Systemic and intrinsic functions of ATRX in glial cell fate and CNS myelination in male mice

Myelin, an extension of the oligodendrocyte plasma membrane, wraps around axons to facilitate nerve conduction. Myelination is compromised in ATR-X intellectual disability syndrome patients, but the causes are unknown. We show that loss of ATRX leads to myelination deficits in male mice that are partially rectified upon systemic thyroxine administration. Targeted ATRX inactivation in either neurons or oligodendrocyte progenitor cells (OPCs) reveals OPC-intrinsic effects on myelination. OPCs lacking ATRX fail to differentiate along the oligodendrocyte lineage and acquire a more plastic state that favors astrocytic differentiation in vitro and in vivo. ATRX chromatin occupancy in OPCs greatly overlaps with that of the chromatin remodelers CHD7 and CHD8 as well as H3K27Ac, a mark of active enhancers. Overall, our data indicate that ATRX regulates the onset of myelination systemically via thyroxine, and by promoting OPC differentiation and suppressing astrogliogenesis. These functions of ATRX identified in mice could explain white matter pathogenesis observed in ATR-X syndrome patients.

Impact and mitigation of lead, cadmium and micro/nano plastics in fragrant rice

Heavy metals (HMs) and micro(nano)plastics (MNPs), represent a significant risk to global food supply as well as a potential risk to humankind. Over 50% of the worldwide population eat rice every day, and rice aroma is a significant qualitative trait that is highly valued by consumers and fetches premium prices in the global market. Despite the huge commercial importance of fragrant rice, limited studies were directed to investigate the influence of HMs and MNPs on yield related traits and 2-Acetyl-1-pyrroline (2-AP) compound, mainly responsible for aroma production in fragrant rice. In this review, we found that the interaction of HMs and MNPs in fragrant rice is complex and accumulation of HMs and MNPs was higher in root as compared to the grains. Nutrients and phytohormones mediated mitigation of HMs and MNPs were most effective sustainable strategies. In addition, monitoring the checkpoints of 2-AP biosynthesis and its interaction with HMs and MNPs is challenging. Finally, we explained the potential challenges that fragrant rice faces considering the continuous rise in environmental pollutants and discussed the future avenues of research to improve fragrant rice's yield and qualitative traits.

DDM1-mediated R-loop resolution and H2A.Z exclusion facilitates heterochromatin formation in Arabidopsis

Programmed constitutive heterochromatin silencing is essential for eukaryotic genome regulation, yet the initial step of this process is ambiguous. A large proportion of R-loops (RNA:DNA hybrids) had been unexpectedly identified within Arabidopsis pericentromeric heterochromatin with unknown functions. Through a genome-wide R-loop profiling screen, we find that DDM1 (decrease in DNA methylation 1) is the primary restrictor of pericentromeric R-loops via its RNA:DNA helicase activity. Low levels of pericentromeric R-loops resolved by DDM1 cotranscriptionally can facilitate constitutive heterochromatin silencing. Furthermore, we demonstrate that DDM1 physically excludes histone H2A variant H2A.Z and promotes H2A.W deposition for faithful heterochromatin initiation soon after R-loop clearance. The dual functions of DDM1 in R-loop resolution and H2A.Z eviction are essential for sperm nuclei structure maintenance in mature pollen. Our work unravels the cotranscriptional R-loop resolution coupled with accurate H2A variants deposition is the primary step of constitutive heterochromatin silencing in Arabidopsis, which might be conserved across eukaryotes.

Biosynthesis of 2-Acetyl-1-pyrroline in Fragrant Rice: Recent Insights into Agro-management, Environmental Factors, and Functional Genomics

Rice is a staple food for more than half of the world's population, and rice fragrance is a key quality attribute which is highly desired by consumers and attracts premium prices in the international market. There are around 200 volatile compounds involved in rice fragrance, but 2-acetyl-1-pyrroline (2-AP) has been considered a master regulator of aroma in fragrant rice. Consequently, efforts were made to increase the 2-AP contents in the grain by managing agronomical practices or by using modern functional genomic tools, which successfully converted nonfragrant cultivars to fragrant rice. Furthermore, environmental factors were also reported to influence the 2-AP contents. However, a comprehensive analysis of 2-AP biosynthesis in response to agro-management practices, environmental factors, and the application of functional genomic tools for fragrant rice production was missing. In this Review, we summarize how micro/macronutrients, cultivation practices, amino acid precursors, growth regulators, and environmental factors, such as drought, salinity, light, and temperature, influence the 2-AP biosynthesis to modulate the aroma of fragrant rice. Furthermore, we also summarized the successful conversion of nonfragrant rice cultivars to fragrant rice using modern gene editing tools, such as RNAi, TALENS, and CRISPR-Cas9. Finally, we discussed and highlighted the future perspective and challenges related to the aroma of fragrant rice.

Homozygous Missense Variant in the N-Terminal Region of ANK3 Gene Is Associated with Developmental Delay, Seizures, Speech Abnormality, and Aggressive Behavior

Introduction

Intellectual disability (ID) is a lifelong disability that affects an individual‧s learning capacity and adaptive behavior. Such individuals depend on their families for day-to-day survival and pose a significant challenge to the healthcare system, especially in developing countries. ID is a heterogeneous condition, and genetic studies are essential to unravel the underlying cellular pathway for brain development and functioning.

