Transcriptome- and proteome-wide effects of a circular RNA encompassing four early exons of the spinal muscular atrophy genes.

Spinal muscular atrophy (SMA) genes, SMN1 and SMN2 (hereinafter referred to as SMN1/2), produce multiple circular RNAs (circRNAs), including C2A-2B-3-4 that encompasses early exons 2A, 2B, 3 and 4. C2A-2B-3-4 is a universally and abundantly expressed circRNA of SMN1/2. Here we report the transcriptome- and proteome-wide effects of overexpression of C2A-2B-3-4 in inducible HEK293 cells. Our RNA-Seq analysis revealed altered expression of ~ 15% genes (4172 genes) by C2A-2B-3-4. About half of the affected genes by C2A-2B-3-4 remained unaffected by L2A-2B-3-4, a linear transcript encompassing exons 2A, 2B, 3 and 4 of SMN1/2. These findings underscore the unique role of the structural context of C2A-2B-3-4 in gene regulation. A surprisingly high number of upregulated genes by C2A-2B-3-4 were located on chromosomes 4 and 7, whereas many of the downregulated genes were located on chromosomes 10 and X. Supporting a cross-regulation of SMN1/2 transcripts, C2A-2B-3-4 and L2A-2B-3-4 upregulated and downregulated SMN1/2 mRNAs, respectively. Proteome analysis revealed 61 upregulated and 57 downregulated proteins by C2A-2B-3-4 with very limited overlap with those affected by L2A-2B-3-4. Independent validations confirmed the effect of C2A-2B-3-4 on expression of genes associated with chromatin remodeling, transcription, spliceosome function, ribosome biogenesis, lipid metabolism, cytoskeletal formation, cell proliferation and neuromuscular junction formation. Our findings reveal a broad role of C2A-2B-3-4, and expands our understanding of functions of SMN1/2 genes.

A qualitative study to assess satisfaction with the Manipal model of telepsychiatry among patients and caregivers.

Context: Telepsychiatry in India is nearly two decades old and is witnessing rapid adaptation in clinical services. This warrants studying the satisfaction with this mode from healthcare seekers' point of view. Aim: This study aimed to study the treatment satisfaction among persons with psychiatric disorders and their caregivers receiving telepsychiatry services via the Manipal model. Settings and Design: This was a qualitative cross-sectional study conducted in three centers, which were part of the Manipal model of telepsychiatry, namely community healthcare centers at Hebri, community healthcare centers at Byndoor, and primary healthcare center (PHC) at Kandlur of Udupi District. Methods and Material: Semi-structured interview schedule and focused group discussions were conducted to assess the treatment satisfaction. Statistical Analysis Used: Descriptive statistics were used to analyze sociodemographic data, and data generated from focused group discussions were qualitatively analyzed. Collected data were coded, and themes were generated from the codes. Results: A total of 45 persons with psychiatric disorders and 28 of the caregivers receiving telepsychiatry services were recruited into this study. Results revealed high satisfaction among patients and caregivers with telepsychiatry services provided to them. Qualitative results of this study revealed high satisfaction among patients and caregivers with telepsychiatry services in different domains such as time, cost of treatment, convenience, doctor-patient communication, and healthcare quality. Conclusion: This study witnessed that patients and caregivers were highly satisfied with telepsychiatry services provided to them. These findings clearly indicate the importance of telepsychiatry services in the country, where the concept of telepsychiatry and its practice is rising.

Synergistic Effect of an Antisense Oligonucleotide and Small Molecule on Splicing Correction of the Spinal Muscular Atrophy Gene.

