A chromosome-scale assembly for 'd'Anjou' pear.

Cultivated pear consists of several Pyrus species with Pyrus communis (European pear) representing a large fraction of worldwide production. As a relatively recently domesticated crop and perennial tree, pear can benefit from genome-assisted breeding. Additionally, comparative genomics within Rosaceae promises greater understanding of evolution within this economically important family. Here, we generate a fully phased chromosome-scale genome assembly of P. communis 'd'Anjou.' Using PacBio HiFi and Dovetail Omni-C reads, the genome is resolved into the expected 17 chromosomes, with each haplotype totaling nearly 540 Megabases and a contig N50 of nearly 14 Mb. Both haplotypes are highly syntenic to each other and to the Malus domestica 'Honeycrisp' apple genome. Nearly 45,000 genes were annotated in each haplotype, over 90% of which have direct RNA-seq expression evidence. We detect signatures of the known whole-genome duplication shared between apple and pear, and we estimate 57% of d'Anjou genes are retained in duplicate derived from this event. This genome highlights the value of generating phased diploid assemblies for recovering the full allelic complement in highly heterozygous crop species.

Maturation of the malarial phosphatidylserine decarboxylase is mediated by high affinity binding to anionic phospholipids.

Decarboxylation of phosphatidylserine (PS) to form phosphatidylethanolamine by PS decarboxylases (PSDs) is an essential process in most eukaryotes. Processing of a malarial PSD proenzyme into its active alpha and beta subunits is by an autoendoproteolytic mechanism regulated by anionic phospholipids, with PS serving as an activator and phosphatidylglycerol (PG), phosphatidylinositol, and phosphatidic acid acting as inhibitors. The biophysical mechanism underlying this regulation remains unknown. We used solid phase lipid binding, liposome-binding assays, and surface plasmon resonance to examine the binding specificity of a processing-deficient Plasmodium PSD (PkPSDS308A) mutant enzyme and demonstrated that the PSD proenzyme binds strongly to PS and PG but not to phosphatidylethanolamine and phosphatidylcholine. The equilibrium dissociation constants (Kd) of PkPSD with PS and PG were 80.4 nM and 66.4 nM, respectively. The interaction of PSD with PS is inhibited by calcium, suggesting that the binding mechanism involves ionic interactions. In vitro processing of WT PkPSD proenzyme was also inhibited by calcium, consistent with the conclusion that PS binding to PkPSD through ionic interactions is required for the proenzyme processing. Peptide mapping identified polybasic amino acid motifs in the proenzyme responsible for binding to PS. Altogether, the data demonstrate that malarial PSD maturation is regulated through a strong physical association between PkPSD proenzyme and anionic lipids. Inhibition of the specific interaction between the proenzyme and the lipids can provide a novel mechanism to disrupt PSD enzyme activity, which has been suggested as a target for antimicrobials, and anticancer therapies.

Identification of tandem repeat families from long-read sequences of Humulus lupulus.

Hop (Humulus lupulus L.) is known for its use as a bittering agent in beer and has a rich history of cultivation, beginning in Europe and now spanning the globe. There are five wild varieties worldwide, which may have been introgressed with cultivated varieties. As a dioecious species, its obligate outcrossing, non-Mendelian inheritance, and genomic structural variability have confounded directed breeding efforts. Consequently, understanding the hop genome represents a considerable challenge, requiring additional resources. In order to facilitate investigations into the transmission genetics of hop, we report here a tandem repeat discovery pipeline developed using k-mer filtering and dot plot analysis of PacBio long-read sequences from the hop cultivar Apollo. From this we identified 17 new and distinct tandem repeat sequence families, which represent candidates for FISH probe development. For two of these candidates, HuluTR120 and HuluTR225, we produced oligonucleotide FISH probes from conserved regions of and demonstrated their utility by staining meiotic chromosomes from wild hop, var. neomexicanus to address, for example, questions about hop transmission genetics. Collectively, these tandem repeat sequence families represent new resources suitable for development of additional cytogenomic tools for hop research.

Early-life injury produces lifelong neural hyperexcitability, cognitive deficit and altered defensive behaviour in the squid Euprymna scolopes.

