bluuebunny/crossref_metadata_2025_split huggingface dataset:
Elevated temperature alters bacterial community from mutualism to antagonism with
Skeletonema costatum
: insights into the role of a novel species,
Tamlana
sp. MS1
Authors: Lin Tenghui , Feng Yumeng , Miao Wenfei , Wang Shuqi , Bao Zhen , Shao Zeyuan , Zhang Demin , Wang Xinwei , Jiang Haibo , Zhang Huajun 
Published: June 2024

ABSTRACT

Skeletonema costatum
, a cosmopolitan diatom primarily inhabiting coastal ecosystems, exhibits a typically close yet variable relationship with heterotrophic bacteria. The increasing temperature of surface seawater is expected to substantially affect the viability and ecological dynamics of
S. costatum
, potentially altering its relationship with bacteria. However, it remains unclear to what extent the elevated temperature could change these relationships. Here, the relationship between axenic
S. costatum
and natural seawater bacteria underwent a dramatic shift from mutualism to antagonism as the co-culture temperature increased from 20°C to 25°C. The co-occurrence network indicated significantly increased complexity of interaction between
S. costatum
and bacteria community after temperature elevation, especially with
Flavobacteriaceae
, implying their potential role in eliminating
S. costatum
under higher temperatures. Additionally, a
Flavobacteriaceae
isolate, namely MS1 identified as
Tamlana
genus, was isolated from the co-culture system at 25°C. MS1 had a remarkable ability to eliminate
S. costatum
, with the mortality rate at 25°C steadily rising from 30.2% at 48 h to 92.4% at 120 h. However, it promoted algal growth to some extent at 20°C. These results demonstrated that increased temperature promotes MS1 shifts from mutualism to antagonism with
S. costatum
. According to the comparative genomics analysis, changes in the lifestyle of MS1 were attributed to the increased gliding motility and attachment of MS1 under elevated temperature, enabling it to exert an algicidal effect through direct contact with alga. This investigation provided an advanced understanding of interactions between phytoplankton and bacteria in future warming oceanic ecosystems.

IMPORTANCE

Ocean warming profoundly influences the growth and metabolism of phytoplankton and bacteria, thereby significantly reshaping their interactions. Previous studies have shown that warming can change bacterial lifestyle from mutualism to antagonism with phytoplankton, but the underlying mechanism remains unclear. In this study, we found that high temperature promotes
Tamlana
sp. MS1 adhesion to
Skeletonema costatum
, leading to algal lysis through direct contact, demonstrating a transition in lifestyle from mutualism to antagonism with increasing temperature. Furthermore, the gliding motility of MS1 appears to be pivotal in mediating the transition of its lifestyle. These findings not only advance our understanding of the phytoplankton-bacteria relationship under ocean warming but also offer valuable insights for predicting the impact of warming on phytoplankton carbon sequestration.
Probing gene function in
Candida albicans
wild-type strains by Cas9-facilitated one-step integration of two dominant selection markers: a systematic analysis of recombination events at the target locus
Authors: Ramírez-Zavala Bernardo , Hoffmann Anna , Krüger Ines , Schwanfelder Sonja , Barker Katherine S. , Rogers P. David , Morschhäuser Joachim 
Published: June 2024

ABSTRACT

The adaptation of gene deletion methods based on the CRISPR-Cas9 system has facilitated the genetic manipulation of the pathogenic yeast
Candida albicans
, because homozygous mutants of this diploid fungus can now be generated in a single step, allowing the rapid screening of candidate genes for their involvement in a phenotype of interest. However, the Cas9-mediated double-strand breaks at the target site may result in an undesired loss of heterozygosity (LOH) on the affected chromosome and cause phenotypic alterations that are not related to the function of the investigated gene. In our present study, we harnessed Cas9-facilitated gene deletion to probe a set of genes that are constitutively overexpressed in strains containing hyperactive forms of the transcription factor Mrr1 for a possible contribution to the fluconazole resistance of such strains. To this aim, we used gene deletion cassettes containing two different dominant selection markers,
caSAT1
and
HygB
, which confer resistance to nourseothricin and hygromycin, respectively, for simultaneous genomic integration in a single step, hypothesizing that this would minimize undesired LOH events at the target locus. We found that selection for resistance to both nourseothricin and hygromycin strongly increased the proportion of homozygous deletion mutants among the transformants compared with selection on media containing only one of the antibiotics, but it did not avoid undesired LOH events. Our results demonstrate that LOH on the target chromosome is a significant problem when using Cas9 for the generation of
C. albicans
gene deletion mutants, which demands a thorough examination of recombination events at the target site.

