Molecular dynamics modeling and simulation of void growth in two dimensions

The mechanisms of growth of a circular void by plastic deformation were studied by means of molecular dynamics in two dimensions (2D). While previous molecular dynamics (MD) simulations in three dimensions (3D) have been limited to small voids (up to ≈10 nm in radius), this strategy allows us to study the behavior of voids of up to 100 nm in radius. MD simulations showed that plastic deformation was triggered by the nucleation of dislocations at the atomic steps of the void surface in the whole range of void sizes studied. The yield stress, defined as stress necessary to nucleate stable dislocations, decreased with temperature, but the void growth rate was not very sensitive to this parameter. Simulations under uniaxial tension, uniaxial deformation and biaxial deformation showed that the void growth rate increased very rapidly with multiaxiality but it did not depend on the initial void radius. These results were compared with previous 3D MD and 2D dislocation dynamics simulations to establish a map of mechanisms and size effects for plastic void growth in crystalline solids.

Characterization of spontaneous combustuion tendency of dried sewage sludge

The general purpose of this study was the determination of the safety conditions to avoid the presence of explosive atmospheres in the wastewater industry. Eight Spanish plants located in Madrid, Barcelona and Málaga were considered and several sludge samples were taken in different seasons. The base for the assessment of the spontaneous ignition behaviour of dust accumulations is the experimental determination of the self-ignition temperature under isothermal conditions. Self-ignition temperatures at four volumes were obtained for one sample of sewage sludge, allowing their extrapolation to large storage facilities. A simple test method, based also on an isothermal study of samples, is the UN classification of substances liable to spontaneous combustion. Two different samples were so tested, obtaining unlike results if transported in packages of different volumes. By means of thermogravimetric techniques it is possible to analyse the thermal susceptibility of dried sewage sludge. Apparent activation energy can be obtained from the rate of weight loss. It is also applied to the study of self-ignition susceptibility by modifying test conditions when oxygen stream is introduced. As a consequence of this oxidant contribution, sample behaviour can be very different during testing and a step drop or sudden loss of weight is observed at a characteristic temperature for every substance, associated to a rapid combustion. Plotting both the activation energy and the characteristic temperature, a map of self-ignition risk was obtained for 10 samples, showing different risk levels for samples taken in different locations and at different seasons. A prediction of the self-ignition risk level can be also determined.

Simulating potential growth and yield of oil palm (Elaeis guineensis) with PALMSIM: Model description, evaluation and application.

Reducing the gap between water-limited potential yield and actual yield in oil palm production systems through intensification is seen as an important option for sustainably increasing palm oil production. Simulation models can play an important role in quantifying water-limited potential yield, and therefore the scope for intensification, but no oil palm model exists that is both simple enough and at the same time incorporates sufficient plant physiological knowledge to be generally applicable across sites with different growing conditions. The objectives of this study therefore were to develop a model (PALMSIM) that simulates, on a monthly time step, the potential growth of oil palm as determined by solar radiation and to evaluate model performance against measured oil palm yields under optimal water and nutrient management for a range of sites across Indonesia and Malaysia. The maximum observed yield in the field matches the corresponding simulated yield for dry bunch weight with a RMSE of 1.7 Mg ha?1 year?1 against an observed yield of 18.8 Mg ha?1. Sensitivity analysis showed that PALMSIM is robust: simulated changes in yield caused by modifying the parameters by 10% are comparable to other tree crop model evaluations. While we acknowledge that, depending on the soils and climatic environment, yields may be often water limited, we suggest a relatively simple physiological approach to simulate potential yield, which can be usefully applied to high rainfall environments and is considered as a first step in developing an oil palm model that also simulates water-limited potential yield. To illustrate the application possibil- ities of the model, PALMSIM was used to create a potential yield map for Indonesia and Malaysia by sim- ulating the growth and yield at a resolution of 0.1?. This map of potential yield is considered as a first step towards a decision support tool that can identify potentially productive, but at the moment degraded sites in Indonesia and Malaysia. ?

