Codon use and the rate of divergence of land plant chloroplast genes

Codon fitnesses for chloroplast genes were estimated using the relative synonymous codon use of psbA, which has a different pattern of codon use than other chloroplast genes and is the major translation product of the chloroplast. These estimates were used to calculate the codon adaptation index (CAI) of chloroplast genes from Marchantia polymorpha, Nicotiana tabacum, and Chlamydomonas reinhardtii. The genes with the highest CAI values in M. polymorpha correspond to those that are expressed at the highest levels. The rate of divergence between M. polymorpha and both C. reinhardtii and N. tabacum is inversely related to the CAI value of the M. polymorpha gene. The data suggest that selection is acting on the synonymous codon use of the highly expressed genes of the M. polymorpha chloroplast genome. The data set is inconclusive about N. tabacum genes, but, as there is a weaker correspondence between CAI value and expression level, it suggests that selection is not operating in this lineage.      

Phenolic extractives in Salix caprea wood and knots

Salix caprea stemwood and knots were found to contain the phenolic extractives vanillic acid, 3-p-coumaryl alcohol, coniferyl alcohol, sinapylaldehyde, dihydrokaempferol, catechin, naringenin, gallocatechin, dihydromyrcetin and taxifolin. The knots contained larger quantities of flavonoids than did stemwood of the same tree.     

Purification and characterization of maltooligosaccharide-forming amylase from Bacillus circulans GRS 313

A maltooligosaccharide-forming amylase that hydrolyzes starch into maltotriose and maltopentaose was found in the culture filtrate of a strain of Bacillus circulans GRS 313 isolated from local soil. The enzyme was purified by organic solvent fractionation, Sephadex G-100 gel filtration and CM-Sephadex column chromatography. Optimum pH and temperature of amylase were evaluated using response surface methodology (RSM) and were found to be 48°C and 4.9, respectively. The enzyme was stable up to 60°C and its pH stability was in the range of 5.0–8.0. The K _m and V _max of the amylase with starch were 11.66 mg/ml and 68.97 U, respectively, and the energy of activation, E _a, was 7.52 kcal/mol. Dextrin inhibited the enzyme competitively, with a K _i of 6.1 mg/ml, and glucose caused noncompetitive inhibition with a K _i of 9.5 mg/ml. The enzyme was inhibited by Hg²⁺, Mn²⁺, Fe³⁺ and Cu²⁺ and enhanced by Co²⁺ and Mg²⁺. EDTA reversed the inhibitory effect of the metals. Paper chromatographic and high-performance liquid chromatography analysis of the products of the amylolytic reaction showed the presence of maltotriose, maltotetraose, maltopentaose, maltose and glucose in the starch hydrolysate. Journal of Industrial Microbiology & Biotechnology (2002) 28, 193–200 DOI: 10.1038/sj/jim/7000220 Received 11 December 2000/ Accepted in revised form 22 October 2001     

Antibacterial effects of knotwood extractives on paper mill bacteria

Hydrophilic knotwood extracts from 18 wood species were assessed in disc diffusion and liquid culture tests for antibacterial effects against three species of paper mill bacteria. The Pinus sylvestris, P. resinosa, P. contorta, and P. banksiana extracts decreased or inhibited bacterial growth. The susceptibility order was P. sylvestris > P. resinosa > P. contorta > P. banksiana, correlating with the concentrations of pinosylvin and pinosylvin monomethyl ether in these wood species. Also, Pseudotsuga menziesii and Thuja occidentalis extracts had a small inhibitory effect. The Gram-positive Bacillus coagulans was more susceptible to the extracts than the Gram-negative Burkholderia multivorans and Alcaligenes xylosoxydans. The main components in the Pinus knotwood extracts were pinosylvin monomethyl ether and pinosylvin, suggesting these to be the active components. Therefore, pure pinosylvin, pinosylvin monomethyl ether, and dihydro-pinosylvin monomethyl ether were also tested. All compounds showed antibacterial effects. However, higher concentrations were needed for these pure compounds than for the knotwood extracts. Pinosylvin had stronger antibacterial effects than pinosylvin monomethyl ether. This work shows that knotwood extracts, especially from Pinus species, have a potential for use as natural biocides in papermaking.     

Diet of bluegill Lepomis macrochirus in a South African reservoir during winter and summer

Alien fishes are considered a major threat to aquatic biodiversity in South Africa, yet relatively little regional information on their biology and ecology is available for many of these species. Seasonal changes in the diet of the bluegill Lepomis macrochirus in Howieson’s Poort Dam, Grahamstown, were assessed during summer and winter in 2014–2015, using stomach content analysis. In winter, juvenile and adult fish diets were dominated by crustacean zooplankton and insects, respectively. In summer, juvenile fish fed on crustaceans and insects, whereas adults consumed mostly fish eggs, indicating a potential impact by these invasive fish on native fish through oophagy.     