Injury occurring in the neonatal period in mammals is known to induce plasticity in pain pathways that may lead to pain dysfunction in later life. Whether these effects are unique to the mammalian nervous system is not well understood. Here, we investigate whether similar effects of early-life injury are found in a large-brained comparative model, the cephalopod Euprymna scolopes. We show that the peripheral nervous system of E. scolopes undergoes profound and permanent plasticity after injury of peripheral tissue in the early post-hatching period, but not after the same injury given in the later juvenile period. Additionally, both innate defensive behaviour and learning are impaired by injury in early life. We suggest that these similar patterns of nervous system and behavioural remodelling that occur in squid and in mammals indicate an adaptive value for long-lasting plasticity arising from early-life injury, and suggest that injuries inflicted in very early life may signal to the nervous system that the environment is highly dangerous. Thus, neonatal pain plasticity may be a conserved pattern whose purpose is to set the developing nervous system's baseline responsiveness to threat. This article is part of the Theo Murphy meeting issue 'Evolution of mechanisms and behaviour important for pain'.

3D Molecular Cytology of Hop (Humulus lupulus) Meiotic Chromosomes Reveals Non-disomic Pairing and Segregation, Aneuploidy, and Genomic Structural Variation.

Hop (Humulus lupulus L.) is an important crop worldwide, known as the main flavoring ingredient in beer. The diversifying brewing industry demands variation in flavors, superior process properties, and sustainable agronomics, which are the focus of advanced molecular breeding efforts in hops. Hop breeders have been limited in their ability to create strains with desirable traits, however, because of the unusual and unpredictable inheritance patterns and associated non-Mendelian genetic marker segregation. Cytogenetic analysis of meiotic chromosome behavior has also revealed conspicuous and prevalent occurrences of multiple, atypical, non-disomic chromosome complexes, including those involving autosomes in late prophase. To explore the role of meiosis in segregation distortion, we undertook 3D cytogenetic analysis of hop pollen mother cells stained with DAPI and FISH. We used telomere FISH to demonstrate that hop exhibits a normal telomere clustering bouquet. We also identified and characterized a new sub-terminal 180 bp satellite DNA tandem repeat family called HSR0, located proximal to telomeres. Highly variable 5S rDNA FISH patterns within and between plants, together with the detection of anaphase chromosome bridges, reflect extensive departures from normal disomic signal composition and distribution. Subsequent FACS analysis revealed variable DNA content in a cultivated pedigree. Together, these findings implicate multiple phenomena, including aneuploidy, segmental aneuploidy, or chromosome rearrangements, as contributing factors to segregation distortion in hop.

Good practices in collecting umbilical cord and placental blood.

OBJECTIVE: to identify the factors related to the quality of umbilical cord and placental blood specimens, and define best practices for their collection in a government bank of umbilical cord and placental blood. METHOD: this was a descriptive study, quantitative approach, performed at a government umbilical cord and placental blood bank, in two steps: 1) verification of the obstetric, neonatal and operational factors, using a specific tool for gathering data as non-participant observers; 2) definition of best practices by grouping non-conformities observed before, during and after blood collection. The data was analyzed using descriptive statistics and the following statistical software: Statistica(r) and R(r). RESULTS: while there was a correlation with obstetrical and neonatal factors, there was a larger correlation with operational factors, resulting in the need to adjust the professional practices of the nursing staff and obstetrical team involved in collecting this type of blood. Based on these non-conformities we defined best practices for nurses before, during and after blood collection. CONCLUSION: the best practices defined in this study are an important management tool for the work of nurses in obtaining blood specimens of high cell quality.

