Design of hypoxia responsive CRISPR-Cas9 for target gene regulation.

The CRISPR-Cas9 system is a widely used gene-editing tool, offering unprecedented opportunities for treating various diseases. Controlling Cas9/dCas9 activity at specific location and time to avoid undesirable effects is very important. Here, we report a conditionally active CRISPR-Cas9 system that regulates target gene expression upon sensing cellular environmental change. We conjugated the oxygen-sensing transcription activation domain (TAD) of hypoxia-inducing factor (HIF-1α) with the Cas9/dCas9 protein. The Cas9-TAD conjugate significantly increased endogenous target gene cleavage under hypoxic conditions compared with that under normoxic conditions, whereas the dCas9-TAD conjugate upregulated endogenous gene transcription. Furthermore, the conjugate system effectively downregulated the expression of SNAIL, an essential gene in cancer metastasis, and upregulated the expression of the tumour-related genes HNF4 and NEUROD1 under hypoxic conditions. Since hypoxia is closely associated with cancer, the hypoxia-dependent Cas9/dCas9 system is a novel addition to the molecular tool kit that functions in response to cellular signals and has potential application for gene therapeutics.

Structural, Hirshfeld surface and three-dimensional inter-action-energy studies of 1,3,5-triethyl 2-amino-3,5-di-cyano-4,6-bis-(4-fluoro-phen-yl)cyclo-hex-1-ene-1,3,5-tri-carboxyl-ate.

In the title compound, C29H27F2N3O6, which crystallizes in the monoclinic space group P21/c, the cyclo-hexenone ring is puckered and adopts an envelope conformation. The crystal structure features various inter-molecular inter-actions, such as N-H⋯O, C-H⋯N and C-H⋯O. These inter-actions were investigated using Hirshfeld surface analysis and the three-dimensional inter-action energies were calculated using the B3LYP/6-31 G(d,p) energy density model.

Ligation-free isothermal nucleic acid amplification.

In this study, we uncover a ligation-free DNA extension method in two adjacent fragmented probes, which are hybridized to target RNA, for developing a ligation-free nucleic acid amplification reaction. In this reaction, DNA elongation occurs from a forward probe to a phosphorothioated-hairpin probe in the presence of target RNA regardless of ligation. The second DNA elongation then occurs simultaneously at the nick site of the phosphorothioated probe and the self-priming region. Therefore, the binding site of the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) 12a is repeatedly amplified, inducing a fluorescence signal in the presence of CRISPR-Cas12a. This ligation-free isothermal gene amplification method enables the detection of target RNA with 49.2 fM sensitivity. Moreover, two types of mRNA detection are feasible, thus, demonstrating the potential of this method for cancer companion diagnostics. Notably, the proposed method also demonstrates efficacy when applied for the detection of mRNA extracted from human cells and tumor-bearing mouse tissue and urine samples. Hence, this newly developed ligation-free isothermal nucleic acid amplification system is expected to be widely used in a variety of gene detection platforms.

Dual extrauterine ectopic pregnancy: double management.

A 30-year-old nulliparous woman was referred with suspected left ovarian ectopic pregnancy. She had undergone laparoscopic left salpingectomy for ruptured tubal ectopic pregnancy 3 weeks earlier, following treatment with medications for ovulation induction. Sonological examination revealed a left ovarian ectopic pregnancy corresponding to 8 0/7 weeks with cardiac activity. She underwent ultrasound-guided intrasac therapy with intrasac instillation of 3 mEq of potassium chloride followed by 50 mg of methotrexate. She was followed with weekly measurements of serum beta human Chorionic Gonadotropin (hCG) which returned to baseline after 65 days of the intrasac therapy. This case not only highlights the need for continued follow-up of the serum beta hCG after definitive management of an ectopic pregnancy in cases with multiple ovulations, but also the option of medical management in cases of advanced ovarian ectopic pregnancy. It also accentuates the necessity for adequate counselling to avoid conception in a multiple ovulation cycle.

Purification and characterization of bioactive compounds extracted from Suaeda maritima leaf and its impact on pathogenicity of Pseudomonas aeruginosa in Catla catla fingerlings.

