bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of hydrothermal temperature on the optical properties of hydrochar-derived dissolved organic matter and their interactions with copper (II)
Authors: Ji Licheng , Yu Zhongpu , Cao Qi , Gui Xiangyang , Fan Xingjun , Wei Chengcheng , Jiang Fei , Wang Jie , Meng Fanbin , Li Feiyue , Wang Jianfei
Published: June 2024

Hydrothermal carbonization (HTC) has been regarded as a promising technique for turning wet biomass into hydrochar due to its low energy consumption, low exhaust gas emissions, etc. In addition, hydrochar is an important source of dissolved organic matter (DOM), which plays a crucial part in the migration and destiny of pollutants in the environmental medium. However, there are limited studies that focus on the factors that influence the formation of DOM in hydrochar, such as hydrothermal temperature. Therefore, the current study comprehensively characterized the optical properties of DOM within hydrochar derived from sawdust (HDOM) under different hydrothermal temperatures (150–300 °C) by Ultraviolet–visible (UV–Vis) and fluorescence spectroscopy, as well as its complexation characteristic with Cu(II). The findings revealed that the organic carbon content of HDOM reached a peak of 37.3 mg L−1 when the temperature rose to 240 °C and then decreased as the temperature increased. UV–Vis spectroscopy analysis showed that the absorption capacity of HDOM at 275 nm increases with temperature and reaches a maximum value at 240 °C, indicating that high temperature promotes the formation of monocyclic aromatic compounds. High temperature enhances the aromaticity, hydrophobicity, and humification degree of HDOM, thus improving its stability and aromaticity. The E3/E4 ratios are all greater than 3.5, confirming that the main component of HDOM is fulvic acid, which corresponds to 3D-EEM and Pearson's correlation coefficient analysis. The humification index (HIX) of HDOM increased with the rise in hydrothermal temperature (150–240 °C), as observed by the three-dimensional excitation-emission matrix spectroscopy (3D-EEMs). After reaching its peak at 240 °C, the HIX value gradually dropped in line with the trend of the DOC change. Moreover, the bioavailability (BIX) value of DOM was all high and greater than 1, indicating all the HDOM are readily bioavailable. Two microbial humic substances (C1 and C4), a humic-like substance (C2), and a protein-like substance (C3) were discovered in DOM by integrating 3D-EEMs with parallel factor analysis (PARAFAC). Their fluorescence intensity decreases as the Cu(II) concentration increases, indicating the formation of complexes with Cu(II). As the temperature rises, the binding ability of DOM and Cu(II) changes significantly, reaching the optimum at 300 °C. Meanwhile, the substance C2 has the strongest binding ability with Cu(II). This research emphasizes the significance of spectroscopy analysis in determining the evolution of hydrochar-derived DOM, the potential for heavy metal binding and migration, and its characteristics and features.

Graphical Abstract
The developments in carbon-modified graphitic carbon nitride for photoelectrochemical water splitting: a mini review
Authors: Yang Yuewen , Xu Tingrui , Zhang Ruiqin
Published: June 2024

Graphitic carbon nitride (g-CN), as a potential photoelectrode for photoelectrochemical water splitting, has garnered significant research attention owing to its favorable attributes, including a suitable bandgap, abundant elemental composition, excellent thermal stability, and non-toxicity. However, the limited efficiency of visible light absorption and poor electrical conductivity of pure g-CN result in low photocurrent density and photocatalytic activity, falling short of meeting the requirements for commercial applications. In contrast, graphitic carbon materials possess high conductivity and stability, appearing to be an excellent candidate for enhancing the photocatalytic performance of g-CN while maintaining its stability. Recently, nitrogen vacancies, surface junction, carbon crystallite introduction, and carbon atom doping methods have been employed to prepare carbon-modified g-CN. The introduced π-electron conjugated system by sp2-hybridized carbon atoms indeed extends the visible light absorption and photocurrent of g-CN, resulting in improved photocatalytic performance. In this review, we highlight recent advancements in the development of carbon-modified g-CN and offer insights into the future prospects of g-CN-based films.
Depth‐Partitioning of Particulate Organic Carbon Composition in the Rising and Falling Stages of the Amazon River
Authors: Rosengard Sarah Z. , Moura Jose Mauro S. , Spencer Robert G. M. , Johnson Carl , McNichol Ann , Steen Andrew D. , Galy Valier
Published: June 2024

The Amazon River mobilizes organic carbon across one of the world's largest terrestrial carbon reservoirs. Quantifying the sources of particulate organic carbon (POC) to this flux is typically challenging in large systems such as the Amazon River due to hydrodynamic sorting of sediments. Here, we analyze the composition of POC collected from multiple total suspended sediment (TSS) profiles in the mainstem at Óbidos, and surface samples from the Madeira, Solimões and Tapajós Rivers. As hypothesized, TSS and POC concentrations in the mainstem increased with depth and fit well to Rouse models for sediment sorting by grain size. Coupling these profiles with Acoustic Doppler Current Profiler discharge data, we estimate a large decrease in POC flux (from 540 to 370 kg per second) between the rising and falling stages of the Amazon River mainstem. The C/N ratio and stable and radiocarbon signatures of bulk POC are less variable within the cross‐section at Óbidos and suggest that riverine POC in the Amazon River is predominantly soil‐derived. However, smaller shifts in these compositional metrics with depth, including leaf wax n‐alkanes and fatty acids, are consistent with the perspective that deeper and larger particles carry fresher, less degraded organic matter sources (i.e., vegetation debris) through the mainstem. Overall, our cross‐sectional surveys at Óbidos highlight the importance of depth‐specific sampling for estimating riverine export fluxes. At the same time, they imply that this approach to sampling is perhaps less essential with respect to characterizing the composition of POC sources exported by the river.
Testing Mantle Convection Simulations With Paleobiology and Other Stratigraphic Observations: Examples From Western North America
Authors: Fernandes Victoria M. , Roberts Gareth G. , Richards Fred
Published: June 2024

