Predicting cancer involvement of genes from heterogeneous data

Background  

Systematic approaches for identifying proteins involved in different types of cancer are needed. Experimental techniques such as microarrays are being used to characterize cancer, but validating their results can be a laborious task. Computational approaches are used to prioritize between genes putatively involved in cancer, usually based on further analyzing experimental data.     

Revised subunit order of mammalian septin complexes explains their in vitro polymerization properties

Septins are conserved GTP-binding cytoskeletal proteins that polymerize into filaments by end-to-end joining of hetero-oligomeric complexes. In human cells, both hexamers and octamers exist, and crystallography studies predicted the order of the hexamers to be SEPT7-SEPT6-SEPT2-SEPT2-SEPT6-SEPT7, while octamers are thought to have the same core, but with SEPT9 at the ends. However, based on this septin organization, octamers and hexamers would not be expected to copolymerize due to incompatible ends. Here we isolated hexamers and octamers of specific composition from human cells and show that hexamers and octamers polymerize individually and, surprisingly, with each other. Binding of the Borg homology domain 3 (BD3) domain of Borg3 results in distinctive clustering of each filament type. Moreover, we show that the organization of hexameric and octameric complexes is inverted compared with its original prediction. This revised septin organization is congruent with the organization and behavior of yeast septins suggesting that their properties are more conserved than was previously thought.     

A new chromone from the stems of Cneorum tricoccum

From the stems of Cneorum tricoccum L. 3,3-dimethylallylspatheliachromene, spatheliabischromene and alloptaeroxylin methyl ether have been isolated as well as the new natural product ptaerochromenol methyl ether, which was chemically interconverted to isoheteropeucenin methyl ether.     

Does biofilm origin matter? Biofilm responses to non-flow period in permanent and temporary streams

1. In some regions, climate change is increasing the variability of rainfall and the frequency of extreme events such as drought. Consequently, non-flow periods have grown in length and frequency, both in temporary and in formerly permanent streams. Water abstraction for human use may further prolong these dry periods.
2. We analysed the resistance and resilience of biofilms from permanent and temporary streams to non-flow conditions. This was achieved by exposing cobbles (collected from permanent and temporary streams) with intact biofilm to 31 days of non-flow, followed by 20 days of stream flow in artificial stream channels. Biofilm resistance and resilience were assessed at a structural (algal biomass, pigment composition, and algae and cyanobacteria composition) and functional level (photosynthetic efficiency and community metabolism).
3. Algal taxa in biofilms from permanent and temporary streams differed throughout the experiment. Biofilms from permanent streams were less resistant to non-flow than those from temporary streams at structural level. Permanent stream biofilms also presented lower resilience at a structural level, but responded similarly to temporary stream biofilms at a functional level.
4. Our investigation shows how the non-flow period disturbed permanent stream biofilms, and suggests that temporary stream biofilms will have greater adaptive capacity as hydroperiod becomes shorter due to climate change.

     

Limit cycle oscillations of the human eye

The altered feedback technique is very suited to display nonlinearities of the human smooth pursuit system. In fact, when the gain of the retinal feedback path is raised, for the horizontal channel, above its normal unitary negative value, a threshold is met beyond which sustained horizontal self-excited smooth oscillations of the eye can be observed, which point out the existence of a stable limit cycle. Furthermore, the characterizing features of both the transient and steady state show a well defined dependence on the total feedback factor K. In particular, the analytical dependence on K of the amplitude and frequency of limit cycle oscillations can be derived. Implications of the experiment with respect to the mathematical modelling of the system are discussed.     

Variation in the free amino acid content of ovary, hepatopancreas and hemolymph of Penaeus schmitti during ovarian maturation (Crustacea, Decapoda, Penaeidae)

Quantitative and qualitative variations of free-amino-acids contents (FAA) of ovaries, hepatopancreas and haemolymph have been studied in the course of ovarian maturation in Penaeus schmitti. In the ovary, FAA content, expressed as microM/g ovary fresh weight, decreases from 56.2 to 23.6 microM between gonadosomatic index (GSI) 0.8 and GSI 7.1. There is an increase of hepatopancreas FAA content of 33.4% till GSI 4. Haemolymph FAA content increases from 0.32 to 1.76 microM/ml, with maximal values of 3.74 microM/ml when GSI are between 3 and 4. FAA content of ovaries, expressed as microM/g of animal, is 3.2 fold higher at the end of maturation, with a main increase in the first stages of ovogenesis. Maturation process has a quantitative effect on all FAA, but, on a qualitative point of view, it concerns mainly lysine, arginine and glycine. The main variations of AA composition (expressed as percentage of total FAA) are observed in haemolymph.     

On the origin and domestication of Olea europaea L. (olive) in Andalucía, Spain, based on the biogeographical distribution of its finds

The remains of Olea europaea in archaeological contexts in the southern Iberian Peninsula have been found in the Epipalaeolithic levels of Cueva de Nerja (10860±160 b.p.). The abundant appearance of charcoal and some seed remains from the Copper Age (3rd millennium b.c.) in the coastal zones of the southeast indicate that this species formed part of the vegetation of the Thermo-mediterranean zone and that its fruits were collected during these periods. However, Olea did not appear in the Meso-mediterranean zone until the Roman period, when olive cultivation was introduced there. The presence of charcoal and olive stones from the 1st century a.d. onwards is abundant, together with remains of structures for oil pressing.     

Image-converter pattern tracker for variable retinal feedback experiments

An optoelectronic device able to change the gain of the retinal feedback path from its natural value (?1) to any other value in the range ?5, +5 is presented. The employement of an image-converter tube with coupled magnetic deflection circuit allows a large variety of targets to be used. Any type of artificial movements, moreover, can be imposed to the target itself. The device can be driven by any eye movement detector able to transduce the horizontal and vertical components of the eye rotation in the form of electrical signals. Experiments were performed to investigate the effects of varying the gain of the retinal feedback loop on the eye behaviour. Evidence was found for the existence of a range of values of such gain where the eye goes into spontaneous smooth sinusoidal-like oscillations. This phenomenon was examined with the control theory methods in terms of stability of the pursuit system. A correlation between the spontaneous oscillations and the well known learning capability of the visual system was found.