A survey of lineage-specific genes in Triticeae reveals de novo gene evolution from genomic raw material

Diploid plant genomes typically contain ~35,000 genes, almost all belonging to highly conserved gene families. Only a small fraction are lineage-specific, which are found in only one or few closely related species. Little is known about how genes arise de novo in plant genomes and how often this occurs; however, they are believed to be important for plants diversification and adaptation. We developed a pipeline to identify lineage-specific genes in Triticeae, using newly available genome assemblies of wheat, barley, and rye. Applying a set of stringent criteria, we identified 5942 candidate Triticeae-specific genes (TSGs), of which 2337 were validated as protein-coding genes in wheat. Differential gene expression analyses revealed that stress-induced wheat TSGs are strongly enriched in putative secreted proteins. Some were previously described to be involved in Triticeae non-host resistance and cold response. Additionally, we show that 1079 TSGs have sequence homology to transposable elements (TEs), ~68% of them deriving from regulatory non-coding regions of Gypsy retrotransposons. Most importantly, we demonstrate that these TSGs are enriched in transmembrane domains and are among the most highly expressed wheat genes overall. To summarize, we conclude that de novo gene formation is relatively rare and that Triticeae probably possess ~779 lineage-specific genes per haploid genome. TSGs, which respond to pathogen and environmental stresses, may be interesting candidates for future targeted resistance breeding in Triticeae. Finally, we propose that non-coding regions of TEs might provide important genetic raw material for the functional innovation of TM domains and the evolution of novel secreted proteins

Resposta de um cultivar de pêssego com caroço aderente à irrigação por défice regulado

Regulated deficit irrigation (RDI) involves inducing water stress during specific fruit growth phases by irrigating at less than full evapotranspiration. The objectives of this research were to study the effects of RDI perfomed at stage II of fruit growth and postharvest, on productivity of clingstone peaches, fruit quality as well as photosynthetic rate and midday leaf water potential. The research was conducted in a commercial clingstone peach (Prunus persica L. Batch cv. A-37) orchard in Greece. Trees were irrigated by means of microsprinklers and their frequency was determined using local meteorological station data and the FAO 56 Pennman-Monteith method. Photosynthetic rate was measured by a portable infrared gas analyzer. Midday leaf water potential was measured by the pressure chamber technique. During the years 2005 and 2006, the treatment RDII with irrigation applied at growth stage II of the peach tree did not affect productivity, fresh and dry mass of fruits. RDII reduced preharvest fruit drop in comparison to the control. RDII as well as the combined treatment RDII plus RDIP with irrigation applied at postharvest, at both years reduced shoot length of the vigorous shoots inside the canopy. RDII in comparison to the control increased the soluble solids content of the fruits and the ratio soluble solids/acidity. However it did not affect fruit acidity and fruit firmness. RDII as well as RDII plus RDIP in 2006 increased 'double' fruits and fruits with open cavity in comparison to the control and RDIP. Water savings were considerable and associated with the climatic conditions of each year.A irrigação por défice regulado (RDI) envolve a indução de défice de água durante fases específicas do crescimento das frutas, irrigando a taxas menores que a evapotranspiração. Os objetivos desse estudo foram verificar os efeitos da RDI no estágio II do crescimento das frutas e no periodo pós-colheita, avaliando a produtividade de pêssegos, a qualidade dos frutos, bem como a taxa fotossintética e o potencial da água na folha. A pesquisa foi desenvolvida em um pomar comercial de pêssegos com caroço aderente (Prunus persica L. Batch cv. A-37) da Grécia. As árvores foram irrigadas por meio de microaspersores e sua frequência foi determinada por meio de dados meteorológicos obtidos em estação automática e o método FAO 56 Pennman-Monteith para determinação de evepotranspiração. A taxa de fotossíntese foi medida por analisador de gás na faixa do infravermelho. O potencial da água na folha foi medido ao meio-dia usando a técnica da câmara de pressão. Durante 2005 e 2006 o tratamento RDII com irrigação aplicada no estágio II não apresentou efeito sobre a produção, pesos seco e fresco dos frutos. RDII reduziu a queda de frutos antes da colheita, em relação ao controle. RDII, como também o tratamento combinado de RDII mais RDIP com irrigação aplicada em pós-colheita, reduziu o comprimento de ramos vigorosos dentro do dossel nos dois anos de estudo. Em comparação com o controle, RDII aumentou o conteúdo de sólidos solúveis dos frutos e a relação sólidos solúveis/acidez, mas não afetou a acidez dos frutos e a firmeza da polpa. Em 2006 RDII e RDII mais RDIP aumentaram os `frutos dobrados' e frutos com cavidade aberta, em comparação com o controle. A economia de água foi considerável e associada às condições climáticas de cada ano

Effect of organic calcium uptake and biostimulants during integrated nutrient management (INM) cultivation of kiwifruit cv. ‘Hayward’

