Elastic turbulence in curvilinear flows of polymer solutions

Following our first report (A. Groisman and V. Steinberg, \sl Nature $\bf 405$, 53 (2000)) we present an extended account of experimental observations of elasticity induced turbulence in three different systems: a swirling flow between two plates, a Couette-Taylor (CT) flow between two cylinders, and a flow in a curvilinear channel (Dean flow). All three set-ups had high ratio of width of the region available for flow to radius of curvature of the streamlines. The experiments were carried out with dilute solutions of high molecular weight polyacrylamide in concentrated sugar syrups. High polymer relaxation time and solution viscosity ensured prevalence of non-linear elastic effects over inertial non-linearity, and development of purely elastic instabilities at low Reynolds number (Re) in all three flows. Above the elastic instability threshold, flows in all three systems exhibit features of developed turbulence. Those include: (i)randomly fluctuating fluid motion excited in a broad range of spatial and temporal scales; (ii) significant increase in the rates of momentum and mass transfer (compared to those expected for a steady flow with a smooth velocity profile). Phenomenology, driving mechanisms, and parameter dependence of the elastic turbulence are compared with those of the conventional high Re hydrodynamic turbulence in Newtonian fluids.Comment: 23 pages, 26 figure

Mice have a transcribed L-threonine aldolase/GLY1 gene, but the human GLY1 gene is a non-processed pseudogene

BACKGROUND: There are three pathways of L-threonine catabolism. The enzyme L-threonine aldolase (TA) has been shown to catalyse the conversion of L-threonine to yield glycine and acetaldehyde in bacteria, fungi and plants. Low levels of TA enzymatic activity have been found in vertebrates. It has been suggested that any detectable activity is due to serine hydroxymethyltransferase and that mammals lack a genuine threonine aldolase. RESULTS: The 7-exon murine L-threonine aldolase gene (GLY1) is located on chromosome 11, spanning 5.6 kb. The cDNA encodes a 400-residue protein. The protein has 81% similarity with the bacterium Thermotoga maritima TA. Almost all known functional residues are conserved between the two proteins including Lys242 that forms a Schiff-base with the cofactor, pyridoxal-5'-phosphate. The human TA gene is located at 17q25. It contains two single nucleotide deletions, in exons 4 and 7, which cause frame-shifts and a premature in-frame stop codon towards the carboxy-terminal. Expression of human TA mRNA was undetectable by RT-PCR. In mice, TA mRNA was found at low levels in a range of adult tissues, being highest in prostate, heart and liver. In contrast, serine/threonine dehydratase, another enzyme that catabolises L-threonine, is expressed very highly only in the liver. Serine dehydratase-like 1, also was most abundant in the liver. In whole mouse embryos TA mRNA expression was low prior to E-15 increasing more than four-fold by E-17. CONCLUSION: Mice, the western-clawed frog and the zebrafish have transcribed threonine aldolase/GLY1 genes, but the human homolog is a non-transcribed pseudogene. Serine dehydratase-like 1 is a putative L-threonine catabolising enzyme

Acute escitalopram treatment inhibits REM sleep rebound and activation of MCH-expressing neurons in the lateral hypothalamus after long term selective REM sleep deprivation.

RATIONALE: Selective rapid eye movement sleep (REMS) deprivation using the platform-on-water ("flower pot") method causes sleep rebound with increased REMS, decreased REMS latency, and activation of the melanin-concentrating hormone (MCH) expressing neurons in the hypothalamus. MCH is implicated in the pathomechanism of depression regarding its influence on mood, feeding behavior, and REMS. OBJECTIVES: We investigated the effects of the most selective serotonin reuptake inhibitor escitalopram on sleep rebound following REMS deprivation and, in parallel, on the activation of MCH-containing neurons. METHODS: Escitalopram or vehicle (10 mg/kg, intraperitoneally) was administered to REMS-deprived (72 h) or home cage male Wistar rats. During the 3-h-long "rebound sleep", electroencephalography was recorded, followed by an MCH/Fos double immunohistochemistry. RESULTS: During REMS rebound, the time spent in REMS and the number of MCH/Fos double-labeled neurons in the lateral hypothalamus increased markedly, and REMS latency showed a significant decrease. All these effects of REMS deprivation were significantly attenuated by escitalopram treatment. Besides the REMS-suppressing effects, escitalopram caused an increase in amount of and decrease in latency of slow wave sleep during the rebound. CONCLUSIONS: These results show that despite the high REMS pressure caused by REMS deprivation procedure, escitalopram has the ability to suppress REMS rebound, as well as to diminish the activation of MCH-containing neurons, in parallel. Escitalopram caused a shift from REMS to slow wave sleep during the rebound. Furthermore, these data point to the potential connection between the serotonergic system and MCH in sleep regulation, which can be relevant in depression and in other mood disorders

