Phylogeny and evolution of Rab7 and Rab9 proteins

<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>Phylogenetic reconstructions of Rab7 and Rab9 proteins were performed by a variety of methods. These Rab GTPases show diversification both at the phylogenetic, expression and structural levels. The presence of many Rab7 and Rab9 isoforms suggests their functional specialization and complexity of subcellular trafficking even in unicellular eukaryotes. The identified less conserved regions in analysed Rab sequences may directly contribute to such a differentiation.</p

The Polemic over Realism, 1945–1948

The polemic over understanding realism and its usefulness in literature was given birth in the early post-war years out of the need to refer to the rich tradition of Great Realism. This was to be a remedy to the problems with the literary presentation of current events and recent history, especially the war years and occupation as well as helping in ‘balancing the ledger’ in the Polish interbellum. The interest in realism swiftly reached beyond literature itself, while the polemic also moved onto the canvas of paining and the plastic arts. In the context of the polemic over realism there evolved also other disputes in the period 1945–1948 such as the discussion on the work Lalka. The subject of polemic under discussion in the present study ebbed and flowed over the columns above all the publications Kuźnica and Odrodzenie, but also Twórczość and Tygodnik Powszechny. Taking part in this exchange of viewpoints was a broad community of literary critics representing a greatly varied kaleidoscope of esthetics and beliefs. Among those clinking swords were Jan Kott, Kazimierz Wyka, Adam Ważyk, Stefan Żółkiewski, Artur Sandauer, Stefan Kisielewski and Melania Kierczyńska.Praca powstała w ramach projektu badawczego NPRH nr 11H 16 0131 84

The Polemic over Realism, 1945–1948

The polemic over understanding realism and its usefulness in literature was given birth in the early post-war years out of the need to refer to the rich tradition of Great Realism. This was to be a remedy to the problems with the literary presentation of current events and recent history, especially the war years and occupation as well as helping in ‘balancing the ledger’ in the Polish interbellum. The interest in realism swiftly reached beyond literature itself, while the polemic also moved onto the canvas of paining and the plastic arts. In the context of the polemic over realism there evolved also other disputes in the period 1945–1948 such as the discussion on the work Lalka. The subject of polemic under discussion in the present study ebbed and flowed over the columns above all the publications Kuźnica and Odrodzenie, but also Twórczość and Tygodnik Powszechny. Taking part in this exchange of viewpoints was a broad community of literary critics representing a greatly varied kaleidoscope of esthetics and beliefs. Among those clinking swords were Jan Kott, Kazimierz Wyka, Adam Ważyk, Stefan Żółkiewski, Artur Sandauer, Stefan Kisielewski and Melania Kierczyńska.Praca powstała w ramach projektu badawczego NPRH nr 11H 16 0131 84

The Polemic over Realism, 1945–1948

The polemic over understanding realism and its usefulness in literature was given birth in the early post-war years out of the need to refer to the rich tradition of Great Realism. This was to be a remedy to the problems with the literary presentation of current events and recent history, especially the war years and occupation as well as helping in ‘balancing the ledger’ in the Polish interbellum. The interest in realism swiftly reached beyond literature itself, while the polemic also moved onto the canvas of paining and the plastic arts. In the context of the polemic over realism there evolved also other disputes in the period 1945–1948 such as the discussion on the work Lalka. The subject of polemic under discussion in the present study ebbed and flowed over the columns above all the publications Kuźnica and Odrodzenie, but also Twórczość and Tygodnik Powszechny. Taking part in this exchange of viewpoints was a broad community of literary critics representing a greatly varied kaleidoscope of esthetics and beliefs. Among those clinking swords were Jan Kott, Kazimierz Wyka, Adam Ważyk, Stefan Żółkiewski, Artur Sandauer, Stefan Kisielewski and Melania Kierczyńska.Praca powstała w ramach projektu badawczego NPRH nr 11H 16 0131 84

The unique settlement microregion of the Lusatian Urnfield culture in Łazy (SW Poland): fieldwalking and geophysical survey results

Cremated cemetery and three settlement sites were surveyed. Magnetics and electrical resistivity provided a suggestive location for the cemetery. Magnetic prospection of the surrounding settlements provided a less clear picture. Surface material indicated the presence of previously unregistered episodes of settlement

Wyłączenia gruntów rolnych z produkcji rolnej a dochody gmin z podatku od nieruchomości

