NmeCas9 is an intrinsically high-fidelity genome-editing platform

Background

The development of CRISPR genome editing has transformed biomedical research. Most applications reported thus far rely upon the Cas9 protein from Streptococcus pyogenes SF370 (SpyCas9). With many RNA guides, wildtype SpyCas9 can induce significant levels of unintended mutations at near-cognate sites, necessitating substantial efforts toward the development of strategies to minimize off-target activity. Although the genome-editing potential of thousands of other Cas9 orthologs remains largely untapped, it is not known how many will require similarly extensive engineering to achieve single-site accuracy within large genomes. In addition to its off-targeting propensity, SpyCas9 is encoded by a relatively large open reading frame, limiting its utility in applications that require size-restricted delivery strategies such as adeno-associated virus vectors. In contrast, some genome-editing-validated Cas9 orthologs are considerably smaller and therefore better suited for viral delivery.

Results

Here we show that wildtype NmeCas9, when programmed with guide sequences of the natural length of 24 nucleotides, exhibits a nearly complete absence of unintended editing in human cells, even when targeting sites that are prone to off-target activity with wildtype SpyCas9. We also validate at least six variant protospacer adjacent motifs (PAMs), in addition to the preferred consensus PAM (5′-N₄GATT-3′), for NmeCas9 genome editing in human cells.

Conclusions

Our results show that NmeCas9 is a naturally high-fidelity genome-editing enzyme and suggest that additional Cas9 orthologs may prove to exhibit similarly high accuracy, even without extensive engineering.

     

Every rose has its thorn: Infants' responses to pointed shapes in naturalistic contexts

Plants produce dangerous chemical and physical defenses that have shaped the physiology and behavior of the herbivorous predators that feed on them. Here we explore the impact that these plant defenses may have had on humans by testing infants' responses to plants with and without sharp-looking thorns. To do this, we presented 8- to 18-month-olds with plants and control stimuli and measured their initial reaching behavior and subsequent object exploration behavior. Half of the stimuli had sharp-looking thorns or pointed parts while the other half did not. We found that infants exhibited both an initial reluctance to touch and minimized subsequent physical contact with plants compared to other object types. Further, infants treated all plants as potentially dangerous, whether or not they possessed sharp-looking thorns. These results reveal novel dimensions of a behavioral avoidance strategy in infancy that would mitigate potential harm from plants.     

Intraepithelial lymphocyte immunophenotype: a useful tool in the diagnosis of celiac disease

According to new ESPGHAN guidelines, gluten challenge is considered necessary when there is doubt about the initial diagnosis of celiac disease (CD). The main aim of this study was to quantify intraepithelial lymphocyte (IEL) immunophenotype on celiac patients on gluten-containing diet (GCD) compared to those on gluten-free diet (GFD). Another aim was to evaluate the clinical utility of IELs in the CD diagnosis, especially in selected patients on GFD where diagnostic uncertainty remains. IEL immunophenotype (TCRγδ and NK-like IELs) were studied by flow cytometry in 111 children with CD (81 children with CD on GCD and 30 celiac patients on GFD) and a control group (10 children). Duration of GFD was 5.4 ± 1.6 years. TCRγδ IELs in celiac patients receiving a GCD or GFD were significantly higher (p < 0.001) than in the control group. NK-like IELs in patients receiving a GCD or GFD were significantly lower than in the control group (p < 0.001). We observed a permanent decrease of NK-like IELs and an increment of TCRγδ IELs after following an adequate establishment and compliance of a long-term GFD in celiac patients. Recognition of IELs changes in the intestinal mucosa on celiac patients after long-term establishment of a GFD could constitute a useful tool for CD diagnosis in various situations: in which there is doubt about the initial diagnosis and repeat biopsy is necessary (avoiding the need of gluten challenges), and in those patients with symptoms/signs suggestive of CD who maintain a low gluten diet.     

Conversion of array‐based single nucleotide polymorphic markers for use in targeted genotyping by sequencing in hexaploid wheat (Triticum aestivum)

Wheat breeders and academics alike use single nucleotide polymorphisms (SNP s) as molecular markers to characterize regions of interest within the hexaploid wheat genome. A number of SNP ‐based genotyping platforms are available, and their utility depends upon factors such as the available technologies, number of data points required, budgets and the technical expertise required. Unfortunately, markers can rarely be exchanged between existing and newly developed platforms, meaning that previously generated data cannot be compared, or combined, with more recently generated data sets. We predict that genotyping by sequencing will become the predominant genotyping technology within the next 5–10 years. With this in mind, to ensure that data generated from current genotyping platforms continues to be of use, we have designed and utilized SNP ‐based capture probes from several thousand existing and publicly available probes from Axiom® and KASP ? genotyping platforms. We have validated our capture probes in a targeted genotyping by sequencing protocol using 31 previously genotyped UK elite hexaploid wheat accessions. Data comparisons between targeted genotyping by sequencing, Axiom® array genotyping and KASP ? genotyping assays, identified a set of 3256 probes which reliably bring together targeted genotyping by sequencing data with the previously available marker data set. As such, these probes are likely to be of considerable value to the wheat community. The probe details, full probe sequences and a custom built analysis pipeline may be freely downloaded from the CerealsDB website (http://www.cerealsdb.uk.net/cerealgenomics/CerealsDB /sequence_capture.php).     

