The virome of maize rough dwarf disease: Molecular genome diversification,phylogeny and selection

The main threat to maize production in the Mediterranean area is maize rough dwarf disease (MRDD) caused by Maize rough dwarf virus (MRDV). The analysis of virus diversification is necessary to assess the risk of MRDD outbreaks. We analysed the virome of MRDD by next-generation sequencing using pooled samples prepared from maize plants collected in Spain between 1999 and 2017. This yielded the sequences of all 10 genomic segments from six MRDV isolates plus an additional variant of S5 in one sample. Five of the genomes were 29,145 nucleotides (nt) in length, and the other was 3 nt longer. The six genomes were AT rich with low codon usage bias and the 13 open reading frames (ORFs) showed low potential expression levels. The highest expression levels were predicted for ORFs encoding the non-structural proteins P6, P5-1 and P9-1, and the structural protein P10. There was a strong correlation between higher level expression and T-ended codons, which were the most over-represented class. The concatenate and three individual segments (S3, S6 and S7) each formed a monophyletic group, whereas the remaining segments split into two groups with different clustering relationships relative to two other European MRDV isolates. The MRDV virome showed certain temporal and geographical diversification, but several proteins were highly conserved, especially P7-2. Three significant recombination hotspots were identified among genomic segments and four within segments. The ORFs encoding structural proteins appear under greater purifying selection.     

Identification of promoter motifs regulating ZmeIF4E expression level involved in maize rough dwarf disease resistance in maize (Zea Mays L.)

Maize rough dwarf disease (MRDD, a viral disease) results in significant grain yield losses, while genetic basis of which is largely unknown. Based on comparative genomics, eukaryotic translation initiation factor 4E (eIF4E) was considered as a candidate gene for MRDD resistance, validation of which will help to understand the possible genetic mechanism of this disease. ZmeIF4E (orthologs of eIF4E gene in maize) encodes a protein of 218 amino acids, harboring five exons and no variation in the cDNA sequence is identified between the resistant inbred line, X178 and susceptible one, Ye478. ZmeIF4E expression was different in the two lines plants treated with three plant hormones, ethylene, salicylic acid, and jasmonates at V3 developmental stage, suggesting that ZmeIF4E is more likely to be involved in the regulation of defense gene expression and induction of local and systemic resistance. Moreover, four cis-acting elements related to plant defense responses, including DOFCOREZM, EECCRCAH1, GT1GAMSCAM4, and GT1CONSENSUS were detected in ZmeIF4E promoter for harboring sequence variation in the two lines. Association analysis with 163 inbred lines revealed that one SNP in EECCRCAH1 is significantly associated with CSI of MRDD in two environments, which explained 3.33 and 9.04 % of phenotypic variation, respectively. Meanwhile, one SNP in GT-1 motif was found to affect MRDD resistance only in one of the two environments, which explained 5.17 % of phenotypic variation. Collectively, regulatory motifs respectively harboring the two significant SNPs in ZmeIF4E promoter could be involved in the defense process of maize after viral infection. These results contribute to understand maize defense mechanisms against maize rough dwarf virus.     

Detection of maize rough dwarf virus by enzyme-linked immunosorbent assay in plant hosts and in the planthopper vector

SVPs were efficiently detected by ELISA in individual male and female insects. Females carried more virus per insect and per unit fresh weight, but no significant difference was detected between males and females in vector efficiency. Of insects positive in ELISA, 15–20% were unable to transmit the virus to host plants. Storage of viruliferous hoppers at-20°C decreased the level of viral antigen detected by half in about 240 days. Subviral particles (SVPs) of maize rough dwarf virus were detected in the planthopper vector Laodelphax striatellus and in maize and barley plants using double antibody sandwich ELISA. In purified preparations diluted in buffer, as little as 36 ng/ml of SVPs was detectable whereas after dilution in extracts of healthy frozen planthoppers the sensitivity was reduced to 50 ng/ml. Freezing the hoppers prior to extraction lowered to one third the background reading due to normal components. Neither the dissociated proteins of the SVP nor the viral double-stranded RNA contributed to the ELISA readings.     

