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Blackberries (Rubus spp.) are the fourth most economically important berry crop worldwide. Genome assemblies and annotations have been developed for Rubus species in subgenus Idaeobatus, including black raspberry (R. occidentalis), red raspberry (R. idaeus), and R. chingii, but very few genomic resources exist for blackberries and their relatives in subgenus Rubus. Here we present a chromosome-length assembly and annotation of the diploid blackberry germplasm accession "Hillquist" (R. argutus). "Hillquist" is the only known source of primocane-fruiting (annual-fruiting) in tetraploid fresh-market blackberry breeding programs and is represented in the pedigree of many important cultivars worldwide. The "Hillquist" assembly, generated using Pacific Biosciences long reads scaffolded with high-throughput chromosome conformation capture sequencing, consisted of 298 Mb, of which 270 Mb (90%) was placed on 7 chromosome-length scaffolds with an average length of 38.6 Mb. Approximately 52.8% of the genome was composed of repetitive elements. The genome sequence was highly collinear with a novel maternal haplotype-resolved linkage map of the tetraploid blackberry selection A-2551TN and genome assemblies of R. chingii and red raspberry. A total of 38,503 protein-coding genes were predicted, of which 72% were functionally annotated. Eighteen flowering gene homologs within a previously mapped locus aligning to an 11.2 Mb region on chromosome Ra02 were identified as potential candidate genes for primocane-fruiting. The utility of the "Hillquist" genome has been demonstrated here by the development of the first genotyping-by-sequencing-based linkage map of tetraploid blackberry and the identification of possible candidate genes for primocane-fruiting. This chromosome-length assembly will facilitate future studies in Rubus biology, genetics, and genomics and strengthen applied breeding programs., Competing Interests: Conflicts of interest None declared., (© The Author(s) 2022. Published by Oxford University Press on behalf of Genetics Society of America.)

This commentary considers the case of Brennan, in which surviving family members successfully brought a Human Rights Act 1998 (HRA) claim against a hospital and a council for the way in which they both treated a body post-mortem. Their failure to freeze it led to such a state of decomposition that it was unfit for viewing. The family argued this constituted an unjustified interference with their rights to family and private life. After a review of Strasbourg case law, the Leeds County Court found for them and awarded them damages under section 8 of the HRA. This commentary evaluates both the Strasbourg law and the way it was utilised and interpreted domestically. While agreeing with the outcome, the authors conclude that the Strasbourg case law does not line up four square-and instead they suggest that a different approach, accepting the legitimacy of a claim based on 'memory-securing', is warranted on the facts. The commentary also questions whether the court was correct in seeing the rights reposed in the surviving family, and offers the view that greater coherence to the law might be achieved if we conceive of the survivors as the vehicle for the exercise of rights by the deceased., (© The Author(s) 2021. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Objective: Access to palliative care (PC) is important for many patients with uncontrolled symptom burden from serious or complex illness. However, many patients who could benefit from PC do not receive it early enough or at all. We sought to address this problem by building a predictive model into a comprehensive clinical framework with the aims to (i) identify in-hospital patients likely to benefit from a PC consult, and (ii) intervene on such patients by contacting their care team., Materials and Methods: Electronic health record data for 68 349 inpatient encounters in 2017 at a large hospital were used to train a model to predict the need for PC consult. This model was published as a web service, connected to institutional data pipelines, and consumed by a downstream display application monitored by the PC team. For those patients that the PC team deems appropriate, a team member then contacts the patient's corresponding care team., Results: Training performance AUC based on a 20% holdout validation set was 0.90. The most influential variables were previous palliative care, hospital unit, Albumin, Troponin, and metastatic cancer. The model has been successfully integrated into the clinical workflow making real-time predictions on hundreds of patients per day. The model had an "in-production" AUC of 0.91. A clinical trial is currently underway to assess the effect on clinical outcomes., Conclusions: A machine learning model can effectively predict the need for an inpatient PC consult and has been successfully integrated into practice to refer new patients to PC., (© The Author(s) 2021. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Background: The king scallop, Pecten maximus, is distributed in shallow waters along the Atlantic coast of Europe. It forms the basis of a valuable commercial fishery and plays a key role in coastal ecosystems and food webs. Like other filter feeding bivalves it can accumulate potent phytotoxins, to which it has evolved some immunity. The molecular origins of this immunity are of interest to evolutionary biologists, pharmaceutical companies, and fisheries management., Findings: Here we report the genome assembly of this species, conducted as part of the Wellcome Sanger 25 Genomes Project. This genome was assembled from PacBio reads and scaffolded with 10X Chromium and Hi-C data. Its 3,983 scaffolds have an N50 of 44.8 Mb (longest scaffold 60.1 Mb), with 92% of the assembly sequence contained in 19 scaffolds, corresponding to the 19 chromosomes found in this species. The total assembly spans 918.3 Mb and is the best-scaffolded marine bivalve genome published to date, exhibiting 95.5% recovery of the metazoan BUSCO set. Gene annotation resulted in 67,741 gene models. Analysis of gene content revealed large numbers of gene duplicates, as previously seen in bivalves, with little gene loss, in comparison with the sequenced genomes of other marine bivalve species., Conclusions: The genome assembly of P. maximus and its annotated gene set provide a high-quality platform for studies on such disparate topics as shell biomineralization, pigmentation, vision, and resistance to algal toxins. As a result of our findings we highlight the sodium channel gene Nav1, known to confer resistance to saxitoxin and tetrodotoxin, as a candidate for further studies investigating immunity to domoic acid., (© The Author(s) 2020. Published by Oxford University Press.)

