DNA topoisomerase IIα controls replication origin cluster licensing and firing time in Xenopus egg extracts

Sperm chromatin incubated in Xenopus egg extracts undergoes origin licensing and nuclear assembly before DNA replication. We found that depletion of DNA topoisomerase IIα (topo IIα), the sole topo II isozyme of eggs and its inhibition by ICRF-193, which clamps topo IIα around DNA have opposite effects on these processes. ICRF-193 slowed down replication origin cluster activation and fork progression in a checkpoint-independent manner, without altering replicon size. In contrast, topo IIα depletion accelerated origin cluster activation, and topo IIα add-back negated overinitiation. Therefore, topo IIα is not required for DNA replication, but topo IIα clamps slow replication, probably by forming roadblocks. ICRF-193 had no effect on DNA synthesis when added after nuclear assembly, confirming that topo IIα activity is dispensable for replication and revealing that topo IIα clamps formed on replicating DNA do not block replication, presumably because topo IIα acts behind and not in front of forks. Topo IIα depletion increased, and topo IIα addition reduced, chromatin loading of MCM2-7 replicative helicase, whereas ICRF-193 did not affect MCM2-7 loading. Therefore, topo IIα restrains MCM2-7 loading in an ICRF-193-resistant manner during origin licensing, suggesting a model for establishing the sequential firing of origin clusters.     

The mechanism of ascus firing – Merging biophysical and mycological viewpoints

The actively discharging ascus is the unique spore-bearing cell that is responsible to dispatch spores into the atmosphere. From a physical perspective, this type of ascus is a sophisticated pressure gun that reliably discharges the spores at an extremely high velocity, without breaking apart. We identify four essential steps in discharge of spores whose order and timing may vary across species. First, asci that fire are mature, so a cue must be present that prevents discharge of immature spores and signals maturity. Second, pressure within the ascus serves to propel the spores forward; therefore a mechanism should be present to pressurize the ascus. Third, in ostiolate fruiting bodies (e.g. perithecia), the ascus extends through an opening to fire spores into the air. The extension process is a relatively unique aspect of the ascus and must be structurally facilitated. Fourth, the ascus must open at its tip for spore release in a controlled rupture. Here we discuss each of these aspects in the context of understanding the process of ascus and fruiting body function. While there is great diversity among fungi, we focus on discharge in a few model species, and then discuss how this framework may vary in other fungi. Our goal is to tie the physiological and molecular studies of ascus function with concepts in engineering that dictate structure.     

Do replication forks control late origin firing in Saccharomyces cerevisiae?

Recent studies of eukaryotic DNA replication timing profiles suggest that the time-dependent rate of origin firing, I(t), has a universal shape, which ensures a reproducible replication completion time. However, measurements of I(t) are based on population averages, which may bias the shape of the I(t) because of imperfect cell synchrony and cell-to-cell variability. Here, we measure the population-averaged I(t) profile from synchronized Saccharomyces cerevisiae cells using DNA combing and we extract the single-cell I(t) profile using numerical deconvolution. The single cell I(t) and the population-averaged I(t) extracted from DNA combing and replication timing profiles are similar, indicating a genome scale invariance of the replication process, and excluding cell-to-cell variability in replication time as an explanation for the shape of I(t). The single cell I(t) correlates with fork density in wild-type cells, which is specifically loosened in late S phase in the clb5Δ mutant. A previously proposed numerical model that reproduces the wild-type I(t) profile, could also describe the clb5Δ mutant I(t) once modified to incorporate the decline in CDK activity and the looser dependency of initiation on fork density in the absence of Clb5p. Overall, these results suggest that the replication forks emanating from early fired origins facilitate origin firing in later-replicating regions.     

Epilithon δ15N signatures indicate the origins of nitrogen loading and its seasonal dynamics in a volcanic Lake

The intensification of agricultural land use and urbanisation has increased nutrient loads in aquatic ecosystems. Nitrogen loads can alter ecosystem structure and functioning, resulting in increased algal productivity, algal blooms and eutrophication. The principal aim of the present paper is to extend the use of epilithic δ¹⁵N signatures to a lake ecosystem in order to evaluate the potential impact of anthropogenic nitrogen discharges (organic and inorganic) that can also reach coastal waters.Epilithic associations were collected from volcanic rocks in different seasons in shallow water along the entire perimeter of Lake Bracciano and analysed for their nitrogen stable isotope signatures. Furthermore, some stones were moved from an unpolluted site to a polluted one in order to verify the effect on the nitrogen signature of the epilithic association. The epilithon’s δ¹⁵N signatures provided strong evidence of the space-time variability of N inputs. The differing quality of nitrogen loads was reflected in high isotopic variation within the lake, especially at the beginning of summer (1.7‰ ≤ δ¹⁵N ≤ 13.3‰), while in winter, when anthropogenic pressure was lowest, the δ¹⁵N signature variation was less accentuated (3.1‰ ≤ δ¹⁵N ≤ 7.6‰). At all sampling times, spatial variability was found to be related to the various human activities along the lake shore (especially tourism and agriculture), while seasonal variation at all sampling sites was related to the intensity of anthropogenic pressures (higher in summer and lower in winter).Our results showed that epilithic algal associations and the physicochemical properties of the water did not influence the δ¹⁵N signature, which in contrast was strongly related to the site-specific effect of human activities around the lake. Thus, the distribution of δ¹⁵N across space and time can be used to direct nutrient reduction strategies in the region and can assist in monitoring the effectiveness of environmental protection measures.     