Incidence of various dreadful microbial infections and the development of antibiotic resistance by infection causative microbes are the main reasons for reducing aquaculture productivity. Hence, there is an immense need for the discovery of alternative and efficient treatment for quick recovery of diseased fishes. In the present study, Suaeda maritima leaf extracts (hexane, diethyl ether, ethanol, and water) were screened for in vitro and in vivo antibacterial and antioxidant activities. Out of all the four extracts, ethanolic extract showed highest antibacterial activity against S. aureus (4.9 ± 1.3 mm), B. subtilis (1.6 ± 0.3 mm), K. pneumoniae (4.2 ± 1.8 mm), and P. aeruginosa (4.1 ± 1.2 mm). Similarly, antioxidant activity was also higher for ethanolic extract (500 µg/mL) based on DPPH radical scavenging ability (71.6 ± 1.4%) and reducing potential (149 µg/mL) assays. Further, ethanolic extract was purified consecutively via column chromatography and preparative TLC where an active fraction was selected based on highest antibacterial (10.1 ± 1.4 mm) and antioxidant properties (82.3 ± 2.8%). Active fraction was loaded onto mass spectroscopy and identified the presence of four active constituents such as 1,2,9,10-tetramethoxy-6-methyl-5,6,6a,7-tetrahydro-4H-dibenzo[de,g]quinolin-3-yl) methanol; 3',7-Dimethoxy-3-hydroxyflavone; Saponin and (19R)9acetyl19hydroxy10,14dimethyl20oxopentacyclo[11.8.0.0 < 2,10 > .0 < 4,9 > .0 < 14,19 >]henicos-17-yl-acetate. Besides, in vivo studies were conducted on Catla catla fingerlings infected with P. aeruginosa under laboratory conditions. The fingerlings were segregated into 5 groups, among which group 4 and 5 were treated with crude and purified extracts. Both the extracts were efficient in treating infected fingerlings and recorded 100% survival rate which is even better than group-3 treated with a synthetic antibiotic (77%). Hence, S. maritima leaf extract can be considered as a possible alternative medicine in aquaculture.

Detection of Infectious Viruses Using CRISPR-Cas12-Based Assay.

The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease-19 (COVID-19), has severely influenced public health and economics. For the detection of SARS-CoV-2, clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR associated protein (Cas)-based assays have been emerged because of their simplicity, sensitivity, specificity, and wide applicability. Herein, we have developed a CRISPR-Cas12-based assay for the detection of SARS-CoV-2. In the assay, the target amplicons are produced by isothermal reverse transcription recombinase polymerase amplification (RT-RPA) and recognized by a CRISPR-Cas12a/guide RNA (gRNA) complex that is coupled with the collateral cleavage activity of fluorophore-tagged probes, allowing either a fluorescent measurement or naked-eye detection on a lateral flow paper strip. This assay enables the sensitive detection of SARS-CoV-2 at a low concentration of 10 copies per sample. Moreover, the reliability of the method is verified by using nasal swabs and sputum of COVID-19 patients. We also proved that the current assay can be applied to other viruses, such as Middle East respiratory syndrome coronavirus (MERS-CoV) and severe acute respiratory syndrome coronavirus (SARS-CoV), with no major changes to the basic scheme of testing. It is anticipated that the CRISPR-Cas12-based assay has the potential to serve as a point-of-care testing (POCT) tool for a wide range of infectious viruses.

Synthesis, structural characterization, and DFT studies of anti-cancer drug N-(2-Aminophenyl)-2-(4-bromophenoxy)acetamide.

Drug design is an integrated and developing system that portends an era of a novel and safe tailored drugs. It involves studying the effects of biologically active synthetic, semi-synthetic, and natural compounds based on molecular interactions in terms of molecular structure with activated functional groups or its unique physicochemical properties involved. The title compound, N-(2-aminophenyl)-2-(4-bromophenoxy) acetamide (c), was synthesized in a good yield and characterized by different spectroscopic techniques (1H, 13CNMR, and LC-MS) and finally, the structure was confirmed by X-ray diffraction (XRD) studies. The XRD data confirms that the cryatal structure is orthorhombic with space group of Pca2 1 . The intermolecular interactions (N-H … O and N-H … Cg) inside the molecule stabilizes the crystal structure. The existence of this intermolecular interactions are computed by the Hirshfeld surfaces (HS) and two-dimensional (2D) fingerprints plot analysis. In addition to this, Energy frame work analysis is performed to quantify the interaction energies between the molecular pairs in a crystal by incorporating new version of CrystalExplorer17 using the energy model of HF/3-21G. Also to calculate the HOMO and LUMO energies, DFT calculations were carried out.

Fetal Adrenal Gland Volume a Novel Predictor of Onset of Labor.

