bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiple genotypes of a quarantine plant pathogen detected in New Zealand indigenous plants located in a botanical garden overseas
Authors: Visnovsky Sandra B. , Kahn Alexandra K. , Nieto‐Jacobo Fernanda , Panda Preeti , Thompson Sarah , Teulon David A. J. , Bojanini Molina Isabel , Marroni M. Virginia , Groenteman Ronny , Rigano Luciano A. , Taylor Robert K. , Forbes Holly , Almeida Rodrigo P. P. 
Published: October 2024

AbstractXylella fastidiosa is a xylem‐limited bacterial plant pathogen transmitted by insect vectors. It infects a wide range of plant species and causes devastating diseases. Botanical gardens are global repositories of plant diversity exposed to local biotic and abiotic stresses. We used molecular diagnostic tools for the detection of X. fastidiosa in a collection of New Zealand indigenous plants grown in a X. fastidiosa‐infected Californian area to determine if any species were infected with this bacterial pathogen and to help inform biosecurity responses. To this end, 130 New Zealand indigenous plant species comprising 72 genera, growing in the University of California Botanical Garden at Berkeley, California, were screened for X. fastidiosa. Multiple PCR‐based methods were used to detect the pathogen at the subspecies and sequence‐type levels directly from plant material; nine plant species tested positive by at least two PCR‐based methods. All nine infections were identified as X. fastidiosa subsp. multiplex sequence types 6 or 7 by the amplification of seven housekeeping genes. Three strains were cultured in vitro and their whole genome sequences were obtained; these strains belonged to three distinct clades within subspecies multiplex, indicating that the infections were not transmitted among these New Zealand indigenous plant species. The information gathered in this study will help to assess the risk of X. fastidiosa to New Zealand indigenous flora and the potential spillover to crops of agricultural importance. The work also shows the applied value of botanical garden collections as sentinels for international plant pathogen biosecurity risk assessment.
The integration of the ecosystem approach in the BBNJ agreement—An initial assessment of limits and opportunities
Authors: De Lucia Vito 
Published: October 2024

AbstractThis paper carries out an initial assessment of the integration of the ecosystem approach in the recently adopted agreement on the conservation and sustainable use of marine biodiversity in areas beyond national jurisdiction (BBNJ). The analysis seeks to assess whether or not such integration is likely to be effective. In this respect, this paper follows up on earlier analyses offered during the negotiating process and aims at offering some initial considerations on, and reactions to, the final text of the BBNJ agreement, in order to map the limits of this integration and the opportunities it may offer, for an effective implementation of the ecosystem approach in the context of the BBNJ agreement, focussing especially on article 7 (on general principles and approaches), on part III (on area‐based management tools, including marine protected areas) and part IV (on environmental impact assessments) with specific focus on strategic environmental assessment.
Inter‐Individual Variability in Muscle Fiber–Type Distribution Affects Running Economy but Not Running Gait at Submaximal Running Speeds
Authors: Swinnen Wannes , Lievens Eline , Hoogkamer Wouter , De Groote Friedl , Derave Wim , Vanwanseele Benedicte 
Published: October 2024

ABSTRACTRunning economy is an important determinant of endurance running performance, yet insights into characteristics contributing to its inter‐individual variability remain limited. Although slow‐twitch muscle fibers are more energy‐efficient than fast‐twitch fibers during the (near‐)isometric contractions common during submaximal running, current literature lacks a consensus on whether a relationship between muscle fiber–type distribution and running economy exists. This study aims to resolve the ongoing debate by addressing potential confounding factors often overlooked in prior research, such as the effect of different running speeds, the homogeneity of investigated groups, and the potential impact of the adopted running gait. We selected two groups with predetermined distinct muscle fiber–type distribution in their triceps surae muscle by measurement of carnosine via 1H‐MRS, one predominantly slow (ST; n = 11; carnosine z‐score = −1.31) and the other predominantly fast (FT; n = 10; z‐score = 0.83). Across a range of running speeds (2–4 m/s), we measured running economy (W/kg) through indirect calorimetry, along with running kinematics, kinetics and muscle activity of the lower limb. The ST‐group exhibited, on average, 7.8% better running economy than the FT‐group (p = 0.01) and this difference was consistent across speeds. Both groups demonstrated almost identical kinematics, kinetics, and muscle activity patterns across submaximal running speeds. Overall, our findings indicate that distinct muscle fiber–type distribution explains some of the observed variability in running economy, for which a predominance of energy‐efficient slow‐twitch fibers appear beneficial. In contrast, muscle fiber–type distribution does not affect running gait substantially.
Are Low‐Income Groups More Dependent on Community Space? A Case Study of Nanjing
Authors: Wang Hui , Kwan Mei‐Po , Hu Mingxing , Qiu Bing 
Published: October 2024

