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ABSTRACT Objective: To identify the genetic markers of spina bifida through a systematic survey of the exome in an Indian cohort. Materials and Methods: Three consecutive patients (P1: 1 year, male; P2: 2.8 years, male; and P3: 10 years, female) with spina bifida (lumbosacral meningomyelocele) underwent whole-exome sequencing (libraries: SureSelect Human All Exon V8; sequencing: 2 150 bp paired-end run, 100x) with NovaSeq 6000. Data analysis was performed using SMART-One™ (secondary analysis) and SMARTer™ (tertiary analysis) for automated quality check, alignment (GRCh38/hg38), variant calling, annotation (ClinVar, OMIM, avsnp150, 1000 Genomes v5b, ExAC v0.3, gnomAD v4.0, and esp6500vi2all v0.0.25), v0.0.25), interpretation. The pathogenic and likely pathogenic (ClinVar/ InterVar), non-synonymous, exonic markers (read depth ≥ 5) were matched with the Familial Neural Tube Defects (Version 1.10) panel (FNTD panel). Results: Pathogenic variants overlapping with the FNTD panel were MTRR, CC2D2A, and ZIC2 in P1 and P2, TGIF1 in P1 only, and none in P3. Novel pathogenic/likely pathogenic variants common to all three patients were PRUNE1, PKD1, PDZD2, and DAB2 in the homozygous state as well as in the heterozygous state, PLK1 and NLGN2. The possible role of such markers in etiopathogenesis was explored through a literatur search. Conclusions: The genetic landscape of the spina bifida in an Indian cohort is diverse compared to that reported from other parts of the world. A comprehensive catalog of single-nucleotide variants in the etiopathogenesis of the spina bifida on a background of the Familial Neural Tube Defects Panel has been generated. Keywords: Gene panel, genetic markers, neural tube defects, spina bifida, whole-exome sequencing, Author(s): Prabudh Goel (corresponding author) [1]; Mahima Sharma [1]; Himani Kaushik [2]; Sourabh Kumar [1]; Harpreet Singh [3]; Vishesh Jain [1]; Anjan Kumar Dhua [1]; Devendra Kumar Yadav [1]; Neeta [...]

The sulfosugar sulfoquinovose (SQ) is produced by photosynthetic plants, algae, and cyanobacteria on a scale of 10 billion tons per annum. Its degradation, which is essential to allow cycling of its constituent carbon and sulfur, involves specialized glycosidases termed sulfoquinovosidases (SQases), which release SQ from sulfolipid glycoconjugates, so SQ can enter catabolism pathways. However, many SQ catabolic gene clusters lack a gene encoding a classical SQase. Here, we report the discovery of a new family of SQases that use an atypical oxidoreductive mechanism involving NAD+as a catalytic cofactor. Three-dimensional X-ray structures of complexes with SQ and NAD+provide insight into the catalytic mechanism, which involves transient oxidation at C3. Bioinformatic survey reveals this new family of NAD+-dependent SQases occurs within sulfoglycolytic and sulfolytic gene clusters that lack classical SQases and is distributed widely including within Roseobacterclade bacteria, suggesting an important contribution to marine sulfur cycling.

The advent of SHG microscopy for biological tissue characterization has opened up avenues in probing ultrastructural features of the sample. The nonlinear polarization properties of collagen manifest in the tissue SHG polarimetry response. As compared to the anisotropic properties of collagen probed using linear polarimetry, SHG probes into the alterations to tropocollagen structures and thus aids in representing early alterations during pathological tissue transformation. This review summarizes SHG polarimetric studies with stromal collagen and correlations with histopathology, primarily for cancerous tissues. Various configurations, such as basic SHG polarization microscopy, polarization in polarization out, and Stokes–Mueller, are discussed with relevant clinical applications.

