Flow Cytometry of Synaptoneurosomes (FCS) Reveals Increased Ribosomal S6 and Calcineurin Proteins in Activated Medial Prefrontal Cortex to Nucleus Accumbens Synapses.

Learning and behavior activate cue-specific patterns of sparsely distributed cells and synapses called ensembles that undergo memory-encoding engram alterations. While Fos is often used to label selectively activated cell bodies and identify neuronal ensembles, there is no comparable endogenous marker to label activated synapses and identify synaptic ensembles. For the purpose of identifying candidate synaptic activity markers, we optimized a flow cytometry of synaptoneurosome (FCS) procedure for assessing protein alterations in activated synapses from male and female rats. After injecting yellow fluorescent protein (YFP)-expressing adeno-associated virus into medial prefrontal cortex (mPFC) to label terminals in nucleus accumbens (NAc) of rats, we injected 20 mg/kg cocaine in a novel context (cocaine+novelty) to activate synapses, and prepared NAc synaptoneurosomes 0-60 min following injections. For FCS, we used commercially available antibodies to label presynaptic and postsynaptic markers synaptophysin and PSD-95 as well as candidate markers of synaptic activity [activity-regulated cytoskeleton protein (Arc), CaMKII and phospho-CaMKII, ribosomal protein S6 (S6) and phospho-S6, and calcineurin and phospho-calcineurin] in YFP-labeled synaptoneurosomes. Cocaine+novelty increased the percentage of S6-positive synaptoneurosomes at 5-60 min and calcineurin-positive synaptoneurosomes at 5-10 min. Electron microscopy verified that S6 and calcineurin levels in synaptoneurosomes were increased 10 min after cocaine+novelty. Pretreatment with the anesthetic chloral hydrate blocked cocaine+novelty-induced S6 and calcineurin increases in synaptoneurosomes, and novel context exposure alone (without cocaine) increased S6, both of which indicate that these increases were due to neural activity per se. Overall, FCS can be used to study protein alterations in activated synapses coming from specifically labeled mPFC projections to NAc.SIGNIFICANCE STATEMENT Memories are formed during learning and are stored in the brain by long-lasting molecular and cellular alterations called engrams formed within specific patterns of cue-activated neurons called neuronal ensembles. While Fos has been used to identify activated ensemble neurons and the engrams within them, we have not had a similar marker for activated synapses that can be used to identify synaptic engrams. Here we developed a procedure for high-throughput in-line analysis of flow cytometry of synaptoneurosome (FCS) and found that ribosomal S6 protein and calcineurin were increased in activated mPFC-NAc synapses. FCS can be used to study protein alterations in activated synapses within specifically labeled circuits.

Efficacy and safety of dolutegravir/lamivudine in virologically suppressed female participants: week 48 data from the pooled TANGO and SALSA studies.

OBJECTIVES: Women represent >50% of people with HIV globally but have historically been underrepresented in clinical trials. We evaluated the efficacy and safety of switching to dolutegravir/lamivudine (DTG/3TC) vs continuing their current antiretroviral regimen (CAR) by sex assigned at birth (female and male) in virologically suppressed adults with HIV-1 without prior virological failure in a pooled analysis of two randomized controlled trials. METHODS: This analysis included 48-week data from the phase 3 TANGO and SALSA studies. Primary and key secondary endpoints included proportions of participants with HIV-1 RNA ≥50 and <50 copies/mL at week 48, respectively. Safety was also assessed. RESULTS: Of 1234 participants, 250 (DTG/3TC, n = 133; CAR, n = 117) were female at birth. Week 48 proportions of participants with Snapshot HIV-1 RNA ≥50 copies/mL were similar regardless of sex at birth (DTG/3TC vs CAR: female, <1% [1/133] vs 2% [2/117]; male, <1% [1/482] vs <1% [3/502]). Proportions with HIV-1 RNA <50 copies/mL were high across sexes and treatment groups (DTG/3TC vs CAR: female, 91% [121/133] vs 89% [104/117]; male, 94% [455/482] vs 94% [471/502]). Immunological response with DTG/3TC was slightly higher in female participants. Incidences of adverse events leading to withdrawal and serious adverse events were low and comparable between treatment groups and across sexes. Weight gain was higher with DTG/3TC than with CAR among female participants aged ≥50 years (treatment difference 2.08 kg [95% confidence interval 0.40-3.75]). CONCLUSIONS: Results confirm the robustness of DTG/3TC as a switch option in virologically suppressed females with HIV-1, with outcomes similar to those in males.

