Pollen-based biome reconstruction for southern Europe and Africa 18,000 yr bp

Pollen data from 18,000 ¹⁴C yr bp were compiled in order to reconstruct biome distributions at the last glacial maximum in southern Europe and Africa. Biome reconstructions were made using the objective biomization method applied to pollen counts using a complete list of dryland taxa wherever possible. Consistent and major differences from present‐day biomes are shown. Forest and xerophytic woods/scrub were replaced by steppe, both in the Mediterranean region and in southern Africa, except in south‐western Cape Province where fynbos (xerophytic scrub) persisted. Sites in the tropical highlands, characterized today by evergreen forest, were dominated by steppe and/or xerophytic vegetation (cf. today’s Ericaceous belt and Afroalpine grassland) at the last glacial maximum. Available data from the tropical lowlands are sparse but suggest that the modern tropical rain forest was largely replaced by tropical seasonal forest while the modern seasonal or dry forests were encroached on by savanna or steppe. Montane forest elements descended to lower elevations than today.     

Pollen–plant–climate relationships in sub-Saharan Africa

Aim  To demonstrate that incorporating the bioclimatic range of possible contributor plants leads to improved accuracy in interpreting the palaeoclimatic record of taxonomically complex pollen types.
Location  North Tropical Africa.
Methods  The geographical ranges of selected African plants were extracted from the literature and geo-referenced. These plant ranges were compared with the pollen percentages obtained from a network of surface sediments. Climate-response surfaces were graphed for each pollen taxon and each corresponding plant species.
Results  Several patterns can be identified, including taxa for which the pollen and plant distributions coincide, and others where the range limits diverge. Some pollen types display a reduced climate range compared with that of the corresponding plant species, due to low pollen production and/or dispersal. For other taxa, corresponding to high pollen producers such as pioneer taxa, pollen types display a larger climatic envelope than that of the corresponding plants. The number of species contained in a pollen taxon is an important factor, as the botanical species included in a taxon may have different geographical and climate distributions.
Main conclusions  The comparison between pollen and plant distributions is an essential step towards more precise vegetation and climate reconstructions in Africa, as it identifies taxa that have a high correspondence between pollen and plant distribution patterns. Our method is a useful tool to reassess biome reconstructions in Africa and to characterize accurately the vegetation and climate conditions at a regional scale, from pollen data.     

Two-dimensional electrophoresis computerized processing

This paper describes various methods suitable for implementation of two-dimensional processing software. The different steps leading to a complete processing are described, from the digitalization of the image to the processing of the resulting data. The characteristics of a convenient digitalization system are discussed. The different software devoted to spot detection is reviewed with respect to the presence or otherwise of a spot model and its characteristics. The major techniques for gel matching are compared as are designs for database structures suitable for tabulation of measurements. Finally, the need for a sophisticated system of data processing is stressed and its main requirements are described.     

D-ASSIRC: distributed program for finding sequence similarities in genomes

MOTIVATION: Locating the regions of similarity in a genome requires the availability of appropriate tools such as 'Accelerated Search for SImilar Regions in Chromosomes' (ASSIRC; Vincens et al., Bioinformatics, 14, 715-725, 1998). The aim of this paper is to present different strategies for improving this program by distributing the operations and data to multiple processing units and to assess the efficiency of the different implementations in terms of running time as a function of the number of processing units. RESULTS: The new version D-ASSIRCis based on three alternative strategies of task sharing: (1) a distributed search using the splitting of studied sequences into large overlapping subsequences (strategy ASS); (2) two distributed searches for repeated exact motifs of fixed size either managed by a central processor (strategy AGD) or locally managed by numerous processors (strategy ALD). The result is that the strategy ASSis suitable for a large number of processing units (the time was divided by a factor of 12 when the number of processing units was increased from 1 to 16) wheras the strategy ALDis better for a small set of processors (typically for four or six).The different proposed strategies are efficient for various applications in genomic research, particularly for locating similarities of nucleic sequences in large genomes. AVAILABILITY: D-ASSIRCis freely available by anonymous FTP at ftp://ftp.ens.fr/pub/molbio/dassirc.tar.gz. Sources and binaries for Solaris and Linux are included in the distribution.     

Use of plots to define pollen-vegetation relationships in densely forested ecosystems of Tropical Africa

Modern soil samples from South Congo were analyzed for pollen content and compared to forest inventories to define modern pollen-vegetation relationships. A correspondence analysis (CA) was applied independently to botanical and pollen data and a hierarchical cluster analysis to pollen data only. Subsequently, a CA using a presence-absence approach has been made to directly compare the two types of data. Results show that the pollen rain and floristic composition of the sampled sites are not directly linked to altitudinal or precipitation gradients, but clear evidence of variation in relation to hygromorphy and soil type is detected. The forests occurring in swampy environments are well differentiated from the forests developed on well-drained soils by pollen and floristic data. Among forests on well-drained soils, a good distinction can be made between those growing on sandy soils and those growing on ferralitic soils. The comparison between pollen spectra and vegetation shows site-to-site variations in pollen assemblages in relation to the floristic heterogeneity of forests, and it appears that few taxa show a good correlation between plant cover and pollen abundance.     

