CRISPcut: A novel tool for designing optimal sgRNAs for CRISPR/Cas9 based experiments in human cells

The ability to direct the CRISPR/Cas9 nuclease to a unique target site within a genome would have broad use in targeted genome engineering. However, CRISPR RNA is reported to bind to other genomic locations that differ from the intended target site by a few nucleotides, demonstrating significant off-target activity. We have developed the CRISPcut tool that screens the off-targets using various parameters and predicts the ideal genomic target for –guide RNAs in human cell lines. sgRNAs for four different types of Cas9 nucleases can be designed with an option for the user to work with different PAM sequences. Direct experimental measurement of genome-wide DNA accessibility is incorporated that effectively restricts the prediction of CRISPR targets to open chromatin. An option to predict target sites for paired CRISPR nickases is also provided. The tool has been validated using a dataset of experimentally used sgRNA and their identified off-targets.URL: http://web.iitd.ac.in/crispcut     

Conservative Management of Urinary Incontinence in Women

Urinary incontinence in women has a high prevalence and causes significant morbidity. Given that urinary incontinence is not generally a progressive disease, conservative therapies play an integral part in the management of these patients. We conducted a nonsystematic review of the literature to identify high-quality studies that evaluated the different components of conservative management of stress urinary incontinence, including behavioral therapy, bladder training, pelvic floor muscle training, lifestyle changes, mechanical devices, vaginal cones, and electrical stimulation. Urinary incontinence can have a severe impact on our healthcare system and patients’ quality of life. There are currently a wide variety of treatment options for these patients, ranging from conservative treatment to surgical treatment. Although further research is required in the area of conservative therapies, nonsurgical treatments are effective and are preferred by some patients.Key words: Urinary incontinence, Women, Conservative managementUrinary incontinence (UI) is a significant cause of decrease in quality of life, especially among women.¹ The prevalence of UI in women is estimated to range from 13% to 46%,^2,3 and studies have shown that incontinence increases with age.⁴ In addition to the significant social impact that UI has on a woman’s quality of life, this condition has a significant financial burden on individual and national healthcare dollars. It has been estimated that the total annual direct and indirect cost for UI in the United States alone is $19.5 billion.⁵UI is defined according to patients’ symptoms. Although definitions vary in the literature, the International Continence Society defines three major subtypes of UI: (1) stress urinary incontinence (SUI) is the complaint of involuntary leakage on effort or exertion, or on sneezing or coughing; (2) urgency urinary incontinence (UUI) is the complaint of involuntary leakage accompanied by or immediately preceded by urgency; and (3) mixed urinary incontinence (MUI) is the complaint of involuntary leakage associated with urgency and also with exertion, effort, sneezing, or coughing.^6,7Although there is a plethora of treatment options, conservative management is the first-line option for most patients with UI. The rationale for conservative treatment is that UI is not necessarily a progressive disease, and that conservative therapies can be effective, well tolerated, and safe. Furthermore, a moderate delay in surgical therapy does not make treatment more difficult or less effective. One of the recommendations of the 1992 Agency for Health Care Policy and Research guideline states that “surgery, except in very specific cases, should be considered only after behavioral and pharmacologic interventions have been tried.”⁸ Similarly, the European Association of Urology guidelines advocate a stepwise approach regarding management of UI, which begins with addressing underlying medical or cognitive issues, progressing to lifestyle modifications, behavioral therapy, and mechanical devices.⁹ In addition, conservative therapies are frequently preferred by many patients. Taking into account the patient’s goals and preferences, it is appropriate to recommend conservative management as an initial approach.     

