bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Enhanced Nonlinear Energy Sink for Hybrid Bifurcation Passive Mitigation and Energy Harvesting From Aeroelastic Galloping Phenomena
Authors: Ignacio da Silva José Augusto , Sanches Leonardo , Michon Guilhem , Marques Flavio Donizeti 
Published: February 2024

Abstract
Galloping is a self-excited vibration problem that structures immersed in fluid flow can experience. Due to its essential nonlinear phenomena, the structure exhibits limit cycle oscillations (LCOs), which, at high levels, can lead to failure of the systems. This work proposes an investigation of electromagnetic-enhanced nonlinear energy sinks (NES-EH) for the hybrid mitigation of aeroelastic LCOs and energy harvesting. The study focuses on a prismatic bluff body with a linear suspension immersed in the airflow, using classical steady nonlinear modeling for aerodynamic loads. The conventional NES approach is adopted, employing cubic stiffness and linear damping. Additionally, a linear electromagnetic transducer is included in the assembly for the energy harvesting process. By combining the method of multiple scales with the Harmonic Balance Method, analytical solutions are derived to characterize the system's dynamics under the influence of the device. The different response domains and their respective boundaries induced by the NES-EH are characterized based on the bifurcation diagrams. Furthermore, a slow invariant manifold (SIM) characterization is presented for each induced response domain, and its significant features are discussed. Parametric studies are carried out based on bifurcation analyses to assess the effect of NES-EH parameters on the galloping system dynamics, which allows for designing the absorber parameters. The electrical resistance is optimized to maximize the harvested power. The optimal design of NES-EH is then compared with classical energy harvesting solutions for the galloping problem. Additionally, a thorough analysis of the Target Energy Transfer phenomenon is performed.
The catabolism of lignin-derived
p
-methoxylated aromatic compounds by
Rhodococcus jostii
RHA1
Authors: Wolf Megan E. , Lalande Anne T. , Newman Brianne L. , Bleem Alissa C. , Palumbo Chad T. , Beckham Gregg T. , Eltis Lindsay D. 
Published: February 2024

ABSTRACT

Emergent strategies to valorize lignin, an abundant but underutilized aromatic biopolymer, include tandem processes that integrate chemical depolymerization and biological catalysis. To date, aromatic monomers from C–O bond cleavage of lignin have been converted to bioproducts, but the presence of recalcitrant C–C bonds in lignin limits the product yield. A promising chemocatalytic strategy that overcomes this limitation involves phenol methyl protection and autoxidation. Incorporating this into a tandem process requires microbial cell factories able to transform the
p
-methoxylated products in the resulting methylated lignin stream. In this study, we assessed the ability of
Rhodococcus jostii
RHA1 to catabolize the major aromatic products in a methylated lignin stream and elucidated the pathways responsible for this catabolism. RHA1 grew on a methylated pine lignin stream, catabolizing the major aromatic monomers:
p
-methoxybenzoate (
p
-MBA), veratrate, and veratraldehyde. Bioinformatic analyses suggested that a cytochrome P450, PbdA, and its cognate reductase, PbdB, are involved in
p
-MBA catabolism. Gene deletion studies established that both
pbdA
and
pbdB
are essential for growth on
p
-MBA and several derivatives. Furthermore, a deletion mutant of a candidate
p-
hydroxybenzoate (
p
-HBA) hydroxylase, Δ
pobA
, did not grow on
p
-HBA. Veratraldehyde and veratrate catabolism required both vanillin dehydrogenase (Vdh) and vanillate
O
-demethylase (VanAB), revealing previously unknown roles of these enzymes. Finally, a Δ
pcaL
strain grew on neither
p
-MBA nor veratrate, indicating they are catabolized through the β-ketoadipate pathway. This study expands our understanding of the bacterial catabolism of aromatic compounds and facilitates the development of biocatalysts for lignin valorization.

