Epitope-directed anti-SARS-CoV-2 scFv engineered against the key spike protein region could block membrane fusion

The newly emerged SARS-CoV-2 causing coronavirus disease (COVID-19) resulted in >500 million infections. A great deal about the molecular processes of virus infection in the host is getting uncovered. Two sequential proteolytic cleavages of viral spike protein by host proteases are prerequisites for the entry of the virus into the host cell. The first cleavage occurs at S1/S2 site by the furin protease, and the second cleavage at a fusion activation site, the S2' site, by the TMPRSS2 protease. S2' cleavage site is present in the S2 domain of spike protein followed by a fusion peptide. Given the S2' site to be conserved among all the SARS-CoV-2 variants, we chose an S2' epitope encompassing the S2' cleavage site and generated single-chain antibodies (scFvs) through an exhaustive phage display library screening. Crystal structure of a scFv in complex with S2' epitope was determined. Incidentally, S2' epitope in the scFv bound structure adopts an alpha-helical conformation equivalent to the conformation of the epitope in the spike protein. Furthermore, these scFvs can bind to the spike protein expressed either in vitro or on the mammalian cell surface. We illustrate a molecular model based on structural and biochemical insights into the antibody-S2' epitope interaction emphasizing scFvs mediated blocking of virus entry into the host cell by restricting the access of TMPRSS2 protease and consequently inhibiting the S2' cleavage competitively.

Sensory Changes Related to Dental Implant Placement: A Scoping Review

AIMS

To perform a scoping review of the literature to elucidate the occurrence of nerve damage related to dental implant placement and the factors causing the sensory changes.

METHODS

An extensive electronic search was conducted using the Cochrane Library, Medline via Ovid, PubMed, Wiley Online, Science Direct, CINAHL, and the Google Scholar databases from the year 1950 to 2020.

RESULTS

The search resulted in 1,067 articles, out of which 76 were selected for this review. The articles were categorized as literature review articles, retrospective studies, prospective studies, and case series/case reports. Altogether, 2,526 subjects were assessed retrospectively, with 5.27% transient and 1.39% persistent sensory changes, and a cohort of 2,750 subjects were followed prospectively, with 6.22% transient and 1.31% persistent sensory changes. A total of 336 subjects were enrolled in various case reports and case series, with 5.95% transient sensory changes and 84.52% persistent neurosensory changes. The articles included were not of high quality and have variations in their study designs and reporting procedures, with limited sensory change data to include in this study.

CONCLUSION

After surgical placement of dental implants in 5,612 patients, the incidence of transient sensory changes was 5.63%, and the incidence of persistent sensory changes was 6.33%. Factors affecting the incidence were: mandibular location of the implant, with the inferior alveolar nerve as the most commonly affected nerve. The common symptoms reported were paresthesia and dysesthesia. Age and gender were among other factors, for which data were not available in all the articles.

Dynamics of lipid displacement inside the hydrophobic cavity of a nonspecific lipid transfer protein from Solanum melongena

Nonspecific lipid transfer proteins are multifunctional and multispecific seed proteins with a characteristic hydrophobic cavity that runs form N-terminal to the C-terminal end. They are capable of binding and transferring different lipid molecules by means of their hydrophobic cavity. Apart from the cavity, lipid molecules bind and interact at key positions on the nsLTP surface as well. The plasticity of the hydrophobic cavity is an unusual property, considered as the primary lipid binding site. Here, we report a crystal structure of nsLTP from Solanum melongena with two lauric acid molecules bound inside the cavity. It has been observed that the extent of the N-terminal entry point and plasticity of the cavity can be extended, upon binding of one or two lipid molecules inside the cavity. The MD simulation further revealed that the lipid molecule shows high mobility inside the cavity and interestingly, was able to change its orientation. An alternate lipid entry site adjacent to the N-terminal end was uncovered during simulation and Arg-84 was implicated to be a potential regulatory residue aside from Tyr-59. Collectively, this study helps to understand that changes in orientation of the lipid inside the cavity could occur intermittently besides entering the cavity via tail-in-mechanism.Communicated by Ramaswamy H. Sarma.

