bluuebunny/crossref_metadata_2025 huggingface dataset:
Ethylene production during Alternaria infections on potato plants and its antagonistic role in virulence of different Alternaria species
Authors: Vandecasteele Michiel , Depaepe Thomas , Abdallah Mohamed Fathi , De Saeger Sarah , Höfte Monica M. , Haesaert Geert , van der Straeten Dominique , Audenaert Kris
Published: November 2023

Alternaria species are notorious pathogens of solanaceous crops and are known to produce a plethora of toxins. Nevertheless, the involvement of toxins or other virulence factors in Alternaria infections on potato plants has never been investigated. In view of this, we analysed whether different Alternaria species produced host‐ and non‐host‐specific toxins in vitro and in vivo. Secondly, we assessed if ethylene (ETH) is involved in potato plant infections, as was previously demonstrated in tomato. Although many toxins were detected in vitro, no toxins were present before symptom appearance in potato leaves. Isolates that made large conidia (A. solani) produced up to six times more ETH in vitro than isolates with small conidia (A. arborescens) in the presence of the ETH precursor α‐keto‐γ‐methylthiobutyric acid (KMBA). In contrast, on potato leaf discs, an inverse relation was found between ETH emission and conidia size after correcting the data according to fungal DNA content, suggesting a role for ETH in symptom development rather than initiation. Moreover, application of a plant ETH biosynthesis inhibitor, 2‐aminoethoxyvinyl glycine (AVG), resulted in a 60% reduction in necrosis after inoculation with a large‐conidia isolate, whereas a 35% increase in necrosis was observed after inoculation with a small‐conidia isolate. Finally, it was concluded that toxin production is not essential for symptom development of Alternaria on potato and that ETH (either from the plant and/or the fungus) is a crucial factor in symptom development by A. solani, whereas its role was found to be antagonistic for A. arborescens.
Writing impactful reviews to rejuvenate public administration: A framework and recommendations
Authors: George Bert , Andersen Lotte B. , Hall Jeremy L. , Pandey Sanjay K.
Published: November 2023

Literature reviews have become widespread in public administration, especially in the past decade. These reviews typically adopt widely‐accepted approaches with many drawing upon systematized approaches to review in fields like medicine and psychology. Public administration, however, is a professional, design‐oriented discipline, focused on enhancing theory to solve real‐life policy, administrative, and managerial challenges. Recognizing the unique traditions and purposes in public administration scholarship, it is important to take stock of how public administration scholars “do” reviews, with the aim of providing recommendations to rejuvenate the state of the art in reviewing. We present a framework to guide review efforts in public administration centered on purpose (why?), object (what?), subject (who?), community (for whom?) and practices (how?). Next, we present different approaches to doing reviews and how those approaches present different answers to the questions raised above. Finally, we discuss examples of public administration reviews within each approach and conclude with specific recommendations for researchers and practitioners who want to use reviews to rejuvenate public administration.
Unpacking the modeling process for energy policy making
Authors: Lo Piano Samuele , Lőrincz Máté János , Puy Arnald , Pye Steve , Saltelli Andrea , Smith Stefán Thor , van der Sluijs Jeroen
Published: November 2023

This article explores how the modeling of energy systems may lead to an undue closure of alternatives by generating an excess of certainty around some of the possible policy options. We retrospectively exemplify the problem with the case of the International Institute for Applied Systems Analysis (IIASA) global modeling in the 1980s. We discuss different methodologies for quality assessment that may help mitigate this issue, which include Numeral Unit Spread Assessment Pedigree (NUSAP), diagnostic diagrams, and sensitivity auditing (SAUD). We illustrate the potential of these reflexive modeling practices in energy policy‐making with three additional cases: (i) the case of the energy system modeling environment (ESME) for the creation of UK energy policy; (ii) the negative emission technologies (NETs) uptake in integrated assessment models (IAMs); and (iii) the ecological footprint indicator. We encourage modelers to adopt these approaches to achieve more robust, defensible, and inclusive modeling activities in the field of energy research.
Intravenous immunoglobulin alteration in response to adverse reactions in neurological conditions: A retrospective cohort study
Authors: Jiang Melinda , Lam Lydia , Kovoor Joshua G. , Kimber James , Gupta Aashray K. , Stretton Brandon , Goh Rudy , Bacchi Stephen
Published: November 2023

Introduction

Intravenous immunoglobulin (IVIg) is an important treatment in a range of neurological conditions. There is currently limited evidence regarding the frequency and management of IVIg‐associated adverse reactions (AR) in neurological disorders.