Spinal muscular atrophy (SMA) is treated by increasing the level of Survival Motor Neuron (SMN) protein through correction of SMN2 exon 7 skipping or exogenous expression of SMN through gene therapy. Currently available therapies have multiple shortcomings, including poor body-wide distribution, invasive delivery, and potential negative consequences due to high doses needed for clinical efficacy. Here we test the effects of a combination treatment of a splice-correcting antisense oligonucleotide (ASO) Anti-N1 with the small compounds risdiplam and branaplam. We show that a low-dose treatment of Anti-N1 with either compound produces a synergistic effect on the inclusion of SMN2 exon 7 in SMA patient fibroblasts. Using RNA-Seq, we characterize the transcriptomes of cells treated with each compound as well as in combination. Although high doses of each individual treatment trigger widespread perturbations of the transcriptome, combination treatment of Anti-N1 with risdiplam and branaplam results in minimal disruption of gene expression. For individual genes targeted by the 3 compounds, we observe little to no additive effects of combination treatment. Overall, we conclude that the combination treatment of a splice-correcting ASO with small compounds represents a promising strategy for achieving a high level of SMN expression while minimizing the risk of off-target effects.

A super minigene with a short promoter and truncated introns recapitulates essential features of transcription and splicing regulation of the SMN1 and SMN2 genes.

Here we report a Survival Motor Neuron 2 (SMN2) super minigene, SMN2Sup, encompassing its own promoter, all exons, their flanking intronic sequences and the entire 3'-untranslated region. We confirm that the pre-mRNA generated from SMN2Sup undergoes splicing to produce a translation-competent mRNA. We demonstrate that mRNA generated from SMN2Sup produces more SMN than an identical mRNA generated from a cDNA clone. We uncover that overexpression of SMN triggers skipping of exon 3 of SMN1/SMN2. We define the minimal promoter and regulatory elements associated with the initiation and elongation of transcription of SMN2. The shortened introns within SMN2Sup preserved the ability of camptothecin, a transcription elongation inhibitor, to induce skipping of exons 3 and 7 of SMN2. We show that intron 1-retained transcripts undergo nonsense-mediated decay. We demonstrate that splicing factor SRSF3 and DNA/RNA helicase DHX9 regulate splicing of multiple exons in the context of both SMN2Sup and endogenous SMN1/SMN2. Prevention of SMN2 exon 7 skipping has implications for the treatment of spinal muscular atrophy (SMA). We validate the utility of the super minigene in monitoring SMN levels upon splicing correction. Finally, we demonstrate how the super minigene could be employed to capture the cell type-specific effects of a pathogenic SMN1 mutation.

Facile Synthesis of Mesoporous Nanohybrid Two-Dimensional Layered Ni-Cr-S and Reduced Graphene Oxide for High-Performance Hybrid Supercapacitors.

This study describes the single-step synthesis of a mesoporous layered nickel-chromium-sulfide (NCS) and its hybridization with single-layered graphene oxide (GO) using a facile, inexpensive chemical method. The conductive GO plays a critical role in improving the physicochemical and electrochemical properties of hybridized NCS/reduced GO (NCSG) materials. The optimized mesoporous nanohybrid NCSG is obtained when hybridized with 20% GO, and this material exhibits a very high specific surface area of 685.84 m2/g compared to 149.37 m2/g for bare NCS, and the pore diameters are 15.81 and 13.85 nm, respectively. The three-fold superior specific capacity of this optimal NCSG (1932 C/g) is demonstrated over NCS (676 C/g) at a current density of 2 A/g. A fabricated hybrid supercapacitor (HSC) reveals a maximum specific capacity of 224 C/g at a 5 A/g current density. The HSC reached an outstanding energy density of 105 Wh/kg with a maximum power density of 11,250 W/kg. A 4% decrement was observed during the cyclic stability study of the HSC over 5000 successive charge-discharge cycles at a 10 A/g current density. These results suggest that the prepared nanohybrid NCSG is an excellent cathode material for gaining a high energy density in an HSC.

Manipal model of telepsychiatry.

