Farm Outlook

With average weather, another big crop of feed grains will be harvested in 1958. That\u27s the obvious conclusion from a glance at the March 1 cropping plans reported by farmers

Is mitochondrial gene expression coordinated or stochastic?

© 2018 Portland Press Ltd. All rights reserved. Mitochondrial biogenesis is intimately dependent on the coordinated expression of the nuclear and mitochondrial genomes that is necessary for the assembly and function of the respiratory complexes to produce most of the energy required by cells. Although highly compacted in animals, the mitochondrial genome and its expression are essential for survival, development, and optimal energy production. The machinery that regulates gene expression within mitochondria is localised within the same compartment and, like in their ancestors, the bacteria, this machinery does not use membrane-based compartmentalisation to order the gene expression pathway. Therefore, the lifecycle of mitochondrial RNAs from transcription through processing, maturation, translation to turnover is mediated by a gamut of RNA-binding proteins (RBPs), all contained within the mitochondrial matrix milieu. Recent discoveries indicate that multiple processes regulating RNA metabolism occur at once but since mitochondria have a new complement of RBPs, many evolved de novo from nuclear genes, we are left wondering how co-ordinated are these processes? Here, we review recently identified examples of the co-ordinated and stochastic processes that govern the mitochondrial transcriptome. These new discoveries reveal the complexity of mitochondrial gene expression and the need for its in-depth exploration to understand how these organelles can respond to the energy demands of the cell

Computational Stem Cell Biology: Open Questions and Guiding Principles

Computational biology is enabling an explosive growth in our understanding of stem cells and our ability to use them for disease modeling, regenerative medicine, and drug discovery. We discuss four topics that exemplify applications of computation to stem cell biology: cell typing, lineage tracing, trajectory inference, and regulatory networks. We use these examples to articulate principles that have guided computational biology broadly and call for renewed attention to these principles as computation becomes increasingly important in stem cell biology. We also discuss important challenges for this field with the hope that it will inspire more to join this exciting area

The FASTK family proteins fine-tune mitochondrial RNA processing.

Funder: The Cancer Council of Western AustraliaFunder: UWA Postgraduate ScholarshipsTranscription of the human mitochondrial genome and correct processing of the two long polycistronic transcripts are crucial for oxidative phosphorylation. According to the tRNA punctuation model, nucleolytic processing of these large precursor transcripts occurs mainly through the excision of the tRNAs that flank most rRNAs and mRNAs. However, some mRNAs are not punctuated by tRNAs, and it remains largely unknown how these non-canonical junctions are resolved. The FASTK family proteins are emerging as key players in non-canonical RNA processing. Here, we have generated human cell lines carrying single or combined knockouts of several FASTK family members to investigate their roles in non-canonical RNA processing. The most striking phenotypes were obtained with loss of FASTKD4 and FASTKD5 and with their combined double knockout. Comprehensive mitochondrial transcriptome analyses of these cell lines revealed a defect in processing at several canonical and non-canonical RNA junctions, accompanied by an increase in specific antisense transcripts. Loss of FASTKD5 led to the most severe phenotype with marked defects in mitochondrial translation of key components of the electron transport chain complexes and in oxidative phosphorylation. We reveal that the FASTK protein family members are crucial regulators of non-canonical junction and non-coding mitochondrial RNA processing

Global analysis of the TRAPPIST Ultra-Cool Dwarf Transit Survey

ABSTRACT We conducted a global analysis of the TRAPPIST Ultra-Cool Dwarf Transit Survey – a prototype of the SPECULOOS transit search conducted with the TRAPPIST-South robotic telescope in Chile from 2011 to 2017 – to estimate the occurrence rate of close-in planets such as TRAPPIST-1b orbiting ultra-cool dwarfs. For this purpose, the photometric data of 40 nearby ultra-cool dwarfs were reanalysed in a self-consistent and fully automated manner starting from the raw images. The pipeline developed specifically for this task generates differential light curves, removes non-planetary photometric features and stellar variability, and searches for transits. It identifies the transits of TRAPPIST-1b and TRAPPIST-1c without any human intervention. To test the pipeline and the potential output of similar surveys, we injected planetary transits into the light curves on a star-by-star basis and tested whether the pipeline is able to detect them. The achieved photometric precision enables us to identify Earth-sized planets orbiting ultra-cool dwarfs as validated by the injection tests. Our planet-injection simulation further suggests a lower limit of 10 per cent on the occurrence rate of planets similar to TRAPPIST-1b with a radius between 1 and 1.3 R⊕ and the orbital period between 1.4 and 1.8 d.</jats:p