Role of genetic analysis of products of conception and PGT in managing early pregnancy loss.

This article considers the addition of comprehensive 24-chromosomal microarray (CMA) analysis of products of conception (POC) to a standard evaluation for recurrent pregnancy loss (RPL) to help direct treatment towards expectant management versus IVF with preimplantation genetic testing for aneuploidies (PGT-A). The review included retrospective data from 65,333 miscarriages, a prospective evaluation of 378 couples with RPL who had CMA testing of POC and the standard workup, and data from an additional 1020 couples who were evaluated for RPL but did not undergo CMA testing of POC. Aneuploidy in POC explained the pregnancy loss in 57.7% (218/378) of cases. In contrast, the full RPL evaluation recommended by the American Society for Reproductive Medicine identified a potential cause in only 42.9% (600/1398). Combining the data from the RPL evaluation and the results of genetic testing of POC provides a probable explanation for the loss in over 90% (347/378) of women. Couples with an unexplained loss after the standard evaluation with POC aneuploidy accounted for 41% of cases; PGT-A may be considered after expectant management. Conversely, PGT-A would have a limited role in those with a euploid loss and a possible explanation after the standard workup. Categorizing a pregnancy loss as an explained versus unexplained loss after the standard evaluation combined with the results of CMA testing of POC may help identify patients who would benefit from expectant management versus PGT-A.

Electronic nicotine delivery systems (ENDS): Frequency of use and smoking-cessation efforts among U.S. women of reproductive age.

OBJECTIVE: Reducing harm from combustible cigarette use among women of reproductive age (WRA) is critical given their potential vulnerability to multigenerational adverse impacts of cigarette smoking. Although electronic nicotine delivery systems (ENDS) are not approved smoking cessation aids in the US, many WRA who smoke report using ENDS to help quit smoking. Associations between ENDS use patterns and smoking-cessation efforts among US WRA remain unclear. METHODS: Using the Population Assessment of Tobacco and Health (PATH) Study, we examined whether baseline (Wave 3 or 4) ENDS use frequency predicted (a) making a cigarette quit attempt (QA) and (b) successful quitting by follow-up (Wave 4 or 5, respectively) among WRA (N = 2834; 72.1% non-Hispanic White). RESULTS: Daily ENDS use predicted greater adjusted odds of making a QA than non-daily (AOR = 1.63, 95% CI = 1.03, 2.59) and no ENDS use (AOR = 1.97, 95% CI = 1.23, 3.14), and greater odds of successful smoking cessation than non-daily use (AOR = 2.37, 95% CI = 1.31, 4.26). Daily ENDS use did not significantly improve odds of successful smoking cessation compared to no ENDS use (AOR = 1.62, 95% CI = 0.97, 2.69). Non-daily ENDS use did not significantly improve odds of making a QA (AOR = 1.21, 95% CI = 0.94, 1.56) and hindered successful smoking cessation compared to no ENDS use (AOR = 0.68, 95% CI = 0.48, 0.98). CONCLUSIONS: These findings suggest that benefits of ENDS for smoking cessation in WRA may be greatest among those who use ENDS daily. WRA who choose to use ENDS to help quit would be well-informed by evidence that non-daily ENDS use may impede smoking cessation.

