bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protein interaction mapping reveals widespread targeting of development‐related host transcription factors by phytoplasma effectors
Authors: Correa Marrero Miguel , Capdevielle Sylvain , Huang Weijie , Al‐Subhi Ali M. , Busscher Marco , Busscher‐Lange Jacqueline , van der Wal Froukje , de Ridder Dick , van Dijk Aalt D. J. , Hogenhout Saskia A. , Immink Richard G. H. 
Published: November 2023

SUMMARYPhytoplasmas are pathogenic bacteria that reprogram plant host development for their own benefit. Previous studies have characterized a few different phytoplasma effector proteins that destabilize specific plant transcription factors. However, these are only a small fraction of the potential effectors used by phytoplasmas; therefore, the molecular mechanisms through which phytoplasmas modulate their hosts require further investigation. To obtain further insights into the phytoplasma infection mechanisms, we generated a protein–protein interaction network between a broad set of phytoplasma effectors and a large, unbiased collection of Arabidopsis thaliana transcription factors and transcriptional regulators. We found widespread, but specific, interactions between phytoplasma effectors and host transcription factors, especially those related to host developmental processes. In particular, many unrelated effectors target specific sets of TCP transcription factors, which regulate plant development and immunity. Comparison with other host‐pathogen protein interaction networks shows that phytoplasma effectors have unusual targets, indicating that phytoplasmas have evolved a unique and unusual infection strategy. This study contributes a rich and solid data source that guides further investigations of the functions of individual effectors, as demonstrated for some herein. Moreover, the dataset provides insights into the underlying molecular mechanisms of phytoplasma infection.
Climate‐resilient crops: Lessons from xerophytes
Authors: Chen Xi , Zhao Chenchen , Yun Ping , Yu Min , Zhou Meixue , Chen Zhong‐Hua , Shabala Sergey 
Published: November 2023

SUMMARYDeveloping climate‐resilient crops is critical for future food security and sustainable agriculture under current climate scenarios. Of specific importance are drought and soil salinity. Tolerance traits to these stresses are highly complex, and the progress in improving crop tolerance is too slow to cope with the growing demand in food production unless a major paradigm shift in crop breeding occurs. In this work, we combined bioinformatics and physiological approaches to compare some of the key traits that may differentiate between xerophytes (naturally drought‐tolerant plants) and mesophytes (to which the majority of the crops belong). We show that both xerophytes and salt‐tolerant mesophytes have a much larger number of copies in key gene families conferring some of the key traits related to plant osmotic adjustment, abscisic acid (ABA) sensing and signalling, and stomata development. We show that drought and salt‐tolerant species have (i) higher reliance on Na for osmotic adjustment via more diversified and efficient operation of Na+/H+ tonoplast exchangers (NHXs) and vacuolar H+‐ pyrophosphatase (VPPases); (ii) fewer and faster stomata; (iii) intrinsically lower ABA content; (iv) altered structure of pyrabactin resistance/pyrabactin resistance‐like (PYR/PYL) ABA receptors; and (v) higher number of gene copies for protein phosphatase 2C (PP2C) and sucrose non‐fermenting 1 (SNF1)‐related protein kinase 2/open stomata 1 (SnRK2/OST1) ABA signalling components. We also show that the past trends in crop breeding for Na+ exclusion to improve salinity stress tolerance are counterproductive and compromise their drought tolerance. Incorporating these genetic insights into breeding practices could pave the way for more drought‐tolerant and salt‐resistant crops, securing agricultural yields in an era of climate unpredictability.
Location Selection of Sectionalizing Valve (SV) Stations in Liquid Hydrocarbon Pipelines: A Case Study
Authors: Singh Akhilesh , Prabhakar Saurabh , Kishore Raj 
Published: November 2023

