A novel approach to designing viral precision vaccines applied to SARS-CoV-2.

Efficient precision vaccines against several highly pathogenic zoonotic viruses are currently lacking. Proteolytic activation is instrumental for a number of these viruses to gain host-cell entry and develop infectivity. For SARS-CoV-2, this process is enhanced by the insertion of a furin cleavage site at the junction of the spike protein S1/S2 subunits upstream of the metalloprotease TMPRSS2 common proteolytic site. Here, we describe a new approach based on specific epitopes selection from the region involved in proteolytic activation and infectivity for the engineering of precision candidate vaccinating antigens. This approach was developed through its application to the design of SARS-CoV-2 cross-variant candidates vaccinating antigens. It includes an in silico structural analysis of the viral region involved in infectivity, the identification of conserved immunogenic epitopes and the selection of those eliciting specific immune responses in infected people. The following step consists of engineering vaccinating antigens that carry the selected epitopes and mimic their 3D native structure. Using this approach, we demonstrated through a Covid-19 patient-centered study of a 500 patients' cohort, that the epitopes selected from SARS-CoV-2 protein S1/S2 junction elicited a neutralizing antibody response significantly associated with mild and asymptomatic COVID-19 (p<0.001), which strongly suggests protective immunity. Engineered antigens containing the SARS-CoV-2 selected epitopes and mimicking the native epitopes 3D structure generated neutralizing antibody response in mice. Our data show the potential of this combined computational and experimental approach for designing precision vaccines against viruses whose pathogenicity is contingent upon proteolytic activation.

Functional and structural responses of a halophilic consortium to oily sludge during biodegradation.

Biotreatment of oily sludge and the involved microbial communities, particularly in saline environments, have been rarely investigated. We enriched a halophilic bacterial consortium (OS-100) from petroleum refining oily sludge, which degraded almost 86% of the aliphatic hydrocarbon (C10-C30) fraction of the oily sludge within 7 days in the presence of 100 g/L NaCl. Two halophilic hydrocarbon-degrading bacteria related to the genera Chromohalobacter and Halomonas were isolated from the OS-100 consortium. Hydrocarbon degradation by the OS-100 consortium was relatively higher compared to the isolated bacteria, indicating potential synergistic interactions among the OS-100 community members. Exclusion of FeCl2, MgCl2, CaCl2, trace elements, and vitamins from the culture medium did not significantly affect the hydrocarbon degradation efficiency of the OS-100 consortium. To the contrary, hydrocarbon biodegradation dropped from 94.1 to 54.4% and 5% when the OS-100 consortium was deprived from phosphate and nitrogen sources in the culture medium, respectively. Quantitative PCR revealed that alkB gene expression increased up to the 3rd day of incubation with 11.277-fold, consistent with the observed increments in hydrocarbon degradation. Illumina-MiSeq sequencing of 16 S rRNA gene fragments revealed that the OS-100 consortium was mainly composed of the genera Halomonas, Idiomarina, Alcanivorax and Chromohalobacter. This community structure changed depending on the culturing conditions. However, remarkable changes in the community structure were not always associated with remarkable shifts in the hydrocarbonoclastic activity and vice versa. The results show that probably synergistic interactions between community members and different subpopulations of the OS-100 consortium contributed to salinity tolerance and hydrocarbon degradation.

How concerning is a SARS-CoV-2 variant of concern? Computational predictions and the variants labeling system.

In this study, we evaluated the use of a predictive computational approach for SARS-CoV-2 genetic variations analysis in improving the current variant labeling system. First, we reviewed the basis of the system developed by the World Health Organization (WHO) for the labeling of SARS-CoV-2 genetic variants and the derivative adapted by the United States Centers for Disease Control and Prevention (CDC). Both labeling systems are based on the virus' major attributes. However, we found that the labeling criteria of the SARS-CoV-2 variants derived from these attributes are not accurately defined and are used differently by the two agencies. Consequently, discrepancies exist between the labels given by WHO and the CDC to the same variants. Our observations suggest that giving the variant of concern (VOC) label to a new variant is premature and might not be appropriate. Therefore, we used a comparative computational approach to predict the effects of the mutations on the virus structure and functions of five VOCs. By linking these data to the criteria used by WHO/CDC for variant labeling, we ascertained that a predictive computational comparative approach of the genetic variations is a good way for rapid and more accurate labeling of SARS-CoV-2 variants. We propose to label all emergent variants, variant under monitoring or variant being monitored (VUM/VBM), and to carry out computational predictive studies with thorough comparison to existing variants, upon which more appropriate and informative labels can be attributed. Furthermore, harmonization of the variant labeling system would be globally beneficial to communicate about and fight the COVID-19 pandemic.