AbstractCommunity dependence reflects individuals' daily needs for community space and facilities and is closely related to the accurate allocation of social resources and human quality of life. This study examines the differences in community use and dependence among different income groups at the overall and community levels from the perspective of the microscale individual activity space. Compared with non‐low‐income groups, low‐income groups are generally more dependent on their communities during their daily lives. However, these differences are diverse among different communities; they are more moderate among different income groups in communities located in central city areas and significant among different income groups in suburban affordable housing communities. The regression models reveal that in addition to income, the characteristics of activities and built environment attributes also affect individuals' community dependence. Social policies should prioritize the quality and quantity of community resources for vulnerable suburban groups.
New Municipalism and the Challenges of Design: Context, Instruments and Implementation
Authors: Ahn Byeongsun , Kazepov Yuri 
Published: October 2024

AbstractThis contribution adds a design approach to our understanding of emancipatory epistemologies within new municipalism. So far, the extant research has rarely discussed its specific opportunities and limitations, regarding their context‐bound formulation and real‐world implementation as a policy process. In contrast, the following article situates their emancipatory potential within the place‐specific ways in which multiple stakeholders define problems, set objectives, choose instruments and convert them into actions, intersecting with significant capacity constraints of the municipal scale. The case of participatory budgeting in Vienna illustrates our approach and theoretical reflection. It shows how and to what extent the design of the relational process influences new municipalism in practice and its outcome with respect to agenda‐setting, formulation and implementation. It concludes by highlighting the contribution of a design approach to the production of emancipatory knowledge and practices in democratic transformation and its analytical value added for comparative research on new municipalism.
A transcriptome atlas of zygotic and somatic embryogenesis in Norway spruce
Authors: Stojkovič Katja , Canovi Camilla , Le Kim‐Cuong , Ahmad Iftikhar , Gaboreanu Ioana , Johansson Sofie , Delhomme Nicolas , Egertsdotter Ulrika , Street Nathaniel R. 
Published: October 2024

SUMMARYSomatic embryogenesis (SE) is a powerful model system for studying embryo development and an important method for scaling up availability of elite and climate‐adapted genetic material of Norway spruce (Picea abies L. Karst). However, there are several steps during the development of the somatic embryo (Sem) that are suboptimal compared to zygotic embryo (Zem) development. These differences are poorly understood and result in substantial yield losses during plant production, which limits cost‐effective large‐scale production of SE plants. This study presents a comprehensive data resource profiling gene expression during zygotic and somatic embryo development to support studies aiming to advance understanding of gene regulatory programmes controlling embryo development. Transcriptome expression patterns were analysed during zygotic embryogenesis (ZE) in Norway spruce, including separated samples of the female gametophytes and Zem, and at multiple stages during SE. Expression data from eight developmental stages of SE, starting with pro‐embryogenic masses (PEMs) up until germination, revealed extensive modulation of the transcriptome between the early and mid‐stage maturing embryos and at the transition of desiccated embryos to germination. Comparative analysis of gene expression changes during ZE and SE identified differences in the pattern of gene expression changes and functional enrichment of these provided insight into the associated biological processes. Orthologs of transcription factors known to regulate embryo development in angiosperms were differentially regulated during Zem and Sem development and in the different zygotic embryo tissues, providing clues to the differences in development observed between Zem and Sem. This resource represents the most comprehensive dataset available for exploring embryo development in conifers.
Identification of lineage‐specific cis–trans regulatory networks related to kiwifruit ripening initiation
Authors: Kuwada Eriko , Takeshita Kouki , Kawakatsu Taiji , Uchida Seiichi , Akagi Takashi 
Published: October 2024