Mantle convection plays a fundamental role in driving evolution of oceanic and continental lithosphere. In turn it impacts a broad suite of processes operating at or close to Earth's surface including landscape evolution, glacio‐eustasy, magmatism, and climate. A variety of theoretical approaches now exist to simulate mantle convection. Outputs from such simulations are being used to parameterize models of landscape evolution and basin formation. However, the substantial body of existing simulations has generated a variety of conflicting views on the history of dynamic topography, its evolution and key parameters for modeling mantle flow. The focus of this study is on developing strategies to use large‐scale quantitative stratigraphic observations to assess model predictions and identify simulation parameters that generate realistic predictions of Earth surface evolution. Spot measurements of uplift or subsidence provide useful target observations for models of dynamic topography, but finding areas where tectonics have not also influenced vertical motions is challenging. To address this issue, we use large inventories of stratigraphic data from across North America with contextual geophysical and geodetic data to constrain the regional uplift and subsidence history. We demonstrate that a suite of typical geodynamic simulations struggle to match the amplitude, polarity and timing of observed vertical motions. Building on recent seismological advances, we then explore strategies for understanding patterns of continental uplift and subsidence that incorporate (and test) predicted evolution of the lithosphere, asthenosphere and deep mantle. Our results demonstrate the importance of contributions from the uppermost mantle in driving vertical motions of continental interiors.
Implementation and Exploration of Parameterizations of Large‐Scale Dynamics in NCAR's Single Column Atmosphere Model SCAM6
Authors: Cohen S. , Sobel A. , Biasutti M. , Wang S. , Simpson I. , Gettelman A. , Hu I.
Published: June 2024

A single column model with parameterized large‐scale (LS) dynamics is used to better understand the response of steady‐state tropical precipitation to relative sea surface temperature under various representations of radiation, convection, and circulation. The large‐scale dynamics are parametrized via the weak temperature gradient (WTG), damped gravity wave (DGW), and spectral weak temperature gradient (Spectral WTG) method in NCAR's Single Column Atmosphere Model (SCAM6). Radiative cooling is either specified or interactive, and the convective parameterization is run using two different values of a parameter that controls the degree of convective inhibition. Results are interpreted in the context of the Global Atmospheric System Studies ‐Weak Temperature Gradient (GASS‐WTG) Intercomparison project. Using the same parameter settings and simulation configuration as in the GASS‐WTG Intercomparison project, SCAM6 under the WTG and DGW methods produces erratic results, suggestive of numerical instability. However, when key parameters are changed to weaken the large‐scale circulation's damping of tropospheric temperature variations, SCAM6 performs comparably to single column models in the GASS‐WTG Intercomparison project. The Spectral WTG method is less sensitive to changes in convection and radiation than are the other two methods, performing qualitatively similarly across all configurations considered. Under all three methods, circulation strength, represented in 1D by grid‐scale vertical velocity, is decreased when barriers to convection are reduced. This effect is most extreme under specified radiative cooling, and is shown to come from increased static stability in the column's reference radiative‐convective equilibrium profile. This argument can be extended to interactive radiation cases as well, though perhaps less conclusively.
Sedimentary Basins Tell Zealandia’s Ancient Story
Authors: Evans Kate
Published: June 2024

New interpretations and mapping of all New Zealand’s offshore sedimentary basins offer clues about the evolution of Earth’s eighth continent.
Sources and Chemical Weathering Implications of Strontium and Hydrochemistry in an Inland Alpine Permafrost Basin
Authors: Zhou Huiling , Li Zongxing , Zhang Baijuan , Du Fa , Xue Jian
Published: June 2024

The hydrochemical characteristics of river water are influenced by a multitude of factors, reflecting the surrounding geographical environment. The Shaliu River, located in the northeastern Tibetan Plateau (TP), serves as a typical inland alpine permafrost watershed. In this study, we compiled data on dissolved strontium (Sr) concentration, 87Sr/86Sr isotopic, and hydrochemical profiles from the Shaliu River during the ablation period (May–October). Additionally, we gathered information on the Sr concentration and 87Sr/86Sr in the sediment of the river. The pattern of spatial heterogeneity in observed strontium (Sr) compositions can largely be attributed to lithological characteristics encountered at different locations along the river. The chemical components of Sr in the waters are derived from a combination of carbonate and silicate materials, with carbonates contributing between 69% and 81% and silicates contributing 19%–31%. The annual dissolved Sr flux is estimated to be 132 t/a. In addition to the influence of lithology and weathering processes, we propose that freeze‐thaw cycles within the permafrost layer may significantly affect the chemical mass flux in alpine permafrost watersheds because they generate substantial amounts of loose and easily erodible materials. Climate warming may further intensify the weathering processes in these watersheds, potentially leading to an increase in the Sr flux. This study is crucial for developing a comprehensive understanding of the geochemical composition of dissolved solutes in alpine permafrost regions, as well as for identifying the factors that regulate river water chemistry.
Accelerating Seafloor Uplift of Submarine Caldera Near Sofugan Volcano, Japan, Resolved by Distant Tsunami Recordings
Authors: Kubota Tatsuya , Sandanbata Osamu , Saito Tatsuhiko , Matsuzawa Takanori
Published: June 2024

