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Chengjiao Duan, Linchuan Fang, Congli Yang, Weibin Chen, Yongxing Cui, Shiqing Li
Enzymes in the soil are vital for assessing heavy metal soil pollution. Although the presence of heavy metals is thought to change the soil enzyme system, the distribution of enzyme activities in heavy metal polluted-soil is still unknown. For the first time, using soil zymography, we analyzed the distribution of enzyme activities of alfalfa rhizosphere and soil surface in the metal-contaminated soil. The results showed that the growth of alfalfa was significantly inhibited, and an impact that was most pronounced in seedling biomass and chlorophyll content...
March 13, 2018: Ecotoxicology and Environmental Safety
Yun-Yan Zhang, En Shi, Zhao-Ping Yang, Qi-Fang Geng, Ying-Xiong Qiu, Zhong-Sheng Wang
Parrotia subaequalis is an endangered palaeoendemic tree from disjunct montane sites in eastern China. Due to the lack of effective genomic resources, the genetic diversity and population structure of this endangered species are not clearly understood. In this study, we conducted paired-end shotgun sequencing (2 × 125 bp) of genomic DNA for two individuals of P. subaequalis on the Illumina HiSeq platform. Based on the resulting sequences, we have successfully assembled the complete chloroplast genome of P...
2018: Frontiers in Plant Science
Ramani Baddam, Narender Kumar, Lothar H Wieler, Aditya Kumar Lankapalli, Niyaz Ahmed, Sharon J Peacock, Torsten Semmler
Pyrazinamide (PZA) is an important first-line anti-tuberculosis drug, resistance to which occurs primarily due to mutations in pncA (Rv2043c) that encodes the pyrazinamidase enzyme responsible for conversion of pro-drug PZA into its active form. Previous studies have reported numerous resistance-conferring mutations distributed across the entire length of pncA without any hotspot regions. As different lineages of Mycobacterium tuberculosis display a strong geographic association, we sought to understand whether the genetic background influenced the distribution of mutations in pncA...
March 15, 2018: Scientific Reports
Yan Li, Zhirong Zhang, Junbo Yang, Guanghui Lv
Fritillaria spp. constitute important traditional Chinese medicinal plants. Xinjiang is one of two diversity hotspots in China in which eight Fritillaria species occur, two of which are endemic to the region. Furthermore, the phylogenetic relationships of Xinjiang Fritillaria species (including F. yuminensis) within the genus are unclear. In the present study, we sequenced the chloroplast (cp) genomes of seven Fritillaria species in Xinjiang using the Illumina HiSeq platform, with the aim of assessing the global structural patterns of the seven cp genomes and identifying highly variable cp DNA sequences...
2018: PloS One
Jinxu Gao, Adelphe Mfuh, Yuka Amako, Christina M Woo
Many therapeutics elicit cell-type specific polypharmacology that is executed by a network of molecular recognition events between a small molecule and the whole proteome. However, measurement of the structures that underpin the molecular associations between the proteome and even common therapeutics, such as the nonsteroidal anti-inflammatory drugs (NSAIDs), is limited by the inability to map the small molecule interactome. To address this gap, we developed a platform termed small molecule interactome mapping by photoaffinity labeling (SIM-PAL) and applied it to the in cellulo direct characterization of specific NSAID binding sites...
March 15, 2018: Journal of the American Chemical Society
Wei Zeng, Bei Hu, Liang Tang, Yan-Yan You, Mara Toderici, Maria Eugenia de la Morena-Barrio, Javier Corral, Yu Hu
[This corrects the article DOI: 10.18632/oncotarget.21365.].
February 16, 2018: Oncotarget
Sumire Terasawa, Asuka Kato, Haruki Nishizawa, Takema Kato, Hikari Yoshizawa, Yoshiteru Noda, Jun Miyazaki, Mayuko Ito, Takao Sekiya, Takuma Fujii, Hiroki Kurahashi
Thanatophoric dysplasia (TD) and achondroplasia (ACH) are allelic disorders caused by a constitutively active mutation in the FGFR3 gene. Because TD is a lethal disorder and ACH is non-lethal, they need to be distinguished after ultrasound identification of fetal growth retardation with short limbs. Accordingly, we have developed a noninvasive prenatal test using cell-free fetal DNA in the maternal circulation to distinguish TD and ACH. A multiplex PCR system encompassing five mutation hotspots in the FGFR3 gene allowed us to efficiently identify the responsible mutation in cell-free DNA in all examined pregnancies with a suspected TD or ACH fetus...
March 14, 2018: Congenital Anomalies
Matthew Dankner, April A N Rose, Shivshankari Rajkumar, Peter M Siegel, Ian R Watson
The RAS-RAF-MEK-ERK signaling cascade is among the most frequently mutated pathways in human cancer. Approximately 50% of melanoma patients possess a druggable hotspot V600E/K mutation in the BRAF protein kinase. FDA-approved combination therapies of BRAF and MEK inhibitors are available that provide survival benefits to patients with a BRAF V600 mutation. Non-V600 BRAF mutants are found in many cancers, and are more prevalent than V600 mutations in certain tumor types. For example, between 50-80% of BRAF mutations in non-small cell lung cancer and 22-30% in colorectal cancer encode for non-V600 mutants...