Sex differences in tobacco use, attempts to quit smoking, and cessation among dual users of cigarettes and e-cigarettes: Longitudinal findings from the US Population Assessment of Tobacco and Health Study.

SIGNIFICANCE: A growing number of adults use more than one tobacco product, with dual use of cigarettes and e-cigarettes being the most common combination. Monitoring sex disparities in tobacco use is a public health priority. However, little is known regarding whether dual users differ by sex. METHODS: Data came from Waves 4-6 (12/2016-11/2021) of the Population Assessment of Tobacco and Health Study, a US nationally-representative longitudinal survey. This analysis included current adult dual users of cigarettes and e-cigarettes. We used weighted generalized estimating equations to assess the association between sex and (1) making a cigarette quit attempt (n = 1882 observations from n = 1526 individuals) and (2) smoking cessation (n = 2081 observations from n = 1688 individuals) across two wave pairs, adjusting for age, education, ethnicity, time-to-first cigarette after waking, and e-cigarette use frequency. RESULTS: Among US dual users, 14.1% (95% Confidence Intervals [Cl] = 11.9-16.4) of females and 23.4% (20.0-26.9) of males were young adults (aged 18-24), 11.7% (9.2-14.2) of females and 14.4% (11.6-17.2) of males had

Sex differences in tobacco use, attempts to quit smoking, and cessation among dual users of cigarettes and e-cigarettes: Longitudinal findings from the US Population Assessment of Tobacco and Health Study.

SIGNIFICANCE: A growing number of adults use more than one tobacco product, with dual use of cigarettes and e-cigarettes being the most common combination. Monitoring sex disparities in tobacco use is a public health priority. However, little is known regarding whether dual users differ by sex. METHODS: Data came from Waves 4-6 (12/2016-11/2021) of the Population Assessment of Tobacco and Health Study, a US nationally-representative longitudinal survey. This analysis included current adult dual users of cigarettes and e-cigarettes. We used weighted generalized estimating equations to assess the association between sex and (1) making a cigarette quit attempt (n = 1882 observations from n = 1526 individuals) and (2) smoking cessation (n = 2081 observations from n = 1688 individuals) across two wave pairs, adjusting for age, education, ethnicity, time-to-first cigarette after waking, and e-cigarette use frequency. RESULTS: Among US dual users, 14.1% (95% Confidence Intervals [Cl] = 11.9-16.4) of females and 23.4% (20.0-26.9) of males were young adults (aged 18-24), 11.7% (9.2-14.2) of females and 14.4% (11.6-17.2) of males had

Characterizing locus specific chromatin structure and dynamics with correlative conventional and super-resolution imaging in living cells.

The dynamic rearrangement of chromatin is critical for gene regulation, but mapping both the spatial organization of chromatin and its dynamics remains a challenge. Many structural conformations are too small to be resolved via conventional fluorescence microscopy and the long acquisition time of super-resolution photoactivated localization microscopy (PALM) precludes the structural characterization of chromatin below the optical diffraction limit in living cells due to chromatin motion. Here we develop a correlative conventional fluorescence and PALM imaging approach to quantitatively map time-averaged chromatin structure and dynamics below the optical diffraction limit in living cells. By assigning localizations to a locus as it moves, we reliably discriminate between bound and unbound dCas9 molecules, whose mobilities overlap. Our approach accounts for changes in DNA mobility and relates local chromatin motion to larger scale domain movement. In our experimental system, we show that compacted telomeres move faster and have a higher density of bound dCas9 molecules, but the relative motion of those molecules is more restricted than in less compacted telomeres. Correlative conventional and PALM imaging therefore improves the ability to analyze the mobility and time-averaged nanoscopic structural features of locus specific chromatin with single molecule sensitivity and yields unprecedented insights across length and time scales.

Association between socioeconomic position of the household head, food insecurity and psychological health: an application of propensity score matching.

