bluuebunny/crossref_metadata_2025 huggingface dataset:
The transcription factor WRKY22 modulates ethylene biosynthesis and root development through transactivating the transcription of ACS5 and ACO5 in Arabidopsis
Authors: Wang Zhaoqiang , Wei Xiangyan , Cui Xing , Wang Jing , Wang Yiqiao , Sun Mengting , Zhao Peiyu , Yang Bo , Wang Qiannan , Jiang Yuan‐Qing
Published: June 2024

The WRKY transcription factor (TF) genes form a large family in higher plants, with 72 members in Arabidopsis (Arabidopsis thaliana). The gaseous phytohormone ethylene (ET) regulates multiple physiological processes in plants. It is known that 1‐aminocyclopropane‐1‐carboxylic acid (ACC) synthases (ACSs, EC 4.4.1.14) limit the enzymatic reaction rate of ethylene synthesis. However, whether WRKY TFs regulate the expression of ACSs and/or ACC oxidases (ACOs, EC 1.14.17.4) remains largely elusive. Here, we demonstrated that Arabidopsis WRKY22 positively regulated the expression of a few ACS and ACO genes, thus promoting ethylene production. Inducible overexpression of WRKY22 caused shorter hypocotyls without ACC treatment. A qRT‐PCR screening demonstrated that overexpression of WRKY22 activates the expression of several ACS and ACO genes. The promoter regions of ACS5, ACS11, and ACO5 were also activated by WRKY22, which was revealed by a dual luciferase reporter assay. A follow‐up chromatin immunoprecipitation coupled with quantitative PCR (ChIP‐qPCR) and electrophoretic mobility shift assay (EMSA) showed that the promoter regions of ACS5 and ACO5 could be bound by WRKY22 directly. Moreover, wrky22 mutants had longer primary roots and more lateral roots than wild type, while WRKY22‐overexpressing lines showed the opposite phenotype. In conclusion, this study revealed that WRKY22 acts as a novel TF activating, at least, the expression of ACS5 and ACO5 to increase ethylene synthesis and modulate root development.
Usability of the Japanese Late‐Stage Elderly Questionnaire for screening major depression
Authors: Sato So , Sasabuchi Yusuke , Okada Akira , Yasunaga Hideo
Published: June 2024

Background

Older adults with major depression are at risk of frailty and long‐term care needs. Consequently, screening for major depression is imperative to prevent such risks. In Japan, the Late‐Stage Elderly Questionnaire was developed to evaluate older adults' holistic health, including mental well‐being. It comprises one specific question to gauge life satisfaction, but the effectiveness of this question to screen for major depression remains unclear. Therefore, we aimed to assess the usability of this question to screen for major depression.

Methods

This retrospective cohort study used a large, commercially available claims database in Japan. Participants were older adults aged ≥75 years who completed the Late‐Stage Elderly Questionnaire and were classified with and without new major depression within 1 year. We evaluated the questionnaire's ability to screen for major depression using C‐statistics, developing three models to assess the cut‐off value based on responses to the life satisfaction question (‘Satisfied’, ‘Somewhat satisfied’, ‘Somewhat unsatisfied’, or ‘Unsatisfied’), estimating the sensitivity and specificity of each model.

Results

Among 11 117 older adults, 77 newly experienced major depression within 1 year. The C‐statistic for screening major depression was 0.587. The model setting the cut‐off between ‘Somewhat unsatisfied’ and ‘Unsatisfied’ the demonstrated lowest sensitivity and highest specificity, while the model setting the cut‐off between ‘Satisfied’ and ‘Somewhat satisfied’ demonstrated highest sensitivity and lowest specificity.

Conclusions

Our results suggest that due to its poor screening ability and high rate of false negatives, the question assessing life satisfaction in the Late‐Stage Elderly Questionnaire may not be useful for screening major depression in older adults and may require modification.
Is it still permissible under EU law to issue new permits for oil and gas extraction?
Authors: Kaupa Clemens
Published: June 2024

This article examines whether the discretion of European Union (EU) Member States to approve new oil and gas extraction projects is restricted by EU law. It shows that greenhouse gas emissions from such projects must be considered in environmental impact assessments under the Environmental Impact Assessment and Strategic Environmental Assessment Directives. This includes emissions from the combustion of extracted oil and gas by end users (scope 3 emissions). The article also shows that Member States' discretion to approve new oil and gas extraction projects is significantly limited by their climate‐related obligations under EU law, as well as by the duty of sincere cooperation in the context of the EU's international commitments under the Paris Agreement.
A single nucleotide substitution in exon 5 generated the novel KIR2DL3*00112 allele
Authors: Li Yunan , Deng Zhihui
Published: June 2024

The novel KIR2DL3*00112 allele differs from the closest allele KIR2DL3*00101 by a single same sense mutation.
HTile: A high‐performance real‐time raster tile service with data‐fusion and data‐hiding approaches
Authors: Chen Jyun‐Yuan , Kuo Chiao‐Ling
Published: June 2024