Abstract
The importance of pipelines can be secondary to none when being vital for the development of a nation and its people. However, like any other project, a pipeline project also has impact on the environment during the installation as well as operation phases. One of the most challenging tasks is the containment of leakage of the fluid in case of damage to the liquid hydrocarbon pipeline. The leakage of hydrocarbon liquid can have detrimental effect on environment especially when it happens at a river crossing. Sectionalizing valve (SV) stations are provided to divide the entire pipeline into sections to minimize the loss of hydrocarbon and limit the damage caused to local environment and its inhabitants. Location of these sectionalizing valve stations is very crucial with regard to the all-weather access and minimal environmental impact in case of leakage. While for liquid hydrocarbons other than LPG the maximum distance of 50 km between successive SV stations is clearly specified in various applicable codes and standards, there is statutory requirement to install Sectionalizing valves (or Mainline block valves) on both sides of major river crossings and public water supply reservoirs as close as possible near the upstream and downstream bank of the river and public water supply reservoirs for isolation of these portions of the pipeline. Although this requirement is necessary for minimizing the environmental impact, a lot of cost is incurred in providing an SV station.
The present case study discusses in detail the methodology adopted for selection of locations to provide SV stations of a 26 inch size Crude oil pipeline of a reputed energy major. Over 200 river crossings are encountered in the route of this pipeline. The methodology for location selection of SV stations intends to optimize number of SV stations by identifying the major river crossings and providing SV stations on their upstream and downstream sides. This involves the usage of modern tool of historical satellite imagery along with the survey data/information of the pipeline route.
Semi-mechanistic population pharmacokinetic/pharmacodynamic modeling of a
Plasmodium
elongation factor 2 inhibitor cabamiquine for prevention and cure of malaria
Authors: Courlet Perrine , Wilkins Justin J. , Oeuvray Claude , Gao Wei , Khandelwal Akash 
Published: November 2023

ABSTRACT

Cabamiquine is a novel antimalarial agent that demonstrates the potential for chemoprevention and treatment of malaria. In this article, the dose–exposure–response relationship of cabamiquine was characterized using a population pharmacokinetic (PK)/pharmacodynamic (PD) model, incorporating the effects of cabamiquine on parasite dynamics at the liver and blood stages of malaria infection. Modeling was performed sequentially. First, a three-compartmental population PK model was developed, comprising linear elimination, a transit absorption model in combination with first-order absorption, and a recirculation model. Second, this model was expanded into a PK/PD model using parasitemia data from an induced blood stage malaria (IBSM) human challenge model. To describe the parasite growth and killing in the blood, a turnover model was used. Finally, the liver stage parasite dynamics were characterized using data from a sporozoite challenge model (SpzCh), and system parameters were fixed based on biological plausibility. Cabamiquine concentration in the central compartment was used to drive parasite killing at the blood and liver stages. Blood stage minimum inhibitory concentrations (MIC
b
) were estimated at 7.12 ng/mL [95% confidence interval (CI
95%
): 6.26–7.88 ng/mL] and 1.28 ng/mL (CI
95%
: 1.12–1.43 ng/mL) for IBSM and SpzCh populations, respectively, while liver stage MIC
l
was lower (0.61 ng/mL; CI
95%
: 0.24–0.96 ng/mL). In conclusion, a population PK/PD model was developed by incorporating parasite dynamics and drug activity at the blood and liver stages based on clinical data and biological knowledge. This model can potentially facilitate antimalarial agent development by supporting the efficient selection of the optimal dosing regimen.
Genome-scale analysis of essential gene knockout mutants to identify an antibiotic target process
Authors: Bailey J. , Gallagher L. , Manoil C. 
Published: November 2023

ABSTRACT

We describe a genome-scale approach to identify the essential biological process targeted by a new antibiotic. The procedure is based on the identification of essential genes whose inactivation sensitizes a Gram-negative bacterium (
Acinetobacter baylyi
) to a drug and employs recently developed transposon mutant screening and single-mutant validation procedures. The approach, based on measuring the rates of loss of newly generated knockout mutants in the presence of antibiotic, provides an alternative to traditional procedures for studying essential functions using conditional expression or activity alleles. As a proof of principle study, we evaluated whether mutations enhancing sensitivity to the β-lactam antibiotic meropenem corresponded to the known essential target process of the antibiotic (septal peptidoglycan synthesis). We found that indeed mutations inactivating most genes needed for peptidoglycan synthesis and cell division strongly sensitized cells to meropenem. Additional classes of sensitizing mutations in essential genes were also identified, including those that inactivated capsule synthesis, DNA replication, or envelope stress response regulation. The essential capsule synthesis mutants appeared to enhance meropenem sensitivity by depleting a precursor needed for both capsule and peptidoglycan synthesis. The replication mutants may sensitize cells by impairing division. Nonessential gene mutations sensitizing cells to meropenem were also identified in the screen and largely corresponded to functions subordinately associated with the essential target process, such as in peptidoglycan recycling. Overall, these results help validate a new approach to identify the essential process targeted by an antibiotic and define the larger functional network determining sensitivity to it.
NADP
+
or CO
2
reduction by
frhAGB
-encoded hydrogenase through interaction with formate dehydrogenase 3 in the hyperthermophilic archaeon
Thermococcus onnurineus
NA1
Authors: Yang Ji-in , Jung Hae-Chang , Oh Hyun-Myung , Choi Bo Gyoung , Lee Hyun Sook , Kang Sung Gyun 
Published: November 2023

