Recombination and replication in DNA repair of heavily irradiated Deinococcus radiodurans.

Deinococcus radiodurans' extreme resistance to ionizing radiation, desiccation, and DNA-damaging chemicals involves a robust DNA repair that reassembles its shattered genome. The repair process requires diploidy and commences with an extensive exonucleolytic erosion of DNA fragments. Liberated single-stranded overhangs prime strand elongation on overlapping fragments and the elongated complementary strands reestablish chromosomal contiguity by annealing. We explored the interdependence of the DNA recombination and replication processes in the reconstitution of the D. radiodurans genome disintegrated by ionizing radiation. The priming of extensive DNA repair synthesis involves RecA and RadA proteins. DNA polymerase III is essential for the initiation of repair synthesis, whereas efficient elongation requires DNA polymerases I and III. Inactivation of both polymerases leads to degradation of DNA fragments and rapid cell death. The present in vivo characterization of key recombination and replication processes dissects the mechanism of DNA repair in heavily irradiated D. radiodurans.

High illness loads (physical and social) do not always force high levels of mass religiosity.

The hypothesis that high levels of religiosity are partly caused by high disease loads is in accord with studies showing that societal dysfunction promotes mass supernaturalism. However, some cultures suffering from high rates of disease and other socioeconomic dysfunction exhibit low levels of popular religiosity. At this point, it appears that religion is hard pressed to thrive in healthy societies, but poor conditions do not always make religion popular, either.

Pre-dispositions and epigenetic inheritance in the Escherichia coli lactose operon bistable switch.

The lactose operon regulation in Escherichia coli is a primary model of phenotypic switching, reminiscent of cell fate determination in higher organisms. Under conditions of bistability, an isogenic cell population partitions into two subpopulations, with the operon's genes turned on or remaining off. It is generally hypothesized that the final state of a cell depends solely on stochastic fluctuations of the network's protein concentrations, particularly on bursts of lactose permease expression. Nevertheless, the mechanisms underlying the cell switching decision are not fully understood. We designed a microfluidic system to follow the formation of a transiently bimodal population within growing microcolonies. The analysis of genealogy and cell history revealed the existence of pre-disposing factors for switching that are epigenetically inherited. Both the pre-induction expression stochasticity of the lactose operon repressor LacI and the cellular growth rate are predictive factors of the cell's response upon induction, with low LacI concentration and slow growth correlating with higher switching probability. Thus, stochasticity at the local level of the network and global physiology are synergistically involved in cell response determination.

A review and reappraisal of the specific gravities of present and past multicellular organisms, with an emphasis on tetrapods.

The density, or specific gravity (SG), of organisms has numerous important implications for their form, function, ecology, and other facets of beings living and dead, and it is especially necessary to apply SG values that are as accurate as practical when estimating their masses which is itself a critical aspect of living things. Yet a comprehensive review and analysis of this notable subject of anatomy has never been conducted and published. This is such an effort, being as extensive as possible with the data on hand, bolstered by some additional observations, and new work focusing on extinct animals who densities are least unknown: pterosaurs and dinosaurs with extensive pneumatic complexes, including the most sophisticated effort to date for a sauropod. Often difficult to determine even via direct observation, techniques for obtaining the best possible SG data are explained and utilized, including observations of floating animals. Neutral specific gravity (NSG) is proposed as the most important value for tetrapods with respiratory tracts of fluctuating volume. SGs of organisms range from 0.08 to 2.6, plant tissues from 0.08 to 1.39, and vertebrates from about 0.75 (some giant pterosaurs) to 1.2 (those with heavy armor and/or skeletons). Tetrapod NSGs tend to be somewhat higher than widely thought, especially those theropod and sauropod dinosaurs and pterosaurs with air-sacs because respiratory system volume is usually measured at maximum inhalation in birds. Also discussed is evidence that the ratio of the mass of skeletons relative to total body mass has not been properly assayed in the past.

Beyond co-localization: inferring spatial interactions between sub-cellular structures from microscopy images.

