Über die wahrscheinlichkeit eines quasiergodischen wortes im grenzfall unendlich grosser wortlänge

According to Rosen (Bull. Math. Biophysics,23, 305–318, 1961) the forming of the first genes in natural history can be understood in terms of stochastic building of words. The genes are supposed to represent quasiergodic words of great length. For a word of lengthN, belonging to the free monoid with base ofn elements, a formula is given for the probability of its belonging to some quasiergodic submonoid. Restricting ourselves ton=2, we give an estimate for an upper and a lower bound of the limit of this probability asN tends to infinity. Result: If the tolerance ε does not exceed a certain value depending only on the mean relative frequencies (p ₁,p ₂,...) of the quasiergodic submonoid, the upper bound for the limit of the probability is zero. Concluding remarks are added to show the meaning of our results to the biologists.     

The origin of the North Indian sugarcanes

The “North Indian sugarcanes”, cultivated by Indian peasants during many centuries, have been studied morphologically very exactly byC. A. Barber from 1910 to 1920. They were named “Saccharum Barberi” byJeswiet. Barber distinguished four groups. In 1931 the present author found the following chromosome numbers in these groups: 2n=116 and 2n=82 in the Sunnabile group; 2n=82 in the Mungo group; 2n=124 and 2n=107 in the Nargori group and about 91 in the Saretha group. The first three groups are sterile, the last is fertile. It is shown that the North Indian sugarcanes are hybrids between ancient indigenous sugar canes with a basic number of 17 chromosomes, and forms ofS. spontaneum withn=40,n=48 andn=56 respectively. Differences in the numbers of chromosomes contributed by the mother type may in part have their origin in endo-duplication, as commonly observed inSaccharum hybrids. Details are presented in Table 2. The differences found between different forms of IndianS. spontaneum in respect to chromosome number, sugar content and mosaic resistance may be attributed to intercrossing with canes of the fertile Saretha group.     

Use of foreign genetic variability to improve the quality of wheat grain

Foreign genetic variability, which is represented by different wild-growing relatives of wheat such as Ae. umbellulata (UU, 2n = 14), Ae. cylindrica (CCDD, 2n = 28), Ae. tauschii (DD, 2n = 14), Ae. ventricosa (DDUnUn, 2n = 28), Ae. variabilis (UUSS, 2n = 28), and T. palmovae (AADD, 2n = 28) is used in interspecies crossings with the wheat cultivar T. aestivum for the purpose of transferring exotic Gli/Glu alleles into the genome of the crop. As a result, a series of new exotic Gli/Glu alleles is introgressed into the genome of wheat cultivar. An essential negative as well as positive influence of the wild exotic alleles on the baking quality indicators of the flour and the consistency of the wheat endosperm is discovered in the course of the study. The new genetic material with the improved grain quality indicators is recommended for use in wheat selection.     

Chromosomes of Ichneumonidae (Hymenoptera): New results and conclusions

New data were obtained on the karyotypes of 12 parasitic wasp species of the family Ichneumonidae: Scambus detritus (2n = 28), S. vesicarius (2n = 28), Pimpla contemplator (2n = 36), Theronia atalantae (2n = 24), Stenomacrus sp. 2 (n = 18, 2n = 36), Phygadeuon sp. 3 (2n = 32), Ichneumon memorator (2n = 24), I. vorax (2n = 22), Lymantrichneumon disparis (2n = 26), Orthopelma mediator (n = 15, 2n = 30), Lissonota buccator (2n = 22), and Trichionotus flexorius (2n = 16). Chromosomes of Anomaloninae were studied for the first time. The data on the karyotype structure of the subfamily Orthopelmatinae were revised. Various aspects of chromosome variability in Ichneumonidae are discussed.     

