CRISPR-STAT: an easy and reliable PCR-based method to evaluate target-specific sgRNA activity

CRISPR/Cas9 has emerged as a versatile genome-engineering tool that relies on a single guide RNA (sgRNA) and the Cas9 enzyme for genome editing. Simple, fast and economical methods to generate sgRNAs have made targeted mutagenesis routine in cultured cells, mice, zebrafish and other model systems. Pre-screening of sgRNAs for target efficacy is desirable both for successful mutagenesis and minimizing wasted animal husbandry on targets with poor activity. Here, we describe an easy, quick and cost-effective fluorescent polymerase chain reaction (PCR)-based method, CRISPR Somatic Tissue Activity Test (CRISPR-STAT), to determine target-specific efficiency of sgRNA. As a proof of principle, we validated our method using 28 sgRNAs with known and varied levels of germline transmission efficiency in zebrafish by analysis of their somatic activity in injected embryos. Our data revealed a strong positive correlation between the fluorescent PCR profiles of the injected embryos and the germline transmission efficiency. Furthermore, the assay was sensitive enough to evaluate multiplex gene targeting. This method is easy to implement by laboratories with access to a capillary sequencer. Although we validated the method using CRISPR/Cas9 and zebrafish, it can be applied to other model systems and other genome targeting nucleases.     

Identifying qualitative effects of different grazing types on below‐ground communities and function in a long‐term field experiment

Herbivory is an important modulator of plant biodiversity and productivity in grasslands, but our understanding of herbivore‐induced changes on below‐ground processes and communities is limited. Using a long‐term (17 years) experimental site, we evaluated impacts of rabbit and invertebrate grazers on some soil functions involved in carbon cycling, microbial diversity, structure and functional composition. Both rabbit and invertebrate grazing impacted soil functions and microbial community structure. All functional community measures (functions, biogeochemical cycling genes, network association between different taxa) were more strongly affected by invertebrate grazers than rabbits. Furthermore, our results suggest that exclusion of invertebrate grazers decreases both microbial biomass and abundance of genes associated with key biogeochemical cycles, and could thus have long‐term consequences for ecosystem functions. The mechanism behind these impacts are likely to be driven by both direct effects of grazing altering the pattern of nutrient inputs and by indirect effects through changes in plant species composition. However, we could not entirely discount that the pesticide used to exclude invertebrates may have affected some microbial community measures. Nevertheless, our work illustrates that human activity that affects grazing intensity may affect ecosystem functioning and sustainability, as regulated by multi‐trophic interactions between above‐ and below‐ground communities.     

Evaluation and elimination of inhibitory effects of salts and heavy metal ions on biodegradation of Congo red by Pseudomonas sp. mutant

In this study, it was attempted to evaluate the influences and also recommended some elimination methods for inhibitory effects offered by salts and heavy metal ions. Congo red dye solution treated with mutant Pseudomonas sp. was taken as a model system for study. The salts used in this study are NaCl, CaCl₂ and MgSO₄·7H₂O. Though the growth was inhibited at concentrations above 4 g/l, toleration was achieved by acclimatization process. In case of heavy metal ions, Cr (VI) showed low inhibition up to 500 mg/l of concentration, compared to Zn (II) and Cu (II). It was due to the presence of chromium reductase enzyme which was confirmed by SDS-PAGE. Zn (II) and Cu (II) ion inhibitions were eliminated by chelation with EDTA. The critical ion concentrations obtained as per Han-Levenspiel model for Cr (VI), Zn (II) and Cu (II) were 0.8958, 0.3028 and 0.204 g/l respectively.     

Discovery of a piperazine urea based compound as a potent, selective, orally bioavailable melanocortin subtype-4 receptor partial agonist

We report the discovery of piperazine urea based compound 1, a potent, selective, orally bioavailable melanocortin subtype-4 receptor partial agonist. Compound 1 shows anti-obesity efficacy without potentiating erectile activity in the rodent models.     