BACKGROUND: Sub-cellular structures interact in numerous direct and indirect ways in order to fulfill cellular functions. While direct molecular interactions crucially depend on spatial proximity, other interactions typically result in spatial correlations between the interacting structures. Such correlations are the target of microscopy-based co-localization analysis, which can provide hints of potential interactions. Two complementary approaches to co-localization analysis can be distinguished: intensity correlation methods capitalize on pattern discovery, whereas object-based methods emphasize detection power. RESULTS: We first reinvestigate the classical co-localization measure in the context of spatial point pattern analysis. This allows us to unravel the set of implicit assumptions inherent to this measure and to identify potential confounding factors commonly ignored. We generalize object-based co-localization analysis to a statistical framework involving spatial point processes. In this framework, interactions are understood as position co-dependencies in the observed localization patterns. The framework is based on a model of effective pairwise interaction potentials and the specification of a null hypothesis for the expected pattern in the absence of interaction. Inferred interaction potentials thus reflect all significant effects that are not explained by the null hypothesis. Our model enables the use of a wealth of well-known statistical methods for analyzing experimental data, as demonstrated on synthetic data and in a case study considering virus entry into live cells. We show that the classical co-localization measure typically under-exploits the information contained in our data. CONCLUSIONS: We establish a connection between co-localization and spatial interaction of sub-cellular structures by formulating the object-based interaction analysis problem in a spatial statistics framework based on nearest-neighbor distance distributions. We provide generic procedures for inferring interaction strengths and quantifying their relative statistical significance from sets of discrete objects as provided by image analysis methods. Within our framework, an interaction potential can either refer to a phenomenological or a mechanistic model of a physico-chemical interaction process. This increased flexibility in designing and testing different hypothetical interaction models can be used to quantify the parameters of a specific interaction model or may catalyze the discovery of functional relations.

Spatial heterogeneity and functional response: an experiment in microcosms with varying obstacle densities.

Spatial heterogeneity of the environment has long been recognized as a major factor in ecological dynamics. Its role in predator-prey systems has been of particular interest, where it can affect interactions in two qualitatively different ways: by providing (1) refuges for the prey or (2) obstacles that interfere with the movements of both prey and predators. There have been relatively fewer studies of obstacles than refuges, especially studies on their effect on functional responses. By analogy with reaction-diffusion models for chemical systems in heterogeneous environments, we predict that obstacles are likely to reduce the encounter rate between individuals, leading to a lower attack rate (predator-prey encounters) and a lower interference rate (predator-predator encounters). Here, we test these predictions under controlled conditions using collembolans (springtails) as prey and mites as predators in microcosms. The effect of obstacle density on the functional response was investigated at the scales of individual behavior and of the population. As expected, we found that increasing obstacle density reduces the attack rate and predator interference. Our results show that obstacles, like refuges, can reduce the predation rate because obstacles decrease the attack rate. However, while refuges can increase predator dependence, we suggest that obstacles can decrease it by reducing the rate of encounters between predators. Because of their opposite effect on predator dependence, obstacles and refuges could modify in different ways the stability of predator-prey communities.

The rationale for consuming protein blends in sports nutrition.

Protein is considered by many to be the most important macronutrient for humans because of the numerous roles protein plays in the body. Protein needs have been compared across several population groups, including athletes and other exercising individuals. Many researchers have compared the effects of ingesting animal and vegetable protein sources and their implications on sports performance. Recently, blends of dairy protein and soy protein have appeared in commercial sports nutrition products such as nutrition bars and ready-to-drink and powdered beverages. This review will focus on the potential nutritional advantages of combining whey protein, casein, and isolated soy protein.

Modeling Point Spread Function in Fluorescence Microscopy With a Sparse Gaussian Mixture: Tradeoff Between Accuracy and Efficiency.

Deblurring is a fundamental inverse problem in bioimaging. It requires modeling the point spread function (PSF), which captures the optical distortions entailed by the image formation process. The PSF limits the spatial resolution attainable for a given microscope. However, recent applications require a higher resolution and have prompted the development of super-resolution techniques to achieve sub-pixel accuracy. This requirement restricts the class of suitable PSF models to analog ones. In addition, deblurring is computationally intensive, hence further requiring computationally efficient models. A custom candidate fitting both the requirements is the Gaussian model. However, this model cannot capture the rich tail structures found in both the theoretical and empirical PSFs. In this paper, we aim at improving the reconstruction accuracy beyond the Gaussian model, while preserving its computational efficiency. We introduce a new class of analog PSF models based on the Gaussian mixtures. The number of Gaussian kernels controls both the modeling accuracy and the computational efficiency of the model: the lower the number of kernels, the lower the accuracy and the higher the efficiency. To explore the accuracy-efficiency tradeoff, we propose a variational formulation of the PSF calibration problem, where a convex sparsity-inducing penalty on the number of Gaussian kernels allows trading accuracy for efficiency. We derive an efficient algorithm based on a fully split formulation of alternating split Bregman. We assess our framework on synthetic and real data, and demonstrate a better reconstruction accuracy in both geometry and photometry in point source localization-a fundamental inverse problem in fluorescence microscopy.

