bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reduction of Roughing Process by Near-Net Shape Manufacturing Using Sheet Metal Laminated Molds
Authors: Ota Chihiro , Nakatsuji Hidenori , Nishida Isamu 
Published: August 2024

Abstract
This study proposes the way to reduce the rouging process by using sheet metal laminated molds to create a near-net shape of a product. To accomplish this, it developed a system that automatically outputs the numerical control (NC) program for laser cutting to create a sheet metal laminated mold from the computer-aided design (CAD) data of the product in standard triangulated language (STL) format. It also developed a system that automatically generates the NC program for medium roughing and finishing. The system eliminates air cut motions of the NC program by using the near-net shape information and the tool path calculated with round bar work materials. By actual machining, the effectiveness of this system was confirmed.
Investigation of Tooth Surface Temperature Based on High-Speed Thermography Monitoring Under Meshing of Hypoid Gear With Small Number of Teeth
Authors: Kikuchi Daiki , Onozeki Shoui , Nakagawa Masao , Hirogaki Toshiki , Aoyama Eiichi , Matsui Shota 
Published: August 2024

Abstract
Improving the noise vibration harshness (NVH) characteristics of systems has recently become a critical issue for meeting user needs in the automotive industry. Note that the accuracy of the tooth surface significantly influences the vibrations of gear meshing. The hypoid gear used in the automobile differential has a complex shape; hence, estimating its contact conditions is difficult. Therefore, we aim to develop a novel method to analyze the tooth contact conditions using highly sensitive infrared thermography measurements with a high response. The proposed method provides a noncontact analysis based on monitoring the temperature distribution during meshing between the pinion and gear surfaces. In this study, we designed three hypoid gear types with high-reduction ratios. Subsequently, a tooth contact analysis was conducted using thermography measurements. As a result, the relationship between the temperature increase at the tooth contact area was clarified.
Study on Dynamic Characteristics Control System of Machine Tools for Avoiding Chatter Vibration
Authors: Hayashi Akio , Takeuchi Shotaro , Morimoto Yoshitaka 
Published: August 2024

Abstract
In cutting process, chatter vibration is a problem that deteriorates machining accuracy. In a previous study, we proposed a method that avoids chatter vibration by changing the dynamic characteristics of the machine tool without changing the machining conditions. However, the method for changing machine tool stiffness was set manually. Then, we have developed new changing method for the dynamic characteristics of machine tools during machining. In this study, the characteristics changes by a brace bar attached to a desktop machine tool is performed automatically by using a servo motor. The effectiveness of the automatic dynamic characteristics control is evaluated by the transition of the stability limit diagram through hammering tests.
Two new Aculus species (Acari: Eriophyoidea) collected on Hypericum spp. in Iran
Authors: Lotfollahi Parisa , Jahandideh-Dogijan Javad , Honarmand Arash 
Published: August 2024

During the year 2023, Hypericaceae plants were sampled in Iran and two new Aculus species were found on them: Aculus quattuorlaminate Lotfollahi, Jahandideh et Honarmand sp. nov. on Hypericum perforatum L. and Aculus hufarighooni Honarmand, Jahandideh et Lotfollahi sp. nov. on Hypericum scabrum L. Both species were vagrant on their host plants. In this study we provided a list of eriophyoid species collected on Hypericaceae plants worldwide, their type host, type locality and habitus, and a key for identification of them.
Engineering of a hydroxysteroid dehydrogenase with simultaneous enhancement in activity and thermostability for efficient biosynthesis of ursodeoxycholic acid
Authors: Li Yuan , Li Shu-Fang , Zhang Lin , Xue Ya-Ping , Zheng Yu-Guo 
Published: August 2024

ABSTRACT

Hydroxysteroid dehydrogenases (HSDHs) catalyze the oxidation/reduction of hydroxyl/keto groups of steroids with high regio- or stereoselectivity, playing an essential role in producing optically pure chemicals. In this work, a novel approach was developed to simultaneously improve the stability and activity of 7β-hydroxysteroid dehydrogenase (7β-HSDH) by combining B-factor analysis and computer-aided prediction. Several advantageous mutants were identified, and the most promising variant, S51Y/P202Y, exhibited 2.3-fold improvements in catalytic activity, 3.3-fold in half-life at 40°C, and 4.7-fold in catalytic efficiency (
k
cat
/K
m
), respectively. Structural modeling analysis showed that the shortened reversible oxidation reaction catalytic distance and the strengthened residue interactions compared to the wild type were attributed to the improved stability and activity of the obtained mutants. To synthesize ursodeoxycholic acid cost-effectively by mutant S51Y/P202Y, a NAD-kinase was employed to facilitate the substitution of nicotinamide adenine dinucleotide phosphate (NADP
+
) with nicotinamide adenine dinucleotide (NAD
+
) in the whole-cell catalysis system. The substrate 7-ketolithocholic acid (100 mM) was converted completely in 0.5 h, achieving a space-time yield of 1,887.3 g L
−1
d
−1
. This work provided a general target-oriented strategy for obtaining stable and highly active dehydrogenase for efficient biosynthesis.

