Differential Retention Research Articles

Evaluating differential nanoparticle accumulation and retention kinetics in a mouse model of traumatic brain injury via Ktrans mapping with MRI

Traumatic brain injury (TBI) is a leading cause of injury-related death worldwide, yet there are no approved neuroprotective therapies that improve neurological outcome post-injury. Transient opening of the blood-brain barrier following injury provides an opportunity for passive accumulation of intravenously administered nanoparticles through an enhanced permeation and retention-like effect. However, a thorough understanding of physicochemical properties that promote optimal uptake and retention kinetics in TBI is still needed. In this study, we present a robust method for magnetic resonance imaging of nanoparticle uptake and retention kinetics following intravenous injection in a controlled cortical impact mouse model of TBI. Three contrast-enhancing nanoparticles with different hydrodynamic sizes and relaxivity properties were compared. Accumulation and retention were monitored by modelling the permeability coefficient, Ktrans, for each nanoparticle within the reproducible mouse model. Quantification of Ktrans for different nanoparticles allowed for non-invasive, multi-time point assessment of both accumulation and retention kinetics in the injured tissue. Using this method, we found that 80 nm poly(lactic-co-glycolic acid) nanoparticles had maximal Ktrans in a TBI when injected 3 hours post-injury, showing significantly higher accumulation kinetics than the small molecule, Gd-DTPA. This robust method will enable optimization of administration time and nanoparticle physicochemical properties to achieve maximum delivery.

Disease Resistance Genetics and Genomics in Octoploid Strawberry

Octoploid strawberry (Fragaria ×ananassa) is a valuable specialty crop, but profitable production and availability are threatened by many pathogens. Efforts to identify and introgress useful disease resistance genes (R-genes) in breeding programs are complicated by strawberry’s complex octoploid genome. Recently-developed resources in strawberry, including a complete octoploid reference genome and high-resolution octoploid genotyping, enable new analyses in strawberry disease resistance genetics. This study characterizes the complete R-gene collection in the genomes of commercial octoploid strawberry and two diploid ancestral relatives, and introduces several new technological and data resources for strawberry disease resistance research. These include octoploid R-gene transcription profiling, dN/dS analysis, expression quantitative trait loci (eQTL) analysis and RenSeq analysis in cultivars. Octoploid fruit eQTL were identified for 76 putative R-genes. R-genes from the ancestral diploids Fragaria vesca and Fragaria iinumae were compared, revealing differential inheritance and retention of various octoploid R-gene subtypes. The mode and magnitude of natural selection of individual F. ×ananassa R-genes was also determined via dN/dS analysis. R-gene sequencing using enriched libraries (RenSeq) has been used recently for R-gene discovery in many crops, however this technique somewhat relies upon a priori knowledge of desired sequences. An octoploid strawberry capture-probe panel, derived from the results of this study, is validated in a RenSeq experiment and is presented for community use. These results give unprecedented insight into crop disease resistance genetics, and represent an advance toward exploiting variation for strawberry cultivar improvement.

Planar Asymmetries in the C. elegans Embryo Emerge by Differential Retention of aPARs at Cell-Cell Contacts.

Formation of the anteroposterior and dorsoventral body axis in Caenorhabditis elegans depends on cortical flows and advection of polarity determinants. The role of this patterning mechanism in tissue polarization after formation of cell-cell contacts is not fully understood. Here, we demonstrate that planar asymmetries are established during left-right symmetry breaking: Centripetal cortical flows asymmetrically and differentially advect anterior polarity determinants (aPARs) from contacts to the medial cortex, resulting in their unmixing from apical myosin. Contact localization and advection of PAR-6 requires balanced CDC-42 activation, while asymmetric retention and advection of PAR-3 can occur independently of PAR-6. Concurrent asymmetric retention of PAR-3, E-cadherin/HMR-1 and opposing retention of antagonistic CDC-42 and Wnt pathway components leads to planar asymmetries. The most obvious mark of planar asymmetry, retention of PAR-3 at a single cell-cell contact, is required for proper cytokinetic cell intercalation. Hence, our data uncover how planar polarity is established in a system without the canonical planar cell polarity pathway through planar asymmetric retention of aPARs.

