3′-End processing of histone pre-mRNAs in Drosophila: U7 snRNP is associated with FLASH and polyadenylation factors

3′-End cleavage of animal replication-dependent histone pre-mRNAs is controlled by the U7 snRNP. Lsm11, the largest component of the U7-specific Sm ring, interacts with FLASH, and in mammalian nuclear extracts these two proteins form a platform that recruits the CPSF73 endonuclease and other polyadenylation factors to the U7 snRNP. FLASH is limiting, and the majority of the U7 snRNP in mammalian extracts exists as a core particle consisting of the U7 snRNA and the Sm ring. Here, we purified the U7 snRNP from Drosophila nuclear extracts and characterized its composition by mass spectrometry. In contrast to the mammalian U7 snRNP, a significant fraction of the Drosophila U7 snRNP contains endogenous FLASH and at least six subunits of the polyadenylation machinery: symplekin, CPSF73, CPSF100, CPSF160, WDR33, and CstF64. The same composite U7 snRNP is recruited to histone pre-mRNA for 3′-end processing. We identified a motif in Drosophila FLASH that is essential for the recruitment of the polyadenylation complex to the U7 snRNP and analyzed the role of other factors, including SLBP and Ars2, in 3′-end processing of Drosophila histone pre-mRNAs. SLBP that binds the upstream stem–loop structure likely recruits a yet-unidentified essential component(s) to the processing machinery. In contrast, Ars2, a protein previously shown to interact with FLASH in mammalian cells, is dispensable for processing in Drosophila. Our studies also demonstrate that Drosophila symplekin and three factors involved in cleavage and polyadenylation—CPSF, CstF, and CF I_m—are present in Drosophila nuclear extracts in a stable supercomplex.     

Never ending story: a lesson in using sampling efficiency methods with ground beetles

Biological inventory is a crucial activity in life sciences field research. However, it is sometimes time-consuming and laborious to take representative samplings of communities, especially in the case of invertebrates. In this paper, we address the issue of sampling efficiency and its influence on obtained results. As a study system, we used data on epigeic carabid beetles (Carabidae) collected in 1999–2001 in the Warta River valley of western Poland. We trapped a total of 17,722 individuals belonging to 108 species. However, due to rarefaction methods, the expected number of species was estimated at 134–140, suggesting that from 26 to 32 species are missing from the material, even expressed as a huge number of collected specimens. The estimated probability that another captured individual will represent a new species (i.e. a species that was not already recorded) is 0.0010. In order to record all the species present in the study area, another 193,338 individuals need to be sampled (abundance-based approach) or another 1,871 samples need to be collected (incidence-based approach). This means that the collected material should be 10.9 times greater (or 7.9 times greater for incidence-based data) than what was actually collected in order to record all the species present in the study area. The results show that, in practice, full inventory is simply nearly impossible to achieve, and this knowledge should be included in inventory planning. Therefore, we argue that species accumulation curves and unseen species estimators need to be carefully examined and threshold probability of detecting a new species should be built into the design of inventory science. The ratio between recorded and estimated species richness and the estimated efficiency of further sampling can be easily computed with available freeware software and should be incorporated when performing biological inventories.     

Molecular diagnosis of cystic echinococcosis in humans from central Poland

The identity of the causative agent of cystic echinococcosis (CE) in humans from central Poland receiving treatment between 2000 and 2010 was determined. A total of 47 samples obtained after hepatectomy were examined and protoscoleces were identified in wet preparations in 27 cases. Using DNA extracted from the samples, two mitochondrial regions (nad1 and cox1 genes) were amplified and the nad1 fragment was sequenced. This PCR analysis confirmed the presence of Echinococcus species in 30 cases and nad1 sequence alignments showed identity with the G7 (pig) strain, Echinococcus canadensis. These data demonstrate that the pig strain of this parasite is the most frequent causative agent of human cystic echinococcosis in central Poland.     

Can Body Condition and Somatic Indices be Used to Evaluate Metal-Induced Stress in Wild Small Mammals?

Wildlife is exposed to natural (e.g., food availability and quality, parasitism) and anthropogenic stressors (e.g., habitat fragmentation, toxicants). Individual variables (e.g., age, gender) affect behaviour and physiology of animals. Together, these parameters can create both great inter-individual variations in health indicators and interpretation difficulties. We investigated the relevance of body condition and somatic indices (liver, kidneys) as indicators of health status in wood mice (Apodemus sylvaticus, n = 560) captured along a metal pollution gradient in four landscape types (30 sampling squares 500-m sided). The indices were calculated using a recently proposed standard major axis regression instead of an ordinary least square regression. After considering age and gender for the body condition index, no landscape type influence was detected in the indices. However, important index variability was observed between sampling squares; this effect was included as a random effect in linear models. After integrating all individual and environmental variables that may affect the indices, cadmium (Cd) concentrations in both the liver and kidneys were negatively related to body condition and liver indices only for individuals from highly contaminated sites. Lead in the liver was negatively related to the liver index, and Cd in kidneys was positively linked to the kidney index, potentially suggesting metal-induced stress. However, interpretation of these indices as a wildlife ecotoxicology tool should be performed with caution due to the sensitivity of potentially confounding variables (e.g., individual factors and environmental parameters).     

