The influence of prey identity and size on selection of prey by two marine fishes

Laboratory experiments were conducted with two predatory fishes, Lagodon rhomboides (Linnaeus) and Syngnathus floridae (Jordan & Gilbert), to determine if prey selection was a result of predator preference or prey accessibility. Prey consisted of two species of caridean shrimp, Tozeuma carolinense (Kingsley) and Hippolyte zostericola (Smith), that commonly inhabit seagrass meadows. Natural diets of both predators revealed that selection ofTozeuma and Hippolyte was not related to their field densities. My experiments demonstrated that natural prey selection was a consequence of prey accessibility, not predator preference. Experiments examining the role of prey size in predator preference revealed that large individuals were significantly preferred over small individuals. Observations of prey behavior indicated that prey motion affected predator choice. These results suggest that predator preference was primarily determined by prey visibility and that the combined effects of prey size and motion contributed to the visibility of these prey.     

The peopling of New Guinea: evidence from class I human leukocyte antigen.

This study utilizes newly developed direct DNA typing methods for human leukocyte antigens (HLA) to provide new information about the peopling of New Guinea. The complete polymorphism of eight Melanesian populations was examined. The groups included were highlanders, northern and southern highlands fringe populations, a Sepik population, northern and southern coastal New Guinea populations, and populations from the Bismarck Archipelago and New Caledonia. The study concluded that, based on HLA and other evidence. Melanesians are likely to have evolved largely from the same ancestral stock as Aboriginal Australians but to have since differentiated. Highlanders are likely to be descendants of earlier migrations who have been isolated for a long period of time. Northern highlands fringe and Sepik populations are likely to share a closer common ancestry but to have differentiated due to long term isolation and the relative proximity to the coast of the Sepik. Southern fringe populations are likely to have a different origin, possibly from the Gulf region, although there may be some admixture with neighboring groups. Coastal populations have a wider range of polymorphisms because of the genetic trail left by later population movement along the coast from Asia that did not reach Australia or remote Oceania. Other polymorphisms found in these populations may have been introduced by the movement of Austronesian-speaking and other more recent groups of people into the Pacific, because they share many polymorphisms with contemporary southeast Asians, Polynesians, and Micronesians that are not found in highlanders or Aboriginal Australians. There is evidence suggestive of later migration to Melanesia from Polynesia and Micronesia.     

Transformation and segregation of GFP fluorescence and glyphosate resistance in horseweed (<Emphasis Type="Italic">Conyza canadensis</Emphasis>) hybrids

The goal of this research was to generate a breeding population of horseweed segregating for glyphosate resistance. In order to generate a marker to select between hybrids of glyphosate resistant (GR) and glyphosate susceptible (GS) horseweed, a GR horseweed accession from western Tennessee was transformed with a green fluorescent protein (GFP) transgene. The GFP marker allowed for the simple and accurate determination of GR hybrid plants by visual observation. GR plants were shown to be transgenic via the green fluorescence under UV light, and resistant to glyphosate when sprayed with the field-use-rate 0.84 kg acid equivalent ha⁻¹ of glyphosate (i.e. Roundup^TM) herbicide. An in vitro screen for glyphosate resistance in seedlings was developed, and a 5 μM glyphosate concentration was found to reduce dry weight in GS seedlings but not in GR seedlings. The GR plants containing GFP were then hand-crossed with GS plants from eastern Tennessee under greenhouse conditions, with GS plants acting as the pollen acceptor. Resulting seed was collected and germinated for GFP fluorescence screening. Seedlings that exhibited the transgenic GFP phenotype were selected as F₁ hybrids between GR and GS horseweed. Thirty GS×GR hybrids were produced on the basis of a green-fluorescent GFP phenotype of GR plants. GS×GFP/GR F₁ hybrids produced F₂ seeds, and F₂ plants were shown to segregate for GFP fluorescence and glyphosate resistance independently. Both traits segregated at a Mendelian 3:1 ratio, indicating a single gene is responsible for each phenotype.     

