The Yeast Telomere Length Counting Machinery Is Sensitive to Sequences at the Telomere-Nontelomere Junction

Saccharomyces cerevisiae telomeres consist of a continuous 325 ± 75-bp tract of the heterogeneous repeat TG_1-3 which contains irregularly spaced, high-affinity sites for the protein Rap1p. Yeast cells monitor or count the number of telomeric Rap1p molecules in a negative feedback mechanism which modulates telomere length. To investigate the mechanism by which Rap1p molecules are counted, the continuous telomeric TG_1-3 sequences were divided into internal TG_1-3 sequences and a terminal tract separated by nontelomeric spacers of different lengths. While all of the internal sequences were counted as part of the terminal tract across a 38-bp spacer, a 138-bp disruption completely prevented the internal TG_1-3 sequences from being considered part of the telomere and defined the terminal tract as a discrete entity separate from the subtelomeric sequences. We also used regularly spaced arrays of six Rap1p sites internal to the terminal TG_1-3 repeats to show that each Rap1p molecule was counted as about 19 bp of TG_1-3 in vivo and that cells could count Rap1p molecules with different spacings between tandem sites. As previous in vitro experiments had shown that telomeric Rap1p sites occur about once every 18 bp, all Rap1p molecules at the junction of telomeric and nontelomeric chromatin (the telomere-nontelomere junction) must participate in telomere length measurement. The conserved arrangement of these six Rap1p molecules at the telomere-nontelomere junction in independent transformants also caused the elongated TG_1-3 tracts to be maintained at nearly identical lengths, showing that sequences at the telomere-nontelomere junction had an effect on length regulation. These results can be explained by a model in which telomeres beyond a threshold length form a folded structure that links the chromosome terminus to the telomere-nontelomere junction and prevents telomere elongation.     

Alien plants associate with widespread generalist arbuscular mycorrhizal fungal taxa: evidence from a continental‐scale study using massively parallel 454 sequencing

Aim The biogeography of arbuscular mycorrhizal (AM) fungi is poorly understood, and consequently the potential of AM fungi to determine plant distribution has been largely overlooked. We aimed to describe AM fungal communities associating with a single host‐plant species across a wide geographical area, including the plant’s native, invasive and experimentally introduced ranges. We hypothesized that an alien AM plant associates primarily with the geographically widespread generalist AM fungal taxa present in a novel range. Location Europe, China. Methods We transplanted the palm Trachycarpus fortunei into nine European sites where it does not occur as a native species, into one site where it is naturalized (Switzerland), and into one glasshouse site. We harvested plant roots after two seasons. In addition, we sampled palms at three sites in the plant’s native range (China). Roots were subjected to DNA extraction, polymerase chain reaction (PCR) and 454 sequencing of AM fungal sequences. We analysed fungal communities with non‐metric multidimensional scaling (NMDS) ordination and cluster analysis and studied the frequency of geographically widespread fungal taxa with log‐linear analysis. We compared fungal communities in the roots of the palm with those in resident plants at one site in the introduced range (Estonia) where natural AM fungal communities had previously been studied. Results We recorded a total of 73 AM fungal taxa. AM fungal communities in the native and introduced ranges differed from one another, while those in the invasive range contained taxa present in both other ranges. Geographically widespread AM fungal taxa were over‐represented in palm roots in all regions, but especially in the introduced range. At the Estonian site, the palm was colonized by the same community of widespread AM fungal taxa as associate with resident habitat‐generalist plants; by contrast, resident forest‐specialist plants were colonized by a diverse community of widespread and other AM fungal taxa. Main conclusions AM fungal communities in the native, invasive and experimentally introduced ranges varied in taxonomic composition and richness, but they shared a pool of geographically widespread, non‐host‐specific taxa that might support the invasion of a generalist alien plant. Our dataset provides the first geographical overview of AM taxon distributions obtained using a single host‐plant species.     

Numerical Exploration of the Planktonic to Benthic Primary Production Ratios in Lakes of the Baltic Sea Catchment

Autotrophic structure refers to the partitioning of whole-ecosystem primary production between benthic and planktonic primary producers. Autotrophic structure remains poorly understood especially because of the paucity of estimates regarding benthic primary production. We used a conceptual model for numerically exploring the autotrophic structure of 13 hemiboreal lakes situated in the Baltic Sea catchment. We also used diel variations in primary production profiles to graphically evaluate levels of light and/or nutrient limitation in lakes. The input morphometric data, light extinction coefficients and dissolved carbon parameters were mostly obtained from in situ measurements. Results revealed that cross- and within-lake autotrophic structure varied greatly: one lake was clearly dominated by benthic production, and three lakes by phytoplankton production. In the rest, phytoplankton production was generally dominant but switch to benthic dominance was possible. The modelled primary production profiles varied according to lake water clarity and bathymetry. Our results clearly indicate that the relative contribution of benthic primary production to whole-lake primary production should be taken into account in studies about hemiboreal and boreal lakes.     

