Denaturation of Circular DNA: Supercoil Mechanism

The denaturation transition which takes place in circular DNA is analyzed by extending the Poland-Scheraga model to include the winding degrees of freedom. We consider the case of a homopolymer whereby the winding number of the double stranded helix, released by a loop denaturation, is absorbed by \emph{supercoils}. We find that as in the case of linear DNA, the order of the transition is determined by the loop exponent $c$. However the first order transition displayed by the PS model for $c>2$ in linear DNA is replaced by a continuous transition with arbitrarily high order as $c$ approaches 2, while the second-order transition found in the linear case in the regime $1<c\le2$ disappears. In addition, our analysis reveals that melting under fixed linking number is a \emph{condensation transition}, where the condensate is a macroscopic loop which appears above the critical temperature.Comment: 9 pages, 4 figure

Differentiation between Vergence and Saccadic Functional Activity within the Human Frontal Eye Fields and Midbrain Revealed through fMRI

Eye movement research has traditionally studied solely saccade and/or vergence eye movements by isolating these systems within a laboratory setting. While the neural correlates of saccadic eye movements are established, few studies have quantified the functional activity of vergence eye movements using fMRI. This study mapped the neural substrates of vergence eye movements and compared them to saccades to elucidate the spatial commonality and differentiation between these systems.The stimulus was presented in a block design where the 'off' stimulus was a sustained fixation and the 'on' stimulus was random vergence or saccadic eye movements. Data were collected with a 3T scanner. A general linear model (GLM) was used in conjunction with cluster size to determine significantly active regions. A paired t-test of the GLM beta weight coefficients was computed between the saccade and vergence functional activities to test the hypothesis that vergence and saccadic stimulation would have spatial differentiation in addition to shared neural substrates.Segregated functional activation was observed within the frontal eye fields where a portion of the functional activity from the vergence task was located anterior to the saccadic functional activity (z>2.3; p<0.03). An area within the midbrain was significantly correlated with the experimental design for the vergence but not the saccade data set. Similar functional activation was observed within the following regions of interest: the supplementary eye field, dorsolateral prefrontal cortex, ventral lateral prefrontal cortex, lateral intraparietal area, cuneus, precuneus, anterior and posterior cingulates, and cerebellar vermis. The functional activity from these regions was not different between the vergence and saccade data sets assessed by analyzing the beta weights of the paired t-test (p>0.2).Functional MRI can elucidate the differences between the vergence and saccade neural substrates within the frontal eye fields and midbrain

SEGMENTATION OF LANDSAT-8 IMAGES FOR BURNED AREA DETECTION WITH DEEP LEARNING

Fires damage nature and living beings. Detection of this damage is important for future. In this study, it was aimed to determine burned areas. For this purpose, Landsat-8 images and U-Net model were used. Python language was preferred. Band combinations 7,5,4; 5,3,7; 5,4,3; 4,3,2; 4,3,2,5 and 2,3,4,5,6,7 have been tried. Train and test processes were carried out separately for each band combination. After the train and test processes were completed, a probability result consisting of values between 0-1 was obtained. Then, a threshold value was used. Thus, binary results consisting of 0 and 1 values were obtained. Three different values were preferred for the threshold: 0.1, 0.5 and 0.9. Thus, the effect of threshold value selection on the test results was examined. The prediction results were evaluated using the masks. For this, general accuracy, recall, precision, F1-score and Jaccard score metrics were used. Recall, precision, and F1-score values were calculated for both burned areas and unburned areas. In addition, minimum, maximum, mean, and standard deviation values were calculated for each metric. When the results are examined, it is seen that the model gives better results when the threshold value is 0.1 and 0.5. Among the band combinations, it is seen that the 7,5,4 combination gave better results than the others. For this band combination, the highest mean accuracy is 0.9743 with the 0.5 threshold value. For this threshold mean recall, mean precision and mean F1-score for burned areas are 0.7203, 0.8411 and 0.7601, respectively. And Jaccard score is 0.6328