Immunoaffinity purification of endogenous proteins from S. cerevisiae for post-translational modification and protein interaction analysis

Protein regulation by post-translational modifications and protein-protein interactions is critical to controlling molecular pathways. Here, we describe an immunoaffinity purification approach in Saccharomyces cerevisiae. The protocol uses an endogenously-expressed epitope-tagged protein and can be applied to the identification of post-translational modifications or protein binding partners. The lysine methyltransferase Set5 is used as an example here to purify phosphorylated Set5 and identify phosphosites; however, this approach can be applied to a diverse set of proteins in yeast.

For complete details on the use and execution of this protocol, please refer to Jaiswal et al. (2020).

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Preparation of yeast for immunoaffinity purification of proteins using the FLAG tag

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Detailed recommendations on optimization of immunoaffinity purifications

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Versatile method for identifying post-translational modifications or protein interactors

Set4 regulates stress response genes and coordinates histone deacetylases within yeast subtelomeres

The yeast chromatin protein Set4 is a member of the Set3-subfamily of SET domain proteins which play critical roles in the regulation of gene expression in diverse developmental and environmental contexts. We previously reported that Set4 promotes survival during oxidative stress and regulates expression of stress response genes via stress-dependent chromatin localization. In this study, global gene expression analysis and investigation of histone modification status identified a role for Set4 in maintaining gene repressive mechanisms within yeast subtelomeres under both normal and stress conditions. We show that Set4 works in a partially overlapping pathway to the SIR complex and the histone deacetylase Rpd3 to maintain proper levels of histone acetylation and expression of stress response genes encoded in subtelomeres. This role for Set4 is particularly critical for cells under hypoxic conditions, where the loss of Set4 decreases cell fitness and cell wall integrity. These findings uncover a new regulator of subtelomeric chromatin that is key to stress defense pathways and demonstrate a function for Set4 in regulating repressive, heterochromatin-like environments.

Set4 is a chromatin-associated protein, promotes survival during oxidative stress, and regulates stress response genes in yeast

The Set4 protein in the yeast Saccharomyces cerevisiae contains both a PHD finger and a SET domain, a common signature of chromatin-associated proteins, and shares sequence homology with the yeast protein Set3, the fly protein UpSET, and the human protein mixed-lineage leukemia 5 (MLL5). However, the biological role for Set4 and its potential function in chromatin regulation has not been well defined. Here, we analyzed yeast cell phenotypes associated with loss of Set4 or its overexpression, which revealed that Set4 protects against oxidative stress induced by hydrogen peroxide. Gene expression analysis indicated that Set4 promotes the activation of stress response genes in the presence of oxidative insults. Using ChIP analysis and other biochemical assays, we also found that Set4 interacts with chromatin and directly localizes to stress response genes upon oxidative stress. However, recombinant Set4 did not show detectable methyltransferase activity on histones. Our findings also suggest that Set4 abundance in the cell is balanced under normal and stress conditions to promote survival. Overall, these results suggest a model in which Set4 is a stress-responsive, chromatin-associated protein that activates gene expression programs required for cellular protection against oxidative stress. This work advances our understanding of mechanisms that protect cells during oxidative stress and further defines the role of the Set3-Set4 subfamily of SET domain-containing proteins in controlling gene expression in response to adverse environmental conditions.

Chromatin Immunoprecipitation (ChIP) of Histone Modifications from Saccharomyces cerevisiae