IMPORTANCE

Candida albicans
is one of the medically most important fungi and a model organism to study fungal pathogenicity. Investigating gene function in this diploid yeast has been facilitated by the adaptation of gene deletion methods based on the bacterial CRISPR-Cas9 system, because they enable the generation of homozygous mutants in a single step. We found that, in addition to increasing the efficiency of gene replacement by selection markers, the Cas9-mediated double-strand breaks also result in frequent loss of heterozygosity on the same chromosome, even when two different selection markers were independently integrated into the two alleles of the target gene. Since loss of heterozygosity for other genes can result in phenotypic alterations that are not caused by the absence of the target gene, these findings show that it is important to thoroughly analyze recombination events at the target locus when using Cas9 to generate gene deletion mutants in
C. albicans
.
Two high-quality
Prototheca zopfii
genomes provide new insights into their evolution as obligate algal heterotrophs and their pathogenicity
Authors: Jian Jianbo , Wang Zhaoyang , Chen Chunhai , Workman Christopher T. , Fang Xiaodong , Larsen Thomas Ostenfeld , Guo Jian , Sonnenschein Eva C. 
Published: June 2024

ABSTRACT

The majority of the nearly 10,000 described species of green algae are photoautotrophs; however, some species have lost their ability to photosynthesize and become obligate heterotrophs that rely on parasitism for survival. Two high-quality genomes of the heterotrophic algae
Prototheca zopfii
Pz20 and Pz23 were obtained using short- and long-read genomic as well as transcriptomic data. The genome sizes were 31.2 Mb and 31.3 Mb, respectively, and contig N50 values of 1.99 Mb and 1.26 Mb. Although
P. zopfii
maintained its plastid genome, the transition to heterotrophy led to a reduction in both plastid and nuclear genome size, including the loss of photosynthesis-related genes from both the nuclear and plastid genomes and the elimination of genes encoding for carotenoid oxygenase and pheophorbide an oxygenase. The loss of genes, including basic leucine-zipper (bZIP) transcription factors, flavin adenine dinucleotide-linked oxidase, and helicase, could have played a role in the transmission of autotrophy to heterotrophs and in the processes of abiotic stress resistance and pathogenicity. A total of 66 (1.37%) and 73 (1.49%) genes were identified as potential horizontal gene transfer events in the two
P. zopfii
genomes, respectively. Genes for malate synthase and isocitrate lyase, which are horizontally transferred from bacteria, may play a pivotal role in carbon and nitrogen metabolism as well as the pathogenicity of
Prototheca
and non-photosynthetic organisms. The two high-quality
P. zopfii
genomes provide new insights into their evolution as obligate heterotrophs and pathogenicity.

IMPORTANCE

The genus
Prototheca
, characterized by its heterotrophic nature and pathogenicity, serves as an exemplary model for investigating pathobiology. The limited understanding of the protothecosis infectious disease is attributed to the lack of genomic resources. Using HiFi long-read sequencing, both nuclear and plastid genomes were generated for two strains of
P. zopfii
. The findings revealed a concurrent reduction in both plastid and nuclear genome size, accompanied by the loss of genes associated with photosynthesis, carotenoid oxygenase, basic leucine-zipper (bZIP) transcription factors, and others. The analysis of horizontal gene transfer revealed the presence of 1.37% and 1.49% bacterial genes, including malate synthase and isocitrate lyase, which play crucial roles in carbon and nitrogen metabolism, as well as pathogenicity and obligate heterotrophy. The two high-quality
P. zopfii
genomes represent valuable resources for investigating their adaptation and evolution as obligate heterotrophs, as well as for developing future prevention and treatment strategies against protothecosis.
Skipped wells and scientific error during fosfomycin agar dilution and broth microdilution lead to inconsistent minimal inhibitory concentrations and may be cause for reevaluating testing methods for
Klebsiella pneumoniae
Authors: Bixby Morgan L. , Daley Ellora C. , Collins Lindsey B. , Salay Jenna M. , Bryson Alexandra L. , Hirsch Elizabeth B. 
Published: June 2024

