Publications by authors named "Oscar RodrÍguez"

88 Publications

Final Selection of Quality Protein Popcorn Hybrids.

Front Plant Sci 2021 24;12:658456. Epub 2021 Mar 24.

Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States.

Quality Protein Popcorn (QPP) BCF inbred lines were produced through an interpopulation breeding system between Quality Protein Maize dent (QPM) and elite popcorn germplasm. In 2019, five QPP F hybrids were selected for further evaluation due to superior agronomics, endosperm protein quality, and popping quality traits. Though these BCF QPP hybrids were phenotypically similar to their popcorn parents, the QPP cultivars conveyed slightly inferior popping characteristics when compared to the original popcorn germplasm. The objective of this study was twofold. First, BCF inbred lines were crossed to their popcorn parents and BCF inbred lines were produced for hybridization to test the agronomic, protein, and popping trait effects from an additional QPP by popcorn backcross. Second, BC- and BC-hybrids were simultaneously evaluated alongside ConAgra Brands elite cultivars and ranked for potential commercialization in the spring of 2020. These 10 QPP hybrids were grown alongside five ConAgra Brands elite popcorn cultivars in three locations and agronomic, protein quality, and popping quality traits were evaluated. Significant improvements in popcorn quality traits were observed in the QPP BC cultivars compared to their BC counterparts, and yield averages were significantly lower in BC-derived QPP hybrids compared to the BC population. Protein quality traits were not significantly different between QPP backcrossing populations and significantly superior to ConAgra elite popcorn varieties. Utilizing a previously published ranking system, six QPP hybrids, three from the BCF population and three from the BCF population, were evaluated as candidates for final selection. The successful evaluation and ranking system methodology employed is transferable to other hybrid production and testing programs. Incorporating this analysis with concurrent sensory studies, two QPP hybrids were chosen as premier cultivars for potential commercialization.
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http://dx.doi.org/10.3389/fpls.2021.658456DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8025670PMC
March 2021

Pervasive cis effects of variation in copy number of large tandem repeats on local DNA methylation and gene expression.

Am J Hum Genet 2021 Mar 24. Epub 2021 Mar 24.

Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Electronic address:

Variable number tandem repeats (VNTRs) are composed of large tandemly repeated motifs, many of which are highly polymorphic in copy number. However, because of their large size and repetitive nature, they remain poorly studied. To investigate the regulatory potential of VNTRs, we used read-depth data from Illumina whole-genome sequencing to perform association analysis between copy number of ∼70,000 VNTRs (motif size ≥ 10 bp) with both gene expression (404 samples in 48 tissues) and DNA methylation (235 samples in peripheral blood), identifying thousands of VNTRs that are associated with local gene expression (eVNTRs) and DNA methylation levels (mVNTRs). Using an independent cohort, we validated 73%-80% of signals observed in the two discovery cohorts, while allelic analysis of VNTR length and CpG methylation in 30 Oxford Nanopore genomes gave additional support for mVNTR loci, thus providing robust evidence to support that these represent genuine associations. Further, conditional analysis indicated that many eVNTRs and mVNTRs act as QTLs independently of other local variation. We also observed strong enrichments of eVNTRs and mVNTRs for regulatory features such as enhancers and promoters. Using the Human Genome Diversity Panel, we define sets of VNTRs that show highly divergent copy numbers among human populations and show that these are enriched for regulatory effects and preferentially associate with genes that have been linked with human phenotypes through GWASs. Our study provides strong evidence supporting functional variation at thousands of VNTRs and defines candidate sets of VNTRs, copy number variation of which potentially plays a role in numerous human phenotypes.
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http://dx.doi.org/10.1016/j.ajhg.2021.03.016DOI Listing
March 2021

European Association of Urology (EAU) Prognostic Factor Risk Groups for Non-muscle-invasive Bladder Cancer (NMIBC) Incorporating the WHO 2004/2016 and WHO 1973 Classification Systems for Grade: An Update from the EAU NMIBC Guidelines Panel.

Eur Urol 2021 Apr 6;79(4):480-488. Epub 2021 Jan 6.

European Association of Urology Non-Muscle-Invasive Bladder Cancer Guidelines Panel, Arnhem, The Netherlands; Department of Surgical Oncology (Urology), University Health Network, Princess Margaret Cancer Center, University of Toronto, Toronto, Canada.

Background: The European Association of Urology (EAU) prognostic factor risk groups for non-muscle-invasive bladder cancer (NMIBC) are used to provide recommendations for patient treatment after transurethral resection of bladder tumor (TURBT). They do not, however, take into account the widely used World Health Organization (WHO) 2004/2016 grading classification and are based on patients treated in the 1980s.

Objective: To update EAU prognostic factor risk groups using the WHO 1973 and 2004/2016 grading classifications and identify patients with the lowest and highest probabilities of progression.

Design, Setting, And Participants: Individual patient data for primary NMIBC patients were collected from the institutions of the members of the EAU NMIBC guidelines panel.

Intervention: Patients underwent TURBT followed by intravesical instillations at the physician's discretion.

Outcome Measurements And Statistical Analysis: Multivariable Cox proportional-hazards regression models were fitted to the primary endpoint, the time to progression to muscle-invasive disease or distant metastases. Patients were divided into four risk groups: low-, intermediate-, high-, and a new, very high-risk group. The probabilities of progression were estimated using Kaplan-Meier curves.

