Deep mutational scanning of hepatitis B virus reveals a mechanism for cis-preferential reverse transcription.

Hepatitis B virus (HBV) is a small double-stranded DNA virus that chronically infects 296 million people. Over half of its compact genome encodes proteins in two overlapping reading frames, and during evolution, multiple selective pressures can act on shared nucleotides. This study combines an RNA-based HBV cell culture system with deep mutational scanning (DMS) to uncouple cis- and trans-acting sequence requirements in the HBV genome. The results support a leaky ribosome scanning model for polymerase translation, provide a fitness map of the HBV polymerase at single-nucleotide resolution, and identify conserved prolines adjacent to the HBV polymerase termination codon that stall ribosomes. Further experiments indicated that stalled ribosomes tether the nascent polymerase to its template RNA, ensuring cis-preferential RNA packaging and reverse transcription of the HBV genome.

Observation and Characterization of Vibrationally Active Surface Species Accessed with Nonthermal Nitrogen Plasmas.

Polycrystalline Ni, Pd, Cu, Ag, and Au foils exposed to nonthermal plasma (NTP)-activated N2 are found to exhibit a vibrational feature near 2200 cm-1 in polarization-modulation infrared reflection-absorption spectroscopy (PM-IRAS) observations that are not present in the same materials exposed to N2 under nonplasma conditions. The feature is similar to that reported elsewhere and is typically assigned to chemisorbed N2. We employ a combination of temperature-dependent experiments, sequential dosing, X-ray photoelectron spectroscopy, isotopic labeling, and density functional theory calculations to characterize the feature. Results are most consistent with a triatomic species, likely NCO, with the C and O likely originating from ppm-level impurities in the ultrahigh-purity (UHP) Ar and/or N2 gas cylinders. The work highlights the potential for nonthermal plasmas to access adsorbates inaccessible thermally as well as the potential contributions of ppm-level impurities to corrupt the interpretation of plasma catalytic chemistry.

Climbing the Hydrogen Evolution Volcano with a NiTi Shape Memory Alloy.

Alkaline water electrolysis is a sustainable way to produce green hydrogen using renewable electricity. Even though the rates of the cathodic hydrogen evolution reaction (HER) are 2-3 orders of magnitude less under alkaline conditions than under acidic conditions, the possibility of using non-precious metal catalysts makes alkaline HER appealing. We identify a novel and facile route for substantially improving HER performance via the use of commercially available NiTi shape memory alloys, which upon heating undergo a phase transformation from the monoclinic martensite to the cubic austenite structure. While the room-temperature performance is modest, austenitic NiTi outperforms Pt (which is the state-of-the-art HER electrocatalyst) in terms of current density by ≤50% at 80 °C. Surface ensembles presented by the austenite phase are computed with density functional theory to bind hydrogen more weakly than either metallic Ni or Ti and to have binding energies ideally suited for HER.

Migratory bats are sensitive to magnetic inclination changes during the compass calibration period.

The Earth's magnetic field is used as a navigational cue by many animals. For mammals, however, there are few data to show that navigation ability relies on sensing the natural magnetic field. In night-time migrating bats, experiments demonstrating a role for the solar azimuth at sunset in the calibration of the orientation system suggest that the magnetic field is a candidate for their compass. Here, we investigated how an altered magnetic field at sunset changes the nocturnal orientation of the bat Pipistrellus pygmaeus. We exposed bats to either the natural magnetic field, a horizontally shifted field (120°), or the same shifted field combined with a reversal of the natural value of inclination (70° to -70°). We later released the bats and found that the take-off orientation differed among all treatments. Bats that were exposed to the 120° shift were unimodally oriented northwards in contrast to controls which exhibited a bimodal north-south distribution. Surprisingly, the orientation of bats exposed to both a 120° shift and reverse inclination was indistinguishable from a uniform distribution. These results suggest that these migratory bats calibrate the magnetic field at sunset, and for the first time, they show that bats are sensitive to the angle of magnetic inclination.

