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Balázs E Helga, Christoph A O Schmid, Ioana Feher, Dorina Podar, Paul-Marian Szatmari, Olivian Marincaş, Zoltan R Balázs, Peter Schröder
Current physical or chemical methods used for remediation of soils contaminated with hexachlocyclohexane (HCH), leave behind significant levels of pollutants. Given the compound's volatility and persistence in the environment, sites contaminated with HCH remain a concern for the population living in nearby areas. By making use of both the recovery capacity and the pollutant uptake ability of spontaneously growing vegetation, our study aimed to identify native plant species able to cover and moreover take up the HCH left at a former lindane production unit in Turda, Romania...
June 19, 2018: Journal of Environmental Management
Yasin F Dagdas, Pooja Pandey, Yasin Tumtas, Nattapong Sanguankiattichai, Khaoula Belhaj, Cian Duggan, Alexandre Y Leary, Maria Segretin, Mauricio Contreras, Zachary Savage, Virendrasinh S Khandare, Sophien Kamoun, Tolga O Bozkurt
During plant cell invasion, the oomycete Phytophthora infestans remains enveloped by host-derived membranes whose functional properties are poorly understood. P. infestans secretes a myriad of effector proteins through these interfaces for plant colonization. Recently we showed that the effector protein PexRD54 reprograms host-selective autophagy by antagonising antimicrobial-autophagy receptor Joka2/NBR1 for ATG8CL binding (Dagdas, 2016). Here, we show that during infection, ATG8CL/Joka2 labelled defense-related autophagosomes are diverted toward the perimicrobial host membrane to restrict pathogen growth...
June 22, 2018: ELife
Ronen Galaiduk, Ben T Radford, Euan S Harvey
Many fishes undergo ontogenetic habitat shifts to meet their energy and resource needs as they grow. Habitat resource partitioning and patterns of habitat connectivity between conspecific fishes at different life-history stages is a significant knowledge gap. Species distribution models were used to examine patterns in the relative abundance, individual biomass estimates and environmental niche associations of different life stages of three iconic West Australian fishes. Continuous predictive maps describing the spatial distribution of abundance and individual biomass of the study species were created as well predictive hotspot maps that identify possible areas for aggregation of individuals of similar life stages of multiple species (i...
June 21, 2018: Scientific Reports
Kateryna Fesko, Dmitry Suplatov, Vytas Švedas
Understanding the role of specific amino acid residues in the molecular mechanism of a protein's function is one of the most challenging problems in modern biology. A systematic bioinformatic analysis of protein families and superfamilies can help in the study of structure-function relationships and in the design of improved variants of enzymes/proteins, but represents a methodological challenge. The pyridoxal-5'-phosphate (PLP)-dependent enzymes are catalytically diverse and include the aspartate aminotransferase superfamily which implements a common structural framework known as type fold I...
June 2018: FEBS Open Bio
Rob Leurs, Xavier Gómez-Santacana, Sabrina M de Munnik, Prashanna Vijayachandran, Daniel Da Costa Pereira, Jan Paul M Bebelman, Iwan J P de Esch, Henry F Vischer, Maikel Wijtmans
In order to obtain optical control of GPCR function, we set out to develop small-molecule ligands with photoswitchable efficacy in which both configurations bind the target protein but exert distinct pharmacological effects, i.e., stimulate or antagonise GPCR activation. Our design was based on a previously identified efficacy hotspot for the peptidergic chemokine receptor CXCR3 and resulted in the synthesis and characterization of five new azobenzene-containing CXCR3 ligands. G protein activation assay and real-time electrophysiology experiments demonstrated a photoswitching from antagonism to partial agonism and even to full agonism (VUF16216)...
June 21, 2018: Angewandte Chemie
Adrian C Pinder, Arunachalam Manimekalan, J D Marcus Knight, Prasannan Krishnankutty, J Robert Britton, Siby Philip, Neelesh Dahanukar, Rajeev Raghavan
Growing to lengths and weights exceeding 1.5 m and 45 kg, the hump-backed mahseer fish of the Western Ghats biodiversity hotspot, India, is an iconic, mega-faunal species that is globally recognized as a premier freshwater game fish. Despite reports of their high extinction risk, conservation approaches are currently constrained by their lack of valid taxonomic identity. Using an integrative approach, incorporating morphology, molecular analysis and historical photographs, this fish can now be revealed to be conspecific with Tor remadevii, a species lacking a common name, that was initially, but poorly, described in 2007 from the River Pambar, a tributary of the River Cauvery in Kerala...
