Rapid generation of single-insertion transgenics by Tol2 transposition in zebrafish.

BACKGROUND: The Tol2 transposable element is the most widely used transgenesis tool in zebrafish. However, its high activity almost always leads to multiple unlinked integrations of the transgenic cassette in F1 fish. Each of these transgenes is susceptible to positional effects from the surrounding regulatory landscape, which can lead to altered expression and, consequently, activity. Scientists therefore must strike a balance between the need to maximize reproducibility by establishing single-insertion transgenic lines and the need to complete experiments within a reasonable timeframe. RESULTS: In this article, we introduce a simple competitive dilution strategy for rapid generation of single-insertion transgenics. By using cry:BFP reporter plasmid as a competitor, we achieved a nearly fourfold reduction in the number of the transgene of interest integrations while simultaneously increasing the proportion of single-insertion F1 generation transgenics to over 50%. We also observed variations in transgene of interest expression among independent single-insertion transgenics, highlighting that the commonly used ubiquitous ubb promoter is susceptible to position effects. CONCLUSIONS: Wide application of our competitive dilution strategy will save time, reduce animal usage, and improve reproducibility of zebrafish research.

Working memory prioritisation effects in tactile immediate serial recall.

There is a growing body of evidence that higher-value information can be prioritised for both visual and auditory working memory. The present study examines whether valuable items can similarly be prioritised for the tactile domain. Employing an immediate serial recall procedure (ISR), participants reconstructed a 6-item tactile sequence by moving their fingers in the order of original stimulation. Participants were informed either that one serial position was worth notionally more points (prioritisation condition) or that all items were of equal value (control condition). For Experiment 1 (N = 48), significant boosts in correct recall were evident when serial positions 4 or 5 were more valuable (i.e., prioritisation effects). Experiment 2 (N = 24) demonstrated that the prioritisation effect persisted with concurrent articulation, suggesting that task performance was not a function of verbal recoding and rehearsal of the tactile information. Importantly, a significant recall cost for low-value (non-prioritised) items within the sequence was evident for both experiments. Taken together, these findings demonstrate that (1) prioritisation effects transfer to the tactile domain and (2) finite attentional resources can be deliberately and strategically redistributed to specific items within a sequence, dependent upon the prevailing task demands.

Transvection between nonallelic genomic positions in Drosophila.

In Drosophila, pairing of maternal and paternal homologous chromosomes can permit trans-interactions between enhancers on one homolog and promoters on another, an example of transvection. Although trans-interactions have been observed at many loci in the Drosophila genome and in other organisms, the parameters that govern enhancer action in trans remain poorly understood. Using a transgenic reporter system, we asked whether enhancers and promoters at nonallelic, but nearby, genomic positions can communication in trans. Using one transgenic insertion carrying the synthetic enhancer GMR and another nearby insertion carrying the hsp70 promoter driving a fluorescent reporter, we show that transgenes separated by 2.6 kb of linear distance can support enhancer action in trans at the 53F8 locus. Furthermore, transvection between the nonallelic insertions can be augmented by a small deletion flanking one insert, likely via changes to the paired configuration of the homologs. Subsequent analyses of other insertions in 53F8 that carry different transgenic sequences demonstrate that the capacity to support transvection between nonallelic sites varies greatly, suggesting that factors beyond the linear distance between insertion sites play an important role. Finally, analysis of transvection between nearby nonallelic sites at other genomic locations shows evidence of position effects, where one locus supported GMR action in trans over a linear distance of over 10 kb, whereas another locus showed no evidence of transvection over a span <200 bp. Overall, our data demonstrate that transvection between nonallelic sites represents a complex interplay between genomic context, interallelic distance, and promoter identity.

Disruption of the serial position effect as an early marker of Alzheimer's disease in Spanish-English bilinguals.

