Use of physiological constraints to identify quantitative design principles for gene expression in yeast adaptation to heat shock

Background: Understanding the relationship between gene expression changes, enzyme activity shifts, and the corresponding physiological adaptive response of organisms to environmental cues is crucial in explaining how cells cope with stress. For example, adaptation of yeast to heat shock involves a characteristic profile of changes to the expression levels of genes coding for enzymes of the glycolytic pathway and some of its branches. The experimental determination of changes in gene expression profiles provides a descriptive picture of the adaptive response to stress. However, it does not explain why a particular profile is selected for any given response. Results: We used mathematical models and analysis of in silico gene expression profiles (GEPs) to understand how changes in gene expression correlate to an efficient response of yeast cells to heat shock. An exhaustive set of GEPs, matched with the corresponding set of enzyme activities, was simulated and analyzed. The effectiveness of each profile in the response to heat shock was evaluated according to relevant physiological and functional criteria. The small subset of GEPs that lead to effective physiological responses after heat shock was identified as the result of the tuning of several evolutionary criteria. The experimentally observed transcriptional changes in response to heat shock belong to this set and can be explained by quantitative design principles at the physiological level that ultimately constrain changes in gene expression. Conclusion: Our theoretical approach suggests a method for understanding the combined effect of changes in the expression of multiple genes on the activity of metabolic pathways, and consequently on the adaptation of cellular metabolism to heat shock. This method identifies quantitative design principles that facilitate understating the response of the cell to stress.

The cell cycle–regulated genes of schizosaccharomyces pombe

Many genes are regulated as an innate part of the eukaryotic cell cycle, and a complex transcriptional network helps enable the cyclic behavior of dividing cells. This transcriptional network has been studied in Saccharomyces cerevisiae (budding yeast) and elsewhere. To provide more perspective on these regulatory mechanisms, we have used microarrays to measure gene expression through the cell cycle of Schizosaccharomyces pombe (fission yeast). The 750 genes with the most significant oscillations were identified and analyzed. There were two broad waves of cell cycle transcription, one in early/mid G2 phase, and the other near the G2/M transition. The early/mid G2 wave included many genes involved in ribosome biogenesis, possibly explaining the cell cycle oscillation in protein synthesis in S.pombe. The G2/M wave included at least three distinctly regulated clusters of genes: one large cluster including mitosis, mitotic exit, and cell separation functions, one small cluster dedicated to DNA replication, and another small cluster dedicated to cytokinesis and division. S. pombe cell cycle genes have relatively long, complex promoters containing groups of multiple DNA sequence motifs, often of two, three, or more different kinds. Many of the genes, transcription factors, and regulatory mechanisms are conserved between S. pombe and S. cerevisiae. Finally, we found preliminary evidence for a nearly genome-wide oscillation in gene expression: 2,000 or more genes undergo slight oscillations in expression as a function of the cell cycle, although whether this is adaptive, or incidental to other events in the cell, such as chromatin condensation, we do not know.

Forage preservation (grazing vs. hay) fed to ewes affects the fatty acid profile of milk and CPT1B gene expression in the sheep mammary gland

