A review of breeding objectives, genomic resources, and marker-assisted methods in common bean (Phaseolus vulgaris L.)

Common bean (Phaseolus vulgaris L.), one of the most important grain legume crops for direct human consumption, faces many challenges as a crop. Domesticated from wild relatives that inhabit a relatively narrow ecological niche, common bean faces a wide range of biotic and abiotic constraints within its diverse agroecological settings. Biotic stresses impacting common bean include numerous bacterial, fungal, and viral diseases and various insect and nematode pests, and abiotic stresses include drought, heat, cold, and soil nutrient deficiencies or toxicities. Breeding is often local, focusing on improvements in responses to biotic and abiotic stresses that are particular challenges in certain locations and needing to respond to conditions such as day-length regimes. This review describes the major breeding objectives for common bean, followed by a description of major genetic and genomic resources, and an overview of current and prospective marker-assisted methods in common bean breeding. Improvements over traditional breeding methods in CB can result from the use of different approaches. Several important germplasm collections have been densely genotyped, and relatively inexpensive SNP genotyping platforms enable implementation of genomic selection and related marker-assisted breeding approaches. Also important are sociological insights related to demand-led breeding, which considers local value chains, from farmers to traders to retailers and consumers

Elementary amenable subgroups of R. Thompson's group F

The subgroup structure of Thompson's group F is not yet fully understood. The group F is a subgroup of the group PL(I) of orientation preserving, piecewise linear self homeomorphisms of the unit interval and this larger group thus also has a poorly understood subgroup structure. It is reasonable to guess that F is the "only" subgroup of PL(I) that is not elementary amenable. In this paper, we explore the complexity of the elementary amenable subgroups of F in an attempt to understand the boundary between the elementary amenable subgroups and the non-elementary amenable. We construct an example of an elementary amenable subgroup up to class (height) omega squared, where omega is the first infinite ordinal.Comment: 20 page

Structurally Complex Osteosarcoma Genomes Exhibit Limited Heterogeneity within Individual Tumors and across Evolutionary Time

Osteosarcoma is an aggressive malignancy characterized by high genomic complexity. Identification of few recurrent mutations in protein coding genes suggests that somatic copy-number aberrations (SCNA) are the genetic drivers of disease. Models around genomic instability conflict-it is unclear whether osteosarcomas result from pervasive ongoing clonal evolution with continuous optimization of the fitness landscape or an early catastrophic event followed by stable maintenance of an abnormal genome. We address this question by investigating SCNAs in >12,000 tumor cells obtained from human osteosarcomas using single-cell DNA sequencing, with a degree of precision and accuracy not possible when inferring single-cell states using bulk sequencing. Using the CHISEL algorithm, we inferred allele- and haplotype-specific SCNAs from this whole-genome single-cell DNA sequencing data. Surprisingly, despite extensive structural complexity, these tumors exhibit a high degree of cell-cell homogeneity with little subclonal diversification. Longitudinal analysis of patient samples obtained at distant therapeutic timepoints (diagnosis, relapse) demonstrated remarkable conservation of SCNA profiles over tumor evolution. Phylogenetic analysis suggests that the majority of SCNAs were acquired early in the oncogenic process, with relatively few structure-altering events arising in response to therapy or during adaptation to growth in metastatic tissues. These data further support the emerging hypothesis that early catastrophic events, rather than sustained genomic instability, give rise to structural complexity, which is then preserved over long periods of tumor developmental time. SIGNIFICANCE: Chromosomally complex tumors are often described as genomically unstable. However, determining whether complexity arises from remote time-limited events that give rise to structural alterations or a progressive accumulation of structural events in persistently unstable tumors has implications for diagnosis, biomarker assessment, mechanisms of treatment resistance, and represents a conceptual advance in our understanding of intratumoral heterogeneity and tumor evolution

Unbiased Characterization of Anopheles Mosquito Blood Meals by Targeted High-Throughput Sequencing

Understanding mosquito host choice is important for assessing vector competence or identifying disease reservoirs. Unfortunately, the availability of an unbiased method for comprehensively evaluating the composition of insect blood meals is very limited, as most current molecular assays only test for the presence of a few pre-selected species. These approaches also have limited ability to identify the presence of multiple mammalian hosts in a single blood meal. Here, we describe a novel high-throughput sequencing method that enables analysis of 96 mosquitoes simultaneously and provides a comprehensive and quantitative perspective on the composition of each blood meal. We validated in silico that universal primers targeting the mammalian mitochondrial 16S ribosomal RNA genes (16S rRNA) should amplify more than 95% of the mammalian 16S rRNA sequences present in the NCBI nucleotide database. We applied this method to 442 female Anopheles punctulatus s. l. mosquitoes collected in Papua New Guinea (PNG). While human (52.9%), dog (15.8%) and pig (29.2%) were the most common hosts identified in our study, we also detected DNA from mice, one marsupial species and two bat species. Our analyses also revealed that 16.3% of the mosquitoes fed on more than one host. Analysis of the human mitochondrial hypervariable region I in 102 human blood meals showed that 5 (4.9%) of the mosquitoes unambiguously fed on more than one person. Overall, analysis of PNG mosquitoes illustrates the potential of this approach to identify unsuspected hosts and characterize mixed blood meals, and shows how this approach can be adapted to evaluate inter-individual variations among human blood meals. Furthermore, this approach can be applied to any disease-transmitting arthropod and can be easily customized to investigate non-mammalian host sources