Unlabelled: High-throughput sequencing technologies survey genetic variation at genome scale and are increasingly used to study the contribution of rare and low-frequency genetic variants to human traits. As part of the Cohorts arm of the UK10K project, genetic variants called from low-read depth (average 7×) whole genome sequencing of 3621 cohort individuals were analysed for statistical associations with 64 different phenotypic traits of biomedical importance. Here, we describe a novel genome browser based on the Biodalliance platform developed to provide interactive access to the association results of the project., Availability and Implementation: The browser is available at http://www.uk10k.org/dalliance.html. Source code for the Biodalliance platform is available under a BSD license from http://github.com/dasmoth/dalliance, and for the LD-display plugin and backend from http://github.com/dasmoth/ldserv., (© The Author 2015. Published by Oxford University Press.)

Mutations in the Plasmodium falciparum K13-propeller domain have recently been shown to be important determinants of artemisinin resistance in Southeast Asia. This study investigated the prevalence of K13-propeller polymorphisms across sub-Saharan Africa. A total of 1212 P. falciparum samples collected from 12 countries were sequenced. None of the K13-propeller mutations previously reported in Southeast Asia were found, but 22 unique mutations were detected, of which 7 were nonsynonymous. Allele frequencies ranged between 1% and 3%. Three mutations were observed in >1 country, and the A578S was present in parasites from 5 countries. This study provides the baseline prevalence of K13-propeller mutations in sub-Saharan Africa., (© The Author 2014. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.)

Pathogen genome sequencing directly from clinical samples is quickly gaining importance in genetic and medical research studies. However, low DNA yield from blood-borne pathogens is often a limiting factor. The problem worsens in extremely base-biased genomes such as the AT-rich Plasmodium falciparum. We present a strategy for whole-genome amplification (WGA) of low-yield samples from P. falciparum prior to short-read sequencing. We have developed WGA conditions that incorporate tetramethylammonium chloride for improved amplification and coverage of AT-rich regions of the genome. We show that this method reduces amplification bias and chimera formation. Our data show that this method is suitable for as low as 10 pg input DNA, and offers the possibility of sequencing the parasite genome from small blood samples., (© The Author 2014. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.)

