Modulating role of RNA structure in alternative splicing of a critical exon in the spinal muscular atrophy genes

Humans have two nearly identical copies of the survival motor neuron (SMN ) gene, SMN1 and SMN2. Homozygous loss of SMN1 causes spinal muscular atrophy (SMA). SMN2 is unable to prevent the disease due to skipping of exon 7. Using a systematic approach of in vivo selection, we have previously demonstrated that a weak 5′ splice site (ss) serves as the major cause of skipping of SMN2 exon 7. Here we show the inhibitory impact of RNA structure on the weak 5′ ss of exon 7. We call this structure terminal stem–loop 2 (TSL2). Confirming the inhibitory nature of TSL2, point mutations that destabilize TSL2 promote exon 7 inclusion in SMN2, whereas strengthening of TSL2 promotes exon 7 skipping even in SMN1. We also demonstrate that TSL2 negatively affects the recruitment of U1snRNP at the 5′ ss of exon 7. Using enzymatic structure probing, we confirm that the sequence at the junction of exon 7/intron 7 folds into TSL2 and show that mutations in TSL2 cause predicted structural changes in this region. Our findings reveal for the first time the critical role of RNA structure in regulation of alternative splicing of human SMN

Filamentous Soil Fungi from Ny-Ålesund, Spitsbergen, and Screening for Extracellular Enzymes

Soil filamentous fungi from Ny-Ålesund, Spitsbergen, were studied. A total of 30 fungal isolates were identified by morpho-taxonomy, and the identity of some morpho-taxonomically complex isolates was authenticated by ITS1-5.8S and ITS2 rDNA domain sequence similarity. The isolates belonged to 19 species under 14 genera (Acremonium, Arthrinium, Aspergillus, Cladosporium, Corynespora, Emericella, Geomyces, Mortierella, Mucor, Myrothecium, Penicillium, Phialophora, Preussia, Xylaria). To the best of our knowledge, Acremonium roseolum, Aspergillus aculeatus, Emericella nidulans, and Preussia sp. are the first northernmost records from Arctic soils. The viable fungal count in different soil samples varied from 0.5 • 104 to 2.0 • 105 g-1. Species richness in different soil samples was also calculated. Mortierella was one of the most dominant genera in Arctic soils. A temperature tolerance study was carried out for all the isolates, and representative species were screened for their extracellular enzyme activity (amylase, cellulase, phosphatase, and pectinase) at 4˚C and 20˚C. Among the 30 isolates, seven showed cellulolytic activity, two were phosphate solubilizers, three had amylolytic activity, and only one showed pectinolytic activity on solid media. CMCase (β1, 4-endoglucanase) activity was quantified in seven isolates that exhibited positive activity during preliminary screening. The records of enzyme activity for amylases, pectinases, and cellulases are the first from the fungi of Spitsbergen. The present study indicates the dominance in Ny-Ålesund of cellulolytic strains, which may serve as potent decomposers in Arctic tundra. These isolates may be used to facilitate the mineralization of cellulolytic wastes generated by human activities in colder hilly areas across the world, including the Himalayas in India.Nous avons étudié des champignons telluriques filamenteux de Ny-Ålesund, Spitzberg. Grâce à la morpho-taxonomie, nous avons identifié 30 isolats fongiques, et l’identité de certains complexes d’isolats morpho-taxonomiques a été authentifiée au moyen des similarités des séquences de domaines ITS1-5.8S et ITS2 DNAr. Les isolats relevaient de 19 espèces faisant partie de 14 genres (Acremonium, Arthrinium, Aspergillus, Cladosporium, Corynespora, Emericella, Geomyces, Mortierella, Mucor, Myrothecium, Penicillium, Phialophora, Preussia, Xylaria). Au meilleur de nos connais­sances, Acremonium roseolum, Aspergillus aculeatus, Emericella nidulans et Preussia sp. constituent les premiers enregis­trements aussi nordiques des sols arctiques. Le dénombrement viable de champignons dans différents échantillons de sol variait de 0,5 • 104 à 2,0 • 105 g-1. Nous avons également calculé la diversité des espèces prélevées dans différents échantillons de sol. Le genre Mortierella était l’un des plus dominants des sols arctiques. Nous avons étudié la tolérance à la température de tous les isolats, et des espèces représentatives ont été examinées du point de vue de l’activité enzymatique extracellulaire (amylase, cellulase, phosphatase et pectinase) à 4 ˚C et 20 ˚C. Parmi les 30 isolats, sept présentaient de l’activité cellulolytique, deux étaient des solubilisants du phosphate, trois présentaient de l’activité amylolytique et seulement un présentait de l’activité pectolytique dans le cas des solides. L’activité CMCase (β1, 4-endoglucanase) a été quantifiée dans sept isolats qui affichaient une activité positive au cours de l’examen préliminaire. Il s’agissait de la première fois que de l’activité enzymatique pour les amylases, pectinases et cellulases a été détectée dans les champignons de Spitzberg. Cette étude indique la dominance de souches cellulolytiques à Ny-Ålesund, souches qui peuvent servir de décomposeurs puissants dans la toundra arctique. Ces isolats peuvent servir à faciliter la minéralisation des déchets cellulolytiques émanant des activités humaines dans les régions montagneuses plus froides du monde entier, y compris l’Himalaya, en Inde