Publication of raster tile services is a widely adopted method for presenting and sharing geographically referenced data, and enhancing geographic information systems (GIS) by serving as either base layers or featured layers. However, the establishment of raster tile services can still be improved in terms of data fusion efficiency and diversity from various raster and vector sources. In addition, addressing data security concerns while maintaining flexibility to meet the requirements and expectations of clients and publishers is crucial. HTile is proposed as a solution to efficiently publish high‐performance real‐time raster tile services. This solution incorporates an innovative tile generation process that enables customized data fusion and data‐hiding and offers dynamic styling while utilizing minimal storage space, ensuring rapid response time to meet the objectives of satisfactory data protection and visualization. Implementations of HTile leverage commonly used raster and vector data, which demonstrate compelling evidence of data‐fusion and data‐hiding capacities with exceptional performance. This study makes a significant contribution to the innovation strategy in publishing raster tile services, proving a novel approach that holds promising potential for GIS paradigms in data management and sharing flexibility.
A serine carboxypeptidase‐like acyltransferase catalyzes consecutive four‐step reactions of hydrolyzable tannin biosynthesis in Camellia oleifera
Authors: Wang Zhihui , Chen Xiangxiang , Zhao Yue , Jin Didi , Jiang Changjuan , Yao Shengbo , Li Zhu , Jiang Xiaolan , Liu Yajun , Gao Liping , Xia Tao
Published: June 2024

Hydrolyzable tannins (HTs), a class of polyphenolic compounds found in dicotyledonous plants, are widely used in food and pharmaceutical industries because of their beneficial effects on human health. Although the biosynthesis of simple HTs has been verified at the enzymatic level, relevant genes have not yet been identified. Here, based on the parent ion‐fragment ion pairs in the feature fragment data obtained using UPLC‐Q‐TOF‐/MS/MS, galloyl phenolic compounds in the leaves of Camellia sinensis and C. oleifera were analyzed qualitatively and quantitatively. Correlation analysis between the transcript abundance of serine carboxypeptidase‐like acyltransferases (SCPL‐ATs) and the peak area of galloyl products in Camellia species showed that SCPL3 expression was highly correlated with HT biosynthesis. Enzymatic verification of the recombinant protein showed that CoSCPL3 from C. oleifera catalyzed the four consecutive steps involved in the conversion of digalloylglucose to pentagalloylglucose. We also identified the residues affecting the enzymatic activity of CoSCPL3 and determined that SCPL‐AT catalyzes the synthesis of galloyl glycosides. The findings of this study provide a target gene for germplasm innovation of important cash crops that are rich in HTs, such as C. oleifera, strawberry, and walnut.
Factores asociados a trastornos musculoesqueléticos entre universitarios del nororiente colombiano durante la pandemia por COVID-19
Authors: Almario Barrera Andrea Johana , Orgulloso Bautista Claudia Alejandra , Padrón Merlano Alison del Carmen , Díaz Cetina Jeison Andrés , Castellanos Domínguez Yeny Zulay
Published: June 2024

Antecedentes: los procesos de formación académica durante la pandemia por COVID-19 fueron soportados por las tecnologías de la información. No obstante, las condiciones del escenario donde se desarrollan los encuentros sincrónicos, así como la disposición de los estudiantes pueden influir en la aparición de trastornos musculoesqueléticos. Objetivo: identificar factores asociados a trastornos musculoesqueléticos en estudiantes de odontología del nororiente colombiano que recibieron clases virtuales mediadas por tecnologías de información durante la pandemia por COVID-19. Métodos: estudio analítico de corte transversal en estudiantes que recibieron clases en modalidad virtual durante el aislamiento social por COVID-19. Se aplicó el cuestionario Kuorinka validado, con variables sociodemográficas y las prácticas posturales durante las clases virtuales. La asociación se evaluó con las pruebas Chi2 o test de Fischer con p <0,05 se consideró significancia estadística. Resultados: en total participaron 170 (71,8 % mujeres), mediana de edad de 20 años (RIC:19-22). En general, el 81,8 % reportó presencia de trastorno musculoesquelético en al menos un sitio anatómico (miembro superior), siendo la espalda de mayor molestia (70 %) y que genera necesidad de cambio del lugar de trabajo (64,1 %). Como factores asociados se identificó el uso de silla inadecuada (trastorno en cuello) y la falta de estiramiento como uso de mesa inadecuada (trastorno en el hombro) (p<0,05). Conclusiones: se reportó alta prevalencia de trastornos musculoesqueléticos en estudiantes de odontología. La higiene postural constituye en un factor determinante para la aparición de estos eventos derivados de las clases remotas mediadas por la tecnología.
Film Cooling Performances Under Various Upstream Roughness Conditions: Experimental Investigations and Similarity Hypothesis
Authors: Huang Weichen , Wang Kechen , Zeng Fei , Chen Wenbin , Zhou Wenwu , Wen Xin , Peng Di , Liu Yingzheng
Published: June 2024

Roughness caused by deposition, erosion, and additive manufacturing can significantly affect gas turbine efficiency. Previous research has often examined film cooling performance under limited roughness configurations, resulting in inconclusive findings. In this study, film cooling performances under various upstream roughness conditions were investigated to simulate the roughness-affected film cooling performance of the suction side and the endwall. Three roughness heights (k/D = 0.1, 0.2, and 0.4) and shapes (ks/k = 0.17, 0.67, and 1.95) were selected to cover a wide range of surface roughness characteristics. Three blowing ratios were examined (M = 0.5, 1.0, and 1.5). The weakly roughened surfaces (ks /k = 0.17) showed improved cooling effectiveness as k/D increased. Meanwhile, the moderately and severely roughened surfaces (ks /k = 0.67 and 1.95) showed a decrease in cooling effectiveness with increasing k/D at M = 0.5 and 1.0 but an increase at M = 1.5. Cases with shallower and higher roughness elements at M = 1.5 outperformed the smooth plate. Subsequently, a similarity hypothesis for film cooling effectiveness was proposed. At all blowing ratios, the scaled cooling effectiveness profiles converged around the smooth plate results for ks /D < 0.391, encompassing common turbine roughness scales, including irregularly roughened surfaces. Deviations emerged at ks /D = 0.782, and they were correlated with the deteriorated regions observed at various blowing ratios. Ensemble-averaged scaled cooling effectiveness exponentially grew with increasing roughness scale for all blowing ratios, and an empirical expression based on the smooth plate result and roughness scale was proposed (R2 > 0.97). Finally, the experimental results and fitting correlations of cooling effectiveness were compared. The results demonstrated that the proposed similarity hypothesis potentially facilitated the fast prediction of the roughness-affected film cooling performance.
Perfect pulsed inline twin-beam squeezers
Authors: Houde Martin , Quesada Nicolás
Published: June 2024

