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Amyotrophic lateral sclerosis (ALS) is a severe neurodegenerative disorder affecting brain and spinal cord motor neurons. Mutations in the copper/zinc superoxide dismutase gene (SOD1) are associated with ∼20% of inherited and 1-2% of sporadic ALS cases. Much has been learned from mice expressing transgenic copies of mutant SOD1, which typically involve high-level transgene expression, thereby differing from ALS patients expressing one mutant gene copy. To generate a model that more closely represents patient gene expression, we created a knock-in point mutation (G85R, a human ALS-causing mutation) in the endogenous mouseSod1gene, leading to mutant SOD1G85Rprotein expression. HeterozygousSod1G85Rmutant mice resemble wild type, whereas homozygous mutants have reduced body weight and lifespan, a mild neurodegenerative phenotype, and express very low mutant SOD1 protein levels with no detectable SOD1 activity. Homozygous mutants exhibit partial neuromuscular junction denervation at 3-4 months of age. Spinal cord motor neuron transcriptome analyses of homozygousSod1G85Rmice revealed up-regulation of cholesterol synthesis pathway genes compared to wild type. Transcriptome and phenotypic features of these mice are similar toSod1knock-out mice, suggesting theSod1G85Rphenotype is largely driven by loss of SOD1 function. By contrast, cholesterol synthesis genes are down-regulated in severely affected humanTgSOD1G93Atransgenic mice at 4 months. Our analyses implicate dysregulation of cholesterol or related lipid pathway genes in ALS pathogenesis. TheSod1G85Rknock-in mouse is a useful ALS model to examine the importance of SOD1 activity in control of cholesterol homeostasis and motor neuron survival.SIGNIFICANCE STATEMENTAmyotrophic lateral sclerosis is a devastating disease involving the progressive loss of motor neurons and motor function for which there is currently no cure. Understanding biological mechanisms leading to motor neuron death is critical for developing new treatments. Using a new knock-in mutant mouse model carrying aSod1mutation that causes ALS in patients, and in the mouse, causes a limited neurodegenerative phenotype similar toSod1loss-of-function, we show that cholesterol synthesis pathway genes are up-regulated in mutant motor neurons, whereas the same genes are down-regulated in transgenicSOD1mice with a severe phenotype. Our data implicate dysregulation of cholesterol or other related lipid genes in ALS pathogenesis and provide new insights that could contribute to strategies for disease intervention.

Circadian rhythms are endogenously generated physiological and molecular rhythms with a cycle length of about 24 h. Bioluminescent reporters have been exceptionally useful for studying circadian rhythms in numerous species. Here, we report development of a reporter mouse generated by modification of a widely expressed and highly rhythmic gene encoding D-site albumin promoter binding protein ( Dbp). In this line of mice, firefly luciferase is expressed from the Dbp locus in a Cre recombinase-dependent manner, allowing assessment of bioluminescence rhythms in specific cellular populations. A mouse line in which luciferase expression was Cre-independent was also generated. The Dbp reporter alleles do not alter Dbp gene expression rhythms in liver or circadian locomotor activity rhythms. In vivo and ex vivo studies show the utility of the reporter alleles for monitoring rhythmicity. Our studies reveal cell-type-specific characteristics of rhythms among neuronal populations within the suprachiasmatic nuclei ex vivo. In vivo studies show Dbp-driven bioluminescence rhythms in the liver of Albumin-Cre;Dbp KI/+ “liver reporter” mice. After a shift of the lighting schedule, locomotor activity achieved the proper phase relationship with the new lighting cycle more rapidly than hepatic bioluminescence did. As previously shown, restricting food access to the daytime altered the phase of hepatic rhythmicity. Our model allowed assessment of the rate of recovery from misalignment once animals were provided with food ad libitum. These studies confirm the previously demonstrated circadian misalignment following environmental perturbations and reveal the utility of this model for minimally invasive, longitudinal monitoring of rhythmicity from specific mouse tissues.

Huntington's disease (HD) is a devastating, autosomal dominant neurodegenerative disease caused by a trinucleotide repeat expansion in the huntingtin (HTT) gene. Inactivation of the mutant allele by clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 based gene editing offers a possible therapeutic approach for this disease, but permanent disruption of normal HTT function might compromise adult neuronal function. Here, we use a novel HD mouse model to examine allele-specific editing of mutant HTT (mHTT), with a BAC97 transgene expressing mHTT and a YAC18 transgene expressing normal HTT. We achieve allele-specific inactivation of HTT by targeting a protein coding sequence containing a common, heterozygous single nucleotide polymorphism (SNP). The outcome is a marked and allele-selective reduction of mHTT protein in a mouse model of HD. Expression of a single CRISPR-Cas9 nuclease in neurons generated a high frequency of mutations in the targeted HD allele that included both small insertion/deletion (InDel) mutations and viral vector insertions. Thus, allele-specific targeting of InDel and insertion mutations to heterozygous coding region SNPs provides a feasible approach to inactivate autosomal dominant mutations that cause genetic disease.

Background: NeoSeekTM STEC is a single-source, service-based method for detection and identification of select Shiga toxin–producing Escherichia coli (STEC), including E. coli O157:H7 and STEC of somatic groups O26, O45, O103, O111, O121, and O145. The method is a multiplex molecular method utilizing more than 80 genetic targets to identify STEC in complex matrices such as food enrichment cultures. Objective: A study was conducted to validate the NeoSeek method for detection of select STEC in raw beef trim. Methods: Performance of the NeoSeek STEC method was compared with that of the U.S. Department of Agriculture, Food Safety and Inspection Service reference methods for E. coli O157:H7 and non-O157 STEC for detection of E. coli O157:H7 and E. coli O26:H11 in raw beef trim. Additionally, inclusivity/exclusivity testing and method robustness testing were performed. Results: Results of raw beef trim testing showed no statistically significant differences in performance between the NeoSeek and reference methods in the ability to detect either E. coli O157:H7 or E.coli O26:H11, as determined by probability of detection analysis. Results of inclusivity and exclusivity testing showed 100% expected results with target and nontarget bacteria, with the exception of a single strain of E. coli O157:H7, which was subsequently verified to be stx-negative by PCR. Conclusions and Highlights: NeoSeek STEC is an accurate, reliable method for rapid detection and identification of select STEC in complex populations such as beef trim enrichment cultures.

