IFN-λ3 is induced by Leishmania donovani and can inhibit parasite growth in cell line models but not in the mouse model, while it shows a significant association with leishmaniasis in humans.

The intracellular protozoan parasite Leishmania donovani causes debilitating human diseases that involve visceral and dermal manifestations. Type 3 interferons (IFNs), also referred to as lambda IFNs (IFNL, IFN-L, or IFN-λ), are known to play protective roles against intracellular pathogens at the epithelial surfaces. Herein, we show that L. donovani induces IFN-λ3 in human as well as mouse cell line-derived macrophages. Interestingly, IFN-λ3 treatment significantly decreased parasite load in infected cells, mainly by increasing reactive oxygen species production. Microscopic examination showed that IFN-λ3 inhibited uptake but not replication, while the phagocytic ability of the cells was not affected. This was confirmed by experiments that showed that IFN-λ3 could decrease parasite load only when added to the medium at earlier time points, either during or soon after parasite uptake, but had no effect on parasite load when added at 24 h post-infection, suggesting that an early event during parasite uptake was targeted. Furthermore, the parasites could overcome the inhibitory effect of IFN-λ3, which was added at earlier time points, within 2-3 days post-infection. BALB/c mice treated with IFN-λ3 before infection led to a significant increase in expression of IL-4 and ARG1 post-infection in the spleen and liver, respectively, and to different pathological changes, especially in the liver, but not to changes in parasite load. Treatment with IFN-λ3 during infection did not decrease the parasite load in the spleen either. However, IFN-λ3 was significantly increased in the sera of visceral leishmaniasis patients, and the IFNL genetic variant rs12979860 was significantly associated with susceptibility to leishmaniasis.

Evidence for a sex-dependent effect modification in the association between IFN-λ DNA polymorphisms and expression of IFN-λ and interferon-stimulated genes in human PBMCs.

Human interferon (IFN) lambda (IFNL, IFN-L or IFN-λ) locus has several functional genetic variants but their role in regulating in vivo gene expression, and whether they associate with antiviral states in healthy individuals, is not clear. In this study, we recruited âˆ¼550 healthy individuals belonging to both sexes, genotyped them for several IFNL genetic variants and measured, by qPCR, the expression of IFNL2/3, IFNL4 and four IFN-stimulated genes (ISGs) (MX1, OAS1, ISG15 and RSAD2) from their peripheral blood mononuclear cells (PBMC) both before and after stimulation with a viral mimic, poly I: C. We also measured secreted levels of several cytokines including IFN-λ1 and IFN-λ3 in poly I:C stimulated PBMCs. We found that males secrete higher levels of IFN-λs than females. The IFNL3/4 genetic variants significantly associated with secreted levels of both IFN-λ1 and IFN-λ3 in opposite directions, only in males. While the IFNL3/4 variants significantly associated with ISG expression either in basal or poly I:C induced or in both states, the direction of effect was opposite for the two sexes, suggesting that sex was a strong effect modifier. We did not see this trend in the association of ISG expression with the IFNL1 polymorphism, rs7247086, whose association with ISG expression and secreted IFN-λ3 levels was seen in females but not in males. Further, expression of several genes was associated with the IFN-λ4 activity-modifying variant rs117648444. However, we neither saw any strong correlation between levels of IFN-λ1/3 and ISG expression, nor did we see any strong evidence of IFNL4 expression that could be responsible for the association between ISG expression and IFNL genetic variants. These results suggest that there are complex interactions involving gender, IFN-λs, IFN-λ genetic variants and antiviral states in humans.

Genetically encoded intrabody sensors report the interaction and trafficking of ß-arrestin 1 upon activation of G-protein-coupled receptors.