INTRODUCTION: There is a definite need to find a highly sensitive and specific, noninvasive, and cost-effective marker for prediction of preterm labor. We hypothesize that a measurement of adrenal gland volume can predict a preterm as well as a term labor. MATERIALS AND METHODS: Two hundred and sixty-eight pregnant women were enrolled in the study at 28-34 weeks' antenatal visit. Final analysis was done in 204. All of them were subjected to 2D ultrasonographic measurement of the corrected fetal adrenal gland volume (cFAGV) and fetal adrenal zone parameters including the width ratio and depth ratio. The cohort was followed up to term, and a reassessment of cFAGV and fetal adrenal zone parameters was repeated between 37 and 39 weeks. Women who presented with features of preterm labor had a scan at the time of presentation to record cFAGV and fetal adrenal zone parameters. RESULTS: Women, who developed features of preterm labor eventually, had a significantly high cFAGV (404.70 mm3/kg body weight) during the first scan compared to those who reached term asymptomatically (241.35 mm3/kg body weight). A cutoff value of 271.16 mm3/kg body weight showed 90% sensitivity and 81.9% specificity. Fetal adrenal gland width ratio had the best efficacy (sensitivity 96.67%, specificity 86.2%) followed by cFAGV (sensitivity 96.67%, specificity 83%) for predicting preterm delivery. CONCLUSION: 2D ultrasound measurement of fetal adrenal gland parameters can be used as a marker for prediction of preterm delivery. cFAGV at term can also be used to predict the possibility of spontaneous onset of labor.

Genome sequencing of herb Tulsi (Ocimum tenuiflorum) unravels key genes behind its strong medicinal properties.

BACKGROUND: Krishna Tulsi, a member of Lamiaceae family, is a herb well known for its spiritual, religious and medicinal importance in India. The common name of this plant is 'Tulsi' (or 'Tulasi' or 'Thulasi') and is considered sacred by Hindus. We present the draft genome of Ocimum tenuiflurum L (subtype Krishna Tulsi) in this report. The paired-end and mate-pair sequence libraries were generated for the whole genome sequenced with the Illumina Hiseq 1000, resulting in an assembled genome of 374 Mb, with a genome coverage of 61 % (612 Mb estimated genome size). We have also studied transcriptomes (RNA-Seq) of two subtypes of O. tenuiflorum, Krishna and Rama Tulsi and report the relative expression of genes in both the varieties. RESULTS: The pathways leading to the production of medicinally-important specialized metabolites have been studied in detail, in relation to similar pathways in Arabidopsis thaliana and other plants. Expression levels of anthocyanin biosynthesis-related genes in leaf samples of Krishna Tulsi were observed to be relatively high, explaining the purple colouration of Krishna Tulsi leaves. The expression of six important genes identified from genome data were validated by performing q-RT-PCR in different tissues of five different species, which shows the high extent of urosolic acid-producing genes in young leaves of the Rama subtype. In addition, the presence of eugenol and ursolic acid, implied as potential drugs in the cure of many diseases including cancer was confirmed using mass spectrometry. CONCLUSIONS: The availability of the whole genome of O.tenuiflorum and our sequence analysis suggests that small amino acid changes at the functional sites of genes involved in metabolite synthesis pathways confer special medicinal properties to this herb.

Draft genome sequence of Staphylococcus aureus 118 (ST772), a major disease clone from India.

We report the draft genome sequence of an ST772 Staphylococcus aureus disease isolate carrying staphylococcal cassette chromosome mec (SCCmec) type V from a pyomyositis patient. Our de novo short read assembly is ∼2.8 Mb and encodes a unique Panton-Valentine leukocidin (PVL) phage with structural genes similar to those of ϕ7247PVL and novel lysogenic genes at the N termini.

Superiority of pediatric en bloc renal allografts over living donor kidneys: a long-term functional study.