Cul4A and DDB1 associate with Skp2 to target p27Kip1 for proteolysis involving the COP9 signalosome

DDB1, a subunit of the damaged-DNA binding protein DDB, has been shown to function also as an adaptor for Cul4A, a member of the cullin family of E3 ubiquitin ligase. The Cul4A-DDB1 complex remains associated with the COP9 signalosome, and that interaction is conserved from fission yeast to human. Studies with fission yeast suggested a role of the Pcu4-Ddb1-signalosome complex in the proteolysis of the replication inhibitor Spd1. Here we provide evidence that the function of replication inhibitor proteolysis is conserved in the mammalian DDB1-Cul4A-signalosome complex. We show that small interfering RNA-mediated knockdown of DDB1, CSN1 (a subunit of the signalosome), and Cul4A in mammalian cells causes an accumulation of p27Kip1. Moreover, expression of DDB1 reduces the level of p27Kip1 by increasing its decay rate. The DDB1-induced proteolysis of p27Kip1 requires signalosome and Cul4A, because DDB1 failed to increase the decay rate of p27Kip1 in cells deficient in CSN1 or Cul4A. Surprisingly, the DDB1-induced proteolysis of p27Kip1 also involves Skp2, an F-box protein that allows targeting of p27Kip1 for ubiquitination by the Skp1-Cul1-F-box complex. Moreover, we provide evidence for a physical association between Cul4A, DDB1, and Skp2. We speculate that the F-box protein Skp2, in addition to utilizing Cul1-Skp1, utilizes Cul4A-DDB1 to induce proteolysis of p27Kip1.     

Qualitative and quantitative resistances to leaf rust finely mapped within two nucleotide-binding site leucine-rich repeat (NBS-LRR)-rich genomic regions of chromosome 19 in poplar

? R(US) is a major dominant gene controlling quantitative resistance, inherited from Populus trichocarpa, whereas R(1) is a gene governing qualitative resistance, inherited from P. deltoides. ? Here, we report a reiterative process of concomitant fine-scale genetic and physical mapping guided by the P. trichocarpa genome sequence. The high-resolution linkage maps were developed using a P. deltoides × P. trichocarpa progeny of 1415 individuals. R(US) and R(1) were mapped in a peritelomeric region of chromosome 19. Markers closely linked to R(US) were used to screen a bacterial artificial chromosome (BAC) library constructed from the P. trichocarpa parent, heterozygous at the locus R(US) . ? Two local physical maps were developed, one encompassing the R(US) allele and the other spanning r(US) . The alignment of the two haplophysical maps showed structural differences between haplotypes. The genetic and physical maps were anchored to the genome sequence, revealing genome sequence misassembly. Finally, the R(US) locus was localized within a 0.8-cM interval, whereas R(1) was localized upstream of R(US) within a 1.1-cM interval. ? The alignment of the genetic and physical maps with the local reorder of the chromosome 19 sequence indicated that R(US) and R(1) belonged to a genomic region rich in nucleotide-binding site leucine-rich repeat (NBS-LRR) and serine threonine kinase (STK) genes.     

Respiration rhythms and heartbeats of diapausing Colorado potato beetles, Leptinotarsa decemlineata, at low temperatures

Discontinuous gas exchange cycles (DGCs), active muscular ventilation, microcycles of repetitive openings, and heartbeats of diapausing adult Colorado potato beetle, Leptinotarsa decemlineata Say (Coleoptera: Chrysomelidae), were studied at low temperatures (0, 5, and 10 °C) using an electrolytic respirometer combined with an infrared actograph. The DGC of the adult constriction-flutter-open type was the main respiration mode in fully quiescent beetles at temperatures from 5 to 10 °C. The CO₂ bursts were actively ventilated at temperatures above 5 °C. During the flutter period, a series of microcycles appeared, but no muscular contractions associated with the microcycles were detected. We identified this respiration mode as discontinuous suction ventilation.
The hydration condition of the beetles did not influence the frequency of the gas exchange cycles, but dehydrated beetles showed significantly longer flutter periods and shorter ventilation periods than hydrated beetles. The heartbeat frequencies were influenced by both temperature and hydration status.
We conclude from the results that DGCs are used at rest in adult L. decemlineata under various environmental conditions and also at low temperatures. Our results showed that DGCs are the main respiration mode of resting adult Colorado potato beetle irrespective of its hydration state and temperature. Our method resolves O₂ uptake and subsequent CO₂ release in flutter and ventilation periods and shows that diffusion is replaced by convection to reduce water loss in adult beetles.     

