Human RIF1 and protein phosphatase 1 stimulate DNA replication origin licensing but suppress origin activation

The human RIF1 protein controls DNA replication, but the molecular mechanism is largely unknown. Here, we demonstrate that human RIF1 negatively regulates DNA replication by forming a complex with protein phosphatase 1 (PP1) that limits phosphorylation‐mediated activation of the MCM replicative helicase. We identify specific residues on four MCM helicase subunits that show hyperphosphorylation upon RIF1 depletion, with the regulatory N‐terminal domain of MCM4 being particularly strongly affected. In addition to this role in limiting origin activation, we discover an unexpected new role for human RIF1‐PP1 in mediating efficient origin licensing. Specifically, during the G1 phase of the cell cycle, RIF1‐PP1 protects the origin‐binding ORC1 protein from untimely phosphorylation and consequent degradation by the proteasome. Depletion of RIF1 or inhibition of PP1 destabilizes ORC1, thereby reducing origin licensing. Consistent with reduced origin licensing, RIF1‐depleted cells exhibit increased spacing between active origins. Human RIF1 therefore acts as a PP1‐targeting subunit that regulates DNA replication positively by stimulating the origin licensing step, and then negatively by counteracting replication origin activation.     

Faecal pellet group counting as a promising method of wild boar population density estimation

The wild boar is a native animal species of the Czech Republic that has significantly increased its population density in recent years. Objective methods of population density estimation are required to inform the intensity of regulation needed for the sustainable management of the wild boar. Population estimation and regulation of the abundance of the wild boar are problematic in comparison to those of other ungulates, and the only widely used method of control is intensive hunting. The purpose of this study was to test if faecal pellet group (FPG) counting was a reliable method of wild boar population censusing in a forest environment. The density of wild boars was evaluated in an area of 22.56 km², circumscribed by both natural and man-made barriers that restrict wild boar migration. As it is essential for proper application of FPG count methods, a separate trial was carried out to determine the daily defecation rate of wild boars. The distribution of faeces in different types of habitat in a forest environment was tested. As the period of faeces accumulation fell within the intensive hunting season, the result is biased by the fact that the calculation includes FPGs produced by animals removed from the population through hunting during winter. The average daily defecation rate of adults and piglets was 4.29 and 5.82, respectively. The corrected (without shot animals) average density of wild boars in the study area estimated by the FPG count at the time of the census was 6.08 individuals (ind.)/km². We have confirmed that an FPG count conducted in winter is applicable for estimation of wild boar abundance on a forested area.     

Intracellular trafficking and subcellular distribution of a large array of HPMA copolymers

The basic physicochemical properties that determine the distribution and fate of synthetic macromolecules in living cells were characterized using fluorescently labeled HPMA (N-(2-hydroxypropyl)methacrylamide) copolymers. Twelve different classes of water-soluble copolymers were created by incorporating eight different functionalized comonomers. These comonomers possessed functional groups with positive or negative charges or contained short hydrophobic peptides. The copolymers were fractionated to create parallel "ladders" consisting of 10 fractions of narrow polydispersity with molecular weights ranging from 10 to 200 kDa. The intracellular distributions were characterized for copolymer solutions microinjected into the cytoplasm of cultured ovarian carcinoma cells. Even the highest molecular weight HPMA copolymers were shown to quickly and evenly diffuse throughout the cytoplasm and remain excluded from membrane-bound organelles, regardless of composition. The exceptions were the strongly cationic copolymers, which demonstrated a pronounced localization to microtubules. For all copolymers, nuclear entry was consistent with passive transport through the nuclear pore complex (NPC). Nuclear uptake was shown to be largely dictated by the molecular weight of the copolymers, however, detailed kinetic analyses showed that nuclear import rates were moderately, but significantly, affected by differences in comonomer composition. HPMA copolymers containing amide-terminated phenylalanine-glycine (FG) sequences, analogous to those found in the NPC channel protein, demonstrated a potential to regulate import to the nuclear compartment. Kinetic analyses showed that 15 kDa copolymers containing GGFG, but not those containing GGLFG, peptide pendant groups altered the size-exclusion characteristics of NPC-mediated nuclear import.     

