bluuebunny/crossref_metadata_2025 huggingface dataset:
Deciphering the β‐carotene hyperaccumulation in Dunaliella by the comprehensive analysis of Dunaliella salina and Dunaliella tertiolecta under high light conditions
Authors: Kim Minjae , Kim Jongrae , Lee Sangmuk , Khanh Nguyen , Li Zhun , Polle Juergen E. W. , Jin EonSeon
Published: September 2023

The green microalga Dunaliella salina hyperaccumulates β‐carotene in the chloroplast, which turns its cells orange. This does not occur in the sister species Dunaliella tertiolecta. However, the molecular mechanisms of β‐carotene hyperaccumulation were still unclear. Here, we discovered the reasons for β‐carotene hyperaccumulation by comparing the morphology, physiology, genome, and transcriptome between the carotenogenic D. salina and the noncarotenogenic D. tertiolecta after transfer to high light. The differences in photosynthetic capacity, cell growth, and the concentration of stored carbon suggest that these species regulate the supply and utilization of carbon differently. The number of β‐carotene‐containing plastid lipid globules increased in both species, but much faster and to a greater extent in D. salina than in D. tertiolecta. Consistent with the accumulation of plastid lipid globules, the expression of the methyl‐erythritol‐phosphate and carotenoid biosynthetic pathways increased only in D. salina, which explains the de novo synthesis of β‐carotene. In D. salina, the concomitantly upregulated expression of the carotene globule proteins suggests that hyperaccumulation of β‐carotene also requires a simultaneous increase in its sink capacity. Based on genomic analysis, we propose that D. salina has genetic advantages for routing carbon from growth to carotenoid metabolism.
AT Hook‐Like 10 phosphorylation determines ribosomal RNA processing 6‐like 1 (RRP6L1) chromatin association and growth suppression during water stress
Authors: Wong Min May , Huang Xin‐Jie , Bau Yu‐Chiuan , Verslues Paul E.
Published: September 2023

Phosphorylation of AT Hook‐Like 10 (AHL10), one of the AT‐hook family of plant‐specific DNA binding proteins, is critical for growth suppression during moderate severity drought (low water potential, ψw) stress. To understand how AHL10 phosphorylation determines drought response, we identified putative AHL10 interacting proteins and further characterized interaction with RRP6L1, a protein involved in epigenetic regulation. RRP6L1 and AHL10 mutants, as well as ahl10‐1rrp6l1‐2, had similar phenotypes of increased growth maintenance during low ψw. Chromatin precipitation demonstrated that RRP6L1 chromatin association increased during low ψw stress and was dependent upon AHL10 phosphorylation. Transcriptome analyses showed that AHL10 and RRP6L1 have concordant effects on expression of stress‐ and development‐related genes. Together these results indicate that stress signalling can act via AHL10 phosphorylation to control the chromatin association of the key regulatory protein RRP6L1. AHL10 and RRP6L1 interaction in meristem cells is part of a mechanism to downregulate growth during low ψw stress. Interestingly, the loss of AHL13, which is homologous to AHL10 and phosphorylated at a similar C‐terminal site, blocked the enhanced growth maintenance of ahl10‐1. Thus, AHL10 and AHL13, despite their close homology, are not redundant but rather have distinct roles, likely related to the formation of AHL hetero‐complexes.
Secretory leucocyte protease inhibitor (SLPI) as an adjunct prognostic biomarker for canine pyometra
Authors: Sasidharan Jisna Kuttiyeri , Patra Manas Kumar , Khan Javid Ahmad , Shah Irfan , Sharma Renu , De Ujjwal Kumar , Saxena Abhishek Chandra , Singh Sanjay Kumar , Kumar Harendra , Krishnaswamy Narayanan
Published: September 2023

Pyometra is a potentially life‐threatening condition that affects intact female dogs in their middle to advance age. Timely diagnosis and appropriate treatment are critical for the survival of patients, especially when pyometra advances to sepsis. This study aimed to investigate the prognostic potential of certain haematology, serum biochemical and inflammatory biomarker, secretory leucocyte protease inhibitor (SLPI) for pyometra in bitches (n = 41). Blood samples were collected after clinical diagnosis of pyometra for haematology and serum biochemistry. Based on the prognosis following medical/surgical treatment, animals were retrospectively categorized into survivor (n = 29) and dead (n = 12). Endometrial tissue sections were obtained from the bitches undergoing ovariohysterectomy (n = 21). Serum concentration of SLPI was quantified using sandwich ELISA and its expression in the endometrium was investigated using RT‐qPCR. A marked increase in the total leucocyte count (TLC), neutrophils, blood urea nitrogen (BUN) and serum creatinine was observed in the female dogs that did not survive. Significant elevation in the serum SLPI concentration (3.49 ± 0.44 vs. 2.38 ± 0.13 ng/mL) was observed in the bitches those died after the treatment, in comparison to those survived (p < .01). Additionally, there was a notable upregulation of SLPI in the endometrium in the bitches those died due to pyometra. Based on the ROC analysis results, it was observed that a cut‐off concentration of 2.93 ng/mL for SLPI, 27.77 mg/dL for BUN and 16.3 × 103/μL for TLC could effectively distinguish the prognosis of pyometra‐affected dogs. From this study, it can be concluded that upregulation of SLPI in the endometrium and its elevated concentration in peripheral circulation along with TLC and BUN concentration could serve as valuable indicators for predicting the prognosis of pyometra in bitches.
Method for high‐plex analysis of immune cells in human skin using the GeoMx system
Authors: Ignatov Borislav , Sortebech Daniel , Emmanuel Thomas , Zhuravleva Ekaterina , Eidsmo Liv
Published: September 2023