The paper addresses the problem of the elimination of agricultural production only from fragments of lots on which building investments are made. The cost of turning farmland to non-agricultural uses and the difference in the rates of the agricultural tax and the property tax are very often the reasons why the elimination involves only a fragment of a lot, while the remaining part is formally still in agricultural use, even though the owner usually does not conduct any farming activity on it. This situation has serious consequences for commune budgets, and it also makes it very hard to establish the actual area of land in agricultural use. The research has shown that in the case of the Bytkowo district located in Rokietnica commune, nearly one-third of the total area of built-up building lots still figures in the Land and Buildings Register as farmland, and is subject to taxation with the agricultural tax. In 2015 the property tax rate for land in Rokietnica commune is 0.47 zlotys/m2, while the agricultural tax is 255,00 zlotys/ha, or 0.0255 zlotys/m2. As a result of taxing this land with the agricultural tax, the income of the commune will be markedly lower than if the property tax were paid. In the Bytkowo district, where 17,225 m2 of built-up building lots are classified as agricultural land, in 2015 this difference will amount to 7,656.51 zlotys. The difference in those taxes, and thus the loss to the commune budget, can be illustrated even more pointedly on the example of a single lot. In the case of a building lot 865 m2 in area, of which 479 m2 are classified in the Land and Buildings Register as B (residential land), while the remaining 386 m2 are R IIIb (arable land), its owner is going to save 171.57 zlotys yearly by paying the agricultural tax instead of the property tax, thus depriving the income of the commune of this sum. In conclusion, one can state that the rules for taking farmland out of agricultural production have led not only to irrational farmland management, but have also opened up the possibility of paying a low agricultural tax on land that in fact is not used for agricultural purposes.W artykule poruszono problem wyłączenia z produkcji rolnej fragmentów działek ewidencyjnych, na których realizowane są inwestycje budowlane. Koszt wyłączenia gruntu z produkcji rolnej oraz różnica wysokości stawek podatku rolnego i podatku od nieruchomości powoduje, że bardzo często wyłączenie dotyczy jedynie części działki, natomiast pozostały fragment formalnie nadal jest terenem użytkowanym rolniczo, mimo że właściciel najczęściej nie prowadzi na nim działalności rolnej. Taki stan rzeczy ma istotne konsekwencje dla budżetów gmin. Ponadto utrudnia on znacznie ustalenie faktycznej powierzchni gruntów użytkowanych rolniczo. Badania wykazały, że w przypadku położonego w gminie Rokietnica obrębu ewidencyjnego Bytkowo blisko 1/3 łącznej powierzchni zabudowanych działek budowlanych w Ewidencji Gruntów i Budynków jest nadal użytkami rolnymi i podlega opodatkowaniu podatkiem rolnym

A new parrot taxon from the Yucatán Peninsula, Mexico—its position within genus Amazona based on morphology and molecular phylogeny

Parrots (Psittaciformes) are a diverse group of birds which need urgent protection. However, many taxa from this order have an unresolved status, which makes their conservation difficult. One species-rich parrot genus is Amazona, which is widely distributed in the New World. Here we describe a new Amazona form, which is endemic to the Yucatán Peninsula. This parrot is clearly separable from other Amazona species in eleven morphometric characters as well as call and behavior. The clear differences in these features imply that the parrot most likely represents a new species. In contrast to this, the phylogenetic tree based on mitochondrial markers shows that this parrot groups with strong support within A. albifrons from Central America, which would suggest that it is a subspecies of A. albifrons. However, taken together tree topology tests and morphometric analyses, we can conclude that the new parrot represents a recently evolving species, whose taxonomic status should be further confirmed. This lineage diverged from its closest relative about 120,000 years ago and was subjected to accelerated morphological and behavioral changes like some other representatives of the genus Amazona. Our phylogenies, which are so far the most comprehensive for Amazona taxa enabled us to consider the most feasible scenarios about parrot colonization of the Greater and Lesser Antilles and Central America from South America mainland. The molecular dating of these migrations and diversification rate were correlated with climatic and geological events in the last five million years, giving an interesting insight into Amazon parrot phylogeography and their evolution in general

Ultrastructural and morphohistochemical study of the influence of benzalkonium chloride on human corneal limbal epithelial cells in vitro