The Yeast La Related Protein Slf1p Is a Key Activator of Translation during the Oxidative Stress Response

The mechanisms by which RNA-binding proteins control the translation of subsets of mRNAs are not yet clear. Slf1p and Sro9p are atypical-La motif containing proteins which are members of a superfamily of RNA-binding proteins conserved in eukaryotes. RIP-Seq analysis of these two yeast proteins identified overlapping and distinct sets of mRNA targets, including highly translated mRNAs such as those encoding ribosomal proteins. In paralell, transcriptome analysis of slf1Δ and sro9Δ mutant strains indicated altered gene expression in similar functional classes of mRNAs following loss of each factor. The loss of SLF1 had a greater impact on the transcriptome, and in particular, revealed changes in genes involved in the oxidative stress response. slf1Δ cells are more sensitive to oxidants and RIP-Seq analysis of oxidatively stressed cells enriched Slf1p targets encoding antioxidants and other proteins required for oxidant tolerance. To quantify these effects at the protein level, we used label-free mass spectrometry to compare the proteomes of wild-type and slf1Δ strains following oxidative stress. This analysis identified several proteins which are normally induced in response to hydrogen peroxide, but where this increase is attenuated in the slf1Δ mutant. Importantly, a significant number of the mRNAs encoding these targets were also identified as Slf1p-mRNA targets. We show that Slf1p remains associated with the few translating ribosomes following hydrogen peroxide stress and that Slf1p co-immunoprecipitates ribosomes and members of the eIF4E/eIF4G/Pab1p ‘closed loop’ complex suggesting that Slf1p interacts with actively translated mRNAs following stress. Finally, mutational analysis of SLF1 revealed a novel ribosome interacting domain in Slf1p, independent of its RNA binding La-motif. Together, our results indicate that Slf1p mediates a translational response to oxidative stress via mRNA-specific translational control

Distance to Galactic globulars using the near-infrared magnitudes of RR Lyrae stars: IV. The case of M5 (NGC5904)

We present new and accurate near-infrared (NIR) J, K-band time series data for the Galactic globular cluster (GC) M5 = NGC5904. Data were collected with SOFI at the NTT (71 J + 120 K images) and with NICS at the TNG (25 J + 22 K images) and cover two orthogonal strips across the center of the cluster of \approx 5 \times 10 arcmin^{2} each. These data allowed us to derive accurate mean K-band magnitudes for 52 fundamental (RR_{ab}) and 24 first overtone (RR_{c}) RR Lyrae stars. Using this sample of RR Lyrae stars, we find that the slope of the K-band Period Luminosity (PLK) relation (-2.33 \pm 0.08) agrees quite well with similar estimates available in the literature. We also find, using both theoretical and empirical calibrations of the PLK relation, a true distance to M5 of (14.44 \pm 0.02) mag. This distance modulus agrees very well (1\sigma) with distances based on main sequence fitting method and on kinematic method (14.44 \pm 0.41 mag, \citealt{rees_1996}), while is systematically smaller than the distance based on the white dwarf cooling sequence (14.67 \pm 0.18 mag, \citealt{layden2005}), even if with a difference slightly larger than 1\sigma. The true distance modulus to M5 based on the PLJ relation (14.50 \pm 0.08 mag) is in quite good agreement with the distance based on the PLK relation further supporting the use of NIR PL relations for RR Lyrae stars to improve the precision of the GC distance scale.Comment: 19 pages, 6 figures, accepted for publication in MNRA

Иммунофенотип макрофагальной популяции при фиброзно-кавернозном туберкулезе легких