Histone post-translational modifications (PTMs), such as acetylation, methylation and phosphorylation, are dynamically regulated by a series of enzymes that add or remove these marks in response to signals received by the cell. These PTMS are key contributors to the regulation of processes such as gene expression control and DNA repair. Chromatin immunoprecipitation (chIP) has been an instrumental approach for dissecting the abundance and localization of many histone PTMs throughout the genome in response to diverse perturbations to the cell. Here, a versatile method for performing chIP of post-translationally modified histones from the budding yeast Saccharomyces cerevisiae (S. cerevisiae) is described. This method relies on crosslinking of proteins and DNA using formaldehyde treatment of yeast cultures, generation of yeast lysates by bead beating, solubilization of chromatin fragments by micrococcal nuclease, and immunoprecipitation of histone-DNA complexes. DNA associated with the histone mark of interest is purified and subjected to quantitative PCR analysis to evaluate its enrichment at multiple loci throughout the genome. Representative experiments probing the localization of the histone marks H3K4me2 and H4K16ac in wildtype and mutant yeast are discussed to demonstrate data analysis and interpretation. This method is suitable for a variety of histone PTMs and can be performed with different mutant strains or in the presence of diverse environmental stresses, making it an excellent tool for investigating changes in chromatin dynamics under different conditions.

Gr/gr deletions on Y-chromosome correlate with male infertility: an original study, meta-analyses, and trial sequential analyses

We analyzed the AZFc region of the Y-chromosome for complete (b2/b4) and distinct partial deletions (gr/gr, b1/b3, b2/b3) in 822 infertile and 225 proven fertile men. We observed complete AZFc deletions in 0.97% and partial deletions in 6.20% of the cases. Among partial deletions, the frequency of gr/gr deletions was the highest (5.84%). The comparison of partial deletion data between cases and controls suggested a significant association of the gr/gr deletions with infertility (P = 0.0004); however, the other partial deletions did not correlate with infertility. In cohort analysis, men with gr/gr deletions had a relatively poor sperm count (54.20 ± 57.45 million/ml) in comparison to those without deletions (72.49 ± 60.06), though the difference was not statistically significant (p = 0.071). Meta-analysis also suggested that gr/gr deletions are significantly associated with male infertility risk (OR = 1.821, 95% CI = 1.39–2.37, p = 0.000). We also performed trial sequential analyses that strengthened the evidence for an overall significant association of gr/gr deletions with the risk of male infertility. Another meta-analysis suggested a significant association of the gr/gr deletions with low sperm count. In conclusion, the gr/gr deletions show a strong correlation with male infertility risk and low sperm count, particularly in the Caucasian populations.

Clinical evaluation of a new art material: Nanoparticulated resin-modified glass ionomer cement

Context:

The success of atraumatic restorative treatment (ART) technique depends on the restorative material; hence, clinical studies with various materials are necessary.

Aim:

The aim of the present study was to clinically evaluate and compare the nanoionomer and high-viscosity glass ionomer using United States Public Health Services (USPHS) Modified Cvar/Ryge Criteria with ART approach.

Materials and Methods:

Two primary molars in 50 healthy children aged between 5 and 8 years were selected for the study. The teeth were treated with ART and divided into two groups. The group 1 teeth were restored with nanoionomer (Ketac Nano 100 3M ESPE) and group 2 with high-viscosity glass ionomer cement (HVGIC), (Fuji IX GC). Each restoration was evaluated using the USPHS Modified Cvar/Ryge Criteria at baseline and 6 months’ and 12 months’ time interval.

Statistical analysis used:

Chi-squared (χ²) test.

Results:

Nanoionomer was significantly better than HVGIC with respect to color match at baseline, 6 months, and 12 months (P<0.001). Nanoionomers were also significantly better than HVGIC in case of cavosurface marginal discoloration and marginal adaptation (P<0.001) at 6 months and 12 months. There was no significant difference between the two materials with respect to secondary caries at 6 months (P>0.05), but at 12 months, nanoionomer was statistically better than HVGIC (P<0.05). There was no statistical significant difference with respect to anatomical form and postoperative sensitivity (P>0.05).

Conclusion:

The results indicate that nanoionomer can be a successful alternative restorative material for use with ART technique.

