Search

Complex plastids, characterized by more than two bounding membranes, still present an evolutionary puzzle for the traditional endosymbiotic theory. Unlike primary plastids that directly evolved from cyanobacteria, complex plastids originated from green or red algae. The Chromalveolata hypothesis proposes a single red alga endosymbiosis that involved the ancestor of all the Chromalveolata lineages: cryptophytes, haptophytes, stramenopiles, and alveolates. As extensive phylogenetic analyses contradict the monophyly of Chromalveolata, serial plastid endosymbiosis models were proposed, suggesting a single secondary red alga endosymbiosis within Cryptophyta, followed by subsequent plastid transfers to other chromalveolates. Our findings based on 97 plastid-encoded markers, 112 species, and robust phylogenetic methods challenge all the existing models. They reveal two independent secondary endosymbioses, one within Cryptophyta and one within stramenopiles, precisely the phylum Ochrophyta, with two different groups of red algae. Consequently, we propose a new model for the emergence of red alga plastid–containing lineages and, through molecular clock analyses, estimate their ages. [ABSTRACT FROM AUTHOR]

This comprehensive study examines fossil remains from Niedźwiedzia Cave in the Eastern Sudetes, offering detailed insights into the palaeobiology and adversities encountered by the Pleistocene cave bear Ursus spelaeus ingressus. Emphasising habitual cave use for hibernation and a primarily herbivorous diet, the findings attribute mortality to resource scarcity during hibernation and habitat fragmentation amid climate shifts. Taphonomic analysis indicates that the cave was extensively used by successive generations of bears, virtually unexposed to the impact of predators. The study also reveals that alkaline conditions developed in the cave during the post-depositional taphonomic processes. Mortality patterns, notably among juveniles, imply dwindling resources, indicative of environmental instability. Skeletal examination reveals a high incidence of forelimb fractures, indicating risks during activities like digging or confrontations. Palaeopathological evidence unveils vulnerabilities to tuberculosis, abscesses, rickets, and injuries, elucidating mobility challenges. The cave's silts exhibit a high zinc concentration, potentially derived from successive bear generations consuming zinc-rich plants. This study illuminates the lives of late cave bears, elucidating unique environmental hurdles faced near their species' end. [ABSTRACT FROM AUTHOR]

Targeting peptides or presequences are N-terminal extensions of proteins that encode information about their cellular localization. They include signal peptides (SP), which target proteins to the endoplasmic reticulum, and transit peptides (TP) directing proteins to the organelles of endosymbiotic origin: chloroplasts and mitochondria. TPs were hypothesized to have evolved from antimicrobial peptides (AMPs), which are responsible for the host defence against microorganisms, including bacteria, fungi and viruses. In this study, we performed comprehensive bioinformatic analyses of amino acid motifs of targeting peptides and AMPs using a curated set of experimentally verified proteins. We identified motifs frequently occurring in each type of presequence showing specific patterns associated with their amino acid composition, and investigated their position within the presequence. We also compared motif patterns among different taxonomic groups and identified taxon-specific features, providing some evolutionary insights. Considering the functional relevance and many practical applications of targeting peptides and AMPs, we believe that our analyses will prove useful for their design, and better understanding of protein import mechanism and presequence evolution. [ABSTRACT FROM AUTHOR]

Mitochondrial DNA (mtDNA) lineages are recognized as important components of intra- and interspecific biodiversity, and allow to reveal colonization routes and phylogeographic structure of many taxa. Among these is the genus Cervus that is widely distributed across the Holarctic. We obtained sequences of complete mitochondrial genomes from 13 Cervus taxa and included them in global phylogenetic analyses of 71 Cervinae mitogenomes. The well-resolved phylogenetic trees confirmed Cervus to be monophyletic. Molecular dating based on several fossil calibration points revealed that ca. 2.6 Mya two main mitochondrial lineages of Cervus separated in Central Asia, the Western (including C. hanglu and C. elaphus) and the Eastern (comprising C. albirostris, C. canadensis and C. nippon). We also observed convergent changes in the composition of some mitochondrial genes in C. hanglu of the Western lineage and representatives of the Eastern lineage. Several subspecies of C. nippon and C. hanglu have accumulated a large portion of deleterious substitutions in their mitochondrial protein-coding genes, probably due to drift in the wake of decreasing population size. In contrast to previous studies, we found that the relic haplogroup B of C. elaphus was sister to all other red deer lineages and that the Middle-Eastern haplogroup E shared a common ancestor with the Balkan haplogroup C. Comparison of the mtDNA phylogenetic tree with a published nuclear genome tree may imply ancient introgressions of mtDNA between different Cervus species as well as from the common ancestor of South Asian deer, Rusa timorensis and R. unicolor, to the Cervus clade. [ABSTRACT FROM AUTHOR]

Mitochondrial genes are placed on one molecule, which implies that they should carry consistent phylogenetic information. Following this advantage, we present a well-supported phylogeny based on mitochondrial genomes from almost 300 representatives of Passeriformes, the most numerous and differentiated Aves order. The analyses resolved the phylogenetic position of paraphyletic Basal and Transitional Oscines. Passerida occurred divided into two groups, one containing Paroidea and Sylvioidea, whereas the other, Passeroidea and Muscicapoidea. Analyses of mitogenomes showed four types of rearrangements including a duplicated control region (CR) with adjacent genes. Mapping the presence and absence of duplications onto the phylogenetic tree revealed that the duplication was the ancestral state for passerines and was maintained in early diverged lineages. Next, the duplication could be lost and occurred independently at least four times according to the most parsimonious scenario. In some lineages, two CR copies have been inherited from an ancient duplication and highly diverged, whereas in others, the second copy became similar to the first one due to concerted evolution. The second CR copies accumulated over twice as many substitutions as the first ones. However, the second CRs were not completely eliminated and were retained for a long time, which suggests that both regions can fulfill an important role in mitogenomes. Phylogenetic analyses based on CR sequences subjected to the complex evolution can produce tree topologies inconsistent with real evolutionary relationships between species. Passerines with two CRs showed a higher metabolic rate in relation to their body mass. [ABSTRACT FROM AUTHOR]

The present distribution of many species is a result of climatic changes during the Pleistocene and human activity. The impact of climate has been accompanied by restrictions of populations into refugia during glacial periods, and subsequent expansions during more favourable conditions, whereas human influence has been associated with hunting practices and translocations. One mammalian species that has been subject to such transformations is the red deer, Cervus elaphus, but the exact nature of these changes has been difficult to determine using only modern DNA. In this study, we obtained new cytochrome b sequences from subfossil remains of deer found in the Crimean Peninsula. A comparison of these sequences with the available recent and ancient sequences allowed to us to reconstruct phylogeographic relationships between Cervus lineages and to determine their potential migration routes at both local and Eurasian scales. Our analyses showed that the Crimean Peninsula was not a glacial refugium for red deer, but rather that red deer colonized Crimea in three independent waves from both Western and Eastern red deer populations. The immigrations were related to local extinctions and replacements of native populations. [ABSTRACT FROM AUTHOR]