Methods

Here we studied a female index patient, born to a consanguineous Pakistani couple, showing clinical symptoms of ID, ataxia, hypotonia, developmental delay, seizures, speech abnormality, and aggressive behavior. Whole exome sequencing (WES) coupled with Sanger sequencing was performed for molecular diagnosis. Further, 3D protein modeling was performed to see the effect of variant on protein structure.

Results

WES identified a novel homozygous missense variant (c.178T>C; p.Tyr60His) in the ANK3 gene. In silico analysis and 3-dimensional (3D) protein modeling supports the deleterious impact of this variant on the encoding protein, which compromises the protein‧s overall structure and function.

Conclusion

Our finding supports the clinical and genetic diversity of the ANK3 gene as a plausible candidate gene for ID syndrome. Intelligence is a complex polygenic human trait, and understanding molecular and biological pathways involved in learning and memory can solve the complex puzzle of how cognition develops. Intellectual disability (ID) is defined as a deficit in an individual‧s learning and adaptive behavior at an early age of onset [American Psychiatric Association, 2013]. It is one of the major medical, and cognitive disorders with a prevalence of 1-3% in the population worldwide [Leonard and Wen, 2002]. ID often exists with other disabling mental conditions such as autism, attention deficit hyperactivity disorder, epilepsy, schizophrenia, bipolar disorder, or depression. Almost half of the cases appear to have a genetic explanation that ranges from cytogenetically visible abnormalities to monogenic defects [Flint, 2001; Ropers, 2010; Tucker-Drob et al., 2013]. Intellectual disability is a genetically heterogeneous condition, and more than 700 genes have been identified to cause ID alone or as a part of the syndrome. Research in X-linked ID has identified more than 100 disease-causing genes on the X chromosome that play a role in cognition; however, research into autosomal causes of ID is still ongoing [Vissers et al., 2016].

CRISPR-Cas9-mediated editing of BADH2 gene triggered fragrance revolution in rice

Fragrance is one of the most important quality traits for breeding in rice. The natural aroma substance 2-acetyl-1-pyrroline (2-AP) is a key fragrance compound among over 200 volatiles identified in fragrant rice. In addition to rice, there are other plant species that contain a germplasm that naturally produces a fragrant aroma. These other plant species all have lower activity levels of the enzyme BETAINE ALDEHYDE DEHYDROGENASE 2 (BADH2). Therefore, improving fragrance efficiency has been a focus of intensive research. Recent studies have engineered BADH2 gene, which is responsible for fragrance trait in non-fragrant cultivars of rice, using CRISPR-Cas9. Although engineering rice BADH2 can be useful for upregulating 2-AP, there are still a lot of restrictions on how it can be applied in practice. In this review article, we discuss the recent developments in BADH2 editing and propose potential future strategies to effectively target BADH2 for transcriptional regulation, with the goal of producing a better fragrance.

Clinical genetics of spondylocostal dysostosis: A mini review

Spondylocostal dysostosis is a genetic defect associated with severe rib and vertebrae malformations. In recent years, extensive clinical and molecular diagnosis advancements enabled us to identify disease-causing variants in different genes for such severe conditions. The identification of novel candidate genes enabled us to understand the developmental biology and molecular and cellular mechanisms involved in the etiology of these rare diseases. Here, we discuss the clinical and molecular targets associated with spondylocostal dysostosis, including clinical evaluation, genes, and pathways involved. This review might help us understand the basics of such a severe disorder, which might help in proper clinical characterization and help in future therapeutic strategies.

Removal of Antibiotic Resistance Genes, Class 1 Integrase Gene and Escherichia coli Indicator Gene in a Microalgae-Based Wastewater Treatment System

Microalgae-based wastewater treatment systems (AWWTS) have recently shown promise in the mitigation of antibiotic resistance genes (ARGs) from municipal wastewater (MWW). However, due to the large number of ARGs that exist in MWW, the use of indirect conventional water quality parameters to monitor ARGs reduction in wastewater would make the process less burdensome and economically affordable. In order to establish a robust relationship between the ARGs and water quality parameters, the current study employed different microalgae strains in monoculture (CM2, KL10) and multi-species combinations (CK and WW) for the MWW treatment under outdoor environmental conditions. The studied genes were quantified in the MWW influents and effluents using real-time PCR. All the cultures substantially improved the physicochemical qualities of the MWW. Out of the 14 genes analyzed in this study, tetO, tetW, tetX and ermB were decreased beyond detection within the first 4 days of treatment in all the cultures. Other genes, including blaCTX, sul1, cmlA, aadA, int1 and uidA were also decreased beyond a 2 log reduction value (LRV). The mobile genetic element, int1, correlated positively with most of the ARGs, especially sul1 (r ≤ 0.99, p < 0.01) and aadA (r ≤ 0.97, p < 0.01). Similarly, the Escherichia coli indicator gene, uidA, correlated positively with the studied genes, especially with aadA, blaCTX, blaTEM and cmlA (r ≤ 0.99 for each, p < 0.01). Some of the studied genes also correlated positively with total dissolved solids (TDS) (r ≤ 0.98, p < 0.01), and/or negatively with total suspended solids (TSS) (r ≤ −0.98, p < 0.01) and pH (r ≤ −0.98, p < 0.01). Among the tested cultures, both monocultures, i.e., KL10 and CM2 were found to be more consistent in gene suppression than their multi-species counterparts. The findings revealed water quality parameters such as TDS, TSS and E. coli as reliable proxies for ARGs mitigation in AWWTS and further highlight the superiority of monocultures over multi-species cultures in terms of gene suppression from the MWW stream.

