Tree growth and management in Ugandan agroforestry systems: effects of root pruning on tree growth and crop yield

Tree root pruning is a potential tool for managing below-ground competition when trees and crops are grown together in agroforestry systems. This study investigates its effects on growth and root distribution of Alnus acuminata (HB & K), Casuarina equisetifolia (L), Grevillea robusta (A. Cunn. ex R. Br), Maesopsis eminii (Engl.), and Markhamia lutea (Benth.) K. Schum. and on yield of adjacent crops in sub-humid Uganda. The trees were 3 years old at the commencement of the study, and most species were competing strongly with crops. Tree roots were pruned 41 months after planting by cutting and back-filling a trench to a depth of 0.3 m, at a distance of 0.3 m from the trees, on one side of the tree row. The trench was re-opened and roots re-cut at 50 and 62 months after planting. Effects on tree growth and root distribution were assessed over a 3 year period, and crop yield after the third root pruning at 62 months is reported here. Overall, root pruning had only a slight effect on tree growth: height growth was unaffected and diameter growth was reduced by only 4 %. A substantial amount of root re-growth was observed by 11 months after pruning. Tree species varied in the number and distribution of their roots, and Casuarina and Markhamia had considerably more roots per unit of trunk volume than the other tree species, especially in the surface soil layers. Casuarina and Maesopsis were the most competitive tree species with crops and Grevillea and Markhamia the least. Crop yield data provides strong evidence of the redistribution of root activity following root pruning, so that competition increased on the unpruned side of tree rows. Thus, one-sided root pruning will only be of use to farmers in a few circumstances. Key words: Alnus acuminata, Casuarina equisetifolia, Grevillea robusta, Maesopsis eminii, Markhamia lutea, root distribution, root functio

Branchpoint translocation by fork remodelers as a general mechanism of R-loop removal.

Co-transcriptional R loops arise from stalling of RNA polymerase, leading to the formation of stable DNA:RNA hybrids. Unresolved R loops promote genome instability but are counteracted by helicases and nucleases. Here, we show that branchpoint translocases are a third class of R-loop-displacing enzyme in vitro. In cells, deficiency in the Fanconi-anemia-associated branchpoint translocase FANCM causes R-loop accumulation, particularly after treatment with DNA:RNA-hybrid-stabilizing agents. This correlates with FANCM localization at R-loop-prone regions of the genome. Moreover, other branchpoint translocases associated with human disease, such as SMARCAL1 and ZRANB3, and those from lower organisms can also remove R loops in vitro. Branchpoint translocases are more potent than helicases in resolving R loops, indicating their evolutionary important role in R-loop suppression. In human cells, FANCM, SMARCAL1, and ZRANB3 depletion causes additive effects on R-loop accumulation and DNA damage. Our work reveals a mechanistic basis for R-loop displacement that is linked to genome stability

The splicing-factor related protein SFPQ/PSF interacts with RAD51D and is necessary for homology-directed repair and sister chromatid cohesion

DNA double-stranded breaks (DSBs) are among the most severe forms of DNA damage and responsible for chromosomal translocations that may lead to gene fusions. The RAD51 family plays an integral role in preserving genome stability by homology directed repair of DSBs. From a proteomics screen, we recently identified SFPQ/PSF as an interacting partner with the RAD51 paralogs, RAD51D, RAD51C and XRCC2. Initially discovered as a potential RNA splicing factor, SFPQ was later shown to have homologous recombination and non-homologous end joining related activities and also to bind and modulate the function of RAD51. Here, we demonstrate that SFPQ interacts directly with RAD51D and that deficiency of both proteins confers a severe loss of cell viability, indicating a synthetic lethal relationship. Surprisingly, deficiency of SFPQ alone also leads to sister chromatid cohesion defects and chromosome instability. In addition, SFPQ was demonstrated to mediate homology directed DNA repair and DNA damage response resulting from DNA crosslinking agents, alkylating agents and camptothecin. Taken together, these data indicate that SFPQ association with the RAD51 protein complex is essential for homologous recombination repair of DNA damage and maintaining genome integrity

A Cortical Attractor Network with Martinotti Cells Driven by Facilitating Synapses

The population of pyramidal cells significantly outnumbers the inhibitory interneurons in the neocortex, while at the same time the diversity of interneuron types is much more pronounced. One acknowledged key role of inhibition is to control the rate and patterning of pyramidal cell firing via negative feedback, but most likely the diversity of inhibitory pathways is matched by a corresponding diversity of functional roles. An important distinguishing feature of cortical interneurons is the variability of the short-term plasticity properties of synapses received from pyramidal cells. The Martinotti cell type has recently come under scrutiny due to the distinctly facilitating nature of the synapses they receive from pyramidal cells. This distinguishes these neurons from basket cells and other inhibitory interneurons typically targeted by depressing synapses. A key aspect of the work reported here has been to pinpoint the role of this variability. We first set out to reproduce quantitatively based on in vitro data the di-synaptic inhibitory microcircuit connecting two pyramidal cells via one or a few Martinotti cells. In a second step, we embedded this microcircuit in a previously developed attractor memory network model of neocortical layers 2/3. This model network demonstrated that basket cells with their characteristic depressing synapses are the first to discharge when the network enters an attractor state and that Martinotti cells respond with a delay, thereby shifting the excitation-inhibition balance and acting to terminate the attractor state. A parameter sensitivity analysis suggested that Martinotti cells might, in fact, play a dominant role in setting the attractor dwell time and thus cortical speed of processing, with cellular adaptation and synaptic depression having a less prominent role than previously thought

