Molecular architecture and functional dynamics of the pre-incision complex in nucleotide excision repair.

Nucleotide excision repair (NER) is vital for genome integrity. Yet, our understanding of the complex NER protein machinery remains incomplete. Combining cryo-EM and XL-MS data with AlphaFold2 predictions, we build an integrative model of the NER pre-incision complex(PInC). Here TFIIH serves as a molecular ruler, defining the DNA bubble size and precisely positioning the XPG and XPF nucleases for incision. Using simulations and graph theoretical analyses, we unveil PInC's assembly, global motions, and partitioning into dynamic communities. Remarkably, XPG caps XPD's DNA-binding groove and bridges both junctions of the DNA bubble, suggesting a novel coordination mechanism of PInC's dual incision. XPA rigging interlaces XPF/ERCC1 with RPA, XPD, XPB, and 5' ssDNA, exposing XPA's crucial role in licensing the XPF/ERCC1 incision. Mapping disease mutations onto our models reveals clustering into distinct mechanistic classes, elucidating xeroderma pigmentosum and Cockayne syndrome disease etiology.

Association between untreated caries and cariogenic bacteria in adolescents in Taiwan.

Background/purpose: There is a paucity of research focused on salivary bacteria analyzed through real-time polymerase chain reaction (qPCR) among adolescents. The current study determined the quantity of Streptococcus mutans (SM) and Lactobacillus (LB) in saliva obtained from Taiwanese adolescents and investigated the association between the oral bacteria and untreated dental caries. Materials and methods: This cross-sectional study recruited Taiwanese students aged 10-18. Saliva was collected using a Salivette kit and then analyzed through qPCR. The relative quantification values of SM and LB were coded based on mean fold ratios, with values > 2 coded as high and other values coded as low. Untreated dental caries was assessed through standard oral examinations. Univariate and multivariate logistic regression models were used to estimate the association between the levels of bacteria in the saliva of the study participants and the presence of untreated caries. Results: The study involved 421 adolescents. 56 (13.3%) had both SM and LB values of >2 and were coded as having high levels of bacteria, whereas the other 365 (86.7%) students were coded as having low levels. The multivariate logistic regression analysis revealed that adolescents who had high combined salivary SM and LB levels had an odds ratio of having untreated dental caries of 2.05 (95% CI = 1.09, 3.86, P = 0.027) compared with those who had low salivary SM and LB levels. Conclusion: The results of the present study indicate that salivary SM and LB levels are significantly associated with adolescents having untreated caries.

Diet induced mitochondrial DNA replication instability in Rad51c mutant mice drives sex-bias in anemia of inflammation.

Anemia of inflammation (AI) is a common comorbidity associated with obesity, diabetes, cardiac disease, aging, and during anti-cancer therapies. Mounting evidence illustrates that males are disproportionally affected by AI, but not why. Here we demonstrate a molecular cause for a sex-bias in inflammation. The data shows that mitochondrial DNA (mtDNA) instability induced by dietary stress causes anemia associated with inflamed macrophages and improper iron recycling in mice. These phenotypes are enhanced in mice with mutations in Fanco/Rad51c , which predisposes to the progeroid disease Fanconi Anemia. The data reveals a striking sex-bias whereby females are protected. We find that estrogen acts as a mitochondrial antioxidant that reduces diet-induced oxidative stress, mtDNA replication instability and the distinctively mtDNA-dependent unphosphorylated STAT1 response. Consequently, treatment of male Rad51c mutant mice with estrogen or mitochondrial antioxidants suppresses the inflammation-induced anemia. Collectively, this study uncovers estrogen-responsive mtDNA replication instability as a cause for sex-specific inflammatory responses and molecular driver for AI.

Chromatin remodeler BRG1 recruits huntingtin to repair DNA double-strand breaks in neurons.

