Genome-Wide Datasets of Chicories (Cichorium intybus L.) for Marker-Assisted Crop Breeding Applications: A Systematic Review and Meta-Analysis

Cichorium intybus L. is the most economically important species of its genus and among the most important of the Asteraceae family. In chicory, many linkage maps have been produced, several sets of mapped and unmapped markers have been developed, and dozens of genes linked to traits of agronomic interest have been investigated. This treasure trove of information, properly cataloged and organized, is of pivotal importance for the development of superior commercial products with valuable agronomic potential in terms of yield and quality, including reduced bitter taste and increased inulin production, as well as resistance or tolerance to pathogens and resilience to environmental stresses. For this reason, a systematic review was conducted based on the scientific literature published in chicory during 1980-2023. Based on the results obtained from the meta-analysis, we created two consensus maps capable of supporting marker-assisted breeding (MAB) and marker-assisted selection (MAS) programs. By taking advantage of the recently released genome of C. intybus, we built a 639 molecular marker-based consensus map collecting all the available mapped and unmapped SNP and SSR loci available for this species. In the following section, after summarizing and discussing all the genes investigated in chicory and related to traits of interest such as reproductive barriers, sesquiterpene lactone biosynthesis, inulin metabolism and stress response, we produced a second map encompassing 64 loci that could be useful for MAS purposes. With the advent of omics technologies, molecular data chaos (namely, the situation where the amount of molecular data is so complex and unmanageable that their use becomes challenging) is becoming far from a negligible issue. In this review, we have therefore tried to contribute by standardizing and organizing the molecular data produced thus far in chicory to facilitate the work of breeders

MIK2 is a candidate gene of the S-locus for sporophytic self-incompatibility in chicory (Cichorium intybus, Asteraceae)

The Cichorium genus offers a unique opportunity to study the sporophytic self-incompatibility (SSI) system, being composed of species characterized by highly efficient self-incompatibility (e.g., C. intybus) and complete self-compatibility (e.g., C. endivia). To this end, the chicory genome was used to map seven previously identified SSI locus-associated markers. The region containing the S-locus was therefore restricted to an similar to 4 M bp window on chromosome 5. Among the genes predicted in this region, MDIS1 INTERACTING RECEPTOR LIKE KINASE 2 (ciMIK2) was particularly promising as a candidate for SSI. Its ortholog in Arabidopsis (atMIK2) is involved in pollen-stigma recognition reactions, and its protein structure is similar to that of S-receptor kinase (SRK), a key component of the SSI system in the Brassica genus. The amplification and sequencing of MIK2 in chicory and endive accessions revealed two contrasting scenarios. In C. endivia, MIK2 was fully conserved even when comparing different botanical varieties (i.e., smooth and curly endive). In C. intybus, 387 polymorphic positions and 3 INDELs were identified when comparing accessions of different biotypes all belonging to the same botanical variety (i.e., radicchio). The polymorphism distribution throughout the gene was uneven, with hypervariable domains preferentially localized in the LRR-rich extracellular region, putatively identified as the receptor domain. The gene was hypothesized to be under positive selection, as the nonsynonymous mutations were more than double the synonymous ones (dN/dS = 2.17). An analogous situation was observed when analyzing the first 500 bp of the MIK2 promoter: no SNPs were observed among the endive samples, whereas 44 SNPs and 6 INDELs were detected among the chicory samples. Further analyses are needed to confirm the role of MIK2 in SSI and to demonstrate whether the 23 species-specific nonsynonymous SNPs in the CDS and/or the species-specific 10 bp-INDEL found in a CCAAT box region of the promoter are responsible for the contrasting sexual behaviors of chicory and endive

Innovating physics teaching through teachers’ learning communities and action research

The paper provides information, foundation and supporting evidence about a possible structure of a research-based in-service program for physics teachers aimed at improving their use of the laboratory. We present our model and we describe the CoLLabora project where the model was first implemented. The results suggest that the program actually produced positive changes in the participants’ ideas about the laboratory, its actual use in their teaching practice, and in students’ outcomes. We also present two case studies and we outline some research lines and the ‘teacher training cascade’ that have developed from the project

Finite-frequency counting statistics of electron transport: Markovian Theory

We present a theory of frequency-dependent counting statistics of electron transport through nanostructures within the framework of Markovian quantum master equations. Our method allows the calculation of finite-frequency current cumulants of arbitrary order, as we explicitly show for the second- and third-order cumulants. Our formulae generalize previous zero-frequency expressions in the literature and can be viewed as an extension of MacDonald's formula beyond shot noise. When combined with an appropriate treatment of tunneling, using, e.g. Liouvillian perturbation theory in Laplace space, our method can deal with arbitrary bias voltages and frequencies, as we illustrate with the paradigmatic example of transport through a single resonant level model. We discuss various interesting limits, including the recovery of the fluctuation-dissipation theorem near linear response, as well as some drawbacks inherent of the Markovian description arising from the neglect of quantum fluctuations.Comment: Accepted in New Journal of Physics. Updated tex

Out-of-Equilibrium Admittance of Single Electron Box Under Strong Coulomb Blockade