Background: Standard coliform count methods require preparation of agar, the use of pour-plate technique, the overlay of agar, and in some cases, the transfer of suspect colonies to broth medium for confirmation. The MC-Media Pad EC for enumeration of Escherichia coli and coliforms is a ready-to-use dehydrated sheet medium with no agar preparation, no spreader, and no confirmation step required. Objective: Using a paired study design, the MC-Media Pad EC was compared with standard method ISO 4832:2006. Ten matrixes including raw ground pork, raw chicken, cream, cream cheese, ready-to-cook vegetable mix, vegetable juice, cooked prawns, crab pâte, ham sandwiches, and cooked rice were evaluated in the study. Methods: Each matrix was tested at three levels of contamination (approximately 10², 10⁴, and 106 CFU/g). Five replicate 10 g test portions per level were tested in a paired comparison by the MC-Media Pad EC, ISO 4832:2006, and ISO 16649-2:2001 (Part 2) methods. In addition, inclusivity/exclusivity, robustness, and product consistency and stability were evaluated. Results: The candidate and reference methods demonstrated standard deviations ranging from 0.034 to 0.188 and 0.028 to 0.181, respectively, for E. coli counts and 0.047-0.188 and 0.025-0.157, respectively, for total coliforms. The difference of means ranged from -0.025 to 0.331 for E. coli and from -0.037 to 0.372 for total coliforms, showing no practical difference between the methods. The MC-Media Pad EC detected 49/50 E. coli and 60/63 coliform inclusivity strains and correctly excluded 30/32 exclusivity organisms for E. coli and 24/31 exclusivity organisms for total coliforms, which was similar to the reference method. Robustness testing demonstrated no significant change in results when small changes were made to sample volume, incubation temperature, and incubation time. The product consistency study demonstrated no significant difference between lots of product and supported the 1.5 year shelf life. Conclusions: The results support the conclusions that the MC-Media Pad EC is a suitable alternative to the ISO 4832:2006 and ISO 16649-2:2001 reference methods for the matrixes examined and the data support AOAC Performance Tested MethodSM certification. Highlights: The MC-Media Pad EC was approved for Performance Tested Method certification No. 011901.

Background: Solus One Salmonella is designed to accurately detect Salmonella species (Salmonella enterica subspecies enterica, salamae, arizonae, diarizonae, houtenae, indica, and Salmonella bongori) from select food matrixes and stainless-steel and plastic environmental surfaces. Solus One Salmonella uses an antibody-based technology test system that is paired with media and our proprietary media supplement, the Solus One Salmonella supplement combined with a manual or automated sample preparation method. Objective: Solus One Salmonella was evaluated for inclusivity and exclusivity, and a matrix comparison study was done for six food matrixes (raw beef trim, pasteurized liquid egg, raw salmon, cheddar cheese, Romaine lettuce, nonfat dry milk) and two environmental surfaces (stainless steel and polystyrene). Methods: Solus One Salmonella was compared with the U.S. Food and Drug Administration Bacteriological Analytical Manual Chapter 5: Salmonella (July 2018) and the U.S. Department of Agriculture Food Safety and Inspection Service Microbiology Laboratory Manual, 4.09 (January 2017) in the matrix study. Both the manual and automated sample preparation methods were performed for cheddar cheese and stainless-steel environmental surfaces. Results: For the inclusivity and exclusivity evaluation, Solus One Salmonella correctly detected all 108 target organism isolates and correctly excluded all 35 nontarget strains that were analyzed. Conclusions: In the method comparison study, both Solus One Salmonella manual and automated sample preparation methods demonstrated no significant differences based on probability of detection (POD) statistical analysis between presumptive and confirmed results or between candidate and reference method results for the six food matrixes after 20–22 h and two environmental surfaces after 16–20 h of enrichment time. POD analysis of Solus One Salmonella method robustness, product consistency, and stability studies using the automated sample preparation method demonstrated no statistically significant differences.

Background: Probe4Cronobacter test kit is based on the use of a fluorescence-labeled peptide nucleic acid probe (PNA) allied to fluorescence microscopy. A sample is taken after a 24 h enrichment of rehydrated 30 g portions of powdered infant formula (PIF). The method uses ready to use dropper solutions applied directly in the sample. This simple process takes less than 2 h to provide a result. In the presence of Cronobacter species, bright red rod-shaped cells will be visible under a fluorescence microscope. Objective: Probe4Cronobacter validation as a new method for the detection Cronobacter species in Powdered Infant Formula (PIF) under the AOAC Performance Tested MethodsSM (License No. 081702). Methods: The validation study encompassed matrix comparison study, inclusivity and exclusivity testing and robustness studies (stability, kit variation, and ruggedness). Results: The inclusivity and exclusivity testing (50 and 35 strains, respectively) yielded no false negative or false positive results. Probe4Cronobacter was compared to the ISO/TS 22964:2006 in 30 g of PIF samples within method comparison in an unpaired study. A total of 30 samples with both low and high level of inoculation were analyzed by Probe4Cronobacter and compared to the same number of samples screened by ISO/TS 22964:2006. No statistically significant differences between presumptive and confirmed results or between candidate and reference method results were observed. Robustness studies showed a high level of consistency and integrity of the kit when different parameters were varied. The deviation conditions tested did not affect the performance of the kit. Conclusions: Probe4Cronobacter test kit has shown to be a accurate, highly sensitive and robust methods for the detection of Cronobacter spp. in PIF samples.

Background: VIP® Gold for Salmonella is a lateral flow immunodetection device that was validated by AOAC in 1999 as Official Method of Analysis 999.09. It was improved upon in 2009 by introducing gold colloid as the detection method. Objective: A simple next-day enrichment protocol using modified enterohemorrhagic Escherichia coli media was developed for the VIP Gold for Salmonella to improve the time-to-results and laboratory work flow. Methods: We tested 128 Salmonella strains, representing all serotypes from A to Z and 51 to 66 as well as 50 non-Salmonella strains for inclusivity/exclusivity. Performance of the VIP using the new enrichment protocol was compared with the U.S. Department of Agriculture (USDA) Microbiology Laboratory Guidebook reference culture procedure for the detection of Salmonella in ready-to-eat poultry, roast beef, and chicken carcass rinsate. VIP performance was also compared with the U.S. Food and Drug Administration (FDA) Bacteriological Analytical Manual (BAM) for the detection of Salmonella from raw spinach, raw almonds, raw pasta, and environmental surfaces (stainless steel, rubber, and plastic). Results: The VIP detected all 128 of Salmonella strains and none of the 50 non-Salmonella strains. There was no statistically significant difference in the numbers of positive results with VIP Gold for Salmonella protocol compared with appropriate USDA-Food Safety and Inspection Service or FDA-BAM reference methods for any of these matrixes. Conclusions: This new enrichment protocol has met all the requirements to be approved as a Performance Tested MethodSM. Highlights: The new enrichment protocol will improve the time-to-results and allow quicker decisions about the contamination of food products.

Background: The gene-based real-time PCR method for identification of Campylobacter jejuni is more simple, rapid and accurate than the traditional biochemical method. Objective: A performance validation of the TadpoleTMCampylobacter jejuni Real-Time PCR Identification Kit was performed. Method: The assay uses TaqMan Real-time PCR technology to amplify target genes from isolated colonies. Bacterial deoxyribonucleic acid (DNA) from inclusivity and exclusivity organisms cultured on Columbia Blood Agar, Campy-Cefex agar and modified Charcoal Cefoperazone Deoxycholate was extracted and analyzed on three instruments: Applied Biosystems (ABI) 7500 Fast, ABI StepOne Plus and Bio-Rad CFX96. Results: When 57 distinct strains of C. jejuni were tested for inclusivity, all 57 strains produced positive results on the three instruments. In exclusivity testing, all 35 strains of related organisms, including 7 non-target Campylobacter strains and other common species, produced negative results on the three instruments. The Independent Laboratory validation consisting of an inclusivity and exclusivity evaluation for 10 C. jejuni isolates and 10 nontarget Campylobacter isolates also showed 100% expected results on the three instruments. In addition, in robustness testing, small, deliberate changes to the assay parameters, including cell suspension turbidity, heat lysis time, and DNA template volume in the PCR reaction, did not affect the kit performance. Finally, the combined lot-to-lot and stability study on both the ABI 7500 Fast and the ABI StepOne Plus showed that the 11 C. jejuni strains and 5 nontarget Campylobacter strains can be correctly identified by the three independently manufactured, lots and it supported a shelf life of 9 months when stored at –20°C. Conclusions: The Tadpole method offers a rapid, accurate, and robust alternative for C. jejuni identification. Highlights: Rapid and accurate method to identify C. jejuni, which has a good robustness and high stability. It is flexible and offers the advantages of reduced labor and time saving.

