bluuebunny/crossref_metadata_2025 huggingface dataset:
Long noncoding RNA CR46040 is essential for injury-stimulated regeneration of intestinal stem cells in Drosophila
Authors: Xu Qi , Liu Jun , Du Xiao , Xue Di , Li Dong , Bi Xiaolin
Published: March 2023

Long noncoding RNAs (lncRNAs) play important regulatory roles in stem cell self-renewal, pluripotency maintenance, and differentiation. Till now, there is very limited knowledge about how lncRNAs regulate intestinal stem cells (ISCs), and lncRNAs mediating ISC regeneration in Drosophila have yet been characterized. Here, we identify a lncRNA, CR46040, that is essential for the injury-induced ISC regeneration in Drosophila. Loss of CR46040 greatly impairs ISC proliferation in response to tissue damage caused by dextran sulfate sodium (DSS) treatment. We demonstrate that CR46040 is a genuine lncRNA that has two isoforms transcribed from the same transcription start site and works in trans to regulate intestinal stem cells. Mechanistically, CR46040 knock-out flies failed to fully activate JNK, JAK/STAT, and HIPPO signaling pathways after tissue damage, which are required for ISC proliferation after intestinal injury. Moreover, CR46040 knock-out flies are highly susceptible to DSS treatment and enteropathogenic bacteria Erwinia carotovora ssp. carotovora 15 (Ecc15) infection. Our findings characterize, for the first time, a lncRNA that mediates damage-induced ISC proliferation in Drosophila and provide new insights into the functional links among the long noncoding RNAs, ISC proliferation, and tissue homeostasis.
The case for supermajority requirements in referendums
Authors: Qvortrup Matt , Trueblood Leah
Published: March 2023

Referendums appear to be the most majoritarian of democratic processes. The simplicity and equality they offer through voting look like the essence of majoritarianism. Indeed, this simplicity and equality are often argued to be central to referendums’ appeal. This article argues that this appearance of majoritarianism is misleading. Paradoxically, without supermajority requirements, binding referendums on constitutional issues cannot offer the simplicity and equality majoritarianism requires. This article identifies three different types of majority requirements and where and when these requirements are used worldwide. It then demonstrates why, at least for binding referendums on constitutional questions, special majority requirements are necessary to maintain the principles of majoritarianism. It shows that there is always a case for turnout thresholds in referendums and further special majority requirements depending on the context. Finally, the article argues that the case for special majority requirements can be context-dependent without collapsing into indeterminacy.
The myth of populist constitutionalism in Hungary and Poland: Populist or authoritarian constitutionalism?
Authors: Szente Zoltán
Published: March 2023

The article seeks to answer the question whether the analytical framework of “populist constitutionalism” adequately describes and explains the constitutional changes that the Hungarian and Polish populist governments have implemented, respectively, since 2010 and 2015. After presenting the similarities and differences between the Hungarian and Polish constitutional developments, the article discusses the conceptual attempts of populist constitutionalism, identifying the primary and secondary characteristics that the literature attributes to this phenomenon. The main point of the article is that these criteria only partially characterize the recent constitutional changes in these two countries, and that the features that do really prevail are more indicative of an unmarked authoritarian transition than of a new, specific version of constitutionalism. It describes the different reasons for the misapplication of constitutional populism to these two countries. Finally, it explains how counterproductive the misconception of populist constitutionalism is for understanding the recent constitutional development in Hungary and Poland.
Exponential state estimate of positive systems with time-varying delays: a Lyapunov–Razumikhin approach
Authors: Ngoc Nguyen Tran
Published: March 2023

In this paper, for the first time, a linear Lyapunov–Razumikhin function is introduced to find an $\alpha$-exponential state estimate for positive systems with time delays. A new set of conditions for the existence of exponential state boundedness of positive systems with bounded time-varying delays is established. Two procedures are then proposed to find the factor vector of $\alpha$-exponential state estimate, in which some techniques of optimization are applied to find the smallest possible factor vector. Numerical experiments are presented to demonstrate the effectiveness of the linear Lyapunov–Razumikhin function as well as of the optimization techniques.
A hybrid high-order scheme for the stationary, incompressible magnetohydrodynamics equations
Authors: Droniou Jérôme , Yemm Liam
Published: March 2023

We propose and analyse a hybrid high-order scheme for the stationary incompressible magnetohydrodynamics equations. The scheme has an arbitrary order of accuracy and is applicable on generic polyhedral meshes. For sources that are small enough, we prove error estimates in energy norm for the velocity and magnetic field, and $L^2$-norm for the pressure; these estimates are fully robust with respect to small faces, and of optimal order with respect to the mesh size. Using compactness techniques, we also prove that the scheme converges to a solution of the continuous problem, irrespective of the source being small or large. Finally, we illustrate our theoretical results through 3D numerical tests on tetrahedral and Voronoi mesh families.
Newton Polygons of Sums on Curves II: Variation in p-adic Families
Authors: Kramer-Miller Joe , Upton James
Published: March 2023