Foliar application with calcium (Ca) fertilizers improves quality and flesh firmness of kiwifruit and affects the mineral composition of leaves and fruits. The impact of preharvest foliar sprays, using a commercial fertilizer with organic Ca content in combination with an integrated nutrient management (INM) fertilizers and biostimulants was assessed for the quality properties and nutritional status of the kiwi cv. ‘Hayward’ over a 2-year period. Fruit flesh firmness increased under all organic Ca applications. In addition, all treatments resulted in elevated dry mass content, which is a common quality index. In leaves, the concentrations of N, P, K and B were higher compared to control. In fruits, the concentrations of N, B, K and Ca increased, in contrast to Mg, which was reduced. The content of Mn, Zn, Fe and Cu was not affected either in leaves or fruits. Application of organic Ca-fertilizers led to increased flesh firmness, total soluble solids, total acidity, and dry mass percentage. Foliar application with the addition of the biostimulant THEOFAST resulted in the elongation of stigmas area in kiwi cv. ‘Hayward’ fruits

Individual Investors and Portfolio Diversification in Late Victorian Britain: How Diversified Were Victorian Financial Portfolios?

This article investigates Victorian investor financial portfolio strategies in England and Wales during the second half of the nineteenth century. We find that investors held on average about half of their gross wealth in the form of four or five liquid financial securities, but were reluctant to adopt fully contemporary financial advice to invest equal amounts in securities or to spread risk across the globe. They generally held under-diversified portfolios and proximity to their investments may have been an alternative to diversification as a means of risk reduction, especially for the less wealthy

Transposable Element Populations Shed Light on the Evolutionary History of Wheat and the Complex Co-Evolution of Autonomous and Non-Autonomous Retrotransposons

Wheat has one of the largest and most repetitive genomes among major crop plants, containing over 85% transposable elements (TEs). TEs populate genomes much in the way that individuals populate ecosystems, diversifying into different lineages, sub-families and sub-populations. The recent availability of high-quality, chromosome-scale genome sequences from ten wheat lines enables a detailed analysis how TEs evolved in allohexaploid wheat, its diploids progenitors, and in various chromosomal haplotype segments. LTR retrotransposon families evolved into distinct sub-populations and sub-families that were active in waves lasting several hundred thousand years. Furthermore, It is shown that different retrotransposon sub-families were active in the three wheat sub-genomes, making them useful markers to study and date polyploidization events and chromosomal rearrangements. Additionally, haplotype-specific TE sub-families are used to characterize chromosomal introgressions in different wheat lines. Additionally, populations of non-autonomous TEs co-evolved over millions of years with their autonomous partners, leading to complex systems with multiple types of autonomous, semi-autonomous and non-autonomous elements. Phylogenetic and TE population analyses revealed the relationships between non-autonomous elements and their mobilizing autonomous partners. TE population analysis provided insights into genome evolution of allohexaploid wheat and genetic diversity of species, and may have implication for future crop breeding

Correction of Pulmonary Arteriovenous Malformation Using Image-Based Surgical Planning

The objectives of this study were to develop an image-based surgical planning framework that 1) allows for in-depth analysis of pre-operative hemodynamics by the use of cardiac magnetic resonance and 2) enables surgeons to determine the optimum surgical scenarios before the operation. This framework is tailored for applications in which post-operative hemodynamics are important. In particular, it is exemplified here for a Fontan patient with severe left pulmonary arteriovenous malformations due to abnormal hepatic flow distribution to the lungs. Patients first undergo cardiac magnetic resonance for 3-dimensional anatomy and flow reconstruction. After analysis of the pre-operative flow fields, the 3-dimensional anatomy is imported into an interactive surgical planning interface for the surgeon to virtually perform multiple surgical scenarios. Associated hemodynamics are predicted by the use of a fully validated computational fluid dynamic solver. Finally, efficiency metrics (e.g., pressure decrease and hepatic flow distribution) are weighted against surgical feasibility to determine the optimal surgical option

Subthalamic deep brain stimulation sweet spots and hyperdirect cortical connectivity in Parkinson’s disease