Methods

A single‐centre 18‐month retrospective cohort study was conducted for all patients at a single tertiary hospital receiving IVIg as an inpatient or the medical day unit. Electronic medical record AR and alerts were reviewed for entries relating to IVIg, and prescribing records associated with recent IVIg administration were reviewed for the use of premedications. Case note review was undertaken to identify AR associated with alterations in IVIg treatment (such as reduction in rate, use of premedications or cessation of IVIg). Demographic, patient, and treatment factors were analysed for associations with AR necessitating alteration in IVIg treatment.

Results

This study included 98 individuals who received IVIg during the study period. Of these, 12 (12.1%) patients required an alteration in their IVIg treatment. In total, 3 (3.1%) of the 98 included patients required a reduced rate of IVIg, and 10 (10.2%) patients received premedication. The most common premedications were normal saline at the time of the infusion, cetirizine, and hydrocortisone. No demographic factors, indications or comorbidities were found to be associated with an increased likelihood of AR. However, an IVIg daily dose of >35 g and >45 g were associated with an increased likelihood of requiring IVIg treatment alteration due to AR.

Conclusions

Alterations to IVIg treatment due to AR are commonly required in neurology patients, and may be associated with higher daily doses of IVIg.
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

Phytoplasmas 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

Developing 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

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.
Fabrication and characterization of a hybrid magnetic structure based on highly ordered metallic nanotube arrays
Authors: Altama Alfreda Krisna , Kong Fanhua , Sugiarto Natanael Ardi , Hsu Peikai , Chen Shih-Yun , Yiu Pakman , Chu Jinn P.
Published: November 2023

Metallic nanotube arrays (MeNTAs) are used in a wide range of applications, including optoelectronic devices, drug delivery, and catalysis. This paper presents a hybrid MeNTA structure in which the nanotubes are filled with Fe3O4 nanoparticles (NPs) to enhance their utility. The proposed fabrication scheme allows the adjustment of the magnetic properties and size of Fe3O4 NPs simply by altering the ratio of reducing agents during the hydrothermal synthesis process. Our research demonstrated that MeNTAs can be functionalized through the application of Fe3O4 magnetic NPs to create a hybrid magnetic structure of high resolution with specific magnetic properties. The vibrating sample magnetometry results revealed that the ferromagnetism of the proposed hybrid MeNTA/Fe3O4 structure was not as strong as that of the Fe3O4 NPs themselves; however, we provide conclusive evidence that the hybrid highly ordered MeNTA structure possesses magnetic properties.
HAXPES reference spectra of KI with Cr Kα excitation
Authors: Zheng Dong , Young Christopher N. , Stickle William F.
Published: November 2023

Hard X-ray Photoelectron Spectroscopy (HAXPES) using monochromatic Cr Kα radiation (5414.8 eV) has been used to acquire XPS and Auger data on a sputtered potassium iodide (KI) sample. Survey data, high-resolution scans of all observed photoelectron peaks, and high-resolution scans of Auger lines are presented herein.
MKL/SRF and Bcl6 mutual transcriptional repression safeguards the fate and positioning of neocortical progenitor cells mediated by RhoA
Authors: Cossard Alexia , Stam Kirsten , Smets Aurore , Jossin Yves
Published: November 2023

