The genome sequence and effector complement of the flax rust pathogen Melampsora lini

Rust fungi cause serious yield reductions on crops, including wheat, barley, soybean, coffee, and represent real threats to global food security. Of these fungi, the flax rust pathogen Melampsora lini has been developed most extensively over the past 80 years as a model to understand the molecular mechanisms that underpin pathogenesis. During infection, M. lini secretes virulence effectors to promote disease. The number of these effectors, their function and their degree of conservation across rust fungal species is unknown. To assess this, we sequenced and assembled de novo the genome of M. lini isolate CH5 into 21,130 scaffolds spanning 189 Mbp (scaffold N50 of 31 kbp). Global analysis of the DNA sequence revealed that repetitive elements, primarily retrotransposons, make up at least 45% of the genome. Using ab initio predictions, transcriptome data and homology searches, we identified 16,271 putative protein-coding genes. An analysis pipeline was then implemented to predict the effector complement of M. lini and compare it to that of the poplar rust, wheat stem rust and wheat stripe rust pathogens to identify conserved and species-specific effector candidates. Previous knowledge of four cloned M. lini avirulence effector proteins and two basidiomycete effectors was used to optimize parameters of the effector prediction pipeline. Markov clustering based on sequence similarity was performed to group effector candidates from all four rust pathogens. Clusters containing at least one member from M. lini were further analyzed and prioritized based on features including expression in isolated haustoria and infected leaf tissue and conservation across rust species. Herein, we describe 200 of 940 clusters that ranked highest on our priority list, representing 725 flax rust candidate effectors. Our findings on this important model rust species provide insight into how effectors of rust fungi are conserved across species and how they may act to promote infection on their hosts.This work was funded by a grant from the CSIRO Transformational Biology Capability Platform to Adnane Nemri. Claire Anderson was supported by an ARC Discovery Grant (DP120104044) awarded to David A. Jones and Peter N. Dodds

Comparative genomics of Australian isolates of the wheat stem rust pathogen Puccinia graminis f. sp. tritici reveals extensive polymorphism in candidate effector genes

The wheat stem rust fungus Puccinia graminis f. sp. tritici (Pgt) is one of the most destructive pathogens of wheat. In this study, a draft genome was built for a founder Australian Pgt isolate of pathotype (pt.) 21-0 (collected in 1954) by next generation DNA sequencing. A combination of reference-based assembly using the genome of the previously sequenced American Pgt isolate CDL 75-36-700-3 (p7a) and de novo assembly were performed resulting in a 92 Mbp reference genome for Pgt isolate 21-0. Approximately 13 Mbp of de novo assembled sequence in this genome is not present in the p7a reference assembly. This novel sequence is not specific to 21-0 as it is also present in three other Pgt rust isolates of independent origin. The new reference genome was subsequently used to build a pan-genome based on five Australian Pgt isolates. Transcriptomes from germinated urediniospores and haustoria were separately assembled for pt. 21-0 and comparison of gene expression profiles showed differential expression in ∼10% of the genes each in germinated spores and haustoria. A total of 1,924 secreted proteins were predicted from the 21-0 transcriptome, of which 520 were classified as haustorial secreted proteins (HSPs). Comparison of 21-0 with two presumed clonal field derivatives of this lineage (collected in 1982 and 1984) that had evolved virulence on four additional resistance genes (Sr5, Sr11, Sr27, SrSatu) identified mutations in 25 HSP effector candidates. Some of these mutations could explain their novel virulence phenotypes.Authors wish to thank the Two Blades Foundation for financial support. Part of this work was supported through access to facilities managed by Bioplatforms Australia and funded by the Australian Government National Collaborative Research Infrastructure Strategy and Education Investment Fund Super Science Initiative

An efficient scheme for interference mitigation in 6G-IoT wireless networks

The Internet of Things (IoT) is the fourth technological revolution in the global information industry after computers, the Internet, and mobile communication networks. It combines radio-frequency identification devices, infrared sensors, global positioning systems, and various other technologies. Information sensing equipment is connected via the Internet, thus forming a vast network. When these physical devices are connected to the Internet, the user terminal can be extended and expanded to exchange information, communicate with anything, and carry out identification, positioning, tracking, monitoring, and triggering of corresponding events on each device in the network. In real life, the IoT has a wide range of applications, covering many fields, such as smart homes, smart logistics, fine agriculture and animal husbandry, national defense, and military. One of the most significant factors in wireless channels is interference, which degrades the system performance. Although the existing QR decomposition-based signal detection method is an emerging topic because of its low complexity, it does not solve the problem of poor detection performance. Therefore, this study proposes a maximum-likelihood-based QR decomposition algorithm. The main idea is to estimate the initial level of detection using the maximum likelihood principle, and then the other layer is detected using a reliable decision. The optimal candidate is selected from the feedback by deploying the candidate points in an unreliable scenario. Simulation results show that the proposed algorithm effectively reduces the interference and propagation error compared with the algorithms reported in the literature

