Flow Cytometry: The Glass Is Half Full.

Accompanied by a historical perspective of the field of cytometry, this introductory chapter provides a broad view of what flow cytometry can do; hence, the glass is half full.

Rabies in an imported dog, Ontario, Canada, 2022.

Importation of rabies-infected dogs results in significant and costly public and animal health risks. In January 2022, a dog in Ontario, Canada, which was imported from Iran in June 2021, developed rabies, leading to an extensive public health investigation and administration of rabies post-exposure prophylaxis to 37 individuals. The dog was infected with a rabies virus variant known to circulate in Iran. This is the second reported case of a rabies-infected dog imported into Canada in 2021 from a high-risk country for canine mediated rabies. This case emphasizes the need for public education regarding the risks associated with importing dogs from high-risk countries for canine-mediated rabies and the benefits of establishing a public health team specializing in rabies exposure investigations.

Genetic modification of flavone biosynthesis in rice enhances biofilm formation of soil diazotrophic bacteria and biological nitrogen fixation.

Improving biological nitrogen fixation (BNF) in cereal crops is a long-sought objective; however, no successful modification of cereal crops showing increased BNF has been reported. Here, we described a novel approach in which rice plants were modified to increase the production of compounds that stimulated biofilm formation in soil diazotrophic bacteria, promoted bacterial colonization of plant tissues and improved BNF with increased grain yield at limiting soil nitrogen contents. We first used a chemical screening to identify plant-produced compounds that induced biofilm formation in nitrogen-fixing bacteria and demonstrated that apigenin and other flavones induced BNF. We then used CRISPR-based gene editing targeting apigenin breakdown in rice, increasing plant apigenin contents and apigenin root exudation. When grown at limiting soil nitrogen conditions, modified rice plants displayed increased grain yield. Biofilm production also modified the root microbiome structure, favouring the enrichment of diazotrophic bacteria recruitment. Our results support the manipulation of the flavone biosynthetic pathway as a feasible strategy for the induction of biological nitrogen fixation in cereals and a reduction in the use of inorganic nitrogen fertilizers.

Draft genome sequence of Solanum aethiopicum provides insights into disease resistance, drought tolerance, and the evolution of the genome.

BACKGROUND: The African eggplant (Solanum aethiopicum) is a nutritious traditional vegetable used in many African countries, including Uganda and Nigeria. It is thought to have been domesticated in Africa from its wild relative, Solanum anguivi. S. aethiopicum has been routinely used as a source of disease resistance genes for several Solanaceae crops, including Solanum melongena. A lack of genomic resources has meant that breeding of S. aethiopicum has lagged behind other vegetable crops. RESULTS: We assembled a 1.02-Gb draft genome of S. aethiopicum, which contained predominantly repetitive sequences (78.9%). We annotated 37,681 gene models, including 34,906 protein-coding genes. Expansion of disease resistance genes was observed via 2 rounds of amplification of long terminal repeat retrotransposons, which may have occurred ∼1.25 and 3.5 million years ago, respectively. By resequencing 65 S. aethiopicum and S. anguivi genotypes, 18,614,838 single-nucleotide polymorphisms were identified, of which 34,171 were located within disease resistance genes. Analysis of domestication and demographic history revealed active selection for genes involved in drought tolerance in both "Gilo" and "Shum" groups. A pan-genome of S. aethiopicum was assembled, containing 51,351 protein-coding genes; 7,069 of these genes were missing from the reference genome. CONCLUSIONS: The genome sequence of S. aethiopicum enhances our understanding of its biotic and abiotic resistance. The single-nucleotide polymorphisms identified are immediately available for use by breeders. The information provided here will accelerate selection and breeding of the African eggplant, as well as other crops within the Solanaceae family.

African Orphan Crops Consortium (AOCC): status of developing genomic resources for African orphan crops.