Are missed- and kept-visit measures capturing different aspects of retention in HIV primary care?

ABSTRACT The literature recognizes six measures of retention in care, an integral component of the HIV Continuum of Care. Given prior research showing that different retention measures are differentially associated with HIV health outcomes (e.g., CD4 count and viral suppression), we hypothesized that different groups of people living with HIV (PLWH) would also have differential retention outcomes based on the retention measure applied. We conducted a cross-sectional analysis of multisite patient-level medical record data (n = 10,053) from six academically-affiliated HIV clinics using six different measures of retention. Principal component analysis indicated two distinct retention constructs: kept-visit-measures and missed-visit measures. Although black (compared to white) PLWH had significantly poorer retention on the three missed-visit measures, race was not significantly associated with any of the three kept-visit measures. Males performed significantly worse than females on all kept-visit measures, but sex differences were not observed for any missed-visit retention measures. IDU risk transmission group and younger age were associated with poorer retention on both missed- and kept-visit retention measures. Missed- and kept-visit measures may capture different aspects of retention, as indicated in the observed differential associations among race, sex, age, and risk transmission group. Multiple measures are needed to effectively assess retention across patient subgroups.

Differential retention of transposable element-derived sequences in outcrossing Arabidopsis genomes

BackgroundTransposable elements (TEs) are genomic parasites with major impacts on host genome architecture and host adaptation. A proper evaluation of their evolutionary significance has been hampered by the paucity of short scale phylogenetic comparisons between closely related species. Here, we characterized the dynamics of TE accumulation at the micro-evolutionary scale by comparing two closely related plant species, Arabidopsis lyrata and A. halleri.ResultsJoint genome annotation in these two outcrossing species confirmed that both contain two distinct populations of TEs with either ‘recent’ or ‘old’ insertion histories. Identification of rare segregating insertions suggests that diverse TE families contribute to the ongoing dynamics of TE accumulation in the two species. Orthologous TE fragments (i.e. those that have been maintained in both species), tend to be located closer to genes than those that are retained in one species only. Compared to non-orthologous TE insertions, those that are orthologous tend to produce fewer short interfering RNAs, are less heavily methylated when found within or adjacent to genes and these tend to have lower expression levels. These findings suggest that long-term retention of TE insertions reflects their frequent acquisition of adaptive roles and/or the deleterious effects of removing nearly neutral TE insertions when they are close to genes.ConclusionOur results indicate a rapid evolutionary dynamics of the TE landscape in these two outcrossing species, with an important input of a diverse set of new insertions with variable propensity to resist deletion.

Functional and cellular localization diversity associated with Fukutin-related protein patient genetic variants.

Genetic variants in Fukutin-related protein (FKRP), an essential enzyme of the glycosylation pathway of α-dystroglycan, can lead to pathologies with different severities affecting the eye, brain, and muscle tissues. Here, we generate an in vitro cellular system to characterize the cellular localization as well as the functional potential of the most common FKRP patient missense mutations. We observe a differential retention in the endoplasmic reticulum (ER), the indication of misfolded proteins. We find data supporting that mutant protein able to overcome this ER-retention through overexpression present functional levels comparable to the wild-type. We also identify a specific region in FKRP protein localized between residues 300 and 321 in which genetic variants found in patients lead to correctly localized proteins but which are nevertheless functionally impaired or catalytically dead in our model, indicating that this particular region might be important for the enzymatic activity of FKRP within the Golgi. Our system thus allows the functional testing of patient-specific mutant proteins and the identification of candidate mutants to be further explored with the aim of finding pharmacological treatments targeting the protein quality control system.

Evolution of nodal and nodal-related genes and the putative composition of the heterodimers that trigger the nodal pathway in vertebrates.