Persistent DNA double-strand breaks (DSBs) are enigmatically implicated in neurodegenerative diseases including Huntington's disease (HD), the inherited late-onset disorder caused by CAG repeat elongations in Huntingtin (HTT). Here we combine biochemistry, computation and molecular cell biology to unveil a mechanism whereby HTT coordinates a Transcription-Coupled Non-Homologous End-Joining (TC-NHEJ) complex. HTT joins TC-NHEJ proteins PNKP, Ku70/80, and XRCC4 with chromatin remodeler Brahma-related Gene 1 (BRG1) to resolve transcription-associated DSBs in brain. HTT recruitment to DSBs in transcriptionally active gene- rich regions is BRG1-dependent while efficient TC-NHEJ protein recruitment is HTT-dependent. Notably, mHTT compromises TC-NHEJ interactions and repair activity, promoting DSB accumulation in HD tissues. Importantly, HTT or PNKP overexpression restores TC-NHEJ in a Drosophila HD model dramatically improving genome integrity, motor defects, and lifespan. Collective results uncover HTT stimulation of DSB repair by organizing a TC-NHEJ complex that is impaired by mHTT thereby implicating dysregulation of transcription-coupled DSB repair in mHTT pathophysiology. Highlights: BRG1 recruits HTT and NHEJ components to transcriptionally active DSBs.HTT joins BRG1 and PNKP to efficiently repair transcription related DSBs in brain.Mutant HTT impairs the functional integrity of TC-NHEJ complex for DSB repair.HTT expression improves DSB repair, genome integrity and phenotypes in HD flies.

BRCA2 C-terminal clamp restructures RAD51 dimers to bind B-DNA for replication fork stability.

Tumor suppressor protein BRCA2 acts with RAD51 in replication-fork protection (FP) and homology-directed DNA break repair (HDR). Critical for cancer etiology and therapy resistance, BRCA2 C-terminus was thought to stabilize RAD51-filaments after they assemble on single-stranded (ss)DNA. Here we determined the detailed crystal structure for BRCA2 C-terminal interaction-domain (TR2i) with ATP-bound RAD51 prior to DNA binding. In contrast to recombinogenic RAD51-filaments comprising extended ATP-bound RAD51 dimers, TR2i unexpectedly reshapes ATP-RAD51 into a unique dimer conformation accommodating double-stranded B-DNA binding unsuited for HDR initiation. Structural, biochemical, and molecular results with interface-guided mutations uncover TR2i's FP mechanism. Proline-driven secondary-structure stabilizes residue triads and spans the RAD51 dimer engaging pivotal interactions of RAD51 M210 and BRCA2 S3291/P3292, the cyclin-dependent kinase (CDK) phosphorylation site that toggles between FP during S-phase and HDR in G2. TR2i evidently acts as an allosteric clamp switching RAD51 from ssDNA to double-stranded and B-DNA binding enforcing FP over HDR.

Athletes with meditation experience counteract the detrimental effect of mental fatigue on endurance performance and neurocognitive functions.

The current study examined whether meditation experience is associated with changes in endurance performance and inhibitory control-relevant neurocognitive functions caused by mental fatigue. Twenty-four athletes with meditation experience (AME) and twenty-five athletes without meditation experience (AWME) underwent a 30-min incongruent Stroop test in mental fatigue condition (MF) and a 30-min congruent Stroop test in control condition (CON) in a randomised-counterbalanced order. Inhibitory control-relevant neurocognitive functions were assessed using Flanker task and event-related potentials, followed by an endurance task using the Bruce treadmill protocol. Visual analogue scale was used to evaluate perceived mental fatigue (VAS-MF) before (T1), after Stroop test (T2) and after Flanker task (T3), and VAS for motivation (VAS-M) was used to evaluate motivation in Flanker task and endurance task. Results indicated that, compared to the CON, AWME in the MF exhibited overall lower accuracy, smaller incongruent N2 amplitude of the Flanker task (ps < .05), and shorter time to exhaustion (TTE) of the endurance task (p < .001), whereas AME did not exhibited difference in these outcomes between the conditions. Along with athletes in the MF reported lower VAS-M in endurance task. These findings suggest the benefits of meditation experience in mitigating the negative effects of mental fatigue.