Science – or not? The status and dynamics of biotechnology

This review traces the emergence of biotechnology as a new scientific discipline since the 1980s, when it became a major economic force. Significant changes in theoretical perception, research strategies, aims, and experimental methods, mainly in genetic engineering techniques, occurred during this period. The article is based on an analysis of its scientific status over four decades: the 60s and 70s when work in the field proceeded in different disciplines with a low level of coherence and little integration, then a significant change during the 80s and 90s when common approaches and the merging of molecular biology and biochemical engineering created a new discipline. The analysis covers scientific highlights and outstanding technical progress, presenting two studies undertaken by scientific and governmental agencies in Germany and the USA, as well as results of interviews and a questionnaire dealing with the scientific status of biotechnology. Answers to the questionnaire were obtained from internationally known scientists and from young scientists with biotechnology degrees. The results collected trace the transition of biotechnology from heterogeneous specialties and approaches towards a scientific discipline of its own. A hypothesis is put forward suggesting a new common paradigm allowing for a coherent perception the of phenomena observed.     

Hemoglobin and Hematocrit Levels in the Prediction of Complicated Crohn's Disease Behavior – A Cohort Study

Background

Markers that predict the occurrence of a complicated disease behavior in patients with Crohn''s disease (CD) can permit a more aggressive therapeutic regimen for patients at risk. The aim of this cohort study was to test the blood levels of hemoglobin (Hgb) and hematocrit (Hct) for the prediction of complicated CD behavior and CD related surgery in an adult patient population.

Methods

Blood samples of 62 CD patients of the German Inflammatory Bowel Disease-network “Kompetenznetz CED” were tested for the levels of Hgb and Hct prior to the occurrence of complicated disease behavior or CD related surgery. The relation of these markers and clinical events was studied using Kaplan-Meier survival analysis and adjusted COX-proportional hazard regression models.

Results

The median follow-up time was 55.8 months. Of the 62 CD patients without any previous complication or surgery 34% developed a complication and/or underwent CD related surgery. Low Hgb or Hct levels were independent predictors of a shorter time to occurrence of the first complication or CD related surgery. This was true for early as well as late occurring complications. Stable low Hgb or Hct during serial follow-up measurements had a higher frequency of complications compared to patients with a stable normal Hgb or Hct, respectively.

Conclusions

Determination of Hgb or Hct in complication and surgery naïve CD patients might serve as an additional tool for the prediction of complicated disease behavior.     

Eukaryotic origins of DNA replication: could you please be more specific?

Initiation of eukaryotic DNA replication commences when the origin recognition complex (ORC) binds to DNA, recruiting helicases, polymerases, and necessary cofactors. While the biochemical mechanism and factors involved in replication initiation appear to be highly conserved, the DNA sequences at which these events take place in different organisms are not. Thus, while ORC appears to bind to specific DNA sequences in budding yeast, there is increasing new evidence that metazoan ORC complexes do not rely on sequence to be directed to origins of replication. Here, we review examples of specific and non-specific initiation, and we consider what, if not DNA sequence, accounts for DNA binding of ORC to defined regions in eukaryotic genomes.     

APC/C – the master controller of origin licensing?

The cyclin kinase inhibitor p27^kip1 acts as a potent tumor supressor protein in a variety of human cancers. Its expression levels correlate closely with the overall prognosis of the affected patient and often predict the outcome to different treatment modalities. In contrast to other tumor suppressor proteins p27 expression levels in tumor cells are frequently regulated by ubiquitin dependent proteolysis. Re-expression of p27 in cancer cells therefore does not require gene therapy but can be achieved by interfering with the protein turnover machinery. In this review we will summarize experimental results which highlight the potential use of p27 as a target for oncological therapies.     