On 8 October 2023 UTC, significant tsunamis were observed around Japan without any major tsunamigenic earthquake, associated with a series of 14 successive minor earthquakes (mb = 4.5–5.4) near Sofugan in the Izu‐Bonin Islands. To examine the cause of this tsunami, we estimated the horizontal locations of the tsunami source and temporal history of the seafloor displacement, using the tsunami data recorded by the ocean‐bottom pressure gauges >∼600 km away. Our results showed the main tsunami source was an uplift located at a caldera‐like bathymetric feature near Sofugan, suggesting the involvement of caldera activity in the tsunami generation. The total seafloor uplift was estimated as ∼4 m, and the uplift amount of each event gradually increased over time, reflecting an accelerating occurrence of volcanic unrest of the submarine caldera within only a few hours.
Dissolved Nitrous Oxide and Hydroxylamine in the Northern South China Sea in Summer
Authors: Zhang L. , Yao F. , Ji Q. , Ma X.
Published: June 2024

Nitrous oxide (N2O) is a potent greenhouse gas and a strong ozone‐depleting substance. Ocean is an important natural source of atmospheric N2O, which has attracted increasing attention recently as to understand the biogeochemical cycles of nitrogen in marine systems. Nitrification is one of the major N2O production pathways during which N2O is produced as a side product and hydroxylamine (NH2OH) is produced as an obligate intermediate. However, few studies have reported the NH2OH variability in natural seawater and its relationship between N2O remains ambiguous. In summer 2022, spatial distribution and influencing factors of N2O and NH2OH in the northern South China Sea (SCS) were investigated. Dissolved N2O varied from 5.79 to 34.80 nmol L−1 in water column and generally increased with water depth above 800 m. N2O was correlated with dissolved oxygen and nitrate, inferring that N2O was mainly produced via nitrification. NH2OH varied from below detection limit to 3.91 nmol L−1. The adoption of multiple standard additions can largely reduce the bias in NH2OH measurement. Structural equation modeling showed that NH2OH has a potential effect favoring excessive N2O. Surface N2O saturation ranged between 102% and 278%, indicating that the northern SCS was a net source of atmospheric N2O in summer.
Ketamine reduces the neural distinction between self- and other-produced affective touch: a randomized double-blind placebo-controlled study
Authors: Kaldewaij Reinoud , Salamone Paula C. , Enmalm Adam , Östman Lars , Pietrzak Michal , Karlsson Hanna , Löfberg Andreas , Gauffin Emelie , Samuelsson Martin , Gustavson Sarah , Capusan Andrea J. , Olausson Håkan , Heilig Markus , Boehme Rebecca
Published: June 2024

A coherent sense of self is crucial for social functioning and mental health. The N-methyl-D-aspartate antagonist ketamine induces short-term dissociative experiences and has therefore been used to model an altered state of self-perception. This randomized double-blind placebo-controlled cross-over study investigated the mechanisms for ketamine’s effects on the bodily sense of self in the context of affective touch. Thirty healthy participants (15 females/15 males, age 19–39) received intravenous ketamine or placebo while performing self-touch and receiving touch by someone else during functional MRI – a previously established neural measure of tactile self-other-differentiation. Afterwards, tactile detection thresholds during self- and other-touch were assessed, as well as dissociative states, interoceptive awareness, and social touch attitudes. Compared to placebo, ketamine administration elicited dissociation and reduced neural activity associated with self-other-differentiation in the right temporoparietal cortex, which was most pronounced during other-touch. This reduction correlated with ketamine-induced reductions in interoceptive awareness. The temporoparietal cortex showed higher connectivity to somatosensory cortex and insula during other- compared to self-touch. This difference was augmented by ketamine, and correlated with dissociation strength for somatosensory cortex. These results demonstrate that disrupting the self-experience through ketamine administration affects neural activity associated with self-other-differentiation in a region involved in touch perception and social cognition, especially with regard to social touch by someone else. This process may be driven by ketamine-induced effects on top-down signaling, rendering the processing of predictable self-generated and unpredictable other-generated touch more similar. These findings provide further evidence for the intricate relationship of the bodily self with the tactile sense.
Biliary atresia: insights into mechanisms using a toxic model of the disease including Wnt and Hippo signaling pathways and microtubules
Authors: Fried Sophia , Har-Zahav Adi , Hamudi Yara , Mahameed Sarah , Mansur Rasha , Dotan Miri , Cozacov Tal , Shamir Raanan , Wells Rebecca G. , Waisbourd-Zinman Orith
Published: June 2024

Background

Mechanisms underlying bile duct injury in biliary atresia (BA) remain unclear and mechanisms of bile duct repair are unknown. This study aimed to explore the roles of microtubule instability and Wnt and Hippo signaling pathways in a biliatresone-induced BA model.

Methods

Using primary murine neonatal cholangiocytes in both 2D and 3D cultures, and ex-vivo extra hepatic bile ducts (EHBD) which also has peri-cholangiocyte area, we analyzed injury and recovery processes. Injury was induced by the toxin biliatresone and recovery was induced by toxin wash-out.

Results

Microtubule stabilizer paclitaxel prevented biliatresone-induced injury, both to cholangiocytes as well as reduced periductal αSMA stain, this process is mediated by decreased glutathione levels. RhoU and Wnt11 (Wnt signaling) and Pard6g and Amotl1 (Hippo signaling) are involved in both injury and recovery processes, with the latter acting upstream to Wnt signaling.

Conclusions

Early stages of biliatresone-induced EHBD injury in cholangiocytes and periductal structures are reversible. Wnt and Hippo signaling pathways play crucial roles in injury and recovery, providing insights into BA injury mechanisms and potential recovery avenues.