Association of the gonadotrophin-regulated testicular RNA helicase gene polymorphism with human male infertility

Gonadotrophin-regulated testicular RNA helicase (GRTH) plays an important role in RNA functions including nuclear transcription, pre-mRNA splicing and it regulates the translation of specific genes required for the progression of spermatogenesis. In this study, we analysed the association of GRTH gene IVS6+55G/T and c.852C/T polymorphisms with human male infertility. The study showed c.852 T allele was associated with an increased risk of male infertility (OR: 3.16, P = 0.008), whereas IVS6+55G/T allele conferred no risk. In Indian population, this is the first report on association of GRTH gene SNP polymorphism and male infertility and it underscores the significance of GRTH genotypes in modulating the risk of male infertility.

Association of the IL1RN gene VNTR polymorphism with human male infertility

Interleukin-1 (IL-1) is a regulatory cytokine that plays an important role in the maintenance of the immune environment of the testis, regulation of junction dynamics and cell differentiation during spermatogenesis. Members of the IL-1 family are pleiotropic cytokines that are involved in inflammation, immunoregulation and other homeostatic functions in the body. IL-1α, IL-1β, and the IL-1 receptor antagonistic molecule (IL-1 Ra) are expressed in the testis under normal homeostasis and they further increase upon infection/inflammation. In the present study we have examined the association of Variable Number Tandem Repeats (VNTR) polymorphism of the Interleukin-1 receptor antagonist gene (IL1RN) with human male infertility. The case-control study comprised of two groups: 331 idiopathic infertile patients and 358 fertile healthy men. The study indicates risk of IL1RN2 variant with male infertility (OR: 1.43, CI: 1.1546 to 1.7804, P = 0.001). To our best knowledge, this is the first report that links IL1RN VNTR polymorphism with human male infertility.

Prevalence of systemic and local disturbances in infants during primary teeth eruption: a clinical study

AIM

The purpose of this study was to find the correlations between local and systemic manifestations during primary teeth eruption and the eruption of various groups of teeth.

MATERIALS AND METHODS

The infants selected for the study purpose were between 6 months to 3 years of age who had at least one erupting tooth. The study group consisted of 894 infants and other 550 infants served as a control group. Questionnaires were distributed to all parents and the data was collected. Chi square test was performed to analyse the information obtained between the two groups. There were 378 girls (42.2%) and 516 boys (57.7%) in the study group. The control group consisted of 195 girls (35.4%) and 355 boys (64.5%).

RESULTS

The most common finding was gingival irritation 821 (95.9%) and the least common symptom observed in the study was running nose 234 (27.3%). The presence of fever diarrhea was seen in 101 (11.7%) infants. In the control group, 92.1% of the infants did not show any clinical manifestations.

CONCLUSION

An association was found between primary teeth eruption and local and systemic manifestations. Most manifestations were found during eruption of the primary incisors.

Long-term phosphorus fertility in wastewater-irrigated cropland

Land treatment of municipal wastewater effluent is a proven method for augmenting freshwater resources and avoiding direct nutrient discharges to surface waters. We assessed changes in soil test phosphorus (P) of the Ap horizon of cropped fields continuously irrigated for 26 yr with secondary effluent from the Penn State University wastewater treatment plant. For annual P additions averaging 97 kg P ha(-1), Mehlich-3 P (M3P) response in the 0- to 20-cm surface soil (initially < 20 mg kg(-1)) was represented by two lines. For the first 12 yr of irrigation, soil test P increased, with 14.5 kg P ha(-1) needed to increase M3P by 1 mg P kg(-1). After the initial buildup, M3P maintained a quasi-steady-state value of approximately 110 mg kg(-1). Over time, the surface soil equilibrium P concentration at zero sorption increased markedly (from < 1 to 5.5 mg P L(-1)), and extractable aluminum (Al) decreased significantly (P < 0.001). Speciation modeling using Visual MINTEQ suggests complexation of Al by dissolved organic carbon at site pH conditions. Loss of Al from the surface layer lowered its P-sorbing capacity, causing added effluent-P to move into the subsoil. Results suggest that current management practices can continue for many years without exceeding the surface soil M3P environmental threshold (200 mg kg(-1)) used in state P-based nutrient policies.

