bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabarcoding read abundances of orchid mycorrhizal fungi are correlated to copy numbers estimated using ddPCR
Authors: Wang Deyi , Trimbos Krijn B. , Gomes Sofia I. F. , Jacquemyn Hans , Merckx Vincent S. F. T. 
Published: November 2023

Summary

Quantifying the abundances of fungi is key to understanding natural variation in mycorrhizal communities in relation to plant ecophysiology and environmental heterogeneity. High‐throughput metabarcoding approaches have transformed our ability to characterize and compare complex mycorrhizal communities. However, it remains unclear how well metabarcoding read counts correlate with actual read abundances in the sample, potentially limiting their use as a proxy for species abundances.

Here, we use droplet digital PCR (ddPCR) to evaluate the reliability of ITS2 metabarcoding data for quantitative assessments of mycorrhizal communities in the orchid species Neottia ovata sampled at multiple sites. We performed specific ddPCR assays for eight families of orchid mycorrhizal fungi and compared the results with read counts obtained from metabarcoding.

Our results demonstrate a significant correlation between DNA copy numbers measured by ddPCR assays and metabarcoding read counts of major mycorrhizal partners of N. ovata, highlighting the usefulness of metabarcoding for quantifying the abundance of orchid mycorrhizal fungi. Yet, the levels of correlation between the two methods and the numbers of false zero values varied across fungal families, which warrants cautious evaluation of the reliability of low‐abundance families.

This study underscores the potential of metabarcoding data for more quantitative analyses of mycorrhizal communities and presents practical workflows for metabarcoding and ddPCR to achieve a more comprehensive understanding of orchid mycorrhizal communities.
Cost of implementing HIV pre‐exposure prophylaxis at community‐based clinics in Indonesia
Authors: Siregar Adiatma Yudistira Manogar , Juwita Mery Nurma , Hardiawan Donny , Akbar Adhadian , Rachman Zulfa Haitan , Haekal Muhammad Dzaki Fahd , Marwah Yuvi Siti , Putri Tarinanda Adzani , Rakhmat Fani Fadillah , Pohan Mawar Nita , Handayani Miasari , Budiarty Tri Indah , Afriana Nurhalina , Prabowo Bagus Rahmat , Wisaksana Rudi 
Published: November 2023

AbstractIntroductionCurrently, Indonesia still has one of the highest rates of new HIV/AIDS infections among countries in Asia and the Pacific region. The WHO has recommended pre‐exposure prophylaxis (PrEP) as an additional HIV epidemic prevention step, which has been applied globally and related to the reduction in the number of HIV cases. However, information on the cost of implementing PrEP is rarely available in developing countries, especially in Southeast Asia. Designing a cost‐effective approach to scale up PrEP and to estimate the potential budget impact requires information on the cost of implementing PrEP. This study aims to estimate the cost of implementing PrEP at community‐based clinics in Indonesia.MethodsWe collected healthcare and non‐healthcare/client costs from nine community‐based clinics in various cities/districts in Indonesia. The healthcare costs included data on resource utilisation and costs to deliver PrEP, divided into recurrent and capital costs using a discount rate of 3%. Non‐healthcare costs included out‐of‐pocket costs (e.g., transportation, meals) and productivity loss by clients and accompanying person(s) in accessing PrEP. On average, we interviewed 27 clients/clinic.ResultsThe annual cost of providing PrEP per client is US $365.03, 39% lower than the yearly cost of antiretroviral treatment (ART) per person (approximately US $600). Drugs and non‐healthcare costs contribute approximately 67% of the cost. The cost of PrEP amounts to US $292,756.45/year, covering 802 clients. The non‐healthcare cost per visit at all sites never reaches more than 10% of the average monthly household expenditure.ConclusionsThe cost of providing PrEP per person is approximately US $365 and is 39% lower than the annual cost of ART per person. Lowering the cost of PrEP ARV drugs would reduce the cost. Scaling up PrEP should recognise this cost structure and strive to reach economies of scale as the intervention gains more clients while simultaneously controlling new HIV infections.
Autoimmune anti‐D in an RhD‐positive young infant: Learning from a rare case
Authors: Malhotra Sheetal , Roy Manisha , Parchure Disha , Kaba Munira , Jain Ashish , Kulkarni Swati , Bansal Deepak , Sharma Ratti Ram 
Published: November 2023

