Miracle-dz/UniFAR-FTUs huggingface dataset:
Alcohol‐responsive genes in the frontal cortex and nucleus accumbens of human alcoholics

The molecular processes underlying alcohol dependence are not fully understood. Many characteristic behaviours result from neuroadaptations in the mesocorticolimbic system. In addition, alcoholism is associated with a distinct neuropathology. To elucidate the molecular basis of these features, we compared the RNA expression profile of the nucleus accumbens and prefrontal cortex of human brain from matched individual alcoholic and control cases using cDNA microarrays. Approximately 6% of genes with a marked alcohol response were common to the two brain regions. Alcohol‐responsive genes were grouped into 11 functional categories. Predominant alcohol‐responsive genes in the prefrontal cortex were those encoding DNA‐binding proteins including transcription factors and repair proteins. There was also a down‐regulation of genes encoding mitochondrial proteins, which could result in disrupted mitochondrial function and energy production leading to oxidative stress. Other alcohol‐responsive genes in the prefrontal cortex were associated with neuroprotection/apoptosis. In contrast, in the nucleus accumbens, alcohol‐responsive genes were associated with vesicle formation and regulation of cell architecture, which suggests a neuroadaptation to chronic alcohol exposure at the level of synaptic structure and function. Our data are in keeping with the previously reported alcoholism‐related pathology characteristic of the prefrontal cortex, but suggest a persistent decrease in neurotransmission and changes in plasticity in the nucleus accumbens of the alcoholic.
Transcriptomic approaches in the brain at cell type resolution : Analysis of neuron-glia interaction in Plp1 and Cnp1 null-mutant mice

Global gene expression profiling is a powerful tool to obtain deep insights into physiological and pathological cellular mechanisms. The enormous cellular complexity of the mammalian brain, however, is a major obstacle for gene expression profiling. Physiologically relevant changes of transcription that occur in specific cell populations are likely to remain undetected in cellularly complex samples. The purification of single populations of neural cell types eliminates these difficulties. We have approached this problem in transgenic mice by labelling genetically-defined neural cell types that express variants of GFP. When combined with isolation techniques such as fluorescence activated cell sorting (FACS) or laser capture microdissection (LCM), the isolation of intact RNA from unfixed cells for global transcriptome analysis is possible. In this study we applied FACS and LCM to isolate neurons and glia to gain insight into cell type specific gene expression. We profiled glial precursor cells, microglia and oligodendrocytes using FACS and generated a transcriptome database for glial cell types. LCM was used to study single isolated callosal projection neurons from the cortex of mouse models, which develop adult onset axonal degeneration a hallmark of many neurodegenerative diseases such as parkinson disease, Alzheimer disease and Multiple Sclerosis (MS). The identification of molecular mechanisms underlying axonal degeneration is critical to design rational therapies for neurodegenerative diseases. Therefore we profiled wild type controls, Cnp1 and Plp1 null mutant mice (myelin specific genes) at 4 different time points during adulthood. Cnp1 and Plp1 null mutants show axonal swellings and with age severe neurodegeneration, although CNS myelin seems ultra structural not affected. In summary, we have shown the feasibility to "snapshot" gene expression profiles of genetically defined neuronal subtypes in vivo and to compare morphologically similar neurons at a given time in pathological conditions. We followed gene expression changes starting from early disease states until stages of severe pathological signs, focusing on cells known to be susceptible to a genetic predisposition. Our analysis revealed several known and novel candidate genes and mechanisms that likely play a role in the early adaptive responses of cortical projection neurons to cope with axonal stress.
photo-hydrogen production by Rhodopseudomonas faecalis RLD-53

abstract In the present study, the effect of Ni 2þ (0–10 mmol/l), Fe (0–200 mmol/l) and Mg 2þ (0–15 mmol/l) concentration on photo-hydrogen production from acetate was investigated bybatch culture. Results showed that under a proper concentration range, Ni 2þ was able toenhance the hydrogen production rate and the hydrogen yield; Fe 2þ was able to increasethe hydrogen yield, and hydrogen production rate was enhanced only when the culturingtime was 24–72 h. Ni 2þ and Fe 2þ at a higher concentration inhibited cell growth. When Ni 2þ and Fe 2þ concentrations were 4 mmol/l and 80 mmol/l, respectively, maximal hydrogen yieldof 2.87 and 2.78 mol H 2 /mol acetate was obtained when batch culturing at 35 C with initialpH 7.0. Mg 2þ did not signiﬁcantly affect hydrogen production and hydrogen yield whichmaintained at about 2.45 mol H 2 /mol acetate, but it was favorable to cell growth.a 2008 International Association for Hydrogen Energy. Published by Elsevier Ltd. All rightsreserved. 1. Introduction
Seasonal diet composition and forage selectivity of Boer goats in a semi-arid gypsophilous grassland