2018: PloS One
Courtney A Miller, Geraud Canis Tasse Taboue, Mary M P Ekane, Matthew Robak, Paul R Sesink Clee, Corinne Richards-Zawacki, Eric B Fokam, Nkwatoh Athanasius Fuashi, Nicola M Anthony
The amphibian disease chytridiomycosis in amphibians is caused by the chytrid fungus Batrachochytrium dendrobatidis (Bd) and has resulted in dramatic declines and extinctions of amphibian populations worldwide. A hypervirulent, globally-dispersed pandemic lineage (Bd-GPL) is thought to be largely responsible for population declines and extinctions, although numerous endemic lineages have also been found. Recent reports of amphibian declines have been linked to the emergence of Bd in Cameroon, a major hotspot of African amphibian diversity...
2018: PloS One
M Z Yang, T Y Zhang, H J Li, T T Yang, Z J Ding, Q Liu
Postmortem interval (PMI) estimation is one of the most challenging problems in the field of forensic science. Vitreous humor is a hotspot which has been used for PMI estimation and postmortem chemical analysis in forensic pathology. In order to provide novel perspectives for the future research of PMI estimation using vitreous humor, the comparison between vitreous humor with other common body fluids, the effect of temperature on vitreous humor, vitreous humor detection method and data fitting method have been reviewed in this paper...
April 2018: Fa Yi Xue za Zhi
Wahida Ghiloufi, Juyoung Seo, Jinhyun Kim, Mohamed Chaieb, Hojeong Kang
Arid ecosystems constitute 41% of land's surface and play an important role in global carbon cycle. In particular, biological soil crusts (BSC) are known to be a hotspot of carbon fixation as well as mineralization in arid ecosystems. However, little information is available on carbon decomposition and microbes in BSC and key controlling variables for microbial activities in arid ecosystems. The current study, carried out in South Mediterranean arid ecosystem, aimed to evaluate the effects of intact and removed cyanobacteria/lichen crusts on soil properties, soil enzyme activities, and microbial abundances (bacteria and fungi)...
June 19, 2018: Microbial Ecology
Panfeng Guan, Lahu Lu, Lijia Jia, Muhammad Rezaul Kabir, Jinbo Zhang, Tianyu Lan, Yue Zhao, Mingming Xin, Zhaorong Hu, Yingyin Yao, Zhongfu Ni, Qixin Sun, Huiru Peng
Major advances in wheat production are needed to address global food insecurity under future climate conditions, such as high temperatures. The grain yield of bread wheat ( Triticum aestivum L.) is a quantitatively inherited complex trait that is strongly influenced by interacting genetic and environmental factors. Here, we conducted global QTL analysis for five yield-related traits, including spike yield, yield components and plant height (PH), in the Nongda3338/Jingdong6 doubled haploid (DH) population using a high-density SNP and SSR-based genetic map...
2018: Frontiers in Plant Science
Leila Hamzehzadeh, Fatemeh Khadangi, Ehsan Ghayoor Karimiani, Alireza Pasdar, Mohammad Amin Kerachian
OBJECTIVES: Mutation analysis of the Epidermal Growth Factor Receptor downstream has been a main part of colorectal carcinoma evaluation. Large prospective clinical trials have shown only colorectal cancer (CRC) with wild-type KRAS and NRAS responds to anti-Epidermal Growth Factor Receptor treatment. Hence, mutation analysis is necessary prior to treatment. It is essential to conduct studies to learn about the mutation signature of such tumors. The aim of this study was to evaluate the frequency of hotspot mutations in KRAS and NRAS genes in Iranian CRC patients and to explore their correlations with clinicopathologic parameters...
May 25, 2018: Current Problems in Cancer
Zinia Jaman, Ahmed Mufti, Samyukta Sah, Larisa Avramova, David H Thompson
Traditional methods to discover optimal reaction conditions for small molecule synthesis is a time-consuming effort that requires large quantities of material and a significant expenditure of labor. High-throughput techniques are a potentially transformative approach for reaction condition screening, however, rapid validation of the reaction hotspots under continuous flow conditions remains necessary to build confidence in high throughput screening hits. Continuous flow technology offers the opportunity to upscale the screening hotspots and optimize their output of the target compounds due to the exceptional heat and mass transfer ability of flow reactions that are conducted in a smaller and safer reaction volume...
June 19, 2018: Chemistry: a European Journal
Sami Ullah, Hanita Daud, Sarat C Dass, Hadi Fanaee-T, Alamgir Khalil
Identifying the abnormally high-risk regions in a spatiotemporal space that contains an unexpected disease count is helpful to conduct surveillance and implement control strategies. The EigenSpot algorithm has been recently proposed for detecting space-time disease clusters of arbitrary shapes with no restriction on the distribution and quality of the data, and has shown some promising advantages over the state-of-the-art methods. However, the main problem with the EigenSpot method is that it cannot be adapted to detect more than one spatiotemporal hotspot...