LBT transmission spectroscopy of HAT-P-12b: confirmation of a cloudy atmosphere with no significant alkali features

The hot sub-Saturn-mass exoplanet HAT-P-12b is an ideal target for transmission spectroscopy because of its inflated radius. We observed one transit of the planet with the multi-object double spectrograph (MODS) on the Large Binocular Telescope (LBT) with the binocular mode and obtained an atmosphere transmission spectrum with a wavelength coverage of $\sim$ 0.4 -- 0.9 $\mathrm{\mu}$m. The spectrum is relatively flat and does not show any significant sodium or potassium absorption features. Our result is consistent with the revised Hubble Space Telescope (HST) transmission spectrum of a previous work, except that the HST result indicates a tentative detection of potassium. The potassium discrepancy could be the result of statistical fluctuation of the HST dataset. We fit the planetary transmission spectrum with an extensive grid of cloudy models and confirm the presence of high-altitude clouds in the planetary atmosphere. The fit was performed on the combined LBT and HST spectrum, which has an overall wavelength range of 0.4 -- 1.6 $\mathrm{\mu}$m. The LBT/MODS spectrograph has unique advantages in transmission spectroscopy observations because it can cover a wide wavelength range with a single exposure and acquire two sets of independent spectra simultaneously.Comment: 14 pages, 12 figures. Accepted for publication in Astronomy & Astrophysic

Fidelity and coordination of mitochondrial protein synthesis in health and disease

The evolutionary acquisition of mitochondria has given rise to the diversity of eukaryotic life. Mitochondria have retained their ancestral α-proteobacterial traits through the maintenance of double membranes and their own circular genome. Their genome varies in size from very large in plants to the smallest in animals and their parasites. The mitochondrial genome encodes essential genes for protein synthesis and has to coordinate its expression with the nuclear genome from which it sources most of the proteins required for mitochondrial biogenesis and function. The mitochondrial protein synthesis machinery is unique because it is encoded by both the nuclear and mitochondrial genomes thereby requiring tight regulation to produce the respiratory complexes that drive oxidative phosphorylation for energy production. The fidelity and coordination of mitochondrial protein synthesis are essential for ATP production. Here we compare and contrast the mitochondrial translation mechanisms in mammals and fungi to bacteria and reveal that their diverse regulation can have unusual impacts on the health and disease of these organisms. We highlight that in mammals the rate of protein synthesis is more important than the fidelity of translation, enabling coordinated biogenesis of the mitochondrial respiratory chain with respiratory chain proteins synthesised by cytoplasmic ribosomes. Changes in mitochondrial protein fidelity can trigger the activation of the diverse cellular signalling networks in fungi and mammals to combat dysfunction in energy conservation. The physiological consequences of altered fidelity of protein synthesis can range from liver regeneration to the onset and development of cardiomyopathy. (Figure presented.)

The Human Mitochondrial Transcriptome

SummaryThe human mitochondrial genome comprises a distinct genetic system transcribed as precursor polycistronic transcripts that are subsequently cleaved to generate individual mRNAs, tRNAs, and rRNAs. Here, we provide a comprehensive analysis of the human mitochondrial transcriptome across multiple cell lines and tissues. Using directional deep sequencing and parallel analysis of RNA ends, we demonstrate wide variation in mitochondrial transcript abundance and precisely resolve transcript processing and maturation events. We identify previously undescribed transcripts, including small RNAs, and observe the enrichment of several nuclear RNAs in mitochondria. Using high-throughput in vivo DNaseI footprinting, we establish the global profile of DNA-binding protein occupancy across the mitochondrial genome at single-nucleotide resolution, revealing regulatory features at mitochondrial transcription initiation sites and functional insights into disease-associated variants. This integrated analysis of the mitochondrial transcriptome reveals unexpected complexity in the regulation, expression, and processing of mitochondrial RNA and provides a resource for future studies of mitochondrial function (accessed at http://mitochondria.matticklab.com)

Modelos de endemicidad a lo largo de un gradiente altitudinal en Sierra Nevada (España) y Lefka Ori (Creta, Grecia)