Broader utilization of origins of DNA replication in cancer cell lines along a 78 kb region of human chromosome 2q34

Human DNA replication depends on the activation of thousands of origins distributed within the genome. The actual distribution of origins is not known, nor whether this distribution is unique to a cell type, or if it changes with the proliferative state of the cell. In this study, we have employed a real‐time PCR‐based nascent strand DNA abundance assay, to determine the location of origins along a 78 kb region on Chr2q34. Preliminary studies using nascent DNA strands isolated from either HeLa and normal skin fibroblast cells showed that in both cell lines peaks of high origin activity mapped in similar locations. However, the overall origin profile in HeLa cells corresponded to broad origin activation zones, whereas in fibroblasts a more punctuated profile of origin activation was observed. To investigate the relevance of this differential origin profile, we compared the origin distribution profiles in breast cancer cell lines MDA‐MB‐231, BT‐474, and MCF‐7, to their normal counterpart MCF‐10A. In addition, the CRL7250 cell line was also used as a normal control. Our results validated our earlier observation and showed that the origin profile in normal cell lines exhibited a punctuated pattern, in contrast to broader zone profiles observed in the cancer cell lines. A quantitative analysis of origin peaks revealed that the number of activated origins in cancer cells is statistically larger than that obtained in normal cells, suggesting that the flexibility of origin usage is significantly increased in cancer cells compared to their normal counterparts. J. Cell. Biochem. 113: 132–140, 2012. © 2011 Wiley Periodicals, Inc.     

Drug-resistant parasites and aggregated infection – early-season dynamics

We investigate the effect of spatial aggregation in the infection dynamics of nematode parasites in ruminants. We show that a high degree of spatial aggregation is likely to lead to a dramatically enhanced rate of invasion by drug-resistant strains. Received: 13 December 1999 / Revised version: 3 April 2000 / Published online: 4 October 2000     

Uncovering the spatio-temporal dynamics of value-based decision-making in the human brain: a combined fMRI–EEG study

While there is a growing body of functional magnetic resonance imaging (fMRI) evidence implicating a corpus of brain regions in value-based decision-making in humans, the limited temporal resolution of fMRI cannot address the relative temporal precedence of different brain regions in decision-making. To address this question, we adopted a computational model-based approach to electroencephalography (EEG) data acquired during a simple binary choice task. fMRI data were also acquired from the same participants for source localization. Post-decision value signals emerged 200 ms post-stimulus in a predominantly posterior source in the vicinity of the intraparietal sulcus and posterior temporal lobe cortex, alongside a weaker anterior locus. The signal then shifted to a predominantly anterior locus 850 ms following the trial onset, localized to the ventromedial prefrontal cortex and lateral prefrontal cortex. Comparison signals between unchosen and chosen options emerged late in the trial at 1050 ms in dorsomedial prefrontal cortex, suggesting that such comparison signals may not be directly associated with the decision itself but rather may play a role in post-decision action selection. Taken together, these results provide us new insights into the temporal dynamics of decision-making in the brain, suggesting that for a simple binary choice task, decisions may be encoded predominantly in posterior areas such as intraparietal sulcus, before shifting anteriorly.     

Liquid-EM goes viral – visualizing structure and dynamics

Liquid-electron microscopy (EM), the room temperature correlate to cryo-EM, is an exciting new technique delivering real-time data of dynamic reactions in solution. Here, we explain how liquid-EM gained popularity in recent years by examining key experiments conducted on viral assemblies and host–pathogen interactions. We describe developing workflows for specimen preparation, data collection, and computing processes that led to the first high-resolution virus structures in a liquid environment. Equally important, we review why liquid-electron tomography may become the next big thing in biomedical research due to its ability to monitor live viruses entering cells within seconds. Taken together, we pose the idea that liquid-EM can serve as a dynamic complement to current cryo-EM methods, inspiring the “real-time revolution” in nanoscale imaging.     

Effects of changes in tree species composition on water flow dynamics – Model applications and their limitations

Water-plant relations play a key role in the water cycling in terrestrial ecosystems. Consequently, changes in tree species composition may have distinct effects on the water retention capacity as well as on the pattern of streamflow generation. Such changes may result from modified interception properties and transpiration related to differences in canopy properties and root distribution. In order to evaluate the potential hydrological effects of the current silvicultural conversion from monocultural conifer stands into mixed or pure deciduous stands the hydrological model BROOK90 was applied to two forested upland catchments in Germany. The Rotherdbach catchment (9.4 ha, 93 yr-old Norway spruce) is situated in the Eastern Ore Mountains. The Schluchsee catchment (11 ha, 55-yr-old Norway spruce) is located in the higher altitudes of the Black Forest. The calibrated model is capable to describe rather well the temporal variation of streamflow but also the portions of the individual flow components. Data for a beech scenario were adapted for each site using a standard parameter set for deciduous trees provided by BROOK90. The annual discharge in the fictional beech stand at Rotherdbach is 30 to 50% higher compared to spruce with an increase of soil moisture and especially the slow streamflow components. This mainly results from low interception rates during winter time. In contrast, the spruce stand has a permanently higher interception rate. Effects of tree species conversion are moderate at Schluchsee. The annual discharge of a fictional beech stand at Schluchsee is 7 to 14% higher compared to spruce. There in contrast to Rotherdbach, effects of tree species conversion on soil moisture dynamics are small since vertical percolation in the highly permeable soil dominates and precipitation is abundant. Practical forestry will favorably establish mixed beech–spruce rather than pure beech stands. However, it is critical to simulate mixed stands with BROOK90. Therefore, a simple summation of model results from spruce and beech according to their respective area in a fictional mixed stand can only be a first approximation. Advanced hydrological simulation of mixed stand conditions should regard interactions of tree species and spatial parameter distribution. However, this is not yet feasible due to a distinct lack of information. As a consequence, there is a strong need to collect relevant hydrological and ecophysiological data in mixed stands in the future.     