Modifying the atlas of low lunar orbits using inert tethers

For long enough tethers, the coupling of the attitude and orbital dynamics may show non-negligible effects in the orbital motion of a tethered satellite about a central body. In the case of fast rotating tethers the attitude remains constant, on average, up to second order effects. Besides, for a tether rotating in a plane parallel to the equatorial plane of the central body, the attitude?orbit coupling effect is formally equal to the perturbation of the Keplerian motion produced by the oblateness of the central body and, therefore, may have a stabilizing effect in the orbital dynamics. In the case of a tethered satellite in a low lunar orbit, it is demonstrated that feasible tether lengths can help in modifying the actual map of lunar frozen orbits

Methods for the analysis of multi-scale cell dynamics from fluorescence microscopy images

La embriogénesis es el proceso mediante el cual una célula se convierte en un ser un vivo. A lo largo de diferentes etapas de desarrollo, la población de células va proliferando a la vez que el embrión va tomando forma y se configura. Esto es posible gracias a la acción de varios procesos genéticos, bioquímicos y mecánicos que interaccionan y se regulan entre ellos formando un sistema complejo que se organiza a diferentes escalas espaciales y temporales. Este proceso ocurre de manera robusta y reproducible, pero también con cierta variabilidad que permite la diversidad de individuos de una misma especie. La aparición de la microscopía de fluorescencia, posible gracias a proteínas fluorescentes que pueden ser adheridas a las cadenas de expresión de las células, y los avances en la física óptica de los microscopios han permitido observar este proceso de embriogénesis in-vivo y generar secuencias de imágenes tridimensionales de alta resolución espacio-temporal. Estas imágenes permiten el estudio de los procesos de desarrollo embrionario con técnicas de análisis de imagen y de datos, reconstruyendo dichos procesos para crear la representación de un embrión digital. Una de las más actuales problemáticas en este campo es entender los procesos mecánicos, de manera aislada y en interacción con otros factores como la expresión genética, para que el embrión se desarrolle. Debido a la complejidad de estos procesos, estos problemas se afrontan mediante diferentes técnicas y escalas específicas donde, a través de experimentos, pueden hacerse y confrontarse hipótesis, obteniendo conclusiones sobre el funcionamiento de los mecanismos estudiados. Esta tesis doctoral se ha enfocado sobre esta problemática intentando mejorar las metodologías del estado del arte y con un objetivo específico: estudiar patrones de deformación que emergen del movimiento organizado de las células durante diferentes estados del desarrollo del embrión, de manera global o en tejidos concretos. Estudios se han centrado en la mecánica en relación con procesos de señalización o interacciones a nivel celular o de tejido. En este trabajo, se propone un esquema para generalizar el estudio del movimiento y las interacciones mecánicas que se desprenden del mismo a diferentes escalas espaciales y temporales. Esto permitiría no sólo estudios locales, si no estudios sistemáticos de las escalas de interacción mecánica dentro de un embrión. Por tanto, el esquema propuesto obvia las causas de generación de movimiento (fuerzas) y se centra en la cuantificación de la cinemática (deformación y esfuerzos) a partir de imágenes de forma no invasiva. Hoy en día las dificultades experimentales y metodológicas y la complejidad de los sistemas biológicos impiden una descripción mecánica completa de manera sistemática. Sin embargo, patrones de deformación muestran el resultado de diferentes factores mecánicos en interacción con otros elementos dando lugar a una organización mecánica, necesaria para el desarrollo, que puede ser cuantificado a partir de la metodología propuesta en esta tesis. La metodología asume un medio continuo descrito de forma Lagrangiana (en función de las trayectorias de puntos materiales que se mueven en el sistema en lugar de puntos espaciales) de la dinámica del movimiento, estimado a partir de las imágenes mediante métodos de seguimiento de células o de técnicas de registro de imagen. Gracias a este esquema es posible describir la deformación instantánea y acumulada respecto a un estado inicial para cualquier dominio del embrión. La aplicación de esta metodología a imágenes 3D + t del pez zebra sirvió para desvelar estructuras mecánicas que tienden a estabilizarse a lo largo del tiempo en dicho embrión, y que se organizan a una escala semejante al del mapa de diferenciación celular y con indicios de correlación con patrones de expresión genética. También se aplicó la metodología al estudio del tejido amnioserosa de la Drosophila (mosca de la fruta) durante el cierre