bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phase-separated CCER1 coordinates the histone-to-protamine transition and male fertility
Authors: Qin Dongdong , Gu Yayun , Zhang Yu , Wang Shu , Jiang Tao , Wang Yao , Wang Cheng , Chen Chang , Zhang Tao , Xu Weiya , Wang Hanben , Zhang Ke , Hu Liangjun , Li Lufan , Xie Wei , Wu Xin , Hu Zhibin 
Published: December 2023

AbstractIdiopathic fertility disorders are associated with mutations in various genes. Here, we report that coiled-coil glutamate-rich protein 1 (CCER1), a germline-specific and intrinsically disordered protein (IDP), mediates postmeiotic spermatid differentiation. In contrast, CCER1 deficiency results in defective sperm chromatin compaction and infertility in mice. CCER1 increases transition protein (Tnp1/2) and protamine (Prm1/2) transcription and mediates multiple histone epigenetic modifications during the histone-to-protamine (HTP) transition. Immiscible with heterochromatin in the nucleus, CCER1 self-assembles into a polymer droplet and forms a liquid-liquid phase-separated condensate in the nucleus. Notably, we identified loss-of-function (LoF) variants of human CCER1 (hCCER1) in five patients with nonobstructive azoospermia (NOA) that were absent in 2713 fertile controls. The mutants led to premature termination or frameshift in CCER1 translation, and disrupted condensates in vitro. In conclusion, we propose that nuclear CCER1 is a phase-separated condensate that links histone epigenetic modifications, HTP transitions, chromatin condensation, and male fertility.
Staphylococcus aureus functional amyloids catalyze degradation of β-lactam antibiotics
Authors: Arad Elad , Pedersen Kasper B. , Malka Orit , Mambram Kunnath Sisira , Golan Nimrod , Aibinder Polina , Schiøtt Birgit , Rapaport Hanna , Landau Meytal , Jelinek Raz 
Published: December 2023

AbstractAntibiotic resistance of bacteria is considered one of the most alarming developments in modern medicine. While varied pathways for bacteria acquiring antibiotic resistance have been identified, there still are open questions concerning the mechanisms underlying resistance. Here, we show that alpha phenol-soluble modulins (PSMαs), functional bacterial amyloids secreted by Staphylococcus aureus, catalyze hydrolysis of β-lactams, a prominent class of antibiotic compounds. Specifically, we show that PSMα2 and, particularly, PSMα3 catalyze hydrolysis of the amide-like bond of the four membered β-lactam ring of nitrocefin, an antibiotic β-lactam surrogate. Examination of the catalytic activities of several PSMα3 variants allowed mapping of the active sites on the amyloid fibrils’ surface, specifically underscoring the key roles of the cross-α fibril organization, and the combined electrostatic and nucleophilic functions of the lysine arrays. Molecular dynamics simulations further illuminate the structural features of β-lactam association upon the fibril surface. Complementary experimental data underscore the generality of the functional amyloid-mediated catalytic phenomenon, demonstrating hydrolysis of clinically employed β-lactams by PSMα3 fibrils, and illustrating antibiotic degradation in actual S. aureus biofilms and live bacteria environments. Overall, this study unveils functional amyloids as catalytic agents inducing degradation of β-lactam antibiotics, underlying possible antibiotic resistance mechanisms associated with bacterial biofilms.
Dissecting the basis for differential substrate specificity of ADAR1 and ADAR2
Authors: Zambrano-Mila Marlon S. , Witzenberger Monika , Rosenwasser Zohar , Uzonyi Anna , Nir Ronit , Ben-Aroya Shay , Levanon Erez Y. , Schwartz Schraga 
Published: December 2023