Specific T cell populations in the skin have been demonstrated as important disease drivers in several dermatoses. Due to the unique skin architecture, these cells are not grouped together in structures but dispersedly spread out throughout the epidermis. Following tissue disruption and isolation, only about 10% of skin T cells are recovered and any in vitro expansion may alter their bona fide phenotype. The Nanostring GeoMx system was developed to address cellular phenotype and protein expression in a tissue spatial context. To do so, regions of interest (ROI) must exceed a certain area threshold (usually 100 μm in diameter) to generate a sufficient signal‐to‐noise ratio. Here, we present an approach that allows for the pooling of numerous smaller ROIs within the skin, enabling T cell and melanocyte phenotyping. Skin samples from healthy individuals and vitiligo patients were analysed using the GeoMx system and several immune profiling panels. A sufficient signal‐to‐noise ratio was achieved by pooling smaller ROIs and analysing them as a single group. While this prevents spatial analysis, this method allows for detailed analysis of cells as a population in the context of their physiological environment, making it possible to investigate in situ phenotype of rare cells in different tissue compartments.
The development of an informative leaflet for children and adolescents suffering from Osgood‐Schlatter disease
Authors: Hansen Rudi , Rathleff Michael Skovdal , Lundgaard‐Nielsen Mathilde , Holden Sinead
Published: September 2023

The mainstay in the treatment of Osgood‐Schlatter Disease (OSD) is guidance on activity modification alongside exercises. The purpose of this study was to create an informative leaflet for patients with OSD, based on evidence and stakeholders perspectives. A synthesis of the literature, including national reference work, clinical research, and systematic reviews informed the initial leaflet. Twelve children with OSD and four clinical experts provided feedback through semi‐structured interviews. After incorporating stakeholder input, the leaflet ‘Osgood‐Schlatter—Information and guidance’ was developed. This provides a resource to assist the provision of information and translation of the current evidence.
Ideological foundations of capitalism and its organizational models: A study using popular management content on LinkedIn
Authors: Duarte Ricardo Mello , Candido Silvio Eduardo Alvarez
Published: September 2023

The paper investigates the ideological foundations of contemporary capitalism and its organizational models in Brazil. Our analysis considers three positions present in the literature: the thesis of the new spirit of capitalism; the literature about financialization and the shareholder value model; and the configuration of a managerial mode of domination. A content analysis was conducted to investigate normative business content from Brazilian “top voices” on the LinkedIn network. A total of 180 influential texts from 32 authors composed our corpus and were assessed based on an abductive approach that had as references the economies of worth model and a related framework for assessing the dynamic configuration of capitalism justifications. Results support the idea that contemporary capitalism is characterized in ideological terms by the fluidity of normative references restricting the market logic, configuring a complex or managerial mode of domination.
The impact of partisanship and religiosity on conspiracy‐theory beliefs in Turkey
Authors: Nefes Türkay Salim , Aksoy Ozan
Published: September 2023

Why do people believe in conspiracy theories? This paper responds to this ever‐significant question by scrutinizing people's belief in conspiracy theories in Turkey. Building on Max Weber's theory of rationalization, it proposes that value‐laden and instrumentally rational predispositions, namely religiosity and partisanship, predict people's beliefs in conspiracy theories. This current study tests this hypothesis by analyzing two nationwide surveys conducted during a period of significant changes in modern Turkish politics: January and July 2013. The findings confirm the hypothesis that people interpret conspiracy theories in line with their instrumental, rational interests and values.
COVID‐19‐related threat perceptions, political identity, and voting in the 2020 presidential election
Authors: Casteigne Maria , O’Mara Kunz Erin M. , Losee Joy , Kerner Liz
Published: September 2023

Perceptions of the COVID‐19 virus varied drastically in the United States, with many people highly concerned by health‐related consequences (realistic threats) and many others concerned by sociocultural implications (symbolic threats). Across three studies, we tested whether differing realistic and symbolic COVID‐19 related threat perceptions varied along gender and political identity near the 2020 US Presidential Election. In all three studies, we found that realistic COVID‐19 related threat perceptions were positively associated with a liberal political identity; this pattern did not vary by gender. In Studies 1 and 3, symbolic COVID‐19 related threat perceptions were positively associated with a conservative political identity and also did not vary by gender. In Study 2, however, the association between symbolic threat and political identity did vary by gender. Symbolic COVID‐19 related threat perceptions were positively associated with a conservative identity for men but not women; for women, threat and political identity were unrelated.
Surgical and oncologic outcomes in dogs with malignant peripheral nerve sheath tumours arising from the brachial or lumbosacral plexus
Authors: Stokes Rebecca , Wustefeld‐Janssens Brandan G. , Hinson Whitney , Wiener Dominique J. , Hollenbeck Danielle , Bertran Judith , Mickelson Megan , Chen Carolyn L. , Selmic Laura , Aly Ali , Hayes Galina
Published: September 2023