Heavy Vacuum Gas Oil Upregulates the Rhamnosyltransferases and Quorum Sensing Cascades of Rhamnolipids Biosynthesis in Pseudomonas sp. AK6U.

We followed a comparative approach to investigate how heavy vacuum gas oil (HVGO) affects the expression of genes involved in biosurfactants biosynthesis and the composition of the rhamnolipid congeners in Pseudomonas sp. AK6U. HVGO stimulated biosurfactants production as indicated by the lower surface tension (26 mN/m) and higher yield (7.8 g/L) compared to a glucose culture (49.7 mN/m, 0.305 g/L). Quantitative real-time PCR showed that the biosurfactants production genes rhlA and rhlB were strongly upregulated in the HVGO culture during the early and late exponential growth phases. To the contrary, the rhamnose biosynthesis genes algC, rmlA and rmlC were downregulated in the HVGO culture. Genes of the quorum sensing systems which regulate biosurfactants biosynthesis exhibited a hierarchical expression profile. The lasI gene was strongly upregulated (20-fold) in the HVGO culture during the early log phase, whereas both rhlI and pqsE were upregulated during the late log phase. Rhamnolipid congener analysis using high-performance liquid chromatography-mass spectrometry revealed a much higher proportion (up to 69%) of the high-molecularweight homologue Rha-Rha-C10-C10 in the HVGO culture. The results shed light on the temporal and carbon source-mediated shifts in rhamonlipids' composition and regulation of biosynthesis which can be potentially exploited to produce different rhamnolipid formulations tailored for specific applications.

Mirabegron versus Solifenacin in Children with Overactive Bladder: Prospective Randomized Single-Blind Controlled Trial.

PURPOSE: The purpose of this study is to investigate the efficacy and safety of mirabegron versus solifenacin in the treatment of newly diagnosed overactive bladder (OAB) in children. METHODS: We conducted a prospective randomized controlled study on pediatric patients with newly diagnosed OAB. Patients were randomized into 3 groups: mirabegron (50 mg once daily) in group I, solifenacin (5 mg) in group II, and placebo in group III. Before starting our treatment and at the end of the 3 months course, we obtained a 3-day voiding diary. This diary included incontinence episode per day, mean voided volume per micturition, mean number of micturition per day, and post-void residual urine. Moreover, the parents/patients were asked to rate symptom relief, and the adverse events were recorded throughout the study period. RESULTS: A total of 190 patients aged from 5 to 14 years completed this study. At the end of this trial, both groups I and II showed significant improvement versus placebo regarding our efficacy parameters with no significant difference between group I and II. The overall success rate based on assessment of symptom relief was significantly higher in the treated groups (87.5% in I and 90.2% in II) versus placebo (55.8%). Dry mouth was reported in 2.8, 10, and 0% and constipation in 2.8, 11.4, and 1.4% in group I, II, and III, respectively, without statistically significant difference between group I and placebo. However, there was a significant difference between group II and placebo regarding these side effects. CONCLUSION: Both mirabegron and solifenacin have comparable efficacy regarding the control of OAB symptoms in the newly diagnosed children, but mirabegrone seems to have less side effects.

Management of 'forgotten' encrusted JJ stents using extracorporeal shockwave lithotripsy: A single-centre experience.

Objective: To evaluate the role of extracorporeal shockwave lithotripsy (ESWL) for the management of 'forgotten' encrusted stents. Patients and Method: This is a retrospective study of 133 patients with forgotten JJ stents, treated between January 2015 and January 2018. Encrustation was mainly found in the renal coil of the stent with distal concomitant encrustation in the vesical and/or ureteric segment. After laboratory and radiological assessment, treatment started with ESWL for the renal encrustation before successful extraction. Auxiliary endourological procedures were used for the encrusted vesical or ureteric segments. Failed cases underwent open surgery. Results: The mean (SD; range) JJ stent indwelling time was 25.84 (10; 14-70) months. In all, 96 (72.2%) patients were seen after treatment for stone disease. In total, 94 patients (70.7%) were managed by ESWL monotherapy, whilst in 36 (27%) additional endourological procedures were required before successful extraction including: cystolithotripsy 19 patients (52.8%), ureteroscopic lithotripsy eight (22.2%), and percutaneous nephrolithotomy nine (25%). Open surgery was required in only three patients (2.3%). A mean of 0.28 procedures per patient was required before smooth stent extraction. The encrusted stents were removed after the first, second, third, and fourth ESWL sessions in 44 patients (33.1%), 43 (32.3%), 26 (19.5%), and 17 (12.8%), respectively. Patients with forgotten indwelling JJ stents for >2 years had significantly larger and harder encrustation at both JJ coils. Conclusion: ESWL proved a feasible first-line treatment for forgotten encrusted JJ stents. The indwelling time of forgotten stents in the urinary tract is associated with greater encrustation burden, density and multiple sites of encrustation. Abbreviations: CLT: cystolithotripsy; ESWL: extracorporeal shockwave lithotripsy; HU: Hounsfield unit; KUB: plain abdominal radiograph of the kidneys, ureters and bladder; PCNL: percutaneous nephrolithotomy; URL: ureteroscopic lithotripsy.

