New data on mollusks from the Miocene (Tarkhanian-Chokrakian) of northern Sinop Province,Turkey

An insufficiently known bivalve and gastropod assemblage from the Early-Middle Miocene (Tarkhanian-Chokrakian) of northern Sinop Province (Turkey), is analyzed. Environments of the assemblage are reconstructed for the Chokrakian as subtidal, with prevailing lime and sandy bottom and good aeration, and partially well vegetated. Impoverishment of the mollusk biocoenose in this part of the marine basin (only 18 bivalve and 22 gastropod species recorded) compared to other areas, including the closest regions, Bulgaria on the west and Georgia on the east, is emphasized. The relatively low diversity of the fauna is probably connected not only with insufficient collecting, but with special hydrological conditions. A special aspect of the fauna is highlighted by the presence of the bivalve Circomphalus foliaceolamellosus subplicatus (Orb.), which is rare in the Chokrakian.     

Immunopathological Changes in the Brain of Immunosuppressed Mice Experimentally Infected with Toxocara canis

Toxocariasis is a soil-transmitted helminthozoonosis due to infection of humans by larvae of Toxocara canis. The disease could produce cognitive and behavioral disturbances especially in children. Meanwhile, in our modern era, the incidence of immunosuppression has been progressively increasing due to increased incidence of malignancy as well as increased use of immunosuppressive agents. The present study aimed at comparing some of the pathological and immunological alterations in the brain of normal and immunosuppressed mice experimentally infected with T. canis. Therefore, 180 Swiss albino mice were divided into 4 groups including normal (control) group, immunocompetent T. canis-infected group, immunosuppressed group (control), and immunosuppressed infected group. Infected mice were subjected to larval counts in the brain, and the brains from all mice were assessed for histopathological changes, astrogliosis, and IL-5 mRNA expression levels in brain tissues. The results showed that under immunosuppression, there were significant increase in brain larval counts, significant enhancement of reactive gliosis, and significant reduction in IL-5 mRNA expression. All these changes were maximal in the chronic stage of infection. In conclusion, the immunopathological alterations in the brains of infected animals were progressive over time, and were exaggerated under the effect of immunosuppression as did the intensity of cerebral infection.     

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.