Malignant peripheral nerve sheath tumours (MPNST) of a plexus nerve or nerve root cause significant morbidity and present a treatment challenge. The surgical approach can be complex and information is lacking on outcomes. The objective of this study was to describe surgical complication rates and oncologic outcomes for canine MPNST of the brachial or lumbosacral plexus. Dogs treated for a naïve MPNST with amputation/hemipelvectomy with or without a laminectomy were retrospectively analysed. Oncologic outcomes were disease free interval (DFI), overall survival (OS), and 1‐ and 2‐year survival rates. Thirty dogs were included. The surgery performed was amputation alone in 17 cases (57%), and amputation/hemipelvectomy with laminectomy in 13 cases (43%). Four dogs (13%) had an intraoperative complication, while 11 dogs (37%) had postoperative complications. Histologic margins were reported as R0 in 12 dogs (40%), R1 in 12 dogs (40%), and R2 in five dogs (17%). No association was found between histologic grade and margin nor extent of surgical approach and margin. Thirteen dogs (46%) had recurrence. The median DFI was 511 days (95% CI: 140–882 days). The median disease specific OST was 570 days (95% CI: 467–673 days) with 1‐ and 2‐year survival rates of 82% and 22% respectively. No variables were significantly associated with recurrence, DFI, or disease specific OST. These data show surgical treatment of plexus MPNST was associated with a high intra‐ and postoperative complication rate but relatively good disease outcomes. This information can guide clinicians in surgical risk management and owner communication regarding realistic outcomes and complications.
Radiografía y ecografía de abdomen como métodos diagnósticos en enterocolitis necrosante
Authors: Sierra Pérez Angie Natali , Otálora Baquero Miguel Andrés , Medellín Alfonso Lozada , Mogollón Portilla Valentina , Rivera Bernal Carlos Andres , Guerrero Restrepo Camila
Published: September 2023

La enterocolitis necrosante (ECN) es la emergencia gastrointestinal adquirida más frecuente en el periodo neonatal, principalmente en recién nacidos pretérmino. Durante el último cuarto de siglo, esta patología ha emergido como un factor de mortalidad neonatal. Los casos graves pueden conducir a perforación intestinal, síndrome de respuesta inflamatoria sistémica, disfunción multiorgánica y muerte. Una vez se ha producido la perforación intestinal, su tasa de mortalidad global varía entre el 20 % y el 40 %, e incluso llega al 60 % en recién nacidos con bajo peso al nacer. Tradicionalmente, el estándar de oro para la evaluación y estadificación por imágenes del intestino neonatal ha sido la radiografía de abdomen. Aun así, este método diagnóstico ha demostrado ser inespecífico para evaluar características tempranas relacionadas con las asas intestinales dilatadas, isquemia y necrosis. Es fundamental un diagnóstico precoz que permita un tratamiento oportuno y disminuya la necesidad de procedimientos quirúrgicos y las complicaciones secundarias. Se ha planteado y descrito en la literatura el uso de la ecografía abdominal con análisis Doppler como método diagnóstico de la ECN. Esta permite evaluar un mayor espectro de anomalías, no produce radiación ionizante y tiene la capacidad de reconocer necrosis intestinal previo a la perforación o al deterioro clínico. Por lo anterior, en el artículo se revisa el tema de la ecografía y radiografía de abdomen como métodos diagnósticos en la ECN.
“Nonlinear” pursuit of understanding pollutant accumulation and chemistry at environmental and biological interfaces
Authors: Carpenter Andrew P. , Golbek Thaddeus W.
Published: September 2023

Over the past few decades, the public recognition of the prevalence of certain classes of pollutants, such as perfluoroalkyl substances and nanoplastics, within the environment, has sparked growing concerns over their potential impact on environmental and human health. Within both environmental and biological systems, the adsorption and structural organization of pollutants at aqueous interfaces can greatly impact the chemical reactivity and transformation. Experimentally probing chemical behavior at interfaces can often pose a problem due to bulk solvated molecules convoluting molecular signatures from interfacial molecules. To solve this problem, there exist interface-specific nonlinear spectroscopy techniques that can directly probe both macroscopic planar interfaces and nanoplastic interfaces in aqueous environments. These techniques can provide essential information such as chemical adsorption, structure, and reactivity at interfaces. In this perspective, these techniques are presented with obvious advantages for studying the chemical properties of pollutants adsorbed to environmental and biological interfaces.
Systematic design and experimental realization of a radially cascaded spherical piezoelectric transducer
Authors: Tang Yifan , Lin Shuyu
Published: September 2023

As a critical component of ultrasonic vibration systems, piezoelectric transducers play an essential role in various practical application scenarios. Recent advances in spherical transducers have been widely used in underwater sound and structural health monitoring, while the cascaded spherical piezoelectric transducer with arbitrary piezoceramic shell thickness has not been investigated. Here, we propose a radially cascaded spherical piezoelectric transducer (RCSPT) and derive its electromechanical equivalent circuit with mechanical losses, dielectric losses, and load mechanical impedances. The resulting device is composed of three concentric spherical metal shells and two radially polarized spherical piezoceramic shells. The underlying physical mechanism is the inverse piezoelectric effect, which converts electrical signals into mechanical vibrations. The effects of the spherical piezoceramic shell's thickness and location on the RCSPT are studied. We also analyze the effects of mechanical losses, dielectric losses, and load mechanical impedances on the modulus of input electric impedance of the cascaded spherical transducer. The experiments are conducted to verify the electromechanical characteristics of the resulting device, which are in good agreement with the simulated results and theoretical predictions. Our methodology will offer new possibilities for designing RCSPTs and may promote applications in various fields, such as underwater acoustic detection and structural health monitoring.
RNA folding studies inside peptide-rich droplets reveal roles of modified nucleosides at the origin of life
Authors: Meyer McCauley O. , Yamagami Ryota , Choi Saehyun , Keating Christine D. , Bevilacqua Philip C.
Published: September 2023