Impact

Microtubule stabilization prevents cholangiocyte injury and lumen obstruction in a toxic model of biliary atresia (biliatresone induced).

Early stages of biliatresone-induced injury, affecting both cholangiocytes and periductal structures, are reversible. Both Wnt and Hippo signaling pathways play a crucial role in bile duct injury and recovery, with a noted interplay between the two.

Understanding mechanisms of cholangiocyte recovery is imperative to unveil potential therapeutic avenues.
Extracellular vesicles from type-2 macrophages increase the survival of chronic lymphocytic leukemia cells ex vivo
Authors: Ikhlef Léa , Ratti Nina , Durand Stéphanie , Formento Rémy , Daverat Héloïse , Boutaud Marie , Guillou Clément , Dmytruk Natalya , Gachard Nathalie , Cosette Pascal , Jauberteau Marie-Odile , Gallet Paul-François
Published: June 2024

The resistance of Chronic Lymphocytic Leukemia (CLL) B-cells to cell death is mainly attributed to interactions within their microenvironment, where they interact with various types of cells. Within this microenvironment, CLL-B-cells produce and bind cytokines, growth factors, and extracellular vesicles (EVs). In the present study, EVs purified from nurse-like cells and M2-polarized THP1 cell (M2-THP1) cultures were added to CLL-B-cells cultures. EVs were rapidly internalized by B-cells, leading to a decrease in apoptosis (P = 0.0162 and 0.0469, respectively) and an increased proliferation (P = 0.0335 and 0.0109). Additionally, they induced an increase in the resistance of CLL-B-cells to Ibrutinib, the Bruton kinase inhibitor in vitro (P = 0.0344). A transcriptomic analysis showed an increase in the expression of anti-apoptotic gene BCL-2 (P = 0.0286) but not MCL-1 and an increase in the expression of proliferation-inducing gene APRIL (P = 0.0286) following treatment with EVs. Meanwhile, an analysis of apoptotic protein markers revealed increased amounts of IGFBP-2 (P = 0.0338), CD40 (P = 0.0338), p53 (P = 0.0219) and BCL-2 (P = 0.0338). Finally, exploration of EVs protein content by mass spectrometry revealed they carry various proteins involved in known oncogenic pathways and the RNAseq analysis of CLL-B-cells treated or not with NLCs EVs show various differentially expressed genes.
IGFBP2/ITGA5 promotes gefitinib resistance via activating STAT3/CXCL1 axis in non-small cell lung cancer
Authors: Lu Hengxiao , Ai Jiangshan , Zheng Yingying , Zhou Wolong , Zhang Liming , Zhu Jiebo , Zhang Heng , Wang Shaoqiang
Published: June 2024

There is a paucity of comprehensive knowledge pertaining to the underlying mechanisms leading to gefitinib resistance in individuals diagnosed NSCLC harboring EGFR-sensitive mutations who inevitably develop resistance to gefitinib treatment within six months to one year. In our preceding investigations, we have noted a marked upregulation of IGFBP2 in the neoplastic tissues of NSCLC, predominantly in the periphery of the tissue, implying its plausible significance in NSCLC. Consequently, in the current research, we delved into the matter and ascertained the molecular mechanisms that underlie the participation of IGFBP2 in the emergence of gefitinib resistance in NSCLC cells. Firstly, the expression of IGFBP2 in the bronchoalveolar lavage fluid and lung cancer tissues of 20 NSCLC patients with gefitinib tolerance was found to be significantly higher than that of non-tolerant patients. Furthermore, in vitro and in vivo experiments demonstrated that IGFBP2 plays a significant role in the acquisition of gefitinib resistance. Mechanistically, IGFBP2 can activate STAT3 to enhance the transcriptional activity of CXCL1, thereby increasing the intracellular expression level of CXCL1, which contributes to the survival of lung cancer cells in the gefitinib environment. Additionally, we identified ITGA5 as a key player in IGFBP2-mediated gefitinib resistance, but it does not function as a membrane receptor in the process of linking IGFBP2 to intracellular signaling transduction. In conclusion, this study demonstrates the promoting role and mechanism of IGFBP2 in acquired gefitinib resistance caused by non-EGFR secondary mutations, suggesting the potential of IGFBP2 as a biomarker for gefitinib resistance and a potential intervention target.
The role of declining ataxia-telangiectasia-mutated (ATM) function in oocyte aging
Authors: Suzuki Reiko , Tan Xiujuan , Szymanska Katarzyna J. , Kubikova Nada , Perez Columba Avila , Wells Dagan , Oktay Kutluk H.
Published: June 2024

Despite the advances in the understanding of reproductive physiology, the mechanisms underlying ovarian aging are still not deciphered. Recent research found an association between impaired ATM-mediated DNA double-strand break (DSB) repair mechanisms and oocyte aging. However, direct evidence connecting ATM-mediated pathway function decline and impaired oocyte quality is lacking. The objective of this study was to determine the role of ATM-mediated DNA DSB repair in the maintenance of oocyte quality in a mouse oocyte knockdown model. Gene interference, in vitro culture, parthenogenesis coupled with genotoxicity assay approaches, as well as molecular cytogenetic analyses based upon next-generation sequencing, were used to test the hypothesis that intact ATM function is critical in the maintenance of oocyte quality. We found that ATM knockdown impaired oocyte quality, resulting in poor embryo development. ATM knockdown significantly lowered or blocked the progression of meiosis in vitro, as well as retarding and reducing embryo cleavage after parthenogenesis. After ATM knockdown, all embryos were of poor quality, and none reached the blastocyst stage. ATM knockdown was also associated with an increased aneuploidy rate compared to controls. Finally, ATM knockdown increased the sensitivity of the oocytes to a genotoxic active metabolite of cyclophosphamide, with increased formation of DNA DSBs, reduced survival, and earlier apoptotic death compared to controls. These findings suggest a key role for ATM in maintaining oocyte quality and resistance to genotoxic stress, and that the previously observed age-induced decline in oocyte ATM function may be a prime factor contributing to oocyte aging.
Comparison of erectile and ejaculatory functional outcomes between unilateral and bilateral cavernosal rupture in penile fractures
Authors: Keskin Emin Taha , Can Osman , Filtekin Yiğit Can , Özdemir Harun , Şahin Mehmet , Çeker Gökhan , Topal Cemal , Canat Halil Lütfi
Published: June 2024