Mixed Inhibition of cPEPCK by Genistein,Using an Extended Binding Site Located Adjacent to Its Catalytic Cleft

Cytosolic phosphoenolpyruvate carboxykinase (cPEPCK) is a critical enzyme involved in gluconeogenesis, glyceroneogenesis and cataplerosis. cPEPCK converts oxaloacetic acid (OAA) into phosphoenol pyruvate (PEP) in the presence of GTP. cPEPCK is known to be associated with type 2 diabetes. Genistein is an isoflavone compound that shows anti-diabetic and anti-obesitic properties. Experimental studies have shown a decrease in the blood glucose level in the presence of genistein by lowering the functional activity of cPEPCK, an enzyme of gluconeogenesis. Using computational techniques such as molecular modeling, molecular docking, molecular dynamics simulation and binding free energy calculations, we identified cPEPCK as a direct target of genistein. We studied the molecular interactions of genistein with three possible conformations of cPEPCK—unbound cPEPCK (u_cPEPCK), GTP bound cPEPCK (GTP_cPEPCK) and GDP bound cPEPCK (GDP_cPEPCK). Binding of genistein was also compared with an already known cPEPCK inhibitor. We analyzed the interactions of genistein with cPEPCK enzyme and compared them with its natural substrate (OAA), product (PEP) and known inhibitor (3-MPA). Our results demonstrate that genistein uses the mechanism of mixed inhibition to block the functional activity of cPEPCK and thus can serve as a potential anti-diabetic and anti-obesity drug candidate. We also identified an extended binding site in the catalytic cleft of cPEPCK which is used by 3-MPA to inhibit cPEPCK non-competitively. We demonstrate that extended binding site of cPEPCK can further be exploited for designing new drugs against cPEPCK.     

Heterogeneity in rabbit liver cytochrome P-450 LM2 observed by cation exchange HPLC: Partial biochemical characterization of the two major LM2 subfractions

Cytochrome P450 LM2 (CYPIIB4) from phenobarbital-induced rabbit liver microsomes, purified to only one band in SDS-PAGE, was further resolved in five peaks by cation exchange HPLC. The two major peaks were partially characterized. Both of them have the amino terminal sequence Met-Glu and the same Cys content. They exhibited the same spectral absorption maximum and similar binding constants for 1-benzylimidazole and imidazole. However, binding of benzphetamine was different. One subfraction presented a Michaelis-Menten type binding curve, but the other presents a non-typical one with an additional high affinity binding site. These subfractions of cytochrome P450 LM2 slightly differed in their catalytic activities with benzyloxy- and pentoxyresorufin substrates. On the contrary, no heterogeneity was observed for P450 LM4.     

Distinct functions for the Drosophila piRNA pathway in genome maintenance and telomere protection

Transposons and other selfish DNA elements can be found in all phyla, and mobilization of these elements can compromise genome integrity. The piRNA (PIWI-interacting RNA) pathway silences transposons in the germline, but it is unclear if this pathway has additional functions during development. Here we show that mutations in the Drosophila piRNA pathway genes, armi, aub, ago3, and rhi, lead to extensive fragmentation of the zygotic genome during the cleavage stage of embryonic divisions. Additionally, aub and armi show defects in telomere resolution during meiosis and the cleavage divisions; and mutations in lig-IV, which disrupt non-homologous end joining, suppress these fusions. By contrast, lig-IV mutations enhance chromosome fragmentation. Chromatin immunoprecipitation studies show that aub and armi mutations disrupt telomere binding of HOAP, which is a component of the telomere protection complex, and reduce expression of a subpopulation of 19- to 22-nt telomere-specific piRNAs. Mutations in rhi and ago3, by contrast, do not block HOAP binding or production of these piRNAs. These findings uncover genetically separable functions for the Drosophila piRNA pathway. The aub, armi, rhi, and ago3 genes silence transposons and maintain chromosome integrity during cleavage-stage embryonic divisions. However, the aub and armi genes have an additional function in assembly of the telomere protection complex.     

