Structure of RecX protein complex with the presynaptic RecA filament: Molecular dynamics simulations and small angle neutron scattering

Using molecular modeling techniques we have built the full atomic structure and performed molecular dynamics simulations for the complexes formed by Escherichia coli RecX protein with a single-stranded oligonucleotide and with RecA presynaptic filament. Based on the modeling and SANS experimental data a sandwich-like filament structure formed two chains of RecX monomers bound to the opposite sides of the single stranded DNA is proposed for RecX::ssDNA complex. The model for RecX::RecA::ssDNA include RecX binding into the grove of RecA::ssDNA filament that occurs mainly via Coulomb interactions between RecX and ssDNA. Formation of RecX::RecA::ssDNA filaments in solution was confirmed by SANS measurements which were in agreement with the spectra computed from the molecular dynamics simulations.     

Size does not matter: size-invariant echo-acoustic object classification

Echolocating bats can not only extract spatial information from the auditory analysis of their ultrasonic emissions, they can also discriminate, classify and identify the three-dimensional shape of objects reflecting their emissions. Effective object recognition requires the segregation of size and shape information. Previous studies have shown that, like in visual object recognition, bats can transfer an echo-acoustic object discrimination task to objects of different size and that they spontaneously classify scaled versions of virtual echo-acoustic objects according to trained virtual-object standards. The current study aims to bridge the gap between these previous findings using a different class of real objects and a classification—instead of a discrimination paradigm. Echolocating bats (Phyllostomus discolor) were trained to classify an object as either a sphere or an hour-glass shaped object. The bats spontaneously generalised this classification to objects of the same shape. The generalisation cannot be explained based on similarities of the power spectra or temporal structures of the echo-acoustic object images and thus require dedicated neural mechanisms dealing with size-invariant echo-acoustic object analysis. Control experiments with human listeners classifying the echo-acoustic images of the objects confirm the universal validity of auditory size invariance. The current data thus corroborate and extend previous psychophysical evidence for sonar auditory-object normalisation and suggest that the underlying auditory mechanisms following the initial neural extraction of the echo-acoustic images in echolocating bats may be very similar in bats and humans.     

Targeting nucleic acids into mitochondria: Progress and prospects

Given the essential functions of these organelles in cell homeostasis, their involvement in incurable diseases and their potential in biotechnological applications, genetic transformation of mitochondria has been a long pursued goal that has only been reached in a couple of unicellular organisms. The challenge led scientists to explore a wealth of different strategies for mitochondrial delivery of DNA or RNA in living cells. These are the subject of the present review. Targeting DNA into the organelles currently shows promise but remarkably a number of alternative approaches based on RNA trafficking were also established and will bring as well major contributions.     

Ricerche Sulla Vegetazione Della Valsesia. VII. Notholaena Marantae (L.) Desv. in Valsesia

Abstract

Researches on the vegetation of Valsesia. VII. «Notholaena marantae» (L.) Desv. in the Sesia Valley. — It's hereby described a station of Notholaena marantae (L.) Desv. near «Giavina Rossa» (Valsesia-Piedmont, Italy). This is probably the only place in the whole valley. The fern grows in a kind of ground formed by peridotitic rocks and on a little dry wall supporting the debris. The fern presence in a wooden valley, and under an oceanic climate could be a very interesting subject for hystorical geobotanic researches.     

Raman spectroscopy of human skin for kidney failure detection

The object of this paper is in vivo study of skin spectral-characteristics in patients with kidney failure by conventional Raman spectroscopy in near infrared region. The experimental dataset was subjected to discriminant analysis with the projection on latent structures (PLS-DA). Application of Raman spectroscopy to investigate the forearm skin in 85 adult patients with kidney failure (90 spectra) and 40 healthy adult volunteers (80 spectra) has yielded the accuracy of 0.96, sensitivity of 0.94 and specificity of 0.99 in terms of identifying the target subjects with kidney failure. The autofluorescence analysis in the near infrared region identified the patients with kidney failure among healthy volunteers of the same age group with specificity, sensitivity, and accuracy of 0.91, 0.84, and 0.88, respectively. When classifying subjects by the presence of kidney failure using the PLS-DA method, the most informative Raman spectral bands are 1315 to 1330, 1450 to 1460, 1700 to 1800 cm⁻¹. In general, the performed study demonstrates that for in vivo skin analysis, the conventional Raman spectroscopy can provide the basis for cost-effective and accurate detection of kidney failure and associated metabolic changes in the skin.     

