Comprehensive deletion landscape of CRISPR-Cas9 identifies minimal RNA-guided DNA-binding modules

Proteins evolve through the modular rearrangement of elements known as domains. Extant, multidomain proteins are hypothesized to be the result of domain accretion, but there has been limited experimental validation of this idea. Here, we introduce a technique for genetic minimization by iterative size-exclusion and recombination (MISER) for comprehensively making all possible deletions of a protein. Using MISER, we generate a deletion landscape for the CRISPR protein Cas9. We find that the catalytically-dead Streptococcus pyogenes Cas9 can tolerate large single deletions in the REC2, REC3, HNH, and RuvC domains, while still functioning in vitro and in vivo, and that these deletions can be stacked together to engineer minimal, DNA-binding effector proteins. In total, our results demonstrate that extant proteins retain significant modularity from the accretion process and, as genetic size is a major limitation for viral delivery systems, establish a general technique to improve genome editing and gene therapy-based therapeutics.

The biogeography of Streptomyces in New Zealand enabled by high-throughput sequencing of genus-specific rpoB amplicons

We evaluated Streptomyces biogeography in soils along a 1200 km latitudinal transect across New Zealand (NZ). Streptomyces diversity was examined using high-throughput sequencing of rpoB amplicons generated with a Streptomyces specific primer set. We detected 1287 Streptomyces rpoB operational taxonomic units (OTUs) with 159 ± 92 (average ± SD) rpoB OTUs per site. Only 12% (n = 149) of these OTUs matched rpoB sequences from cultured specimens (99% nucleotide identity cutoff). Streptomyces phylogenetic diversity (Faith's PD) was correlated with soil pH, mean annual temperature and plant community richness (Spearman's r: 0.77, 0.64 and -0.79, respectively; P < 0.05), but not with latitude. In addition, soil pH and plant community richness both explained significant variation in Streptomyces beta diversity. Streptomyces communities exhibited both high dissimilarity and strong dominance of one or a few species at each site. Taken together, these results suggest that dispersal limitation due to competitive interactions limits the colonization success of spores that relocate to new sites. Cultivated Streptomyces isolates represent a major source of clinically useful antibiotics, but only a small fraction of extant diversity within the genus have been identified and most species of Streptomyces have yet to be described.

Rapid and Programmable Protein Mutagenesis Using Plasmid Recombineering

Comprehensive and programmable protein mutagenesis is critical for understanding structure-function relationships and improving protein function. There is thus a need for robust and unbiased molecular biological approaches for the construction of the requisite comprehensive protein libraries. Here we demonstrate that plasmid recombineering is a simple and robust in vivo method for the generation of protein mutants for both comprehensive library generation as well as programmable targeting of sequence space. Using the fluorescent protein iLOV as a model target, we build a complete mutagenesis library and find it to be specific and comprehensive, detecting 99.8% of our intended mutations. We then develop a thermostability screen and utilize our comprehensive mutation data to rapidly construct a targeted and multiplexed library that identifies significantly improved variants, thus demonstrating rapid protein engineering in a simple protocol.

A Comprehensive Analysis of Replicative Lifespan in 4,698 Single-Gene Deletion Strains Uncovers Conserved Mechanisms of Aging

Many genes that affect replicative lifespan (RLS) in the budding yeast Saccharomyces cerevisiae also affect aging in other organisms such as C. elegans and M. musculus. We performed a systematic analysis of yeast RLS in a set of 4,698 viable single-gene deletion strains. Multiple functional gene clusters were identified, and full genome-to-genome comparison demonstrated a significant conservation in longevity pathways between yeast and C. elegans. Among the mechanisms of aging identified, deletion of tRNA exporter LOS1 robustly extended lifespan. Dietary restriction (DR) and inhibition of mechanistic Target of Rapamycin (mTOR) exclude Los1 from the nucleus in a Rad53-dependent manner. Moreover, lifespan extension from deletion of LOS1 is nonadditive with DR or mTOR inhibition, and results in Gcn4 transcription factor activation. Thus, the DNA damage response and mTOR converge on Los1-mediated nuclear tRNA export to regulate Gcn4 activity and aging.