Perfect inline squeezers are both spectrally pure and have identical input and output temporal modes, allowing one to squeeze an arbitrary input quantum state in the sole input mode on which the device acts, while the quantum states of any other modes are unaffected. We study theoretically how to obtain a perfect pulsed inline squeezer in twin-beam systems by considering three commonly used configurations: unpoled single pass, poled single pass, and poled double pass. By obtaining analytical relations between the input and output temporal modes from the Bloch–Messiah decomposition of the discretized Heisenberg-picture propagator, we find that a double-pass structure produces a perfect pulsed inline squeezer when operated in a frequency degenerate, symmetric group-velocity matched type-II configuration.
A modal approach for wall impedance estimate in a test section of a cavitation tunnel
Authors: Boucheron Romuald
Published: June 2024

The measurement of the underwater radiated noise at a model scale is generally the preferred way to predict this important feature at sea, using scaling laws. The accuracy of such method depends on many parameters. The measurement accuracy in a test section of a cavitation depends on the model used for the transfer function or for the propagation model. Thus, the knowledge of the wall acoustic impedance appears as an important parameter in such studies. The proposed study presents a modal method dedicated to the estimate of the wall impedance of a cavitation tunnel test section. It is based on a reverse method to estimate the impedance from measurements assuming that the sensor locations are known.
Effect of Data and Gap Characteristics on the Nonlinear Calculation of Motion During Locomotor Activities
Authors: Mohammadzadeh Gonabadi Arash , Buster Thad W. , Cesar Guilherme M. , Burnfield Judith M.
Published: June 2024

This study investigated how data series length and gaps in human kinematic data impact the accuracy of Lyapunov exponents (LyE) calculations with and without cubic spline interpolation. Kinematic time series were manipulated to create various data series lengths (28% and 100% of original) and gap durations (0.05–0.20 s). Longer gaps generally resulted in significantly higher LyE% error values in each plane in noninterpolated data. During cubic spline interpolation, only the 0.20-second gap in frontal plane data resulted in a significantly higher LyE% error. Data series length did not significantly affect LyE% error in noninterpolated data. During cubic spline interpolation, sagittal plane LyE% errors were significantly higher at shorter versus longer data series lengths. These findings suggest that not interpolating gaps in data could lead to erroneously high LyE values and mischaracterization of movement variability. When applying cubic spline, a long gap length (0.20 s) in the frontal plane or a short sagittal plane data series length (1000 data points) could also lead to erroneously high LyE values and mischaracterization of movement variability. These insights emphasize the necessity of detailed reporting on gap durations, data series lengths, and interpolation techniques when characterizing human movement variability using LyE values.
Stiffness sensing via Piezo1 enhances macrophage efferocytosis and promotes the resolution of liver fibrosis
Authors: Wang Yang , Wang Jin , Zhang Jiahao , Wang Yina , Wang Yuanyuan , Kang Haixia , Zhao Wenying , Bai Wenjuan , Miao Naijun , Wang Jing
Published: June 2024

Tissue stiffening is a predominant feature of fibrotic disorders, but the response of macrophages to changes in tissue stiffness and cellular context in fibrotic diseases remains unclear. Here, we found that the mechanosensitive ion channel Piezo1 was up-regulated in hepatic fibrosis. Macrophages lacking Piezo1 showed sustained inflammation and impaired spontaneous resolution of early liver fibrosis. Further analysis revealed an impairment of clearance of apoptotic cells by macrophages in the fibrotic liver. Macrophages showed enhanced efferocytosis when cultured on rigid substrates but not soft ones, suggesting stiffness-dependent efferocytosis of macrophages required Piezo1 activation. Besides, Piezo1 was involved in the efficient acidification of the engulfed cargo in the phagolysosomes and affected the subsequent expression of anti-inflammation genes after efferocytosis. Pharmacological activation of Piezo1 increased the efferocytosis capacity of macrophages and accelerated the resolution of inflammation and fibrosis. Our study supports the antifibrotic role of Piezo1-mediated mechanical sensation in liver fibrosis, suggesting that targeting PIEZO1 to enhance macrophage efferocytosis could induce fibrosis regression.
Plasticity and lineage commitment of individual TH1 cells are determined by stable T-bet expression quantities
Authors: Hegazy Ahmed N. , Peine Caroline , Niesen Dominik , Panse Isabel , Vainshtein Yevhen , Kommer Christoph , Zhang Qin , Brunner Tobias M. , Peine Michael , Fröhlich Anja , Ishaque Naveed , Marek Roman M. , Zhu Jinfang , Höfer Thomas , Löhning Max
Published: June 2024

