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Decoding the structural integrity and multifunctional role of Era protein in the survival of <i>Mycobacterium tuberculosis</i> H<sub>37</sub>Rv
No full textEra, a widely known GTP binding protein found in many organisms including prokaryotes and eukaryotes and plays a significant role in many fundamental cellular processes like cell growth, differentiation and signaling. In Mycobacterium tuberculosis (Mtb) H37Rv, Era protein had been proved as a GTPase protein but its structural and functional insights are still lacking. Through comparative analysis, structural modeling, docking and using various bioinformatic tools, a detailed investigation of Era was carried out to deduce the structure, function and residues involved in the activity of the protein. Intriguingly, docking results revealed high binding affinity of Era not only with GTP but also with ATP. Myristoylation modifications and phosphorylations on Era were predicted to possibly aid in regulating Era activity and localization; and also the role of Era in translation regulation was foreseen by showing its association with 16s rRNA. Moreover, point mutation of Era residues revealed the effect of W288G and K19G in highly destabilizing the protein structure and activity. Additionally, Era protein was docked with 25 GTPase/ATPase inhibitors, where, Dynasore inhibitor showed the highest affinity for the protein’s GTP binding sites and can be used for further drug trials to inhibit growth of mycobacteria. Communicated by Ramaswamy H. Sarma MtEra protein carries five GTP binding motifs (G1, G2, G3, G4 and G5) and one KH domain for RNA binding.Multifunctional role of MtEra predicted in processes like catabolic, metabolic and ribosome biogenesis.Point mutation analysis showed the importance of tryptophan (W) and lysine (K) residues at position 288 and 19 in stability and activity of the protein, respectively.Dynasore inhibitor showed the highest binding energy of −9 kcal/mol for MtEra. MtEra protein carries five GTP binding motifs (G1, G2, G3, G4 and G5) and one KH domain for RNA binding. Multifunctional role of MtEra predicted in processes like catabolic, metabolic and ribosome biogenesis. Point mutation analysis showed the importance of tryptophan (W) and lysine (K) residues at position 288 and 19 in stability and activity of the protein, respectively. Dynasore inhibitor showed the highest binding energy of −9 kcal/mol for MtEra.</p
<i>In-vitro</i> antimicrobial activity of AF-DP protein and <i>in-silico</i> approach of cell membrane disruption
No full textMicrobial resistance against common antibiotics has become one of the most serious threats to human health. The increasing statistics on this problem show the necessity of finding a way to deal with it. In recent years, antimicrobial peptides with unique properties and the capability of targeting a wide range of pathogens, have been considered as a potential for replacing common antibiotics. A small chitin-binding protein with anticandidal activity was isolated from Moringa oleifera seeds by Neto and colleagues in 2017, which very much resembled antimicrobial peptides. In this study, the antimicrobial protein ‘AF-DP’ was identified and characterized. AF-DP was heterologously expressed, purified, and characterized, and its 3D structure was predicted. Six molecular dynamic simulations were performed to investigate how the protein interacts with Gram-negative inner and outer, Gram-positive, fungal, cancerous, and normal mammalian membranes. Also, its antimicrobial and anticancer activity was assessed in vitro via minimum inhibition concentration (MIC) and MTT assays, respectively. This protein with 111 amino acids and a total net charge (of 10.5) has been predicted to be mainly composed of alpha helix and random coils. Its MIC affecting the growth of Escherichia coli, Staphylococcus aureus, and Candida albicans was 30 µg/ml, 100 µg/ml, and 100 µg/ml, respectively; AF-DP showed anticancer activity against MCF-7 breast cancer cell line. Scanning electron microscopic analysis confirmed the creation of pores and scratches on the surface of the bacterial membrane. The results of this research show that AF-DP can be a candidate for the production of new drugs as an AMP with antimicrobial activity. Communicated by Ramaswamy H. Sarma</p
Supplementary Material for: Survival of a Rhino-Orbital-Cerebral Mucormycosis Patient after Localized Combination Liposomal Amphotericin B Medications: A Case Report