Chemometric characterization of gamma irradiated chestnuts from Turkey

Chestnut (Castanea sativa Miller) is a valuable natural resource, with high exportation levels. Due to their water content, chestnuts are susceptible to storage problems like dehydration or development of insects and microorganisms. Irradiation has been revealing interesting features to be considered as an alternative conservation technology, increasing food products shelf-life. Any conservation methodology should have a wide application range. Hence, and after evaluating Portuguese cultivars, the assessment of irradiation effects in foreign cultivars might act as an important indicator of the versatility of this technology. In this work, the effects of gamma irradiation (0.0, 0.5 and 3.0 kGy) on proximate composition, sugars, fatty acids (FA) and tocopherols composition of Turkish chestnuts stored at 4 ºC for different periods (0, 15 and 30 days) were evaluated. Regarding proximate composition, the storage time (ST) had higher influence than irradiation dose (ID), especially on fat, ash, carbohydrates and energetic value. Sucrose exhibited similar behavior in response to the assayed ST and ID. The prevalence of ST influence was also verified for FA, tocopherols and sucrose. Lauric, palmitoleic and linolenic acids, were the only FA that undergone some differences with ID. Saturated, monounsaturated and polyunsaturated fatty acids levels were not affected neither by storage nor irradiation. α-Tocopherol was the only vitamer with significant differences among the assayed ST and ID. Overall, Turkish cultivars showed a compositional profile closely related with Portuguese cultivars, and seemed to confirm that gamma irradiation in the applied doses did not change chestnut chemical and nutritional composition

Gamma irradiation improves the nutritional profile of dried and sliced wild Boletus edulis Bull.

Boletus edulis Bull. is a seasonal mushroom with high perishability (shelf-life: 1-3 days at room temperature) [1]. Drying is a widely used postharvest technology, which overcomes those problems. Nevertheless, after slicing, mushrooms need special care to keep their quality [2]. A possible treatment is applying ionizing radiation. Herein, the effects of gamma irradiation (2, 6 and 10 kGy) on nutritional parameters were analyzed in wild B. edulis dried and sliced samples (Bragança, Northeast of Portugal, 2013). Irradiation was performed at Gamma-Pak Sterilizasyon (Çerkezköy, Turkey). The nutritional parameters were determined throughout the storage time (0, 6 and 12 months) according to official procedures. The results were compared considering the mean value of each storage time (ST), including all gamma irradiation (GI) doses, and also the mean value of each dose, with all ST included, allowing verifying the effect of each factor independently. Despite the detected significance in the interaction among ST and GI for all assayed factors, some defined conclusions were obtained: fat, protein and ash contents gave maximal contents in samples irradiated with 10 kGy, while the lowest values were detected in non-irradiated samples. Regarding the effect of ST, these same parameters presented minimal values in samples stored during 12 months. The variation in carbohydrates, which was calculated by difference, was precisely the opposite of the previously described. The variation in energy was less pronounced for both effects. Overall, irradiation treatment, particularly the 10 kGy dose, tended to improve the nutritional profile of sliced-dried B. edulis samples. References [1] Jaworska, G., Bernaś, E. (2009). Food Chemistry, 113, 936-943. [2] Oliveira, F., Sousa-Gallagher, M. J., Mahajan, P. V., & Teixeira, J. A. (2012). Journal of Food Engineering, 108, 507–514.FCT and COMPETE/QREN/UE- strategic projects PEst-OE/AGR/UI0690/2014 (CIMO) and PEst-C/EQB/LA0006/2014 (REQUIMTE); grants SFRH/BD/76019/2011 and SFRH/BPD/72802/2010 to A. Fernandes and J.C.M. Barreira, respectively

Effect of gamma irradiation and extended storage on selected chemical constituents and antioxidant activities of sliced mushroom

