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Bioinformation 2022CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas9 (CRISPR-associated system) is used to edit specific genomic sequences with precision and...
CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas9 (CRISPR-associated system) is used to edit specific genomic sequences with precision and efficacy. There are many online platforms/software for the design of gRNAs and related primers. However, there are concerns in design regarding off-site deletions besides knocking out sequences in the target genes. Nonetheless, a well known robust platform for CRISPR/gRNA primers design is CRISPRdirect. We demonstrate the use of this tool in the design of CRISPR/gRNA primers for soluble starch synthases (SSS) II-1, 2, and 3 genes in the Oryza sativa genome followed by the PCR-mediated amplification of SSS genes with corresponding confirmation towards genome editing having improved phenotype features.
PubMed: 36945226
DOI: 10.6026/97320630018471 -
JAAD Case Reports Jul 2022
PubMed: 35898669
DOI: 10.1016/j.jdcr.2022.02.044 -
Bioinformatics Advances 2022Recently, several computational modeling approaches, such as agent-based models, have been applied to study the interaction dynamics between immune and tumor cells in...
MOTIVATION
Recently, several computational modeling approaches, such as agent-based models, have been applied to study the interaction dynamics between immune and tumor cells in human cancer. However, each tumor is characterized by a specific and unique tumor microenvironment, emphasizing the need for specialized and personalized studies of each cancer scenario.
RESULTS
We present MAST, a hybrid Multi-Agent Spatio-Temporal model which can be informed using a data-driven approach to simulate unique tumor subtypes and tumor-immune dynamics starting from high-throughput sequencing data. It captures essential components of the tumor microenvironment by coupling a discrete agent-based model with a continuous partial differential equations-based model.The application to real data of human colorectal cancer tissue investigating the spatio-temporal evolution and emergent properties of four simulated human colorectal cancer subtypes, along with their agreement with current biological knowledge of tumors and clinical outcome endpoints in a patient cohort, endorse the validity of our approach.
AVAILABILITY AND IMPLEMENTATION
MAST, implemented in Python language, is freely available with an open-source license through GitLab (https://gitlab.com/sysbiobig/mast), and a Docker image is provided to ease its deployment. The submitted software version and test data are available in Zenodo at https://dx.doi.org/10.5281/zenodo.7267745.
SUPPLEMENTARY INFORMATION
Supplementary data are available at online.
PubMed: 36699399
DOI: 10.1093/bioadv/vbac092 -
ACS Omega Jul 2022Mulberry () is commonly cultivated in Asian countries as a traditional medicine and food supplement. Four Kashmiri varieties (, , , and ) were evaluated for their...
Mulberry () is commonly cultivated in Asian countries as a traditional medicine and food supplement. Four Kashmiri varieties (, , , and ) were evaluated for their proximate composition, mineral content, total phenolic and flavonoid content, antioxidant potential, and antihyperglycemic activity. Furthermore, TLC-MS-bioautography was used for the identification of antioxidant and antidiabetic compounds in the best active extract. Lastly, UPLC-MS was employed for metabolomic profiling of the best variety of . Among all the varieties, the variety was found to have the highest phenolic (71.10 ± 0.44 mg GAE/g DW) and flavonoid (53.22 ± 0.69 mg rutin/g DW) content. The highest antioxidant potential (DPPH) with an IC value of 107.88 ± 3.8 μg/mL was recorded for the variety. Similarly, α-amylase and α-glucosidase inhibition for antidiabetic potential with IC 74.76 ± 6.76 and 109.19 ± 5.78 μg/mL, respectively, was recorded in variety. TLC-MS-bioautography for identification of bioactive compounds revealed the presence of chlorogenic acid for antioxidant potential and 1-deoxynojirimycin (DNJ) and syringic acid for antidiabetic potential. Further, bioactive compounds responsible for diverse functions of were confirmed by UPLC-MS in both negative and positive modes. However, major compounds in the variety were identified as chlorogenic acid, moracin N, gallic acid, ferulic acid, morin, 1-deoxynojirimycin, and syringic acid. Hence, based on our findings, it can be concluded that leaves can be consumed as a promising dietary supplement and can be formulated as phytopharmaceutical for the management of various metabolic disorders.