SUMMARYPrevious research on the ripening process of many fruit crop varieties typically involved analyses of the conserved genetic factors among species. However, even for seemingly identical ripening processes, the associated gene expression networks often evolved independently, as reflected by the diversity in the interactions between transcription factors (TFs) and the targeted cis‐regulatory elements (CREs). In this study, explainable deep learning (DL) frameworks were used to predict expression patterns on the basis of CREs in promoter sequences. We initially screened potential lineage‐specific CRE–TF interactions influencing the kiwifruit ripening process, which is triggered by ethylene, similar to the corresponding processes in other climacteric fruit crops. Some novel regulatory relationships affecting ethylene‐induced fruit ripening were identified. Specifically, ABI5‐like bZIP, G2‐like, and MYB81‐like TFs were revealed as trans‐factors modulating the expression of representative ethylene signaling/biosynthesis‐related genes (e.g., ACS1, ERT2, and ERF143). Transient reporter assays and DNA affinity purification sequencing (DAP‐Seq) analyses validated these CRE–TF interactions and their regulatory relationships. A comparative analysis with co‐expression networking suggested that this DL‐based screening can identify regulatory networks independently of co‐expression patterns. Our results highlight the utility of an explainable DL approach for identifying novel CRE–TF interactions. These imply that fruit crop species may have evolved lineage‐specific fruit ripening‐related cis–trans regulatory networks.
All convex bodies are in the subdifferential of some everywhere differentiable locally Lipschitz function
Authors: Daniilidis Aris , Deville Robert , Tapia‐García Sebastián 
Published: October 2024

AbstractWe construct a differentiable locally Lipschitz function in with the property that for every convex body there exists such that coincides with the set of limits of derivatives of sequences converging to . The technique can be further refined to recover all compact connected subsets with nonempty interior, disclosing an important difference between differentiable and continuously differentiable functions. It stems out from our approach that the class of these pathological functions contains an infinite‐dimensional vector space and is dense in the space of all locally Lipschitz functions for the uniform convergence.
Exploration of novel mechanisms of azole resistance in
Candida auris
Authors: Li Jizhou , Brandalise Danielle , Coste Alix T. , Sanglard Dominique , Lamoth Frederic 
Published: October 2024

ABSTRACT

Candida auris
is a pathogenic yeast of particular concern because of its ability to cause nosocomial outbreaks of invasive candidiasis (IC) and to develop resistance to all current antifungal drug classes. Most
C. auris
clinical isolates are resistant to fluconazole, an azole drug that is used for the treatment of IC. Azole resistance may arise from diverse mechanisms, such as mutations of the target gene (
ERG11
) or upregulation of efflux pumps via gain of function mutations of the transcription factors
TAC1
and/or
MRR1
. To explore novel mechanisms of azole resistance in
C. auris
, we applied an
in vitro
evolutionary protocol to induce azole resistance in a
TAC1A
/
TAC1B
/
MRR1
triple-deletion strain. Azole-resistant isolates without
ERG11
mutations were further analyzed. In addition to a whole chromosome aneuploidy of chromosome 5, amino acid substitutions were recovered in the transcription factor Upc2 (N592S, L499F), the ubiquitin ligase complex consisting of Ubr2 (P708T, H1275P) and Mub1 (Y765*), and the mitochondrial protein Mrs7 (D293H). Genetic introduction of these mutations in an azole-susceptible wild-type
C. auris
isolate of clade IV resulted in significantly decreased azole susceptibility. Real-time reverse transcription PCR analyses were performed to assess the impact of these mutations on the expression of genes involved in azole resistance, such as
ERG11
, the efflux pumps
CDR1
and
MDR1
or the transcription factor
RPN4
. In conclusion, this work provides further insights in the complex and multiple pathways of azole resistance of
C. auris
. Further analyses would be warranted to assess their respective role in azole resistance of clinical isolates.
Application of sodium hypochlorite for human norovirus and hepatitis A virus inactivation in groundwater
Authors: Jeon Eun Bi , Roy Anamika , Park Shin Young 
Published: October 2024

