Characterizing Various Posterior Fossa Tumors in Children and Adults With Diffusion-Weighted Imaging and Spectroscopy.

Background The posterior fossa is situated between the tentorium cerebelli above and the foramen magnum below. Vital structures like the cerebellum, the pons, and the medulla are situated within it; hence, tumors within the posterior fossa are considered one of the most critical brain lesions. Children are more likely to develop posterior fossa tumors than adults. Diffusion-weighted imaging (DWI) and magnetic resonance spectroscopy (MRS) sequences along with the conventional MRI help in providing additional information in the characterization of the various posterior fossa tumors. We hereby present a series of 30 patients with clinically suspected posterior fossa masses who underwent preoperative MRI. Objectives This study aims to differentiate the neoplastic from non-neoplastic posterior fossa mass by evaluating the diffusion restriction pattern on DWI, quantifying the apparent diffusion coefficient (ADC) map in various posterior fossa tumors, and comparing the different metabolites of various posterior fossa tumors on MRS. Results Out of the 30 patients with posterior fossa lesions, 18 were males and 12 were females. Eight of them were in the pediatric age group, while twenty-two of them were adults. Metastasis was the most common posterior fossa lesion in our study sample and was found in six patients (20%), followed by vestibular schwannomas (17%) and arachnoid cysts (13%), meningiomas, medulloblastoma, and pilocytic astrocytoma (10% each) and epidermoid, ependymoma, and hemangioblastoma (7% each). The mean ADC value of benign tumors was higher than that of malignant tumors, and this difference was found to be significant (p = 0.012). The cut-off ADC value 1.21x 10-3mm2/s had a sensitivity of 81.82% and specificity of 80.47%. MRS metabolites played an additional role in differentiating benign from malignant tumors. Conclusion A combination of conventional MRI, DWI, ADC values, and MRS metabolites showed good diagnostic accuracy to differentiate between the various posterior fossa neoplastic tumors both in adults and children.

Development of a Covalent Inhibitor of c-Jun N-Terminal Protein Kinase (JNK) 2/3 with Selectivity over JNK1.

The c-Jun N-terminal kinases (JNKs) are members of the mitogen-activated protein kinase (MAPK) family, which includes JNK1-JNK3. Interestingly, JNK1 and JNK2 show opposing functions, with JNK2 activity favoring cell survival and JNK1 stimulating apoptosis. Isoform-selective small molecule inhibitors of JNK1 or JNK2 would be useful as pharmacological probes but have been difficult to develop due to the similarity of their ATP binding pockets. Here, we describe the discovery of a covalent inhibitor YL5084, the first such inhibitor that displays selectivity for JNK2 over JNK1. We demonstrated that YL5084 forms a covalent bond with Cys116 of JNK2, exhibits a 20-fold higher Kinact/KI compared to that of JNK1, and engages JNK2 in cells. However, YL5084 exhibited JNK2-independent antiproliferative effects in multiple myeloma cells, suggesting the existence of additional targets relevant in this context. Thus, although not fully optimized, YL5084 represents a useful chemical starting point for the future development of JNK2-selective chemical probes.

Mutations of Rad6 E2 ubiquitin-conjugating enzymes at alanine-126 in helix-3 affect ubiquitination activity and decrease enzyme stability.

Rad6, an E2 ubiquitin-conjugating enzyme conserved from yeast to humans, functions in transcription, genome maintenance, and proteostasis. The contributions of many conserved secondary structures of Rad6 and its human homologs UBE2A and UBE2B to their biological functions are not understood. A mutant RAD6 allele with a missense substitution at alanine-126 (A126) of helix-3 that causes defects in telomeric gene silencing, DNA repair, and protein degradation was reported over 2 decades ago. Here, using a combination of genetics, biochemical, biophysical, and computational approaches, we discovered that helix-3 A126 mutations compromise the ability of Rad6 to ubiquitinate target proteins without disrupting interactions with partner E3 ubiquitin-ligases that are required for their various biological functions in vivo. Explaining the defective in vitro or in vivo ubiquitination activities, molecular dynamics simulations and NMR showed that helix-3 A126 mutations cause local disorder of the catalytic pocket of Rad6 in addition to disorganizing the global structure of the protein to decrease its stability in vivo. We also show that helix-3 A126 mutations deform the structures of UBE2A and UBE2B, the human Rad6 homologs, and compromise the in vitro ubiquitination activity and folding of UBE2B. Providing insights into their ubiquitination defects, we determined helix-3 A126 mutations impair the initial ubiquitin charging and the final discharging steps during substrate ubiquitination by Rad6. In summary, our studies reveal that the conserved helix-3 is a crucial structural constituent that controls the organization of catalytic pockets, enzymatic activities, and biological functions of the Rad6-family E2 ubiquitin-conjugating enzymes.