We study admittance and energy dissipation in an out-of-equlibrium single electron box. The system consists of a small metallic island coupled to a massive reservoir via single tunneling junction. The potential of electrons in the island is controlled by an additional gate electrode. The energy dissipation is caused by an AC gate voltage. The case of a strong Coulomb blockade is considered. We focus on the regime when electron coherence can be neglected but quantum fluctuations of charge are strong due to Coulomb interaction. We obtain the admittance under the specified conditions. It turns out that the energy dissipation rate can be expressed via charge relaxation resistance and renormalized gate capacitance even out of equilibrium. We suggest the admittance as a tool for a measurement of the bosonic distribution corresponding collective excitations in the system

Measurement of finite-frequency current statistics in a single-electron transistor

Electron transport in nano-scale structures is strongly influenced by the Coulomb interaction which gives rise to correlations in the stream of charges and leaves clear fingerprints in the fluctuations of the electrical current. A complete understanding of the underlying physical processes requires measurements of the electrical fluctuations on all time and frequency scales, but experiments have so far been restricted to fixed frequency ranges as broadband detection of current fluctuations is an inherently difficult experimental procedure. Here we demonstrate that the electrical fluctuations in a single electron transistor (SET) can be accurately measured on all relevant frequencies using a nearby quantum point contact for on-chip real-time detection of the current pulses in the SET. We have directly measured the frequency-dependent current statistics and hereby fully characterized the fundamental tunneling processes in the SET. Our experiment paves the way for future investigations of interaction and coherence induced correlation effects in quantum transport.Comment: 7 pages, 3 figures, published in Nature Communications (open access

Measurements of the Correlation Function of a Microwave Frequency Single Photon Source

At optical frequencies the radiation produced by a source, such as a laser, a black body or a single photon source, is frequently characterized by analyzing the temporal correlations of emitted photons using single photon counters. At microwave frequencies, however, there are no efficient single photon counters yet. Instead, well developed linear amplifiers allow for efficient measurement of the amplitude of an electromagnetic field. Here, we demonstrate how the properties of a microwave single photon source can be characterized using correlation measurements of the emitted radiation with such detectors. We also demonstrate the cooling of a thermal field stored in a cavity, an effect which we detect using a cross-correlation measurement of the radiation emitted at the two ends of the cavity.Comment: 5 pages, 4 figure

Correspondence Between Cognitive and Audiological Evaluations Among the Elderly: A Preliminary Report of an Audiological Screening Model of Subjects at Risk of Cognitive Decline With Slight to Moderate Hearing Loss

Epidemiological studies show increasing prevalence rates of cognitive decline and hearing loss with age, particularly after the age of 65 years. These conditions are reported to be associated, although conclusive evidence of causality and implications is lacking. Nevertheless, audiological and cognitive assessment among elderly people is a key target for comprehensive and multidisciplinary evaluation of the subject's frailty status. To evaluate the use of tools for identifying older adults at risk of hearing loss and cognitive decline and to compare skills and abilities in terms of hearing and cognitive performances between older adults and young subjects, we performed a prospective cross-sectional study using supraliminal auditory tests. The relationship between cognitive assessment results and audiometric results was investigated, and reference ranges for different ages or stages of disease were determined. Patients older than 65 years with different degrees of hearing function were enrolled. Each subject underwent an extensive audiological assessment, including tonal and speech audiometry, Italian Matrix Sentence Test, and speech audiometry with logatomes in quiet. Cognitive function was screened and then verified by experienced clinicians using the Montreal Cognitive Assessment Score, the Geriatric Depression Scale, and further investigations in some. One hundred twenty-three subjects were finally enrolled during 2016-2019: 103 were >65 years of age and 20 were younger participants (as controls). Cognitive functions showed a correlation with the audiological results in post-lingual hearing-impaired patients, in particular in those affected by slight to moderate hearing loss and aged more than 70 years. Audiological testing can thus be useful in clinical assessment and identification of patients at risk of cognitive impairment. The study was limited by its sample size (CI 95%; CL 10%), strict dependence on language, and hearing threshold. Further investigations should be conducted to confirm the reported results and to verify similar screening models

Structural basis of nSH2 regulation and lipid binding in PI3Kα

We report two crystal structures of the wild-type phosphatidylinositol 3-kinase α (PI3Kα) heterodimer refined to 2.9 Å and 3.4 Å resolution: the first as the free enzyme, the second in complex with the lipid substrate, diC4-PIP2, respectively. The first structure shows key interactions of the N-terminal SH2 domain (nSH2) and iSH2 with the activation loop that suggest a mechanism by which the enzyme is inhibited in its basal state. In the second structure, the lipid substrate binds in a positively charged pocket adjacent to the ATP-binding site, bordered by the P-loop, the activation loop and the iSH2 domain. An additional lipid-binding site was identified at the interface of the ABD, iSH2 and kinase domains. The ability of PI3Kα to bind an additional PIP2 molecule was confirmed in vitro by fluorescence quenching experiments. The crystal structures reveal key differences in the way the nSH2 domain interacts with wild-type p110α and with the oncogenic mutant p110αH1047R. Increased buried surface area and two unique salt-bridges observed only in the wild-type structure suggest tighter inhibition in the wild-type PI3Kα than in the oncogenic mutant. These differences may be partially responsible for the increased basal lipid kinase activity and increased membrane binding of the oncogenic mutant