Tuning Molecular Motion Enhances Intrinsic Fluorescence in Peptide Amphiphile Nanofibers.

Peptide amphiphiles (PAs) are highly tunable molecules that were recently found to exhibit aggregation-induced emission (AIE) when they self-assemble into nanofibers. Here, we leverage decades of molecular design and self-assembly study of PAs to strategically tune their molecular motion within nanofibers to enhance AIE, making them a highly useful platform for applications such as sensing, bioimaging, or materials property characterization. Since AIE increases when aggregated molecules are rigidly and closely packed, we altered the four most closely packed amino acids nearest to the hydrophobic core by varying the order and composition of glycine, alanine, and valine pairs. Of the six PA designs studied, C16VVAAK2 had the highest quantum yield at 0.17, which is a more than 10-fold increase from other PA designs including the very similar C16AAVVK2, highlighting the importance of precise amino acid placement to anchor rigidity closest to the core. We also altered temperature to increase AIE. C16VVAAK2 exhibited an additional 4-fold increase in maximum fluorescence intensity when the temperature was raised from 5 to 65 °C. As the temperature increased, the secondary structure transitioned from ß-sheet to random coil, indicating that further packing an already aligned molecular system makes it even more readily able to transfer energy between the electron-rich amides. This work both unveils a highly fluorescent AIE PA system design and sheds insights into the molecular orientation and packing design traits that can significantly enhance AIE in self-assembling systems.

Single-cell RNA-seq reveals developmental plasticity with coexisting oncogenic states and immune evasion programs in ETP-ALL.

Lineage plasticity and stemness have been invoked as causes of therapy resistance in cancer, because these flexible states allow cancer cells to dedifferentiate and alter their dependencies. We investigated such resistance mechanisms in relapsed/refractory early T-cell progenitor acute lymphoblastic leukemia (ETP-ALL) carrying activating NOTCH1 mutations via full-length single-cell RNA sequencing (scRNA-seq) of malignant and microenvironmental cells. We identified 2 highly distinct stem-like states that critically differed with regard to cell cycle and oncogenic signaling. Fast-cycling stem-like leukemia cells demonstrated Notch activation and were effectively eliminated in patients by Notch inhibition, whereas slow-cycling stem-like cells were Notch independent and rather relied on PI3K signaling, likely explaining the poor efficacy of Notch inhibition in this disease. Remarkably, we found that both stem-like states could differentiate into a more mature leukemia state with prominent immunomodulatory functions, including high expression of the LGALS9 checkpoint molecule. These cells promoted an immunosuppressive leukemia ecosystem with clonal accumulation of dysfunctional CD8+ T cells that expressed HAVCR2, the cognate receptor for LGALS9. Our study identified complex interactions between signaling programs, cellular plasticity, and immune programs that characterize ETP-ALL, illustrating the multidimensionality of tumor heterogeneity. In this scenario, combination therapies targeting diverse oncogenic states and the immune ecosystem seem most promising to successfully eliminate tumor cells that escape treatment through coexisting transcriptional programs.

Effects of a Home-Based Intervention on HIV Prevention Health Behaviors in Pregnant/Postpartum Kenyan Women: Estimating Moderating Effects of Depressive Symptoms.

We estimated effects of maternal depressive symptoms, utilizing the Patient Health Questionnaire-8 (PHQ-8), on women's HIV prevention behaviors in Migori County, Kenya. Pregnant women ≥ 18 years old, with gestational age of < 37 weeks, were randomized into standard care or three home visits (2 during pregnancy, 1 postpartum) promoting couple HIV testing and counseling (CHTC) and HIV prevention. Of 105 female participants, 37 (35.24%) reported depressive symptoms and 50 (47.62%) were HIV-positive. Three Poisson regressions with robust variance (univariable, multivariable, and multivariable with depressive symptoms/study arm interaction) were modeled for three outcomes: CHTC, infant HIV testing, health-seeking postpartum. In multivariable analysis with interaction, a moderating trend for the interaction between depressive symptoms and individual health-seeking was observed (p-value = 0.067). Women scoring ≤ 9 (n = 68) on the PHQ-8 and participating in home visits were 1.76 times more likely to participate in individual health-seeking compared to participants in standard care (ARR 1.76, 95% CI 1.17-2.66).