Telepsychiatry can be understood as an interactive mental health service providing mode using information and communication technology. In recent decades, services provided under the umbrella term of telepsychiatry expanded to cater clinical services, diagnostic services, interventions, therapies, education, and research. Since telepsychiatry has been practiced in India for two decades, various models have emerged to meet the country's demands and the logistics that are available. Both synchronous and asynchronous modes of telepsychiatry had been in practice in India depending on the availability of logistics. Most of the telepsychiatry services in India had focused on providing clinical care to reach the unreached population. Furthermore, telepsychiatry had been used to train mental health professionals and healthcare workers from other disciplines. However, not many models had incorporated the idea of hands-on training of the postgraduates/trainees of psychiatric social work (PSW) in telepsychiatry under supervision. This was addressed in the Manipal model of telepsychiatry. Manipal model of telepsychiatry has begun in 2016 with a novel idea to train mental health profession trainees in addition to cover other clinical services, research, and education. In the last eight years, four centers of Karnataka state have been covered under this model with progressive growth in a number of patients and this acted as a hands-on training model for the postgraduate trainees in starting telepsychiatry services independently. Furthermore, it provided an opportunity to develop the organization skills of trainees, improved their oratory skills, and improved their expertise in using information technology for mental healthcare delivery.

Diverse targets of SMN2-directed splicing-modulating small molecule therapeutics for spinal muscular atrophy.

Designing an RNA-interacting molecule that displays high therapeutic efficacy while retaining specificity within a broad concentration range remains a challenging task. Risdiplam is an FDA-approved small molecule for the treatment of spinal muscular atrophy (SMA), the leading genetic cause of infant mortality. Branaplam is another small molecule which has undergone clinical trials. The therapeutic merit of both compounds is based on their ability to restore body-wide inclusion of Survival Motor Neuron 2 (SMN2) exon 7 upon oral administration. Here we compare the transcriptome-wide off-target effects of these compounds in SMA patient cells. We captured concentration-dependent compound-specific changes, including aberrant expression of genes associated with DNA replication, cell cycle, RNA metabolism, cell signaling and metabolic pathways. Both compounds triggered massive perturbations of splicing events, inducing off-target exon inclusion, exon skipping, intron retention, intron removal and alternative splice site usage. Our results of minigenes expressed in HeLa cells provide mechanistic insights into how these molecules targeted towards a single gene produce different off-target effects. We show the advantages of combined treatments with low doses of risdiplam and branaplam. Our findings are instructive for devising better dosing regimens as well as for developing the next generation of small molecule therapeutics aimed at splicing modulation.

Electroconvulsive Therapy in Patients With Cardiac Implantable Electronic Devices: A Case Report and Systematic Review of Published Cases.

OBJECTIVE: The aims of the study were to report the case of a 54-year-old man with recurrent depressive disorder with multiple medical comorbidities having a dual-chamber pacemaker, treated successfully with 11 sessions of electroconvulsive therapy, and to conduct a systematic review of published cases documenting the use of electroconvulsive therapy (ECT) in patients with cardiac implantable electronic devices (CIEDs) for treating major psychiatric disorders. METHODS: We searched electronic databases (MEDLINE, PubMed, Google Scholar, Embase, Cochrane Library, PsycINFO, and Crossref) and included studies reporting on the use of electroconvulsive therapy in patients with CIEDs. RESULTS: Thirty-five publications across 53 years (1967-2021) reported on 76 patients (including current report) who received a pooled total of 979 modified ECT sessions. The most common adverse events were premature ventricular contraction and hypertension. There have been no reports of serious adverse effects that necessitated the cessation of ECT. CONCLUSIONS: Electroconvulsive therapy is a safe and efficacious treatment for major psychiatric disorders, and the presence of CIEDs should not delay or deter the use of ECT in these patients.

Structural Context of a Critical Exon of Spinal Muscular Atrophy Gene.