AbstractMillions of adenosines are deaminated throughout the transcriptome by ADAR1 and/or ADAR2 at varying levels, raising the question of what are the determinants guiding substrate specificity and how these differ between the two enzymes. We monitor how secondary structure modulates ADAR2 vs ADAR1 substrate selectivity, on the basis of systematic probing of thousands of synthetic sequences transfected into cell lines expressing exclusively ADAR1 or ADAR2. Both enzymes induce symmetric, strand-specific editing, yet with distinct offsets with respect to structural disruptions: −26 nt for ADAR2 and −35 nt for ADAR1. We unravel the basis for these differences in offsets through mutants, domain-swaps, and ADAR homologs, and find it to be encoded by the differential RNA binding domain (RBD) architecture. Finally, we demonstrate that this offset-enhanced editing can allow an improved design of ADAR2-recruiting therapeutics, with proof-of-concept experiments demonstrating increased on-target and potentially decreased off-target editing.
Projecting future carbon emissions from cement production in developing countries
Authors: Cheng Danyang , Reiner David M. , Yang Fan , Cui Can , Meng Jing , Shan Yuli , Liu Yunhui , Tao Shu , Guan Dabo 
Published: December 2023

AbstractAchieving low-carbon development of the cement industry in the developing countries is fundamental to global emissions abatement, considering the local construction industry’s rapid growth. However, there is currently a lack of systematic and accurate accounting and projection of cement emissions in developing countries, which are characterized with lower basic economic country condition. Here, we provide bottom-up quantifications of emissions from global cement production and reveal a regional shift in the main contributors to global cement CO2 emissions. The study further explores cement emissions over 2020-2050 that correspond to different housing and infrastructure conditions and emissions mitigation options for all developing countries except China. We find that cement emissions in developing countries except China will reach 1.4-3.8 Gt in 2050 (depending on different industrialization trajectories), compared to their annual emissions of 0.7 Gt in 2018. The optimal combination of low-carbon measures could contribute to reducing annual emissions by around 65% in 2050 and cumulative emissions by around 48% over 2020-2050. The efficient technological paths towards a low carbon future of cement industry vary among the countries and infrastructure scenarios. Our results are essential to understanding future emissions patterns of the cement industry in the developing countries and can inform policies in the cement sector that contribute to meeting the climate targets set out in the Paris Agreement.
Nanophotonics for pair production
Authors: Di Giulio Valerio , García de Abajo F. Javier 
Published: December 2023

AbstractThe transformation of electromagnetic energy into matter represents a fascinating prediction of relativistic quantum electrodynamics that is paradigmatically exemplified by the creation of electron-positron pairs out of light. However, this phenomenon has a very low probability, so positron sources rely instead on beta decay, which demands elaborate monochromatization and trapping schemes to achieve high-quality beams. Here, we propose to use intense, strongly confined optical near fields supported by a nanostructured material in combination with high-energy photons to create electron-positron pairs. Specifically, we show that the interaction between near-threshold γ-rays and polaritons yields higher pair-production cross sections, largely exceeding those associated with free-space photons. Our work opens an unexplored avenue toward generating tunable pulsed positrons from nanoscale regions at the intersection between particle physics and nanophotonics.
The emergence of modern zoogeographic regions in Asia examined through climate–dental trait association patterns
Authors: Liu Liping , Galbrun Esther , Tang Hui , Kaakinen Anu , Zhang Zhongshi , Zhang Zijian , Žliobaitė Indrė 
Published: December 2023

AbstractThe complex and contrasted distribution of terrestrial biota in Asia has been linked to active tectonics and dramatic climatic changes during the Neogene. However, the timings of the emergence of these distributional patterns and the underlying climatic and tectonic mechanisms remain disputed. Here, we apply a computational data analysis technique, called redescription mining, to track these spatiotemporal phenomena by studying the associations between the prevailing herbivore dental traits of mammalian communities and climatic conditions during the Neogene. Our results indicate that the modern latitudinal zoogeographic division emerged after the Middle Miocene climatic transition, and that the modern monsoonal zoogeographic pattern emerged during the late Late Miocene. Furthermore, the presence of a montane forest biodiversity hotspot in the Hengduan Mountains alongside Alpine fauna on the Tibetan Plateau suggests that the modern distribution patterns may have already existed since the Pliocene.
The 5α condensate state in 20Ne
Authors: Zhou Bo , Funaki Yasuro , Horiuchi Hisashi , Ma Yu-Gang , Röpke Gerd , Schuck Peter , Tohsaki Akihiro , Yamada Taiichi 
Published: December 2023