Ants accelerate succession from mountain grassland towards spruce forest

Question: What is the role of mound‐building ants (Lasius flavus) in successional changes of a grassland ecosystem towards a spruce forest? Location: Slovenské Rudohorie Mountains, Slovakia; ca. 950 m a.s.l. near the Obrubovanec point (1020 m a.s.l.; 48°41′N, 19°39′E). Methods: Both chronosequence data along a successional gradient and temporal data from long‐term permanent plots were collected on ants, spruce establishment, and vegetation structure, together with additional data on spruce growth. Results: There are more spruce seedlings on ant mounds (4.72 m^?2) than in the surrounding vegetation (0.81 m^?2). Spruce seedlings grow faster on these mounds compared to surrounding areas. The first colonization wave of seedlings was rapid and probably occurred when grazing prevailed over mowing. Ant colony presence, mound volume, and plant species composition change along the successional gradient. Mounds become bigger when partly shaded but shrink in closed forest, when ant colonies disappear. Shade‐tolerant acidophylic species replace grassland plants both on the mounds and in surrounding areas. Conclusions: The massive occurrence of Lasius flavus anthills contributes to a runaway feedback process that accelerates succession towards forest. The effect of ants as ecosystem engineers is scale‐dependent: although they stabilize the system at the scale of an individual mound, they may destabilize the whole grassland system over a longer time scale if combined with changes in mowing regime.     

The decline of Afro‐Palaearctic migrants and an assessment of potential causes

There is compelling evidence that Afro‐Palaearctic (A‐P) migrant bird populations have declined in Europe in recent decades, often to a greater degree than resident or short‐distance migrants. There appear to have been two phases of decline. The first in the 1960s–1970s, and in some cases into the early 1980s, largely affected species wintering predominantly in the arid Sahelian zone, and the second since the 1980s has mostly affected species wintering in the humid tropics and Guinea forest zone. Potential drivers of these declines are diverse and are spread across and interact within the migratory cycle. Our knowledge of declining species is generally better for the breeding than the non‐breeding parts of their life cycles, but there are significant gaps in both for many species. On the breeding grounds, degradation of breeding habitats is the factor affecting the demography of the largest number of species, particularly within agricultural systems and woodland and forests. In the non‐breeding areas, the interacting factors of anthropogenic habitat degradation and climatic conditions, particularly drought in the Sahel zone, appear to be the most important factors. Based on our synthesis of existing information, we suggest four priorities for further research: (1) use of new and emerging tracking technologies to identify migratory pathways and strategies, understand migratory connectivity and enable field research to be targeted more effectively; (2) undertake detailed field studies in sub‐Saharan Africa and at staging sites, where we understand little about distribution patterns, habitat use and foraging ecology; (3) make better use of the wealth of data from the European breeding grounds to explore spatial and temporal patterns in demographic parameters and relate these to migratory pathways and large‐scale patterns of habitat change and climatic factors; and (4) make better use of remote sensing to improve our understanding of how and where land cover is changing across these extensive areas and how this impacts A‐P migrants. This research needs to inform and underpin a flyway approach to conservation, evaluating a suite of drivers across the migratory cycle and combining this with an understanding of land management practices that integrate the needs of birds and people in these areas.     