Botanical and chemical compositions of Boer goat diets, determined with repeated collection of forage samples taken from the goat’s mouth, were studied in a gypsophilous grassland during four seasons of the year. Ten pluriparous goats were used to collect selected forage species. Shrubs were a minor dietary component throughout the year (<7.5%). Goats selected more (p < 0.01) grass during autumn and winter (34.2–37.8%) than during spring (21.2%) and summer (29.0%). During all seasons goat diets were dominated by forbs (>59%). Diets were lowest (p < 0.05) in percentage of crude protein during spring, summer and autumn (13.2 ± 3.5, 13.2 ± 2.4 and 14.2 ± 3.9, respectively) than winter (17.5 ± 2.9) with levels above the recommended quantities for goats throughout the year. In vitro dry matter digestibility of forages selected by goats did not differ between seasons (range 47.4–53.3%). It was concluded that in this particular ecosystem goats preferred forb species over grasses across all seasons. In addition, goats maintained relatively stable diet quality by forage-class mixing of diets.
Control of vasculo-proliferative processes by the NO-cGMP-cGKI pathway

Nitric oxide (NO) is of crucial importance for smooth muscle cell (SMC) function and exerts numerous, sometimes opposing, effects on vascular proliferative diseases. Among these disorders is restenosis, the narrowing of an artery after intra-arterial intervention, such as balloon angioplasty or stent placement. The molecular downstream effectors of NO in restenosis are not clear. In SMCs, NO exerts many of its effects via the second messenger cyclic guanosine-3´,5´-monophosphate (cGMP). The cGMP-dependent protein kinase type I (cGKI) is presumably the major mediator of NO-cGMP signaling in SMCs. The purpose of this study was to examine the functional role of the SMC NO-cGMP-cGKI pathway in restenosis. By using the Cre-loxP site-specific recombination system, tissue-specific mouse mutants were generated in which the cGKI protein was efficiently ablated in SMCs and, to a lesser extent, also in cardiomyocytes. It was tested whether this conditional inactivation of cGKI would effect vascular remodeling after carotid ligation. Remodeling was analyzed by morphometry and immunohistochemistry. Based on the neointima/media ratio and other vessel parameters as well as on various immunostainings, no significant differences were detected between the conditional cGKI mutants and controls at different time points after injury, in normolipidemic as well as in apolipoprotein E-deficient mice. Moreover, continuous treatment of injured wild-type mice with the phosphodiesterase 5 inhibitor sildenafil (Viagra) indicated that elevated cGMP levels had no influence on ligation-induced remodeling. Thus, vascular remodeling after mechanical injury was altered neither by the deletion of smooth muscle cGKI nor by sildenafil treatment. Finally, this work addressed the effects of different cGMP-elevating agents, such as sildenafil, 2-(N,N-diethylamino)-diazenolate-2-oxide (DEA-NO), and natriuretic peptides, on cyclic nucleotide signaling in primary vascular SMCs. These experiments indicated that endogenously generated cGMP might cross-activate cAMP-dependent protein kinase (cAK), at least in the absence of cGKI. Together, the results of the present study indicate that NO signaling in restenosis is independent of the cGMP-cGKI pathway and perhaps mediated via an unconventional NO-cGMP-cAK pathway.
Novel effects of n-3 LC-PUFA on adipose tissue and liver in diet-induced obesity in mice

In this study, high fat diet (HF) induced obesity in mice, which was less by feeding HF rich in n-3 polyunsaturated fatty acids (PUFA) due to reduced adipose tissue (AT) mass and hepatic lipid deposition and improved insulin levels. Unexpectedly, AT expression of pro- and anti-inflammatory genes was increased by HF/n-3 but less pronounced in mesenteric AT, while other organs showed anti-inflammatory effects. This AT-specific response challenges the known anti-inflammatory role of n-3 PUFA.
Effects of Isotretinoin on the Phosphoinositide-3-kinase/Akt/FoxO1 Pathway and Molecular Functions of SZ95 Sebocytes In vitro

