AI-Based Homology Modelling of Fatty Acid Transport Protein 1 Using AlphaFold: Structural Elucidation and Molecular Dynamics Exploration

Fatty acid transport protein 1 (FATP1) is an integral transmembrane protein that is involved in facilitating the translocation of long-chain fatty acids (LCFA) across the plasma membrane, thereby orchestrating the importation of LCFA into the cell. FATP1 also functions as an acyl-CoA ligase, catalyzing the ATP-dependent formation of fatty acyl-CoA using LCFA and VLCFA (very-long-chain fatty acids) as substrates. It is expressed in various types of tissues and is involved in the regulation of crucial signalling pathways, thus playing a vital role in numerous physiological and pathological conditions. Structural insight about FATP1 is, thus, extremely important for understanding the mechanism of action of this protein and developing efficient treatments against its anomalous expression and dysregulation, which are often associated with pathological conditions such as breast cancer. As of now, there has been no prior prediction or evaluation of the 3D configuration of the human FATP1 protein, hindering a comprehensive understanding of the distinct functional roles of its individual domains. In our pursuit to unravel the structure of the most commonly expressed isoforms of FATP1, we employed the cutting-edge ALPHAFOLD 2 model for an initial prediction of the entire protein's structure. This prediction was complemented by molecular dynamics simulations, focusing on the most promising model. We predicted the structure of FATP1 in silico and thoroughly refined and validated it using coarse and molecular dynamics in the absence of the complete crystal structure. Their relative dynamics revealed the different properties of the characteristic FATP1.

Report of terbinafine resistant Trichophyton spp. in Italy: Clinical presentations, molecular identification, antifungal susceptibility testing and mutations in the squalene epoxidase gene

BACKGROUND

Numerous reports of resistance to terbinafine in Trichophyton spp. from all over the world are arousing justified attention and concern. Point mutations in the gene that encodes the squalene epoxidase (SQLE) enzyme are responsible for these therapeutic resistances.

OBJECTIVES

Primary objective of the study was to describe first isolates of Trichophyton spp. resistant to terbinafine among the patients treated between September 2019 and June 2022 at the Dermatology Units of Ospedale Maggiore Policlinico and San Bortolo Hospital. Secondary objective was to study the resistance mechanism.

METHODS

Patients with confirmed Trichophyton spp. infection has been treated with systemic and topical terbinafine. Patients were then re-evaluated 12 weeks after the therapy. Patients with incomplete or absent response to terbinafine underwent a new skin scraping for direct mycological examination, new identification of dermatophyte species from culture and MALDI-TOF, molecular species identification, antifungal susceptibility testing and molecular analysis of SQLE gene.

RESULTS

We identified five patients without clinical response to treatment with terbinafine. The DNA sequencing of the ITS region identified one Trichophyton rubrum and four Trichophyton indotineae. The T. rubrum strain showed minimum inhibitory concentration (MIC) (90% growth inhibition) of 4 mg/L for terbinafine. The four T. indotineae strains showed a MICs range of 0.25-4 mg/L for terbinafine. The analysis of the SQLE gene in the T. rubrum strain showed a nucleotide substitution generating a missense mutation (L393F). The SQLE gene sequencing in the T. indotineae strains showed a nucleotide substitution generating a missense mutation (F397L) in two strains, a nucleotide substitution L393S in one strain and a nucleotide substitution F415C in another strain.

CONCLUSIONS

We report the first cases of terbinafine-resistant Trichophyton isolates in the Italian population. Solid antifungal management programs will be needed to promote more responsible use of antimycotics and preserve their therapeutic efficacy to control antifungal resistance.

Extent of multifocality with corneal manipulation in manual small incision cataract surgery with monofocal posterior chamber intraocular lens implantation

Purpose:

To compare the visual outcome in terms of multifocality in Manual Small Incision Cataract Surgery (MSICS) with and without intraoperative manipulation of corneal curvature.

Methods:

This was a prospective study on 80 subjects (80 eyes) who underwent MSICS with monofocal posterior chamber intraocular lens (PCIOL) implantation between January 2018 and October 2019. Intraoperative manipulation of corneal curvature using viscoelastics was performed during MSICS in 40 subjects (cases) while this intraoperative manipulation was not performed in the remaining 40 subjects (controls). Uncorrected distance visual acuity (UDVA) and uncorrected near visual acuity (UNVA) were compared at day 1, 7, 30 and 180postoperatively.