Limiting transport steps and novel interactions of Connexin-43 along the secretory pathway

Connexins are four-transmembrane-domain proteins expressed in all vertebrates which form permeable gap junction channels that connect cells. Here, we analysed Connexin-43 (Cx43) transport to the plasma membrane and studied the effects of small GTPases acting along the secretory pathway. We show that both GTP- and GDP-restricted Sar1 prevents exit of Cx43 from the endoplasmic reticulum (ER), but only GTP-restricted Sar1 arrests Cx43 in COP II-coated ER exit sites and accumulates 14-3-3 proteins in the ER fraction. FRET-FLIM data confirm that already in ER exit sites Cx43 exists in oligomeric form, suggesting an in vivo role for 14-3-3 in Cx43 oligomerization. Exit of Cx43 from the ER can be blocked by other factors—such as expression of the β subunit of the COP I coat or p50/dynamitin that acts on the microtubule-based dynein motor complex. GTP-restricted Arf1 blocks Cx43 in the Golgi. Lastly, we show that GTP-restricted Arf6 removes Cx43 gap junction plaques from the cell–cell interface and targets them to degradation. These data provide a molecular explanation of how small GTPases act to regulate Cx43 transport through the secretory pathway, facilitating or abolishing cell–cell communication through gap junctions.     

Characterization of the catalase of the genus Porphyromonas isolated from cats

Crude cell extracts from members of the genus Porphyromonas isolated from catswere examined in SDS-PAGE and nondenaturing PAGE. In eachof the species catalase activitywas detected as a single band with characteristics of typical bacterial catalases, i.e. each catalase functioned over a broad pH range (pH 5—10), was not inhibited by chloroform-ethanol, did not possess detectable peroxidase activity, and was irreversibly inhibited by3-amino-1,2,4 triazole. The catalase enzyme of P. gingivalis VPB 3492, P. circumdentaria NCTC 12469^T, P. salivosa VPB 3313 and VPB 3444 was inactivated at 71, 66·5, 63·5 and 57°C respectively. The molecular weights of the enzymes from P. gingivalis VPB 3492, P. circumdentaria NCTC 12469^T, P. salivosa NCTC 11632^T and P. salivosa VPB 3444 were 200000, 216000, 209000 and 200000 Da respectively.     

Cigarette smoking during pregnancy: comparison of biomarkers for inclusion in epidemiological studies

Using proteomic approach in cerebrospinal fluid (CSF) we identified pigment epithelium-derived factor (PEDF) and Haptoglobin (Hp) as putative markers that could discriminate between AD and other dementias. ELISA assays were developed to measure the levels of PEDF and Hp in CSF from patients with AD (AD, n?=?27), non-AD (NAD, n?=?30) and in non-demented patients (ND, n?=?27). The combined assessment of PEDF, Hp and Tau levels, using Iterative Marginal Optimization, improved the differential diagnosis of AD, especially in patients with moderate to severe dementia (p<0.002). This pilot study highlights the probable different contribution of oxidative mechanisms in dementia.     

Short-Lived Tree Species and Their Role as Indicators for Plant Diversity in the Restoration of Natural Forests

Anthropogenic forests, particularly conifer monocultures, today constitute a large proportion of Central European woodland. Conversion of such forest stands into abundantly structured mixed‐species woodland is within the focus of ecosystem restoration and is considered to affect forest biodiversity. Short‐lived tree species play an important role in such conversion processes and may serve as focal species. However, not much is known about their relationship with forest biodiversity. In this study, the short‐lived tree species, European mountain ash (Sorbus aucuparia L.), European white birch (Betula pendula Roth), Downy birch (B. pubescens Ehrh.), and Glossy buckthorn (Frangula alnus P. Mill.), commonly occurring throughout Central Europe, are investigated with regard to their relationship with plant diversity. The focus is on their occurrences in Scots pine (Pinus sylvestris L.)–dominated forests in the Northeast German lowlands. A significant increase in vascular plant diversity is revealed in stands with the selected species’ presence, in comparison to stands without them. Increase in plant species numbers is highest where the respective species occurs in the tree and/or shrub layer, compared with their presence only in the herb layer. For bryophyte species, there is a less strong inverse relationship. An analysis of different species groups, such as threatened, woody, and typical forest species of higher plants, reveals no decrease in species numbers in these groups if short‐lived tree species are present. It is concluded that short‐lived tree species can be indicators for plant diversity assessment within forest restoration processes. As to causal explanations, effects of differing site conditions, assessed by use of Ellenberg indicator values, are discussed as well as possible active effects of the tree species changing their environment.