BACKGROUND: Mental health outcomes can be influenced by various factors, one of which has recently gained attention, namely food security. Food security is paramount to maintaining not only physical, but also mental health. There is an increasing need to understand the interplay between food insecurity (FI) and mental health outcomes, especially among vulnerable populations. The objective of this study was to investigate the effect of FI on psychological health (anxiety and depression) as well as to examine the modifying effect of socioeconomic position on this relationship. METHODS: A cross-sectional study was conducted in Maputo City, Mozambique, in 1,842 participants. Data were collected through structured interviews using a modified version of the US Department of Agriculture Household Food Security Module to measure FI, and the Hospital Anxiety and Depression Scale to measure anxiety and depression. A composite variable for psychological health was created. Propensity score matching and interaction effect analyses were employed to examine the effects of FI on psychological health and the moderating role of socioeconomic position. RESULTS: Of the 1,174 participants randomly assigned to propensity score matching, 787 were exposed to FI while 387 were unexposed. The analysis revealed stark disparities in psychological health outcomes associated with FI. The risk of poor psychological health among those exposed to FI was 25.79%, which was significantly higher than the 0.26% in unexposed individuals. The risk difference was 25.54% points (95% CI: 22.44-28.63), with a risk ratio of 99.82. Our assessment of population attributable fractions indicated that nearly all the risk for poor psychological health in the exposed group could be ascribed to FI. The interaction effects analysis revealed that socioeconomic status modifies this relationship. Specifically, heads of food-insecure households with a lower socioeconomic position tended to report poor mental health compared to their food-secure counterparts with a higher position. CONCLUSIONS: The findings underscore the profound impact of FI on the mental health of household heads in Maputo City, socioeconomic position being a significant modifier. Addressing household FI along with the socioeconomic position of household heads could be pivotal to mental health promotion, especially among vulnerable populations.

The Effects of Long-Term Dienogest Therapy on In Vitro Fertilization Outcomes in Women with Endometriosis: A Systematic Review and Meta-Analysis.

OBJECTIVES: Assessing dienogest's efficacy in endometriosis patients undergoing in vitro fertilization (IVF). DATA SOURCES: Systematic search in databases (PubMed, MEDLINE, Embase, Web of Science, Cochrane CENTRAL, Google Scholar) until 1 October 2022. STUDY SELECTIONS: Randomized trials and observational studies comparing extended dienogest pre-treatment, no pre-treatment, or gonadotropin-releasing hormone (GnRH) agonist pre-treatment in endometriosis-linked IVF. OUTCOME MEASURES: live birth, clinical pregnancy rates, oocytes collected, miscarriage rate, gonadotropin consumption. DATA EXTRACTIONS AND SYNTHESES: Two authors independently assessed eligibility. Dichotomous variables were analyzed via a random-effect model and Mantel-Haenszel method to calculate weighted estimates and 95% confidence intervals (CI). I2 statistic gauged study heterogeneity; GRADE criteria evaluated evidence quality. CONCLUSIONS: Out of 191 publications, five studies with 723 participants were included. Uncertainty persists on whether prolonged dienogest affects live birth (RR 1.42, 95% CI 0.29 to 6.84; 3 studies, n = 289; I2 86%) and clinical pregnancy rates (RR 1.33, 95% CI 0.31 to 5.65; 3 studies, n = 289; I2 86%) compared to conventional IVF. Moreover, uncertainty remains regarding intervention impact on live birth (RR 1.46, 95% CI 0.63 to 3.37; 1 study, n = 34) and clinical pregnancy rates (RR 1.32, 95% CI 0.78 to 2.23; 3 studies, n = 288; I2 0%) versus long-term GnRH agonist therapy before IVF. Given limited data and very low evidence quality, doubts arise about the benefits of long-term dienogest pre-treatment before conventional IVF in endometriosis patients.

