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 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.

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.

Animal movement on the hoof and on the cart and its implications for understanding exchange within the Indus Civilisation

Movement of resources was essential to the survival and success of early complex societies. The sources and destinations of goods and the means of transportation - be it by boats, carts and/or foot - can often be inferred, but the logistics of these movements are inherently more difficult to ascertain. Here, we use strontium isotopic analysis to test hypotheses about the role of animal and animal-powered transport in medium and long-distance movement and exchange, using the Indus Civilization as a case study. Across the wide geographical spread of the Indus Civilisation, there is strong evidence for long-distance exchange of raw materials and finished objects and this process is presumed to involve boats and animal-driven transport, although there is little evidence as to the relative importance of each mode of movement. Strontium isotopic analysis of animal remains from four sites analysed for this study combined with results from nine other sites indicates limited long-distance animal movement between different geological zones within the Indus Civilisation. These findings suggest that individual animals primarily moved short- or medium-distances, though there are several significant exceptions seen in some pigs and cattle found at two large urban sites. We infer that long-distance transport of goods, be it raw materials, finished objects, other goods, or the animals themselves, could have occurred through the use of boats and waterways, by traction animals moving over long distances that did not end up in the archaeological record, and/or by different animals participating in many short to medium-distance movements.

Combining biophysical parameters with thermal and RGB indices using machine learning models for predicting yield in yellow rust affected wheat crop

Evaluating crop health and forecasting yields in the early stages are crucial for effective crop and market management during periods of biotic stress for both farmers and policymakers. Field experiments were conducted during 2017-18 and 2018-19 with objective to evaluate the effect of yellow rust on various biophysical parameters of 24 wheat cultivars, with varying levels of resistance to yellow rust and to develop machine learning (ML) models with improved accuracy for predicting yield by integrating thermal and RGB indices with crucial plant biophysical parameters. Results revealed that as the level of rust increased, so did the canopy temperature and there was a significant decrease in crop photosynthesis, transpiration, stomatal conductance, leaf area index, membrane stability index, relative leaf water content, and normalized difference vegetation index due to rust, and the reductions were directly correlated with levels of rust severity. The yield reduction in moderate resistant, low resistant and susceptible cultivars as compared to resistant cultivars, varied from 15.9-16.9%, 28.6-34.4% and 59-61.1%, respectively. The ML models were able to provide relatively accurate early yield estimates, with the accuracy increasing as the harvest approached. The yield prediction performance of the different ML models varied with the stage of the crop growth. Based on the validation output of different ML models, Cubist, PLS, and SpikeSlab models were found to be effective in predicting the wheat yield at an early stage (55-60 days after sowing) of crop growth. The KNN, Cubist, SLR, RF, SpikeSlab, XGB, GPR and PLS models were proved to be more useful in predicting the crop yield at the middle stage (70 days after sowing) of the crop, while RF, SpikeSlab, KNN, Cubist, ELNET, GPR, SLR, XGB and MARS models were found good to predict the crop yield at late stage (80 days after sowing). The study quantified the impact of different levels of rust severity on crop biophysical parameters and demonstrated the usefulness of remote sensing and biophysical parameters data integration using machine-learning models for early yield prediction under biotically stressed conditions.

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.

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.

Interactive effect of elevated tropospheric ozone and carbon dioxide on radiation utilisation, growth and yield of chickpea (Cicer arietinum L.)

An experiment was conducted in the Free Air Ozone and Carbon dioxide Enrichment (FAOCE) facility to study the impact of elevated O₃, CO₂ and their interaction on chickpea crop (cv. Pusa-5023) in terms of phenology, biophysical parameters, yield components, radiation interception and use efficiency. The crop was exposed to elevated O₃ (EO:60ppb), CO₂ (EC:550 ppm) and their combined interactive treatment (ECO: EC+EO) during the entire growing season. Results revealed that the crop's total growth period was shortened by 10, 14 and 17 days under elevated CO₂, elevated O₃ and the combined treatment, respectively. Compared to ambient condition, the leaf area index (LAI) under elevated CO₂ was higher by 4 to 28%, whilst it is reduced by 7.3 to 23.8% under elevated O₃. The yield based radiation use efficiency (RUE_y) was highest under elevated CO₂ (0.48 g MJ^-1), followed by combined (0.41 g MJ^-1), ambient (0.38 g MJ^-1) and elevated O₃ (0.32 g MJ^-1) treatments. Elevated O₃ decreased RUE_y by 15.78% over ambient, and the interaction results in a 7.8% higher RUE_y. The yield was 31.7% more under elevated CO₂ and 21.9% lower in elevated O₃ treatment as compared to the ambient. The combined interactive treatment recorded a higher yield as compared to ambient by 9.7%. Harvest index (HI) was lowest under elevated O₃ (36.10%), followed by ambient (39.18%), combined (40.81%), and highest was under elevated CO₂ (44.18%). Chickpea showed a positive response to elevated CO₂ resulting a 5% increase in HI as compared to ambient condition. Our findings quantified the positive and negative impacts of elevated O₃, CO₂ and their interaction on chickpea and revealed that the negative impacts of elevated O₃ can be compensated by elevated CO₂ in chickpea. This work promotes the understanding of crop behaviour under elevated O₃, CO₂ and their interaction, which can be used as valuable inputs for radiation-based crop simulation models to simulate climate change impact on chickpea crop.

Lipid residues in pottery from the Indus Civilisation in northwest India

This paper presents novel insights into the archaeology of food in ancient South Asia by using lipid residue analysis to investigate what kinds of foodstuffs were used in ceramic vessels by populations of the Indus Civilisation in northwest India. It examines how vessels were used in urban and rural Indus settlements during the Mature Harappan period (c.2600/2500-1900 BC), the relationship between vessels and the products within them, and identifies whether changes in vessel use occurred from the Mature Harappan to Late Harappan periods, particularly during climatic instability after 4.2 ka BP (c.2100 BC). Despite low lipid concentrations, which highlight challenges with conducting residue analysis in arid, seasonally-wet and alkaline environments, 71% of the vessels yielded appreciable quantities of lipid. Lipid profiles revealed the use of animal fats in vessels, and contradictory to faunal evidence, a dominance of non-ruminant fats, with limited evidence of dairy processing. The absence of local modern reference fats makes this dataset challenging to interpret, and it is possible that plant products or mixtures of plant and animal products have led to ambiguous fatty acid-specific isotopic values. At the same time, it appears that urban and rural populations processed similar types of products in vessels, with limited evidence for change in vessel use from the urban to the post-urban period. This study is a systematic investigation into pot lipid residues from multiple sites, demonstrating the potential of the method for examining ancient Indus foodways and the need for the development of further research in ancient organic residues in South Asia.