Results:

At 1 month and 6 months of follow up, UDVA was comparable in the 2 groups. UNVA was better in cases than controls at 1 month and6 months (P < 0.001). At 6 months of follow up,76% of cases with UDVA of 6/9 or better had UNVA of N8 while only 15% of controls with UDVA of 6/9 or better had UNVA of N8 (P <0.001). Mean near add requirement to achieve a best corrected near vision (BCNV)of N6 at 6 months was significantly lesser (P =0.002) in cases (+2.05 D) compared to controls (+2.43D).

Conclusion:

MSICS with intra operative manipulation of corneal curvature resulted in better unaided near visual acuity compared to that without intra operative manipulation of corneal curvature, without compromising unaided distant visual acuity.

Exploring the Potential of Capsaicin Against Cancer Metastasis Based on TGF-β Signaling Modulation Through Module-based Network Pharmacology Approachx

BACKGROUND

Capsaicin is an active alkaloid /principal component of red pepper responsible for the pungency of chili pepper. Capsaicin by changing the intracellular redox homeostasis regulate a variety of signaling pathways ultimately producing a divergent cellular outcome. Several reports showed the potential of capsaicin against cancer metastasis, however unexplored molecular mechanism is still an active part of the research. Several growth factors have a critical role during cancer metastasis among them TGF- β signaling play a vital role.

METHODS

The present study aimed at analyzing capsaicin modulation of TGF-β signaling using network pharmacology approach. The chemical and protein interaction data of capsaicin was curated and abstracted using STITCH4.0, PubChem and ChEMBL database. Further, the compiled data set was subjected to the pathway and functional enrichment analysis using Protein Analysis THrough Evolutionary Relationship (PANTHER) and, Database for Annotation, Visualization, and Integrated Discovery (DAVID) database. Meanwhile, the pattern of amino acid composition across the capsaicin targets was analyzed using the EMBOSS Pepstat tool. Capsaicin targets involved in TGF- β were identified and their Protein-Protein Interaction (PPI) network constructed using STRING v10 and Cytoscape (v 3.2.1). From the above-constructed network, the clusters were mined using the MCODE clustering algorithm and finally binding affinity of capsaicin with its targets involved in TGF-β signaling pathway was analyzed using Autodock Vina.

RESULTS

The analysis explored capsaicin targets and, their associated functional and pathway annotations. Besides, the analysis also provides a detailed distinct pattern of amino acid composition across the capsaicin targets. The capsaicin targets described as MAPK14, JUN, SMAD3, MAPK3, MAPK1 and MYC involved in TGF-β signaling pathway through pathway enrichment analysis. The binding mode analysis of capsaicin with its targets has shown high affinity with MAPK3, MAPK1, JUN and MYC.

CONCLUSION

The study explores the potential of capsaicin as a potent modulator of TGF-β signaling pathway during cancer metastasis and proposes new methodology and mechanism of action of capsaicin against TGF- β signaling pathway.

Aqueous extract from Madhuca indica bark protects cells from oxidative stress caused by electron beam radiation: in vitro, in vivo and in silico approach

In an endeavor to find the novel natural radioprotector to secure normal cells surrounding cancerous cell during radiation exposure, Madhuca indica (M. indica) aqueous stem bark extract was evaluated for radioprotective activity using in vitro, in vivo, and in silico models. M. indica extract exhibited concentration dependent protective effect on electron beam radiation (EBR) induced damage to pBR322 DNA; the highest protection was achieved at 150 μg concentrations. Similarly, M. indica extract (400 mg/kg) administrated to mice prior to irradiation protected DNA from the radiation damage, which was confirmed by inhibiting comet parameters. The study showed a significant increase in the levels of glutathione and superoxide dismutase levels. The study also revealed that administration of M. Indica at the different dose to mice significantly reduced EBR induced MDA, sialic acid and nitric acid levels. Further extract prevented histophatological changes of skin and liver. In contrast, protein-protein interaction studies were performed to find the hub protein, involved in radiation-induced DNA damage. Among 437 proteins that are found expressed during radiation, p53 was found to be a master protein regulating the whole pathway. Molecular interaction between p53 and M. indica extract was predicted by quantitative structure-activity relationship and ADMET properties. Biomolecules such as quercetin, myricetin, and 7-hydroxyflavone were found to be promising inhibitors of p53 protein and may help in the protection of EBR induced DNA damage during cancer treatment.