Sulfoquinovose (SQ) is the anionic headgroup of the ubiquitous plant sulfolipid, sulfoquinovosyl diacylglycerol (SQDG). SQDG can undergo delipidation to give sulfoquinovosyl glycerol (SQGro) and further glycoside cleavage to give SQ, which can be metabolized through microbial sulfoglycolytic pathways. Exogenous SQDG metabolites are imported into bacteria through membrane spanning transporter proteins. The recently discovered sulfoglycolytic sulfoquinovose monooxygenase (sulfo-SMO) pathway in Agrobacterium tumefaciensfeatures a periplasmic sulfoquinovosyl glycerol binding protein, SmoF, and an ATP-binding cassette (ABC) transporter. Here, we use X-ray crystallography, differential scanning fluorimetry and isothermal titration calorimetry to study SQ glycoside recognition by SmoF. This work reveals that in addition to SQGro, SmoF can also bind SQ, a simple methyl glycoside and even a short-chain SQDG analogue. Molecular recognition of these substrates is achieved through conserved interactions with the SQ-headgroup together with more plastic interactions with the aglycones. This suggests that the solute binding protein of A. tumefaciens,and related SQ-binding proteins from other sulfoglycolytic pathways, can provide their host organisms direct access to most of the SQ metabolites known to be produced by phototrophs.

Optical polarimetry has increased interest in probing finer details of soft tissue components representing alterations during pathological tissue transformation. Stromal collagen, a potential candidate for optical polarimetry, plays a vital role during the developmental stages of cancer. This review presents an overview of the biology and optical response of stromal collagen followed by instrumentation and image analysis in various optical polarimetry configurations that help extract the relevant features for efficient tissue classification for diagnostic applications. Part 1 deals with the linear optical polarization properties of collagen, while Part 2 probes the extraction of finer structural details of collagen with the help of nonlinear optical polarimetry. Both in vivo and extracted tissue measurements are discussed, and directions for future research are recommended.

AbstractCulex quinquefasciatusCqm1 protein acts as the receptor for Lysinibacillus sphaericusmosquito-larvicidal binary (BinAB) toxin that is used worldwide for mosquito control. We found amino acid transporter protein, rBAT, as phylogenetically closest Cqm1 homolog in humans. The present study reveals large evolutionary distance between Cqm1 and rBAT, and rBAT ectodomain lacks the sequence motif which serves as binding-site for the BinAB toxin. Thus, BinAB toxin can be expected to remain safe for humans. rBAT (heavy subunit; SLC3A1) and catalytic b0,+AT (light subunit; SLC7A9), linked by single disulfide bond, mediate renal reabsorption of cystine and dibasic amino acids in Na+independent manner. Mutations in rBAT cause type I Cystinuria disease which shows global prevalence, and rBAT can be thought as an important pharmacological target. However, 3D structures of rBAT and b0,+AT, the two components of b0,+heteromeric amino acid transporter systems, are not available. We constructed a reliable homology model of rBAT using Cqm1 coordinates and that of transmembrane b0,+AT subunit using LAT1 coordinates. Mapping of pathogenic mutations onto rBAT ectodomain revealed their scattered distribution throughout the rBAT protein. Further, our computational simulations-based scoring of several known deleterious mutations of rBAT revealed that mutations those do not compromise the protein fold and stability, are localized on the same face of the molecule. These residues are expected to interact with the b0,+AT transporter. The present study thus identifies druggable sites on rBAT that could be targeted for the treatment of type I Cystinuria.Communicated by Ramaswamy H. Sarma