Genetic diversity of the house mouse <Emphasis Type="Italic">Mus musculus</Emphasis> and geographic distribution of its subspecies-specific RAPD markers on the territory of Russia

Genetic diversity and geographic distribution of taxon-specific RAPD markers was examined in ten local populations of the house mouse Mus musculus (n = 42). The house mice were generally characterized by moderate genetic variation: polymorphism P ₉₉ = 60%, P ₉₅ = 32.57%; heterozygosity H = 0.12; the observed allele number n _a = 1.6; the effective allele number n _e = 1.18; the within-population differentiation ?_s = 0.388; and Shannon index I = 0.19. The degree of genetic isolation of individual local populations was greatly variable. The genetic subdivision index G _st varied from 0.162 to 0.770 at the gene flow of Nm = 2.58?0.149, while the among-population distances D _N varied from 0.026 to 0.178. The largest part of the genetic diversity was found among the populations (H _T = 0.125), while the within-population diversity was twice lower (H _S = 0.06). The samples examined were well discriminated relative to the sets of RAPD markers. The character distribution pattern provided conditional subdivision of the mice into the “western” and the “eastern” groups with the putative boarder along the Baikal Lake. The first group was characterized by the prevalence of the markers typical of M. m. musculus and M. m. domesticus. The second group was characterized by the prevalence of the markers typical of M. m. musculus, M. m. gansuensis, M. m. castaneus, M. m. domesticus, and M. m. wagneri. The genotype of the nominative subspecies M. m. musculus was background for all populations. In the populations examined some of earlier described subspecies-specific molecular markers were found at different frequencies, pointing to the involvement of several subspecies of M. musculus in the process of hybridization.     

Identification of alcohol stress tolerance genes of <Emphasis Type="Italic">Synechocystis</Emphasis> sp. PCC 6803 using adaptive laboratory evolution

Background

Synechocystis sp. PCC 6803 is an attractive organism for the production of alcohols, such as isobutanol and ethanol. However, because stress against the produced alcohol is a major barrier for industrial applications, it is highly desirable to engineer organisms with strong alcohol tolerance.

Results

Isobutanol-tolerant strains of Synechocystis sp. PCC 6803 were obtained by long-term passage culture experiments using medium containing 2 g/L isobutanol. These evolved strains grew on medium containing 5 g/L isobutanol on which the parental strain could not grow. Mutation analysis of the evolved strains revealed that they acquired resistance ability due to combinatorial malfunctions of slr1044 (mcpA) and slr0369 (envD), or slr0322 (hik43) and envD. The tolerant strains demonstrated stress resistance against isobutanol as well as a wide variety of alcohols such as ethanol, n-butanol, and isopentanol. As a result of introducing an ethanol-producing pathway into the evolved strain, its productivity successfully increased to 142% of the control strain.

Conclusions

Novel mutations were identified that improved the stress tolerance ability of various alcohols in Synechocystis sp. PCC 6803.

     

New data on chromosomes of parasitic wasps of the subfamily Ichneumoninae (Hymenoptera,Ichneumonidae)

The new data on chromosomes of parasitic wasps of the subfamily Ichneumoninae: Centeterus major (2n = 22), Diadromus troglodytes (2n = 22), D. varicolor (2n = 22), Tycherus infimus (2n = 22), Cratichneumon rufifrons (2n = 26), Eristicus clarigator (2n =.26), and Ctenichneumon funereus (2n = 16) were obtained. Some aspects of the chromosomal variability of Ichneumoninae are discussed.     

The Karyotype of <Emphasis Type="Italic">Amoeba borokensis</Emphasis> from a “<Emphasis Type="Italic">proteus</Emphasis>-like” Amoeba Group (Amoebozoa: Euamoebida)

The karyotype of Amoeba borokensis was studied for the first time. At the metaphase of mitosis, this species has a haploid set of chromosomes (n = 27). This is exactly half of the diploid karyotype in Amoeba proteus (strain B). At first glance, it confirms the idea that has recently appeared that one species arises from another via multiple changes in chromosome number. However, comparative cytogenetic analysis revealed that four orthologous chromosomes from haploid sets of these two species were not distinguished by the pattern of DAPI-stained bands. It shows that the genetic distance between A. proteus and A. borokensis is higher than was believed earlier and these two species have diverged from each other. Analysis of data on the life cycles of A. proteus and A. borokensis shows that a kind of so-called “cyclic polyploidy” takes place in “proteus-like” amoebae. “Cyclic polyploidy” has recently been considered as an alternative to the sexual process for genetic recombination in agamic protists from different macrotaxons.     