No full textIntroduction: The aim of this study was to report a case of ROCM related to nasogastric intubation who was survived by liposomal amphotericin B (LAmB) combination therapy in situ without orbital exenteration. Case Presentation: A 44-year-old woman presented with a 1-week history of rapidly enlarging swelling on the right nose, cheek, and lower eyelid after underwent gastrointestinal decompression. The lesions were derived from the nasal area where the nasogastric tube had been placed. Based on the biopsy results and clinical manifestations, ROCM was diagnosed. Immediate combination therapy with intravenous LAmB and micafungin and multisection debridement of the right facial region were applied. Postoperative treatment included cleaning, irrigating, and local dressing of the wound area using LAmB. LAmB was also used daily as binocular eye drops against deep infection on the eyeballs. The patient recovered well 4 months later and remained free of disease after 40 months of follow-up. Conclusion: This case adds to our knowledge on the potential risk of nasogastric intubation for mucormycosis infection. Nasogastric tube may be the source of infection associated with ROCM. This report evaluates the beneficial effect of LAmB combination therapy in situ for cleaning, irrigating, local wound dressing, and eye drops on lesion areas. The combination of LAmB as cleaning, irrigating, local dressing solution, and eye drops to control intraocular and intraorbital ROCM infection has not been previously reported to our knowledge. These methods provide multiple choices to substitute for orbital exenteration on the survival of ROCM patients
U.S. and State GHG emissions by sector (2012-2020) - Supporting Figures
No full textThese figures were produced using the 2012-2020 Greenhouse Gas National- and State-Level Emission Totals by Industry datasets. These datasets are described in the paper 'Dataset of 2012-2020 U.S. National- and State-Level Greenhouse Gas Emissions by Sector' in Data in Brief. As the original dataset values are by kg gas, for some figures we combine the GHGs into a total CO2e using the AR5 100-yr global warming potentials compatible with the FEDEFL. We further aggregate the sectors from the original sets of 118 (aggregate) and 540 (detailed) in the datasets for easier representation and also for comparison to an older model. Sector names for the figures where names are not included on the axis are provided in the attached csvs "aggregate_sector_names.csv" and "detail_sector_names.csv". A mapping of the sectors in the detailed dataset to the BEA Detail 2012 schema in the figure is provided in "detailed_to_BEA_detail_mapping.csv". Figures fit the following naming schema:{figuretype}_{dataset}_{gas}_{years}Figuretype is the figure type. One of three types are included:Totals show one or more point totals by the given sector on the vertical axis for the given year of the data points. The national models compare the changes across years as well as by sector. In the figures created from the detailed_US dataset, NGHGIAM is added as an additional data point for the National GHG Industry Attribution Model, a previous version of the model, which was used to previously estimate 2016 totals. These detailed level figures use the BEA Detail sector schema (405 sectors) to further aggregate the totals for visualization from the 540 sectors in the original dataset. Totals figures using the aggregate_State dataset show the range of emissions by sector across all 50 U.S. states for 2020 only.DirectvAllocated figures show total GHGs by type split by those with direct attribution (no need for allocation), and those where the emissions were allocated.Relative. Like the Totals figures but NGHGIAM totals were set equal to 1 and the new dataset values from 2012-2020 are presented a values relative to the NGHGIAM total for that sector.dataset is the dataset that the figures were created with (from the file below). This is either aggregate_US, aggregate_State, or detailed_US.gas is the chemical formula of the greenhouse gas and or is in carbon dioxide equivalents which is designated as CO2e. The latter are calculated from all the GHGs using their 100 yr Global warming potentials from the IPCC AR5 report, as present in the IPCC AR4, AR5, and AR6 20-, 100-, and 500-year GWPs dataset.years are either a range of years or single year which the data represent.</p
A Full-Spectrum ZnS Photocatalyst with Gradient Distribution of Atomic Copper Dopants and Concomitant Sulfur Vacancies for Highly Efficient Hydrogen Evolution
No full textA rarely discussed phenomenon in the realm of photocatalytic
materials
involves the presence of gradient distributed dopants and defects
from the interior to the surface. This intriguing characteristic has
been successfully achieved in the case of ZnS through the incorporation
of atomic monovalent copper ions (Cu+) and concurrent sulfur
vacancies (Vs), resulting in a photocatalyst denoted as
G-CZS1–x. Through the cooperative
action of these atomic Cu dopants and Vs, G-CZS1–x significantly extends its photoabsorption range
to encompass the full spectrum (200–2100 nm), which improves
the solar utilization ability. This alteration enhances the efficiency
of charge separation and optimizes Δ(H*) (free energy of hydrogen
adsorption) to approach 0 eV for the hydrogen evolution reaction (HER).
