (MMCs) in the liver and spleen of the roach Rutilus rutilus and the amount of pigments in MMCs during the Haff disease outbreak and the death of fish in Lake Kotokel in relation to these parameters in the roach from Lake Baikal are described. Pathological changes in the microvasculature and parenchyma in the liver of the roach from Lake Kotokel were found. The area of melanomacrophage centers in the liver of the roach from this lake was significantly smaller, whereas the number and size of these centers in the spleen was significantly larger than in the roaches from Lake Baikal. Among the pigments studied, the strongest response to the content of this toxin in the water body was shown by hemosiderin. An increase in its amount in the spleen MMCs testifies to an enhanced degradation of erythrocytes and iron release, which may be caused by the damage of cells of the erythrocyte lineage by the toxin.     

A novel Netrin-1–sensitive mechanism promotes local SNARE-mediated exocytosis during axon branching

Developmental axon branching dramatically increases synaptic capacity and neuronal surface area. Netrin-1 promotes branching and synaptogenesis, but the mechanism by which Netrin-1 stimulates plasma membrane expansion is unknown. We demonstrate that SNARE-mediated exocytosis is a prerequisite for axon branching and identify the E3 ubiquitin ligase TRIM9 as a critical catalytic link between Netrin-1 and exocytic SNARE machinery in murine cortical neurons. TRIM9 ligase activity promotes SNARE-mediated vesicle fusion and axon branching in a Netrin-dependent manner. We identified a direct interaction between TRIM9 and the Netrin-1 receptor DCC as well as a Netrin-1–sensitive interaction between TRIM9 and the SNARE component SNAP25. The interaction with SNAP25 negatively regulates SNARE-mediated exocytosis and axon branching in the absence of Netrin-1. Deletion of TRIM9 elevated exocytosis in vitro and increased axon branching in vitro and in vivo. Our data provide a novel model for the spatial regulation of axon branching by Netrin-1, in which localized plasma membrane expansion occurs via TRIM9-dependent regulation of SNARE-mediated vesicle fusion.     

Evaluation of <Emphasis Type="Italic">in silico</Emphasis> algorithms for use with ACMG/AMP clinical variant interpretation guidelines

Background

The American College of Medical Genetics and American College of Pathologists (ACMG/AMP) variant classification guidelines for clinical reporting are widely used in diagnostic laboratories for variant interpretation. The ACMG/AMP guidelines recommend complete concordance of predictions among all in silico algorithms used without specifying the number or types of algorithms. The subjective nature of this recommendation contributes to discordance of variant classification among clinical laboratories and prevents definitive classification of variants.

Results

Using 14,819 benign or pathogenic missense variants from the ClinVar database, we compared performance of 25 algorithms across datasets differing in distinct biological and technical variables. There was wide variability in concordance among different combinations of algorithms with particularly low concordance for benign variants. We also identify a previously unreported source of error in variant interpretation (false concordance) where concordant in silico predictions are opposite to the evidence provided by other sources. We identified recently developed algorithms with high predictive power and robust to variables such as disease mechanism, gene constraint, and mode of inheritance, although poorer performing algorithms are more frequently used based on review of the clinical genetics literature (2011–2017).

Conclusions

Our analyses identify algorithms with high performance characteristics independent of underlying disease mechanisms. We describe combinations of algorithms with increased concordance that should improve in silico algorithm usage during assessment of clinically relevant variants using the ACMG/AMP guidelines.

     

A graphical method for identifying the six types of non‐deep physiological dormancy in seeds

We present a new seed dormancy classification scheme for the non‐deep level of the class physiological dormancy (PD), which contains six types. Non‐deep PD is divided into two sublevels: one for seeds that exhibit a dormancy continuum (types 1, 2 and 3) and the other for those that do not exhibit a dormancy continuum (types 4, 5 and 6). Analysis of previous studies showed that different types of non‐deep PD also can be identified using a graphical method. Seeds with a dormancy (D) ? conditional dormancy (CD) ? non‐dormancy (ND) cycle have a low germination percentage in the early stages of CD, and during dormancy loss the germination capacity increases. However, seeds with a CD/ND (i.e. D→CD?ND) cycle germinate to a high percentage at a narrow range of temperatures in the early stages of CD. Cardinal temperatures for seeds with either a D/ND or a CD/ND cycle change during dormancy loss: the ceiling temperature increases in seeds with Type 1, the base temperature decreases in seeds with Type 2 and the base and ceiling temperatures decrease and increase, respectively, in seeds with Type 3. Criteria for distinguishing the six types of non‐deep PD and models of the temperature functions of seeds with types 1, 2 and 3 with both types of dormancy cycles are presented. The relevancy of our results to modelling the timing of weed seedling emergence is briefly discussed.     

Evolution of the claustrum in Cnidaria: comparative anatomy reveals that it is exclusive to some species of Staurozoa and absent in Cubozoa

The claustrum in Cnidaria is a tissue in the gastrovascular cavity delimited by a central layer of mesoglea surrounded by gastrodermis (i.e., gastrodermis-mesoglea-gastrodermis), without communication with epidermis. By dividing the gastrovascular cavity, the four claustra provide an additional level of complexity. The presence of claustra in Cubozoa and Staurozoa has been used as evidence supporting a close relationship between these two cnidarian classes. However, the detailed anatomy of the claustrum has never been comparatively analyzed, rendering the evolution of this character among Cnidaria and its homology in Staurozoa and Cubozoa uncertain. This study provides a comparative investigation of the internal anatomy of the claustrum in Staurozoa and Cubozoa, addressing its evolutionary history based on recent phylogenetic hypotheses for Cnidaria. We conclude that the claustrum is a character exclusive to some species of Staurozoa, with a homoplastic evolution in the class, and that the structure called the “claustrum” in Cubozoa corresponds to the valve of gastric ostium, a structure at the base of the manubrium, which is also present in Staurozoa with and without claustrum. Thus, the claustrum cannot be a synapomorphy of a hypothetical clade uniting Staurozoa and Cubozoa, nor can its hypothetical presence in enigmatic fossils be used to support cubozoan affinities.