Ecological factors driving the long-term evolution of influenza's host range

The evolution of a pathogen''s host range is shaped by the ecology of its hosts and by the physiological traits that determine host specificity. For many pathogen traits, there is a trade-off: a phenotype suitable for infecting one set of hosts poorly infects another. Introducing and analysing a simple evo-epidemiological model, here we study how such a trade-off is expected to affect evolution of the host ranges of influenza viruses. We examine a quantitative trait underlying host specificity, given by an influenza virus''s degree of adaptation to certain conformations of sialic acid receptors, and investigate how this receptor preference evolves in a minimal network of host species, including humans, that differ in life history and receptor physiology. Using adaptive dynamics theory, we establish thresholds in interspecific transmission rates and host population sizes that govern the emergence and persistence of human-adapted viruses. These ecological thresholds turn out to be largely independent of the strength of the evolutionary trade-off, underscoring the importance of ecological conditions in determining a disease''s host range.     

Population-based incidence of lymphoid neoplasms: Twenty years of epidemiological data in the Girona province,Spain

BackgroundThe aim of this study was to describe incidence patterns of lymphoid neoplasms in the Girona province (Spain) (1996–2015), and to predict the number of cases in Spain during 2020.MethodsData were extracted from the Girona cancer registry. Incident cases were classified using the ICD-O-3, third revision, and grouped according to the WHO 2008 classification scheme. Age-adjusted incidence rates to the European standard population (ASRE) were estimated and incidence trends were modeled using Joinpoint.Results4367 lymphoid neoplasms were diagnosed in the Girona province. The ASRE for overall lymphoma was 37.1 (95% CI: 36.0; 38.2), with a marked male predominance in almost all subtypes. During 1996–2015, incidence trends remained stable for broader lymphoma categories. According to our predictions, 17,950 new cases of LNs will be diagnosed in Spain in 2020.ConclusionsThis ‘real-world’ data will provide valuable information to better inform etiological hypotheses and plan future health-care services.     

The influence of temperature, relative humidity and host factors on the attachment and survival of Boophilus microplus (Canestrini) larvae to skin slices

Attachment of B. microplus larvae was examined using slices (0.5 mm) of bovine skin stretched over a suitable medium. Optimal temperature for attachment lay between 31 and 38°C. At 38°C, 70 to 80% had attached by 4 h but this was followed 6–7 h after the release of the larvae by a significant decrease in the percentage attached. By 8 h, the percentage attached had risen again and remained at 70–80% for the subsequent 16 h. Attachment was not influenced by ambient relative humidity within the range 20–75 % on the time scale studied (16 h). Most larvae denied access to the skin surface at 20 or 45 % R.H. (38°C) died within 24 h. Those allowed to feed survived at 45% but most died at 20% R.H. There was no difference in attachment when bovine or rabbit serum or phosphate buffered saline was used, nor when skin was taken from Zebu × European cattle or Herefords. Attachment was no different when skin was taken from neck, rib or rump, or from cattle with different levels of resistance to B. microplus but there was reduced attachment with mouse skin. Attachment was reduced on skin which had been stored at ? 15°C for 1 day but storage at 10°C for 16 h had no effect. These results are related to problems of tick water balance, host specificity and stimuli for tick attachment.     

Genetic and environmental factors reducing the incidence of the storage pest Sitotroga cerealella in maize

The Angoumois grain moth, Sitotroga cerealella (Olivier) (Lepidoptera: Gelechiidae), is found worldwide and infests maize grains in the field and during storage. Transgenic maize resistant to kernel attack by S. cerealella has been developed, but could pose a nutritional risk to humans and livestock. Therefore, alternative sources of resistance posing no threat to consumption should be identified. In this study, our main objectives were to assess genetic variability for kernel damage by S. cerealella under natural infestation and to determine genetic and environmental factors contributing to genotype, year, and genotype*year variability. Factorial regression was performed to obtain a biological explanation for the number of kernels damaged per ear. Seventy-seven Spanish maize landraces along with six hybrid checks were evaluated in 2004, 2005, and 2006. There was variability for kernel damage by natural infestation of S. cerealella among the landraces: popcorn landraces were among the least damaged, whereas hybrid checks were among the most susceptible genotypes. Plant characteristics associated with ear appearance could be the main stimulatory factors for oviposition and feeding of S. cerealella moths, followed by husk coverage of the ear. It was confirmed that temperature is the main environmental factor affecting S. cerealella development. Genotypes sensitive to infestation by S. cerealella were more negatively affected by higher temperatures than the least attractive genotypes, and lower temperatures reduced the number of kernels damaged on the most susceptible genotypes more than on the least susceptible.     