IMPORTANCE

Hydroxysteroid dehydrogenases have emerged as indispensable tools in the synthesis of steroids, bile acids, and other steroid derivatives for the pharmaceutical and chemical industries. In this study, a novel approach was developed to simultaneously improve the stability and activity of a hydroxysteroid dehydrogenase by combining B-factor analysis and computer-aided prediction. This semi-rational method was demonstrated to be highly effective for enzyme engineering. In addition, NAD kinase was introduced to convert NAD
+
to NADP
+
for effective coenzyme regeneration in the whole-cell multienzyme-catalyzed system. This strategy reduces the significant economic costs associated with externally supplemented cofactors in NADP-dependent biosynthetic pathways.
VP3 protein of Senecavirus A promotes viral IRES-driven translation and attenuates innate immunity by specifically relocalizing hnRNPA2B1
Authors: Li Lu , Li Xinwei , Zhong Han , Li Mingyang , Wan Bo , He Wenrui , Zhang Yuhang , Du Yongkun , Chen Dongjie , Zhang Wei , Ji Pengchao , Jiang Dawei , Han Shichong 
Published: August 2024

ABSTRACT

Viruses deploy sophisticated strategies to hijack the host’s translation machinery to favor viral protein synthesis and counteract innate cellular defenses. However, little is known about the mechanisms by which Senecavirus A (SVA) controls the host’s translation. Using a series of sophisticated molecular cell manipulation techniques, heterogeneous nuclear ribonucleoprotein A2B1 (hnRNPA2B1) was identified as an essential host factor involved in translation control in SVA-infected cells. It was also determined that the SVA structural protein, VP3, binds to and relocalizes hnRNPA2B1, which interferes with the host’s protein synthesis machinery to establish a cellular environment that facilitates viral propagation via a two-pronged strategy: first, hnRNPA2B1 serves as a potent internal ribosome entry site (IRES)
trans
-acting factor, which is selectively co-opted to promote viral IRES-driven translation by supporting the assembly of translation initiation complexes. Second, a strong repression of host cell translation occurs in the context of the VP3-hnRNPA2B1 interaction, resulting in attenuation of the interferons response. This is the first study to demonstrate the interaction between SVA VP3 and hnRNPA2B1, and to characterize their key roles in manipulating translation. This novel dual mechanism, which regulates selective mRNA translation and immune evasion of virus-infected cells, highlights the VP3-hnRNPA2B1 complex as a potential target for the development of modified antiviral or oncolytic reagents.

IMPORTANCE
Viral reproduction is contingent on viral protein synthesis, which relies entirely on the host's translation machinery. As such, viruses often need to control the cellular translational apparatus to favor viral protein production and avoid host innate defenses. Senecavirus A (SVA) is an important virus, both as an emerging pathogen in the pork industry and as a potential oncolytic virus for neuroendocrine cancers. Here, heterogeneous nuclear ribonucleoprotein A2B1 (hnRNPA2B1) was identified as a critical regulator of the translational landscape during SVA infection. This study supports a model whereby the VP3 protein of SVA efficiently subverts the host’s protein synthesis machinery through its ability to bind to and relocalize hnRNPA2B1, not only selectively promoting viral internal ribosome entry site-driven translation but also resulting in global translation shutdown and immune evasion. Together, these data provide new insights into how the complex interactions between translation machinery, SVA, and innate immunity contribute to the pathogenicity of the SVA.
Small archaea may form intimate partnerships to maximize their metabolic potential
Authors: Baker Brett J. , Sarno Natalie 
Published: August 2024