Nodal is a signaling molecule that belongs to the transforming growth factor-β superfamily that plays key roles during the early stages of development of animals. In vertebrates Nodal forms an heterodimer with a GDF1/3 protein to activate the Nodal pathway. Vertebrates have a paralog of nodal in their genomes labeled Nodal-related, but the evolutionary history of these genes is a matter of debate, mainly because of the presence of a variable numbers of genes in the vertebrate genomes sequenced so far. Thus, the goal of this study was to investigate the evolutionary history of the Nodal and Nodal-related genes with an emphasis in tracking changes in the number of genes among vertebrates. Our results show the presence of two gene lineages (Nodal and Nodal-related) that can be traced back to the ancestor of jawed vertebrates. These lineages have undergone processes of differential retention and lineage-specific expansions. Our results imply that Nodal and Nodal-related duplicated at the latest in the ancestor of gnathostomes, and they still retain a significant level of functional redundancy. By comparing the evolution of the Nodal/Nodal-related with GDF1/3 gene family, it is possible to infer that there are several types of heterodimers that can trigger the Nodal pathway among vertebrates.

Retention marker excretion suggests incomplete digesta mixing across the order primates

The digestive tract of animals, and the patterns how passage markers are excreted from them, have been fruitfully compared to chemical reactor models from engineering science. An important characteristic of idealized reactor models is the smoothness of the curves plotting marker concentrations in outflow (i.e., faeces) over time, which is the result of the assumed complete mixing of the marker with the reactor contents. Published excretion patterns from passage experiments in non-primate mammals appear to indicate a high degree of digesta mixing. In order to assess whether marker excretion graphs from primates differ from ideal outflow graphs, we performed passage experiments in eight individuals of three foregut-fermenting species (Pygathrix nemaeus, Trachypithecus auratus and Semnopithecus vetulus), and added them to available marker excretion curves from the literature. In the resulting collection, 23 out of a total of 25 patterns in foregut fermenters (21 individuals of 10 species from 7 studies), and 13 out of 15 in hindgut fermenters (9 individuals of 2 species from 2 studies), showed an irregular, ‘spiky’ pattern. We consider this proportion to be too high to be explained by experimental errors, and suggest that this may indicate a taxon-wide characteristic of particularly incomplete digesta mixing, acknowledging that further data from less related primate species are required for corroboration. Our hypothesis is in accordance with previous findings of a comparatively low degree of ‘digesta washing’ (differential retention of particulate and fluid digesta) in primates. Together with literature findings that suggest a low chewing efficiency in primates compared to other mammals, these observations indicate that in contrast to other herbivores, the success of the primate order is not derived from particularly elaborate adaptations of their ingestive and digestive physiology.

Pursuing an engineering major: social capital of women and underrepresented minorities

ABSTRACTAs part of a longitudinal research effort that examines the influence of social capital on differential persistence and retention among undergraduate engineering majors, this study examines how engineering degree-related social capital differs for first-year engineering students by gender and ethno-racial groups. Social capital is operationalized as a person’s network of relationships with individuals who hold influential positions (e.g. parent, teacher, advisers) and access to resources that support persistence in engineering programs. Our data comprise survey responses from 2186 first-year engineering students, from eleven diverse colleges and universities, who provided information about their participation in engineering-related courses, activities, and programs while in high school as well as the individuals who influenced their decision to pursue an engineering major. We found few differences in social capital between men and women, but found many differences among ethno-racial groups, which suggests that different levels of social capital could influence students’ persistence and retention.

