Solution structure of the DNA-binding domain of RPA from Saccharomyces cerevisiae and its interaction with single-stranded DNA and SV40 T antigen

Replication protein A (RPA) is a three-subunit complex with multiple roles in DNA metabolism. DNA-binding domain A in the large subunit of human RPA (hRPA70A) binds to single-stranded DNA (ssDNA) and is responsible for the species-specific RPA–T antigen (T-ag) interaction required for Simian virus 40 replication. Although Saccharomyces cerevisiae RPA70A (scRPA70A) shares high sequence homology with hRPA70A, the two are not functionally equivalent. To elucidate the similarities and differences between these two homologous proteins, we determined the solution structure of scRPA70A, which closely resembled the structure of hRPA70A. The structure of ssDNA-bound scRPA70A, as simulated by residual dipolar coupling-based homology modeling, suggested that the positioning of the ssDNA is the same for scRPA70A and hRPA70A, although the conformational changes that occur in the two proteins upon ssDNA binding are not identical. NMR titrations of hRPA70A with T-ag showed that the T-ag binding surface is separate from the ssDNA-binding region and is more neutral than the corresponding part of scRPA70A. These differences might account for the species-specific nature of the hRPA70A–T-ag interaction. Our results provide insight into how these two homologous RPA proteins can exhibit functional differences, but still both retain their ability to bind ssDNA

The complete mitochondrial genome of the sea spider Achelia bituberculata (Pycnogonida, Ammotheidae): arthropod ground pattern of gene arrangement

<p>Abstract</p> <p>Background</p> <p>The phylogenetic position of pycnogonids is a long-standing and controversial issue in arthropod phylogeny. This controversy has recently been rekindled by differences in the conclusions based on neuroanatomical data concerning the chelifore and the patterns of <it>Hox </it>expression. The mitochondrial genome of a sea spider, <it>Nymphon gracile </it>(Pycnogonida, Nymphonidae), was recently reported in an attempt to address this issue. However, <it>N. gracile </it>appears to be a long-branch taxon on the phylogenetic tree and exhibits a number of peculiar features, such as 10 tRNA translocations and even an inversion of several protein-coding genes. Sequences of other pycnogonid mitochondrial genomes are needed if the position of pycnogonids is to be elucidated on this basis.</p> <p>Results</p> <p>The complete mitochondrial genome (15,474 bp) of a sea spider (<it>Achelia bituberculata</it>) belonging to the family Ammotheidae, which combines a number of anatomical features considered plesiomorphic with respect to other pycnogonids, was sequenced and characterized. The genome organization shows the features typical of most metazoan animal genomes (37 tightly-packed genes). The overall gene arrangement is completely identical to the arthropod ground pattern, with one exception: the position of the <it>trnQ </it>gene between the <it>rrnS </it>gene and the control region. Maximum likelihood and Bayesian inference trees inferred from the amino acid sequences of mitochondrial protein-coding genes consistently indicate that the pycnogonids (<it>A. bituberculata </it>and <it>N. gracile</it>) may be closely related to the clade of Acari and Araneae.</p> <p>Conclusion</p> <p>The complete mitochondrial genome sequence of <it>A. bituberculata </it>(Family Ammotheidae) and the previously-reported partial sequence of <it>Endeis spinosa </it>show the gene arrangement patterns typical of arthropods (<it>Limulus</it>-like), but they differ markedly from that of <it>N. gracile</it>. Phylogenetic analyses based on mitochondrial protein-coding genes showed that Pycnogonida may be authentic arachnids (= aquatic arachnids) within Chelicerata <it>sensu lato</it>, as indicated by the name 'sea spider,' and suggest that the Cormogonida theory – that the pycnogonids are a sister group of all other arthropods – should be rejected. However, in view of the relatively weak node confidence, strand-biased nucleotide composition and long-branch attraction artifact, further more intensive studies seem necessary to resolve the exact position of the pycnogonids.</p