OBJECTIVES: The present study examined if disruption of serial position effects in list recall could serve as an early marker of Alzheimer's disease (AD) in Spanish-English bilinguals. METHODS: We tested 20 participants initially diagnosed as cognitively normal or with mild cognitive impairment who declined and eventually received a diagnosis of AD (decliners), and 37 who remained cognitively stable (controls) over at least 2 years. Participants were tested on the Consortium to Establish a Registry for Alzheimer's Disease (CERAD) Word List Learning Test in English or Spanish as part of an annual neuropsychological evaluation. RESULTS: Compared to controls, decliners exhibited significantly reduced recall including reduced primacy scores (i.e., items recalled from the first three list items on Trial 1), whereas recency scores (i.e., items recalled from the last 3 list items on Trial 1) were equivalent in decliners and controls. Further analyses suggested that the sensitivity of the primacy effect to preclinical AD was initially stronger in participants tested in Spanish, a surprising finding given that the CERAD was developed for English speakers. However, in the subsequent year of testing, primacy scores declined to the same level regardless of language of testing. CONCLUSIONS: Several list learning measures may facilitate early diagnosis of AD in Spanish-English bilinguals, possibly including the relatively understudied primacy effect. Additional studies are needed to investigate the possibility that linguistic or demographic variables might modulate sensitivity of list learning tests to preclinical AD, which could lead to broader improvements in their utility for early diagnosis of AD in all populations.

The item position effects in international examinations: the roles of gender.

The goal of the present study was to evaluate the roles of item position in terms of item difficulty levels in the assessment of aptitude. Using data from a National Examination in Saudi Arabia, the item position effect was evaluated as a teacher licensure test (GTLT) was administered using five different forms with the same items appearing in a different order. Results indicated minuscule in magnitude position effects estimates, overall, with initially 11.1% of the tests being significant but all of them failing to reach significance using the Holm-Bonferroni's and Sidak corrective procedures. With regard to gender, item position effects emerged in 47.6% of the tests after adjusting the level of significance using the Sidak correction. Interestingly, the direction of effect was consistent so that in 87% of the significant gender comparisons, item position effects were in the direction where females were spending more time on items when they appeared in later positions on the test compared to males. Assuming that items appearing later on the test are likely more difficult, the present findings suggest a profile of deep processing and active engagement in females when facing achievement tests.

Glucocorticoid stimulation induces regionalized gene responses within topologically associating domains.

Transcription-factor binding to cis-regulatory regions regulates the gene expression program of a cell, but occupancy is often a poor predictor of the gene response. Here, we show that glucocorticoid stimulation led to the reorganization of transcriptional coregulators MED1 and BRD4 within topologically associating domains (TADs), resulting in active or repressive gene environments. Indeed, we observed a bias toward the activation or repression of a TAD when their activities were defined by the number of regions gaining and losing MED1 and BRD4 following dexamethasone (Dex) stimulation. Variations in Dex-responsive genes at the RNA levels were consistent with the redistribution of MED1 and BRD4 at the associated cis-regulatory regions. Interestingly, Dex-responsive genes without the differential recruitment of MED1 and BRD4 or binding by the glucocorticoid receptor were found within TADs, which gained or lost MED1 and BRD4, suggesting a role of the surrounding environment in gene regulation. However, the amplitude of the response of Dex-regulated genes was higher when the differential recruitment of the glucocorticoid receptor and transcriptional coregulators was observed, reaffirming the role of transcription factor-driven gene regulation and attributing a lesser role to the TAD environment. These results support a model where a signal-induced transcription factor induces a regionalized effect throughout the TAD, redefining the notion of direct and indirect effects of transcription factors on target genes.

Functional Clustering of Metabolically Related Genes Is Conserved across Dikarya.

Transcriptional regulation is vital for organismal survival, with many layers and mechanisms collaborating to balance gene expression. One layer of this regulation is genome organization, specifically the clustering of functionally related, co-expressed genes along the chromosomes. Spatial organization allows for position effects to stabilize RNA expression and balance transcription, which can be advantageous for a number of reasons, including reductions in stochastic influences between the gene products. The organization of co-regulated gene families into functional clusters occurs extensively in Ascomycota fungi. However, this is less characterized within the related Basidiomycota fungi despite the many uses and applications for the species within this clade. This review will provide insight into the prevalence, purpose, and significance of the clustering of functionally related genes across Dikarya, including foundational studies from Ascomycetes and the current state of our understanding throughout representative Basidiomycete species.