Characterization of biofilm-forming marine bacteria and their effect on attachment and germination of algal spores

In this work, 37 bacterial strains isolated from biofouling of marine organisms and from the Museum of Heterotrophic Bacteria of the National Scientific Center of Marine Biology were studied. The strains were identified based on their phenotypic characteristics and on the fatty acid composition of their cell wall lipids. Members of the genus Pseudoalteromonas prevailed both in associated microflora of two dinoflagellate clones and in the biofilms from marine hydrobionts. Associated microflora included also members of the CFB cluster, Bacillus, Sulfitobacter, Acinetobacter, Shewanella, and Psychrobacter. A considerable portion of strains (48.6%) exhibited antimicrobial activity. Antifouling activity against algal spores was studied using single-species bacterial biofilms and the spores of Ulva lactuca и Undaria pinnatifida, the algae most common in the Sea of Japan. Strong inhibitory effect on attachment of Ulva and Undaria spores was observed for 75 and 51% of the strains, respectively. Attached spores were, however, less sensitive to the inhibitory action of biofilms. Species specificity of algal response to bacteria was shown, with a strain having different effect on the spores of different algal species. Biotechnologically promising strains were determined, which exhibited high activity against the spores of macroalgae and could probably be used as producers of antifouling substances and as components of antifouling coatings. No relation was found between antifouling activity of bacteria and the source of their isolation. Our results indicate wide occurrence of bacteria with antifouling activity among associated microflora of marine hydrobionts and demonstrate the extent of complexity and diversity of relations between bacterial biofilms and algal spores.     

<Emphasis Type="Italic">Hsp70</Emphasis> genes of the <Emphasis Type="Italic">Megaphragma amalphitanum</Emphasis> (Hymenoptera: Trichogrammatidae) parasitic wasp

Miniaturization is an evolutionary process that is widely represented in both invertebrates and vertebrates. Miniaturization frequently affects not only the size of the organism and its constituent cells, but also changes the genome structure and functioning. The structure of the main heat shock genes (hsp70 and hsp83) was studied in one of the smallest insects, the Megaphragma amalphitanum (Hymenoptera: Trichogrammatidae) parasitic wasp, which is comparable in size with unicellular organisms. An analysis of the sequenced genome has detected six genes that relate to the hsp70 family, some of which are apparently induced upon heat shock. Both induced and constitutively expressed hsp70 genes contain a large number of introns, which is not typical for the genes of this family. Moreover, none of the found genes form clusters, and they are all very heterogeneous (individual copies are only 75–85% identical), which indicates the absence of gene conversion, which provides the identity of genes of this family in Drosophila and other organisms. Two hsp83 genes, one of which contains an intron, have also been found in the M. amalphitanum genome.     

Competition of Multiple Species in Advective Environments

We study the effect of changes in flow speed on competition of an arbitrary number of species living in advective environments, such as streams and rivers. We begin with a spatial Lotka–Volterra model which is described by n reaction–diffusion–advection equations with Danckwerts boundary conditions. Using the dominant eigenvalue \(\lambda \le 0\) of the diffusion–advection operator subject to boundary conditions, we reduce the model to a system of ordinary differential equations. We impose a “transitive arrangement” of the competitors in terms of their interspecific coefficients and growth rates, which means that in the absence of advection, we have the following situation: for all \(1\le i<j\le n\), species i out-competes species j, while species j has higher intrinsic growth rate than species i. Changing advection speed in the original spatial model corresponds to changing the value of \(\lambda \) in the spatially implicit model. Considering the cases of the odd and even n separately, we obtain explicit intervals of the values of \(\lambda \) that allow all n species to be present in the habitat (coexistence interval). Stability of this equilibrium is shown for \(n\le 4\).     