Results And Limitations: A total of 3401 patients treated with TURBT ± intravesical chemotherapy were included. From the multivariable analyses, tumor stage, WHO 1973/2004-2016 grade, concomitant carcinoma in situ, number of tumors, tumor size, and age were used to form four risk groups for which the probability of progression at 5 yr varied from <1% to >40%. Limitations include the retrospective collection of data and the lack of central pathology review.

Conclusions: This study provides updated EAU prognostic factor risk groups that can be used to inform patient treatment and follow-up. Incorporating the WHO 2004/2016 and 1973 grading classifications, a new, very high-risk group has been identified for which urologists should be prompt to assess and adapt their therapeutic strategy when necessary.

Patient Summary: The newly updated European Association of Urology prognostic factor risk groups for non-muscle-invasive bladder cancer provide an improved basis for recommending a patient's treatment and follow-up schedule.
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http://dx.doi.org/10.1016/j.eururo.2020.12.033DOI Listing
April 2021

Optimization of training sets for genomic prediction of early-stage single crosses in maize.

Theor Appl Genet 2021 Feb 4;134(2):687-699. Epub 2021 Jan 4.

Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA.

Key Message: Training population optimization algorithms are useful for efficiently training genomic prediction models for single-cross performance, especially if the population is extended beyond only realized crosses to all possible single crosses. Genomic prediction of single-cross performance could allow effective evaluation of all possible single crosses between all inbreds developed in a hybrid breeding program. The objectives of the present study were to investigate the effect of different levels of relatedness on genomic predictive ability of single crosses, evaluate the usefulness of deterministic formula to forecast prediction accuracy in advance, and determine the potential for TRS optimization based on prediction error variance (PEVmean) and coefficient of determination (CDmean) criteria. We used 481 single crosses made by crossing 89 random recombinant inbred lines (RILs) belonging to the Iowa stiff stalk synthetic group with 103 random RILs belonging to the non-stiff stalk synthetic heterotic group. As expected, predictive ability was enhanced by ensuring close relationships between TRSs and target sets, even when TRS sizes were smaller. We found that designing a TRS based on PEVmean or CDmean criteria is useful for increasing the efficiency of genomic prediction of maize single crosses. We went further and extended the sampling space from that of all observed single crosses to all possible single crosses, providing a much larger genetic space within which to design a training population. Using all possible single crosses increased the advantage of the PEVmean and CDmean methods based on expected prediction accuracy. This finding suggests that it may be worthwhile using an optimization algorithm to select a training population from all possible single crosses to maximize efficiency in training accurate models for hybrid genomic prediction.
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http://dx.doi.org/10.1007/s00122-020-03722-wDOI Listing
February 2021

Lethality of SARS-CoV-2 infection in K18 human angiotensin-converting enzyme 2 transgenic mice.

Nat Commun 2020 11 30;11(1):6122. Epub 2020 Nov 30.

Texas Biomedical Research Institute, San Antonio, TX, 78227, USA.

Vaccine and antiviral development against SARS-CoV-2 infection or COVID-19 disease would benefit from validated small animal models. Here, we show that transgenic mice expressing human angiotensin-converting enzyme 2 (hACE2) by the human cytokeratin 18 promoter (K18 hACE2) represent a susceptible rodent model. K18 hACE2 transgenic mice succumbed to SARS-CoV-2 infection by day 6, with virus detected in lung airway epithelium and brain. K18 ACE2 transgenic mice produced a modest TH1/2/17 cytokine storm in the lung and spleen that peaked by day 2, and an extended chemokine storm that was detected in both lungs and brain. This chemokine storm was also detected in the brain at day 6. K18 hACE2 transgenic mice are, therefore, highly susceptible to SARS-CoV-2 infection and represent a suitable animal model for the study of viral pathogenesis, and for identification and characterization of vaccines (prophylactic) and antivirals (therapeutics) for SARS-CoV-2 infection and associated severe COVID-19 disease.
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http://dx.doi.org/10.1038/s41467-020-19891-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7705712PMC
November 2020

A Novel Framework for Characterizing Genomic Haplotype Diversity in the Human Immunoglobulin Heavy Chain Locus.

Front Immunol 2020 23;11:2136. Epub 2020 Sep 23.

Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United States.

An incomplete ascertainment of genetic variation within the highly polymorphic immunoglobulin heavy chain locus (IGH) has hindered our ability to define genetic factors that influence antibody-mediated processes. Due to locus complexity, standard high-throughput approaches have failed to accurately and comprehensively capture IGH polymorphism. As a result, the locus has only been fully characterized two times, severely limiting our knowledge of human IGH diversity. Here, we combine targeted long-read sequencing with a novel bioinformatics tool, IGenotyper, to fully characterize IGH variation in a haplotype-specific manner. We apply this approach to eight human samples, including a haploid cell line and two mother-father-child trios, and demonstrate the ability to generate high-quality assemblies (>98% complete and >99% accurate), genotypes, and gene annotations, identifying 2 novel structural variants and 15 novel IGH alleles. We show multiplexing allows for scaling of the approach without impacting data quality, and that our genotype call sets are more accurate than short-read (>35% increase in true positives and >97% decrease in false-positives) and array/imputation-based datasets. This framework establishes a desperately needed foundation for leveraging IG genomic data to study population-level variation in antibody-mediated immunity, critical for bettering our understanding of disease risk, and responses to vaccines and therapeutics.
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http://dx.doi.org/10.3389/fimmu.2020.02136DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7539625PMC
September 2020

A Survey of Rare Epigenetic Variation in 23,116 Human Genomes Identifies Disease-Relevant Epivariations and CGG Expansions.