U1 snRNA interactions with deep intronic sequences regulate splicing of multiple exons of spinal muscular atrophy genes

Introduction: The U1 small nuclear RNA (snRNA) forms ribonucleoprotein particles (RNPs) such as U1 snRNP and U1-TAF15 snRNP. U1 snRNP is one of the most studied RNPs due to its critical role in pre-mRNA splicing in defining the 5 splice site (5ss) of every exon through direct interactions with sequences at exon/intron junctions. Recent reports support the role of U1 snRNP in all steps of transcription, namely initiation, elongation, and termination. Functions of U1-TAF15 snRNP are less understood, though it associates with the transcription machinery and may modulate pre-mRNA splicing by interacting with the 5ss and/or 5ss-like sequences within the pre-mRNA. An anti-U1 antisense oligonucleotide (ASO) that sequesters the 5 end of U1 snRNA inhibits the functions of U1 snRNP, including transcription and splicing. However, it is not known if the inhibition of U1 snRNP influences post-transcriptional regulation of pre-mRNA splicing through deep intronic sequences. Methods: We examined the effect of an anti-U1 ASO that sequesters the 5 end of U1 snRNA on transcription and splicing of all internal exons of the spinal muscular atrophy (SMA) genes, SMN1 and SMN2. Our study was enabled by the employment of a multi-exon-skipping detection assay (MESDA) that discriminates against prematurely terminated transcripts. We employed an SMN2 super minigene to determine if anti-U1 ASO differently affects splicing in the context of truncated introns. Results: We observed substantial skipping of multiple internal exons of SMN1 and SMN2 triggered by anti-U1 treatment. Suggesting a role for U1 snRNP in interacting with deep intronic sequences, early exons of the SMN2 super minigene with truncated introns were resistant to anti-U1 induced skipping. Consistently, overexpression of engineered U1 snRNAs targeting the 5ss of early SMN1 and SMN2 exons did not prevent exon skipping caused by anti-U1 treatment. Discussion: Our results uncover a unique role of the U1 snRNA-associated RNPs in splicing regulation executed through deep intronic sequences. Findings are significant for developing novel therapies for SMA based on deep intronic targets.This article is published as Ottesen, Eric W., Natalia N. Singh, Joonbae Seo, and Ravindra N. Singh. "U1 snRNA interactions with deep intronic sequences regulate splicing of multiple exons of spinal muscular atrophy genes." Frontiers in Neuroscience 18: 1412893. doi: https://doi.org/10.3389/fnins.2024.1412893. © 2024 Ottesen, Singh, Seo and Singh. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY)