Background: Alterations in lipid metabolism occur when animals are exposed to different feeding systems. In the last few decades, the characterisation of genes involved in fat metabolism and technological advances have enabled the study of the effect of diet on the milk fatty acid (FA) profile in the mammary gland and aided in the elucidation of the mechanisms of the response to diet. The aim of this study was to evaluate the effect of different forage diets (grazing vs. hay) near the time of ewe parturition on the relationship between the fatty acid profile and gene expression in the mammary gland of the Churra Tensina sheep breed. Results: In this study, the forage type affected the C18:2 cis-9 trans-11 (CLA) and long-chain saturated fatty acid (LCFA) content, with higher percentages during grazing than during hay feeding. This may suggest that these FAs act as regulatory factors for the transcriptional control of the carnitine palmitoyltransferase 1B (CPT1B) gene, which was more highly expressed in the grazing group (GRE). The most highly expressed gene in the mammary gland at the fifth week of lactation is CAAT/ enhancer- binding protein beta (CEBPB), possibly due to its role in milk fat synthesis in the mammary gland. More stable housekeeping genes in the ovine mammary gland that would be appropriate for use in gene expression studies were ribosomal protein L19 (RPL19) and glyceraldehyde- 3- phosphate dehydrogenase (GAPDH). Conclusions: Small changes in diet, such as the forage preservation (grazing vs. hay), can affect the milk fatty acid profile and the expression of the CPT1B gene, which is associated with the oxidation of fatty acids. When compared to hay fed indoors, grazing fresh low mountain pastures stimulates the milk content of CLA and LCFA via mammary uptake. In this sense, LCFA in milk may be acting as a regulatory factor for transcriptional control of the CPT1B gene, which was more highly expressed in the grazing group.

The role of fibroblast growth factor (FGF) and type beta transforming growth factot beta (TGF beta1, beta2 and beta3) during rat craniofacial development

Growth factors seem to be part of a complex cellular signalling language, in which individual growth factors are the equivalents of the letters that compose words. According to this analogy, informational content lies, not in an individual growth factor, but in the entire set of growth factors and others signals to which a cell is exposed. The ways in which growth factors exert their combinatorial effects are becoming clearer as the molecular mechanisms of growth factors actions are being investigated. A number of related extracellular signalling molecules that play widespread roles in regulating development in both invertebrates and vertebrates constitute the Fibroblast Growth Factor (FGF) and type beta Transforming Growth Factor ((TGF beta). The latest research literature about the role and fate of these Growth factors and their influence in the craniofacial bone growth ad development is reviewed

The role of fibroblast growth factor (FGF) and type beta transforming growth factot beta (TGF beta1, beta2 and beta3) during rat craniofacial development

Growth factors seem to be part of a complex cellular signalling language, in which individual growth factors are the equivalents of the letters that compose words. According to this analogy, informational content lies, not in an individual growth factor, but in the entire set of growth factors and others signals to which a cell is exposed. The ways in which growth factors exert their combinatorial effects are becoming clearer as the molecular mechanisms of growth factors actions are being investigated. A number of related extracellular signalling molecules that play widespread roles in regulating development in both invertebrates and vertebrates constitute the Fibroblast Growth Factor (FGF) and type beta Transforming Growth Factor ((TGF beta). The latest research literature about the role and fate of these Growth factors and their influence in the craniofacial bone growth ad development is reviewed

Quantum black holes: Nonperturbative corrections and no-veil scenario

A common belief is that further quantum corrections near the singularity of a large black hole should not substantially modify the semiclassical picture of black hole evaporation; in particular, the outgoing spectrum of radiation should be very close to the thermal spectrum predicted by Hawking. In this paper we explore a possible counterexample: in the context of dilaton gravity, we find that nonperturbative quantum corrections which are important in strong-coupling regions may completely alter the semiclassical picture, to the extent that the presumptive spacelike boundary becomes timelike, changing in this way the causal structure of the semiclassical geometry. As a result, only a small fraction of the total energy is radiated outside the fake event horizon; most of the energy comes in fact at later retarded times and there is no problem of information loss. This may constitute a general characteristic of quantum black holes, that is, quantum gravity might be such as to prevent the formation of global event horizons.