Am J Hum Genet 2020 10 15;107(4):654-669. Epub 2020 Sep 15.

Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, Hess Center for Science and Medicine, New York, NY 10029, USA. Electronic address:

There is growing recognition that epivariations, most often recognized as promoter hypermethylation events that lead to gene silencing, are associated with a number of human diseases. However, little information exists on the prevalence and distribution of rare epigenetic variation in the human population. In order to address this, we performed a survey of methylation profiles from 23,116 individuals using the Illumina 450k array. Using a robust outlier approach, we identified 4,452 unique autosomal epivariations, including potentially inactivating promoter methylation events at 384 genes linked to human disease. For example, we observed promoter hypermethylation of BRCA1 and LDLR at population frequencies of ∼1 in 3,000 and ∼1 in 6,000, respectively, suggesting that epivariations may underlie a fraction of human disease which would be missed by purely sequence-based approaches. Using expression data, we confirmed that many epivariations are associated with outlier gene expression. Analysis of variation data and monozygous twin pairs suggests that approximately two-thirds of epivariations segregate in the population secondary to underlying sequence mutations, while one-third are likely sporadic events that occur post-zygotically. We identified 25 loci where rare hypermethylation coincided with the presence of an unstable CGG tandem repeat, validated the presence of CGG expansions at several loci, and identified the putative molecular defect underlying most of the known folate-sensitive fragile sites in the genome. Our study provides a catalog of rare epigenetic changes in the human genome, gives insight into the underlying origins and consequences of epivariations, and identifies many hypermethylated CGG repeat expansions.
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http://dx.doi.org/10.1016/j.ajhg.2020.08.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7536611PMC
October 2020

Comparison of the performances of the ADXBLADDER test and urinary cytology in the follow-up of non-muscle-invasive bladder cancer: a blinded prospective multicentric study.

BJU Int 2021 02 29;127(2):198-204. Epub 2020 Aug 29.

Department of Urology, Fundacio Puigvert, Barcelona, Spain.

Objective: To compare directly the performance of the ADXBLADDER test with that of cytology in the detection of non-muscle-invasive bladder cancer (NMIBC) recurrences.

Background: ADXBLADDER is a urine test based on the detection of MCM5, a DNA licensing factor expressed in all cells capable of dividing. Expression is usually restricted to the basal stem cell compartment; however, in malignancy, MCM5-expressing cells can be found throughout the epithelium. Detection of MCM5 in urine sediment can be indicative of the presence of a bladder tumour.

Patients And Methods: A multicentre prospective, blinded study was carried out from August 2017 and July 2019 at 21 European Union centres, 14 of which collected matching cytology data. Urine was collected from patients prior to cystoscopy. Urine cytology and ADXBLADDER were performed and compared to the diagnosis obtained by cystoscopy. The performance of cytology and ADXBLADDER were then compared.

Results: The overall performance of ADXBLADDER demonstrated a sensitivity of 51.9%, a specificity of 66.4%, and a negative predictive value (NPV) of 92%. The sensitivity of ADXBLADDER for low- and high-grade recurrences was 44.1% and 58.8%, respectively. By contrast, cytology sensitivity was 16.7%, specificity was 98% and NPV was 90.7%. Cytology sensitivity for both low- and high-grade disease was 17.6%.

Conclusions: ADXBLADDER detection of both low- and high-grade NMIBC recurrence is superior to that of cytology, with ADXBLADDER able to exclude the presence of high-grade recurrence in 97.8% of cases compared to 97.1% with cytology. These results show that ADXBLADDER has promise as a more reliable alternative to urine cytology in the follow-up of NMIBC.
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http://dx.doi.org/10.1111/bju.15194DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7891338PMC
February 2021

Production and Selection of Quality Protein Popcorn Hybrids Using a Novel Ranking System and Combining Ability Estimates.

Front Plant Sci 2020 23;11:698. Epub 2020 Jun 23.

Department of Agronomy and Horticulture, University of Nebraska - Lincoln, Lincoln, NE, United States.

Popcorn varieties are agronomically sub-optimal and genetically limited compared to other maize subspecies. To increase genetic diversity and improve popcorn agronomics, dent germplasm has been introduced to popcorn with limited success and generally, major loss of popping. Between 2013 and 2018, 12 Quality Protein Popcorn (QPP) inbreds containing Quality Protein Maize (QPM) and popcorn germplasm were produced that maintained popping while carrying the allele conferring elevated kernel lysine. This is an opportune trait in the growing market for healthier snacks and a model for mining QPM traits into popcorn. We crossed QPP inbreds to explore the effects of heterosis on popcorn protein, popping quality, and plant agronomics and selected hybrids for further production. To rank and intermediately prescreen hybrids, we utilized a novel hybrid-ranking model adapted from a rank summation index while examining the inbred general combining ability and hybrid specific combining ability estimates for all traits. We observed a biological manifestation of heterosis by categorizing hybrids by pedigree that resulted in a stepwise progression of trait improvement. These results corroborated our hybrid selection and offered insight in basic heterosis research. Estimates for popcorn quality and agronomic trait covariances also suggest the synergistic introgression of highly vitreous dent maize (QPM) into popcorn, providing a likely explanation for the successfully maintained vitreous endosperm, protein quality and popping traits in line with a remodeled proteome. QPP hybrids maintained improved amino acid profiles although different popping methods variably affected popcorn's protein bound and free amino acid levels. This preliminary screening of QPP hybrids is enabling further quantitative selection for large-scale, complex trait comparison to currently marketed elite popcorn varieties.
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http://dx.doi.org/10.3389/fpls.2020.00698DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7325744PMC
June 2020