Basal subtype, as approximated by triple-negative phenotype, is associated with locoregional recurrence in a case-control study of women with 0-3 positive lymph nodes after mastectomy

PURPOSE

Basal subtype, as approximated by the triple-negative phenotype (ER-PR-Her2-), has correlated with higher LRR in recent studies. Indications for postmastectomy RT (PMRT) in women with 0-3 positive lymph nodes remain unclear. We evaluated the importance of biologic subtype in a cohort of women with LRR after mastectomy.

METHODS

We identified 22 women with 0-3 positive lymph nodes at our institution who were initially treated with mastectomy (without post-mastectomy radiation), suffered LRRs, and had paraffin-embedded tissue blocks from the primary mastectomy specimen available for staining. None of these women received PMRT. We case-control matched these to 29 women with 0-3 positive nodes who had mastectomy (no PMRT) and remained without evidence of disease at last follow-up and had available primary specimens for processing. We matched controls for age (±3 years) and follow-up duration (<5 year vs. more). Paraffin-embedded specimens were used to construct a triple-redundant tissue microarray. We used conditional logistic regressions to study the association between each predictor and LRR. Results were summarized based on odds ratio (OR).

RESULTS

On univariate analysis, ER+, PR+, or the combination was strongly associated with lower odds of LRR. Basal subtype, as approximated by ER-PR-Her2- (TN), was associated with higher LRR (OR 8.5, p = 0.048). Use of chemotherapy also was associated with lower LRR (OR 0.126, p = 0.0073).

CONCLUSIONS

Our data are concordant with reports from others demonstrating that TN phenotype is associated with higher LRR and can be considered along with other predictors of LRR when selecting women for PMRT.

Androgen ablation augments prostate cancer vaccine immunogenicity only when applied after immunization

BACKGROUND

Androgen ablation (AA) causes apoptosis of normal and neoplastic prostate cells. It is a standard treatment for advanced prostate cancer. Androgen ablation-mediated immunological effects include bone marrow hyperplasia, thymic regeneration, T and B cell lymphopoeisis and restoration of age-related peripheral T cell dysfunction. Androgens also regulate the transcription of several cytokines. Dendritic cells (DC) are the most potent antigen presenting cells that can activate antigen-specific naïve T cells. Despite myriad clinical trials involving DC-based prostate cancer immunotherapies, the effects of AA on DC function remain largely uncharacterized. Therefore, we investigated the effects of AA on DC and whether it could improve the efficacy of prostate cancer immunotherapy.

METHODS

Cytokine expression changes due to AA were quantified by multiplex ELISA. Flow cytometry was used to assess AA-mediated effects on DC maturation and expression of costimulatory markers. Mixed leukocyte reactions and cell-mediated lysis assays elucidated the role of androgens in DC function. The effect of AA on the efficacy of vaccination against a prostate tumor-associated antigen was tested using Elispot assays.

RESULTS

Androgen ablation increased dendritic cell maturation and costimulatory marker expression, but had no effect on DC costimulatory function. However, DC isolated from castrated mice increased the expression of key cytokines by antigen-experienced T cells while decreasing their expression in naïve cells. Finally, androgen ablation improved immune responses to vaccination only when applied after immunization.

CONCLUSION

Androgen ablation causes differential effects of DC on primary and secondary T cell responses, thus augmenting vaccine immunogenicity only when applied after immunization.

Immunological consequences of using three different clinical/laboratory techniques of emulsifying peptide-based vaccines in incomplete Freund's adjuvant

Incomplete Freund's adjuvant (IFA) serves as a carrier for water-in-oil emulsion (W/O) vaccines. The stability of such emulsions greatly affects vaccine safety and efficacy since continued presence of antigen depots at lymphoid organs releasing low-level antigens is known to stimulate a potent immune response and high-level systemic release of antigens can lead to tolerance. W/O emulsions for the purpose of clinical and laboratory peptide-based vaccinations have been prepared using the techniques of syringe extrusion, vortex or high-speed homogenization. There is no consensus in the field over which technique would be best to use and no immunological data are available that compare the three techniques. In this study, we compared the immune responses induced by a peptide-based vaccine prepared using vortex, syringe-extrusion and homogenization. The vaccination led to tumor rejection by mice vaccinated with the peptide-based vaccine prepared using all three techniques. The immunological data from the in vivo cytotoxicity assay showed a trend for lower responses and a higher variability and greater range in the immune responses induced by a vaccine that was emulsified by the vortex or homogenizer techniques as compared to the syringe-extrusion technique. There were statistically significant lower numbers of IFNγ-secreting cells induced when the mice were vaccinated with a peptide-based vaccine emulsion prepared using the vortex compared to the syringe-extrusion technique. At a suboptimal vaccine dose, the mice vaccinated with a peptide-based vaccine emulsion prepared using the vortex technique had the largest tumors compared to the syringe-extrusion or the homogenizer technique. In the setting of a busy pharmacy that prepares peptide-based vaccine emulsions for clinical studies, the vortex technique can still be used but we urge investigators to take special care in their choice of mixing vessels for the vortex technique as that can influence the stability of the emulsion. However, in instances where the optimal dose is unknown, we caution investigators against using the vortex technique to prepare the peptide-based vaccine emulsions. Overall, we report that all three techniques can be used to prepare peptide-based vaccine emulsions under optimal dose conditions and we discuss important details regarding the proper preparation of the emulsions.