Applying a dynamic membrane filtration (DMF) process for domestic wastewater preconcentration: Organics recovery and bioenergy production potential analysis

Wastewater is increasingly recognized as a valuable resource rather than as a waste, motivating a shift in the perspective of wastewater treatment from pollution control to resource recovery. This study proposes the recovery of organic matter from domestic wastewater for the production of bioenergy through a novel process of wastewater preconcentration based on dynamic membrane filtration (DMF). The selection of a dynamic membrane (DM) supporting material, the preconcentration performance of organics, and the biomethane production potential (BMP) of the organic concentrate were investigated. The process optimization results indicated that a DM module with a supporting material of a 25 μm stainless steel mesh with a three-layer structure, assisted by internal suspended particles derived from raw wastewater, enabled the rapid DM layer formation within 1 h. The DMF process operated under a constant high flux of 30–60 L/m2 h at a trans-membrane pressure (TMP) of less than 40 kPa. During the continuous DMF operation, the average chemical oxygen demand (COD) of the influent, effluent and concentrate was 305, 113 and 2000–2500 mg/L, respectively, while the removal performance of other pollutants(such as nitrogen and phosphorus) varied, indicating differential retention effects for the various pollutants by the DM layer. Air back-flushing can effectively regenerate the DM layer and maintain long-term stable operation, but higher rates of TMP increase were observed for later filtration cycles, probably due to the accumulation of physically irremovable fouling. The BMP of the DMF concentrate was 0.20 L CH4/g COD, which was comparable to the ordinary biogas yield from municipal wastewater by anaerobic digestion. The DMF process integrated with anaerobic digestion can be a promising alternative for energy-sufficient wastewater treatment.

Persistent DNA-break potential near telomeres increases initiation of meiotic recombination on short chromosomes

Faithful meiotic chromosome inheritance and fertility rely on the stimulation of meiotic crossover recombination by potentially genotoxic DNA double-strand breaks (DSBs). To avoid excessive damage, feedback mechanisms down-regulate DSBs, likely in response to initiation of crossover repair. In Saccharomyces cerevisiae, this regulation requires the removal of the conserved DSB-promoting protein Hop1/HORMAD during chromosome synapsis. Here, we identify privileged end-adjacent regions (EARs) spanning roughly 100 kb near all telomeres that escape DSB down-regulation. These regions retain Hop1 and continue to break in pachynema despite normal synaptonemal complex deposition. Differential retention of Hop1 requires the disassemblase Pch2/TRIP13, which preferentially removes Hop1 from telomere-distant sequences, and is modulated by the histone deacetylase Sir2 and the nucleoporin Nup2. Importantly, the uniform size of EARs among chromosomes contributes to disproportionately high DSB and repair signals on short chromosomes in pachynema, suggesting that EARs partially underlie the curiously high recombination rate of short chromosomes.

Angiosperm-Wide and Family-Level Analyses of AP2/ERF Genes Reveal Differential Retention and Sequence Divergence After Whole-Genome Duplication.

Plants are immobile and often face stressful environmental conditions, prompting the evolution of genes regulating environmental responses. Such evolution is achieved largely through gene duplication and subsequent divergence. One of the most important gene families involved in regulating plant environmental responses and development is the AP2/ERF superfamily; however, the evolutionary history of these genes is unclear across angiosperms and in major angiosperm families adapted to various ecological niches. Specifically, the impact on gene copy number of whole-genome duplication events occurring around the time of the origins of several plant families is unknown. Here, we present the first angiosperm-wide comparative study of AP2/ERF genes, identifying 75 Angiosperm OrthoGroups (AOGs), each derived from an ancestral angiosperm gene copy. Among these AOGs, 21 retain duplicates with increased copy number in many angiosperm lineages, while the remaining 54 AOGs tend to maintain low copy number. Further analyses of multiple species in the Brassicaceae family indicated that family-specific duplicates experienced differential selective pressures in coding regions, with some paralogs showing signs of positive selection. Further, cis regulatory elements also exhibit extensive divergence between duplicates in Arabidopsis. Moreover, comparison of expression levels suggested that AP2/ERF genes with frequently retained duplicates are enriched for broad expression patterns, offering increased opportunities for functional diversification via changes in expression patterns, and providing a mechanism for repeated duplicate retention in some AOGs. Our results represent the most comprehensive evolutionary history of the AP2/ERF gene family, and support the hypothesis that AP2/ERF genes with broader expression patterns are more likely to be retained as duplicates than those with narrower expression profiles, which could lead to a higher chance of duplicate gene subfunctionalization. The greater tendency of some AOGs to retain duplicates, allowing expression and functional divergence, may facilitate the evolution of complex signaling networks in response to new environmental conditions.