This study aimed to compare the erectile and ejaculatory functional outcomes of unilateral and bilateral ruptures of the corpus cavernosum in penile fractures. Sixty patients’ data were analyzed retrospectively between June 2020 and January 2023. The patients were divided into two groups based on the affected corpus cavernosum (unilateral and bilateral). Preoperative and postoperative 3rd-, 6th-, and 12th-month self-estimated intravaginal-ejaculation-latency-time (IELT), and international index of erectile function-erectile function (IIEF-EF) scores as well as the presence of urethral injury were compared. Bilateral corpus cavernosum fractures were detected in 18.3% of the patients. The IIEF-EF scores of both groups at 3rd-, 6th-, and 12th-month were found to be significantly lower than the preoperative scores (unilateral group:24.1 ± 2.7 vs 23.2 ± 3.5 and 23.3 ± 3.4, respectively, p = 0.011 and 0.014, respectively; bilateral group: 24 ± 1.9 vs 23 ± 1.8 and 23.2 ± 1.5, respectively, p = 0.027 and 0.047, respectively). No significant difference was found between the preoperative and the postoperative 12th month IIEF-EF scores in either group (unilateral group: 24.1 ± 2.7 vs 23.4 ± 3.6, p = 0.207;bilateral group:24 ± 1.9 vs 23.2 ± 1.5, p = 0.057). The self-estimated IELTs of both groups at the postoperative 3rd, 6th, and 12th months demonstrated a significant increase from the preoperative values (unilateral group: 221.6 ± 81.8 vs 252 ± 94.6, 256.5 ± 97.6, and 250.5 ± 104.8, respectively, p < 0.001; bilateral group:241.8 ± 61.6 vs 278.1 ± 55.4, 281.8 ± 56.1, and 283.6 ± 54.2, respectively, p = 0.041, 0.030, and 0.047, respectively). The changes in self-estimated IELTs and IIEF-EF scores between the preoperative period and the postoperative 3rd, 6th, and 12th-months were compared, and no statistical difference was found between patients with unilateral and bilateral corpus cavernosum fractures (p > 0.05). In conclusion, no significant difference in erectile function was found in either group at the 12-month follow-up, and the self-estimated IELTs were found to be prolonged in both groups. Furthermore, no difference was noted between the groups at any follow-up. To explain the effects of unilateral and bilateral injuries on erectile and ejaculatory functions, further studies with a larger-number of patients are necessary.
Personalized and muscle-specific OXPHOS measurement with integrated CrCEST MRI and proton MR spectroscopy
Authors: Armbruster Ryan R. , Kumar Dushyant , Benyard Blake , Jacobs Paul , Khandavilli Aditi , Liu Fang , Nanga Ravi Prakash Reddy , McCormack Shana , Cappola Anne R. , Wilson Neil , Reddy Ravinder
Published: June 2024

Creatine chemical exchange saturation transfer (CrCEST) MRI is an emerging high resolution and noninvasive method for measuring muscle specific oxidative phosphorylation (OXPHOS). However, CrCEST measurements are sensitive to changes in muscle pH, which might confound the measurement and interpretation of creatine recovery time (τCr). Even with the same prescribed exercise stimulus, the extent of acidification and hence its impact on τCr is expected to vary between individuals. To address this issue, a method to measure pH pre- and post-exercise and its impact on CrCEST MRI with high temporal resolution is needed. In this work, we integrate carnosine 1H- magnetic resonance spectroscopy (MRS) and 3D CrCEST to establish “mild” and “moderate/intense” exercise stimuli. We then test the dependence of CrCEST recovery time on pH using different exercise stimuli. This comprehensive metabolic imaging protocol will enable personalized, muscle specific OXPHOS measurements in both healthy aging and myriad other disease states impacting muscle mitochondria.
Raman micro-spectroscopy reveals the spatial distribution of fumarate in cells and tissues
Authors: Kamp Marlous , Surmacki Jakub , Segarra Mondejar Marc , Young Tim , Chrabaszcz Karolina , Joud Fadwa , Zecchini Vincent , Speed Alyson , Frezza Christian , Bohndiek Sarah E.
Published: June 2024