From room for books to room for users: an old infantry barrack as an answer to the lack of space

At the beginning of the 21st century, some Catalan university libraries detected a need stemming from the lack of space and the reconversion of physical libraries within the new European educational panorama. With the same cooperative spirit that characterized previous CBUC (Consortium of Academic Libraries of Catalonia) programs and services, the Consortium set in motion a project to address this need. An initial study was commissioned in 2002, and in 2003 a suitable building (old infantry barracks) was found in Lleida. The official opening took place in 2008. GEPA (Guaranteed Space for the Preservation of Access) facility is a cooperative repository, whose objectives are to store and preserve low use documents, ensuring their future access when needed, to convert room for books into room for library users, and doing it saving both space and money. The paper presents a brief historical introduction about the physical management of collections in libraries, and a short overview about high density library repositories all over the world, as an answer to the pressing problem of lack of spaces. The main goals of the communication are to comment the architectural project and its librarian issues, and to show how the GEPA facility allowed to change the spaces in university libraries in Catalonia. On the one hand, the paper deals with the selection of an old building to be renovated, the determination of the librarian needs, the compact shelving system chosen to store the documents in the building, the relation between physical space and information management, and the logistics involved in the load of low use documents from the libraries into the facility. On the other hand, we will show some examples of physical changes in Catalan libraries after large loads of documents to GEPA.

Contribution of femoral and proximal sciatic nerve branches to the sensory innervation of hindlimb digits in the rat

The present study was performed to investigate the possibility of 'aberrant' innervation of the tips of the hindlimb digits in the rat, i.e., from other sources than the femoral and the main sciatic branches (tibial, peroneal, sural). Cutaneous injections of fluorescent tracers in the digits were combined with either selective nerve transections to restrict afferent routes followed by detection of labeled neurons in dorsal root ganglia (DRGs), or by a delayed application of a second tracer to afferent nerves under study to detect double labeled neurons in DRGs. The results show that the tips of the digits were represented in DRGs L3-6. The femoral nerve afferents from digits 1 and 2 projected primarily to DRG L3 and to a smaller extent to DRG L4. A small number of neurons from primarily medial digits 1 and 2, but also from lateral digits 3-5, were found to project to DRGs L4 and L5 via a proximal branch that leaves the sciatic nerve near the sciatic notch and runs distally in the posterior part of the thigh, here called the musculocutaneous nerve of the hindlimb. We also have some evidence indicating innervation of the tips of the digits from the posterior cutaneous nerve of the thigh. Aberrant innervation such as that described here might contribute to remaining and perhaps abnormal sensibility after nerve injury and is of interest for the interpretation of results in experimental studies of collateral and regenerative sprouting after such injury

A Database of >20 keV Electron Green's Functions of Interplanetary Transport at 1 AU

We use interplanetary transport simulations to compute a database of electron Green's functions, i.e., differential intensities resulting at the spacecraft position from an impulsive injection of energetic (>20 keV) electrons close to the Sun, for a large number of values of two standard interplanetary transport parameters: the scattering mean free path and the solar wind speed. The nominal energy channels of the ACE, STEREO, and Wind spacecraft have been used in the interplanetary transport simulations to conceive a unique tool for the study of near-relativistic electron events observed at 1 AU. In this paper, we quantify the characteristic times of the Green's functions (onset and peak time, rise and decay phase duration) as a function of the interplanetary transport conditions. We use the database to calculate the FWHM of the pitch-angle distributions at different times of the event and under different scattering conditions. This allows us to provide a first quantitative result that can be compared with observations, and to assess the validity of the frequently used term beam-like pitch-angle distribution.

The proportional distribution in a cooperative model with external opportunities

[cat] En aquest article es considera un problema de cooperació entre agents on cada agent realitza una contribució (diners, capital, treball, esforç) per tal d'obtenir un benefici comú a repartir. El repartiment proporcional respecte a les contribucions és una distribució que pertany al nucli del joc cooperatiu associat. A partir d'aquest model bàsic s'introdueix un agent extern que pot realitzar una determinada aportació que serveix per avaluar el potencial benefici de cada subcoalició d'agents si aquest nou agent finalment entrés. Aquesta anàlisi pot produir que el poder relatiu dels agents hagi variat. en concret s'avalua si la distribució proporcional és encara robusta des del punt de vista de la seva pertinença al conjunt de negociació. Amb aquest objectiu, analitzem el problema utilitzant el model de joc cooperatius amb estructura de coalició. Donat que, en general, la distribució proporcional, no pertany al conjunt de negociació, s'estudia una condició suficient per a que així sigui. També enunciem una condició necessària, i finalment es proposa una condició suficient que garanteix que el repartiment proporcional és la única distribució existent dins del conjunt de negociació.