It is noteworthy that both surface-exposed atomic Cu and Vs act as active sites for photocatalysis. G-CZS1–x exhibits a significant H2 evolution rate
of 1.01 mmol h–1 in the absence of a cocatalyst.
This performance exceeds the majority of previously reported photocatalysts,
exhibiting approximately 25-fold as ZnS, and 5-fold as H-CZS1–x with homogeneous distribution of
equal content Cu dopants and Vs. In contrast to G-CZS1–x, the H adsorption on Cu sites for H-CZS1–x (ΔG(H*) = −1.22 eV)
is excessively strong to inhibit the H2 release, and the
charge separation efficiency for H-CZS1–x is relatively sluggish, revealing the positive role of a gradient
distribution model of dopants and defects on activity enhancement.
This work highlights the synergy of atomic dopants and defects in
advancing photoactivity, as well as the significant benefit of the
controllable distribution model of dopants and defects for photocatalysis
DataSheet1_Effect of TraN key residues involved in DNA binding on pIP501 transfer rates in Enterococcus faecalis.pdf
No full textConjugation is a major mechanism that facilitates the exchange of antibiotic resistance genes among bacteria. The broad-host-range Inc18 plasmid pIP501 harbors 15 genes that encode for a type IV secretion system (T4SS). It is a membrane-spanning multiprotein complex formed between conjugating donor and recipient cells. The penultimate gene of the pIP501 operon encodes for the cytosolic monomeric protein TraN. This acts as a transcriptional regulator by binding upstream of the operon promotor, partially overlapping with the origin of transfer. Additionally, TraN regulates traN and traO expression by binding upstream of the PtraNO promoter. This study investigates the impact of nine TraN amino acids involved in binding to pIP501 DNA through site-directed mutagenesis by exchanging one to three residues by alanine. For three traN variants, complementation of the pIP501∆traN knockout resulted in an increase of the transfer rate by more than 1.5 orders of magnitude compared to complementation of the mutant with native traN. Microscale thermophoresis (MST) was used to assess the binding affinities of three TraN double-substituted variants and one triple-substituted variant to its cognate pIP501 double-stranded DNA. The MST data strongly correlated with the transfer rates obtained by biparental mating assays in Enterococcus faecalis. The TraN variants TraN_R23A-N24A-Q28A, TraN_H82A-R86A, and TraN_G100A-K101A not only exhibited significantly lower DNA binding affinities but also, upon complementation of the pIP501∆traN knockout, resulted in the highest pIP501 transfer rates. This confirms the important role of the TraN residues R23, N24, Q28, H82, R86, G100, and K101 in downregulating pIP501 transfer. Although TraN is not part of the mating pair formation complex, TraE, TraF, TraH, TraJ, TraK, and TraM were coeluted with TraN in a pull-down. Moreover, TraN homologs are present not only in Inc18 plasmids but also in RepA_N and Rep_3 family plasmids, which are frequently found in enterococci, streptococci, and staphylococci. This points to a widespread role of this repressor in conjugative plasmid transfer among Firmicutes.</p
A modification to the extended Rytov theory