PubMed: 35874221
DOI: 10.1021/acsomega.2c01623 -
Annals of Dermatology Apr 2022Oral-facial-digital syndrome type 1 (OFD1), first described by Papillon-Léage in 1954, is transmitted as an X-linked dominant condition and is characterized by a...
Oral-facial-digital syndrome type 1 (OFD1), first described by Papillon-Léage in 1954, is transmitted as an X-linked dominant condition and is characterized by a combination of malformations in the face, oral cavity, and digits. Malformations of the brain and polycystic kidney disease are also commonly associated with OFD1. An 11-month-old female presented with multiple tiny whitish papules on her face that had been present since birth. The histopathologic examination was consistent with milium. She also had congenital anomalies, including incomplete cleft palate, bifid tongue, short frenulum, anomalous deformities of both toes, and clino-brachy-syndactyly. Based on the characteristic dysmorphic features of her face, mouth, and hands, a clinical diagnosis of OFD1 was made. Herein, we report a rare case of OFD1 featuring congenital milia, which has not been previously reported in the Korean literature.
PubMed: 35450320
DOI: 10.5021/ad.2022.34.2.132 -
Foods (Basel, Switzerland) Jan 2022and are prokaryotic microalgae commercially marketed as spirulina. The pigments extracted from these algae are widely used for cosmetic and nutraceutical applications....
and are prokaryotic microalgae commercially marketed as spirulina. The pigments extracted from these algae are widely used for cosmetic and nutraceutical applications. This work aimed to evaluate the influence of three light-emitting lamps (white, orange and blue) on the growth and biomass composition of two strains of (M2 and M2M) and one of . The obtained data show strain- and light-dependent responses of the microalgae. In addition, white and orange lights led to a similar overall effect by increasing the levels of chlorophyll and carotenoids. However, exposure to orange light resulted in the highest dry weight (5973.3 mg L in M2M), whereas white light stimulated an increase in the carbohydrate fraction (up to 42.36 g 100 g in ). Conversely, blue light led to a constant increase in the concentration of phycocyanin (14 g 100 g in ) and a higher content of proteins in all strains. These results provide important environmental information for modulating the growth of different spirulina strains, which can be used to address the synthesis of biochemical compounds of strategic importance for the development of new nutraceutical foods.
PubMed: 35159549
DOI: 10.3390/foods11030399 -
Cureus Jan 2024Seizures are the most common neurological disorder in pediatrics, and their initial approach aims at clinical stabilization. A thorough patient evaluation may provide...
Seizures are the most common neurological disorder in pediatrics, and their initial approach aims at clinical stabilization. A thorough patient evaluation may provide important clues for the etiological diagnosis. A 12-month-old female child was observed in the emergency department after experiencing her first apyretic seizure. She had a history of congenital alopecia and, on physical examination, presented subtotal alopecia and milia. Initial investigation revealed hypocalcemia; therefore, intravenous calcium correction was started with a partial response. The analytical study was extended, revealing hypophosphatemia, elevated parathormone, and 1,25(OH) vitamin D with normal 25(OH) vitamin D. The genetic analysis confirmed hereditary vitamin D-resistant rickets (HVDRR). The integration of the findings was crucial to diagnostic reasoning and to guide further investigation. HVDRR is a rare disorder, with more severe clinical presentations associated with alopecia. Early diagnosis and treatment are fundamental to minimize the impact on growth and the development of other comorbidities.
PubMed: 38425628
DOI: 10.7759/cureus.53233 -
Nature Communications Jun 2021While mass-scale vaccination campaigns are ongoing worldwide, genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical to monitor...
While mass-scale vaccination campaigns are ongoing worldwide, genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical to monitor the emergence and global spread of viral variants of concern (VOC). Here, we present a streamlined workflow-COVseq-which can be used to generate highly multiplexed sequencing libraries compatible with Illumina platforms from hundreds of SARS-CoV-2 samples in parallel, in a rapid and cost-effective manner. We benchmark COVseq against a standard library preparation method (NEBNext) on 29 SARS-CoV-2 positive samples, reaching 95.4% of concordance between single-nucleotide variants detected by both methods. Application of COVseq to 245 additional SARS-CoV-2 positive samples demonstrates the ability of the method to reliably detect emergent VOC as well as its compatibility with downstream phylogenetic analyses. A cost analysis shows that COVseq could be used to sequence thousands of samples at less than 15 USD per sample, including library preparation and sequencing costs. We conclude that COVseq is a versatile and scalable method that is immediately applicable for SARS-CoV-2 genomic surveillance and easily adaptable to other pathogens such as influenza viruses.