Identification of extremely halophilic archaea associated with adult <Emphasis Type="Italic">Artemia urmiana</Emphasis>

The brine shrimp, Artemia is the dominant macrozooplankton present in many hypersaline environments. Artemia urmiana is the only macroscopic organism in Urmia Salt Lake (Iran), and the high salinity of the lake makes it a suitable environment for halophilic archaea too. Because of common environment for Artemia and extreme halophiles; this investigation is concentrated on studying the relationship between Artemia and halophilic archaea in Urmia Lake. In this study first the procedure of arhaea isolation was done. Then, isolated strains were sub-cultured and DNA was extracted and amplified by PCR using specific primers for amplifying archaeal 16S rRNA. The amplified archeal DNA fragments were purified, and sequenced. 16S rRNA sequences were compared to known sequences using the NCBI BLAST program. Sequences relating to Halorubrum, Haloarcula and Halobacterium species were identified in Urmia Salt Lake water and Artemia adults and the phylogenetic tree of different species was constructed. Only Halorubrum species were present in association with Artemia. They belong to Halobacteriaceae family of archeae which are isolated from different salt lakes in different parts of world and we could show their existence in adult Artemia, another organism living in hypersaline enviroments.     

On the nature of the domination of oligomeric (dA:dT)<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript> tracts in the structure of eukaryotic genomes

The comparative analysis of the frequency of oligomeric W- and S-tracts was conducted in the genomes of different eukaryotic species that differ in their GC-composition. The domination of mononucleotide and mixed (A/T) _n -sequences compared with (G/C) _n -sequences was detected in the studied eukaryotic genomes, including Dictyostelium discoideum (GC ~ 25.7%), Caenorhabditis elegans (GC ~ 36.9%), Arabidopsis thaliana (GC ~ 38.0%), Drosophila melanogaster (GC ~ 38.8%), Homo sapiens (GC ~ 40.0%), Gallus gallus (GC ~ 50.0%), Leishmania major (GC ~ 59.1%). Using the results of quantum–chemical calculations, a theoretical rationale of the important role of existing differences in the initial hidden structural polymorphism of the hydrogen bonding of the Watson–Crick AT and GC pairs in the development of this phenomenon is given. It is concluded that a decreased structural polymorphism of AT pairs compared with the high fourfold polymorphism of the main state of GC pairs may be the most probable source of the preference and reliability of the “use” of AT pairs by nature in genomic DNA of many species.     

High-throughput sequencing of <Emphasis Type="Italic">Prunus ferganensis</Emphasis> indicates that it is a geographical population of <Emphasis Type="Italic">P. persica</Emphasis>

Peach belongs to the genus Prunus, which includes Prunus persica and its relative species, P. mira, P. davidiana, P. kansuensis, and P. ferganensis. Of these, P. ferganensis have been classified as a species, subspecies, or geographical population of P. persica. To explore the genetic difference between P. ferganensis and P. persica, high-throughput sequencing was used in different peach accessions belonging to different species. First, low-depth sequencing data of peach accessions belonging to four categories revealed that similarity between P. ferganensis and P. persica was similar to that between P. persica accessions from different geographical populations. Then, to further detect the genomic variation in P. ferganensis, the P. ferganensis accession “Xinjiang Pan Tao 1” and the P. persica accession “Xia Miao 1” were sequenced with high depth, and sequence reads were assembled. The results showed that the collinearity of “Xinjiang Pan Tao 1” with the reference genome “Lovell” was higher than that of “Xia Miao 1” and “Lovell” peach. Additionally, the number of genetic variants, including single nucleotide polymorphisms (SNPs), structural variations (SVs), and the specific genes annotated from unmapped sequence in “Xia Miao 1” was higher than that in “Xinjiang Pan Tao 1” peach. The data showed that there was a close distance between “Xinjiang Pan Tao 1” (P. ferganensis) and reference genome which belong to P. persica, comparing “Xia Miao 1” (P. persica) and reference ones. The results accompany with phylogenetic tree and structure analysis confirmed that P. ferganensis should be considered as a geographic population of P. persica rather than a subspecies or a distinct species. Furthermore, gene ontology analysis was performed using the gene comprising large-effect variation to understand the phenotypic difference between two accessions. The result revealed that the pathways of gene function affected by SVs but SNPs and insertion-deletions markedly differed between the two peach accessions.     