During embryogenesis, multiple intricate and intertwined cellular signaling pathways coordinate cell behavior. Their slightest alterations can have dramatic consequences for the cells and the organs they form. The transcriptional repressor Bcl6 was recently found as important for brain development. However, its regulation and integration with other signals is unknown. Using in vivo functional approaches combined with molecular mechanistic analysis, we identified a reciprocal regulatory loop between B cell lymphoma 6 (Bcl6) and the RhoA-regulated transcriptional complex megakaryoblastic leukemia/serum response factor (MKL/SRF). We show that Bcl6 physically interacts with MKL/SRF, resulting in a down-regulation of the transcriptional activity of both Bcl6 and MKL/SRF. This molecular cross-talk is essential for the control of proliferation, neurogenesis, and spatial positioning of neural progenitors. Overall, our data highlight a regulatory mechanism that controls neuronal production and neocortical development and reveal an MKL/SRF and Bcl6 interaction that may have broader implications in other physiological functions and in diseases.
Temporal and spatial tracking of ultrafast light-induced strain and polarization modulation in a ferroelectric thin film
Authors: Gu Ruizhe , Juvé Vincent , Laulhé Claire , Bouyanfif Houssny , Vaudel Gwenaëlle , Poirier Aurélie , Dkhil Brahim , Hollander Philippe , Paillard Charles , Weber Mads C. , Sando Daniel , Fusil Stéphane , Garcia Vincent , Ruello Pascal
Published: November 2023

Ultrashort light pulses induce rapid deformations of crystalline lattices. In ferroelectrics, lattice deformations couple directly to the polarization, which opens the perspective to modulate the electric polarization on an ultrafast time scale. Here, we report on the temporal and spatial tracking of strain and polar modulation in a single-domain BiFeO
3
thin film by ultrashort light pulses. To map the light-induced deformation of the BiFeO
3
unit cell, we perform time-resolved optical reflectivity and time-resolved x-ray diffraction. We show that an optical femtosecond laser pulse generates not only longitudinal but also shear strains. The longitudinal strain peaks at a large amplitude of 0.6%. The access of both the longitudinal and shear strains enables to quantitatively reconstruct the ultrafast deformation of the unit cell and to infer the corresponding reorientation of the ferroelectric polarization direction in space and time. Our findings open new perspectives for ultrafast manipulation of strain-coupled ferroic orders.
Centromere innovations within a mouse species
Authors: Gambogi Craig W. , Pandey Nootan , Dawicki-McKenna Jennine M. , Arora Uma P. , Liskovykh Mikhail A. , Ma Jun , Lamelza Piero , Larionov Vladimir , Lampson Michael A. , Logsdon Glennis A. , Dumont Beth L. , Black Ben E.
Published: November 2023

Mammalian centromeres direct faithful genetic inheritance and are typically characterized by regions of highly repetitive and rapidly evolving DNA. We focused on a mouse species,
Mus pahari,
that we found has evolved to house centromere-specifying centromere protein-A (CENP-A) nucleosomes at the nexus of a satellite repeat that we identified and termed π-satellite (π-sat), a small number of recruitment sites for CENP-B, and short stretches of perfect telomere repeats. One
M. pahari
chromosome, however, houses a radically divergent centromere harboring ~6 mega–base pairs of a homogenized π-sat–related repeat, π-sat
B
, that contains >20,000 functional CENP-B boxes. There, CENP-B abundance promotes accumulation of microtubule-binding components of the kinetochore and a microtubule-destabilizing kinesin of the inner centromere. We propose that the balance of pro- and anti-microtubule binding by the new centromere is what permits it to segregate during cell division with high fidelity alongside the older ones whose sequence creates a markedly different molecular composition.
A printed luminescent flier inspired by plant seeds for eco-friendly physical sensing
Authors: Cikalleshi Kliton , Nexha Albenc , Kister Thomas , Ronzan Marilena , Mondini Alessio , Mariani Stefano , Kraus Tobias , Mazzolai Barbara
Published: November 2023

Continuous and distributed monitoring of environmental parameters may pave the way for developing sustainable strategies to tackle climate challenges. State-of-the-art technologies, made with electronic systems, are often costly, heavy, and generate e-waste. Here, we propose a new generation of self-deployable, biocompatible, and luminescent artificial flying seeds for wireless, optical, and eco-friendly monitoring of environmental parameters (i.e., temperature). Inspired by naturalAcer campestreplant seeds, we developed three-dimensional functional printed luminescent seed–like fliers, selecting polylactic acid as a biocompatible matrix and temperature as a physical parameter to be monitored. The artificial seeds mimic the aerodynamic and wind dispersal performance of the natural ones. The sensing properties are given by the integration of fluorescent lanthanide–doped particles, whose photoluminescence properties depend on temperature. The luminescent artificial flying seeds can be optically read from a distance using eye-safe near-infrared wavelengths, thus acting as a deployable sensor for distributed monitoring of topsoil environmental temperatures.
Manipulating nitration and stabilization to achieve high energy
Authors: Singh Jatinder , Staples Richard J. , Shreeve Jean’ne M.
Published: November 2023