Little is known of the interactions between insect-only flaviviruses and other arboviruses in their mosquito hosts, or the potential public health significance of these associations. The specific aims of this study were to describe the geographic distribution, prevalence, and seasonal infection rates of Culex flavivirus (CxFV) and West Nile virus (WNV) in Culex quinquefasciatus Say in the Southeastern United States, investigate the potential association between CxFV and WNV prevalence in Cx. quinquefasciatus and describe the phylogenetic relationship among CxFV and WNV isolates from the Southeastern United States and around the world. Using ArboNET records, 11 locations were selected across Georgia, Mississippi, and Louisiana that represented a range of WNV human case incidence levels. Cx. quinquefasciatus were trapped weekly throughout the summer of 2009 and pools were screened for flavivirus RNA by reverse transcriptase polymerase chain reaction. Cx. quinquefasciatus from Georgia had significantly higher CxFV infection rates than either Mississippi or Louisiana. CxFV was not detected in Mississippi after July, and no CxFV was detected in Cx. quinquefasciatus in Louisiana. In Georgia, CxFV infection rates were variable between and within counties and over time. WNV infection rates were not significantly different across states or months, and WNV sequences from all three states were identical to each other in the envelope and NS5 gene regions. Phylogenetically, NS5 and E gene sequences from Georgia CxFV isolates clustered with CxFV from Japan, Iowa, and Texas. Multiple CxFV genetic variants were found circulating simultaneously in Georgia. No evidence was found supporting an association between WNV and CxFV infection prevalence in Cx. quinquefasciatus.

Despite recent advances in sequencing, complete finishing of large genomes and analysis of novel proteins they encode typically require cloning of specific regions. However, many of these fragments are extremely difficult to clone in current vectors. Superhelical stress in circular plasmids can generate secondary structures that are substrates for deletion, particularly in regions that contain numerous tandem or inverted repeats. Common vectors also induce transcription and translation of inserted fragments, which can select against recombinant clones containing open reading frames or repetitive DNA. Conversely, transcription from cloned promoters can interfere with plasmid stability. We have therefore developed a novel Escherichia coli cloning vector (termed 'pJAZZ' vector) that is maintained as a linear plasmid. Further, it contains transcriptional terminators on both sides of the cloning site to minimize transcriptional interference between vector and insert. We show that this vector stably maintains a variety of inserts that were unclonable in conventional plasmids. These targets include short nucleotide repeats, such as those of the expanded Fragile X locus, and large AT-rich inserts, such as 20-kb segments of genomic DNA from Pneumocystis, Plasmodium, Oxytricha or Tetrahymena. The pJAZZ vector shows decreased size bias in cloning, allowing more uniform representation of larger fragments in libraries.

Vesicular stomatitis New Jersey virus (VSNJV) is an insect-transmitted Rhabdovirus causing vesicular disease in domestic livestock including cattle, horses, and pigs. Natural transmission during epidemics remains poorly understood, particularly in cattle, one of the most affected species during outbreaks. This study reports the first successful transmission of VSNJV to cattle by insect bite resulting in clinical disease. When infected black flies (Simulium vittatum Zetterstedt) fed at sites where VS lesions are usually observed (mouth, nostrils, and foot coronary band), infection occurred, characterized by local viral replication, vesicular lesions, and high neutralizing antibody titers (> 1: 256). Viral RNA was detected up to 9 d postinfection in tissues collected during necropsy from lesion sites and lymph nodes draining those sites. Interestingly, when flies were allowed to feed on flank or neck skin, viral replication was poor, lesions were not observed, and low levels of neutralizing antibodies (range, 1:8-1:32) developed. Viremia was never observed in any of the animals and infectious virus was not recovered from tissues on necropsies performed between 8 and 27 d postinfection. Demonstration that VSNJV transmission to cattle by infected black flies can result in clinical disease contributes to a better understanding of the epidemiology and potential prevention and control methods for this important disease.

Historically, malaria was a significant cause of morbidity and mortality throughout the western United States, and Anopheles freeborni Aitken was thought to be the vector west of the Continental Divide. In 1989, Anopheles hermsi Barr & Guptavanij was described and subsequently found to be an effective laboratory vector of Plasmodium. The adults of these two species are morphologically indistinguishable, and therefore polymerase chain reaction was used to analyze the DNA from 48 mosquitoes collected in Arizona and Colorado (identified morphologically as An. freeborni). All specimens were identified as An. hermsi. This was the first report of An. hermsi in Arizona and Colorado and indicated that this Anopheles species historically may have been a malaria vector in these two western states.