Transcranial ultrasound with electrical stimulation of the cerebello-parietal nucleus on cerebral blood flow and limb function in patients with stroke.

OBJECTIVE: To investigate the efficacy of transcranial ultrasound stimulation (TUS) combined with Fastigial nucleus stimulation (FNS) on cerebral blood flow and limb function in patients in the acute phase of ischemic stroke. METHODS: A total of 90 patients in the acute phase of ischemic stroke were randomly divided into an FNS, TUS, and TUS + FNS group (30 patients each), and all patients also received conventional treatment. The FNS group was treated with FNS alone. The TUS group was treated with TUS alone. The TUS + FNS group was treated with both TUS and FNS. The three groups were treated once a day for 6 days a week. RESULTS: The simplified Fugl-Meyer Assessment (FMA) and Barthel index scores (BI), and the peak systolic blood flow velocity (Vs) and the mean blood flow velocity (Vm) of the anterior cerebral artery, middle cerebral artery, and posterior cerebral artery, were significantly higher in all three groups compared with before treatment (P < 0.05). The scores for the TUS group were higher than for the FNS group (P < 0.05), and the scores of the TUS + FNS group were higher than the TUS and FNS groups, respectively (P < 0.05). The total effective rate was 63.3%, 70.0%, and 90.0% in the FNS, TUS, and TUS + FNS groups, respectively, and the difference between the three groups was statistically significant (P < 0.05). CONCLUSION: The FNS and TUS treatments improved the function of and accelerated cerebral blood flow in patients with acute ischemic stroke to different degrees, and the combined use of both treatment types was overall more effective.

Lexical Morphology as a Source of Risk and Resilience for Learning to Read With Dyslexia: An fNIRS Investigation.

PURPOSE: We examined the neurocognitive bases of lexical morphology in children of varied reading abilities to understand the role of meaning-based skills in learning to read with dyslexia. METHOD: Children completed auditory morphological and phonological awareness tasks during functional near-infrared spectroscopy neuroimaging. We first examined the relation between lexical morphology and phonological processes in typically developing readers (Study 1, N = 66, Mage = 8.39), followed by a more focal inquiry into lexical morphology processes in dyslexia (Study 2, N = 50, Mage = 8.62). RESULTS: Typical readers exhibited stronger engagement of language neurocircuitry during the morphology task relative to the phonology task, suggesting that morphological analyses involve synthesizing multiple components of sublexical processing. This effect was stronger for more analytically complex derivational affixes (like + ly) than more semantically transparent free base morphemes (snow + man). In contrast, children with dyslexia exhibited stronger activation during the free base condition relative to derivational affix condition. Taken together, the findings suggest that although children with dyslexia may struggle with derivational morphology, they may also use free base morphemes' semantic information to boost word recognition. CONCLUSION: This study informs literacy theories by identifying an interaction between reading ability, word structure, and how the developing brain learns to recognize words in speech and print. SUPPLEMENTAL MATERIAL: https://doi.org/10.23641/asha.25944949.

Nardilysin-regulated scission mechanism activates polo-like kinase 3 to suppress the development of pancreatic cancer.

Pancreatic ductal adenocarcinoma (PDAC) develops through step-wise genetic and molecular alterations including Kras mutation and inactivation of various apoptotic pathways. Here, we find that development of apoptotic resistance and metastasis of KrasG12D-driven PDAC in mice is accelerated by deleting Plk3, explaining the often-reduced Plk3 expression in human PDAC. Importantly, a 41-kDa Plk3 (p41Plk3) that contains the entire kinase domain at the N-terminus (1-353 aa) is activated by scission of the precursor p72Plk3 at Arg354 by metalloendopeptidase nardilysin (NRDC), and the resulting p32Plk3 C-terminal Polo-box domain (PBD) is removed by proteasome degradation, preventing the inhibition of p41Plk3 by PBD. We find that p41Plk3 is the activated form of Plk3 that regulates a feed-forward mechanism to promote apoptosis and suppress PDAC and metastasis. p41Plk3 phosphorylates c-Fos on Thr164, which in turn induces expression of Plk3 and pro-apoptotic genes. These findings uncover an NRDC-regulated post-translational mechanism that activates Plk3, establishing a prototypic regulation by scission mechanism.

