Assay for lipid peroxides in animal tissues by thiobarbituric acid reaction

Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N^2) space and O(N^2 L) time, but FastTree requires just O( NLa + N sqrt(N) ) memory and O( N sqrt(N) log(N) L a ) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.

/pdf/fast-tree-computing-large-minimum-evolution-trees-with-4grq0gwfpy.pdf

Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix

Pyrethroids are now the fourth most used group of insecticides worldwide. Employed in agriculture and in urban areas, they are detected in waterways at concentrations that are lethally and sublethally toxic to aquatic organisms. Highly lipophilic, pyrethroids accumulate in sediments and bioaccumulate in fishes. Additionally, these compounds are demonstrated to act as endocrine disrupting compounds (or EDCs) in mammals and fishes, and therefore interfere with endocrine signaling by blocking, mimicking, or synergizing endogenous hormones through direct receptor interactions, and indirectly via upstream signaling pathways. Pyrethroid metabolites have greater endocrine activity than their parent structures, and this activity is dependent on the enantiomer present, as some pyrethroids are chiral. Many EDCs studied thus far in fish have known estrogenic or antiestrogenic effects, and as such cause the inappropriate or altered expression of genes or proteins (i.e., Vtg–vitellogenin, Chg–choriogenin), often leadi...

Pyrethroid Pesticides as Endocrine Disruptors: Molecular Mechanisms in Vertebrates with a Focus on Fishes.

In March 2020, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. At the genus rank, 20 new genera were added, two were deleted, one was moved, and three were renamed. At the species rank, 160 species were added, four were deleted, ten were moved and renamed, and 30 species were renamed. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.

/pdf/2020-taxonomic-update-for-phylum-negarnaviricota-riboviria-2n5y73t4uf.pdf

2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

Developmental toxicity of cypermethrin in embryo-larval stages of zebrafish.

Beta-cypermethrin impairs reproductive function in male mice by inducing oxidative stress.

Citrus plants are natural hosts of five viroid species and large numbers of sequence variants. In this paper a simple and sensitive one step multiplex RT-PCR protocol with an internal control was utilised to simultaneously detect and differentiate five citrus viroids: Citrus exocortis viroid (CEVd), Citrus bent leaf viroid (CBLVd), Hop stunt viroid (HSVd), Citrus viroid-III (CVd-III) and Citrus viroid-IV (CVd-IV). In addition, a micro and rapid total nucleic acid extraction method was developed and the protocol applied to evaluate the occurrence and distribution of citrus viroids in China.

A rapid one-step multiplex RT-PCR assay for the simultaneous detection of five citrus viroids in China

An emerging virus-like flower yellowing disease (FYD) of green Sichuan pepper (Zanthoxylum armatum v. novemfolius) has been recently reported. Four new RNA viruses were discovered in the FYD-affected plant by the virome analysis using high-throughput sequencing of transcriptome and small RNAs. The complete genomes were determined, and based on the sequence and phylogenetic analysis, they are considered to be new members of the genera Nepovirus (Secoviridae), Idaeovirus (unassigned), Enamovirus (Luteoviridae), and Nucleorhabdovirus (Rhabdoviridae), respectively. Therefore, the tentative names corresponding to these viruses are green Sichuan pepper-nepovirus (GSPNeV), -idaeovirus (GSPIV), -enamovirus (GSPEV), and -nucleorhabdovirus (GSPNuV). The viral population analysis showed that GSPNeV and GSPIV were dominant in the virome. The small RNA profiles of these viruses are in accordance with the typical virus-plant interaction model for Arabidopsis thaliana. Rapid and sensitive RT-PCR assays were developed for viral detection, and used to access the geographical distributions. The results revealed a correlation between GSPNeV and the FYD. The viruses pose potential threats to the normal production of green Sichuan pepper in the affected areas due to their natural transmission and wide spread in fields. Collectively, our results provide useful information regarding taxonomy, transmission and pathogenicity of the viruses as well as management of the FYD.

https://www.mdpi.com/1999-4915/11/8/696/pdf

Discovery of Four Novel Viruses Associated with Flower Yellowing Disease of Green Sichuan Pepper ( Zanthoxylum armatum ) by Virome Analysis