Post-transcriptional regulation of 2-acetyl-1-pyrroline (2-AP) biosynthesis pathway, silicon, and heavy metal transporters in response to Zn in fragrant rice

Fragrant rice (Oryza sativa L.) has a high economic and nutritional value, and the application of micronutrients regulates 2-acetyl-1-pyrroline (2-AP) production, which is responsible for aroma in fragrant rice. Alternative splicing (AS) is an important post-transcriptional regulatory mechanism to generate transcript variability and proteome diversity in plants. However, no systematic investigation of AS events in response to micronutrients (Zn) has been performed in fragrant rice. Furthermore, the post-transcriptional regulation of genes involved in 2-AP biosynthesis is also not known. In this study, a comprehensive analysis of AS events under two gradients of Zn treatment in two different fragrant rice cultivars (Meixiangzhan-2 and Xiangyaxiangzhan) was performed based on RNA-seq analysis. A total of 386 and 598 significant AS events were found in Meixiangzhan-2 treated with low and high doses of Zn, respectively. In Xiangyaxiangzhan, a total of 449 and 598 significant AS events were found in low and high doses of Zn, respectively. Go analysis indicated that these genes were highly enriched in physiological processes, metabolism, and cellular processes in both cultivars. However, genotype and dose-dependent AS events were also detected in both cultivars. By comparing differential AS (DAS) events with differentially expressed genes (DEGs), we found a weak overlap among DAS and DEGs in both fragrant rice cultivars indicating that only a few genes are post-transcriptionally regulated in response to Zn treatment. We further report that Zn differentially regulates the expression of 2-AP biosynthesis-related genes in both cultivars and Zn treatment altered the editing frequency of single nucleotide polymorphism (SNPs) in the genes involved in 2-AP biosynthesis. Finally, we showed that epigenetic modifications associated with active gene transcription are generally enriched over 2-AP biosynthesis-related genes. Similar to the 2-AP pathway, we found that heavy metal transporters (genes related to silicon, iron, Zn and other metal transport) are also regulated at transcriptional and post-transcriptional levels in response to Zn in fragrant rice. Taken together, our results provide evidence of the post-transcriptional gene regulation in fragrant rice in response to Zn treatment and highlight that the 2-AP biosynthesis pathway and heavy metal transporters may also be regulated through epigenetic modifications. These findings will serve as a cornerstone for further investigation to understand the molecular mechanisms of 2-AP biosynthesis and regulation of heavy metal transporters in fragrant rice.

Transcriptional cascades in the regulation of 2-AP biosynthesis under Zn supply in fragrant rice

Transcription factors (TFs) regulate gene expression to control certain genetic programs, such as growth and development, phytohormone regulation, and environmental stresses. 2-acetyl-1-pyrroline (2-AP) is the key element involved in aroma biosynthesis pathway, and the application of micronutrients can increase the 2-AP levels. However, little is known about the micronutrient-induced TFs involved in 2-AP biosynthesis. Here, we identify a number of TF families in two fragrant rice varieties, "Meixiangzhan-2" (M) and "Xiangyaxiangzhan" (X), in response to Zinc (Zn) application through transcriptomic analysis. A total of ~678 TFs were identified and grouped into 26 TF families, each of which was found to be involved in numerous signaling pathways. The WRKY TF family was found to be the most abundant, followed by bHLH and MYB. Furthermore, members of the WRKY, bHLH, MYB, ERF, HSF, MADS-box, NFY, and AP2 TF families were significantly upregulated and may be involved in the transcriptional regulation of aroma biosynthesis. In brief, this study enhances our understanding of the molecular mechanism of 2-AP biosynthesis and highlights the key TFs potentially involved in the production of aroma in fragrant rice.

Homozygous missense variant in POPDC3 causes recessive limb girdle muscular dystrophy type 26

BACKGROUND

Limb-girdle muscular dystrophy (LGMD) is a heterogeneous group of diseases, which affects different muscles, predominantly skeletal muscles and cardiac muscles of the body. LGMD is classified into two main sub-types A and B, which are further sub-classified into eight dominant and thirty recessive sub-types. Three genes, mainly POPDC1, POPDC2 and POPDC3, encodes popeye domain-containing protein (POPDC), and the variants of POPDC1 and POPDC3 genes have been associated with LGMD.

METHODS

In this study, we performed whole-exome sequencing (WES) analysis on a single-family to investigate the hallmark features of LGMD. The results of WES were further confirmed by Sanger sequencing and 3D protein modeling was also performed.

RESULTS

WES data analysis and sanger sequencing revealed a homozygous missense variant (c.460A>G; p.Lys154Glu) at a highly conserved amino acid position in the POPDC3. Mutations in the POPDC3 gene have been previously associated with recessive limb-girdle muscular dystrophy type 26. 3D protein modeling further suggested that the identified variant might affect the POPDC3 structure and proper function.