Although cave bear remains have been described since the end of 18th century, recent discoveries and methods provide new knowledge about the typical representative of Pleistocene megafauna, which did not survive the Last Glacial Maximum. Genetic studies supplemented by morphometric analyses showed that this mammal differentiated in the Late Pleistocene into two main forms called Ursus spelaeus and U. ingressus. The latter is regarded more expansive and replaced the native U. spelaeus in some areas of Western Europe. Taking into account the differences between these bears, it is interesting to determine if these forms became extinct at different or similar times. Therefore, we assessed their extinction times, applying seven methods using 205 dated records of cave bear ascribed to these two forms. The average extinction time of U. spelaeus was about 25,600 cal. yr BP (Before Present) and of U. ingressus about 24,800 cal. yr BP. The estimations showed that that U. ingressus could survive up to ca. 1,000 years longer than its relative U. spelaeus. The longer survival of the former could be related to its greater morphological variability and better adaptation to arid continental environments, as well as a stronger tendency to occasional omnivory. Both bears became extinct within the coldest phase of the last glacial period, Greenland Stadial 3, which implies that climate cooling was the main factor of their extinction. The climate deterioration decreased vegetation productivity, and could also have had negative consequences on the prolonged hibernation period when the bears were more susceptible to the activity of humans and predators. [ABSTRACT FROM AUTHOR]

Shrews of the Sorex genus are an evolutionarily successful group that includes more than 77 species widely distributed in Eurasia and North America. The genus is one of the rare cases where karyotypic changes reflect well the evolutionary relationships among its species. The taxa showing the greatest variation in karyotype are usually classified into the Sorex araneus group. Its evolution was associated with chromosomal rearrangements, which could have promoted fast diversification of this group into many chromosomal races and species. These processes were additionally complicated by introgressions of mitochondrial DNA, which made the evolutionary history of this group quite complex and difficult to infer. To tackle the problem, we performed multi-method phylogenetic analyses based on mitochondrial cytochrome b that is considered a good molecular marker available for many representatives of Sorex. The results were compared with phylogenies based on chromosomal rearrangement data and put into temporal and spatial context using molecular dating and historical biogeography methods. We complemented the study with the estimation of diversification rates within the S. araneus group as well as comparing the results with paleontological records and climatic oscillations within the last 4 million years. Based on the gathered data, we proposed a hypothetical scenario for the evolution and geographic dispersion of species belonging to the S. araneus group. The shrews began to diversify about 2.7 million years ago in Eurasia and then migrated at least twice to North America. The evolution of shrews was driven by Pleistocene glacial and interglacial cycles, which increased their speciation rate and the emergence of new lineages. The migrations of populations were accompanied by introgressions of mitochondrial DNA into native shrews and occurred at least twice. [ABSTRACT FROM AUTHOR]

The rhizarian amoeba Paulinella chromatophora harbors two photosynthetic cyanobacterial endosymbionts (chromatophores), acquired independently of primary plastids of glaucophytes, red algae and green plants. These endosymbionts have lost many essential genes, and transferred substantial number of genes to the host nuclear genome via endosymbiotic gene transfer (EGT), including those involved in photosynthesis. This indicates that, similar to primary plastids, Paulinella endosymbionts must have evolved a transport system to import their EGT-derived proteins. This system involves vesicular trafficking to the outer chromatophore membrane and presumably a simplified Tic-like complex at the inner chromatophore membrane. Since both sequenced Paulinella strains have been shown to undergo differential plastid gene losses, they do not have to possess the same set of Toc and Tic homologs. We searched the genome of Paulinella FK01 strain for potential Toc and Tic homologs, and compared the results with the data obtained for Paulinella CCAC 0185 strain, and 72 cyanobacteria, eight Archaeplastida as well as some other bacteria. Our studies revealed that chromatophore genomes from both Paulinella strains encode the same set of translocons that could potentially create a simplified but fully-functional Tic-like complex at the inner chromatophore membranes. The common maintenance of the same set of translocon proteins in two Paulinella strains suggests a similar import mechanism and/or supports the proposed model of protein import. Moreover, we have discovered a new putative Tic component, Tic62, a redox sensor protein not identified in previous comparative studies of Paulinella translocons. [ABSTRACT FROM AUTHOR]

One of the key evolutionary events on the scale of the biosphere was an endosymbiosis between a heterotrophic eukaryote and a cyanobacterium, resulting in a primary plastid. Such an organelle is characteristic of three eukaryotic lineages, glaucophytes, red algae and green plants. The three groups are usually united under the common name Archaeplastida or Plantae in modern taxonomic classifications, which indicates they are considered monophyletic. The methods generally used to verify this monophyly are phylogenetic analyses. In this article we review up-to-date results of such analyses and discussed their inconsistencies. Although phylogenies of plastid genes suggest a single primary endosymbiosis, which is assumed to mean a common origin of the Archaeplastida, different phylogenetic trees based on nuclear markers show monophyly, paraphyly, polyphyly or unresolved topologies of Archaeplastida hosts. The difficulties in reconstructing host cell relationships could result from stochastic and systematic biases in data sets, including different substitution rates and patterns, gene paralogy and horizontal/endosymbiotic gene transfer into eukaryotic lineages, which attract Archaeplastida in phylogenetic trees. Based on results to date, it is neither possible to confirm nor refute alternative evolutionary scenarios to a single primary endosymbiosis. Nevertheless, if trees supporting monophyly are considered, relationships inferred among Archaeplastida lineages can be discussed. Phylogenetic analyses based on nuclear genes clearly show the earlier divergence of glaucophytes from red algae and green plants. Plastid genes suggest a more complicated history, but at least some studies are congruent with this concept. Additional research involving more representatives of glaucophytes and many understudied lineages of Eukaryota can improve inferring phylogenetic relationships related to the Archaeplastida. In addition, alternative approaches not directly dependent on phylogenetic methods should be developed. [ABSTRACT FROM AUTHOR]

The migration of Ursus ingressus from Southern to Western Europe, where it replaced native forms of Ursus spelaeus , is well documented. However, its occurrence in Central and Eastern European countries is unexplored. We have characterized the cave bear population inhabiting the Sudetes Mountains during the Late Pleistocene. DNA analyses were performed on 39 cave bear specimens from the Niedzwiedzia Cave. Ten successfully yielded the 254-bp sequences of an mtDNA control region. Phylogenetic analyses allowed assignment of nine samples to the U. ingressus haplogroup and one to brown bear ( Ursus arctos ). The mtDNA haplotypes of U. ingressus formed a single cluster and differed from haplotypes obtained for cave bears from other excavation sites in Europe. Uranium-thorium and radiocarbon dating of selected samples has shown that U. ingressus appeared in the Sudetes region at least 80,000 years ago. This finding may suggest that the appearance of U. ingressus in this area resulted from migration that occurred earlier than the colonization of the Alps and Swabian Jura. It is possible that migration of U. ingressus proceeded along the Carpathian and Sudetes arc. [ABSTRACT FROM AUTHOR]

The Yellow-shouldered Amazon (Amazona barbadensis) is the sole parrot of the genus Amazona that inhabits only dry forests. Its population has been dropping; therefore it has been the topic of many studies and conservation efforts. However, the phylogenetic relationship of this species to potential relatives classified within the Yellow-Headed Amazon (YHA) complex are still not clear. Therefore, we used more extensive data sets, including the newly sequenced mitochondrial genome of A. barbadensis, to conduct phylogenetic analyses. Various combinations of genes and many phylogenetic approaches showed that A. barbadensis clustered significantly with A. ochrocephala ochrocephala from Colombia and Venezuela, which created the Northern South American (NSA) lineage, clearly separated from two other lineages within the YHA complex, the Central (CA) and South American (SA). Tree topology tests and exclusion of rapidly evolving sites provided support for a NSA+SA grouping. We propose an evolutionary scenario for the YHA complex and its colonization of the American mainland. The NSA lineage likely represents the most ancestral lineage, which derived from Lesser Antillean Amazons and colonized the northern coast of Venezuela about a million years ago. Then, Central America was colonized through the Isthmus of Panama, which led to the emergence of the CA lineage. The southward expansion to South America and the origin of the SA lineage happened almost simultaneously. However, more intensive or prolonged gene flow or migrations have led to much weaker geographic differentiation of genetic markers in the SA than in the CA lineage. [ABSTRACT FROM AUTHOR]