Stem injection of (15)N-labeled ammonium sulfate was used to determine effects of pruning on canopy nitrogen dynamics in open-grown Pinus radiata D. Don in New Zealand. Trees were planted in July 1990 and the isotope introduced in December 1994. Tree crowns were divided into three zones: base section, from which branches of pruned trees were removed; mid section, between the pruned zone and the height of the trees at the start of the year in which they were pruned; and top section, which grew predominantly after the isotope was applied. Pruning removed 32% of the green crown length, representing 75% of foliage biomass. Needles were sampled from each region of the crown until July 1996. Branch growth was used to predict foliage biomass for each sampling occasion. Approximately 45% of the applied isotope was recovered from needles sampled in December 1994 (1 week after application and immediately before pruning), two-thirds of which occurred in needles in the base section. Thereafter, changes in isotope content of needles in the base section of unpruned trees largely reflected foliage biomass fluctuations and dilution of the isotope by continued uptake from the unlabeled soil nitrogen pool. Recovery of isotope in needles from the mid-crown section increased by 58 and 86% from December 1994 to July 1995 in control and pruned trees, respectively. Within this crown section, there was evidence of isotope translocation from old to new needles, with both isotope dilution and efflux observed in the needle cohorts that had been present at the time the isotope was applied. Therefore, isotope dynamics did not reflect the dynamics of the total nitrogen pool in the mid-crown section. By July 1996, a small proportion of the applied isotope was recovered from the new foliage formed in the top section of the crown. Within the top section, isotope dynamics closely matched total nitrogen fluxes. Pruning the lower crown did not affect nitrogen dynamics elsewhere in the crown for the following 18 months.

Laboratory-reared female black flies (Simulium vittatum Zetterstedt) were infected experimentally with a 1997 vesicular stomatitis virus New Jersey serotype isolate and allowed to feed on susceptible laboratory mice. All mice exposed to black fly bite seroconverted by day 21 after infection, an indication of virus transmission. In addition, viral RNA was detected in the spleen of several mice. These findings are consistent with the hypothesis that black flies are involved in VSV-NJ transmission during epizootics in the western USA and represent the 1st confirmed example of biological transmission of an arbovirus by a member of the Simuliidae using an animal model.

R.CviJI is unique among site-specific restriction endonucleases in that its activity can be modulated to recognize either a two or three base sequence. Normally R.CviJI cleaves RGCY sites between the G and C to leave blunt ends. In the presence of ATP R.CviJI* cleaves RGCN and YGCY sites, but not YGCR sites. The gene encoding R.CviJI was cloned from the eukaryotic Chlorella virus IL-3A and expressed in Escherichia coli. The primary E.coli cviJIR gene product is a 278 amino acid protein initiated from a GTG codon, rather than the expected 358 amino acid protein initiated from an in-frame upstream ATG codon. Interestingly, the 278 amino acid protein displays the normal restriction activity but not the R.CviJI* activity of the native enzyme. Nine restriction and modification proteins which recognize a central GC or CG sequence share short regions of identity with R.CviJI amino acids 144-235, suggesting that this region is the recognition and/or catalytic domain.

Males and females of Lutzomyia anthophora Addis were collected by vacuum aspiration from woodrat, Neotoma albigula Hartley, and rock squirrel, Citellus variegatus Bailey, nests along Arivaca Creek in Pima County, Arizona. Additional flies were collected from the same location using CDC miniature light traps supplemented with CO2. These collections extend the recorded geographic distribution of this vector of Leishmania mexicana Biagi westward by approximately 724 km and place Lu. anthophora in a Sonoran desert habitat.

The conversion of an anonymous DNA sample into numerous oligonucleotides is enzymatically feasible using an unusual restriction endonuclease, CviJI. Depending on reaction conditions, CviJI is capable of digesting DNA at a two or three base recognition sequence. CviJI normally cleaves RGCY sites between the G and C to leave blunt ends. Under 'relaxed' conditions CviJI* cleaves RGCY, and RGCR/YGCY, but not YGCR sites. In theory, CviJI* restriction of pUC19 (2686 bp) should produce 157 fragments, 75% of which are smaller than 20 bp. Instead, 96% of the CviJI* fragments were 18-56 bp long and none of the fragments were smaller than 18 bp. Thermal denaturation of these fragments generates sequence specific oligonucleotides homologous for the cognate template. The enzymatic conversion of anonymous DNA into sequence specific oligomers has implications for several conventional and novel molecular biology procedures.