Outcome of Modification of Dose and Time of Administration of Tamsulosin in Men with Abnormal Ejaculation.

INTRODUCTION: Alpha-adrenergic blockers are now the cornerstone medication in management of lower urinary tract symptom (LUTS); however, the associated treatment-related abnormal ejaculation could be a bothersome event. This is a comparative study among different methods of tamsulosin administration in terms of efficacy, recoverability of ejaculatory function, and quality of life (QoL) in men with tamsulosin-related abnormal ejaculation. PATIENTS AND METHODS: Sexually active men receiving tamsulosin for LUTS who were bothered by treatment-related abnormal ejaculation following initiation of tamsulosin were randomized into 3 groups; group A received intermittent-full-standard-dose, group B received low-dose-tamsulosin, and group C received full-standard-dose tamsulosin The status of ejaculatory function, IPSS, QoL score, and Q-Max were measured at baseline and 3 months later. RESULTS: A total of 93 men with mean age of 53.1 years were included in the study, 3-months after randomization, statistically significant improvements in IPSS, QoL index, and Q-Max in comparison to pre-treatment levels were noted. Restoration of normal ejaculation was reported by 74.1 and 90.3% of patients in group A and B, respectively, versus none in group C. The QoL score was significant when comparing group A to the other groups; finally, the Q-Max was significant when comparing group C to the other groups. CONCLUSION: For patients bothered by tamsulosin-related abnormal ejaculation, a significant improvement in the QoL, without deviation from the therapeutic purpose of treatment, can be achieved by administration of 0.4 mg tamsulosin every other day.

A prospective randomised controlled study comparing bipolar plasma vaporisation of the prostate to monopolar transurethral resection of the prostate.

OBJECTIVES: To compare the safety and efficacy of bipolar transurethral plasma vaporisation (B-TUVP) as an alternative to the 'gold standard' monopolar transurethral resection of the prostate (M-TURP) for the treatment of benign prostatic hyperplasia (BPH) in a prospective randomised controlled study. PATIENTS AND METHODS: In all, 82 patients indicated for prostatectomy were assigned to two groups, group I (40 patients) underwent B-TUVP and group II (42 patients) underwent M-TURP. The safety of both techniques was evaluated by reporting perioperative changes in serum Na+, serum K+, haematocrit (packed cell volume), and any perioperative complications. For the efficacy assessment, patients were evaluated subjectively by comparing the improvement in International Prostate Symptom Score and objectively by measuring the maximum urinary flow rate (Qmax) and post-void residual urine volume (PVR) before and after the procedures. RESULTS: In group II, there was a significant perioperative drop in serum Na+ (from 137.5 to 129.4 mmol/L) and haematocrit (from 42.9% to 38.2%) (both P < 0.001). Moreover, one patient in group II had TUR syndrome. The remote postoperative complication rate was (15%) in group I and comprised of stress urinary incontinence (5%), bladder outlet obstruction (5%), and residual adenoma (5%). In group II, the remote postoperative complication rate was (4.8%), as two patients developed urethral stricture. There were statistically significant improvements in micturition variables postoperatively in both arms, but the magnitude of improvement was statistically more significant in group II. CONCLUSION: B-TUPV seems to be safer than M-TURP; however, the lack of a tissue specimen and the relatively high retreatment rate are major disadvantages of the B-TUVP technique. Moreover, M-TURP appears to be more effective than B-TUPV and its safety can be improved by careful case selection and adequate haemostasis.

Sulfur source-mediated transcriptional regulation of the rhlABC genes involved in biosurfactants production by Pseudomonas sp. strain AK6U.