Humans contain two nearly identical copies of Survival Motor Neuron genes, SMN1 and SMN2. Deletion or mutation of SMN1 causes spinal muscular atrophy (SMA), one of the leading genetic diseases associated with infant mortality. SMN2 is unable to compensate for the loss of SMN1 due to predominant exon 7 skipping, leading to the production of a truncated protein. Antisense oligonucleotide and small molecule-based strategies aimed at the restoration of SMN2 exon 7 inclusion are approved therapies of SMA. Many cis-elements and transacting factors have been implicated in regulation of SMN exon 7 splicing. Also, several structural elements, including those formed by a long-distance interaction, have been implicated in the modulation of SMN exon 7 splicing. Several of these structures have been confirmed by enzymatic and chemical structure-probing methods. Additional structures formed by inter-intronic interactions have been predicted by computational algorithms. SMN genes generate a vast repertoire of circular RNAs through inter-intronic secondary structures formed by inverted Alu repeats present in large number in SMN genes. Here, we review the structural context of the exonic and intronic cis-elements that promote or prevent exon 7 recognition. We discuss how structural rearrangements triggered by single nucleotide substitutions could bring drastic changes in SMN2 exon 7 splicing. We also propose potential mechanisms by which inter-intronic structures might impact the splicing outcomes.

Association mapping of autumn-seeded rye (Secale cereale L.) reveals genetic linkages between genes controlling winter hardiness and plant development.

Winter field survival (WFS) in autumn-seeded winter cereals is a complex trait associated with low temperature tolerance (LTT), prostrate growth habit (PGH), and final leaf number (FLN). WFS and the three sub-traits were analyzed by a genome-wide association study of 96 rye (Secale cereal L.) genotypes of different origins and winter-hardiness levels. A total of 10,244 single nucleotide polymorphism (SNP) markers were identified by genotyping by sequencing and 259 marker-trait-associations (MTAs; p < 0.01) were revealed by association mapping. The ten most significant SNPs (p < 1.49e-04) associated with WFS corresponded to nine strong candidate genes: Inducer of CBF Expression 1 (ICE1), Cold-regulated 413-Plasma Membrane Protein 1 (COR413-PM1), Ice Recrystallization Inhibition Protein 1 (IRIP1), Jasmonate-resistant 1 (JAR1), BIPP2C1-like protein phosphatase, Chloroplast Unusual Positioning Protein-1 (CHUP1), FRIGIDA-like 4 (FRL4-like) protein, Chalcone Synthase 2 (CHS2), and Phenylalanine Ammonia-lyase 8 (PAL8). Seven of the candidate genes were also significant for one or several of the sub-traits supporting the hypothesis that WFS, LTT, FLN, and PGH are genetically interlinked. The winter-hardy rye genotypes generally carried additional allele variants for the strong candidate genes, which suggested allele diversity was a major contributor to cold acclimation efficiency and consistent high WFS under varying field conditions.

Layer-by-layer nanohybrids of Ni-Cr-LDH intercalated with 0D polyoxotungstate for highly efficient hybrid supercapacitor.

The layer-by-layer mesoporous nanohybrids of Ni-Cr-layered double hydroxide (Ni-Cr-LDH) and polyoxotungstate nanoclusters (Ni-Cr-LDH-POW) are prepared via exfoliation reassembling strategy. The intercalative hybridization of Ni-Cr-LDH with POW nanoclusters leads to forming a layer-by-layer stacking framework with significant expansion of the interplanar spacing and surface area. The aqueous hybrid supercapacitor (AHSC) and all-solid-state hybrid supercapacitor (SSHSC) devices are fabricated using Ni-Cr-LDH-POW nanohybrid as a cathode and reduced graphene oxide (rGO) as an anode material. Notably, the NCW-2//rGO AHSC device delivers an ED of 43 Wh kg-1 at PD of 1.33 kW kg-1 and excellent electrochemical stability over 10,000 charge-discharge cycles. Moreover, NCW-2//rGO SSHSC exhibits an ED of 34 Wh kg-1 at PD of 1.32 kW kg-1 with capacitance retention of 86% after 10,000 cycles. These results highlight the excellent electrochemical functionality and advantages of the Ni-Cr-LDH-POW nanohybrids as a cathode for hybrid supercapacitors.

Nutritional Composition and In Vitro Starch Digestibility of Crackers Supplemented with Faba Bean Whole Flour, Starch Concentrate, Protein Concentrate and Protein Isolate.