The proportional distribution in a cooperative model with external opportunities

[cat] En aquest article es considera un problema de cooperació entre agents on cada agent realitza una contribució (diners, capital, treball, esforç) per tal d'obtenir un benefici comú a repartir. El repartiment proporcional respecte a les contribucions és una distribució que pertany al nucli del joc cooperatiu associat. A partir d'aquest model bàsic s'introdueix un agent extern que pot realitzar una determinada aportació que serveix per avaluar el potencial benefici de cada subcoalició d'agents si aquest nou agent finalment entrés. Aquesta anàlisi pot produir que el poder relatiu dels agents hagi variat. en concret s'avalua si la distribució proporcional és encara robusta des del punt de vista de la seva pertinença al conjunt de negociació. Amb aquest objectiu, analitzem el problema utilitzant el model de joc cooperatius amb estructura de coalició. Donat que, en general, la distribució proporcional, no pertany al conjunt de negociació, s'estudia una condició suficient per a que així sigui. També enunciem una condició necessària, i finalment es proposa una condició suficient que garanteix que el repartiment proporcional és la única distribució existent dins del conjunt de negociació.

The snow storm of the 8th of March 2010 in Barcelona: a paradigmatic case

A heavy precipitation event swept over Catalonia (NE Spain) on 8 March 2010, with a total amount that ex- ceeded 100mm locally and snowfall of more than 60cm near the coast. Unusual for this region and at this time of the year, this snowfall event affected mainly the coastal region and was accompanied by thunderstorms and strong wind gusts in some areas. Most of the damage was due to"wet snow", a kind of snow that favours accretion on power lines and causes line-breaking and subsequent interruption of the electricity supply. This paper conducts an interdisciplinary analysis of the event to show its great societal impact and the role played by the recently developed social networks (it has been called the first"Snowfall 2.0"), as well to analyse the meteorologi- cal factors associated with the major damage, and to propose an indicator that could summarise them. With this aim, the paper introduces the event and its societal impact and com- pares it with other important snowfalls that have affected the Catalan coast, using the PRESSGAMA database. The sec- ond part of the paper shows the event"s main meteorological features and analyses the near-surface atmospheric variables responsible for the major damage through the application of the SAFRAN (Système d"analyse fournissant des renseigne- ments atmosphériques à la neige) mesoscale analysis, which, together with the proposed"wind, wet-snow index" (WWSI), allows to estimate the severity of the event. This snow storm provides further evidence of our vulnerability to natural haz- ards and highlights the importance of a multidisciplinary ap- proach in analysing societal impact and the meteorological factors responsible for this kind of event.

Structural Insight into the Mode of Action of a Direct Inhibitor of Coregulator Binding to the Thyroid Hormone Receptor.

The development of nuclear hormone receptor antagonists that directly inhibit the association of the receptor with its essential coactivators would allow useful manipulation of nuclear hormone receptor signaling. We previously identified 3-(dibutylamino)-1-(4-hexylphenyl)-propan-1-one (DHPPA), an aromatic β-amino ketone that inhibits coactivator recruitment to thyroid hormone receptor β (TRβ), in a high-throughput screen. Initial evidence suggested that the aromatic β-enone 1-(4-hexylphenyl)-prop-2-en-1-one (HPPE), which alkylates a specific cysteine residue on the TRβ surface, is liberated from DHPPA. Nevertheless, aspects of the mechanism and specificity of action of DHPPA remained unclear. Here, we report an x-ray structure of TRβ with the inhibitor HPPE at 2.3-Å resolution. Unreacted HPPE is located at the interface that normally mediates binding between TRβ and its coactivator. Several lines of evidence, including experiments with TRβ mutants and mass spectroscopic analysis, showed that HPPE specifically alkylates cysteine residue 298 of TRβ, which is located near the activation function-2 pocket. We propose that this covalent adduct formation proceeds through a two-step mechanism: 1) β-elimination to form HPPE; and 2) a covalent bond slowly forms between HPPE and TRβ. DHPPA represents a novel class of potent TRβ antagonist, and its crystal structure suggests new ways to design antagonists that target the assembly of nuclear hormone receptor gene-regulatory complexes and block transcription.