AbstractBackground and ObjectivesAnti‐D is usually immune in nature and is formed in individuals lacking D antigen or having variants/altered D phenotypes. In the Indian population, 93.8% are RhD positive, and R1R1 is the commonest Rh phenotype. Here we report a rare and interesting case of autoimmune anti‐D in an RhD‐positive 3‐month‐old infant leading to warm autoimmune haemolytic anaemia.Study Design and MethodsAuto‐anti‐D was detected serologically by immunohaematological techniques such as direct antiglobulin test, antibody detection and identification, dithiothreitol, enzyme treatment, antibody titration and elution. Molecular studies were performed to rule out genetic variants of RhD.ResultsAnti‐D was confirmed in eluate and blood group post elution was B RhD positive. On genotyping using the Indian‐specific RHD genotyping assay, the sample was found to be negative for the RHD*01W.150 (most common RhD variant in Indians) but positive for RHD exon 5 and RHD exon 10 along with glyceraldehyde‐3‐phosphate dehydrogenase (GAPDH). The sample was further sequenced for RHD exons 1–10 by Sanger sequencing and found to be a wild type, thus, ruling out the presence of an RhD variant.ConclusionThis case is of interest because of the rare occurrence of autoimmune anti‐D in an RhD‐positive patient of such a young age (3 months). To the best of our knowledge, only two case reports have been published on autoimmune anti‐D in infancy (in 1961 and 1964).
A note on lc‐trivial fibrations
Authors: Hashizume Kenta 
Published: November 2023

AbstractFor every lc‐trivial fibration from an lc pair, we prove that after a base change, there exists a positive integer , depending only on the dimension of , the Cartier index of , and the sufficiently general fibers of , such that is linearly equivalent to the pullback of a Cartier divisor.
Multi-Fidelity Physics-Informed Generative Adversarial Network for Solving Partial Differential Equations
Authors: Taghizadeh Mehdi , Nabian Mohammad Amin , Alemazkoor Negin 
Published: November 2023

Abstract
We propose a novel method for solving partial differential equations using multi-fidelity physics-informed generative adversarial networks. Our approach incorporates physics supervision into the adversarial optimization process to guide the learning of the generator and discriminator models. The generator has two components: one that approximates the low-fidelity response of the input and another that combines the input and low-fidelity response to generate an approximation of high-fidelity responses. The discriminator identifies whether the input–output pairs accord not only with the actual high-fidelity response distribution, but also with physics. The effectiveness of the proposed method is demonstrated through numerical examples and compared to existing methods.
The Influence of a Warm-Up on Vigilance in University Students
Authors: González-Fernández Francisco Tomás , Castillo-Rodriguez Alfonso , González-Víllora Sixto , Hortigüela-Alcalá David 
Published: November 2023

The present study aimed to analyze the effects of conducting a warm-up (WC) or not (WWC) on students of the Science Degree in Physical Activity and Sport before starting a practical class. Thirty-two students of the Science Degree in Physical Activity and Sport (age: 22.38 ± 1.81 years; height: 176.09 ± 8.52 cm; weight: 22.38 ± 1.81 kg; body fat: 25.17 ± 3.20%) participated in a counterbalanced cross-sectional study in which three conditions were tested: (a) basal lineal, (b) WC, and (c) WWC. Participants recorded longer times (worse performance) in the Illinois dribbling test (basal lineal condition [20.17 ± 1.35], WWC [20.13 ± 1.37], and WC [19.32 ± 1.35]) and the Psychomotor Vigilance Task test (basal lineal condition [397.88 ± 75.98 ms]; WWC [412.19 ± 91.39 ms], and WC [368.53 ± 68.65 ms]). The warm-up prior to physical activity classes had positive effects on vigilance linked to executive functioning, and physical performance. In this sense, more research on different types of warm-up may be in order to contrast them with each other, as well as to carry out attention measurements according to the content to be imparted after the warm-ups. The present study represents a big opportunity for all physical education teachers due to warm-up is a crucial aspect that occurs in all practical sessions, also linked to the attention processes and motivational factors of the students.
Jumbo phages are active against extensively drug-resistant eyedrop-associated
Pseudomonas aeruginosa
infections
Authors: Cobián Güemes Ana Georgina , Ghatbale Pooja , Blanc Alisha N. , Morgan Chase J. , Garcia Andrew , Leonard Jesse , Huang Lina , Kovalick Grace , Proost Marissa , Chiu Megan , Kuo Peiting , Oh Joseph , Karthikeyan Smruthi , Knight Rob , Pogliano Joe , Schooley Robert T. , Pride David T. 
Published: November 2023