dorsal, obteniendo indicios de un acoplamiento entre escalas subcelulares, celulares y supracelulares, que genera patrones complejos en respuesta a la fuerza generada por los esqueletos de acto-myosina. En definitiva, esta tesis doctoral propone una estrategia novedosa de análisis de la dinámica celular multi-escala que permite cuantificar patrones de manera inmediata y que además ofrece una representación que reconstruye la evolución de los procesos como los ven las células, en lugar de como son observados desde el microscopio. Esta metodología por tanto permite nuevas formas de análisis y comparación de embriones y tejidos durante la embriogénesis a partir de imágenes in-vivo. ABSTRACT The embryogenesis is the process from which a single cell turns into a living organism. Through several stages of development, the cell population proliferates at the same time the embryo shapes and the organs develop gaining their functionality. This is possible through genetic, biochemical and mechanical factors that are involved in a complex interaction of processes organized in different levels and in different spatio-temporal scales. The embryogenesis, through this complexity, develops in a robust and reproducible way, but allowing variability that makes possible the diversity of living specimens. The advances in physics of microscopes and the appearance of fluorescent proteins that can be attached to expression chains, reporting about structural and functional elements of the cell, have enabled for the in-vivo observation of embryogenesis. The imaging process results in sequences of high spatio-temporal resolution 3D+time data of the embryogenesis as a digital representation of the embryos that can be further analyzed, provided new image processing and data analysis techniques are developed. One of the most relevant and challenging lines of research in the field is the quantification of the mechanical factors and processes involved in the shaping process of the embryo and their interactions with other embryogenesis factors such as genetics. Due to the complexity of the processes, studies have focused on specific problems and scales controlled in the experiments, posing and testing hypothesis to gain new biological insight. However, methodologies are often difficult to be exported to study other biological phenomena or specimens. This PhD Thesis is framed within this paradigm of research and tries to propose a systematic methodology to quantify the emergent deformation patterns from the motion estimated in in-vivo images of embryogenesis. Thanks to this strategy it would be possible to quantify not only local mechanisms, but to discover and characterize the scales of mechanical organization within the embryo. The framework focuses on the quantification of the motion kinematics (deformation and strains), neglecting the causes of the motion (forces), from images in a non-invasive way. Experimental and methodological challenges hamper the quantification of exerted forces and the mechanical properties of tissues. However, a descriptive framework of deformation patterns provides valuable insight about the organization and scales of the mechanical interactions, along the embryo development. Such a characterization would help to improve mechanical models and progressively understand the complexity of embryogenesis. This framework relies on a Lagrangian representation of the cell dynamics system based on the trajectories of points moving along the deformation. This approach of analysis enables the reconstruction of the mechanical patterning as experienced by the cells and tissues. Thus, we can build temporal profiles of deformation along stages of development, comprising both the instantaneous events and the cumulative deformation history. The application of this framework to 3D + time data of zebrafish embryogenesis allowed us to discover mechanical profiles that stabilized through time forming structures that organize in a scale comparable to the map of cell differentiation (fate map), and also suggesting correlation with genetic patterns. The framework was also applied to the analysis of the amnioserosa tissue in the drosophila’s dorsal closure, revealing that the oscillatory contraction triggered by the acto-myosin network organized complexly coupling different scales: local force generation foci, cellular morphology control mechanisms and tissue geometrical constraints. In summary, this PhD Thesis proposes a theoretical framework for the analysis of multi-scale cell dynamics that enables to quantify automatically mechanical patterns and also offers a new representation of the embryo dynamics as experienced by cells instead of how the microscope captures instantaneously the processes. Therefore, this framework enables for new strategies of quantitative analysis and comparison between embryos and tissues during embryogenesis from in-vivo images.