Agonist stimulation of G-protein-coupled receptors (GPCRs) typically leads to phosphorylation of GPCRs and binding to multifunctional proteins called ß-arrestins (ßarrs). The GPCR-ßarr interaction critically contributes to GPCR desensitization, endocytosis, and downstream signaling, and GPCR-ßarr complex formation can be used as a generic readout of GPCR and ßarr activation. Although several methods are currently available to monitor GPCR-ßarr interactions, additional sensors to visualize them may expand the toolbox and complement existing methods. We have previously described antibody fragments (FABs) that recognize activated ßarr1 upon its interaction with the vasopressin V2 receptor C-terminal phosphopeptide (V2Rpp). Here, we demonstrate that these FABs efficiently report the formation of a GPCR-ßarr1 complex for a broad set of chimeric GPCRs harboring the V2R C terminus. We adapted these FABs to an intrabody format by converting them to single-chain variable fragments and used them to monitor the localization and trafficking of ßarr1 in live cells. We observed that upon agonist simulation of cells expressing chimeric GPCRs, these intrabodies first translocate to the cell surface, followed by trafficking into intracellular vesicles. The translocation pattern of intrabodies mirrored that of ßarr1, and the intrabodies co-localized with ßarr1 at the cell surface and in intracellular vesicles. Interestingly, we discovered that intrabody sensors can also report ßarr1 recruitment and trafficking for several unmodified GPCRs. Our characterization of intrabody sensors for ßarr1 recruitment and trafficking expands currently available approaches to visualize GPCR-ßarr1 binding, which may help decipher additional aspects of GPCR signaling and regulation.

Functional genetic variants of the IFN-λ3 (IL28B) gene and transcription factor interactions on its promoter.

Interferon lambda 3 (IFN-λ3 or IFNL3, formerly IL28B), a type III interferon, modulates immune responses during infection/inflammation. Several human studies have reported an association of single nucleotide polymorphisms (SNP) in the IFNL3 locus with expression level of IFNL3. Previous genetic studies, in the context of hepatitis C virus infections, had predicted three regulatory SNPs: rs4803219, rs28416813 and rs4803217 that could have functional/causal roles. Subsequent studies confirmed this prediction for rs28416813 and rs4803217. A dinucleotide TA-repeat variant (rs72258881) has also been reported to be regulating the IFN-λ3 promoter. In this study, we tested all these genetic variants using a sensitive reporter assay. We show that the minor/ancestral alleles of both rs28416813 and rs4803217, together have a strong inhibitory effect on reporter gene expression. We also show an interaction between the two principal transcription factors regulating IFNL3 promoter: IRF7 and NF-kB RelA/p65. We show that IRF7 and p65 physically interact with each other. By using a transient ChIP assay, we show that presence of p65 increases the promoter occupancy of IRF7, thereby leading to synergistic activation of the IFNL3 promoter. We reason that, in contrast to p65, a unique nature of IRF7 binding to its specific DNA sequence makes it more sensitive to changes in DNA phasing. As a result, we see that IRF7, but not p65-mediated transcriptional activity is affected by the phase changes introduced by the TA-repeat polymorphism. Overall, we see that three genetic variants: rs28416813, rs4803217 and rs72258881 could have functional roles in controlling IFNL3 gene expression.

Purification of native CCL7 and its functional interaction with selected chemokine receptors.

Chemokine receptors form a major sub-family of G protein-coupled receptors (GPCRs) and they are involved in a number of cellular and physiological processes related to our immune response and regulation. A better structural understanding of ligand-binding, activation, signaling and regulation of chemokine receptors is very important to design potentially therapeutic interventions for human disorders arising from aberrant chemokine signaling. One of the key limitations in probing the structural details of chemokine receptors is the availability of large amounts of purified, homogenous and fully functional chemokine ligands, and the commercially available products, are not affordable for in-depth structural studies. Moreover, production of uniformly isotope-labeled chemokines, for example, suitable for NMR-based structural investigation, also remains challenging. Here, we have designed a streamlined approach to express and purify the human chemokine CCL7 as well as its 15N-, 15N/13C-, 2H/15N/13C- isotope-labeled derivatives, at milligram levels using E. coli expression system. Purified CCL7 not only maintains a well-folded three-dimensional structure as analyzed using circular dichroism and 1H/15N NMR but it also induces coupling of heterotrimeric G-proteins and ß-arrestins for selected chemokine receptors in cellular system. We compared cAMP response induced by histidine tagged CCL7 and native CCL7 and found that modification of the N-terminus of CCL7 compromises its functionality. Our strategy presented here may be applicable to other chemokines and therefore, provide a potentially generic and cost-effective approach to produce chemokines in large amounts for functional and structural studies.

Gender-dependent multiple cross-phenotype association of interferon lambda genetic variants with peripheral blood profiles in healthy individuals.