No full textThis paper proposes a heuristic modification to the extended Rytov theory of strong scintillation [Andrews L, Phillips R. Laser beam propagation through random media. 2nd ed., Washington, USA: SPIE Press; 2005, Andrews LC, Al-Habash MA, Hopen CY, et al. Theory of optical scintillation: Gaussian-beam wave model. Waves Random Media. 2001;11(3):271–291]. This is done by dividing the large and small scales in the extended Rytov theory into further sub-scales. Expressions for the induced irradiance variance, and log-irradiance, due to each sub-scale are presented. The modified theory is used to derive and justify recent results in irradiance fluctuation modeling and hence answer a question initially proposed in [Shishter YM, Young RC, Ali FH. Irradiance probability density function for turbulence induced fading in free space optics. JOSA A. 2022;39(7):1267–1274, Shishter YM, Young RC, Ali FH. General statistical model of irradiance fluctuations in free space optics. JOSA A. 2023;40(1):53–63]. Plots of the irradiance pdf under the modified theory are in support of the theory. The validity of the theory presented would result in modifications to the classical scintillation analysis of waves in random media, with applications to the design of optical systems. Moreover, it is observed that the mathematical framework developed also follows from the assumption of variations in the turbulence along a horizontal path. The work presented in this paper suggests the need of further theoretical and experimental investigations into the effect of variations in atmospheric turbulence characteristics along horizontal paths in the received signal irradiance distribution.</p
Virtual reality immerses you in your mind: the experience and stress-reduction benefits of VR mindfulness modules in persons with TBI
No full textThis pilot study tested the feasibility and stress reduction effectiveness of a one-time virtual reality mindfulness module (VRMM) in individuals with mild-to-moderate traumatic brain injury (TBI). Thirty-eight participants participated in a pilot study utilizing a mixed methods convergent parallel design. Pretest and posttest stress levels were collected; participants engaged in a brief 4-question qualitative interview. Mann Whitney U and Wilcoxon Signed Rank Tests were used. Qualitative analysis utilized grounded theory. Post-VRMM, two-thirds (24) of participants had a statistically significant decrease in stress levels. A key qualitative finding indicated that participants found the immersiveness and realism of the VR environments helpful in compensating for cognitive deficits resulting from TBI. There were no adverse side effects reported, indicating that well-designed VRMMs that minimize motion-induced adverse effects are well tolerated in persons with TBI. A guided mindfulness activity in a VR environment was well tolerated, and participants overall found VRMM effective in reducing stress levels. VR-based environments have potential to harness guided mindfulness practice and may support persons with TBI to enhance concentration. Further application of this technology in TBI rehabilitation is promising and warrants future research to explore the benefit of VR in improving rehabilitation outcomes.</p
Pengujian Bahan Semen: Seri 1-Uji Laboratorium Bahan Beton dan Beton
No full textSemen merupakan suatu hasil industri yang dapat menjadi sangat kompleks dengan campuran serta susunan yang berbeda-beda. Semen dapat dibedakan menjadi dua kelompok (Mulyono, 2003), yaitu: semen non-hidrolik dan semen hidrolik . Semen non-Hidrolik merupakan semen yang tidak dapat mengikat dan mengeras di dalam air, akan tetapi memerlukan udara untuk dapat mengeras, contoh utama dari semen non-hidralik adalah kapur. Semen hidrolik mempunyai kemampuan untuk mengikat dan mengeras di dalam air, semenhidrolik antara lain: Kapur hydrolik, semen pozollan, semen terak , semen alam, semen portland , semen portland-pozolan , semen portland terak tanur tinggi, semen alumina, semen expansif , dan jenis lainnya, seperti, semen porland putih, semen warna, dan semen-semen untuk keperluan khusus.</p
Extended data
No full textA prospective study on health-seeking behavior and post exposure prophylaxis received by animal bite victims at an anti-rabies clinic in a tertiary care center in urban Bangalore </p