De novo assembled expressed gene catalog of a fast-growing Eucalyptus tree produced by Illumina mRNA-Seq

<p>Abstract</p> <p>Background</p> <p><it>De novo </it>assembly of transcript sequences produced by short-read DNA sequencing technologies offers a rapid approach to obtain expressed gene catalogs for non-model organisms. A draft genome sequence will be produced in 2010 for a <it>Eucalyptus </it>tree species (<it>E. grandis</it>) representing the most important hardwood fibre crop in the world. Genome annotation of this valuable woody plant and genetic dissection of its superior growth and productivity will be greatly facilitated by the availability of a comprehensive collection of expressed gene sequences from multiple tissues and organs.</p> <p>Results</p> <p>We present an extensive expressed gene catalog for a commercially grown <it>E. grandis </it>× <it>E. urophylla </it>hybrid clone constructed using only Illumina mRNA-Seq technology and <it>de novo </it>assembly. A total of 18,894 transcript-derived contigs, a large proportion of which represent full-length protein coding genes were assembled and annotated. Analysis of assembly quality, length and diversity show that this dataset represent the most comprehensive expressed gene catalog for any <it>Eucalyptus </it>tree. mRNA-Seq analysis furthermore allowed digital expression profiling of all of the assembled transcripts across diverse xylogenic and non-xylogenic tissues, which is invaluable for ascribing putative gene functions.</p> <p>Conclusions</p> <p><it>De novo </it>assembly of Illumina mRNA-Seq reads is an efficient approach for transcriptome sequencing and profiling in <it>Eucalyptus </it>and other non-model organisms. The transcriptome resource (Eucspresso, <url>http://eucspresso.bi.up.ac.za/</url>) generated by this study will be of value for genomic analysis of woody biomass production in <it>Eucalyptus </it>and for comparative genomic analysis of growth and development in woody and herbaceous plants.</p

Genetic diversity and population structure analysis reveals the unique genetic composition of South African selected macadamia accessions

Macadamia nuts are known globally for their high quality and economic value. Global macadamia commercial nut production amounts to 60,000 metric tonnes and is increasing steadily. South Africa is the leading producer with 29% of worldwide kernel production. Commercial macadamia germplasm was originally selected from a small genepool (mainly Macadamia integrifolia species) from a limited geographic distribution in Australia. These accessions were subsequently bred, cloned and exported across the world to start local macadamia industries. The South African macadamia industry was established with pre-commercial and commercial macadamia from different parts of the world, and local selections were also performed. Many of these accessions have unique genetic compositions that have not been characterized yet. We used 13 nuclear microsatellite markers to study the genetic diversity and structure of macadamia germplasm cultivated in South Africa. We compared four groups of accessions including 31 originating from the Hawaiian Agricultural Experimental Station (HAES), 19 from Australia (AUS), two from California and one from Israel (OTH), 31 from South Africa’s locally selected accessions (SA) and 26 from two local Farmers (FARM). We used STRUCTURE, PCoA and neighbour-joining phylogenetic analyses to show that the South African selected accessions include diverse hybrid genotypes with strong Macadamia tetraphylla composition, unlike the Hawaiian commercially released and Australian representative collections that mostly have M. integrifolia or hybrid composition. Our results suggest that the South African selections represent a unique and diverse set of germplasm for future macadamia improvement efforts that will benefit from genomic breeding technologies.The National Research Foundation (NRF) of South Africa and Macadamias South Africa.https://link.springer.com/journal/11295hj2023BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

Ecology of the plant-dwelling spiders (Arachnida: Araneae) of the Erfenis Dam Nature Reserve, South Africa