Serial position effects and mild cognitive impairment: a comparison of measures and scoring approaches.

INTRODUCTION: Serial position effects (SPEs) have shown promise as predictors of future cognitive decline and conversion from mild cognitive impairment (MCI) to Alzheimer's disease (AD), even when accounting for total learning and memory scores. However, conflicting results have been found in the literature, which may be at least partially related to the many ways in which SPEs are calculated. The current study aimed to address the discrepancies in the literature by examining whether one method of analyzing SPEs is more sensitive at distinguishing those with and without psychometrically defined MCI. METHOD: 86 older adult participants (57 healthy comparison, 29 MCI) completed the California Verbal Learning Test, Third Edition (CVLT3) and the Rey Auditory Verbal Learning Test (RAVLT), along with measures assessing multiple cognitive domains. Each participant completed two visits, between 3 and 9 days apart, with a different memory measure administered on each day. The standard scoring approach and the regional scoring approach to calculating SPEs were compared. RESULTS: Results showed that, when significant differences were found, SPEs were always reduced in the MCI group compared to the healthy comparison group when using regional scoring; however, results were not as consistent when using standard scoring. Further, lower primacy than recency scores were only consistently seen in the MCI group when using the RAVLT but not the CVLT3. ROC analyses showed that only regional scoring of SPEs from delayed recall of the RAVLT and the CVLT3 accurately discriminated between those with and without MCI. CONCLUSION: Regional scoring of SPEs may be more sensitive at identifying subtle cognitive decline compared to standard scoring. However, the specific measure that is used to analyze SPEs can impact the interpretation of findings.

Dynamic Response Strategies: Accounting for Response Process Heterogeneity in IRTree Decision Nodes.

It is essential to control self-reported trait measurements for response style effects to ensure a valid interpretation of estimates. Traditional psychometric models facilitating such control consider item responses as the result of two kinds of response processes-based on the substantive trait, or based on response styles-and they assume that both of these processes have a constant influence across the items of a questionnaire. However, this homogeneity over items is not always given, for instance, if the respondents' motivation declines throughout the questionnaire so that heuristic responding driven by response styles may gradually take over from cognitively effortful trait-based responding. The present study proposes two dynamic IRTree models, which account for systematic continuous changes and additional random fluctuations of response strategies, by defining item position-dependent trait and response style effects. Simulation analyses demonstrate that the proposed models accurately capture dynamic trajectories of response processes, as well as reliably detect the absence of dynamics, that is, identify constant response strategies. The continuous version of the dynamic model formalizes the underlying response strategies in a parsimonious way and is highly suitable as a cognitive model for investigating response strategy changes over items. The extended model with random fluctuations of strategies can adapt more closely to the item-specific effects of different response processes and thus is a well-fitting model with high flexibility. By using an empirical data set, the benefits of the proposed dynamic approaches over traditional IRTree models are illustrated under realistic conditions.

Using serial position effects to investigate memory dysfunction in homeless and precariously housed persons.

Background: Homeless and precariously housed persons exhibit significant memory impairment, but the component processes underlying memory dysfunction have not been explored. We examined the serial position profile (i.e., primacy and recency effects) of verbal memory and its neuroanatomical correlates to identify the nature of memory difficulties in a large cohort of homeless and precariously housed adults. Method: The sample included 227 community-dwelling homeless and precariously housed adults. Serial position scores (primacy, middle, recency) were computed using the Hopkins Verbal Learning Test-Revised. Paired sample t-tests were used to compare percent recall from each word list region. Age-adjusted correlations assessed associations between serial position scores and other cognitive domains (attention, processing speed, executive functioning). Regression analyses were conducted to examine regional brain volumes of interest (hippocampus, entorhinal cortex, dorsolateral prefrontal cortex [DLPFC]) and their differential associations with serial position scores. Results: The serial position profile was characterized by a diminished recency effect in relation to the primacy effect. Serial position scores positively correlated with sustained attention and cognitive control. Larger hippocampal volume was associated with better primacy item recall. DLPFC volume was not associated with serial position recall after adjustment for false discovery rate. There were no associations between regional brain volumes and recency item recall. Conclusion: Our results suggest that commonly reported memory difficulties in homeless and precariously housed adults are likely secondary to a core deficit in executive control due to compromised frontal lobe functioning. These findings have implications for cognitive rehabilitation in this complex and vulnerable group.