Background: Listeria Right NowTM is a novel, enrichment-free molecular method for detection of Listeria spp. in swab samples from environmental surfaces. The test provides results in real time, indicating the current or recent presence of Listeria spp. in the environment. After sampling, the entire contents of the swab are subject to sample processing, releasing large quantities of target ribosomal RNA molecules into the lysate. A portion of the lysate is then tested using the ANSR® for Listeria isothermal nucleic acid amplification assay. Objective: A Performance Tested MethodSM study was conducted to validate the method for detection of Listeria spp. in swab samples from stainless steel and sealed concrete surfaces. Methods and Results: In inclusivity testing, 60 of 60 Listeria spp. strains tested positive. In exclusivity testing, 31 of 31 nontarget bacterial strains tested negative. In LOD testing, the test was able to detect as few as 2 CFU of L. monocytogenes applied to a stainless steel surface. In matrix testing of inoculated stainless steel and sealed concrete surfaces, there were no statistically significant differences in method performance comparing the Listeria Right Now and U.S. Food and Drug Administration Bacteriological Analytical Manual reference culture procedures as determined by probability of detection analysis. In robustness testing, modest changes to three assay operating parameters simultaneously did not significantly affect performance of the test. Conclusions and Highlights: Results can be obtained in less than 1 h using the Listeria Right Now test, allowing food industry personnel to take immediate corrective action in the case of Listeria contamination incidents.

Background: Solus One Listeria is designed to accurately detect Listeria species (Listeria grayi, L. innocua, L. ivanovii, L. marthii, L. monocytogenes, L. seeligeri, and L. welshimeri) from stainless steel and plastic environmental surface matrixes using an antibody-based technology test system paired with proprietary SOLO+ media and combined with manual or automated sample preparation method. Objective: Solus One Listeria was evaluated for inclusivity and exclusivity and a matrix comparison study fortwo environmental surfaces. Methods: Solus One Listeria was comparedwith the following reference method for the method comparison study: the U.S. Food and Drug Administration Bacteriological Analytical Manual Chapter 10 from stainless steel and plastic environmental surfaces. Both the manual and automatedpreparation methods were performed for stainless steel and plastic environmental surfaces. Results: For the inclusivity and exclusivityevaluation, Solus One Listeria correctly identified all 50 target organism isolates and correctly excluded all 30 nontarget strains that were analyzed. In the method comparison study, bothSolus One Listeria manual and automated preparation methods demonstrated no significant differences based on probability of detection statistical analysis between presumptive and confirmed results or between candidate and reference methodresults for two environmental surfaces after 22–30 h of enrichment time. Probability of detection analysis of Solus One Listeria method robustness, product consistency (lot-to-lot), and stability studies using the automated preparation method demonstrated no statistically significant differences. Conclusions: The data from the study support the product claims of Solus One Listeria for the accurate detection of Listeria species, using both the manual and automated methods (using theDynex DS2 instrument), on both environmental surfaces analyzed.

Background: The Thermo Scientific RapidFinder™ Salmonella species, Typhimurium and Enteritidis Multiplex PCR Kit is a real-time multiplex PCR assay for the detection and differentiation of Salmonella species, Salmonella Typhimurium, and S. Enteritidis from poultry, pork, and environmental samples. The method has previously been granted certification as Performance Tested Method SM (PTM) 081701, validated according to the AOAC Research Institute (RI) PTM program for poultry (chicken thighs with skin, chicken wings with skin, and chicken nuggets), raw pork sausage matrixes, and stainless steel environmental surface sponges. Objective: This report details the method modification study to validate ground turkey (375 g sample size), chicken carcass rinse, and shell egg matrixes. Methods: The candidate method was compared with the U.S. Food and Drug Administration’s Bacteriological Analytical Manual Chapter 5 for shell eggs and the U.S. Department of Agriculture Food Safety and Inspection Service’s Microbiology Laboratory Guidebook 4.09 for ground turkey (375 g) and chicken carcass rinse matrixes. Results: The statistically significant differences found between the candidate and reference methods upon analysis by probability of detection were in favor of the candidate method. Inclusivity and exclusivity testing demonstrated that the RapidFinder Salmonella species, Typhimurium and Enteritidis Multiplex PCR Kit was able to detect all the major groups of Salmonella. All exclusivity isolates were correctly excluded. Conclusions: The data presented in this report show that the candidate is suitable for the detection and differentiation of Salmonellae from shell egg, chicken carcass rinse, and ground turkey (375 g) matrixes. Highlights: Thermo Scientific RapidFinder Salmonella species, Typhimurium and Enteritidis Multiplex PCR Kit (candidate method) matrix claims extended to include ground turkey (375 g), chicken carcass rinse and shell egg samples.

The AOAC Research Institute Performance Tested MethodsSM Program certified Sample6 DETECT/L™ in April 2014 (Certification No. 041401) for the detection of Listeria species (L. monocytogenes, L. innocua, L. ivanovii, L. seeligeri, L. marthii, L. welshimeri) on stainless steel environmental surfaces. A modification was approved in January 2016, increasing the concentration of sanitizer-neutralizing reagents in detection reagents, increasing the number of phage in the detection solution, and increasing the sample test volume. Moreover, changes to reduce the number of negative controls and add compatibility with polyurethane sponges were also approved. In this modification, to ensure that DETECT/L continues to meet performance expectations, Sample6 evaluated workflow changes to enhance sensitivity and the ease-of-use of the assay. Changes to the phage concentration and detection threshold, plus the inclusion of a confirmation step (DETECT Check), were validated to obtain better accuracy and optimize assay performance. Inclusivity, exclusivity, and robustness testing were conducted by Sample6 to evaluate the changes. A third-party laboratory compared the DETECT/L assay and the U.S. Department of Agriculture reference method in a stainless steel environmental surface matrix study. The data presented in this report demonstrate that the changes proposed to the DETECT/L assay meet or exceed the performance in the current configuration.

Circadian rhythms are endogenously generated physiological and molecular rhythms with a cycle length of about 24 h. Bioluminescent reporters have been exceptionally useful for studying circadian rhythms in numerous species. Here, we report development of a reporter mouse generated by modification of a widely expressed and highly rhythmic gene encoding D-site albumin promoter binding protein (Dbp). In this line of mice, firefly luciferase is expressed from the Dbp locus in a Cre-recombinase-dependent manner, allowing assessment of bioluminescence rhythms in specific cellular populations. A mouse line in which luciferase expression was Cre-independent was also generated. The Dbp reporter alleles do not alter Dbp gene expression rhythms in liver or circadian locomotor activity rhythms. In vivo and ex vivo studies show the utility of the reporter alleles for monitoring rhythmicity. Our studies reveal cell-type specific characteristics of rhythms among neuronal populations within the suprachiasmatic nuclei ex vivo. In vivo studies show Dbp-driven bioluminescence rhythms in the liver of Albumin-Cre;DbpKI/+ “liver reporter” mice. After a shift of the lighting schedule, locomotor activity achieved the proper phase relationship with the new lighting cycle more rapidly than hepatic bioluminescence did. As previously shown, restricting food access to the daytime altered the phase of hepatic rhythmicity. Our model allowed assessment of the rate of recovery from misalignment once animals were provided with food ad libitum. These studies confirm the previously demonstrated circadian misalignment following environmental perturbations and reveal the utility of this model for minimally invasive, longitudinal monitoring of rhythmicity from specific mouse tissues.