Objectives Firstly, to identify subthalamic region stimulation clusters that predict maximum improvement in rigidity, bradykinesia and tremor, or emergence of side-effects; and secondly, to map-out the cortical fingerprint, mediated by the hyperdirect pathways which predict maximum efficacy. Methods High angular resolution diffusion imaging in twenty patients with advanced Parkinson’s disease was acquired prior to bilateral subthalamic nucleus deep brain stimulation. All contacts were screened one-year from surgery for efficacy and side-effects at different amplitudes. Voxel-based statistical analysis of volumes of tissue activated models was used to identify significant treatment clusters. Probabilistic tractography was employed to identify cortical connectivity patterns associated with treatment efficacy. Results All patients responded well to treatment (46% mean improvement off medication UPDRS-III [p<0.0001]) without significant adverse events. Cluster corresponding to maximum improvement in tremor was in the posterior, superior and lateral portion of the nucleus. Clusters corresponding to improvement in bradykinesia and rigidity were nearer the superior border in a further medial and posterior location. The rigidity cluster extended beyond the superior border to the area of the zona incerta and Forel-H2 field. When the clusters where averaged, the coordinates of the area with maximum overall efficacy was X=-10(-9.5), Y=-13(-1) and Z=-7(-3) in MNI(AC-PC) space. Cortical connectivity to primary motor area was predictive of higher improvement in tremor; whilst that to supplementary motor area was predictive of improvement in bradykinesia and rigidity; and connectivity to prefrontal cortex was predictive of improvement in rigidity. Interpretation These findings support the presence of overlapping stimulation sites within the subthalamic nucleus and its superior border, with different cortical connectivity patterns, associated with maximum improvement in tremor, rigidity and bradykinesia

Financial diversification before modern portfolio theory: UK financial advice documents in the late nineteenth and the beginning of the twentieth century

The paper offers textual evidence from a series of financial advice documents in the late nineteenth century and the early twentieth century of how UK investors perceived of and managed risk. In the world’s largest financial centre of the time, UK investors were familiar with the concept of correlation and financial advisers’ suggestions were consistent with the recommendations of modern portfolio theory in relation to portfolio selection strategies. From the 1870s, there was an increased awareness of the benefits of financial diversification - primarily putting equal amounts into a number of different securities - with much of the emphasis being on geographical rather than sectoral diversification and some discussion of avoiding highly correlated investments. Investors in the past were not so naïve as mainstream financial discussions suggest today

Ancient variation of the AvrPm17 gene in powdery mildew limits the effectiveness of the introgressed rye Pm17 resistance gene in wheat

Introgressions of chromosomal segments from related species into wheat are important sources of resistance against fungal diseases. The durability and effectiveness of introgressed resistance genes upon agricultural deployment is highly variable-a phenomenon that remains poorly understood, as the corresponding fungal avirulence genes are largely unknown. Until its breakdown, the Pm17 resistance gene introgressed from rye to wheat provided broad resistance against powdery mildew (Blumeria graminis). Here, we used quantitative trait locus (QTL) mapping to identify the corresponding wheat mildew avirulence effector AvrPm17. It is encoded by two paralogous genes that exhibit signatures of reoccurring gene conversion events and are members of a mildew sublineage specific effector cluster. Extensive haplovariant mining in wheat mildew and related sublineages identified several ancient virulent AvrPm17 variants that were present as standing genetic variation in wheat powdery mildew prior to the Pm17 introgression, thereby paving the way for the rapid breakdown of the Pm17 resistance. QTL mapping in mildew identified a second genetic component likely corresponding to an additional resistance gene present on the 1AL.1RS translocation carrying Pm17. This gene remained previously undetected due to suppressed recombination within the introgressed rye chromosomal segment. We conclude that the initial effectiveness of 1AL.1RS was based on simultaneous introgression of two genetically linked resistance genes. Our results demonstrate the relevance of pathogen-based genetic approaches to disentangling complex resistance loci in wheat. We propose that identification and monitoring of avirulence gene diversity in pathogen populations become an integral part of introgression breeding to ensure effective and durable resistance in wheat

Microtubule-associated protein tau is essential for long-term depression in the hippocampus

The microtubule-associated protein tau is a principal component of neurofibrillary tangles, and has been identified as a key molecule in Alzheimer's disease and other tauopathies. However, it is unknown how a protein that is primarily located in axons is involved in a disease that is believed to have a synaptic origin. To investigate a possible synaptic function of tau, we studied synaptic plasticity in the hippocampus and found a selective deficit in long-term depression (LTD) in tau knockout mice in vivo and in vitro, an effect that was replicated by RNAi knockdown of tau in vitro. We found that the induction of LTD is associated with the glycogen synthase kinase-3-mediated phosphorylation of tau. These observations demonstrate that tau has a critical physiological function in LTD.A.T. was supported by the research funding for longevity sciences (23-39) from National Center for Geriatrics and Gerontology, and the Strategic Research Programme for Brain Science ('Integrated Research on Neuropsychiatric Disorders') and Grant in Aid for Scientific Research on Innovative Areas ('Brain Environment') from the Ministry of Education, Science, Sports and Culture of Japan. K.C., D.J.W. and G.L.C. were supported by UK Wellcome Trust-MRC Neurodegenerative Disease Initiative Programme. K.C. was supported by the Korea-UK Alzheimer's Disease Research Consortium programme from the Ministry of Health and Welfare (Korea). G.L.C. was supported by the WCU Programme (Korea). I.S. was supported by the British Council. The collaboration between K.C. and A.T. was supported by a Sasakawa Foundation grant awarded to K.C. K.C. was supported by the Wolfson Research Merit Award and the Royal Society, London