Compartmentalization of RNA in biopolymer-rich membraneless organelles is now understood to be pervasive and critical for the function of extant biology and has been proposed as a prebiotically plausible way to accumulate RNA. However, compartment-RNA interactions that drive encapsulation have the potential to influence RNA structure and function in compartment- and RNA sequence–dependent ways. Here, we detail next-generation sequencing (NGS) experiments performed in membraneless compartments called complex coacervates to characterize the fold of many different transfer RNAs (tRNAs) simultaneously under the potentially denaturing conditions of these compartments. Notably, we find that natural modifications favor the native fold of tRNAs in these compartments. This suggests that covalent RNA modifications could have played a critical role in metabolic processes at the origin of life.
Intentional creation of carbon-rich dark earth soils in the Amazon
Authors: Schmidt Morgan J. , Goldberg Samuel L. , Heckenberger Michael , Fausto Carlos , Franchetto Bruna , Watling Jennifer , Lima Helena , Moraes Bruno , Dorshow Wetherbee B. , Toney Joshua , Kuikuro Yamalui , Waura Kumessi , Kuikuro Huke , Kuikuro Taku Wate , Kuikuro Takumã , Kuikuro Yahila , Kuikuro Afukaka , Teixeira Wenceslau , Rocha Bruna , Honorato Vinicius , Tavares Hugo , Magalhães Marcos , Barbosa Carlos Augusto , da Fonseca João Aires , Mendes Kelton , Alleoni Luís Reynaldo Ferracciú , Cerri Carlos Eduardo Pellegrino , Arroyo-Kalin Manuel , Neves Eduardo , Perron J. Taylor
Published: September 2023

Fertile soil known as Amazonian dark earth is central to the debate over the size and ecological impact of ancient human populations in the Amazon. Dark earth is typically associated with human occupation, but it is uncertain whether it was created intentionally. Dark earth may also be a substantial carbon sink, but its spatial extent and carbon inventory are unknown. We demonstrate spatial and compositional similarities between ancient and modern dark earth and document modern Indigenous practices that enrich soil, which we use to propose a model for the formation of ancient dark earth. This comparison suggests that ancient Amazonians managed soil to improve fertility and increase crop productivity. These practices also sequestered and stored carbon in the soil for centuries, and we show that some ancient sites contain as much carbon as the above-ground rainforest biomass. Our results demonstrate the intentional creation of dark earth and highlight the value of Indigenous knowledge for sustainable rainforest management.
Using robotics to move a neurosurgeon’s hands to the tip of their endoscope
Authors: Price Karl , Peine Joseph , Mencattelli Margherita , Chitalia Yash , Pu David , Looi Thomas , Stone Scellig , Drake James , Dupont Pierre E.
Published: September 2023

A major advantage of surgical robots is that they can reduce the invasiveness of a procedure by enabling the clinician to manipulate tools as they would in open surgery but through small incisions in the body. Neurosurgery has yet to benefit from this advantage. Although clinical robots are available for the least invasive neurosurgical procedures, such as guiding electrode insertion, the most invasive brain surgeries, such as tumor resection, are still performed as open manual procedures. To investigate whether robotics could reduce the invasiveness of major brain surgeries while still providing the manipulation capabilities of open surgery, we created a two-armed joystick-controlled endoscopic robot. To evaluate the efficacy of this robot, we developed a set of neurosurgical skill tasks patterned after the steps of brain tumor resection. We also created a patient-derived brain model for pineal tumors, which are located in the center of the brain and are normally removed by open surgery. In comparison, testing with existing manual endoscopic instrumentation, we found that the robot provided access to a much larger working volume at the trocar tip and enabled bimanual tasks without compression of brain tissue adjacent to the trocar. Furthermore, many tasks could be completed faster with the robot. These results suggest that robotics has the potential to substantially reduce the invasiveness of brain surgery by enabling certain procedures currently performed as open surgery to be converted to endoscopic interventions.
A multi-laboratory preclinical trial in rodents to assess treatment candidates for acute ischemic stroke
Authors: Lyden Patrick D. , Diniz Márcio A. , Bosetti Francesca , Lamb Jessica , Nagarkatti Karisma A. , Rogatko André , Kim Sungjin , Cabeen Ryan P. , Koenig James I. , Akhter Kazi , Arbab Ali S. , Avery Brooklyn D. , Beatty Hannah E. , Bibic Adnan , Cao Suyi , Simoes Braga Boisserand Ligia , Chamorro Angel , Chauhan Anjali , Diaz-Perez Sebastian , Dhandapani Krishnan , Dhanesha Nirav , Goh Andrew , Herman Alison L. , Hyder Fahmeed , Imai Takahiko , Johnson Conor W. , Khan Mohammad B. , Kamat Pradip , Karuppagounder Senthilkumar S. , Kumskova Mariia , Mihailovic Jelena M. , Mandeville Joseph B. , Morais Andreia , Patel Rakesh B. , Sanganahalli Basavaraju G. , Smith Cameron , Shi Yanrong , Sutariya Brijesh , Thedens Daniel , Qin Tao , Velazquez Sofia E. , Aronowski Jaroslaw , Ayata Cenk , Chauhan Anil K. , Leira Enrique C. , Hess David C. , Koehler Raymond C. , McCullough Louise D. , Sansing Lauren H.
Published: September 2023

