Direct electrochemical oxidation of Clostridium pasteurianum ferredoxin: Identification of facile electron-transfer processes relevant to cluster degradation

Rapid oxidation processes relevant to the degradation of [4Fe4S] clusters in Clostridium pasteurianum ferredoxin were studied via direct (unmediated) heterogeneous electron transfer at a pyrolytic graphite electrode. Differential-pulse voltammograms of native [4Fe4S] ferredoxin showed two well-defined oxidation peaks corresponding to apparent E-values of +793 and +1120 mV at 5°C. Direct involvement of the cluster was established through parallel experiments with the 2[4Fe4Se] derivative for which peak positions were shifted. Square-wave voltammetry showed that the product of the first electron transfer, which may correspond to the ‘super-oxidised’ [4Fe4S]³⁺ oxidation level, undergoes rapid degradation (t_{$\text{1}\text{2}$} < 1.6 ms at 5°C). The second oxidation process, as characterised by a significant (?100 mV) negative shift upon selenium substitution, very likely represents oxidation of S(Se) still associated with the protein and possibly contained within the remaining FES(Se) substructure.     

A method for subgrouping the S-type of CMS forms in maize

Summary Simple correlations were calculated between nine different cms sources (cms-S, -R, -ML, -L, -CA, -EK, -C, -Rb, -T) on the basis of the weighted restoring reactions of 41 inbred lines. The Principal Component Analysis was applied to a 9 × 9 matrix which clearly grouped cytoplasms according to their similarities. The Principal Component I included S, R, ML, L, CA and EK cytoplasms; the Principal Component II contained C and Rb cytoplasms while T-cytoplasms was placed in Principal Component III. This corresponds to the main groupings indicated in the literature (Beckett 1971). However, after varimax rotation of the Principal Components, the S main group, including the 6 tested cytoplasms, fell into 3 subgroups: I.: S, R, ML; II.: L, CA; III.: EK.These data indicate that the Principal Component Analysis can be used to select a limited number of cms sources from the S group, representing the variability of the cytoplasmic gene pool of that group.     

Un modèle d'ontogenèse: La croissancede Toxaster granosus kiliani (Lambert)), échinide spatangoide du Valanginien

A complete study of the ontogeny of the irregular urchin Toxaster granosus kiliani (Lambert)) was achieved from an important lower cretaceous sample. In a first time, ontogenic variations of each character were analysed versus length chosen as size reference. This first step had shown that very important changes in shape take place during the development of the young urchin: increase in height, downward migration of the periproct, forward movement of the peristome… In a second time, a growth crisis was proved and described. Such a crisis occurs, from 12 mm to 16 mm length, as a momentary acceleration of the growth (i.e. the rate of growth increases during a short time). The reality of this crisis was demonstrated by both mathematical and biological ways and also by comparing with other actual and fossil populations. The whole of these results leads to a synthetical pattern of growth divided into three main stages which are successively a juvenile, a preadult and an adult stage. This division was proved also by a principal components analysis.     

Amino acid sequence and immunological properties of chachalaca egg white lysozyme

Summary The amino acid sequence of lysozyme c from chachalaca egg white was determined. Like other bird lysozymes c, that of the chachalaca has 129 amino acid residues. It differs from other avian lysozymes c by 27 to 31 amino acid substitutions as well as by being devoid of phenylalanine. It contains substitutions at 9 positions which are invariant in the other 7 bird lysozymes of known sequence. Although the chachalaca is classified zoologically in the order Galliformes, which includes chickens and other pheasant-like birds, its lysozyme differs more from those of pheasant-like birds than do the lysozymes c of ducks. Phylogenetic analysis of the sequence comparisons confirms that the lineage leading to chachalaca lysozyme c separated from that leading to other galliform lysozymes c before the duck lysozyme c lineage did. This indicates a contrast between protein evolution and evolution at the organismal level. Immunological comparison of chachalacalysozyme c with other lysozymes of known sequence provides further support for the proposal that immunological cross-reactivity is strongly dependent on degree of sequence resemblance among bird lysozymes.103rd communication on lysozymes from the Laboratory of P. Jollès. Supported in part by grants from C.N.R.S. (ER 102), I.N.S.E.R.M. (Groupe de recherche U-116), N.S.F. (GB-42028X), and N.I.H. (GM-21509).     

Identification of marker genes in Alzheimer's disease using a machine-learning model

Alzheimer''s Disease (AD) is one of the most common causes of dementia, mostly affecting the elderly population. Currently, there is no proper diagnostic tool or method available for the detection of AD. The present study used two distinct data sets of AD genes, which could be potential biomarkers in the diagnosis. The differentially expressed genes (DEGs) curated from both datasets were used for machine learning classification, tissue expression annotation and co-expression analysis. Further, CNPY3, GPR84, HIST1H2AB, HIST1H2AE, IFNAR1, LMO3, MYO18A, N4BP2L1, PML, SLC4A4, ST8SIA4, TLE1 and N4BP2L1 were identified as highly significant DEGs and exhibited co-expression with other query genes. Moreover, a tissue expression study found that these genes are also expressed in the brain tissue. In addition to the earlier studies for marker gene identification, we have considered a different set of machine learning classifiers to improve the accuracy rate from the analysis. Amongst all the six classification algorithms, J48 emerged as the best classifier, which could be used for differentiating healthy and diseased samples. SMO/SVM and Logit Boost further followed J48 to achieve the classification accuracy.     