Draft Genome Sequence of Corynebacterium sanguinis Strain Marseille-P8776.

In 2018, Corynebacterium sanguinis strain Marseille-P8776 was isolated from the blood of a 64-year-old woman suffering from breast cancer who had undergone chemotherapy and radiotherapy. Following whole-genome sequencing, the chromosome of strain Marseille-P8776 was 2,613,836 bp long with a G+C content of 64.92%, 2,568 protein-coding genes, and 64 RNA genes.

Pangenome analysis and virulence profiling of Streptococcus intermedius.

BACKGROUND: Streptococcus intermedius, a member of the S. anginosus group, is a commensal bacterium present in the normal microbiota of human mucosal surfaces of the oral, gastrointestinal, and urogenital tracts. However, it has been associated with various infections such as liver and brain abscesses, bacteremia, osteo-articular infections, and endocarditis. Since 2005, high throughput genome sequencing methods enabled understanding the genetic landscape and diversity of bacteria as well as their pathogenic role. Here, in order to determine whether specific virulence genes could be related to specific clinical manifestations, we compared the genomes from 27 S. intermedius strains isolated from patients with various types of infections, including 13 that were sequenced in our institute and 14 available in GenBank. RESULTS: We estimated the theoretical pangenome size to be of 4,020 genes, including 1,355 core genes, 1,054 strain-specific genes and 1,611 accessory genes shared by 2 or more strains. The pangenome analysis demonstrated that the genomic diversity of S. intermedius represents an "open" pangenome model. We identified a core virulome of 70 genes and 78 unique virulence markers. The phylogenetic clusters based upon core-genome sequences and SNPs were independent from disease types and sample sources. However, using Principal Component analysis based on presence/ absence of virulence genes, we identified the sda histidine kinase, adhesion protein LAP and capsular polysaccharide biosynthesis protein cps4E as being associated to brain abscess or broncho-pulmonary infection. In contrast, liver and abdominal abscess were associated to presence of the fibronectin binding protein fbp54 and capsular polysaccharide biosynthesis protein cap8D and cpsB. CONCLUSIONS: Based on the virulence gene content of 27 S. intermedius strains causing various diseases, we identified putative disease-specific genetic profiles discriminating those causing brain abscess or broncho-pulmonary infection from those causing liver and abdominal abscess. These results provide an insight into S. intermedius pathogenesis and highlights putative targets in a diagnostic perspective.

Genomic description and characterization of Nigeribacterium massiliense gen. nov., sp. nov., isolated from the human gut.

Strain Marseille-P1302 was isolated from the stool of a 2-year-old Nigerian boy suffering from Kwashiorkor, a form of severe acute malnutrition. The strain grows in aerobic atmosphere and bacterial cells are Gram-positive cocci ranging in diameter from 0.8 to 1 µm. Among species with standing in nomenclature, strain Marseille-P1302 exhibited a highest 16S rRNA sequence similarity of 94.97% with Brevilactibacter flavus strain VG341T, but was phylogenetically-closest to Brevilactibacter sinopodophylli strains KCTC 33808T. The draft genome of strain Marseille-P1302 was 2,934,258-bp-long with a 70.38% G + C content, and contained 2704 protein-coding genes and 55 RNAs that included 9 rRNA genes. On the basis of these data, we propose the creation of the new genus Nigeribacterium gen. nov., with strain Marseille-P1302T (= CSUR P1302 = DSM 29084) being the type strain of the new species Nigeribacterium. massiliense gen. nov., sp. nov.

Generation of acoustic-Brownian noise in nuclear magnetic resonance under non-equilibrium thermal fluctuations.

We present an analytical study on generation of acoustic-Brownian noise in nuclear magnetic resonance (NMR) induced as a result of thermal fluctuations of the magnetic moments under non-equilibrium thermal interactions which has not been explored independent of Nyquist-Johnson noise until now. The mechanism of physical coupling between non-equilibrium thermal fluctuations and magnetic moments is illustrated using Lighthill's formulation on suspension dynamics. We discover that unlike Nyquist-Johnson noise which has a uniform spectral density across a range of frequencies, the spectral dependence of acoustic-Brownian noise decreases with an increase in frequency and resembles Brownian noise associated with a particle in a potential well. The results have applications in the field of image enhancement algorithm as well as noise reduction instrumentation in NMR systems.

