- Phylogenetic and crystallographic analysis of Nostoc phycocyanin having blue-shifted spectral properties. [Journal Article]
- SRSci Rep 2019 Jul 08; 9(1):9863
- The distinct sequence feature and spectral blue-shift (~10 nm) of phycocyanin, isolated from Nostoc sp. R76DM (N-PC), were investigated by phylogenetic and crystallographic analyses. Twelve conserved…
The distinct sequence feature and spectral blue-shift (~10 nm) of phycocyanin, isolated from Nostoc sp. R76DM (N-PC), were investigated by phylogenetic and crystallographic analyses. Twelve conserved substitutions in N-PC sequence were found distributed unequally among α- and β-subunit (3 in α- and 9 in β-subunit). The phylogenetic analysis suggested that molecular evolution of α- and β-subunit of Nostoc-phycocyanin is faster than evolution of Nostoc-species. The divergence events seem to have occurred more frequently in β-subunit, compared to α-subunit (relative divergence, 7.38 for α-subunit and 9.66 for β-subunit). Crystal structure of N-PC was solved at 2.35 Å resolution to reasonable R-factors (Rwork/RFree = 0.199/0.248). Substitutions congregate near interface of two αβ-monomer in N-PC trimer and are of compensatory nature. Six of the substitutions in β-subunit may be involved in maintaining topology of β-subunit, one in inter-monomer interaction and one in interaction with linker-protein. The β153Cys-attached chromophore adopts high-energy conformational state resulting due to reduced coplanarity of B- and C-pyrrole rings. Distortion in chromophore conformation can result in blue-shift in N-PC spectral properties. N-PC showed significant in-vitro and in-vivo antioxidant activity comparable with other phycocyanin. Since Nostoc-species constitute a distinct phylogenetic clade, the present structure would provide a better template to build a model for phycocyanins of these species.
- Quantitative assessment of phased array coils with different numbers of receiving channels in terms of signal-to-noise ratio and spatial noise variation in magnetic resonance imaging. [Journal Article]
- PlosPLoS One 2019; 14(7):e0219407
- The neuroimaging of humans using 7T magnetic resonance imaging (MRI) has been conducted using phased array (PA) coils with different numbers of receiving channels. PA coils with a high number of chan…
The neuroimaging of humans using 7T magnetic resonance imaging (MRI) has been conducted using phased array (PA) coils with different numbers of receiving channels. PA coils with a high number of channels may offer parallel imaging (PI) with a high reduction (R)-factor, which is enabled via under-sampling and coil geometry (g) factor, increasing the radiofrequency signal sensitivity provided by a small coil. The goals of this study were to assess and validate the coil performance of PA coils with different numbers of receiver (Rx)-channels in and to propose the coil selection guidelines by visualizing 7T brain images. The combined magnetic flux density (||B1||) distributions of four configurations of PA coils-4-, 8-, 12-, and 16-channel Rx-only mode under the local transmit (Tx) mode of birdcage coils-were evaluated using electromagnetic (EM) calculations. These four configurations of PA coils and a local Tx coil were designed and built for a 7T MRI experiment. For 7T brain imaging experiments, all PA coils with (w/) and without (w/o) R-factors were compared in terms of signal-to-noise ratio (SNR) and spatial noise variation (SNV). EM simulation results clearly demonstrated that PA coils with a high number of Rx channels showed more homogeneously distributed ||B1|| fields than a PA coils with a low number of Rx coils. The results of this study demonstrate that a collection of smaller surface coils can contribute to high RF signal sensitivity in terms of the anatomical coverage of the brain and may facilitate PI. With further improvement in coil technology, researchers and clinicians will be provided with PA coils with different numbers of channels, which can ensure the optimum SNR and PI benefits for 7T brain MR imaging.
- Crystal structure of phycocyanin from heterocyst-forming filamentous cyanobacterium Nostoc sp. WR13. [Journal Article]
- IJInt J Biol Macromol 2019 Aug 15; 135:62-68
- Phycocyanin (PC) is the principal pigment protein in the light-harvesting antenna of cyanobacteria. Here the biochemical characterization and the 1.51 Å crystal structure of PC from cyanobacterium No…
Phycocyanin (PC) is the principal pigment protein in the light-harvesting antenna of cyanobacteria. Here the biochemical characterization and the 1.51 Å crystal structure of PC from cyanobacterium Nostoc sp. WR13 (Nst-PC) is reported. The P63 crystal lattice is composed of the minimal biological entities of Nst-PC, the (αβ)3 trimeric rings. The structure has been refined to R factor 11.5% (Rfree 15.4%) using anisotropic atomic B factors. A phylogenetic study shows that the α and β chains of Nst-PC are significantly clustered in a distinct clade with Acaryochloris marina. The structure was examined to look for any significant differences between Nst-PC and PC from non-desert species. Only minor differences were found in the chromophore microenvironments. The tentative energy transfer pathways in Nst-PC were modeled based on simple structural considerations.