The First Orally Deliverable Small Molecule for the Treatment of Spinal Muscular Atrophy

Spinal muscular atrophy (SMA) is 1 of the leading causes of infant mortality. SMA is mostly caused by low levels of Survival Motor Neuron (SMN) protein due to deletion of or mutation in the SMN1 gene. Its nearly identical copy, SMN2, fails to compensate for the loss of SMN1 due to predominant skipping of exon 7. Correction of SMN2 exon 7 splicing by an antisense oligonucleotide (ASO), nusinersen (Spinraza™), that targets the intronic splicing silencer N1 (ISS-N1) became the first approved therapy for SMA. Restoration of SMN levels using gene therapy was the next. Very recently, an orally deliverable small molecule, risdiplam (Evrysdi™), became the third approved therapy for SMA. Here we discuss how these therapies are positioned to meet the needs of the broad phenotypic spectrum of SMA patients.

Characteristics of circular RNAs generated by human Survival Motor Neuron genes

Circular RNAs (circRNAs) belong to a diverse class of stable RNAs expressed in all cell types. Their proposed functions include sponging of microRNAs (miRNAs), sequestration and trafficking of proteins, assembly of multimeric complexes, production of peptides, and regulation of transcription. Backsplicing due to RNA structures formed by an exceptionally high number of Alu repeats lead to the production of a vast repertoire of circRNAs by human Survival Motor Neuron genes, SMN1 and SMN2, that code for SMN, an essential multifunctional protein. Low levels of SMN due to deletion or mutation of SMN1 result in spinal muscular atrophy (SMA), a major genetic disease of infants and children. Mild SMA is also recorded in adult population, expanding the spectrum of the disease. Here we review SMN circRNAs with respect to their biogenesis, sequence features, and potential functions. We also discuss how SMN circRNAs could be exploited for diagnostic and therapeutic purposes.

A survey of transcripts generated by spinal muscular atrophy genes

Human Survival Motor Neuron (SMN) genes code for SMN, an essential multifunctional protein. Complete loss of SMN is embryonic lethal, while low levels of SMN lead to spinal muscular atrophy (SMA), a major genetic disease of children and infants. Reduced levels of SMN are associated with the abnormal development of heart, lung, muscle, gastro-intestinal system and testis. The SMN loci have been shown to generate a vast repertoire of transcripts, including linear, back- and trans-spliced RNAs as well as antisense long noncoding RNAs. However, functions of the majority of these transcripts remain unknown. Here we review the nature of RNAs generated from the SMN loci and discuss their potential functions in cellular metabolism.

RNA in spinal muscular atrophy: therapeutic implications of targeting

INTRODUCTION

Spinal muscular atrophy (SMA) is caused by low levels of the Survival Motor Neuron (SMN) protein due to deletions of or mutations in the SMN1 gene. Humans carry another nearly identical gene, SMN2, which mostly produces a truncated and less stable protein SMNΔ7 due to predominant skipping of exon 7. Elevation of SMN upon correction of SMN2 exon 7 splicing and gene therapy have been proven to be the effective treatment strategies for SMA.

AREAS COVERED

This review summarizes existing and potential SMA therapies that are based on RNA targeting.We also discuss the mechanistic basis of RNA-targeting molecules.

EXPERT OPINION

The discovery of intronic splicing silencer N1 (ISS-N1) was the first major step towards developing the currently approved antisense-oligonucleotide (ASO)-directed therapy (SpinrazaTM) based on the correction of exon 7 splicing of the endogenous SMN2pre-mRNA. Recently, gene therapy (Zolgensma) has become the second approved treatment for SMA. Small compounds (currently in clinical trials) capable of restoring SMN2 exon 7 inclusion further expand the class of the RNA targeting molecules for SMA therapy. Endogenous RNA targets, such as long non-coding RNAs, circular RNAs, microRNAs and ribonucleoproteins, could be potentially exploited for developing additional SMA therapies.

Human Survival Motor Neuron genes generate a vast repertoire of circular RNAs

Circular RNAs (circRNAs) perform diverse functions, including the regulation of transcription, translation, peptide synthesis, macromolecular sequestration and trafficking. Inverted Alu repeats capable of forming RNA:RNA duplexes that bring splice sites together for backsplicing are known to facilitate circRNA generation. However, higher limits of circRNAs produced by a single Alu-rich gene are currently not predictable due to limitations of amplification and analyses. Here, using a tailored approach, we report a surprising diversity of exon-containing circRNAs generated by the Alu-rich Survival Motor Neuron (SMN) genes that code for SMN, an essential multifunctional protein in humans. We show that expression of the vast repertoire of SMN circRNAs is universal. Several of the identified circRNAs harbor novel exons derived from both intronic and intergenic sequences. A comparison with mouse Smn circRNAs underscored a clear impact of primate-specific Alu elements on shaping the overall repertoire of human SMN circRNAs. We show the role of DHX9, an RNA helicase, in splicing regulation of several SMN exons that are preferentially incorporated into circRNAs. Our results suggest self- and cross-regulation of biogenesis of various SMN circRNAs. These findings bring a novel perspective towards a better understanding of SMN gene function.