The Noether current in Maxwell's equations and radiation under symmetry breaking.

Symmetries in physical systems are defined in terms of conserved Noether Currents of the associated Lagrangian. In electrodynamic systems, global symmetry is defined through conservation of charges, which is reflected in gauge symmetry; however, loss of charges from a radiating system can be interpreted as localized loss of the Noether current which implies that electrodynamic symmetry has been locally broken. Thus, we propose that global symmetries and localized symmetry breaking are interwoven into the framework of Maxwell's equations which appear as globally conserved and locally non-conserved charges in an electrodynamic system and define the geometric topology of the electromagnetic field. We apply the ideas in the context of explaining radiation from dielectric materials with low physical dimensions. We also briefly look at the nature of reversibility in electromagnetic wave generation which was initially proposed by Planck, but opposed by Einstein and in recent years by Zoh.This article is part of the theme issue 'Celebrating 125 years of Oliver Heaviside's 'Electromagnetic Theory''.

Crystal structure of a novel domain of the motor subunit of the Type I restriction enzyme EcoR124 involved in complex assembly and DNA binding.

Although EcoR124 is one of the better-studied Type I restriction-modification enzymes, it still presents many challenges to detailed analyses because of its structural and functional complexity and missing structural information. In all available structures of its motor subunit HsdR, responsible for DNA translocation and cleavage, a large part of the HsdR C terminus remains unresolved. The crystal structure of the C terminus of HsdR, obtained with a crystallization chaperone in the form of pHluorin fusion and refined to 2.45 Å, revealed that this part of the protein forms an independent domain with its own hydrophobic core and displays a unique α-helical fold. The full-length HsdR model, based on the WT structure and the C-terminal domain determined here, disclosed a proposed DNA-binding groove lined by positively charged residues. In vivo and in vitro assays with a C-terminal deletion mutant of HsdR supported the idea that this domain is involved in complex assembly and DNA binding. Conserved residues identified through sequence analysis of the C-terminal domain may play a key role in protein-protein and protein-DNA interactions. We conclude that the motor subunit of EcoR124 comprises five structural and functional domains, with the fifth, the C-terminal domain, revealing a unique fold characterized by four conserved motifs in the IC subfamily of Type I restriction-modification systems. In summary, the structural and biochemical results reported here support a model in which the C-terminal domain of the motor subunit HsdR of the endonuclease EcoR124 is involved in complex assembly and DNA binding.

A residue of motif III positions the helicase domains of motor subunit HsdR in restriction-modification enzyme EcoR124I.

Type I restriction-modification enzymes differ significantly from the type II enzymes commonly used as molecular biology reagents. On hemi-methylated DNAs type I enzymes like the EcoR124I restriction-modification complex act as conventional adenine methylases at their specific target sequences, but unmethylated targets induce them to translocate thousands of base pairs through the stationary enzyme before cleaving distant sites nonspecifically. EcoR124I is a superfamily 2 DEAD-box helicase like eukaryotic double-strand DNA translocase Rad54, with two RecA-like helicase domains and seven characteristic sequence motifs that are implicated in translocation. In Rad54 a so-called extended region adjacent to motif III is involved in ATPase activity. Although the EcoR124I extended region bears sequence and structural similarities with Rad54, it does not influence ATPase or restriction activity as shown in this work, but mutagenesis of the conserved glycine residue of its motif III does alter ATPase and DNA cleavage activity. Through the lens of molecular dynamics, a full model of HsdR of EcoR124I based on available crystal structures allowed interpretation of functional effects of mutants in motif III and its extended region. The results indicate that the conserved glycine residue of motif III has a role in positioning the two helicase domains.

PknB remains an essential and a conserved target for drug development in susceptible and MDR strains of M. Tuberculosis.