Aberrantly accumulated metabolites elicit intra- and inter-cellular pro-oncogenic cascades, yet current measurement methods require sample perturbation/disruption and lack spatio-temporal resolution, limiting our ability to fully characterize their function and distribution. Here, we show that Raman spectroscopy (RS) can directly detect fumarate in living cells in vivo and animal tissues ex vivo, and that RS can distinguish between Fumarate hydratase (Fh1)-deficient and Fh1-proficient cells based on fumarate concentration. Moreover, RS reveals the spatial compartmentalization of fumarate within cellular organelles in Fh1-deficient cells: consistent with disruptive methods, we observe the highest fumarate concentration (37 ± 19 mM) in mitochondria, where the TCA cycle operates, followed by the cytoplasm (24 ± 13 mM) and then the nucleus (9 ± 6 mM). Finally, we apply RS to tissues from an inducible mouse model of FH loss in the kidney, demonstrating RS can classify FH status. These results suggest RS could be adopted as a valuable tool for small molecule metabolic imaging, enabling in situ non-destructive evaluation of fumarate compartmentalization.
SNM1A is crucial for efficient repair of complex DNA breaks in human cells
Authors: Swift Lonnie P. , Lagerholm B. Christoffer , Henderson Lucy R. , Ratnaweera Malitha , Baddock Hannah T. , Sengerova Blanka , Lee Sook , Cruz-Migoni Abimael , Waithe Dominic , Renz Christian , Ulrich Helle D. , Newman Joseph A. , Schofield Christopher J. , McHugh Peter J.
Published: June 2024

DNA double-strand breaks (DSBs), such as those produced by radiation and radiomimetics, are amongst the most toxic forms of cellular damage, in part because they involve extensive oxidative modifications at the break termini. Prior to completion of DSB repair, the chemically modified termini must be removed. Various DNA processing enzymes have been implicated in the processing of these dirty ends, but molecular knowledge of this process is limited. Here, we demonstrate a role for the metallo-β-lactamase fold 5′−3′ exonuclease SNM1A in this vital process. Cells disrupted for SNM1A manifest increased sensitivity to radiation and radiomimetic agents and show defects in DSB damage repair. SNM1A is recruited and is retained at the sites of DSB damage via the concerted action of its three highly conserved PBZ, PIP box and UBZ interaction domains, which mediate interactions with poly-ADP-ribose chains, PCNA and the ubiquitinated form of PCNA, respectively. SNM1A can resect DNA containing oxidative lesions induced by radiation damage at break termini. The combined results reveal a crucial role for SNM1A to digest chemically modified DNA during the repair of DSBs and imply that the catalytic domain of SNM1A is an attractive target for potentiation of radiotherapy.
Structural and mechanistic insights into a lysosomal membrane enzyme HGSNAT involved in Sanfilippo syndrome
Authors: Zhao Boyang , Cao Zhongzheng , Zheng Yi , Nguyen Phuong , Bowen Alisa , Edwards Robert H. , Stroud Robert M. , Zhou Yi , Van Lookeren Campagne Menno , Li Fei
Published: June 2024

Heparan sulfate (HS) is degraded in lysosome by a series of glycosidases. Before the glycosidases can act, the terminal glucosamine of HS must be acetylated by the integral lysosomal membrane enzyme heparan-α-glucosaminide N-acetyltransferase (HGSNAT). Mutations of HGSNAT cause HS accumulation and consequently mucopolysaccharidosis IIIC, a devastating lysosomal storage disease characterized by progressive neurological deterioration and early death where no treatment is available. HGSNAT catalyzes a unique transmembrane acetylation reaction where the acetyl group of cytosolic acetyl-CoA is transported across the lysosomal membrane and attached to HS in one reaction. However, the reaction mechanism remains elusive. Here we report six cryo-EM structures of HGSNAT along the reaction pathway. These structures reveal a dimer arrangement and a unique structural fold, which enables the elucidation of the reaction mechanism. We find that a central pore within each monomer traverses the membrane and controls access of cytosolic acetyl-CoA to the active site at its luminal mouth where glucosamine binds. A histidine-aspartic acid catalytic dyad catalyzes the transfer reaction via a ternary complex mechanism. Furthermore, the structures allow the mapping of disease-causing variants and reveal their potential impact on the function, thus creating a framework to guide structure-based drug discovery efforts.
Myeloid-derived miR-6236 potentiates adipocyte insulin signaling and prevents hyperglycemia during obesity
Authors: Paneru Bam D. , Chini Julia , McCright Sam J. , DeMarco Nicole , Miller Jessica , Joannas Leonel D. , Henao-Mejia Jorge , Titchenell Paul M. , Merrick David M. , Lim Hee-Woong , Lazar Mitchell A. , Hill David A.
Published: June 2024

Adipose tissue macrophages (ATMs) influence obesity-associated metabolic dysfunction, but the mechanisms by which they do so are not well understood. We show that miR-6236 is a bona fide miRNA that is secreted by ATMs during obesity. Global or myeloid cell-specific deletion of miR-6236 aggravates obesity-associated adipose tissue insulin resistance, hyperglycemia, hyperinsulinemia, and hyperlipidemia. miR-6236 augments adipocyte insulin sensitivity by inhibiting translation of negative regulators of insulin signaling, including PTEN. The human genome harbors a miR-6236 homolog that is highly expressed in the serum and adipose tissue of obese people. hsa-MIR-6236 expression negatively correlates with hyperglycemia and glucose intolerance, and positively correlates with insulin sensitivity. Together, our findings establish miR-6236 as an ATM-secreted miRNA that potentiates adipocyte insulin signaling and protects against metabolic dysfunction during obesity.
Impact of whole-genome duplications on structural variant evolution in Cochlearia
Authors: Hämälä Tuomas , Moore Christopher , Cowan Laura , Carlile Matthew , Gopaulchan David , Brandrud Marie K. , Birkeland Siri , Loose Matthew , Kolář Filip , Koch Marcus A. , Yant Levi
Published: June 2024