March 15, 2018: Oncogene
Bo Li, Yanan Zhang, Lin Fu, Tong Yu, Shujie Zhou, Luyuan Zhang, Longwei Yin
Owing to inevitable thermal/moisture instability for organic-inorganic hybrid perovskites, pure inorganic perovskite cesium lead halides with both inherent stability and prominent photovoltaic performance have become research hotspots as a promising candidate for commercial perovskite solar cells. However, it is still a serious challenge to synthesize desired cubic cesium lead iodides (CsPbI3 ) with superior photovoltaic performance for its thermodynamically metastable characteristics. Herein, polymer poly-vinylpyrrolidone (PVP)-induced surface passivation engineering is reported to synthesize extra-long-term stable cubic CsPbI3 ...
March 14, 2018: Nature Communications
Henrik Devitt Møller, Marghoob Mohiyuddin, Iñigo Prada-Luengo, M Reza Sailani, Jens Frey Halling, Peter Plomgaard, Lasse Maretty, Anders Johannes Hansen, Michael P Snyder, Henriette Pilegaard, Hugo Y K Lam, Birgitte Regenberg
The human genome is generally organized into stable chromosomes, and only tumor cells are known to accumulate kilobase (kb)-sized extrachromosomal circular DNA elements (eccDNAs). However, it must be expected that kb eccDNAs exist in normal cells as a result of mutations. Here, we purify and sequence eccDNAs from muscle and blood samples from 16 healthy men, detecting ~100,000 unique eccDNA types from 16 million nuclei. Half of these structures carry genes or gene fragments and the majority are smaller than 25 kb...
March 14, 2018: Nature Communications
Hasmik Grigoryan, William M B Edmands, Qing Lan, Henrik Carlsson, Roel Vermeulen, Luoping Zhang, Song-Nian Yin, Gui-Lan Li, Martyn T Smith, Nathaniel Rothman, Stephen M Rappaport
Although benzene has long been recognized as a cause of human leukemia, the mechanism by which this simple molecule causes cancer has been problematic. A complicating factor is benzene metabolism, which produces many reactive intermediates, some specific to benzene and others derived from redox processes. Using archived serum from 20 nonsmoking Chinese workers, 10 with and 10 without occupational exposure to benzene (exposed: 3.2 - 88.9 ppm, controls: 0.002 - 0.020 ppm), we employed an adductomic pipeline to characterize protein modifications at Cys34 of human serum albumin (HSA), a nucleophilic hotspot in extracellular fluids...
March 10, 2018: Carcinogenesis
Jennifer A Sheridan, Bryan L Stuart
Accurately delimiting species and their geographic ranges is imperative for conservation, especially in areas experiencing rapid habitat loss. Southeast Asia currently has one of the highest rates of deforestation in the world, is home to multiple biodiversity hotspots, and the majority of its countries have developing economies with limited resources for biodiversity conservation. Thus, accurately delimiting species and their ranges is particularly important in this region. We examined genetic and morphological variation in the widespread frog species Sylvirana nigrovittata (and its long-treated junior synonym S...
2018: PloS One
Sona Gregorova, Vaclav Gergelits, Irena Chvatalova, Tanmoy Bhattacharyya, Barbora Valiskova, Vladana Fotopulosova, Petr Jansa, Diana Wiatrowska, Jiri Forejt
Hybrid sterility is one of the reproductive isolation mechanisms leading to speciation. Prdm9 , the only known vertebrate hybrid sterility gene, causes failure of meiotic chromosome synapsis and infertility in male hybrids between two mouse subspecies. But within species Prdm9 determines the sites of programmed DNA double-strand breaks and meiotic recombination hotspots. To investigate the relation between Prdm9 -controlled meiotic arrest and asynapsis, we inserted random stretches of consubspecific homology on several autosomal pairs in sterile hybrids and analyzed their ability to form synaptonemal complexes and rescue male fertility...
March 14, 2018: ELife
Barbara Manachini, Giuseppe Bazan, Rosario Schicchi
The general increase of the cultivation and trade of Bt transgenic plants resistant to Lepidoptera pests raises concerns regarding the conservation of animal and plant biodiversity. Demand for biofuels has increased the cultivation and importation of oilseed rape (Brassica napus L.), including transgenic lines. In environmental risk assessments (ERAs) for its potential future cultivation as well as for food and feed uses, the impact on wild Brassicaeae relatives and on non-target Lepidoptera should be assessed...