High-Cot sequence analysis of the maize genome

Higher eukaryotic genomes, including those from plants, contain large amounts of repetitive DNA that complicate genome analysis. We have developed a technique based on DNA renaturation which normalizes repetitive DNA, and thereby allows a more efficient outcome for full genome shotgun sequencing. The data indicate that sequencing the unrenatured outcome of a Cot experiment, otherwise known as High-Cot DNA, enriches genic sequences by more than fourfold in maize, from 5% for a random library to more than 20% for a High-Cot library. Using this approach, we predict that gene discovery would be greater than 95% and that the number of sequencing runs required to sequence the full gene space in maize would be at least fourfold lower than that required for full-genome shotgun sequencing.     

The complete sequence of a sugarcane mosaic virus isolate causing maize dwarf mosaic disease in China

The complete sequence of a potyvirus from maize in Zhejiang Province was determined. The RNA was 9596 nucleotides long, excluding the 3′-poly (A) tail, and there was a single long open reading frame (ORF) of 9192 nts encoding a 346.1 ku polyprotein. The polyprotein had substantial amino acid sequence homology with those encoded by the RNAs of a Chinese isolate of sorghum mosaic virus (SrMV-C) and a Bulgarian isolate of maize dwarf mosaic virus, but it was most closely related to sugarcane mosaic virus (SCMV) isolates, for which only partial sequences have been published. According to the published criteria for distinguishing potyviruses, the sequence reported here is clearly a strain of SCMV, but it also showed a surprisingly high amino acid homology with SrMV-C in the HC-Pro, P3 and Cl proteins.     

The complete sequence of a sugarcane mosaic virus isolate causing maize dwarf mosaic disease in China

The complete sequence of a potyvirus from maize in Zhejiang Province was determined. The RNA was 9596 nucleotides long, excluding the 3'-poly (A) tail, and there was a single long open reading frame (ORF) of 9192 nts encoding a 346.1 ku polyprotein. The polyprotein had substantial amino acid sequence homology with those encoded by the RNAs of a Chinese isolate of sorghum mosaic virus (SrMV-C) and a Bulgarian isolate of maize dwarf mosaic virus, but it was most closely related to sugarcane mosaic virus (SCMV) isolates, for which only partial sequences have been published. According to the published criteria for distinguishing potyviruses, the sequence reported here is clearly a strain of SCMV, but it also showed a surprisingly high amino acid homology with SrMV-C in the HC-Pro, P3 and Cl proteins.     

Molecular and Morphological Characterization of Anncaliia azovica sp. n. (Microsporidia) Infecting Niphargogammarus intermedius (Crustacea,Amphipoda) from the Azov Sea

Five out of one hundred adults of Niphargogammarus intermedius caught at the Azov sea shore were found to be infected with microsporidia. The infection was found in the subcuticular fat body and myocytes. Parasites developed in direct contact with host cells, displayed a disporoblastic sporogony and diplokaryotic arrangement of nuclei at all stages. Spores were oval, 4.6–5.8 × 2.6–3.0 μm. Exospore appendages, vesicular–tubular secretions, and the anisofilar polar filament indicated a similarity to Anncaliia species. Sporont surfaces displayed ridges of amorphous material. Meronts and sporonts formed protoplastic extensions, similar to A. vesicularum and A. meligheti. Mature spores possessed a bipartite polaroplast. The polar tube was arranged in one row of 13–18 coils including 0–3 distal coils of lesser diameter. Partial sequencing of SSU, ITS, and LSU regions of rRNA gene (GenBank accessions: KY288064 – KY288065 ) confirmed this new species to be congeneric with A. algerae (# AF069063 ) and A. meligheti (# AY894423 ). The SSU gene of this novel microsporidium shared 99.4% sequence similarity to A. algerae and 98.9% to A. meligheti. Genes for HSP70 and RPB1 amplified with primers designed for A. algerae orthologs displayed 99.7% and 97.4% similarity, respectively, between A. algerae and the novel microsporidium. A new species, Anncaliia azovica, is described based on morphological and molecular characterization.     

Understanding the interacting factors that determine ecological effectiveness of terrestrial protected areas

Protected areas are recognized as an essential tool to safeguard habitat integrity and biodiversity in the Anthropocene. Substantial efforts have been made to clarify the conditions under which they deliver conservation outcomes effectively. Location, spatial design, management strategy and threats, have commonly been identified as key factors. The impacts of these factors have, however, often been evaluated independently, and there is limited information on how their combined and interactive effects can improve or hinder protected area effectiveness. Here we develop a framework for understanding the combined effects of these factors. This has important implications for how protected areas are established and maintained.     