As part of the South African National Survey of Arachnida in the Grassland Biome, foliagedwelling and grass-dwelling spiders (Arachnida: Araneae) were collected in the Erfenis Dam Nature Reserve in the central Free State Province from November 2005 to August 2007. Foliage-dwelling spiders were collected from three common tree or shrub species (Acacia karroo, Searsia ciliata and Searsia lancea) and grass-dwellers from four contrasting grasslands (uniform Themeda triandra, mixed, weedy and woodland grasslands). From the grass layer, 1649 spiders were collected, representing 15 families and 82 species, whilst 496 tree-dwelling spiders were collected that represented 17 families and 52 species. There was some overlap in the fauna of the two strata, resulting in a total of 108 species from 18 families being collected. The Araneidae, Philodromidae, Salticidae and Thomisidae were consistently the most abundant in all grassland types and tree species, although Salticidae were scarce on A. karroo. Assemblage analysis indicates high similarity and overlap in the fauna of the four grassland types, suggesting that the structural complexity of grasslands has a limited effect on species composition. In contrast, the foliage-dwelling assemblages were more distinct, with only some overlap between the faunas of S. ciliata and A. karroo, suggesting a stronger vegetation structural effect in shaping arboreal spider assemblages. The isolation of trees and shrubs within the extensive grassy habitat may contribute to the more unique fauna and lower species richness of the woody vegetation. CONSERVATION IMPLICATIONS: This study uncovered a rich diversity of plant-dwelling spiders from central South Africa. Grassland faunas show considerable temporal variation and some variability in microhabitat preferences, and sampling protocols should take this into account when spiders are considered in management plans and biodiversity surveys in reserves and private land.Additional supporting information may be found in the online version of this article as an Online Appendix: http://dx.doi. org/10.4102/koedoe. v55i1.1113-1.Scan this QR code with your smart phone or mobile device to read online.This study formed part of R.F.’s (University of the Free State) MSc on spider ecology in the Erfenis Dam Nature Reserve. R.F. conducted field work, sorted and tallied specimens, performed some statistical analyses and wrote part of the manuscript. C.R.H. (University of the Free State) supervised R.F., performed initial identifications, performed some statistical analyses and wrote part of the manuscript. A.S.D-S. (Agricultural Research Council – Plant Protection Research Institute) conducted final identifications and contributed to writing the manuscript. A.G. (University of the Free State) assisted with field work and sorting specimens.This study forms part of the first author’s MSc at the University of the Free State and funded through a National Research Foundation of South Africa (NRF) grant in the NRF Thuthuka programme to the second author (Grant number TTK2008050500003).http://www.koedoe.co.zaam2013ab201

Effects of a fast-burning spring fire on the ground-dwelling spider assemblages (Arachnida : Araneae) in a central South African grassland habitat

Fire is widely used as a management strategy in grasslands to maintain vegetation structure and improve grazing quality for large herbivores. The impacts of burning on invertebrates in South Africa remain poorly understood. A study was initiated in spring 2005 to determine the impact of a fast hot burn on ground-dwelling spider assemblages in a grassland habitat in the central Free State. Pitfall traps were set out at six sites in the reserve, with three sites each in the burnt and unburnt areas, to sample spiders over a 12-month period. A total of 5 253 spiders were collected, representing 33 families and 120 species. Spider abundance was significantly lower in the burnt (n = 1 956) than unburnt sites (n = 3 297), and burnt sites had, on average, considerably fewer species than unburnt sites. The dominant families in the burnt sites were Lycosidae (29.5%), Gnaphosidae (16.9%), Ammoxenidae (9.6%) and Zodariidae (5.7%), whereas Ammoxenidae (22.7%), Lycosidae (20.6%), Gnaphosidae (15.3%) and Amaurobiidae (10.2%) dominated the unburnt sites. Of the nine most abundant families collected, only Caponiidae were more abundant in the burnt than unburnt sites. Our data suggest that fast-burning hot spring fires cause a considerable initial post-fire decline in spider abundance, and have a negative influence on the abundance as well as the resistance of assemblages to disturbances other than fire (e.g. rain). However, most of the dominant families had abundances comparable to unburnt areas within a year post-burn.http://www.tandfonline.com/loi/tafz202016-12-31hb201

Achievement of therapeutic antibiotic exposures using Bayesian dosing software in critically unwell children and adults with sepsis