Childcare Subsidy Employment and Copayment Requirements and Child Maltreatment.

Economic support programs for low-income families may play an important role in preventing child abuse and neglect. In the United States, childcare subsidies are provided to low-income families who meet certain requirements to offset the high cost of childcare. States have flexibility in setting many policies related to the provision of childcare subsidies, which results in a great deal of variation in how the programs operate between states. One policy dimension on which states vary is the number of employment hours required to receive childcare subsidies. A small body of work has begun to investigate the ways in which these state policy variations might relate to child maltreatment. Using 11 years of administrative data from the United States, the current study sought to estimate the relationship between two sources of variation in childcare subsidy policies: employment requirements and copayment size; and child neglect, physical abuse, and emotional abuse substantiations. The study found a nuanced relationship between required employment and neglect substantiations. Specifically, requiring some level of work was not associated with neglect substantiations, but requiring 30 hours of employment was associated with higher rates. The study did not find a relationship between copayment size and maltreatment substantiations.

Blood Group Serology and "Race": Looking Back to Move Forward.

Less than a decade after the discovery of the ABO antigens as a Mendelian inherited trait, blood group antigen frequencies were first used to define racial groups. This approach, known as seroanthropology, was the basis for collecting large amounts of blood group frequency data in different populations and was also sometimes used for racist purposes. Ultimately, population geneticists used these data to disprove race as a biological construct. Through understanding the history of seroanthropology, and recognizing the harms of its lingering presence, healthcare providers can better practice race-conscious, as opposed to race-based, transfusion medicine.

Oculomotor Abnormalities in a Sheep (Ovis aries) Model of Huntington's Disease: Towards a Biomarker for Assessing Therapeutic Efficacy.

BACKGROUND: Huntington's disease (HD) is characterized by a loss of control of motor function that causes the presence of abnormal eye movements at early stages. OBJECTIVE: To determine if, compared to normal sheep, HD sheep have abnormal eye movements. METHODS: We measured eye movements in a transgenic sheep (Ovis aries) model of HD using a purpose-built, head-mounted sheep oculometer. This allows us to measure saccades without the need for either behavioral training or head fixation. At the age of testing (6 years old), the HD sheep were pre-manifest. We used 21 sheep (11 HD, 10 normal). RESULTS: We found small but significant differences in eye movements between normal (control) and HD sheep during vestibular ocular reflex (VOR)- and vestibular post-rotational nystagmus (PRN)-based tests. CONCLUSIONS: Two measures were identified that could distinguish normal from HD sheep; the number of PRN oscillations when tested in the dark and the gain (eye movement to head movement ratio) during the VOR when tested in the light. To our knowledge, this is the first study in which eye movements have been quantified in sheep. It demonstrates the feasibility of measuring and quantifying human-relevant eye movements in this species. The HD-relevant deficits show that even in 'premanifest' sheep there are measurable signs of neurological dysfunction that are characterized by loss of control of eye movements.

An RNA-based system to study hepatitis B virus replication and evaluate antivirals.

Hepatitis B virus (HBV) chronically infects an estimated 300 million people, and standard treatments are rarely curative. Infection increases the risk of liver cirrhosis and hepatocellular carcinoma, and consequently, nearly 1 million people die each year from chronic hepatitis B. Tools and approaches that bring insights into HBV biology and facilitate the discovery and evaluation of antiviral drugs are in demand. Here, we describe a method to initiate the replication of HBV, a DNA virus, using synthetic RNA. This approach eliminates contaminating background signals from input virus or plasmid DNA that plagues existing systems and can be used to study multiple stages of HBV replication. We further demonstrate that this method can be uniquely applied to identify sequence variants that confer resistance to antiviral drugs.

Home, but Left Alone: Time at Home and Child Abuse and Neglect During COVID-19.