ABSTRACT

It has been reported that the
frhAGB
-encoded hydrogenase from
Thermococcus onnurineus
NA1 is homologous to the F
420
-reducing hydrogenase from methanogens and can reduce thioredoxin reductase (TrxR) via direct electron transfer from H
2
oxidation. In this study, to find other interaction targets of
frhAGB
-encoded hydrogenase, we searched for structural homologs of TrxR using the Position-Specific Iterative Basic Local Alignment Search Tool (PSI-BLAST) protein database search program and AlphaFold Protein Structure Database. Fdh3B (TON_0542), a subunit of the formate dehydrogenase 3 (Fdh3), showed the most similar structure to TrxR in its domains. The interaction potential of Fdh3B with
frhAGB
-encoded hydrogenase was demonstrated by measuring H
2
-dependent NADP
+
reduction by a mixture of purified proteins. Similarly, the H
2
-dependent NADP
+
-reducing activity of Fdh3 whole complex and two other TrxR homologs encoded by TON_0702 and TON_1376 was determined. It was also demonstrated that the Fdh3 complex could reduce CO
2
to formate in the presence of the
frhAGB
-encoded hydrogenase and H
2
, as shown for the H
2
-dependent CO
2
reductase (HDCR) of acetogen. The
in vivo
contribution of the
frhAGB
-encoded hydrogenase and Fdh3 to H
2
-dependent CO
2
reduction was investigated using a resting cell assay, and formate production was significantly decreased in
fdh3A
or
frhA
deletion mutants. In conclusion, the
frhAGB
-encoded hydrogenase was identified to directly transfer electrons to Fdh3 without an electron carrier, similar to the mechanism observed for TrxR. These results expand our understanding of the functional role of the
frhAGB
-encoded hydrogenase in non-methanogenic
Thermococcus
species.

IMPORTANCE

The strategy using structural homology with the help of structure prediction by AlphaFold was very successful in finding potential targets for the
frhAGB
-encoded hydrogenase of
Thermococcus onnurineus
NA1. The finding that the hydrogenase can interact with FdhB to reduce the cofactor NAD(P)
+
is significant in that the enzyme can function to supply reducing equivalents, just as F
420
-reducing hydrogenases in methanogens use coenzyme F
420
as an electron carrier. Additionally, it was identified that
T. onnurineus
NA1 could produce formate from H
2
and CO
2
by the concerted action of
frhAGB
-encoded hydrogenase and formate dehydrogenase Fdh3.
Essential role of the conserved oligomeric Golgi complex in
Toxoplasma gondii
Authors: Marsilia Clem , Batra Mrinalini , Pokrovskaya Irina D. , Wang Changqi , Chaput Dale , Naumova Daria A. , Lupashin Vladimir V. , Suvorova Elena S. 
Published: November 2023

ABSTRACT

Survival of the apicomplexan parasite
Toxoplasma gondii
depends on the proper functioning of many glycosylated proteins. Glycosylation is performed in the major membranous organelles ER and Golgi apparatus that constitute a significant portion of the intracellular secretory system. The secretory pathway is bidirectional: cargo is delivered to target organelles in the anterograde direction, while retrograde flow maintains the membrane balance and proper localization of glycosylation machinery. Despite the vital role of the Golgi in parasite infectivity, little is known about its biogenesis in apicomplexan parasites. In this study, we examined the
T. gondii
conserved oligomeric Golgi (COG) complex and determined that contrary to predictions,
T. gondii
expresses the entire eight-subunit complex and that each complex subunit is essential for tachyzoite growth. Deprivation of the COG complex induces a pronounced effect on Golgi and ER membranes, which suggests that the
T. gondii
COG complex has a wider role in intracellular membrane trafficking. We demonstrated that besides its conservative role in retrograde intra-Golgi trafficking, the COG complex also interacted with anterograde and novel transport machinery. Furthermore, we identified coccidian-specific components of the Golgi transport system: TgUlp1 and TgGlp1. Protein structure and phylogenetic analyses revealed that TgUlp1 is an adaptation of the conservative Golgi tethering factor Uso1/p115. TgUlp1 and together with Golgi-localized TgGlp1 showed dominant interactions with the trafficking machinery that was predicted to operate endosome-to-Golgi recycling. Together, our study showed that
T. gondii
has expanded the function of the conservative Golgi tethering COG complex and evolved additional regulators of transport that are likely to serve parasite-specific secretory organelles.

