Day Plots of Bacterial Magnetite from Sediments of Shira Lake (Khakassia, Russia)

The domain state of magnetite detected in sediments of Shira lake (Khakassia, Russia) was examined by means of magnetic hysteresis. Analysis of experimental data obtained on samples from different parts of bottom sediment cores in terms of Day plots allowed us to conclude that magnetite particles are in the pseudo-single-domain state. This indicates respectively small size of magnetite particles (< 100 nm) and reveals their bacterial origin. Biogenic magnetite buried in the bottom sediments can indicate the climatic changes in the Shira lake level in the Late Holocen

Genome-wide changes in protein translation efficiency are associated with autism

We previously proposed that changes in the efficiency of protein translation are associated with autism spectrum disorders (ASDs). This hypothesis connects environmental factors and genetic factors because each can alter translation efficiency. For genetic factors, we previously tested our hypothesis using a small set of ASD-associated genes, a small set of ASD-associated variants, and a statistic to quantify by how much a single nucleotide variant (SNV) in a protein coding region changes translation speed. In this study, we confirm and extend our hypothesis using a published set of 1,800 autism quartets (parents, one affected child and one unaffected child) and genome-wide variants. Then, we extend the test statistic to combine translation efficiency with other possibly relevant variables: ribosome profiling data, presence/absence of CpG dinucleotides, and phylogenetic conservation. The inclusion of ribosome profiling abundances strengthens our results for male–male sibling pairs. The inclusion of CpG information strengthens our results for female–female pairs, giving an insight into the significant gender differences in autism incidence. By combining the single-variant test statistic for all variants in a gene, we obtain a single gene score to evaluate how well a gene distinguishes between affected and unaffected siblings. Using statistical methods, we compute gene sets that have some power to distinguish between affected and unaffected siblings by translation efficiency of gene variants. Pathway and enrichment analysis of those gene sets suggest the importance of Wnt signaling pathways, some other pathways related to cancer, ATP binding, and ATP-ase pathways in the etiology of ASDs

Evolution of alternative and constitutive regions of mammalian 5'UTRs

<p>Abstract</p> <p>Background</p> <p>Alternative splicing (AS) in protein-coding sequences has emerged as an important mechanism of regulation and diversification of animal gene function. By contrast, the extent and roles of alternative events including AS and alternative transcription initiation (ATI) within the 5'-untranslated regions (5'UTRs) of mammalian genes are not well characterized.</p> <p>Results</p> <p>We evaluated the abundance, conservation and evolution of putative regulatory control elements, namely, upstream start codons (uAUGs) and open reading frames (uORFs), in the 5'UTRs of human and mouse genes impacted by alternative events. For genes with alternative 5'UTRs, the fraction of alternative sequences (those present in a subset of the transcripts) is much greater than that in the corresponding coding sequence, conceivably, because 5'UTRs are not bound by constraints on protein structure that limit AS in coding regions. Alternative regions of mammalian 5'UTRs evolve faster and are subject to a weaker purifying selection than constitutive portions. This relatively weak selection results in over-abundance of uAUGs and uORFs in the alternative regions of 5'UTRs compared to constitutive regions. Nevertheless, even in alternative regions, uORFs evolve under a stronger selection than the rest of the sequences, indicating that some of the uORFs are conserved regulatory elements; some of the non-conserved uORFs could be involved in species-specific regulation.</p> <p>Conclusion</p> <p>The findings on the evolution and selection in alternative and constitutive regions presented here are consistent with the hypothesis that alternative events, namely, AS and ATI, in 5'UTRs of mammalian genes are likely to contribute to the regulation of translation.</p

Optical and transport properties of short period InAs/GaAs superlattices near quantum dot formation

We have investigated the optical and transport properties of MBE grown short-period superlattices of InAs/GaAs with different numbers of periods (3 <= N <= 24) and a total thickness 14 nm. Bandstructure calculations show that these superlattices represent a quantum well with average composition In_0.16Ga_0.84As. The electron wave functions are only slightly modulated by the superlattice potential as compared to a single quantum well with the same composition, which was grown as a reference sample. The photoluminescence, the resistance, the Shubnikov-de Haas effect and the Hall effect have been measured as a function of the InAs layer thickness Q in the range 0.33 <= Q <= 2.7 monolayers (ML). The electron densities range from 6.8 to 11.5x10^11 cm^-2 for Q <= 2.0 ML. The photoluminescence and magnetotransport data show that only one subband is occupied. When Q >= 2.7 ML quantum dots are formed and the metallic type of conductivity changes to variable range hopping conductivity.Comment: 15 pages (incl.7 figures); pdf file; submitted to Semicond. Sci. Techno