The taxonomic status of Trochulus phorochaetius and its phylogenetic relationships to Trochulus plebeius and Trochulus hispidus were evaluated based on molecular, morphological, and genital anatomy data. The canonical discriminant analysis ( CDA) of shell morphology allowed the clear differentiation between these three nominal species, whereas the genitalia revealed their high similarity. Analyses of cytochrome c oxidase subunit I ( COI) sequences were not always congruent with the differentiation between these three species by shell characters. None of them formed a monophyletic group covering all its sequences. Instead, many sequences obtained from individuals classified to the same morphospecies, and/or usually collected from the same region or country, created highly supported separate clades and delimited clusters. Three distinct clades containing sequences of two morphospecies originating from the same country were identified in molecular phylogenetic and species delimitation studies: (1) T. plebeius + T. hispidus from Great Britain; (2) T. plebeius + T. hispidus from Poland; and (3) T. phorochaetius + T. hispidus from France. In the latter case some of the sequences were even identical. Their genetic similarity could indicate the ability to hybridize, which may be evidenced by the lack of major differences in their reproductive system. The assignment of distinctive morphospecies, and thus existing taxonomic names, to genetically defined evolutionary lineages is premature and arbitrary to some extent at this stage. © 2013 The Linnean Society of London [ABSTRACT FROM AUTHOR]

Organelle genomes lose their genes by transfer to host nuclear genomes, but only occasionally are enriched by foreign genes from other sources. In contrast to mitochondria, plastid genomes are especially resistant to such horizontal gene transfer (HGT), and thus every gene acquired in this way is notable. An exceptional case of HGT was recently recognized in the peculiar peridinin plastid genome of dinoflagellates, which is organized in plasmid-like minicircles. Genomic and phylogenetic analyses of Ceratium horridum and Pyrocystis lunula minicircles revealed four genes and one unannotated open reading frame that probably were gained from bacteria belonging to the Bacteroidetes. Such bacteria seem to be a good source of genes because close endosymbiotic associations between them and dinoflagellates have been observed. The HGT-acquired genes are involved in plastid functions characteristic of other photosynthetic eukaryotes, and their arrangement resembles bacterial operons. These studies indicate that the peridinin plastid genome, usually regarded as having resulted from reduction and fragmentation of a typical plastid genome derived from red algae, may have a chimeric origin that includes bacterial contributions. Potential contamination of the Ceratium and Pyrocystis plastid genomes by bacterial sequences and the controversial localization of their minicircles in the nucleus are also discussed. [ABSTRACT FROM AUTHOR]

The rhizarian amoeba Paulinella chromatophora harbors two photosynthetically active and deeply integrated cyanobacterial endosymbionts acquired ~60 million years ago. Recent genomic analyses of P. chromatophora have revealed the loss of many essential genes from the endosymbiont's genome, and have identified more than 30 genes that have been transferred to the host cell's nucleus through endosymbiotic gene transfer (EGT). This indicates that, similar to classical primary plastids, Paulinella endosymbionts have evolved a transport system to import their nuclear-encoded proteins. To deduce how these proteins are transported, we searched for potential targeting signals in genes for 10 EGT-derived proteins. Our analyses indicate that five proteins carry potential signal peptides, implying they are targeted via the host endomembrane system. One sequence encodes a mitochondrial-like transit peptide, which suggests an import pathway involving a channel protein residing in the outer membrane of the endosymbiont. No N-terminal targeting signals were identified in the four other genes, but their encoded proteins could utilize non-classical targeting signals contained internally or in C-terminal regions. Several amino acids more often found in the Paulinella EGT-derived proteins than in their ancestral set (proteins still encoded in the endosymbiont genome) could constitute such signals. Characteristic features of the EGT-derived proteins are low molecular weight and nearly neutral charge, which both could be adaptations to enhance passage through the peptidoglycan wall present in the intermembrane space of the endosymbiont's envelope. Our results suggest that Paulinella endosymbionts/plastids have evolved several different import routes, as has been shown in classical primary plastids. [ABSTRACT FROM AUTHOR]

Bacteriophage KP34 is a novel virus belonging to the subfamily Autographivirinae lytic for extended-spectrum β-lactamase-producing Klebsiella pneumoniae strains. Its biological features, morphology, susceptibility to chemical and physical agents, burst size, host specificity and activity spectrum were determined. As a potential antibacterial agent used in therapy, KP34 molecular features including genome sequence and protein composition were examined. Phylogenetic analyses and clustering of KP34 phage genome sequences revealed its clear relationships with 'phiKMV-like viruses'. Simultaneously, whole-genome analyses permitted clustering and classification of all phages, with completely sequenced genomes, belonging to the Podoviridae. [ABSTRACT FROM AUTHOR]

The article focuses on the evolution of plastid proteins of plants. It cites that according to the endosymbiotic theory, there is a proof that plastids are evolving from free-living cyanobacteria which is confined by heterotrophic eukaryotic cells. It states that some of the nuclear-encoded proteins are brought in higher plastids through the endomembrane (EM) system. Moreover, the loss of the phagosomal membrane occur very soon in the primary plastids evolution.

Background: An important role in the evolution of intracellular trafficking machinery in eukaryotes played small GTPases belonging to the Rab family known as pivotal regulators of vesicle docking, fusion and transport. The Rab family is very diversified and divided into several specialized subfamilies. We focused on the VII functional group comprising Rab7 and Rab9, two related subfamilies, and analysed 210 sequences of these proteins. Rab7 regulates traffic from early to late endosomes and from late endosome to vacuole/lysosome, whereas Rab9 participates in transport from late endosomes to the trans-Golgi network. Results: Although Rab7 and Rab9 proteins are quite small and show heterogeneous rates of substitution in different lineages, we found a phylogenetic signal and inferred evolutionary relationships between them. Rab7 proteins evolved before radiation of main eukaryotic supergroups while Rab9 GTPases diverged from Rab7 before split of choanoflagellates and metazoans. Additional duplication of Rab9 and Rab7 proteins resulting in several isoforms occurred in the early evolution of vertebrates and next in teleost fishes and tetrapods. Three Rab7 lineages emerged before divergence of monocots and eudicots and subsequent duplications of Rab7 genes occurred in particular angiosperm clades. Interestingly, several Rab7 copies were identified in some representatives of excavates, ciliates and amoebozoans. The presence of many Rab copies is correlated with significant differences in their expression level. The diversification of analysed Rab subfamilies is also manifested by non-conserved sequences and structural features, many of which are involved in the interaction with regulators and effectors. Individual sites discriminating different subgroups of Rab7 and Rab9 GTPases have been identified. [ABSTRACT FROM AUTHOR]