Human diseases may be modeled in animals to allow preclinical assessment of putative new clinical interventions. Recent, highly publicized failures of large clinical trials called into question the rigor, design, and value of preclinical assessment. We established the Stroke Preclinical Assessment Network (SPAN) to design and implement a randomized, controlled, blinded, multi-laboratory trial for the rigorous assessment of candidate stroke treatments combined with intravascular thrombectomy. Efficacy and futility boundaries in a multi-arm multi-stage statistical design aimed to exclude from further study highly effective or futile interventions after each of four sequential stages. Six independent research laboratories performed a standard focal cerebral ischemic insult in five animal models that included equal numbers of males and females: young mice, young rats, aging mice, mice with diet-induced obesity, and spontaneously hypertensive rats. The laboratories adhered to a common protocol and efficiently enrolled 2615 animals with full data completion and comprehensive animal tracking. SPAN successfully implemented treatment masking, randomization, prerandomization inclusion and exclusion criteria, and blinded assessment of outcomes. The SPAN design and infrastructure provide an effective approach that could be used in similar preclinical, multi-laboratory studies in other disease areas and should help improve reproducibility in translational science.
Targeted C-to-T and A-to-G dual mutagenesis system for RhtA transporter
in vivo
evolution
Authors: Wei Zhandong , Zhao Dongdong , Wang Jie , Li Ju , Xu Ning , Ding Chao , Liu Jun , Li Siwei , Zhang Chunzhi , Bi Changhao , Zhang Xueli
Published: September 2023

T7 RNA polymerase (T7RNAP) has been fused with cytosine or adenine deaminase individually, enabling
in vivo
C-to-T or A-to-G transitions on DNA sequence downstream of T7 promoter, and greatly accelerated directed protein evolution. However, its base conversion type is limited. In this study, we created a dual-functional system for simultaneous C-to-T and A-to-G
in vivo
mutagenesis, called T7-DualMuta, by fusing T7RNAP with both cytidine deaminase (PmCDA1) and a highly active adenine deaminase (TadA-8e). The C-to-T and A-to-G mutagenesis frequencies of T7-DualMuta were 4.02 × 10
−3
and 1.20 × 10
−2
, respectively, with 24 h culturing and distributed mutations evenly across the target gene. The T7-DualMuta system was used to
in vivo
directed evolution of L-homoserine transporter RhtA, resulting in efficient variants that carried the four types of base conversions by T7-DualMuta. The evolved variants greatly increased the host growth rates at L-homoserine concentrations of 8 g/L, which was not previously achieved, and demonstrated the great
in vivo
evolution capacity. The novel molecular device T7-DualMuta efficiently provides both C/G-to-T/A and A/T-to-G/C mutagenesis on target regions, making it useful for various applications and research in Enzymology and Synthetic Biology studies. It also represents an important expansion of the base editing toolbox.

Importance

A T7-DualMuta system for simultaneous C-to-T and A-to-G
in vivo
mutagenesis was created. The mutagenesis frequency was 4.02 × 10
7
fold higher than the spontaneous mutation, which was reported to be approximately 10
−10
bases per nucleotide per generation. This mutant system can be utilized for various applications and research in Enzymology and Synthetic Biology studies.
Comparative genomic analysis of
Periweissella
and the characterization of novel motile species
Authors: Qiao Nanzhen , Bechtner Julia , Cnockaert Margo , Depoorter Eliza , Díaz-Muñoz Christian , Vandamme Peter , De Vuyst Luc , Gänzle Michael G.
Published: September 2023

The genus
Periweissella
was proposed as a novel genus in the
Lactobacillaceae
in 2022. However, the phylogenetic relationship between
Periweissella
and other heterofermentative lactobacilli, and the genetic and physiological properties of this genus remain unclear. This study aimed to determine the phylogenetic relationship between
Periweissella
and the two closest genera,
Weissella
and
Furfurilactobacillus
, by the phylogenetic analysis and calculation of (core gene) pairwise average amino acid identity. Targeted genomic analysis showed that fructose bisphosphate aldolase was only present in the genome of
Pw. cryptocerci
. Mannitol dehydrogenase was found in genomes of
Pw. beninensis
,
Pw. fabaria
, and
Pw. fabalis
. Untargeted genomic analysis identified the presence of flagellar genes in
Periweissella
but not in other closely related genera. Phenotypes related to carbohydrate fermentation and motility matched the genotypes. Motility genes were organized in a single operon and the proteins shared a high amino acid similarity in the genus
Periweissella
. The relatively low similarity of motility operons between
Periweissella
and other motile lactobacilli indicated the acquisition of motility by the ancestral species. Our findings facilitate the phylogenetic, genetic, and phenotypic understanding of the genus
Periweissella
.

Importance

The genus
Periweissella
is a heterofermentative genus in the
Lactobacillaceae
which includes predominantly isolates from cocoa fermentations in tropical climates. Despite the relevance of the genus in food fermentations, genetic and physiological properties of the genus are poorly characterized and genome sequences became available only after 2020. This study characterized strains of the genus by functional genomic analysis, and by determination of metabolic and physiological traits. Phylogenetic analysis revealed that
Periweissella
is the evolutionary link between rod-shaped heterofermentative lactobacilli and the coccoid
Leuconostoc
clade with the genera
Weissella
and
Furfurilactobacillus
as closest relatives.
Periweissella
is the only heterofermentative genus in the
Lactobacillaceae
which comprises predominantly motile strains. The genomic, physiological, and metabolic characterization of
Periweissella
may facilitate the potential use of strains of the genus as starter culture in traditional or novel food fermentations.
The alternative sigma factor SigN of
Bacillus subtilis
is intrinsically toxic
Authors: Burton Aisha T. , Pospíšilová Debora , Sudzinova Petra , Snider Elizabeth V. , Burrage Andrew M. , Krásný Libor , Kearns Daniel B.
Published: September 2023

