Effect of Replacing Race With Apolipoprotein L1 Genotype in Calculation of Kidney Donor Risk Index.

Renal allografts from deceased African American donors with two apolipoprotein L1 gene (APOL1) renal-risk variants fail sooner than kidneys from donors with fewer variants. The Kidney Donor Risk Index (KDRI) was developed to evaluate organ offers by predicting allograft longevity and includes African American race as a risk factor. Substituting APOL1 genotype for race may refine the KDRI. For 622 deceased African American kidney donors, we applied a 10-fold cross-validation approach to estimate contribution of APOL1 variants to a revised KDRI. Cross-validation was repeated 10 000 times to generate distribution of effect size associated with APOL1 genotype. Average effect size was used to derive the revised KDRI weighting. Mean current-KDRI score for all donors was 1.4930 versus mean revised-KDRI score 1.2518 for 529 donors with no or one variant and 1.8527 for 93 donors with two variants. Original and revised KDRIs had comparable survival prediction errors after transplantation, but the spread in Kidney Donor Profile Index based on presence or absence of two APOL1 variants was 37 percentage points. Replacing donor race with APOL1 genotype in KDRI better defines risk associated with kidneys transplanted from deceased African American donors, substantially improves KDRI score for 85-90% of kidneys offered, and enhances the link between donor quality and recipient need.

Modeling community COVID-19 transmission risk associated with U.S. universities.

The ongoing COVID-19 pandemic is among the worst in recent history, resulting in excess of 520,000,000 cases and 6,200,000 deaths worldwide. The United States (U.S.) has recently surpassed 1,000,000 deaths. Individuals who are elderly and/or immunocompromised are the most susceptible to serious sequelae. Rising sentiment often implicates younger, less-vulnerable populations as primary introducers of COVID-19 to communities, particularly around colleges and universities. Adjusting for more than 32 key socio-demographic, economic, and epidemiologic variables, we (1) implemented regressions to determine the overall community-level, age-adjusted COVID-19 case and mortality rate within each American county, and (2) performed a subgroup analysis among a sample of U.S. colleges and universities to identify any significant preliminary mitigation measures implemented during the fall 2020 semester. From January 1, 2020 through March 31, 2021, a total of 22,385,335 cases and 374,130 deaths were reported to the CDC. Overall, counties with increasing numbers of university enrollment showed significantly lower case rates and marginal decreases in mortality rates. County-level population demographics, and not university level mitigation measures, were the most significant predictor of adjusted COVID-19 case rates. Contrary to common sentiment, our findings demonstrate that counties with high university enrollments may be more adherent to public safety measures and vaccinations, likely contributing to safer communities.

Dynamics of data availability in disease modeling: An example evaluating the trade-offs of ultra-fine-scale factors applied to human West Nile virus disease models in the Chicago area, USA.

BACKGROUND: Since 1999, West Nile virus (WNV) has moved rapidly across the United States, resulting in tens of thousands of human cases. Both the number of human cases and the minimum infection rate (MIR) in vector mosquitoes vary across time and space and are driven by numerous abiotic and biotic forces, ranging from differences in microclimates to socio-demographic factors. Because the interactions among these multiple factors affect the locally variable risk of WNV illness, it has been especially difficult to model human disease risk across varying spatial and temporal scales. Cook and DuPage Counties, comprising the city of Chicago and surrounding suburbs, experience some of the highest numbers of human neuroinvasive cases of WNV in the United States. Despite active mosquito control efforts, there is consistent annual WNV presence, resulting in more than 285 confirmed WNV human cases and 20 deaths from the years 2014-2018 in Cook County alone. METHODS: A previous Chicago-area WNV model identified the fifty-five most high and low risk locations in the Northwest Mosquito Abatement District (NWMAD), an enclave » the size of the combined Cook and DuPage county area. In these locations, human WNV risk was stratified by model performance, as indicated by differences in studentized residuals. Within these areas, an additional two-years of field collections and data processing was added to a 12-year WNV dataset that includes human cases, MIR, vector abundance, and land-use, historical climate, and socio-economic and demographic variables, and was assessed by an ultra-fine-scale (1 km spatial x 1 week temporal resolution) multivariate logistic regression model. RESULTS: Multivariate statistical methods applied to the ultra-fine-scale model identified fewer explanatory variables while improving upon the fit of the previous model. Beyond MIR and climatic factors, efforts to acquire additional covariates only slightly improved model predictive performance. CONCLUSIONS: These results suggest human WNV illness in the Chicago area may be associated with fewer, but increasingly critical, key variables at finer scales. Given limited resources, these findings suggest large variations in model performance occur, depending on covariate availability, and provide guidance in variable selection for optimal WNV human illness modeling.