T helper 1 (TH1) cell identity is defined by the expression of the lineage-specifying transcription factor T-bet. Here, we examine the influence of T-bet expression heterogeneity on subset plasticity by leveraging cell sorting of distinct in vivo–differentiated TH1 cells based on their quantitative expression of T-bet and interferon-γ. Heterogeneous T-bet expression states were regulated by virus-induced type I interferons and were stably maintained even after secondary viral infection. Exposed to alternative differentiation signals, the sorted subpopulations exhibited graded levels of plasticity, particularly toward the TH2 lineage: T-bet quantities were inversely correlated with the ability to express the TH2 lineage–specifying transcription factor GATA-3 and TH2 cytokines. Reprogramed TH1 cells acquired graded mixed TH1 + TH2 phenotypes with a hybrid epigenetic landscape. Continuous presence of T-bet in differentiated TH1 cells was essential to ensure TH1 cell stability. Thus, innate cytokine signals regulate TH1 cell plasticity via an individual cell-intrinsic rheostat to enable T cell subset adaptation to subsequent challenges.
High-entropy alloy electrocatalysts go to (sub-)nanoscale
Authors: Li Menggang , Lin Fangxu , Zhang Shipeng , Zhao Rui , Tao Lu , Li Lu , Li Junyi , Zeng Lingyou , Luo Mingchuan , Guo Shaojun
Published: June 2024

Alloying has proven power to upgrade metallic electrocatalysts, while the traditional alloys encounter limitation for optimizing electronic structures of surface metallic sites in a continuous manner. High-entropy alloys (HEAs) overcome this limitation by manageably tuning the adsorption/desorption energies of reaction intermediates. Recently, the marriage of nanotechnology and HEAs has made considerable progresses for renewable energy technologies, showing two important trends of size diminishment and multidimensionality. This review is dedicated to summarizing recent advances of HEAs that are rationally designed for energy electrocatalysis. We first explain the advantages of HEAs as electrocatalysts from three aspects: high entropy, nanometer, and multidimension. Then, several structural regulation methods are proposed to promote the electrocatalysis of HEAs, involving the thermodynamically nonequilibrium synthesis, regulating the (sub-)nanosize and anisotropic morphologies, as well as engineering the atomic ordering. The general relationship between the electronic structures and electrocatalytic properties of HEAs is further discussed. Finally, we outline remaining challenges of this field, aiming to inspire more sophisticated HEA-based nanocatalysts.
The PCNA–Pol δ complex couples lagging strand DNA synthesis to parental histone transfer for epigenetic inheritance
Authors: Serra-Cardona Albert , Hua Xu , McNutt Seth W. , Zhou Hui , Toda Takenori , Jia Songtao , Chu Feixia , Zhang Zhiguo
Published: June 2024

Inheritance of epigenetic information is critical for maintaining cell identity. The transfer of parental histone H3-H4 tetramers, the primary carrier of epigenetic modifications on histone proteins, represents a crucial yet poorly understood step in the inheritance of epigenetic information. Here, we show the lagging strand DNA polymerase, Pol δ, interacts directly with H3-H4 and that the interaction between Pol δ and the sliding clamp PCNA regulates parental histone transfer to lagging strands, most likely independent of their roles in DNA synthesis. When combined, mutations at Pol δ and Mcm2 that compromise parental histone transfer result in a greater reduction in nucleosome occupancy at nascent chromatin than mutations in either alone. Last, PCNA contributes to nucleosome positioning on nascent chromatin. On the basis of these results, we suggest that the PCNA–Pol δ complex couples lagging strand DNA synthesis to parental H3-H4 transfer, facilitating epigenetic inheritance.
A large-scale transcontinental river system crossed West Antarctica during the Eocene
Authors: Zundel Maximilian , Spiegel Cornelia , Mark Chris , Millar Ian , Chew David , Klages Johann , Gohl Karsten , Hillenbrand Claus-Dieter , Najman Yani , Salzmann Ulrich , Ehrmann Werner , Titschack Jürgen , Bauersachs Thorsten , Uenzelmann-Neben Gabriele , Bickert Torsten , Müller Juliane , Larter Rober , Lisker Frank , Bohaty Steve , Kuhn Gerhard ,   the Science Team of Expedition PS104
Published: June 2024

Extensive ice coverage largely prevents investigations of Antarctica’s unglaciated past. Knowledge about environmental and tectonic development before large-scale glaciation, however, is important for understanding the transition into the modern icehouse world. We report geochronological and sedimentological data from a drill core from the Amundsen Sea shelf, providing insights into tectonic and topographic conditions during the Eocene (~44 to 34 million years ago), shortly before major ice sheet buildup. Our findings reveal the Eocene as a transition period from >40 million years of relative tectonic quiescence toward reactivation of the West Antarctic Rift System, coinciding with incipient volcanism, rise of the Transantarctic Mountains, and renewed sedimentation under temperate climate conditions. The recovered sediments were deposited in a coastal-estuarine swamp environment at the outlet of a >1500-km-long transcontinental river system, draining from the rising Transantarctic Mountains into the Amundsen Sea. Much of West Antarctica hence lied above sea level, but low topographic relief combined with low elevation inhibited widespread ice sheet formation.
Rules for dissipationless topotronics
Authors: Yan Qing , Li Hailong , Jiang Hua , Sun Qing-Feng , Xie X. C.
Published: June 2024

Topological systems hosting gapless boundary states have attracted huge attention as promising components for next-generation information processing, attributed to their capacity for dissipationless electronics. Nevertheless, recent theoretical and experimental inquiries have revealed the emergence of energy dissipation in precisely quantized electrical transport. Here, we present a criterion for the realization of truly no-dissipation design, characterized as
N
in
=
N
tunl
+
N
bs
, where
N
in
,
N
tunl
, and
N
bs
represent the number of modes participating in injecting, tunneling, and backscattering processes, respectively. The key lies in matching the number of injecting, tunneling, and backscattering modes, ensuring the equilibrium among all engaged modes inside the device. Among all the topological materials, we advocate for the indispensability of Chern insulators exhibiting higher Chern numbers to achieve functional devices and uphold the no-dissipation rule simultaneously. Furthermore, we design the topological current divider and collector, evading dissipation upon fulfilling the established criterion. Our work paves the path for developing the prospective topotronics.
Case Commentary: Dual β-lactam as part of regimen to treat
Mycobacterium abscessus
lung disease
Authors: Lippincott Christopher K. , Lamichhane Gyanu
Published: June 2024