How RNA structure dictates the usage of a critical exon of spinal muscular atrophy gene

Role of RNA structure in pre-mRNA splicing has been implicated for several critical exons associated with genetic disorders. However, much of the structural studies linked to pre-mRNA splicing regulation are limited to terminal stem-loop structures (hairpins) sequestering splice sites. In few instances, role of long-distance interactions is implicated as the major determinant of splicing regulation. With the recent surge of reports of circular RNA (circRNAs) generated by backsplicing, role of Alu-associated RNA structures formed by long-range interactions are taking central stage. Humans contain two nearly identical copies of Survival Motor Neuron (SMN) genes, SMN1 and SMN2. Deletion or mutation of SMN1 coupled with the inability of SMN2 to compensate for the loss of SMN1 due to exon 7 skipping causes spinal muscular atrophy (SMA), one of the leading genetic diseases of children. In this review, we describe how structural elements formed by both local and long-distance interactions are being exploited to modulate SMN2 exon 7 splicing as a potential therapy for SMA. We also discuss how Alu-associated secondary structure modulates generation of a vast repertoire of SMN circRNAs. This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm.

High-affinity RNA targets of the Survival Motor Neuron protein reveal diverse preferences for sequence and structural motifs

The Survival Motor Neuron (SMN) protein is essential for survival of all animal cells. SMN harbors a nucleic acid-binding domain and plays an important role in RNA metabolism. However, the RNA-binding property of SMN is poorly understood. Here we employ iterative in vitro selection and chemical structure probing to identify sequence and structural motif(s) critical for RNA–SMN interactions. Our results reveal that motifs that drive RNA–SMN interactions are diverse and suggest that tight RNA–SMN interaction requires presence of multiple contact sites on the RNA molecule. We performed UV crosslinking and immunoprecipitation coupled with high-throughput sequencing (HITS-CLIP) to identify cellular RNA targets of SMN in neuronal SH-SY5Y cells. Results of HITS-CLIP identified a wide variety of targets, including mRNAs coding for ribosome biogenesis and cytoskeleton dynamics. We show critical determinants of ANXA2 mRNA for a direct SMN interaction in vitro. Our data confirms the ability of SMN to discriminate among close RNA sequences, and represent the first validation of a direct interaction of SMN with a cellular RNA target. Our findings suggest direct RNA–SMN interaction as a novel mechanism to initiate the cascade of events leading to the execution of SMN-specific functions.

A novel role of U1 snRNP: Splice site selection from a distance

Removal of introns by pre-mRNA splicing is fundamental to gene function in eukaryotes. However, understanding the mechanism by which exon-intron boundaries are defined remains a challenging endeavor. Published reports support that the recruitment of U1 snRNP at the 5'ss marked by GU dinucleotides defines the 5'ss as well as facilitates 3'ss recognition through cross-exon interactions. However, exceptions to this rule exist as U1 snRNP recruited away from the 5'ss retains the capability to define the splice site, where the cleavage takes place. Independent reports employing exon 7 of Survival Motor Neuron (SMN) genes suggest a long-distance effect of U1 snRNP on splice site selection upon U1 snRNP recruitment at target sequences with or without GU dinucleotides. These findings underscore that sequences distinct from the 5'ss may also impact exon definition if U1 snRNP is recruited to them through partial complementarity with the U1 snRNA. In this review we discuss the expanded role of U1 snRNP in splice-site selection due to U1 ability to be recruited at more sites than predicted solely based on GU dinucleotides.

Pre-mRNA Splicing Modulation by Antisense Oligonucleotides

Pre-mRNA splicing, a dynamic process of intron removal and exon joining, is governed by a combinatorial control exerted by overlapping cis-elements that are unique to each exon and its flanking intronic sequences. Splicing cis-elements are usually 4-to-8-nucleotide-long linear motifs that provide binding sites for specific proteins. Pre-mRNA splicing is also influenced by secondary and higher order RNA structures that affect accessibility of splicing cis-elements. Antisense oligonucleotides (ASOs) that block splicing cis-elements and/or affect RNA structure have been shown to modulate splicing in vivo. Therefore, ASO-based strategies have emerged as a powerful tool for therapeutic manipulation of splicing in pathological conditions. Here we describe an ASO-based approach to increase the production of the full-length SMN2 mRNA in spinal muscular atrophy patient cells.

Correction: Journey to the east: Diverse routes and variable flowering times for wheat and barley en route to prehistoric China

[This corrects the article DOI: 10.1371/journal.pone.0187405.].

Mechanism of Splicing Regulation of Spinal Muscular Atrophy Genes

Spinal muscular atrophy (SMA) is one of the major genetic disorders associated with infant mortality. More than 90% cases of SMA result from deletions or mutations of Survival Motor Neuron 1 (SMN1) gene. SMN2, a nearly identical copy of SMN1, does not compensate for the loss of SMN1 due to predominant skipping of exon 7. However, correction of SMN2 exon 7 splicing has proven to confer therapeutic benefits in SMA patients. The only approved drug for SMA is an antisense oligonucleotide (Spinraza™/Nusinersen), which corrects SMN2 exon 7 splicing by blocking intronic splicing silencer N1 (ISS-N1) located immediately downstream of exon 7. ISS-N1 is a complex regulatory element encompassing overlapping negative motifs and sequestering a cryptic splice site. More than 40 protein factors have been implicated in the regulation of SMN exon 7 splicing. There is evidence to support that multiple exons of SMN are alternatively spliced during oxidative stress, which is associated with a growing number of pathological conditions. Here, we provide the most up to date account of the mechanism of splicing regulation of the SMN genes.

Activation of a cryptic 5' splice site reverses the impact of pathogenic splice site mutations in the spinal muscular atrophy gene

Spinal muscular atrophy (SMA) is caused by deletions or mutations of the Survival Motor Neuron 1 (SMN1) gene coupled with predominant skipping of SMN2 exon 7. The only approved SMA treatment is an antisense oligonucleotide that targets the intronic splicing silencer N1 (ISS-N1), located downstream of the 5' splice site (5'ss) of exon 7. Here, we describe a novel approach to exon 7 splicing modulation through activation of a cryptic 5'ss (Cr1). We discovered the activation of Cr1 in transcripts derived from SMN1 that carries a pathogenic G-to-C mutation at the first position (G1C) of intron 7. We show that Cr1-activating engineered U1 snRNAs (eU1s) have the unique ability to reprogram pre-mRNA splicing and restore exon 7 inclusion in SMN1 carrying a broad spectrum of pathogenic mutations at both the 3'ss and 5'ss of the exon 7. Employing a splicing-coupled translation reporter, we demonstrate that mRNAs generated by an eU1-induced activation of Cr1 produce full-length SMN. Our findings underscore a wider role for U1 snRNP in splicing regulation and reveal a novel approach for the restoration of SMN exon 7 inclusion for a potential therapy of SMA.