IMPORTANCE

Lignin, an abundant aromatic polymer found in plant biomass, is a promising renewable replacement for fossil fuels as a feedstock for the chemical industry. Strategies for upgrading lignin include processes that couple the catalytic fractionation of biomass and biocatalytic transformation of the resulting aromatic compounds with a microbial cell factory. Engineering microbial cell factories for this biocatalysis requires characterization of bacterial pathways involved in catabolizing lignin-derived aromatic compounds. This study identifies new pathways for lignin-derived aromatic degradation in
Rhodococcus
, a genus of bacteria well suited for biocatalysis. Additionally, we describe previously unknown activities of characterized enzymes on lignin-derived compounds, expanding their utility. This work advances the development of strategies to replace fossil fuel-based feedstocks with sustainable alternatives.
Diversity, origin, and evolution of the ESCRT systems
Authors: Makarova Kira S. , Tobiasson Victor , Wolf Yuri I. , Lu Zhongyi , Liu Yang , Zhang Siyu , Krupovic Mart , Li Meng , Koonin Eugene V. 
Published: February 2024

ABSTRACT

Endosomal sorting complexes required for transport (ESCRT) play key roles in protein sorting between membrane-bounded compartments of eukaryotic cells. Homologs of many ESCRT components are identifiable in various groups of archaea, especially in Asgardarchaeota, the archaeal phylum that is currently considered to include the closest relatives of eukaryotes, but not in bacteria. We performed a comprehensive search for ESCRT protein homologs in archaea and reconstructed ESCRT evolution using the phylogenetic tree of Vps4 ATPase (ESCRT IV) as a scaffold and using sensitive protein sequence analysis and comparison of structural models to identify previously unknown ESCRT proteins. Several distinct groups of ESCRT systems in archaea outside of Asgard were identified, including proteins structurally similar to ESCRT-I and ESCRT-II, and several other domains involved in protein sorting in eukaryotes, suggesting an early origin of these components. Additionally, distant homologs of CdvA proteins were identified in Thermoproteales which are likely components of the uncharacterized cell division system in these archaea. We propose an evolutionary scenario for the origin of eukaryotic and Asgard ESCRT complexes from ancestral building blocks, namely, the Vps4 ATPase, ESCRT-III components, wH (winged helix-turn-helix fold) and possibly also coiled-coil, and Vps28-like domains. The last archaeal common ancestor likely encompassed a complex ESCRT system that was involved in protein sorting. Subsequent evolution involved either simplification, as in the TACK superphylum, where ESCRT was co-opted for cell division, or complexification as in Asgardarchaeota. In Asgardarchaeota, the connection between ESCRT and the ubiquitin system that was previously considered a eukaryotic signature was already established.

IMPORTANCE
All eukaryotic cells possess complex intracellular membrane organization. Endosomal sorting complexes required for transport (ESCRT) play a central role in membrane remodeling which is essential for cellular functionality in eukaryotes. Recently, it has been shown that Asgard archaea, the archaeal phylum that includes the closest known relatives of eukaryotes, encode homologs of many components of the ESCRT systems. We employed protein sequence and structure comparisons to reconstruct the evolution of ESCRT systems in archaea and identified several previously unknown homologs of ESCRT subunits, some of which can be predicted to participate in cell division. The results of this reconstruction indicate that the last archaeal common ancestor already encoded a complex ESCRT system that was involved in protein sorting. In Asgard archaea, ESCRT systems evolved toward greater complexity, and in particular, the connection between ESCRT and the ubiquitin system that was previously considered a eukaryotic signature was established.
Uncultivated DPANN archaea are ubiquitous inhabitants of global oxygen-deficient zones with diverse metabolic potential
Authors: Zhang Irene H. , Borer Benedict , Zhao Rui , Wilbert Steven , Newman Dianne K. , Babbin Andrew R. 
Published: February 2024

ABSTRACT

Archaea belonging to the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have been found in an expanding number of environments and perform a variety of biogeochemical roles, including contributing to carbon, sulfur, and nitrogen cycling. Generally characterized by ultrasmall cell sizes and reduced genomes, DPANN archaea may form mutualistic, commensal, or parasitic interactions with various archaeal and bacterial hosts, influencing the ecology and functioning of microbial communities. While DPANN archaea reportedly comprise a sizeable fraction of the archaeal community within marine oxygen-deficient zone (ODZ) water columns, little is known about their metabolic capabilities in these ecosystems. We report 33 novel metagenome-assembled genomes (MAGs) belonging to the DPANN phyla Nanoarchaeota, Pacearchaeota, Woesearchaeota, Undinarchaeota, Iainarchaeota, and SpSt-1190 from pelagic ODZs in the Eastern Tropical North Pacific and the Arabian Sea. We find these archaea to be permanent, stable residents of all three major ODZs only within anoxic depths, comprising up to 1% of the total microbial community and up to 25%–50% of archaea as estimated from read mapping to MAGs. ODZ DPANN appear to be capable of diverse metabolic functions, including fermentation, organic carbon scavenging, and the cycling of sulfur, hydrogen, and methane. Within a majority of ODZ DPANN, we identify a gene homologous to nitrous oxide reductase. Modeling analyses indicate the feasibility of a nitrous oxide reduction metabolism for host-attached symbionts, and the small genome sizes and reduced metabolic capabilities of most DPANN MAGs suggest host-associated lifestyles within ODZs.