Aging and death in an organism that reproduces by morphologically symmetric division.

In macroscopic organisms, aging is often obvious; in single-celled organisms, where there is the greatest potential to identify the molecular mechanisms involved, identifying and quantifying aging is harder. The primary results in this area have come from organisms that share the traits of a visibly asymmetric division and an identifiable juvenile phase. As reproductive aging must require a differential distribution of aged and young components between parent and offspring, it has been postulated that organisms without these traits do not age, thus exhibiting functional immortality. Through automated time-lapse microscopy, we followed repeated cycles of reproduction by individual cells of the model organism Escherichia coli, which reproduces without a juvenile phase and with an apparently symmetric division. We show that the cell that inherits the old pole exhibits a diminished growth rate, decreased offspring production, and an increased incidence of death. We conclude that the two supposedly identical cells produced during cell division are functionally asymmetric; the old pole cell should be considered an aging parent repeatedly producing rejuvenated offspring. These results suggest that no life strategy is immune to the effects of aging, and therefore immortality may be either too costly or mechanistically impossible in natural organisms.

A Bayesian framework for the analog reconstruction of kymographs from fluorescence microscopy data.

Kymographs are widely used to represent and analyse spatio-temporal dynamics of fluorescence markers along curvilinear biological compartments. These objects have a singular geometry, thus kymograph reconstruction is inherently an analog image processing task. However, the existing approaches are essentially digital: the kymograph photometry is sampled directly from the time-lapse images. As a result, such kymographs rely on raw image data that suffer from the degradations entailed by the image formation process and the spatio-temporal resolution of the imaging setup. In this work, we address these limitations and introduce a well-grounded Bayesian framework for the analog reconstruction of kymographs. To handle the movement of the object, we introduce an intrinsic description of kymographs using differential geometry: a kymograph is a photometry defined on a parameter space that is embedded in physical space by a time-varying map that follows the object geometry. We model the kymograph photometry as a Lévy innovation process, a flexible class of non-parametric signal priors. We account for the image formation process using the virtual microscope framework. We formulate a computationally tractable representation of the associated maximum a posteriori problem and solve it using a class of efficient and modular algorithms based on the alternating split Bregman. We assess the performance of our Bayesian framework on synthetic data and apply it to reconstruct the fluorescence dynamics along microtubules in vivo in the budding yeast S. cerevisiae. We demonstrate that our framework allows revealing patterns from single time-lapse data that are invisible on standard digital kymographs.

Quantitative spatial analysis of haematopoiesis-regulating stromal cells in the bone marrow microenvironment by 3D microscopy.

Sinusoidal endothelial cells and mesenchymal CXCL12-abundant reticular cells are principal bone marrow stromal components, which critically modulate haematopoiesis at various levels, including haematopoietic stem cell maintenance. These stromal subsets are thought to be scarce and function via highly specific interactions in anatomically confined niches. Yet, knowledge on their abundance, global distribution and spatial associations remains limited. Using three-dimensional quantitative microscopy we show that sinusoidal endothelial and mesenchymal reticular subsets are remarkably more abundant than estimated by conventional flow cytometry. Moreover, both cell types assemble in topologically complex networks, associate to extracellular matrix and pervade marrow tissues. Through spatial statistical methods we challenge previous models and demonstrate that even in the absence of major specific interaction forces, virtually all tissue-resident cells are invariably in physical contact with, or close proximity to, mesenchymal reticular and sinusoidal endothelial cells. We further show that basic structural features of these stromal components are preserved during ageing.

Prototype of the novel CAMEA concept-A backend for neutron spectrometers.

The continuous angle multiple energy analysis concept is a backend for both time-of-flight and analyzer-based neutron spectrometers optimized for neutron spectroscopy with highly efficient mapping in the horizontal scattering plane. The design employs a series of several upward scattering analyzer arcs placed behind each other, which are set to different final energies allowing a wide angular coverage with multiple energies recorded simultaneously. For validation of the concept and the model calculations, a prototype was installed at the Swiss neutron source SINQ, Paul Scherrer Institut. The design of the prototype, alignment and calibration procedures, experimental results of background measurements, and proof-of-concept inelastic measurements on LiHoF4 and h-YMnO3 are presented here.

Restoring Maximum Vertical Browsing Reach in Sauropod Dinosaurs.