Multiplex PCR for detection of three exfoliative toxin serotype genes inStaphylococcus aureus

Rapid and specific detection of exfoliative toxin (ET)-producing Staphylococcus aureus strains by multiplex polymerase chain reaction (PCR) was used for identification of exfoliative toxin genes in a diverse set of 115 clinical S. aureus strains isolated in 14 Czech cities between 1998 and 2004. Fifty-nine wild-type ET-positive isolates of which 40 strains were the causative agents of toxic epidermolysis in neonates were classified into 4 PCR types. The genes coding for ETA, ETB or ETD were not detected in any of non-ET-producing isolates. The PCR method using the multiplex and specific primer set was shown to be reliable in rapid identification of the exfoliative toxin producing S. aureus and can be used as a convenient tool for hospital epidermolytic infection control.     

Synthesis of α-carboxyphosphinopeptides derived from norleucine

In the present study, we describe in detail the synthesis of a relatively rare class of phosphorus compounds, α-carboxyphosphinopeptides. We prepared several norleucine-derived α-carboxyphosphinic pseudopeptides of the general formula Nle-Ψ[PO(OH)]-Gly. These compounds could have important applications as transition state-mimicking inhibitors for methionine or leucine aminopeptidases or other enzymes. For the preparation of the key α-carboxyphosphinate protected precursors, we investigated, compared and improved two different synthetic methods described in literature: the Arbuzov reaction of a silylated N-protected phosphinic acid with a bromoacetate ester and the nucleophilic addition of a mixed O-methyl S-phenyl N-protected phosphonic acid or a methyl N-protected phosphonochloridate with tert-butyl lithioacetate. We also prepared two N-Fmoc protected synthons, Fmoc-Nle-Ψ[PO(OH)]-Gly-COOH and Fmoc-Nle-Ψ[PO(OAd)]-Gly-COOH, and demonstrated that these precursors are suitable building blocks for the solid-phase synthesis of α-carboxyphosphinopeptides.     

Identifying hybridizing taxa within the <Emphasis Type="Italic">Daphnia longispina</Emphasis> species complex: a comparison of genetic methods and phenotypic approaches

Daphnia galeata Sars, D. longispina O. F. Müller and D. cucullata Sars (Crustacea: Cladocera) are closely related species which often produce interspecific hybrids in natural populations. Several marker systems are available for taxon determination in this hybridizing complex, but their performance and reliability has not been systematically assessed. We compared results from identifications by three molecular methods. More than 1,200 individuals from 10 localities in the Czech Republic were identified as parental species or hybrids by allozyme electrophoresis and the analysis of the restriction fragment length polymorphism of the internal transcribed spacer (ITS-RFLP); over 440 of them were additionally analyzed and identified by 12 microsatellite loci. Identification by microsatellite markers corresponded well with allozyme analyses. However, consistent discrepancies between ITS-RFLP and other markers were observed in two out of 10 studied localities. Although some marker discrepancies may have been caused by occasional recent introgression, consistent deviations between ITS-RFLP and other markers suggest a long-term maintenance of introgressed alleles. These results warn against its use as a sole identification method in field studies. Additionally, we quantitatively evaluated the discriminatory power of geometric morphometric (elliptic Fourier) analysis of body shapes based on photos of over 1,300 individuals pre-classified by allozyme markers. Furthermore, a randomly selected subset of 240 individuals was independently determined from photos by several experts. Despite a tendency for morphological divergence among parental Daphnia species, some taxa (especially D. galeata, D. longispina, and their hybrids) substantially overlapped in their body shapes. This was reflected in different determination success for particular species and hybrids in discriminant analysis based on shape data as well as from photographs.     

Mycobacteria in the light of modern genetics development

It is generally assumed that genetic research of mycobacteria is delayed as compared with other, more commonly used, bacterial models, particularly in the field of genetic transfers. In the field of mutagenesis the problems have been studied to such an extent that replication maps of the chromosome of M. phlei and M. tuberculosis H37 Rv have already been constructed and a new model of the cell cycle of bacteria exhibiting a slow growth rate has been worked out. When the problems of mycobacterial genetics are looked upon in the light of gene manipulations it may be concluded that mycobacteria belong to a few models whose genes are used for cloning and that problems of practical significance will be studied by means of the most modern approaches.