DISCUSSION/CONCLUSIONS

This study confirms the role of POPDC3 in LGMD, and will facilitate in genetic counseling of the family to mitigate the risks of the carrier or affected in future pregnancies.

Selective isolation of mouse glial nuclei optimized for reliable downstream omics analyses

BACKGROUND

Isolation of cell types of interest from the brain for molecular applications presents several challenges, including cellular damage during tissue dissociation or enrichment procedures, and low cell number in the tissue in some cases. Techniques have been developed to enrich distinct cell populations using immunopanning or fluorescence activated cell/nuclei sorting. However, these techniques often involve fixation, immunolabeling and DNA staining steps, which could potentially influence downstream omics applications.

NEW METHOD

Taking advantage of readily available genetically modified mice with fluorescent-tagged nuclei, we describe a technique for the purification of cell-type specific brain nuclei, optimized to decrease sample preparation time and to limit potential artefacts for downstream omics applications. We demonstrate the applicability of this approach for the purification of glial cell nuclei and show that the resulting cell-type specific nuclei obtained can be used effectively for omics applications, including ATAC-seq and RNA-seq.

RESULTS

We demonstrate excellent enrichment of fluorescently-tagged glial nuclei, yielding high quality RNA and chromatin. We identify several critical steps during nuclei isolation that help limit nuclei rupture and clumping, including quick homogenization, dilution before filtration and loosening of the pellet before resuspension, thus improving yield. Sorting of fluorescent nuclei can be achieved without fixation, antibody labelling, or DAPI staining, reducing potential artifactual results in RNA-seq and ATAC-seq analyses. We show that reproducible glial cell type-specific profiles can be obtained in transcriptomic and chromatin accessibility assays using this rapid protocol.

COMPARISON WITH EXISTING METHODS

Our method allows for rapid enrichment of glial nuclei populations from the mouse brain with minimal processing steps, while still providing high quality RNA and chromatin required for reliable omics analyses.

CONCLUSIONS

We provide a reproducible method to obtain nucleic material from glial cells in the mouse brain with a quick and limited sample preparation.

Atrx Deletion in Neurons Leads to Sexually Dimorphic Dysregulation of miR-137 and Spatial Learning and Memory Deficits

ATRX gene mutations have been identified in syndromic and non-syndromic intellectual disabilities in humans. ATRX is known to maintain genomic stability in neuroprogenitor cells, but its function in differentiated neurons and memory processes remains largely unresolved. Here, we show that the deletion of neuronal Atrx in mice leads to distinct hippocampal structural defects, fewer presynaptic vesicles, and an enlarged postsynaptic area at CA1 apical dendrite-axon junctions. We identify male-specific impairments in long-term contextual memory and in synaptic gene expression, linked to altered miR-137 levels. We show that ATRX directly binds to the miR-137 locus and that the enrichment of the suppressive histone mark H3K27me3 is significantly reduced upon the loss of ATRX. We conclude that the ablation of ATRX in excitatory forebrain neurons leads to sexually dimorphic effects on miR-137 expression and on spatial memory, identifying a potential therapeutic target for neurological defects caused by ATRX dysfunction.

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Loss of ATRX in neurons has sexually dimorphic effects on long-term spatial memory

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Targeted deletion of neuronal ATRX in mice causes ultrastructural synaptic defects

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ATRX null neurons show sex-specific changes in miR-137 and target synaptic transcripts

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ATRX directly binds and suppresses miR-137 in males via enrichment of H3K27me3

Eco-Environmental Aspects of COVID-19 Pandemic and Potential Control Strategies

A new coronavirus-strain from a zoonotic reservoir (probably bat)-termed as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-has recently claimed more than two million deaths worldwide. Consequently, a burst of scientific reports on epidemiology, symptoms, and diagnosis came out. However, a comprehensive understanding of eco-environmental aspects that may contribute to coronavirus disease 2019 (COVID-19) spread is still missing, and we therefore aim to focus here on these aspects. In addition to human-human direct SARS-CoV-2 transmission, eco-environmental sources, such as air aerosols, different public use objects, hospital wastes, livestock/pet animals, municipal wastes, ventilation facilities, soil and groundwater potentially contribute to SARS-CoV-2 transmission. Further, high temperature and humidity were found to limit the spread of COVID-19. Although the COVID-19 pandemic led to decrease air and noise pollution during the period of lockdown, increased use of masks and gloves is threatening the environment by water and soil pollutions. COVID-19 badly impacted all the socio-economic groups in different capacities, where women, slum dwellers, and the people lacking social protections are the most vulnerable. Finally, sustainable strategies, waste management, biodiversity reclaim, eco-friendly lifestyle, improved health infrastructure and public awareness, were proposed to minimize the COVID-19 impact on our society and environment. These strategies will seemingly be equally effective against any future outbreak.