Continuous monitoring of noise levels in the Gulf of Catania (Ionian Sea). Study of correlation with ship traffic

Acoustic noise levels were measured in the Gulf of Catania (Ionian Sea) from July 2012 to May 2013 by a low frequency (<1000Hz) hydrophone, installed on board the NEMO-SN1 multidisciplinary observatory. NEMO-SN1 is a cabled node of EMSO-ERIC, which was deployed at a water depth of 2100m, 25km off Catania. The study area is characterized by the proximity of mid-size harbors and shipping lanes. Measured noise levels were correlated with the passage of ships tracked with a dedicated AIS antenna. Noise power was measured in the frequency range between 10Hz and 1000Hz. Experimental data were compared with the results of a fast numerical model based on AIS data to evaluate the contribution of shipping noise in six consecutive 1/3 octave frequency bands, including the 1/3 octave frequency bands centered at 63Hz and 125Hz, indicated by the Marine Strategy Framework Directive (2008/56/EC).

Italy introduces pre and post operation monitoring phases for offshore seismic exploration activities

Concern is growing that marine fauna can be affected by noise such as naval sonar, pile driving or geophysical surveys, among others. Literature reports a variety of animal reactions to human noise (from apparently null or negligible to strong). However, conclusive results on its effects on marine mammals at individual and population level are still lacking. In 2015, the Italian Environmental Impact Assessment Commission mandated seismic operators apply a standard scientific protocol comparing marine mammal presence before, during, and after offshore seismic survey. For 60days before and after the survey, marine mammals are monitored using visual and acoustic methods. One or more acoustic autonomous recorders, depending on area size, must also be deployed throughout the three phases for continuous monitoring. Consistent data gathered from many surveys will enable robust statistical analysis of results. Diffusion of this monitoring method internationally would improve the study of far-reaching, intense, low frequency noise.

Pharmacogenetic study of long-term response to interferon-β treatment in multiple sclerosis

The aim of the study is the identification of genetic factors that influence the long-term response to interferon-β (IFNβ) (4-year follow-up). We performed a genome-wide association study in 337 IFNβ-treated Italian multiple sclerosis patients at the extreme of treatment response, and we meta-analyzed association effects, integrating results with pathway analysis, gene-expression profiling of IFNβ-stimulated peripheral blood mononuclear cells from 20 healthy controls (HC) and expression quantitative locus (eQTL) analyses. From meta-analysis, 43 markers were associated at P<10-4, and two of them (rs7298096 and rs4726460) pointed to two genes, NINJ2 and TBXAS1, that were significantly downregulated after IFNβ stimulation in HC (P=3.1 × 10-9 and 5.6 × 10-10). We also observed an eQTL effect for the allele associated with favorable treatment response (rs4726460A); moreover, TBXAS1 appeared downregulated upon IFNβ administration (β=-0.39; P=0.02). Finally, we found an enrichment of pathways related to inflammatory processes and presynaptic membrane, the latter with involvement of genes related to glutamatergic system (GRM3 and GRIK2), confirming its potential role in the response to IFNβ.

Risk mapping for sensitive species to underwater anthropogenic sound emissions: model development and validation in two Mediterranean areas

Recent observations of cetacean mass strandings, coincident with anthropogenic sounds emissions, have raised concerns on the potential environmental impact of underwater noise. Cuvier's beaked whale (Ziphius cavirostris) was reported in all the cited stranding events. Within the NATO Marine Mammal Risk Mitigation project (MMRM), multiple interdisciplinary sea trials have been conducted in the Mediterranean Sea with the objective of developing tools and procedures to mitigate the impact of underwater sound emissions. During these cruises, visual observations, passive acoustic detections and environmental data were collected. The aim of this study was to evaluate "a priori" predictions of Cuvier's beaked whale presence in the Alboran Sea, using models developed in the Ligurian Sea that employ bathymetric and chlorophyll features as predictors. The accuracy of these predictions was found adequate and elements are given to account for the uncertainties associated to the use of models developed in areas different from their calibration site.