Las teorías del gótico y su representación gráfica en España el último tercio del siglo XIX. Un estudio sobre: Some Account of Gothic Architecture in Spain, de George Edmund Street

La tesis se centra en el estudio, descripción y análisis del libro publicado por el arquitecto británico George Edmund Street en 1865, bajo el título Some Account of Gothic Architecture in Spain. El libro dio a conocer una de la colecciones más importantes de dibujos realizada en el siglo XIX sobre la arquitectura gótica española, y por lo tanto fue una primera referencia para su estudio, hasta bien entrado el siglo veinte. El volumen incluyó 107 grabados de diversos tipos de edificios con perspectivas y detalles, y 25 láminas con 45 planos de plantas de iglesias y claustros, muchos de ellos publicados por primera vez. Gracias a varias campañas de verano por la mitad norte del país, la casi inexplorada -desde un punto de vista académico- arquitectura española medieval fue finalmente descubierta. Este hecho conduce a una pregunta intrigante que está en el origen de esta investigación ¿cómo pudo Street en pocos viajes sentar las bases de la historia del gótico español que hasta entonces los estudiosos españoles no habían sido capaces de definir? Esta tesis comienza describiendo la obra de Street en su contexto cultural con un breve repaso a su biografía y a su posición profesional y teórica. También su relación con las personas más representativas que participaron en el estudio de la arquitectura gótica, como Robert Willis, William Whewell, Augustus Pugin, o George G. Scott. Se ha prestado especial atención, en explicar su papel relevante en el Gothic Revival, para entender el significado de su interés en la arquitectura gótica continental. Estos capítulos preliminares son seguidos por una revisión del papel del dibujo como herramienta para la arquitectura de los viajeros en sus rutas en busca de la arquitectura gótica. También se trata la influencia de la Royal Academy y sus académicos, (entre los cuales estuvo Street) y su formación académica. Finalmente la tesis entra en el estudio de los planos arquitectónicos que Street hizo durante sus viajes continentales de arquitectura, seguido por una descripción detallada de sus dibujos de España, analizando su método, su técnica, y las nuevas características aportadas, que fueron una novedad en el contexto español. También se lleva a cabo algunos estudios comparativos de los dibujos de España, gracias a una recopilación exhaustiva de bocetos y dibujos originales de Street, que en su gran mayoría se conservan en los archivos del RIBA, cotejándolos con sus versiones finales, con dibujos de la época de otros autores sobre los mismos edificios, y con fotos recientes. La tesis deja claro por qué y cómo Street, gracias a su soporte teórico y habilidades para el dibujo, pudo realizar algo que había pasado desapercibido para los estudiosos españoles de la época (construcción, historia de los estilos, señalamiento de períodos constructivos), lo que le permitió encontrar el lugar adecuado de la arquitectura gótica española en la historia y en el mapa de la arquitectura gótica europea. ABSTRACT This thesis focuses on the study, description and analysis of the book published by the British architect George Edmund Street in 1865, under the title Some Account of Gothic Architecture in Spain. The book displayed one of the most significant collections of drawings on Spanish Gothic Architecture made in the nineteenth century, and therefore was a first reference for its study, until well into the twentieth century. The book included 107 engravings, the surveying of various types of buildings with perspectives and details, and 25 sheets containing 45 ground plans of churches and cloisters, many of them new and published for the first time. Thanks to several summer campaigns in the north half of the country, the almost unexplored -from a scholar point of view- medieval Spanish architecture was eventually revealed. This fact lead to an intriguing question that is at the origin of this research: how could Street in a few trips lay the foundations of the history of Spanish Gothic that until then Spanish scholars had not been able to define? This thesis begins inscribing this Street's work in his cultural context. A brief review of his biography and professional and theoretical positions has been seen as necessary. Also his debts and relationship with the most representative people involved in the study of Gothic architecture, like Robert Willis, William Whewell, Augustus Pugin, or George G. Scott are discussed. Special attention has been paid, taken into account his relevant role in the Gothic Revival, to understand the significance of his interest in continental Gothic architecture. These preliminary chapters are followed by a review of role of drawing as a tool for Architectural travellers in their Tours in search of the Gothic architecture. The influence of the Royal Academy and its academicians, (among which was Street) and his educational background are here tackled. Eventually this thesis enters into the study of the architectural drawings Street made during his continental architectural journeys, which is followed by a detailed description and analysis of the Spanish ones: his methods, his technique, and the new features which were a novelty in the Spanish context are explored. Also in this thesis is carried out some comparative studies thanks to a previous exhaustive gathering of Street's sketches and original drawings, most of which are preserved in the RIBA archives. Their final versions, drawings of the same buildings from other contemporary draughtsman and pictures of their current state are compared with them. This thesis makes clear why and how Street thanks to his theoretical back-ground and portraying skills could realize what have passed unnoticed by contemporary Spanish scholars (construction, genealogy of forms, dating of periods) allowing him to find the proper place of the Spanish architecture in the history and the map of European Gothic architecture.