The Thermo Scientific RapidFinder™ Salmonella Species, Typhimurium, and Enteritidis Multiplex PCR Kit (candidate method) is a real-time PCR assay for the detection and differentiation of Salmonella spp., and the serovars S. Typhimurium, and S. Enteritidis from poultry, pork, and environmental samples. The method was validated in comparison to the U.S. Department of Agriculture Food Safety and Inspection Service and the U.S. Food and Drug Administration reference methods. Thermo Fisher Scientific (Basingstoke, United Kingdom) tested all matrixes. In addition, two matrixes were analyzed independently by Q Laboratories, Inc. (Cincinnati, OH). Few statistically significant differences were found between the candidate and reference methods when analyzed by probability of detection. When differences were observed, these were in favor of the candidate method. All 200 inclusivity strains and none of the 45 exclusivity strains were detected, which demonstrated that the RapidFinder Salmonella Species, Typhimurium, and Enteritidis Multiplex PCR Kit was able to detect all the major groups of Salmonella, the less common subspecies of S. enterica, and the rarely encountered S. bongori. None of the exclusivity isolates analyzed were detected. Robustness testing demonstrated that the assay gave reliable performance, with specific method deviations outside the recommended parameters. Accelerated stability testing was conducted, validating the assay shelf life.

The MC-Media Pad ACplus™ is a dry, rehydratable film medium for the enumeration of aerobic bacterial colonies. The performance of the method in a variety of foods was compared to that of U.S. reference methods: U.S. Department of Agriculture (USDA) Food Safety and Inspection Service (FSIS) Microbiology Laboratory Guidebook (MLG) Chapter 3.02 “Quantitative Analysis of Bacteria in Foods as Sanitary Indicators” (USDA/FSIS MLG 3.02); Standard Methods for the Examination of Dairy Products (SMEDP) Chapter 6 “Microbiological Count Methods, Standard Plate Count Method” (SMEDP 6); AOAC Official MethodSM966.23Microbiological Methods; and ISO 4833-1:2013 “Microbiology of the food chain—Horizontal method for the enumeration of microorganisms—Part 1: Colony count at 30 degrees C by the pour plate technique.” The validated matrixes included raw chicken breast and raw ground pork for USDA/FSIS MLG 3.02; cream cheese and yogurt drink for SMEDP 6; parsley, vegetable juice, prawns, tuna pate, sandwiches, and pasta salad for AOAC Method 966.23, and raw chicken breast, raw ground pork, cream cheese, yogurt drink, parsley, vegetable juice, prawns, tuna pate, sandwiches, and pasta salad for ISO 4833-1:2013. In each matrix study, five replicates at each of three contamination levels were tested as paired test portions. All 10 matrixes were compared to the appropriate U.S. reference methods under MC-Media Pad ACplus standard-usage conditions (35 ± 1°C for 48 ± 2 h). Across all matrixes, the difference of mean log10 values ranged from –0.43 to 0.44, within the acceptable range of –0.50 to 0.50. The candidate method repeatability SD (sr) varied from 0.03 to 0.23 log10 CFU/g, comparing favorably to the reference method SD, which ranged from 0.06 to 0.30 log10 CFU/g. Seven matrixes were compared to the appropriate U.S. reference methods under MC-Media Pad ACplus rapid-usage conditions (35 ± 1°C for 24 ± 2 h). Of the 21 matrix/concentration combinations, only three instances of difference of mean >0.5 log were observed. The ranges of sr values of the rapid-usage candidate method (0.023–0.324) and the reference method (0.013–0.236) were similar for the seven matrixes tested. All 10 matrixes were compared to the International Organization for Standardization (ISO) reference method under MC-Media Pad ACplus alternate-method conditions (30 ± 1°C for 72 ± 3 h). All 10 matrixes yielded a mean difference between methods of

Two candidate method modifications for the Atlas Listeria Environmental LE Detection Assay were compared with the U.S. Department of Agriculture (USDA)-Food Safety and Inspection Service Microbiology Laboratory Guidebook 8.09 (MLG 8.09) method for detection of Listeria spp. on stainless steel, polyvinyl chloride (PVC), and sealed concrete surfaces. For LE candidate method 1, samples were enriched in FoodChek Actero Listeria Enrichment Media [ALEM; Performance Tested MethodSM (PTM) 111201] at 35 ± 2°C for 18 to 24 h and evaluated for a range of analytical sample volumes. For LE candidate method 2, the current Roka PTM using 90 mL of Half-Fraser broth for enrichment at 35 ± 2°C was evaluated at 24 h with a reduced sample volume. These comparisons were made in multiple studies across the three environmental surfaces. Within each method and study, a total of 5 samples were uninoculated, 20 samples were inoculated with Listeria spp. at a low level to target fractional positivity, and 5 samples were inoculated with Listeria spp. at a high level to approach a probability of detection of 1. Inclusivity and exclusivity studies were also conducted for the LE method in combination with Half-Fraser and ALEM. The Atlas Listeria Environmental LE Detection Assay detected all 50 inclusive organisms, including 25 strains of L. monocytogenes and 5 strains of each of the other five common species of Listeria (L. innocua, L. welshimeri, L. ivanovii, L. seeligeri, and L. grayi) and none of the 30 exclusive organisms across all media and with both 200 and 2000 µL sample volumes. For the LE candidate method 1 studies, no significant differences were observed within the Roka ALEM method at 18, 20, or 24 h and for both the 200 and 2000 µL sample volumes as compared with the paired culture outcome. However, the ALEM method performed significantly better as compared with the unpaired reference method for sealed concrete and stainless steel. For the LE candidate method 2 studies, no significant differences were observed within the Roka HF method at 24 h for the 200 and 2000 µL samples as compared with the paired culture outcomes and unpaired reference method outcomes across the surfaces. The independent laboratory studies observed no significant differences in performance between the USDA/MLG 8.09 reference method and candidate methods 1 or 2, respectively, across the evaluated parameters. Overall, the candidate method 1 modification parameters and candidate method 2 sample parameters for the Atlas Listeria Environmental LE Detection Assay were statistically equivalent to or better than the reference method for detection of Listeria spp. on stainless steel, PVC, and sealed concrete surfaces, providing greater flexibility in method application for end users.