SOD1 in amyotrophic lateral sclerosis development – in silico analysis and molecular dynamics of A4F and A4V variants

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease that is characterized by the selective loss of motor neurons. Approximately 5% to 10% of patients with ALS have a family history of the disease, and approximately 20% of familial amyotrophic lateral sclerosis (fALS) cases are associated with mutations in Cu/Zn superoxide dismutase (SOD1). In this study, we evaluated the structural and functional effects of human A4F and A4V SOD1 protein mutations. We performed an in silico analysis using prediction algorithms of nonsynonymous single-nucleotide polymorphisms (nsSNPs) associated with the fALS development. Our structural conservation results show that the mutations analyzed (A4V and A4F) were in a highly conserved region. Molecular dynamics simulations using the Linux GROMACS package revealed how these mutations affect protein structure, protein stability, and aggregation. These results suggest that there might be an effect on the SOD1 function. Understanding the molecular basis of disease provides new insights useful for rational drug design and advancing our understanding of the ALS development.     

Rana temporaria metamorph production and population dynamics in the field – Effects of tadpole density,predation and pond drying

This study investigates factors of importance for tadpoles survival and metamorph production in the common frog Rana temporaria. It also assess the importance of this for the population dynamics of the species. Eighteen ponds were studied for up to 8 years. Data collected each year included: number of spawn clumps deposited, tadpole number and metamorph number. The permanency of the ponds was also recorded each year. Measures were taken of predator density. There was no suggestion of density dependence in the survival of tadpoles. In contrast, the number of spawn clumps deposited per pond area was highest for ponds with high survival. Density of predators (sticklebacks, newts and invertebrates) was negatively correlated to tadpole and metamorph survival. This was true both within (among years) and among ponds. Several of the study ponds dried completely before metamorphosis in some years. However, those ponds also were those with the smallest number of predators and in years with successful metamorphosis, these ponds produced more metamorphs than more permanent ponds. An analysis of the year to year dynamics showed that population size (number of deposited spawn clumps) was correlated to that in the previous year, suggesting a fairly high adult survival, but also on the number of metamorphs emerging two or three years before (corresponding to the age of sexual maturity of the species). It is concluded that the aquatic stage is not strongly limiting in these ponds but conservation efforts should be focused on the terrestrial habitat. Also, the study stresses the value of temporary ponds, despite the fact that recruitment often fails totally in these.     

Seasonal dynamics of chemotypes in a freshwater phytoplankton community – A metabolomic approach

Cyanobacteria are known to produce a huge variety of secondary metabolites. Many of these metabolites are toxic to zooplankton, fish, birds and mammals. Therefore, the toxicity of cyanobacterial blooms is strongly dependent on the cyanobacterial strain composition. These strains produce distinct bouquets of secondary metabolites, and thus constitute different chemotypes. Some of the cyanobacterial metabolites are potent inhibitors of gut proteases of the filter-feeder Daphnia. Here, we investigate the seasonal dynamics of secondary metabolites in a phytoplankton community from a hypertrophic pond, making use of a new metabolomic approach. Using liquid chromatography coupled with high-resolution mass spectrometry (LCMS), we obtained mass spectra of phytoplankton samples taken on different dates throughout the summer season. By applying multivariate statistics, we combined these data with the protease inhibition capacity of the same samples. This led to the identification of metabolites with cyanobacterial origin and as well of distinct cyanobacterial chemotypes being dominant on different dates. The protease inhibition capacity varied strongly with season, and only one out of 73 known cyanobacterial protease inhibitors could be confirmed in the natural samples. Instead, several so far unknown, putative protease inhibitors were detected. In conclusion, the creation of time series of mass spectral data of a natural phytoplankton community proved to be useful for elucidating seasonal chemotype succession in a cyanobacterial community. Additionally, correlating mass spectral data with a biological assay provides a promising tool for facilitating the search for new harmful metabolites prior to structure elucidation.