Extent of genomic rearrangement after genome duplication in yeast

Whole-genome duplication approximately 108 years ago was proposed as an explanation for the many duplicated chromosomal regions in Saccharomyces cerevisiae. Here we have used computer simulations and analytic methods to estimate some parameters describing the evolution of the yeast genome after this duplication event. Computer simulation of a model in which 8% of the original genes were retained in duplicate after genome duplication, and 70–100 reciprocal translocations occurred between chromosomes, produced arrangements of duplicated chromosomal regions very similar to the map of real duplications in yeast. An analytical method produced an independent estimate of 84 map disruptions. These results imply that many smaller duplicated chromosomal regions exist in the yeast genome in addition to the 55 originally reported. We also examined the possibility of determining the original order of chromosomal blocks in the ancestral unduplicated genome, but this cannot be done without information from one or more additional species. If the genome sequence of one other species (such as Kluyveromyces lactis) were known it should be possible to identify 150–200 paired regions covering the whole yeast genome and to reconstruct approximately two-thirds of the original order of blocks of genes in yeast. Rates of interchromosome translocation in yeast and mammals appear similar despite their very different rates of homologous recombination per kilobase.

Proteomic definition of normal human luminal and myoepithelial breast cells purified from reduction mammoplasties

Normal human luminal and myoepithelial breast cells separately purified from a set of 10 reduction mammoplasties by using a double antibody magnetic affinity cell sorting and Dynabead immunomagnetic technique were used in two-dimensional gel proteome studies. A total of 43,302 proteins were detected across the 20 samples, and a master image for each cell type comprising a total of 1,738 unique proteins was derived. Differential analysis identified 170 proteins that were elevated 2-fold or more between the two breast cell types, and 51 of these were annotated by tandem mass spectrometry. Muscle-specific enzyme isoforms and contractile intermediate filaments including tropomyosin and smooth muscle (SM22) alpha protein were detected in the myoepithelial cells, and a large number of cytokeratin subclasses and isoforms characteristic of luminal cells were detected in this cell type. A further 134 nondifferentially regulated proteins were also annotated from the two breast cell types, making this the most extensive study to date of the protein expression map of the normal human breast and the basis for future studies of purified breast cancer cells.

Localization of the C terminus of the assembly domain of hepatitis B virus capsid protein: Implications for morphogenesis and organization of encapsidated RNA