Influence of Guar Gum on the In Vitro Starch Digestibility—Rheological and Microstructural Characteristics

The present study investigates the effect of guar gum on the digestibility of a waxy maize starch in vitro under simulated gastric and intestinal conditions. A detailed rheology and confocal scanning laser microscopy of the digesta were performed in order to study the possible mechanisms of interactions involved during in vitro hydrolysis of starch. No starch hydrolysis was observed under simulated gastric conditions, whereas more than 90% hydrolysis was observed at the end of digestion under simulated intestinal conditions. In the presence of guar gum, the starch hydrolysis was reduced by nearly 25% during the first 10 min and by 15% at the end of in vitro intestinal digestion. The rheological behavior of the digesta was significantly affected in the presence of the gum. The viscosity of digesta decreased during intestinal digestion; however, the extent of decrease was quite low in the presence of guar gum. The consistency index increased and flow behavior index of digesta decreased in the presence of gum after 1 min of intestinal digestion. All the samples (digested or undigested) displayed a pseudoplastic behavior as their apparent viscosity (η _a) decreased with an increase in shear rate. A negative correlation between the starch hydrolysis (%) and storage modulus for the starch sample without gum and a positive correlation for the starch sample with gum were found. Large granule remnants observed through confocal micrographs have shown that the solubilization of starch granule remnants during in vitro digestion is significantly reduced in the presence of gum.     

Discovery of diacylphloroglucinols as a new class of GPR40 (FFAR1) agonists

In this letter, we report discovery of diacylphloroglucinol compounds as a new class of GPR40 (FFAR1) agonists. Several diacylphloroglucinols with varying length of acyl functionality and substitution on aromatic hydroxyls were synthesized and evaluated for GPR40 agonism using functional calcium-flux assay. Out of 17 compounds evaluated, 14, 17, 19 and 25 exhibited good GPR40 agonistic activity with EC(50) values ranging from 0.07 to 8 microM (pEC(50) 7.12-5.09), respectively, with maximal agonistic response of 84-102%.     

Adaptation to P element transposon invasion in Drosophila melanogaster

Transposons evolve rapidly and can mobilize and trigger genetic instability. Piwi-interacting RNAs (piRNAs) silence these genome pathogens, but it is unclear how the piRNA pathway adapts to invasion of new transposons. In Drosophila, piRNAs are encoded by heterochromatic clusters and maternally deposited in the embryo. Paternally inherited P element transposons thus escape silencing and trigger a hybrid sterility syndrome termed P-M hybrid dysgenesis. We show that P-M hybrid dysgenesis activates both P elements and resident transposons and disrupts the piRNA biogenesis machinery. As dysgenic hybrids age, however, fertility is restored, P elements are silenced, and P element piRNAs are produced de novo. In addition, the piRNA biogenesis machinery assembles, and resident elements are silenced. Significantly, resident transposons insert into piRNA clusters, and these new insertions are transmitted to progeny, produce novel piRNAs, and are associated with reduced transposition. P element invasion thus triggers heritable changes in genome structure that appear to enhance transposon silencing.     

Performance and preference of sugarcane borer,Diatraea saccharalis,on rice cultivars

The sugarcane borer, Diatraea saccharalis (Fabricius) (Lepidoptera: Crambidae), is a major agronomic pest in the southeastern USA. This study was conducted to investigate the performance of D. saccharalis on eight rice cultivars widely grown in Louisiana and to assess the relationship between oviposition preference and offspring performance. In a previous study, oviposition preference of sugarcane borers was found to vary on the same eight rice cultivars. In this study, variation in larval performance on the eight cultivars was observed. The overall performance of larvae in terms of relative growth rate and boring success of larvae was highest on Priscilla and Cocodrie. Larval performance was lower on the hybrid XL723, the Clearfield (herbicide‐resistant) variety CL161, and the medium grain Bengal. Also, larvae took more time to enter into the stem of the hybrid XL723 compared with Cocodrie. Significant positive correlations were observed among relative growth rate and boring success and between larval performance and oviposition preference. Significant positive correlations among measures of larval performance and oviposition preference suggest the operation of a common resistance mechanism. Results in laboratory and greenhouse extended into the field, where Cocodrie and Cheniere were the most damaged cultivars, whereas CL161 and the medium grain Jupiter were least injured in terms of average number of stem borer entry/exit holes per plant. Results from this study could contribute to the use of resistant cultivars in an integrated management program for stem borers and the resistant cultivars identified in this study could be used as sources of resistance in breeding programs for resistance against stem borers.