On-Line Optical and Morphological Studies of Silver Nanoparticles Growth Formed by Nanosecond Laser Irradiation of Silver-Exchanged Silicate Glass

Silver-exchanged silicate glass has been irradiated by 532-nm pulsed Nd:YAG laser in order to locally form metallic nanoparticles. The particular interest of this process is to locally control the silver nanoparticles (NPs) growth. Silver ions are exchanged with sodium ions near the glass surface after dumping of a silicate glass few minutes in silver and sodium nitrates molten salt. A low-energy density laser exposure (0.239 J/cm²) chosen at the ablation threshold allows to observe the kinetics of the silver NPs growth according to the increasing shots number. An on-line optical measurement is carried out after each shot to identify the most important steps during the irradiation process. According to this measurement, we have determined four steps highlighted by UV/Visible spectrophotometry and we have identified the influence of located surface plasmon resonance. Three combined material analysis methods were used to understand the glass/laser interaction mechanism: we outlined the material volume variations by profilometric method, the element distribution by scanning electron microscopy and finally the structural distribution of the irradiated region by a local infrared investigation. The trend for NPs formation revealed by the UV/Visible spectrophotometry is thus explained by the formation of a ring expelled from a central hole. We highlight that the on-line extinction measurement can be used to data process the NPs evolution.     

Factors Associated with Post-Seasonal Serological Titer and Risk Factors for Infection with the Pandemic A/H1N1 Virus in the French General Population

The CoPanFlu-France cohort of households was set up in 2009 to study the risk factors for infection by the pandemic influenza virus (H1N1pdm) in the French general population. The authors developed an integrative data-driven approach to identify individual, collective and environmental factors associated with the post-seasonal serological H1N1pdm geometric mean titer, and derived a nested case-control analysis to identify risk factors for infection during the first season. This analysis included 1377 subjects (601 households). The GMT for the general population was 47.1 (95% confidence interval (CI): 45.1, 49.2). According to a multivariable analysis, pandemic vaccination, seasonal vaccination in 2009, recent history of influenza-like illness, asthma, chronic obstructive pulmonary disease, social contacts at school and use of public transports by the local population were associated with a higher GMT, whereas history of smoking was associated with a lower GMT. Additionally, young age at inclusion and risk perception of exposure to the virus at work were identified as possible risk factors, whereas presence of an air humidifier in the living room was a possible protective factor. These findings will be interpreted in light of the longitudinal analyses of this ongoing cohort.     

Patterns of sclerobiont colonization on the rugose coral Schlotheimophyllum patellatum (Schlotheim, 1820) from the Silurian of Gotland,Sweden

Analysis of mushroom-shaped rugose corals Schlotheimophyllum patellatum (Schlotheim, 1820) from the Silurian (Upper Visby Beds, Lower Wenlock, Sheinwoodian) of Gotland, Sweden, showed that they were colonized on both the upper (exposed) and lower (cryptic) sides by a variety of encrusting and boring (sclerobiont) biotas, represented by 10 taxa and at least 23 species. Bryozoans and microconchid tubeworms, the most abundant encrusters, dominated on the cryptic undersides of the corals, while the dominant endobionts responsible for Trypanites borings overwhelmingly dominated the exposed surfaces. Except for cnidarian sphenothallids, which were exclusive colonizers of the underside of only one coral host, no other encrusters could be referred to as obligate cryptobionts. Because the upper surface of these corals was likely covered by soft-tissues during life, in specimens lifted off the sea-floor sclerobionts must have settled on the cryptic sides first. They could colonize the upper side only after the coral’s death, unless it was covered by sediment as could be the case in some flat specimens. With time, the space on the underside of the coral skeleton may have progressively been filled by sediment as well, precluding further colonization by sclerobionts. In that respect, the colonization patterns of these corals by encrusters and borers were controlled by the complex interplay of environmental factors, sclerobiont dynamics and coral growth in a given Silurian habitat. Compared with Silurian stromatoporoid hosts, the sclerobiont diversity and abundance noted on the Schlotheimophyllum corals may be regarded as representative for the Silurian as a whole.     

Schisandra henryi C. B. Clarke in vitro cultures: a promising tool for the production of lignans and phenolic compounds

Plant Cell, Tissue and Organ Culture (PCTOC) - We initiated and optimized in vitro culture conditions of the endemic Chinese plant species—Schisandra henryi C. B. Clarke. Different types of...     

Light at Night Co‐distributes with Incident Breast but not Lung Cancer in the Female Population of Israel

Recent studies of shift‐working women have reported that excessive exposure to light at night (LAN) may be a risk factor for breast cancer. However, no studies have yet attempted to examine the co‐distribution of LAN and breast cancer incidence on a population level with the goal to assess the coherence of these earlier findings with population trends. Coherence is one of Hill's “criteria” (actually, viewpoints) for an inference of causality. Nighttime satellite images were used to estimate LAN levels in 147 communities in Israel. Multiple regression analysis was performed to investigate the association between LAN and breast cancer incidence rates and, as a test of the specificity of our method, lung cancer incidence rates in women across localities under the prediction of a link with breast cancer but not lung cancer. After adjusting for several variables available on a population level, such as ethnic makeup, birth rate, population density, and local income level, a strong positive association between LAN intensity and breast cancer rate was revealed (p<0.05), and this association strengthened (p<0.01) when only statistically significant factors were filtered out by stepwise regression analysis. Concurrently, no association was found between LAN intensity and lung cancer rate. These results provide coherence of the previously reported case‐control and cohort studies with the co‐distribution of LAN and breast cancer on a population basis. The analysis yielded an estimated 73% higher breast cancer incidence in the highest LAN exposed communities compared to the lowest LAN exposed communities.