CRISPR/Cas9-mediated targeted T-DNA integration in rice

Key message

Combining with a CRISPR/Cas9 system, Agrobacterium-mediated transformation can lead to precise targeted T-DNA integration in the rice genome.

Abstract

Agrobacterium-mediated T-DNA integration into the plant genomes is random, which often causes variable transgene expression and insertional mutagenesis. Because T-DNA preferentially integrates into double-strand DNA breaks, we adapted a CRISPR/Cas9 system to demonstrate that targeted T-DNA integration can be achieved in the rice genome. Using a standard Agrobacterium binary vector, we constructed a T-DNA that contains a CRISPR/Cas9 system using SpCas9 and a gRNA targeting the exon of the rice AP2 domain-containing protein gene Os01g04020. The T-DNA also carried a red fluorescent protein and a hygromycin resistance (hptII) gene. One version of the vector had hptII expression driven by an OsAct2 promoter. In an effort to detect targeted T-DNA insertion events, we built another T-DNA with a promoterless hptII gene adjacent to the T-DNA right border such that integration of T-DNA into the targeted exon sequence in-frame with the hptII gene would allow hptII expression. Our results showed that these constructs could produce targeted T-DNA insertions with frequencies ranging between 4 and 5.3% of transgenic callus events, in addition to generating a high frequency (50?80%) of targeted indel mutations. Sequencing analyses showed that four out of five sequenced T-DNA/gDNA junctions carry a single copy of full-length T-DNA at the target site. Our results indicate that Agrobacterium-mediated transformation combined with a CRISPR/Cas9 system can efficiently generate targeted T-DNA insertions.

     

Quantitative Trait Loci (QTL) and Mendelian Trait Loci (MTL) Analysis in Prunus: a Breeding Perspective and Beyond

Trait loci analysis, a classic procedure in quantitative (quantitative trait loci, QTL) and qualitative (Mendelian trait loci, MTL) genetics, continues to be the most important approach in studies of gene labeling in Prunus species from the Rosaceae family. Since 2011, the number of published Prunus QTLs and MTLs has doubled. With increased genomic resources, such as whole genome sequences and high-density genotyping platforms, trait loci analysis can be more readily converted to markers that can be directly utilized in marker-assisted breeding. To provide this important resource to the community and to integrate it with other genomic, genetic, and breeding data, a global review of the QTLs and MTLs linked to agronomic traits in Prunus has been performed and the data made available in the Genome Database for Rosaceae. We describe detailed information on 760 main QTLs and MTLs linked to a total of 110 agronomic traits related to tree development, pest and disease resistance, flowering, ripening, and fruit and seed quality. Access to these trait loci enables the application of this information in the post-genomic era, characterized by the availability of a high-quality peach reference genome and new high-throughput DNA and RNA analysis technologies.     

Hepatitis B Virus Infection in HIV-Positive Individuals in the UK Collaborative HIV Cohort (UK CHIC) Study

Background

Hepatitis B virus (HBV) infection is an increasingly important cause of morbidity and mortality in HIV-infected adults. This study aimed to determine the prevalence and incidence of HBV in the UK CHIC Study, a multicentre observational cohort.

Methods and Findings

12 HIV treatment centres were included. Of 37,331 patients, 27,450 had at least one test (HBsAg, anti-HBs or anti-HBc) result post-1996 available. 16,043 were white, 8,130 black and 3,277 other ethnicity. Route of exposure was homosexual sex 15,223 males, heterosexual sex 3,258 males and 5,384 females, injecting drug use 862 and other 2,723. The main outcome measures used were the cumulative prevalence and the incidence of HBV coinfection. HBV susceptible patients were followed up until HBsAg and/or anti-HBc seroconversion incident infection, evidence of vaccination or last visit. Poisson regression was used to determine associated factors. 25,973 had at least one HBsAg test result. Participants with HBsAg results were typically MSM (57%) and white (59%) (similar to the cohort as a whole). The cumulative prevalence of detectable HBsAg was 6.9% (6.6 to 7.2%). Among the 3,379 initially HBV-susceptible patients, the incidence of HBV infection was 1.7 (1.5 to 1.9)/100 person-years. Factors associated with incident infection were older age and IDU. The main limitation of the study was that 30% of participants did not have any HBsAg results available. However baseline characteristics of those with results did not differ from those of the whole cohort. Efforts are on-going to improve data collection.