The population genetic test Tajima's D identifies genes encoding pathogen‐associated molecular patterns and other virulence‐related genes in Ralstonia solanacearum

The detection of pathogen‐associated molecular patterns (PAMPs) by plant pattern recognition receptors (PRRs) is an essential part of plant immunity. Until recently, elf18, an epitope of elongation factor‐Tu (EF‐Tu), was the sole confirmed PAMP of Ralstonia solanacearum, the causal agent of bacterial wilt disease, limiting our understanding of R. solanacearum–plant interactions. Therefore, we set out to identify additional R. solanacearum PAMPs based on the hypothesis that genes encoding PAMPs are under selection to avoid recognition by plant PRRs. We calculated Tajima's D, a population genetic test statistic which identifies genes that do not evolve neutrally, for 3003 genes conserved in 37 R. solanacearum genomes. The screen flagged 49 non‐neutrally evolving genes, including not only EF‐Tu but also the gene for Cold Shock Protein C, which encodes the PAMP csp22. Importantly, an R. solanacearum allele of this PAMP was recently identified in a parallel independent study. Genes coding for efflux pumps, some with known roles in virulence, were also flagged by Tajima's D. We conclude that Tajima's D is a straightforward test to identify genes encoding PAMPs and other virulence‐related genes in plant pathogen genomes.     

Label‐free imaging of healthy and infarcted fetal sheep hearts by two‐photon microscopy

Coronary heart disease is one of the largest causes of death worldwide, making this a significant health care issue. A critical problem for the adult human heart is that it does not undergo effective repair in response to damage, leaving patients with a poor prognosis. Unlike the adult, fetal hearts have the ability to repair after myocardial damage. Using two‐photon microscopy, we have visualised the morphological and metabolic changes following myocardial infarction in sheep fetuses, to characterise response to cardiac injury in a mammalian model. Following myocardial infarction, fetal hearts showed no significant increase in collagen deposition in the region of the infarction, when compared to either the surrounding tissue or shams. In contrast, metabolic activity (i. e. NAD(P)H and FAD) was significantly reduced in the region of myocardial infarction, when compared to either the surrounding tissue or sham hearts. For comparison, we also imaged two hearts from preadolescent sheep (sham and myocardial infarction) and showed highly ordered collagen deposition with decreased metabolic activity within the infarcted area. Therefore, two‐photon imaging had the capacity to image both morphological and metabolic changes in response to myocardial infarction and showed differences in the response with age. Picture : Two‐photon imaging of myocardial infarction ( b and d ) enabled the visualisation of increased collagen (blue; Em=431 nm) and changes in other tissue autofluorescence (green; Em=489–606 nm) in fetal ( a and b ) and preadolescent ( c and d ) hearts, compared to shams ( a and c ). The excitation wavelength was 840 nm. Scale bars: 10 μm.

     

Probiotic Features of Lactic Acid Bacteria Isolated from a Diverse Pool of Traditional Greek Dairy Products Regarding Specific Strain-Host Interactions

Probiotics and Antimicrobial Proteins - The increased consumers’ interest on the positive role of food in wellbeing and health underscores the need to determine new probiotic microorganisms....     

Ant-partners play a minor role on occurrence of the myrmecophilous butterfly <Emphasis Type="Italic">Leptotes cassius</Emphasis> in its host plant

Ant-related oviposition in facultatively myrmecophilous lycaenid butterflies is common, but not universal. In fact, our knowledge of ant-related oviposition in lycaenids is based on some common species (e.g., Rekoa marius, Allosmaitia strophius, Parrhasius polibetes), which limits generalizations about these systems. In this study, we experimentally investigated whether the oviposition pattern of the florivorous lycaenid Leptotes cassius was influenced by the presence of Camponotus ants and whether larvae were attended, rather than attacked, by ants. This might be evidence of myrmecophily. Both L. cassius and Camponotus ants occur on Bionia coriacea, an extrafloral nectaried legume shrub that grows in the Brazilian cerrado. Plants were randomly assigned to ant-present and ant-excluded treatments and were observed twice throughout the short reproductive season. Larvae of L. cassius were tended by ants, whose attendance was characterized by active antennation on the last body segments of the caterpillars. Therefore, Camponotus can be considered a partner of L. cassius. Lycaenid abundance was on average 1.9- and 1.21-fold higher in plants with ants in each sampling period, respectively, indicating a tendency of L. cassius to occur in plants with ants. Nonetheless, results were not statistically significant, suggesting that in this case ants are not a major cue for lycaenid oviposition. In many ant–lycaenid mutualisms, butterfly immatures benefit from reduced parasitism rates. However, no L. cassius immature, regardless of ant presence or absence, was parasitized. Furthermore, larvae may occur inside flower buds that may provide protection from natural enemies; thus, ants may not be required for immature protection.