ABSTRACT

Antibiotic-resistant bacteria present an emerging challenge to human health. Their prevalence has been increasing across the globe due in part to the liberal use of antibiotics that has pressured them to develop resistance. Those bacteria that acquire mobile genetic elements are especially concerning because those plasmids may be shared readily with other microbes that can then also become antibiotic resistant. Serious infections have recently been related to the contamination of preservative-free eyedrops with extensively drug-resistant (XDR) isolates of
Pseudomonas aeruginosa
, already resulting in three deaths. These drug-resistant isolates cannot be managed with most conventional antibiotics. We sought to identify alternatives to conventional antibiotics for the lysis of these XDR isolates and identified multiple bacteriophages (viruses that attack bacteria) that killed them efficiently. We found both jumbo phages (>200 kb in genome size) and non-jumbo phages that were active against these isolates, the former killing more efficiently. Jumbo phages effectively killed the three separate XDR
P. aeruginosa
isolates both on solid and liquid medium. Given the ongoing nature of the XDR
P. aeruginosa
eyedrop outbreak, the identification of phages active against them provides physicians with several novel potential alternatives for treatment.
Enhancing the antibacterial function of probiotic
Escherichia coli
Nissle: when less is more
Authors: Bartram Emma , Asai Masanori , Gabant Philippe , Wigneshweraraj Sivaramesh 
Published: November 2023

ABSTRACT

Probiotic bacteria confer multiple health benefits, including preventing the growth, colonization, or carriage of harmful bacteria in the gut. Bacteriocins are antibacterial peptides produced by diverse bacteria, and their production is tightly regulated and coordinated at the transcriptional level. A popular strategy for enhancing the antibacterial properties of probiotic bacteria is to retrofit them with the ability to overproduce heterologous bacteriocins. This is often achieved from non-native constitutive promoters or in response to host or pathogen signal from synthetic promoters. How the dysregulated overproduction of heterologous bacteriocins affects the fitness and antibacterial efficacy of the retrofitted probiotic bacteria is often overlooked. We have conferred the prototypical probiotic
Escherichia coli
strain Nissle (EcN) the ability to produce microcin C (McC) from the wild-type promoter and two mutant promoters that allow, relative to the wild-type promoter, high and low amounts of McC production. This was done by introducing specific changes to the sequence of the wild-type promoter driving transcription of the McC operon while ensuring that the modified promoters respond to native regulation. By studying the transcriptomic responses and antibacterial efficacy of the retrofitted EcN bacteria in a
Galleria mellonella
infection model of enterohemorrhagic
E. coli
, we show that EcN bacteria that produce the lowest amount of McC display the highest antibacterial efficacy with little-to-none undesired collateral impact on their fitness. The results highlight considerations researchers may take into account when retrofitting probiotic bacteria with heterogenous gene products for therapeutic, prophylactic, or diagnostic applications.

Bacteria that resist killing by antibiotics are a major risk to modern medicine. The use of beneficial “probiotic” bacteria to make antibiotic-like compounds at the site of infection in the body is emerging as a popular alternative to the use of conventional antibiotics. A potential drawback of engineering probiotic bacteria in this way is that producing antibiotic-like compounds could impart undesired side effects on the performance of such bacteria, thereby compromising their intended use. This study highlights considerations researchers may take into account when engineering probiotic bacteria for therapeutic, prophylactic, or diagnostic applications.
Regulation of the general stress response sigma factor σ
T
by Lon-mediated proteolysis
Authors: Akar Roya , Fink Matthias J. , Omnus Deike J. , Jonas Kristina 
Published: November 2023

ABSTRACT

The Lon protease is widely conserved in both prokaryotic and eukaryotic organisms and fulfills important regulatory functions. Nevertheless, the number of identified Lon substrates is limited in most organisms, and the precise role of Lon in regulating these proteins is poorly understood. Here, we describe the α-proteobacterial general stress response sigma factor σ
T
as a novel Lon substrate in
Caulobacter crescentus
. Based on previously published quantitative proteomics data, we find σ
T
to be a promising putative Lon substrate and confirm a direct role of Lon in degrading σ
T
. We show that Lon contributes to the downregulation of σ
T
abundance under optimal conditions and during recovery from sucrose-induced osmotic stress. Furthermore, the presence of the Lon activity regulator LarA enhances Lon-mediated degradation of σ
T
in vitro
and reduces σ
T
levels
in vivo
indicating a role of LarA in modulating Lon-mediated degradation of σ
T
. Together, our results highlight the importance of Lon during the recovery phase following stress exposure by adjusting the concentrations of critical regulators of stress responses.