A Multilayered Control of the Human Survival Motor Neuron Gene Expression by Alu Elements

Humans carry two nearly identical copies of Survival Motor Neuron gene: SMN1 and SMN2. Mutations or deletions of SMN1, which codes for SMN, cause spinal muscular atrophy (SMA), a leading genetic disease associated with infant mortality. Aberrant expression or localization of SMN has been also implicated in other pathological conditions, including male infertility, inclusion body myositis, amyotrophic lateral sclerosis and osteoarthritis. SMN2 fails to compensate for the loss of SMN1 due to skipping of exon 7, leading to the production of SMNΔ7, an unstable protein. In addition, SMNΔ7 is less functional due to the lack of a critical C-terminus of the full-length SMN, a multifunctional protein. Alu elements are specific to primates and are generally found within protein coding genes. About 41% of the human SMN gene including promoter region is occupied by more than 60 Alu-like sequences. Here we discuss how such an abundance of Alu-like sequences may contribute toward SMA pathogenesis. We describe the likely impact of Alu elements on expression of SMN. We have recently identified a novel exon 6B, created by exonization of an Alu-element located within SMN intron 6. Irrespective of the exon 7 inclusion or skipping, transcripts harboring exon 6B code for the same SMN6B protein that has altered C-terminus compared to the full-length SMN. We have demonstrated that SMN6B is more stable than SMNΔ7 and likely functions similarly to the full-length SMN. We discuss the possible mechanism(s) of regulation of SMN exon 6B splicing and potential consequences of the generation of exon 6B-containing transcripts.

Journey to the east: Diverse routes and variable flowering times for wheat and barley en route to prehistoric China

Today, farmers in many regions of eastern Asia sow their barley grains in the spring and harvest them in the autumn of the same year (spring barley). However, when it was first domesticated in southwest Asia, barley was grown between the autumn and subsequent spring (winter barley), to complete their life cycles before the summer drought. The question of when the eastern barley shifted from the original winter habit to flexible growing schedules is of significance in terms of understanding its spread. This article investigates when barley cultivation dispersed from southwest Asia to regions of eastern Asia and how the eastern spring barley evolved in this context. We report 70 new radiocarbon measurements obtained directly from barley grains recovered from archaeological sites in eastern Eurasia. Our results indicate that the eastern dispersals of wheat and barley were distinct in both space and time. We infer that barley had been cultivated in a range of markedly contrasting environments by the second millennium BC. In this context, we consider the distribution of known haplotypes of a flowering-time gene in barley, Ppd-H1, and infer that the distributions of those haplotypes may reflect the early dispersal of barley. These patterns of dispersal resonate with the second and first millennia BC textual records documenting sowing and harvesting times for barley in central/eastern China.

TIA1 is a gender-specific disease modifier of a mild mouse model of spinal muscular atrophy

Spinal muscular atrophy (SMA) is caused by deletions or mutations of Survival Motor Neuron 1 (SMN1) gene. The nearly identical SMN2 cannot compensate for SMN1 loss due to exon 7 skipping. The allele C (C ^+/+) mouse recapitulates a mild SMA-like phenotype and offers an ideal system to monitor the role of disease-modifying factors over a long time. T-cell-restricted intracellular antigen 1 (TIA1) regulates SMN exon 7 splicing. TIA1 is reported to be downregulated in obese patients, although it is not known if the effect is gender-specific. We show that female Tia1-knockout (Tia1 ^-/-) mice gain significant body weight (BW) during early postnatal development. We next examined the effect of Tia1 deletion in novel C ^+/+/Tia1 ^-/- mice. Underscoring the opposing effects of Tia1 deletion and low SMN level on BW gain, both C ^+/+ and C ^+/+/Tia1 ^-/- females showed similar BW gain trajectory at all time points during our study. We observed early tail necrosis in C ^+/+/Tia1 ^-/- females but not in males. We show enhanced impairment of male reproductive organ development and exacerbation of the C ^+/+/Tia1 ^-/- testis transcriptome. Our findings implicate a protein factor as a gender-specific modifier of a mild mouse model of SMA.

Antimycobacterial, antimicrobial activity, experimental (FT-IR, FT-Raman, NMR, UV-Vis, DSC) and DFT (transition state, chemical reactivity, NBO, NLO) studies on pyrrole-isonicotinyl hydrazine

As part of a study of pyrrole hydrazone, we have investigated quantum chemical calculations, molecular geometry, relative energy, vibrational properties and antimycobacterial/antimicrobial activity of pyrrole-2-carboxaldehyde isonicotinyl hydrazone (PCINH), by applying the density functional theory (DFT) and Hartree Fock (HF). Good reproduction of experimental values is obtained and with small percentage error in majority of the cases in comparison to theoretical result (DFT). The experimental FT-IR and Raman wavenumbers were compared with the respective theoretical values obtained from DFT calculations and found to agree well. In crystal structure studies the hydrated PCINH (syn-syn conformer) shows different conformation than from anhydrous form (syn-anti conformer). The rotational barrier between syn-syn and syn-anti conformers of PCINH is 12.7kcal/mol in the gas phase. In this work, use of FT-IR, FT-Raman, ¹H NMR, ¹³C NMR and UV-Vis spectroscopies has been made for full characterization of PCINH. A detailed interpretation of the vibrational spectrum was carried out with the aid of normal coordinate analysis using single scaling factor. Our results support the hydrogen bonding pattern proposed by reported crystalline structure. The calculated nature of electronic transitions within molecule found to be π→π*. The electronic descriptors study indicates that PCINH can be used as robust synthon for synthesis of new heterocyclic compounds. The first static hyperpolarizability (β₀) of PCINH is calculated as 33.89×10^-30esu_, (gas phase); 68.79×10^-30 (CHCl₃), esu; 76.76×10^-30esu (CH₂Cl₂), 85.16×10^-30esu (DMSO). The solvent induced effects on the first static hyperpolarizability were studied and found to increase as dielectric constants of the solvents increases. Investigated molecule shows better NLO value than Para nitroaniline (PNA). The compound PCINH shows good antifungal and antibacterial activity against Aspergillus niger and gram-positive bacteria Bacillus subtilis, respectively. The compound also shows good antituberculosis activity against Mycobacterium tuberculosis H37Rv using the microplate alamar blue assay (MABA).