Multi-Color Luminescence Transition of Upconversion Nanocrystals via Crystal Phase Control with SiO2 for High Temperature Thermal Labels

Upconversion nanocrystals (UCNs)-embedded microarchitectures with luminescence color transition capability and enhanced luminescence intensity under extreme conditions are suitable for developing a robust labeling system in a high-temperature thermal industrial process. However, most UCNs based labeling systems are limited by the loss of luminescence owing to the destruction of the crystalline phase or by a predetermined luminescence color without color transition capability. Herein, an unusual crystal phase transition of UCNs to a hexagonal apatite phase in the presence of SiO2 nanoparticles is reported with the enhancements of 130-fold green luminescence and 52-fold luminance as compared to that of the SiO2-free counterpart. By rationally combining this strategy with an additive color mixing method using a mask-less flow lithography technique, single to multiple luminescence color transition, scalable labeling systems with hidden letters-, and multi-luminescence colored microparticles are demonstrated for a UCNs luminescence color change-based high temperature labeling system

Identification of protein functions using a machine-learning approach based on sequence-derived properties

<p>Abstract</p> <p>Background</p> <p>Predicting the function of an unknown protein is an essential goal in bioinformatics. Sequence similarity-based approaches are widely used for function prediction; however, they are often inadequate in the absence of similar sequences or when the sequence similarity among known protein sequences is statistically weak. This study aimed to develop an accurate prediction method for identifying protein function, irrespective of sequence and structural similarities.</p> <p>Results</p> <p>A highly accurate prediction method capable of identifying protein function, based solely on protein sequence properties, is described. This method analyses and identifies specific features of the protein sequence that are highly correlated with certain protein functions and determines the combination of protein sequence features that best characterises protein function. Thirty-three features that represent subtle differences in local regions and full regions of the protein sequences were introduced. On the basis of 484 features extracted solely from the protein sequence, models were built to predict the functions of 11 different proteins from a broad range of cellular components, molecular functions, and biological processes. The accuracy of protein function prediction using random forests with feature selection ranged from 94.23% to 100%. The local sequence information was found to have a broad range of applicability in predicting protein function.</p> <p>Conclusion</p> <p>We present an accurate prediction method using a machine-learning approach based solely on protein sequence properties. The primary contribution of this paper is to propose new <it>PNPRD </it>features representing global and/or local differences in sequences, based on positively and/or negatively charged residues, to assist in predicting protein function. In addition, we identified a compact and useful feature subset for predicting the function of various proteins. Our results indicate that sequence-based classifiers can provide good results among a broad range of proteins, that the proposed features are useful in predicting several functions, and that the combination of our and traditional features may support the creation of a discriminative feature set for specific protein functions.</p

Large‐Scale, Ultrapliable, and Free‐Standing Nanomembranes

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/97443/1/adma_201204619_sm_suppl.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/97443/2/2167_ftp.pd

Analysis of abnormal muscle activities in patients with loss of cervical lordosis: a cross-sectional study

Background This study aimed to detect the differences in cervical muscle activation patterns in people with versus without cervical lordosis and explore the possible mechanism of cervical pain originating therein. Methods This cross-sectional design included 39 participants without and 18 with normal cervical lordosis. Muscular activation was measured for 5 s in both groups using surface electromyography. Subsequently, the root mean square (RMS) of muscle amplitude was obtained at the bilateral splenius capitis, upper and lower parts of the splenius cervicis, upper and lower parts of the semispinalis cervicis, sternocleidomastoid, upper trapezius, and rhomboid muscles in five cervical positions: 0° (resting), 30° of flexion, 30° of extension, 60° of extension, and upon a 1-kg load on the head in a resting posture. Results The RMS values of the upper trapezius muscle at all postures and the rhomboid muscles at 60° of extension were significantly lower in the loss of lordosis than control group. Comparing the RMS ratio of each posture to the resting position, the ratio of the upper trapezius at flexion was significantly higher and that of the rhomboids at 60° of extension and upon loading was significantly lower in the loss of lordosis than control group. Moreover, the pattern changes in the RMS values according to posture showed a similar shape in these two muscles, and lower in the loss of lordosis than the normal group. Conclusions The loss of normal cervical alignment may correlate with predisposed conditions such as reduced muscle activation of the trapezius and rhomboid muscle, and may also provoke over-firing of the upper trapezius muscle, possibly increasing neck musculoskeletal pain. Trial registration. Clinicaltrials.gov, registration number: NCT03710785.This research was supported by a grant of the Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea (grant number: HI18C1169