March 14, 2018: Insect Science
J Hou, W Jiang, L Zhu, S Zhong, H Zhang, J Li, S Zhou, S Yang, Y He, D Wang, X Chen, F Deng, Q Zhang, J Wang, J Hu, W Zhang, L Ding, J Zhao, J Tang
Circular RNAs (CircRNAs) are a type of non-coding RNAs (NcRNAs) with a closed annular structure. Until next-generation sequencing (NGS) is developed, the misunderstanding of circRNAs 'splicing error' has changed, and the mysterious veil of circRNAs has been revealed. NGS provides an approach to investigate circRNAs. Many scholars point out that circRNAs may play an important role in many diseases, especially cancer. At the same time, exosomes, as a kind of extracellular vesicles loaded with many contents, are a hotspot in recent years...
March 13, 2018: Clinical & Translational Oncology
Meenakshi Mehrotra, Rajesh R Singh, Sanam Loghavi, Dzifa Yawa Duose, Bedia A Barkoh, Carmen Behrens, Keyur P Patel, Mark J Routbort, Scott Kopetz, Russell R Broaddus, L Jeffrey Medeiros, Ignacio I Wistuba, Rajyalakshmi Luthra
A suitable clinical-grade platform is required for detection of somatic mutations with high sensitivity in cell-free DNA (cfDNA) of patients with solid tumors. In this study, we evaluated in parallel ultra-deep NGS with MassARRAY and allele-specific droplet digital PCR (ddPCR) for cfDNA genotyping and correlated cfDNA yield and mutation status with overall survival (OS) of patients. We assessed plasma samples from 46 patients with various advanced metastatic solid tumors and known mutations by deep sequencing using an Ampliseq cancer hotspot panel V2 on Ion Proton...
February 13, 2018: Oncotarget
Aleš Hnízda, Milan Fábry, Takaya Moriyama, Petr Pachl, Michael Kugler, Vítězslav Brinsa, David B Ascher, William L Carroll, Petr Novák, Markéta Žaliová, Jan Trka, Pavlína Řezáčová, Jun J Yang, Václav Veverka
Activating mutations in NT5C2, a gene encoding cytosolic purine 5'-nucleotidase (cN-II), confer chemoresistance in relapsed acute lymphoblastic leukemia. Here we show that all mutants became independent of allosteric effects of ATP and thus constitutively active. Structural mapping of mutations described in patients demonstrates that 90% of leukemia-specific allelles directly affect two regulatory hotspots within the cN-II molecule-the helix A region: residues 355-365, and the intersubunit interface: helix B (232-242) and flexible interhelical loop L (400-418)...
February 25, 2018: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
Hossein Tabari, Patrick Willems
Climate change is expected to alter precipitation patterns; however, the amplitude of the change may broadly differ across seasons. Combining different seasons may mask contrasting climate change signals in individual seasons, leading to weakened signals and misleading impact results. A realistic assessment of future climate change is of great importance for arid regions, which are more vulnerable to any change in extreme events as their infrastructure is less experienced or not well adapted for extreme conditions...
March 13, 2018: Scientific Reports
Mitsuko Nakashima, Mitsuhiro Kato, Kazushi Aoto, Masaaki Shiina, Hazrat Belal, Souichi Mukaida, Satoko Kumada, Atsushi Sato, Ayelet Zerem, Tally Lerman-Sagie, Dorit Lev, Huey Yin Leong, Yoshinori Tsurusaki, Takeshi Mizuguchi, Satoko Miyatake, Noriko Miyake, Kazuhiro Ogata, Hirotomo Saitsu, Naomichi Matsumoto
OBJECTIVE: The cytoplasmic fragile X mental retardation 1 interacting proteins 2 (CYFIP2) is a component of the WAVE regulatory complex, which is involved in actin dynamics. An obvious association of CYFIP2 variants with human neurological disorders has never been reported. Here, we identified de novo hotspot CYFIP2 variants in neurodevelopmental disorders and explore the possible involvement of the CYFIP2 mutants in the WAVE signaling pathway. METHODS: We performed trio-based whole exome sequencing (WES) in 210 families and case-only WES in 489 individuals with epileptic encephalopathies...
March 13, 2018: Annals of Neurology
Francles Blanco-Guillot, M Lucía Castañeda-Cediel, Pablo Cruz-Hervert, Leticia Ferreyra-Reyes, Guadalupe Delgado-Sánchez, Elizabeth Ferreira-Guerrero, Rogelio Montero-Campos, Miriam Bobadilla-Del-Valle, Rosa Areli Martínez-Gamboa, Pedro Torres-González, Norma Téllez-Vazquez, Sergio Canizales-Quintero, Mercedes Yanes-Lane, Norma Mongua-Rodríguez, Alfredo Ponce-de-León, José Sifuentes-Osornio, Lourdes García-García
BACKGROUND: Genotyping and georeferencing in tuberculosis (TB) have been used to characterize the distribution of the disease and occurrence of transmission within specific groups and communities. OBJECTIVE: The objective of this study was to test the hypothesis that diabetes mellitus (DM) and pulmonary TB may occur in spatial and molecular aggregations. MATERIAL AND METHODS: Retrospective cohort study of patients with pulmonary TB. The study area included 12 municipalities in the Sanitary Jurisdiction of Orizaba, Veracruz, México...
2018: PloS One
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