Lack of correlation between different measurements of proprioception in the knee

Current methods of measurement of proprioceptive function depend on the ability to detect passive movement (kinaesthesia) or the awareness of joint position (joint position sense, JPS). However, reports of proprioceptive function in healthy and pathological joints are quite variable, which may be due to the different methods used. We have compared the validity of several frequently used methods to quantify proprioception. Thirty healthy subjects aged between 24 and 72 years underwent five established tests of proprioception. Two tests were used for the measurement of kinaesthesia (KT1 and KT2). Three tests were used for the measurement of JPS, a passive reproduction test (JPS1), a relative reproduction test (JPS2) and a visual estimation test (JPS3). There was no correlation between the tests for kinaesthesia and JPS or between the different JPS tests. There was, however, a significant correlation between the tests for kinaesthesia (r = 0.86). We conclude therefore that a subject with a given result in one test will not automatically obtain a similar result in another test for proprioception. Since they describe different functional proprioceptive attributes, proprioceptive ability cannot be inferred from independent tests of either kinaesthesia or JPS.

Chemoradiation as primary or adjuvant treatment for locally advanced carcinoma of the vulva

PURPOSE

To determine the impact of primary or adjuvant chemotherapy and radiation (CRT) on the survival rates of patients with locally advanced vulvar carcinoma.

METHODS AND MATERIALS

Between 1973 and 1998, 54 patients with vulvar cancer were treated with radiation therapy, among which 20 received CRT, while 34 patients received radiation therapy (RT) alone. Of the 20 patients, 14 were treated for primary or recurrent disease (pCRT), and 6 after radical vulvectomy for high-risk disease (aCRT). Of the 34 patients, 12 were treated primarily (pRT) and 22 received adjuvant treatment (aRT). Chemotherapy consisted of 2 courses of 5-fluorouracil (5-FU) and mitomycin C administered during RT. Six patients received cisplatin in place of mitomycin C. In CRT groups, radiation was administered to the vulva, pelvic, and inguinal lymph nodes to a median dose of 45 Gy with additional 6-17 Gy to gross disease. In RT groups, the median dose to the microscopic diseases was 45 Gy. Nine patients received external beam boost and 16 patients received supplementary brachytherapy in the forms of (226)Ra or (241)Am plaques to sites of macroscopic disease.

RESULTS

Overall survival was superior in the patients treated with pCRT versus pRT with statistical significance (p = 0.04). There was also a statistically significant improvement in disease-specific (p = 0.03) and relapse-free survival (p = 0.01) favoring pCRT. No statistically significant trends of improved survival rates favoring aCRT over aRT were observed.

CONCLUSION

Concurrent radiation therapy and chemotherapy decreases local relapse rate, improves disease-specific and overall survival over RT alone as primary treatment for locally advanced vulvar cancer.

Hodgkin's disease with spinal cord compression. A case report and a review of the literature

BACKGROUND

Spinal cord compression is a rare complication of Hodgkin's disease, occurring in only 5% of cases, usually in the setting of progressive, advanced disease. As the initial symptom of Hodgkin's disease, it is extremely rare, with only a few cases reported in the literature.

METHODS

A case report of a 46-year-old man who presented with signs and symptoms of spinal cord compression and was found to have an extradural mass in the cervical and thoracic spine is described. Biopsy revealed Hodgkin's disease. This case report represents a unique case of a patient with Hodgkin's disease presenting with epidural disease, with spinal cord compression as the only apparent site of initial clinical involvement. A review of the literature of patients with Hodgkin's disease presenting with spinal cord compression from 1970 to the present is presented.