Sigma factors bind and direct the RNA polymerase core to specific promoter sequences, and alternative sigma factors direct transcription of different regulons of genes. Here, we study the pBS32 plasmid-encoded sigma factor SigN of
Bacillus subtilis
to determine how it contributes to DNA damage-induced cell death. We find that SigN causes cell death when expressed at high levels and does so in the absence of its regulon suggesting it is intrinsically toxic. One way toxicity was relieved was by curing the pBS32 plasmid, which eliminated a positive feedback loop that led to SigN hyper-accumulation. Another way toxicity was relieved was through mutating the chromosomally encoded transcriptional repressor protein AbrB, thereby derepressing a potent antisense transcript that antagonized SigN expression. SigN efficiently competed with the vegetative sigma factor SigA
in vitro
, and SigN accumulation in the absence of positive feedback reduced SigA-dependent transcription suggesting that toxicity may be due to competitive inhibition of one or more essential transcripts. Why
B. subtilis
encodes a toxic sigma factor is unclear but SigN may function in host-inhibition during lytic conversion, as phage lysogen genes are also encoded on pBS32.

IMPORTANCE

Alternative sigma factors activate entire regulons of genes to improve viability in response to environmental stimuli. The pBS32 plasmid-encoded alternative sigma factor SigN of
Bacillus subtilis
however
,
is activated by the DNA damage response and leads to cellular demise. Here we find that SigN impairs viability by hyper-accumulating and outcompeting the vegetative sigma factor for the RNA polymerase core. Why
B. subtilis
retains a plasmid with a deleterious alternative sigma factor is unknown.
Expanding our grasp of two-component signaling in
Clostridioides difficile
Authors: Berumen Alvarez Orlando , Purcell Erin B.
Published: September 2023

The intestinal pathogen
Clostridioides difficile
encodes roughly 50 TCS, but very few have been characterized in terms of their activating signals or their regulatory roles. A. G. Pannullo, B. R. Zbylicki, and C. D. Ellermeier (J Bacteriol 205:e00164-23, 2023,
https://doi.org/10.1128/jb.00164-23
) have identified both for the novel
C. difficile
TCD DraRS. DraRS responds to antibiotics that target lipid-II molecules in the bacterial cell envelope, and regulates the production of a novel glycolipid necessary for bacitracin and daptomycin resistance in
C. difficile
.
Multi-site performance evaluation of the Alinity m Molecular assay for quantifying Epstein-Barr virus DNA in plasma samples
Authors: Wessels Els , Albert Eliseo , Vreeswijk Tom , Claas Eric C. J. , Giménez Estela , Reinhardt Birgit , Sasaki Mark M. , Navarro David
Published: September 2023

Detection and monitoring of acute infection or reactivation of Epstein-Barr virus (EBV) are critical for treatment decision-making and to reduce the risk of EBV-related malignancies and other associated diseases in immunocompromised individuals. The analytical and clinical performance of the Alinity m EBV assay was evaluated at two independent study sites; analytical performance was assessed by evaluating precision with a commercially available 5-member EBV verification panel, while the clinical performance of the Alinity m EBV assay was compared to the RealTi
me
EBV assay and a laboratory-developed test (LDT) as the routine test of record (TOR). Analytical analysis demonstrated standard deviation (SD) between 0.08 and 0.13 Log IU/mL. A total of 300 remnant plasma specimens were retested with the Alinity m EBV assay, and results were compared to those of the TOR at the respective study sites (
n
= 148 with the RealTi
m
e EBV assay and
n
= 152 with the LDT EBV assay). Agreement between Alinity m EBV and RealTi
m
e EBV or LDT EBV assays had kappa values of 0.88 and 0.84, respectively, with correlation coefficients
r
of 0.956 and 0.912, while the corresponding observed mean bias was −0.02 and −0.19 Log IU/mL. The Alinity m EBV assay had a short median onboard turnaround time of 2:40 h. Thus, the Alinity m system can shorten the time to results and, therefore, to therapy.
Functional comparisons of the virus sensor RIG-I from humans, the microbat
Myotis daubentonii
, and the megabat
Rousettus aegyptiacus
, and their response to SARS-CoV-2 infection
Authors: Schoen Andreas , Hölzer Martin , Müller Marcel A. , Wallerang Kai B. , Drosten Christian , Marz Manja , Lamp Benjamin , Weber Friedemann
Published: September 2023

Bats (order
Chiroptera
) are a major reservoir for emerging and re-emerging zoonotic viruses. Their tolerance toward highly pathogenic human viruses led to the hypothesis that bats may possess an especially active antiviral interferon (IFN) system. Here, we cloned and functionally characterized the virus RNA sensor, retinoic acid-inducible gene-I (RIG-I), from the “microbat”
Myotis daubentonii
(suborder
Yangochiroptera
) and the “megabat”
Rousettus aegyptiacus
(suborder Yinpterochiroptera) and compared them to the human ortholog. Our data show that the overall sequence and domain organization are highly conserved and that all three RIG-I orthologs can mediate a similar IFN induction in response to viral RNA at 37° and 39°C but not at 30°C. Like human RIG-I, bat RIG-Is were optimally activated by double stranded RNA containing a 5’-triphosphate end and required mitochondrial antiviral-signaling protein (MAVS) for antiviral signaling. Moreover, the RIG-I orthologs of humans and of
R. aegyptiacus
, but not of
M. daubentonii
, enable innate immune sensing of SARS-CoV-2 infection. Our results thus show that microbats and megabats express a RIG-I that is not substantially different from the human counterpart with respect to function, temperature dependency, antiviral signaling, and RNA ligand properties, and that human and megabat RIG-I are able to sense SARS-CoV-2 infection.