Effect of Curcuma longa freeze dried rhizome powder with milk in STZ induced diabetic rats

This study deals with the effects of freeze dried rhizome powder of Curcuma longa (C. longa) dissolved in milk on normal as well as diabetic models. Diabetes of type II and type I was within 3 days of a single administration of doses of 45 and 65 mg kg(-1) of streptozotocin respectively. Various parameters such as blood glucose levels, triglycerides, total cholesterol, high density lipoprotein, very low density lipoprotein, low density lipoprotein, serum glutamic oxaloacetic transaminase, serum glutamic pyruvate transaminase, alkaline phosphatase, creatinine, hemoglobin, urine protein and urine sugar in addition to body weight were taken in to consideration and were analyzed after administration of variable doses of rhizome powder. The dose of 200 mg kg(-1) was identified as the most effective dose as it increased HDL, Hb and bw (P<0.05) with significant decrease in the levels of blood glucose, lipid profile and hepatoprotective enzymes (P<0.001).

Managing biosolids runoff phosphorus using buffer strips enhanced with drinking water treatment residuals

Vegetated buffers strips typically have limited ability to reduce delivery of dissolved phosphorus (DP) from agricultural fields to surface waters. A field study was conducted to evaluate the ability of buffer strips enhanced with drinking water treatment residuals (WTRs) to control runoff P losses from surface-applied biosolids characterized by high water-extractable P (4 g kg(-)(1)). Simulated rainfall (62.4 mm h(-1)) was applied to grassed plots (3 m x 10.7 m including a 2.67 m downslope buffer) surface-amended with biosolids at 102 kg P ha(-1) until 30 min of runoff was collected. With buffer strips top-dressed with WTR (20 Mg ha(-1)), runoff total P (TP = 2.5 mg L(-1)) and total DP (TDP = 1.9 mg L(-1)) were not statistically lower (alpha = 0.05) compared to plots with unamended grass buffers (TP = 2.7 mg L(-1); TDP = 2.6 mg L(-1)). Although the applied WTR had excess capacity (Langmuir P maxima of 25 g P kg(-1)) to sorb all runoff P, kinetic experiments suggest that sheet flow travel time across the buffers ( approximately 30 s) was insufficient for significant P reduction. Effective interception of dissolved P in runoff water by WTR-enhanced buffer strips requires rapid P sorption kinetics and hydrologic flow behavior ensuring sufficient runoff residence time and WTR contact in the buffer. Substantial phosphate-adsorbent contact opportunity may be more easily achieved by incorporating WTRs into P-enriched soils or blending WTRs with applied P sources.

Effects of exercise on heart rate, QT, QTc and QT/QS2 in the Romano-Ward inherited long QT syndrome

Patients with the Romano-Ward inherited long QT syndrome have an incompletely defined cardiac sympathetic system abnormality, and exhibit ventricular arrhythmias during exercise, fear and anxiety. Treadmill and bicycle exercise were used to modulate cardiac autonomic activity in 27 Romano-Ward subjects and 27 normal controls. The heart rate, and the QT, QTc and QT/QS2 (ratio of electrical to mechanical systole) intervals were compared. Subjects with long QT were compared with normals. Those with a long QT interval had the following results: similar resting heart rates; lower rates during moderate (151.6 vs 169.6 beats/min, p = 0.04) and maximal (155.9 vs 182.1 beats/min, p = less than 0.001) exercise; an abnormal QT cycle-length relationship, with failure of the QT to shorten normally with increasing heart rate; an increase in QTc versus a decrease in normals; supine rest QT/QS2 ratio of 1.12 vs 0.93, p = 0.001; and an exercise QT/QS2 that increased by 30%, from 1.12 at rest to 1.45, versus 15%, in normals, from 0.93 to 1.07, p = 0.001. The lower heart rates and excessively prolonged QT/QS2 ratios during exercise further support an abnormality of, or abnormal cardiac response to, sympathetic activity. A QT/QS2 greater than 1.0 at rest, an exercise QT/QS2 ratio greater than 1.17, and an increase in QTc during moderate exercise may be helpful diagnostic findings in patients with borderline long QTc intervals at rest.