Hypercalcified segmented sponges (“sphinctozoans”) from the Upper Triassic (Norian) reef boulders of Taurus Mountains (southern Turkey)

Upper Triassic Norian reef boulders, exposed in a locality near the fountain “Tavuk Cesme” (“Chicken Fountain”) in Taurus Mountains, southern Turkey yielded a large number of hypercalcified sponges, including “sphinctozoans”, “inozoans”, “spongiomorphids”, and “chaetetids”. The sphinctozoans from this locality are described in this paper. Geologically, this locality belongs to the Anamas-Akseki autochthonous. The reef boulders of this locality are exposed near the “Tavuk Cesme” fountain, located at the road, leading from the town of Aksu to Yenisarbademli. The following taxa are described: Amblysiphonella taurica nov. sp., Anthalythalamia riedeli Senowbari-Daryan, Calabrisiphonella sphaerica nov. sp., Calabrisiphonella cuifi nov. sp., Cinnabaria minima Senowbari-Daryan, Colospongia recta nov. sp., Colospongia sp. 1, Colospongia sp. 2, Colospongia sp. 3, Cryptocoelia compacta nov. sp., Cryptocoelia? sp., Deningeria crassireticulata Senowbari-Daryan, Zühlke, Bechstädt and Flügel, Discosiphonella minima Senowbari-Daryan and Link, Gigantothalamia ovoidalis Senowbari-Daryan, Hajarispongia dipoyrazensis nov. sp., Hajarispongia cortexifera nov. sp., Kashanella irregularis Senowbari-Daryan, Kashanella cylindrica nov. sp., Parauvanella ferdowsensis Senowbari-Daryan, Parastylothalamia cylindrica nov. gen., nov. sp., Asiphothalamia polyosculata nov. gen, nov. sp., Sollasia norica nov. sp., and Thaumastocoelia sphaeroida Senowbari-Daryan. The most abundant sponge is Amblysiphonella taurica nov. sp. followed by Hajarispongia dipoyrazensis nov. sp., Colospongia and Discosiphonella minima Senowbari-Daryan and Link are also relatively abundant. The stylothalamid sponge Parastylothalamia nov. gen. is an abundant sponge genus in other Norian reefs of the Taurus Mountains, but is rare at the “Tavuk Cesme” locality.     

Initial growth deceleration as an immanent property of plants

A previously published sectional model of the system of tree branches (spruce) was expanded in the range (0,1) of the fractal model parameter μ, which links the value of green biomass of a “tree” to its size. The presence of branches in this range indicates the realization of green biomass in the form of photosynthe-sizing “points”, and is interpreted as endosymbiosis of cyanobacteria with protists. Using the method of box dimensionality, the parameter μ was estimated for the sets of points within an interval. The properties of the uniform and group distributions are shown to be different. For the group distribution, the trajectories of parameter μ are fundamentally different, depending on the method of point grouping, i.e., they decrease with an increase in the total number of points for a fixed number of points n _g in the groups and increase for a fixed number N _g groups. The initial endosymbiosis of cyanobacteria and “protists” is characterized by a lack of the necessary infrastructure in protists for feeding cyanobacteria and distributing their products and, thus, by a fixed number of “points” in the group. As the infrastructure of protists developed in the course of evolution, endosymbiosis tended to move towards an increased number of points in the group and, accordingly, increased μ. A special form of the dependence of parameter μ(N _g *n _g ) provides the inherent nature of the initial growth deceleration and modularity of architecture, which are occasionally observed in extant plants.     