Individuals with compromised lung function and immunity are susceptible to developing chronic
Mycobacterium abscessus
infection. Current treatment recommendations typically involve using one β-lactam antibiotic in combination with non-β-lactam antibiotics. However, a recent case study (B. Becken, K. M. Dousa, J. L. Johnson, S. M. Holland, and R. A. Bonomo, Antimicrob Agents Chemother 68:e00319-24, 2024,
https://doi.org/10.1128/aac.00319-24
) demonstrated successful treatment of chronic
M. abscessus
lung disease in a child using two β-lactam antibiotics simultaneously. This commentary reviews the emerging evidence and outstanding questions regarding dual β-lactam therapy for
M. abscessus
infections.
The catabolism of ethylene glycol by
Rhodococcus jostii
RHA1 and its dependence on mycofactocin
Authors: Roccor Raphael , Wolf Megan E. , Liu Jie , Eltis Lindsay D.
Published: June 2024

Ethylene glycol (EG) is a widely used industrial chemical with manifold applications and also generated in the degradation of plastics such as polyethylene terephthalate.
Rhodococcus jostii
RHA1 (RHA1), a potential biocatalytic chassis, grows on EG. Transcriptomic analyses revealed four clusters of genes potentially involved in EG catabolism: the
mad
locus, predicted to encode
m
ycofactocin-dependent
a
lcohol
d
egradation, including the catabolism of EG to glycolate; two GCL clusters, predicted to encode glycolate and glyoxylate catabolism; and the
mft
genes, predicted to specify mycofactocin biosynthesis. Bioinformatic analyses further revealed that the
mad
and
mft
genes are widely distributed in mycolic acid-producing bacteria such as RHA1. Neither Δ
madA
nor Δ
mftC
RHA1 mutant strains grew on EG but grew on acetate. In resting cell assays, the Δ
madA
mutant depleted glycolaldehyde but not EG from culture media. These results indicate that
madA
encodes a mycofactocin-dependent alcohol dehydrogenase that initiates EG catabolism. In contrast to some mycobacterial strains, the
mad
genes did not appear to enable RHA1 to grow on methanol as sole substrate. Finally, a strain of RHA1 adapted to grow ~3× faster on EG contained an overexpressed gene,
aldA2
, predicted to encode an aldehyde dehydrogenase. When incubated with EG, this strain accumulated lower concentrations of glycolaldehyde than RHA1. Moreover, ecotopically expressed
aldA2
increased RHA1’s tolerance for EG further suggesting that glycolaldehyde accumulation limits growth of RHA1 on EG. Overall, this study provides insights into the bacterial catabolism of small alcohols and aldehydes and facilitates the engineering of
Rhodococcus
for the upgrading of plastic waste streams.

IMPORTANCE

Ethylene glycol (EG), a two-carbon (C2) alcohol, is produced in high volumes for use in a wide variety of applications. There is burgeoning interest in understanding and engineering the bacterial catabolism of EG, in part to establish circular economic routes for its use. This study identifies an EG catabolic pathway in
Rhodococcus
, a genus of bacteria well suited for biocatalysis. This pathway is responsible for the catabolism of methanol, a C1 feedstock, in related bacteria. Finally, we describe strategies to increase the rate of degradation of EG by increasing the transformation of glycolaldehyde, a toxic metabolic intermediate. This work advances the development of biocatalytic strategies to transform C2 feedstocks.
Lamotrigine-mediated rescue of RsgA-deficient
Escherichia coli
reveals another role of IF2 in ribosome biogenesis
Authors: Singh Sudhir , Singh Jitendra , Varshney Umesh
Published: June 2024

RsgA (small ribosomal subunit, 30S, GTPase), a late-stage biogenesis factor, releases RbfA from 30S-RbfA complex.
Escherichia coli
Δ
rsgA
(deleted for
rsgA
) shows a slow growth phenotype and an increased accumulation of 17S rRNA (precursor of 16S rRNA) and the ribosomal subunits. Here, we show that the rescue of the Δ
rsgA
strain by multicopy
infB
(IF2) is enhanced by simultaneous overexpression of initiator tRNA (i-tRNA), suggesting a role of initiation complex formation in growth rescue. The synergistic effect of IF2/i-tRNA is accompanied by increased processing of 17S rRNA (to 16S), and protection of the 16S rRNA 3′-minor domain. Importantly, we show that an IF2-binding anticonvulsant drug, lamotrigine (Ltg), also rescues the Δ
rsgA
strain growth. The rescue is accompanied by increased processing of 17S rRNA, protection of the 3′-minor domain of 16S rRNA, and increased 70S ribosomes in polysome profiles. However, Ltg becomes inhibitory to the
ΔrsgA
strain whose growth was already rescued by an L83R mutation in
rbfA
. Interestingly, like wild-type
infB
, overproduction of Ltg
R
infB
alleles (having indel mutations in their domain II) also rescues the Δ
rsgA
strain (independent of Ltg). Our observations suggest the dual role of IF2 in rescuing the Δ
rsgA
strain. First, together with i-tRNA, IF2 facilitates the final steps of processing of 17S rRNA. Second, a conformer of IF2 functionally compensates for RsgA, albeit poorly, during 30S biogenesis.