Expression of human AID in yeast induces mutations in context similar to the context of somatic hypermutation at G-C pairs in immunoglobulin genes

BACKGROUND: Antibody genes are diversified by somatic hypermutation (SHM), gene conversion and class-switch recombination. All three processes are initiated by the activation-induced deaminase (AID). According to a DNA deamination model of SHM, AID converts cytosine to uracil in DNA sequences. The initial deamination of cytosine leads to mutation and recombination in pathways involving replication, DNA mismatch repair and possibly base excision repair. The DNA sequence context of mutation hotspots at G-C pairs during SHM is DGYW/WRCH (G-C is a hotspot position, R = A/G, Y = T/C, W = A/T, D = A/G/T). RESULTS: To investigate the mechanisms of AID-induced mutagenesis in a model system, we studied the genetic consequences of AID expression in yeast. We constructed a yeast vector with an artificially synthesized human AID gene insert using codons common to highly expressed yeast genes. We found that expression of the artificial hAIDSc gene was moderately mutagenic in a wild-type strain and highly mutagenic in an ung1 uracil-DNA glycosylase-deficient strain. A majority of mutations were at G-C pairs. In the ung1 strain, C-G to T-A transitions were found almost exclusively, while a mixture of transitions with 12% transversions was characteristic in the wild-type strain. In the ung1 strain mutations that could have originated from deamination of the transcribed stand were found more frequently. In the wild-type strain, the strand bias was reversed. DGYW/WRCH motifs were preferential sites of mutations. CONCLUSION: The results are consistent with the hypothesis that AID-mediated deamination of DNA is a major cause of mutations at G-C base pairs in immunoglobulin genes during SHM. The sequence contexts of mutations in yeast induced by AID and those of somatic mutations at G-C pairs in immunoglobulin genes are significantly similar. This indicates that the intrinsic substrate specificity of AID itself is a primary determinant of mutational hotspots at G-C base pairs during SHM

Ecological features of cyanobacteria and algae communities of the littoral of the meromictic Lake Shira (Khakassia Republic, Russia)

During the study of cyanobacteria and algae from littoral of the meromictic Lake Shira (Republic of Khakas- sia, Russia) forty-eight taxa were identified: Cyanobacteria – 7, Chlorophyta – 5, and Bacillariophyta – 36 species. Cyanobacteria were represented by cosmopolitan taxa Leptolyngbya voronichiniana, cf. Trichocoleus hospitus and widely distributed in the freshwater ecosystems species Phormidium cf. paulsenianum, Pseudophormidium cf. golenkinianum, P. pauciramosum, Leptolyngbya perforans, and L. subtilissima. Among green algae typical freshwater taxa Chloroidium saccharophilum, Desmodesmus abundans, Oocystis lacustris, Chlorella sp., Stigeoclonium sp. were detected. Among Bacillariophyta the most frequent species were Amphora ovalis, Cymbella affinis, Encyonema silesiacum, Eunotia fallax, Gomphonella olivacea, G. parvulum, Kobayasiella subtilissima, Navicula minima, N. radiosa, N. veneta, Nitzchia fonti- cola, N. palea, Grunowia tabellaria, Surirella undulata. Several rare species cf. Fragilaria tenera, Grunowia tabellaria and cf. Ulnaria capitata were found. In relation to mineralization indifferents was the largest group (73%). In relation to pH, a unique feature of the investigated lake was the predominance of alkaliphilic species of diatoms (56%), such as Amphora ovalis, Cymbella affinis, Gomphonema truncatum, Hantzschia amphioxys, Navicula minima, N. veneta, Nitzschia cf. linearis, N. palea, Planothidium lanceolatum and other. In the geographic structure cosmopolitan group included 25 species (69%), boreal group – 4 species (11%), arcto-apline group – 2 species (6%). To obtain more accurate informa- tion on the biodiversity of cyanobacteria and algae of Lake Shira further studies using molecular-genetic and electron microscopic methods are needed