Recent developments in genetics and medically assisted reproduction : from research to clinical applications

Two leading European professional societies, the European Society of Human Genetics and the European Society for Human Reproduction and Embryology, have worked together since 2004 to evaluate the impact of fast research advances at the interface of assisted reproduction and genetics, including their application into clinical practice. In September 2016, the expert panel met for the third time. The topics discussed highlighted important issues covering the impacts of expanded carrier screening, direct-to-consumer genetic testing, voiding of the presumed anonymity of gamete donors by advanced genetic testing, advances in the research of genetic causes underlying male and female infertility, utilisation of massively parallel sequencing in preimplantation genetic testing and non-invasive prenatal screening, mitochondrial replacement in human oocytes, and additionally, issues related to cross-generational epigenetic inheritance following IVF and germline genome editing. The resulting paper represents a consensus of both professional societies involved.Peer reviewe

Poor Long-Term Patient Compliance with the Tennis Ball Technique for Treating Positional Obstructive Sleep Apnea

Study Objectives: Little is known regarding long-term patient compliance with the tennis ball technique (TBT), one of the original simple methods of positional therapy (i.e., avoiding the supine posture during sleep) for posture-dependent obstructive sleep apnea patients. The purpose of this study was to investigate long-term patient compliance with TBT. Methods: A follow-up questionnaire was mailed to all patients prescribed TBT at the Adelaide Institute for Sleep Health between July 2004 and March 2008 (n = 108). Results: Sixty-seven patients replied to the questionnaire. Baseline demographic/clinical characteristics were not significantly different from non-respondents. Among the respondents, follow-up time was (mean ± SD) 2.5 ± 1.0 years. Four (6.0%) reported they were still using TBT (group A); 9 (13.4%) were no longer using TBT, claiming to have learned to avoid the supine position during sleep (group B); and 54 (80.6%) were neither using TBT nor avoiding the supine posture (group C). The main reason for ceasing TBT use in group C was that TBT was too uncomfortable (34/54 patients). Conclusions: Long-term patient compliance with TBT appears to be very poor, with less than 10% of patients reporting continued use (group A) ~30 months after prescription. With most TBT non-compliers reporting it to be too uncomfortable, alternative forms of positional therapy appear to be needed.James J. Bignold, Georgina Deans-Costi, Mitchell R. Goldsworthy, Claire A. Robertson, Douglas McEvoy, Peter G. Catcheside and Jeremy D. Mercerhttp://www.aasmnet.org/JCSM/ViewAbstract.aspx?pid=2759

Preparation and purification of mono-ubiquitinated proteins using Avi-tagged ubiquitin.

Site-specific conjugation of ubiquitin onto a range of DNA repair proteins regulates their critical functions in the DNA damage response. Biochemical and structural characterization of these functions are limited by an absence of tools for the purification of DNA repair proteins in purely the ubiquitinated form. To overcome this barrier, we designed a ubiquitin fusion protein that is N-terminally biotinylated and can be conjugated by E3 RING ligases onto various substrates. Biotin affinity purification of modified proteins, followed by cleavage of the affinity tag leads to release of natively-mono-ubiquitinated substrates. As proof-of-principle, we applied this method to several substrates of mono-ubiquitination in the Fanconi anemia (FA)-BRCA pathway of DNA interstrand crosslink repair. These include the FANCI:FANCD2 complex, the PCNA trimer and BRCA1 modified nucleosomes. This method provides a simple approach to study the role of mono-ubiquitination in DNA repair or any other mono-ubiquitination signaling pathways

No evidence that CDKN1B (p27) polymorphisms modify breast cancer risk in BRCA1 and BRCA2 mutation carriers

The p27kip1 protein functions as an inhibitor of cyclin dependent kinase-2, and shows loss of expression in a large percentage of BRCA1 and BRCA2 breast cancer cases. We investigated the association between CDKN1B gene variants and breast cancer risk in 2359 female BRCA1 and BRCA2 mutation carriers from Australia, the UK, and the USA. Samples were genotyped for five single nucleotide polymorphisms, including coding variant rs2066827 (V109G). Cox regression provided no convincing evidence that any of the polymorphisms modified disease risk for BRCA1 or BRCA2 carriers, either alone or as a haplotype. Borderline associations were observed for homozygote carriers of the rs3759216 rare allele, but were opposite in effect for BRCA1 and BRCA2 carriers (adjusted hazard ratio (HR) 0.72 (95% CI = 0.53–0.99; P = 0.04 for BRCA1, HR 1.47 (95% CI = 0.99–2.18; P = 0.06 for BRCA2). The 95% confidence intervals for per allele risk estimates excluded a twofold risk, indicating that common CDKN1B polymorphisms do not markedly modify breast cancer risk among BRCA1 or BRCA2 carriers