Near-infrared fluorescent northern blot.

Northern blot analysis detects RNA molecules immobilized on nylon membranes through hybridization with radioactive 32P-labeled DNA or RNA oligonucleotide probes. Alternatively, nonradioactive northern blot relies on chemiluminescent reactions triggered by horseradish peroxidase (HRP) conjugated probes. The use of regulated radioactive material and the complexity of chemiluminescent reactions and detection have hampered the adoption of northern blot techniques by the wider biomedical research community. Here, we describe a sensitive and straightforward nonradioactive northern blot method, which utilizes near-infrared (IR) fluorescent dye-labeled probes (irNorthern). We found that irNorthern has a detection limit of ∼0.05 femtomoles (fmol), which is slightly less sensitive than 32P-Northern. However, we found that the IR dye-labeled probe maintains the sensitivity after multiple usages as well as long-term storage. We also present alternative irNorthern methods using a biotinylated DNA probe, a DNA probe labeled by terminal transferase, or an RNA probe labeled during in vitro transcription. Furthermore, utilization of different IR dyes allows multiplex detection of different RNA species. Therefore, irNorthern represents a more convenient and versatile tool for RNA detection compared to traditional northern blot analysis.

Engineered CRISPR prime editors with compact, untethered reverse transcriptases.

The CRISPR prime editor PE2 consists of a Streptococcus pyogenes Cas9 nickase (nSpCas9) fused at its C-terminus to a Moloney murine leukemia virus reverse transcriptase (MMLV-RT). Here we show that separated nSpCas9 and MMLV-RT proteins function as efficiently as intact PE2 in human cells. We use this Split-PE system to rapidly identify and engineer more compact prime editor architectures that also broaden the types of RTs used for prime editing.

Differences in colonization and shedding patterns after oral challenge of cattle with three Escherichia coli O157:H7 strains.

Experimental oral challenge studies with three different genotypes of Escherichia coli O157:H7 were conducted in cattle to determine the genotype-specific variability in shedding frequencies and concentrations and the frequency and extent of contamination of the environment. The results indicated that the E. coli O157:H7 genotype and ecological origin maybe important factors for the occurrence and concentration in the cattle host. Four groups of six young Holstein steers each were orally challenged with 10(6) CFU of one of three E. coli O157:H7 strains: FRIK 47 (groups 1 and 2), FRIK 1641 (group 3), and FRIK 2533 (group 4). Recto-anal mucosal swabs (RAMS) and environmental samples were taken on alternate days over 30 days. The numbers of E. coli O157:H7 cells and generic E. coli cells per sample were determined. Also, the presence and absence of 28 gene targets were determined for 2,411 isolates using high-throughput real-time PCR. Over the study period, strains FRIK 47, FRIK 1641, and FRIK 2533 were detected in 52%, 42%, and 2% of RAMS, respectively. Environmental detection of the challenge strains was found mainly in samples of the hides and pen floors, with strains FRIK 47, FRIK 1641, and FRIK 2533 detected in 22%, 27%, and 0% of environmental samples, respectively. Based on the panel of 28 gene targets, genotypes of enterohemorrhagic E. coli (EHEC) and generic E. coli from the experimental samples were clustered into three subgroups. In conclusion, the results suggested that the type and intensity of measures to control this pathogen at the preharvest level may need to be strain specific.

Factors Associated with "Survivor Identity" in Men with Breast Cancer.

Cancer patients vary in their comfort with the label "survivor". Here, we explore how comfortable males with breast cancer (BC) are about accepting the label cancer "survivor". Separate univariate logistic regressions were performed to assess whether time since diagnosis, age, treatment status, and cancer stage were associated with comfort with the "survivor" label. Of the 70 males treated for BC who participated in the study, 58% moderately-to-strongly liked the term "survivor", 26% were neutral, and 16% moderately-to-strongly disliked the term. Of the factors we explored, only a longer time since diagnosis was significantly associated with the men endorsing a survivor identity (OR = 1.02, p = 0.05). We discuss how our findings compare with literature reports on the comfort with the label "survivor" for women with BC and men with prostate cancer. Unlike males with prostate cancer, males with BC identify as "survivors" in line with women with BC. This suggests that survivor identity is more influenced by disease type and treatments received than with sex/gender identities.