Heterogeneric conjugal transfer of the pheromone-responsive plasmid pIP964 (IncHlyI) of Enterococcus faecalis in the apparent absence of pheromone induction

Abstract Erythromycin-resistant derivatives of the pheromone-responsive plasmid pIP964 from Enterococcus faecalis were constructed to study its host range. This was done by inserting the integrative vector pAT112 and the related replicon pTCR1 harboring oriR of the broad host range plasmid pAMβ1 into the hemolysin-bacteriocin operon of pIP964, to give pTCR2 and pTCR3, respectively. Plasmid pTCR2 was transferred by filter matings from E. faecalis to Enterococcus faecium and Listeria monocytogenes at frequencies of 2×10⁻⁷ and 5×10⁻⁷ per donor, respectively, in the apparent absence of pheromone induction and cellular aggregation. In these hosts, pTCR2 remained intact as a self-replicating element and maintained its transfer capabilities. Plasmid pTCR3, but not pTCR2, was transferred at similar frequencies from E. faecalis to Lactococcus lactis and Streptococcus agalactiae . Thus, the transfer system of pIP964 possesses a broader host-range than its replication system.     

Localization of an origin of replication in Corynebacterium diphtheriae broad host range plasmid pNG2 that also functions in Escherichia coli

Subcloning and protoplast transformation studies identified a 2.6 kb fragment of Corynebacterium diphtheriae plasmid pNG2 which contains an origin of replication (oriR). Molecular combination of the 2.6 kb oriR cartridge with Escherichia coli plasmid pUC18CmR enabled the E. coli cloning vector to replicate within several species of Corynebacterium host cells. A 2.6 kb plasmid formed from the oriR cartridge alone is capable of replicating in E. coli. This suggests that a single origin could be used in vectors shuttling between Corynebacterium spp. and E. coli.     

灰飞虱Bursicon基因的克隆、序列分析及在不同发育阶段的表达

Bursicon是通过G蛋白受体调节昆虫表皮硬化及展翅的功能蛋白, 它在昆虫蜕皮后的表皮硬化过程中起着关键作用。为探讨灰飞虱Laodelphax striatellus的 bursicon的功能, 利用RT-PCR和RACE技术克隆获得1 126 bp的bursicon α和761 bp的bursicon β全长序列, 将其分别命名为Lsburs-α和Lsburs-β。生物信息学分析表明： Lsburs-α开放阅读框长483 bp, 编码160个氨基酸, 该蛋白具有2个N-豆蔻酰化位点、 3个酪蛋白激酶Ⅱ磷酸化位点以及2个蛋白激酶C磷酸化位点。Lsburs-β开放阅读框长417 bp, 编码138个氨基酸, 该蛋白具有2个N-豆蔻酰化位点、 3个酪蛋白激酶Ⅱ磷酸化位点以及1个酪氨酸激酶磷酸化位点。qRT-PCR结果表明： Lsburs-α和Lsburs-β在灰飞虱各龄期均有转录表达, 并在若虫期随龄期增加呈上升趋势, 在羽化期达到峰值, 成虫期表达量逐渐降低。结果提示bursicon与灰飞虱蜕皮后的外表皮硬化关系密切。本文结果为深入研究bursicon的功能、受体调节和信号通路等奠定了基础。     

Identification and Genomic Variability of Prune dwarf virus Variants Infecting Stone Fruit Trees in Turkey

Prune dwarf virus (PDV), a pathogen of stone fruit trees worldwide, shows a great variability in its biological, serological and molecular properties. The coat protein sequences of ten PDV variants from different stone fruit tree species in Turkey were determined. The sequence for each variant was 657 nucleotides in length. The phylogenetic analyses of the sequences of the Turkish variants and of additional sequences of other PDV variants from international databases indicate the existence of four groups of PDV variants: one contains cherry variants that differs in group specific conserved amino acids; a second contains one apricot and cherry variants, most members of the group being Turkish variants; a third contains mixed variants from cherry, peach, plum trees and an almond tree; and a fourth contains only variants from almond trees. Based on their hosts, we propose the nomenclature of these groups as cherry I, cherry II, mixed and almond groups, respectively.     

