Control of inflorescence architecture in tomato by BTB/POZ transcriptional regulators

Plant productivity depends on inflorescences, flower-bearing shoots that originate from the stem cell populations of shoot meristems. Inflorescence architecture determines flower production, which can vary dramatically both between and within species. In tomato plants, formation of multiflowered inflorescences depends on a precisely timed process of meristem maturation mediated by the transcription factor gene TERMINATING FLOWER (TMF), but the underlying mechanism is unknown. We show that TMF protein acts together with homologs of the Arabidopsis BLADE-ON-PETIOLE (BOP) transcriptional cofactors, defined by the conserved BTB (Broad complex, Tramtrack, and Bric-a-brac)/POZ (POX virus and zinc finger) domain. TMF and three tomato BOPs (SlBOPs) interact with themselves and each other, and TMF recruits SlBOPs to the nucleus, suggesting formation of a transcriptional complex. Like TMF, SlBOP gene expression is highest during vegetative and transitional stages of meristem maturation, and CRISPR/Cas9 elimination of SlBOP function causes pleiotropic defects, most notably simplification of inflorescences into single flowers, resembling tmf mutants. Flowering defects are enhanced in higher-order slbop tmf mutants, suggesting that SlBOPs function with additional factors. In support of this, SlBOPs interact with TMF homologs, mutations in which cause phenotypes like slbop mutants. Our findings reveal a new flowering module defined by SlBOP-TMF family interactions that ensures a progressive meristem maturation to promote inflorescence complexity

The evolution of inflorescence diversity in the nightshades and heterochrony during meristem maturation

One of the most remarkable manifestations of plant evolution is the diversity for floral branching systems. These "inflorescences" arise from stem cell populations in shoot meristems that mature gradually to reproductive states in response to environmental and endogenous signals. The morphology of the shoot meristem maturation process is conserved across distantly related plants, raising the question of how diverse inflorescence architectures arise from seemingly common maturation programs. In tomato and related nightshades (Solanaceae), inflorescences range from solitary flowers to highly branched structures bearing hundreds of flowers. Since reproductive barriers between even closely related Solanaceae have precluded a genetic dissection, we captured and compared meristem maturation transcriptomes from five domesticated and wild species reflecting the evolutionary continuum of inflorescence complexity. We find these divergent species share hundreds of dynamically expressed genes, enriched for transcription factors. Meristem stages are defined by distinct molecular states and point to modified maturation schedules underlying architectural variation. These modified schedules are marked by a peak of transcriptome expression divergence during the reproductive transition, driven by heterochronic shifts of dynamic genes, including transcriptional regulators with known roles in flowering. Thus, evolutionary diversity in Solanaceae inflorescence complexity is determined by subtle modifications of transcriptional programs during a critical transitional window of meristem maturation, which we propose underlies similar cases of plant architectural variation. More broadly, our findings parallel the recently described transcriptome "inverse hourglass" model for animal embryogenesis, suggesting both plant and animal morphological variation is guided by a mid-development period of transcriptome divergence

Tomato yield heterosis is triggered by a dosage sensitivity of the florigen pathway that fine-tunes shoot architecture

The superiority of hybrids has long been exploited in agriculture, and although many models explaining "heterosis" have been put forth, direct empirical support is limited. Particularly elusive have been cases of heterozygosity for single gene mutations causing heterosis under a genetic model known as overdominance. In tomato (Solanum lycopersicum), plants carrying mutations in SINGLE FLOWER TRUSS (SFT) encoding the flowering hormone florigen are severely delayed in flowering, become extremely large, and produce few flowers and fruits, but when heterozygous, yields are dramatically increased. Curiously, this overdominance is evident only in the background of "determinate" plants, in which the continuous production of side shoots and inflorescences gradually halts due to a defect in the flowering repressor SELF PRUNING (SP). How sp facilitates sft overdominance is unclear, but is thought to relate to the opposing functions these genes have on flowering time and shoot architecture. We show that sft mutant heterozygosity (sft/+) causes weak semi-dominant delays in flowering of both primary and side shoots. Using transcriptome sequencing of shoot meristems, we demonstrate that this delay begins before seedling meristems become reproductive, followed by delays in subsequent side shoot meristems that, in turn, postpone the arrest of shoot and inflorescence production. Reducing SFT levels in sp plants by artificial microRNAs recapitulates the dose-dependent modification of shoot and inflorescence production of sft/+ heterozygotes, confirming that fine-tuning levels of functional SFT transcripts provides a foundation for higher yields. Finally, we show that although flowering delays by florigen mutant heterozygosity are conserved in Arabidopsis, increased yield is not, likely because cyclical flowering is absent. We suggest sft heterozygosity triggers a yield improvement by optimizing plant architecture via its dosage response in the florigen pathway. Exploiting dosage sensitivity of florigen and its family members therefore provides a path to enhance productivity in other crops, but species-specific tuning will be required