ABSTRACT

DPANN archaea have characteristically small cells and unique genomes that were long overlooked in diversity surveys. Their reduced genomes often lack essential metabolic pathways, requiring symbiotic relationships with other archaeal and bacterial hosts for survival. Yet a long-standing question remains, what is the advantage of maintaining ultrasmall cells. A recent study by Zhang et al. examined genomes of DPANN archaea from marine oxygen deficient zones (ODZs) (I. H. Zhang, B. Borer, R. Zhao, S. Wilbert, et al., mBio 15:e02918-23, 2024,
https://doi.org/10.1128/mbio.02918-23
). Surprisingly, these genomes contain a broad array of metabolic pathways including genes predicted to be involved in nitrous oxide (N
2
O) reduction. However, N
2
O levels are likely too low in ODZs to make this metabolically feasible. Modeling co-localization of DPANN archaea (N
2
O consumers) with other larger cells (N
2
O producers) demonstrates that N
2
O uptake rates can be optimized by maximizing the producer-to-consumer size ratio and proximity of consumer cells to producers. This may explain why such a diversity of archaea maintain extremely small cell sizes.
Role of IgA1 protease-producing bacteria in SARS-CoV-2 infection and transmission: a hypothesis
Authors: Russell Michael W. , Kilian Mogens , Mestecky Jiri 
Published: August 2024

ABSTRACT

Secretory (S) IgA antibodies against severe acute respiratory syndrome (SARS)-CoV-2 are induced in saliva and upper respiratory tract (URT) secretions by natural infection and may be critical in determining the outcome of initial infection. Secretory IgA1 (SIgA1) is the predominant isotype of antibodies in these secretions. Neutralization of SARS-CoV-2 is most effectively accomplished by polymeric antibodies such as SIgA. We hypothesize that cleavage of SIgA1 antibodies against SARS-CoV-2 by unique bacterial IgA1 proteases to univalent Fabα antibody fragments with diminished virus neutralizing activity would facilitate the descent of the virus into the lungs to cause serious disease and also enhance its airborne transmission to others. Recent studies of the nasopharyngeal microbiota of patients with SARS-CoV-2 infection have revealed significant increases in the proportions of IgA1 protease-producing bacteria in comparison with healthy subjects. Similar considerations might apply also to other respiratory viral infections including influenza, possibly explaining the original attribution of influenza to
Haemophilus influenzae
, which produces IgA1 protease.
Diagnosis and mitigation of the systemic impact of genome reduction in
Escherichia coli
DGF-298
Authors: Champie Antoine , Lachance Jean-Christophe , Sastry Anand , Matteau Dominick , Lloyd Colton J. , Grenier Frédéric , Lamoureux Cameron R. , Jeanneau Simon , Feist Adam M. , Jacques Pierre-Étienne , Palsson Bernhard O. , Rodrigue Sébastien 
Published: August 2024

ABSTRACT

Microorganisms with simplified genomes represent interesting cell chassis for systems and synthetic biology. However, genome reduction can lead to undesired traits, such as decreased growth rate and metabolic imbalances. To investigate the impact of genome reduction on
Escherichia coli
strain DGF-298, a strain in which ~ 36% of the genome has been removed, we reconstructed a strain-specific metabolic model (
i
AC1061), investigated the regulation of gene expression using iModulon-based transcriptome analysis, and performed adaptive laboratory evolution to let the strain correct potential imbalances that arose during its simplification. The model notably predicted that the removal of all three key pathways for glycolaldehyde disposal in this microorganism would lead to a metabolic bottleneck through folate starvation. Glycolaldehyde is also known to cause self-generation of reactive oxygen species, as evidenced by the increased expression of oxidative stress resistance genes in the SoxS iModulon. The reintroduction of the
aldA
gene, responsible for one native glycolaldehyde disposal route, alleviated the constitutive oxidative stress response. Our results suggest that systems-level approaches and adaptive laboratory evolution have additive benefits when trying to repair and optimize genome-engineered strains.