Pathways for HIV Prevention Behaviors Following a Home-Based Couples Intervention for Pregnant Women and Male Partners in Kenya.

Pregnancy is a time of heightened HIV risk, but also a phase when a couple can prioritize family health. We conducted secondary analysis of a home-based intervention in rural Kenya to explore couple-level adherence to HIV prevention behaviors. The intervention included health education, relationship-building skills, and Couples HIV Testing and Counseling. Pregnant women were randomized to the intervention (n = 64) or standard care (n = 63) along with male partners. Of 96 couples, 82 (85.0%) were followed to 3 months postpartum, when 31.0% of couples reported perfect adherence to HIV prevention. In logistic regression, intervention condition couples had three-fold higher odds of perfect adherence (AOR = 3.07, 95% CI = 1.01-9.32). A structural equation model found the intervention had moderate effects on couple communication, large effects on couple efficacy to take action around HIV, which in turn improved HIV prevention behaviors (CFI = 0.969; TLI = 0.955; RMSEA = 0.049). Strengthening couple communication and efficacy may help prevent the spread of HIV to infants or partners around the time of pregnancy.

Medical student volunteerism and interest in working with underserved and vulnerable populations.

BACKGROUND: The desire of medical students to eventually work with underserved and vulnerable populations (hereafter 'service interest'), has been shown to be shaped by individual factors including job satisfaction and financial considerations. School-level factors such as required longitudinal primary care experiences and the availability of extracurricular opportunities to work with underserved patients also affect service interest, but little is known about the impact of student volunteer activities. METHODS: This cross-sectional study gathered data from preclinical medical students via an online questionnaire. The data were linked to academic records, deidentified, and analysed using an ordinal logistic regression model with interest in caring 'primarily for underserved or vulnerable populations' as the outcome variable. RESULTS: Of 121 respondents (33% response rate), 24.8% expressed a definite interest, 55.3% expressed possible interest, and 19.9% expressed no service interest. Intent to work with the underserved was not related to age, sex, race/ethnicity, being from a rural hometown, academic qualifications prior to medical school, or anticipated debt at medical school graduation. Students with no service interest had a higher average academic performance in medical school and plans of subspecialising. When considering volunteerism prior to medical school, students in the highest and middle volunteerism tertiles had 5.68 (95% CI: 1.63, 19.81) and 4.34 (1.32, 14.32) times the odds, respectively, of having definite or possible service interest relative to those who were in the lowest volunteerism tertile, after adjusting for potential confounders. Volunteerism in a student-run clinic for the underserved during medical school was not correlated with service interest. CONCLUSIONS: Medical schools looking to enroll more students interested in working with underserved or vulnerable populations may choose to emphasise applicant premedical volunteerism record in their admissions decisions.

A conceptual framework for the impact of obesity on risk of cesarean delivery.

Cesarean deliveries accounted for 32.2% of nearly 4 million births in the United States in 2014. Obesity affects a third of reproductive-age women and is associated with worse cesarean delivery outcomes. Studies have shown that increasing maternal body mass index correlates linearly with cesarean delivery rates, but little is known about the potential mediating and moderating mechanisms. Thus, a conceptual framework for understanding how obesity correlates with risk of cesarean delivery is crucial to determining safe ways to reduce the cesarean delivery rate among obese gravidas. Based on an extensive review and synthesis of the literature, we present a conceptual framework that posits how obesity may operate through several pathways to lead to a cesarean delivery. Our framework explores the complexity of obesity as an exposure that operates through potential mediating pathways, a moderator of cesarean delivery risk, and a covariate with other cesarean delivery risk factors. Among nulliparas, obesity appears to operate through 3 main proximal mediating mechanisms to increase risk of cesarean delivery including: (1) preexisting comorbidities and obstetric complications; (2) a slower progression of first-stage labor, potentially increasing the risk of cesarean delivery secondary to failure to progress; and (3) a prolongation of pregnancy, which is associated with risk of maternal postdates. For multiparas, a fourth proximal mediator of prior uterine scar may also increase cesarean delivery risk. Distal mediating mechanisms, which operate through one of the proximal mechanisms, may include an induction of labor or planned prelabor cesarean delivery. Obesity may also moderate the likelihood of cesarean delivery by interacting with clinician-level or hospital-level factors. Future research should assess the validity of this framework and seek to understand the relative contributions of each potential pathway between obesity and cesarean delivery. This will allow for evidence-based recommendations to reduce preventable cesareans among obese women by targeting modifiable mediators and moderators of the relationship between obesity and increased risk of cesarean delivery.