Contamination of staple crops by heavy metals in Sibaté, Colombia.

Heliyon 2020 Jul 1;6(7):e04212. Epub 2020 Jul 1.

Environmental Engineering Program, Faculty of Engineering, El Bosque University, CHOC-IZONE Research Group. Av., Carrera 9 N° 131 A - 02, Bogotá, Colombia.

Heavy metal contamination in water resources, soil, and food sources is an issue that compromises food safety in Sibaté, Colombia. In the present study concentration of heavy metals [HMs], such as Cu, As, Pb, Cr, Zn, Co, Cd and Ni, present in vegetables included in the typical Colombian diet were measured. The study was conducted as follows: samples of parsley, artichoke and carrots produced in a location near the Muña dam were collected, where the Bogotá River water is treated for use as a water resource. To determine food safety, national and international [HMs] established limits were compared with quantified [HMs] in samples of different vegetable parts and of the surrounding soil. Fresh samples were separated in their respective parts for cold acid digestion with HCl and HNO (1:1) for 15 days. Heavy metal mean ± standard error (SE) were as follows (mg/kg) As 2.36 ± 0.185, Cd 0.16 ± 0.009, Co 0.43 ± 0.019, Cr 12.1 ± 0.453, Cu 13.1 ± 1.68, Ni 0.00, Pb 7.07 ± 0.482 and Zn 3.976 ± 0.332. Cd, Cr, As, Co and Ni showed high transfer factor in Moreover, high Pb, Cu and Zn transfer factor were present in . Except for roots, there was a high metal transfer specifically in leaves and other different plant parts, with high transfer factor for Cr, As, Co, Pb, Cu and Zn.
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http://dx.doi.org/10.1016/j.heliyon.2020.e04212DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7334423PMC
July 2020

A robust benchmark for detection of germline large deletions and insertions.

Nat Biotechnol 2020 11 15;38(11):1347-1355. Epub 2020 Jun 15.

Joint Initiative for Metrology in Biology, SLAC National Accelerator Lab, Stanford University, Stanford, CA, USA.

New technologies and analysis methods are enabling genomic structural variants (SVs) to be detected with ever-increasing accuracy, resolution and comprehensiveness. To help translate these methods to routine research and clinical practice, we developed a sequence-resolved benchmark set for identification of both false-negative and false-positive germline large insertions and deletions. To create this benchmark for a broadly consented son in a Personal Genome Project trio with broadly available cells and DNA, the Genome in a Bottle Consortium integrated 19 sequence-resolved variant calling methods from diverse technologies. The final benchmark set contains 12,745 isolated, sequence-resolved insertion (7,281) and deletion (5,464) calls ≥50 base pairs (bp). The Tier 1 benchmark regions, for which any extra calls are putative false positives, cover 2.51 Gbp and 5,262 insertions and 4,095 deletions supported by ≥1 diploid assembly. We demonstrate that the benchmark set reliably identifies false negatives and false positives in high-quality SV callsets from short-, linked- and long-read sequencing and optical mapping.
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http://dx.doi.org/10.1038/s41587-020-0538-8DOI Listing
November 2020

Diagnostic Accuracy of MCM5 for the Detection of Recurrence in Nonmuscle Invasive Bladder Cancer Followup: A Blinded, Prospective Cohort, Multicenter European Study.

J Urol 2020 10 21;204(4):685-690. Epub 2020 Apr 21.

Department of Urology, Fundacio Puigvert, Barcelona, Spain.

Purpose: Detection of MCM5 containing cells in urine has been shown to be indicative of the presence of a bladder tumor on primary diagnosis. In this study we evaluate diagnostic performance of ADXBLADDER in patients undergoing cystoscopic surveillance in nonmuscle invasive bladder cancer followup.

Materials And Methods: A multicenter prospective blinded study was performed at 21 European centers with patients undergoing cystoscopy for nonmuscle invasive bladder cancer surveillance, diagnosed in the preceding 2 years. Urine was collected from all eligible patients and ADXBLADDER-MCM5 testing was performed. Performance characteristics were calculated by comparing MCM5 results to the outcome of cystoscopy plus pathological assessment.

Results: Of 1,431 eligible patients enrolled 127 were diagnosed with a bladder cancer recurrence. The overall sensitivity for the ADXBLADDER-MCM5 test in detecting bladder cancer recurrence was 44.9% (95% CI 36.1-54) with a 75.6% sensitivity for nonpTaLG tumors (95% CI 59.7-87.6). Specificity was 71.1% (95% CI 68.5-73.5). The overall negative predictive value was 93% (95% CI 91.2-94.5). However, ADXBLADDER was able to rule out the presence of a nonpTaLG recurrent tumor with a negative predictive value of 99.0% (95% CI 98.2-99.5). No statistically significant differences in the performance of ADXBLADDER were observed as a result of age or sex.