The Phenolic Contents and Antimicrobial Activities of Some Marine Algae from the Mediterranean Sea (Algeria)

In this study, three marine algae collected from western coast of algerian mediteranean sea (Ulva lactuca, Dictyota dichotoma, and Corallina elongata) were tested using the agar-well diffusion method for their production of antibacterial and antifungal agents on various organisms that cause diseases of humans and plants (Eschirichia coli ATCC 25922, Staphylococcus aureus ATCC 25923, Salmonella sp, Candida albicans, and Penicillium sp.). The total phenol content and antimicrobial activity were determined using different crude seaweeds extracts (methanol, diethylether, and chloroform). The results show that the chloroform extracts of (Ulva lactuca and Corallina elongata) had the highest activity against E. coli and Salmonella sp. The methanol extract obtained from (Ulva lactuca, Dictyota dichotoma, and Corallina elongata) showed antifungal activity for Candida albicans. The results of the study revealed that the seaweeds from Algeria appear to have immense potential as a source of antibacterial and antifungal compounds; they can be used in treating diseases caused by these organisms.     

Reexamination of structures,stabilities, and electronic properties of holmium-doped silicon clusters HoSi<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript> (<Emphasis Type="Italic">n</Emphasis> = 12–20)

The total energies, growth patterns, equilibrium geometries, relative stabilities, hardnesses, intramolecular charge transfer, and magnetic moments of HoSi _n (n?=?12–20) clusters have been reexamined theoretically using two different density functional schemes in combination with relativistic small-core Stuttgart effective core potentials (ECP28MWB) for the Ho atoms. The results show that when n?=?12–15, the most stable structures are predicted to be exohedral frameworks with a quartet ground state, but when n?=?16–20, they are predicted to be endohedral frameworks with a sextuplet ground state. These trend in stability across the clusters (gauged from their dissociation energies) was found to be approximately the same regardless of the DFT scheme used in the calculations, with HoSi₁₃, HoSi₁₆, HoSi₁₈, and HoSi₂₀ calculated to be more stable than the other clusters. The results obtained for cluster hardness indicated that doping the Ho atom into Si₁₃ and Si₁₆ leads to the most stable HoSi _n clusters, while doping Ho into the other Si _n clusters increases the photochemical sensitivity of the cluster. Analyses of intracluster charge transfer and magnetic moments revealed that charge always shifts from the Ho atom to the Si _n cluster during the creation of exohedral HoSi _n (n?=?12–15) structures. However, the direction of charge transfer is reversed during the creation of endohedral HoSi _n (n?=?16–20) structures, which implies that Ho acts as an electron acceptor when it is encapsulated in the Si _n cage. Furthermore, when the most stable exohedral HoSi _n (n?=?12–15) structures are generated, the 4f electrons of Ho are virtually unchanged and barely participate in intracluster bonding. However, in the most stable endohedral HoSi _n (n?=?16–20) frameworks, a 4f electron does participate in bonding. It does this by transferring to the 5d orbital, which hybridizes with the 6s and 6p orbitals and then interacts with Si valence sp orbitals. Meanwhile, the total magnetic moments of the HoSi _n (n?=?16–20) clusters are considerably higher than those of HoSi _n (n?=?12–15). Interestingly, the endohedral HoSi₁₆ and HoSi₂₀ clusters can be viewed as the most suitable building blocks for novel high-density magnetic storage nanomaterials and for novel optical and optoelectronic photosensitive nanomaterials, respectively.