RESULTS

The patient, whom we report, received chemotherapy followed by external beam radiation therapy and achieved complete resolution of symptoms and a complete response by radiologic criteria. Based on a review of the literature, Hodgkin's disease involving the spinal epidural space is very responsive to radiation therapy and chemotherapy with a good prognosis for both functional recovery (86%), complete response (61%), and long term survival.

CONCLUSIONS

Chemotherapy and/or radiation therapy is successful treatment for Hodgkin's disease presenting with spinal cord compression. For the rare patient who presents with spinal cord compression as the initial symptom of Hodgkin's disease, the therapeutic options include chemotherapy alone, radiation therapy alone, or combined modality therapy.

Evaluation of reference ranges for fatty acids in serum

Long chain fatty acid fractionation has become a valuable tool in the management of patients maintained on total parenteral nutrition. While many clinicians prefer to use absolute concentrations to monitor a patient's fatty acid status, reference ranges are not available. Previous reference range studies reported values in terms of percentages only and calculated ranges parametrically. However, due to the non-Gaussian distributions of some serum fatty acids, it is necessary to calculate reference ranges non-parametrically. Serum from blood donors (n = 130) were collected and analyzed for total fatty acids by gas-liquid chromatography. Results for each of the fatty acids were calculated both as a concentration and as a percentage of the total fatty acids measured.

Evaluation of the Behring Nephelometer for detection of low level urinary albumin

Mildly increased urinary albumin excretion rates and concentrations, below the quantity normally detected by conventional urinary protein and albumin methods, have prognostic significance for the development of nephropathy in patients with diabetes mellitus. The authors evaluated the automated Behring Nephelometer using Behring reagents for the detection of low level urinary albumin. Within run coefficients of variation (CVs, N = 20) are 1.7%, 1.3%, and 2.4% at mean urinary albumin levels of 16, 70, and 217 mg/L, respectively. Between run CVs (N = 20) are 4.5%, 2.6%, and 4.4% at mean albumin levels of 19, 71, and 239 mg/L, respectively. The method is sensitive to 3 mg/L. Hemoglobin, immunoglobulins, bilirubin, urea, and radiographic contrast media beyond a few hours of injection show no significant interference at levels normally expected from clinical specimens. Analysis is unaffected by pH within the physiologic range. Most urine specimens are stable for at least eight days when refrigerated at 4 degrees C. Specimen centrifugation before analysis is essential to avoid a negative bias that occurs when analyzing uncentrifuged refrigerated samples. Preanalytical freezing produces results higher than those observed in fresh or refrigerated samples. The authors conclude that automated nephelometry using the Behring Nephelometer is a convenient, simple, and accurate technique for the determination of low level urinary albumin.

Definitive characterization of human thymine glycol N-glycosylase activity

An N-glycosylase activity that released cis-[3H]-5,6-dihydroxy-5,6-dihydrothymine (thymine glycol, TG) from chemically oxidized poly(dA-[3H]dT) was unambiguously characterized both in extracts of HeLa cells and in purified Escherichia coli endonuclease III. This was accomplished by use of microderivatization procedure that quantitatively converted cis-TG to 5-hydroxy-5-methylhydantoin (HMH). The reaction products were analyzed by high-pressure liquid chromatography before and after derivatization by using cis-[14C]TG and [14C]HMH, which had been independently synthesized, as reference compounds. This technique facilitated construction of a v/[E]t plot for the enzyme activity in HeLa cells, permitting estimation of its specific activity. The results obtained prove the existence of both human and bacterial N-glycosylase activities that effect removal of TG from DNA.

Activity rhythms in the Mongolian gerbil under natural light conditions

Male and female Mongolian gerbils (Meriones unguiculatus) were maintained from birth under natural light conditions. They were observed in adulthood over 24-hour periods for the occurrence of locomotion, digging, scrabbling, sleeping, grooming, eating and drinking. The animals exhibited a crepuscular activity rhythm in all behaviors except drinking. Peak activity levels occurred at approximately 6-8 a.m. and 6-8 p.m., the hours of day which encompassed dawn and dusk. There were no sex differences in the rhythmic cycling of activity. Results are discussed in relation to basal metabolic rate of the animals, nutritional requirements and ambient temperature conditions.