Men's hopes, fears and challenges in engagement in perinatal health and the prevention of mother-to-child transmission of HIV in rural Kenya.

Male involvement in antenatal care has been shown to improve health outcomes for women and infants. However, little is known about how best to encourage male partners to support essential perinatal health activities. We explored men's perceptions of facilitators and barriers to involvement in antenatal care and HIV prevention including fears, hopes and challenges. Forty in-depth interviews were conducted with the male partners of HIV-positive and HIV-negative pregnant women in southwest Kenya. Most male partners believed engaging in pregnancy health-related activities was beneficial for keeping families healthy. However, thematic analysis revealed several obstacles that hindered participation. Poor couple relationship dynamics seemed negatively to influence male engagement. Some men were apprehensive that clinic staff might force them to test for HIV and disclose the results; if HIV-positive, men feared being labelled as 'victimisers' in situations of serodiscordancy, and described fears of abandonment by their wives. Some men avoided accompanying their wives, citing local culture as rationale for avoiding the 'effeminate' act of antenatal care attendance. Amidst these obstacles, some men chose to use their partners' HIV status as proxy for their own. Findings suggest that improving male engagement in essential maternal and child health-related activities will require addressing both structural and interpersonal barriers.

Susceptibility of Escherichia coli O157:H7 to Disinfectants In Vitro and in Simulated Footbaths Amended with Manure.

Escherichia coli O157:H7 is a human pathogen associated with gastrointestinal disease and hemolytic uremic syndrome. Direct contact with ruminants and their feces at agritourism or livestock interaction events is a known source of transmission. Footbath use is a pathogen reduction strategy that may decrease the transmission of E. coli O157:H7 at these interactions. The efficacy of chemical disinfectants in footbaths is not well reported. Our objective was to determine the susceptibility of E. coli O157:H7 toward commonly used disinfectants in vitro and within contaminated footbaths. The minimum inhibitory concentration and the minimum bactericidal concentration (MIC and MBC) and the time-to-kill were determined in vitro for seven E. coli O157:H7 strains using five disinfectant compounds (didecyldimethylammonium chloride [DDAC], glutaraldehyde, hydrogen peroxide, phenol, and sodium hypochlorite). Time-kill assays were performed within simulated footbaths at 22°C, 37°C, and 42°C with and without organic contamination using three commercial disinfectants with similar active ingredients (0.26% Clorox® Bleach, 0.034% Virex® II 256, and 1% Virkon™ S). The MBCs of disinfectants toward E. coli O157:H7 were 3.2, 625, 40, 5000, and 320 ppm of DDAC, glutaraldehyde, hydrogen peroxide, phenol, and sodium hypochlorite, respectively. At 2 × MIC, E. coli O157:H7 reached a 3 log10(colony-forming unit [CFU]/mL) reduction on contact with glutaraldehyde, by 20 min with DDAC and sodium hypochlorite, and by 4 h with phenol and hydrogen peroxide. In simulated footbaths, the commercial disinfectants reduced concentrations by 3 log10(CFU/mL) on contact in the absence of organic contamination, but viable E. coli O157:H7 was recovered from organically contaminated Clorox Bleach and Virex II 256 footbaths. No E. coli O157:H7 was recovered from the Virkon S footbaths after 10 min. This study highlights the ability for organic contamination to compromise the efficacy of disinfectants in footbaths and the importance of choosing an appropriate footbath disinfectant to retain the efficacy.

Economic Evaluations Comparing a Trial of Labor with an Elective Repeat Cesarean Delivery: A Systematic Review.