Topics: Animals; COVID-19; Cells, Cultured; Chlorocebus aethiops; Cost-Benefit Analysis; Epidemiological Monitoring; Genome, Viral; High-Throughput Nucleotide Sequencing; Humans; Phylogeny; SARS-CoV-2; Workflow
PubMed: 34162869
DOI: 10.1038/s41467-021-24078-9 -
Journal of Dental Anesthesia and Pain... Aug 2021Achieving profound anesthesia in mandibular molars with irreversible pulpitis is a tedious task. This review aimed at evaluating the success of buccal/lingual... (Review)
Review
Anesthetic efficacy of primary and supplemental buccal/lingual infiltration in patients with irreversible pulpitis in human mandibular molars: a systematic review and meta-analysis.
Achieving profound anesthesia in mandibular molars with irreversible pulpitis is a tedious task. This review aimed at evaluating the success of buccal/lingual infiltrations administered with a primary inferior alveolar nerve block (IANB) injection or as a supplemental injection after the failure of the primary injection in symptomatic and asymptomatic patients with irreversible pulpitis in human mandibular molars. The review question was "What will be the success of primary and supplemental infiltration injection in the endodontic treatment of patients with irreversible pulpitis in human mandibular molars?" We searched electronic databases, including Pubmed, Scopus, and Ebsco host and we did a comprehensive manual search. The review protocol was framed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) checklist. We included clinical studies that evaluated and compared the anesthetic outcomes of primary IANB with primary and/or supplementary infiltration injections. Standard evaluation of the included studies was performed and suitable data and inferences were assessed. Twenty-six studies were included, of which 13 were selected for the meta-analysis. In the forest plot representation of the studies evaluating infiltrations, the combined risk ratio (RR) was 1.88 (95% CI: 1.49, 2.37), in favor of the secondary infiltrations with a statistical heterogeneity of 77%. The forest plot analysis for studies comparing primary IANB + infiltration versus primary IANB alone showed a low heterogeneity (0%). The included studies had similar RRs and the combined RR was 1.84 (95% CI: 1.44, 2.34). These findings suggest that supplemental infiltrations given along with a primary IANB provide a better success rate. L'Abbe plots were generated to measure the statistical heterogeneity among the studies. Trial sequential analysis suggested that the number of patients included in the analysis was adequate. Based on the qualitative and quantitative analyses, we concluded that the infiltration technique, either as a primary injection or as a supplementary injection, given after the failure of primary IANB, increases the overall anesthetic efficacy.
PubMed: 34395897
DOI: 10.17245/jdapm.2021.21.4.283 -
International Journal of Environmental... Nov 2021Uterine myomas or uterine fibroids are the most common benign uterine masses affecting women. The management of large myoma during pregnancy is challenging, and surgical...
Uterine myomas or uterine fibroids are the most common benign uterine masses affecting women. The management of large myoma during pregnancy is challenging, and surgical treatment is a possible option. We report nine cases of pregnant women affected by uterine masses larger than 10 cm, who underwent surgical treatment during the second trimester of pregnancy. In all cases, the masses were preconceptionally unknown and diagnosed during the first trimester. In eight cases, no maternal and fetal complications arose during or after surgical treatment and delivery occurred at full term of pregnancy. In one case, spontaneous abortion was recorded. In all cases, histologic diagnosis demonstrated the benign nature. Women affected by large uterine masses diagnosed for the first time in pregnancy could be taken into consideration for surgical treatment in a referral center during the second trimester.
Topics: Abortion, Spontaneous; Female; Humans; Leiomyoma; Pregnancy; Uterine Neoplasms; Uterus
PubMed: 34831895
DOI: 10.3390/ijerph182212139