Influence of Friction Stir Welding on Mechanical Properties of Butt Joints of AZ61 Magnesium Alloy

In this study, the effect of heat input on the mechanical properties and fracture behaviors of AZ61 magnesium alloy joints has been studied. Magnesium alloy AZ61 plates with thickness of 5 mm were welded at different ratios of tool rotational speed to welding speed (ω/ν). The average ultimate tensile strength of all weld conditions satisfying a ω/ν ratio of 3 reached 100% of the strength of the base material. Fractures occurred at the interface between the thermomechanical affected zone at advancing side and the stir zone in all welded specimens. From the scanning electron microscope and electron backscatter diffraction analysis, it was determined that the interface between the thermomechanical affected zone and the stir zone, which is the region where the grain orientation changes, was the weakest part; the advancing side region was relatively weaker than the retreating side region because the grain orientation change occurred more dramatically in the advancing side region

Comparison of Clinical Outcomes Following Gefitinib and Erlotinib Treatment in Non–Small-Cell Lung Cancer Patients Harboring an Epidermal Growth Factor Receptor Mutation in Either Exon 19 or 21

Background:Gefitinib and erlotinib, small-molecule kinase inhibitors that block epidermal growth factor receptor (EGFR) signaling, have demonstrated a dramatic response rate and prolonged progression-free survival (PFS) in patients harboring an activating EGFR mutation. We compared the clinical outcomes in gefitinib- and erlotinib-treated patients harboring EGFR mutations who had recurrent or metastatic non–small-cell lung cancer (NSCLC).Methods:A total of 375 patients with recurrent or metastatic stage IIIB/IV NSCLC, who had either exon 19 deletion or the L858R mutation in exon 21, and had received either gefitinib (n = 228) or erlotinib (n = 147), were included in the study. A matched-pair case-control study design was implemented in the analysis, where 121 pairs of gefitinib-treated and erlotinib-treated patients were matched according to sex, smoking history, Eastern Cooperative Oncology Group performance status, and types of EGFR mutation.Results:The median age of all patients was 58 years (range, 30–84), and more than half of patients had never been smokers (63.6%). Most patients had adenocarcinoma (98.3%) and good Eastern Cooperative Oncology Group performance status (0, 1) (90.9%). The median number of cycles of EGFR tyrosine kinase inhibitor (TKI) treatment was 12.7 in the gefitinib group and 10.8 in the erlotinib group. Of the 242 patients, 63 (26%) received EGFR TKI as first-line therapy. The overall response rates and disease control rates in the gefitinib- or erlotinib-treated groups were 76.9% versus 74.4% (p = 0.575) and 90.1% versus 86.8%, respectively (p = 0.305). There was no statistically significant difference with regard to PFS (median, 11.7 versus 9.6; p = 0.056) between the gefitinib- and erlotinib-treated groups. For patients receiving EGFR TKI as the first-line treatment, there was no significant difference between the two treatment groups in overall response rates (76.7% and 90.0%) (p = 0.431) and median PFS (11.7 versus 14.5 months) (p = 0.507).Conclusion:In NSCLC patients harboring EGFR mutation, treatment with gefitinib and erlotinib resulted in similar effectiveness