BACKGROUND: For women who have had a previous low transverse cesarean delivery, the decision to undergo a trial of labor after cesarean (TOLAC) or an elective repeat cesarean delivery (ERCD) has important clinical and economic ramifications. OBJECTIVES: To evaluate the cost-effectiveness of the alternative choices of a TOLAC and an ERCD for women with low-risk, singleton gestation pregnancies. METHODS: We searched EMBASE, MEDLINE, CINAHL, Cochrane Library, EconLit, and the Cost-Effectiveness Analysis Registry with no language, publication, or date restrictions up until October 2015. Studies were included if they were primary research, compared a TOLAC with an ERCD, and provided information on the relative cost of the alternatives. Abstracts and partial economic evaluations were excluded. RESULTS: Of 310 studies initially reviewed, 7 studies were included in the systematic review. In the base-case analyses, 4 studies concluded that TOLAC was dominant over ERCD, 1 study found ERCD to be dominant, and 2 studies found that although TOLAC was more costly, it offered more benefits and was thus cost-effective from a population perspective when considering societal willingness to pay for better outcomes. In sensitivity analyses, cost-effectiveness was found to be dependent on a high likelihood of TOLAC success, low risk of uterine rupture, and low relative cost of TOLAC compared with ERCD. CONCLUSIONS: For women who are likely to have a successful vaginal delivery, routine ERCD may result in excess morbidity and cost from a population perspective.

Association between Perceived Discrimination in Healthcare Settings and HIV Medication Adherence: Mediating Psychosocial Mechanisms.

There is insufficient research on the impact of perceived discrimination in healthcare settings on adherence to antiretroviral therapy (ART), particularly among women living with HIV, and even less is known about psychosocial mechanisms that may mediate this association. Cross-sectional analyses were conducted in a sample of 1356 diverse women living with HIV enrolled in the Women's Interagency HIV Study (WIHS), a multi-center cohort study. Indirect effects analysis with bootstrapping was used to examine the potential mediating roles of internalized stigma and depressive symptoms in the association between perceived discrimination in healthcare settings and ART adherence. Perceived discrimination in healthcare settings was negatively associated with optimal (95% or better) ART adherence (adjusted odds ratio (AOR) = 0.81, p = 0.02, 95% confidence interval (CI) [0.68, 0.97]). Furthermore, internalization of stigma and depressive symptoms mediated the perceived discrimination-adherence association: Serial mediation analyses revealed a significant indirect effect of perceived discrimination in healthcare settings on ART adherence, first through internalized HIV stigma, and then through depressive symptoms (B = - 0.08, SE = 0.02, 95% CI [- 0.12, - 0.04]). Perceiving discrimination in healthcare settings may contribute to internalization of HIV-related stigma, which in turn may lead to depressive symptoms, with downstream adverse effects on ART adherence among women. These findings can guide the design of interventions to reduce discrimination in healthcare settings, as well as interventions targeting psychosocial mechanisms that may impact the ability of women living with HIV to adhere to ART regimens.

Efficacy of an Escherichia coli O157:H7 SRP Vaccine in Orally Challenged Goats and Strain Persistence Over Time.

Small ruminants have been implicated in outbreaks of Escherichia coli O157:H7 at livestock exhibitions throughout the United States. Additionally, goat meat or milk may serve as a reservoir for foodborne transmission of the organism. These associations highlight the public health importance of an effective strategy to reduce E. coli O157:H7 shedding in goats. We examined the efficacy of the SRP® vaccine in goats orally challenged with E. coli O157:H7. Mixed-breed goats (n = 14) were randomly allocated into vaccinated and unvaccinated treatments (n = 7 per treatment). Goats were housed with a vaccinated and unvaccinated animal in each pen. Feces were collected for 3 weeks, then at necropsy, gastrointestinal contents were collected to determine the concentration of E. coli O157:H7. Three isolates per positive sample were saved and evaluated by pulsed-field gel electrophoresis (PFGE) to assess strain persistence over time. The mean concentration of E. coli O157:H7 in the feces of goats was numerically reduced in the vaccinated treatment; however, it was not statistically significant. In addition, the total number of days goats were fecal positive for E. coli O157:H7 were not different between vaccinated and unvaccinated treatments. Pulsotypes of isolates revealed that goats initially shed two of the four challenge strains of E. coli O157:H7, after which there was a distinct shift to two different strains. Further work is needed to evaluate cost-effective intervention strategies that reliably reduce E. coli O157:H7 shedding in goats, particularly those that may reduce the risk of transmission at public events, including petting zoos and fairs.