IMPORTANCE

A common hypothesis holds that bats (order
Chiroptera
) are outstanding reservoirs for zoonotic viruses because of a special antiviral interferon (IFN) system. However, functional studies about key components of the bat IFN system are rare. RIG-I is a cellular sensor for viral RNA signatures that activates the antiviral signaling chain to induce IFN. We cloned and functionally characterized RIG-I genes from two species of the suborders
Yangochiroptera
and
Yinpterochiroptera
. The bat RIG-Is were conserved in their sequence and domain organization, and similar to human RIG-I in (i) mediating virus- and IFN-activated gene expression, (ii) antiviral signaling, (iii) temperature dependence, and (iv) recognition of RNA ligands. Moreover, RIG-I of
Rousettus aegyptiacus
(suborder
Yinpterochiroptera
) and of humans were found to recognize SARS-CoV-2 infection. Thus, members of both bat suborders encode RIG-Is that are comparable to their human counterpart. The ability of bats to harbor zoonotic viruses therefore seems due to other features.
Microbial activity contributes to spatial heterogeneity of wetland methane fluxes
Authors: Arnold Wyatt , Taylor Meghan , Bradford Mark , Raymond Peter , Peccia Jordan
Published: September 2023

The emission of methane from wetlands is spatially heterogeneous, as concurrently measured surface fluxes can vary by orders of magnitude within the span of a few meters. Despite extensive study and the climatic significance of these emissions, it remains unclear what drives large, within-site variations. While geophysical factors (e.g., soil temperature) are known to correlate with methane (CH
4
) flux, measurable variance in these parameters often declines as spatial and temporal scales become finer. As methane emitted from wetlands is the direct, net product of microbial metabolisms which both produce and degrade CH
4
, it stands to reason that characterizing the spatial variability of microbial communities within a wetland—both horizontally and vertically—may help explain observed variances in flux. To that end, we surveyed microbial communities to a depth of 1 m across an ombrotrophic peat bog in Maine, USA using amplicon sequencing and gene expression techniques. Surface methane fluxes and geophysical factors were concurrently measured. Across the first meter of peat at the site, we observed significant changes in the abundance and composition of methanogenic taxa at every depth sampled, with variance in methanogen abundance explaining 70% of flux heterogeneity at a subset of plots. Among measured environmental factors, only peat depth emerged as correlated with flux, and had significant impact on the abundance and composition of methane-cycling communities. These conclusions suggest that a heightened awareness of how microbial communities are structured and spatially distributed within wetlands could offer improved insights into predicting CH
4
flux dynamics.

IMPORTANCE

Globally, wetlands are one of the largest sources of methane (CH
4
), a greenhouse gas with a warming impact significantly greater than CO
2
. Methane produced in wetlands is the byproduct of a group of microorganisms which convert organic carbon into CH
4
. Despite our knowledge of how this process works, it is still unclear what drives dramatic, localized (<10 m) variance in emission rates from the surface of wetlands. While environmental conditions, like soil temperature or water table depth, correlate with methane flux when variance in these factors is large (e.g., spring vs fall), the explanatory power of these variables decline when spatial and temporal scales become smaller. As methane fluxes are the direct product of microbial activity, we profiled how the microbial community varied, both horizontally and vertically, across a peat bog in Maine, USA, finding that variance in microbial communities was likely contributing to much of the observed variance in flux.
Erratum to: Novel Samarium Cobaltate/Silicon Carbide Composite Catalyst for Dry Reforming of Methane into Synthesis Gas
Authors: Loktev A. S. , Arkhipova V. A. , Bykov M. A. , Sadovnikov A. A. , Dedov A. G.
Published: September 2023

Erratum
Type IIIb jejunal atresia treated surgically with two end-to-end anastomoses
Authors: Harper Alexander James , Das Susmit , Williamson Emma , Sah Rajesh
Published: September 2023

A term newborn presented after birth with abdominal distension and vomiting in a developing country in Asia. Ultrasonography suggested intestinal obstruction and abdominal X-ray showed a ‘double-bubble’ sign suggestive of intestinal atresia. The newborn was diagnosed with early-onset neonatal sepsis secondary to intestinal obstruction and transferred to the neonatal intensive care unit. Surgery was performed and type IIIb jejunal atresia was found. Type IIIa/b jejunal atresia is associated with high incidence of poor outcome in lower socioeconomic countries. The affected intestinal segment and a distal serosal tear were resected and two end-to-end anastomoses formed. Oral feeding commenced on day 13 postoperatively. The patient was discharged on day 20 with adequate nutritional status. At follow-up, the patient continued to thrive. An operation involving resection of two different segments of bowel repaired with two end-to-end anastomoses in a neonate had a successful outcome for the patient.
Sulfasalazine as a cause of false-positive elevation of urinary normetanephrine in patients with adrenal mass and suspected phaeochromocytoma: a diagnostic challenge
Authors: Zuling Eunice Ter , Debono Miguel , Rab Edmund , Balasubramanian Sabapathy
Published: September 2023

In patients with suspected phaeochromocytoma, biochemical screening of urine or blood for excess secretion catecholamines and/or their metabolites is performed. Elevated levels of catecholamines and metanephrines help in establishing the diagnosis of phaeochromocytoma. In two patients with adrenal lesions who were subjected to biochemical testing significantly elevated urinary normetanephrines appeared to establish the diagnosis of phaeochromocytoma. However, on subsequent investigations, this was demonstrated to be a ‘false positive’ finding. Both these patients were on sulfasalazine, an anti-inflammatory drug used in inflammatory bowel disease, rheumatoid arthritis and ankylosing spondylitis. Sulfasalazine can cause analytical interference in some assays for urinary normetanephrine and result in spuriously elevated levels, leading to misdiagnosis of phaeochromocytoma. In this report, one patient underwent adrenalectomy and another had conservative management.