PURPOSE: Early recognition and effective treatment of sepsis improves outcomes in critically ill patients. However, antibiotic exposures are frequently suboptimal in the intensive care unit (ICU) setting. We describe the feasibility of the Bayesian dosing software Individually Designed Optimum Dosing Strategies (ID-ODS™), to reduce time to effective antibiotic exposure in children and adults with sepsis in ICU. METHODS: A multi-centre prospective, non-randomised interventional trial in three adult ICUs and one paediatric ICU. In a pre-intervention Phase 1, we measured the time to target antibiotic exposure in participants. In Phase 2, antibiotic dosing recommendations were made using ID-ODS™, and time to target antibiotic concentrations were compared to patients in Phase 1 (a pre-post-design). RESULTS: 175 antibiotic courses (Phase 1 = 123, Phase 2 = 52) were analysed from 156 participants. Across all patients, there was no difference in the time to achieve target exposures (8.7 h vs 14.3 h in Phase 1 and Phase 2, respectively, p = 0.45). Sixty-one courses in 54 participants failed to achieve target exposures within 24 h of antibiotic commencement (n = 36 in Phase 1, n = 18 in Phase 2). In these participants, ID-ODS™ was associated with a reduction in time to target antibiotic exposure (96 vs 36.4 h in Phase 1 and Phase 2, respectively, p < 0.01). These patients were less likely to exhibit subtherapeutic antibiotic exposures at 96 h (hazard ratio (HR) 0.02, 95% confidence interval (CI) 0.01-0.05, p < 0.01). There was no difference observed in in-hospital mortality. CONCLUSIONS: Dosing software may reduce the time to achieve target antibiotic exposures. It should be evaluated further in trials to establish its impact on clinical outcomes

Omecamtiv mecarbil in chronic heart failure with reduced ejection fraction, GALACTIC‐HF: baseline characteristics and comparison with contemporary clinical trials

Aims: The safety and efficacy of the novel selective cardiac myosin activator, omecamtiv mecarbil, in patients with heart failure with reduced ejection fraction (HFrEF) is tested in the Global Approach to Lowering Adverse Cardiac outcomes Through Improving Contractility in Heart Failure (GALACTIC‐HF) trial. Here we describe the baseline characteristics of participants in GALACTIC‐HF and how these compare with other contemporary trials. Methods and Results: Adults with established HFrEF, New York Heart Association functional class (NYHA) ≥ II, EF ≤35%, elevated natriuretic peptides and either current hospitalization for HF or history of hospitalization/ emergency department visit for HF within a year were randomized to either placebo or omecamtiv mecarbil (pharmacokinetic‐guided dosing: 25, 37.5 or 50 mg bid). 8256 patients [male (79%), non‐white (22%), mean age 65 years] were enrolled with a mean EF 27%, ischemic etiology in 54%, NYHA II 53% and III/IV 47%, and median NT‐proBNP 1971 pg/mL. HF therapies at baseline were among the most effectively employed in contemporary HF trials. GALACTIC‐HF randomized patients representative of recent HF registries and trials with substantial numbers of patients also having characteristics understudied in previous trials including more from North America (n = 1386), enrolled as inpatients (n = 2084), systolic blood pressure &lt; 100 mmHg (n = 1127), estimated glomerular filtration rate &lt; 30 mL/min/1.73 m2 (n = 528), and treated with sacubitril‐valsartan at baseline (n = 1594). Conclusions: GALACTIC‐HF enrolled a well‐treated, high‐risk population from both inpatient and outpatient settings, which will provide a definitive evaluation of the efficacy and safety of this novel therapy, as well as informing its potential future implementation

A revision of the purse-web spider genus Calommata Lucas, 1837 (Araneae, Atypidae) in the Afrotropical Region

The purse-web spider genus Calommata Lucas, 1837 is revised in the Afrotropical Region. Following examination of the female type material, C. transvaalica Hewitt, 1916 is removed from synonymy with C. simoni Pocock, 1903 and revalidated. The females of both species are redescribed and their males described for the first time. While C. simoni is very widespread across tropical Africa, C. transvaalica is endemic to northern South Africa. Four new species are described, all known only from males: C. megae sp. n. (Zimbabwe), C. meridionalis sp. n. (South Africa), C. namibica sp. n. (Namibia) and C. tibialis sp. n. (Ivory Coast and Togo). Notes are presented on the biology of each species