The nutritional quality of common wheat-based foods can be improved by adding flours from whole pulses or their carbohydrate and protein constituents. Faba bean (Vicia faba L.) is a pulse with high protein concentration. In this study, prepared faba bean (FB) flours were added to wheat based baked crackers. Wheat cracker recipes were modified by substituting forty percent wheat flour with flours from whole faba bean, starch enriched flour (starch 60%), protein concentrate (protein 60%) or protein isolate (protein 90%). Baked crackers were ground into meal and analyzed for their macronutrient composition, starch characteristics and in vitro starch hydrolysis. Faba bean supplemented crackers had lower (p ≤ 0.001) total starch concentrations, but proportionally higher protein (16.8-43%), dietary fiber (6.7-12.1%), fat (4.8-7.1%) and resistant starch (3.2-6%) (p ≤ 0.001) than wheat crackers (protein: 16.2%, dietary fiber: 6.3%, fat: 4.2, resistant starch: 1.2%). The increased amylose, amylopectin B1- chain and fat concentration from faba bean flour and starch flour supplementation in cracker recipe contributed to increased resistant starch. Flours from whole faba bean, starch or protein fractions improved the nutritional properties and functional value of the wheat-based crackers. The analytical analysis describing protein, starch composition and structure and in vitro enzymatic hydrolysis advance understanding of factors that account for the in vivo benefits of faba bean flours added to crackers in human physiological functions as also previously shown for pasta. The findings can be used to guide development of improve nutritional quality of similar wheat-based food products.

Surface sterilization for isolation of endophytes: Ensuring what (not) to grow.

Endophytic microbiota opens a magnificent arena of metabolites that served as a potential source of medicines for treating a variety of ailments and having prospective uses in agriculture, food, cosmetics, and many more. There are umpteen reports of endophytes improving the growth and tolerance of plants. In addition, endophytes from lifesaving drug-producing plants such as Taxus, Nothapodytes, Catharanthus, and so forth have the ability to produce host mimicking compounds. To harness these benefits, it is imperative to isolate the true endophytes, not the surface microflora. The foremost step in endophyte isolation is the removal of epiphytic microbes from plant tissues, called as surface sterilization. The success of surface sterilization decides "what to grow" (the endophytes) and "what not to grow" (the epiphytes). It is very crucial to use an appropriate sterilant solution, concentration, and exposure time to ensure thorough surface disinfection with minimal damage to the endophytic diversity. Commonly used surface sterilants include sodium hypochlorite (2%-10%), ethanol (70%-90%), mercuric chloride (0.1%), formaldehyde (40%), and so forth. In addition, the efficiency could further be improved by pretreatment with surfactants such as Triton X-100, Tween 80, and Tween 20. This review comprehensively deals with the various sterilants and sterilization methods for the isolation of endophytic microbes. In addition, the mechanisms and rationale behind using specific surface sterilants have also been elaborated at length.

A new strategy for using historical imbalanced yield data to conduct genome-wide association studies and develop genomic prediction models for wheat breeding.

Using imbalanced historical yield data to predict performance and select new lines is an arduous breeding task. Genome-wide association studies (GWAS) and high throughput genotyping based on sequencing techniques can increase prediction accuracy. An association mapping panel of 227 Texas elite (TXE) wheat breeding lines was used for GWAS and a training population to develop prediction models for grain yield selection. An imbalanced set of yield data collected from 102 environments (year-by-location) over 10 years, through testing yield in 40-66 lines each year at 6-14 locations with 38-41 lines repeated in the test in any two consecutive years, was used. Based on correlations among data from different environments within two adjacent years and heritability estimated in each environment, yield data from 87 environments were selected and assigned to two correlation-based groups. The yield best linear unbiased estimation (BLUE) from each group, along with reaction to greenbug and Hessian fly in each line, was used for GWAS to reveal genomic regions associated with yield and insect resistance. A total of 74 genomic regions were associated with grain yield and two of them were commonly detected in both correlation-based groups. Greenbug resistance in TXE lines was mainly controlled by Gb3 on chromosome 7DL in addition to two novel regions on 3DL and 6DS, and Hessian fly resistance was conferred by the region on 1AS. Genomic prediction models developed in two correlation-based groups were validated using a set of 105 new advanced breeding lines and the model from correlation-based group G2 was more reliable for prediction. This research not only identified genomic regions associated with yield and insect resistance but also established the method of using historical imbalanced breeding data to develop a genomic prediction model for crop improvement. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-022-01287-8.