How the discovery of ISS-N1 led to the first medical therapy for spinal muscular atrophy

Spinal muscular atrophy (SMA), a prominent genetic disease of infant mortality, is caused by low levels of survival motor neuron (SMN) protein owing to deletions or mutations of the SMN1 gene. SMN2, a nearly identical copy of SMN1 present in humans, cannot compensate for the loss of SMN1 because of predominant skipping of exon 7 during pre-mRNA splicing. With the recent US Food and Drug Administration approval of nusinersen (Spinraza), the potential for correction of SMN2 exon 7 splicing as an SMA therapy has been affirmed. Nusinersen is an antisense oligonucleotide that targets intronic splicing silencer N1 (ISS-N1) discovered in 2004 at the University of Massachusetts Medical School. ISS-N1 has emerged as the model target for testing the therapeutic efficacy of antisense oligonucleotides using different chemistries as well as different mouse models of SMA. Here, we provide a historical account of events that led to the discovery of ISS-N1 and describe the impact of independent validations that raised the profile of ISS-N1 as one of the most potent antisense targets for the treatment of a genetic disease. Recent approval of nusinersen provides a much-needed boost for antisense technology that is just beginning to realize its potential. Beyond treating SMA, the ISS-N1 target offers myriad potentials for perfecting various aspects of the nucleic-acid-based technology for the amelioration of the countless number of pathological conditions.

Diverse role of survival motor neuron protein

The multifunctional Survival Motor Neuron (SMN) protein is required for the survival of all organisms of the animal kingdom. SMN impacts various aspects of RNA metabolism through the formation and/or interaction with ribonucleoprotein (RNP) complexes. SMN regulates biogenesis of small nuclear RNPs, small nucleolar RNPs, small Cajal body-associated RNPs, signal recognition particles and telomerase. SMN also plays an important role in DNA repair, transcription, pre-mRNA splicing, histone mRNA processing, translation, selenoprotein synthesis, macromolecular trafficking, stress granule formation, cell signaling and cytoskeleton maintenance. The tissue-specific requirement of SMN is dictated by the variety and the abundance of its interacting partners. Reduced expression of SMN causes spinal muscular atrophy (SMA), a leading genetic cause of infant mortality. SMA displays a broad spectrum ranging from embryonic lethality to an adult onset. Aberrant expression and/or localization of SMN has also been associated with male infertility, inclusion body myositis, amyotrophic lateral sclerosis and osteoarthritis. This review provides a summary of various SMN functions with implications to a better understanding of SMA and other pathological conditions.

A novel human-specific splice isoform alters the critical C-terminus of Survival Motor Neuron protein

Spinal muscular atrophy (SMA), a leading genetic disease of children and infants, is caused by mutations or deletions of Survival Motor Neuron 1 (SMN1) gene. SMN2, a nearly identical copy of SMN1, fails to compensate for the loss of SMN1 due to skipping of exon 7. SMN2 predominantly produces SMNΔ7, an unstable protein. Here we report exon 6B, a novel exon, generated by exonization of an intronic Alu-like sequence of SMN. We validate the expression of exon 6B-containing transcripts SMN6B and SMN6BΔ7 in human tissues and cell lines. We confirm generation of SMN6B transcripts from both SMN1 and SMN2. We detect expression of SMN6B protein using antibodies raised against a unique polypeptide encoded by exon 6B. We analyze RNA-Seq data to show that hnRNP C is a potential regulator of SMN6B expression and demonstrate that SMN6B is a substrate of nonsense-mediated decay. We show interaction of SMN6B with Gemin2, a critical SMN-interacting protein. We demonstrate that SMN6B is more stable than SMNΔ7 and localizes to both the nucleus and the cytoplasm. Our finding expands the diversity of transcripts generated from human SMN genes and reveals a novel protein isoform predicted to be stably expressed during conditions of stress.

Oxidative Stress Triggers Body-Wide Skipping of Multiple Exons of the Spinal Muscular Atrophy Gene

Humans carry two nearly identical copies of Survival Motor Neuron gene: SMN1 and SMN2. Loss of SMN1 leads to spinal muscular atrophy (SMA), the most frequent genetic cause of infant mortality. While SMN2 cannot compensate for the loss of SMN1 due to predominant skipping of exon 7, correction of SMN2 exon 7 splicing holds the promise of a cure for SMA. Previously, we used cell-based models coupled with a multi-exon-skipping detection assay (MESDA) to demonstrate the vulnerability of SMN2 exons to aberrant splicing under the conditions of oxidative stress (OS). Here we employ a transgenic mouse model and MESDA to examine the OS-induced splicing regulation of SMN2 exons. We induced OS using paraquat that is known to trigger production of reactive oxygen species and cause mitochondrial dysfunction. We show an overwhelming co-skipping of SMN2 exon 5 and exon 7 under OS in all tissues except testis. We also show that OS increases skipping of SMN2 exon 3 in all tissues except testis. We uncover several new SMN2 splice isoforms expressed at elevated levels under the conditions of OS. We analyze cis-elements and transacting factors to demonstrate the diversity of mechanisms for splicing misregulation under OS. Our results of proteome analysis reveal downregulation of hnRNP H as one of the potential consequences of OS in brain. Our findings suggest SMN2 as a sensor of OS with implications to SMA and other diseases impacted by low levels of SMN protein.