Good practices in collecting umbilical cord and placental blood / Boas práticas para a coleta de sangue de cordão umbilical e placentário / Buenas prácticas para la recolección de sangre del cordón umbilical y de la placenta

Abstract Objective: to identify the factors related to the quality of umbilical cord and placental blood specimens, and define best practices for their collection in a government bank of umbilical cord and placental blood. Method: this was a descriptive study, quantitative approach, performed at a government umbilical cord and placental blood bank, in two steps: 1) verification of the obstetric, neonatal and operational factors, using a specific tool for gathering data as non-participant observers; 2) definition of best practices by grouping non-conformities observed before, during and after blood collection. The data was analyzed using descriptive statistics and the following statistical software: Statistica(r) and R(r). Results: while there was a correlation with obstetrical and neonatal factors, there was a larger correlation with operational factors, resulting in the need to adjust the professional practices of the nursing staff and obstetrical team involved in collecting this type of blood. Based on these non-conformities we defined best practices for nurses before, during and after blood collection. Conclusion: the best practices defined in this study are an important management tool for the work of nurses in obtaining blood specimens of high cell quality.

Resumo Objetivos: identificar fatores relacionados à qualidade das amostras do sangue de cordão umbilical e placentário e definir boas práticas para sua coleta em um banco público de sangue de cordão umbilical e placentário. Método: pesquisa descritiva, abordagem quantitativa, realizada em um banco público de sangue de cordão umbilical e placentário, desenvolvida em duas etapas: 1) verificação dos fatores obstétricos, neonatais e operacionais, obtidos por coleta em instrumento próprio e observação não participante; 2) definição das boas práticas, por meio do agrupamento de não-conformidades observadas antes, durante e após a coleta do sangue. Os dados foram analisados por meio da estatística descritiva, utilizando-se dos softwares Statistica(r) e R(r). Resultados: houve correlação da influência dos fatores obstétricos e neonatais em menor escala quando comparados aos fatores operacionais, resultando na necessidade de readequar a prática profissional do enfermeiro e da equipe obstétrica envolvida no processo da coleta desse tipo de sangue. A partir das não-conformidades foram definidas boas práticas para o enfermeiro antes, durante e após a coleta. Conclusão: as boas práticas definidas neste estudo são importante ferramenta gerencial para o trabalho do enfermeiro na obtenção de amostras de sangue com alta qualidade celular.

Resumen Objetivos: identificar factores relacionados a la calidad de las muestras de la sangre del cordón umbilical y de la placenta y definir buenas prácticas para su recolección en un banco público de sangre del cordón umbilical y de la placenta. Método: investigación - descriptiva, abordaje cuantitativo, realizada en un banco público de sangre - del cordón umbilical y de la placenta, desarrollada en dos etapas: 1) verificación de los factores obstétricos, neonatales y operacionales, obtenidos por recolección con instrumento propio y observación no participante; 2) definición de las buenas prácticas, por medio del agrupamiento de no-conformidades observadas antes, durante y después de la recolección de la sangre. Los datos fueron analizados por medio de la estadística descriptiva, utilizando los softwares Statistica(r) y R(r). Resultados: hubo correlación de la influencia de los factores obstétricos y neonatales en menor escala cuando comparados a los factores operacionales, resultando en la necesidad de readecuar la práctica profesional del enfermero y del equipo obstétrico que participa en el proceso de la recolección de ese tipo de sangre. A partir de las no-conformidades fueron definidas buenas prácticas para el enfermero antes, durante y después de la recolección. Conclusión: las buenas prácticas definidas en este estudio son importante herramienta administrativa para el trabajo del enfermero en la obtención de muestras de sangre con alta calidad celular.

Boas práticas para a coleta de sangue de cordão umbilical e placentário: atuação do enfermeiro / Good practices for umbilical and placental cord blood collection: nurses' performance