Nitro groups have played a central and decisive role in the development of the most powerful known energetic materials. Highly nitrated compounds are potential oxidizing agents, which could replace the environmentally hazardous used materials such as ammonium perchlorate. The scarcity of azole compounds with a large number of nitro groups is likely due to their inherent thermal instability and the limited number of ring sites available for bond formation. Now, the formation of the first azole molecule bonded to seven nitro groups, 4-nitro-3,5-bis(trinitromethyl)-1
H
-pyrazole (
4
), by the stepwise nitration of 3,5-dimethyl-1
H
-pyrazole is reported. Compound
4
exhibits exceptional physicochemical properties with a positive oxygen balance (OB
CO2
= 13.62%) and an extremely high calculated density (2.04 g cm
−3
at 100 K). This is impressively high for a C, H, N, O compound. This work is a giant step forward to highly nitrated and dense azoles and will accelerate further exploration in this challenging field.
Parathyroid hormone treatment partially reverses endplate remodeling and attenuates low back pain in animal models of spine degeneration
Authors: Ling Zemin , Crane Janet , Hu Hao , Chen Yan , Wan Mei , Ni Shuangfei , Demehri Shadpour , Mohajer Bahram , Peng Xinsheng , Zou Xuenong , Cao Xu
Published: November 2023

Low back pain (LBP) is one of the most prevalent diseases affecting quality of life, with no disease-modifying therapy. During aging and spinal degeneration, the balance between the normal endplate (EP) bilayers of cartilage and bone shifts to more bone. The aged/degenerated bony EP has increased porosity because of osteoclastic remodeling activity and may be a source of LBP due to aberrant sensory innervation within the pores. We used two mouse models of spinal degeneration to show that parathyroid hormone (PTH) treatment induced osteogenesis and angiogenesis and reduced the porosity of bony EPs. PTH increased the cartilaginous volume and improved the mechanical properties of EPs, which was accompanied by a reduction of the inflammatory factors cyclooxygenase-2 and prostaglandin E
2
. PTH treatment furthermore partially reversed the innervation of porous EPs and reversed LBP-related behaviors. Conditional knockout of PTH 1 receptors in the nucleus pulposus (NP) did not abolish the treatment effects of PTH, suggesting that the NP is not the primary source of LBP in our mouse models. Last, we showed that aged rhesus macaques with spontaneous spinal degeneration also had decreased EP porosity and sensory innervation when treated with PTH, demonstrating a similar mechanism of PTH action on EP sclerosis between mice and macaques. In summary, our results suggest that PTH treatment could partially reverse EP restructuring during spinal regeneration and support further investigation into this potentially disease-modifying treatment strategy for LBP.
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

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

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

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

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

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

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

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

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

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.
Bacterial community dynamics during distilled spirit fermentation: influence of mash recipes and fermentation processes
Authors: Liu Shuang , Greenhut Isaac V. , Heist E. Patrick , Heist Melanie R. , Moe Luke A.
Published: November 2023

The popularity and production of whiskey have grown dramatically in recent years. During whiskey fermentation, lactic acid bacteria (LAB) are a major concern since they can outcompete yeast and spoil the fermentation. However, some bacteria present in the fermentation could potentially counter this effect and promote fermentation efficiency. To better understand the possible roles bacteria play in yeast-based whiskey fermentations, we examined bacterial community dynamics across fermentation stages and investigated how variation in the mash recipe affects bacterial community composition and fermentation efficiency. To this end, we collected 193 samples from three distilleries at the beginning (Cook/set), middle (Fermentation), and end (Drop) of whiskey fermentation, with six mash recipes sampled from one distillery. We used high-performance liquid chromatography (HPLC) to quantify the contents of sugars, organic acids, and ethanol, which revealed distinct differences between distilleries and mash recipes. High-throughput Illumina Miseq sequencing of the 16S rRNA gene V4 region revealed that bacterial communities shifted toward Firmicutes during the fermentative conversion of sugar to ethanol, especially Lactobacillales. Mash recipes also influenced sugar composition, fermentation efficiency, and microbial dynamics. Recipe-specific operational taxonomic unit (OTU) biomarkers in Drop samples included
Leuconostoc
for corn,
Lactococcus
for wheat, and
Lactobacillaceae_unclassified
for rye, while
Escherichia/Shigella
was associated with sorghum, suggesting potential suppression of LAB.