Conclusions: This large blinded prospective study demonstrates that in the followup of patients with nonmuscle invasive bladder cancer ADXBLADDER is able to exclude the presence of the most aggressive tumors with a negative predictive value of 99%. These results indicate that ADXBLADDER could be incorporated in the followup strategy of nonmuscle invasive bladder cancer.
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http://dx.doi.org/10.1097/JU.0000000000001084DOI Listing
October 2020

State-of-the-Art Production Chains for Peas, Beans and Chickpeas-Valorization of Agro-Industrial Residues and Applications of Derived Extracts.

Molecules 2020 Mar 18;25(6). Epub 2020 Mar 18.

Institute for Ecopreneurship, School of Life Sciences, Fachhochschule Nordwestschweiz, Hofackerstrasse 30, CH-4132 Muttenz, Switzerland.

The world is confronted with the depletion of natural resources due to their unsustainable use and the increasing size of populations. In this context, the efficient use of by-products, residues and wastes generated from agro-industrial and food processing opens the perspective for a wide range of benefits. In particular, legume residues are produced yearly in very large amounts and may represent an interesting source of plant proteins that contribute to satisfying the steadily increasing global protein demand. Innovative biorefinery extraction cascades may also enable the recovery of further bioactive molecules and fibers from these insufficiently tapped biomass streams. This review article gives a summary of the potential for the valorization of legume residual streams resulting from agro-industrial processing and more particularly for pea, green bean and chickpea by-products/wastes. Valuable information on the annual production volumes, geographical origin and state-of-the-art technologies for the extraction of proteins, fibers and other bioactive molecules from this source of biomass, is exhaustively listed and discussed. Finally, promising applications, already using the recovered fractions from pea, bean and chickpea residues for the formulation of feed, food, cosmetic and packaging products, are listed and discussed.
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http://dx.doi.org/10.3390/molecules25061383DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7144388PMC
March 2020

Impedimetric Detection of Ammonia and Low Molecular Weight Amines in the Gas Phase with Covalent Organic Frameworks.

Sensors (Basel) 2020 Mar 3;20(5). Epub 2020 Mar 3.

Grupo de Electroquímica y Termodinámica Computacional, Department of Chemistry, National University of Colombia, Bogotá 111321, Colombia.

Two Covalent Organic Frameworks (COF), named TFP-BZ and TFP-DMBZ, were synthesized using the imine condensation between 1,3,5-triformylphloroglucinol (TFP) with benzidine (BZ) or 3,3-dimethylbenzidine (DMBZ). These materials were deposited, such as films over interdigitated electrodes (IDE), by chemical bath deposition, giving rise to TFP-BZ-IDE and TFP-DMBZ-IDE systems. The synthesized COFs powders were characterized by Powder X-Ray Diffraction (PXRD), Fourier Transform Infrared spectroscopy (FT-IR), solid-state Nuclear Magnetic Resonance (ssNMR), nitrogen adsorption isotherms, Scanning Electron Microscopy (SEM), and Raman spectroscopy, while the films were characterized by SEM and Raman. Ammonia and low molecular weight amine sensing were developed with the COF film systems using the impedance electrochemical spectroscopy (EIS). Results showed that the systems TFP-BZ-IDE and TFP-DMBZ-IDE detect low molecular weight amines selectively by impedimetric analysis. Remarkably, with no significant interference by other atmospheric gas compounds such as nitrogen, carbon dioxide, and methane. Additionally, both COF films presented a range of sensitivity at low amine concentrations below two ppm at room temperature.
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http://dx.doi.org/10.3390/s20051385DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7085617PMC
March 2020

Maize genomes to fields (G2F): 2014-2017 field seasons: genotype, phenotype, climatic, soil, and inbred ear image datasets.

BMC Res Notes 2020 Feb 12;13(1):71. Epub 2020 Feb 12.

University of Wisconsin, Madison, WI, 53706, USA.

Objectives: Advanced tools and resources are needed to efficiently and sustainably produce food for an increasing world population in the context of variable environmental conditions. The maize genomes to fields (G2F) initiative is a multi-institutional initiative effort that seeks to approach this challenge by developing a flexible and distributed infrastructure addressing emerging problems. G2F has generated large-scale phenotypic, genotypic, and environmental datasets using publicly available inbred lines and hybrids evaluated through a network of collaborators that are part of the G2F's genotype-by-environment (G × E) project. This report covers the public release of datasets for 2014-2017.

Data Description: Datasets include inbred genotypic information; phenotypic, climatic, and soil measurements and metadata information for each testing location across years. For a subset of inbreds in 2014 and 2015, yield component phenotypes were quantified by image analysis. Data released are accompanied by README descriptions. For genotypic and phenotypic data, both raw data and a version without outliers are reported. For climatic data, a version calibrated to the nearest airport weather station and a version without outliers are reported. The 2014 and 2015 datasets are updated versions from the previously released files [1] while 2016 and 2017 datasets are newly available to the public.
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http://dx.doi.org/10.1186/s13104-020-4922-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7017475PMC
February 2020

Elucidation of de novo small insertion/deletion biology with parent-of-origin phasing.