ABSTRACT

In this study, the effect of sodium hypochlorite (10–200 ppm of Cl
2
) on the inactivation of human norovirus (HuNV) GII.4 and hepatitis A virus (HAV) in groundwater was investigated using propidium monoazide (PMA)/reverse transcription quantitative real-time PCR (RT-qPCR). Initially, 4.00 log
10
genome copies/μL of HuNV GII.4 or 5.50 log
10
genome copies/μL of HAV were artificially inoculated in groundwater. The titers of HuNV GII.4 and HAV decreased significantly (
P
< 0.05) with increasing Cl
2
concentrations. Groundwater was treated with 10, 30, 50, 100, 150, and 200 ppm of Cl
2
, and the viable HuNV GII.4 was significantly (
P
< 0.05) reduced to 3.28 (0.21-log reduction), 3.18 (0.31-log reduction), 3.01 (0.48 log reduction), 2.75 (0.74 log reduction), 2.54 (0.95 log reduction), and 2.34 (1.15 log reduction) log
10
genome copies/μL, respectively. The viable HAV was also significantly (
P
< 0.05) reduced to 4.99 (0.23 log reduction), 4.76 (0.46 log reduction), 4.55 (0.67 log reduction), 4.21 (1.01-log reduction), 3.89 (1.33 log reduction), and 3.64 (1.58 log reduction) log
10
genome copies/μL, respectively. The decimal reduction times (
D
values) (1-log
10
genome reduction) of HuNV GII.4 and HAV infectivity in groundwater were predicted as 116.7 and 98.9 ppm of Cl
2
, respectively, using the first-order kinetics model (HuNV GII.4:
y
= −0.0054
x
+ 3.3585, correlation coefficient (
R
2
) = 0.97; HAV:
y
= −0.0091
x
+ 5.0470,
R
2
= 0.97). The result specifically suggests that 150- to 200-ppm Cl
2
can potentially be used for the inactivation of >1-log
10
genome copy/μL HuNV GII.4 and HAV in groundwater.

IMPORTANCE
Groundwater represents a vital component of the global water supply, serving as a crucial source of potable water for humans. It serves as a source of potable water for up to 50% of the global population and accounts for 43% of all water used for irrigation. It thus follows that the sustainable management of groundwater represents a pivotal solution. However, the regrowth of pathogens in water that is not treated with chlorine or where proper residual chlorine is not maintained represents a risk to public health.
PEDV evades MHC-I-related immunity through nsp1-mediated NLRC5 translation inhibition
Authors: Liu Xiang , Zhang Meng , Yin Lingdan , Kang Li , Luo Yi , Wang Xiaodong , Ren Li , Zhang Guozhong , Yao Yao , Liu Pinghuang 
Published: October 2024

ABSTRACT

Major histocompatibility complex class I (MHC-I) plays crucial roles against viral infections not only by initiating CD8
+
T cell immunity but also by modulating natural killer (NK) cell cytotoxicity. Understanding how viruses precisely regulate MHC-I to optimize their infection is important; however, the manipulation of MHC-I molecules by porcine epidemic diarrhea virus (PEDV) remains unclear. In this study, we demonstrate that PEDV infection promotes the transcription of NLRC5, a key transactivator of MHC-I, in several porcine cell lines and
in vivo
. Paradoxically, no increase in MHC-I expression is observed after PEDV infection both
in vitro
and
in vivo
. Mechanistic studies revealed that PEDV infection inhibits the translation of PEDV-elicited NLRC5 mRNA and the expression of downstream MHC-I proteins, without affecting the expression of physiological NLRC5 and MHC-I proteins. Through viral protein screening, we identified PEDV nonstructural protein 1 (nsp1) as the critical antagonist that inhibits NLRC5-mediated upregulation of MHC-I, and the nsp1’s inhibitory effect on MHC-I requires the motif of 15 amino acids at its C-terminus. Notably, our results revealed that the cytotoxic ability of NK cells against PEDV-infected cells is similar to that against healthy cells. Collectively, our findings uncover an immune evasion mechanism by which PEDV-infected cells masquerade as healthy cells to evade NK and T cell immunity. This is achieved by targeting NLRC5, a key MHC-I transcriptional regulator, via nsp1.

IMPORTANCE

Porcine epidemic diarrhea virus (PEDV) is a highly contagious enteric coronavirus that inflicts substantial financial losses on the swine industry. Major histocompatibility complex class I (MHC-I) is a critical factor influencing both CD8
+
T cell and natural killer (NK) cell immunity. However, how PEDV manipulates MHC-I expression to optimize its infection process remains largely unknown. In this study, we demonstrate that PEDV’s nonstructural protein 1 (nsp1) inhibits virus-mediated induction of MHC-I expression by directly targeting NLRC5, a key MHC-I transactivator. Intriguingly, nsp1 does not reduce physiological NLRC5 and MHC-I expression. This selective inhibition of virus-elicited NLRC5 mRNA translation allows PEDV-infected cells to masquerade as healthy cells, thereby evading CD8
+
T cell and NK cell cytotoxicity. Our findings provide unique insights into the mechanisms by which PEDV evades CD8
+
T cell and NK cell immunity.
SydR, a redox-sensing MarR-type regulator of
Sinorhizobium meliloti
, is crucial for symbiotic infection of
Medicago truncatula
roots
Authors: Nazaret Fanny , Farajzadeh Davoud , Mejias Joffrey , Pacoud Marie , Cosi Anthony , Frendo Pierre , Alloing Geneviève , Mandon Karine 
Published: October 2024