The capsid protein of hepatitis B virus, consisting of an “assembly” domain (residues 1–149) and an RNA-binding “protamine” domain (residues 150–183), assembles from dimers into icosahedral capsids of two different sizes. The C terminus of the assembly domain (residues 140–149) functions as a morphogenetic switch, longer C termini favoring a higher proportion of the larger capsids, it also connects the protamine domain to the capsid shell. We now have defined the location of this peptide in capsids assembled in vitro by engineering a mutant assembly domain with a single cysteine at its C terminus (residue 150), labeling it with a gold cluster and visualizing the cluster by cryo-electron microscopy. The labeled protein is unimpaired in its ability to form capsids. Our density map reveals a single undecagold cluster under each fivefold and quasi-sixfold vertex, connected to sites at either end of the undersides of the dimers. Considering the geometry of the vertices, the C termini must be more crowded at the fivefolds. Thus, a bulky C terminus would be expected to favor formation of the larger (T = 4) capsids, which have a greater proportion of quasi-sixfolds. Capsids assembled by expressing the full-length protein in Escherichia coli package bacterial RNAs in amounts equivalent to the viral pregenome. Our density map of these capsids reveals a distinct inner shell of density—the RNA. The RNA is connected to the protein shell via the C-terminal linkers and also makes contact around the dimer axes.

Representation of sound localization cues in the auditory thalamus of the barn owl

Barn owls can localize a sound source using either the map of auditory space contained in the optic tectum or the auditory forebrain. The auditory thalamus, nucleus ovoidalis (N.Ov), is situated between these two auditory areas, and its inactivation precludes the use of the auditory forebrain for sound localization. We examined the sources of inputs to the N.Ov as well as their patterns of termination within the nucleus. We also examined the response of single neurons within the N.Ov to tonal stimuli and sound localization cues. Afferents to the N.Ov originated with a diffuse population of neurons located bilaterally within the lateral shell, core, and medial shell subdivisions of the central nucleus of the inferior colliculus. Additional afferent input originated from the ipsilateral ventral nucleus of the lateral lemniscus. No afferent input was provided to the N.Ov from the external nucleus of the inferior colliculus or the optic tectum. The N.Ov was tonotopically organized with high frequencies represented dorsally and low frequencies ventrally. Although neurons in the N.Ov responded to localization cues, there was no apparent topographic mapping of these cues within the nucleus, in contrast to the tectal pathway. However, nearly all possible types of binaural response to sound localization cues were represented. These findings suggest that in the thalamo-telencephalic auditory pathway, sound localization is subserved by a nontopographic representation of auditory space.

Identification of a thiamin-dependent synthase in Escherichia coli required for the formation of the 1-deoxy-d-xylulose 5-phosphate precursor to isoprenoids, thiamin, and pyridoxol

In Escherichia coli, 1-deoxy-d-xylulose (or its 5-phosphate, DXP) is the biosynthetic precursor to isopentenyl diphosphate [Broers, S. T. J. (1994) Dissertation (Eidgenössische Technische Hochschule, Zürich)], thiamin, and pyridoxol [Himmeldirk, K., Kennedy, I. A., Hill, R. E., Sayer, B. G. & Spenser, I. D. (1996) Chem. Commun. 1187–1188]. Here we show that an open reading frame at 9 min on the chromosomal map of E. coli encodes an enzyme (deoxyxylulose-5-phosphate synthase, DXP synthase) that catalyzes a thiamin diphosphate-dependent acyloin condensation reaction between C atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield DXP. We have cloned and overexpressed the gene (dxs), and the enzyme was purified 17-fold to a specific activity of 0.85 unit/mg of protein. The reaction catalyzed by DXP synthase yielded exclusively DXP, which was characterized by 1H and 31P NMR spectroscopy. Although DXP synthase of E. coli shows sequence similarity to both transketolases and the E1 subunit of pyruvate dehydrogenase, it is a member of a distinct protein family, and putative DXP synthase sequences appear to be widespread in bacteria and plant chloroplasts.