Antimicrobial activity, structural evaluation and vibrational (FT-IR and FT-Raman) study of pyrrole containing vinyl derivatives

In this paper we present structural and vibrational study of three vinylpyrrole derivatives: 2-Cyano-3-(1H-pyrrol-2-yl)-acrylamide (CPA), 1-(1H-Pyrrol-2-yl)-Pent-1-en-3-one (PP) and 1-(1H-Pyrrol-2-yl)-but-1-en-3-one (PB), using ab initio, DFT and experimental approaches. The quantum chemical calculation have been performed on B3LYP method and 6-311+G(d,p) basis set. The experimental FT-IR and Raman wavenumbers were compared with the respective theoretical values obtained from DFT calculations and found to agree well. The experimental FT-IR and Raman study clearly indicate that the compound exist as dimer in solid state. The binding energies of (CPA), (PP) and (PB) dimers are found to be 20.95, 18.75 and 19.18 kcal/mol, respectively. The vibrational analysis shows red shifts in v(N-H) and v(C=O) stretching as result of dimer formation. Stability of the molecule arising from hyperconjugative interactions and charge delocalization has been analyzed using NBO analysis. Topological and energetic parameters reveal the nature of interactions in dimer. The local electronic descriptors analyses were used to predict the reactive sites in the molecule. Calculated first static hyperpolarizability of CPA, PP and PB is found to be 10.41×10(-30), 18.93×10(-30), 18.29×10(-30) esu, respectively, shows that investigated molecules will have non-linear optical response and might be used as non-linear optical (NLO) material. These vinylpyrrole compounds (CPA), (PP) and (PB) showed antifungal and antibacterial activity against Aspergillus niger and gram-positive bacteria Bacillus subtili.

Severe impairment of male reproductive organ development in a low SMN expressing mouse model of spinal muscular atrophy

Spinal muscular atrophy (SMA) is caused by low levels of survival motor neuron (SMN), a multifunctional protein essential for higher eukaryotes. While SMN is one of the most scrutinized proteins associated with neurodegeneration, its gender-specific role in vertebrates remains unknown. We utilized a mild SMA model (C/C model) to examine the impact of low SMN on growth and development of mammalian sex organs. We show impaired testis development, degenerated seminiferous tubules, reduced sperm count and low fertility in C/C males, but no overt sex organ phenotype in C/C females. Underscoring an increased requirement for SMN expression, wild type testis showed extremely high levels of SMN protein compared to other tissues. Our results revealed severe perturbations in pathways critical to C/C male reproductive organ development and function, including steroid biosynthesis, apoptosis, and spermatogenesis. Consistent with enhanced apoptosis in seminiferous tubules of C/C testes, we recorded a drastic increase in cells with DNA fragmentation. SMN was expressed at high levels in adult C/C testis due to an adult-specific splicing switch, but could not compensate for low levels during early testicular development. Our findings uncover novel hallmarks of SMA disease progression and link SMN to general male infertility.

A Rare Presentation Of An Ectopic Breast Tissue In Axilla

Accessory breast tissue is rare accounting to less than 1% cases seen in females. It is usually bilateral. We report a case of 24-year-old woman with a lump in the left axilla in view of its rarity and made a differential diagnosis of fibroadenoma, which following the investigations and histopathological report was confirmed as revealed fibroadenoma in the axilla. It should also be considered as a differential diagnosis for all axillary swellings.

Assessment of conformational, spectral, antimicrobial activity, chemical reactivity and NLO application of Pyrrole-2,5-dicarboxaldehyde bis(oxaloyldihydrazone)

An orange colored pyrrole dihydrazone: Pyrrole-2,5-dicarboxaldehyde bis(oxaloyldihydrazone) (PDBO) has been synthesized by reaction of oxalic acid dihydrazide with 2,5 diformyl-1H-pyrrole and has been characterized by spectroscopic analysis (1H, 13C NMR, UV-visible, FT-IR and DART Mass). The properties of the compound has been evaluated using B3LYP functional and 6-31G(d,p)/6-311+G(d,p) basis set. The symmetric (3319, 3320 cm(-1)) and asymmetric (3389, 3382 cm(-1)) stretching wave number confirm free NH2 groups in PDBO. NBO analysis shows, inter/intra molecular interactions within the molecule. Topological parameters have been analyzed by QTAIM theory and provide the existence of intramolecular hydrogen bonding (N-H⋯O). The local reactivity descriptors analyses determine the reactive sites within molecule. The calculated first hyperpolarizability value (β0=23.83×10(-30) esu) of pyrrole dihydrazone shows its suitability for non-linear optical (NLO) response. The preliminary bioassay suggested that the PDBO exhibits relatively good antibacterial and fungicidal activity against Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus pyogenes, Candida albicans, Aspergillus niger. The local reactivity descriptors--Fukui functions (fk+, fk-), local softnesses (sk+, sk-) and electrophilicity indices (ωk+, ωk-) analyses have been used to determine the reactive sites within molecule.

Splicing regulation in spinal muscular atrophy by an RNA structure formed by long-distance interactions

Humans carry two copies of the survival motor neuron gene: SMN1 and SMN2. Loss of SMN1 coupled with skipping of SMN2 exon 7 causes spinal muscular atrophy (SMA), a leading genetic disease associated with infant mortality. Our discovery of intronic splicing silencer N1 (ISS-N1) is a promising target, currently in a phase III clinical trial, for an antisense oligonucleotide-mediated splicing correction in SMA. We have recently shown that the first residue of ISS-N1 is locked in a unique RNA structure that we term ISTL1 (internal stem through long-distance interaction-1). Complementary strands of ISTL1 are separated from each other by 279 nucleotides. Using site-specific mutations and chemical structure probing, we confirmed the formation and functional significance of ISTL1. Located in the middle of intron 7, the 3' strand of ISTL1 falls within an inhibitory region that we term ISS-N2. We demonstrate that an antisense oligonucleotide-mediated sequestration of ISS-N2 fully corrects SMN2 exon 7 splicing and restores high levels of SMN in SMA patient cells. These results underscore the therapeutic potential of the regulatory information present in a secondary and high-order RNA structure of a human intron.