Objective: For more than 3 decades, isotretinoin [13-cis retinoic acid (13-cis RA)] is established as the most potent oral treatment for severe acne. However, the molecular mechanisms of isotretinoin action have not been fully elucidated. Recently, we showed that insulin and insulin-like growth factor 1 (IGF-1) increase differentiation and decrease proliferation of SZ95 sebocytes in vitro via activation of the phosphoinositide 3-kinase (PI3K)/Akt/forkhead box-O1 (FoxO1) pathway. Furthermore, this pathway is activated in patient acne biopsies in vivo. Using SZ95 sebocytes as an in vitro model, the aim of this study was to investigate the effect of isotretinoin on PI3K pathway activation. Methods: SZ95 sebocytes were treated under light protection with 0.1 μM isotretinoin in the presence or absence of 1.0 and 0.1 μM IGF-1 or insulin or 50 μM LY294002 inhibitor in a time- dependent manner. The expression of p-Akt and its downstream target p-FoxO1 was analyzed by Western blot. FoxO transcriptional activity was measured by dual luciferase assay. Nuclear and cytoplasmic mobilization of FoxO1, p-FoxO1, and p-Akt were also determined by immunofluorescence microscopy.Proliferation of sebocytes was measured by [3H]-thymidine incorporation and sebocyte differentiation by oil red O staining. Results: We show that isotretinoin activates the PI3K/Akt pathway and decreases the nuclear content of FoxO1 and its transcriptional activity in sebocytes in vitro and in sebaceous gland biopsies from an isotretinoin-treated acne patient. Isotretinoin reduces the proliferation of IGF-1- or insulin-stimulated sebocytes more effectively than IGF-1 and insulin alone. However, it normalizes the increased lipid accumulation in IGF-1- or insulin-stimulated sebocytes via a PI3K-independent pathway. Conclusion: Our data from the SZ95 sebocyte in vitro model suggest that the potent therapeutic effect of isotretinoin in acne is not mediated via the PI3K/Akt/FoxO1 pathway.
Bilateral processing of thermoreception in the olfactory system of larval Xenopus laevis

This study of the ventral olfactory bulb of larval Xenopus laevis shows for the first time the existence of a thermosensitive olfactory glomerulus. This thermosensitive olfactory glomerulus was found to be innervated by axons of olfactory sensory neurons emerging from the ipsilateral olfactory epithelium as well as from the contralateral olfactory epithelium. The perfusion of the ipsilateral or contralateral olfactory epithelium with cold, odor-free Ringer solution elicited a transient [Ca2+]i response within the axons of olfactory sensory neurons and in mitral cells. The activation of mitral cells demonstrated that the response to temperature stimulation is transmitted across the first olfactory synapse. The thermoreception was spatially restricted to this glomerulus, which did not respond to any of the tested odors. Adjacent olfactory glomeruli responded to olfactory and mechanical stimulation without showing any response to temperature changes. The spatially restricted, bilateral processing of temperature stimuli at the level of the olfactory glomerulus and mitral cells indicates that temperature represents a novel, adequate quality for the vertebrate olfactory system.
An optimized strategy for cloning-based locus-specific bisulfite sequencing PCR

In this methods paper, we describe a successful strategy to investigate locus-specific methylation by cloning-based bisulfite sequencing. We cover sample handling, DNA isolation, DNA quality control before bisulfite conversion, bisulfite conversion, DNA quality control after bisulfite conversion, in silico identification of CpG islands, methylation-independent bisulfite sequencing PCR (BSP) assay design, methylation-independent BSP, cloning strategy, sequencing and data analysis. Methods that are described nicely elsewhere will not be covered in detail. Instead, the focus will be on tips/tricks and new methods/strategies used in this protocol, including quality control assessment of the DNA before and after bisulfite conversion and a pooled cloning strategy to reduce time, costs and effort during this step. In addition we comment on dealing with bias and improving overall protocol efficiency.
Molecular mapping of major genes influencing flowering time in wheat (Triticum aestivum L. em. Thell)

For genetic mapping of major photoperiod (Ppd-B1) and vernalisation (Vrn-D1) genes in wheat, four segregating populations were employed. For this purpose, AFLP and SSR were chosen as molecular techniques. The use of different populations carrying the same gene enabled to answer the crucial question in marker assisted selection (MAS) whether the markers found in a specific cross can be also applied in different crosses. Furthermore, a simple method for scoring the presence of Ppd-B1 gene was also developed by converting a co-segregating AFLP to a simple PCR marker.
New and interesting lichens from Panama

Abstract The following five new species are described from Panama: Anisomeridium trichialis, Arthothelium isidiatum, Astrothelium flavomegaspermum, Mycocalicium chiodectonicola and Polymeridium xanthopleurothecium. In addition, 41 species are reported from Panama for the first time.
Acute and sub-chronic oral toxicity studies on the methanol leaf extract of Gnetum africanum Welw in wistar rats.