MC-Media Pad SA (formerly known as Sanita-kun SA) is a dry rehydratable film medium for the enumeration of Staphylococcus aureus. The performance of the method in a variety of foods was compared with that of ISO 6888-1:1999, Microbiology of Food and Animal Feeding Stuffs - Horizontal Method for the Enumeration of Coagulase-Positive Staphylococci (Staphylococcus aureus and Other Species) - Part 1: Technique Using Baird–Parker Agar Medium. The validated matrixes included pastrami, a sliced cooked chicken roll, cooked prawns, cold-smoked salmon, pasta salad, sandwich spread, fresh uncooked pasta, infant cereal, custard, and raw-milk Brie cheese. In the matrix study, five replicates at each of three contamination levels were tested as paired test portions. Across all matrixes, the difference in mean log10 values ranged from –0.32 to 0.10, which was within the acceptable range of –0.50 to 0.50. Thus, all 10 matrixes met the acceptance criterion at all concentration levels. Further, only two matrixes, cooked prawns and raw-milk Brie cheese, had 95% confidence limits outside the –0.50 to 0.50 criterion, and these were at the lowest concentration level for each matrix. The candidate method sr varied from 0.03 to 0.22 log10 CFU/g. This compares favorably with the reference method SD, which ranged from 0.06 to 0.30 log10 CFU/g. The candidate and reference methods detected 51 of 53 inclusivity strains, with both methods not detecting the same two strains. The candidate method did not detect any of the 32 exclusivity strains, whereas the reference method did not detect 30 of the 32 exclusivity strains; the 2 strains detected by the reference method were S. delphini and S. hyicus, both developing atypical colonies on Baird–Parker plates. The product consistency study demonstrated no significant difference between lots of product and supported the 1 year shelf life. Robustness testing yielded no significant differences when small variations were made in sample volume, incubation temperature, and incubation time. Thus, the data show equivalent or better performance of the Sanita-kun SA/MC-Media Pad SA method compared with the International Organization for Standardization reference method, in support of AOAC Performance Tested MethodSM certification.

Chronic obstructive pulmonary disease affects 10% of the worldwide population, and the leading genetic cause is α-1 antitrypsin (AAT) deficiency. Due to the complexity of the murine locus, which includes up to six Serpina1 paralogs, no genetic animal model of the disease has been successfully generated until now. Here we create a quintuple Serpina1a–e knockout using CRISPR/Cas9-mediated genome editing. The phenotype recapitulates the human disease phenotype, i.e., absence of hepatic and circulating AAT translates functionally to a reduced capacity to inhibit neutrophil elastase. With age, Serpina1 null mice develop emphysema spontaneously, which can be induced in younger mice by a lipopolysaccharide challenge. This mouse models not only AAT deficiency but also emphysema and is a relevant genetic model and not one based on developmental impairment of alveolarization or elastase administration. We anticipate that this unique model will be highly relevant not only to the preclinical development of therapeutics for AAT deficiency, but also to emphysema and smoking research.

The Applied Biosystems™ RapidFinder™ STEC Detection Workflow (Thermo Fisher Scientific) is a complete protocol for the rapid qualitative detection of Escherichia coli (E. coli) O157:H7 and the “Big 6” non-O157 Shiga-like toxin-producing E. coli (STEC) serotypes (defined as serogroups: O26, O45, O103, O111, O121, and O145). The RapidFinder STEC Detection Workflow makes use of either the automated preparation of PCR-ready DNA using the Applied Biosystems PrepSEQ™ Nucleic Acid Extraction Kit in conjunction with the Applied Biosystems MagMAX™ Express 96-well magnetic particle processor or the Applied Biosystems PrepSEQ Rapid Spin kit for manual preparation of PCR-ready DNA. Two separate assays comprise the RapidFinder STEC Detection Workflow, the Applied Biosystems RapidFinder STEC Screening Assay and the Applied Biosystems RapidFinder STEC Confirmation Assay. The RapidFinder STEC Screening Assay includes primers and probes to detect the presence of stx1 (Shiga toxin 1), stx2 (Shiga toxin 2), eae (intimin), and E. coli O157 gene targets. The RapidFinder STEC Confirmation Assay includes primers and probes for the “Big 6” non-O157 STEC and E. coli O157:H7. The use of these two assays in tandem allows a user to detect accurately the presence of the “Big 6” STECs and E. coli O157:H7. The performance of the RapidFinder STEC Detection Workflow was evaluated in a method comparison study, in inclusivity and exclusivity studies, and in a robustness evaluation. The assays were compared to the U.S. Department of Agriculture (USDA), Food Safety and Inspection Service (FSIS) Microbiology Laboratory Guidebook (MLG) 5.09: Detection, Isolation and Identification of Escherichia coli O157:H7 from Meat Products and Carcass and Environmental Sponges for raw ground beef (73% lean) and USDA/FSIS-MLG 5B.05: Detection, Isolation and Identification of Escherichia coli non-O157:H7 from Meat Products and Carcass and Environmental Sponges for raw beef trim. No statistically significant differences were observed between the reference method and the individual or combined kits forming the candidate assay using either of the DNA preparation kits (manual or automated extraction). For the inclusivity and exclusivity evaluation, the RapidFinder STEC Detection Workflow, comprising both RapidFinder STEC screening and confirmation kits, correctly identified all 50 target organism isolates and correctly excluded all 30 nontarget strains for both of the assays evaluated. The results of these studies demonstrate the sensitivity and selectivity of the RapidFinder STEC Detection Workflow for the detection of E. coli O157:H7 and the “Big 6” STEC serotypes in both raw ground beef and beef trim. The robustness testing demonstrated that minor variations in the method parameters did not impact the accuracy of the assay and highlighted the importance of following the correct incubation temperatures

Five laboratories compared the quantitative recovery of heterotrophic bacteria, yeasts and molds, coliforms, Escherichia coli , Pseudomonas aeruginosa , and Staphylococcus aureus from a variety of naturally contaminated food and water samples, using traditional incubation procedures and a delayed-incubation method. Refrigeration of inoculated media for up to 3 days prior to incubation was shown to be a viable option for many quantitative analyses, but needs to be validated for each application. Some inoculated media withstood refrigeration for up to 7 days prior to incubation without any detrimental effect on the recovery of target cells, while the incubation of other media for similar types of analyses could not be delayed even for 3 days.

A survey was conducted in the Toronto region in 1988/89 to determine the overall microbiological quality of both hot- and cold-smoked, ready-to-eat fish at the retail level. Of the samples collected, 34 were analyzed immediately after purchase (day 0) and 66 were analyzed at day 0 and after 30 d at 4°C. There was a wide variation in initial aerobic colony count (ACC) values, but most (77%) were under 105 CFU/g; 39% were under 103 CFU/g. After storage, just over half (56%) the samples had an ACC greater than 107 CFU/g, but some (12%) had an ACC less than 103 CFU/g. While coliforms were not detected in 70% of samples at day 0, or in 66% after 30 d, four samples initially had over 103 coliforms per g, and after 30 d, 15 samples had over 103 coliforms per g. Escherichia coli , Staphylococcus aureus , Salmonella , and Clostridium botulinum were not detected in any sample at either time. The water activity of samples varied greatly; the average water activity was 0.947, and the range was from 0.727 to 0.997 (n=98). Based on the ACC guidelines for cold-smoked fish of the International Commission on Microbiological Specifications for Foods, four samples would have been rejected at day 0, and 37 at day 30.

