Geographic separation and genetic differentiation of populations are not coupled with niche differentiation in threatened Kaiser's spotted newt (Neurergus kaiseri)

The combination of niche modelling and landscape genetics (genomics) helps to disentangle processes that have shaped population structure in the evolutionary past and presence of species. Herein, we integrate a comprehensive genomic dataset with ecological parameters and niche modelling for the threatened Kaiser's newt, a newt species adapted to mountain spring-ponds in Iran. Genomic analysis suggests the existence of two highly differentiated clades North and South of the Dez River. Genetic variation between the two clades (76.62%) was much greater than within clades (16.25%), suggesting that the Dez River prevented gene flow. River disconnectivity, followed by geographic distance, contributed mostly to genetic differentiation between populations. Environmental niche and landscape resistance had no significant influence. Though a significant difference between climatic niches occupied by each clade at the landscape-scale, habitat niches at the local-scale were equivalent. 'Niche similarity analysis' supported niche conservatism between the two clades despite the southward shift in the climatic niche of the Southern clade. Accordingly, populations of different clades may occupy different climatic niches within their ancestral niche. Our results indicate that the change of climatic conditions of geographically and genetically separated populations does not necessarily result in the shift of an ecological niche

Real-time Internet of Things Architecture for Wireless Livestock Tracking

Automatic livestock tracking is necessary for countries facing stock theft problems, like South Africa and Kenya. This paper presents a conceptual design of architecture for real-time wireless livestock tracking based on Internet of Things paradigm. It is a hierarchical model consisting of three building blocks, where the first block is represented with wireless sensor network. Additionally, we have developed a low-power device for livestock tracking in an outdoor environment. The animal tracking device (AnTrack) is self-sustainable with a watertight solar panel(s), designed as a collar to be worn by the animals. A detailed analysis of the AnTrack power consumption proves that the device is capable to generate enough supply power, even when there is no sunshine for a week. This device can be used as a robust building block of future real-time Internet of Things livestock tracking solutions

Deep learning improves pancreatic cancer diagnosis using RNA-based variants

For optimal pancreatic cancer treatment, early and accurate diagnosis is vital. Blood-derived biomarkers and genetic predispositions can contribute to early diagnosis, but they often have limited accuracy or applicability. Here, we seek to exploit the synergy between them by combining the biomarker CA19-9 with RNA-based variants. We use deep sequencing and deep learning to improve differentiating pancreatic cancer and chronic pancreatitis. We obtained samples of nucleated cells found in peripheral blood from 268 patients suffering from resectable, non-resectable pancreatic cancer, and chronic pancreatitis. We sequenced RNA with high coverage and obtained millions of variants. The high-quality variants served as input together with CA19-9 values to deep learning models. Our model achieved an area under the curve (AUC) of 96% in differentiating resectable cancer from pancreatitis using a test cohort. Moreover, we identified variants to estimate survival in resectable cancer. We show that the blood transcriptome harbours variants, which can substantially improve noninvasive clinical diagnosis

The antioxidant and antiproliferative activities of methanolic extracts from Njavara rice bran

<p>Abstract</p> <p>Background</p> <p>Free radical-induced oxidative stress is the root cause for many human diseases. Naturally occurring antioxidant supplements from plants are vital to counter the oxidative damage in cells. The main objective of the present study was to characterize the antioxidant and antiproliferative potential of rice bran extracted from an important Indian rice variety, Njavara and to compare the same with two commercially available basmati rice varieties: Vasumathi, Yamini and a non medicinal variety, Jyothi.</p> <p>Methods</p> <p>Methanolic extracts of rice bran from four varieties; Vasumathi, Yamini, Jyothi and Njavara were used to study their total phenolic and flavonoid contents, <it>in vitro </it>antioxidant activities including total antioxidant activity, scavenging of nitric oxide and 1,1-Diphenyl-2-picrylhydrazyl (DPPH) radical, reducing power and cytotoxic activity in C6 glioma cells. Correlation coefficient and regression analysis were done by using Sigmastat version 3.1 and Stata statistical package respectively.</p> <p>Results</p> <p>Rice bran methanolic extract from Njavara showed the highest antioxidant and cell cytotoxic properties compared to the other three rice varieties. IC₅₀values for scavenging DPPH and nitric oxide were in the range of 30.85-87.72 μg/ml and 52.25-107.18 μg/ml respectively. Total antioxidant activity and reducing power were increased with increasing amounts of the extract. Total phenolic and flavonoid contents were in the range of 3.2-12.4 mg gallic acid-equivalent (GAE)/g bran and 1.68-8.5 mg quercetin-equivalent (QEE)/g bran respectively. IC₅₀values of cytotoxic assay (MTT assay) were 17.53-57.78 μg/ml. Correlation coefficient and regression analysis of phenolic content with DPPH and NO scavenging, MTT (-[4,5-dimethylthiazol-2-yl]-2,5-diphenyl tetrazolium bromide) assay, total antioxidant assay and reducing power showed a highly significant correlation coefficient values (96-99%) and regression values (91-98%).</p> <p>Conclusion</p> <p>The results of the present study show that the crude methanolic extract from Njavara rice bran contains significantly high polyphenolic compounds with superior antioxidant activity as evidenced by scavenging of free radicals including DPPH and NO. Njavara extracts also showed highest reducing power activity, anti-proliferative property in C6 glioma cells. In conclusion, it is conceivable that the Njavara rice variety could be exploited as one of the potential sources for plant - based pharmaceutical products.</p