MENGGUNAKAN METODE DISKUSI UNTUK MENINGKATKAN KEMAMPUAN MENULIS PADA SISWA KELAS IV SD NEGERI NEUHEUN KABUPATEN ACEH BESAR

Banda Ace

Adaptation to Variable Environments, Resilience to Climate Change: Investigating Land, Water and Settlement in Indus Northwest India

This paper explores the nature and dynamics of adaptation and resilience in the face of a diverse and varied environmental and ecological context using the case study of South Asia’s Indus Civilization (ca. 3000–1300 BC). Most early complex societies developed in regions where the climatic parameters faced by ancient subsistence farmers were varied but rain falls primarily in one season. In contrast, the Indus Civilization developed in a specific environmental context that spanned a very distinct environmental threshold, where winter and summer rainfall systems overlap. There is now evidence to show that this region was directly subject to climate change during the period when the Indus Civilization was at its height (ca. 2500–1900 BC). The Indus Civilization, therefore, provides a unique opportunity to understand how an ancient society coped with diverse and varied ecologies and change in the fundamental environmental parameters. This paper integrates research carried out as part of the Land, Water and Settlement project in northwest India between 2007 and 2014. Although coming from only one of the regions occupied by Indus populations, these data necessitate the reconsideration of several prevailing views about the Indus Civilization as a whole and invigorate discussion about human-environment interactions and their relationship to processes of cultural transformation

Role of diffusion weighted MR imaging in differentiating benign from malignant prostate lesions

Background: The purpose of the study was to determine the diagnostic accuracy of diffusion weighted MR imaging and to propose a cut off ADC value in differentiating benign from malignant prostatic lesions considering histopathology as gold standard.Methods: It is a descriptive type of observational study done on 40 patients with clinical suspicion of prostate carcinoma and elevated PSA level more than 4ng/ml. The patients underwent Multiparametric prostate MRI and ADC values were calculated using ADC maps.Results: Of the 40 cases included in the study histopathology revealed a diagnosis of abscess (1), chronic prostatitis (2), BPH with chronic prostatitis (4), BPH (12), and malignancy (21). The mean and standard deviation (SD) of ADC values for the abscess (0.59), CP (0.83+0.16), BPH with CP (0.94+0.22), BPH (1.14+0.14) and malignancy (0.72+0.15) (x10-3mm2/s) were found in our study. The mean ADC value of malignant lesion was lower (0.727+0.149) as compare to benign lesion (1.034+0.216) and this difference was found to be statistically significant with p<0.001. By using ROC curve, ADC cut off value was calculated as 0.92 x 10-3mm2/s and sensitivity, specificity at this cut off value of ADC were 95.24% and 73.68% respectively. The PPV, NPV, diagnostic accuracy of at this cut off value of ADC were 80%, 93.33%, 85% respectively.Conclusions: Our study shows that DWI with ADC calculation helps in differentiation of Benign from Malignant prostatic lesions with high accuracy and this quantitative analysis should be incorporated in routine MRI evaluation of prostatic lesion

Role Of Kunapa Jala For The Overall Enhancement And Growth Of Prishnaparni

Vrikshayurveda is a traditional branch of botany that studies plant growth and development. This science mostly recommends using Kunapa jala and Pancha gavya to increase crop output. This idea is around using organic farming to grow plants effectively. Kunapajala, is an organic liquid manure that is a by-product of fermentation and serves as a source of plant nutrients, was stated by Vrikshayurveda. The two main forms of Kunapajala used in practises are herbal and non-herbal, and both are made in accordance with the steps outlined in Vrikshayurvedha. Given its significance, we designed a study to examine the contribution of the Vrikshayurvedha idea to the evolution of medicinal plants; Prishniparni. Present study evaluated role of Kunapajala in the growth and % yield of plant Prishniparni. This study observed that Kunapajala treatment provides best response with respect to root yield and soil physico-chemical parameters. The yield of plant improved quantitatively as well as qualitatively after the use of Kunapajala