Aim: Acute and sub-chronic toxicity studies were performed on Gnetum africanum Welw leaves using well established guidelines and methods. In spite of its use as a herbal remedy, there is dearth of data on toxicity studies of the plant extract. Methods: Gnetum africanum leaves were identified by a plant taxonomist, air-dried, pulverized and extracted with 80 % methanol for 48 hours in July, 2015. The extract was concentrated in-vacuo and stored as Gnetum africanum extract (GAE) at 4oC. Thirty five male albino rats randomly divided into 7 groups (n=5) were used for acute toxicity test which was done in August, 2015. Rats in groups 1-6 were given GAE at 500, 1000, 2000, 3000, 4000 and 5000 mg/kg, respectively while group 7 rats received 10 ml/kg distilled water. Feed and water were provided and they were observed for signs of toxicity for 48 h. A 90-day sub-chronic toxicity study was conducted using 56 rats of 4 groups (n=14) in December 2015-March, 2016. Group 1 received feed without GAE, while groups 2-4 were given feed with GAE at 10, 20 and 40 mg/kg respectively. Four rats from each group were bled on days 30, 60 and 90 for clinical biochemistry and sacrificed for histopathological examination. Results: LD50 was greater than 5000 mg/kg while no-observed-adverse-effect-level was 40 mg/kg. Serum marker enzymes and creatinine were not increased in rats given extract in feed while there were no histopathological lesions in the organs studied. Conclusions: The extract is safe at both acute and sub-chronic levels.
Weak interactions between groups and physical drivers of community dynamics in coastal phytoplankton

Phytoplanktonic communities maintain a high diversity in a seemingly homogeneous environment, competing for the same set of resources. Many theories have been proposed to explain this coexistence despite likely competition, such as contrasted responses to temporal environmental variation. However, theory has developed at a faster pace than its empirical evaluation using field data, that requires to infer biotic and abiotic drivers of community dynamics from observational time series. Here, we combine autoregressive models with a data set spanning more than 20 years of biweekly plankton counts and abiotic variables, including nutrients and physical variables. By comparing models dominated by nutrients or physical variables (hydrodynamics and climate), we first explore which abiotic factors contribute more to phytoplankton growth and decline. We find that physical drivers - such as irradiance, wind, and salinity - explain some of the variability in abundances unexplained by biotic interactions. In contrast, responses to nutrients explain less of phytoplankton variability. Concerning biotic drivers of community dynamics, multivariate autoregressive models reveal that competition between different groups (at the genus level for most) has a much weaker effect on population growth rates than competition within a group. In fact, the few biotic interactions between genera that are detected are frequently positive. Hence, our system is unlikely to be best represented as a set of competitors whose differing responses to fluctuating environments allow coexistence, as in “paradox of the plankton” models with a storage effect or a relative nonlinearity of competition. Coexistence is more likely to result from stabilizing niche differences, manifested through high intragroup density-dependence. Competition between planktonic groups and nutrients are often invoked as drivers of phytoplankton dynamics; our findings suggest instead that more attention should be given to the physical structure of the environment and natural enemies, for coastal phytoplankton at least.
In search of a meaningful classification for Amazonian marmosets: Should dwarf marmosets be considered Mico congenerics?