Implementation of repeat HIV testing during pregnancy in Kenya: a qualitative study.

BACKGROUND: Repeat HIV testing in late pregnancy has the potential to decrease rates of mother-to-child transmission of HIV by identifying mothers who seroconvert after having tested negative for HIV in early pregnancy. Despite being national policy in Kenya, the available data suggest that implementation rates are low. METHODS: We conducted 20 in-depth semi-structured interviews with healthcare providers and managers to explore barriers and enablers to implementation of repeat HIV testing guidelines for pregnant women. Participants were from the Nyanza region of Kenya and were purposively selected to provide variation in socio-demographics and job characteristics. Interview transcripts were coded and analyzed in Dedoose software using a thematic analysis approach. Four themes were identified a priori using Ferlie and Shortell's Framework for Change and additional themes were allowed to emerge from the data. RESULTS: Participants identified barriers and enablers at the client, provider, facility, and health system levels. Key barriers at the client level from the perspective of providers included late initial presentation to antenatal care and low proportions of women completing the recommended four antenatal visits. Barriers to offering repeat HIV testing for providers included heavy workloads, time limitations, and failing to remember to check for retest eligibility. At the facility level, inconsistent volume of clients and lack of space required for confidential HIV retesting were cited as barriers. Finally, at the health system level, there were challenges relating to the HIV test kit supply chain and the design of nationally standardized antenatal patient registers. Enablers to improving the implementation of repeat HIV testing included client dissemination of the benefits of antenatal care through word-of-mouth, provider cooperation and task shifting, and it was suggested that use of an electronic health record system could provide automatic reminders for retest eligibility. CONCLUSIONS: This study highlights some important barriers to improving HIV retesting rates among pregnant women who attend antenatal clinics in the Nyanza region of Kenya at the client, provider, facility, and health system levels. To successfully implement Kenya's national repeat HIV testing guidelines during pregnancy, it is essential that these barriers be addressed and enablers capitalized on through a multi-faceted intervention program.

Evaluation of levonorgestrel intrauterine system upon presumed nonintact removal.

A 51 year old woman presented for removal of her expired levonorgestrel intrauterine device (IUD). The IUD arms appeared absent upon IUD removal. Further examination of the device revealed that the arms were concealed inside the hormonal cylinder. Recognizing abnormal presentations of the levonorgestrel IUD upon removal can avoid unnecessary procedures.

Histone variant H2A.Z and linker histone H1 influence chromosome condensation in Saccharomyces cerevisiae.

Chromosome condensation is essential for the fidelity of chromosome segregation during mitosis and meiosis. Condensation is associated both with local changes in nucleosome structure and larger-scale alterations in chromosome topology mediated by the condensin complex. We examined the influence of linker histone H1 and variant histone H2A.Z on chromosome condensation in budding yeast cells. Linker histone H1 has been implicated in local and global compaction of chromatin in multiple eukaryotes, but we observe normal condensation of the rDNA locus in yeast strains lacking H1. However, deletion of the yeast HTZ1 gene, coding for variant histone H2A.Z, causes a significant defect in rDNA condensation. Loss of H2A.Z does not change condensin association with the rDNA locus or significantly affect condensin mRNA levels. Prior studies reported that several phenotypes caused by loss of H2A.Z are suppressed by eliminating Swr1, a key component of the SWR complex that deposits H2A.Z in chromatin. We observe that an htz1Δ swr1Δ strain has near-normal rDNA condensation. Unexpectedly, we find that elimination of the linker histone H1 can also suppress the rDNA condensation defect of htz1Δ strains. Our experiments demonstrate that histone H2A.Z promotes chromosome condensation, in part by counteracting activities of histone H1 and the SWR complex.

Using sequences of life-events to predict human lives.