We use high-frequency mobile phone movement data and quick-release administrative data from Georgia to examine how time at home during the COVID-19 pandemic is related to child maltreatment referrals. Findings show that referrals plummeted by 58% relative to previous years, driven by fewer referrals from education personnel. After this initial decline, however, each 15 minutes at home was associated with an increase in referrals of material neglect by 3.5% and supervisory neglect by 1%. Our results describe how children have fared during the initial wave of the pandemic, and the results have long-term implications for child development and well-being.

Paid Family Leave: An Upstream Intervention to Prevent Family Violence.

Purpose: Family violence imposes tremendous costs on victims and society. Rarely are policies focused on the primary prevention of family violence. Given the prevalence of family violence-including child maltreatment and intimate partner violence (IPV)-during the perinatal period, policies targeting this vulnerable time period may be successful in primary prevention. Paid family leave (PFL) programs provide income-replacement during particularly stressful family events, such as the birth of a child. Method: In this commentary, we describe the conceptual links between PFL, child maltreatment, and IPV, suggesting that PFL may be a promising strategy for the primary prevention of child maltreatment and IPV. Results: There is emerging evidence that policies targeting the early years of life may reduce child maltreatment and IPV. Conclusion: Addressing the concrete and economic challenges faced by caregivers is one promising strategy for the prevention of family violence.

DDX60 selectively reduces translation off viral type II internal ribosome entry sites.

Co-opting host cell protein synthesis is a hallmark of many virus infections. In response, certain host defense proteins limit mRNA translation globally, albeit at the cost of the host cell's own protein synthesis. Here, we describe an interferon-stimulated helicase, DDX60, that decreases translation from viral internal ribosome entry sites (IRESs). DDX60 acts selectively on type II IRESs of encephalomyocarditis virus (EMCV) and foot and mouth disease virus (FMDV), but not by other IRES types or by 5' cap. Correspondingly, DDX60 reduces EMCV and FMDV (type II IRES) replication, but not that of poliovirus or bovine enterovirus 1 (BEV-1; type I IRES). Furthermore, replacing the IRES of poliovirus with a type II IRES is sufficient for DDX60 to inhibit viral replication. Finally, DDX60 selectively modulates the amount of translating ribosomes on viral and in vitro transcribed type II IRES mRNAs, but not 5' capped mRNA. Our study identifies a novel facet in the repertoire of interferon-stimulated effector genes, the selective downregulation of translation from viral type II IRES elements.

Human hepatocyte PNPLA3-148M exacerbates rapid non-alcoholic fatty liver disease development in chimeric mice.

Advanced non-alcoholic fatty liver disease (NAFLD) is a rapidly emerging global health problem associated with pre-disposing genetic polymorphisms, most strikingly an isoleucine to methionine substitution in patatin-like phospholipase domain-containing protein 3 (PNPLA3-I148M). Here, we study how human hepatocytes with PNPLA3 148I and 148M variants engrafted in the livers of broadly immunodeficient chimeric mice respond to hypercaloric diets. As early as four weeks, mice developed dyslipidemia, impaired glucose tolerance, and steatosis with ballooning degeneration selectively in the human graft, followed by pericellular fibrosis after eight weeks of hypercaloric feeding. Hepatocytes with the PNPLA3-148M variant, either from a homozygous 148M donor or overexpressed in a 148I donor background, developed microvesicular and severe steatosis with frequent ballooning degeneration, resulting in more active steatohepatitis than 148I hepatocytes. We conclude that PNPLA3-148M in human hepatocytes exacerbates NAFLD. These models will facilitate mechanistic studies into human genetic variant contributions to advanced fatty liver diseases.

A Step Towards Validation of High-Throughput Sequencing for the Identification of Plant Pathogenic Oomycetes.