AbstractThe formed 4He (α) clusters consisting of two neutrons and two protons can be a building block in light nuclear systems. Intriguingly, these alpha clusters could potentially form alpha condensate states within the nuclear system. The Hoyle state at 7.65 MeV in 12C, which plays an essential role in stellar nucleosynthesis, is now considered to be a phase transition, namely the 3α Bose-Einstein condensate. Confirming the existence of Hoyle-analog states in Nα nuclei (N > 3) remains a major challenge. Here we show microscopic five-body calculations for the 20Ne nucleus. We find that one excited 0+ state has a distinct gas-like characteristic and represents the condensate state. Identifying the 5α condensate state is an important step in establishing the concept of α condensation in nuclear fermion systems.
Nearly complete structure of bacteriophage DT57C reveals architecture of head-to-tail interface and lateral tail fibers
Authors: Ayala Rafael , Moiseenko Andrey V. , Chen Ting-Hua , Kulikov Eugene E. , Golomidova Alla K. , Orekhov Philipp S. , Street Maya A. , Sokolova Olga S. , Letarov Andrey V. , Wolf Matthias 
Published: December 2023

AbstractThe T5 family of viruses are tailed bacteriophages characterized by a long non-contractile tail. The bacteriophage DT57C is closely related to the paradigmal T5 phage, though it recognizes a different receptor (BtuB) and features highly divergent lateral tail fibers (LTF). Considerable portions of T5-like phages remain structurally uncharacterized. Here, we present the structure of DT57C determined by cryo-EM, and an atomic model of the virus, which was further explored using all-atom molecular dynamics simulations. The structure revealed a unique way of LTF attachment assisted by a dodecameric collar protein LtfC, and an unusual composition of the phage neck constructed of three protein rings. The tape measure protein (TMP) is organized within the tail tube in a three-stranded parallel α-helical coiled coil which makes direct contact with the genomic DNA. The presence of the C-terminal fragment of the TMP that remains within the tail tip suggests that the tail tip complex returns to its original state after DNA ejection. Our results provide a complete atomic structure of a T5-like phage, provide insights into the process of DNA ejection as well as a structural basis for the design of engineered phages and future mechanistic studies.
Nonuniversal impact of cholesterol on membranes mobility, curvature sensing and elasticity
Authors: Pöhnl Matthias , Trollmann Marius F. W. , Böckmann Rainer A. 
Published: December 2023

AbstractBiological membranes, composed mainly of phospholipids and cholesterol, play a vital role as cellular barriers. They undergo localized reshaping in response to environmental cues and protein interactions, with the energetics of deformations crucial for exerting biological functions. This study investigates the non-universal role of cholesterol on the structure and elasticity of saturated and unsaturated lipid membranes. Our study uncovers a highly cooperative relationship between thermal membrane bending and local cholesterol redistribution, with cholesterol showing a strong preference for the compressed membrane leaflet. Remarkably, in unsaturated membranes, increased cholesterol mobility enhances cooperativity, resulting in membrane softening despite membrane thickening and lipid compression caused by cholesterol. These findings elucidate the intricate interplay between thermodynamic forces and local molecular interactions that govern collective properties of membranes.
An archetype and scaling of developmental tissue dynamics across species
Authors: Morishita Yoshihiro , Lee Sang-Woo , Suzuki Takayuki , Yokoyama Hitoshi , Kamei Yasuhiro , Tamura Koji , Kawasumi-Kita Aiko 
Published: December 2023

AbstractMorphometric studies have revealed the existence of simple geometric relationships among various animal shapes. However, we have little knowledge of the mathematical principles behind the morphogenetic dynamics that form the organ/body shapes of different species. Here, we address this issue by focusing on limb morphogenesis in Gallus gallus domesticus (chicken) and Xenopus laevis (African clawed frog). To compare the deformation dynamics between tissues with different sizes/shapes as well as their developmental rates, we introduce a species-specific rescaled spatial coordinate and a common clock necessary for cross-species synchronization of developmental times. We find that tissue dynamics are well conserved across species under this spacetime coordinate system, at least from the early stages of development through the phase when basic digit patterning is established. For this developmental period, we also reveal that the tissue dynamics of both species are mapped with each other through a time-variant linear transformation in real physical space, from which hypotheses on a species-independent archetype of tissue dynamics and morphogenetic scaling are proposed.
DeepRTAlign: toward accurate retention time alignment for large cohort mass spectrometry data analysis
Authors: Liu Yi , Yang Yun , Chen Wendong , Shen Feng , Xie Linhai , Zhang Yingying , Zhai Yuanjun , He Fuchu , Zhu Yunping , Chang Cheng 
Published: December 2023