The sulfosugar sulfoquinovose (SQ) is produced by essentially all photosynthetic organisms on Earth and is metabolized by bacteria through the process of sulfoglycolysis. The sulfoglycolytic Embden–Meyerhof–Parnas pathway metabolizes SQ to produce dihydroxyacetone phosphate and sulfolactaldehyde and is analogous to the classical Embden–Meyerhof–Parnas glycolysis pathway for the metabolism of glucose-6-phosphate, though the former only provides one C3 fragment to central metabolism, with excretion of the other C3 fragment as dihydroxypropanesulfonate. Here, we report a comprehensive structural and biochemical analysis of the three core steps of sulfoglycolysis catalyzed by SQ isomerase, sulfofructose (SF) kinase, and sulfofructose-1-phosphate (SFP) aldolase. Our data show that despite the superficial similarity of this pathway to glycolysis, the sulfoglycolytic enzymes are specific for SQ metabolites and are not catalytically active on related metabolites from glycolytic pathways. This observation is rationalized by three-dimensional structures of each enzyme, which reveal the presence of conserved sulfonate binding pockets. We show that SQ isomerase acts preferentially on the β-anomer of SQ and reversibly produces both SF and sulforhamnose (SR), a previously unknown sugar that acts as a derepressor for the transcriptional repressor CsqR that regulates SQ-utilization. We also demonstrate that SF kinase is a key regulatory enzyme for the pathway that experiences complex modulation by the metabolites SQ, SLA, AMP, ADP, ATP, F6P, FBP, PEP, DHAP, and citrate, and we show that SFP aldolase reversibly synthesizes SFP. This body of work provides fresh insights into the mechanism, specificity, and regulation of sulfoglycolysis and has important implications for understanding how this biochemistry interfaces with central metabolism in prokaryotes to process this major repository of biogeochemical sulfur.

The use of bioactive compounds and probiotic bacteria against the viral diseases in human is known for a long time. Anti-viral, anti-inflammatory and anti-allergic properties of bioactive compounds and bacteria with probiotic properties in respiratory viral diseases may have significance to enhance immunity. This review highlights some of the important bioactive compounds and probiotic bacteria, suggesting them as a ray of hope in the milieu of the COVID-19 management.

The Pictet–Spengler reaction is a valuable route to 1,2,3,4-tetrahydro-β-carboline (THBC) and isoquinoline scaffolds found in many important pharmaceuticals. Strictosidine synthase (STR) catalyzes the Pictet–Spengler condensation of tryptamine and the aldehyde secologanin to give (S)-strictosidine as a key intermediate in indole alkaloid biosynthesis. STRs also accept short-chain aliphatic aldehydes to give enantioenriched alkaloid products with up to 99% ee STRs are thus valuable asymmetric organocatalysts for applications in organic synthesis. The STR catalysis of reactions of small aldehydes gives an unexpected switch in stereopreference, leading to formation of the (R)-products. Here we report a rationale for the formation of the (R)-configured products by the STR enzyme from Ophiorrhiza pumila(OpSTR) using a combination of X-ray crystallography, mutational, and molecular dynamics (MD) studies. We discovered that short-chain aldehydes bind in an inverted fashion compared to secologanin leading to the inverted stereopreference for the observed (R)-product in those cases. The study demonstrates that the same catalyst can have two different productive binding modes for one substrate but give different absolute configuration of the products by binding the aldehyde substrate differently. These results will guide future engineering of STRs and related enzymes for biocatalytic applications.

The present study entails a simple chemical method for the preparation of high-quality silver / reduced graphene oxide (Ag/rGO) nanocomposite. Ag/rGO nanocomposite was characterized using UV–Visible spectroscopy, High Resolution Transmission Spectroscopy (HR-TEM), Scanning Electron Microscopy (SEM), Atomic Force Microscopy (AFM), Brunauer–Emmett–Teller (BET) analysis and X-ray Diffraction spectroscopy (XRD). SEM results showed the Silver (Ag) nanoparticles were deposited on graphene oxide (GO) nanosheets. XRD results confirmed the crystalline structure of Ag/rGO nanocomposite. The photocatalytic activity and stability of Ag/rGO nanocomposite for the degradation of methyl orange (MeO) dye was significantly increased in comparison to GO nanosheets under visible light. The adsorption capacity of Total Dissolved Solids (TDS) by Ag/rGO nanocomposite and GO nanosheets were further studied by utilizing wastewater as sample. The adsorption isothermal and kinetic studies suggest that 0.4 g/L Ag/rGO nanocomposite produce optimum separation capacity. Therefore, considering the excellent photocatalytic activity and adsorptivity nature of Ag/rGO nanocomposite, the present investigation can be effective in energy and environment related application.