Septic shock, pneumonia, and soft tissue infection due to Myroides odoratimimus: report of a case and review of Myroides infections

The genus Myroides comprises aerobic, yellow-pigmented, non-motile, non-fermenting gram-negative rods formerly classified as Flavobacterium odoratum. Members of the genus are widely distributed in the environment, especially in water, and usually behave as low-grade opportunistic pathogens, having been found to cause urinary tract infection, endocarditis, ventriculitis, and cutaneous infections in severely immunocompromised patients. We report a case of soft tissue infection, septic shock, and pneumonia due to M. odoratimimus in an immunocompetent male. To our knowledge, this is the first description of life-threatening infection caused by this organism in an immunocompetent host. We have also reviewed the medical literature on the genus Myroides.

Acquired perforating dermatoses in patients with diabetic kidney disease on hemodialysis

Acquired perforating dermatoses (APD) is an uncommon skin disorder seen in patients with diabetes mellitus, chronic kidney disease, or both together. We present the clinicopathological features of APD in patients with diabetic kidney disease and discuss the recent advances in management. We retrospectively analyzed the data of 8 patients with APD presenting to our center. All patients were known cases of Type 2 diabetes and chronic kidney disease requiring maintenance dialysis. Acquired perforating dermatoses was diagnosed based on clinical presentation of itchy, keratotic papulonodular lesions, and characteristic histopathological features of transepithelial elimination on skin biopsy. The patients were subdivided into 4 types of APD based on the biopsy features. All our patients had Type 2 diabetes over 5 years duration and were on maintenance dialysis for more than 6 months before presentation. Acquired perforating dermatoses symptoms appeared 2 to 6 months before presentation. The majority of patients (6/8) had a subtype of reactive perforating collagenosis. All the patients showed significant resolution with topical glucocorticoid therapy. Acquired perforating dermatoses is a skin complication seen in Type 2 diabetes, chronic kidney disease, or when both are present together. Early identification and therapy prevents the associated morbidity.

Time patterns of sperm whale codas recorded in the Mediterranean Sea 1985-1996

A distinctive vocalization of the sperm whale, Physeter macrocephalus (=P. catodon), is the coda: a short click sequence with a distinctive stereotyped time pattern [Watkins and Schevill, J. Acoust. Soc. Am. 62, 1485-1490 (1977)]. Coda repertoires have been found to vary both geographically and with group affiliation [Weilgart and Whitehead, Behav. Ecol. Sociobiol. 40, 277-285 (1997)]. In this work, the click timings and repetition patterns of sperm whale codas recorded in the Mediterranean Sea are characterized statistically, and the context in which the codas occurred are also taken into consideration. A total of 138 codas were recorded in the central Mediterranean in the years 1985-1996 by several research groups using a number of different detection instruments, including stationary and towed hydrophones, sonobuoys and passive sonars. Nearly all (134) of the recorded codas share the same "3+1" (/// /) click pattern. Coda durations ranged from 456 to 1280 ms, with an average duration of 908 ms and a standard deviation of 176 ms. Most of the codas (a total of 117) belonged to 20 coda series. Each series was produced by an individual, in most cases by a mature male in a small group, and consisted of between 2 and 16 codas, emitted in one or more "bursts" of 1 to 13 codas spaced fairly regularly in time. The mean number of codas in a burst was 3.46, and the standard deviation was 2.65. The time interval ratios within a coda are parameterized by the coda duration and by the first two interclick intervals normalized by coda duration. These three parameters remained highly stable within each coda series, with coefficients of variation within the series averaging less than 5%. The interval ratios varied somewhat across the data sets, but were highly stable over 8 of the 11 data sets, which span 11 years and widely dispersed geographic locations. Somewhat different interval ratios were observed in the other three data sets; in one of these data sets, the variant codas were produced by a young whale. Two sets of presumed sperm whale codas recorded in 1996 had 5- and 6-click patterns; the observation of these new patterns suggests that sperm whale codas in the Mediterranean may have more variations than previously believed.