Estimating 750 years of temperature variations and uncertainties in the Pyrenees by tree-ring reconstructions and climate simulations.

Past temperature variations are usually inferred from proxy data or estimated using general circulation models. Comparisons between climate estimations derived from proxy records and from model simulations help to better understand mechanisms driving climate variations, and also offer the possibility to identify deficiencies in both approaches. This paper presents regional temperature reconstructions based on tree-ring maximum density series in the Pyrenees, and compares them with the output of global simulations for this region and with regional climate model simulations conducted for the target region. An ensemble of 24 reconstructions of May-to-September regional mean temperature was derived from 22 maximum density tree-ring site chronologies distributed over the larger Pyrenees area. Four different tree-ring series standardization procedures were applied, combining two detrending methods: 300-yr spline and the regional curve standardization (RCS). Additionally, different methodological variants for the regional chronology were generated by using three different aggregation methods. Calibration verification trials were performed in split periods and using two methods: regression and a simple variance matching. The resulting set of temperature reconstructions was compared with climate simulations performed with global (ECHO-G) and regional (MM5) climate models. The 24 variants of May-to-September temperature reconstructions reveal a generally coherent pattern of inter-annual to multi-centennial temperature variations in the Pyrenees region for the last 750 yr. However, some reconstructions display a marked positive trend for the entire length of the reconstruction, pointing out that the application of the RCS method to a suboptimal set of samples may lead to unreliable results. Climate model simulations agree with the tree-ring based reconstructions at multi-decadal time scales, suggesting solar variability and volcanism as the main factors controlling preindustrial mean temperature variations in the Pyrenees. Nevertheless, the comparison also highlights differences with the reconstructions, mainly in the amplitude of past temperature variations and in the 20th century trends. Neither proxy-based reconstructions nor model simulations are able to perfectly track the temperature variations of the instrumental record, suggesting that both approximations still need further improvements.

Current Sheet Regulation of Solar Near-relativistic Electron Injection Histories

We present a sample of three large near-relativistic (>50 keV) electron events observed in 2001 by both the ACE and the Ulysses spacecraft, when Ulysses was at high-northern latitudes (>60◦) and close to 2 AU. Despite the large latitudinal distance between the two spacecraft, electrons injected near the Sun reached both heliospheric locations. All three events were associated with large solar flares, strong decametric type II radio bursts and accompanied by wide (>212◦) and fast (>1400 km s−1) coronal mass ejections (CMEs). We use advanced interplanetary transport simulations and make use of the directional intensities observed in situ by the spacecraft to infer the electron injection profile close to the Sun and the interplanetary transport conditions at both low and high latitudes. For the three selected events, we find similar interplanetary transport conditions at different heliolatitudes for a given event, with values of the mean free path ranging from 0.04 AU to 0.27 AU. We find differences in the injection profiles inferred for each spacecraft. We investigate the role that sector boundaries of the heliospheric current sheet (HCS) have on determining the characteristics of the electron injection profiles. Extended injection profiles, associated with coronal shocks, are found if the magnetic footpoints of the spacecraft lay in the same magnetic sector as the associated flare, while intermittent sparse injection episodes appear when the spacecraft footpoints are in the opposite sector or a wrap in the HCS bounded the CME structure.