IMPORTANCE

RsgA is a late-stage ribosome biogenesis factor. Earlier,
infB
(IF2) was isolated as a multicopy suppressor of the
Escherichia coli
Δ
rsgA
strain. How IF2 rescued the strain growth remained unclear. This study reveals that (i) the multicopy
infB
-mediated growth rescue of
E. coli
Δ
rsgA
and the processing of 17S precursor to 16S rRNA in the strain are enhanced upon simultaneous overexpression of initiator tRNA and (ii) a conformer of IF2, whose occurrence increases when IF2 is overproduced or when
E. coli
Δ
rsgA
is treated with Ltg (an anticonvulsant drug that binds to domain II of IF2), compensates for the function of RsgA. Thus, this study reveals yet another role of IF2 in ribosome biogenesis.
Interferon-γ inducible factor 16 (IFI16) restricts adeno-associated virus type 2 (AAV2) transduction in an immune-modulatory independent way
Authors: Sutter Sereina O. , Tobler Kurt , Seyffert Michael , Lkharrazi Anouk , Zöllig Joël , Schraner Elisabeth M. , Vogt Bernd , Büning Hildegard , Fraefel Cornel
Published: June 2024

We determined the transcription profile of adeno-associated virus type 2 (AAV2)-infected primary human fibroblasts. Subsequent analysis revealed that cells respond to AAV infection through changes in several significantly affected pathways, including cell cycle regulation, chromatin modulation, and innate immune responses. Various assays were performed to validate selected differentially expressed genes and to confirm not only the quality but also the robustness of the raw data. One of the genes upregulated in AAV2-infected cells was interferon-γ inducible factor 16 (IFI16). IFI16 is known as a multifunctional cytosolic and nuclear innate immune sensor for double-stranded as well as single-stranded DNA, exerting its effects through various mechanisms, such as interferon response, epigenetic modifications, or transcriptional regulation. IFI16 thereby constitutes a restriction factor for many different viruses among them, as shown here, AAV2 and thereof derived vectors. Indeed, the post-transcriptional silencing of
IFI16
significantly increased AAV2 transduction efficiency, independent of the structure of the virus/vector genome. We also show that IFI16 exerts its inhibitory effect on AAV2 transduction in an immune-modulatory independent way by interfering with Sp1-dependent transactivation of wild-type AAV2 and AAV2 vector promoters.

IMPORTANCE

Adeno-associated virus (AAV) vectors are among the most frequently used viral vectors for gene therapy. The lack of pathogenicity of the parental virus, the long-term persistence as episomes in non-proliferating cells, and the availability of a variety of AAV serotypes differing in their cellular tropism are advantageous features of this biological nanoparticle. To deepen our understanding of virus-host interactions, especially in terms of antiviral responses, we present here the first transcriptome analysis of AAV serotype 2 (AAV2)-infected human primary fibroblasts. Our findings indicate that interferon-γ inducible factor 16 acts as an antiviral factor in AAV2 infection and AAV2 vector-mediated cell transduction in an immune-modulatory independent way by interrupting the Sp1-dependent gene expression from viral or vector genomes.
An efficient
trans
complementation system for
in vivo
replication of defective poliovirus mutants
Authors: Arita Minetaro
Published: June 2024

The picornavirus genome encodes a large, single polyprotein that is processed by viral proteases to form an active replication complex. The replication complex is formed with the viral genome, host proteins, and viral proteins that are produced/translated directly from each of the viral genomes (viral proteins provided in
cis
). Efficient complementation
in vivo
of replication complex formation by viral proteins provided in
trans
, thus exogenous or ectopically expressed viral proteins, remains to be demonstrated. Here, we report an efficient
trans
complementation system for the replication of defective poliovirus (PV) mutants by a viral polyprotein precursor in HEK293 cells. Viral 3AB in the polyprotein, but not 2BC, was processed exclusively in
cis
. Replication of a defective PV replicon mutant, with a disrupted cleavage site for viral 3C
pro
protease between 3C
pro
and 3D
pol
(3C/D[A/G] mutant) could be rescued by a viral polyprotein provided in
trans
. Only a defect of 3D
pol
activity of the replicon could be rescued in
trans
; inactivating mutations in 2C
ATPase/hel
, 3B, and 3C
pro
of the replicon completely abrogated the
trans
-rescued replication. An intact N-terminus of the 3C
pro
domain of the 3CD
pro
provided in
trans
was essential for the
trans
-active function. By using this
trans
complementation system, a high-titer defective PV pseudovirus (PV
pv
) (>10
7
infectious units per mL) could be produced with the defective mutants, whose replication was completely dependent on
trans
complementation. This work reveals potential roles of exogenous viral proteins in PV replication and offers insights into protein/protein interaction during picornavirus infection.