Two hundred-fifty freshly formed cheese samples produced by 32 provincially inspected cheese plants were analyzed by 7 regional laboratories of the Ontario Ministry of Health. Coliforms were detected in 61 (25.8%) and fecal coliforms confirmed in 46 (19.5%) of the 236 samples tested, with geometric mean counts per g of 133 and 136, respectively. The incidence of coliforms was highest in Cheddar cheeses made from pasteurized milk (29.7%) compared with the incidence of raw milk cheese (22.0%) and cheese made from milk which had been subjected to sub-pasteurization heat treatment (28.2%). Conversely, the incidence of fecal coliforms was lowest in pasteurized milk cheese (17.8%), followed by raw milk cheese (22.0%) and highest in heat-treated milk cheeses (25.6%). Staphylococcus aureus above the screening level of 1000 per g was not found in any of the 237 samples analyzed. Salmonella spp. were not detected in any of the 250 samples. These results suggest that producers of Cheddar cheese should have no difficulty in meeting the microbiological standards adopted by the Health Protection Branch, Health and Welfare Canada.

The Biotran II automated colony counter was compared with a manual procedure for accuracy in counting bacterial colonies using both spread agar plate and membrane filter techniques. Comparative total bacterial counts of 250 samples (14 food, 124 water and 112 raw milk) were analyzed using the spread agar plate technique. Compared to manual enumeration, the Biotran II was found to be inaccurate for counting bacterial colonies on spread agar plates. Only 60 (24%) and 79 (31.6%) Biotran II counts fell within 10 and 20%, respectively, of the corresponding manual counts. Two samples from each of three river and four effluent sources were analyzed for total aerobic, total coliform, fecal coliform, fecal streptococci and total staphylococci bacterial counts using non-gridded membrane filters. A yellow acetate filter was used to mask the background growth and enhance the target colonies on the membrane filter. However, the method had limited success. Only 12 (20.7%) and 20 (34.5%) Biotran II counts fell within 10 and 20%, respectively, of the corresponding manual counts. Until the effect of background growth can be eliminated, the Biotran II cannot be relied upon to accurately count bacterial colonies on membrane filters.

A collaborative evaluation of the plate loop count technique was undertaken involving 13 laboratories with 29 technologists and 27 plate loops, The log variance of the Plate Loop Count (PLC) was 0.007, compared with a log variance of 0.001 for the reference Standard Plate Count (SPC), both of which fell within the tolerance limit of 0.012 considered acceptable for reproducibility by Standard Methods. The overall log10 mean PLC (1.975) compared favourably with the log10 mean SPC (1.960). Despite this overall image of precision and accuracy of the PLC, comparative data between individual technicians and/or loops was significantly different. Factors which contributed to this inaccuracy and imprecision of the PLC included improper loop calibration and significant variation in technique not only between analysts but also by individual analysts between loops.

Adoption of a streamlined version of the bacterial clustered regular interspersed short palindromic repeat (CRISPR)/Cas9 defense system has accelerated targeted genome engineering. The Streptococcus pyogenes Cas9 protein, directed by a simplified, CRISPR-like single-guide RNA, catalyzes a double-stranded DNA break at a specific genomic site; subsequent repair by end joining can introduce mutagenic insertions or deletions, while repair by homologous recombination using an exogenous DNA template can incorporate new sequences at the target locus. However, the efficiency of Cas9-directed mutagenesis is low in Drosophila melanogaster. Here, we describe a strategy that reduces the time and effort required to identify flies with targeted genomic changes. The strategy uses editing of the white gene, evidenced by altered eye color, to predict successful editing of an unrelated gene-of-interest. The red eyes of wild-type flies are readily distinguished from white-eyed (end-joining-mediated loss of White function) or brown-eyed (recombination-mediated conversion to the whitecoffee allele) mutant flies. When single injected G0 flies produce individual G1 broods, flies carrying edits at a gene-of-interest were readily found in broods in which all G1 offspring carried white mutations. Thus, visual assessment of eye color substitutes for wholesale PCR screening of large numbers of G1 offspring. We find that end-joining-mediated mutations often show signatures of microhomology-mediated repair and that recombination-based mutations frequently involve donor plasmid integration at the target locus. Finally, we show that gap repair induced by two guide RNAs more reliably converts the intervening target sequence, whereas the use of Lig4169 mutants to suppress end joining does not improve recombination efficacy.

The pathogenesis of human type 1 diabetes, characterized by immune-mediated damage of insulin-producing β-cells of pancreatic islets, may involve viral infection. Essential components of the innate immune antiviral response, including type I interferon (IFN) and IFN receptor–mediated signaling pathways, are candidates for determining susceptibility to human type 1 diabetes. Numerous aspects of human type 1 diabetes pathogenesis are recapitulated in the LEW.1WR1 rat model. Diabetes can be induced in LEW.1WR1 weanling rats challenged with virus or with the viral mimetic polyinosinic:polycytidylic acid (poly I:C). We hypothesized that disrupting the cognate type I IFN receptor (type I IFN α/β receptor [IFNAR]) to interrupt IFN signaling would prevent or delay the development of virus-induced diabetes. We generated IFNAR1 subunit–deficient LEW.1WR1 rats using CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats–associated protein 9) genome editing and confirmed functional disruption of the Ifnar1 gene. IFNAR1 deficiency significantly delayed the onset and frequency of diabetes and greatly reduced the intensity of insulitis after poly I:C treatment. The occurrence of Kilham rat virus–induced diabetes was also diminished in IFNAR1-deficient animals. These findings firmly establish that alterations in innate immunity influence the course of autoimmune diabetes and support the use of targeted strategies to limit or prevent the development of type 1 diabetes.

Assurance GDS® MPX ID for Top Shiga toxin-producing Escherichia coli (STEC; MPX ID) was validated according to the AOAC INTERNATIONAL Methods Committee Guidelines for Validation of Microbiological Methods for Foods and Environmental Surfaces as (1) a secondary screening method for specific detection of the Top 6 STEC serogroups (O26, O45, O103, O111, O121, and O145) in raw beef trim, raw ground beef, raw spinach, and on stainless steel; and (2) as a confirmatory method for the identification of pure culture isolates as Top 6 STEC. MPX ID is used in conjunction with the upfront BCS Assurance GDS MPX Top 7 STEC assay. This Performance Tested MethodSM validation has two main parts: Method Developer studies and the Independent Laboratory study. A total of 180 samples and controls were analyzed. Results showed that MPX ID had no statistically significant differences with the reference culture methods for the detection of Top 6 STEC in the food matrixes (raw beef trim, raw ground beef, and raw spinach) and environmental sponges (stainless steel) studied. Inclusivity/exclusivity studies were also conducted. One hundred percent inclusivity among the 50 Top 6 STEC serovars tested and 100% exclusivity for the 30 non-Top 6 STEC organisms tested were demonstrated. For validation of MPX ID as a confirmatory method for isolated colonies, all inclusivity and exclusivity organisms were streaked for isolation onto five STEC plating media: modified rainbow agar, Levine's eosin-methylene blue (L-EMB) agar, rainbow agar with novobiocin and cefixime, and enterohemolysin agar with selective agents as well as trypticase soy agar with yeast extract. These isolated colonies were suspended and analyzed by Assurance GDS MPX Top 7 STEC and MPX ID. MPX ID was able to correctly confirm all inclusivity organisms from all plate types, except two STEC isolates from L-EMB agar plates only in the Independent Laboratory study. All exclusivity organisms were correctly determined by MPX ID as non-Top 6 STEC from the STEC plating media. An additional but separate part of these studies was a comparison of immunomagnetic separation (IMS) efficiency using the Assurance GDS procedure with a PickPen® device and the U.S. Department of Agriculture procedure using the OctoMACS™ Separator device for plating onto chromogenic agar. Results demonstrated the equivalence of the two IMS procedures for plate confirmation of Top 7 STEC.