IMPORTANCE

Genomic streamlining can be employed in model organisms to reduce complexity and enhance strain predictability. One of the most striking examples is the bacterial strain
Escherichia coli
DGF-298, notable for having over one-third of its genome deleted. However, such extensive genome modifications raise the question of how similar this simplified cell remains when compared with its parent, and what are the possible unintended consequences of this simplification. In this study, we used metabolic modeling along with iModulon-based transcriptomic analysis in different growth conditions to assess the impact of genome reduction on metabolism and gene regulation. We observed little impact of genomic reduction on the regulatory network of
E. coli
DGF-298 and identified a potential metabolic bottleneck leading to the constitutive activity of the SoxS iModulon. We then leveraged the model's predictions to successfully restore SoxS activity to the basal level.
Uncovering the roles of the scaffolding protein CsoS2 in mediating the assembly and shape of the α-carboxysome shell
Authors: Li Tianpei , Chen Taiyu , Chang Ping , Ge Xingwu , Chriscoli Vincent , Dykes Gregory F. , Wang Qiang , Liu Lu-Ning 
Published: August 2024

ABSTRACT

Carboxysomes are proteinaceous organelles featuring icosahedral protein shells that enclose the carbon-fixing enzymes, ribulose-1,5-bisphosphate carboxylase oxygenase (Rubisco), along with carbonic anhydrase. The intrinsically disordered scaffolding protein CsoS2 plays a vital role in the construction of α-carboxysomes through bridging the shell and cargo enzymes. The N-terminal domain of CsoS2 binds Rubisco and facilitates Rubisco packaging within the α-carboxysome, whereas the C-terminal domain of CsoS2 (CsoS2-C) anchors to the shell and promotes shell assembly. However, the role of the middle region of CsoS2 (CsoS2-M) has remained elusive. Here, we conducted in-depth examinations on the function of CsoS2-M in the assembly of the α-carboxysome shell by generating a series of recombinant shell variants in the absence of cargos. Our results reveal that CsoS2-M assists CsoS2-C in the assembly of the α-carboxysome shell and plays an important role in shaping the α-carboxysome shell through enhancing the association of shell proteins on both the facet-facet interfaces and flat shell facets. Moreover, CsoS2-M is responsible for recruiting the C-terminal truncated isoform of CsoS2, CsoS2A, into α-carboxysomes, which is crucial for Rubisco encapsulation and packaging. This study not only deepens our knowledge of how the carboxysome shell is constructed and regulated but also lays the groundwork for engineering and repurposing carboxysome-based nanostructures for diverse biotechnological purposes.

IMPORTANCE

Carboxysomes are a paradigm of organelle-like structures in cyanobacteria and many proteobacteria. These nanoscale compartments enclose Rubisco and carbonic anhydrase within an icosahedral virus-like shell to improve CO
2
fixation, playing a vital role in the global carbon cycle. Understanding how the carboxysomes are formed is not only important for basic research studies but also holds promise for repurposing carboxysomes in bioengineering applications. In this study, we focuses on a specific scaffolding protein called CsoS2, which is involved in facilitating the assembly of α-type carboxysomes. By deciphering the functions of different parts of CsoS2, especially its middle region, we provide new insights into how CsoS2 drives the stepwise assembly of the carboxysome at the molecular level. This knowledge will guide the rational design and reprogramming of carboxysome nanostructures for many biotechnological applications.
Rubella virus assembly requirements and evolutionary relationships with novel rubiviruses
Authors: Das Pratyush Kumar , Kielian Margaret 
Published: August 2024

ABSTRACT

Rubella virus (RuV) is an enveloped virus that usually causes mild disease in children, but can produce miscarriage or severe congenital birth defects. While in nature RuV only infects humans, the discovery of the related Ruhugu (RuhV) and Rustrela (RusV) viruses highlights the spillover potential of mammalian rubiviruses to humans. RuV buds into the Golgi, but its assembly and exit are not well understood. We identified a potential late domain motif
278
PPAY
281
at the C-terminus of the RuV E2 envelope protein. Such late domain motifs can promote virus budding by recruiting the cellular ESCRT machinery. An E2 Y281A mutation reduced infectious virus production by >3 logs and inhibited virus particle production. However, RuV was insensitive to inhibition by dominant-negative VPS4, and thus appeared ESCRT-independent. The E2 Y281A mutation did not significantly inhibit the production of the viral structural proteins capsid (Cp), E2, and E1, or dimerization, glycosylation, Golgi transport, and colocalization of E2 and E1. However, E2 Y281A significantly reduced glycoprotein-Cp colocalization and interaction, and inhibited Cp localization to the Golgi. Revertants of the E2 Y281A mutant contained an E2 281V substitution or the second site mutations [E2 N277I + Cp D215A]. These mutations promoted virus growth, particle production, E2/Cp colocalization and Cp-Golgi localization. Both the E2 substitutions 281V and 277I were found at the corresponding positions in the RuhV E2 protein. Taken together, our data identify a key interaction of the RuV E2 endodomain with the Cp during RuV biogenesis, and support the close evolutionary relationship between human and animal rubiviruses.