ABSTRACT

Despite the first-line recommendation of fosfomycin for uncomplicated urinary tract infections (UTIs), there are pressing barriers for optimizing its use for the treatment of non-
Escherichia coli
Enterobacterales UTI. There are no approved breakpoints for oral use against other Enterobacterales, and the recommended agar dilution (AD) reference method for minimal inhibitory concentration (MIC) determination is largely impractical. Using 160 clinical
Klebsiella pneumoniae
isolates, we sought to understand rates of skipped wells and MIC imprecision in broth microdilution (BMD) and how that compares to rates of error using AD. Though the Clinical and Laboratory Standards Institute refers to the skipped well phenomena in their recommendation against the use of BMD, there is a paucity of data on its frequency. While AD and BMD produced similar MIC
50/90
values (32/256 µg/mL for AD and 64/256 µg/mL for BMD), essential agreement was poor. No-growth wells at concentrations below the MIC occurred in up to 10.9% of wells at a given concentration, as the most frequent scientific error. Growth in concentrations above the measured MIC occurred in up to 3.3% of wells and was seen within three dilutions of the MIC for BMD. Observation of single colonies either at or beyond the measured MIC for AD was also common and occurred up to 8.3% and 2.5% of the time, respectively. The frequent scientific error in both testing methods should prompt re-evaluation of AD guidelines and expansion of MIC testing methods for fosfomycin susceptibility testing, as poor agreement with another method prone to scientific error should not be the main detractor from BMD use.

IMPORTANCE
Despite the recommendation of fosfomycin for uncomplicated urinary tract infections (UTIs), there are barriers for optimizing its use. There are no approved breakpoints for oral use against other Enterobacterales, and the recommended agar dilution (AD) reference method for MIC determination is largely impractical. The use of broth microdilution (BMD) for fosfomycin testing is not recommended by the Clinical and Laboratory Standards Institute due to unsatisfactory precision and skipped wells—occurrence of no-growth in a single well before the minimal inhibitory concentration (MIC)—and trailing endpoints. We sought to understand rates of skipped wells and growth at concentrations above measured MICs in BMD and how that compares to scientific error using AD. No-growth wells at concentrations below the MIC occurred in up to 10.9% of wells for BMD and single colonies at or beyond measured MICs for AD were also common. Frequent scientific error in both methods should prompt re-evaluation of both AD and BMD for fosfomycin susceptibility testing.
A westerly dominated Early Cretaceous eolian system in the Hami Basin, NW China
Authors: Zhang Dehai , Wang Guocan , Pullen Alex , Abell Jordan T. , Cheng Feng , Shen Tianyi , Ji Junliang , Zhang Meng 
Published: June 2024