IMPORTANCE
Archaea from the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have diverse metabolic capabilities and participate in multiple biogeochemical cycles. While metagenomics and enrichments have revealed that many DPANN are characterized by ultrasmall genomes, few biosynthetic genes, and episymbiotic lifestyles, much remains unknown about their biology. We report 33 new DPANN metagenome-assembled genomes originating from the three global marine oxygen-deficient zones (ODZs), the first from these regions. We survey DPANN abundance and distribution within the ODZ water column, investigate their biosynthetic capabilities, and report potential roles in the cycling of organic carbon, methane, and nitrogen. We test the hypothesis that nitrous oxide reductases found within several ODZ DPANN genomes may enable ultrasmall episymbionts to serve as nitrous oxide consumers when attached to a host nitrous oxide producer. Our results indicate DPANN archaea as ubiquitous residents within the anoxic core of ODZs with the potential to produce or consume key compounds.
Two
Toxoplasma gondii
putative pore-forming proteins, GRA47 and GRA72, influence small molecule permeability of the parasitophorous vacuole
Authors: Bitew Mebratu A. , Gaete Pablo S. , Swale Christopher , Maru Parag , Contreras Jorge E. , Saeij Jeroen P. J. 
Published: February 2024

ABSTRACT

Toxoplasma gondii
, a medically important intracellular parasite, uses GRA proteins secreted from dense granule organelles to mediate nutrient flux across the parasitophorous vacuole membrane (PVM). GRA17 and GRA23 are known pore-forming proteins on the PVM involved in this process, but the roles of additional proteins have remained largely uncharacterized. We recently identified
GRA72
as synthetically lethal with
GRA17
. Deleting
GRA72
produced similar phenotypes to Δ
gra17
parasites, and computational predictions suggested it forms a pore. To understand how GRA72 functions, we performed immunoprecipitation experiments and identified GRA47 as an interactor of GRA72. Deletion of
GRA47
resulted in an aberrant “bubble vacuole” morphology with reduced small molecule permeability, mirroring the phenotype observed in
GRA17
and
GRA72
knockouts. Structural predictions indicated that GRA47 and GRA72 form heptameric and hexameric pores, respectively, with conserved histidine residues lining the pore. Mutational analysis highlighted the critical role of these histidines for protein functionality. Validation through electrophysiology confirmed alterations in membrane conductance, corroborating their pore-forming capabilities. Furthermore, Δ
gra47
parasites and parasites expressing GRA47 with a histidine mutation had reduced
in vitro
proliferation and attenuated virulence in mice. Our findings show the important roles of GRA47 and GRA72 in regulating PVM permeability, thereby expanding the repertoire of potential therapeutic targets against
Toxoplasma
infections.

IMPORTANCE

Toxoplasma gondii
is a parasite that poses significant health risks to those with impaired immunity. It replicates inside host cells shielded by the PVM, which controls nutrient and waste exchange with the host. GRA72, previously identified as essential in the absence of the GRA17 nutrient channel, is implicated in forming an alternative nutrient channel. Here we found that GRA47 associates with GRA72 and is also important for the PVM's permeability to small molecules. Removal of GRA47 leads to distorted vacuoles and impairs small molecule transport across the PVM, resembling the effects of GRA17 and GRA72 deletions. Structural models suggest GRA47 and GRA72 form distinct pore structures, with a pore-lining histidine critical to their function.
Toxoplasma
strains lacking GRA47 or those with a histidine mutation have impaired growth and reduced virulence in mice, highlighting these proteins as potential targets for new treatments against toxoplasmosis.
A novel
Bartonella
-like bacterium forms an interdependent mutualistic symbiosis with its host, the stored-product mite
Tyrophagus putrescentiae
Authors: Xiong Qing , Sopko Bruno , Klimov Pavel B. , Hubert Jan 
Published: February 2024