Although this has been previously reported, increased awareness of the possibility of false-positive results on urinary metanephrines testing is important to reduce the potential for misdiagnosis and unnecessary treatment.
Aortic sarcoma: a challenging diagnosis
Authors: Bui Thi Huong Giang , Do Ngoc Son , Pham The Thach , Ho Duc Trieu
Published: September 2023

Sarcomas of the aorta are rare tumours with various clinical presentations. The most common symptoms are embolic events, constitutional symptoms, claudication, abdominal complaints, aneurysm/pseudoaneurysm, back pain and hypertension. We present a case of a woman in her early 60s having fever, fatigue and cough for 3 months. The chest CT revealed an aneurysm measuring 64.1×65.6 mm. The oncology and thoracic surgical teams were consulted and decided to do an open repair of the aorta and take specimens for histopathological examination, which later confirmed a pleomorphic undifferentiated sarcoma of the aorta. She was temporarily discharged on day 9th after the surgery, followed up by chemotherapy in subsequent admission.
Exploring the association between household access to water, sanitation and hygiene (WASH) services and common childhood diseases using data from the 2017–2018 Demographic and Health Survey in Benin: focus on diarrhoea and acute respiratory infection
Authors: Gaffan Nicolas , Degbey Cyriaque , Kpozehouen Alphonse , Ahanhanzo Yolaine Glele , Paraïso Moussiliou Noël
Published: September 2023

Objective

The paper aimed to study the association between household access to water, sanitation and hygiene (WASH) services and the occurrence of diarrhoea and acute respiratory infection among children under 5 years in Benin.

Design

We performed secondary analyses using Benin’s Fifth Demographic and Health Survey datasets. The dependent variables were diarrhoea and acute respiratory infection (yes=1, no=0). Among the independent variables were the household access to individual WASH services, grouped as follows: ‘basic’, ‘limited’, ‘unimproved’ and ‘no service’. Multivariate logistic regression was used to determine the association between household access to WASH services and the occurrence of diarrhoea and acute respiratory infection. Results from the multivariate logistic regression were presented using adjusted Odds Ratios (aORs) with 95% Confidence Intervals (95% CIs).

Setting

Benin.

Participants

Children under 5 years successfully surveyed during Benin’s Fifth Demographic and Health Survey.

Outcome measures

Diarrhoea and acute respiratory infection.

Results

In the current study, 12 034 children under 5 years met the selection criteria and were included in the analyses. The prevalence of diarrhoea and acute respiratory infection was 10.5% (95% CI=9.8% to 11.3%) and 2.9% (95% CI=2.5% to 3.4%), respectively. Children living in households without sanitation service, that is, practising open defecation (aOR=1.9, 95% CI=1.4 to 2.6), and with unimproved (aOR=1.9, 95% CI=1.3 to 2.7) and limited (aOR=1.5, 95% CI=1.1 to 2.2) services were more likely to have diarrhoea compared with children with basic sanitation services. Household access to WASH services was not associated with acute respiratory infection.

Conclusion

We suggest reinforcing household access to basic sanitation services to combat diarrhoea in children under 5 years. Further research is needed on the effects of WASH interventions on diarrhoea and acute respiratory infection in children under 5 years.
Impact of Long Covid on the school experiences of children and young people: a qualitative study
Authors: MacLean Alice , Wild Cervantee , Hunt Kate , Nettleton Sarah , Skea Zoë C , Ziebland Sue
Published: September 2023

Objectives

To explore the impact of Long Covid (LC) on the school experiences of children and young people (CYP).

Design

Qualitative study using narrative interviews.

Participants

22 CYP (aged 10–18 years, 15 female) with LC and 15 parents/caregivers (13 female) of CYP (aged 5–18 years) with LC.

Setting

Interviews were conducted between October 2021 and July 2022 via online video call or telephone. Recruitment routes included social media, LC support groups, clinicians, community groups and snowballing.

Results

Three key findings were identified. Finding 1: Going to school is a valued part of CYP’s lives and participants viewed educational attainment as important for their future trajectories. Returning to school full time was highlighted as a key part of regaining ‘normal life’. Finding 2: Attending school (in-person or online) with LC is extremely difficult; even a gradual return required CYP to balance the impact of being at and engaging with school, with the need to manage symptoms to prevent relapse. Often this meant prioritising school and rest over other aspects of their lives. Finding 3: School responses to CYP with LC were reported to be mixed and hampered by difficulties communicating with healthcare professionals during the pandemic and a lack of awareness of LC among healthcare and education professionals. Participants viewed supportive school responses as staff believing, understanding and taking them seriously, alongside schools offering tailored and flexible adaptations which allowed engagement with school while limiting any deterioration of symptoms.

Conclusions

This study describes how LC affects the school experiences of CYP and generates recommendations for supportive school responses alongside supportive healthcare professionals. Further research could explore the approaches that facilitate a successful return to school for CYP with LC and investigate education professionals’ perspectives on support they require to positively engage with returning pupils.