Objetivos: O objetivo geral deste estudo foi definir as boas práticas para a coleta de sangue de cordão umbilical e placentário (SCUP) em um Banco Público de SCUP (BPSCUP) da Rede BrasilCord, enquanto que os objetivos específicos foram descrever a atuação do enfermeiro em um BPSCUP da Rede BrasilCord; identificar os fatores que influenciam no volume e celularidade de amostras de SCUP em um BPSCUP da Rede BrasilCord; investigar as causas de descartes de amostras de SCUP em um BPSCUP da Rede BrasilCord; estabelecer o padrão de descarte de amostras de SCUP em um BPSUP da Rede BrasilCord. Método: Pesquisa de intervenção de abordagem quantitativa, realizada com 50 doadoras de SCUP e 14 profissionais da equipe de obstetrícia, em uma unidade de coleta externa de um BPSCUP do Sul do Brasil. A coleta de dados ocorreu no período de abril de 2013 a agosto de 2014, pela análise documental, observação não-participante (12 horas e 50 minutos no total) e diário de campo. Os dados foram tabulados em planilha eletrônica do Excell® e pelos softwares estatísticos R® e Statistica®, sofrendo ajustes de normalidade não-paramétrica, considerando 5% como nível de significância. Resultados: Foram identificadas como influências no volume e celularidade do SCUP, os fatores obstétricos peso placentário (rs=0,382923, p=0,006057; rs=0,339155, p=0,015978) e características do cordão umbilical quanto ao calibre (p=0,0051, p= 0,0095) e fluxo sanguíneo (p=0,00001, p=0,00001); os fatores neonatais peso do recém-nato (rs=0,362558, p=0,009667) e os fatores operacionais volume e celularidade (rs=0,873151, p=0,000000), características do cordão umbilical quanto ao aspecto (p=0,0003, p=0,0001), secção inadequada do segmento do cordão umbilical (p=0,00054, p=0,0005), excesso de pressão manual durante a dequitação placentária por tração controlada (p=0,0004, p=0,0004), ruptura ou laceração do segmento do cordão umbilical (p=0,021, p=0,036), desclampeamento do segmento de cordão umbilical por esquecimento do profissional (p=0,0007, p=0,024), desclampeamento do segmento do cordão umbilical para esvaziamento placentário (p=0,024), desclampeamento do segmento do cordão umbilical para coleta de tipagem sanguínea (p=0,006), sequencia de clampeamentos no segmento do cordão umbilical (p=0,036) e tempo entre coleta, transporte e processamento de amostras de SCUP (p=0,0355, p=0,0233). O padrão de descartes das amostras foi estabelecido pelos fatores obstétricos e neonatais identificados. As boas práticas para a coleta de SCUP foram definidas a partir da descrição da atuação do enfermeiro em BPSCUP e das não-conformidades encontradas baseadas nos fatores operacionais de influencia no volume e celularidade de SCUP e foram validadas com profissionais da equipe obstétrica da instituição. Conclusão: As boas práticas para a coleta de SCUP definidas neste estudo surgem como uma importante ferramenta gerencial para o trabalho do enfermeiro de BPSCUP na perspectiva da obtenção de volume e celularidade adequadas para o suprimento de amostras de alta qualidade celular para o BPSCUP. Desta forma, a atuação do enfermeiro em um serviço de ponta, de alta complexidade, visa atender às necessidades da demanda dos TCTH advindos do SCUP à inúmeros candidatos, principalmente crianças, contribuindo para a melhoria da qualidade do SCUP armazenado nos BPSCUP.

