Comparative analysis of algorithms for signal quantitation from oligonucleotide microarrays

MOTIVATION: Recent years' exponential increase in DNA microarrays experiments has motivated the development of many signal quantitation (SQ) algorithms. These algorithms perform various transformations on the actual measurements aimed to enable researchers to compare readings of different genes quantitatively within one experiment and across separate experiments. However, it is relatively unclear whether there is a 'best' algorithm to quantitate microarray data. The ability to compare and assess such algorithms is crucial for any downstream analysis. In this work, we suggest a methodology for comparing different signal quantitation algorithms for gene expression data. Our aim is to enable researchers to compare the effect of different SQ algorithms on the specific dataset they are dealing with. We combine two kinds of tests to assess the effect of an SQ algorithm in terms of signal to noise ratio. To assess noise, we exploit redundancy within the experimental dataset to test the variability of a given SQ algorithm output. For the effect of the SQ on the signal we evaluate the overabundance of differentially expressed genes using various statistical significance tests. RESULTS: We demonstrate our analysis approach with three SQ algorithms for oligonucleotide microarrays. We compare the results of using the dChip software and the RMAExpress software to the ones obtained by using the standard Affymetrix MAS5 on a dataset containing pairs of repeated hybridizations. Our analysis suggests that dChip is more robust and stable than the MAS5 tools for about 60% of the genes while RMAExpress is able to achieve an even greater improvement in terms of signal to noise, for more than 95% of the genes.     

Oxytocin during pregnancy and early postpartum: individual patterns and maternal-fetal attachment

Oxytocin (OT), a nanopeptide hormone, plays a role in the emergence of maternal behavior, yet few studies examined OT in humans across pregnancy and the postpartum. We followed healthy women at three points: first trimester of pregnancy, third trimester, and first postpartum month. Plasma OT levels showed high individual stability. A third of the sample showed consistent OT levels, whereas others showed increasing or decreasing trends or peak in late pregnancy. The increase in OT from early to late pregnancy correlated with higher maternal-fetal bonding. These data may help set standards for OT levels and underscore links with maternal-infant attachment.     

Global effects of non‐native tree species on multiple ecosystem services

Non‐native tree (NNT) species have been transported worldwide to create or enhance services that are fundamental for human well‐being, such as timber provision, erosion control or ornamental value; yet NNTs can also produce undesired effects, such as fire proneness or pollen allergenicity. Despite the variety of effects that NNTs have on multiple ecosystem services, a global quantitative assessment of their costs and benefits is still lacking. Such information is critical for decision‐making, management and sustainable exploitation of NNTs. We present here a global assessment of NNT effects on the three main categories of ecosystem services, including regulating (RES), provisioning (PES) and cultural services (CES), and on an ecosystem disservice (EDS), i.e. pollen allergenicity. By searching the scientific literature, country forestry reports, and social media, we compiled a global data set of 1683 case studies from over 125 NNT species, covering 44 countries, all continents but Antarctica, and seven biomes. Using different meta‐analysis techniques, we found that, while NNTs increase most RES (e.g. climate regulation, soil erosion control, fertility and formation), they decrease PES (e.g. NNTs contribute less than native trees to global timber provision). Also, they have different effects on CES (e.g. increase aesthetic values but decrease scientific interest), and no effect on the EDS considered. NNT effects on each ecosystem (dis)service showed a strong context dependency, varying across NNT types, biomes and socio‐economic conditions. For instance, some RES are increased more by NNTs able to fix atmospheric nitrogen, and when the ecosystem is located in low‐latitude biomes; some CES are increased more by NNTs in less‐wealthy countries or in countries with higher gross domestic products. The effects of NNTs on several ecosystem (dis)services exhibited some synergies (e.g. among soil fertility, soil formation and climate regulation or between aesthetic values and pollen allergenicity), but also trade‐offs (e.g. between fire regulation and soil erosion control). Our analyses provide a quantitative understanding of the complex synergies, trade‐offs and context dependencies involved for the effects of NNTs that is essential for attaining a sustained provision of ecosystem services.     