CRISPR C-to-G base editors for inducing targeted DNA transversions in human cells.

CRISPR-guided DNA cytosine and adenine base editors are widely used for many applications1-4 but primarily create DNA base transitions (that is, pyrimidine-to-pyrimidine or purine-to-purine). Here we describe the engineering of two base editor architectures that can efficiently induce targeted C-to-G base transversions, with reduced levels of unwanted C-to-W (W = A or T) and indel mutations. One of these C-to-G base editors (CGBE1), consists of an RNA-guided Cas9 nickase, an Escherichia coli-derived uracil DNA N-glycosylase (eUNG) and a rat APOBEC1 cytidine deaminase variant (R33A) previously shown to have reduced off-target RNA and DNA editing activities5,6. We show that CGBE1 can efficiently induce C-to-G edits, particularly in AT-rich sequence contexts in human cells. We also removed the eUNG domain to yield miniCGBE1, which reduced indel frequencies but only modestly decreased editing efficiency. CGBE1 and miniCGBE1 enable C-to-G edits and will serve as a basis for optimizing C-to-G base editors for research and therapeutic applications.

A dual-deaminase CRISPR base editor enables concurrent adenine and cytosine editing.

Existing adenine and cytosine base editors induce only a single type of modification, limiting the range of DNA alterations that can be created. Here we describe a CRISPR-Cas9-based synchronous programmable adenine and cytosine editor (SPACE) that can concurrently introduce A-to-G and C-to-T substitutions with minimal RNA off-target edits. SPACE expands the range of possible DNA sequence alterations, broadening the research applications of CRISPR base editors.

Northern Blot with IR Fluorescent Probes: Strategies for Probe Preparation.

Northern blot is a molecular biology technique that can detect, quantify, and determine the molecular weight of RNA. Recently, we published a protocol utilizing near-infrared (IR) fluorescent probes in Northern blot (irNorthern). Our method is as sensitive as other non-radioactive methods but is more straightforward and versatile. Additionally, we found that IR-labeled probes can be used to multiplex or detect different species of RNA at the same time. Here we describe three methods for generating an IR-labeled probe as well as how to perform irNorthern blot. In conclusion, our irNorthern protocol offers a convenient method for RNA detection.

Cesarean section in alpacas and llamas: 34 cases (1997-2010).

OBJECTIVE: To determine indications for cesarean section in alpacas and llamas, and clinical management and outcome of alpacas and llamas undergoing cesarean section. DESIGN: Retrospective case series. ANIMALS: 27 alpacas and 7 llamas. PROCEDURES: Medical records were reviewed and information gathered on signalment, anamnesis including reproductive history, physical examination findings, indication for cesarean section, anesthetic protocol, surgical technique, number of crias delivered (alive or dead), additional treatment, duration of hospitalization, and postoperative complications. Follow-up information was gathered via email or telephone interview with owners. RESULTS: Uterine torsion (13/34 [38%]) was the most common reason for cesarean section. The most common surgical approach was the left proximal lateral abdominal approach (21/34 [62%]). Thirty-four crias were delivered via cesarean section. Twenty (59%) were born alive and discharged from the hospital. Retained placenta was the most common complication observed after surgery. A significant association was found between prolonged dystocia and fetal death. Of the 34 dams that underwent cesarean section, 21 were rebred, and 19 of the 21 (90.5%) dams that were rebred became pregnant. Fifteen of 19 dams were confirmed to have ≥ 1 normal vaginal delivery with a live cria following cesarean section. CONCLUSIONS AND CLINICAL RELEVANCE: The results of the present study indicated that cesarean section was an effective method of resolving dystocia in camelids without negatively affecting future fertility or parturition by the dam. Prompt referral of patients with dystocia is advised to improve fetal viability. Retained fetal membranes seemed to be a common complication of cesarean section in camelids but was not associated with negative outcomes.