HDAC6/aggresome processing pathway importance for inflammasome formation is context-dependent.

The inflammasome is a large multiprotein complex that assembles in the cell cytoplasm in response to stress or pathogenic infection. Its primary function is to defend the cell and promote the secretion of pro-inflammatory cytokines, including IL-1ß and IL-18. Previous research has shown that in immortalized bone marrow-derived macrophages (iBMDMs) inflammasome assembly is dependent on the deacetylase HDAC6 and the aggresome processing pathway (APP), a cellular pathway involved in the disposal of misfolded proteins. Here we used primary BMDMs from mice in which HDAC6 is ablated or impaired and found that inflammasome activation was largely normal. We also used human peripheral blood mononuclear cells and monocyte cell lines expressing a synthetic protein blocking the HDAC6-ubiquitin interaction and impairing the APP and found that inflammasome activation was moderately affected. Finally, we used a novel HDAC6 degrader and showed that inflammasome activation was partially impaired in human macrophage cell lines with depleted HDAC6. Our results therefore show that HDAC6 importance in inflammasome activation is context-dependent.

Examining the Association Between Trauma Characteristics and Adult Depression and Anxiety: Analysis of Types, Variety, Repetition, and Timing of Past Trauma.

Past research has emphasized the impact of prior trauma on adult depression and anxiety rates. However, few studies have examined the simultaneous connection between various trauma characteristics (e.g., type, variety, repetition, timing) and symptoms of depression and anxiety in adults. Understanding how these different trauma characteristics relate to mental health issues can offer valuable insight into predicting the onset of such problems. We conducted a cross-sectional analysis with 356 adult participants to explore the associations between lifetime trauma history and depression/anxiety scores. Participants retrospectively reported on five different traumatic experiences from birth to the present, including childhood physical abuse, witnessing parental violence, lifetime experiences of rape, witnessing trauma to loved ones, and the unexpected death of loved ones. For each trauma type, participants indicated the timing of their first exposure and the frequency of subsequent occurrences. Depression and anxiety symptoms in the past 2 weeks were also self-reported. Multiple regression analyses with covariates were employed. On average, participants experienced two out of the five trauma types. Regardless of the type, having at least one traumatic experience was linked to higher depression and anxiety scores. Those who experienced all five trauma types reported the highest levels of depression and anxiety. Repeated instances of rape, witnessing trauma to loved ones, and the death of loved ones were significantly associated with elevated depression and anxiety scores. The timing of exposure to the unexpected death of loved ones predicted higher depression scores in childhood compared to adulthood, while no relationship between timing and anxiety scores was observed. Other trauma types did not show significant associations. Our study enhances knowledge of the link between trauma and depression/anxiety by elucidating how various trauma characteristics, such as type, variety, repetition, and timing of trauma, have differential influences on depression and anxiety scores.

Studying Cell Migration (Random and Wound Healing) Parameters with Imaging and MATLAB Analysis.

Cell migration is an essential biological process for organisms, in processes including embryonic development, immune response, and cancer metastasis. To elucidate the regulatory machinery of this vital process, methods that mimic in vivo migration, including in vitro wound healing assay and random migration assay, are widely used for cell behavior investigation. However, several concerns are raised with traditional cell migration experiment analysis. First, a manually scratched wound often presents irregular edges, causing the speed analysis difficult. Second, only the migration speed of leading cells is considered in the wound healing assay. Here, we provide a reliable analysis method to trace each cell in the time-lapse images, eliminating the concern about wound shape and creating a more comprehensive understanding of cell migration-not only of collective migration speed but also single-cell directionality and coordination between cells.

Studying Cellular Focal Adhesion Parameters with Imaging and MATLAB Analysis.