Cause-Specific Neonatal Mortality at the Armed Forces Hospital, Southern Region Khamis Mushayt, Kingdom of Saudi Arabia

Abstract Objective: To document the perinatal and neonatal characteristics in a single hospital setting, to identify the main causes of neonatal deaths and to review the trends in neonatal mortality over a 6-year period. Methodology: This is a 6-year retrospective analysis of perinatal and neonatal data at the Armed Force Hospital, Southern Region, Saudi Arabia. Results: During the study period, there were 3 7,3 84 births resulting in 4,352 (11%) admissions to the neonatal intensive care unit (NICU). The average stillbirths rate was 54/1000 of the total births, and perinatal mortality rate was 9.6/1000 live births. Of the total NICU admissions, 2,698 (62%) were preterm, low-birth-weight (LBW) babies and 234 (5.4%) were extreme low birth-weight neonates (ELBW<1000gm). Overall neonatal mortality was 5.3% of the total admissions. Mortality rate was highest among ELBW babies (n=85; 36%). Prematurity-related conditions and multiple congenital anomalies accounted for the majority of deaths in the unit (61% and 44%, respectively), followed by birth asphyxia (10%). In ELBW infants, respiratory failure (45%) and grade IV intraventricular hemorrhage (40%) were the leading causes of early deaths, while sepsis accounted for 50% of late neonatal deaths. The mortality rate was significantly lower for larger neonates (10% for 1000-1500gm birth weight infants and only 3.3% of near-term neonates above 1500gm). The major cause of death was respiratory failure in smaller babies (52%) and multiple congenital anomalies in near-term infants. The presence of multiple congenital anomalies and extreme prematurity were the major contributing factors to neonatal mortality. Conclusions: There is a pressing need to study neonatal mortality to ascertain the cause of neonatal deaths in the Kingdom of Saudi Arabia

The genome sequence and effector complement of the flax rust pathogen Melampsora lini

Rust fungi cause serious yield reductions on crops, including wheat, barley, soybean, coffee, and represent real threats to global food security. Of these fungi, the flax rust pathogen Melampsora lini has been developed most extensively over the past 80 years as a model to understand the molecular mechanisms that underpin pathogenesis. During infection, M. lini secretes virulence effectors to promote disease. The number of these effectors, their function and their degree of conservation across rust fungal species is unknown. To assess this, we sequenced and assembled de novo the genome of M. lini isolate CH5 into 21, 130 scaffolds spanning 189 Mbp (scaffold N50 of 31 kbp). Global analysis of the DNA sequence revealed that repetitive elements, primarily retrotransposons, make up at least 45% of the genome. Using ab initio predictions, transcriptome data and homology searches, we identified 16, 271 putative protein-coding genes. An analysis pipeline was then implemented to predict the effector complement of M. lini and compare it to that of the poplar rust, wheat stem rust and wheat stripe rust pathogens to identify conserved and species-specific effector candidates. Previous knowledge of four cloned M. lini avirulence effector proteins and two basidiomycete effectors was used to optimize parameters of the effector prediction pipeline. Markov clustering based on sequence similarity was performed to group effector candidates from all four rust pathogens. Clusters containing at least one member from M. lini were further analyzed and prioritized based on features including expression in isolated haustoria and infected leaf tissue and conservation across rust species. Herein, we describe 200 of 940 clusters that ranked highest on our priority list, representing 725 flax rust candidate effectors. Our findings on this important model rust species provide insight into how effectors of rust fungi are conserved across species and how they may act to promote infection on their hosts

Genome analysis and avirulence gene cloning using a high-density RADseq linkage map of the flax rust fungus, Melampsora lini

Agroinfiltration of avirulence gene constructs. The response of flax cultivars and near-isogenic lines to expression of avirulence gene candidates (AvrM14-A, AvrM14-B and AvrL2-A) using Agrobacterium tumefaciens-mediated transient transformation. (PDF 2637 kb

Influence of Shear-Thinning Rheology on the Mixing Dynamics in Taylor-Couette Flow