Conclusions

The prevalence of HBV in UK CHIC is in line with estimates from other studies and low by international standards. Incident infection continued to occur even after entry to the cohort, emphasising the need to ensure early vaccination.     

Ante-mortem detection of chronic wasting disease in recto-anal mucosa-associated lymphoid tissues from elk (Cervus elaphus nelsoni) using real-time quaking-induced conversion (RT-QuIC) assay: A blinded collaborative study

Prion diseases are transmissible spongiform encephalopathies (TSEs) characterized by fatal, progressive neurologic diseases with prolonged incubation periods and an accumulation of infectious misfolded prion proteins. Antemortem diagnosis is often difficult due to a long asymptomatic incubation period, differences in the pathogenesis of different prions, and the presence of very low levels of infectious prion in easily accessible samples. Chronic wasting disease (CWD) is a TSE affecting both wild and captive populations of cervids, including mule deer, white-tailed deer, elk, moose, muntjac, and most recently, wild reindeer. This study represents a well-controlled evaluation of a newly developed real-time quaking-induced conversion (RT-QuIC) assay as a potential CWD diagnostic screening test using rectal biopsy sections from a depopulated elk herd. We evaluated 69 blinded samples of recto-anal mucosa-associated lymphoid tissue (RAMALT) obtained from USDA Veterinary Services. The results were later un-blinded and statistically compared to immunohistochemical (IHC) results from the USDA National Veterinary Services Laboratories (NVSL) for RAMALT, obex, and medial retropharyngeal lymph node (MRPLN). Comparison of RAMALT RT-QuIC assay results with the IHC results of RAMALT revealed 92% relative sensitivity (95% confidence limits: 61.52–99.8%) and 95% relative specificity (95% confidence limits: 85.13–99%). Collectively, our results show a potential utility of the RT-QuIC assay to advance the development of a rapid, sensitive, and specific prion diagnostic assay for CWD prions.     

Genotyping‐by‐sequencing‐based genome‐wide association studies on Verticillium wilt resistance in autotetraploid alfalfa (Medicago sativa L.)

Verticillium wilt (VW) is a fungal disease that causes severe yield losses in alfalfa. The most effective method to control the disease is through the development and use of resistant varieties. The identification of marker loci linked to VW resistance can facilitate breeding for disease‐resistant alfalfa. In the present investigation, we applied an integrated framework of genome‐wide association with genotyping‐by‐sequencing (GBS) to identify VW resistance loci in a panel of elite alfalfa breeding lines. Phenotyping was performed by manual inoculation of the pathogen to healthy seedlings, and scoring for disease resistance was carried out according to the standard test of the North America Alfalfa Improvement Conference (NAAIC). Marker–trait association by linkage disequilibrium identified 10 single nucleotide polymorphism (SNP) markers significantly associated with VW resistance. Alignment of the SNP marker sequences to the M. truncatula genome revealed multiple quantitative trait loci (QTLs). Three, two, one and five markers were located on chromosomes 5, 6, 7 and 8, respectively. Resistance loci found on chromosomes 7 and 8 in the present study co‐localized with the QTLs reported previously. A pairwise alignment (blastn ) using the flanking sequences of the resistance loci against the M. truncatula genome identified potential candidate genes with putative disease resistance function. With further investigation, these markers may be implemented into breeding programmes using marker‐assisted selection, ultimately leading to improved VW resistance in alfalfa.