ABSTRACT

A novel
Bartonella
-like symbiont (BLS) of
Tyrophagus putrescentiae
was characterized. BLS formed a separate cluster from the
Bartonella
clade together with an ant symbiont. BLS was present in mite bodies (103 16S DNA copies/mite) and feces but was absent in eggs. This indicated the presence of the BLS in mite guts. The BLS showed a reduction in genome size (1.6 Mb) and indicates gene loss compared to
Bartonella apis
. The BLS can be interacted with its host by using host metabolic pathways (e.g., the histidine and arginine metabolic pathways) as well as by providing its own metabolic pathways (pantothenate and lipoic acid) to the host, suggesting the existence of a mutualistic association. Our experimental data further confirmed these potential mutualistic nutritional associations, as cultures of
T. putrescentiae
with low BLS abundance showed the strongest response after the addition of vitamins. Despite developing an arguably tight dependency on its host, the BLS has probably retained flagellar mobility, as evidenced by the 32 proteins enriched in KEGG pathways associated with flagellar assembly or chemotaxis (e.g., fliC, flgE, and flgK, as highly expressed genes). Some of these proteins probably also facilitate adhesion to host gut cells. The microcin C transporter was identified in the BLS, suggesting that microcin C may be used in competition with other gut bacteria. The 16S DNA sequence comparison indicated a mite clade of BLSs with a broad host range, including house dust and stored-product mites. Our phylogenomic analyses identified a unique lineage of arachnid specific BLSs in mites and scorpions.

IMPORTANCE

A
Bartonella
-like symbiont was found in an astigmatid mite of allergenic importance. We assembled the genome of the bacterium from metagenomes of different stored-product mite (
T. putrescentiae
) cultures. The bacterium provides pantothenate and lipoic acid to the mite host. The vitamin supply explains the changes in the relative abundance of BLSs in
T. putrescentiae
as the microbiome response to nutritional or pesticide stress, as observed previously. The phylogenomic analyses of available 16S DNA sequences originating from mite, scorpion, and insect samples identified a unique lineage of arachnid specific forming large
Bartonella
clade. BLSs associated with mites and a scorpion. The
Bartonella
clade included the previously described
Ca
. Tokpelaia symbionts of ants.
Carboniferous bimodal volcanic sequences along the Northeastern Pamir: Evidence for back-arc extension due to northward subduction of the Paleo-Tethys
Authors: Song Zhi-Hao , Zhang Chuan-Lin , Sargazi Masumeh , Hussain Zahid , Liu Xiao-Qiang , Ye Xian-Tao , Wang Hong-Ran 
Published: February 2024

Abstract
The Pamir plateau lies at the western end of the Tethys domain recording the entire evolution from the opening of the Proto-Tethys to the final closure of the Neo-Tethys. During this long-term evolution, the details of the initial subduction of the Paleo-Tethys and the final amalgamation of the main terranes in the Pamir are still controversial. The Carboniferous bimodal volcanic sequences along the Northern Pamir may supply the key evidence to reveal the subduction process of the Paleo-Tethys Ocean. This study presents the detailed stratigraphic architecture, petrography, geochronological and geochemical data of the Carboniferous–Permian volcanic rocks along the Northern Pamir in western China bordering Tajikistan. Zircons from two plagioclase phenocryst-rich basalts, and an andesite, volcanic agglomerate, and granitic sill emplaced in the basalts yield concordant ages of 319.5 ± 2 Ma, 322.7 ± 1.6 Ma, 288.7 ± 2.5 Ma, 301.6 ± 4.2 Ma, and 300.4 ± 1.5 Ma, respectively. The basalts show mid-oceanic-ridge basalt–like geochemical features with flat to depleted light rare earth element trends [(La/Yb)N = 0.68–1.82], depleted whole-rock εNd(t) (6.44–7.85), and zircon εHf(t) (6.3–10.1) values, suggesting they are primitive magmas derived from a depleted mantle source metasomatized by earlier subduction in line with their low Nb/La ratios (0.30–0.64). As for the intermediate-acid volcanic rocks (andesite and dacite), they show enrichment of large ionic lithophile elements (e.g., Rb, Ba, and Sr) and depletion of high field strength elements (e.g., Nb, Ta, and Ti) as well as negative εNd(t) values ranging from −0.97 to −0.75, demonstrating that they are primitive magmas derived from partial melting of the metasomatized lithospheric mantle source, followed by crystal fraction of hornblende, plagioclase, and minor quartz. Taking together the stratigraphic features, rock associations, and geochemical signatures, the Carboniferous basalts share most features with the Okinawa and the Mariana back-arc basalts. Integrating the new data with the previous studies, we construct a detailed evolution process of the Paleo-Tethys Ocean at the Pamir, i.e., extension of the filled residual Proto-Tethys Ocean between the Tarim and the Northern Pamir induced by the northward Paleo-Tethys subduction in the early Carboniferous, gradually waning of the back-arc basin from the late Carboniferous to the Early Permian, and finally, the closure of the Paleo-Tethys Ocean led to the amalgamation of the Northern, the Central, and the Southern Pamir, resulting in the initial architecture of the Pamir.
Geophysical constraints on continental rejuvenation in central China: Implications for outward growth of the Tibetan Plateau
Authors: Zhang Yi-Peng , Zhang Pei-Zhen , Lease Richard O. , Li Min-Juan , Zhou Renjie , Xu Bin-Bin , Cheng Si-Yuan , Shen Xu-Zhang , Zheng Wen-Jun , He Xiao-Hui , Wang Wei-Tao , Wang Yue-Jun 
Published: February 2024