The recency ratio assessed by story recall is associated with cerebrospinal fluid levels of neurodegeneration biomarkers.

Recency refers to the information learned at the end of a study list or task. Recency forgetting, as tracked by the ratio between recency recall in immediate and delayed conditions, i.e., the recency ratio (Rr), has been applied to list-learning tasks, demonstrating its efficacy in predicting cognitive decline, conversion to mild cognitive impairment (MCI), and cerebrospinal fluid (CSF) biomarkers of neurodegeneration. However, little is known as to whether Rr can be effectively applied to story recall tasks. To address this question, data were extracted from the database of the Alzheimer's Disease Research Center at the University of Wisconsin - Madison. A total of 212 participants were included in the study. CSF biomarkers were amyloid-beta (Aß) 40 and 42, phosphorylated (p) and total (t) tau, neurofilament light (NFL), neurogranin (Ng), and α-synuclein (a-syn). Story Recall was measured with the Logical Memory Test (LMT). We carried out Bayesian regression analyses with Rr, and other LMT scores as predictors; and CSF biomarkers (including the Aß42/40 and p-tau/Aß42 ratios) as outcomes. Results showed that models including Rr consistently provided best fits with the data, with few exceptions. These findings demonstrate the applicability of Rr to story recall and its sensitivity to CSF biomarkers of neurodegeneration, and encourage its inclusion when evaluating risk of neurodegeneration with story recall.

How retrieval practice and semantic generation affect subsequently studied material: an analysis of item-level effects.

The forward testing effect (FTE) refers to the finding that retrieval practice of previously studied material can facilitate recall of newly studied (critical) material. Such interim retrieval practice can also lead to a differential FTE, i.e., a more pronounced FTE for items at early than later serial positions in the critical material. The present study examined whether this differential FTE also holds with interim semantic generation of extra-list items, and whether it is influenced by study material. Consistent with prior work, the results of two experiments showed that both interim retrieval practice and interim semantic generation induce the general (list-level) FTE when unrelated study lists are applied, whereas retrieval practice only creates the effect with categorised study lists. Critically, however, the differential FTE was present in response to retrieval practice but absent in response to semantic generation. This pattern held regardless of which material was studied, thus experimentally dissociating the general (list-level) from the differential (item-level) FTE. The findings may suggest that retrieval practice, but not semantic generation, induces a reset of the encoding process which promotes attentional encoding such that a more pronounced FTE arises for early than middle and late serial positions in the critical list.

Chunking, boosting, or offloading? Using serial position to investigate long-term memory's enhancement of verbal working memory performance.

Individuals can use information stored in episodic long-term memory (LTM) to optimize performance in a working memory (WM) task, and the WM system negotiates the exchange of information between WM and LTM depending on the current memory load. In this study, we assessed the ability of different accounts of interactions between LTM and WM to explain these findings, by investigating whether the position of pre-learnt information within a memory list encoded into WM affects the benefit it provides to immediate memory. In two experiments we varied the input position of previously learned word-word pairs within a set of four to-be-remembered pairs. We replicated previous findings of superior performance when these LTM pairs were included in the WM task and show that the position in the list in which these LTM pairs were included not seem to matter. These results are most consistent with the idea that having access to information in LTM reduces or removes the need to rely on WM for its storage, implying that people "offload" information in conditions containing LTM pairs.

Intentional and incidental odour-colour binding in working memory.