Dentistry from Ancient Phoenicia to Contemporary Lebanon: The USJ Faculty of Dental Medicine in Beirut.

In 2023, the Faculty of Dental Medicine, Saint Joseph University of Beirut (USJ) celebrated its 100th anniversary, marking a century of unwavering commitment to academic excellence. This milestone offers a valuable opportunity to navigate the history and evolution of dentistry in Lebanon, from its ancient roots in Phoenicia to its modern developments. It chronicles the transformative journey of dentistry while recognizing the key role played against all odds by the Society of Jesus and Saint Joseph University of Beirut in fostering the growth of dentistry as a distinct medical discipline.

Nucleosome landscape reflects phenotypic differences in Trypanosoma cruzi life forms.

Trypanosoma cruzi alternates between replicative and nonreplicative life forms, accompanied by a shift in global transcription levels and by changes in the nuclear architecture, the chromatin proteome and histone posttranslational modifications. To gain further insights into the epigenetic regulation that accompanies life form changes, we performed genome-wide high-resolution nucleosome mapping using two T. cruzi life forms (epimastigotes and cellular trypomastigotes). By combining a powerful pipeline that allowed us to faithfully compare nucleosome positioning and occupancy, more than 125 thousand nucleosomes were mapped, and approximately 20% of them differed between replicative and nonreplicative forms. The nonreplicative forms have less dynamic nucleosomes, possibly reflecting their lower global transcription levels and DNA replication arrest. However, dynamic nucleosomes are enriched at nonreplicative regulatory transcription initiation regions and at multigenic family members, which are associated with infective-stage and virulence factors. Strikingly, dynamic nucleosome regions are associated with GO terms related to nuclear division, translation, gene regulation and metabolism and, notably, associated with transcripts with different expression levels among life forms. Finally, the nucleosome landscape reflects the steady-state transcription expression: more abundant genes have a more deeply nucleosome-depleted region at putative 5' splice sites, likely associated with trans-splicing efficiency. Taken together, our results indicate that chromatin architecture, defined primarily by nucleosome positioning and occupancy, reflects the phenotypic differences found among T. cruzi life forms despite the lack of a canonical transcriptional control context.

Linkage drag analysis in three Aegilops speltoides introgressions carrying Sr47 in modern durum and hard red spring wheat germplasm.

KEY MESSAGE: Yield and quality tests of wheat lines derived from RWG35 show they carry little, or no linkage drag and are the preferred source of Sr47 for stem rust resistance. Three durum wheat (Triticum turgidum L. subsp. durum) lines, RWG35, RWG36, and RWG37 carrying slightly different Aegilops speltoides introgressions, but each carrying the Sr47 stem rust resistance gene, were backcrossed to three durum and three hard red spring (HRS) wheat (Triticum aestivum L.) cultivars to produce 18 backcross populations. Each population was backcrossed to the recurrent parent six times and prepared for yield trials to test for linkage drag. Lines carrying the introgression (S-lines) were compared to euploid sibling lines (W-lines) and their parent. Yield trials were conducted from 2018 to 2021 at three locations. Three agronomic and several quality traits were studied. In durum, lines derived from RWG35 had little or no linkage drag. Lines derived from RWG36 and RWG37 still retained linkage drag, most notably involving yield and thousand kernel weight, but also test weight, falling number, kernel hardness index, semolina extract, semolina protein content, semolina brightness, and peak height. In HRS wheat, the results were more complex, though the general result of RWG35 lines having little or no linkage drag and RWG36 and RWG37 lines retaining linkage drag still applied. But there was heterogeneity in the Glenn35S lines, and Linkert lines had problems combining with the Ae. speltoides introgressions. We concluded that introgressions derived from RWG35 either had eliminated linkage drag or any negative effects were minor in nature. We recommend that breeders who wish to incorporate Sr47 into their cultivars should work exclusively with germplasm derived from RWG35.