VereBeef™ Detection Kit, incorporating both multiplex PCR and microarray technologies on a lab-on-chip platform, is intended for qualitative detection and differentiation of Escherichia coli O157:H7, E. coli O26, E. coli O45, E. coli O103, E. coli O111, E. coli O121, E. coli O145, Shiga toxin-producing E. coli (STEC) virulence factors (stx1A, stx2A, eae), and Salmonella species in one test using raw beef trim samples. This product underwent extensive evaluations, including inclusivity-exclusivity, method comparison, robustness, lot-to-lot variability, and stability studies. The inclusivity/exclusivity study demonstrated that VereBeef Detection Kit specifically detects and identifies target analytes without occurrence of false-positive and false-negative detection. In the method comparison study, the performance of the VereBeef Detection Kit was compared with U.S. Department of Agriculture Food Safety and Inspection Service Microbiology Laboratory Guidebook’s methods for target organism detection in raw beef trim using E. coli O157:H7 single inoculation and Salmonella and non-O157 STEC dual inoculation. Data demonstrated equivalence in both methods. The robustness study showed that changesin the test parameters do not impact assay performance. Collectively, VereBeef Detection Kit is able to detect target pathogens in raw beef trim with a minimum enrichment time of 8 h for E. coli O157:H7 detection and 10 h for Salmonella and non-O157 STEC detection.

RNA-based drugs depend on chemical modifications to increase potency and to decrease immunogenicity in vivo. Chemical modification will likely improve the guide RNAs involved in CRISPR-Cas9-based therapeutics as well. Cas9 orthologs are RNA-guided microbial effectors that cleave DNA. Here, we explore chemical modifications at all positions of the crRNA guide and tracrRNA cofactor. We identify several heavily modified versions of crRNA and tracrRNA that are more potent than their unmodified counterparts. In addition, we describe fully chemically modified crRNAs and tracrRNAs (containing no 2′-OH groups) that are functional in human cells. These designs will contribute to Cas9-based therapeutics since heavily modified RNAs tend to be more stable in vivo (thus increasing potency). We anticipate that our designs will improve the use of Cas9 via RNP and mRNA delivery for in vivo and ex vivo purposes., Resistance of gRNA to ubiquitous ribonucleases is required for CRISPR-Cas9-based therapeutics. Here, the authors explore chemical modifications at all positions of the crRNA guide and tracrRNA cofactor, and identify modified versions that are more potent and stable than their unmodified counterparts in editing human cells.

Significance Chronic obstructive pulmonary disease affects 10% of the worldwide population, and the leading genetic cause is a genetic disease, α-1 antitrypsin (AAT) deficiency. Humans have only one gene that codes for the AAT protein, but mice have up to six, which made it impossible for decades to create a mouse model of the disease. Here we succeeded in creating this mouse model using CRISPR technology to target all of the mouse genes at once. Importantly, this mouse model spontaneously develops lung disease and recapitulates many aspects of the human disease. We anticipate that this model will be highly relevant not only to the preclinical development of therapeutics for AAT deficiency, but also to emphysema and smoking research., Chronic obstructive pulmonary disease affects 10% of the worldwide population, and the leading genetic cause is α-1 antitrypsin (AAT) deficiency. Due to the complexity of the murine locus, which includes up to six Serpina1 paralogs, no genetic animal model of the disease has been successfully generated until now. Here we create a quintuple Serpina1a–e knockout using CRISPR/Cas9-mediated genome editing. The phenotype recapitulates the human disease phenotype, i.e., absence of hepatic and circulating AAT translates functionally to a reduced capacity to inhibit neutrophil elastase. With age, Serpina1 null mice develop emphysema spontaneously, which can be induced in younger mice by a lipopolysaccharide challenge. This mouse models not only AAT deficiency but also emphysema and is a relevant genetic model and not one based on developmental impairment of alveolarization or elastase administration. We anticipate that this unique model will be highly relevant not only to the preclinical development of therapeutics for AAT deficiency, but also to emphysema and smoking research.

Rationale: The most prevalent genetic cause of chronic obstructive pulmonary disease is alpha-1 antitrypsin (A1AT) deficiency, a disorder that has yet to be widely modeled in animals because of species-specific differences between rodents and humans. Objectives: To address these challenges, we engineered two A1AT ferret models using zygote gene editing to test the hypothesis that unopposed protease activity within the lung leads to emphysema and bronchitis. Methods: Guide RNAs targeting exon 2 (for knockout) and exon 5 (for Z-allele mutation, Pi*Z) of the ferret A1AT gene were injected into ferret zygotes with Cas9 mRNA. For PI*Z targeting, a short oligonucleotide carrying the mutation was included. Offspring were genotyped and plasma levels of A1AT determined by Western blot before entry into a longitudinal study. Adult A1AT ferrets underwent bronchoscopy and FlexiVent over time to characterize lung disease. Control animals were wild-type (WT) and age, sex, and size matched. Results: A1AT-deficient ferrets spontaneously develop hallmarks of emphysema as early as 3 months when compared with matched WT control ferrets. Over time, A1AT-KO ferrets reached an inspiratory capacity of 117% ± 5% (WT, 57.4 ml; A1AT, 67.5 ml) and compliance of 111% ± 4% (WT, 5.5 ml/cm H(2)O; A1AT, 6.1 ml/cm H(2)O; N = 8 pairs A1AT/WT, P

The CRISPR-Cas9 system is commonly employed in biomedical research; however, the precision of Cas9 is sub-optimal for gene therapy applications that involve editing a large population of cells. Variations on the standard Cas9 system have yielded improvements in the precision of targeted DNA cleavage, but often restrict the range of targetable sequences. It remains unclear whether these variants can limit lesions to a single site within the human genome over a large cohort of treated cells. Here, we demonstrate that fusing a programmable DNA-binding domain (pDBD) to Cas9 combined with the attenuation of Cas9’s inherent DNA binding affinity produces a Cas9-pDBD chimera with dramatically improved precision and increased targeting range. Because the specificity and affinity of this framework is easily tuned, Cas9-pDBDs provide a flexible system that can be tailored to achieve extremely precise genome editing at nearly any genomic locus – characteristics that are ideal for gene therapy applications.

Characterization of cell type specific regulatory networks and elements is a major challenge in genomics, and emerging strategies frequently employ high-throughput genome-wide assays of transcription factor (TF) to DNA binding, histone modifications or chromatin state. However, these experiments remain too difficult/expensive for many laboratories to apply comprehensively to their system of interest. Here, we explore the potential of elucidating regulatory systems in varied cell types using computational techniques that rely on only data of gene expression, low-resolution chromatin accessibility, and TF–DNA binding specificities (‘motifs’). We show that static computational motif scans overlaid with chromatin accessibility data reasonably approximate experimentally measured TF–DNA binding. We demonstrate that predicted binding profiles and expression patterns of hundreds of TFs are sufficient to identify major regulators of ∼200 spatiotemporal expression domains in the Drosophila embryo. We are then able to learn reliable statistical models of enhancer activity for over 70 expression domains and apply those models to annotate domain specific enhancers genome-wide. Throughout this work, we apply our motif and accessibility based approach to comprehensively characterize the regulatory network of fruitfly embryonic development and show that the accuracy of our computational method compares favorably to approaches that rely on data from many experimental assays.

