Alignathon: a competitive assessment of whole-genome alignment methods.

Multiple sequence alignments (MSAs) are a prerequisite for a wide variety of evolutionary analyses. Published assessments and benchmark data sets for protein and, to a lesser extent, global nucleotide MSAs are available, but less effort has been made to establish benchmarks in the more general problem of whole-genome alignment (WGA). Using the same model as the successful Assemblathon competitions, we organized a competitive evaluation in which teams submitted their alignments and then assessments were performed collectively after all the submissions were received. Three data sets were used: Two were simulated and based on primate and mammalian phylogenies, and one was comprised of 20 real fly genomes. In total, 35 submissions were assessed, submitted by 10 teams using 12 different alignment pipelines. We found agreement between independent simulation-based and statistical assessments, indicating that there are substantial accuracy differences between contemporary alignment tools. We saw considerable differences in the alignment quality of differently annotated regions and found that few tools aligned the duplications analyzed. We found that many tools worked well at shorter evolutionary distances, but fewer performed competitively at longer distances. We provide all data sets, submissions, and assessment programs for further study and provide, as a resource for future benchmarking, a convenient repository of code and data for reproducing the simulation assessments.

The Mysterious Amurian Grig Paracyphoderris erebeus Storozhenko, 1980 (Orthoptera: Prophalangopsidae): New Data on Its Distribution, Ecology and Biology.

New data on distribution, ecology and biology of the rare extant species Paracyphoderris erebeus of the almost completely ancient family Prophalangopsidae (Orthoptera) are given. This montane species prefers humid areas with relatively low summer temperatures. Habits, mating behaviour and life history of P. erebeus are extremely similar to those of the North American representatives of the genus Cyphoderris. Nowadays, the Amurian grig is known from the Myaochan, Badzhalsky, Dusse-Alin, Bureinsky and Aezop ridges in the Khabarovsk Territory (north of the Amur River) and Bydyr Mountain in the Jewish Autonomous Region of Russia only. The analysis of the predicted distribution of P. erebeus based on the occurrence data reveals that the populations of the species may be more widely distributed over the southern part of the Russian Far East, at least up to 56° N. The ecologo-geographic model of the species distribution over its range is generated using the Maxent 3.4.4 software for the first time. Modelling of the P. erebeus distribution for 2021-2040 and 2041-2060 shows that the position of the species range appears to be relatively stable but a weak decline in the foretold suitability during climate warming may result in a reduction in population sizes and the subsequent fragmentation of the species population system. In this case, the Amurian grig will become a prospective to be included on the IUCN Red List.

The Handsome Cross Grasshopper Oedaleus decorus (Germar, 1825) (Orthoptera: Acrididae) as a Neglected Pest in the South-Eastern Part of West Siberian Plain.

Oedaleus decorus is a widely distributed acridid over the Eurasian semi-arid territories, from the Atlantic coast to the Pacific coast. In many semi-arid territories, O. decorus was and is the most important pest, but in the south-eastern part of West Siberian Plain, it was not considered a pest until the 1960s. We compared two sets of data on the acridid distribution in the region: before 1960 and from 1961 until 2021. Until the 1960s, the species occurred mainly in the southern steppes. Since the 1960s, its distribution changed significantly. Nowadays, it occupies almost all local steppes and the southern part of the forest-steppes and can be also found on the eastern side of the Ob River. These shifts may be explained by both climatic changes and changes in human activities. During upsurges the densities of O. decorus were often more than one to two adults per square meter. It is often abundant in the same habitats and in the same periods as the Italian locust (Calliptamus italicus)-one of the most important acridid pests. This means during joint outbreaks these two species can simultaneously damage almost all spectrum of plants.

Gene expression profiling of tumor-initiating stem cells from mouse Krebs-2 carcinoma using a novel marker of poorly differentiated cells.

Using the ability of poorly differentiated cells to natively internalize fragments of extracellular double-stranded DNA as a marker, we isolated a tumorigenic subpopulation present in Krebs-2 ascites that demonstrated the features of tumor-inducing cancer stem cells. Having combined TAMRA-labeled DNA probe and the power of RNA-seq technology, we identified a set of 168 genes specifically expressed in TAMRA-positive cells (tumor-initiating stem cells), these genes remaining silent in TAMRA-negative cancer cells. TAMRA+ cells displayed gene expression signatures characteristic of both stem cells and cancer cells. The observed expression differences between TAMRA+ and TAMRA- cells were validated by Real Time PCR. The results obtained corroborated the biological data that TAMRA+ murine Krebs-2 tumor cells are tumor-initiating stem cells. The approach developed can be applied to profile any poorly differentiated cell types that are capable of immanent internalization of double-stranded DNA.