Regeneration in starved planarians depends on TRiC/CCT subunits modulating the unfolded protein response.

Planarians are able to stand long periods of starvation by maintaining adult stem cell pools and regenerative capacity. The molecular pathways that are needed for the maintenance of regeneration during starvation are not known. Here, we show that down-regulation of chaperonin TRiC/CCT subunits abrogates the regeneration capacity of planarians during starvation, but TRiC/CCT subunits are dispensable for regeneration in fed planarians. Under starvation, they are required to maintain mitotic fidelity and for blastema formation. We show that TRiC subunits modulate the unfolded protein response (UPR) and are required to maintain ATP levels in starved planarians. Regenerative defects in starved CCT-depleted planarians can be rescued by either chemical induction of mild endoplasmic reticulum stress, which leads to induction of the UPR, or by the supplementation of fatty acids. Together, these results indicate that CCT-dependent UPR induction promotes regeneration of planarians under food restriction.

A call to action: Contingency management to improve post-release treatment engagement among people with opioid use disorder who are incarcerated.

People with opioid use disorder (OUD) are overrepresented in US correctional facilities and experience disproportionately high risk for illicit opioid use and overdose after release. A growing number of correctional facilities offer medication for OUD (MOUD), which is effective in reducing these risks. However, a recent evaluation found that <50% of those prescribed MOUD during incarceration continued MOUD within 30 days after release, demonstrating a need to improve post-release continuity of care. We describe available evidence on contingency management (CM), an intervention wherein patients receive incentives contingent on behavior change, to achieve this goal. A prior systematic review reported strong evidence in support of CM for increasing treatment adherence in MOUD programs, but the trials reviewed did not include incarcerated participants. Research on CM to increase treatment adherence among participants in the criminal justice system is limited with mixed findings. However, in comparison to the trials that supported CM's efficacy in the community, CM trials in the criminal justice system provided smaller rewards with greater delays in the delivery of rewards to patients, which likely contributed to null findings. Indeed, a prior meta-analysis demonstrates a dose-response relationship between the magnitude and immediacy of reward and CM effectiveness. Thus, CM involving larger and more immediately delivered rewards are likely necessary to improve MOUD adherence during the critical period following release from incarceration. Future research on the effectiveness and implementation of CM to improve MOUD retention after release from incarceration is warranted.

Effect of Surfactant Selectivity on Shape and Inner Morphology of Triblock Terpolymer Microparticles.

The confined assembly of block copolymers (BCPs) has become a useful tool to prepare microparticles with controlled anisotropy and inner structure. While a solid understanding of the behavior of AB diblock copolymers exists, knowledge on the parameters affecting ABC triblock terpolymer assembly is much more limited. In this work, the effect of block-selective surfactants, sodium-4-vinylbenzenesulfonate (VBS) and sodium dodecylsulfate (SDS), is analyzed in the evaporation-induced confined assembly (EICA) of a polystyrene-block-polybutadiene-block-poly(methyl methacrylate) triblock terpolymer (SBM). Despite using the same terpolymer and emulsification process, SDS results in ellipsoidal microparticles with axially stacked lamellae, while VBS results in spherical microparticles with concentric lamellae or 3D spiral morphology. This change in morphology upon switching the surfactant is further substantiated by molecular simulations and enhances the understanding of terpolymer microphase separation in confinement.

Interest in quitting e-cigarette use by device type and smoking history in US adults.