Dendritic Spine Shape Analysis: A Clustering Perspective

Functional properties of neurons are strongly coupled with their morphology. Changes in neuronal activity alter morphological characteristics of dendritic spines. First step towards understanding the structure-function relationship is to group spines into main spine classes reported in the literature. Shape analysis of dendritic spines can help neuroscientists understand the underlying relationships. Due to unavailability of reliable automated tools, this analysis is currently performed manually which is a time-intensive and subjective task. Several studies on spine shape classification have been reported in the literature, however, there is an on-going debate on whether distinct spine shape classes exist or whether spines should be modeled through a continuum of shape variations. Another challenge is the subjectivity and bias that is introduced due to the supervised nature of classification approaches. In this paper, we aim to address these issues by presenting a clustering perspective. In this context, clustering may serve both confirmation of known patterns and discovery of new ones. We perform cluster analysis on two-photon microscopic images of spines using morphological, shape, and appearance based features and gain insights into the spine shape analysis problem. We use histogram of oriented gradients (HOG), disjunctive normal shape models (DNSM), morphological features, and intensity profile based features for cluster analysis. We use x-means to perform cluster analysis that selects the number of clusters automatically using the Bayesian information criterion (BIC). For all features, this analysis produces 4 clusters and we observe the formation of at least one cluster consisting of spines which are difficult to be assigned to a known class. This observation supports the argument of intermediate shape types.Comment: Accepted for BioImageComputing workshop at ECCV 201

RaGOO: fast and accurate reference-guided scaffolding of draft genomes

We present RaGOO, a reference-guided contig ordering and orienting tool that leverages the speed and sensitivity of Minimap2 to accurately achieve chromosome-scale assemblies in minutes. After the pseudomolecules are constructed, RaGOO identifies structural variants, including those spanning sequencing gaps. We show that RaGOO accurately orders and orients 3 de novo tomato genome assemblies, including the widely used M82 reference cultivar. We then demonstrate the scalability and utility of RaGOO with a pan-genome analysis of 103 Arabidopsis thaliana accessions by examining the structural variants detected in the newly assembled pseudomolecules. RaGOO is available open source at https://github.com/malonge/RaGOO

Interplay between magnetism and superconductivity and appearance of a second superconducting transition in alpha-FeSe at high pressure

We synthesized tetragonal alpha-FeSe by melting a powder mixture of iron and selenium at high pressure. Subsequent annealing at normal pressure results in removing traces of hexagonal beta- FeSe, formation of a rather sharp transition to superconducting state at Tc ~ 7 K, and the appearance of a magnetic transition near Tm = 120 K. Resistivity and ac-susceptibility were measured on the annealed sample at hydrostatic pressure up to 4.5 GPa. A magnetic transition visible in ac-susceptibility shifts down under pressure and the resistive anomaly typical for a spin density wave (SDW) antiferromagnetic transition develops near the susceptibility anomaly. Tc determined by the appearance of a diamagnetic response in susceptibility, increases linearly under pressure at a rate dTc/dP = 3.5 K/GPa. Below 1.5 GPa, the resistive superconducting transition is sharp; the width of transition does not change with pressure; and, Tc determined by a peak in drho/dT increases at a rate ~ 3.5 K/GPa. At higher pressure, a giant broadening of the resistive transition develops. This effect cannot be explained by possible pressure gradients in the sample and is inherent to alpha-FeSe. The dependences drho(T)/dT show a signature for a second peak above 3 GPa which is indicative of the appearance of another superconducting state in alpha-FeSe at high pressure. We argue that this second superconducting phase coexists with SDW antiferromagnetism in a partial volume fraction and originates from pairing of charge carriers from other sheets of the Fermi surface

Gap structure in the electron-doped Iron-Arsenide Superconductor Ba(Fe0.92Co0.08)2As2: low-temperature specific heat study

We report the field and temperature dependence of the low-temperature specific heat down to 400 mK and in magnetic fields up to 9 T of the electron-doped Ba(Fe0.92Co0.08)2As2 superconductor. Using the phonon specific heat obtained from pure BaFe2As2 we find the normal state Sommerfeld coefficient to be 18 mJ/mol.K^2 and a condensation energy of 1.27 J/mol. The temperature dependence of the electronic specific heat clearly indicate the presence of the low-energy excitations in the system. The magnetic field variation of field-induced specific heat cannot be described by single clean s- or d-wave models. Rather, the data require an anisotropic gap scenario which may or may not have nodes. We discuss the implications of these results.Comment: New Journal of Physics in press, 10 pages, 5 figure

Spectroscopic scanning tunneling microscopy insights into Fe-based superconductors