Vibrational spectra, electronic absorption, nonlinear optical properties, evaluation of bonding, chemical reactivity and thermodynamic properties of ethyl 4-(1-(2-(hydrazinecarbonothioyl)hydrazono)ethyl)-3,5-dimethyl-1H-pyrrole-2-carboxylate molecule by ab initio HF and density functional methods

In this work, detailed vibrational spectral analysis of ethyl 4-(1-(2-(hydrazinecarbonothioyl)hydrazono)ethyl)-3,5-dimethyl-1H-pyrrole-2-carboxylate (EHCHEDPC) molecule has been carried out using FT-IR spectroscopy and potential energy distribution (PED). Theoretical calculations were performed by ab initio RHF and density functional theory (DFT) method, using 6-31G(d,p) and 6-311+G(d,p) basis sets. The other carried outwork cover: structural, thermodynamic properties, electronic transitions, bonding, multiple interaction, chemical reactivity and hyperpolarizability analysis. The results of the calculation were applied to the simulated spectra of (EHCHEDPC), which show excellent agreement with observed spectra. The vibrational analysis shows red shift in both group, the proton donor (pyrrole N-H) and proton acceptor (C=O of ester) indicating the presence of intermolecular hydrogen bonding. Time dependent density functional theory (TD-DFT) has been used to find electronic excitations and their nature. The results of natural bond orbital (NBOs) analysis show the charges transfer and delocalization in various intra- and intermolecular interactions. The binding energy of intermolecular multiple interactions is calculated to be 12.54 kcal mol(-1) using QTAIM calculation. The electronic descriptors analyses reveal the investigated molecule used as precursor for heterocyclic derivatives synthesis. First hyperpolarizability (β0) has been computed to evaluate non-linear optical (NLO) response.

Antisense methods to modulate pre-mRNA splicing

The dynamic process of pre-mRNA splicing is regulated by combinatorial control exerted by overlapping cis-elements that are unique to every exon and its flanking intronic sequences. Splicing cis-elements are usually 4-8-nucleotide-long linear motifs that furnish interaction sites for specific proteins. Secondary and higher-order RNA structures exert an additional layer of control by providing accessibility to cis-elements. Antisense oligonucleotides (ASOs) that block splicing cis-elements and/or affect RNA structure have been shown to modulate alternative splicing in vivo. Consistently, ASO-based strategies have emerged as a powerful tool for therapeutic manipulation of aberrant splicing in pathological conditions. Here we describe the application of an ASO-based approach for the enhanced production of the full-length mRNA of SMN2 in spinal muscular atrophy patient cells.

Synthesis, molecular structure, hydrogen-bonding, NBO and chemical reactivity analysis of a novel 1,9-bis(2-cyano-2-ethoxycarbonylvinyl)-5-(4-hydroxyphenyl)-dipyrromethane: a combined experimental and theoretical (DFT and QTAIM) approach

The spectroscopic analysis of a newly synthesized 1,9-bis(2-cyano-2-ethoxycarbonylvinyl)-5-(4-hydroxyphenyl)-dipyrromethane (3) has been carried out using (1)H NMR, UV-Visible, FT-IR and Mass spectroscopic techniques. All the quantum chemical calculations have been carried out using DFT level of theory, B3LYP functional and 6-31G(d,p) as basis set. Thermodynamic parameters (H, G, S) of all the reactants and products have been used to determine the nature of the chemical reaction. The chemical shift of pyrrolic NH in (1)H NMR spectrum appears at 9.4 ppm due to intramolecular hydrogen bonding. TD-DFT calculation shows the nature of electronic transitions as π→π(*) within the molecule. A combined experimental and theoretical vibrational analysis designates the existence of H-bonding between pyrrole N-H as proton donor and nitrogen of cyanide as proton acceptor, therefore, lowering in stretching vibration of NH and CN. To investigate the strength and nature of H-bonding, topological parameters at bond critical points (BCPs) are analyzed by 'Quantum theory of Atoms in molecules' (QTAIMs). Natural bond orbitals (NBOs) analysis has been carried out to investigate the intramolecular conjugative and hyperconjugative interactions within molecule and their second order stabilization energy (E((2))). Global electrophilicity index (ω=4.528 eV) shows that title molecule (3) is a strong electrophile. The maximum values of local electrophilic reactivity descriptors (fk(+),sk(+),ωk(+)) at vinyl carbon (C6/C22) of (3) indicate that these sites are more prone to nucleophilic attacks.

An intronic structure enabled by a long-distance interaction serves as a novel target for splicing correction in spinal muscular atrophy

Here, we report a long-distance interaction (LDI) as a critical regulator of alternative splicing of Survival Motor Neuron 2 (SMN2) exon 7, skipping of which is linked to spinal muscular atrophy (SMA), a leading genetic disease of children and infants. We show that this LDI is linked to a unique intra-intronic structure that we term internal stem through LDI-1 (ISTL1). We used site-specific mutations and Selective 2'-Hydroxyl Acylation analyzed by Primer Extension to confirm the formation and functional significance of ISTL1. We demonstrate that the inhibitory effect of ISTL1 is independent of hnRNP A1/A2B1 and PTB1 previously implicated in SMN2 exon 7 splicing. We show that an antisense oligonucleotide-mediated sequestration of the 3' strand of ISTL1 fully corrects SMN2 exon 7 splicing and restores high levels of SMN and Gemin2, a SMN-interacting protein, in SMA patient cells. Our results also reveal that the 3' strand of ISTL1 and upstream sequences constitute an inhibitory region that we term intronic splicing silencer N2 (ISS-N2). This is the first report to demonstrate a critical role of a structure-associated LDI in splicing regulation of an essential gene linked to a genetic disease. Our findings expand the repertoire of potential targets for an antisense oligonucleotide-mediated therapy of SMA.

Spinal muscular atrophy: an update on therapeutic progress

Humans have two nearly identical copies of survival motor neuron gene: SMN1 and SMN2. Deletion or mutation of SMN1 combined with the inability of SMN2 to compensate for the loss of SMN1 results in spinal muscular atrophy (SMA), a leading genetic cause of infant mortality. SMA affects 1 in ~6000 live births, a frequency much higher than in several genetic diseases. The major known defect of SMN2 is the predominant exon 7 skipping that leads to production of a truncated protein (SMNΔ7), which is unstable. Therefore, SMA has emerged as a model genetic disorder in which almost the entire disease population could be linked to the aberrant splicing of a single exon (i.e. SMN2 exon 7). Diverse treatment strategies aimed at improving the function of SMN2 have been envisioned. These strategies include, but are not limited to, manipulation of transcription, correction of aberrant splicing and stabilization of mRNA, SMN and SMNΔ7. This review summarizes up to date progress and promise of various in vivo studies reported for the treatment of SMA.