AbstractRetention time (RT) alignment is a crucial step in liquid chromatography-mass spectrometry (LC-MS)-based proteomic and metabolomic experiments, especially for large cohort studies. The most popular alignment tools are based on warping function method and direct matching method. However, existing tools can hardly handle monotonic and non-monotonic RT shifts simultaneously. Here, we develop a deep learning-based RT alignment tool, DeepRTAlign, for large cohort LC-MS data analysis. DeepRTAlign has been demonstrated to have improved performances by benchmarking it against current state-of-the-art approaches on multiple real-world and simulated proteomic and metabolomic datasets. The results also show that DeepRTAlign can improve identification sensitivity without compromising quantitative accuracy. Furthermore, using the MS features aligned by DeepRTAlign, we trained and validated a robust classifier to predict the early recurrence of hepatocellular carcinoma. DeepRTAlign provides an advanced solution to RT alignment in large cohort LC-MS studies, which is currently a major bottleneck in proteomics and metabolomics research.
Interactions between climate change, urban infrastructure and mobility are driving dengue emergence in Vietnam
Authors: Gibb Rory , Colón-González Felipe J. , Lan Phan Trong , Huong Phan Thi , Nam Vu Sinh , Duoc Vu Trong , Hung Do Thai , Dong Nguyễn Thanh , Chien Vien Chinh , Trang Ly Thi Thuy , Kien Quoc Do , Hoa Tran Minh , Tai Nguyen Hữu , Hang Tran Thi , Tsarouchi Gina , Ainscoe Eleanor , Harpham Quillon , Hofmann Barbara , Lumbroso Darren , Brady Oliver J. , Lowe Rachel 
Published: December 2023

AbstractDengue is expanding globally, but how dengue emergence is shaped locally by interactions between climatic and socio-environmental factors is not well understood. Here, we investigate the drivers of dengue incidence and emergence in Vietnam, through analysing 23 years of district-level case data spanning a period of significant socioeconomic change (1998-2020). We show that urban infrastructure factors (sanitation, water supply, long-term urban growth) predict local spatial patterns of dengue incidence, while human mobility is a more influential driver in subtropical northern regions than the endemic south. Temperature is the dominant factor shaping dengue’s distribution and dynamics, and using long-term reanalysis temperature data we show that warming since 1950 has expanded transmission risk throughout Vietnam, and most strongly in current dengue emergence hotspots (e.g., southern central regions, Ha Noi). In contrast, effects of hydrometeorology are complex, multi-scalar and dependent on local context: risk increases under either short-term precipitation excess or long-term drought, but improvements in water supply mitigate drought-associated risks except under extreme conditions. Our findings challenge the assumption that dengue is an urban disease, instead suggesting that incidence peaks in transitional landscapes with intermediate infrastructure provision, and provide evidence that interactions between recent climate change and mobility are contributing to dengue’s expansion throughout Vietnam.
Ultrafast THz probing of nonlocal orbital current in transverse multilayer metallic heterostructures
Authors: Kumar Sandeep , Kumar Sunil 
Published: December 2023

AbstractTHz generation from femtosecond photoexcited spintronic heterostructures has become a versatile tool for investigating ultrafast spin-transport and transient charge-current in a non-contact and non-invasive manner. The equivalent effect from the orbital degree of freedom is still in the primitive stage. Here, we experimentally demonstrate orbital-to-charge current conversion in metallic heterostructures, consisting of a ferromagnetic layer adjacent to either a light or a heavy metal layer, through detection of the emitted THz pulses. Our temperature-dependent experiments help to disentangle the orbital and spin components that are manifested in the respective Hall-conductivities, contributing to THz emission. NiFe/Nb shows the strongest inverse orbital Hall effect with an experimentally extracted value of effective intrinsic Hall-conductivity, $${({\sigma }_{{SOH}}^{{{{{\mathrm{int}}}}}})}^{{eff}} \sim 195{\varOmega }^{-1}{{cm}}^{-1}$$