The advancement in high-throughput sequencing (HTS) technology allows the detection of pathogens without the need for isolation or template amplification. Plant regulatory agencies worldwide are adopting HTS as a prescreening tool for plant pathogens in imported plant germplasm. The technique is a multipronged process and, often, the bioinformatic analysis complicates detection. Previously, we developed E-probe diagnostic nucleic acid analysis (EDNA), a bioinformatic tool that detects pathogens in HTS data. EDNA uses custom databases of signature nucleic acid sequences (e-probes) to reduce computational effort and subjectivity when determining pathogen presence in a sample. E-probes of Pythium ultimum and Phytophthora ramorum were previously validated only using simulated HTS data. However, HTS samples generated from infected hosts or pure culture may vary in pathogen concentration, sequencing bias, and data quality, suggesting that each pathosystem requires further validation. Here, we used metagenomic and genomic HTS data generated from infected hosts and pure culture, respectively, to further validate and curate e-probes of Pythium ultimum and Phytophthora ramorum. E-probe length was found to be a determinant of diagnostic sensitivity and specificity; 80-nucleotide e-probes increased the diagnostic specificity to 100%. Curating e-probes to increase specificity affected diagnostic sensitivity only for 80-nucleotide Pythium ultimum e-probes. Comparing e-probes with alternative databases and bioinformatic tools in their speed and ability to find Pythium ultimum and Phytophthora ramorum demonstrated that, although pathogen sequence reads were detected by other methods, they were less specific and slower when compared with e-probes.

Observation and rationalization of nitrogen oxidation enabled only by coupled plasma and catalyst.

Heterogeneous catalysts coupled with non-thermal plasmas (NTP) are known to achieve reaction yields that exceed the contributions of the individual components. Rationalization of the enhancing potential of catalysts, however, remains challenging because the background contributions from NTP or catalysts are often non-negligible. Here, we first demonstrate platinum (Pt)-catalyzed nitrogen (N2) oxidation in a radio frequency plasma afterglow at conditions at which neither catalyst nor plasma alone produces significant concentrations of nitric oxide (NO). We then develop reactor models based on reduced NTP- and surface-microkinetic mechanisms to identify the features of each that lead to the synergy between NTP and Pt. At experimental conditions, NTP and thermal catalytic NO production are suppressed by radical reactions and high N2 dissociation barrier, respectively. Pt catalyzes NTP-generated radicals and vibrationally excited molecules to produce NO. The model construction further illustrates that the optimization of productivity and energy efficiency involves tuning of plasma species, catalysts properties, and the reactor configurations to couple plasma and catalysts. These results provide unambiguous evidence of synergism between plasma and catalyst, the origins of that synergy for N2 oxidation, and a modeling approach to guide material selection and system optimization.

Geography of mobility and parenting behavior in low income families.

BACKGROUND: The geographic location of birth has implications for low-income children's upward economic mobility, as Chetty, Hendren, Kline, and Saez (2014) found in an examination of millions of income tax records from each county in the US. Additional work indicates that low income children in higher economic mobility counties have higher language scores and fewer behavioral problems (Donnelly et al., 2017). However, the processes by which the geography of opportunity influences parenting are less well-understood. OBJECTIVE: This study examines whether living in higher intergenerational mobility counties is associated with less harsh parenting, material hardship, household violence and substance use, and low child supervision - parenting behaviors that increase the risk for child maltreatment - for low-income families. DATA: Data come from the Fragile Families and Child Wellbeing Study, a longitudinal birth cohort of low income families in 20 cities in the U.S (N ~, 2841; 76% lower (household income of $41,994 or less) and 24% higher-income) linked to county level data on intergenerational mobility from the Equality of Opportunity Project. METHODS: We estimate OLS and Linear Probability regressions of the association between (1) exposure to county-level intergenerational mobility and (2) number of waves of exposure to county intergenerational mobility 1 standard deviation above the mean and maternal parenting behaviors. RESULTS: A 1 standard deviation increase in county level intergenerational mobility is associated with decreases in harsh parenting, but not indicators of neglect. Longer exposure to high intergenerational mobility areas was associated with decreased maternal harsh parenting and risk for child maltreatment. CONCLUSIONS: For low-income children, higher intergenerational mobility is associated with decreased risk of harsh parenting, particularly at younger ages, as is longer exposure to high intergenerational mobility areas. That lower-income families are less likely to live in economically mobile geographies may exacerbate inequalities among income groups.