Abstract: Three hundred commensal Escherichia coli recovered from healthy herbivorous, carnivorous, and omnivorous mammals from one zoo were characterized for their phylogenetic origin, intestinal virulence gene (VG) prevalence, and genomic diversity. The phylogenetic structure of the E. coli (groups A, B1, B2, and D) from the herbivores was homogenous, with a prevailing representation of group B1. In the carnivores and omnivores, the phylogenetic diversity was species specific with a higher representation of group A compared to the herbivores. Of 16 intestinal VGs in the whole set, 8 were detected and they formed 13 VG profiles. In the herbivores, all the VG-positive isolates belonged to group B1 and harboured the genes eaeA, eastI, ehxA, stx1, and stx2, which separately or in combination formed 8 VG profiles. In the carnivores and omnivores, the VG-positive isolates frequently belonged to group A and harboured the estI and estII genes or a combination of eastI and estI, forming three VG profiles. Single genes cnf2, in group B2, and eastI, in group D, were found. Similarity analysis of pulsed-field gel electrophoresis (PFGE) patterns revealed closer relatedness between the isolates from carnivores and omnivores than those from herbivores. The comparison between the prevalence of phylogenetic groups and the phylogenetic origin of VG-positive isolates in the examined E. coli suggested, that E. coli from group B1 in herbivores and E. coli from group A rather than B1 in carnivores and omnivores are “best adapted” to the host organism. The groups revealed different preferences in the acquisition and maintenance of intestinal VGs. [Copyright &y& Elsevier]

One of the proteins targeted to the peridinin plastid of the dinoflagellate Lingulodinium polyedrum is the iron-containing superoxide dismutase (LpSOD). Like dinoflagellate plastid proteins of class II, LpSOD carries a bipartite presequence comprising a signal peptide followed by a transit peptide. Our bioinformatic studies suggest that its signal peptide is atypical, however, and that the entire presequence may function as a mitochondrial targeting signal. It is possible that LpSOD represents a new class of proteins in algae with complex plastids, which are co-targeted to the plastid and mitochondrion. In addition to the ambiguous N-terminal targeting signal, LpSOD contains a potential type-1 peroxisome-targeting signal (PTS1) located at its C-terminus. In accordance with a peroxisome localization of this dismutase, its mRNA has two in-frame AUG codons. Our bioinformatic analyses indicate that the first start codon resides in a much weaker oligonucleotide context than the second one. This suggests that synthesis of the plastid/mitochondrion-targeted and peroxisome-targeted isoforms could proceed through so-called leaky scanning. Moreover, our results show that expression of the two isoforms could be regulated by a ‘hairpin’ structure located between the first and second start codons. [ABSTRACT FROM AUTHOR]

AUG as the Translation Start Codon in Circular RNA Molecules: A Connection between Protein-Coding Genes and Transfer RNAs? The AUG codon is a classical signal that tells the ribosome where protein synthesis (translation) should start. Additionally, the RNA ring structure is a well-known motif in some mitochondrial tRNAs, whose sequences contain conserved stop codons between two stems and codon AUG, that is, between the hypervariable loop and a sidearm. [Extracted from the article]

Genome‐wide technologies open up new possibilities to clarify questions on genetic structure and phylogeographic history of taxa previously studied with microsatellite loci and mitochondrial sequences. Here, we used 736 individual red deer (Cervus elaphus) samples genotyped at 35,701 single nucleotide polymorphism loci (SNPs) to assess the population structure of the species throughout Europe. The results identified 28 populations, with higher degrees of genetic distinction in peripheral compared to mainland populations. Iberian red deer show high genetic differentiation, with lineages in Western and Central Iberia maintaining their distinctiveness, which supports separate refugial ranges within Iberia along with little recent connection between Iberian and the remaining Western European populations. The Norwegian population exhibited the lowest variability and the largest allele frequency differences from mainland European populations, compatible with a history of bottlenecks and drift during post‐glacial colonization from southern refugia. Scottish populations showed high genetic distance from the mainland but high levels of diversity. Hybrid zones were found between Eastern and Western European lineages in Central Europe as well as in the Pyrenees, where red deer from France are in close contact with Iberian red deer. Anthropogenic restocking has promoted the Pyrenean contact zone, admixture events in populations on the Isle of Rum and in the Netherlands, and at least partly the admixture of the two main lineages in central‐eastern Europe. Our analysis enabled detailed resolution of population structure of a large mammal widely distributed throughout Europe and contributes to resolving the evolutionary history, which can also inform conservation and management policies. [ABSTRACT FROM AUTHOR]

Six genera of the Arini tribe form morphologically diverse group termed as Macaws. The presence of bare facial area distinguishes them from other members of the tribe. Genera and species of Macaw group differ in pattern of this bare skin as well as in body size. The genus Ara contains eight extant species. Two of them are classified as medium-sized Macaws and other six species are classified as large Macaws. Based on morphological similarities and differences, large Macaw species can be segregated into three pairs according to their plumage coloration. So far, representative mitochondrial genomes were sequenced only for Ara glaucogularis (blue and yellow coloration), Ara macao (predominantly red/scarlet) and Ara militaris (predominantly green) species. Ara ararauna is the second of two Ara species with predominant blue and yellow plumage. Hitherto, close phylogenetic relation of these two species was shown using only ND2 genes or incomplete combined COI/Cytb/ND2 sequences. Therefore, Ara ararauna mitogenome, which was sequenced in this study, will be indispensable to refine the phylogenetic relationships within Macaws group. [ABSTRACT FROM AUTHOR]

The presence of bare facial area distinguishes Macaws from other members of theArinitribe. Genera and species of the Macaw group differ in pattern of this bare skin as well as in body size. Individuals of the genera:Diopsittaca,Orthopsittaca,andPrimoliusare significantly smaller than the members of the genera:Anodorhynchus,Cyanopsitta,and the most species of the genusAra. The genusPrimoliuscontains three species:P. auricollis,P. couloni,andP. maracana, which are classified as medium-sized Macaws. So far, mitochondrial genome representative for the genus was sequenced only forPrimolius coulonispecies.Primolius maracanamitogenome, which was sequenced in this study, will be indispensable to refine the phylogenetic relationships betweenPrimoliusspecies, as results of molecular researches seems to be inconsistent withPrimoliusspecies morphology. [ABSTRACT FROM PUBLISHER]

The Mitred Conure (Psittacara mitratus) is a species native to the forests and woodlands in the Andes in central Peru, south through west-central Bolivia, to northwestern Argentina. The genusPsittacarahave recently been distinguished on the basis of molecular revision of theAratingaspecies. In consequence, it became one of the nine genera, which form morphologically diverse group termed as Conures. Although, the number of species/subspecies belonging toPsittacararemains controversial, it is now believed that the genus is represented by 11 species. Taxonomic position of Mitred Conure was determined by molecular research and makes the species crucial for examination of evolutionary diversification of the genus. Therefore, we sequenced complete mitochondrial genome ofP. mitratusmitogenome to gain a source of comprehensive molecular data. It will be indispensable to refine the phylogenetic relationships within “Psittacaragroup” as well as within the tribe Arini. [ABSTRACT FROM AUTHOR]

According to some taxonomists the Red-throated Conure (Psittacara rubritorquis) is considered a subspecies of Green Conure (Psittacara holochlora). Some other classifications treatrubritorquisas a separate species based on relatively minor morphological differences between both species/subspecies. So far, taxonomic position ofP. rubritorquiswas determined by molecular researches using only ND2 gene sequence or incomplete combined mitochondrial ND2, COI and CYTB gene sequences. Obtained outcomes found thatP. rubritorquisshould be treated as a subspecies ofP. holochlora. However, the lack ofP. h. brewsteriiandP. h. strenuasamples as well as incompleteness of combined mitochondrial sequence do not exclude opposite scenario. Therefore, we sequencedP. rubritorquismitogenome to gain a source of molecular data appropriate for future examination of evolutionary diversification of theP. holochloragroup. [ABSTRACT FROM AUTHOR]