Cell signaling is highly integrated for the process of various cell activities. Although previous studies have shown how individual genes contribute to cell migration, it remains unclear how the integration of these signaling pathways is involved in the modulation of cell migration. In our two-hit migration screen, we revealed that serine-threonine kinase 40 (STK40) and mitogen-activated protein kinase (MAPK) worked synergistically, and the suppression of both genes could further lead to suppression in cell migration. Furthermore, based on our analysis of cellular focal adhesion (FA) parameters using MATLAB analysis, we are able to find out the synergistic reduction of STK40 and MAPK that further abolished the increased FA by shSTK40. While FA identification in previous studies includes image analysis using manual selection, our protocol provides a semi-automatic manual selection of FAs using MATLAB. Here, we provide a method that can shorten the amount of time required for manual identification of FAs and increase the precision for discerning individual FAs for various analyses, such as FA numbers, area, and mean signals.

Newly Generated Ca-Feldspar during Sintering Processes Enhances the Mechanical Strength of Coal Gangue-Based Insulation Bricks.

Coal gangue is a solid waste with low carbon content discharged during the course of the coal mining process. The resource utilization of coal gangue could solve environmental problems caused by its excessive production, such as soil contamination and land occupation. This study proposed to produce high-strength thermal insulation bricks using coal gangue as the primary material and three other mineral powders as auxiliary materials, including K-feldspar, CaCO3 and fly ash. A systematic analysis was conducted to explore the optimum raw material addition ratio and optimum sintering temperature; then, the intrinsic structure of thermal insulation bricks and their sintering formation mechanisms were revealed. The results showed that the optimal ratios of coal gangue, K-feldspar, CaCO3 and fly ash were 65 wt%, 15 wt%, 10 wt% and 10 wt%, respectively; the compressive strength of the thermal insulation brick produced under this ratio was 22.5 MPa; thermal conductivity was 0.39 W m-1 k-1. During sintering processes, mineral powders sufficiently fused to form a skeleton, and the CO2 derived from CaCO3 formed pores. The optimum sintering temperature was 1150 °C, because at this temperature, K-feldspar had the best effect in promoting the conversion of CaCO3 to Ca-feldspar. The high level of the relative crystallinity of Ca-feldspar (about 76.0%) helped raise the Si-O network's polymerization degree (NBO/T = 1.24), finally raising the compressive strength of thermal insulation bricks. The innovative method of using coal gangue to make thermal insulation bricks not only solved the environmental pollution caused by coal gangue but also provided excellent construction materials with high practical application value.

Impact of asymmetric electrodes on ferroelectricity of sub-10 nm HZO thin films.

In this study, platinum (Pt) and tungsten (W), two materials with dissimilar coefficients of thermal expansion (CTE) and work functions (WF), are used as the top electrode (TE) and the bottom electrode (BE) in metal/ferroelectric/metal (MFM) structures to explore the ferroelectricity of hafnium zirconium oxide (HZO) with a thickness less than 10 nm. The electrical measurements indicate that a higher CTE mismatch between HZO and TE/BE is beneficial for enhancing the ferroelectric properties of nanoscale HZO thin films. The different WFs of TE and BE generate a built-in electric field in the HZO layer, leading to shifts in the hysteresis loops and the capacitance-voltage characteristics. The structural characterizations reveal that the preferred formation of the orthorhombic phase in HZO is dominated by the W BE. The device in which W is used as the TE and BE (the W/HZO/W MFM structure) presents the optimal ferroelectric performance of a high remanent polarization (2Pr= 55.2µC cm-2). The presence of tungsten oxide (WOx) at the W/HZO interfaces, as revealed by high-resolution transmission microscopy, is also responsible for the enhancement of ferroelectric properties. This study demonstrates the significant effects of different CTEs and WFs of TE and BE on the properties of ferroelectric HZO thin films.

The development of a broad-spectrum retaining ß-exo-galactosidase activity-based probe.