In this article, we study the behavior of Newton polygons along $\mathbb{Z}_p$-towers of curves. Fix an ordinary curve $X$ over a finite field $\mathbb{F}_q$ of characteristic $p$. By a $\mathbb{Z}_p$-tower $X_\infty /X$, we mean a tower of covers $ \dots \to X_2 \to X_1 \to X$ with $\textrm{Gal}(X_n/X) \cong \mathbb{Z}/p^n\mathbb{Z}$. We show that if the ramification along the tower is sufficiently moderate, then the slopes of the Newton polygon of $X_n$ are equidistributed in the interval $[0,1]$ as $n$ tends to $\infty $. Under a stronger congruence assumption on the ramification invariants, we completely determine the slopes of the Newton polygon of each curve. This is the first result towards “regularity” in Newton polygon behavior for $\mathbb{Z}_p$-towers over higher genus curves. We also obtain similar results for $\mathbb{Z}_p$-towers twisted by a generic tame character.
The Kobayashi–Hitchin Correspondence of Generalized Holomorphic Vector Bundles Over Generalized Kähler Manifolds of Symplectic Type
Authors: Goto Ryushi
Published: March 2023

In this paper, we establish the Kobayashi–Hitchin correspondence, that is, the equivalence of the existence of an Einstein–Hermitian metric and $\psi $-polystability of a generalized holomorphic vector bundle over a compact generalized Kähler manifold of symplectic type. Poisson modules provide intriguing generalized holomorphic vector bundles, and we obtain $\psi $-stable Poisson modules over complex surfaces that are not stable in the ordinary sense.
Biotypes of Central Nervous System Complications in People With Human Immunodeficiency Virus: Virology, Immunology, and Neuropathology
Authors: Joseph Sarah B , Gianella Sara , Burdo Tricia H , Cinque Paola , Gisslen Magnus , Letendre Scott , Nath Avindra , Morgello Susan , Ndhlovu Lishomwa C , Spudich Serena
Published: March 2023

Despite viral suppression with antiretroviral therapy (ART), people with human immunodeficiency virus (HIV) continue to experience central nervous system (CNS) complications, primarily in the form of mild cognitive impairment and mental health disorders (eg, depression, anxiety, other neuropsychiatric problems). The multifactorial pathogenesis and heterogeneity of mechanisms likely underlying CNS complications must be addressed in the development of preventive interventions and effective treatments. The biotyping approach has previously been useful to define phenotypes of other CNS diseases based on underlying mechanisms and could be translated to the field of neuroHIV. The purpose of the Biotype Workshop series, and the Virology, Immunology and Neuropathology Working Group in particular, is to capitalize on current and new technologies and guide future research efforts using the wealth of available immunological, virologic, and neuropathological data collected from people with HIV on and off ART.
Neither promoting nor projecting democracy: Indonesia’s middlepowermanship in the Bali democracy forum under Joko Widodo
Authors: Rosyidin Mohamad , Kusumawardhana Indra
Published: March 2023

Despite the pragmatic character of Indonesian President Joko Widodo’s foreign policy and the regression of the country’s democracy index, Indonesia remains eager for the continuation of Bali Democracy Forum (BDF). This article aims to solve this apparent contradiction using the concept of middle power diplomacy. This article argues that, in contrast to his predecessor, Widodo does not perceive BDF as an instrument to promote or project democracy abroad. Rather, Widodo considers the BDF to accentuate Indonesia’s leadership role in multilateral fora. This ‘middlepowermanship’ challenges the elite-based approach in explaining Indonesia’s foreign policy, which puts a strong emphasis on Jokowi’s personal character traits. The continuation of the BDF under Widodo reflects Indonesia’s default thinking of its status as a middle power.
Staphylococcus coagulanspossesses many virulence factors ofStaph. aureusandStaph. pseudintermedius
Authors: Murugesan Ananda Chitra , Ramachandran Maya , Varughese Hridya Susan , Kumaragurubaran Karthik
Published: March 2023

Aims

To understand the Staphylococcus coagulans prevalence in causing skin infections in dogs and detection of various virulence genes in Staph. coagulans isolates.

Methods and Results

Staph. coagulans was isolated from pus swabs collected from dogs with skin infection and identified by detecting thermonuclease, coagulase, and urease genes. The presence of methicillin-resistant gene (mecA) was performed by PCR. Antimicrobial susceptibility test was carried out by disc diffusion method. In total, 38 Staph. coagulans clinical isolates and 42 Staph. coagulans genomes available in NCBI database were screened for 19 virulence genes by PCR and in silico prediction, respectively. A prevalence of 13.8% (38/275) of Staph. coagulans dog skin infection was observed and 15.8% (6/38) of Staph. coagulans isolates carried mecA gene. Many Staph. coagulans isolates were susceptible to all tested antimicrobials. Twenty nine per cent isolates were resistant to ciprofloxacin. Genes encoding leukotoxins, DNase, exfoliative toxin, superantigen-like exotoxin, immunoglobulin-binding proteins, fibrinogen-binding proteins, autolysin, and rod shape-determining protein were detected in almost all the Staph. coagulans clinical isolates and genomes from NCBI database, whereas anti-adhesin plasma-sensitive protein genes were present in relatively lesser number of Staph. coagulans clinical isolates and genomes from NCBI database.