Hum Mutat 2020 04 16;41(4):800-806. Epub 2020 Jan 16.

Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York.

The mechanisms underlying de novo insertion/deletion (indel) genesis, such as polymerase slippage, have been hypothesized but not well characterized in the human genome. We implemented two methodological improvements, which were leveraged to dissect indel mutagenesis. We assigned de novo variants to parent-of-origin (i.e., phasing) with low-coverage long-read whole-genome sequencing, achieving better phasing compared to short-read sequencing (medians of 84% and 23%, respectively). We then wrote an application programming interface to classify indels into three subtypes according to sequence context. Across three cohorts with different phasing methods (N  = 540, all cohorts), we observed that one de novo indel subtype, change in copy count (CCC), was significantly correlated with father's (p = 7.1 × 10 ) but not mother's (p = .45) age at conception. We replicated this effect in three cohorts without de novo phasing (p  = 1.9 × 10 , p  = .61; N  = 3,391, all cohorts). Although this is consistent with polymerase slippage during spermatogenesis, the percentage of variance explained by paternal age was low, and we did not observe an association with replication timing. These results suggest that spermatogenesis-specific events have a minor role in CCC indel mutagenesis, one not observed for other indel subtypes nor for maternal age in general. These results have implications for indel modeling in evolution and disease.
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http://dx.doi.org/10.1002/humu.23971DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7069802PMC
April 2020

Papillary urothelial neoplasm of low malignant potential (PUN-LMP): Still a meaningful histo-pathological grade category for Ta, noninvasive bladder tumors in 2019?

Urol Oncol 2020 05 5;38(5):440-448. Epub 2019 Nov 5.

EAU Guidelines Office Board, European Association of Urology, Arnhem, the Netherlands.

Background: Papillary urothelial neoplasm of low malignant potential (PUN-LMP) was introduced as a noninvasive, noncancerous lesion and a separate grade category in 1998. Subsequently, PUN-LMP was reconfirmed by World Health Organization (WHO) 2004 and WHO 2016 classifications for urothelial bladder tumors.

Objectives: To analyze the proportion of PUN-LMP diagnosis over time and to determine its prognostic value compared to Ta-LG (low-grade) and Ta-HG (high-grade) carcinomas. To assess the intraobserver variability of an experienced uropathologist assigning (WHO) 2004/2016 grades at 2 time points.

Materials And Methods: Individual patient data of 3,311 primary Ta bladder tumors from 17 hospitals in Europe and Canada were available. Transurethral resection of the tumor was performed between 1990 and 2018. Time to recurrence and progression were analyzed with cumulative incidence functions, log-rank tests and multivariable Cox-regression stratified by institution. Intraobserver variability was assessed by examining the same 314 transurethral resection of the tumorslides twice, in 2004 and again in 2018.

Results: PUN-LMP represented 3.8% (127/3,311) of Ta tumors. The same pathologist found 71/314 (22.6%) PUN-LMPs in 2004 and only 20/314 (6.4%) in 2018. Overall, the proportion of PUN-LMP diagnosis substantially decreased over time from 31.3% (1990-2000) to 3.2% (2000-2010) and to 1.1% (2010-2018). We found no difference in time to recurrence between the three WHO 2004/2016 Ta-grade categories (log-rank, P = 0.381), nor for LG vs. PUN-LMP (log-rank, P = 0.238). Time to progression was different for all grade categories (log-rank, P < 0.001), but not between LG and PUN-LMP (log-rank, P = 0.096). Multivariable analyses on recurrence and progression showed similar results for all 3 grade categories and for LG vs. PUN-LMP.

Conclusions: The proportion of PUN-LMP has decreased to very low levels in the last decade. Contrary to its reconfirmation in the WHO 2016 classification, our results do not support the continued use of PUN-LMP as a separate grade category in Ta tumors because of the similar prognosis for PUN-LMP and Ta-LG carcinomas.
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http://dx.doi.org/10.1016/j.urolonc.2019.10.002DOI Listing
May 2020

Relative importance of gene effects for nitrogen-use efficiency in popcorn.

PLoS One 2019 26;14(9):e0222726. Epub 2019 Sep 26.

Department of Agronomy and Horticulture, University of Nebraska, Nebraska, United States of America.

The objective of this study was to evaluate the effects of additive and non-additive genes on the efficiency of nitrogen (N) use and N responsiveness in inbred popcorn lines. The parents, hybrids and reciprocal crosses were evaluated in a 10x10 triple lattice design at two sites and two levels of N availability. To establish different N levels in the two experiments, fertilization was carried out at sowing, according to soil analysis reports. However, for the experiments with ideal nitrogen availability, N was sidedressed according to the crop requirement, whereas for the N-poor experiments sidedressing consisted of 30% of that applied in the N-rich environment. Two indices were evaluated, the Harmonic Mean of the Relative Performance (HMRP) and Agronomic Efficiency under Low Nitrogen Availability (AELN), both based on grain yield at both N levels. Both additive and non-additive gene effects were important for selection for N-use efficiency. Moreover, there was allelic complementarity between the lines and a reciprocal effect for N-use efficiency, indicating the importance of the choice of the parents used as male or female. The best hybrids were obtained from inbred popcorn lines with contrasting N-use efficiency and N responsiveness.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0222726PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6762054PMC
April 2020

A unified encyclopedia of human functional DNA elements through fully automated annotation of 164 human cell types.