Endocytic response of type I alveolar epithelial cells to hypertonic stress

We present plasma membrane (PM) internalization responses of type I alveolar epithelial cells to a 50 mosmol/l increase in tonicity. Our research is motivated by interest in ATI repair, for which endocytic retrieval of PM appears to be critical. We validated pharmacological and molecular tools to dissect the endocytic machinery of these cells and used these tools to test the hypothesis that osmotic stress triggers a pathway-specific internalization of PM domains. Validation experiments confirmed the fluorescent analogs of lactosyl-ceramide, transferrin, and dextran as pathway-specific cargo of caveolar, clathrin, and fluid-phase uptake, respectively. Pulse-chase experiments indicate that hypertonic exposure causes a downregulation of clathrin and fluid-phase endocytosis while stimulating caveolar endocytosis. The tonicity-mediated increase in caveolar endocytosis was associated with the translocation of caveolin-1 from the PM and was absent in cells that had been transfected with dominant-negative dynamin constructs. In separate experiments we show that hypertonic exposure increases the probability of PM wound repair following micropuncture from 82 ± 4 to 94 ± 2% (P < 0.01) and that this effect depends on Src pathway activation-mediated caveolar endocytosis. The therapeutic and biological implications of our findings are discussed.     

Oxidative stress in zinc-induced dopaminergic neurodegeneration: implications of superoxide dismutase and heme oxygenase-1

The study was undertaken to investigate the effect of zinc (Zn) on glutathione S-transferase (GST) and superoxide dismutases (SOD) activities and on the expressions of cytosolic Cu, Zn-SOD (SOD1), mitochondrial Mn-SOD (SOD2), γ-glutamyl cysteine synthetase (γ-GCS) and heme oxygenase-1 (HO-1) in the nigrostriatal tissue of rats. Additionally, Zn-induced alterations in the neurobehavioral parameters, lipid peroxidation (LPO), striatal dopamine and its metabolites and tyrosine hydroxylase (TH) protein expression were measured to assess their correlations with the oxidative stress. Zn exposure reduced the locomotor activity, rotarod performance, striatal dopamine and its metabolites and TH protein expression. LPO, total SOD, SOD1 and SOD2 activities were increased while GST and catalase were reduced in a dose and time dependent manner. Expressions of SOD1 and HO-1 were increased while no change was observed in SOD2 and γ-GCS expressions. The results obtained suggest that Zn-induced augmentation of total SOD, SOD1, SOD2 and HO-1 was associated with increased oxidative stress and neurodegenerative indexes indicating the involvement of both cytosolic and mitochondrial machinery in Zn-induced oxidative stress leading to dopaminergic neurodegeneration.     

Construction and nanomechanical properties of the exoskeleton of the barnacle, Amphibalanus reticulatus

Barnacles are some of the major inhabitants of intertidal zones and have calcite-based exoskeleton to anchor and armor their tissues. Structural characterization studies of the specie Ambhibalanus reticulatus were performed to understand the construction of the exoskeleton which forms a light-weight yet stiff structure. The parietal shell is constructed of six compartments to yield a truncated cone geometry, which is neatly fixed onto the basal shell that attaches the organism to the substrate surface. The connections among the different compartments happen through sutured edges and also have chemical interlocking to make the junctions impermeable. Also, the shell parts are furnished with hollow channels reducing the overall mass of the construction. The structure and functions of different parts of the exoskeleton are identified and outlined. Finally, the mechanical properties such as modulus, hardness and fracture toughness of the exoskeleton obtained by indentation techniques are discussed.     

Revisiting the hetero-fertilization phenomenon in maize

Development of a seed DNA-based genotyping system for marker-assisted selection (MAS) has provided a novel opportunity for understanding aberrant reproductive phenomena such as hetero-fertilization (HF) by observing the mismatch of endosperm and leaf genotypes in monocot species. In contrast to conventional approaches using specific morphological markers, this approach can be used for any population derived from diverse parental genotypes. A large-scale experiment was implemented using seven F(2) populations and four three-way cross populations, each with 534 to 1024 individuals. The frequency of HF within these populations ranged from 0.14% to 3.12%, with an average of 1.46%. The highest frequency of HF in both types of population was contributed by the pollen gametes. Using three-way crosses allowed, for the first time, detection of the HF contributed by maternal gametes, albeit at very low frequency (0.14%-0.65%). Four HF events identified from each of two F(2) populations were tested and confirmed using 1032 single nucleotide polymorphic markers. This analysis indicated that only 50% of polymorphic markers can detect a known HF event, and thus the real HF frequency can be inferred by doubling the estimate obtained from using only one polymorphic marker. As expected, 99% of the HF events can be detected by using seven independent markers in combination. Although seed DNA-based analysis may wrongly predict plant genotypes due to the mismatch of endosperm and leaf DNA caused by HF, the relatively low HF frequencies revealed with diverse germplasm in this study indicates that the effect on the accuracy of MAS is limited. In addition, comparative endosperm and leaf DNA analysis of specific genetic stocks could be useful for revealing the relationships among various aberrant fertilization phenomena including haploidy and apomixis.