Overview of the Rapid Response data.

The Type I Diabetes Genetics Consortium (T1DGC) Rapid Response Workshop was established to evaluate published candidate gene associations in a large collection of affected sib-pair (ASP) families. We report on our quality control (QC) and preliminary family-based association analyses. A random sample of blind duplicates was analyzed for QC. Quality checks, including examination of plate-panel yield, marker yield, Hardy-Weinberg equilibrium, mismatch error rate, Mendelian error rate, and allele distribution across plates, were performed. Genotypes from 2324 families within nine cohorts were obtained from a panel of 21 candidate genes, including 384 single-nucleotide polymorphisms on two genotyping platforms performed at the Broad Institute Center for Genotyping and Analysis (Cambridge, MA, USA). The T1DGC Rapid Response project, following rigorous QC procedures, resulted in a 2297 family, 9688 genotyped individual database on a single-candidate gene panel. The available data include 9005 individuals with genotype data from both platforms and 683 individuals genotyped (276 in Illumina; 407 in Sequenom) on only one platform.

Tandem duplication of D-loop and ribosomal RNA sequences in lizard mitochondrial DNA.

Some Cnemidophorus exsanguis have mitochondrial DNA's (mtDNA's) that are 22.2 kilobases (kb) in size, whereas most have mtDNA's of 17.4 kb. Restriction site mapping, DNA transfer hybridization experiments, and electron microscopy show that the size increment stems from the tandem duplication of a 4.8-kb region that includes regulatory sequences and transfer and ribosomal RNA genes. This observation is notable in that sequences outside of the control region are involved in major length variation. Besides revealing a novel form of mtDNA evolution in animals, these duplications provide a useful system for investigating the molecular and evolutionary biology of animal mtDNA.

Nuclear and mitochondrial DNA comparisons reveal extreme rate variation in the molecular clock.

The discovery that the rate of evolution of vertebrate mitochondrial DNA is rapid, compared to the rate for vertebrate nuclear DNA, has resulted in its widespread use in evolutionary studies. Comparison of mitochondrial and nuclear DNA divergences among echinoid and vertebrate taxa of similar ages indicates that the rapid rate of vertebrate mitochondrial DNA evolution is, in part, an artifact of a widely divergent rate of nuclear DNA evolution. This disparity in relative rates of mitochondrial and nuclear DNA divergence suggests that the controls and constraints under which the mitochondrial and nuclear genomes operate are evolving independently, and provides evidence that is independent of fossil dating for a robust rejection of a generalized molecular clock hypothesis of DNA evolution.

Mitochondrial DNA analyses and the origin and relative age of parthenogenetic lizards (genus Cnemidophorus).

Morphological, karyological, and allozyme analyses indicate that the parthenogenetic lizards Cnemidophorus neomexicanus and diploid C. tesselatus are hybrids formed, respectively, by crosses involving the bisexual species C. tigris and C. inornatus, and C. tigris and C. septemvittatus. Mitochondrial DNA, which is inherited maternally, was obtained from each of these species. Analyses of the mitochondrial DNA's and their restriction endonuclease digestion products by electron microscopy and agarose gel electrophoresis support the hybridization hypothesis by indicating that C. tigris (specifically the subspecies marmoratus) was the maternal parent species for both C. neomexicanus and C. tesselatus. Furthermore, these data imply that these two parthenogenetic species are younger than some races of C. tigris.