BACKGROUND: The use of e-cigarettes has been increasing, especially since the introduction of 'pod' devices to the marketplace since 2018. Most adults who vape report interest in quitting. The present study examined level of interest in e-cigarette cessation between users with varying cigarette smoking histories and device types. METHODS: Data obtained from wave 5 (2018-2019) of the Population Assessment of Tobacco and Health study (n=34 309). Analyses were conducted on adult current established e-cigarette users, categorised on cigarette smoking history (current, former or never) and device type (disposable, cartridge/pod, tank or mod). Participants reported if they planned to ever quit e-cigarettes, attempted to quit in the past year and attempted to quit by cutting back in the past year. RESULTS: Of the 2922 established e-cigarette users, 68.21% reported plans to quit vaping; 17.27% reported attempting to quit e-cigarettes in the past year; and 29.28% reported attempting to quit by cutting back in the past year. Cartridge users had higher odds of interest in quitting than tank and mod users. Disposable and cartridge users had higher odds of reporting a past year quit attempt than tank and mod users. Individuals with no smoking history had higher odds of reporting a past year quit attempt or cutting back relative to those reporting dual use (of both e-cigarettes and cigarettes) and former smoking. CONCLUSIONS: Tobacco control should consider the type of e-cigarette device that is being used, alongside users' cigarette smoking history, when developing interventions and other resources for vaping cessation.

Latent Classes of Perceived Addictiveness Predict Marijuana, Alcohol, and Tobacco Use in Youth and Young Adults.

Background: Mass media substance use prevention efforts target addiction perceptions in young people. This study examined youth and young adults' (YAs) perceived addictiveness across several substances and the associations between addiction perceptions and substance use. Methods: Data were collected in 2019 in an online cohort study of Vermonters aged 12-25. Latent class analyses grouped participants by perceived addictiveness of nicotine, caffeine, alcohol, marijuana, cigarettes, electronic vapor products (EVPs), and opioids. Bivariate multinomial logistic and modified Poisson regression estimated associations between sociodemographics, substance use correlates, and subsequent use across latent classes. Results: Four latent classes captured addiction perceptions: high perceived addictiveness of EVPs, cigarettes, marijuana, and alcohol (Class 1: n = 317; 31.3%), low perceived addictiveness of marijuana, alcohol, and caffeine (Class 2: n = 151; 14.3%), low perceived addictiveness of marijuana (Class 3: n = 581; 46.5%), and low perceived addictiveness of nicotine, cigarettes, and EVPs (Class 4: n = 83; 7.9%). For each year increase in age, there was a 36% increased likelihood of being in Class 2 (vs. Class 1) and a 148% increased likelihood of belonging to Class 3 (vs. Class 1). Low perceived addictiveness classes were associated with ever and past 30-day marijuana and alcohol use and predicted past 30-day alcohol use at three-month follow-up. Membership in Classes 2 and 3 also predicted past 30-day marijuana use at Wave 3. Discussion: The strong association between age and latent classes defined by low perceived addictiveness suggests age group differences in addiction perceptions. Findings suggest that YAs may benefit from prevention messaging on addictiveness.

Sensitive, Highly Multiplexed Sequencing of Microhaplotypes From the Plasmodium falciparum Heterozygome.

BACKGROUND: Targeted next-generation sequencing offers the potential for consistent, deep coverage of information-rich genomic regions to characterize polyclonal Plasmodium falciparum infections. However, methods to identify and sequence these genomic regions are currently limited. METHODS: A bioinformatic pipeline and multiplex methods were developed to identify and simultaneously sequence 100 targets and applied to dried blood spot (DBS) controls and field isolates from Mozambique. For comparison, whole-genome sequencing data were generated for the same controls. RESULTS: Using publicly available genomes, 4465 high-diversity genomic regions suited for targeted sequencing were identified, representing the P. falciparum heterozygome. For this study, 93 microhaplotypes with high diversity (median expected heterozygosity = 0.7) were selected along with 7 drug resistance loci. The sequencing method achieved very high coverage (median 99%), specificity (99.8%), and sensitivity (90% for haplotypes with 5% within sample frequency in dried blood spots with 100 parasites/µL). In silico analyses revealed that microhaplotypes provided much higher resolution to discriminate related from unrelated polyclonal infections than biallelic single-nucleotide polymorphism barcodes. CONCLUSIONS: The bioinformatic and laboratory methods outlined here provide a flexible tool for efficient, low-cost, high-throughput interrogation of the P. falciparum genome, and can be tailored to simultaneously address multiple questions of interest in various epidemiological settings.