VGLL2-NCOA2 leverages developmental programs for pediatric sarcomagenesis

Clinical sequencing efforts are rapidly identifying sarcoma gene fusions that lack functional validation. An example is the fusion of transcriptional coactivators, VGLL2-NCOA2, found in infantile rhabdomyosarcoma. To delineate VGLL2-NCOA2 tumorigenic mechanisms and identify therapeutic vulnerabilities, we implement a cross-species comparative oncology approach with zebrafish, mouse allograft, and patient samples. We find that VGLL2-NCOA2 is sufficient to generate mesenchymal tumors that display features of immature skeletal muscle and recapitulate the human disease. A subset of VGLL2-NCOA2 zebrafish tumors transcriptionally cluster with embryonic somitogenesis and identify VGLL2-NCOA2 developmental programs, including a RAS family GTPase, ARF6. In VGLL2-NCOA2 zebrafish, mouse, and patient tumors, ARF6 is highly expressed. ARF6 knockout suppresses VGLL2-NCOA2 oncogenic activity in cell culture, and, more broadly, ARF6 is overexpressed in adult and pediatric sarcomas. Our data indicate that VGLL2-NCOA2 is an oncogene that leverages developmental programs for tumorigenesis and that reactivation or persistence of ARF6 could represent a therapeutic opportunity

Galaxy groups in the 2dFGRS: the group-finding algorithm and the 2PIGG catalogue

The construction of a catalogue of galaxy groups from the Two-degree Field Galaxy Redshift Survey (2dFGRS) is described. Groups are identified by means of a friends-of-friends percolation algorithm which has been thoroughly tested on mock versions of the 2dFGRS generated from cosmological N-body simulations. The tests suggest that the algorithm groups all galaxies that it should be grouping, with an additional 40 per cent of interlopers. About 55 per cent of the ∼190 000 galaxies considered are placed into groups containing at least two members of which ∼29 000 are found. Of these, ∼7000 contain at least four galaxies, and these groups have a median redshift of 0.11 and a median velocity dispersion of 260 km s−1. This 2dFGRS Percolation-Inferred Galaxy Group (2PIGG) catalogue represents the largest available homogeneous sample of galaxy groups. It is publicly available on the World Wide We

Dissipative Chaos in Semiconductor Superlattices

We consider the motion of ballistic electrons in a miniband of a semiconductor superlattice (SSL) under the influence of an external, time-periodic electric field. We use the semi-classical balance-equation approach which incorporates elastic and inelastic scattering (as dissipation) and the self-consistent field generated by the electron motion. The coupling of electrons in the miniband to the self-consistent field produces a cooperative nonlinear oscillatory mode which, when interacting with the oscillatory external field and the intrinsic Bloch-type oscillatory mode, can lead to complicated dynamics, including dissipative chaos. For a range of values of the dissipation parameters we determine the regions in the amplitude-frequency plane of the external field in which chaos can occur. Our results suggest that for terahertz external fields of the amplitudes achieved by present-day free electron lasers, chaos may be observable in SSLs. We clarify the nature of this novel nonlinear dynamics in the superlattice-external field system by exploring analogies to the Dicke model of an ensemble of two-level atoms coupled with a resonant cavity field and to Josephson junctions.Comment: 33 pages, 8 figure

Searching for a Stochastic Background of Gravitational Waves with LIGO

The Laser Interferometer Gravitational-wave Observatory (LIGO) has performed the fourth science run, S4, with significantly improved interferometer sensitivities with respect to previous runs. Using data acquired during this science run, we place a limit on the amplitude of a stochastic background of gravitational waves. For a frequency independent spectrum, the new limit is $\Omega_{\rm GW} < 6.5 \times 10^{-5}$. This is currently the most sensitive result in the frequency range 51-150 Hz, with a factor of 13 improvement over the previous LIGO result. We discuss complementarity of the new result with other constraints on a stochastic background of gravitational waves, and we investigate implications of the new result for different models of this background.Comment: 37 pages, 16 figure

Galaxy groups in the Two-degree Field Galaxy Redshift Survey: the luminous content of the groups

The Two-degree Field Galaxy Redshift Survey (2dFGRS) Percolation-Inferred Galaxy Group (2PIGG) catalogue of ∼29 000 objects is used to study the luminous content of galaxy systems of various sizes. Mock galaxy catalogues constructed from cosmological simulations are used to gauge the accuracy with which intrinsic group properties can be recovered. It is found that a Schechter function is a reasonable fit to the galaxy luminosity functions in groups of different mass in the real data, and that the characteristic luminosity L⋆ is slightly larger for more massive groups. However, the mock data show that the shape of the recovered luminosity function is expected to differ from the true shape, and this must be allowed for when interpreting the data. Luminosity function results are presented in both the bJ and rF wavebands. The variation of the halo mass-to-light ratio, ϒ, with group size is studied in both of these wavebands. A robust trend of increasing ϒ with increasing group luminosity is found in the 2PIGG data. Going from groups with bJ luminosities equal to 1010h−2 L⊙ to those 100 times more luminous, the typical bJ-band mass-to-light ratio increases by a factor of 5, whereas the rF-band mass-to-light ratio grows by a factor of 3.5. These trends agree well with the predictions of the simulations which also predict a minimum in the mass-to-light ratio on a scale roughly corresponding to the Local Group. The data indicate that if such a minimum exists, then it must occur at L≲ 1010h−2 L⊙, below the range accurately probed by the 2PIGG catalogue. According to the mock data, the bJ mass-to-light ratios of the largest groups are expected to be approximately 1.1 times the global value. Assuming that this correction applies to the real data, the mean bJ luminosity density of the Universe yields an estimate of Ωm= 0.26 ± 0.03 (statistical error only). Various possible sources of systematic error are considered, with the conclusion that these could affect the estimate of Ωm by a few tens of per cen