Heteroplasmy suggests limited biparental inheritance of Mytilus mitochondrial DNA.

Strict maternal inheritance of mitochondrial DNA is commonly observed in animals. There is usually only one mitochondrial DNA population (homoplasmy) within an individual. Mussels of the Mytilus edulis species group appear to be exceptions in both respects. Of 150 Mytilus individuals examined, 85 were heteroplasmic. Mitochondrial DNA types within heteroplasmic individuals differed greatly; in one comparison, the inferred sequence difference was 20 +/- 5 percent. Homoplasmic individuals with mitochondrial DNA similar to the heteroplasmic mitochondrial DNA types were found. These observations are best explained by the hypothesis that biparental inheritance of mitochondrial DNA can occur in Mytilus.

Real-time landslide warning during heavy rainfall.

A real-time system for issuing warnings of landslides during major storms is being developed for the San Francisco Bay region, California. The system is based on empirical and theoretical relations between rainfall and landslide initiation, geologic determination of areas susceptible to landslides, real-time monitoring of a regional network of telemetering rain gages, and National Weather Service precipitation forecasts. This system was used to issue warnings during the storms of 12 to 21 February 1986, which produced 800 millimeters of rainfall in the region. Although analysis after the storms suggests that modifications and additional development are needed, the system successfully predicted the times of major landslide events. It could be used as a prototype for systems in other landslide-prone regions.

Overview of the MHC fine mapping data.

AIM: The aim of this study was to perform quality control (QC) and initial family-based association analyses on the major histocompatibility complex (MHC) single nucleotide polymorphism (SNP) and microsatellite marker data for the MHC Fine Mapping Workshop through the Type 1 Diabetes Genetics Consortium (T1DGC). METHODS: A random sample of blind duplicates was sent for analysis of QC. DNA samples collected from participants were shipped to the genotyping laboratory from several T1DGC DNA Repository sites. Quality checks including examination of plate-panel yield, marker yield, Hardy-Weinberg equilibrium, mismatch error rate, Mendelian error rate and allele distribution across plates were performed. RESULTS: Genotypes from 2325 families within nine cohorts were obtained and subjected to QC procedures. The MHC project consisted of three marker panels - two 1536 SNP sets (Illumina Golden Gate platform performed at the Wellcome Trust Sanger Institute, Cambridge, UK) and one 66 microsatellite marker panel (performed at deCODE). In the raw SNP data, the overall concordance rate was 99.1% (+/-0.02). CONCLUSIONS: The T1DGC MHC Fine Mapping project resulted in a 2300 family, 9992 genotyped individuals database comprising of two 1536 SNP panels and a 66 microsatellite panel to densely cover the 4 Mb MHC core region for use in statistical genetic analyses.

Light Harvesting with Guide-Slide Superabsorbing Condensed-Matter Nanostructures.

We establish design principles for light-harvesting antennae whose energy capture scales superlinearly with system size. Controlling the absorber dipole orientations produces sets of "guide-slide" states that promote steady-state superabsorbing characteristics in noisy condensed-matter nanostructures. Inspired by natural photosynthetic complexes, we discuss the example of ringlike dipole arrangements and show that, in our setup, vibrational relaxation enhances rather than impedes performance. Remarkably, the superabsorption effect proves to be robust to O(5%) disorder simultaneously for all relevant system parameters, showing promise for experimental exploration across a broad range of platforms.

The scented brain: pheromonal responses in humans.

Using PET, Savic et al., in this issue of Neuron, found a sexually dimorphic neural response to two putative human pheromones. The specific regions activated combined with the pronounced sex difference depict a pheromonal-type brain response in humans. Here, we preview this finding and suggest that human pheromones exist.

Big trees from little genomes: mitochondrial gene order as a phylogenetic tool.