IMPORTANCE

Viral polyprotein processing is an elaborately controlled step by viral proteases encoded in the polyprotein; fully processed proteins and processing intermediates need to be correctly produced for replication, which can be detrimentally affected even by a small modification of the polyprotein. Purified/isolated viral proteins can retain their enzymatic activities required for viral replication, such as protease, helicase, polymerase, etc. However, when these proteins of picornavirus are exogenously provided (provided in
trans
) to the viral replication complex with a defective viral genome, replication is generally not rescued/complemented, suggesting the importance of viral proteins endogenously provided (provided in
cis
) to the replication complex. In this study, I discovered that only the viral polymerase activity of poliovirus (PV) (the typical member of picornavirus family) could be efficiently rescued by exogenously expressed viral proteins. The current study reveals potential roles for exogenous viral proteins in viral replication and offers insights into interactions during picornavirus infection.
Shotgun metagenomic sequencing of swab samples from Japanese university campuses
Authors: Tsujimoto Megumu , Dewi Dewa A. P. Rasmika , Mason Christopher E. , Shiwa Yuh , Suzuki Haruo
Published: June 2024

We obtained shotgun metagenome sequences from swab samples obtained through 3-minute swabbing of different surfaces and the air within buildings at three university campuses in part of the Greater Tokyo Area in Japan. These data aid in understanding built environment microbial communities and elucidate various microbial profiles across different locations.
Exploring the potential of isorhapontigenin: attenuating
Staphylococcus aureus
virulence through MgrA-mediated regulation
Authors: Yuan Lei , Xi Huimin , Luo Zhaoxia , Liu Mei-fang , Chen Qiang , Zhu Qing , Zhao Rui , Sheng Yi-yun
Published: June 2024

The emerging prevalence of drug-resistant
Staphylococcus aureus
isolates underscores the urgent need for alternative therapeutic strategies due to the declining effectiveness of traditional antibiotics in clinical settings. MgrA, a key virulence regulator in
S. aureus
, orchestrates the expression of numerous virulence factors. Here, we report the discovery of isorhapontigenin, a methoxylated analog of resveratrol, as a potential anti-virulence agent against
S. aureus
. Isorhapontigenin effectively inhibits the hemolytic activity of
S. aureus
in a non-bactericidal manner. Additionally, it significantly reduces the cytotoxicity of
S. aureus
and impairs its ability to survive in macrophages. Mechanistically, isorhapontigenin modulates the expression of virulence factors, dose-dependently downregulating
hla
and upregulating the MgrA-regulated gene
spa
. Electrophoretic mobility shift assays demonstrated that isorhapontigenin inhibits the binding of MgrA to the
hla
promoter in a dose-dependent manner. Thermal shift assays confirmed the direct interaction between isorhapontigenin and the MgrA protein. The
in vivo
experiments demonstrated that isorhapontigenin significantly reduced the area of skin abscesses and improved survival in a pneumonia model while decreasing bacterial burden and inflammation in the lungs. In conclusion, isorhapontigenin holds potential as a candidate drug for further development as an anti-virulence agent for treating
S. aureus
infections.

IMPORTANCE

The emergence of antibiotic-resistant
Staphylococcus aureus
strains presents a formidable challenge to public health, necessitating novel approaches in combating these pathogens. Traditional antibiotics are becoming increasingly ineffective, leading to a pressing need for innovative therapeutic strategies. In this study, targeting virulence factors that play a crucial role in the pathogenesis of bacterial infections offers a promising alternative to circumvent resistance mechanisms. The discovery of isorhapontigenin as an inhibitor of
S. aureus
virulence represents a significant advance in anti-virulence therapy.
Expanded trade: tripartite interactions in the mycorrhizosphere
Authors: Charakas Christos , Khokhani Devanshi
Published: June 2024

Interactions between arbuscular mycorrhizal fungi (AMF), plants, and the soil microbial community have the potential to increase the availability and uptake of phosphorus (P) and nitrogen (N) in agricultural systems. Nutrient exchange between plant roots, AMF, and the adjacent soil microbes occurs at the interface between roots colonized by mycorrhizal fungi and soil, referred to as the mycorrhizosphere. Research on the P exchange focuses on plant–AMF or AMF–microbe interactions, lacking a holistic view of P exchange between the plants, AMF, and other microbes. Recently, N exchange at both interfaces revealed the synergistic role of AMF and bacterial community in N uptake by the host plant. Here, we highlight work carried out on each interface and build upon it by emphasizing research involving all members of the tripartite network. Both nutrient systems are challenging to study due to the complex chemical and biological nature of the mycorrhizosphere. We discuss some of the effective methods to identify important nutrient processes and the tripartite members involved in these processes. The extrapolation of
in vitro
studies into the field is often fraught with contradiction and noise. Therefore, we also suggest some approaches that can potentially bridge the gap between laboratory-generated data and their extrapolation to the field, improving the applicability and contextual relevance of data within the field of mycorrhizosphere interactions. Overall, we argue that the research community needs to adopt a holistic tripartite approach and that we have the means to increase the applicability and accuracy of
in vitro
data in the field.
Isoforms of the Cytoskeletal LIM-Domain Protein Zyxin in the Early Embryogenesis of Xenopus laevis
Authors: Ivanova E. D. , Parshina E. A. , Zaraisky A. G. , Martynova N. Y.
Published: June 2024