Abstract
Continental rejuvenation results from the tectonic reactivation of crustal structures and lithospheric reworking by mantle flow. Geochemical observations and field mapping have traditionally provided the primary evidence for the secular evolution of crustal composition and tectonic processes during continental rejuvenation. Nonetheless, the impact of continental rejuvenation on the observed present-day strain rate and orogenic-scale lithospheric structure has not been well constrained. The pre-existing E-W–trending Central China Orogenic Belt has been overprinted by the N-S–trending Central Longitudinal Seismic Belt and constitutes the intracontinental West Qinling Syntaxis in central China, where the tectonic setting changes eastward from contraction to extension. Combining updated global positioning system data and high-resolution crustal seismic tomography, we reveal a modern continental rejuvenation process within the West Qinling Syntaxis in central China. The northward extrusion of the Tibetan Plateau's weak lithospheric layer (middle-lower crust and lithospheric mantle) of southwestern China relative to the rigid Sichuan Basin/Ordos Block of the eastern West Qinling Syntaxis results in regional dextral shearing that shapes the Central Longitudinal Seismic Belt and defines the eastern Tibetan Plateau margin. The pre-existing E-W–trending Central China Orogenic Belt has been preserved above the brittle-ductile transition zone, and the northward movement of the deep lithospheric layer drives the deformation of the upper crust in the West Qinling Syntaxis. Our results, along with previous studies, suggest the presence of an intracontinental lithospheric interchange structure in central China. The continental rejuvenation of the West Qinling Syntaxis results from a combination of fault reactivation in the upper crust (Stage I, Eocene–Oligocene) and reworking of the deep lithosphere (Stage II, middle–late Miocene) related to the plateau-wide shift in stress accommodation ultimately driven by the redistribution of mass outward from the central Tibetan Plateau. At present, the transition zone between the high- and low-velocity anomalies along the Central Longitudinal Seismic Belt not only shapes the landscape boundary but controls the size and recurrence interval of earthquakes within the West Qinling Syntaxis in central China.
Eocene crustal thickening in the Tethyan Himalaya: Insights from Barrovian metamorphism and granite geochemistry from the Ramba area
Authors: Shi Shuai , Jiang Yingde , Weinberg Roberto F. , Zhang Zhi , Wang Qiang 
Published: February 2024

Abstract
Magmatism, structures, and metamorphism in the Ramba dome of the Tethyan Himalaya were investigated to shed light on orogenic processes during the early stages of the India-Asia collision. Deformed granite dikes in the dome envelope yield zircon U-Pb ages of ca. 45 Ma. These Eocene granites have adakitic, Na-rich compositions (K2O/Na2O = 0.20–0.61), weak to no Eu anomaly, enrichment in Sr, depletion in heavy rare earth elements and Y, and low MgO and Mg# contents. These characteristics contrast with the Miocene potassic granites in the core of the dome and suggest that the Eocene adakites were derived from the high-pressure melting of crustal amphibolites in a thick crust. The mica schists of the dome envelope have an early foliation (S1) that is overprinted by upright folds (F2). Phase-equilibria modeling of garnet and staurolite mica schists suggests a Barrovian-type, prograde P-T evolution in association with S1, with peak conditions of 6.7–7.2 kbar/590–605 °C and 7.3–7.8 kbar/650–670 °C, respectively, which are typical of crustal thickening metamorphism. Monazites from S1-dominated staurolite mica schists yield metamorphic ages of ca. 51–49 Ma, while those from the late foliation (S2) that transposed S1 give younger ages of ca. 10 Ma. The integration of geochemical, structural, metamorphic, and geochronological data suggests that peak Barrovian D1 metamorphism and adakitic magmatism occurred in the Eocene in response to crustal thickening. The results provide critical constraints for addressing the crustal shortening deficit of the region.