Gene arrangement comparisons are a powerful tool for phylogenetic studies, especially those focused on ancient relationships. Recent reports using metazoan mitochondrial genomes address evolutionary relationships as well as rates and mechanisms of rearrangement. Mitochondrial systems serve as a model for larger-scale comparisons of whole organismal genomes and a stimulus for developing methods for reconstructing the patterns of rearrangement.

Assessing human risk of illness with West Nile virus mosquito surveillance data to improve public health preparedness.

Surveillance for West Nile virus (WNV) and other mosquito-borne pathogens involves costly and time-consuming collection and testing of mosquito samples. One difficulty faced by public health personnel is how to interpret mosquito data relative to human risk, thus leading to a failure to fully exploit the information from mosquito testing. The objective of our study was to use the information gained from historic West Nile virus mosquito testing to determine human risk relative to mosquito infection and to assess the usefulness of our mosquito infection forecasting models to give advance warning. We compared weekly mosquito infection rates from 2004 to 2013 to WNV case numbers in Illinois. We then developed a weather-based forecasting model to estimate the WNV mosquito infection rate one to 3 weeks ahead of mosquito testing both statewide and for nine regions of Illinois. We further evaluated human illness risk relative to both the measured and the model-estimated infection rates to provide guidelines for public health messages. We determined that across 10 years, over half of human WNV cases occurred following the 29 (of 210) weeks with the highest mosquito infection rates. The values forecasted by the models can identify those time periods, but model results and data availability varied by region with much stronger results obtained from regions with more mosquito data. The differences among the regions may be related to the amount of surveillance or may be due to diverse landscape characteristics across Illinois. We set the stage for better use of all surveillance options available for WNV and described an approach to modelling that can be expanded to other mosquito-borne illnesses.

Barley yellow rust in North America.

Yellow rust of barley is an invasive disease that was found in the past 10 years in North America. The causal agent, Puccinia striiformis f. sp. hordei, was introduced into Colombia, South America, from Europe in 1975. It spread to all major barley-producing areas in South America by 1982. In 1988 it was found in Mexico and in 1991 in Texas. Since then it has been found in all major barley-producing areas of the American West. Originally described as race (R) 24, barley yellow rust in North America is now known to be a very heterogeneous population. Resistance has been identified, evaluated, and is being introduced into commercial malting and other barley cultivars. Cultural and chemical controls are effective and available. An integrated approach using general field resistance and other tactics is described for sustainable management of barley yellow rust.

Predicting West Nile Virus Infection Risk From the Synergistic Effects of Rainfall and Temperature.

Mosquito-based surveillance is a practical way to estimate the risk of transmission of West Nile virus (WNV) to people. Variations in temperature and precipitation play a role in driving mosquito infection rates and transmission of WNV, motivating efforts to predict infection rates based on prior weather conditions. Weather conditions and sequential patterns of meteorological events can have particularly important, but regionally distinctive, consequences for WNV transmission, with high temperatures and low precipitation often increasing WNV mosquito infection. Predictive models that incorporate weather can thus be used to provide early indications of the risk of WNV infection. The purpose of this study was first, to assess the ability of a previously published model of WNV mosquito infection to predict infection for an area within the region for which it was developed, and second, to improve the predictive ability of this model by incorporating new weather factors that may affect mosquito development. The legacy model captured the primary trends in mosquito infection, but it was improved considerably when calibrated with local mosquito infection rates. The use of interaction terms between precipitation and temperature improved model performance. Specifically, temperature had a stronger influence than rainfall, so that lower than average temperature greatly reduced the effect of low rainfall on increased infection rates. When rainfall was lower, high temperature had an even stronger positive impact on infection rates. The final model is practical, stable, and operationally valid for predicting West Nile virus infection rates in future weeks when calibrated with local data.

The nucleotide sequence of the murine Hox-D3 (Hox-4.1) gene reveals extensive identity with the human protein.