- Permutimin: Factor Rotation to Simple Structure with Permutation of Variables. [Journal Article]
- MBMultivariate Behav Res 2019 Apr 25; :1-13
- Factor rotation is usually performed for a p-variables × r -factors loading matrix so that the resulting rotated matrix has a simple structure. This simple structure was originally defined by Thursto…
Factor rotation is usually performed for a p-variables × r -factors loading matrix so that the resulting rotated matrix has a simple structure. This simple structure was originally defined by Thurstone (1947) by specifying how zero elements are arranged in the loading matrix. In this article, we propose a new rotation technique, which is directly based on Thurstone's definition. It can give a p-variables × r -factors target matrix of zero and nonzero elements, which stands for the properties to be possessed by the rotated loading matrix. However, it is unknown how the rows of the target matrix are associated with those of the loading matrix. In the proposed procedure, a loading matrix is rotated simultaneously with a permutation of the rows of the target matrix, so that the rotated loading matrix is optimally matched to the permuted target matrix in a least squares sense. Its novel feature is the use of permutation, thus we call the technique Permutimin. Its algorithm is presented, with Thurstone's definition of simple structure modified so as to specify the target matrix uniquely. Permutimin is illustrated with real data examples. Finally, we discuss the relationships between Permutimin and Procrustes rotation.
- Mapping Local Conformational Landscapes of Proteins in Solution. [Journal Article]
- SStructure 2019 May 07; 27(5):853-865.e5
- The ability of proteins to adopt multiple conformational states is essential to their function, and elucidating the details of such diversity under physiological conditions has been a major challenge…
The ability of proteins to adopt multiple conformational states is essential to their function, and elucidating the details of such diversity under physiological conditions has been a major challenge. Here we present a generalized method for mapping protein population landscapes by NMR spectroscopy. Experimental NOESY spectra are directly compared with a set of expectation spectra back-calculated across an arbitrary conformational space. Signal decomposition of the experimental spectrum then directly yields the relative populations of local conformational microstates. In this way, averaged descriptions of conformation can be eliminated. As the method quantitatively compares experimental and expectation spectra, it inherently delivers an R factor expressing how well structural models explain the input data. We demonstrate that our method extracts sufficient information from a single 3D NOESY experiment to perform initial model building, refinement, and validation, thus offering a complete de novo structure determination protocol.
- Exercise is Medicine®: Knowledge and Awareness among Exercise Science and Medical School Students. [Journal Article]
- IJInt J Exerc Sci 2019; 12(3):505-514
- The purpose of this exploratory study was twofold: to determine whether exercise science and medical students are aware of the Exercise is Medicine® (EIM®) program and to construct a tool that would …
The purpose of this exploratory study was twofold: to determine whether exercise science and medical students are aware of the Exercise is Medicine® (EIM®) program and to construct a tool that would permit assessment of EIM® variables with students enrolled in both programs. The study consisted of a quantitative, cross-sectional design, using a self-report electronic questionnaire. An Exploratory Factor Analysis (EFA) using principal component analysis extraction method with Varimax factor rotation was employed to validate the survey instrument based on the expected constructs, which posited five (5) contending factors: Value, Familiarity, Preparedness, Curricular Perceptions, and Opinions. A pairwise comparison was then performed to compare elements of the EIM® scale identified from the factor analysis by student type (medical and exercise science student) using multiple independent sample t-tests. Based on the pairwise comparisons, there were statistically significant differences of all EIM® factors by student type with the exception of Opinions (p = 0.109). Based on the trends observed in the data, exercise science students had a more positive report for each EIM® factor compared to medical students. These findings suggest a discrepancy in the delivery, acceptance, and implementation of the EIM® initiative between exercise professionals and medical healthcare providers. Future investigation is warranted to validate this experimental instrument and study the differences in EIM® factors among current medical and exercise professionals.