BACKGROUND: The Mycobacterium tuberculosis (M.tb) protein kinase B (PknB) which is now proved to be essential for the growth and survival of M.tb, is a transmembrane protein with a potential to be a good drug target. However it is not known if this target remains conserved in otherwise resistant isolates from clinical origin. The present study describes the conservation analysis of sequences covering the inhibitor binding domain of PknB to assess if it remains conserved in susceptible and resistant clinical strains of mycobacteria picked from three different geographical areas of India. METHODS: A total of 116 isolates from North, South and West India were used in the study with a variable profile of their susceptibilities towards streptomycin, isoniazid, rifampicin, ethambutol and ofloxacin. Isolates were also spoligotyped in order to find if the conservation pattern of pknB gene remain consistent or differ with different spoligotypes. The impact of variation as found in the study was analyzed using Molecular dynamics simulations. RESULTS: The sequencing results with 115/116 isolates revealed the conserved nature of pknB sequences irrespective of their susceptibility status and spoligotypes. The only variation found was in one strains wherein pnkB sequence had G to A mutation at 664 position translating into a change of amino acid, Valine to Isoleucine. After analyzing the impact of this sequence variation using Molecular dynamics simulations, it was observed that the variation is causing no significant change in protein structure or the inhibitor binding. CONCLUSIONS: Hence, the study endorses that PknB is an ideal target for drug development and there is no pre-existing or induced resistance with respect to the sequences involved in inhibitor binding. Also if the mutation that we are reporting for the first time is found again in subsequent work, it should be checked with phenotypic profile before drawing the conclusion that it would affect the activity in any way. Bioinformatics analysis in our study says that it has no significant effect on the binding and hence the activity of the protein.

The helical domain of the EcoR124I motor subunit participates in ATPase activity and dsDNA translocation.

Type I restriction-modification enzymes are multisubunit, multifunctional molecular machines that recognize specific DNA target sequences, and their multisubunit organization underlies their multifunctionality. EcoR124I is the archetype of Type I restriction-modification family IC and is composed of three subunit types: HsdS, HsdM, and HsdR. DNA cleavage and ATP-dependent DNA translocation activities are housed in the distinct domains of the endonuclease/motor subunit HsdR. Because the multiple functions are integrated in this large subunit of 1,038 residues, a large number of interdomain contacts might be expected. The crystal structure of EcoR124I HsdR reveals a surprisingly sparse number of contacts between helicase domain 2 and the C-terminal helical domain that is thought to be involved in assembly with HsdM. Only two potential hydrogen-bonding contacts are found in a very small contact region. In the present work, the relevance of these two potential hydrogen-bonding interactions for the multiple activities of EcoR124I is evaluated by analysing mutant enzymes using in vivo and in vitro experiments. Molecular dynamics simulations are employed to provide structural interpretation of the functional data. The results indicate that the helical C-terminal domain is involved in the DNA translocation, cleavage, and ATPase activities of HsdR, and a role in controlling those activities is suggested.

Quantum Calculations Indicate Effective Electron Transfer between FMN and Benzoquinone in a New Crystal Structure of Escherichia coli WrbA.

UNLABELLED: Quantum mechanical calculations using the Marcus equation are applied to compare the electron-transfer probability for two distinct crystal structures of the Escherichia coli protein WrbA, an FMN-dependent NAD(P)H: quinone oxidoreductase, with the bound substrate benzoquinone. The calculations indicate that the position of benzoquinone in a new structure reported here and solved at 1.33 Å resolution is more likely to be relevant for the physiological reaction of WrbA than a previously reported crystal structure in which benzoquinone is shifted by ∼5 Å. Because the true electron-acceptor substrate for WrbA is not yet known, the present results can serve to constrain computational docking attempts with potential substrates that may aid in identifying the natural substrate(s) and physiological role(s) of this enzyme. The approach used here highlights a role for quantum mechanical calculations in the interpretation of protein crystal structures.

Electromagnetic radiation under explicit symmetry breaking.

We report our observation that radiation from a system of accelerating charges is possible only when there is explicit breaking of symmetry in the electric field in space within the spatial configuration of the radiating system. Under symmetry breaking, current within an enclosed area around the radiating structure is not conserved at a certain instant of time resulting in radiation in free space. Electromagnetic radiation from dielectric and piezoelectric material based resonators are discussed in this context. Finally, it is argued that symmetry of a resonator of any form can be explicitly broken to create a radiating antenna.

Molecular dynamics comparison of E. coli WrbA apoprotein and holoprotein.