Function and evolution of allelic variations of Sr13 conferring resistance to stem rust in tetraploid wheat (Triticum turgidum L.).

The resistance gene Sr13 is one of the most important genes in durum wheat for controlling stem rust caused by Puccinia graminis f. sp. tritici (Pgt). The Sr13 functional gene CNL13 has haplotypes R1, R2 and R3. The R1/R3 and R2 haplotypes were originally designated as alleles Sr13a and Sr13b, respectively. To detect additional Sr13 alleles, we developed Kompetitive allele specific PCR (KASP™) marker KASPSr13 and four semi-thermal asymmetric reverse PCR markers, rwgsnp37-rwgsnp40, based on the CNL13 sequence. These markers were shown to detect R1, R2 and R3 haplotypes in a panel of diverse tetraploid wheat accessions. We also observed the presence of Sr13 in durum line CAT-A1, although it lacked any of the known haplotypes. Sequence analysis revealed that CNL13 of CAT-A1 differed from the susceptible haplotype S1 by a single nucleotide (C2200T) in the leucine-rich repeat region and differed from the other three R haplotypes by one or two additional nucleotides, confirming that CAT-A1 carries a new (R4) haplotype. Stem rust tests on the monogenic, transgenic and mutant lines showed that R1 differed from R3 in its susceptibility to races TCMJC and THTSC, whereas R4 differed from all other haplotypes for susceptibility to TTKSK, TPPKC and TCCJC. Based on these differences, we designate the R1, R3 and R4 haplotypes as alleles Sr13a, Sr13c and Sr13d, respectively. This study indicates that Sr13d may be the primitive functional allele originating from the S1 haplotype via a point mutation, with the other three R alleles probably being derived from Sr13d through one or two additional point mutations.

Genome-wide association study and functional validation implicates JADE1 in tauopathy.

Primary age-related tauopathy (PART) is a neurodegenerative pathology with features distinct from but also overlapping with Alzheimer disease (AD). While both exhibit Alzheimer-type temporal lobe neurofibrillary degeneration alongside amnestic cognitive impairment, PART develops independently of amyloid-ß (Aß) plaques. The pathogenesis of PART is not known, but evidence suggests an association with genes that promote tau pathology and others that protect from Aß toxicity. Here, we performed a genetic association study in an autopsy cohort of individuals with PART (n = 647) using Braak neurofibrillary tangle stage as a quantitative trait. We found some significant associations with candidate loci associated with AD (SLC24A4, MS4A6A, HS3ST1) and progressive supranuclear palsy (MAPT and EIF2AK3). Genome-wide association analysis revealed a novel significant association with a single nucleotide polymorphism on chromosome 4 (rs56405341) in a locus containing three genes, including JADE1 which was significantly upregulated in tangle-bearing neurons by single-soma RNA-seq. Immunohistochemical studies using antisera targeting JADE1 protein revealed localization within tau aggregates in autopsy brains with four microtubule-binding domain repeats (4R) isoforms and mixed 3R/4R, but not with 3R exclusively. Co-immunoprecipitation in post-mortem human PART brain tissue revealed a specific binding of JADE1 protein to four repeat tau lacking N-terminal inserts (0N4R). Finally, knockdown of the Drosophila JADE1 homolog rhinoceros (rno) enhanced tau-induced toxicity and apoptosis in vivo in a humanized 0N4R mutant tau knock-in model, as quantified by rough eye phenotype and terminal deoxynucleotidyl transferase dUTP nick end-labeling (TUNEL) in the fly brain. Together, these findings indicate that PART has a genetic architecture that partially overlaps with AD and other tauopathies and suggests a novel role for JADE1 as a modifier of neurofibrillary degeneration.