Comparative transcriptome analysis revealed key factors for differential cadmium transport and retention in roots of two contrasting peanut cultivars

BackgroundPeanut is the world’s fourth largest oilseed crop that exhibits wide cultivar variations in cadmium (Cd) accumulation. To establish the mechanisms of Cd distribution and accumulation in peanut plants, eight cDNA libraries from the roots of two contrasting cultivars, Fenghua 1 (low-Cd cultivar) and Silihong (high-Cd cultivar), were constructed and sequenced by RNA-sequencing. The expression patterns of 16 candidate DEGs were validated by RT-qPCR analysis.ResultsA total of 75,634 genes including 71,349 known genes and 4484 novel genes were identified in eight cDNA libraries, among which 6798 genes were found to be Cd-responsive DEGs and/or DEGs between these two cultivars. Interestingly, 183 DEGs encoding ion transport related proteins and 260 DEGs encoding cell wall related proteins were identified. Among these DEGs, nine metal transporter genes (PDR1, ABCC4 and ABCC15, IRT1, ZIP1, ZIP11, YSL7, DTX43 and MTP4) and nine cell wall related genes (PEs, PGIPs, GTs, XYT12 CYP450s, LACs, 4CL2, C4H and CASP5) showed higher expression in Fenghua 1 than in Silihong.ConclusionsBoth the metal transporters and cell wall modification might be responsible for the difference in Cd accumulation and translocation between Fenghua 1 and Silihong. These findings would be useful for further functional analysis, and reveal the molecular mechanism responsible for genotype difference in Cd accumulation.

RETENTION STRATEGY AND EMPLOYEE’S TURNOVER AMONG ACADEMIC STAFF OF LAGOS STATE OWNED TERTIARY INSTITUTIONS

The study investigated the influence of retention strategies of tertiary institutions on academic staff turnover. Employing exploratory study, the Key Informant Interview (KII) combined with Focused Group Discussion (FGD) was deployed to elicit responses from third party respondents in two (2) Lagos State owned tertiary institutions. Descriptive statistics were used to describe the responses obtained. It was found that the same pattern of retention strategic offerings obtained in the two institutions. The distinguishing turnover factor (TF) for the two institutions was the differences in agency (leadership/management) dispositions to academic staff in terms of creating an enabling environment and climate that meet the expectations of academic staff in an ideal academic milieu. The study also established that differential academic status (cadres) require differential retention strategies to reduce the risk of turnover among the cadres. It was recommended among other things that tertiary institutions’ management need to periodically examine the existing value propositions profile offered to their academic staff in terms of their sufficiency and adequacy in comparison to what obtain in other global clime if they are not to further lose competent staff to competitors at both local and international academic market space

A mechanistic assessment of the relationship between gut morphology and endozoochorous seed dispersal by waterfowl.

Many plants and invertebrates rely on internal transport by animals for long‐distance dispersal. Their dispersal capacity is greatly influenced by interactions with the animal's digestive tract. Omnivorous birds adjust their digestive tract morphology to seasonally variable diets. We performed feeding trials in waterfowl to unravel how changing organ size, in combination with seed size, affects dispersal potential. We subjected captive mallards to mimics of summer (animal‐based), winter (plant‐based), and intermediate diets, and analyzed gut passage of seeds before and after the treatment (trials 1 and 2). To test the effect of gut morphology on seed digestion, we measured digestive organ size after euthanasia. Three hours before euthanasia, differently sized seeds were fed to test how seed size affects gut passage by determining their relative position in the digestive tract (trial 3). Trials 1 and 2 showed that intact seed passage was lower in the plant‐based than in the animal‐based diet group. Retention time changed only within groups, decreasing in the animal‐based, and increasing in the plant‐based diet group. No post‐diet differences in organ size were detected, probably due to large between‐individual variation within groups. Digestive tract measures did not explain variation in seed survival or retention time. Trial 3 revealed that small seeds pass the digestive tract rapidly, while large seeds are retained longer, particularly in the gizzard. Differential retention in the gizzard, the section where seeds can be destroyed, is likely why larger seeds have a lower probability to pass the digestive tract intact. Our results confirm that rapid, flexible adaptation to diet shifts affects seed digestion in waterfowl, although we could not conclusively relate this to organ size. Large interindividual variation in digestive efficiency between mallards feeding on the same diet may provide opportunities for seed dispersal in the field throughout the annual cycle.