IMPORTANCE

The Golgi is an essential eukaryotic organelle and a major place for protein sorting and glycosylation. Among apicomplexan parasites,
Toxoplasma gondii
retains the most developed Golgi structure and produces many glycosylated factors necessary for parasite survival. Despite its importance, Golgi function received little attention in the past. In the current study, we identified and characterized the conserved oligomeric Golgi complex and its novel partners critical for protein transport in
T. gondii
tachyzoites. Our results suggest that
T. gondii
broadened the role of the conserved elements and reinvented the missing components of the trafficking machinery to accommodate the specific needs of the opportunistic parasite
T. gondii
.
Draft genomes of seven isolates from Danish wastewater facilities belonging to
Pseudomonas
,
Bacillus
,
Pseudochrobactrum
,
Brevundimonas
, and
Pandoraea
Authors: Maccario Lorrie , Silva Ana F. , Nesme Joseph , Amador Cristina I. , Sørensen Søren J. , Cooper Vaughn S. , Røder Henriette L. 
Published: November 2023

ABSTRACT

We report here seven draft genomes of bacterial strains from two Danish wastewater facilities, two of which might be characterized as a new group within the
Pseudomonas
and
Pseudochrobactrum
genera, respectively. These genomes will provide useful references for understanding bacterial interactions and horizontal gene transfer within bacterial communities.
Draft genome sequences of six
Pseudomonas
spp. and one
Rheinheimera
sp. isolated from oil sands process-affected water from Alberta, Canada
Authors: Goff Kira L. , Gauthier Jeff , Shideler Steven M. , Bookout Tyson , Kukavica-Ibrulj Irena , Lewenza Shawn , Levesque Roger C. 
Published: November 2023

ABSTRACT

We report the draft genomes of seven bacterial strains (six
Pseudomonas
spp. and one
Rheinheimera
sp.) isolated from environmental water samples from oil sands tailings ponds that have accumulated a wide variety of organic compounds, salts and metals.
Draft genome sequence of active gold mine isolate
Pseudomonas iranensis
strain ABS_30
Authors: Adeniji Adetomiwa A. , Ayangbenro Ayansina S. , Babalola Olubukola O. 
Published: November 2023

ABSTRACT

Pseudomonas iranensis
ABS_30, isolated from gold mining soil, exhibits metal-resistant properties valuable for heavy metal removal. We report the draft genome sequencing of the
P. iranensis
ABS_30 strain, which is 5.9 Mb in size.
Alleviation of DSS-induced colitis via bovine colostrum-derived extracellular vesicles with microRNA
let-7a-5p
is mediated by regulating
Akkermansia
and
β
-hydroxybutyrate in gut environments
Authors: Mun Daye , Kang Minkyoung , Shin Minhye , Choi Hye Jin , Kang An Na , Ryu Sangdon , Unno Tatsuya , Maburutse Brighton E. , Oh Sangnam , Kim Younghoon 
Published: November 2023