Objective: to study the immunophenotype of the macrophage population and the mechanisms of their vectorial redistribution in fibrous cavernous pulmonary tuberculosis.Materials and methods. The material for the study was fragments of the fibrous cavern wall and pericavernous lung tissue of the dead or surgical patients diagnosed with fibrous cavernous tuberculosis (n = 163). All patients were divided into 2 main groups: patients with active bacteria excretion (MTB+, n = 84) and patients with clinical abacillation (MTB–, n = 79) for immunohistochemistry with a panel of markers for: macrophages and histiocytes – CD68; vascular growth factor A – VEGF-A; T-helpers – CD4, and T-cytotoxic lymphocytes – CD8.Results. Following the analysis of CD68 expression, the population heterogeneity of macrophages was revealed depending on the intensity of the cytoplasmic reaction, functional activity, localization and quantitative characteristics. Three groups were identified: highly active, moderately active and weakly active. Based on the reaction with vascular growth factor A, it was determined that VEGF+ cells correspond to weakly active CD68+ macrophages and are located on the border between the specific granulation tissue and fibrous layer as well as in the pericavernous zone and intact lung tissue with a statistically significant predominance in patients with MTB– (p < 0.05). Regardless of the scope of bacterial secretion, the number of VEGF+ cells in the lymphoid follicle zone directly correlates with that of CD68+ macrophages in the pericavernous zone (R = 0.68) and indirectly correlates with the number of diffusely scattered VEGF+ cells in the fibrous capsule (R = –0.75). In the meantime, CD68+/VEGF+ are visualized in the zone of CD8+ T-lymphocytes, and CD68+/VEGF- – in the zone of CD4+ cell clusters. Such correlation indicates the redistribution of macrophages into type 2, which has a remodeling effect on the surrounding tissues with the potentiating participation of lymphoid cells.Цель исследования: изучение иммунофенотипа макрофагальной популяции и механизмов их векторного перераспределения при фиброзно-кавернозном туберкулезе легких.Материалы и методы. Материалом для исследования явились фрагменты стенки каверны и перикавернозной легочной ткани прооперированных по поводу фиброзно-кавернозного туберкулеза (ФКТ) легких (n = 163). Все пациенты были разделены на две основные группы (с активным бактериовыделением (МБТ+, n = 84) и клиническим абациллированием (МБТ–, n = 79)) для проведения иммуногистохимического исследования с панелью маркеров: макрофагов и гистиоцитов – CD68; сосудистого фактора роста А – VEGF-A; Т-хелперов CD4, цитотоксических Т-лимфоцитов CD8.Результаты. При анализе экспрессии маркера CD68 установлена популяционная неоднородность макрофагов в зависимости от интенсивности цитоплазматической реакции функциональной активности с различными локализационными и количественными характеристиками: высокоактивные (тип 1), умеренно активные (тип 2) и слабоактивные (тип 3). На основании реакции с сосудистым фактором ростом A определено, что клетки VEGF+ соответствуют слабоактивным макрофагам CD68+ и локализуются на границе перехода специфической грануляционной ткани в фиброзный слой, перикавернозной зоне и интактной легочной ткани со статистически значимым преобладанием у пациентов с МБТ– (р < 0,05). Независимо от активности бактериовыделения число клеток VEGF+ в зоне лимфоидных фолликулов прямо коррелирует с количеством макрофагов CD68+ в перикавернозной зоне (R = 0,68) и обратно – с числом VEGF+ диффузно рассеянных клеток в фиброзной капсуле (R = макрофагов 0,75). При этом CD68+/VEGF+ визуализируются в зоне CD8+ Т-лимфоцитов, а CD68+/VEGF- – в зоне скоплений клеток CD4+. Такой характер корреляционной взаимосвязи свидетельствует о перераспределении макрофагов во второй тип, обладающих ремоделирующим действием на окружающие ткани при потенцирующем участии клеток лимфоидной популяции

Dynamic changes in eIF4F-mRNA interactions revealed by global analyses of environmental stress responses