MAIN CONCLUSION: The African Orphan Crops Consortium (AOCC) successfully initiated the ambitious genome sequencing project of 101 African orphan crops/trees with 6 genomes sequenced, 6 near completion, and 20 currently in progress. Addressing stunting, malnutrition, and hidden hunger through nutritious, economic, and resilient agri-food system is one of the major agricultural challenges of this century. As sub-Saharan Africa harbors a large portion of the severely malnourished population, the African Orphan Crops Consortium (AOCC) was established in 2011 with an aim to reduce stunting and malnutrition by providing nutritional security through improving locally adapted nutritious, but neglected, under-researched or orphan African food crops. Foods from these indigenous or naturalized crops and trees are rich in minerals, vitamins, and antioxidant, and are an integral part of the dietary portfolio and cultural, social, and economic milieu of African farmers. Through stakeholder consultations supported by the African Union, 101 African orphan and under-researched crop species were prioritized to mainstream into African agri-food systems. The AOCC, through a network of international-regional-public-private partnerships and collaborations, is generating genomic resources of three types, i.e., reference genome sequence, transcriptome sequence, and re-sequencing 100 accessions/species, using next-generation sequencing (NGS) technology. Furthermore, the University of California Davis African Plant Breeding Academy under the AOCC banner is training 150 lead African scientists to breed high yielding, nutritious, and climate-resilient (biotic and abiotic stress tolerant) crop varieties that meet African farmer and consumer needs. To date, one or more forms of sequence data have been produced for 60 crops. Reference genome sequences for six species have already been published, 6 are almost near completion, and 19 are in progress.

The draft genomes of five agriculturally important African orphan crops.

BACKGROUND: The expanding world population is expected to double the worldwide demand for food by 2050. Eighty-eight percent of countries currently face a serious burden of malnutrition, especially in Africa and south and southeast Asia. About 95% of the food energy needs of humans are fulfilled by just 30 species, of which wheat, maize, and rice provide the majority of calories. Therefore, to diversify and stabilize the global food supply, enhance agricultural productivity, and tackle malnutrition, greater use of neglected or underutilized local plants (so-called orphan crops, but also including a few plants of special significance to agriculture, agroforestry, and nutrition) could be a partial solution. RESULTS: Here, we present draft genome information for five agriculturally, biologically, medicinally, and economically important underutilized plants native to Africa: Vigna subterranea, Lablab purpureus, Faidherbia albida, Sclerocarya birrea, and Moringa oleifera. Assembled genomes range in size from 217 to 654 Mb. In V. subterranea, L. purpureus, F. albida, S. birrea, and M. oleifera, we have predicted 31,707, 20,946, 28,979, 18,937, and 18,451 protein-coding genes, respectively. By further analyzing the expansion and contraction of selected gene families, we have characterized root nodule symbiosis genes, transcription factors, and starch biosynthesis-related genes in these genomes. CONCLUSIONS: These genome data will be useful to identify and characterize agronomically important genes and understand their modes of action, enabling genomics-based, evolutionary studies, and breeding strategies to design faster, more focused, and predictable crop improvement programs.

Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota.

Plants are associated with a complex microbiota that contributes to nutrient acquisition, plant growth, and plant defense. Nitrogen-fixing microbial associations are efficient and well characterized in legumes but are limited in cereals, including maize. We studied an indigenous landrace of maize grown in nitrogen-depleted soils in the Sierra Mixe region of Oaxaca, Mexico. This landrace is characterized by the extensive development of aerial roots that secrete a carbohydrate-rich mucilage. Analysis of the mucilage microbiota indicated that it was enriched in taxa for which many known species are diazotrophic, was enriched for homologs of genes encoding nitrogenase subunits, and harbored active nitrogenase activity as assessed by acetylene reduction and 15N2 incorporation assays. Field experiments in Sierra Mixe using 15N natural abundance or 15N-enrichment assessments over 5 years indicated that atmospheric nitrogen fixation contributed 29%-82% of the nitrogen nutrition of Sierra Mixe maize.

Lasers for Flow Cytometry: Current and Future Trends.

Lasers are the principal light sources for flow cytometers. Virtually all cytometers are equipped with at least one (and often many more) lasers. This unit covers the various types of lasers available and the qualities that make them suitable or unsuitable for use in flow cytometers. Also included is a discussion of future directions, particularly in the area of tunable laser development. Practical tips are provided for building multilaser cytometer systems. © 2018 by John Wiley & Sons, Inc.

Flow Cytometry: The Glass Is Half Empty.

In hopes of broadening the reader's perspective, this closing chapter discusses what flow cytometry cannot do; hence, the glass is half empty. Alternative methods using affordable and sustainable simple imaging cytometers are presented.

Flow Cytometry: The Glass Is Half Full.

Accompanied by a historical perspective of the field of cytometry, this introductory chapter provides a broad view of what flow cytometry can do; hence, the glass is half full.

Impact of Cataract Surgery during Treatment with Ranibizumab in Patients with Diabetic Macular Edema.