The ongoing controversy centered on neck posture and function in sauropod dinosaurs is misplaced for a number of reasons. Because of an absence of pertinent data it is not possible to accurately restore the posture and range of motion in long necked fossil animals, only gross approximations are possible. The existence of a single "neutral posture" in animals with long, slender necks may not exist, and its relationship to feeding habits is weak. Restorations of neutral osteological neck posture based on seemingly detailed diagrams of cervical articulations are not reliable because the pictures are not sufficiently accurate due to a combination of illustration errors, and distortion of the fossil cervicals. This is all the more true because fossil cervical series lack the critical inter-centra cartilage. Maximum vertical reach is more readily restorable and biologically informative for long necked herbivores. Modest extension of 10° between each caudal cervical allowed high shouldered sauropods to raise the cranial portion of their necks to vertical postures that allowed them to reach floral resources far higher than seen in the tallest mammals. This hypothesis is supported by the dorsally extended articulation of the only known co-fused sauropod cervicals. Many sauropods appear to have been well adapted for rearing in order to boost vertical reach, some possessed retroverted pelves that may have allowed them to walk slowly while bipedal. A combination of improved high browsing abilities and sexual selection probably explains the unusually long necks of tall ungulates and super tall sauropods. Anat Rec, 2017. © 2017 Wiley Periodicals, Inc. Anat Rec, 300:1802-1825, 2017. © 2017 Wiley Periodicals, Inc.

Internal modifications in the CENP-A nucleosome modulate centromeric dynamics.

BACKGROUND: Posttranslational modifications of core histones are correlated with changes in transcriptional status, chromatin fiber folding, and nucleosome dynamics. However, within the centromere-specific histone H3 variant CENP-A, few modifications have been reported, and their functions remain largely unexplored. In this multidisciplinary report, we utilize in silico computational and in vivo approaches to dissect lysine 124 of human CENP-A, which was previously reported to be acetylated in advance of replication. RESULTS: Computational modeling demonstrates that acetylation of K124 causes tightening of the histone core and hinders accessibility to its C-terminus, which in turn diminishes CENP-C binding. Additionally, CENP-A K124ac/H4 K79ac containing nucleosomes are prone to DNA sliding. In vivo experiments using a CENP-A acetyl or unacetylatable mimic (K124Q and K124A, respectively) reveal alterations in CENP-C levels and a modest increase in mitotic errors. Furthermore, mutation of K124 results in alterations in centromeric replication timing. Purification of native CENP-A proteins followed by mass spectrometry analysis reveals that while CENP-A K124 is acetylated at G1/S, it switches to monomethylation during early S and mid-S phases. Finally, we provide evidence implicating the histone acetyltransferase (HAT) p300 in this cycle. CONCLUSIONS: Taken together, our data suggest that cyclical modifications within the CENP-A nucleosome contribute to the binding of key kinetochore proteins, the integrity of mitosis, and centromeric replication. These data support the paradigm that modifications in histone variants can influence key biological processes.

Visual scanning of faces in autism.

The visual scanpaths of five high-functioning adult autistic males and five adult male controls were recorded using an infrared corneal reflection technique as they viewed photographs of human faces. Analyses of the scanpath data revealed marked differences in the scanpaths of the two groups. The autistic participants viewed nonfeature areas of the faces significantly more often and core feature areas of the faces (i.e., eyes, nose, and mouth) significantly less often than did control participants. Across both groups of participants, scanpaths generally did not differ as a function of the instructions given to the participants (i.e., "Please look at the faces in any manner you wish." vs. "Please identify the emotions portrayed in these faces."). Autistic participants showed a deficit in emotion recognition, but this effect was driven primarily by deficits in the recognition of fear. Collectively, these results indicate disorganized processing of face stimuli in autistic individuals and suggest a mechanism that may subserve the social information processing deficits that characterize autism spectrum disorders.

Segmentation and quantification of subcellular structures in fluorescence microscopy images using Squassh.

Detection and quantification of fluorescently labeled molecules in subcellular compartments is a key step in the analysis of many cell biological processes. Pixel-wise colocalization analyses, however, are not always suitable, because they do not provide object-specific information, and they are vulnerable to noise and background fluorescence. Here we present a versatile protocol for a method named 'Squassh' (segmentation and quantification of subcellular shapes), which is used for detecting, delineating and quantifying subcellular structures in fluorescence microscopy images. The workflow is implemented in freely available, user-friendly software. It works on both 2D and 3D images, accounts for the microscope optics and for uneven image background, computes cell masks and provides subpixel accuracy. The Squassh software enables both colocalization and shape analyses. The protocol can be applied in batch, on desktop computers or computer clusters, and it usually requires <1 min and <5 min for 2D and 3D images, respectively. Basic computer-user skills and some experience with fluorescence microscopy are recommended to successfully use the protocol.