Non‐Newtonian rheology can have a significant effect on mixing efficiency, which remains poorly understood. The effect of shear‐thinning rheology in a Taylor‐Couette reactor is studied using a combination of particle image velocimetry and flow visualization. Shear‐thinning is found to alter the critical Reynolds numbers for the formation of Taylor vortices and the higher‐order wavy instability, and is associated with an increase in the axial wavelength. Strong shear‐thinning and weak viscoelasticity can also lead to sudden transitions in wavelength as the Reynolds number is varied. Finally, it is shown that shear‐thinning causes an increase in the mixing time within vortices, due to a reduction in their circulation, but enhances the axial dispersion of fluid in the reactor

Reprogramming of orientation columns in visual cortex : a domino effect

Abstract : Cortical organization rests upon the fundamental principle that neurons sharing similar properties are co-located. In the visual cortex, neurons are organized into orientation columns. In a column, most neurons respond optimally to the same axis of an oriented edge, that is, the preferred orientation. This orientation selectivity is believed to be absolute in adulthood. However, in a fully mature brain, it has been established that neurons change their selectivity following sensory experience or visual adaptation. Here, we show that after applying an adapter away from the tested cells, neurons whose receptive fields were located remotely from the adapted site also exhibit a novel selectivity in spite of the fact that they were not adapted. These results indicate a robust reconfiguration and remapping of the orientation domains with respect to each other thus removing the possibility of an orientation hole in the new hypercolumn. These data suggest that orientation columns transcend anatomy, and are almost strictly functionally dynamic

Visual Cells Remember Earlier Applied Target: Plasticity of Orientation Selectivity

BACKGROUND: A canonical proposition states that, in mature brain, neurons responsive to sensory stimuli are tuned to specific properties installed shortly after birth. It is amply demonstrated that that neurons in adult visual cortex of cats are orientation-selective that is they respond with the highest firing rates to preferred oriented stimuli. METHODOLOGY/PRINCIPAL FINDINGS: In anesthetized cats, prepared in a conventional fashion for single cell recordings, the present investigation shows that presenting a stimulus uninterruptedly at a non-preferred orientation for twelve minutes induces changes in orientation preference. Across all conditions orientation tuning curves were investigated using a trial by trial method. Contrary to what has been previously reported with shorter adaptation duration, twelve minutes of adaptation induces mostly attractive shifts, i.e. toward the adapter. After a recovery period allowing neurons to restore their original orientation tuning curves, we carried out a second adaptation which produced three major results: (1) more frequent attractive shifts, (2) an increase of their magnitude, and (3) an additional enhancement of responses at the new or acquired preferred orientation. Additionally, we also show that the direction of shifts depends on the duration of the adaptation: shorter adaptation in most cases produces repulsive shifts, whereas adaptation exceeding nine minutes results in attractive shifts, in the same unit. Consequently, shifts in preferred orientation depend on the duration of adaptation. CONCLUSION/SIGNIFICANCE: The supplementary response improvements indicate that neurons in area 17 keep a memory trace of the previous stimulus properties, thereby upgrading cellular performance. It also highlights the dynamic nature of basic neuronal properties in adult cortex since repeated adaptations modified both the orientation tuning selectivity and the response strength to the preferred orientation. These enhanced neuronal responses suggest that the range of neuronal plasticity available to the visual system is broader than anticipated

Summation of connectivity strengths in the visual cortex reveals stability of neuronal microcircuits after plasticity

Abstract : Background: Within sensory systems, neurons are continuously affected by environmental stimulation. Recently, we showed that, on cell-pair basis, visual adaptation modulates the connectivity strength between similarly tuned neurons to orientation and we suggested that, on a larger scale, the connectivity strength between neurons forming sub-networks could be maintained after adaptation-induced-plasticity. In the present paper, based on the summation of the connectivity strengths, we sought to examine how, within cell-assemblies, functional connectivity is regulated during an exposure-based adaptation. Results: Using intrinsic optical imaging combined with electrophysiological recordings following the reconfiguration of the maps of the primary visual cortex by long stimulus exposure, we found that within functionally connected cells, the summed connectivity strengths remain almost equal although connections among individual pairs are modified. Neuronal selectivity appears to be strongly associated with neuronal connectivity in a “homeodynamic” manner which maintains the stability of cortical functional relationships after experience-dependent plasticity. Conclusions: Our results support the “homeostatic plasticity concept” giving new perspectives on how the summation in visual cortex leads to the stability within labile neuronal ensembles, depending on the newly acquired properties by neurons