BACKGROUND: Type III interferons (IFN), also called as lambda IFNs (IFN-λs), are antiviral and immunomodulatory cytokines that are evolutionarily important in humans. Given their central roles in innate immunity, they could be influencing other aspects of human biology. This study aimed to examine the association of genetic variants that control the expression and/or activity of IFN-λ3 and IFN-λ4 with multiple phenotypes in blood profiles of healthy individuals. METHODS: In a cohort of about 550 self-declared healthy individuals, after applying several exclusion criteria to determine their health status, we measured 30 blood parameters, including cellular, biochemical, and metabolic profiles. We genotyped them at rs12979860 and rs28416813 using competitive allele-specific PCR assays and tested their association with the blood profiles under dominant and recessive models for the minor allele. IFN-λ4 variants rs368234815 and rs117648444 were also genotyped or inferred. RESULTS: We saw no association in the combined cohort under either of the models for any of the phenotypes. When we stratified the cohort based on gender, we saw a significant association only in males with monocyte (p = 1 × 10-3 ) and SGOT (p = 7 × 10-3 ) levels under the dominant model and with uric acid levels (p = 0.01) under the recessive model. When we tested the IFN-λ4 activity modifying variant within groupings based on absence or presence of one or two copies of IFN-λ4 and on different activity levels of IFN-λ4, we found significant (p < 0.05) association with several phenotypes like monocyte, triglyceride, VLDL, ALP, and uric acid levels, only in males. All the above significant associations did not show any confounding when we tested for the same with up to ten different demographic and lifestyle variables. CONCLUSIONS: These results show that lambda interferons can have pleiotropic effects. However, gender seems to be an effect modifier, with males being more sensitive than females to the effect.

Identification and analysis of gamma-irradiation-induced Stemphylium blight tolerant lentil (Lens culinaris) mutant.

In the short-season winter environment of India and Bangladesh, lentil growth and seed yield are significantly hindered by foliar blight caused by Stemphylium botryosum. As the international germplasm pool lacks a resistance source, the study aims to develop a mutant population to identify a high-yielding mutant resistance against the pathogen. A gamma-irradiated population was developed based on its GR50 dose of 248.8 Gy. The screening of almost 130,000 M2 plants identified a tolerant lentil mutant, MM216. The multi-location trials revealed that MM216 showed an impressive and robust resistance; the selected mutant line could be recommended as a donor in the lentil breeding program against the pathogen globally. A 100 g seed was exposed to a GR50 dose to develop the M1 population. At maturity, at least 100 M2 seeds of each 1300 M1 plant were harvested individually. So, almost 130,000 M2 plants were screened in the disease hot spot. The selected mutants were advanced to M7 by screening in the field and challenged in controlled conditions with the pure pathogen isolate. A resistance mutant, MM216, with a per cent disease index (PDI) of <10, was identified where the mean of the check varieties, WBL 77, was >55. The resistance ability was confirmed further in controlled conditions. The fungal and plant DNA ratio was almost negligible in the tolerant mutant, whereas it was 0.17 in WBL77 at 196 h post-inoculation. The selected mutant did not display any yield penalty, but there was a delay in flowering by a week compared to WBL77.

Machine learning and DFT-based combined framework for predicting transmission spectra of quantum-confined bio-molecular nanotube.

CONTEXT: The Adenine-based nanotube is theoretically designed, and its transmission spectra are investigated. The quantum-confined Adenine nanotube shows electronic transmission of the carrier at minimum stress. In this paper, the prediction of transmission spectra of the quantum-confined bio-molecular nanotube is investigated and deeply studied. Molecular level structure prediction and their electronic characterization can be possible with ab initio accuracy using a machine learning algorithmic approach. At the molecular level, it is difficult to predict quantum transmission spectra as these results are always hampered by the carrier backscattering effect. However, mostly these predictive models are available for intrinsic semi-conducting materials and other inorganic structures. METHODS: Machine learning algorithms are designed to predict the electronic properties of the nano-scale structure. This task is even more difficult when quantum-confined molecular arrangements are considered, whose transmission spectra are sensitive to the confinements applied. This paper presents an effective machine learning algorithms framework for predicting transmission spectra of quantum-confined nanotubes from their geometries. In this paper, we consider regression machine learning algorithms to find maximum accuracy with varying configurations and geometries to excerpt their atoms' local environment information. The Hamiltonian components are then used to enable the utilization of the information to predict the electronic structure at any arbitrary sampling point or k-point. The theoretical basics introduced in this process help to capture and incorporate minor changes in quantum confinements into transmission spectra and provide the framework algorithm with more accuracy. This paper shows the ability to predict the accurate algorithmic models of the Adenine nanotube. In this framework, we have considered a tiny data set to achieve a rapid and reliable method for electronic structure determination and also propose the best algorithm for predictive model analysis.