We studied the distribution and retranslocation of N in 11-year-old Pinus contorta Dougl. trees following a winter application of N at 100 kg ha(-1) as (15)N-urea, (15)NH(4)NO(3) or NH(4) (15)NO(3). In all treatments, there was little uptake of (15)N after the first growing season although labeled N was still present in the soil. In subsequent years, (15)N in the trees was partly retranslocated, and, at the same time, it was diluted by uptake of unlabeled N from the soil. Between Years 1 and 8 after N fertilization, net retranslocation of (15)N from the lower crown (branches formed before fertilization) was 14%, and 18-25% of the (15)N in the trees was translocated to the upper and mid-crown. Overall, uptake of (15)N from nitrate was less than from urea or ammonium. However, when compared with the urea- and ammonium-N sources, (15)N from the nitrate source initially moved as rapidly into the foliage, but a greater proportion of it was retranslocated from the foliage during the second growing season. Nitrogen in foliage and wood formed in the growing season following fertilization was more highly labeled (measured as % N derived from the fertilizer) than in recently formed tissues. Labeling was substantially higher in foliage formed before fertilization than in wood of a similar age. In contrast, N in foliage formed after fertilization had only slightly higher labeling than wood of a similar age, indicating a relatively stable labeling throughout the trees once (15)N uptake had ceased. The concentrations of total and labeled N were substantially higher in foliage than in either wood or bark. There was evidence of N movement into wood tissues formed before fertilization, presumably along rays, and also of N retranslocation out of xylem cells as they matured. This study of internal N cycles was facilitated by the use of (15)N labeling because there was little uptake of labeled N after the first growing season, whereas interpretation based on total N was obscured by substantial uptake of N from the soil. We conclude that retranslocation studies based on measurements of total N content should be avoided.

Cultivation of Campylobacter jejuni with INT 407 cell monolayer cultures results in new or enhanced synthesis of a number of proteins compared with bacteria cultured in the absence of the epithelial cells. These proteins were detected within 60 min after the addition of the bacteria to the epithelial cell cultures, and their synthesis was temporally associated with an increase in C. jejuni internalization. A rabbit antiserum raised against bacteria that were cultivated with INT 407 cells recognized nine proteins that were not recognized by an antiserum against C. jejuni cultivated in medium alone. The former antiserum inhibited the internalization, but not the binding, of Campylobacter jejuni in a dose-dependent fashion. The results suggest that one or more of the proteins synthesized by C. jejuni in response to cocultivation with epithelial cells plays a role in facilitating internalization.

The ability of Campylobacter jejuni isolates to translocate across an epithelial cell barrier was investigated by using polarized Caco-2 cell monolayers grown on microporous membrane filters. The 4 C. jejuni isolates tested all traversed the Caco-2 cell monolayers and displayed similar translocation kinetics. The number of bacteria crossing the polarized cell monolayers continued to increase with time until 4 h after inoculation, at which time a maximum rate of translocation was observed. Transmission electron microscopy revealed that C. jejuni translocated across polarized Caco-2 cell monolayers by passing both through and between cells. Chloramphenicol, an inhibitor of bacterial protein synthesis, reduced the translocation of C. jejuni. Bacterial attachment, internalization, and translocation were inhibited at low temperature. These data indicate that adherence, penetration, and translocation of C. jejuni require active bacterial and target cell processes and further suggest a role for cellular translocation in the pathogenesis of C. jejuni-mediated enteritis.