Objectives: This study aims to define the best practices for umbilical cord and placental blood (UCPB) collecting in a umbilical cord blood and placental public bank (UCPPBB) of BrasilCord network, while the specific objectives were to describe the nurse's role in a UCPPBB of BrasilCord network; identify the factors that influence the volume and cellularity of samples UCPB in a UCPPBB of BrasilCord network; investigate the causes of discharges of samples UCPB in a UCPPBB BrasilCord network; setting standards for disposal of samples UCPB in a UCPPBB BrasilCord Network. Method: Intervention quantitative research, performed with 50 donors and 14 UCPB professional obstetrics team in an external unity collection of a UCPPBB in the South of Brazil. Data collection realized between April 2013 and August 2014, by documentary analysis, non-participant observation (12 hours and 50 minutes in total) and a field journal. The data were tabulated in a spreadsheet and the Excell® and the statistical software R® and the Statistica®, suffering adjustments nonparametric normality, considering 5% level of significance. Results: We identified the influence on the volume and cellularity of the UCPB linked obstetric factors like a placental weight (rs=0.382923, p=0.006057; rs=0.339155, p=0.015978) and characteristics of the umbilical cord as size (p=0.0051, p=0.0095) and blood flow (p=0.00001, p=0.00001); neonatal factors newborn weight (rs=0.362558, p=0.009667) and operational factors volume and cellularity (rs=0.873151, p=0.000000), characteristics of the umbilical cord in appearance (p=0,0003, p=0.0001), inadequate section of the umbilical cord (p=0.00054, p=0.0005) manual excess pressure for blood placental expulsion by a controlled traction (p=0.0004, p=0.0004), rupturing or lacerating the umbilical cord (p=0.021, p=0.036) segment unclamping the umbilical cord segment through forgetfulness professional (p=0.0007, p=0.024), unclamping the umbilical cord segment for placental deflating (p=0.024), unclamping the umbilical cord segment for collecting blood type (p=0.006), the sequence of clamping umbilical cord (p=0.036) and related time for collection, transportation and processing of samples UCPB (p=0.0355, p=0.0233). The discharges pattern of the samples were established by identified obstetric and neonatal factors. Best practices for UCPB collecting were defined from description of the nurse works in UCPPBB and non-conformities found based on operational factors influencing the volume and cellularity of UCPB and were validated by a professional obstetric staff. Conclusion: The best practices of UCPB collecting, defined in this study, emerged as an important management tool for the job of UCPB nurse, prospect of obtaining volume and suitable for the supply of high quality samples for UCPPBB cell cellularity. Thus, the nurses work in a rush service with a high complexity, which aims to meet the needs of the demand arising from UCPB HSCT for many candidates, especially children, contributing to improve the quality of UCPB stored in UCPPBB.

Gerenciamento de materiais e custos hospitalares em UTI neonatal / Materials management and hospital costs in neonatal ICU / Gerenciamento de materiales y costos hospitalarios en UTI neonatal

Esta pesquisa objetivou quantificar e qualificar o uso indevido de materiais de consumo em uma Unidade de Terapia Intensiva Neonatal de um hospital universitário da cidade de Curitiba/PR. Foi realizada observação não participante na unidade no período de 17 de março a 2 de abril de 2009, em todos os turnos de trabalho, totalizando 100 horas. Os resultados revelaram o emprego indevido de materiais de consumo; uso de materiais de baixa qualidade; uso irracional; e improvisos, além de falhas no manuseio por profissionais. A pesquisa mostrou o volume e o valor de gastos impróprios na unidade, com alguns destaques para cateteres venosos periféricos, gazes, sondas nasogástricas, ampolas de glicose, cabos de oxímetros, entre outros. Sugere-se que a unidade melhore a gestão, por meio de auditoria de materiais e custos hospitalares, com olhar crítico e consciente sobre racionalização de uso de materiais.

This study aimed to quantify and qualify the improper use of consumables in a Neonatal Intensive Care Unit of a university hospital in Curitiba / PR. Non-participant observation was conducted in the unit during the period of March 17 to April 2, 2009, on all shifts, totaling 100 hours. The results revealed the improper use of consumables, the use of low quality materials, irrational use, and improvisation, as well as failures in handling the materials by professionals. The survey showed the volume and value of improper spending in the unit, with some highlights for peripheral venous catheters, gauzes, nasogastric tubes, ampoules of glucose, oximeters cables, among others. It is suggested that the unit must improve the management of materials and hospital costs through auditing, critically and consciously about the rational use of materials.

Esta investigación objetivó cuantificar y cualificar el uso indebido de materiales de consumo en una Unidad de Terapia Intensiva Neonatal de un hospital universitario de la ciudad de Curitiba/PR. Fue realizada observación no participante en la unidad en el periodo de 17 de marzo a 2 de abril de 2009, en todos los turnos de trabajo, totalizando 100 horas. Los resultados revelaron el empleo indebido de materiales de consumo; uso de materiales de baja calidad; uso irracional; e improvisados, además de fallas en el manoseo por profesionales. La investigación mostró el volumen y el valor de gastos impropios en la unidad, con algunos destaques para catéteres venosos periféricos, gasas, sondas nasogástricas, ampollas de glucosa, cables de oximetros, entre otros. Se sugiere que la unidad mejore la gestión, por medio de auditoría de materiales y costos hospitalarios, con visión crítica y consciente sobre racionalización de uso de materiales.