Succession of mycorrhizal fungi in stands of Pinus sylvestris in the Netherlands

The mycorrhizal mycoflora was investigated in 35 stands of Pinus sylvestris in three types of young (4-13 yr) and three of old (50-80 yr) stands in the Netherlands, differing in number of rotations and soil type. A plot of 1050 m² (30 m x 35 m) within each stand was searched for carpophores during the autumns of 1986 and 1987. 10 soil samples per plot were taken in October 1987 in order to assess the mycorrhizal status of the tree roots. The composition of mycorrhizal mycoflora in the different plots was subjected to TWINSPAN cluster analysis and Detrended Correspondence Analysis. Plot groupings generated by these analyses largely parallelled the stand types, indicating that each stand type has its own mycoflora. Differences in myco-floristic composition between stand types were parallelled by differences in the composition of green vegetation. The young stand types had 3.5–27 x more carpophores and 1.4–6.8 x more species than two of the old stand types One old stand type was intermediate. Considerable differences in species composition between the young stand types were observed. It is concluded that the succession of mycorrhizal fungi is not primarily influenced by ageing of the trees, but rather by changes in the soil. The results were compared with data on changes in the occurrence of fruiting species of mycorrhizal fungi in the Netherlands during this century. It appeared that species which have declined according to these data were more frequent in the young plots than in the old plots. However, these species are reported to be frequent in old stands of P. sylvestris in Estonia and Finland. It is argued that this difference is related to the high nitrogen deposition in the Netherlands.     

Cis-regulatory characterization of sequence conservation surrounding the Hox4 genes

Hox genes are key regulators of anterior-posterior axis patterning and have a major role in hindbrain development. The zebrafish Hox4 paralogs have strong overlapping activities in hindbrain rhombomeres 7 and 8, in the spinal cord and in the pharyngeal arches. With the aim to predict enhancers that act on the hoxa4a, hoxb4a, hoxc4a and hoxd4a genes, we used sequence conservation around the Hox4 genes to analyze all fish:human conserved non-coding sequences by reporter assays in stable zebrafish transgenesis. Thirty-four elements were functionally tested in GFP reporter gene constructs and more than 100 F1 lines were analyzed to establish a correlation between sequence conservation and cis-regulatory function, constituting a catalog of Hox4 CNEs. Sixteen tissue-specific enhancers could be identified. Multiple alignments of the CNEs revealed paralogous cis-regulatory sequences, however, the CNE sequence similarities were found not to correlate with tissue specificity. To identify ancestral enhancers that direct Hox4 gene activity, genome sequence alignments of mammals, teleosts, horn shark and the cephalochordate amphioxus, which is the most basal extant chordate possessing a single prototypical Hox cluster, were performed. Three elements were identified and two of them exhibited regulatory activity in transgenic zebrafish, however revealing no specificity. Our data show that the approach to identify cis-regulatory sequences by genome sequence alignments and subsequent testing in zebrafish transgenesis can be used to define enhancers within the Hox clusters and that these have significantly diverged in their function during evolution.     

Using species traits to assess human impacts on near shore benthic ecosystems in the Canadian Arctic

Human activities have the potential to alter the diversity and composition of biological communities in natural environments, which can cause changes in ecosystem functioning. This has led to the development of environmental assessment techniques that take into account species identity, as species can contribute differently to various ecosystem processes. Biological Traits Analysis (BTA) is used to compare the abundances of specific biological traits in samples to produce information about how ecosystem functioning may change across a specific terrestrial or aquatic system. In the present study, BTA was used to assess the influence of municipal wastewater effluent on benthic marine communities in near shore soft sediments in four locations across the Canadian Arctic Territory of Nunavut, Canada. Shifts in trait composition were assessed relative to indicators of sediment enrichment (sediment chlorophyll, organic content, degree of anoxia), and natural variation in habitat characteristics (water depth, porosity, average grain size) at a site receiving wastewater and a reference site in each sampling location. The results indicated a mild enrichment effect of wastewater, as evidenced by changes in trait composition at three of the four sites that received wastewater inputs. However, the amount of variance in trait composition explained by metrics of wastewater enrichment in these locations were generally equal to or lower than the amount of variance explained by sediment characteristics related to natural processes. These results provide greater insight into the underlying causes and consequences of human activities than more traditional methods for environmental impact assessment, and can be directly applied in a management context.     

High day-to-day repeatability of lower extremity muscle activation patterns and joint biomechanics of dual-belt treadmill gait: A reliability study in healthy young adults

PurposeThe reliability of lower extremity muscle activation patterns has not been clearly studied in a dual-belt instrumented treadmill environment. The primary study objective was to quantify the day-to-day reliability of quadriceps, hamstrings, gastrocnemius and gluteus medius activation patterns in healthy young adult gait. Secondarily, the reliability of spatiotemporal, and knee/hip motion and moment-based gait outcomes was assessed.Scope: 20 young adults were recruited and tested on two separate days. Using standardized procedures, participants were prepared for surface electromyography and lower extremity motion capture. All individuals walked on a dual-belt instrumented treadmill while muscle activation, segment motions and ground reaction forces were recorded. Sagittal plane motion and net external sagittal and frontal plane moments were calculated. Discrete biomechanical and muscle activation measures were calculated, and non-negative matrix factorization extracted amplitude and temporal muscle activation features. Intraclass Correlation Coefficients, Standard Error of Measurement and Minimum Detectable Change were calculated.ConclusionsHigh to excellent Intraclass correlation coefficients were found between visits for most primary and secondary outcomes. The absolute and relative reliability, including Minimum Detectable Change values, provided in this study support the use of dual-belt instrumented treadmill walking as an acceptable medium to collect biomechanical and lower extremity EMG outcomes for future studies.