ABSTRACT

Rhizobia associate with legumes and induce the formation of nitrogen-fixing nodules. The regulation of bacterial redox state plays a major role in symbiosis, and reactive oxygen species produced by the plant are known to activate signaling pathways. However, only a few redox-sensing transcriptional regulators (TRs) have been characterized in the microsymbiont. Here, we describe SydR, a novel redox-sensing TR of
Sinorhizobium meliloti
that is essential for the establishment of symbiosis with
Medicago truncatula
. SydR, a MarR-type TR, represses the expression of the adjacent gene SMa2023 in growing cultures, and this repression is alleviated by NaOCl,
tert-
butyl hydroperoxide, or H
2
O
2
treatment. Transcriptional
psydR-gfp
and
p
SMa2023-
gfp
fusions, as well as gel shift assays, showed that SydR binds two independent sites of the
sydR
-SMa2023 intergenic region. This binding is redox-dependent, and site-directed mutagenesis demonstrated that the conserved C16 is essential for SydR redox sensing. The inactivation of
sydR
did not alter the sensitivity of
S. meliloti
to NaOCl,
tert
-butyl hydroperoxide, or H
2
O
2
, nor did it affect the response to oxidants of the roGFP2-Orp1 redox biosensor expressed within bacteria. However,
in planta
, Δ
sydR
mutation impaired the formation of root nodules. Microscopic observations and analyses of plant marker gene expression showed that the Δ
sydR
mutant is defective at an early stage of the bacterial infection process. Altogether, these results demonstrated that SydR is a redox-sensing MarR-type TR that plays a key role in the regulation of nitrogen-fixing symbiosis with
M. truncatula
.

IMPORTANCE

The nitrogen-fixing symbiosis between rhizobia and legumes has an important ecological role in the nitrogen cycle, contributes to nitrogen enrichment of soils, and can improve plant growth in agriculture. This interaction is initiated in the rhizosphere by a molecular dialog between the two partners, resulting in plant root infection and the formation of root nodules, where bacteria reduce the atmospheric nitrogen into ammonium. This symbiosis involves modifications of the bacterial redox state in response to reactive oxygen species produced by the plant partner. Here, we show that SydR, a transcriptional regulator of the
Medicago
symbiont
Sinorhizobium meliloti
, acts as a redox-responsive repressor that is crucial for the development of root nodules and contributes to the regulation of bacterial infection in
S. meliloti/Medicago truncatula
symbiotic interaction.
Emerging mosquito-borne flaviviruses
Authors: Nelson Amy N. , Ploss Alexander 
Published: October 2024

ABSTRACT

Flaviviruses comprise a genus of enveloped, positive-sense, single-stranded RNA viruses typically transmitted between susceptible and permissive hosts by arthropod vectors. Established flavivirus threats include dengue viruses (DENV), yellow fever virus (YFV), Zika virus (ZIKV), and West Nile virus (WNV), which continue to cause over 400 million infections annually and are significant global health and economic burdens. Additionally, numerous closely related but largely understudied viruses circulate in animals and can conceivably emerge in human populations. Previous flaviviruses that were recognized to have this potential include ZIKV and WNV, which only became extensively studied after causing major outbreaks in humans. More than 50 species exist within the flavivirus genus, which can be further classified as mosquito-borne, tick-borne, insect-specific, or with no known vector. Historically, many of these flaviviruses originated in Africa and have mainly affected tropical and subtropical regions due to the ecological niche of mosquitoes. However, climate change, as well as vector and host migration, has contributed to geographical expansion, thereby posing a potential risk to global populations. For the purposes of this minireview, we focus on the mosquito-borne subgroup and highlight viruses that cause significant pathology or lethality in at least one animal species and/or have demonstrated an ability to infect humans. We discuss current knowledge of these viruses, existing animal models to study their pathogenesis, and potential future directions. Emerging viruses discussed include Usutu virus (USUV), Wesselsbron virus (WSLV), Spondweni virus (SPOV), Ilheus virus (ILHV), Rocio virus (ROCV), Murray Valley encephalitis virus (MVEV), and Alfuy virus (ALFV).