Lead, Cadmium and Zinc Phytotoxicity Alter DNA Methylation Levels to Confer Heavy Metal Tolerance in Wheat

Being a staple food, wheat (Triticum aestivum) nutritionally fulfills all requirements of human health and also serves as a significant link in the food chain for the ingestion of pollutants by humans and animals. Therefore, the presence of the heavy metals such as lead (Pb) and cadmium (Cd) in soil is not only responsible for the reduction of wheat crop yield but also the potential threat for human and animal health. However, the link between DNA methylation and heavy metal stress tolerance in wheat has not been investigated yet. In this study, eight high yielding wheat varieties were screened based on their phenotype in response to Pb stress. Out of these, Pirsabak 2004 and Fakhar-e-sarhad were identified as Pb resistant and sensitive varieties, respectively. In addition, Pirsabak 2004 and Fakhar-e-sarhad varieties were also found resistant and sensitive to Cd and Zinc (Zn) stress, respectively. Antioxidant activity was decreased in Fakhar-e-sarhad compared with control in response to Pb/Cd/Zn stresses, but Fakhar-e-sarhad and Pirsabak 2004 accumulated similar levels of Pb, Cd and Zn in their roots. The expression of Heavy Metal ATPase 2 (TaHMA2) and ATP-Binding Cassette (TaABCC2/3/4) metal detoxification transporters are significantly upregulated in Pirsabak 2004 compared with Fakhar-e-sarhad and non-treated controls in response to Pb, Cd and Zn metal stresses. Consistent with upregulation of metal detoxification transporters, CG DNA hypomethylation was also found at the promoter region of these transporters in Pirsabak 2004 compared with Fakhar-e-sarhad and non-treated control, which indicates that DNA methylation regulates the expression of metal detoxification transporters to confer resistance against metal toxicity in wheat. This study recommends the farmers to cultivate Pirsabak 2004 variety in metal contaminated soils and also highlights that DNA methylation is associated with metal stress tolerance in wheat.

Genetic, structural and pharmacological characterization of polymannuronate synthesized by algG mutant indigenous soil bacterium Pseudomonas aeruginosa CMG1421

AIMS

It was aimed to study the genetic, structural and pharmacological characteristics of polymannuronate synthesized by Pseudomonas aeruginosa CMG1421.

METHODS AND RESULTS

Synthesis was analysed by transmission electron microscopy, FT/IR, ¹ H-NMR and gel permeation chromatography followed by in vitro bioassays. Colony PCR followed by sequence analysis was employed for screening of structural genes. FT/IR analysis indicated the presence of hydroxyl, carboxyl and O-acetyl groups linked to mannuronate. ¹ H-NMR analysis indicated M-M bond characteristics for mannuronic acid residues. The average relative molecular weight was found in range of 20 000-250 000 Da. The amplified DNA fragments were identified as 16S rRNA, algD, alg8, alg44, algG, algE and algX genes showing 99-100% homology with those of P. aeruginosa. However, in algG there were transition mutations of adenine and cytosine at nucleotide position 766 and 769, and 878 and 881 respectively. Polymannuronate and its oligomannuronates respectively showed moderate and significant antioxidant, anti-inflammatory, anti-obesity and antidiabetic activities.

CONCLUSIONS

Alginate synthesized by ∆algG mutant P. aeruginosa CMG1421 was bioactive and solely consists of acetylated d-mannuronates.

SIGNIFICANCE AND IMPACT OF THE STUDY

We investigated biocompatible, nonimmunogenic and nontoxic pharmacological agents for treatment and attenuation of degenerative, inflammatory, autoimmune disease, and metabolic disorders such as obesity and diabetes.

DNA Topoisomerase 1 Prevents R-loop Accumulation to Modulate Auxin-Regulated Root Development in Rice

R-loop structures (RNA:DNA hybrids) have important functions in many biological processes, including transcriptional regulation and genome instability among diverse organisms. DNA topoisomerase 1 (TOP1), an essential manipulator of DNA topology during RNA transcription and DNA replication processes, can prevent R-loop accumulation by removing the positive and negative DNA supercoiling that is made by RNA polymerases during transcription. TOP1 is required for plant development, but little is known about its function in preventing co-transcriptional R-loop accumulation in various biological processes in plants. Here we show that knockdown of OsTOP1 strongly affects rice development, causing defects in root architecture and gravitropism, which are the consequences of misregulation of auxin signaling and transporter genes. We found that R-loops are naturally formed at rice auxin-related gene loci, and overaccumulate when OsTOP1 is knocked down or OsTOP1 protein activity is inhibited. OsTOP1 therefore sets the accurate expression levels of auxin-related genes by preventing the overaccumulation of inherent R-loops. Our data reveal R-loops as important factors in polar auxin transport and plant root development, and highlight that OsTOP1 functions as a key to link transcriptional R-loops with plant hormone signaling, provide new insights into transcriptional regulation of hormone signaling in plants.

Combination of needle aspiration and core needle biopsy: A new technique of stereotactic biopsy

Aim:

The study aims at describing the results of using a new technique to acquire the tissue sample in stereotactic biopsy of brain lesions.

Materials and Methods:

The study was performed in 19 patients over a period of 5 years in which we used the new technique, i.e., Abrar and Afzal technique (AT) of obtaining tissue biopsy. It is a combination of core tissue biopsy and needle aspiration techniques. The technique was devised to acquire greater amount of tissue for pathologic study.

Results:

While we could give pathologic diagnosis in 18 patients out of 19 (94.7%), in one patient, the tissue sample revealed only inflammatory cells and definitive diagnosis could not be reached. There was no significant morbidity or any mortality in the series.

Conclusion:

Abrar and Afzal technique is a reasonably accurate technique of acquiring larger tissue sample in stereotactic brain biopsy without any additional risks. It can be done with little modification of the conventional equipment available with the stereotactic system.