IMPORTANCE

Regulated protein degradation is a critical process in all cell types, which contributes to the precise regulation of protein amounts in response to internal and external cues. In bacteria, protein degradation is carried out by ATP-dependent proteases. Although past work revealed detailed insights into the operation principles of these proteases, there is limited knowledge about the substrate proteins that are degraded by distinct proteases and the regulatory role of proteolysis in cellular processes. This study reveals a direct role of the conserved protease Lon in regulating σ
T
, a transcriptional regulator of the general stress response in α-proteobacteria. Our work is significant as it underscores the importance of regulated proteolysis in modulating the levels of key regulatory proteins under changing conditions.
SARS-CoV-2 NSP12 associates with TRiC and the P323L substitution acts as a host adaption
Authors: Alruwaili Muhannad , Armstrong Stuart , Prince Tessa , Erdmann Maximillian , Matthews David A. , Luu Lisa , Davidson Andrew , Aljabr Waleed , Hiscox Julian A. 
Published: November 2023

ABSTRACT

SARS-CoV-2 emerged in the human population in late 2019, and human-to-human transmission has dominated the evolutionary landscape and driven the selection of different lineages. The first major change that resulted in increased transmission was the D614G substitution in the spike protein. This was accompanied by the P323L substitution in the viral RNA-dependent RNA polymerase (NSP12). Together with D614G, these changes are the root of the predominant global SARS-CoV-2 landscape. Here, we found that NSP12 formed an interactome with cellular proteins. The functioning of NSP12 was dependent on the T-complex protein ring complex, a molecular chaperone. In contrast, there was a differential association between NSP12 variants and components of a phosphatase complex (PP2/PP2A and STRN3). The virus expressing NSP12
L323
was less sensitive to perturbations in PP2A and supports the paradigm that ongoing genotype to phenotype adaptation of SARS-CoV-2 in humans is not exclusively restricted to the spike protein.

IMPORTANCE
SARS-CoV-2 has caused a worldwide health and economic crisis. During the course of the pandemic, genetic changes occurred in the virus, which have resulted in new properties of the virus—particularly around gains in transmission and the ability to partially evade either natural or vaccine-acquired immunity. Some of these viruses have been labeled Variants of Concern (VoCs). At the root of all VoCs are two mutations, one in the viral spike protein that has been very well characterized and the other in the virus polymerase (NSP12). This is the viral protein responsible for replicating the genome. We show that NSP12 associates with host cell proteins that act as a scaffold to facilitate the function of this protein. Furthermore, we found that different variants of NSP12 interact with host cell proteins in subtle and different ways, which affect function.
Bacillus subtilis
partially inhibits African swine fever virus infection
in vivo
and
in vitro
based on its metabolites arctiin and genistein interfering with the function of viral topoisomerase II
Authors: Lv Changjie , Yang Jingyu , Zhao Li , Zou Zhong , Kang Chao , Zhang Qiang , Wu Chao , Yang Li , Cheng Chuxing , Zhao Ya , Liao Qi , Hu Xiaotong , Li Chengfei , Sun Xiaomei , Jin Meilin 
Published: November 2023

ABSTRACT

African swine fever virus (ASFV) is an infectious disease with a mortality rate of nearly 100% in pigs; however, no safe commercial vaccines or antiviral drugs are currently available, which seriously threatens the global pig industry. Therefore, effective biologics against ASFV are urgently needed. Here, we screened 138
Bacillus subtilis
strains, four of which evidently inhibited ASFV replication
in vitro
. Pigs fed with biologics of different types from the four
B. subtilis
strains showed reduced pathological changes and viral loads in tissues, with a survival rate of up to 100%. The antiviral activity of
B. subtilis
was attributed to small-molecule metabolites, rather than to secretory proteins. A total of 169 small molecules were obtained from the metabolites of
B. subtilis
using liquid chromatograph mass spectrometer/mass spectrometer (LC-MS/MS), arctiin, and genistein, which showed the highest inhibition efficiency, suppressing ASFV proliferation at the mid-stage of infection. These molecules acted as competitive inhibitors by complexing the ATP-binding domain of viral topoisomerase II, as demonstrated using molecular docking, biolayer interferometry binding, and a competitive decatenation assay, thereby disrupting the catalytic activity of the enzyme and inhibiting ASFV replication. Furthermore, pigs administered arctiin and genistein orally showed decreased mortality and tissue damage. Collectively, these results suggest that the four
B. subtilis
strains screened may be preventative biologics against ASFV infection. Our findings pave the way for ASFV prevention and control strategies in the pig industry to curb the economic losses caused by the disease.