The question of how features are bound together in working memory has become a topic of much research in recent years. However, this is typically focused on visual and/or auditory stimuli. The purpose of this study is to apply established feature binding procedures to investigate odour binding in working memory. Across three experiments, memory for intentionally and incidentally formed odour-colour pairings was tested. Experiment 1 showed that following explicit instruction to remember the odour-colour combinations, young adults can recall lists of 3-pairings at levels above that of chance and exhibit a recency advantage for the last pairing. In Experiment 2 participants were asked to prioritise the first pairing in the list or treat all pairings equally. We observed only limited evidence of prioritisation affecting the serial position function. Experiment 3 explored incidental odour-colour binding. Using a yes/no recognition procedure, accuracy did not differ for positive test probes presented in the same (bound) or different (unbound) colour to encoding. This study is one of the first to examine odour-colour binding in working memory and, taking the evidence together, suggests that odour-colour bindings can be formed in working memory; however, functionality may be limited compared to that of visual feature binding.

Uncovering the Complexity of Item Position Effects in a Low-Stakes Testing Context.

Previous researchers have only either adopted an item or examinee perspective to position effects, where they focused on exploring the relationships among position effects and item or examinee variables separately. Unlike previous researchers, we adopted an integrated perspective to position effects, where we focused on exploring the relationships among position effects, item variables, and examinee variables simultaneously. We evaluated the degree to which position effects on two separate low-stakes tests administered to two different samples were moderated by different item (item length, number of response options, mental taxation, and graphic) and examinee (effort, change in effort, and gender) variables. Items exhibited significant negative linear position effects on both tests, with the magnitude of the position effects varying from item to item. Longer items were more prone to position effects than shorter items; however, the level of mental taxation required to answer the item, the presence of a graphic, and the number of response options were not related to position effects. Examinee effort levels, change in effort patterns, and gender did not moderate the relationships among position effects and item features.

The transcription factor Atf1 lowers the transition barrier for nucleosome-mediated establishment of heterochromatin.

Transcription factors can exert opposite effects depending on the chromosomal context. The fission yeast transcription factor Atf1 both activates numerous genes in response to stresses and mediates heterochromatic gene silencing in the mating-type region. Investigating this context dependency, we report here that the establishment of silent heterochromatin in the mating-type region occurs at a reduced rate in the absence of Atf1 binding. Quantitative modeling accounts for the observed establishment profiles by a combinatorial recruitment of histone-modifying enzymes: locally by Atf1 at two binding sites and over the whole region by dynamically appearing heterochromatic nucleosomes, a source of which is the RNAi-dependent cenH element. In the absence of Atf1 binding, the synergy is lost, resulting in a slow rate of heterochromatin formation. The system shows how DNA-binding proteins can influence local nucleosome states and thereby potentiate long-range positive feedback on histone-modification reactions to enable heterochromatin formation over large regions in a context-dependent manner.

Standardized item selection for alternate computerized versions of Rey Auditory Verbal Learning Test(-based) word lists.

INTRODUCTION: Despite an increasing need for new Rey Auditory Verbal Learning Test (RAVLT)-based word lists in computerized testing, no criteria or standardized procedures exist for its development. To lay a foundation for future development of new and alternate computerized RAVLT(-based) word lists, we present cross-lingual word criteria, developed new lists using the criteria and evaluated performance on the lists using online assessment. METHOD: Based on psycholinguistic literature, we identified relevant word selection criteria. To validate the criteria, we developed two new American-English word lists and one new Dutch list, and administered the RAVLT using visual presentation of the new or original list in an online American (n = 248) and Dutch sample (n = 246) of healthy people. We compared performance of the new and original word lists on trial scores and serial position effects using Bayesian correlations and analyses of variance. Additionally, we compared proportions of correct responses per item, corrected for serial position. RESULTS: We identified 13 relevant word selection criteria. The criteria led to two new highly comparable American-English word lists with lower trial scores compared to the original American-English list, indicating that the criteria helped to develop parallel lists with fewer associations between items. The new Dutch word list showed similar trial scores, serial position effects, and proportions of correct responses per item corrected for serial position compared to the original Dutch version. CONCLUSIONS: The systematic use of word selection criteria can facilitate development of new parallel word lists, including in new language areas. Future studies should evaluate the use of the word criteria for the other sections of the RAVLT (such as delayed recall and recognition), performance using original test modalities (auditory presentation and recall of words) as well as performance in clinical samples.