The trxG family histone methyltransferase SET DOMAIN GROUP 26 promotes flowering via a distinctive genetic pathway

Histone methylation is a major component in numerous processes such as determination of flowering time, which is fine-tuned by multiple genetic pathways that integrate both endogenous and environmental signals. Previous studies identified SET DOMAIN GROUP 26 (SDG26) as a histone methyltransferase involved in the activation of flowering, as loss of function of SDG26 caused a late-flowering phenotype in Arabidopsis thaliana. However, the SDG26 function and the underlying molecular mechanism remain largely unknown. In this study, we undertook a genetic analysis by combining the sdg26 mutant with mutants of other histone methylation enzymes, including the methyltransferase mutants Arabidopsis trithorax1 (atx1), sdg25 and curly leaf (clf), as well as the demethylase double mutant lsd1-like1 lsd1-like2 (ldl1 ldl2). We found that the early-flowering mutants sdg25, atx1 and clf interact antagonistically with the late-flowering mutant sdg26, whereas the late-flowering mutant ldl1 ldl2 interacts synergistically with sdg26. Based on microarray analysis, we observed weak overlaps in the genes that were differentially expressed between sdg26 and the other mutants. Our analyses of the chromatin of flowering genes revealed that the SDG26 protein binds at the key flowering integrator SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1/AGAMOUS-LIKE 20 (SOC1/AGL20), and is required for histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 lysine 36 trimethylation (H3K36me3) at this locus. Together, our results indicate that SDG26 promotes flowering time through a distinctive genetic pathway, and that loss of function of SDG26 causes a decrease in H3K4me3 and H3K36me3 at its target gene SOC1, leading to repression of this gene and the late-flowering phenotype.

Combinatorial functions of diverse histone methylations in Arabidopsis thaliana flowering time regulation

Previous studies in Arabidopsis thaliana have identified several histone methylation enzymes, including Arabidopsis trithorax1 (ATX1)/set domain group 27 (SDG27), ATX2/SDG30, LSD1-LIKE1 (LDL1), LDL2, SDG8, SDG25, and curly leaf (CLF)/SDG1, as regulators of the key flowering repressor flowering locus C (FLC) and the florigen flowering locus T (FT). However, the combinatorial functions of these enzymes remain largely uninvestigated. Here, we investigated functional interplays of different histone methylation enzymes by studying higher order combinations of their corresponding gene mutants. We showed that H3K4me2/me3 and H3K36me3 depositions occur largely independently and that SDG8-mediated H3K36me3 overrides ATX1/ATX2-mediated H3K4me2/me3 or LDL1/LDL2-mediated H3K4 demethylation in regulating FLC expression and flowering time. By contrast, a reciprocal inhibition was observed between deposition of the active mark H3K4me2/me3 and/or H3K36me3 and deposition of the repressive mark H3K27me3 at both FLC and FT chromatin; and the double mutants sdg8 clf and sdg25 clf displayed enhanced early-flowering phenotypes of the respective single mutants. Collectively, our results provide important insights into the interactions of different types of histone methylation and enzymes in the regulation of FLC and FT expression in flowering time control.

Histone modifications in transcriptional activation during plant development

In eukaryotic cell nuclei, chromatin states dictated by different combinations of post-translational modifications of histones, such as acetylation, methylation and monoubiquitination of lysine residues, are part of the multitude of epigenomes involved in the fine-tuning of all genetic functions and in particular transcription. During the past decade, an increasing number of 'writers', 'readers' and 'erasers' of histone modifications have been identified. Characterization of these factors in Arabidopsis has unraveled their pivotal roles in the regulation of essential processes, such as floral transition, cell differentiation, gametogenesis, and plant response/adaptation to environmental stresses. In this review we focus on histone modification marks associated with transcriptional activation to highlight current knowledge on Arabidopsis 'writers', 'readers' and 'erasers' of histone modifications and to discuss recent findings on molecular mechanisms of integration of histone modifications with the RNA polymerase II transcriptional machinery during transcription of the flowering repressor gene FLC.

Production, characterization, in vitro and ex vivo studies of babchi oil-encapsulated nanostructured solid lipid carriers produced by a hot aqueous titration method

An aqueous dispersion of solid fat nanoparticles of babchi oil (BOSLN) was prepared by means of the hot water titration method. Surface morphology was determined by HR-TEM which revealed a fairly spherical shape of the formulations. Further they were evaluated for in vitro drug release characteristics and ex vivo skin permeation profile, zeta potential and particle diameter, rheological measures and droplet size distribution. Highest values for steady state flux (Jss), permeability coefficient (Kp) and enhancement ratio (Er) were observed for formulation, BOSLN3 comprised of oil [10% v/v; BO (3.33%), CAT (6.67%)], Tween 80 (9.25% v/v), transcutol-P (28.75% v/v) and distilled water (53% v/v). These results suggest that the studied SLN might be promising vehicles for babchi oil in the management of psoriasis.