Valproate-associated hair abnormalities: Pathophysiology and management strategies.

OBJECTIVE: To review the literature on valproate-associated hair abnormalities and the available treatment options. METHODS: We searched PubMed and Google Scholar with keywords including "valproate", "valproic acid", "hair", "alopecia", and "effluvium," supplemented with hand search from cross-references. We included all types of studies including case reports in this review. RESULTS: The pathophysiology of hair loss includes telogen effluvium, biotin, mineral deficiency, and possibly hyperandrogenism. Diagnosis is based on history of hair loss or abnormalities following valproate treatment, and is confirmed by use of simple clinical tests such as pull test and modified wash test. Treatment involves reassurance and advice on hair care, and if possible drug discontinuation or dose reduction. Medications such as biotin and other vitamins with minerals supplementation is effective for most individuals with hair loss. Other treatment options are agomelatine, topical valproate or minoxidil, though these lack evidence. CONCLUSION: Hair abnormalities with valproate are common, benign adverse effects, and management includes general measures and specific treatment options.

Genome-wide QTL mapping of yield and agronomic traits in two widely adapted winter wheat cultivars from multiple mega-environments.

Quantitative trait loci (QTL) analysis could help to identify suitable molecular markers for marker-assisted breeding (MAB). A mapping population of 124 F5:7recombinant inbred lines derived from the cross 'TAM 112'/'TAM 111' was grown under 28 diverse environments and evaluated for grain yield, test weight, heading date, and plant height. The objective of this study was to detect QTL conferring grain yield and agronomic traits from multiple mega-environments. Through a linkage map with 5,948 single nucleotide polymorphisms (SNPs), 51 QTL were consistently identified in two or more environments or analyses. Ten QTL linked to two or more traits were also identified on chromosomes 1A, 1D, 4B, 4D, 6A, 7B, and 7D. Those QTL explained up to 13.3% of additive phenotypic variations with the additive logarithm of odds (LOD(A)) scores up to 11.2. The additive effect increased yield up to 8.16 and 6.57 g m-2 and increased test weight by 2.14 and 3.47 kg m-3 with favorable alleles from TAM 111 and TAM 112, respectively. Seven major QTL for yield and six for TW with one in common were of our interest on MAB as they explained 5% or more phenotypic variations through additive effects. This study confirmed previously identified loci and identified new QTL and the favorable alleles for improving grain yield and agronomic traits.

The Relationships between Plant Developmental Traits and Winter Field Survival in Rye (Secale cereale L.).

Overwintering cereals accumulate low temperature tolerance (LTT) during cold acclimation in the autumn. Simultaneously, the plants adjust to the colder season by making developmental changes at the shoot apical meristem. These processes lead to higher winter hardiness in winter rye varieties (Secale cereale L.) adapted to Northern latitudes as compared to other cereal crops. To dissect the winter-hardiness trait in rye, a panel of 96 genotypes of different origins and growth habits was assessed for winter field survival (WFS), LTT, and six developmental traits. Best Linear Unbiased Estimates for WFS determined from five field trials correlated strongly with LTT (r = 0.90, p < 0.001); thus, cold acclimation efficiency was the major contributor to WFS. WFS also correlated strongly (p < 0.001) with final leaf number (r = 0.80), prostrate growth habit (r = 0.61), plant height (r = 0.34), but showed weaker associations with top internode length (r = 0.30, p < 0.01) and days to anthesis (r = 0.25, p < 0.05). The heritability estimates (h2) for WFS-associated traits ranged from 0.45 (prostrate growth habit) to 0.81 (final leaf number) and were overall higher than for WFS (h2 = 0.48). All developmental traits associated with WFS and LTT are postulated to be regulated by phytohormone levels at shoot apical meristem.