Role of intrinsic synaptic circuitry in collicular sensorimotor integration

The superficial gray layer of the superior colliculus contains a map that represents the visual field, whereas the underlying intermediate gray layer contains a vector map of the saccades that shift the direction of gaze. These two maps are aligned so that a particular region of the visual field is represented directly above the neurons that orient the highest acuity area of the retina toward that region. Although it has been proposed that the transmission of information from the visuosensory to the motor map plays an important role in the generation of visually guided saccades, experiments have failed to demonstrate any functional linkage between the two layers. We examined synaptic transmission between these layers in vitro by stimulating the superficial layer while using whole-cell patch-clamp methods to measure the responses of intermediate layer neurons. Stimulation of superficial layer neurons evoked excitatory postsynaptic currents in premotor cells. This synaptic input was columnar in organization, indicating that the connections between the layers link corresponding regions of the visuosensory and motor maps. Excitatory postsynaptic currents were large enough to evoke action potentials and often occurred in clusters similar in duration to the bursts of action potentials that premotor cells use to command saccades. Our results indicate the presence of functional connections between the superficial and intermediate layers and show that such connections could play a significant role in the generation of visually guided saccades.

The small ribosomal subunit from Thermus thermophilus at 4.5 Å resolution: Pattern fittings and the identification of a functional site

The electron density map of the small ribosomal subunit from Thermus thermophilus, constructed at 4.5 Å resolution, shows the recognizable morphology of this particle, as well as structural features that were interpreted as ribosomal RNA and proteins. Unbiased assignments, carried out by quantitative covalent binding of heavy atom compounds at predetermined sites, led to the localization of the surface of the ribosomal protein S13 at a position compatible with previous assignments, whereas the surface of S11 was localized at a distance of about twice its diameter from the site suggested for its center by neutron scattering. Proteins S5 and S7, whose structures have been determined crystallographically, were visually placed in the map with no alterations in their conformations. Regions suitable to host the fold of protein S15 were detected in several positions, all at a significant distance from the location of this protein in the neutron scattering map. Targeting the 16S RNA region, where mRNA docks to allow the formation of the initiation complex by a mercurated mRNA analog, led to the characterization of its vicinity.

Comparative mapping of Andropogoneae: Saccharum L. (sugarcane) and its relation to sorghum and maize

Comparative genetic maps of Papuan Saccharum officinarum L. (2n = 80) and S. robustum (2n = 80) were constructed by using single-dose DNA markers (SDMs). SDM-framework maps of S. officinarum and S. robustum were compared with genetic maps of sorghum and maize by way of anchor restriction fragment length polymorphism probes. The resulting comparisons showed striking colinearity between the sorghum and Saccharum genomes. There were no differences in marker order between S. officinarum and sorghum. Furthermore, there were no alterations in SDM order between S. officinarum and S. robustum. The S. officinarum and S. robustum maps also were compared with the map of the polysomic octoploid S. spontaneum ‘SES 208’ (2n = 64, x = 8), thus permitting relations to homology groups (“chromosomes”) of S. spontaneum to be studied. Investigation of transmission genetics in S. officinarum and S. robustum confirmed preliminary results that showed incomplete polysomy in these species. Because of incomplete polysomy, multiple-dose markers could not be mapped for lack of a genetic model for their segregation. To coalesce S. officinarum and S. robustum linkage groups into homology groups (composed of homologous pairing partners), they were compared with sorghum (2n = 20), which functioned as a synthetic diploid. Groupings suggested by comparative mapping were found to be highly concordant with groupings based on highly polymorphic restriction fragment length polymorphism probes detecting multiple SDMs. The resulting comparative maps serve as bridges to allow information from one Andropogoneae to be used by another, for breeding, ecology, evolution, and molecular biology.

In vitro reconstruction of the Aspergillus (= Emericella) nidulans genome

A physical map of the 31-megabase Aspergillus nidulans genome is reported, in which 94% of 5,134 cosmids are assigned to 49 contiguous segments. The physical map is the result of a two-way ordering process, in which clones and probes were ordered simultaneously on a binary DNA/DNA hybridization matrix. Compression by elimination of redundant clones resulted in a minimal map, which is a chromosome walk. Repetitive DNA is nonrandomly dispersed in the A. nidulans genome, reminiscent of heterochromatic banding patterns of higher eukaryotes. We hypothesize gene clusters may arise by horizontal transfer and spread by transposition to explain the nonrandom pattern of repeats along chromosomes.