Genome Biol 2019 08 28;20(1):180. Epub 2019 Aug 28.

Department of Genome Sciences, University of Washington, Seattle, USA.

Semi-automated genome annotation methods such as Segway take as input a set of genome-wide measurements such as of histone modification or DNA accessibility and output an annotation of genomic activity in the target cell type. Here we present annotations of 164 human cell types using 1615 data sets. To produce these annotations, we automated the label interpretation step to produce a fully automated annotation strategy. Using these annotations, we developed a measure of the importance of each genomic position called the "conservation-associated activity score." We further combined all annotations into a single, cell type-agnostic encyclopedia that catalogs all human regulatory elements.
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http://dx.doi.org/10.1186/s13059-019-1784-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6714098PMC
August 2019

MsPAC: a tool for haplotype-phased structural variant detection.

Bioinformatics 2020 02;36(3):922-924

Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.

Summary: While next-generation sequencing (NGS) has dramatically increased the availability of genomic data, phased genome assembly and structural variant (SV) analyses are limited by NGS read lengths. Long-read sequencing from Pacific Biosciences and NGS barcoding from 10x Genomics hold the potential for far more comprehensive views of individual genomes. Here, we present MsPAC, a tool that combines both technologies to partition reads, assemble haplotypes (via existing software) and convert assemblies into high-quality, phased SV predictions. MsPAC represents a framework for haplotype-resolved SV calls that moves one step closer to fully resolved, diploid genomes.

Availability And Implementation: https://github.com/oscarlr/MsPAC.

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/btz618DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7523683PMC
February 2020

An Interesting Breathing Pattern.

Ann Am Thorac Soc 2019 07;16(7):920-922

2 Department of Pediatric Pulmonary and Sleep Medicine, University of Mississippi Medical Center, Jackson, Mississippi.

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http://dx.doi.org/10.1513/AnnalsATS.201807-452CCDOI Listing
July 2019

Slow Delivery Immunization Enhances HIV Neutralizing Antibody and Germinal Center Responses via Modulation of Immunodominance.

Cell 2019 05 9;177(5):1153-1171.e28. Epub 2019 May 9.

Division of Vaccine Discovery, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA. Electronic address:

Conventional immunization strategies will likely be insufficient for the development of a broadly neutralizing antibody (bnAb) vaccine for HIV or other difficult pathogens because of the immunological hurdles posed, including B cell immunodominance and germinal center (GC) quantity and quality. We found that two independent methods of slow delivery immunization of rhesus monkeys (RMs) resulted in more robust T follicular helper (T) cell responses and GC B cells with improved Env-binding, tracked by longitudinal fine needle aspirates. Improved GCs correlated with the development of >20-fold higher titers of autologous nAbs. Using a new RM genomic immunoglobulin locus reference, we identified differential IgV gene use between immunization modalities. Ab mapping demonstrated targeting of immunodominant non-neutralizing epitopes by conventional bolus-immunized animals, whereas slow delivery-immunized animals targeted a more diverse set of epitopes. Thus, alternative immunization strategies can enhance nAb development by altering GCs and modulating the immunodominance of non-neutralizing epitopes.
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http://dx.doi.org/10.1016/j.cell.2019.04.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6619430PMC
May 2019

Parallels between natural selection in the cold-adapted crop-wild relative Tripsacum dactyloides and artificial selection in temperate adapted maize.

Plant J 2019 09 26;99(5):965-977. Epub 2019 Jun 26.

Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.

Artificial selection has produced varieties of domesticated maize that thrive in temperate climates around the world. However, the direct progenitor of maize, teosinte, is indigenous only to a relatively small range of tropical and subtropical latitudes and grows poorly or not at all outside of this region. Tripsacum, a sister genus to maize and teosinte, is naturally endemic to the majority of areas in the western hemisphere where maize is cultivated. A full-length reference transcriptome for Tripsacum dactyloides generated using long-read Iso-Seq data was used to characterize independent adaptation to temperate climates in this clade. Genes related to phospholipid biosynthesis, a critical component of cold acclimation in other cold-adapted plant lineages, were enriched among those genes experiencing more rapid rates of protein sequence evolution in T. dactyloides. In contrast with previous studies of parallel selection, we find that there is a significant overlap between the genes that were targets of artificial selection during the adaptation of maize to temperate climates and those that were targets of natural selection in temperate-adapted T. dactyloides. Genes related to growth, development, response to stimulus, signaling, and organelles were enriched in the set of genes identified as both targets of natural and artificial selection.
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http://dx.doi.org/10.1111/tpj.14376DOI Listing
September 2019

Palladium-Catalyzed Direct α-C(sp3) Heteroarylation of Ketones under Microwave Irradiation.

J Org Chem 2019 06 1;84(12):7652-7663. Epub 2019 May 1.

Department of Chemistry & Biochemistry , Northern Kentucky University , Nunn Drive , Highland Heights , Kentucky 41099 , United States.