IMPORTANCE

Rubella virus (RuV) is an enveloped virus that only infects humans, where transplacental infection can cause miscarriage or congenital birth defects. We identified a potential late domain,
278
PPAY
281
, at the C terminus of the E2 envelope protein. However, rather than this domain recruiting the cellular ESCRT machinery as predicted, our data indicate that E2 Y281 promotes a critical interaction of the E2 endodomain with the capsid protein, leading to capsid's localization to the Golgi where virus budding occurs. Revertant analysis demonstrated that two substitutions on the E2 protein could partially rescue virus growth and Cp-Golgi localization. Both residues were found at the corresponding positions in Ruhugu virus E2, supporting the close evolutionary relationship between RuV and Ruhugu virus, a recently discovered rubivirus from bats.
From microbes to mind: germ-free models in neuropsychiatric research
Authors: Delgado-Ocaña Susana , Cuesta Santiago 
Published: August 2024

ABSTRACT

The gut–microbiota–brain axis refers to the bidirectional communication system between the gut, its microbial community, and the brain. This interaction involves a complex interplay of neural pathways, chemical transmitters, and immunological mechanisms. Germ-free animal models have been extensively employed to investigate gut–microbiota–brain interactions, significantly contributing to our current understanding of the role of intestinal microbes in brain function. However, despite the many benefits, this absence of microbiota is not futile. Germ-free animals present physiological and neurodevelopmental alterations that can persist even after reconstitution with normal microbiota. Therefore, the main goal of this minireview is to discuss how some of the inherent limitations of this model can interfere with the conclusion obtained when using these animals to study the complex nature of neuropsychiatric disorders. Furthermore, we examine the inclusion and use of antibiotic-based treatments as an alternative in the research of gut–brain interactions.
Hypermigration of macrophages through the concerted action of GRA effectors on NF-κB/p38 signaling and host chromatin accessibility potentiates
Toxoplasma
dissemination
Authors: ten Hoeve Arne L. , Rodriguez Matias E. , Säflund Martin , Michel Valentine , Magimel Lucas , Ripoll Albert , Yu Tianxiong , Hakimi Mohamed-Ali , Saeij Jeroen P. J. , Ozata Deniz M. , Barragan Antonio 
Published: August 2024

ABSTRACT

Mononuclear phagocytes facilitate the dissemination of the obligate intracellular parasite
Toxoplasma gondii
. Here, we report how a set of secreted parasite effector proteins from dense granule organelles (GRA) orchestrates dendritic cell-like chemotactic and pro-inflammatory activation of parasitized macrophages. These effects enabled efficient dissemination of the type II
T. gondii
lineage, a highly prevalent genotype in humans. We identify novel functions for effectors GRA15 and GRA24 in promoting CCR7-mediated macrophage chemotaxis by acting on NF-κB and p38 mitogen-activated protein kinase signaling pathways, respectively, with contributions by GRA16/18 and counter-regulation by effector TEEGR. Furthermore, GRA28 boosted chromatin accessibility and GRA15/24/NF-κB-dependent transcription at the
Ccr7
gene locus in primary macrophages.
In vivo
, adoptively transferred macrophages infected with wild-type
T. gondii
outcompeted macrophages infected with a GRA15/24 double mutant in migrating to secondary organs in mice. The data show that
T. gondii
, rather than being passively shuttled, actively promotes its dissemination by inducing a finely regulated pro-migratory state in parasitized human and murine phagocytes via co-operating polymorphic GRA effectors.

IMPORTANCE

Intracellular pathogens can hijack the cellular functions of infected host cells to their advantage, for example, for intracellular survival and dissemination. However, how microbes orchestrate the hijacking of complex cellular processes, such as host cell migration, remains poorly understood. As such, the common parasite
Toxoplasma gondii
actively invades the immune cells of humans and other vertebrates and modifies their migratory properties. Here, we show that the concerted action of a number of secreted effector proteins from the parasite, principally GRA15 and GRA24, acts on host cell signaling pathways to activate chemotaxis. Furthermore, the protein effector GRA28 selectively acted on chromatin accessibility in the host cell nucleus to selectively boost host gene expression. The joint activities of GRA effectors culminated in pro-migratory signaling within the infected phagocyte. We provide a molecular framework delineating how
T. gondii
can orchestrate a complex biological phenotype, such as the migratory activation of phagocytes to boost dissemination.