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, while CoFeB/Pt shows maximum contribution from the inverse spin Hall effect. In addition, we observe a nearly ten-fold enhancement in the THz emission due to pronounced orbital-transport in W-insertion heavy metal layer in CoFeB/W/Ta heterostructure as compared to CoFeB/Ta bilayer counterpart.
The formation of the Indo-Pacific montane avifauna
Authors: Reeve Andrew Hart , Kennedy Jonathan David , Pujolar José Martín , Petersen Bent , Blom Mozes P. K. , Alström Per , Haryoko Tri , Ericson Per G. P. , Irestedt Martin , Nylander Johan A. A. , Jønsson Knud Andreas 
Published: December 2023

AbstractThe processes generating the earth’s montane biodiversity remain a matter of debate. Two contrasting hypotheses have been advanced to explain how montane populations form: via direct colonization from other mountains, or, alternatively, via upslope range shifts from adjacent lowland areas. We seek to reconcile these apparently conflicting hypotheses by asking whether a species’ ancestral geographic origin determines its mode of mountain colonization. Island-dwelling passerine birds at the faunal crossroads between Eurasia and Australo-Papua provide an ideal study system. We recover the phylogenetic relationships of the region’s montane species and reconstruct their ancestral geographic ranges, elevational ranges, and migratory behavior. We also perform genomic population studies of three super-dispersive montane species/clades with broad island distributions. Eurasian-origin species populated archipelagos via direct colonization between mountains. This mode of colonization appears related to ancestral adaptations to cold and seasonal climates, specifically short-distance migration. Australo-Papuan-origin mountain populations, by contrast, evolved from lowland ancestors, and highland distribution mostly precludes their further colonization of island mountains. Our study explains much of the distributional variation within a complex biological system, and provides a synthesis of two seemingly discordant hypotheses for montane community formation.
Immunoproximity biotinylation reveals the axon initial segment proteome
Authors: Zhang Wei , Fu Yu , Peng Luxin , Ogawa Yuki , Ding Xiaoyun , Rasband Anne , Zhou Xinyue , Shelly Maya , Rasband Matthew N. , Zou Peng 
Published: December 2023

AbstractThe axon initial segment (AIS) is a specialized neuronal compartment required for action potential generation and neuronal polarity. However, understanding the mechanisms regulating AIS structure and function has been hindered by an incomplete knowledge of its molecular composition. Here, using immuno-proximity biotinylation we further define the AIS proteome and its dynamic changes during neuronal maturation. Among the many AIS proteins identified, we show that SCRIB is highly enriched in the AIS both in vitro and in vivo, and exhibits a periodic architecture like the axonal spectrin-based cytoskeleton. We find that ankyrinG interacts with and recruits SCRIB to the AIS. However, loss of SCRIB has no effect on ankyrinG. This powerful and flexible approach further defines the AIS proteome and provides a rich resource to elucidate the mechanisms regulating AIS structure and function.
Dispersal from the Qinghai-Tibet plateau by a high-altitude butterfly is associated with rapid expansion and reorganization of its genome
Authors: Zhao Youjie , Su Chengyong , He Bo , Nie Ruie , Wang Yunliang , Ma Junye , Song Jingyu , Yang Qun , Hao Jiasheng 
Published: December 2023

AbstractParnassius glacialis is a typical “Out of the QTP” alpine butterfly that originated on the Qinghai-Tibet Plateau (QTP) and dispersed into relatively low-altitude mountainous. Here we assemble a chromosome-level genome of P. glacialis and resequence 9 populations in order to explore the genome evolution and local adaptation of this species. These results indicated that the rapid accumulation and slow unequal recombination of transposable elements (TEs) contributed to the formation of its large genome. Several ribosomal gene families showed extensive expansion and selective evolution through transposon-mediated processed pseudogenes. Additionally, massive structural variations (SVs) of TEs affected the genetic differentiation of low-altitude populations. These low-altitude populations might have experienced a genetic bottleneck in the past and harbor genes with selective signatures which may be responsible for the potential adaptation to low-altitude environments. These results provide a foundation for understanding genome evolution and local adaptation for “Out of the QTP” of P. glacialis.