Heteroaryl compounds are valuable building blocks in medicinal chemistry and chemical industry. A palladium-catalyzed direct α-C(sp3) heteroarylation of ketones under microwave irradiation is developed and reported in this study. Under optimized conditions, twenty-eight (28) heteroarylated ketones were prepared in this study to demonstrate the substrate scope of this reaction. The ground-state optimized structure of Pd(0) active catalyst with 2-dicyclohexylphosphino-2',4',6'-triisopropylbiphenyl (XPhos) in toluene, and the products of its reaction with 3-bromopyridine and acetophenone were studied using all-atom density functional theory. This study provided insightful information for palladium catalytic system design to generate heteroaryl compounds.
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http://dx.doi.org/10.1021/acs.joc.9b00446DOI Listing
June 2019

Multi-platform discovery of haplotype-resolved structural variation in human genomes.

Nat Commun 2019 04 16;10(1):1784. Epub 2019 Apr 16.

The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.

The incomplete identification of structural variants (SVs) from whole-genome sequencing data limits studies of human genetic diversity and disease association. Here, we apply a suite of long-read, short-read, strand-specific sequencing technologies, optical mapping, and variant discovery algorithms to comprehensively analyze three trios to define the full spectrum of human genetic variation in a haplotype-resolved manner. We identify 818,054 indel variants (<50 bp) and 27,622 SVs (≥50 bp) per genome. We also discover 156 inversions per genome and 58 of the inversions intersect with the critical regions of recurrent microdeletion and microduplication syndromes. Taken together, our SV callsets represent a three to sevenfold increase in SV detection compared to most standard high-throughput sequencing studies, including those from the 1000 Genomes Project. The methods and the dataset presented serve as a gold standard for the scientific community allowing us to make recommendations for maximizing structural variation sensitivity for future genome sequencing studies.
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http://dx.doi.org/10.1038/s41467-018-08148-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6467913PMC
April 2019

Generation and Evaluation of Modified Popcorn Suggests a Route to Quality Protein Popcorn.

Front Plant Sci 2018 6;9:1803. Epub 2018 Dec 6.

Department of Agronomy and Horticulture, University of Nebraska - Lincoln, Lincoln, NE, United States.

Introducing traits from dent corn to popcorn is challenging because it is difficult to recover adequate popping characteristics. QPM (Quality Protein Maize) is a dent corn variety carrying the () mutation, specifying increased amounts of normally limiting essential amino acids, and modifier genes which restore the wild type vitreous kernel phenotype. In this study, we introgressed and selected for endosperm modification using vitreousness and high 27-kD gamma zein content. In this way, we recovered high-lysine, fully poppable Quality Protein Popcorn (QPP). BCF individuals with vitreous kernels were confirmed to be mutants by both genotyping and SDS-PAGE. Amino acid profiling of BCF individuals showed that they all have significantly increased lysine compared with popcorn parental lines. Principal Component Analysis of the amino acid profiles showed that all introgressions were grouped with corresponding QPM parental lines. Popping analysis of the BCF individuals showed that while there is variability in popping volume between lines, some lines show equivalent popping to the popcorn parent. In this proof-of-concept study for QPP, we have shown that it is possible to rapidly recover sufficient popcorn characteristics in a modified background using simple phenotypic, biochemical and genetic selection. Furthermore, this shows increased γ-zein is an acceptable substitute for α-zein for full poppability. Since we have developed multiple QPP introgressions, this gives good scope for ongoing hybrid production and future evaluation of agronomic performance and selection of elite hybrids. In a wider context, this study shows the potential for breeding beneficial traits into popcorn for agronomic improvement.
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http://dx.doi.org/10.3389/fpls.2018.01803DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6291453PMC
December 2018

Ultrasound assisted low-temperature drying of kiwifruit: Effects on drying kinetics, bioactive compounds and antioxidant activity.

J Sci Food Agric 2019 Apr 7;99(6):2901-2909. Epub 2019 Jan 7.

Department of Chemistry, University of the Balearic Islands, Palma de Mallorca, Spain.

Background: Low-temperature drying is considered to be a promising technique for food processing. It preserves thermolabile compounds and might be intensified by acoustic assistance. The effect of acoustic assistance (20.5 kW m ) during low-temperature drying of kiwifruit (at 5, 10 and 15 °C, and 1 m s ) on drying kinetics, bioactive compounds (such as ascorbic acid, vitamin E, and total polyphenols), and antioxidant activity was studied.

Results: Drying time was shortened by 55-65% when using power ultrasound. A diffusion model was used to evaluate the drying kinetics. The effective diffusion coefficient increased by 154 ± 30% and the external mass transfer coefficient increased by 158 ± 66% when ultrasound was applied during drying, compared with drying without ultrasound application. With regard to bioactive compounds and antioxidant activity, although samples dried at 15 °C presented significantly higher (P < 0.05) losses (39-54% and 57-69%, respectively) than samples dried at 5 °C (14-43% and 23-50%, respectively) when ultrasound was not applied, the application of ultrasound during drying at 15 °C significantly reduced (P < 0.05) those losses in all quality parameters (15-47% and 47-58%, respectively).

Conclusion: Overall, low-temperature drying of kiwifruit was enhanced by acoustic assistance preserving bioactive compounds and antioxidant activity, especially at 15 °C. © 2018 Society of Chemical Industry.
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http://dx.doi.org/10.1002/jsfa.9503DOI Listing
April 2019