BACKGROUND: Growing waiting list for kidney transplantation in the United States makes it imperative to expand donor pool to use of pediatric kidneys. Because en bloc pediatric kidneys double nephron numbers, it would be interesting to learn how they fare compared to living donor kidneys long term. METHODS: Retrospective chart review was performed on all 72 pediatric en bloc and 75 live adult donor kidney recipients transplanted between January 1990 and December 2001. Long term graft function was assessed with glomerular filtration rate (GFR) using the abbreviated modification of diet in renal disease (MDRD) formula. RESULTS: Pediatric donor was 16.9 +/- 11.2 months old and weighed 10.7 +/- 3.8 kg. Nine en bloc kidneys thrombosed at a mean of 4.2 days posttransplantation. Proteinuria was detected later posttransplantation in en bloc group (45.6 +/- 33.6 months vs. 23.4 +/- 16.3 months, P = 0.002). Pediatric en bloc recipients had significantly higher GFR up to 8 years posttransplantation. One-year graft survival was significantly better in live donor group (93.3% vs. 81.9%, P = 0.041) but five-year graft survival rates were similar (86.7% vs. 76.3%, P = 0.125). One-year and five-year patient survival rates were similar between en bloc and live donor groups (97.3% vs. 98.6%, P = 0.585 and 94.6% vs. 93.0%, P = 0.688, respectively). CONCLUSION: Early postoperative graft thrombosis remain a challenge with pediatric en bloc renal transplants, but once the allografts survive early postoperative course, they provide better long-term function than living donor kidney transplants. In order to alleviate burden on waiting list, pediatric en bloc kidneys should be transplanted more often when available.

Heterogeneity in 2-deoxy-D-glucose-induced modifications in energetics and radiation responses of human tumor cell lines.

PURPOSE: The glucose analog and glycolytic inhibitor, 2-deoxy-D-glucose (2-DG), has been shown to differentially enhance the radiation damage in tumor cells by inhibiting the postirradiation repair processes. The present study was undertaken to examine the relationship between 2-DG-induced modification of energy metabolism and cellular radioresponses and to identify the most relevant parameter(s) for predicting the tumor response to the combined treatment of radiation + 2-DG. METHODS AND MATERIALS: Six human tumor cell lines (glioma: BMG-1 and U-87, squamous cell carcinoma: 4451 and 4197, and melanoma: MeWo and Be-11) were investigated. Cells were exposed to 2 Gy of Co-60 gamma-rays or 250 kVP X-rays and maintained under liquid-holding conditions 2-4 h to facilitate repair. 2-DG (5 mM, equimolar with glucose) that was added at the time of irradiation was present during the liquid holding. Glucose utilization, lactate production (enzymatic assays), and adenine nucleotides (high performance liquid chromatography and capillary isotachophoresis) were investigated as parameters of energy metabolism. Induction and repair of DNA damage (comet assay), cytogenetic damage (micronuclei formation), and cell death (macrocolony assay) were analyzed as parameters of radiation response. RESULTS: The glucose consumption and lactate production of glioma cell lines (BMG-1 and U-87) were nearly 2-fold higher than the squamous carcinoma cell lines (4197 and 4451). The ATP content varied from 3.0 to 6.5 femto moles/cell among these lines, whereas the energy charge (0.86-0.90) did not show much variation. Presence of 2-DG inhibited the rate of glucose usage and glycolysis by 30-40% in glioma cell lines and by 15-20% in squamous carcinoma lines, while ATP levels reduced by nearly 40% in all the four cell lines. ATP:ADP ratios decreased to a greater extent ( approximately 40%) in glioma cells than in squamous carcinoma 4451 and MeWo cells; in contrast, presence of 2-DG reduced ADP:AMP ratios by 3-fold in the squamous carcinoma 4451, whereas an increase was noted in the glioma cell line BMG-1. 2-DG significantly reduced the initial rates of DNA repair in all cells, resulting in an excess residual damage after 2 h of repair in BMG-1, U-87, and 4451 cell lines, whereas no significant differences could be observed in the other cell lines. Recovery from potentially lethal damage was also significantly inhibited in BMG-1 cells. 2-DG increased the radiation-induced micronuclei formation in the melanoma line (MeWo) by nearly 60%, while a moderate (25-40%) increase was observed in the glioma cell lines (BMG-1 and U-87). Presence of 2-DG during liquid holding (4 h) enhanced the radiation-induced cell death by nearly 40% in both the glioma cell lines, while significant effects were not observed in others. CONCLUSIONS: The modifications in energetics and radiation responses by 2-DG vary considerably among different human tumor cell lines, and the relationships between energy metabolism and various radiobiologic parameters are complex in nature. The 2-DG-induced modification of radiation response does not strictly correlate with changes in the levels of ATP. However, a significant enhancement of the radiation damage by 2-DG was observed in cells with high rates of glucose usage and glycolysis, which appear to be the two most important factors determining the tumor response to the combined treatment of 2-DG + radiation therapy.