2018: PloS One
Emily B Graham, Alex R Crump, David W Kennedy, Evan Arntzen, Sarah Fansler, Samuel O Purvine, Carrie D Nicora, William Nelson, Malak M Tfaily, James C Stegen
Biogeochemical hotspots are pervasive at terrestrial-aquatic interfaces, particularly within groundwater-surface water mixing zones (hyporheic zones), and they are critical to understanding spatiotemporal variation in biogeochemical cycling. Here, we use multi 'omic comparisons of hotspots to low-activity sediments to gain mechanistic insight into hyporheic zone organic matter processing. We hypothesized that microbiome structure and function, as described by metagenomics and metaproteomics, would distinguish hotspots from low-activity sediments by shifting metabolism towards carbohydrate-utilizing pathways and elucidate discrete mechanisms governing organic matter processing in each location...
June 16, 2018: Science of the Total Environment
Viktor R Tóth
Littoral zones of freshwater lakes are exposed to environmental impacts from both terrestrial and aquatic sides, while substantial anthropogenic pressure also affects the high spatial, and temporal variability of the ecotone. In this study, the possibility of monitoring seasonal and spatial changes in reed ( Phragmites australis ) stands using an unmanned aerial vehicle (UAV) based remote sensing technique was examined. Stands in eutrophic and mesotrophic parts of Lake Balaton including not deteriorating (stable) and deteriorating (die-back) patches, were tracked throughout the growing season using a UAV equipped with a Normalized Difference Vegetation Index (NDVI) camera...
2018: Frontiers in Plant Science
Wei Yan, Shuzhen Wei, Qiong Wang, Xilin Xiao, Qinglu Zeng, Nianzhi Jiao, Rui Zhang
Prochlorococcus is the most abundant and smallest known free-living photosynthetic microorganism and is a key player in marine ecosystems and biogeochemical cycles. Prochlorococcus can be broadly divided into high-light-adapted (HL) and low-light-adapted (LL) clades. In this study, we isolated two low-light-adapted I (LLI) strains from the western Pacific Ocean and obtained their genomic data. We reconstructed Prochlorococcus evolution based on genome rearrangement. Our results showed that genome rearrangement might have played an important role in Prochlorococcus evolution...
June 18, 2018: Applied and Environmental Microbiology
Live L Nesse, Roger Simm
Bacteria have the ability to adapt to changing environments through rapid evolution mediated by modification of existing genetic information, as well as by horizontal gene transfer (HGT). This makes bacteria a highly successful life form when it comes to survival. Unfortunately, this genetic plasticity may result in emergence and dissemination of antimicrobial resistance and virulence genes, and even the creation of multiresistant "superbugs" which may pose serious threats to public health. As bacteria commonly reside in biofilms, there has been an increased interest in studying these phenomena within biofilms in recent years...
2018: Advances in Applied Microbiology
Qiuming Luo, Chao Guo, Yi Jun Zhang, Ye Cai, Gang Liu
BACKGROUND: With the reduction of gene sequencing cost and demand for emerging technologies such as precision medical treatment and deep learning in genome, it is an era of gene data outbreaks today. How to store, transmit and analyze these data has become a hotspot in the current research. Now the compression algorithm based on reference is widely used due to its high compression ratio. There exists a big problem that the data from different gene banks can't merge directly and share information efficiently, because these data are usually compressed with different references...
June 18, 2018: BMC Bioinformatics
Ming-Yeng Lin, Yi-Xin Guo, Yu-Cheng Chen, Wei-Ting Chen, Li-Hao Young, Kuo-Jung Lee, Zhu-You Wu, Perng-Jy Tsai
People living near roadways are exposed to high concentrations of ultrafine particles (UFP, diameter < 100 nm). This can result in adverse health effects such as respiratory illness and cardiovascular diseases. However, accurately characterizing the UFP number concentration requires expensive sets of instruments. The development of an UFP surrogate with cheap and convenient measures is needed. In this study, we used a mobile measurement platform with a Fast Mobility Particle Sizer (FMPS) and sound level meter to investigate the spatiotemporal relations of noise and UFP and identify the hotspots of UFP...
September 15, 2018: Science of the Total Environment
Maria Jose Martinez-Harms, Brett A Bryan, Spencer A Wood, David M Fisher, Elizabeth Law, Jonathan R Rhodes, Cynnamon Dobbs, Duan Biggs, Kerrie A Wilson
Experiences with nature through visits to protected areas provide important cultural ecosystem services that have the potential to strengthen pro-environmental attitudes and behavior. Understanding accessibility to protected areas and likely preferences for enjoying the benefits of nature visits are key factors in identifying ways to reduce inequality in access and inform the planning and management for future protected areas. We develop, at a regional scale, a novel social media database of visits to public protected areas in part of the Chilean biodiversity hotspot using geotagged photographs and assess the inequality of access using the home locations of the visitors and socio-economic data...
September 15, 2018: Science of the Total Environment
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