ABSTRACT

Inflammatory bowel disease (IBD) is an inflammatory disease caused by the interaction of environmental and genetic factors, including diet and microbiota. Recent studies have suggested the effects of extracellular vesicles (EVs) on controlling host intestinal immune responses, although the specified mechanisms have not yet been fully elucidated. In the current study, we investigated the effects of EVs isolated from bovine colostrum on attenuating dextran sodium sulfate-induced colitis in mice. Multiomic approaches were used to assess host gene expression and gut microbiota profiles and to explain the roles of EVs in modulating the host immune system. Transcriptomic analyses suggested a possible immunoregulatory mechanism mediated by the cell cycle regulator CDK6 and pro-inflammatory responses. The gut microbiome composition and fecal metabolite profiles showed that EV supplementation promoted the microbial abundance of
Akkermansia
and short-chain fatty acid production in mice with colitis. Further
in vivo
analysis revealed that β-hydroxybutyrate and
Akkermansia muciniphila
, which are elevated by the administration with EVs, are involved in lessening colitis through modulating the immune system. Additionally, the bta-let-7a-5p, one of the most abundant microRNAs in bovine colostrum-derived EVs, alleviated the indications of colitis in mice by modulating their intestinal immunity and by regulating the cell cycle-related target gene Cdk6. Overall, these results suggest that bovine colostrum EVs and bta-let-7a-5p could be promising alternative strategies for preventing the onset of IBD.

IMPORTANCE
Even though studying on the possible involvement of extracellular vesicles (EVs) in host-microbe interactions, how these relationships mediate host physiology has not clarified yet. Our current findings provide insights into the encouraging benefits of dietary source-derived EVs and microRNAs (miRNAs) on organic acid production and ultimately stimulating gut microbiome for human health, suggesting that supplementation of dietary colostrum EVs and miRNAs is a novel preventive strategy for the treatment of inflammatory bowel disease.
Quantitative detection of the
Ralstonia solanacearum
species complex in soil by qPCR combined with a recombinant internal control strain
Authors: Chen Wei , Zhang Jun-Wei , Qin Bi-Xia , Xie Hui-Ting , Zhang Zhi , Qiao Xiu-Ze , Li Shan-Kui , Asif Muhammad , Guo Song , Cui Li-Xian , Wang Pei-Pei , Dong Li-Hong , Guo Qing-Gang , Jiang Wen-Jun , Ma Ping , Xia Zhen-Yuan , Lu Can-Hua , Zhang Li-Qun 
Published: November 2023

ABSTRACT

The detection of soil-borne pathogens by quantitative PCR (qPCR) has been challenging due to the pronounced influence of soil type on DNA extraction and PCR reactions. In the present study, we developed a novel qPCR system and an internal sample process control (ISPC) strain, RsPC, for the detection of
Ralstonia solanacearum
species complex (RSSC), the pathogens causing bacterial wilt. Specific primers and TaqMan probe were designed based on analyses of 16S rRNA gene sequences from 581
Ralstonia
genomes, and the RsPC was constructed by insertion of an artificial fragment, which consisted of two fragments from the kanamycin-resistant gene and the
gfp
gene, into the chromosome of a phylogenetically closely related strain,
Ralstonia pickettii
JCM 5969. The qPCR target sequences of RSSC and RsPC shared primers; however, different TaqMan probes were used to distinguish them from each other. The interaction assay between ISPC and target DNA showed no influence on sensitivity when their difference in concentration was <10
4
-fold. We tested 10 different soils with co-spiked RsPC and
R. pseudosolanacearum
LMG 9673 and found comparable recovery efficiencies (REs) of two strains in most samples, and the REs of LMG 9673 after correction by RsPC were closer to theoretical values. The RE of LMG 9673 improved most (2.98-fold) in a heavy clay soil. Similar results were obtained in three representative soils co-spiked with RsPC and LMG 9673 (at three concentrations),
R. solanacearum
NCPPB 325, and
R. syzygii
LLRS-1, respectively . The qPCR system and ISPC strain developed in this study could be applied for the accurate detection of RSSC in soil, and similar ISPCs can be developed in the future for other soil-borne animal and plant pathogens.

IMPORTANCE

DNA-based detection and quantification of soil-borne pathogens, such as the
Ralstonia solanacearum
species complex (RSSC), plays a vital role in risk assessment, but meanwhile, precise quantification is difficult due to the poor purity and yield of the soil DNA retrieved. The internal sample process control (ISPC) strain RsPC we developed solved this problem and significantly improved the accuracy of quantification of RSSC in different soils. ISPC-based quantitative PCR detection is a method especially suitable for the quantitative detection of microbes in complex matrices (such as soil and sludge) containing various PCR inhibitors and for those not easy to lyse (like Gram-positive bacteria, fungi, and thick-wall cells like resting spores). In addition, the use of ISPC strains removes additional workload on the preparation of high-quality template DNA and facilitates the development of high-throughput quantitative detection techniques for soil microbes.