WrbA is a novel multimeric flavodoxin-like protein of unknown function. A recent high-resolution X-ray crystal structure of E. coli WrbA holoprotein revealed a methionine sulfoxide residue with full occupancy in the FMN-binding site, a finding that was confirmed by mass spectrometry. In an effort to evaluate whether methionine sulfoxide may have a role in WrbA function, the present analyses were undertaken using molecular dynamics simulations in combination with further mass spectrometry of the protein. Methionine sulfoxide formation upon reconstitution of purified apoWrbA with oxidized FMN is fast as judged by kinetic mass spectrometry, being complete in ∼5 h and resulting in complete conversion at the active-site methionine with minor extents of conversion at heterogeneous second sites. Analysis of methionine oxidation states during purification of holoWrbA from bacterial cells reveals that methionine is not oxidized prior to reconstitution, indicating that methionine sulfoxide is unlikely to be relevant to the function of WrbA in vivo. Although the simulation results, the first reported for WrbA, led to no hypotheses about the role of methionine sulfoxide that could be tested experimentally, they elucidated the origins of the two major differences between apo- and holoWrbA crystal structures, an alteration of inter-subunit distance and a rotational shift within the tetrameric assembly.

Ideal graphene/silicon Schottky junction diodes.

The proper understanding of semiconductor devices begins at the metal-semiconductor interface. The metal/semiconductor interface itself can also be an important device, as Schottky junctions often forms when the doping in the semiconductors is low. Here, we extend the analysis of metal-silicon Schottky junctions by using graphene, an atomically thin semimetal. We show that a fundamentally new transport model is needed to describe the graphene-silicon Schottky junction. While the current-voltage behavior follows the celebrated ideal diode behavior, the details of the diode characteristics is best characterized by the Landauer transport formalism, suggesting that the injection rate from graphene ultimately determines the transport properties of this new Schottky junction.

Interdomain communication in the endonuclease/motor subunit of type I restriction-modification enzyme EcoR124I.

Restriction-modification systems protect bacteria from foreign DNA. Type I restriction-modification enzymes are multifunctional heteromeric complexes with DNA-cleavage and ATP-dependent DNA translocation activities located on endonuclease/motor subunit HsdR. The recent structure of the first intact motor subunit of the type I restriction enzyme from plasmid EcoR124I suggested a mechanism by which stalled translocation triggers DNA cleavage via a lysine residue on the endonuclease domain that contacts ATP bound between the two helicase domains. In the present work, molecular dynamics simulations are used to explore this proposal. Molecular dynamics simulations suggest that the Lys-ATP contact alternates with a contact with a nearby loop housing the conserved QxxxY motif that had been implicated in DNA cleavage. This model is tested here using in vivo and in vitro experiments. The results indicate how local interactions are transduced to domain motions within the endonuclease/motor subunit.

Quantum efficiency and capture cross section of first and second excitonic transitions of single-walled carbon nanotubes measured through photoconductivity.

Comparing photoconductivity measurements, using p-n diodes formed along individual single-walled carbon nanotubes (SWNT), with modeling results, allows determination of the quantum efficiency, optical capture cross section, and oscillator strength of the first (E11) and second (E22) excitonic transitions of SWNTs. This is in the infrared region of the spectrum, where little experimental work on SWNT optical absorption has been reported to date. We estimate quantum efficiency (η) ~1-5% and provide a correlation of η, capture cross section, and oscillator strength for E11 and E22 with nanotube diameter. This study uses the spectral weight of the exciton resonances as the determining parameter in optical measurements.

Hidden markov model for the prediction of transmembrane proteins using MATLAB.

UNLABELLED: Since membranous proteins play a key role in drug targeting therefore transmembrane proteins prediction is active and challenging area of biological sciences. Location based prediction of transmembrane proteins are significant for functional annotation of protein sequences. Hidden markov model based method was widely applied for transmembrane topology prediction. Here we have presented a revised and a better understanding model than an existing one for transmembrane protein prediction. Scripting on MATLAB was built and compiled for parameter estimation of model and applied this model on amino acid sequence to know the transmembrane and its adjacent locations. Estimated model of transmembrane topology was based on TMHMM model architecture. Only 7 super states are defined in the given dataset, which were converted to 96 states on the basis of their length in sequence. Accuracy of the prediction of model was observed about 74 %, is a good enough in the area of transmembrane topology prediction. Therefore we have concluded the hidden markov model plays crucial role in transmembrane helices prediction on MATLAB platform and it could also be useful for drug discovery strategy. AVAILABILITY: The database is available for free at bioinfonavneet@gmail.comvinaysingh@bhu.ac.in.