PURPOSE: To determine how best-corrected visual acuity (BCVA) was affected by cataract surgery in patients with diabetic macular edema (DME) who were treated with ranibizumab during the RIDE/RISE phase III trials. DESIGN: Post hoc analysis of data from RIDE and RISE, 2 phase III, parallel, randomized, multicenter, double-masked trials (clinicaltrials.gov identifiers, NCT00473382 and NCT00473330). PARTICIPANTS: Patients with DME (N = 759) who were randomized 1:1:1 to monthly intravitreal ranibizumab 0.3 mg or 0.5 mg, or sham injections for 24 months. METHODS: Patient records in the electronic RIDE/RISE study database were examined for cataract surgeries using the terms "cataract extraction," "cataract removal," "cataract surgery," "lens implant," and "lensectomy." The last study visit immediately before cataract surgery served as the redefined baseline to examine subsequent BCVA changes. The t test was performed to compare times to cataract surgery for the sham and pooled ranibizumab groups. MAIN OUTCOME MEASURES: Mean change in BCVA from redefined baseline to 1, 2, and 3 months (±15 days) after surgery. RESULTS: Among study eyes that underwent cataract surgery, mean BCVA at original study baseline was 54.6 letters in the pooled ranibizumab arms and 56.6 letters in the sham arm (approximate Snellen equivalent 20/80). At the redefined presurgery baseline, mean BCVA was 54.2 letters for the pooled ranibizumab group and 46.6 letters for the sham-treated study eyes. Compared with the redefined baseline, at 1 month after surgery, mean BCVA changes were +10.6 letters for ranibizumab-treated patients and +10.3 letters for sham-treated patients. Compared with the original baseline, at 1 month after surgery, on average, ranibizumab-treated study eyes experienced mean BCVA improvement (+11.3 letters), whereas sham-treated eyes (-0.5 letters) and fellow eyes (+1.8 and +1.7 letters for ranibizumab and sham, respectively) had a mean BCVA similar to the original baseline. CONCLUSIONS: In patients undergoing ranibizumab treatment for DME and who had cataract surgery, an average of 2 lines of vision were gained from the last visit before surgery to 1 month after surgery.

The Gut Microbiota, Food Science, and Human Nutrition: A Timely Marriage.

Analytic advances are enabling more precise definitions of the molecular composition of key food staples incorporated into contemporary diets and how the nutrient landscapes of these staples vary as a function of cultivar and food processing methods. This knowledge, combined with insights about the interrelationship between consumer microbiota configurations and biotransformation of food ingredients, should have a number of effects on agriculture, food production, and strategies for improving the nutritional value of foods and health status. These effects include decision-making about which cultivars of current or future food staples to incorporate into existing and future food systems, and which components of waste streams from current or future food manufacturing processes have nutritional value that is worth capturing. They can also guide which technologies should be applied, or need to be developed, to produce foods that support efficient microbial biotransformation of their ingredients into metabolic products that sustain health.

Arsenic from community water fluoridation: quantifying the effect.

Community water fluoridation is a WHO recommended strategy to prevent dental carries. One debated concern is that hydrofluorosilicic acid, used to fluoridate water, contains arsenic and poses a health risk. This study was undertaken to determine if fluoridation contributes to arsenic in drinking water, to estimate the amount of additional arsenic associated with fluoridation, and compare this to the National Sanitation Foundation/American National Standards Institute (NSF/ANSI) standard and estimates from other researchers. Using surveillance data from Ontario drinking water systems, mixed effects linear regression was performed to examine the effect of fluoridation status on the difference in arsenic concentration between raw water and treated water samples. On average, drinking water treatment was found to reduce arsenic levels in water in both fluoridated and non-fluoridated systems by 0.2 µg/L. However, fluoridated systems were associated with an additional 0.078 µg/L (95% CI 0.021, 0.136) of arsenic in water when compared to non-fluoridated systems (P = 0.008) while controlling for raw water arsenic concentrations, types of treatment processes, and source water type. Our estimate is consistent with concentrations expected from other research and is less than 10% of the NSF/ANSI standard of 1 µg/L arsenic in water. This study provides further information to inform decision-making regarding community water fluoridation.

Patterns of Early and Delayed Visual Response to Ranibizumab Treatment for Neovascular Age-Related Macular Degeneration.