Effect of a 6-month vegan low-carbohydrate ('Eco-Atkins') diet on cardiovascular risk factors and body weight in hyperlipidaemic adults: a randomised controlled trial.

OBJECTIVE: Low-carbohydrate diets may be useful for weight loss. Diets high in vegetable proteins and oils may reduce the risk of coronary heart disease. The main objective was to determine the longer term effect of a diet that was both low-carbohydrate and plant-based on weight loss and low-density lipoprotein cholesterol (LDL-C). DESIGN, SETTING, PARTICIPANTS: A parallel design study of 39 overweight hyperlipidaemic men and postmenopausal women conducted at a Canadian university-affiliated hospital nutrition research centre from April 2005 to November 2006. INTERVENTION: Participants were advised to consume either a low-carbohydrate vegan diet or a high-carbohydrate lacto-ovo vegetarian diet for 6 months after completing 1-month metabolic (all foods provided) versions of these diets. The prescribed macronutrient intakes for the low-carbohydrate and high-carbohydrate diets were: 26% and 58% of energy from carbohydrate, 31% and 16% from protein and 43% and 25% from fat, respectively. PRIMARY OUTCOME: Change in body weight. RESULTS: 23 participants (50% test, 68% control) completed the 6-month ad libitum study. The approximate 4 kg weight loss on the metabolic study was increased to -6.9 kg on low-carbohydrate and -5.8 kg on high-carbohydrate 6-month ad libitum treatments (treatment difference (95% CI) -1.1 kg (-2.1 to 0.0), p=0.047). The relative LDL-C and triglyceride reductions were also greater on the low-carbohydrate treatment (treatment difference (95% CI) -0.49 mmol/L (-0.70 to -0.28), p<0.001 and -0.34 mmol/L (-0.57 to -0.11), p=0.005, respectively), as were the total cholesterol:HDL-C and apolipoprotein B:A1 ratios (-0.57 (-0.83, -0.32), p<0.001 and -0.05 (-0.09, -0.02), p=0.003, respectively). CONCLUSIONS: A self-selected low-carbohydrate vegan diet, containing increased protein and fat from gluten and soy products, nuts and vegetable oils, had lipid lowering advantages over a high-carbohydrate, low-fat weight loss diet, thus improving heart disease risk factors. TRIAL REGISTRATION: clinicaltrials.gov (http://www.clinicaltrials.gov/), #NCT00256516.

E5501: phase II study of topotecan sequenced with etoposide/cisplatin, and irinotecan/cisplatin sequenced with etoposide for extensive-stage small-cell lung cancer.

PURPOSE: Sequence-dependent improved efficacy of topoisomerase I followed by topoisomerase 2 inhibitors was assessed in a randomized phase II study in extensive-stage small-cell lung cancer (SCLC). METHODS: Patients with previously untreated extensive-stage SCLC with measurable disease, ECOG performance status of 0-3 and stable brain metastases were eligible. Arm A consisted of topotecan (0.75 mg/m(2)) on days 1, 2 and 3, etoposide (70 mg/m(2)) and cisplatin (20 mg/m(2)) (PET) on days 8, 9 and 10 in a 3-week cycle. Arm B consisted of irinotecan (50 mg/m(2)) and cisplatin (20 mg/m(2)) on days 1 and 8 followed by etoposide (85 mg/m(2) PO bid) on days 3 and 10 (PIE) in a 3-week cycle. RESULTS: We enrolled 140 patients and randomized 66 eligible patients to each arm. Only 54.5 % of all patients completed the planned maximum 6 cycles. There were grade ≥3 treatment-related adverse events in approximately 70 % of the patients on both arms including 6 treatment-related grade 5 events. The overall response rates (CR + PR) were 69.7 % (90 % CI 59.1-78.9, 95 % CI 57.1-80.4 %) for arm A and 57.6 % (90 % CI 46.7-67.9, 95 % CI 44.8-69.7 %) for arm B. The median progression-free survival and overall survival were 6.4 months (95 % CI 5.4-7.5 months) and 11.9 months (95 % CI 9.6-13.7 months) for arm A and 6.0 months (95 % CI 5.4-7.0 months) and 11.0 months (95 % CI 8.6-13.1 months) for arm B. CONCLUSION: Sequential administration of topoisomerase inhibitors did not improve on the historical efficacy of standard platinum-doublet chemotherapy for extensive-stage SCLC.