Effect of Labrasol on self-nanoemulsification efficiency of ramipril nanoemulsion

The purpose of the present investigation was to evaluate the capacity of Labrasol as surfactant for self-nanoemulsification efficiency of ramipril nanoemulsion formulation. Based on the solubility profile of ramipril, Sefsol-218, Labrasol and Carbitol were selected as oil phase, surfactant and cosurfactant, respectively. Based on the stability profile of ramipril, standard buffer solution of pH 5.0 was selected as an aqueous phase for the development of ramipril nanoemulsion formulation. Nanoemulsion formulations of ramipril were developed using an aqueous phase titration method. Pseudoternary phase diagrams were constructed to identify the nanoemulsion region. Selected formulations were subjected to different thermodynamic stability tests using centrifugation, heating cooling cycles and freeze thaw cycles. The formulations which were stable at thermodynamic stability tests were taken for self-nanoemulsification efficiency test. No creaming, cracking, coalescence or phase inversion was observed on most of the formulations upon thermodynamic stability tests. All the formulations passed self-nanoemulsification tests in grade C, D and E but not in grade A and B. Because none of the formulation passed self-nanoemulsification efficiency test in grade A and B, it was concluded that Labrasol is not suitable as surfactant for oral or self nanoemulsifying drug delivery system of ramipril.

Enhanced anti-inflammatory effects of celecoxib from a transdermally applied nanoemulsion

The aim of the present study was to evaluate the enhanced anti-inflammatory effects of celecoxib (CXB) from a transdermally applied nanoemulsion. The anti-inflammatory effects of an optimized nanoemulsion formulation were compared with those of conventional CXB gel and nanoemulsion gel on carrageenan-induced paw edema in rats. These tests were compared using the Dunnett test of one-way analysis of variance (ANOVA). The % inhibition value after 24 h application was significant for optimized formulation C2 (85.4%) compared with CXB gel and nanoemulsion gel (p < 0.05). These results suggest that nanoemulsions can be successfully used to enhance the anti-inflammatory effects of CXB.

Skin permeation mechanism of aceclofenac using novel nanoemulsion formulation

The aim of the present study was to investigate the skin permeation mechanism of aceclofenac using a novel nanoemulsion formulation. An optimized oil-in-water nanoemulsion of aceclofenac was prepared by the spontaneous emulsification method. The optimized nanoemulsion contained 2% w/w aceclofenac, 10% w/w Labrafil, 5% w/w Triacetin, 35.33% w/w Tween 80, 17.66% w/w Transcutol P and 32% w/w distilled water. The skin permeation mechanism was evaluated by FTIR spectroscopy, DSC thermography, activation energy measurement and histopathological examination. FTIR spectra of skin treated with the nanoemulsion formulation indicated breaking of the hydrogen bond network at the head of ceramides. DSC thermograms indicated that intracellular transport could be a possible mechanism of permeation enhancement and that permeation occurred due to the extraction of SC lipids by the nanoemulsion. The significant decrease in activation energy for aceclofenac permeation across rat skin indicated that the SC lipid bilayers were significantly disrupted (p < 0.05). Photomicrography of skin showed disruption and extraction of lipid bilayers as distinct voids and empty spaces visible in the epidermal region. Overall these findings indicated that nanoemulsions can be successfully used to enhance skin permeation of drugs.

Differential effects of doxorubicin on atrial natriuretic peptide expression in vivo and in vitro

Doxorubicin (Dox) is a potent anti-cancer agent with cardiotoxic side-effects but the mechanism of its cardiotoxicity and its effect on expression of the vasoactive atrial natriuretic peptide (ANP), an important marker for cardiac hypertrophy, are little understood. The present study examined Dox-induced changes in vivo in hearts of 6 mongrel dogs and 5 Sprague-Dawley rats and in vitro in cardiac cultures of neonatal rats. Quantitative RT-PCR analysis using gamma 32-p labeled primers for beta-actin, phospholamban (PLB) and ANP showed a selective 5-fold increase of ANP mRNA in Dox-treated dog hearts in comparison to controls. Similarly, northern analysis of GAPD, beta-actin, cardiac alpha-actin and ANP gave a selective 4.5-fold increase in ANP transcripts in Dox-treated rat hearts. On the other hand, there was a selective decrease (approximately 39%) of ANP transcripts in Dox-treated cardiac cultures relative to controls. Immunohistochemistry localized the ANP changes both in tissue sections and in cultures to the cardiomyocytes. The data clearly showed that Dox selectively increases ANP expression in dog and rat hearts in absence of cardiocyte hypertrophy but selectively decreases it in cardiac cultures. This differential effect of Dox on cardiocytes in vivo and in vitro should be a useful parameter for studies of transcriptional control of ANP expression.

Ventricular myosin light chain-2 gene expression in developing heart of chicken embryos

Recent gene knock-out studies in mice have suggested that ventricular myosin light chain-2 (vMLC2) has a role in the regulation of cardiogenic development and that perturbation in expression of vMLC2 is linked to the onset of dilated cardiomyopathy. In an attempt to develop an avian model for such studies, we examined the expression pattern of vMLC2 in chicken embryos at various stages and analyzed the effect of antisense oligonucleotide-mediated interference of vMLC2 function in cultures of whole embryos. Our results showed vMLC2 to be a specific marker for ventricular chamber throughout chicken embryonic development and antisense vMLC2 treatment of primitive streak stage (stage 4) embryos to produce pronounced dilation of heart tube with severe deficiency in formation of striated myofibrils. Further studies with antisense mRNA techniques of whole embryo cultures should, therefore, be useful to evaluate the role of vMLC2 and other putative regulatory factors in cardiac myofibrillogenesis.