IMPORTANCE

African swine fever virus (ASFV) is a highly fatal swine disease that severely affects the pig industry. Although ASFV has been prevalent for more than 100 years, effective vaccines or antiviral strategies are still lacking. In this study, we identified four
Bacillus subtilis
strains that inhibited ASFV proliferation
in vitro
. Pigs fed with liquid biologics or powders derived from four
B. subtilis
strains mixed with pellet feed showed reduced morbidity and mortality when challenged with ASFV. Further analysis showed that the antiviral activity of
B. subtilis
was based on its metabolites arctiin and genistein interfering with the function of viral topoisomerase II. Our findings offer a promising new strategy for the prevention and control of ASFV that may significantly alleviate the economic losses in the pig industry.
Pelagic metagenome-assembled genomes from an estuarine salinity gradient in San Francisco Bay
Authors: Rasmussen Anna N. , Francis Christopher A. 
Published: November 2023

ABSTRACT
San Francisco Bay (SFB) is a large and highly human-impacted estuarine system. We produced 449 metagenome-assembled genomes from SFB waters, collected along the salinity gradient, providing a rich data set to compare the metabolic potential of microorganisms from different salinity zones within SFB and to other estuarine systems.
The presence of
Ixodes pavlovskyi
and
I. pavlovskyi
–borne microorganisms in Rishiri Island: an ecological survey
Authors: Zamoto-Niikura Aya , Saigo Akiko , Sato Masahiko , Kobayashi Hirotaka , Sasaki Mizuki , Nakao Minoru , Suzuki Tadaki , Morikawa Shigeru 
Published: November 2023

ABSTRACT

Rishiri Island, towering toward the Sea of Japan, has been volcanically dormant for approximately 8,000 years. This small inhabited island is free of middle- to large-sized wildlife and a crucial stopover for wild birds migrating along various routes of the East Asian Flyway. A 5-year survey was conducted to explore the biogeography of ticks and tick-borne microorganisms. By flagging vegetation,
Ixodes pavlovskyi
(Pomerantzev, 1948), distributed in limited spots in the Far East, was predominantly collected (60%–80% collection) throughout the survey period. The
I. pavlovskyi
consisted of two haplogroups, Asahikawa-type and Rishiri-type, with the prevalence and nucleotide diversity of Rishiri-type being over 90% and 0.068, respectively. A survey of wild animals revealed that red-backed voles and wild birds, including Oriental greenfinches and black-faced buntings, are their hosts for blood feeding. Furthermore, the red-backed voles were infected with tick-borne
Candidatus
Ehrlichia khabarensis (5/21, 24%). Till date, microorganisms with identical gene sequences have only been reported from Khabarovsk and Vancouver.
Ca
. E. khabarensis gene has also been detected in host-seeking adult
I. pavlovskyi
. These results indicated that Rishiri Island is a refuge for both
I. pavlovskyi and I. pavlovskyi
–borne microorganisms. Additionally, the
Babesia microti
US lineage, which is vectored by
Ixodes persulcatus
in the Far East, appears to be maintained between
I. pavlovskyi
and wild rodents. Various factors have influenced the unique ecosystem of the island. The historical and ecological biogeography of Rishiri Island helps us understand the origin, evolution, and expansion of ticks and associated microorganisms.

IMPORTANCE

Understanding the ecology of ticks and tick-borne microorganisms is important to assess the risk of emerging tick-borne diseases. Despite the fact that the
Ixodes pavlovskyi
tick bites humans, we lack information including population genetics and the reason for the inadequate distribution in Japan. A 5-year survey revealed that Rishiri Island, the main stopover in the East Asian Flyway of wild birds in the northern Sea of Japan, was a refuge of
I. pavlovskyi
. The
I. pavlovskyi
included two haplogroups, which were supposed to diverge a long time before the island separated from the continent and Hokkaido mainland. The detection of microorganisms from wildlife revealed that wild birds and rodents play a role in diffusion and settlement, respectively, of not only
I. pavlovskyi
but also
I. pavlovskyi
–borne microorganisms including
Candidatus
Ehrlichia khabarensis and
Babesia microti
US lineage. Various island-specific factors control
I. pavlovskyi
dominance and tick-borne pathogen maintenance. The results may enable us to explain how tick-borne infectious microorganisms are transported.