The oligomeric architecture of the archaeal exosome is important for processive and efficient RNA degradation

The exosome plays an important role in RNA degradation and processing. In archaea, three Rrp41:Rrp42 heterodimers assemble into a barrel like structure that contains a narrow RNA entrance pore and a lumen that contains three active sites. Here, we demonstrate that this quaternary structure of the exosome is important for efficient RNA degradation. We find that the entrance pore of the barrel is required for nM substrate affinity. This strong interaction is crucial for processive substrate degradation and prevents premature release of the RNA from the enzyme. Using methyl TROSY NMR techniques, we establish that the 3′ end of the substrate remains highly flexible inside the lumen. As a result, the RNA jumps between the three active sites that all equally participate in substrate degradation. The RNA jumping rate is, however, much faster than the cleavage rate, indicating that not all active site:substrate encounters result in catalysis. Enzymatic turnover therefore benefits from the confinement of the active sites and substrate in the lumen, which ensures that the RNA is at all times bound to one of the active sites. The evolution of the exosome into a hexameric complex and the optimization of its catalytic efficiency were thus likely co-occurring events.     

Crude bacterial extracts of two new Streptomyces sp. isolates as bio-colorants for textile dyeing

Renewed demand for incorporation of natural dyes (bio-colorants) in textile industry could be met through biotechnological production of bacterial pigments. Two new Streptomyces strains (NP2 and NP4) were isolated for the remarkable ability to produce diffusible deep blue and deep red pigment into fermentation medium. Crude mycelial extracts of both strains were used as bio-colorants in conventional textile dyeing procedures avoiding downstream purification procedures. The yields of bio-colorants obtained in this way were 62 and 84 mg per g of mycelia for Streptomyces sp. NP2 and Streptomyces sp. NP4, respectively. Through nuclear magnetic resonance analysis of crude extracts before and after dyeing procedures, it was shown that both extracts contained prodigiosin-like family of compounds that exhibited different dyeing capabilities towards different textile fibers. Polyamide and acrylic fibers were colored to the deepest shade, polyester and triacetate fibers to a noticeable, but much lower shade depth, while cotton and cellulosic fibers stained weakly. These results confirmed that crude bacterial extracts had the characteristics similar to those of ionic and disperse dyes, which was consistent with the identified polypyrrolic prodigiosin-like structures.     

Inhibition of glycolytic enzymes by endogenous aldehydes: a possible relation to diabetic neuropathies

Endogenous saturated and unsaturated aldehydes were found in significant elevations in serum of diabetic humans and rats. These compounds, originating from the lipid peroxidation processes, are shown here to be potent inhibitors of the glycolytic enzymes, phosphofructokinase and glyceraldehyde-3-phosphate dehydrogenase. The inhibition process is non-competitive and progressive. The aldehyde mixture, when supplemented to the standard rat diet at $\text{1}\text{100}$ ratio, caused nerve damage that is reminiscent of diabetic polyneuropathies.     

Effects of arm and leg loading on sprint performance

The effects of loading on sprint kinematics were examined in 24 male students. The moment of inertia of either the arms or legs was increased by up to 50% of their unloaded values and the time for distances of 0.5–15 m and 15–30 m from a sprint start was measured. An increase in leg loading was associated with a gradual decrease in velocity of both sprint phases, while the change associated with arm loading was modest and significant only in the second phase. The decrease in sprint velocity was predominantly due to a reduction in stride rate, while the stride length remained almost unchanged. It was concluded that leg loading affected sprint velocity more than arm loading, and also that the velocity was reduced due to a decrease in the stride rate rather than in the stride length. Accepted: 10 November 1997     

The presence of prtP proteinase gene in natural isolate Lactobacillus plantarum BGSJ3–18