Background: Bird mitogenomes differ from other vertebrates in gene rearrangement. The most common avian gene order, identified first in Gallus gallus, is considered ancestral for all Aves. However, other rearrangements including a duplicated control region and neighboring genes have been reported in many representatives of avian orders. The repeated regions can be easily overlooked due to inappropriate DNA amplification or genome sequencing. This raises a question about the actual prevalence of mitogenomic duplications and the validity of the current view on the avian mitogenome evolution. In this context, Palaeognathae is especially interesting because is sister to all other living birds, i.e. Neognathae. So far, a unique duplicated region has been found in one palaeognath mitogenome, that of Eudromia elegans. Results: Therefore, we applied an appropriate PCR strategy to look for omitted duplications in other palaeognaths. The analyses revealed the duplicated control regions with adjacent genes in Crypturellus, Rhea and Struthio as well as ND6 pseudogene in three moas. The copies are very similar and were subjected to concerted evolution. Mapping the presence and absence of duplication onto the Palaeognathae phylogeny indicates that the duplication was an ancestral state for this avian group. This feature was inherited by early diverged lineages and lost two times in others. Comparison of incongruent phylogenetic trees based on mitochondrial and nuclear sequences showed that two variants of mitogenomes could exist in the evolution of palaeognaths. Data collected for other avian mitogenomes revealed that the last common ancestor of all birds and early diverging lineages of Neoaves could also possess the mitogenomic duplication. Conclusions: The duplicated control regions with adjacent genes are more common in avian mitochondrial genomes than it was previously thought. These two regions could increase effectiveness of replication and transcription as well as the number of replicating mitogenomes per organelle. In consequence, energy production by mitochondria may be also more efficient. However, further physiological and molecular analyses are necessary to assess the potential selective advantages of the mitogenome duplications. [ABSTRACT FROM AUTHOR]

The family Rhinocerotidae is a key component of the Cenozoic European fauna. It reached its peak diversity during Miocene and began to decline in the Pliocene; the last representatives became extinct in Europe during the Quaternary. The present state-of-the-art review takes stock of the knowledge accumulated on Central and Eastern European Pleistocene rhinos to date. Eight species were present in Central and Eastern Europe in the Quaternary; five belonged to the genus Stephanorhinus (S. etruscus , S. jeanvireti , S. hundsheimensis , S. hemitoechus , and S. kirchbergensis), one was the woolly rhino Coelodonta antiquitatis , and two species were members of the genus Elasmotherium (E. peii and E. caucasicum). This review also offered the opportunity to critically reconsider some aspects of the systematics and stratigraphic location of the finds. Coelodonta antiquitatis is shown to have still been present as late as the Interplenivistulian and the Last Glacial Maximum; radiocarbon dating of its latest remains provided the timing of the final disappearance of the woolly rhino from the studied region. The Late Pleistocene distribution of Coelodonta antiquitatis in Central and Eastern Europe was found to largely overlap that of the woolly mammoth. [ABSTRACT FROM AUTHOR]

The distinct structure and universality of the standard genetic code (SGC) have fascinated the scientists ever since the first amino acid assignments were discovered. There are several hypotheses trying to explain the origin and evolution of this code. One of them postulates that the SGC evolved to minimize harmful effects of amino acid replacements in proteins, caused by mutations and translational errors. Many investigations concerning this hypothesis have already been carried out, but they were focused mainly on the consequences of single-point mutations. Therefore, we decided to check the influence of other types of mutations, i.e. insertions and deletions, on the robustness to amino acid replacements of the SGC. Such mutations cause shifts in the reading frame during the translation process which result in more harmful consequences in coded proteins than in the case of single-point mutations. We applied a multi-objective optimization algorithm to find the best and the worst genetic codes, regarding their robustness to both single-point and frameshift mutations, for various amino acid properties. Then we compared the features of the found codes with the properties of the standard genetic code. The results show that the SGC is not fully optimized for minimizing the effects of frameshift mutations but it is, nevertheless, much closer to the best solutions than to the worst ones. It implies that a certain tendency to minimize the costs of amino acids replacements resulting from various kinds of mutations is present in the standard genetic code. [ABSTRACT FROM AUTHOR]

Endosymbiotic relationships are common across the tree of life and have had profound impacts on cellular evolution and diversity. Recent molecular investigations of the amoeba Paulinella chromatophora have raised a timely and important question: should obligatory intracellular cyanobacteria in Paulinella be considered new organelles, or do plastids and mitochondria hold a unique stature in the history of endosymbiotic events? We argue that drawing a sharp distinction between these two organelles and all other endosymbionts is not supported by accumulating data, neither is it a productive framework for investigating organelle evolution. [Copyright &y& Elsevier]

Lactoferrin, an iron-binding glycoprotein, plays a significant role in the innate immune system, with antibacterial, antivirial, antifungal, anticancer, antioxidant and immunomodulatory functions reported. It is worth emphasizing that not only the whole protein but also its derived fragments possess antimicrobial peptide (AMP) activity. Using AmpGram, a top-performing AMP classifier, we generated three novel human lactoferrin (hLF) fragments: hLF 397-412, hLF 448-464 and hLF 668-683, predicted with high probability as AMPs. For comparative studies, we included hLF 1-11, previously confirmed to kill some bacteria. With the four peptides, we treated three Gram-negative and three Gram-positive bacterial strains. Our results indicate that none of the three new lactoferrin fragments have antimicrobial properties for the bacteria tested, but hLF 1-11 was lethal against Pseudomonas aeruginosa. The addition of serine protease inhibitors with the hLF fragments did not enhance their activity, except for hLF 1-11 against P. aeruginosa, which MIC dropped from 128 to 64 µg/mL. Furthermore, we investigated the impact of EDTA with/without serine protease inhibitors and the hLF peptides on selected bacteria. We stress the importance of reporting non-AMP sequences for the development of next-generation AMP prediction models, which suffer from the lack of experimentally validated negative dataset for training and benchmarking. [ABSTRACT FROM AUTHOR]

Due to their complex history, plastids possess proteins encoded in the nuclear and plastid genome. Moreover, these proteins localize to various subplastid compartments. Since protein localization is associated with its function, prediction of subplastid localization is one of the most important steps in plastid protein annotation, providing insight into their potential function. Therefore, we create a novel manually curated data set of plastid proteins and build an ensemble model for prediction of protein subplastid localization. Moreover, we discuss problems associated with the task, e.g. data set sizes and homology reduction. PlastoGram classifies proteins as nuclear- or plastid-encoded and predicts their localization considering: envelope, stroma, thylakoid membrane or thylakoid lumen; for the latter, the import pathway is also predicted. We also provide an additional function to differentiate nuclear-encoded inner and outer membrane proteins. PlastoGram is available as a web server at https://biogenies.info/PlastoGram and as an R package at https://github.com/BioGenies/PlastoGram. The code used for described analyses is available at https://github.com/BioGenies/PlastoGram-analysis. [ABSTRACT FROM AUTHOR]