A new approach has been developed for the rapid fragmentation and fractionation of DNA into a size suitable for shotgun cloning and sequencing. The restriction endonuclease CviJI normally cleaves the recognition sequence PuGCPy between the G and C to leave blunt ends. Atypical reaction conditions which alter the specificity of this enzyme (CviJI**) yield a quasi-random distribution of DNA fragments from the small molecule pUC19 (2686 base pairs). To quantitatively evaluate the randomness of this fragmentation strategy, a CviJI** digest of pUC19 was size fractionated by a rapid gel filtration method and directly ligated, without end repair, to a lacZ minus M13 cloning vector. Sequence analysis of 76 clones showed that CviJI** restricts PyGCPy and PuGCPu, in addition to PuGCPy sites, and that new sequence data is accumulated at a rate consistent with random fragmentation. Advantages of this approach compared to sonication and agarose gel fractionation include: smaller amounts of DNA are required (0.2-0.5 micrograms instead of 2-5 micrograms), fewer steps are involved (no preligation, end repair, chemical extraction, or agarose gel electrophoresis and elution are needed), and higher cloning efficiencies are obtained (CviJI** digested and column fractionated DNA transforms 3-16 times more efficiently than sonicated, end-repaired, and agarose fractionated DNA).

A major challenge of the Human Genome Initiative is the development of a rapid, accurate, and efficient DNA sequencing technology. A major limitation of current technology is the relatively long time required to perform the gel electrophoretic separations of DNA fragments produced in the sequencing reactions. We demonstrate here that it is possible to increase the speed of sequence analysis by over an order of magnitude by performing the electrophoresis and detection in ultra thin capillary gels. An instrument which utilizes these high speed separations to simultaneously analyze many samples will constitute a second generation automated DNA sequencer suitable for large-scale sequence analysis.

The intergenic region of bacteriophage f1 has been subcloned into the bacteriophage SP6 promoter plasmids, pSP64 and pSP65, in both orientations. Coinfection of E. coli with these SP6 promoter/phage f1 chimeric plasmids and the interference resistance phage, IR1, results in the replication and secretion of the pSP6.f1 plasmids as single stranded DNA. Bovine preProPTH cDNAs in both the native form and a form containing an insertion of 117 base pairs in the protein coding region have been inserted in these plasmids. The RNA transcribed from the SP6.f1/preProPTH cDNA constructs was efficiently translated in the wheat germ or reticulocyte cell free systems without addition of a 7-methylguanosine cap to the RNA. In the presence of dog pancreatic or chicken oviduct microsomal membranes, conversion of the resultant pre-proteins to pro-proteins was observed. Confirmation of the "mutated" preProPTH cDNA was determined by dideoxyribonucleotide DNA sequencing of single stranded plasmid DNA. These vectors are suitable for the efficient biosynthesis of large amounts of single or double stranded DNA, and translationally active RNA. The combined properties of single stranded DNA replication and the SP6 promoter simplify the engineering of mutant RNAs and their corresponding proteins. In addition, single stranded DNA or RNA corresponding to either complementary strand may be synthesized as nucleic acid hybridization probes.

Chimeric phage-plasmid expression vectors were constructed from pUC18/19 plasmids by cloning a single-stranded DNA (ssDNA) origin of replication from bacteriophage f1 and inserting a bacteriophage T7 promoter within the beta-galactosidase gene. A T7 promoter permits in vivo or in vitro expression of single proteins by the translation of T7 RNA polymerase transcripts. Insertional inactivation of the T7 promoter-containing beta-galactosidase gene permits a simple blue-to-white color cloning assay. Compared with several helper phages that were examined, superinfection with M13K07 resulted in the highest yields of the pTZ plasmids as ssDNA viral particles. These ssDNA promoter plasmids are uniquely suited for protein engineering because they simplify cloning, oligonucleotide directed mutagenesis, verification by enzymatic sequence analysis, and expression of mutant proteins from a single vector. These vectors were utilized to eliminate an efficient transcriptional terminator of T7 RNA polymerase in the cDNA of bovine preproparathyroid hormone by oligonucleotide directed mutagenesis. The mutation changed the codon for phenylalanine-19 in the signal peptide to alanine. In a cell-free system the mutant cDNA transcripts were translated into preproparathyroid hormone, which was converted to proparathyroid hormone in the presence of microsomal membranes.