Metacognitive control, serial position effects, and effective transfer to self-paced study.

Serial position effects involve the differential recall of information based on its temporal order at encoding. Previous research indicates that learners may be aware of these effects under certain encoding conditions, but it is unclear whether metacognitive control is sensitive to serial position effects. The current study examined whether there are serial position effects in participants' study time and whether they can learn about serial position effects under fixed encoding conditions and then transfer what they have learned to self-paced study conditions. Specifically, participants were given lists of to-be-remembered words and studied each word for a fixed duration on initial lists, but self-paced their study time on later lists. Results revealed that self-paced study times oppositely mirrored serial position effects (i.e., briefer study times in the beginning and end of each list), and serial position effects were reduced in self-paced study conditions, particularly in participants initially studying under fixed conditions before self-pacing their study time. Specifically, participants may have monitored their output and, based on observations of forgetting middle items, transferred their learning of serial position effects from prior lists. Thus, participants may use forgetting and serial position information to guide encoding, indicating that fundamental properties of the memory system can be incorporated into the processes that guide metacognitive control.

Fine Breakpoint Mapping by Genome Sequencing Reveals the First Large X Inversion Disrupting the NHS Gene in a Patient with Syndromic Cataracts.

Inversions are structural variants that are generally balanced. However, they could lead to gene disruptions or have positional effects leading to diseases. Mutations in the NHS gene cause Nance-Horan syndrome, an X-linked disorder characterised by congenital cataracts and dental anomalies. Here, we aimed to characterise a balanced pericentric inversion X(p22q27), maternally inherited, in a child with syndromic bilateral cataracts by breakpoint mapping using whole-genome sequencing (WGS). 30× Illumina paired-end WGS was performed in the proband, and breakpoints were confirmed by Sanger sequencing. EdU assays and FISH analysis were used to assess skewed X-inactivation patterns. RNA expression of involved genes in the breakpoint boundaries was evaluated by droplet-digital PCR. We defined the breakpoint position of the inversion at Xp22.13, with a 15 bp deletion, disrupting the unusually large intron 1 of the canonical NHS isoform, and also perturbing topologically-associated domains (TADs). Moreover, a microhomology region of 5 bp was found on both sides. RNA analysis confirmed null and reduced NHS expression in the proband and his unaffected mother, respectively. In conclusion, we report the first chromosomal inversion disrupting NHS, fine-mapped by WGS. Our data expand the clinical spectrum and the pathogenic mechanisms underlying the NHS defects.

The dynamics of memory for United States presidents in younger and older adults.

ABSTRACTSerial position effects are often observed within the free recall of unassociated words but also when recalling items from a semantic category like U.S. presidents. We investigated the dynamics of recall for U.S. presidents in younger and older adults to examine potential age-related differences in the organisation of retrieval from semantic long-term memory. Older adults recalled more presidents than younger adults and also demonstrated dual serial position effects such that, in addition to overall serial position effects, primacy (e.g., Eisenhower) and recency presidents (e.g., Obama) within older adults' lifetime were better recalled than presidents from the middle of their lives (e.g., Ford). Additionally, participants initiated recall with the most distinct presidents (highly familiar or memorable presidents like Washington, Obama, Trump), and conditional-response probabilities revealed that presidents from similar eras were recalled in close proximity, indicating that the retrieval of distinct presidents can facilitate memory for presidents from a similar era. Collectively, we demonstrate the potential interplay of the mechanisms that influence the organisation of retrieval such that distinctiveness and temporal contiguity effects may simultaneously impact recall. Specifically, semantic and temporal-contextual associations can drive semantic autobiographical memory and people likely organise retrieval from long-term memory according to familiarity and distinctiveness.