Background: Conures are a morphologically diverse group of Neotropical parrots classified as members of the tribe Arini, which has recently been subjected to a taxonomic revision. The previously broadly defined Aratinga genus of this tribe has been split into the 'true' Aratinga and three additional genera, Eupsittula, Psittacara and Thectocercus. Popular markers used in the reconstruction of the parrots' phylogenies derive from mitochondrial DNA. However, current phylogenetic analyses seem to indicate conflicting relationships between Aratinga and other conures, and also among other Arini members. Therefore, it is not clear if the mtDNA phylogenies can reliably define the species tree. The inconsistencies may result from the variable evolution rate of the markers used or their weak phylogenetic signal. To resolve these controversies and to assess to what extent the phylogenetic relationships in the tribe Arini can be inferred from mitochondrial genomes, we compared representative Arini mitogenomes as well as examined the usefulness of the individual mitochondrial markers and the efficiency of various phylogenetic methods. Results: Single molecular markers produced inconsistent tree topologies, while different methods offered various topologies even for the same marker. A significant disagreement in these tree topologies occurred for cytb, nd2 and nd6 genes, which are commonly used in parrot phylogenies. The strongest phylogenetic signal was found in the control region and RNA genes. However, these markers cannot be used alone in inferring Arini phylogenies because they do not provide fully resolved trees. The most reliable phylogeny of the parrots under study is obtained only on the concatenated set of all mitochondrial markers. The analyses established significantly resolved relationships within the former Aratinga representatives and the main genera of the tribe Arini. Such mtDNA phylogeny can be in agreement with the species tree, owing to its match with synapomorphic features in plumage colouration. Conclusions: Phylogenetic relationships inferred from single mitochondrial markers can be incorrect and contradictory. Therefore, such phylogenies should be considered with caution. Reliable results can be produced by concatenated sets of all or at least the majority of mitochondrial genes and the control region. The results advance a new view on the relationships among the main genera of Arini and resolve the inconsistencies between the taxa that were previously classified as the broadly defined genus Aratinga. Although gene and species trees do not always have to be consistent, the mtDNA phylogenies for Arini can reflect the species tree. [ABSTRACT FROM AUTHOR]

Morphological variation of snails from the genus Trochulus is so huge that their taxonomy is unclear. The greatest variability concerns forms hispidus and sericeus/plebeius, which are often considered as separate species. To evidence the species barriers, we carried out crossbreeding experiments between these two sympatric morphs. Moreover, we compared the shell morphology of laboratory-bred offspring with their wild parents to test if the variation can be explained by the phenotypic plasticity model. We found that the two Trochulus morphs show no reproductive barriers. The fecundity rates, the mean clutch size, and F1 viability observed for all crosses were not significantly different. In hybrid crosses (in F2 generation), we also recorded reproduction compatibility, similar fecundity, and hatching success as in their parents. Accordingly, phylogenetic analyses revealed the significant grouping of sequences from these different morphs and supported no constrains in reproduction between them. Comparison of shell morphology between wild and laboratory samples showed that various characters appeared highly plastic. The average shell shape of the hispidus morph changed significantly from flat with wide umbilicus to elevated with narrower umbilicus such as in the sericeus/plebeius morph. All these findings indicate that the examined morphs do not represent separate biological species and the evolutionary process is not advanced enough to separate their genetic pool. Therefore, phenotypic plasticity has played a significant role in the evolution of Trochulus shell polymorphism. The two morphs can evolve independently in separate phylogenetic lineages under the influence of local environmental conditions. [ABSTRACT FROM AUTHOR]

One of theories explaining the present structure of canonical genetic code assumes that it was optimized to minimize harmful effects of amino acid replacements resulting from nucleotide substitutions and translational errors. A way to testify this concept is to find the optimal code under given criteria and compare it with the canonical genetic code. Unfortunately, the huge number of possible alternatives makes it impossible to find the optimal code using exhaustive methods in sensible time. Therefore, heuristic methods should be applied to search the space of possible solutions. Evolutionary algorithms (EA) seem to be ones of such promising approaches. This class of methods is founded both on mutation and crossover operators, which are responsible for creating and maintaining the diversity of candidate solutions. These operators possess dissimilar characteristics and consequently play different roles in the process of finding the best solutions under given criteria. Therefore, the effective searching for the potential solutions can be improved by applying both of them, especially when these operators are devised specifically for a given problem. To study this subject, we analyze the effectiveness of algorithms for various combinations of mutation and crossover probabilities under three models of the genetic code assuming different restrictions on its structure. To achieve that, we adapt the position based crossover operator for the most restricted model and develop a new type of crossover operator for the more general models. The applied fitness function describes costs of amino acid replacement regarding their polarity. Our results indicate that the usage of crossover operators can significantly improve the quality of the solutions. Moreover, the simulations with the crossover operator optimize the fitness function in the smaller number of generations than simulations without this operator. The optimal genetic codes without restrictions on their structure minimize the costs about 2.7 times better than the canonical genetic code. Interestingly, the optimal codes are dominated by amino acids characterized by polarity close to its average value for all amino acids. [ABSTRACT FROM AUTHOR]

Summary: It is commonly assumed that transformations of endosymbionts into organelles are exceptionally rare evolutionary events because of hypothetical difficulties in the origin of an import apparatus for nuclear-encoded, organelle-targeted proteins along with their targeting signals. A challenge to this view comes from recent studies of protein import into the cyanobacterial endosymbionts/organelles of Paulinella chromatophora. [ABSTRACT FROM AUTHOR]

Synonymous codon usage can be influenced by mutations and/or selection, e.g., for speed of protein translation and correct folding. However, this codon bias can also be affected by a general selection at the amino acid level due to differences in the acceptance of the loss and generation of these codons. To assess the importance of this effect, we constructed a mutation–selection model model, in which we generated almost 90,000 stationary nucleotide distributions produced by mutational processes and applied a selection based on differences in physicochemical properties of amino acids. Under these conditions, we calculated the usage of fourfold degenerated (4FD) codons and compared it with the usage characteristic of the pure mutations. We considered both the standard genetic code (SGC) and alternative genetic codes (AGCs). The analyses showed that a majority of AGCs produced a greater 4FD codon bias than the SGC. The mutations producing more thymine or adenine than guanine and cytosine increased the differences in usage. On the other hand, the mutational pressures generating a lot of cytosine or guanine with a low content of adenine and thymine decreased this bias because the nucleotide content of most 4FD codons stayed in the compositional equilibrium with these pressures. The comparison of the theoretical results with those for real protein coding sequences showed that the influence of selection at the amino acid level on the synonymous codon usage cannot be neglected. The analyses indicate that the effect of amino acid selection cannot be disregarded and that it can interfere with other selection factors influencing codon usage, especially in AT-rich genomes, in which AGCs are usually used. [ABSTRACT FROM AUTHOR]

Amyloids and antimicrobial peptides (AMPs) have many similarities, e.g., both kill microorganisms by destroying their membranes, form aggregates, and modulate the innate immune system. Given these similarities and the fact that the antimicrobial properties of short amyloids have not yet been investigated, we chose a group of potentially antimicrobial short amyloids to verify their impact on bacterial and eukaryotic cells. We used AmpGram, a best-performing AMP classification model, and selected ten amyloids with the highest AMP probability for our experimental research. Our results indicate that four tested amyloids: VQIVCK, VCIVYK, KCWCFT, and GGYLLG, formed aggregates under the conditions routinely used to evaluate peptide antimicrobial properties, but none of the tested amyloids exhibited antimicrobial or cytotoxic properties. Accordingly, they should be included in the negative datasets to train the next-generation AMP prediction models, based on experimentally confirmed AMP and non-AMP sequences. In the article, we also emphasize the importance of reporting non-AMPs, given that only a handful of such sequences have been officially confirmed. [ABSTRACT FROM AUTHOR]