Due to its exquisite odor and taste, Boletus edulis Bull.: Fr. mushroom is being increasingly used throughout the world. However, the availability of this product is highly restrained by its seasonality and perishability, demanding special care to keep its quality. Furthermore, mushrooms are often distributed in sliced form, and the slicing operation requires special treatments, besides augmenting the possibility of microbial contamination. Some techniques are currently applied to sliced mushrooms, but these processes had adverse effects on nutrients, odor, texture and taste, besides requiring expensive equipment. Food irradiation is being studied as an alternative technology to improve the quality and durability of determined products, having been previously applied in several mushroom species. Herein, gamma irradiation was applied to dried and sliced samples of B. edulis, at high doses (2, 6 and 10 kGy), and the effects on nutritional, chemical and antioxidant parameters were evaluated throughout storage (6 and 12 months). The results obtained for the chemical parameters do not advised storing B. edulis for such extended periods, since some relevant changes were detected, especially in samples stored for 12 months. In general, the gamma irradiation treatment did not cause further changes in the chemical composition, besides having a slightly positive effect in keeping the antioxidant activity and most of the bioactive compounds profiled in this work, contributing to maintain the potential health effects of this exquisite food, even after extended storage periods.The authors are grateful to the Foundation for Science and Technology, COMPETE/QREN/EU - strategic projects PEst-OE/AGR/UI0690/2014 (CIMO) and PEst-C/EQB/LA0006/2014 (REQUIMTE), FCT/MEC through national funds and co-financed by FEDER, under the Partnership Agreement (PT2020UID/QUI/50006/2013 - POCI/01/0145/FERDER/007265). A. Fernandes and J.C.M. Barreira thank FCT for their grants SFRH/BD/76019/2011 and SFRH/BPD/72802/2010, respectively.info:eu-repo/semantics/publishedVersio

Denaturation of Circular DNA: Supercoils and Overtwist

The denaturation transition of circular DNA is studied within a Poland-Scheraga type approach, generalized to account for the fact that the total linking number (LK), which measures the number of windings of one strand around the other, is conserved. In the model the LK conservation is maintained by invoking both overtwisting and writhing (supercoiling) mechanisms. This generalizes previous studies which considered each mechanism separately. The phase diagram of the model is analyzed as a function of the temperature and the elastic constant $\kappa$ associated with the overtwisting energy for any given loop entropy exponent, $c$. As is the case where the two mechanisms apply separately, the model exhibits no denaturation transition for $c \le 2$. For $c>2$ and $\kappa=0$ we find that the model exhibits a first order transition. The transition becomes of higher order for any $\kappa>0$. We also calculate the contribution of the two mechanisms separately in maintaining the conservation of the linking number and find that it is weakly dependent on the loop exponent $c$.Comment: 10 pages, 6 figure

Reconstructing complex regions of genomes using long-read sequencing technology

Cataloged from PDF version of article.Obtaining high-quality sequence continuity of complex regions of recent segmental duplication remains one of the major challenges of finishing genome assemblies. In the human and mouse genomes, this was achieved by targeting large-insert clones using costly and laborious capillary-based sequencing approaches. Sanger shotgun sequencing of clone inserts, however, has now been largely abandoned, leaving most of these regions unresolved in newer genome assemblies generated primarily by next-generation sequencing hybrid approaches. Here we show that it is possible to resolve regions that are complex in a genome-wide context but simple in isolation for a fraction of the time and cost of traditional methods using long-read single molecule, real-time (SMRT) sequencing and assembly technology from Pacific Biosciences (PacBio). We sequenced and assembled BAC clones corresponding to a 1.3-Mbp complex region of chromosome 17q21.31, demonstrating 99.994% identity to Sanger assemblies of the same clones. We targeted 44 differences using Illumina sequencing and find that PacBio and Sanger assemblies share a comparable number of validated variants, albeit with different sequence context biases. Finally, we targeted a poorly assembled 766-kbp duplicated region of the chimpanzee genome and resolved the structure and organization for a fraction of the cost and time of traditional finishing approaches. Our data suggest a straightforward path for upgrading genomes to a higher quality finished state