Polyploidy, the result of whole-genome duplication (WGD), is a major driver of eukaryote evolution. Yet WGDs are hugely disruptive mutations, and we still lack a clear understanding of their fitness consequences. Here, we study whether WGDs result in greater diversity of genomic structural variants (SVs) and how they influence evolutionary dynamics in a plant genus, Cochlearia (Brassicaceae). By using long-read sequencing and a graph-based pangenome, we find both negative and positive interactions between WGDs and SVs. Masking of recessive mutations due to WGDs leads to a progressive accumulation of deleterious SVs across four ploidal levels (from diploids to octoploids), likely reducing the adaptive potential of polyploid populations. However, we also discover putative benefits arising from SV accumulation, as more ploidy-specific SVs harbor signals of local adaptation in polyploids than in diploids. Together, our results suggest that SVs play diverse and contrasting roles in the evolutionary trajectories of young polyploids.
Room temperature, cascadable, all-optical polariton universal gates
Authors: Sannikov Denis A. , Baranikov Anton V. , Putintsev Anton D. , Misko Mikhail , Zasedatelev Anton V. , Scherf Ullrich , Lagoudakis Pavlos G.
Published: June 2024

Today, almost all information processing is performed using electronic logic circuits operating at several gigahertz frequency. All-optical logic holds the promise to allow for up to three orders of magnitude higher speed. Whereas essential all-optical transistor functionalities were demonstrated across a range of platforms, utilising them to implement a complete Boolean logic gate set and in particular negation, i.e. switching off an optical signal with another, weaker, optical signal, poses a major challenge. Here, we realize a cascadable NOT gate by introducing the concept of non-ground-state polariton amplification in organic semiconductor microcavities under non-resonant optical excitation. We unravel the importance of vibron-mediated stimulated scattering in room temperature operation of the inverter. Moreover, we extend the concept to a multi-input universal NOR logic gate, where in the presence of any of the input signals non-ground-state amplification supersedes spontaneous ground-state condensation, resulting in a NOR gate with ~1 ps switching time. The realisation of an ultrafast universal logic gate constitutes an essential step for more complex optical circuitry that could boost information processing applications.
The tyrosine kinase KDR is essential for the survival of HTLV-1-infected T cells by stabilizing the Tax oncoprotein
Authors: Mohanty Suchitra , Suklabaidya Sujit , Lavorgna Alfonso , Ueno Takaharu , Fujisawa Jun-ichi , Ngouth Nyater , Jacobson Steven , Harhaj Edward W.
Published: June 2024

Human T-cell leukemia virus type 1 (HTLV-1) infection is linked to the development of adult T-cell leukemia/lymphoma (ATLL) and the neuroinflammatory disease, HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). The HTLV-1 Tax oncoprotein regulates viral gene expression and persistently activates NF-κB to maintain the viability of HTLV-1-infected T cells. Here, we utilize a kinome-wide shRNA screen to identify the tyrosine kinase KDR as an essential survival factor of HTLV-1-transformed cells. Inhibition of KDR specifically induces apoptosis of Tax expressing HTLV-1-transformed cell lines and CD4 + T cells from HAM/TSP patients. Furthermore, inhibition of KDR triggers the autophagic degradation of Tax resulting in impaired NF-κB activation and diminished viral transmission in co-culture assays. Tax induces the expression of KDR, forms a complex with KDR, and is phosphorylated by KDR. These findings suggest that Tax stability is dependent on KDR activity which could be exploited as a strategy to target Tax in HTLV-1-associated diseases.
Shape of the first mitotic spindles impacts multinucleation in human embryos
Authors: Ono Yuki , Shirasawa Hiromitsu , Takahashi Kazumasa , Goto Mayumi , Ono Takahiro , Sakaguchi Taichi , Okabe Motonari , Hirakawa Takeo , Iwasawa Takuya , Fujishima Akiko , Sugawara Tae , Makino Kenichi , Miura Hiroshi , Fukunaga Noritaka , Asada Yoshimasa , Kumazawa Yukiyo , Terada Yukihiro
Published: June 2024

During human embryonic development, early cleavage-stage embryos are more susceptible to errors. Studies have shown that many problems occur during the first mitosis, such as direct cleavage, chromosome segregation errors, and multinucleation. However, the mechanisms whereby these errors occur during the first mitosis in human embryos remain unknown. To clarify this aspect, in the present study, we image discarded living human two-pronuclear stage zygotes using fluorescent labeling and confocal microscopy without microinjection of DNA or mRNA and investigate the association between spindle shape and nuclear abnormality during the first mitosis. We observe that the first mitotic spindles vary, and low-aspect-ratio-shaped spindles tend to lead to the formation of multiple nuclei at the 2-cell stage. Moreover, we observe defocusing poles in many of the first mitotic spindles, which are strongly associated with multinucleation. Additionally, we show that differences in the positions of the centrosomes cause spindle abnormality in the first mitosis. Furthermore, many multinuclei are modified to form mononuclei after the second mitosis because the occurrence of pole defocusing is firmly reduced. Our study will contribute markedly to research on the occurrence of mitotic errors during the early cleavage of human embryos.
Dietary fibre directs microbial tryptophan metabolism via metabolic interactions in the gut microbiota
Authors: Sinha Anurag K. , Laursen Martin F. , Brinck Julius E. , Rybtke Morten L. , Hjørne Anna Pii , Procházková Nicola , Pedersen Mikael , Roager Henrik M. , Licht Tine R.
Published: June 2024