Abstract
Cretaceous eolian deposits provide evidence of variations in the tropical-subtropical atmospheric circulation under greenhouse conditions. However, the misinterpretation of many such deposits as fluvial or deltaic originally hindered precise paleoclimatic reconstructions. Here we report a newly identified Early Cretaceous desert in the Hami Basin, China, which helps understand spatial-temporal variations in aridity and atmospheric circulations within central East Asia during the Early Cretaceous. The Liushuquan Formation is composed of &gt;300-m-thick eolian deposits interpreted as an intermontane erg environment. Paleocurrent indicators within the straight-crested dunes of the Liushuquan Formation yield a mean trend of 101.3° (± 10.1°, 1 standard deviation) throughout the formation, consistent with near-surface westerly winds. Paleo-atmospheric circulation superimposed on topographic effects led to widespread eolianite accumulation during the Early Cretaceous. Combined with the spatiotemporal changes in desert distributions and prevailing surface wind patterns in East Asia, these observations are consistent with the migration of the subtropical high-pressure belt during the Early Cretaceous. We propose the following paleo-atmospheric model: (1) During the late Berriasian–Valanginian, the subtropical high belt drifted southward and northward over shorter time scales within the spatial domain of the paleo-Ordos Basin, then shifted southward at least past the Ordos Basin; (2) until the late Hauterivian–Barremian, the subtropical high-pressure zone was primarily located between the northwestern Tarim Basin and the Ordos Basin; and (3) a significant southward shift of the subtropical high-pressure zone occurred during the Aptian–Albian.
How predictive is peer review for gauging impact? The association between reviewer rating scores, publication status, and article impact measured by citations in a pain subspecialty journal
Authors: Weitzner Aidan S , Davis Matthew , Han Andrew H , Liu Olivia O , Patel Anuj B , Sites Brian D , Cohen Steven P 
Published: June 2024

BackgroundPeer review represents a cornerstone of the scientific process, yet few studies have evaluated its association with scientific impact. The objective of this study is to assess the association of peer review scores with measures of impact for manuscripts submitted and ultimately published.Methods3173 manuscripts submitted toRegional Anesthesia & Pain Medicine (RAPM)between August 2018 and October 2021 were analyzed, with those containing an abstract included. Articles were categorized by topic, type, acceptance status, author demographics and open-access status. Articles were scored based on means for the initial peer review where each reviewer’s recommendation was assigned a number: 5 for ‘accept’, 3 for ‘minor revision’, 2 for ‘major revision’ and 0 for ‘reject’. Articles were further classified by whether any reviewers recommended ‘reject’. Rejected articles were analyzed to determine whether they were subsequently published in an indexed journal, and their citations were compared with those of accepted articles when the impact factor was<1.4 points lower thanRAPM’s 5.1 impact factor. The main outcome measure was the number of Clarivate citations within 2 years from publication. Secondary outcome measures were Google Scholar citations within 2 years and Altmetric score.Results422 articles met inclusion criteria for analysis. There was no significant correlation between the number of Clarivate 2-year review citations and reviewer rating score (r=0.038, p=0.47), Google Scholar citations (r=0.053, p=0.31) or Altmetric score (p=0.38). There was no significant difference in 2-year Clarivate citations between accepted (median (IQR) 5 (2–10)) and rejected manuscripts published in journals with impact factors>3.7 (median 5 (2–7); p=0.39). Altmetric score was significantly higher forRAPM-published papers compared withRAPM-rejected ones (median 10 (5–17) vs 1 (0–2); p<0.001).ConclusionsPeer review rating scores were not associated with citations, though the impact of peer review on quality and association with other metrics remains unclear.
Hydrogeology of southeastern coastal parts of Great Nicobar Island, India: development of an integrated conceptual model for a hitherto unexplored island in the Indian Ocean
Authors: Roy Indranil , Sarkar Sujit , Kumar Awadhesh , Mukherjee Mahasweta , Nandi Rajyashree , Chowdhuri Atalanta Narayan , Barman Nilamoni , Choudhury Anirvan , Gayen Anadi 
Published: June 2024

