Induction of linear tracks of DNA double-strand breaks by alpha-particle irradiation of cells

Understanding how cells maintain genome integrity when challenged with DNA double-strand breaks (DSBs) is of major importance, particularly since the discovery of multiple links of DSBs with genome instability and cancer-predisposition disorders. Ionizing radiation is the agent of choice to produce DSBs in cells; however, targeting DSBs and monitoring changes in their position over time can be difficult. Here we describe a procedure for induction of easily recognizable linear arrays of DSBs in nuclei of adherent eukaryotic cells by exposing the cells to alpha particles from a small Americium source (Box 1). Each alpha particle traversing the cell nucleus induces a linear array of DSBs, typically 10-20 DSBs per 10 mum track length. Because alpha particles cannot penetrate cell-culture plastic or coverslips, it is necessary to irradiate cells through a Mylar membrane. We describe setup and irradiation procedures for two types of experiments: immunodetection of DSB response proteins in fixed cells grown in Mylar-bottom culture dishes (Option A) and detection of fluorescently labeled DSB-response proteins in living cells irradiated through a Mylar membrane placed on top of the cells (Option B). Using immunodetection, recruitment of repair proteins to individual DSB sites as early as 30 s after irradiation can be detected. Furthermore, combined with fluorescence live-cell microscopy of fluorescently tagged DSB-response proteins, this technique allows spatiotemporal analysis of the DSB repair response in living cells. Although the procedures might seem a bit intimidating, in our experience, once the source and the setup are ready, it is easy to obtain results. Because the live-cell procedure requires more hands-on experience, we recommend starting with the fixed-cell application.     

Factors affecting Common Quail’s Coturnix coturnix occurrence in farmland of Poland: is agriculture intensity important?

Over the last four decades, the majority of European farmland birds have shown marked population declines attributed to the intensification of agriculture. The Common Quail is a widespread farmland breeder across most of Europe. Its populations have shown marked decline, particularly pronounced at the end of the previous century. Ongoing agriculture intensification may be the factor responsible for the observed declines; however, links between species occurrence and farming intensification have not been addressed so far. We analyzed factors affecting the occurrence of the Quail in Poland using data from 722 1 × 1-km study plots and a set of 22 environmental variables, including proxies for agriculture intensification. Predictors were aggregated using PCAs and related to species presence/absence data using GAMs. The best-supported model of the species’ occurrence included eight variables and was clearly better (AIC weight = 0.54) than other models. Quails preferred open fields, showing high photosynthetic activity in March or June, with rather low precipitation and often at relatively high altitudes (up to 900 m a.s.l.). Importantly, quails were more frequent on plots located in regions with rather high inorganic fertilizer input, and showed no avoidance of areas with a high level of agriculture mechanization. We postulate that singing male quails are attracted to areas with medium or high intensity of agriculture but it may represent a maladaptive habitat choice enhanced by changing agriculture practices and peculiarities of the quail’s breeding strategy. Given the results, the quail cannot be classified as a good indicator of extensive traditional agriculture.     

Body mass patterns of Little Stints at different latitudes during incubation and chick-rearing

Due to the ‘double‐clutch’ mating system found in the arctic‐breeding Little Stint Calidris minuta, each parent cares for a clutch and brood alone. The resulting constraint on feeding time, combined with the cold climate and a small body size, may cause energetic bottlenecks. Based on the notion that mass stores in birds serve as an ‘insurance’ for transient periods of negative energy balance, but entail certain costs as well, body mass may vary in relation to climatic conditions and stage of the breeding cycle. We studied body mass in Little Stints in relation to breeding stage and geographical location, during 17 expeditions to 12 sites in the Eurasian Arctic, ranging from north Norway to north‐east Taimyr. Body mass was higher during incubation than during chick‐rearing. Structural size, as estimated by wing length, increased with latitude. This was probably caused by relatively more females (the larger sex) incubating further north, possibly after leaving a first clutch to be incubated by a male further south. Before and after correction for structural size, body mass was strongly related to latitude during both incubation and chick‐rearing. In analogy to a similar geographical pattern in overwintering shorebirds, we interpret the large energy stores of breeding Little Stints as an insurance against periods of cold weather which are a regular feature of arctic summers. Climate data showed that the risk of encountering cold spells lasting several days increases with latitude over the species’ breeding range, and is larger in June than in July. Maintaining these stores is therefore less necessary at southern sites and during the chick‐rearing period than in the incubation period. When guarding chicks, feeding time is less constrained than during incubation, temperatures tend to be higher than in the incubation period, reducing energy expenditure, and the availability of insect prey reaches a seasonal maximum. However, the alternative interpretation that the chick‐tending period is more energetically stressful than the incubation period, resulting in a negative energy balance for the parent, could not be rejected on the present evidence.     