Here we represent human lives in a way that shares structural similarity to language, and we exploit this similarity to adapt natural language processing techniques to examine the evolution and predictability of human lives based on detailed event sequences. We do this by drawing on a comprehensive registry dataset, which is available for Denmark across several years, and that includes information about life-events related to health, education, occupation, income, address and working hours, recorded with day-to-day resolution. We create embeddings of life-events in a single vector space, showing that this embedding space is robust and highly structured. Our models allow us to predict diverse outcomes ranging from early mortality to personality nuances, outperforming state-of-the-art models by a wide margin. Using methods for interpreting deep learning models, we probe the algorithm to understand the factors that enable our predictions. Our framework allows researchers to discover potential mechanisms that impact life outcomes as well as the associated possibilities for personalized interventions.

Selective Posterior Cerebral Artery Wada Better Predicts Good Memory and Naming Outcomes Following Selective Stereotactic Thermal Ablation for Medial Temporal Lobe Epilepsy Than Internal Carotid Artery Wada.

The conventional intracarotid amobarbital (Wada) test has been used to assess memory function in patients being considered for temporal lobe epilepsy (TLE) surgery. Minimally invasive approaches that target the medial temporal lobe (MTL) and spare neocortex are increasingly used, but a knowledge gap remains in how to assess memory and language risk from these procedures. We retrospectively compared results of two versions of the Wada test, the intracarotid artery (ICA-Wada) and posterior cerebral artery (PCA-Wada) approaches, with respect to predicting subsequent memory and language outcomes, particularly after stereotactic laser amygdalohippocampotomy (SLAH). We included all patients being considered for SLAH who underwent both ICA-Wada and PCA-Wada at a single institution. Memory and confrontation naming assessments were conducted using standardized neuropsychological tests to assess pre- to post-surgical changes in cognitive performance. Of 13 patients who initially failed the ICA-Wada, only one patient subsequently failed the PCA-Wada (p=0.003, two-sided binomial test with p 0 =0.5) demonstrating that these tests assess different brain regions or networks. PCA-Wada had a high negative predictive value for the safety of SLAH, compared to ICA-Wada, as none of the patients who underwent SLAH after passing the PCA-Wada experienced catastrophic memory decline (0 of 9 subjects, p <.004, two-sided binomial test with p 0 =0.5), and all experienced a good cognitive outcome. In contrast, the single patient who received a left anterior temporal lobectomy after failed ICA- and passed PCA-Wada experienced a persistent, near catastrophic memory decline. On confrontation naming, few patients exhibited disturbance during the PCA-Wada. Following surgery, SLAH patients showed no naming decline, while open resection patients, whose surgeries all included ipsilateral temporal lobe neocortex, experienced significant naming difficulties (Fisher's exact test, p <.05). These findings demonstrate that (1) failing the ICA-Wada falsely predicts memory decline following SLAH, (2) PCA-Wada better predicts good memory outcomes of SLAH for MTLE, and (3) the MTL brain structures affected by both PCA-Wada and SLAH are not directly involved in language processing.

Relating Antimicrobial Resistance and Virulence in Surface-Water E. coli.

The role of the environment in the emergence and spread of antimicrobial resistance (AMR) is being increasingly recognized, raising questions about the public health risks associated with environmental AMR. Yet, little is known about pathogenicity among resistant bacteria in environmental systems. Existing studies on the association between AMR and virulence are contradictory, as fitness costs and genetic co-occurrence can be opposing influences. Using Escherichia coli isolated from surface waters in eastern North Carolina, we compared virulence gene prevalence between isolates resistant and susceptible to antibiotics. We also compared the prevalence of isolates from sub-watersheds with or without commercial hog operations (CHOs). Isolates that had previously been evaluated for phenotypic AMR were paired by matching isolates resistant to any tested antibiotic with fully susceptible isolates from the same sample date and site, forming 87 pairs. These 174 isolates were evaluated by conventional PCR for seven virulence genes (bfp, fimH, cnf-1, STa (estA), EAST-1 (astA), eae, and hlyA). One gene, fimH, was found in 93.1% of isolates. Excluding fimH, at least one virulence gene was detected in 24.7% of isolates. Significant negative associations were found between resistance to at least one antibiotic and presence of at least one virulence gene, tetracycline resistance and presence of a virulence gene, resistance and STa presence, and tetracycline resistance and STa presence. No significant associations were found between CHO presence and virulence, though some sub-significant associations merit further study. This work builds our understanding of factors controlling AMR dissemination through the environment and potential health risks.