From Bacteria to Piscivorous Fish: Estimates of Whole-Lake and Component-Specific Metabolism with an Ecosystem Approach

The influence of functional group specific production and respiration patterns on a lake''s metabolic balance remains poorly investigated to date compared to whole-system estimates of metabolism. We employed a summed component ecosystem approach for assessing lake-wide and functional group-specific metabolism (gross primary production (GPP) and respiration (R)) in shallow and eutrophic Lake Võrtsjärv in central Estonia during three years. Eleven functional groups were considered: piscivorous and benthivorous fish; phyto-, bacterio-, proto- and metazooplankton; benthic macroinvertebrates, bacteria and ciliates; macrophytes and their associated epiphytes. Metabolism of these groups was assessed by allometric equations coupled with daily records of temperature and hydrology of the lake and measurements of food web functional groups biomass. Results revealed that heterotrophy dominated most of the year, with a short autotrophic period observed in late spring. Most of the metabolism of the lake could be attributed to planktonic functional groups, with phytoplankton contributing the highest share (90% of GPP and 43% of R). A surge of protozooplankton and bacterioplankton populations forming the microbial loop caused the shift from auto- to heterotrophy in midsummer. Conversely, the benthic functional groups had overall a very small contribution to lake metabolism. We validated our ecosystem approach by comparing the GPP and R with those calculated from O₂ measurements in the lake. Our findings are also in line with earlier productivity studies made with ¹⁴C or chlorophyll a (chl-a) based equations. Ideally, the ecosystem approach should be combined with diel O₂ approach for investigating critical periods of metabolism shifts caused by dynamics in food-web processes.     

The effect of treating goat's milk with transglutaminase on chemical,structural, and sensory properties of labneh

Labneh (a concentrated type of Mediterranean-Middle-East yogurt) was prepared by inoculating goat's milk with/without transglutaminase (TGase, at ranges of 0–4 units/g protein), followed by heat inactivation. Application of TGase did not change the chemical composition of the product. However, TGase treatment at rate of 2–4 U/g protein increased the firmness of the labneh samples by 14–15 folds, compared to the untreated sample. Scanning electron microscopy pictures revealed that the protein matrices in labneh from TGase treated samples appeared to be relatively more compact than the control. SDS-PAGE scans show crosslinking of proteins in labneh samples treated with TGase, and conversely, the bands corresponding to casein fractions became less intense as the concentration of TGase increased. Scores of firmness by sensory evaluation indicated that TGase treated samples at 2 U/g had a value of 27.4 compared to 12.5 in non-treated samples.     

Body movements and their role as triggers of heartbeats in pupae of the Colorado potato beetle Leptinotarsa decemlineata

Rhythmic body movements and their role as triggers of intermittent heartbeats were studied in pupae of Leptinotarsa decemlineata Say. Heartbeats and body movements were recorded simultaneously by means of an optical method (infra‐red cardiography) combined with respirometry. IR‐cardiography allows heartbeats and body movements to be distinguished on the basis of their different rates (40–80 min^?1 and 4–8 min^?1, respectively) and amplitude. In the mid‐interecdysial period, abdominal movements in the pupae were always accompanied by heart activity beginning after the first 5–12 abdominal strokes. Simultaneous periods of abdominal movements and heartbeats lasted 2–5 min, while the intervening pause ranged from 40 to 72 min at 24°C. Experiments of forced heart activity showed that a slight external tactile stimulus (prodding once with a single hair), applied prior to an expected heartbeat bout, evoked abdominal movements followed soon afterwards by contractions of the dorsal vessel. Repeated prodding with a hair evoked body rotating movements (1–3 strokes) at any time with heartbeats starting at the first movement. We surmise that rhythmic body movements play an active role in the triggering of heart activity in pupae according to the principle of cardiac reflex response. This is a possible mechanism for synchronizing periods of heart activity with periods of rhythmic body movements. Haemolymph circulation in pupae is favoured when heartbeat bouts are accompanied by active body movements.