A Unique haplotype found in apple accessions exhibiting early bud-break could serve as a marker for breeding apples with low chilling requirements

Most commercial apple cultivars have high to medium chilling requirements and consequently are not grown in regions with warm winters. Furthermore, global climate changes raise the concern that some regions where apples are currently being produced will become unsuitable in the future. Therefore, mapping and understanding the factors governing chilling requirements are important goals towards the breeding of new apple varieties. In this study, we characterized 73 apple accessions: old local accessions, modern cultivars, and selected hybrids, all grown in the Newe Ya’ar germplasm collection in Israel under moderate winter conditions. We measured the time of vegetative bud-break as an indicator of chilling requirements and genotyped the accessions for known genetic markers and for markers we developed by re-sequencing the genome of ‘Anna’, a cultivar with very low chilling requirements. Our results show that while most of the accessions that were characterized as having early bud-break are genetically different from each other, they all share a unique haplotype in a region of ～190 kb, within a previously identified QTL for bud-break time, on chromosome 9. The alleles in the early bud-break-associated haplotype were not found in any of the late accessions tested, suggesting that the causative difference leading to the variation in bud-break time lays within or near this region, and that there is a common ancestor carrying early bud-break trait of the early accessions tested. Moreover, the markers of the unique haplotype can serve as genetic markers to accelerate the breeding of apple cultivars better adapted to warm climates.     

The SMC5/6 complex compacts and silences unintegrated HIV-1 DNA and is antagonized by Vpr

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NDNF interneurons in layer 1 gain-modulate whole cortical columns according to an animal’s behavioral state

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Functional analysis of the apple fruit microbiome based on shotgun metagenomic sequencing of conventional and organic orchard samples

Fruits harbour abundant and diverse microbial communities that protect them from post-harvest pathogens. Identification of functional traits associated with a given microbiota can provide a better understanding of their potential influence. Here, we focused on the epiphytic microbiome of apple fruit. We suggest that shotgun metagenomic data can indicate specific functions carried out by different groups and provide information on their potential impact. Samples were collected from the surface of ‘Golden Delicious’ apples from four orchards that differ in their geographic location and management practice. Approximately 1 million metagenes were predicted based on a high-quality assembly. Functional profiling of the microbiome of fruits from orchards differing in their management practice revealed a functional shift in the microbiota. The organic orchard microbiome was enriched in pathways involved in plant defence activities; the conventional orchard microbiome was enriched in pathways related to the synthesis of antibiotics. The functional significance of the variations was explored using microbial network modelling algorithms to reveal the metabolic role of specific phylogenetic groups. The analysis identified several associations supported by other published studies. For example, the analysis revealed the nutritional dependencies of the Capnodiales group, including the Alternaria pathogen, on aromatic compounds.     

Arabidopsis leaf hydraulic conductance is regulated by xylem sap pH,controlled, in turn,by a P-type H+-ATPase of vascular bundle sheath cells

The leaf vascular bundle sheath cells (BSCs) that tightly envelop the leaf veins, are a selective and dynamic barrier to xylem sap water and solutes radially entering the mesophyll cells. Under normal conditions, xylem sap pH below 6 is presumably important for driving and regulating the transmembranal solute transport. Having discovered recently a differentially high expression of a BSC proton pump, AHA2, we now test the hypothesis that it regulates the xylem sap pH and leaf radial water fluxes. We monitored the xylem sap pH in the veins of detached leaves of wild-type Arabidopsis, AHA mutants and aha2 mutants complemented with AHA2 gene solely in BSCs. We tested an AHA inhibitor (vanadate) and stimulator (fusicoccin), and different pH buffers. We monitored their impact on the xylem sap pH and the leaf hydraulic conductance (K_leaf), and the effect of pH on the water osmotic permeability (P_f) of isolated BSCs protoplasts. We found that AHA2 is necessary for xylem sap acidification, and in turn, for elevating K_leaf. Conversely, AHA2 knockdown, which alkalinized the xylem sap, or, buffering its pH to 7.5, reduced K_leaf, and elevating external pH to 7.5 decreased the BSCs P_f. All these showed a causative link between AHA2 activity in BSCs and leaf radial hydraulic water conductance.     

CloneSeq: A highly sensitive analysis platform for the characterization of 3D-cultured single-cell-derived clones

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Notes on an interspecific interaction between distant taxa: Observation of active cohabitation and communal nesting resources between Gehyra mutilata (Wiegmann, 1834) and two vespid wasp species

Tropical ecosystems are biodiverse and ecologically complex, supporting nearly half of the global herpetofauna. Ecological interactions play a role in the maintenance of species diversity with a range of ecological interactions occurring within and among species in tropical ecosystems. Incidental observations of ecological interactions provide an important contribution to the understanding of the ecology and natural history of species. Here, we report an interspecific interaction between distant taxa, the Four-Clawed Gecko (Gehyra mutilata) utilizing an active communal nesting site and shared nesting resources with two vespid wasp species (Eumeninae and Polistinae), where previous observations documented species utilizing abandoned nesting resources. This is the first known record of three species actively cohabitating in a shared nesting resource. This observation, with one or all species positively benefiting from the ecological interaction, likely indicates a mutualistic or commensal ecological interaction. Incidental observations such as the present study are likely to reveal that interspecific ecological interactions including communal nesting are more widespread than previously thought and the co-utilization of existing nesting resources presents an advantage for taxa. Observations such as these provide the basis for understanding the complex network of ecological interactions occurring in tropical rainforests.     

The DAP-kinase interactome

DAP-kinase (DAPK) is a Ca²⁺/calmodulin regulated Ser/Thr kinase that activates a diverse range of cellular activities. It is subject to multiple layers of regulation involving both intramolecular signaling, and interactions with additional proteins, including other kinases and phosphatases. Its protein stability is modulated by at least three distinct ubiquitin-dependent systems. Like many kinases, DAPK participates in several signaling cascades, by phosphorylating additional kinases such as ZIP-kinase and protein kinase D (PKD), or Pin1, a phospho-directed peptidyl-prolyl isomerase that regulates the function of many phosphorylated proteins. Other substrate targets have more direct cellular effects; for example, phosphorylation of the myosin II regulatory chain and tropomyosin mediate some of DAPK’s cytoskeletal functions, including membrane blebbing during cell death and cell motility. DAPK induces distinct death pathways of apoptosis, autophagy and programmed necrosis. Among the substrates implicated in these processes, phosphorylation of PKD, Beclin 1, and the NMDA receptor has been reported. Interestingly, not all cellular effects are mediated by DAPK’s catalytic activity. For example, by virtue of protein–protein interactions alone, DAPK activates pyruvate kinase isoform M2, the microtubule affinity regulating kinases and inflammasome protein NLRP3, to promote glycolysis, influence microtubule dynamics, and enhance interleukin-1β production, respectively. In addition, a number of other substrates and interacting proteins have been identified, the physiological significance of which has not yet been established. All of these substrates, effectors and regulators together comprise the DAPK interactome. By presenting the components of the interactome network, this review will clarify both the mechanisms by which DAPK function is regulated, and by which it mediates its various cellular effects.