Codon optimality modulates protein output by tuning translation initiation.

The impact of synonymous codon choice on protein output has important implications for understanding endogenous gene expression and design of synthetic mRNAs. Previously, we used a neural network model to design a series of synonymous fluorescent reporters whose protein output in yeast spanned a seven-fold range corresponding to their predicted translation speed. Here, we show that this effect is not due primarily to the established impact of slow elongation on mRNA stability, but rather, that an active mechanism further decreases the number of proteins made per mRNA. We combine simulations and careful experiments on fluorescent reporters to argue that translation initiation is limited on non-optimally encoded transcripts. Using a genome-wide CRISPRi screen to discover factors modulating the output from non-optimal transcripts, we identify a set of translation initiation factors including multiple subunits of eIF3 whose depletion restored protein output of a non-optimal reporter. Our results show that codon usage can directly limit protein production, across the full range of endogenous variability in codon usage, by limiting translation initiation.

Environment-specific genomic prediction ability in maize using environmental covariates depends on environmental similarity to training data.

Technology advances have made possible the collection of a wealth of genomic, environmental, and phenotypic data for use in plant breeding. Incorporation of environmental data into environment-specific genomic prediction is hindered in part because of inherently high data dimensionality. Computationally efficient approaches to combining genomic and environmental information may facilitate extension of genomic prediction models to new environments and germplasm, and better understanding of genotype-by-environment (G × E) interactions. Using genomic, yield trial, and environmental data on 1,918 unique hybrids evaluated in 59 environments from the maize Genomes to Fields project, we determined that a set of 10,153 SNP dominance coefficients and a 5-day temporal window size for summarizing environmental variables were optimal for genomic prediction using only genetic and environmental main effects. Adding marker-by-environment variable interactions required dimension reduction, and we found that reducing dimensionality of the genetic data while keeping the full set of environmental covariates was best for environment-specific genomic prediction of grain yield, leading to an increase in prediction ability of 2.7% to achieve a prediction ability of 80% across environments when data were masked at random. We then measured how prediction ability within environments was affected under stratified training-testing sets to approximate scenarios commonly encountered by plant breeders, finding that incorporation of marker-by-environment effects improved prediction ability in cases where training and test sets shared environments, but did not improve prediction in new untested environments. The environmental similarity between training and testing sets had a greater impact on the efficacy of prediction than genetic similarity between training and test sets.

Genomic prediction for the Germplasm Enhancement of Maize project.

The Germplasm Enhancement of Maize (GEM) project was initiated in 1993 as a cooperative effort of public- and private-sector maize (Zea mays L.) breeders to enhance the genetic diversity of the U.S. maize crop. The GEM project selects progeny lines with high topcross yield potential from crosses between elite temperate lines and exotic parents. The GEM project has released hundreds of useful breeding lines based on phenotypic selection within selfing generations and multienvironment yield evaluations of GEM line topcrosses to elite adapted testers. Developing genomic selection (GS) models for the GEM project may contribute to increases in the rate of genetic gain. Here we evaluated the prediction ability of GS models trained on 6 yr of topcross evaluations from the two GEM programs in Raleigh, NC, and Ames, IA, documenting prediction abilities ranging from 0.36 to 0.75 for grain yield and from 0.78 to 0.96 for grain moisture when models were cross-validated within program and heterotic group. Predicted genetic gain from GS ranged from 0.95 to 2.58 times the gain from phenotypic selection. Prediction ability across program and heterotic group was generally poorer than within groups. Based on observed genomic relationships between GEM breeding lines and their tropical ancestors, GS for either yield or moisture would reduce recovery of exotic germplasm only slightly. Using GS models trained within program, the GEM programs should be able to more effectively deliver on its mission to broaden the genetic base of U.S. germplasm.