Functional neuroimaging of associative learning and generalization in specific phobia

BackgroundTheoretical models have implicated classical fear conditioning, fear generalization, and extinction learning in the development of anxiety disorders. To date, it is largely unknown to what extent these mechanisms and the underlying neurobiology may be altered in specific phobia, a disorder characterized by focal fears. The current study systematically examined fear conditioning, fear generalization, extinction learning, and extinction recall in a sample of individuals with a specific phobia. MethodsParticipants with a specific phobia (SP) of spiders (n = 46) and healthy controls (HC) (n = 48) underwent a 3-day fMRI cue-conditioning protocol, including a fear acquisition and a fear generalization phase (day 1), an extinction learning phase (day 2), and an extinction recall phase (day 3). Stimuli were phobia-irrelevant, as geometrical shapes served as conditioned threat (CS+) and safety stimuli (CS-), and an electrical shock as the unconditioned stimulus (US). Self-reported fear, US expectancy, and blood-oxygen-level dependent responses were measured. ResultsBehavioral results only revealed enhanced CS+/CS-differentiation in fear scores during acquisition retention in SP. Some neural differences were observed during other task phases. During early fear acquisition, SP showed enhanced differential activation in the angular gyrus and lateral occipital cortex, and during extinction recall, more precuneus deactivation was found in SP compared to HC. There were no clear indications of altered neural fear generalization or extinction learning mechanisms in the SP group. ConclusionsResults indicate that spider phobia may be characterized by enhanced differential fear retention and altered brain activation patterns during fear acquisition and extinction recall. The findings provide insight into the nature of fear learning alterations in specific phobia, and how these may differ from those found in disorders characterized by broad anxious distress.

Optimization of nitrogen and phosphorus removal from pig slaughterhouse and packing plant wastewater through electrocoagulation in a batch reactor

This work evaluated the removal of total Kjeldahl nitrogen (TKN) and total phosphorus (P) through electrocoagulation and used aluminum electrodes to optimize the potential differential (pd) and hydraulic retention time (HRT) variables in a batch reactor. The experimental design used was Rotatable Central Composite Design (RCCD). The application of the electrocoagulation in the treatment of effluents from pig slaughterhouses and packing plants proved to be efficient in relation to the removal of TKN and total phosphorus, obtaining maximum efficiency equal to 67.15% and 99%, respectively. The maximum TKN removal value was found in Test 12, where treatment conditions were 30 minutes for HRT and 20 volts for pd, which corresponds to 0.86 A of electric current and a current density of 17.2 mA cm-2. For P, the only test that removed below 99% was the first. Through statistical analyses, it was only possible to obtain a mathematical model for TKN removal. While the response surface graph did not present a defined range of the best conditions for the independent variables, it was possible to observe the tendency for better removal, a wide range of pd and values over 30 minutes for retention time.