Eureka lemon (Citrus limon) is an economically important crop in China. In 2009, a new disease was observed on Eureka lemon in an orchard of Ruili city in Yunnan Province. Nearly 10% of the plants were symptomatic with yellow vein clearing on lateral veins, combined with leaf crinkling and warping of young leaves. Water-soaked appearances were also seen on the adaxial leaf veins. The symptoms were present on mature leaves, resulting in almost 20% yield reduction. The symptoms on leaves were more severe in spring and autumn than in summer. This disease was transmitted by grafting from infected Eureka lemon to six lemon (C. limon) varieties (Femminello, Fino, Villafranca, Verna, Kutdiken, and Monachello) and two sour orange (C. aurantium) varieties (Daidai, Morocco), with inoculated plants showing similar symptoms. Variable symptoms were observed on other hosts, including severe yellowing and vein clearing on Dweet tangor (C. reticulata × C. sinensis), slight vein clearing on Tongshui 72-1 sweet orange (C. sinensis) and Marsh grapefruit (C. paradisi), but no symptoms were observed on Etrog citron (C. medica), Mexican lime (C. aurantifolia), or Ponkan (C. reticulata). When infected branches from Etrog citron, Mexican lime, and Ponkan were grafted onto healthy Morocco sour orange, typical yellowing and vein clearing symptoms were observed. In the mechanical transmission trials using eight herbaceous plant species, leaf rolling, shrinking, and pointed necrosis were observed on Vigna unguiculata, slight leaf rolling symptoms were observed on Capsicum frutescens, whereas Lycopersicum esculenum, Nicotiana benthamiana, Momordica charantia, Solanum melongena, Cucumis sativus, and Sesamum indicum remained symptomless. Symptom expression was influenced by temperature, being visible between 18 and 24°C but disappearing over 32°C. Crude extracts from young symptomatic lemon leaves were negatively stained for transmission electron microscopy observation (1) and showed filamentous virus particles of 13 to 15 × 400 to 1,000 nm. The described combination of symptoms in citrus species and herbaceous indicators, and virus morphology revealed by electron microscopy, suggested presence of Citrus yellow vein clearing virus (CYVCV). RNA extractions were made from 52 samples of Eureka lemon with yellow vein clearing symptoms. A one-step RT-PCR using primer pair (sense: 5'-TACCGCAGCTATCCATTTCC-3' and antisense: 5'-GCAGAAATCCCGAACCACTA-3'), designed from coat protein gene of CYVCV genome (GenBank Accession No. JX040635) (1), was performed. All of the symptomatic samples yielded the expected cDNA fragment and no amplicon was obtained from healthy plants. Three PCR amplicons were selected for cloning and sequencing. BLAST analysis showed that these nucleotide sequences (KJ859679 to 81) had greater than 97% nucleotide identity with the corresponding region of CYVCV reference genome (2), and therefore, this disease was associated with CYVCV. Symptoms resembling CYVCV infection were observed in China before (3); however, to our knowledge, this is the first proven report of CYVCV present in China. The identification of the pathogen now allows for appropriate field management and control measures. References: (1) V. Grimaldi et al. 13th IOCV Conference, 343-345, 1996. (2) G. Loconsole et al. Phytopathology 102:1168, 2012. (3) C. Zhou et al. 18th IOCV Conference, 44, 2010.

First Report of Citrus yellow vein clearing virus on Lemon in Yunnan, China

In 2009, a new citrus viral disease caused by Citrus yellow vein clearing virus (CYVCV) was discovered in China. To more effectively monitor the presence of CYVCV, a survey was conducted in 166 citrus orchards from 11 major citrus-growing provinces in China from May 2014 to April 2016. In all, 458 of a total of 2,350 citrus samples tested positive for CYVCV, demonstrating that the virus is widely distributed in China. In this study, the complete genome sequences of 19 CYVCV isolates from different provinces and hosts were sequenced and characterized. Comparisons of the whole-genome sequences of these 19 CYVCV isolates as well as 4 isolates previously reported from around the world revealed that the sequence identity ranged from 97.1 to 99.8%, indicating that there is a very low level of sequence heterogeneity among CYVCV isolates of different geographic origins and hosts. Phylogenetic analysis of these 23 genomic sequences suggested that all of the isolates from China were clustered into the same clade, clearly apart from the CYVCV isolates from Turkey and Pakistan. To our knowledge, this is the first extensive survey conducted in China for CYVCV incidence.

https://apsjournals.apsnet.org/doi/pdf/10.1094/PDIS-05-16-0679-RE

Yan Zhou

Papers

Beta-cypermethrin impairs reproductive function in male mice by inducing oxidative stress.

A rapid one-step multiplex RT-PCR assay for the simultaneous detection of five citrus viroids in China

Discovery of Four Novel Viruses Associated with Flower Yellowing Disease of Green Sichuan Pepper ( Zanthoxylum armatum ) by Virome Analysis

First Report of Citrus yellow vein clearing virus on Lemon in Yunnan, China

Occurrence, Distribution, and Molecular Characterization of Citrus yellow vein clearing virus in China