An improved procedure for gene selection from microarray experiments using false discovery rate criterion

Background  

A large number of genes usually show differential expressions in a microarray experiment with two types of tissues, and the p-values of a proper statistical test are often used to quantify the significance of these differences. The genes with small p-values are then picked as the genes responsible for the differences in the tissue RNA expressions. One key question is what should be the threshold to consider the p-values small. There is always a trade off between this threshold and the rate of false claims. Recent statistical literature shows that the false discovery rate (FDR) criterion is a powerful and reasonable criterion to pick those genes with differential expression. Moreover, the power of detection can be increased by knowing the number of non-differential expression genes. While this number is unknown in practice, there are methods to estimate it from data. The purpose of this paper is to present a new method of estimating this number and use it for the FDR procedure construction.     

Antiproliferative effect of growth hormone-releasing hormone (GHRH) antagonist on ovarian cancer cells through the EGFR-Akt pathway

Background  

Antagonists of growth hormone-releasing hormone (GHRH) are being developed for the treatment of various human cancers.     

Activin-A up-regulates type I activin receptor mRNA levels in human immortalized extravillous trophoblast cells.

Activin is known to play an important regulatory role in reproduction, including pregnancy. To further examine the role and signaling mechanism of activin in regulating placental function, the steady-state level of activin type I receptor (ActRI) mRNA in immortalized extravillous trophoblasts (IEVT) cells was measured using competitive PCR (cPCR). An internal standard of ActRI cDNA for cPCR was constructed for the quantification of ActRI mRNA levels in IEVT cells. ActRI mRNA levels were increased in a dose-dependent manner by activin-A with the maximal effect observed at the dose of 10 ng/ml. Time course studies revealed that activin-A had maximal effects on ActRI mRNA levels at 6 hours after treatment. The effects of activin-A on ActRI mRNA levels was blocked by follistatin, an activin binding protein, in a dose-dependent manner. In addition, inhibin-A inhibited basal, as well as activin-A-induced ActRI mRNA levels. These findings provide evidence, for the first time, that activin-A modulates ActRI mRNA levels in human trophoblast cells.     

A flavonoid mutant of barley (Hordeum vulgare L.) exhibits increased sensitivity to UV-B radiation in the primary leaf

The aim of the present investigation was to define the role of soluble flavonoids as UV-B protectants in the primary leaf of barley (Hordeum vulgare L.). For this purpose we used a mutant line (Ant 287) from the Carlsberg collection of proanthocyanidin-free barley containing only 7% of total extractable flavonoids in the primary leaf as compared to the mother variety (Hiege 550/75). Seven-day-old leaves from plants grown under high visible light with or without supplementary UV-B radiation were used for the determination of UV-B sensitivity. UV-B-induced changes were assessed from parameters of chlorophyll fluorescence of photosystem II, including initial and maximum fluorescence, apparent quantum yield, and photochemical and non-photochemical quenching. A quartz fibre-optic microprobe was used to evaluate the amount of potentially harmful UV-B (310 nm radiation) penetrating into the leaf as a direct consequence of flavonoid deficiency. Our data indicate an essential role of flavonoids in UV-B protection of barley primary leaves. In leaves of the mutant line grown under supplementary UV-B, an increase in 310nm radiation in the mesophyll and a strong decrease in the quantum yield of photosynthesis were observed as compared to the corresponding mother variety. Primary leaves of liege responded to supplementary UV-B radiation with a 30% increase in the major flavonoid saponarin and a 500% increase in the minor compound lutonarin. This is assumed to be an efficient protective response since no changes in variable chlorophyll fluorescence were apparent. In addition, a further reduction in UV-B penetration into the mesophyll was recorded in these leaves.     

Effects of elevated ozone on CO2 uptake and leaf structure in sugar maple under two light environments

The interactive effects of ozone and light on leaf structure, carbon dioxide uptake and short-term carbon allocation of sugar maple ( Acer saccharum Marsh.) seedlings were examined using gas exchange measurements and ¹⁴C-macroautoradiographic techniques. Two-year-old sugar maple seedlings were fumigated from budbreak for 5 months with ambient or 3 × ambient ozone in open-top chambers, receiving either 35% (high light) or 15% (low light) of full sunlight. Ozone accelerated leaf senescence, and reduced net photosynthesis, ¹⁴CO₂ uptake and stomatal conductance, with the effects being most pronounced under low light. The proportion of intercellular space increased in leaves of seedlings grown under elevated ozone and low light, possibly enhancing the susceptibility of mesophyll cells to ozone by increasing the cumulative dose per mesophyll cell. Indeed, damage to spongy mesophyll cells in the elevated ozone × low light treatment was especially frequent. ¹⁴C macroautoradioraphy revealed heterogeneous uptake of ¹⁴CO₂ in well defined areole regions, suggesting patchy stomatal behaviour in all treatments. However, in seedlings grown under elevated ozone and low light, the highest ¹⁴CO₂ uptake occurred along larger veins, while interveinal regions exhibited little or no uptake. Although visible symptoms of ozone injury were not apparent in these seedlings, the cellular damage, reduced photosynthetic rates and reduced whole-leaf chlorophyll levels corroborate the visual scaling of whole-plant senescence, suggesting that the ozone × low light treatment accelerated senescence or senescence-like injury in sugar maple.     

Assessment of the phytochemical constituents and antioxidant activity of a bloom forming microalgae Euglena tuba

Background

Unstable generation of free radicals in the body are responsible for many degenerative diseases. A bloom forming algae Euglena tuba growing abundantly in the aquatic habitats of Cachar district in the state of Assam in North-East India was analysed for its phytochemical contents, antioxidant activity as well as free radical scavenging potentials.

Results

Based on the ability of the extract in ABTS^•+ radical cation inhibition and Fe³⁺ reducing power, the obtained results revealed the prominent antioxidant activity of the algae, with high correlation coefficient of its TEAC values to the respective phenolic and flavonoid contents. The extract had shown its scavenging activity for different free radicals and 41.89 ± 0.41 μg/ml, 5.83 ± 0.07 μg/ml, 278.46 ± 15.02 μg/ml and 223.25 ± 4.19 μg/ml were determined as the IC₅₀ values for hydroxyl, superoxide, nitric oxide and hypochlorous acid respectively, which are lower than that of the corresponding reference standards. The phytochemical analysis also revealed that the phenolics, flavonoids, alkaloids, tannins and carbohydrates are present in adequate amount in the extract which was confirmed by HPLC analysis.

Conclusions

The results showed that 70% methanol extract of the algae possesses excellent antioxidant and free radical scavenging properties.     

Disproportional risk for habitat loss of high‐altitude endemic species under climate change

The expected upward shift of trees due to climate warming is supposed to be a major threat to range‐restricted high‐altitude species by shrinking the area of their suitable habitats. Our projections show that areas of endemism of five taxonomic groups (vascular plants, snails, spiders, butterflies, and beetles) in the Austrian Alps will, on average, experience a 77% habitat loss even under the weakest climate change scenario (+1.8 °C by 2100). The amount of habitat loss is positively related with the pooled endemic species richness (species from all five taxonomic groups) and with the richness of endemic vascular plants, snails, and beetles. Owing to limited postglacial migration, hotspots of high‐altitude endemics are situated in rather low peripheral mountain chains of the Alps, which have not been glaciated during the Pleistocene. There, tree line expansion disproportionally reduces habitats of high‐altitude species. Such legacies of climate history, which may aggravate extinction risks under future climate change have to be expected for many temperate mountain ranges.