We report the sequence of the murine Hox-D3 gene, formerly referred to as Hox-4, Hox-4.1 and Hox-4A. This gene is located on murine chromosome 2 in the Hox-D complex. The predicted Hox-D3 protein comprises 417 amino acids and displays 95% identity to the human protein. We have demonstrated that Hox-D3 is expressed in the skin, kidney and thymus, but not in lung, liver, spleen or stomach.

Rates and patterns of base change in the small subunit ribosomal RNA gene.

The small subunit ribosomal RNA gene (srDNA) has been used extensively for phylogenetic analyses. One common assumption in these analyses is that substitution rates are biased toward transitions. We have developed a simple method for estimating relative rates of base change that does not assume rate constancy and takes into account base composition biases in different structures and taxa. We have applied this method to srDNA sequences from taxa with a noncontroversial phylogeny to measure relative rates of evolution in various structural regions of srRNA and relative rates of the different transitions and transversions. We find that: (1) the long single-stranded regions of the RNA molecule evolve slowest, (2) biases in base composition associated with structure and phylogenetic position exist, and (3) the srDNAs studied lack a consistent transition/transversion bias. We have made suggestions based on these findings for refinement of phylogenetic analyses using srDNA data.

Complete sequence of the mitochondrial DNA of the annelid worm Lumbricus terrestris.

We have determined the complete nucleotide (nt) sequence of the mitochondrial genome of an oligochaete annelid, the earthworm Lumbricus terrestris. This genome contains the 37 genes typical of metazoan mitochondrial DNA (mtDNA), including ATPase8, which is missing from some invertebrate mtDNAs. ATPase8 is not immediately upstream of ATPase6, a condition found previously only in the mtDNA of snails. All genes are transcribed from the same DNA strand. The largest noncoding region is 384 nt and is characterized by several homopolymer runs, a tract of alternating TA pairs, and potential secondary structures. All protein-encoding genes either overlap the adjacent downstream gene or end at an abbreviated stop codon. In Lumbricus mitochondria, the variation of the genetic code that is typical of most invertebrate mitochondrial genomes is used. Only the codon ATG is used for translation initiation. Lumbricus mtDNA is A + T rich, which appears to affect the codon usage pattern. The DHU arm appears to be unpaired not only in tRNAser(AGN), as is typical for metazoans, but perhaps also in tRNAser(UCN), a condition found previously only in a chiton and among nematodes. Relating the Lumbricus gene organization to those of other major protostome groups requires numerous rearrangements.

Complete DNA sequence of the mitochondrial genome of the black chiton, Katharina tunicata.

The DNA sequence of the 15,532-base pair (bp) mitochondrial DNA (mtDNA) of the chiton Katharina tunicata has been determined. The 37 genes typical of metazoan mtDNA are present: 13 for protein subunits involved in oxidative phosphorylation, 2 for rRNAs and 22 for tRNAs. The gene arrangement resembles those of arthropods much more than that of another mollusc, the bivalve Mytilus edulis. Most genes abut directly or overlap, and abbreviated stop codons are inferred for four genes. Four junctions between adjacent pairs of protein genes lack intervening tRNA genes; however, at each of these junctions there is a sequence immediately adjacent to the start codon of the downstream gene that is capable of forming a stem-and-loop structure. Analysis of the tRNA gene sequences suggests that the D arm is unpaired in tRNA(ser)(AGN), which is typical of metazoan mtDNAs, and also in tRNA(ser)(UCN), a condition found previously only in nematode mtDNAs. There are two additional sequences in Katharina mtDNA that can be folded into structures resembling tRNAs; whether these are functional genes is unknown. All possible codons except the stop codons TAA and TAG are used in the protein-encoding genes, and Katharina mtDNA appears to use the same variation of the mitochondrial genetic code that is used in Drosophila and Mytilus. Translation initiates at the codons ATG, ATA and GTG. A + T richness appears to have affected codon usage patterns and, perhaps, the amino acid composition of the encoded proteins. A 142-bp non-coding region between tRNA(glu) and CO3 contains a 72-bp tract of alternating A and T.