A posteriori correction of camera characteristics from large image data sets

Large datasets are emerging in many fields of image processing including: electron microscopy, light microscopy, medical X-ray imaging, astronomy, etc. Novel computer-controlled instrumentation facilitates the collection of very large datasets containing thousands of individual digital images. In single-particle cryogenic electron microscopy (“cryo-EM”), for example, large datasets are required for achieving quasi-atomic resolution structures of biological complexes. Based on the collected data alone, large datasets allow us to precisely determine the statistical properties of the imaging sensor on a pixel-by-pixel basis, independent of any “a priori” normalization routinely applied to the raw image data during collection (“flat field correction”). Our straightforward “a posteriori” correction yields clean linear images as can be verified by Fourier Ring Correlation (FRC), illustrating the statistical independence of the corrected images over all spatial frequencies. The image sensor characteristics can also be measured continuously and used for correcting upcoming images

Impact of COVID-19 and the Ukrainian War on FDI in a Panel of Eastern European Economies

The COVID-19 pandemic, coupled with the Russia-Ukraine war, has had disastrous consequences for the global economy. As a result of the crisis, the normal way of conducting business has changed drastically, and, with the ongoing Russian invasion in Ukraine, many governments and companies have taken immediate investment-related measures. Undoubtedly, the majority of Eastern European countries have been severely hit. It is therefore crucial to find out what impact these challenges have on foreign direct investment in these countries. To do so, the paper employs the panel data technique to estimate the impact of COVID-19 and the Ukrainian war on FDI in Eastern European economies from 1995 to 2022. The regression results show that both the pandemic and the war have discouraged foreign investment in the panel of countries considered in the sample. The results further indicate that per capita growth and trade openness are important determinants of FDI. COVID-19, Ukrainian war, Eastern Europe, Fixed effect model

Observational and metabarcoding approaches reveal the ecology, natural history and conservation status of Scolopendra abnormis, a threatened centipede endemic to Mauritius

The Serpent Island centipede Scolopendra abnormis is a threatened centipede species found on only 2 small islands in the Indian Ocean: Round Island, located 22.5 km northeast of Mauritius, and Serpent Island, 4 km northwest of Round Island. Current understanding of its ecology is based on limited direct observations from 30 yr ago. Round Island has since undergone significant habitat restoration. Hyperabundant non-native ants are also present, which may impact centipede nesting behaviour, ecology, and survival. Recent methodological advances, such as high-throughput sequencing of dietary DNA, can extend our understanding of invertebrate ecology and provide data complementary to direct observation. Using a combination of dietary metabarcoding and observational approaches, we provide new insights into the ecology and natural history of this threatened invertebrate predator. S. abnormis nest most consistently in the root network found beneath endemic Pandanus vandermeeschii trees. They are also found in areas with good soil cover, herbaceous growth, and areas of bare rock slab. Only 4 of 43 centipedes in this study were found near an ant foraging trail, which may have significant implications for S. abnormis nesting habits. These centipedes primarily consume insect prey (particularly taxa within Lepidoptera, Hymenoptera, Diptera), irrespective of centipede body size. A quarter of centipedes also consumed endemic lizards. We also found marked differences in diet composition between wet and dry seasons arising from the changing availability of prey. We provide additional natural history observations and conclude by suggesting conservation actions that would help better understand and safeguard S. abnormis populations

Ribosomal RNAs are tolerant toward genetic insertions: evolutionary origin of the expansion segments