IMPORTANCE

Production of ethanol from sugars and yeast is an ancient, ostensibly simple process. The source of sugars varies depending on the desired product and can include fruits, vegetables, molasses, honey, or grains, among other things. The source of yeast can be natural in the case of spontaneous ferments, but dry yeast addition is typical for large-scale fermentations. While the polymicrobial nature of some alcoholic fermentations is appreciated (e.g., for wine), most grain-based ethanol producers view microbes, apart from the added yeast, as “contaminants” meant to be controlled in order to maximize efficiency of ethanol production per unit of sugar. Nonetheless, despite rigorous cleaning-in-place measures and cooking the mash, bacteria are routinely cultured from these fermentations. We now know that bacteria can contribute to fermentation efficiency on an industrial scale, yet nothing is known about the makeup and stability of microbial communities in distilled spirit fermentations. The work here establishes the roles of mash recipes and distillery practices in microbial community assembly and dynamics over the course of fermentation. This represents an important first step in appreciating the myriad roles of bacteria in the production of distilled spirits.
Transcriptional regulation of the fidaxomicin gene cluster and cellular development in
Actinoplanes deccanensis
YP-1 by the pleiotropic regulator MtrA
Authors: Xie Huang , Ruan Jing-Yi , Bu Qing-Ting , Li Yue-Ping , Su Yi-Ting , Zhao Qing-Wei , Du Yi-Ling , Li Yong-Quan
Published: November 2023

Fidaxomicin is an 18-membered glycosidic macrolide polyketide that was clinically used in the treatment of
Clostridium difficile
infection in 2011. Although the biosynthetic mechanism and pathway-specific regulator of fidaxomicin were well elaborated, little is known about the pleiotropic regulators outside the fidaxomicin gene cluster. To further reveal the transcriptional regulatory mechanism of fidaxomicin biosynthesis in
Actinoplanes deccanensis
YP-1, we used the 5′-biotin-labeled
fadR1
promoter (
fadS5R1p
) as a probe to affinity isolate the
fadS5R1p
-interactive protein MtrA, a response regulator of the two-component system MtrAB, from the proteome of mycelia. MtrA is bound directly to
fadS5R1p
to positively regulate gene cluster expression and fidaxomicin production. Fidaxomicin production was improved by 37% in the
mtrA
overexpressed strain. Furthermore, we revealed that MtrA tends to bind GTKAYS motifs and influence genes involved in secondary metabolites, phosphate transport, methionine transport, nitrogen metabolism, drug transport, membrane properties, etc. Overall, for the first time at the transcriptional level, we comprehensively revealed a pleiotropic regulator, MtrA, that not only directly mediates the FadR1-specific pathway to regulate the proper production of fidaxomicin but also participates in bacterial growth and development.

IMPORTANCE

Cascade regulation networks are almost present in various kinds of microorganisms, but locating and systematically elucidating specific pleiotropic regulators related to a certain gene cluster can be a tricky problem. Here, based on the promoter of the fidaxomicin pathway-specific regulator FadR1, we utilized a “DNA to Proteins” affinity purification method and captured a global regulator MtrA, which positively regulates fidaxomicin biosynthesis. In the
mtrA
overexpressed strain, the production of fidaxomicin was improved by 37% compared to the native strain. Then, we combined the “Protein to DNAs” affinity purification method (DAP-seq) with the results of RNA-seq and systematically elucidated the primary and secondary metabolic processes in which MtrA directly or indirectly participates. Thus, our work brought up a new way to improve fidaxomicin production from the perspective of global regulation and analyzed the regulatory mechanism of MtrA. Meanwhile, we provided a novel methodology for the research of cascade regulation networks and vital secondary metabolites.