Cell-free DNA in Human Follicular Microenvironment: New Prognostic Biomarker to Predict in vitro Fertilization Outcomes

Cell-free DNA (cfDNA) fragments, detected in blood and in other biological fluids, are released from apoptotic and/or necrotic cells. CfDNA is currently used as biomarker for the detection of many diseases such as some cancers and gynecological and obstetrics disorders. In this study, we investigated if cfDNA levels in follicular fluid (FF) samples from in vitro fertilization (IVF) patients, could be related to their ovarian reserve status, controlled ovarian stimulation (COS) protocols and IVF outcomes. Therefore, 117 FF samples were collected from women (n = 117) undergoing IVF/Intra-cytoplasmic sperm injection (ICSI) procedure and cfDNA concentration was quantified by ALU-quantitative PCR. We found that cfDNA level was significantly higher in FF samples from patients with ovarian reserve disorders (low functional ovarian reserve or polycystic ovary syndrome) than from patients with normal ovarian reserve (2.7 ± 2.7 ng/μl versus 1.7 ± 2.3 ng/μl, respectively, p = 0.03). Likewise, FF cfDNA levels were significant more elevated in women who received long ovarian stimulation (> 10 days) or high total dose of gonadotropins (≥ 3000 IU/l) than in women who received short stimulation duration (7–10 days) or total dose of gonadotropins < 3000 IU/l (2.4 ± 2.8 ng/μl versus 1.5 ± 1.9 ng/μl, p = 0.008; 2.2 ± 2.3 ng/μl versus 1.5 ± 2.1 ng/μl, p = 0.01, respectively). Finally, FF cfDNA level was an independent and significant predictive factor for pregnancy outcome (adjusted odds ratio = 0.69 [0.5; 0.96], p = 0.03). In multivariate analysis, the Receiving Operator Curve (ROC) analysis showed that the performance of FF cfDNA in predicting clinical pregnancy reached 0.73 [0.66–0.87] with 88% specificity and 60% sensitivity. CfDNA might constitute a promising biomarker of follicular micro-environment quality which could be used to predict IVF prognosis and to enhance female infertility management.     

Androgen metabolism in hirsute patients treated with cyproterone acetate

Cyproterone acetate (CPA) in association with percutaneously administered estradiol has been used for the treatment of 150 hirsute patients for periods ranging from 6 months to 3 years. A spectacular clinical improvement ensued. Plasma testosterone (T) and androstenedione (A) fell from 69.0 +/- 24 to 33.0 +/- 8 and 210 +/- 103 to 119 +/- 25 ng/dl (mean +/- SD) respectively after 3 months of treatment and remained low thereafter. In contrast, T glucuronide (TG) and 3 alpha-androstanediol (Adiol) remained high during the whole course of treatment: 37 +/- 9 and 115 +/- 43 micrograms/24 h respectively. In vitro T 5 alpha-reductase activity (5 alpha-R) in pubic skin decreased from 147 +/- 34 to 79 +/- 17 fmol/mg skin after 1 year of treatment. To elucidate the discrepancy between plasma and urinary androgens levels, T production rate (PR) and metabolic clearance rate (MCR) were measured with the constant infusion technique in 7 patients before and after 6 months of treatment. PR decreased from 988 +/- 205 to 380 +/- 140 micrograms/24 h (mean +/- SD). In contrast MCRT increased from 1275 +/- 200 to 1632 +/- 360 1/24 h; this increase in MCRT explains the striking plasma T concentration fall and the high TG and Adiol excretion relative to the decrease in PR. Antipyrine clearance rate (n = 8) increased from 36.3 +/- 5.2 to 51.5 +/- 7.4 ml/min whereas 6 beta hydroxycortisol remained unchanged. In conclusion, CPA acts through several mechanisms: (1) it lowers the androgen input to the target cells by (a) depressing T production through its antigonadotropic effect and (b) accelerating T metabolic inactivation due to a partial enzymatic inducer effect on the liver; (2) at the target cell level it competes with any remaining T for the receptor binding sites; (3) the decrease in the androgen-dependent skin 5 alpha-R is a consequence of both actions of androgen suppression and androgen receptor blockade; it reinforces the antiandrogenic effect of CPA.     

Changes in nuclear proteins induced by heat shock in Drosophila culture cells

Nuclear proteins of normal and heat-shocked Drosophila cells were analysed by two-dimensional electrophoresis. The computerized processing of the gels allowed us to detect 6 proteins strongly induced by the heat treatment, but which were different from the usually described heat-shock proteins. The possible role of these proteins in genetic regulation is discussed, as is the value of this type of approach for the study of other genetic regulation phenomena.     

Influence of rainfall seasonality on African lowland vegetation during the Late Quaternary: pollen evidence from Lake Masoko, Tanzania

Aim  To determine if changes in the key bioclimatic parameters associated with rainfall seasonality can be quantified from fossil sequences and to distinguish them from changes in the total annual rainfall.
Location  Lake Masoko, southern Tanzania (9°20' S, 33°45' E, 840 m a.s.l.).
Methods  Fossil pollen was extracted from a long and well-dated sedimentary sequence spanning the period 45,000–4400 cal. yr bp . The modern habitat, geographical distribution and climatic range (mean annual rainfall and temperature, and length of the dry season) of selected East African plants were used to infer past rainfall attributes for the most characteristic fossil pollen taxa identified from the sediments of Lake Masoko.
Results  In the Masoko pollen sequence it has been possible to identify changes in the length/severity of the dry season during the last 45,000 cal. yr bp , which are interpreted to reflect shifts in the mean position of the Intertropical Convergence Zone (ITCZ) over the southern tropics. We suggest that this bioclimatic parameter has been the main driver of the vegetation dynamics in this area. The major inferred change occurred at the Younger Dryas–Holocene transition c . 11,800 cal. yr bp , when semi-deciduous forest disappeared, being replaced in the lake catchment by woodland, which persists to the present day in spite of locally high rainfall.
Main conclusions  In tropical regions under the influence of the ITCZ, the position and strength of which determine the distribution of rainfall through the year, more attention must be paid to the impact of the length and intensity of the dry season on the modern and past distribution and dynamics of the vegetation. This climatic parameter is as important as the total annual amount of rainfall, and probably one of the most relevant in lowland areas.