A mis-splicing early flowering 3 (elf3) allele of lentil is associated with yield enhancement under terminal heat stress.

There is a vast scope of area expansion of lentils after harvesting wet rice in South Asia. However, due to the photoperiod effect and terminal heat, the existing short-duration varieties failed to minimize yield loss under late-sown conditions. A mis-splicing causing A/G SNP present in the last nucleotide of exon 3 of early flowering 3 (ELF3) gene (elf3 allele) in a lentil line, L4710, is associated with the photoperiod insensitive flowering and the fast absolute growth rate (AGR). None of the Indian cultivars tested in this study, either early or late, possesses the non-functional elf3 allele. However, the A to G transition in ELF3-exon2 replaces glycine with aspartic acid at the 403rd amino acid in all the Indian varieties tested, compared to the reference sequence of Mediterranean accession, ILL5588. Therefore, targeting A/G SNP of exon 3, a PCR-based codominant marker is developed. The elf3 allele is correlated with the fast AGR and early flowering, but low yield and biomass, in an L4710 × LL56-derived RIL-population, compared to ELF3 carrying alleles when sown on 15th November. However, in a month of delayed sowing (20th December), the same elf3-RILs revealed a higher yield and biomass with slower AGR Moreover, three elf3-carrying lines, grown in delayed condition (20 December) for two consecutive years in three locations, outyielded three popular high-yielding cultivars that carry functional ELF3. Thus, elf3-carrying high-yielding lines could be the breeder's choice to expand and enhance lentil yield in short-season environments and in vast rice fallows of south Asia, where delayed rice harvest occurs frequently.

Measuring surface expression and endocytosis of GPCRs using whole-cell ELISA.

G protein-coupled receptors (GPCRs) constitute a large class of cell surface receptors that recognize a wide array of ligands and mediate a diverse spectrum of signaling pathways. Measuring their surface expression in cellular context is a critical aspect of studying their signaling pathways and cellular outcomes. Upon addition of agonist, GPCRs typically undergo internalization and traffic from the plasma membrane to endosomal compartments. Although radioligand binding has been the primary assay to measure GPCR surface expression and internalization, whole-cell ELISA has now emerged as a powerful alternative approach. Here, we present a step-by-step whole-cell ELISA protocol for measuring relative surface expression and agonist-induced internalization of GPCRs containing engineered N-terminal epitope tag and recombinantly expressed in heterologous cells.

Cone-beam computed tomography a reliable tool for morphometric analysis of the foramen magnum and a boon for forensic odontologists.

BACKGROUND/AIM: The aim of this pilot study was to perform morphometric analysis of the foramen magnum (FM) using cone-beam computed tomography (CBCT). MATERIALS AND METHODS: This study included CBCT images of 120 individuals (60 males and 60 females). The sagittal and transverse diameters and circumference of the FM were measured. The data were statistically analyzed with Chi-square and t-tests to assess the level of significance for sex and age. RESULTS: The means of its sagittal and transverse diameters and also circumference were higher in males than in females. Statistically significant differences were found between transverse and circumference in case of males and females for all variables (P < 0.05). No statistically significant difference (P > 0.05) was found in sagittal diameter and age groups for all variables. CONCLUSION: CBCT images can provide valuable information regarding FM and the measurements of its sagittal and transvers diameters and also its circumference may be reliably used for sexual dimorphism in anthropometric analysis and forensic medicine.

Conformational Sensors and Domain Swapping Reveal Structural and Functional Differences between ß-Arrestin Isoforms.

Desensitization, signaling, and trafficking of G-protein-coupled receptors (GPCRs) are critically regulated by multifunctional adaptor proteins, ß-arrestins (ßarrs). The two isoforms of ßarrs (ßarr1 and 2) share a high degree of sequence and structural similarity; still, however, they often mediate distinct functional outcomes in the context of GPCR signaling and regulation. A mechanistic basis for such a functional divergence of ßarr isoforms is still lacking. By using a set of complementary approaches, including antibody-fragment-based conformational sensors, we discover structural differences between ßarr1 and 2 upon their interaction with activated and phosphorylated receptors. Interestingly, domain-swapped chimeras of ßarrs display robust complementation in functional assays, thereby linking the structural differences between receptor-bound ßarr1 and 2 with their divergent functional outcomes. Our findings reveal important insights into the ability of ßarr isoforms to drive distinct functional outcomes and underscore the importance of integrating this aspect in the current framework of biased agonism.