- Sexual Sadism and Psychopathy in Sexual Homicide Offenders: An Exploration of Their Associates in a Clinical Sample. [Journal Article]
- IJInt J Offender Ther Comp Criminol 2019; 63(9):1738-1765
- Sexual sadism and psychopathy are often considered synonymous with sexual homicide, but there is limited research on their associates in sexual homicide offenders. Associates of dimensional measures …
Sexual sadism and psychopathy are often considered synonymous with sexual homicide, but there is limited research on their associates in sexual homicide offenders. Associates of dimensional measures of sexual sadism (Sexual Sadism Scale; SeSaS) and psychopathy (Psychopathy Check List-Revised [PCL-R] total, Factor 1, and Factor 2) were examined in 51 male Scottish cases. Over a third were DSM-IV (Diagnostic and Statistical Manual of Mental Disorders-IV) sexual sadists, just under a third screened in with the SeSaS, and a quarter were "Hare psychopaths." Sexual sadism and PCL-R measures were moderately associated. Sexual sadism predicted control, sexual deviance, and unusual behaviour at crime scenes; attempted homicide and having a co-accused; and multiple sexual homicides and previous sexual offending. PCL-R Factor 1 predicted violent, exploitative, and evading detection behaviours at crime scenes; completed homicide; and previous violent offending. PCL-R Factor 2 predicted impulsive behaviours at crime scenes, substance misuse, and previous general offending. Psychopathy and sexual sadism play key roles in sexual homicide, interact with each other, and determine different aspects of offences and offenders.
- Nonimmunologic Donor-Recipient Pairing, HLA Matching, and Graft Loss in Deceased Donor Kidney Transplantation. [Journal Article]
- TDTransplant Direct 2019; 5(1):e414
- CONCLUSIONS: D-R pairing is valuable in predicting patient and graft outcomes after kidney transplant. D-R size matching could offset the benefit and harm seen with 0 and 6 HLA MM, respectively. This is a novel finding.
- Molecular Antimicrobial Resistance of Neisseria gonorrhoeae in a Moroccan Area. [Journal Article]
- IDInfect Dis Obstet Gynecol 2018; 2018:7263849
- CONCLUSIONS: Resistance to penicillin, tetracycline, and ciprofloxacin among NG samples positives remained at high levels in Morocco as determined by molecular profile. So, the use of molecular tools for NG antimicrobial resistance detection can help in the management and spread limitation of this infection.
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- Conjugative Selectivity of Plasmids Is Affected by Coexisting Recipient Candidates. [Journal Article]
- MmSphere 2018 12 19; 3(6)
- Understanding the mechanisms underlying plasmid behavior under conditions of various environments is important to predict the fate of plasmids in nature. Most previous studies on plasmid transfer emp…
Understanding the mechanisms underlying plasmid behavior under conditions of various environments is important to predict the fate of plasmids in nature. Most previous studies on plasmid transfer employed two strains: one as a donor and the other as a recipient. However, in natural environments, there are usually different recipient cells available to which plasmid can be transferred. In this study, to reveal the underlying mechanisms, we assessed the transferability of plasmids from one donor strain to either of two recipient candidates as the most simplified model. We used Pseudomonas putida KT2440 and Pseudomonas resinovorans CA10dm4 as model hosts and pCAR1 (IncP-7), NAH7 (IncP-9), pB10 (IncP-1β), and R388 (IncW) as model plasmids. As expected, in most cases these plasmids were generally transferred more frequently to a recipient of the same species than to a recipient of a different one under conditions of liquid and filter mating, although NAH7 was transferred from P. resinovorans more frequently to P. putida than to P. resinovorans during filter mating. With the exception of pCAR1, which was less affected, the coexistence of other recipients enhanced the preferences of conjugative transfer to the same species. In particular, preferences corresponding to transfer from P. putida to a different recipient (P. resinovorans) were reduced by the presence of a coexisting same recipient (P. putida) during transfer of NAH7 in liquid and transfer of R388 in filter mating. We determined that large cell aggregates and substances secreted into culture supernatant were not responsible for this phenomenon. Overall, the results of this study suggest the existence of unknown factors determining optimal plasmid transfer to native recipients.IMPORTANCE Most previous studies on plasmid conjugal transfer employed experimental setups with two strains: one as a donor and the other as a recipient. However, the results obtained sometimes failed to agree with observations obtained under natural environmental conditions or in a model microcosm using natural soil and water samples. Therefore, we consider that there is a "gap" in our understanding of plasmid behavior in the context of bacterial consortia that exist under the actual environmental conditions. In this study, we clearly showed that the conjugation selectivity of a plasmid can be affected by the recipient candidates existing around the donor strain by the use of a simplified experimental setup with one strain as the donor and two strains as recipients. These phenomena could not be explained by factors known to affect plasmid transfer as suggested by previous studies. Therefore, we suggest the presence of novel elements regulating plasmid transfer within consortia.