In the first three years since the discovery of Fe-based high Tc superconductors, scanning tunneling microscopy (STM) and spectroscopy have shed light on three important questions. First, STM has demonstrated the complexity of the pairing symmetry in Fe-based materials. Phase-sensitive quasiparticle interference (QPI) imaging and low temperature spectroscopy have shown that the pairing order parameter varies from nodal to nodeless s\pm within a single family, FeTe1-xSex. Second, STM has imaged C4 -> C2 symmetry breaking in the electronic states of both parent and superconducting materials. As a local probe, STM is in a strong position to understand the interactions between these broken symmetry states and superconductivity. Finally, STM has been used to image the vortex state, giving insights into the technical problem of vortex pinning, and the fundamental problem of the competing states introduced when superconductivity is locally quenched by a magnetic field. Here we give a pedagogical introduction to STM and QPI imaging, discuss the specific challenges associated with extracting bulk properties from the study of surfaces, and report on progress made in understanding Fe-based superconductors using STM techniques.Comment: 36 pages, 23 figures, 229 reference

De novo domestication of wild tomato using genome editing

Breeding of crops over millennia for yield and productivity1 has led to reduced genetic diversity. As a result, beneficial traits of wild species, such as disease resistance and stress tolerance, have been lost2. We devised a CRISPR–Cas9 genome engineering strategy to combine agronomically desirable traits with useful traits present in wild lines. We report that editing of six loci that are important for yield and productivity in present-day tomato crop lines enabled de novo domestication of wild Solanum pimpinellifolium. Engineered S. pimpinellifolium morphology was altered, together with the size, number and nutritional value of the fruits. Compared with the wild parent, our engineered lines have a threefold increase in fruit size and a tenfold increase in fruit number. Notably, fruit lycopene accumulation is improved by 500% compared with the widely cultivated S. lycopersicum. Our results pave the way for molecular breeding programs to exploit the genetic diversity present in wild plants

HIV self-testing among young women in rural South Africa: A randomized controlled trial comparing clinic-based HIV testing to the choice of either clinic testing or HIV self-testing with secondary distribution to peers and partners

Background: HIV testing rates in many hyper-endemic areas are lower than needed to curtail the HIV epidemic. New HIV testing strategies are needed to overcome barriers to traditional clinic based testing; HIV self-testing is one modality that offers promise in reaching individuals who experience barriers to clinic-based testing. Methods: We conducted a randomized control trial among young women ages 18-26 living in rural Mpumalanga, South Africa where they were randomized in a 1:1 allocation to either the: (1) HIV Counseling and Testing (HCT) arm: an invitation to test at one of the 9 local government clinics where free HCT is provided and is standard of care (SOC), or (2) choice arm: choice of either a clinic-based HCT invitation or oral HIV Self-Testing (HIVST) kits. Depending on the arm, participants were also provided either: (1) 4 HCT invitations to provide to peers/partners for HIV testing at one of the 9 local clinics, or (2) 4 HIV self-test kits to provide to peers/partners (thus 5 total HIVST kits or HCT invitations). Young women were asked to return 3 months and 9 months after enrollment to assess testing uptake and invitation or kit distribution to peers and partners and experiences with testing. Peers and partners who were reported by index participants to have received kits/invitations during follow-up visits were also invited to attend a study visit to assess their testing experiences. The trial is registered at clinical trials.gov NCT03162965. Findings: 287 young women were enrolled and randomized, with 146 randomized to the HCT arm and 141 to the choice (HCT or HIVST) arm. Of those randomized to the choice arm, over 95% (n=135) chose the HIV self-testing kit and only 6 individuals chose HCT. At the 3-month follow-up visit, 92% of index participants in the choice arm reported having tested for HIV compared to 43% of participants in the HCT arm, resulting in a significant risk difference of 49% (95% CI 40%, 58%). By 9 months, this difference decreased to a risk difference of 25% (95% CI 17%, 33%) between arms (96% in the choice arm and 72% in the HCT arm). Participants in the choice arm were also more likely to invite peers and partners to test compared to the HCT arm (94% vs. 76% or an average of 4.97 vs 2.79 tests). Few male partners were invited to test by index participants; however, index participants in the choice arm were more likely to have their male partners test than index participants in the HCT arm (RR 2.99, 95% CI 1.45, 6.16). Interpretation: When given a choice between clinic-based HIV testing and HIV oral self-testing, the overwhelming majority of young women chose HIVST. In addition, those offered a choice of HIV testing modality were much more likely to test, distribute test kits to peers and partners, and to have peers and partners who reported testing compared to the HCT arm. Self-testing offers an important opportunity to significantly increase testing rates among young women and their peers and partners compared to clinic-based HCT. Other strategies to reach men with testing are needed. Funding: US National Institutes of Healt