The vulnerability of oceanic islands in the face of climate change, vis-a-vis human development, is a serious issue at present. The island of Great Nicobar in the Nicobar archipelago in the Indian Ocean will face major challenges owing to its impending development activities. The eastern coastal part of the island was investigated through exploratory drilling, geophysical investigations, and water-table monitoring. Field investigations show that coralline sand is the major groundwater repository and is commonly developed through dug wells. Exploratory drilling down to 100 m depth revealed that the underlying Tertiary consolidated aquifer is of limited potential and showed increased salinity with depth. Water is also present along the contacts of shale–sandstone. The mean seasonal fluctuations in the depth to the water table was 0.18 m. Geoelectrical sections identified promising fresh groundwater zones along the east coast, with freshwater-bearing semi-weathered coralline limestone and coralline sand having a resistivity of 146–622 ohm m. Based on generated data, a 3D model of the aquifer system was constructed. The observed soil infiltration rate was 0.3–0.5 cm h
−1
. The specific capacity of the dug wells was
c
. 5 m
2
min
−1
. The permeability of the phreatic aquifer was 5–11 m/day and the transmissivity was 0.11–0.2 m
2
min
−1
. The optimum yield of the unconfined aquifer was 17–21 m
3
/day. The tidal influences on the aquifer system also added complexity to the island's hydrogeological dynamics. Despite the challenges of restricted access due to the presence of aboriginal tribes in the island, the present study provides the maiden set of hydrogeological data for the island, revealing the disposition of the aquifers, their properties and their spatio-temporal behaviour.
Abundance and microhabitat association of Barbourula busuangensis (Anura: Bombinatoridae) in Busuanga Island, Philippines
Authors: Flores Gerrie Mae A. , Flores Andrie Bon A. , Mabitasan Ronnie Jann Ian B. , Lopus Jay Martin F. , Paguntalan Lisa J. 
Published: June 2024

Barbourula busuangensis, popularmente conhecida como rã-de- cabeça-chata-das-filipinas, é uma espécie quase ameaçada e endêmica de Palau, Filipinas. Apesar de seu nicho ecológico distinto e características únicas, como a cabeça e o corpo achatados que suportam seu estilo de vida totalmente aquático, são limitados os estudos efetuados para compreender seus requisitos de habitat e status populacional. Realizamos levantamentos visuais e capturas manuais ao longo de transectos de 30–100 m em dois distritos, Cheey e New Busuanga. Um total de 270 indivíduos foi registado, e as variáveis de micro-habitat foram comparadas entre os dois locais. A abundância de B. busuangensis foi significativamente maior em Cheey do que em New Busuanga. Encontramos diferenças significativas em seis variáveis-chave do micro-habitat (umidade relativa, temperatura, profundidade e largura do riacho/rio, percentagem de rochas, fluxo e turbidez da água) entre os dois locais, sugerindo condições ambientais diversas com impacto nas populações. Além disso, 14% das rãs capturadas (23 indivíduos) apresentavam deformações morfológicas, embora a causa permaneça indeterminada. Nossas descobertas ressaltam a necessidade urgente de mais pesquisas e esforços de conservação direcionados a garantir a sobrevivência dessa espécie. Este estudo fornece dados essenciais sobre a distribuição e as preferências de habitat de B. busuangensis, sugerindo estratégias de conservação para mitigar o declínio da população e abordar os desafios ambientais que afetam esse anfíbio único.
The Art and Chemistry of Replicating Oil Paintings into Woven Textiles
Authors: Linden Delanie 
Published: June 2024

Abstract
The prominence of chiaroscuro in late eighteenth-century French oil painting posed significant challenges for tapestry weavers, which led artisans and chemists to seek chemical solutions for replicating in textiles the style’s high contrast between light and dark. Textile manufacturers struggled to reproduce the intense gradations of painters like Jacques-Louis David, and innovations in dye technology were driven by the need to match the naturalism and Enlightenment symbolism of contemporary paintings. Napoleon’s investment in dye chemistry and the establishment of a dyeing school aimed to standardize colorants and rebrand traditional arts with political imagery. The integration of scientific expertise in the decorative arts led to advancements that laid the groundwork for future developments in synthetic colorants.
Institutions as Intangible Assets in the Evolution of Italian Fashion, 1950–2000
Authors: Merlo Elisabetta , Pinchera Valeria 
Published: June 2024

Abstract
Institutions, as intangible factors, influenced the development and configuration of the Italian fashion system in the second half of the twentieth century. Historians have recognized the importance of institutions in understanding historical change, economic trends, and path dependence. This approach is well established in historical studies, but the application of the institutional logics theoretical framework to detailed analyses of specific cases and contexts remains unexplored. In this respect, the institutions and institutional logics in the emergence and configuration of the Italian fashion system exemplify how institutions influence organizational structure and behavior as well as market evolution. The evolution of Italian fashion therefore underscores the cultural dimensions of institutions and, eventually, their significance as intangible factors.