Modulation of MLC-2v gene expression by AP-1: complex regulatory role of Jun in cardiac myocytes

Hypertrophic stimulation of cardiac myocytes results in rapid induction of a number of transcription factors, including members of the AP-1 family, which is followed by a programmed alteration in the pattern of gene expression. In the ventricular cardiocytes there is re-expression of the fetal atrial natriuretic factor (ANF) gene and upregulation of its myosin light chain-2 (MLC-2v). The mechanism(s) by which the induction ofAP-1 is coupled to the promoters of these target genes is largely unknown. In this report, we demonstrate that in transient co-transfection assay, c-Jun inhibited while Jun B stimulated the MLC-2v promoter activity. Mutant c-Jun recombinants, in which the activation domains were deleted, still remained inhibitory, but a specific mutation in the leucine zipper, which changes the alignment of Jun with its dimerization partner, caused a reversal of its effect on the target MLC-2v promoter. Based on these findings, we propose that in chicken cardiac myocytes, the regulation of MLC-2v promoter by Jun may occur via its interaction with other proteins, possibly of the leucine zipper family.

Identification of a novel cardiac lineage-associated protein(cCLP-1): A candidate regulator of cardiogenesis

We describe the isolation and characterization of a cDNA clone, called cCLP-1, that is a candidate for the previously described early cardiac-specific transcription factor BBF-1. BBF-1 binds the MEF2 (or element B) binding site within the cardiac myosin light chain 2 (MLC2) gene promoter. We used the element B sequence as a probe to screen an expression library constructed from mRNA obtained from the presumptive heart-forming regions of stage 6 chicken embryos. This yielded the cCLP-1 cDNA clone. Gel-shift analysis of stage 6 embryonic chicken protein extracts suggests that a protein that is recognized by the anti-cCLP-1 antibody binds to the same element B binding site to which BBF-1 binds. cCLP-1 mRNA was detected early in chicken development, prior to cardiac fate assignment at stage 4. The expression pattern of cCLP-1, based on whole mount in situ hybridization, coincides remarkably well with the established morphogenetic field of early heart formation. The nuclear localization of cCLP-1 is phosphorylation-dependent, suggesting that cCLP-1 may be a member of that class of transcription factors whose activity is regulated by cytoplasm to nucleus transport. Taken together, these data suggest that cCLP-1 may encode a novel transcription factor whose expression pattern is in agreement with that of the cardiogenic precursor cells of the early chicken embryo.

The effect of protease inhibitors, leupeptin and E64d, on differentiation of C2C12 myoblasts in tissue culture

Intracellular calcium levels play an important role in myofibril disintegration and regeneration of muscle fibers. Earlier studies have shown that the calcium activated protease, calpain, is involved in the removal of Z-discs from myofibrils of striated muscle and the tripeptide-aldehyde, leupeptin, which is an inhibitor of calpain, inhibits this activity. In the present communication, we demonstrate that leupeptin and another calpain inhibitor, E64d, inhibit the fusion of mouse skeletal muscle C2C12 myoblasts to form multinucleated myotubes in tissue culture.

The effect of protease inhibitors, leupeptin and E64d, on differentiation of C2C12 myoblasts in tissue culture

Intracellular calcium levels play an important role in myofibril disintegration and regeneration of muscle fibers. Earlier studies have shown that the calcium activated protease, calpain, is involved in the removal of Z-discs from myofibrils of striated muscle and the tripeptide-aldehyde, leupeptin, which is an inhibitor of calpain, inhibits this activity. In the present communication, we demonstrate that leupeptin and another calpain inhibitor, E64d, inhibit the fusion of mouse skeletal muscle C2C12 myoblasts to form multinucleated myotubes in tissue culture.

In vitro antibacterial studies of some newly synthesized phenacyl-thiosemicarbazones

Four different phenacyl-thiosemicarbazone compounds were studied for their antibacterial activity against seventeen different species/strains. Of the four compounds under study, O-methoxy- phenacyl-thiosemicarbazone was found to be highly active against almost all the cultures under study. The other compounds were also found to possess antibacterial spectrum, but in very high concentrations for some of the cultures.

Isoforms of C-protein in adult chicken skeletal muscle: detection with monoclonal antibodies

Monoclonal antibodies (McAbs) specific for the C-proteins of chicken pectoralis major and anterior latissimus dorsi (ALD) muscles have been produced and characterized. Antibody specificity was demonstrated by solid phase radioimmunoassay (RIA), immunoblots, and immunofluorescence cytochemistry. Both McAbs MF-1 (or MF-21) and ALD-66 bound to myofibrillar proteins of approximately 150,000 daltons; the former antibody reacted with pectoralis but not ALD myofibrils, whereas the latter recognized ALD but not pectoralis myofibrils. Chromatographic elution of the antigens from DEAE-Sephadex, and their distribution in the A-band, support the conclusion that both of these antibodies recognize variant isoforms of C-protein. Since both McAbs react with a protein of similar molecular weight in the A-band of all myofibrils of the posterior latissimus dorsi (PLD) muscle, we suggest that either another isoform of C-protein exists in the PLD muscle or both pectoralis and ALD-like isoforms coexist in the A-bands of PLD muscle.