Differential retention of pollen grains on clothing and the effectiveness of laboratory retrieval methods in forensic settings

Forensic palynology has been important in criminal investigation since the 1950s and often provides evidence that is vital in identifying suspects and securing convictions. However, for such evidence to be used appropriately, it is necessary to understand the factors affecting taphonomic variability (i.e. the variability in the fate of pollen grains before they are found during forensic examination). Here, we test the relative amount of pollen retained on clothing after a period of simulated light or heavy wear based on pollen and fabric characteristics. We also test the efficiency of forensic laboratory protocols for retrieving pollen from fabrics for analysis. There was no statistically significant difference in retention of fresh or dried pollen on any fabric type. There was a substantial difference in pollen retention according to wear intensity, with considerably more pollen being retained after light wear than after heavy wear. Pollen from insect-pollinated species was retained at higher concentrations than pollen from wind-pollinated species. This pattern was consistent regardless of wear intensity but pollination type explained more of the variability in pollen retention after light wear. Fabric type was significantly related to pollen retention, but interacted strongly with plant species such that patterns were both complex and highly species-specific. The efficiency of removing pollen with the standard washing protocol differed substantially according to plant species, fabric type, and the interaction between these factors. The average efficiency was 67.7% but this ranged from 21% to 93%, demonstrating that previous assumptions on the reliability of the technique providing a representative sample for forensic use should be reviewed. This paper highlights the importance of understanding pollen and fabric characteristics when creating a pollen profile in criminal investigations and to ensure that evidence used in testimony is accurate and robust.

Alterations in sperm DNA methylation, non-coding RNA expression, and histone retention mediate vinclozolin-induced epigenetic transgenerational inheritance of disease.

Epigenetic transgenerational inheritance of disease and phenotypic variation can be induced by several toxicants, such as vinclozolin. This phenomenon can involve DNA methylation, non-coding RNA (ncRNA) and histone retention, and/or modification in the germline (e.g. sperm). These different epigenetic marks are called epimutations and can transmit in part the transgenerational phenotypes. This study was designed to investigate the vinclozolin-induced concurrent alterations of a number of different epigenetic factors, including DNA methylation, ncRNA, and histone retention in rat sperm. Gestating females (F0 generation) were exposed transiently to vinclozolin during fetal gonadal development. The directly exposed F1 generation fetus, the directly exposed germline within the fetus that will generate the F2 generation, and the transgenerational F3 generation sperm were studied. DNA methylation and ncRNA were altered in each generation rat sperm with the direct exposure F1 and F2 generations being distinct from the F3 generation epimutations. Interestingly, an increased number of differential histone retention sites were found in the F3 generation vinclozolin sperm, but not in the F1 or F2 generations. All three different epimutation types were affected in the vinclozolin lineage transgenerational sperm (F3 generation). The direct exposure generations (F1 and F2) epigenetic alterations were distinct from the transgenerational sperm epimutations. The genomic features and gene pathways associated with the epimutations were investigated to help elucidate the integration of these different epigenetic processes. Our results show that the three different types of epimutations are involved and integrated in the mediation of the epigenetic transgenerational inheritance phenomenon.

Epigenetic Transgenerational Inheritance of Altered Sperm Histone Retention Sites

A variety of environmental toxicants and factors have been shown to induce the epigenetic transgenerational inheritance of disease and phenotypic variation. Epigenetic alterations in the germline (sperm or egg) are required to transmit transgenerational phenotypes. The current study was designed to investigate the potential role of histones in sperm to help mediate the epigenetic transgenerational inheritance. The agricultural fungicide vinclozolin and the pesticide DDT (dichlorodiphenyltrichloroethane) were independently used to promote the epigenetic transgenerational inheritance of disease. Purified cauda epididymal sperm were collected from the transgenerational F3 generation control and exposure lineage male rats for histone analysis. A reproducible core of histone H3 retention sites was observed using an H3 chromatin immunoprecipitation (ChIP-Seq) analysis in control lineage sperm. Interestingly, the same core group of H3 retention sites plus additional differential histone retention sites (DHRs) were observed in the F3 generation exposure lineage sperm. Although new histone H3 retention sites were observed, negligible change in histone modification (methylation of H3K27me3) was observed between the control and exposure lineages. Observations demonstrate that in addition to alterations in sperm DNA methylation and ncRNA previously identified, the induction of differential histone retention sites (DHRs) also appear to be involved in environmentally induced epigenetic transgenerational inheritance.