Ribosomal RNAs (rRNAs), assisted by ribosomal proteins, form the basic structure of the ribosome, and play critical roles in protein synthesis. Compared to prokaryotic ribosomes, eukaryotic ribosomes contain elongated rRNAs with several expansion segments and larger numbers of ribosomal proteins. To investigate architectural evolution and functional capability of rRNAs, we employed a Tn5 transposon system to develop a systematic genetic insertion of an RNA segment 31 nt in length into Escherichia coli rRNAs. From the plasmid library harboring a single rRNA operon containing random insertions, we isolated surviving clones bearing rRNAs with functional insertions that enabled rescue of the E. coli strain (Δ7rrn) in which all chromosomal rRNA operons were depleted. We identified 51 sites with functional insertions, 16 sites in 16S rRNA and 35 sites in 23S rRNA, revealing the architecture of E. coli rRNAs to be substantially flexible. Most of the insertion sites show clear tendency to coincide with the regions of the expansion segments found in eukaryotic rRNAs, implying that eukaryotic rRNAs evolved from prokaryotic rRNAs suffering genetic insertions and selections

Multiple capsid-stabilizing interactions revealed in a high-resolution structure of an emerging picornavirus causing neonatal sepsis

The poorly studied picornavirus, human parechovirus 3 (HPeV3) causes neonatal sepsis with no therapies available. Our 4.3-Å resolution structure of HPeV3 on its own and at 15 Å resolution in complex with human monoclonal antibody Fabs demonstrates the expected picornavirus capsid structure with three distinct features. First, 25% of the HPeV3 RNA genome in 60 sites is highly ordered as confirmed by asymmetric reconstruction, and interacts with conserved regions of the capsid proteins VP1 and VP3. Second, the VP0 N terminus stabilizes the capsid inner surface, in contrast to other picornaviruses where on expulsion as VP4, it forms an RNA translocation channel. Last, VP1's hydrophobic pocket, the binding site for the antipicornaviral drug, pleconaril, is blocked and thus inappropriate for antiviral development. Together, these results suggest a direction for development of neutralizing antibodies, antiviral drugs based on targeting the RNA-protein interactions and dissection of virus assembly on the basis of RNA nucleation.Peer reviewe

‘RNA walk’ a novel approach to study RNA–RNA interactions between a small RNA and its target

In this study we describe a novel method to investigate the RNA–RNA interactions between a small RNA and its target that we termed ‘RNA walk’. The method is based on UV-induced AMT cross-linking in vivo followed by affinity selection of the hybrid molecules and mapping the intermolecular adducts by RT–PCR or real-time PCR. Domains carrying the cross-linked adducts fail to efficiently amplify by PCR compared with non-cross-linked domains. This method was calibrated and used to study the interaction between a special tRNA-like molecule (sRNA-85) that is part of the trypanosome signal recognition particle (SRP) complex and the ribosome. Four contact sites between sRNA-85 and rRNA were identified by ‘RNA walk’ and were further fine-mapped by primer extension. Two of the contact sites are expected; one contact site mimics the interaction of the mammalian Alu domain of SRP with the ribosome and the other contact sites include a canonical tRNA interaction. The two other cross-linked sites could not be predicted. We propose that ‘RNA walk, is a generic method to map target RNA small RNAs interactions in vivo

Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA

Explicit solvent molecular dynamics (MD) was used to describe the intrinsic flexibility of the helix 42–44 portion of the 23S rRNA (abbreviated as Kt-42+rGAC; kink-turn 42 and GTPase-associated center rRNA). The bottom part of this molecule consists of alternating rigid and flexible segments. The first flexible segment (Hinge1) is the highly anharmonic kink of Kt-42. The second one (Hinge2) is localized at the junction between helix 42 and helices 43/44. The rigid segments are the two arms of helix 42 flanking the kink. The whole molecule ends up with compact helices 43/44 (Head) which appear to be modestly compressed towards the subunit in the Haloarcula marismortui X-ray structure. Overall, the helix 42–44 rRNA is constructed as a sophisticated intrinsically flexible anisotropic molecular limb. The leading flexibility modes include bending at the hinges and twisting. The Head shows visible internal conformational plasticity, stemming from an intricate set of base pairing patterns including dynamical triads and tetrads. In summary, we demonstrate how rRNA building blocks with contrasting intrinsic flexibilities can form larger architectures with highly specific patterns of preferred low-energy motions and geometries

The structure of the Escheria coli 50S ribosomal subunit by cryo- transmission electron microscopy

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