Myomesin and M protein: Differential expression in embryonic fibers during pectoral muscle development

By applying immunocytochemistry using monoclonal antibodies, we found that the myofibrillar M band of both presumptive type-I and -II fibers in the pectoralis major muscle of chickens contains two high-molecular-weight proteins, i.e., myomesin (Mr, 185,000) and M protein (Mr, 165,000), early in embryonic development (7 days in ovo), even though adult type-I fibers lack M protein. The developmental expression of M protein is unusual in that, from 10 to 14 days in ovo, it is gradually suppressed not only in presumptive type-I fibers but also in presumptive type-II fibers formed from primary-generation myotubes. This latter suppression is transient, as M protein is expressed in all adult type-II fibers derived from both the primary- and second-generation myotubes. Myomesin, on the other hand, is continuously expressed in all myotubes throughout development. This finding shows that myomesin and M protein expression is regulated independently in different myotube populations, and that the suppression of M protein in primary-generation myotubes accounts for the delayed accumulation of M protein during development, as previously revealed by biochemical analysis. Presumptive type-I fibers, which form in the deep portion of the muscle, become concentrated in a narrow band known as the red strip.     

Familial frontotemporal dementia with neuronal intranuclear inclusions is not a polyglutamine expansion disease

Background  

Many cases of frontotemporal dementia (FTD) are familial, often with an autosomal dominant pattern of inheritance. Some are due to a mutation in the tau- encoding gene, on chromosome 17, and show an accumulation of abnormal tau in brain tissue (FTDP-17T). Most of the remaining familial cases do not exhibit tau pathology, but display neuropathology similar to patients with dementia and motor neuron disease, characterized by the presence of ubiquitin-immunoreactive (ub-ir), dystrophic neurites and neuronal cytoplasmic inclusions in the neocortex and hippocampus (FTLD-U). Recently, we described a subset of patients with familial FTD with autopsy-proven FTLD-U pathology and with the additional finding of ub-ir neuronal intranuclear inclusions (NII). NII are a characteristic feature of several other neurodegenerative conditions for which the genetic basis is abnormal expansion of a polyglutamine-encoding trinucleotide repeat region. The genetic basis of familial FTLD-U is currently not known, however the presence of NII suggests that a subset of cases may represent a polyglutamine expansion disease.     

Sugar composition of biofilms produced by paper mill bacteria

Biofilms of paper mill bacteria were cultivated in paper mill white water-simulating conditions on glass slides or stainless steel coupons in a laboratory culture system. The sugar content and composition of the biofilms were analysed and compared with the sugar composition of paper mill slimes. Acid methanolysis followed by gas chromatography revealed that Burkholderia was the major biofilm producer in pure culture, producing up to 50 microg of biofilm sugar cm(-2) in 5 days in rich medium and 10 microg in paper mill simulating medium. A mixture of simulated paper mill water with a culture medium yielded more biofilm (100 microg cm(-2)) than either of the media alone, so the biofilm accumulation was not proportional to the available substrate. More biofilm accumulated on stainless steel coupons than on glass slides, and the steel-coupon biofilms contained slightly more uronic acids. The biofilm sugars contained mainly galactose, glucose, mannose, and rhamnose. In paper mill medium, the Burkholderia biofilm contained more galactose and glucose, and less rhamnose, than in rich laboratory medium. The sugar composition of paper mill slimes was quite similar to those of steel-cultured Burkholderia cepacia biofilms. This suggests that Burkholderia cepacia is responsible for much of the slime in the paper mill.     

Enzyme and immunohistochemical assessment of myocardial damage after ischaemia and reperfusion in a closed-chest pig model.

The usefulness of different enzyme and immunohistochemical stains to distinguish reversible and irreversible myocardial cell injury after experimental coronary artery occlusion of varying duration and reperfusion with or without superoxide dismutase as adjunct was investigated. Biopsies or parts of the infarcted and non-infarcted area were rapidly frozen and sectioned in series for enzyme and immunohistochemical evaluation. Sections were stained for the demonstration of phosphorylase, myofibrillar ATPase and mitochondrial oxidative enzymes and also with periodic acid-Schiff, alizarin red S and routine histological stains. Other sections in series were stained with antibodies against fibronectin and the intermediate filament proteins desmin and vimentin. In 49 biopsies a blind quantitative estimation of the area stained for fibronectin, phosphorylase and alizarin red S was performed and evaluated statistically. Phosphorylase, periodic acid-Schiff, fibronectin and alizarin red S allowed delineation of affected myocardium after 30 min of ischaemia followed by reperfusion whereas with the other stains, affected myocardium was readily detectable only after 60 or 90 min of ischaemia followed by reperfusion as well as after 24 h of ischaemia without reperfusion. The immunostaining for fibronectin was very distinct and inversely related to the phosphorylase activity. We show that fibronectin is an excellent marker for damaged cells and that these positively stained myocytes are necrotic as confirmed ultrastructurally. Using alizarin red S as a marker of calcium accumulation in myocytes, a marked discrepancy was observed between the area of fibronectin-containing myocytes and that of myocytes stained by alizarin red S. Calcium accumulation in mitochondria is thus not a prerequisite for myocyte necrosis but does occur only in some of the irreversibly damaged cells. Of special interest is the finding that there was a significant reduction of intracellular calcium in pigs where superoxide dismutase had been used as an adjunct at reperfusion, thus supporting the theory that free radicals do play a role during reperfusion of ischaemic myocardium.