Within the corneal limbal epithelium there exist limbal stem cells (LSC) which under suitable conditions can regenerate their population or differentiate into corneal epithelial cells. However, upon limbal damage, the cells differentiate irreversibly and do not self-renew. One of the causes of the damage of progenitor cells and their niche is a long-term use of eye drops containing preservatives. While the side effects are related to the antimicrobial activity of such eye drops, damage to cellular and cytoplasmic membranes as well as enzymatic reactions can concurrently cause disorders of normal ocular surface tissue. The aim of this study was to evaluate the toxic effects of the preservative used in eye drops – benzalkonium chloride (BAK) – on human corneal limbal epithelial cells in vitro, and to define the mechanisms of acute limbal cell damage caused by the action of BAK. Ten corneoscleras rims, which were not qualified for transplantation by the Eye Tissue Bank, were obtained from 5 deceased donors aged 39 to 43 years. The tissue fragments (explants) containing corneal limbal epithelial cells were immediately after the explantation subjected to the action of the experimental substance being benzalkonium chloride (BAK) in concentrations of 0.005% and 0.01%. The qualitative analysis of microscopic images of the corneal limbus specimens was performed on tissue sections stained with hematoxylin and eosin using the immunohistochemical method for vimentin and with the use of a transmission electron microscope. The structure of the area of corneal limbus, as well as the morphological characteristics and the ultrastructure of the very limbal cells were evaluated with careful attention to the basal epithelial cells of the limbus. The BAK-treated groups of explants in sections stained by H & E featured characteristics of severe structural disorders of the corneal limbus area. Depletion of the epithelial cells was visible and involved both superficial and deep layers. Immunohistochemical staining for vimentin did not show the expression of this protein. This might have been connected with the damage to the cytoskeleton of limbal epithelial cells and large depletion of cells reaching down to the basement membrane. The images obtained with electron microscopy demonstrate serious defects of cell ultrastructure and, indirectly, abnormal cellular metabolism, including water and electrolyte balance and energy metabolism.This experiment confirmed the significant adverse effect of benzalkonium chloride on the limbal epithelial cells and the possibility of their damage

The quality of life of farmers with chronic obstructive pulmonary disease (COPD)

Introduction and objective COPD is a medical state characterized by chronically poor airflow, and typically worsens over time. Farmers have an increased risk of COPD because of being exposed to ammonia, hydrogen sulfide, inorganic dust, and organic dust. The quality of life of the ill depends on biomedical as well as psychosocial factors, the impact of which has not been a frequent subject of studies among COPD patients. The aim of the study was to indicate the factors that have negative and positive influence on the quality of life of farmers suffering from COPD. Material and Methods The study was conducted among 84 farmers treated for COPD in the Department of Pneumology, Oncology and Allergology of the Medical University in Lublin, Poland. The differences between the farmers concerned: severity of the disease, level of education and income, frequency of smoking tobacco and drinking alcohol, kinds of support they receive from their families, and the level of depression and anxiety experienced by the patients. Results The study revealed that most patients suffered from depressive and anxiety disorders, and the level of depression higher among the patients who smoked more. Lack of family support had significant influence on exacerbation of the patient’s depressive and anxiety symptoms. Patients who had recently experienced a critical situation presented with more severe COPD symptoms, lower quality of life and a higher level of depression. Higher income of the patients had positive influence on their quality of life. Farmers addicted to alcohol suffered from a higher level of anxiety

The quality of life of farmers with chronic obstructive pulmonary disease (COPD)

Introduction and objective COPD is a medical state characterized by chronically poor airflow, and typically worsens over time. Farmers have an increased risk of COPD because of being exposed to ammonia, hydrogen sulfide, inorganic dust, and organic dust. The quality of life of the ill depends on biomedical as well as psychosocial factors, the impact of which has not been a frequent subject of studies among COPD patients. The aim of the study was to indicate the factors that have negative and positive influence on the quality of life of farmers suffering from COPD. Material and Methods The study was conducted among 84 farmers treated for COPD in the Department of Pneumology, Oncology and Allergology of the Medical University in Lublin, Poland. The differences between the farmers concerned: severity of the disease, level of education and income, frequency of smoking tobacco and drinking alcohol, kinds of support they receive from their families, and the level of depression and anxiety experienced by the patients. Results The study revealed that most patients suffered from depressive and anxiety disorders, and the level of depression higher among the patients who smoked more. Lack of family support had significant influence on exacerbation of the patient’s depressive and anxiety symptoms. Patients who had recently experienced a critical situation presented with more severe COPD symptoms, lower quality of life and a higher level of depression. Higher income of the patients had positive influence on their quality of life. Farmers addicted to alcohol suffered from a higher level of anxiety