Next-generation sequencing, FISH mapping and synteny-based modeling reveal mechanisms of decreasing dysploidy in Cucumis

In the large Cucurbitaceae genus Cucumis, cucumber (C. sativus) is the only species with 2n = 2x = 14 chromosomes. The majority of the remaining species, including melon (C. melo) and the sister species of cucumber, C. hystrix, have 2n = 2x = 24 chromosomes, implying a reduction from n = 12 to n = 7. To understand the underlying mechanisms, we investigated chromosome synteny among cucumber, C. hystrix and melon using integrated and complementary approaches. We identified 14 inversions and a C. hystrix lineage-specific reciprocal inversion between C. hystrix and melon. The results reveal the location and orientation of 53 C. hystrix syntenic blocks on the seven cucumber chromosomes, and allow us to infer at least 59 chromosome rearrangement events that led to the seven cucumber chromosomes, including five fusions, four translocations, and 50 inversions. The 12 inferred chromosomes (AK1-AK12) of an ancestor similar to melon and C. hystrix had strikingly different evolutionary fates, with cucumber chromosome C1 apparently resulting from insertion of chromosome AK12 into the centromeric region of translocated AK2/AK8, cucumber chromosome C3 originating from a Robertsonian-like translocation between AK4 and AK6, and cucumber chromosome C5 originating from fusion of AK9 and AK10. Chromosomes C2, C4 and C6 were the result of complex reshuffling of syntenic blocks from three (AK3, AK5 and AK11), three (AK5, AK7 and AK8) and five (AK2, AK3, AK5, AK8 and AK11) ancestral chromosomes, respectively, through 33 fusion, translocation and inversion events. Previous results (Huang, S., Li, R., Zhang, Z. et al., , Nat. Genet. 41, 1275-1281; Li, D., Cuevas, H.E., Yang, L., Li, Y., Garcia-Mas, J., Zalapa, J., Staub, J.E., Luan, F., Reddy, U., He, X., Gong, Z., Weng, Y. 2011a, BMC Genomics, 12, 396) showing that cucumber C7 stayed largely intact during the entire evolution of Cucumis are supported. Results from this study allow a fine-scale understanding of the mechanisms of dysploid chromosome reduction that has not been achieved previously.

Modeling and inferring cleavage patterns in proliferating epithelia

The regulation of cleavage plane orientation is one of the key mechanisms driving epithelial morphogenesis. Still, many aspects of the relationship between local cleavage patterns and tissue-level properties remain poorly understood. Here we develop a topological model that simulates the dynamics of a 2D proliferating epithelium from generation to generation, enabling the exploration of a wide variety of biologically plausible cleavage patterns. We investigate a spectrum of models that incorporate the spatial impact of neighboring cells and the temporal influence of parent cells on the choice of cleavage plane. Our findings show that cleavage patterns generate "signature" equilibrium distributions of polygonal cell shapes. These signatures enable the inference of local cleavage parameters such as neighbor impact, maternal influence, and division symmetry from global observations of the distribution of cell shape. Applying these insights to the proliferating epithelia of five diverse organisms, we find that strong division symmetry and moderate neighbor/maternal influence are required to reproduce the predominance of hexagonal cells and low variability in cell shape seen empirically. Furthermore, we present two distinct cleavage pattern models, one stochastic and one deterministic, that can reproduce the empirical distribution of cell shapes. Although the proliferating epithelia of the five diverse organisms show a highly conserved cell shape distribution, there are multiple plausible cleavage patterns that can generate this distribution, and experimental evidence suggests that indeed plants and fruitflies use distinct division mechanisms.

Cell shapes and patterns as quantitative indicators of tissue stress in the plant epidermis

In a confluent, single-cell tissue layer, we show that cell shapes and statistics correlate directly with the tissue's mechanical properties, described by an energy functional with generic interfacial terms only. Upon increasing the cohesive component of the model, we observe a clear transition from a tense state with isotropic cells to a relaxed state with anisotropic cells. Signatures of the transition are present in the interfacial mechanics, the domain geometry, and the domain statistics, thus linking all three fields of study. This transition persists for all cell size distributions, but its exact position is crucially dependent on fluctuations in the parameter values of the functional (quenched disorder). The magnitude of fluctuations can be matched to the observed shape distribution of cells, so that visual observation of cell shapes and statistics provides information about the mechanical state of the tissue. Comparing with experimental data from the Cucumis epidermis, we find that the system is located right at the transition, allowing the tissue to relieve most of the local stress while maintaining integrity.

Fourier domain mode-locked swept source at 1050 nm based on a tapered amplifier

While swept source optical coherence tomography (OCT) in the 1050 nm range is promising for retinal imaging, there are certain challenges. Conventional semiconductor gain media have limited output power, and the performance of high-speed Fourier domain mode-locked (FDML) lasers suffers from chromatic dispersion in standard optical fiber. We developed a novel light source with a tapered amplifier as gain medium, and investigated the FDML performance comparing two fiber delay lines with different dispersion properties. We introduced an additional gain element into the resonator, and thereby achieved stable FDML operation, exploiting the full bandwidth of the tapered amplifier despite high dispersion. The light source operates at a repetition rate of 116 kHz with an effective average output power in excess of 30 mW. With a total sweep range of 70 nm, we achieved an axial resolution of 15 microm in air (approximately 11 microm in tissue) in OCT measurements. As our work shows, tapered amplifiers are suitable gain media for swept sources at 1050 nm with increased output power, while high gain counteracts dispersion effects in an FDML laser.

A simple landscape of metastable state energies for two-dimensional cellular matter

The mechanical behavior of cellular matter in two dimensions can be inferred from geometric information near its energetic ground state. Here it is shown that the much larger set of all metastable state energies is universally described by a systematic expansion in moments of the joint probability distribution of size (area) and topology (number of neighbors). The approach captures bounds to the entire range of metastable state energies and quantitatively identifies any such state. The resulting energy landscape is invariant across different classes of energy functionals, across simulation techniques, and across system polydispersities. The theory also finds a threshold in tissue adhesion beyond which no metastable states are possible. Mechanical properties of cellular matter in biological and technological applications can thus be identified by visual information only.

CYTOGENETICAL TREATISE OF INDIAN REPRESENTATIVE SPECIES OF CUCUMIS. A KARYOTYPIC APPROACH

Karyomorphological studies have been carried out in nine species and five varieties of the genus Cucumis representing Indian gene pool. The present investigations reveal the occurrence of two somatic chromosome numbers 2n = 14, 24 in the genus. C. ritchiei and C. indicus the two new species, were found to be having somatic chromosome numbers of 2n = 24 and 2n = 20 respectively. The wild species viz. C. hystrix, C. setosus, C. prophetarum, C. dipsaceus, C. indicus have very less number of median-centromeric chromosomes, high asymmetry indices, while melon groups have intermediate number of median -centromeric chromosomes. C. sativus, C. callosus, C. ritchiei show lesser number median-cen-tromeric chromosomes and very less asymmetry indices. The importance of karyotypic variation with respect to speciation within the genus Cucumis have been discussed.