Ethnic groups and biological diversity in medieval Spain: analysis of a Jew Necropolis from Sevilla

The skulls and mandibles of adults individuals from a Jewish necropolis of Sevilla (La Buhayra), (V–IX Cent. A.D.) have been analyzed. The results show that Sevillian Jews, both males and females, present narrow skulls with a notable dolichocrany. Sexual differences in both the height of the skull and the mandible robustness have been found. A comparison between Sevillian Jews and other Iberian samples from different epochs (Neolithic-Bronze to Centuries A.D.) has been carried out by means of a principal component analysis taken only into account the variability between groups. Results of the analysis showed a certain degree of biological differentiation between Sevillian and Catalonian Jews (XI–XIVth Centuries A.D.) which can be justified not only by the geographical distance and the temporal gap between the two groups, but also by the intrinsic heterogeneity of Jews (Nathan, 1961a, b; Nathan et al., 1963; Arensburg et al., 1980). The existence of some degree of biological variability between several ethnic-religious groups (Jew, Christians and Moslems) can be detected although they share a common Mediterranean background. Paper presented at the 4^th congress of the European Anthropology Association (Florence, Sept. 1984).     

Identifying the factors that determine the severity and type of alien bird impacts

Aim

To identify traits related to the severity and type of environmental impacts generated by alien bird species, in order to improve our ability to predict which species may have the most damaging impacts.

Location

Global.

Methods

Information on traits hypothesized to influence the severity and type of alien bird impacts was collated for 113 bird species. These data were analysed using mixed effects models accounting for phylogenetic non‐independence of species.

Results

The severity and type of impacts generated by alien bird species are not randomly distributed with respect to their traits. Alien range size and habitat breadth were strongly associated with impact severity. Predation impacts were strongly associated with dietary preference, but also with alien range size, relative brain size and residence time. Impacts mediated by interactions with other alien species were related to alien range size and diet breadth.

Main conclusions

Widely distributed generalist alien birds have the most severe environmental impacts. This may be because these species have greater opportunity to cause environmental impacts through their sheer number and ubiquity, but this could also be because they are more likely to be identified and studied. Our study found little evidence for an effect of per capita impact on impact severity.

     

Native-range research assists risk analysis for non-targets in weed biological control: the cautionary tale of the broom seed beetle

Abstract  This case study considers the broom seed beetle, Bruchidius villosus , a narrowly oligophagous species within the Fabaceae, subtribe Genistinae for which in-depth native-range studies have been vital to help understand the likely field host specificity following release. Bruchidius villosus has been used in three countries as a classical biological control agent against Scotch broom, Cytisus scoparius . Original host-specificity testing of a UK population, where this species had only been observed developing on C. scoparius , suggested this population was specific to the target. The beetle was released in New Zealand. Following release, however, the agent exhibited a broader host range than in the tests, but not a broader host range than that of the species as a whole. Subsequent studies in the native range using surveys and field testing have helped to show why B. villosus populations exhibit higher specificity in the native range than would be expected from the species' host range. This case is used to illustrate the contribution native-range studies can make to science-based risk analysis of biological control agents against weeds. By doing so, they also highlight the associated risks of ignoring native-range studies and adopting of a 'grab-and-run' approach to obtaining classical biological control agents.     

Host selectivity,haustorial anatomy and impact of the invasive parasite Parentucellia viscosa on floodplain vegetative communities in Japan

The parasitic plant Parentucellia viscosa has been introduced recently to the Japanese floodplain. Because of its parasitic nature and high fecundity, P. viscosa may well become a major plant invader with a significant impact on floodplain ecosystems. Thus, a knowledge of the host selectivity of P. viscosa will not only provide basic biological information, but will also contribute to the understanding of floodplain vegetation conservation. We evaluated the host selectivity by comparing the observed numbers of haustoria with those expected from the relative below‐ground biomass. In addition, we examined the haustorial anatomy to determine whether haustoria are functional, and compared the above‐ground biomass of three functional plant groups (grasses, legumes and nonleguminous forbs) in intact and parasite removal quadrats. We found that haustoria were nonrandomly distributed amongst host species, suggesting host preference for Poaceae and Fabaceae. In addition, haustoria attached to certain forbs did not penetrate into the stele. The above‐ground biomass of grasses and legumes was increased significantly by the removal of P. viscosa, but the biomass of forbs did not change significantly. These results suggest that host preference depresses the performance of Poaceae and Fabaceae, thus affecting the competitive relationships among plants, meaning that P. viscosa may pose a serious threat to indigenous endangered legumes and grasses. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 170 , 69–78.