Reductive amination is one of the most important methods for the synthesis of chiral amines. Here we report the discovery of an NADP(H)-dependent reductive aminase from Aspergillus oryzae(AspRedAm, Uniprot code Q2TW47) that can catalyse the reductive coupling of a broad set of carbonyl compounds with a variety of primary and secondary amines with up to >98% conversion and with up to >98% enantiomeric excess. In cases where both carbonyl and amine show high reactivity, it is possible to employ a 1:1 ratio of the substrates, forming amine products with up to 94% conversion. Steady-state kinetic studies establish that the enzyme is capable of catalysing imine formation as well as reduction. Crystal structures of AspRedAm in complex with NADP(H) and also with both NADP(H) and the pharmaceutical ingredient (R)-rasagiline are reported. We also demonstrate preparative scale reductive aminations with wild-type and Q240A variant biocatalysts displaying total turnover numbers of up to 32,000 and space time yields up to 3.73 g l−1d−1.

Infertility is a big problem in present scenario as around 8–12% of couples are experiencing infertility worldwide. A nationwide survey of Indian council of Medical Research projected infertility rate around 15–18%. Statistical data suggest that all over world 40% infertility is due to male factor. More than 90% of male infertility problems occur due to poor sperm counts, poor sperm quality, or both. The remaining cases of male infertility can be caused by a variety of conditions involving anatomical problems, hormonal imbalances, and genetic defects.

•Synthesis of high-yield AC using algae Chlamydomonas sp.•Magnetic nanocomposite IAC examined for its removal efficiency for Cr(VI) and DFS•IAC resulted in 95.2 and 82.1% removal efficiency for Cr(VI) and DFS in 4 h•5 cycles of regeneration exhibited only 6.6% reduction in removal efficiency by IAC

•Binary (BinAB) toxin is primarily responsible for the larvicidal action of the WHO recognized mosquito-larvicidal bacterium Lysinibacillus sphaericus.•BinAB is a single receptor-specific toxin, active against larvae of Culex and Anopheles, but not Aedes aegypti.•The target receptor in Culex is Cqm1 protein, a GPI-anchored amylomaltase located apically in the lipid-rafts of the larval-midgut epithelium.•Interaction of the toxin components with the receptor is critical for the larvicidal activity of the toxin.•Evidences support the pore formation model for BinAB toxin internalization and the role of toxin-glycan interactions in the endoplasmic reticulum in mediating larval death.•Targeted R&D efforts are required to maintain the sustainability and improve efficacy of the eco-friendly BinAB proteins for efficient mosquito control interventions.

Owing to the incline in oil spills and oily wastewater released in marine waters, development of cost-effective and eco-friendly strategies is in urgent demand. Herein, we report a simple and cost-effective method for the fabrication of superhydrophobic-super oleophilic and eco-friendly polyurethane sponge for the sorption of oil from wastewater. Sponge was refurbished by applying textile sludge derived biochar and polydimethylsiloxane using dip coating method. Structural and chemical characterization of the Biochar: Polydimethylsiloxane nanohybrid embedded PU sponge was examined by Field Emission-Scanning Electron Microscopy, Energy Dispersive X-Ray Spectroscopy, Fourier Transform Infrared Spectroscopy, Brunauer-Emmett-Teller and X-Ray Diffraction. The prepared adsorbent efficiently separated diesel from wastewater with maximum sorption capacity of 26.88 g g-1followed by benzene, petrol and toluene with sorption capacities of 20.92 g g-1, 20.91 g g-1and 20.44 g g-1, respectively within seconds of immersion. Least sorption capacity (13.01 g g-1) was recorded for Kerosene. Quadrupole-inductively coupled plasma mass spectrometry accredited for nanohybrid’s stability. The synthesized adsorbent showed excellent reusability up-to 8 cycles, suggesting its practical applicability. Thus, the current study inferred that Biochar: Polydimethylsiloxane nanohybrid embedded Polyurethane sponge could be used as a proficient adsorbent for the removal of various contaminants in oil wastewater.