The criteria to classify the diversity of Neotropical Primates have recently taken the discussion boards due to the reappraisal on the phylogenetic relationship of some groups. Such controversial and arbitrary decisions, however, can hamper conservation actions in as much as it becomes difficult to prioritise and set meaningful targets. It is the case for dwarf marmosets from central Amazonia. Today, the classification of dwarf marmosets in Mico or Callibella genus has not been satisfactorily settled. Aiming to contribute to the taxonomic and conservation assessment of dwarf marmosets, we conducted new data collection during 3‐year fieldwork in the Aripuanã River, where the species was discovered. We present the first phylogenomic analysis of the evolutionary relationships between marmosets, new data from mitochondrial DNA and morphology, as well new records to clarify geographic distribution. With this new evidence, we support dwarf marmosets as the genus Callibella. We further discuss the implications for the conservation of this marmoset.
The role of meiosis-specific cohesins in accurate chromosome segregation

of the Dissertation . ii Acknowlegdements . iv Dedication . v List of Tables . viii List of Illustrations. ix Chapter 1: Introduction . 1 Aneuploidy and maternal age . 1 Meiosis . 3 Synaptonemal complex and the chromosome axis . 4 Mitotic cohesion . 8 Meiotic cohesion . 10 Crossing over . 14 The Drosophila ovary system . 14 Using the Gal4/UAS system to control expression of transgenics . 17 Chapter 2: Dynamic and stable cohesins regulate synaptonemal complex assembly and chromosome segregation . 20 I. Preface . 20 II. Graphical abstract . 21 III. Abstract . 22 IV. Introduction . 22 V. Results . 24 Stromalin is required for SC assembly . 24 SMC1 on the chromosome arms but not the centromeres depends on SA . 27 SA functions in the same pathway as C(2)M but not ORD or SUNN . 29 SA depletion does not result in sister centromere defects at meiosis I . 32 C(2)M is integrated into the SC throughout pachytene . 35 C(2)M is also removed from the SC throughout pachytene . 41 Centromere cohesins SUNN and SOLO are not integrated during pachytene . 41 VI. Discussion . 44 The two complexes are directed towards either sister or homolog interactions . 44 Differential regulation and dynamics of meiotic cohesins . 45 Evolutionary conservation and function of multiple cohesins complexes . 46 vii VI. Materials and Methods . 47 Chapter 3: Meiosis specific Kleisin,C(2)M, functions with other cohesin subunits, but possibly not in traditional ring structure . 53 I. Preface . 53 II. Abstract . 53 II
A new Global Climate Model to explore the rich dynamics of Saturn's stratosphere

New observations, new questions Recent observations of the Saturn’s atmosphere have shed a new light on its thermal structure, chemistry, and dynamics. In particular, a leap forward on our knowledge of Saturn’s stratosphere has resulted from the combination of orbital observations on board the Cassini spacecraft and state-of-the-art ground-based observations. Maps of temperature and hydrocarbons in Saturn’s stratosphere revealed puzzling anomalies: equatorial oscillations with a period of about half a Saturn year [3, 10], meridional circulations affecting the hydrocarbons’ distribution, including possible effects of rings shadowing [5], “beacons” associated with the powerful 2010 Great White Spot [1]. Those signatures, reminiscent of fundamental dynamical phenomena in the Earth’s middle atmosphere (e.g., Quasi-Biennal Oscillation, Brewer-Dobson circulation), cannot be explained by photochemical and radiative models. A rich, wave-driven atmospheric dynamics plays a crucial role in Saturn’s stratosphere, hence the need to develop new three-dimensional dynamical models to understand it.
Highly masculinized and younger males attain higher reproductive success in a social rodent

Alternative morphotypes have been reported in males of different taxa. In some mammals, highly masculinized and slightly masculinized males represent 2 opposite ends along a gradient of phenotypic variation in males. This phenotypical gradient originates during prenatal development. Laboratory studies have documented how highly and slightly masculinized males differ in several traits, including their reproductive success. However, the extent to which these reported differences materialize in natural populations remains unknown. We quantified the impact of male morphotype on male reproductive success in a natural population of Octodon degus, a highly social rodent. We assessed male morphotype through a continuous gradient of anogenital distance. We also tested the hypothesis that the social environment interacts with male morphotype to influence male reproductive success. We found that individual attributes, including masculinization level and age, impacted male reproductive success. Highly masculinized and younger males had greater reproductive success. Additionally, male body weight had a small magnitude but positive effect on male reproductive success. Male reproductive success was not affected by social attributes such as group composition. Thus, the number of males and females within a group did not affect male reproductive success, nor did the average male anogenital distance within a group. Our results support the hypothesis that the prenatal environment can result in long-term effects on individual life history and cause intrasexual phenotypical variation in natural populations. Our findings suggest that male phenotypical masculinization could be an adaptive trait, regardless of the social environment.