BACKGROUND: Translation factors eIF4E and eIF4G form eIF4F, which interacts with the messenger RNA (mRNA) 5' cap to promote ribosome recruitment and translation initiation. Variations in the association of eIF4F with individual mRNAs likely contribute to differences in translation initiation frequencies between mRNAs. As translation initiation is globally reprogrammed by environmental stresses, we were interested in determining whether eIF4F interactions with individual mRNAs are reprogrammed and how this may contribute to global environmental stress responses. RESULTS: Using a tagged-factor protein capture and RNA-sequencing (RNA-seq) approach, we have assessed how mRNA associations with eIF4E, eIF4G1 and eIF4G2 change globally in response to three defined stresses that each cause a rapid attenuation of protein synthesis: oxidative stress induced by hydrogen peroxide and nutrient stresses caused by amino acid or glucose withdrawal. We find that acute stress leads to dynamic and unexpected changes in eIF4F-mRNA interactions that are shared among each factor and across the stresses imposed. eIF4F-mRNA interactions stabilised by stress are predominantly associated with translational repression, while more actively initiating mRNAs become relatively depleted for eIF4F. Simultaneously, other mRNAs are insulated from these stress-induced changes in eIF4F association. CONCLUSION: Dynamic eIF4F-mRNA interaction changes are part of a coordinated early translational control response shared across environmental stresses. Our data are compatible with a model where multiple mRNA closed-loop complexes form with differing stability. Hence, unexpectedly, in the absence of other stabilising factors, rapid translation initiation on mRNAs correlates with less stable eIF4F interactions

riboviz: analysis and visualization of ribosome profiling datasets

Abstract Background Using high-throughput sequencing to monitor translation in vivo, ribosome profiling can provide critical insights into the dynamics and regulation of protein synthesis in a cell. Since its introduction in 2009, this technique has played a key role in driving biological discovery, and yet it requires a rigorous computational toolkit for widespread adoption. Description We have developed a database and a browser-based visualization tool, riboviz, that enables exploration and analysis of riboseq datasets. In implementation, riboviz consists of a comprehensive and flexible computational pipeline that allows the user to analyze private, unpublished datasets, along with a web application for comparison with published yeast datasets. Source code and detailed documentation are freely available from https://github.com/shahpr/RiboViz . The web-application is live at www.riboviz.org. Conclusions riboviz provides a comprehensive database and analysis and visualization tool to enable comparative analyses of ribosome-profiling datasets. This toolkit will enable both the community of systems biologists who study genome-wide ribosome profiling data and also research groups focused on individual genes to identify patterns of transcriptional and translational regulation across different organisms and conditions

Pichia pastoris regulates its gene-specific response to different carbon sources at the transcriptional, rather than the translational, level

Background: The methylotrophic, Crabtree-negative yeast Pichia pastoris is widely used as a heterologous protein production host. Strong inducible promoters derived from methanol utilization genes or constitutive glycolytic promoters are typically used to drive gene expression. Notably, genes involved in methanol utilization are not only repressed by the presence of glucose, but also by glycerol. This unusual regulatory behavior prompted us to study the regulation of carbon substrate utilization in different bioprocess conditions on a genome wide scale. Results: We performed microarray analysis on the total mRNA population as well as mRNA that had been fractionated according to ribosome occupancy. Translationally quiescent mRNAs were defined as being associated with single ribosomes (monosomes) and highly-translated mRNAs with multiple ribosomes (polysomes). We found that despite their lower growth rates, global translation was most active in methanol-grown P. pastoris cells, followed by excess glycerol- or glucose-grown cells. Transcript-specific translational responses were found to be minimal, while extensive transcriptional regulation was observed for cells grown on different carbon sources. Due to their respiratory metabolism, cells grown in excess glucose or glycerol had very similar expression profiles. Genes subject to glucose repression were mainly involved in the metabolism of alternative carbon sources including the control of glycerol uptake and metabolism. Peroxisomal and methanol utilization genes were confirmed to be subject to carbon substrate repression in excess glucose or glycerol, but were found to be strongly de-repressed in limiting glucose-conditions (as are often applied in fed batch cultivations) in addition to induction by methanol. Conclusions: P. pastoris cells grown in excess glycerol or glucose have similar transcript profiles in contrast to S. cerevisiae cells, in which the transcriptional response to these carbon sources is very different. The main response to different growth conditions in P. pastoris is transcriptional; translational regulation was not transcript-specific. The high proportion of mRNAs associated with polysomes in methanol-grown cells is a major finding of this study; it reveals that high productivity during methanol induction is directly linked to the growth condition and not only to promoter strength

Circuit-based interrogation of sleep control.

Sleep is a fundamental biological process observed widely in the animal kingdom, but the neural circuits generating sleep remain poorly understood. Understanding the brain mechanisms controlling sleep requires the identification of key neurons in the control circuits and mapping of their synaptic connections. Technical innovations over the past decade have greatly facilitated dissection of the sleep circuits. This has set the stage for understanding how a variety of environmental and physiological factors influence sleep. The ability to initiate and terminate sleep on command will also help us to elucidate its functions within and beyond the brain