Detection of serum antibodies against Chlamydia pneumoniae by in vitro neutralization and microimmunofluorescence assays

Antibodies to Chlamydia pneumoniae (IOL-207) were studied by the microimmunofluorescence (MIF) assay and in vitro neutralization in serum samples from 230 healthy adults and 332 patients at risk of C. pneumoniae infection. In the MIF test, the prevalence of immunoglobulin G (IgG) antibody was 53.9% among healthy subjects and 40.7% in the patients. An MIF antibody titre of > or = 1 : 512, consistent with acute infection by C. pneumoniae was documented in 23 out of 332 patients, and in none of the healthy adults. C. pneumoniae complement-dependent neutralizing antibody was detected in 25.8% and 31.2%, respectively of MIF-positive sera from healthy subjects and patients. The neutralizing antibody detection rate was 52.2% among the 23 patients with MIF titres of > or = 1 : 512. Complement-independent neutralization was observed in only 5 sera from healthy subjects and in 3 sera from patients. The complement-dependent neutralizing ability of sera significantly (p < 0.001) correlated with MIF titres.

Differences in the envelope proteins of Chlamydia pneumoniae, Chlamydia trachomatis, and Chlamydia psittaci shown by two-dimensional gel electrophoresis

Analysis by two-dimensional gel electrophoresis of the N-laurylsarkosinate(Sarkosyl)-insoluble envelope complexes of L-[35]S-cysteine-labeled elementary bodies of Chlamydia pneumoniae strain IOL-207, Chlamydia trachomatis serovar LGV2, D, and F, and Chlamydia psittaci strain 6BC showed differences in the molecular charges of chlamydial outer membrane proteins. The apparent isoelectric point (pI) of the major outer membrane protein of C. pneumoniae strain IOL-207 was 6.4, whereas the pI of the major outer membrane protein of the C. trachomatis and C. psittaci strains differed little from one another, ranging from 5.3 to 5.5. The 60-kDa cysteine-rich protein of C. pneumoniae was the only 60-kDa chlamydial protein with a pI value (5.9) more acidic than that of the corresponding major outer membrane protein. As a general rule, the charges of both the 60-kDa and the low-molecular-mass (12-15 kDa) cysteine-rich proteins were widely variable, depending on the strain. However, in each individual strain, the variation of the charge of the 60-kDa protein had a compensatory change in the low-molecular-mass cysteine-rich protein.

An immunofluorescence assay in microwell plate (IFA) for detecting serum antibodies to Chlamydia pneumoniae

An indirect immunofluorescence assay using a 96 microwell cell culture plate (IFA) was developed for the detection of antibodies to C. pneumoniae. The results obtained by IFA on 230 sera of healthy subjects were compared with those obtained with the microimmunofluorescence test. The correlation coefficient for IgG detection with the two methods was 0.96 showing good agreement.

Influence of centrifugation on the infectivity of Chlamydia pneumoniae IOL-207

The influence of centrifugation on the infectivity of Chlamydia pneumoniae IOL-207 was compared with seven serovars of C. trachomatis biovar trachoma, the three serovars of C. trachomatis biovar lymphogranuloma and four C. psittaci strains. Prolonged centrifugation from 1 to 4 hours resulted in a 3-fold increase in the infectivity of C. pneumoniae and variable or no increase in the infectivity of the other Chlamydia strains studied. These findings indicate that a 4 hour centrifugation of C. pneumoniae is recommended to improve the isolation procedures of this organism in cell cultures.

Assessment of the "Amplicor" PCR test in the diagnosis of Chlamydia trachomatis infection

We compared a commercially available PCR assay (Amplicor, Roche, Switzerland) and tissue culture isolation for the detection of C. trachomatis in urethral and/or endocervical swabs. Of the 200 patients studied (130 men and 70 women) PCR and tissue culture gave concordant results in 199 cases; in one case PCR was positive and culture negative. The Amplicor PCR assay proved fast and sensitive and suitable for routine use in most clinical microbiology laboratories.