Objective: The study of highly conserved mechanosensitive proteins, such as zyxin, is essential due to their role in shaping embryos of all animals during embryogenesis through coordinated morphogenetic processes and controlled cell differentiation. This study aims to identify endogenous zyxin isoforms in Xenopus laevis and investigate changes in their abundance and intracellular localization during embryogenesis. Methods: Endogenous proteins were primarily detected using specific antibodies. Polyclonal antibodies targeting the C-terminal region of zyxin containing the NES and three LIM domains (438–663 aa), as well as antibodies against the N-terminal proline-rich region of Zyxin (1–373 aa) crucial for interactions with actinin and cytoskeletal proteins, were employed. Western blotting with these antibodies was conducted on Xenopus laevis embryo cell samples after fractionation into nuclear and cytoplasmic fractions. Results and Discussion: The study revealed multiple isoforms of zyxin in Xenopus laevis, including a full-length modified protein (105 kDa), an unmodified form (70 kDa), and two truncated forms of 45 and 37 kDa. The number and subcellular distribution of the truncated forms were found to vary based on the developmental stage, with increased levels of the 45 and 37 kDa isoforms observed in the early stages. Conclusions: This work provides novel insights into changes in the abundance and localization of zyxin isoforms during embryonic development, shedding light on the dynamics of this mechanosensitive protein in the embryo.
A New Protein Glosaxin Composed of Noncatalytic Domains of Class PIII Metalloproteinase from the Pit Viper Gloydius saxatilis Venom Inhibits Nicotinic Acetylcholine Receptor
Authors: Osipov A. V. , Kryukova E. V. , Ojomoko L. O. , Shelukhina I. V. , Ziganshin R. H. , Starkov V. G. , Andreeva T. V. , Tsetlin V. I. , Utkin Yu. N.
Published: June 2024

Objective: Although main components of the venoms from Viperidae snakes are hemotoxins, several studies indicate the presence of neurotoxins in these venoms. We previously found that the venom of pit viper Gloydius saxatilis inhibited the muscle-type nicotinic acetylcholine receptor (nAChR). The objective of present work is to isolate and characterize a neurotoxic protein from this venom. Methods: The protein was isolated by liquid chromatography and characterized using high resolution mass-spectrometry. Results and Discussion: The isolated protein called glosaxin inhibited the binding of the α-bungarotoxin to the nAChR of muscle type from Torpedo californica. Investigation of the amino acid sequence of the isolated protein by high resolution mass spectrometry and the subsequent bioinformatic analysis showed that it is homologous to the amino acid sequences of disintegrin-like proteins, consisting of non-catalytic domains of class PIII metalloproteinases from the venom of pit vipers of genus Gloydius. Glosaxin was shown to inhibit the binding of α-bungarotoxin to T. californica nAChR with IC50 = 51 μM. It also inhibited ACh-induced functional responses of the human neuronal nAChR of α3β2 subtype. Conclusions: This is the first evidence for the ability of proteins consisting of non-catalytic domains of snake venom class PIII metalloproteinase to inhibit the nAChR.
Digital ray: enhancing cataractous fundus images using style transfer generative adversarial networks to improve retinopathy detection
Authors: Liu Lixue , Hong Jiaming , Wu Yuxuan , Liu Shaopeng , Wang Kai , Li Mingyuan , Zhao Lanqin , Liu Zhenzhen , Li Longhui , Cui Tingxin , Tsui Ching-Kit , Xu Fabao , Hu Weiling , Yun Dongyuan , Chen Xi , Shang Yuanjun , Bi Shaowei , Wei Xiaoyue , Lai Yunxi , Lin Duoru , Fu Zhe , Deng Yaru , Cai Kaimin , Xie Yi , Cao Zizheng , Wang Dongni , Zhang Xulin , Dongye Meimei , Lin Haotian , Wu Xiaohang
Published: June 2024

Background/aims

The aim of this study was to develop and evaluate digital ray, based on preoperative and postoperative image pairs using style transfer generative adversarial networks (GANs), to enhance cataractous fundus images for improved retinopathy detection.

Methods

For eligible cataract patients, preoperative and postoperative colour fundus photographs (CFP) and ultra-wide field (UWF) images were captured. Then, both the original CycleGAN and a modified CycleGAN (C2ycleGAN) framework were adopted for image generation and quantitatively compared using Frechet Inception Distance (FID) and Kernel Inception Distance (KID). Additionally, CFP and UWF images from another cataract cohort were used to test model performances. Different panels of ophthalmologists evaluated the quality, authenticity and diagnostic efficacy of the generated images.

Results

A total of 959 CFP and 1009 UWF image pairs were included in model development. FID and KID indicated that images generated by C2ycleGAN presented significantly improved quality. Based on ophthalmologists’ average ratings, the percentages of inadequate-quality images decreased from 32% to 18.8% for CFP, and from 18.7% to 14.7% for UWF. Only 24.8% and 13.8% of generated CFP and UWF images could be recognised as synthetic. The accuracy of retinopathy detection significantly increased from 78% to 91% for CFP and from 91% to 93% for UWF. For retinopathy subtype diagnosis, the accuracies also increased from 87%–94% to 91%–100% for CFP and from 87%–95% to 93%–97% for UWF.

Conclusion

Digital ray could generate realistic postoperative CFP and UWF images with enhanced quality and accuracy for overall detection and subtype diagnosis of retinopathies, especially for CFP.\

Trial registration number

This study was registered with ClinicalTrials.gov (NCT05491798).
Hospitals as medical device manufacturers: keeping to the Medical Device Regulation (MDR) in the EU
Authors: Boyle Gerard , Melvin Tom , Verdaasdonk Rudolf M , Van Boxtel Robert A , Reilly Richard B
Published: June 2024

In the European Union, the introduction of the Medical Device Regulation (MDR) 2017/745 in 2021 increased the regulatory requirements for ‘in-hospital’ manufacture of medical devices. Depending on the exact scenario, a hospital manufacturing devices will need to consider applying one of three sets of regulatory requirements defined in the MDR: a reduced set of rules called the ‘health institution exemption’, which can be availed of under certain conditions; rules that apply for the manufacture of custom-made devices; or, exceptionally and most onerously, the same ‘full’ set of rules that apply to commercial medical device manufacturers. The purpose of this discussion is to provide an introductory guide to compliance with the MDR for in-hospital manufacture, highlighting the main regulatory requirements and the factors which determine which of the three ‘routes’ is the most appropriate.