Tryptophan is catabolized by gut microorganisms resulting in a wide range of metabolites implicated in both beneficial and adverse host effects. How gut microbial tryptophan metabolism is directed towards indole, associated with chronic kidney disease, or towards protective indolelactic acid (ILA) and indolepropionic acid (IPA) is unclear. Here we used in vitro culturing and animal experiments to assess gut microbial competition for tryptophan and the resulting metabolites in a controlled three-species defined community and in complex undefined human faecal communities. The generation of specific tryptophan-derived metabolites was not predominantly determined by the abundance of tryptophan-metabolizing bacteria, but rather by substrate-dependent regulation of specific metabolic pathways. Indole-producing Escherichia coli and ILA- and IPA-producing Clostridium sporogenes competed for tryptophan within the three-species community in vitro and in vivo. Importantly, fibre-degrading Bacteroides thetaiotaomicron affected this competition by cross-feeding monosaccharides to E. coli. This inhibited indole production through catabolite repression, thus making more tryptophan available to C. sporogenes, resulting in increased ILA and IPA production. The fibre-dependent reduction in indole was confirmed using human faecal cultures and faecal-microbiota-transplanted gnotobiotic mice. Our findings explain why consumption of fermentable fibres suppresses indole production but promotes the generation of other tryptophan metabolites associated with health benefits.
Control of mitophagy initiation and progression by the TBK1 adaptors NAP1 and SINTBAD
Authors: Adriaenssens Elias , Nguyen Thanh Ngoc , Sawa-Makarska Justyna , Khuu Grace , Schuschnig Martina , Shoebridge Stephen , Skulsuppaisarn Marvin , Watts Emily Maria , Csalyi Kitti Dora , Padman Benjamin Scott , Lazarou Michael , Martens Sascha
Published: June 2024

Mitophagy preserves overall mitochondrial fitness by selectively targeting damaged mitochondria for degradation. The regulatory mechanisms that prevent PTEN-induced putative kinase 1 (PINK1) and E3 ubiquitin ligase Parkin (PINK1/Parkin)-dependent mitophagy and other selective autophagy pathways from overreacting while ensuring swift progression once initiated are largely elusive. Here, we demonstrate how the TBK1 (TANK-binding kinase 1) adaptors NAP1 (NAK-associated protein 1) and SINTBAD (similar to NAP1 TBK1 adaptor) restrict the initiation of OPTN (optineurin)-driven mitophagy by competing with OPTN for TBK1. Conversely, they promote the progression of nuclear dot protein 52 (NDP52)-driven mitophagy by recruiting TBK1 to NDP52 and stabilizing its interaction with FIP200. Notably, OPTN emerges as the primary recruiter of TBK1 during mitophagy initiation, which in return boosts NDP52-mediated mitophagy. Our results thus define NAP1 and SINTBAD as cargo receptor rheostats, elevating the threshold for mitophagy initiation by OPTN while promoting the progression of the pathway once set in motion by supporting NDP52. These findings shed light on the cellular strategy to prevent pathway hyperactivity while still ensuring efficient progression.
Multistage time-to-event models improve survival inference by partitioning mortality processes of tracked organisms
Authors: Sethi Suresh A. , Koeberle Alex L. , Poulton Anna J. , Linden Daniel W. , Diefenbach Duane , Buderman Frances E. , Casalena Mary Jo , Duren Kenneth
Published: June 2024

Advances in tagging technologies are expanding opportunities to estimate survival of fish and wildlife populations. Yet, capture and handling effects could impact survival outcomes and bias inference about natural mortality processes. We developed a multistage time-to-event model that can partition the survival process into sequential phases that reflect the tagged animal experience, including handling and release mortality, post-release recovery mortality, and subsequently, natural mortality. We demonstrate performance of multistage survival models through simulation testing and through fish and bird telemetry case studies. Models are implemented in a Bayesian framework and can accommodate left, right, and interval censorship events. Our results indicate that accurate survival estimates can be achieved with reasonable sample sizes ($$n\approx 100+)$$

n
≈
100
+
)

and that multimodel inference can inform hypotheses about the configuration and length of survival stages needed to adequately describe mortality processes for tracked specimens. While we focus on survival estimation for tagged fish and wildlife populations, multistage time-to-event models could be used to understand other phenomena of interest such as migration, reproduction, or disease events across a range of taxa including plants and insects.
Genomic barcoding for clonal diversity monitoring and control in cell-based complex antibody production
Authors: Bauer Niels , Oberist Christoph , Poth Michaela , Stingele Julian , Popp Oliver , Ausländer Simon
Published: June 2024

Engineered mammalian cells are key for biotechnology by enabling broad applications ranging from in vitro model systems to therapeutic biofactories. Engineered cell lines exist as a population containing sub-lineages of cell clones that exhibit substantial genetic and phenotypic heterogeneity. There is still a limited understanding of the source of this inter-clonal heterogeneity as well as its implications for biotechnological applications. Here, we developed a genomic barcoding strategy for a targeted integration (TI)-based CHO antibody producer cell line development process. This technology provided novel insights about clone diversity during stable cell line selection on pool level, enabled an imaging-independent monoclonality assessment after single cell cloning, and eventually improved hit-picking of antibody producer clones by monitoring of cellular lineages during the cell line development (CLD) process. Specifically, we observed that CHO producer pools generated by TI of two plasmids at a single genomic site displayed a low diversity (< 0.1% RMCE efficiency), which further depends on the expressed molecules, and underwent rapid population skewing towards dominant clones during routine cultivation. Clonal cell lines from one individual TI event demonstrated a significantly lower variance regarding production-relevant and phenotypic parameters as compared to cell lines from distinct TI events. This implies that the observed cellular diversity lies within pre-existing cell-intrinsic factors and that the majority of clonal variation did not develop during the CLD process, especially during single cell cloning. Using cellular barcodes as a proxy for cellular diversity, we improved our CLD screening workflow and enriched diversity of production-relevant parameters substantially. This work, by enabling clonal diversity monitoring and control, paves the way for an economically valuable and data-driven CLD process.