IMPORTANCE: Understanding the range of temporal responses to ranibizumab is critical for the assessment of individualized treatment regimens for neovascular age-related macular degeneration. OBJECTIVE: To examine patterns of visual and anatomical response to ranibizumab treatment. DESIGN, SETTING, AND PARTICIPANTS: This study is a retrospective subanalysis of HARBOR (a phase 3, double-masked, multicenter, randomized, active treatment-controlled study of the efficacy and safety of 0.5 mg and 2.0 mg ranibizumab administered monthly or on an as-needed basis (PRN) in patients with subfoveal neovascular age-related macular degeneration). A total of 1097 patients with neovascular age-related macular degeneration were randomized to intravitreal ranibizumab, 0.5 or 2.0 mg, administered monthly or as needed (PRN) with monthly monitoring. Of the 1097 patients, 1057 were included in the analysis for early responders (best-corrected visual acuity [BCVA] obtained at baseline and month 3), and 988 patients were included in the analysis for delayed responders (BCVA obtained at baseline, month 3, and month 12). The HARBOR study began July 7, 2009, with the primary 12-month end point completed on August 5, 2011, ongoing to 24 months. Data analysis for the subgroup was performed from January 4, 2013, through December 17, 2015. INTERVENTIONS: Patients were categorized based on BCVA outcomes as early 15-letter responders (gained ≥15 letters from baseline at month 3) or delayed 15-letter responders (did not gain ≥15 letters from baseline at month 3 but did so at month 12). MAIN OUTCOMES AND MEASURES: Changes from baseline in BCVA and central foveal thickness (CFT). RESULTS: In total, 266 early and 135 delayed 15-letter responders were identified. In the 0.5-mg monthly, 0.5-mg PRN, 2.0-mg monthly, and 2.0-mg PRN treatment groups, 63 (24.0%) of 263, 65 (24.6%) of 264, 68 (25.7%) of 265, and 70 (26.4%) of 265 patients were early responders, respectively, and 40 (16.3%) of 246, 31 (12.6%) of 247, 35 (14.1%) of 248, and 29 (11.7%) of 247 patients were delayed responders, respectively. By month 12, early vs delayed responders in the PRN treatment groups received 7.5 vs 7.4 ranibizumab injections, respectively (P = .84). More than 80% of early responders receiving PRN treatment maintained 15-letter or greater gains at month 24. At baseline, early vs delayed responders had worse BCVA (49.8 vs 55.4 letters; P < .001) and greater CFT (374.9 vs 339.0 µm; P = .02), although anatomical results were comparable by month 3 (CFT, 187.7 vs 188.9 µm). CONCLUSIONS AND RELEVANCE: Improvement of 15 letters or more from baseline occurred in 266 (25.2%) of 1057 patients within 3 months of beginning ranibizumab treatment, whereas an additional 135 (13.7%) of 988 patients achieved this gain by 12 months. The 2 cohorts had similar anatomical temporal response patterns. PRN treatment with monthly monitoring was effective in maintaining early vision gains and allowing delayed vision gains. These results suggest that vision improvement can continue in some patients after macular edema resolves and CFT decreases stabilize.

Predicting vision gains with anti-VEGF therapy in neovascular age-related macular degeneration patients by using low-luminance vision.

BACKGROUND/AIMS: To evaluate baseline low-luminance visual acuity (LLVA) as a predictor of visual acuity improvement in patients with neovascular (wet) age-related macular degeneration (wAMD) receiving antivascular endothelial growth factor A (anti-VEGF) therapy. METHODS: In the HARBOR trial, 1084 treatment-naïve patients ≥50 years of age with subfoveal wAMD received intravitreal ranibizumab 0.5 or 2.0 mg monthly or as needed. To measure LLVA, patients read a normally illuminated ETDRS (Early Treatment Diabetic Retinopathy Study) chart with a neutral density filter placed in front of the study eye. Patients were assigned into quartiles based on the magnitude of the difference between best-corrected visual acuity under optimal luminance (BCVA) and LLVA (BCVA-LLVA gap). The association between mean change in BCVA from baseline and BCVA-LLVA gap at baseline was analysed using a general linear model. RESULTS: A smaller baseline BCVA-LLVA gap predicted significantly higher BCVA gains over 24 months (p<0.0001 at each month; Pearson correlation), even after controlling for baseline BCVA or stratifying by treatment arm. Patients in the smallest baseline BCVA-LLVA gap quartile gained an average of +13.4 letters compared with +2.4 letters for patients in the widest baseline BCVA-LLVA gap quartile. At months 12 and 24, the smallest baseline BCVA-LLVA gap quartile had the highest proportion of ≥15-≥30-letter gain, and the widest baseline BCVA-LLVA gap quartile had the highest proportion of ≥15-/≥30-letter loss (p<0.0001; Fisher's exact test). CONCLUSIONS: The baseline BCVA-LLVA gap is a significant predictor of visual acuity response to anti-VEGF treatment in patients with wAMD. TRIAL REGISTRATION NUMBER: NCT00891735; Post-results.