Antimicrobial peptides (AMPs) are a heterogeneous group of short polypeptides that target not only microorganisms but also viruses and cancer cells. Due to their lower selection for resistance compared with traditional antibiotics, AMPs have been attracting the ever-growing attention from researchers, including bioinformaticians. Machine learning represents the most cost-effective method for novel AMP discovery and consequently many computational tools for AMP prediction have been recently developed. In this article, we investigate the impact of negative data sampling on model performance and benchmarking. We generated 660 predictive models using 12 machine learning architectures, a single positive data set and 11 negative data sampling methods; the architectures and methods were defined on the basis of published AMP prediction software. Our results clearly indicate that similar training and benchmark data set, i.e. produced by the same or a similar negative data sampling method, positively affect model performance. Consequently, all the benchmark analyses that have been performed for AMP prediction models are significantly biased and, moreover, we do not know which model is the most accurate. To provide researchers with reliable information about the performance of AMP predictors, we also created a web server AMPBenchmark for fair model benchmarking. AMPBenchmark is available at http://BioGenies.info/AMPBenchmark. [ABSTRACT FROM AUTHOR]

Brown bear Ursus arctos is a permanent member of European Middle and Late Pleistocene carnivore assemblages, which shows great body size fluctuation over time. To study this subject we carried out extensive comparison of 37 cranial metric features based on 2954 measurements coming from 263 specimens. In the statistical analyses we included a new complete brown bear calvarium which was found in Bukovynka Cave in Ukraine and dated to postglacial period. The cranial material was divided into male and female sets and classified according to geographic and stratigraphic affiliation of the samples. Analyses revealed clear decrease in many skull dimensions from the Middle Pleistocene specimens through the Late Pleistocene and postglacial to the Holocene skulls. The trend is probably related with general climatic changes during this period. However, Late Pleistocene specimens from Iberian Peninsula were significantly smaller from other Late Pleistocene European skulls or even a bit younger from the Late Glacial and postglacial period for some dimensions. The deviation from the global trend could result from their isolation from other European populations. These conclusions can be drawn both for male and female skulls. The decrease in body size showed that U. arctos is dynamically evolving species. Thus, the size does not seem to be a perfect criterion in determining the biochronological age of the brown bear findings although a general decreasing trend in size with time is clearly visible. The size of brown bear is under the influence of many factors such as great sexual dimorphism, individual and population variability as well as global and local climatic conditions. [ABSTRACT FROM AUTHOR]

Organisms with limited dispersal capabilities should show phenotypic plasticity in situ to keep pace with environmental changes. Therefore, to study the influence of environmental variation on the phenotypic diversity, we chose land snails, Trochulus hispidus and T. sericeus, characterized by high population variability. We performed long-term field studies as well as laboratory and common garden experiments, which revealed that temporal environmental changes generate visible variation in shell size and shape of these snails. Many shell measurements of T. hispidus varied significantly with temperature and humidity in individual years. According to this, the first generation of T. hispidus, bred in controlled laboratory conditions, became significantly different in higher spire and narrower umbilicus from its wild parents. Interestingly, offspring produced by this generation and transplanted to wild conditions returned to the 'wild' flat and wide-umbilicated shell shape. Moreover, initially different species T. hispidus and T. sericeus transferred into common environment conditions revealed rapid and convergent shell modifications within one generation. Such morphological flexibility and high genetic variation can be evolutionarily favored, when the environment is heterogeneous in time. The impact of climate change on the shell morphometry can lead to incorrect taxonomic classification or delimitation of artificial taxa in land snails. These findings have also important implications in the context of changing climate and environment. [ABSTRACT FROM AUTHOR]

The standard genetic code (SGC) is the set of rules by which genetic information is translated into proteins, from codons, i.e. triplets of nucleotides, to amino acids. The questions about the origin and the main factor responsible for the present structure of the code are still under a hot debate. Various methodologies have been used to study the features of the code and assess the level of its potential optimality. Here, we introduced a new general approach to evaluate the quality of the genetic code structure. This methodology comes from graph theory and allows us to describe new properties of the genetic code in terms of conductance. This parameter measures the robustness of codon groups against the potential changes in translation of the protein-coding sequences generated by single nucleotide substitutions. We described the genetic code as a partition of an undirected and unweighted graph, which makes the model general and universal. Using this approach, we showed that the structure of the genetic code is a solution to the graph clustering problem. We presented and discussed the structure of the codes that are optimal according to the conductance. Despite the fact that the standard genetic code is far from being optimal according to the conductance, its structure is characterised by many codon groups reaching the minimum conductance for their size. The SGC represents most likely a local minimum in terms of errors occurring in protein-coding sequences and their translation. [ABSTRACT FROM AUTHOR]

The present phylogeographic pattern of red deer in Eurasia is not only a result of the contraction of their distribution range into glacial refugia and postglacial expansion, but probably also an effect of replacement of some red deer s.l. mtDNA lineages by others during the last 50 000 years. To better recognize this process, we analysed 501 sequences of mtDNA cytochrome b , including 194 ancient and 75 contemporary samples newly obtained for this study. The inclusion of 161 radiocarbon-dated samples enabled us to study the phylogeny in a temporal context and conduct divergence-time estimation and molecular dating. Depending on methodology, our estimate of divergence between Cervus elaphus and Cervus canadensis varied considerably (370 000 or 1.37 million years BP, respectively). The divergence times of genetic lineages and haplogroups corresponded to large environmental changes associated with stadials and interstadials of the Late Pleistocene. Due to the climatic oscillations, the distribution of C. elaphus and C. canadensis fluctuated in north–south and east–west directions. Some haplotypes dated to pre-Last Glacial Maximum periods were not detected afterwards, representing possibly extinct populations. We indicated with a high probability the presence of red deer sensu lato in south-eastern Europe and western Asia during the Last Glacial Maximum. [ABSTRACT FROM AUTHOR]

Background: It is commonly assumed that a heterotrophic ancestor of the supergroup Archaeplastida/Plantae engulfed a cyanobacterium that was transformed into a primary plastid; however, it is still unclear how nuclearencoded proteins initially were imported into the new organelle. Most proteins targeted to primary plastids carry a transit peptide and are transported post-translationally using Toc and Tic translocons. There are, however, several proteins with N-terminal signal peptides that are directed to higher plant plastids in vesicles derived from the endomembrane system (ES). The existence of these proteins inspired a hypothesis that all nuclear-encoded, plastidtargeted proteins initially carried signal peptides and were targeted to the ancestral primary plastid via the host ES. Results: We present the first phylogenetic analyses of Arabidopsis thaliana α-carbonic anhydrase (CAH1), Oryza sativa nucleotide pyrophosphatase/phosphodiesterase (NPP1), and two O. sativa α-amylases (αAmy3, αAmy7), proteins that are directed to higher plant primary plastids via the ES. We also investigated protein disulfide isomerase (RB60) from the green alga Chlamydomonas reinhardtii because of its peculiar dual post- and cotranslational targeting to both the plastid and ES. Our analyses show that these proteins all are of eukaryotic rather than cyanobacterial origin, and that their non-plastid homologs are equipped with signal peptides responsible for co-translational import into the host ES. Our results indicate that vesicular trafficking of proteins to primary plastids evolved long after the cyanobacterial endosymbiosis (possibly only in higher plants) to permit their glycosylation and/or transport to more than one cellular compartment. Conclusions: The proteins we analyzed are not relics of ES-mediated protein targeting to the ancestral primary plastid. Available data indicate that Toc- and Tic-based translocation dominated protein import into primary plastids from the beginning. Only a handful of host proteins, which already were targeted through the ES, later were adapted to reach the plastid via the vesicular trafficking. They represent a derived class of higher plant plastidtargeted proteins with an unusual evolutionary history. [ABSTRACT FROM AUTHOR]