Viral Reservoir Capacity of Wild Prunus Alternative Hosts of Plum Pox Virus Through Multiple Cycles of Transmission and Dormancy.

Plum pox virus (PPV) is a significant pathogen of Prunus worldwide and is known for having a broad experimental host range. Many of these hosts represent epidemiological risks as potential wild viral reservoirs. A comparative study of the PPV reservoir capacity of three commonly found native North American species, western choke cherry (Prunus virginiana var. demissa), black cherry (Prunus serotina), and American plum (Prunus americana) was conducted. Pennsylvania isolates of PPV-D were transmitted from the original host peach (Prunus persica cv. GF305) to all three species. Viral accumulation and transmission rates to alternative hosts and peach were monitored over the course of five vegetative growth and cold induced dormancy (CID) cycles. The three alternative host species demonstrated differences in their ability to maintain PPV-D and the likelihood of transmission to additional alternative hosts or back transmission to peach. Western choke cherry had low (5.8%) initial infection levels, PPV-D was not transmissible to additional western choke cherry, and transmission of PPV-D from western choke cherry to peach was only possible before the first CID cycle. Black cherry had intermediate initial infection levels (26.6%) but did not maintain high infection levels after repeated CID cycles. Conversely, American plum had a high level (50%) of initial infection that was not significantly different from initial infection in peach (72.2%) and maintained moderate levels (15 to 25%) of infection and PPV-D transmission to both American plum and peach through all five cycles of CID. Our results indicate that American plum has the greatest potential to act as a reservoir host for Pennsylvania isolates of PPV-D.

The power of the future: Intergenerational income mobility and child maltreatment in the United States.

BACKGROUND: Recent research has shown that the likelihood of children experiencing intergenerational, upward income mobility depends on the community in which they are raised. Whether parents consider their children's economic chances in their parenting decisions, however, is not well understood. OBJECTIVE: To examine the relationship between county-level income mobility-distinct from income inequality and poverty-and child maltreatment. PARTICIPANTS AND SETTING: Administrative data from the National Child Abuse and Neglect Data System: Child File for 2406 counties were merged with measures of intergenerational income mobility from Chetty et al. (2014a), including the probability that a child born in the bottom quintile of the national income distribution reaches the top quintile by age thirty. METHODS: Weighted least squares analyses were used to empirically estimate the relationship between intergenerational income mobility and child maltreatment report rates. Maltreatment reports were also divided into subgroups by age and metropolitan status. RESULTS: Counties where children have a greater chance of moving up the income ladder have lower child maltreatment report rates, independent from income inequality and poverty rates. This relationship is consistent across all child ages (0-17). The relationship between upward income mobility and substantiated child maltreatment is also negatively correlated among non-metropolitan counties. CONCLUSIONS: Children experience a lower risk for maltreatment if they are more likely to move up the income ladder in adulthood. Macroeconomic factors and policies that reduce income inequality and enhance economic mobility are likely to prevent child maltreatment.

Flavivirus-host interactions: an expanding network of proviral and antiviral factors.

Flaviviruses are zoonotic pathogens transmitted by the bite of infected mosquitos and ticks and represent a constant burden to human health. Here we review recent literature aimed at uncovering how flaviviruses interact with the cells that they infect. A better understanding of these interactions may ultimately lead to novel therapeutic targets. We highlight several studies that employed low-biased methods to discover new protein-protein, protein-RNA, and genetic interactions, and spotlight recent work characterizing the host protein, TMEM41B, which has been shown to be critical for infection by diverse flaviviruses and coronaviruses.