A combined experimental and theoretical (DFT and AIM) studies on synthesis, molecular structure, spectroscopic properties and multiple interactions analysis in a novel ethyl-4-[2-(thiocarbamoyl)hydrazinylidene]-3,5-dimethyl-1H-pyrrole-2-carboxylate and its dimer

In the present work, ethyl-4-[2-(thiocarbamoyl)hydrazinylidene]-3,5-dimethyl-1H-pyrrole-2-carboxylate (3) has been synthesized and characterized by (1)H NMR, UV-Vis, FT-IR and Mass spectroscopy. The formation of the compound and its properties have also been evaluated by quantum chemical calculations using DFT, B3LYP functional and 6-31G(d,p) as basis set. The calculated thermodynamic parameters show that the formation of 3 is an exothermic and spontaneous reaction at room temperature. (1)H NMR chemical shifts are calculated using gauge including atomic orbitals (GIAO) approach in DMSO-d6 as solvent. Time dependent density functional theory (TD-DFT) is used to calculate the energy (E), oscillator strength (f) and wavelength absorption maxima (λ(max)) of various electronic transitions and their nature within the molecule. NBO analysis is carried out to investigate the charge transfer or charge delocalization in various intra- and intermolecular interactions of molecular system. The vibrational analysis indicates the formation of dimer in the solid state by intermolecular heteronuclear hydrogen bonding (NH···O). Topological parameters at bond critical points (BCP) are calculated to analyze the strength and nature of various types of intra and intermolecular interactions in dimer by Bader's 'Atoms in molecules' AIM theory in detail. The binding energy of intermolecular multiple interactions is calculated to be 15.54 kcal/mol, using AIM calculation. The local reactivity descriptors such as Fukui functions (f(k)(+),f(k)(-)), local softnesses (s(k)(+),s(k)(-)) and electrophilicity indices (ω(k)(+),ω(k)(-)) analyses are performed to determine the reactive sites within molecule.

Food and feeding pattern of Channa punctatus in two different habitats at Tarai region of Uttarakhand

A comparative study was conducted for the food items and feeding pattern of Channa punctatus in pond environment and in reservoir of Tarai region in Uttarakhand state. Observation was made for body length, gut length, food and feeding frequency and qualitative and quantitative analysis of gut content. Both, body length and gut length were in higher side with a ratio of 1:2.1 for the natural fish stock of reservoir. Gut content mainly consists of crustacean, insects, mollusks, small fishes and semi-digested material. There was significant difference for the percent occurrence of the food items (p < 0.01) of natural stock of reservoir and pond reared stock. The study revealed that seasonal variability of natural food items in different habitats and their biological diversity put impacts on the biological needs in terms of food and feeding pattern of the same fish species.

Antisense oligonucleotide mediated therapy of spinal muscular atrophy

Spinal muscular atrophy (SMA) is the leading genetic cause of infant mortality. SMA results from deletions or mutations of survival motor neuron 1 (SMN1), an essential gene. SMN2, a nearly identical copy, can compensate for SMN1 loss if SMN2 exon 7 skipping is prevented. Among the many cis-elements involved in the splicing regulation of SMN exon 7, intronic splicing silencer N1 (ISS-N1) has emerged as the most effective target for an antisense oligonucleotide (ASO)-mediated splicing correction of SMN2 exon 7. Blocking of ISS-N1 by an ASO has been shown to fully restore SMN2 exon 7 inclusion in SMA patient cells as well as in vivo. Here we review how ISS-N1 targeting ASOs that use different chemistries respond differently in the various SMA mouse models. We also compare other ASO-based strategies for therapeutic splicing correction in SMA. Given that substantial progress on ASO-based strategies to promote SMN2 exon 7 inclusion in SMA has been made, and that similar approaches in a growing number of genetic diseases are possible, this report has wide implications.

Phase diagram and thermodynamic properties of H2

A statistical mechanical-based theory is used to develop the equation of state for the molecular fluid of H(2). We incorporate in this equation the long-range correlations through the double Yukawa potential, dimerization of the H(2) molecule by treating the fluid as a hard convex body fluid, and first-order quantum correction which is important at low temperatures. We use this to calculate the liquid-vapor equilibrium of H(2), including the temperature and pressure dependence of compressibility factor, entropy, specific heat, compressibility, and sound velocity.

A multi-exon-skipping detection assay reveals surprising diversity of splice isoforms of spinal muscular atrophy genes

Humans have two near identical copies of Survival Motor Neuron gene: SMN1 and SMN2. Loss of SMN1 coupled with the predominant skipping of SMN2 exon 7 causes spinal muscular atrophy (SMA), a neurodegenerative disease. SMA patient cells devoid of SMN1 provide a powerful system to examine splicing pattern of various SMN2 exons. Until now, similar system to examine splicing of SMN1 exons was unavailable. We have recently screened several patient cell lines derived from various diseases, including SMA, Alzheimer’s disease, Parkinson’s disease and Batten disease. Here we report a Batten disease cell line that lacks functional SMN2, as an ideal system to examine pre-mRNA splicing of SMN1. We employ a multiple-exon-skipping detection assay (MESDA) to capture simultaneously skipping of multiple exons. Our results show surprising diversity of splice isoforms and reveal novel splicing events that include skipping of exon 4 and co-skipping of three adjacent exons of SMN. Contrary to the general belief, MESDA captured oxidative-stress induced skipping of SMN1 exon 5 in several cell types, including non-neuronal cells. We further demonstrate that the predominant SMN2 exon 7 skipping induced by oxidative stress is modulated by a combinatorial control that includes promoter sequence, endogenous context, and the weak splice sites. We also show that an 8-mer antisense oligonucleotide blocking a recently described GC-rich sequence prevents SMN2 exon 7 skipping under the conditions of oxidative stress. Our findings bring new insight into splicing regulation of an essential housekeeping gene linked to neurodegeneration and infant mortality.