There is growing interest in models of regulatory sequence evolution. However, existing models specifically designed for regulatory sequences consider the independent evolution of individual transcription factor (TF)-binding sites, ignoring that the function and evolution of a binding site depends on its context, typically the cis-regulatory module (CRM) in which the site is located. Moreover, existing models do not account for the gene-specific roles of TF-binding sites, primarily because their roles often are not well understood. We introduce two models of regulatory sequence evolution that address some of the shortcomings of existing models and implement simulation frameworks based on them. One model simulates the evolution of an individual binding site in the context of a CRM, while the other evolves an entire CRM. Both models use a state-of-the art sequence-to-expression model to predict the effects of mutations on the regulatory output of the CRM and determine the strength of selection. We use the new framework to simulate the evolution of TF-binding sites in 37 well-studied CRMs belonging to the anterior-posterior patterning system in Drosophila embryos. We show that these simulations provide accurate fits to evolutionary data from 12 Drosophila genomes, which includes statistics of binding site conservation on relatively short evolutionary scales and site loss across larger divergence times. The new framework allows us, for the first time, to test hypotheses regarding the underlying cis-regulatory code by directly comparing the evolutionary implications of the hypothesis with the observed evolutionary dynamics of binding sites. Using this capability, we find that explicitly modeling self-cooperative DNA binding by the TF Caudal (CAD) provides significantly better fits than an otherwise identical evolutionary simulation that lacks this mechanistic aspect. This hypothesis is further supported by a statistical analysis of the distribution of intersite spacing between adjacent CAD sites. Experimental tests confirm direct homodimeric interaction between CAD molecules as well as self-cooperative DNA binding by CAD. We note that computational modeling of the D. melanogaster CRMs alone did not yield significant evidence to support CAD self-cooperativity. We thus demonstrate how specific mechanistic details encoded in CRMs can be revealed by modeling their evolution and fitting such models to multispecies data.

Regulation of eukaryotic gene transcription is often combinatorial in nature, with multiple transcription factors (TFs) regulating common target genes, often through direct or indirect mutual interactions. Many individual examples of cooperative binding by directly interacting TFs have been identified, but it remains unclear how pervasive this mechanism is during animal development. Cooperative TF binding should be manifest in genomic sequences as biased arrangements of TF-binding sites. Here, we explore the extent and diversity of such arrangements related to gene regulation during Drosophila embryogenesis. We used the DNA-binding specificities of 322 TFs along with chromatin accessibility information to identify enriched spacing and orientation patterns of TF-binding site pairs. We developed a new statistical approach for this task, specifically designed to accurately assess inter-site spacing biases while accounting for the phenomenon of homotypic site clustering commonly observed in developmental regulatory regions. We observed a large number of short-range distance preferences between TF-binding site pairs, including examples where the preference depends on the relative orientation of the binding sites. To test whether these binding site patterns reflect physical interactions between the corresponding TFs, we analyzed 27 TF pairs whose binding sites exhibited short distance preferences. In vitro protein–protein binding experiments revealed that >65% of these TF pairs can directly interact with each other. For five pairs, we further demonstrate that they bind cooperatively to DNA if both sites are present with the preferred spacing. This study demonstrates how DNA-binding motifs can be used to produce a comprehensive map of sequence signatures for different mechanisms of combinatorial TF action.

Cys2-His2 zinc finger proteins (ZFPs) are the largest group of transcription factors in higher metazoans. A complete characterization of these ZFPs and their associated target sequences is pivotal to fully annotate transcriptional regulatory networks in metazoan genomes. As a first step in this process, we have characterized the DNA-binding specificities of 129 zinc finger sets from Drosophila using a bacterial one-hybrid system. This data set contains the DNA-binding specificities for at least one encoded ZFP from 70 unique genes and 23 alternate splice isoforms representing the largest set of characterized ZFPs from any organism described to date. These recognition motifs can be used to predict genomic binding sites for these factors within the fruit fly genome. Subsets of fingers from these ZFPs were characterized to define their orientation and register on their recognition sequences, thereby allowing us to define the recognition diversity within this finger set. We find that the characterized fingers can specify 47 of the 64 possible DNA triplets. To confirm the utility of our finger recognition models, we employed subsets of Drosophila fingers in combination with an existing archive of artificial zinc finger modules to create ZFPs with novel DNA-binding specificity. These hybrids of natural and artificial fingers can be used to create functional zinc finger nucleases for editing vertebrate genomes.

Motivation: Recognition models for protein-DNA interactions, which allow the prediction of specificity for a DNA-binding domain based only on its sequence or the alteration of specificity through rational design, have long been a goal of computational biology. There has been some progress in constructing useful models, especially for C2H2 zinc finger proteins, but it remains a challenging problem with ample room for improvement. For most families of transcription factors the best available methods utilize k-nearest neighbor (KNN) algorithms to make specificity predictions based on the average of the specificities of the k most similar proteins with defined specificities. Homeodomain (HD) proteins are the second most abundant family of transcription factors, after zinc fingers, in most metazoan genomes, and as a consequence an effective recognition model for this family would facilitate predictive models of many transcriptional regulatory networks within these genomes. Results: Using extensive experimental data, we have tested several machine learning approaches and find that both support vector machines and random forests (RFs) can produce recognition models for HD proteins that are significant improvements over KNN-based methods. Cross-validation analyses show that the resulting models are capable of predicting specificities with high accuracy. We have produced a web-based prediction tool, PreMoTF (Predicted Motifs for Transcription Factors) (http://stormo.wustl.edu/PreMoTF), for predicting position frequency matrices from protein sequence using a RF-based model. Contact: stormo@wustl.edu

FlyFactorSurvey (http://pgfe.umassmed.edu/TFDBS/) is a database of DNA binding specificities for Drosophila transcription factors (TFs) primarily determined using the bacterial one-hybrid system. The database provides community access to over 400 recognition motifs and position weight matrices for over 200 TFs, including many unpublished motifs. Search tools and flat file downloads are provided to retrieve binding site information (as sequences, matrices and sequence logos) for individual TFs, groups of TFs or for all TFs with characterized binding specificities. Linked analysis tools allow users to identify motifs within our database that share similarity to a query matrix or to view the distribution of occurrences of an individual motif throughout the Drosophila genome. Together, this database and its associated tools provide computational and experimental biologists with resources to predict interactions between Drosophila TFs and target cis-regulatory sequences.

DNA damage or unprotected telomeres can trigger apoptosis via signaling pathways that directly sense abnormal DNA structures and activate the p53 transcription factor. We describe a p53-independent mechanism that acts in parallel to the canonical DNA damage response pathway in Drosophila to induce apoptosis after exposure to ionizing radiation. Following recovery from damage-induced cell cycle arrest, p53 mutant cells activate the JNK pathway and expression of the pro-apoptotic gene hid. Mutations in grp, a cell cycle checkpoint gene, and puc, a negative regulator of the JNK pathway, sensitize p53 mutant cells to ionizing radiation (IR)-induced apoptosis. Induction of chromosome aberrations by DNA damage generates cells with segmental aneuploidy and heterozygous for mutations in ribosomal protein genes. p53-independent apoptosis limits the formation of these aneuploid cells following DNA damage. We propose that reduced copy number of haploinsufficient genes following chromosome damage activates apoptosis and helps maintain genomic integrity.