Acid ß-galactosidase (GLB1) and galactocerebrosidase (GALC) are retaining exo-ß-galactosidases involved in lysosomal glycoconjugate metabolism. Deficiency of GLB1 may result in the lysosomal storage disorders GM1 gangliosidosis, Morquio B syndrome, and galactosialidosis, and deficiency of GALC may result in Krabbe disease. Activity-based protein profiling (ABPP) is a powerful technique to assess the activity of retaining glycosidases in relation to health and disease. This work describes the use of fluorescent and biotin-carrying activity-based probes (ABPs) to assess the activity of both GLB1 and GALC in cell lysates, culture media, and tissue extracts. The reported ABPs, which complement the growing list of retaining glycosidase ABPs based on configurational isomers of cyclophellitol, should assist in fundamental and clinical research on various ß-galactosidases, whose inherited deficiencies cause debilitating lysosomal storage disorders.

Phonological and morphological literacy skills in English and Chinese: A cross-linguistic neuroimaging comparison of Chinese-English bilingual and monolingual English children.

Over the course of literacy development, children learn to recognize word sounds and meanings in print. Yet, they do so differently across alphabetic and character-based orthographies such as English and Chinese. To uncover cross-linguistic influences on children's literacy, we asked young Chinese-English simultaneous bilinguals and English monolinguals (N = 119, ages 5-10) to complete phonological and morphological awareness (MA) literacy tasks. Children completed the tasks in the auditory modality in each of their languages during functional near-infrared spectroscopy neuroimaging. Cross-linguistically, comparisons between bilinguals' two languages revealed that the task that was more central to reading in a given orthography, such as phonological awareness (PA) in English and MA in Chinese, elicited less activation in the left inferior frontal and parietal regions. Group comparisons between bilinguals and monolinguals in English, their shared language of academic instruction, revealed that the left inferior frontal was less active during phonology but more active during morphology in bilinguals relative to monolinguals. MA skills are generally considered to have greater language specificity than PA skills. Bilingual literacy training in a skill that is maximally similar across languages, such as PA, may therefore yield greater automaticity for this skill, as reflected in the lower activation in bilinguals relative to monolinguals. This interpretation is supported by negative correlations between proficiency and brain activation. Together, these findings suggest that both the structural characteristics and literacy experiences with a given language can exert specific influences on bilingual and monolingual children's emerging brain networks for learning to read.

Real-world effectiveness of national pit and fissure sealants program in Taiwan.

OBJECTIVES: This study investigated the effectiveness of a national population-based pit and fissure sealants (PFS) program in Taiwan. METHODS: Part 1 (effectiveness of national PFS program) involved children who had participated in the PFS program from 2015 to 2019. After propensity score matching, 670,840 children were selected for analysis until the end of 2019. During follow-up, the permanent first molars of the participants were assessed for caries-related treatments by employing multilevel Cox proportional hazards models. In Part 2 (effectiveness of retained sealants), which involved 1,561 children, sealant retention was evaluated 3 years after placement. A structured questionnaire was employed to collect information on family and individual factors. The endpoints were the same as in Part 1. RESULTS: In Part 1, the adjusted hazard ratios (HRs) for caries-related treatments among participants in the PFS program were 0.90 (95% confidence interval [CI] = 0.89, 0.91) for dental restoration, 0.42 (95% CI = 0.38, 0.46) for initiation of endodontic treatment, 0.46 (95% CI = 0.41, 0.52) for completion of endodontic treatment, and 0.25 (95% CI = 0.18, 0.34, all Ps < 0.0001) for extraction. In Part 2, the adjusted HR for dental restoration of teeth with retained sealants was 0.70 (95% CI = 0.58, 0.85), significantly lower than that for teeth without retained sealants (P = 0.0002). CONCLUSIONS: Participation in the national PFS program was associated with a significant reduction of at least 10% in the risk of caries-related treatments, and an additional 30% risk reduction may have been attributed to sealant retention. CLINICAL SIGNIFICANCE: In a real-world setting, schoolchildren in the national PFS program were associated with a significant reduction of at least 10% in the likelihood of caries-related treatments. The program provided moderate protection against caries for the study population and could be improved by increasing the sealant retention rate.