Aim: High mountains in the Mediterranean region of Europe are particularly rich in endemic vascular plants. We aimed to compare the altitudinal patterns of vascular plant species richness and the proportion of endemic species in two Mediterranean region: Lefka Ori on the island of Crete (Greece) and Sierra Nevada on the Iberian peninsula. Location: Sierra Nevada, Granada (Spain); Lefka Ori, Crete (Greece). Methods: Data from standardised permanent plots settings on summit sites (comprising eight plot sectors, covering the upeermost 10 altitudinal metres) of different elevations were used (GLORIA Multi-Summit approach; www.gloria.ac.at). Species numbers, rates of endemic species, and soils temperature were compared by means of ANCOVA and linear regression. Results: The two regions, though climatically similar, showed strikingly different patterns: In Sierra Nevada, the proportion of endemic vascular plants (species restricted to Sierra Nevada) showed a stepwise increase from the lowest to the highest summit. In contrast, the proportion of endemic species restricted to Crete was not significantly different between the four summits in Lefka Ori. In both regions the observed trends were largely consistent with the altitudinal distribution of the endemic species obtained from standard floras. Main conclusions: The geographic positions of the two regions, i.e. island versus mainland and the higher elevation of Sierra Nevada are suggested to be the primary causes of the observed differences. The high degree of endemism in the cold environments of Mediterranean mountains’ upper bioclimatic zones indicates a pronounced vulnerability to the impacts of climate change. A continued and intensified species monitoring in the mountains around the Mediterranean basin, therefore, should be considered as a priority research task.Objetivo: Las zonas de alta montaña en la región mediterránea europea son particularmente ricas en plantas vasculares endémicas. Nuestro objetivo es comparar los modelos altitudinales para la riqueza de plantas vasculares y la proporción de endemismos en dos regiones mediterráneas: Lefka Ori en la isla de Creta (Grecia) y Sierra Nevada en la Península Ibérica. Localización: Sierra Nevada, Granada (España); Lefka Ori, Creta (Grecia). Método: Los datos proceden de un muestreo estandarizado en varias cimas situadas a diferentes altitudes (GLORIA Multi-Summit approach; www.gloria.ac.at). El número de especies, tasas de endemicidad, y temperatura del suelo se compararon por medio de ANCOVA y regresión lineal. Resultados: Las dos regiones objeto de análisis, aunque similares climáticamente, muestran patrones llamativamente diferentes: en Sierra Nevada, la proporción de plantas vasculares endémicas (especies restringidas a Sierra Nevada) muestra un incremento gradual desde la cima más baja a la más alta. En contraste, la proporción de endemismos restringidos a Creta no fue significativamente diferente entre las cuatro cimas de Lefka Ori. Las tendencias observadas en ambas regiones fueron en gran parte consistentes con la distribución de las especies endémicas obtenida de las floras para cada región. Conclusiones principales: La posición geográfica de ambas regiones, por ejemplo. isla frente a continente, y la mayor elevación de Sierra Nevada se sugieren como las principales causas de las diferencias observadas. El alto grado de endemicidad en los ambientes fríos de las zonas bioclimáticas superiores de las montañas mediterráneas evidencia una marcada vulnerabilidad a los impactos del cambio climático. Por lo tanto, el seguimiento continuado e intensivo de las especies de montaña alrededor de la cuenca mediterránea, debería considerarse como una tarea investigadora prioritaria.He set up of the permanent plots and data collection was supported by the FP-5 project GLORIA-Europe (2001-2003) No EVK2-2000-00056 of the European Commission

RNA polymerase II primes Polycomb-repressed developmental genes throughout terminal neuronal differentiation

Polycomb repression in mouse embryonic stem cells (ESCs) is tightly associated with promoter co-occupancy of RNA polymerase II (RNAPII) which is thought to prime genes for activation during early development. However, it is unknown whether RNAPII poising is a general feature of Polycomb repression, or is lost during differentiation. Here, we map the genome-wide occupancy of RNAPII and Polycomb from pluripotent ESCs to non-dividing functional dopaminergic neurons. We find that poised RNAPII complexes are ubiquitously present at Polycomb-repressed genes at all stages of neuronal differentiation. We observe both loss and acquisition of RNAPII and Polycomb at specific groups of genes reflecting their silencing or activation. Strikingly, RNAPII remains poised at transcription factor genes which are silenced in neurons through Polycomb repression, and have major roles in specifying other, non-neuronal lineages. We conclude that RNAPII poising is intrinsically associated with Polycomb repression throughout differentiation. Our work suggests that the tight interplay between RNAPII poising and Polycomb repression not only instructs promoter state transitions, but also may enable promoter plasticity in differentiated cells