Aims:  The study of proteolytic activity and examination of proteinase gene region organization in proteolytically active Lactobacillus plantarum strains from different natural sources.
Methods and Results:  A set of 37 lactobacilli was distinguished by using multiplex PCR assay. Results showed that 34 strains were Lact. plantarum and three of them were Lact. paraplantarum . The examination of proteolytic activity revealed that 28 Lact.   plantarum and two Lact.   paraplantarum hydrolyse β-casein. Further analyses of all proteolytically active Lact. plantarum with primers specific for different types of CEPs demonstrated that strain BGSJ3–18 has prtP catalytic domain as well as prtP – prtM intergenic region showing more than 95% sequence identity with the same regions present in Lact. paracasei , Lact. casei and L. lactis . No presence of prtB , prtH or prtR proteinase genes was detected in any of tested Lact. plantarum strains.
Conclusions:  One out of 28 analysed Lact. plantarum strains harbours the prtP -like gene. The other proteolytically active Lact. plantarum probably possesses a different type of extracellular proteinase(s).
Significance and Impact of the Study:  It is the first report about the presence of the prtP –like gene in Lact. plantarum , which illustrates the mobility of this gene and its presence in different species.     

Efficient Peak-Labeling Algorithms for Whole-Sample Mass Spectrometry Proteomics

Whole-sample mass spectrometry (MS) proteomics allows for a parallel measurement of hundreds of proteins present in a variety of biospecimens. Unfortunately, the association between MS signals and these proteins is not straightforward. The need to interpret mass spectra demands the development of methods for accurate labeling of ion species in such profiles. To aid this process, we have developed a new peak-labeling procedure for associating protein and peptide labels with peaks. This computational method builds upon characteristics of proteins expected to be in the sample, such as the amino sequence, mass weight, and expected concentration within the sample. A new probabilistic score that incorporates this information is proposed. We evaluate and demonstrate our method's ability to label peaks first on simulated MS spectra and then on MS spectra from human serum with a spiked-in calibration mixture.     

Assessment of cortical bone fracture resistance curves by fusing artificial neural networks and linear regression

Bone injures (BI) represents one of the major health problems, together with cancer and cardiovascular diseases. Assessment of the risks associated with BI is nontrivial since fragility of human cortical bone is varying with age. Due to restrictions for performing experiments on humans, only a limited number of fracture resistance curves (R-curves) for particular ages have been reported in the literature. This study proposes a novel decision support system for the assessment of bone fracture resistance by fusing various artificial intelligence algorithms. The aim was to estimate the R-curve slope, toughness threshold and stress intensity factor using the two input parameters commonly available during a routine clinical examination: patients age and crack length. Using the data from the literature, the evolutionary assembled Artificial Neural Network was developed and used for the derivation of Linear regression (LR) models of R-curves for arbitrary age. Finally, by using the patient (age)-specific LR models and diagnosed crack size one could estimate the risk of bone fracture under given physiological conditions. Compared to the literature, we demonstrated improved performances for estimating nonlinear changes of R-curve slope (R² = 0.82 vs. R² = 0.76) and Toughness threshold with ageing (R² = 0.73 vs. R² = 0.66).     

Dynamics of pigment pattern formation in the zebrafish, Brachydanio rerio. III. Effect of anteroposterior location of three-day lateral line melanophores on colonization by the second wave of melanophores

The mode of colonization of the lateral line melanophore band of the zebrafish, Brachydanio rerio, by the second wave of melanophores has been investigated. This stripe forms in two consecutive stages. First, there is an initial migration and reorientation of pigment cells in an anteroposterior wave into the site to form an interrupted stripe. Following this, a round of melanophores differentiates directly at the site and fills in the gaps between the initial cells. An analysis of the distributions of initial and second wave melanophores along the stripe site has shown that both groups of cells are selective as to localization. Initial wave melanophores colonize more anterior somite areas than do second wave melanophores. However, both groups of cells exhibit preferential colonization of the same anterior sites. It is suggested that second wave melanophores attempt to colonize the same somite areas of the stripe as the initial wave of melanophores but are forced to move to more posterior locations due to the presence of initial wave melanophores anteriorly. Observations were also made on later stages of development of the lateral line melanophore band. These melanophores retain the ability to migrate. Some of them reorient out onto the flank and contribute to the juvenile flank pigment pattern.