New species in the Old World: Europe as a frontier in biodiversity exploration, a test bed for 21st century taxonomy

The number of described species on the planet is about 1.9 million, with ca. 17,000 new species described annually, mostly from the tropics. However, taxonomy is usually described as a science in crisis, lacking manpower and funding, a politically acknowledged problem known as the Taxonomic Impediment. Using data from the Fauna Europaea database and the Zoological Record, we show that contrary to general belief, developed and heavily-studied parts of the world are important reservoirs of unknown species. In Europe, new species of multicellular terrestrial and freshwater animals are being discovered and named at an unprecedented rate: since the 1950s, more than 770 new species are on average described each year from Europe, which add to the 125,000 terrestrial and freshwater multicellular species already known in this region. There is no sign of having reached a plateau that would allow for the assessment of the magnitude of European biodiversity. More remarkably, over 60% of these new species are described by non-professional taxonomists. Amateurs are recognized as an essential part of the workforce in ecology and astronomy, but the magnitude of non-professional taxonomist contributions to alpha-taxonomy has not been fully realized until now. Our results stress the importance of developing a system that better supports and guides this formidable workforce, as we seek to overcome the Taxonomic Impediment and speed up the process of describing the planetary biodiversity before it is too late.     

Transmembrane helix 11 is a genuine regulator of the endoplasmic reticulum Ca2+ pump and acts as a functional parallel of β-subunit on α-Na+,K+-ATPase

The housekeeping sarco(endo)plasmic reticulum Ca(2+) ATPase SERCA2b transports Ca(2+) across the endoplasmic reticulum membrane maintaining a vital Ca(2+) gradient. Compared with the muscle-specific isoforms SERCA2a and SERCA1a, SERCA2b houses an 11th transmembrane segment (TM11) and a short luminal extension (LE) at its C terminus (2b-tail). The 2b-tail imposes a 2-fold higher apparent Ca(2+) affinity and lower V(max). Previously, we assumed that LE is the sole functional region of the 2b-tail and that TM11 is a passive element providing an additional membrane passage. However, here we show that peptides corresponding to the TM11 region specifically modulate the activity of the homologous SERCA1a in co-reconstituted proteoliposomes and mimic the 2b-tail effect (i.e. lower V(max) and higher Ca(2+) affinity). Using truncated 2b-tail variants we document that TM11 regulates SERCA1a independently from LE, confirming that TM11 is a second, previously unrecognized functional region of the 2b-tail. A phylogenetic analysis further indicates that TM11 is the oldest and most conserved feature of the 2b-tail, found in the SERCA pump of all Bilateria, whereas LE is only present in Nematoda and vertebrates. Considering remarkable similarities with the Na(+),K(+)-ATPase α-β interaction, we now propose a model for interaction of TM11 with TM7 and TM10 in the anchoring subdomain of the Ca(2+) pump. This model involves a TM11-induced helix bending of TM7. In conclusion, more than just a passive structural feature, TM11 acts as a genuine regulator of Ca(2+) transport through interaction with the pump.     

Sarco(endo)plasmic Reticulum Calcium ATPase (SERCA) Inhibition by Sarcolipin Is Encoded in Its Luminal Tail

The sarco(endo)plasmic reticulum calcium ATPase (SERCA) is regulated in a tissue-dependent manner via interaction with the short integral membrane proteins phospholamban (PLN) and sarcolipin (SLN). Although defects in SERCA activity are known to cause heart failure, the regulatory mechanisms imposed by PLN and SLN could have clinical implications for both heart and skeletal muscle diseases. PLN and SLN have significant sequence homology in their transmembrane regions, suggesting a similar mode of binding to SERCA. However, unlike PLN, SLN has a conserved C-terminal luminal tail composed of five amino acids (²⁷RSYQY), which may contribute to a distinct SERCA regulatory mechanism. We have functionally characterized alanine mutants of the C-terminal tail of SLN using co-reconstituted proteoliposomes of SERCA and SLN. We found that Arg²⁷ and Tyr³¹ are essential for SLN function. We also tested the effect of a truncated variant of SLN (Arg²⁷stop) and extended chimeras of PLN with the five luminal residues of SLN added to its C terminus. The Arg²⁷stop form of SLN resulted in loss of function, whereas the PLN chimeras resulted in superinhibition with characteristics of both PLN and SLN. Based on our results, we propose that the C-terminal tail of SLN is a distinct, essential domain in the regulation of SERCA and that the functional properties of the SLN tail can be transferred to PLN.     

An ultrasoft X-ray multi-microbeam irradiation system for studies of DNA damage responses by fixed- and live-cell fluorescence microscopy

Localized induction of DNA damage is a valuable tool for studying cellular DNA damage responses. In recent decades, methods have been developed to generate DNA damage using radiation of various types, including photons and charged particles. Here we describe a simple ultrasoft X-ray multi-microbeam system for high dose-rate, localized induction of DNA strand breaks in cells at spatially and geometrically adjustable sites. Our system can be combined with fixed- and live-cell microscopy to study responses of cells to DNA damage. This article has been submitted as a contribution to the Festschrift entitled “Uncovering cellular sub-structures by light microscopy” in honour of Professor Cremer’s 65th birthday. C. van Oven and P. M. Krawczyk contributed equally to this work.