Despite the nutritional significance of sulfur, its influence on biosurfactants production has not been sufficiently studied. We investigated the expression of key biosurfactants production genes, rhlABC, in cultures of Pseudomonas sp. AK6U grown with inorganic or organic sulfur sources. AK6U grew with either inorganic sulfate (MgSO4), dibenzothiophene (DBT), or DBT-sulfone as a sole sulfur source in the presence of glucose as a carbon source. The AK6U cultures produced variable amounts of biosurfactants depending on the utilized sulfur source. Biosurfactants production profile of the DBT cultures was significantly different from that of the DBT-sulfone and inorganic sulfate cultures. The last two cultures were very similar in terms of biosurfactants productivity. Biosurfactants yield in the DBT cultures (1.3 g/L) was higher than that produced by the DBT-sulfone (0.5 g/L) and the inorganic sulfate (0.44 g/L) cultures. Moreover, the surface tension reduction in the DBT cultures (33 mN/m) was much stronger than that measured in the DBT-sulfone (58 mN/m) or inorganic sulfate (54 mN/m) cultures. RT-qPCR revealed variations in the expression levels of the rhlABC genes depending on the sulfur source. The DBT cultures had higher expression levels for the three genes as compared to the DBT-sulfone and inorganic sulfate cultures. There was no significant difference in the expression profiles between the DBT-sulfone and the MgSO4 cultures. The increased expression of rhlC in the DBT cultures is indicative for production of higher amounts of dirhamnolipids compared to the DBT-sulfone and inorganic sulfate cultures. The gene expression results were in good agreement with the biosurfactants production yields and surface tension measurements. The sulfur source mediates a fine-tuned mechanism of transcriptional regulation of biosurfactants production genes. Our findings can have an impact on industrial production of biosurfactants and other biotechnological processes like biodesulfurization.

The development of ureteric strictures after ureteroscopic treatment for ureteric calculi: A long-term study at two academic centres.

OBJECTIVE: To determine the incidence of symptomatic and 'silent' obstruction after ureteroscopic procedures. PATIENTS AND METHODS: In all, 1980 patients underwent ureteroscopy for ureteric calculi in two large centres. The methods of disintegration, auxiliary procedures used and type of stenting were considered. Intraoperative complications, in addition to the size and site of the stone, were assessed in relation to postoperative obstruction. The mean (range) follow-up was 42 (12-68) months, with patients assessed after 3-6 months and yearly thereafter. The postoperative evaluation included an assessment of pain, renal ultrasonography, a plain abdominal film, intravenous urography, and a diuretic renal scan in some cases to confirm obstruction. RESULTS: The success rate of stone removal was 98.5%. The failures were related to the size of the stone (>2 cm; P < 0.001). In eight patients there was a ureteric perforation, and six of these developed a ureteric stricture. A stricture also occurred in 12 patients (0.6%) during the follow-up; these included nine of 204 with stones of >2 cm (4.4%), compared to three (0.17%) of 1746 patients with stones of <2 cm (P < 0.001). Fourteen patients presented with pain (0.7%), and five had no obstruction, while in nine (0.46%) the pain was associated with obstruction. There was silent obstruction in three cases (0.15%). The negative and positive predictive values for pain were 99.8% and 64.3%, respectively. CONCLUSIONS: Radiographic surveillance for stricture formation and obstruction is mandatory in patients who are symptomatic after ureteroscopy, and for up to 18 months in patients with intraoperative complications or with a stone of >2 cm in the proximal ureter.

Endoscopic urethroplasty using small intestinal submucosal patch in cases of recurrent urethral stricture: a preliminary study.

OBJECTIVES: The objective of this study was to evaluate the results of internal urethrotomy with endoscopically placed small intestinal submucosa (SIS) graft for treatment of selected cases of recurrent urethral stricture. PATIENTS AND METHODS: This prospective study included 10 patients with recurrent inflammatory bulbar urethral stricture of 0.5-2 cm in length with no dense spongiofibrosis. Following the 12 o'clock visual internal urethrotomy, a prepared 12F Foley's silicon catheter with the SIS patch was introduced into the urethra over a preplaced super-stiff guidewire. The advancement of this catheter was monitored via a 15F urethroscope to enable us to put its balloon with the overlying SIS patch at the site of the urethral incision. Thereafter, the balloon was inflated with saline and the catheter was secured with a silk suture to the glans. In addition, a suprapubic cystostomy was fixed for bladder drainage. These catheters were kept in place for 2 weeks. The patients were followed up at regular intervals using uroflowmetry and ascending urethrography. RESULTS: At 3-month follow-up, only two cases showed mild recurrent stricture and the rest of cases had a normally patent functional urethra. The subsequent follow-up studies of all the eight successful cases for 12-18 months revealed no evidence of recurrent stricture in all of them and no more interventions were required for any of them. On the other hand, the two cases with recurrent stricture showed a satisfactory response to regular monthly urethral dilatation. CONCLUSION: Endoscopic urethroplasty using SIS patch can be considered as a minimally invasive solution for cases with recurrent, short urethral stricture that are associated with mild spongiofibrosis.