Porphyromonas gingivalis, a major etiological agent of chronic periodontitis, acquires heme from host hemoproteins using the HmuY hemophore. The aim of this study was to develop a specific P. gingivalis marker based on a hmuY gene sequence. Subgingival samples were collected from 66 patients with chronic periodontitis and 40 healthy subjects and the entire hmuY gene was analyzed in positive samples. Phylogenetic analyses demonstrated that both the amino acid sequence of the HmuY protein and the nucleotide sequence of the hmuY gene are unique among P. gingivalis strains/isolates and show low identity to sequences found in other species (below 50 and 56%, respectively). In agreement with these findings, a set of hmuY gene-based primers and standard/real-time PCR with SYBR Green chemistry allowed us to specifically detect P. gingivalis in patients with chronic periodontitis (77.3%) and healthy subjects (20%), the latter possessing lower number of P. gingivalis cells and total bacterial cells. Isolates from healthy subjects possess the hmuY gene-based nucleotide sequence pattern occurring in W83/W50/A7436 (n = 4), 381/ATCC 33277 (n = 3) or TDC60 (n = 1) strains, whereas those from patients typically have TDC60 (n = 21), W83/W50/A7436 (n = 17) and 381/ATCC 33277 (n = 13) strains. We observed a significant correlation between periodontal index of risk of infectiousness (PIRI) and the presence/absence of P. gingivalis (regardless of the hmuY gene-based sequence pattern of the isolate identified [r = 0.43; P = 0.0002] and considering particular isolate pattern [r = 0.38; P = 0.0012]). In conclusion, we demonstrated that the hmuY gene sequence or its fragments may be used as one of the molecular markers of P. gingivalis. [ABSTRACT FROM AUTHOR]

Background: Considerable evidence supports the concept of active communication between the nervous and immune systems. One class of such communicators are the neuropeptides (NPs). Recent reports have highlighted the antimicrobial activity of neuropeptides, placing them among the integral components of innate immune defense. This study examined the action of four human neuropeptides: calcitonin gene-related peptide (CGRP), neuropeptide Y (NPY), substance P (SP) and somatostatin (SOM), which are accessible in the upper respiratory tract, against two human-specific respiratory pathogens. We studied: (i) neuropeptide-mediated direct antibacterial activity exerted against Moraxella catarrhalis and nontypeable Haemophilus influenzae, and (ii) indirect immunomodulatory role of these neuropeptides in the neutrophil-mediated phagocytosis of indicated pathogens. Results: We found that 100 micromolar concentrations of CGRP, NPY, SP, and SOM effectively permeabilized bacterial membranes and showed (except SOM) bactericidal activity against both pathogens. SOM acted only bacteriostatically. However the killing efficacy was dependent on the bactericidal assay used. The rank order of killing NP effect was: NPY ≥ CGRP > SP >> SOM and correlated with their potency to permeabilize bacterial membranes. The killing and permeabilization activity of the analyzed NPs showed significant correlation with several physicochemical properties and amino acid composition of the neuropeptides. M. catarrhalis was more sensitive to neuropeptides than nontypeable H. influenzae. The immunomodulatory bimodal effect of physiological concentrations of CGRP, NPY, and SP on the phagocytic function of human neutrophils against M. catarrhalis and H. influenzae was observed both in the ingestion (pathogen uptake) and reactive oxygen species generation stages. This effect was also dependent on the distinct type of pathogen recognition (opsonic versus nonopsonic). Conclusions: The present results indicate that neuropeptides such as CGRP, NPY, and SP can effectively participate in the direct and indirect elimination of human-specific respiratory pathogens. Because the studied NPs show both direct and indirect modulating antimicrobial potency, they seem to be important molecules involved in the innate host defense against M. catarrhalis and nontypeable H. influenzae. [ABSTRACT FROM AUTHOR]

Abstract: The Emine-Bair-Khosar Cave (EBK), situated on the northern edge of the Lower Plateau of the Chatyrdag Massif (Crimean Mountains) is rich in palaeontological material accumulated over most of the Pleistocene. mtDNA was isolated from bones of three specimens of red deer (Cervus elaphus) dated to the late Pleistocene (MIS 3). These are the first ancient DNA sequences obtained for this species. The position of the three red deer individuals on the phylogeographic tree is based on mtDNA sequences of contemporary representatives of the Cervinae inhabiting the Northern Hemisphere. The results confirm the notion that the Crimean Peninsula was the north-easternmost refugium in Europe, and that during and after the Late Pleistocene it played a major role in recolonisation and dispersal of temperate species in the whole Eurasian continent. [Copyright &y& Elsevier]

The rearrangement of 37 genes with one control region, firstly identified in Gallus gallus mitogenome, is believed to be ancestral for all Aves. However, mitogenomic sequences obtained in recent years revealed that many avian mitogenomes contain duplicated regions that were omitted in previous genomic versions. Their evolution and mechanism of duplication are still poorly understood. The order of Accipitriformes is especially interesting in this context because its representatives contain a duplicated control region in various stages of degeneration. Therefore, we applied an appropriate PCR strategy to look for duplications within the mitogenomes of the early diverged species Sagittarius serpentarius and Cathartiformes, which is a sister order to Accipitriformes. The analyses revealed the same duplicated gene order in all examined taxa and the common ancestor of these groups. The duplicated regions were subjected to gradual degeneration and homogenization during concerted evolution. The latter process occurred recently in the species of Cathartiformes as well as in the early diverged lineages of Accipitriformes, that is, Sagittarius serpentarius and Pandion haliaetus. However, in other lineages, that is, Pernis ptilorhynchus , as well as representatives of Aegypiinae, Aquilinae, and five related subfamilies of Accipitriformes (Accipitrinae, Circinae, Buteoninae, Haliaeetinae, and Milvinae), the duplications were evolving independently for at least 14–47 Myr. Different portions of control regions in Cathartiformes showed conflicting phylogenetic signals indicating that some sections of these regions were homogenized at a frequency higher than the rate of speciation, whereas others have still evolved separately. [ABSTRACT FROM AUTHOR]

Reprogramming of the standard genetic code to include non-canonical amino acids (ncAAs) opens new prospects for medicine, industry, and biotechnology. There are several methods of code engineering, which allow us for storing new genetic information in DNA sequences and producing proteins with new properties. Here, we provided a theoretical background for the optimal genetic code expansion, which may find application in the experimental design of the genetic code. We assumed that the expanded genetic code includes both canonical and non-canonical information stored in 64 classical codons. What is more, the new coding system is robust to point mutations and minimizes the possibility of reversion from the new to old information. In order to find such codes, we applied graph theory to analyze the properties of optimal codon sets. We presented the formal procedure in finding the optimal codes with various number of vacant codons that could be assigned to new amino acids. Finally, we discussed the optimal number of the newly incorporated ncAAs and also the optimal size of codon groups that can be assigned to ncAAs. [ABSTRACT FROM AUTHOR]