Diabetes modulates differentially creatine kinase-specific activity responsiveness to estradiol-17beta and to raloxifene in rat organs

Diabetes mellitus increases the risk for CVD in women. While there is considerable evidence suggesting beneficial effects of estrogen on decreasing lipid peroxidation, atherosclerotic processes, and cardiovascular diseases, diabetes negates most estrogen protective effects as well as the skeletal protective effects of estrogens, which are not discernable in diabetic women. In the present study, we examined the in vivo effects of estradiol-17beta (E2), on creatine kinase (CK)-specific activity, in estrogen-responsive organs from healthy and diabetic rats. Healthy or diabetic (streptozotocin-induced) female rats were injected with either E2 (10-50 microg/rat) or raloxifene (Ral; 500-1,000 microg/rat). Twenty-four hours following the injection, animals were sacrificed; their organs removed and assayed for CK-specific activity. CK-specific activity in different organs [Left ventricle of heart (Lv), uterus (Ut), aorta (Ao), para uterine adipose tissue (Ad), epiphyseal cartilage (Ep), and diaphyseal bone (Di)] from healthy animals, was stimulated with increased doses of E2, with maximum at 20 microg/rat. Age-matched diabetic female rats exhibited a remarkable decreased response to E2 in all organs except Ut. In contrast, the response to Ral was not altered in diabetic rats. Similar results were observed in organs from ovariectomized female rats (Ovx), healthy or diabetic. These results support our previous in vitro findings, demonstrating that hyperglycemia decreases CK response to E2 but not to Ral in cultured human vascular and bone cells. In summary, diabetes mellitus decreases CK response to E2 but not that of Ral in skeletal and vascular tissues. The decreased response to E2 detected in organs derived from diabetic rats might be due to changes in nuclear and/or membrane estrogen receptors and/or other genomic and non-genomic pathways, as was shown in in vitro cellular models.     

Static mechanical stretching accelerates lipid production in 3T3-L1 adipocytes by activating the MEK signaling pathway

Understanding mechanotransduction in adipocytes is important for research of obesity and related diseases. We cultured 3T3-L1 preadipocytes on elastic substrata and applied static tensile strains of 12% to the substrata while inducing differentiation. Using an image processing method, we monitored lipid production for a period of 3-4 wk. The ratio of %-lipid area per field of view (FOV) in the stretched over nonstretched cultures was significantly greater than unity (P < 0.05), reaching ～1.8 on average starting from experimental day ～10. The superior coverage of the FOV by lipids in the stretched cultures was due to significantly greater sizes of lipid droplets (LDs) with respect to nonstretched cultures, starting from experimental day ～10 (P < 0.05), and due to significantly more LDs per cell between days ～10 and ～17 (P < 0.05). The statically stretched cells also differentiated significantly faster than the nonstretched cells within the first ～10 days (P < 0.05). Adding peroxisome proliferator-activated receptor-γ (PPARγ) antagonist did not change these trends, as the %-lipid area per FOV in the stretched cultures that received this treatment was still significantly greater than in the nonstretched cultures without the PPARγ antagonist (14.44 ± 1.96% vs. 10.21 ± 3%; P < 0.05). Hence, the accelerated adipogenesis in the stretched cultures was not mediated through PPARγ. Nonetheless, inhibiting the MEK/MAPK signaling pathway reduced the extent of adipogenesis in the stretched cultures (13.53 ± 5.63%), bringing it to the baseline level of the nonstretched cultures without the MEK inhibitor (10.21 ± 3.07%). Our results hence demonstrate that differentiation of adipocytes can be enhanced by sustained stretching, which activates the MEK signaling pathway.     

A role for the FEAR pathway in nuclear positioning during anaphase

In budding yeast, cells lacking separase function exit mitosis with an undivided nucleus localized to the daughter cell. Here we show that the inability to separate sister chromatids per se is not sufficient to cause the daughter preference. Rather, separase affects nuclear positioning as part of the Cdc14 early anaphase release (FEAR) pathway. The role of the FEAR pathway in nuclear positioning is exerted during anaphase and is not shared by the mitotic exit network. We find that the nuclear segregation defect in FEAR mutants does not stem from nonfunctional spindle poles or the absence of cytoplasmic microtubules. Instead, the concomitant inactivation of sister chromatid separation and the FEAR pathway uncovered a mother-directed force in anaphase that was previously masked by the elongating spindle. We propose that at anaphase onset, the FEAR pathway activates cytoplasmic microtubule-associated forces that facilitate chromosome segregation to the mother cell.