A Phylogeny and Timescale for the Evolution of Pseudocheiridae (Marsupialia: Diprotodontia) in Australia and New Guinea

Pseudocheiridae (Marsupialia: Diprotodontia) is a family of endemic Australasian arboreal folivores, more commonly known as ringtail possums. Seventeen extant species are grouped into six genera (Pseudocheirus, Pseudochirulus, Hemibelideus, Petauroides, Pseudochirops, Petropseudes). Pseudochirops and Pseudochirulus are the only genera with representatives on New Guinea and surrounding western islands. Here, we examine phylogenetic relationships among 13 of the 17 extant pseudocheirid species based on protein-coding portions of the ApoB, BRCA1, ENAM, IRBP, Rag1, and vWF genes. Maximum parsimony, maximum likelihood, and Bayesian methods were used to estimate phylogenetic relationships. Two different relaxed molecular clock methods were used to estimate divergence times. Bayesian and maximum parsimony methods were used to reconstruct ancestral character states for geographic provenance and maximum elevation occupied. We find robust support for the monophyly of Pseudocheirinae (Pseudochirulus + Pseudocheirus), Hemibelidinae (Hemibelideus + Petauroides), and Pseudochiropsinae (Pseudochirops + Petropseudes), respectively, and for an association of Pseudocheirinae and Hemibelidinae to the exclusion of Pseudochiropsinae. Within Pseudochiropsinae, Petropseudes grouped more closely with the New Guinean Pseudochirops spp. than with the Australian Pseudochirops archeri, rendering Pseudochirops paraphyletic. New Guinean species belonging to Pseudochirops are monophyletic, as are New Guinean species belonging to Pseudochirulus. Molecular dates and ancestral reconstructions of geographic provenance combine to suggest that the ancestors of extant New Guinean Pseudochirops spp. and Pseudochirulus spp. dispersed from Australia to New Guinea ∼12.1–6.5 Ma (Pseudochirops) and ∼6.0–2.4 Ma (Pseudochirulus). Ancestral state reconstructions support the hypothesis that occupation of high elevations (>3000 m) is a derived feature that evolved on the terminal branch leading to Pseudochirops cupreus, and either evolved in the ancestor of Pseudochirulus forbesi, Pseudochirulus mayeri, and Pseudochirulus caroli, with subsequent loss in P. caroli, or evolved independently in P. mayeri and P. forbesi. Divergence times within the New Guinean Pseudochirops clade are generally coincident with the uplift of the central cordillera and other highlands. Diversification within New Guinean Pseudochirulus occurred in the Plio-Pleistocene after the establishment of the Central Range and other highlands

Design of a RFID System for Real-Time Tracking of Laboratory Animals

In this paper, a real-time RFID system capable of tracking laboratory animals for behavior analysis purposes was designed and implemented. Four passive RFID tags based on low frequency (LF) were designed and implemented from first principles. The tags can be read by any RFID reader that operates on the low frequency range 125-134 kHz. The tags were designed through the investigation of various antenna, encoding, modulation, and energy harvesting techniques. The tag receives the electromagnetic signal via the antenna, and converts it to a DC signal that the microcontroller can use to manipulate the electromagnetic signal with the data such that the reader can decode the unique tag identifier. RFID sensors were designed and implemented to collect data from various monitored areas of a semi natural environment. The data is sent to a central data coordinator for pre-processing and middleware for data error checking, display and storage. The data is stored in an online database which is used to produce statistical information about the area within which the RFID system is deployed. The RFID system can successfully detect and store movement data in real time. A read range of 14.5cm was achieved.http://link.springer.com/journal/112772018-08-30hb2017Electrical, Electronic and Computer Engineerin

Comparison of Geostatistical Methods to Determine the Best Bioclimatic Data Interpolation Method for Modelling Species Distribution in Central Iran

Climatic change can impose physiological constraints on species and can therefore affect species distribution. Bioclimatic predictors, including annual trends, regimes, thresholds and bio-limiting factors are the most important independent variables in species distribution models. Water and temperature are the most limiting factors in arid ecosystem in central Iran. Therefore, mapping of climatic factors in species distribution models seems necessary. In this study, we describe the extraction of 20 important bioclimatic variables from climatic data and compare different interpolation methods including inverse distance weighting, ordinary kriging, kriging with external trend, cokriging, and five radial basis functions. Normal climatic data (1950-2010) in 26 synoptic stations in central Iran were used to extract bioclimatic data. Spatial correlation, heterogeneity and trend in data were evaluated using three models of semivariogram (spherical, exponential and Gaussian) and the best model was selected using cross validation. The optimum model for bioclimatic variables was assessed based on the root mean square error and mean bias error. Exponential model was considered to be the best fit mathematical model to empirical semivariogram. IDW and cokriging were recognised as the best interpolating methods for average annual temperature and annual precipitation, respectively. Use of elevation as an auxiliary variable appeared to be necessary for optimizing interpolation methods of climatic and bioclimatic variables