Conclusions

Staph. coagulans possesses many virulence factors that are present in other coagulase-positive staphylococci, such as Staph. aureus and Staph. pseudintermedius. The presence of two bi-component leukotoxin genes in tandem with other virulence factor genes in a single pathogenic island in the Staph. coagulans genomes explained their eminence in the virulence of Staph. coagulans causing infections. Staph. coagulans was classified as a separate species in the year 2020 and primarily causes skin infections in dogs. Identification of this species is not included in any of the automated bacterial identification systems. Hence, many veterinary laboratories do not have a strategy to identify this bacterium. This study will help in the identification of Staph. coagulans in veterinary laboratories by PCR apart from detecting various virulence factors present in this pathogen. The existence of many virulence factors and prevalence in different animals in varied geographical locations suggest that Staph. coagulans is an important coagulase-positive staphylococcal pathogen in animals.
Probiotic lactobacilli mediate their immunoregulatory functions in intestinal cells via modulation of H3 histone acetylation
Authors: Kumari Ankita , Bhawal Shalaka , Kapila Suman , Kapila Rajeev
Published: March 2023

Aims

Probiotics are known to maintain intestinal homeostasis through the regulation of the immune response of the host. Hence, the role of histone modifications as epigenetic agents on immune modulations by potential probiotic bacteria has been investigated.

Methods and Results

Human colonic epithelial cells (Caco-2) pre-treated with class I histone deacetylase (HDAC) specific inhibitor, MS-275, were incubated either with potential probiotic bacteria (Limosilactobacillus fermentum MTCC 5898 and Lacticaseibacillus rhamnosus MTCC 5897) or Escherichia coli (ATCC 14948) as an inflammatory agent. Initially, transcriptional expression of potential immune-related genes (IL-6, IL-8, and hBD-2) was analyzed using RT-qPCR, and later H3 histone acetylation (H3Ac) at the promoter region of these genes was confirmed with a chromatin immunoprecipitation (ChIP) assay respectively. Potential probiotic L. fermentum (MTCC 5898) significantly suppressed (P < 0.05) the inhibitor-mediated elevated expression of immune-related genes while another strain L. rhamnosus (MTCC 5897), did not influence these gene expression results. In contrast, as an inflammatory agent, E. coli (ATCC 14948) synergistically augmented the expression of immune-related genes. Later, ChIP analysis confirmed the occurrence of H3 acetylation at these genes’ promoter regions, which was directly related to the transcriptional activity of host epithelial cells stimulated by L. fermentum and E. coli, respectively. But in the case of L. rhamnosus, MTCC 5897, acetylation did not follow the transcription pattern and potentiated H3Ac on the promoter regions of these genes.

Conclusions

Potential probiotics used in the study were found to regulate the immune response of host cells through histone acetylation in a strain-specific manner.

Significance and Impact of Study

Occurrence of probiotic-mediated regulation of immune genes by H3 acetylation in a strain-specific manner.
Isolation, identification, and evaluation of the biocontrol potential of aBacillus velezensisstrain against tobacco root rot caused byFusarium oxysporum
Authors: Li X J , Yao C X , Qiu R , Bai J K , Liu C , Chen Y G , Li S J
Published: March 2023

Aims

Tobacco (Nicotiana tabacum) is an economically important crop. Root rot caused by Fusarium oxysporum has become a damaging disease in N. tabacum crops grown in Henan province of China. Therefore, the objectives of this study were to screen bacterial isolates against F. oxysporum from rhizosphere soils of tobacco growing areas and to evaluate their antifungal activities, biocontrol effects, and effects on plant growth.

Methods and results

Nineteen strains with antifungal inhibition effects of >60% against F. oxysporum were obtained using the method of flat confrontation; the strain Ba-0321 was the strongest, with an antifungal effect of 75%. Moreover, this strain had broad spectrum antimicrobial activity to eight additional tobacco pathogens. The strain was identified as Bacillus velezensis by morphology and the 16S rDNA sequence. The B. velezensis strain Ba-0321 had strong UV resistance as well as tolerance to high temperatures and low nutrition. The bacteria inhibited spore germination and mycelial growth of F. oxysporum under in vitro co-culture conditions. In vivo assays demonstrated that the Ba-0321 strain significantly reduced the pathogenicity of F. oxysporum, resulting in a control effect on tobacco root rot of 81.00%. Simultaneously, the bacteria significantly promoted root development and the growth of tobacco plants.

Conclusion

Our results confirmed that the B. velezensis strain Ba-0321 has a strong antifungal effect and stress resistance that enable it to be used as a biological control agent for tobacco root rot caused by F. oxysporum.

Significance and impact of the study

Tobacco root rot caused by F. oxysporum has become a damaging disease in China. The B. velezensis strain Ba-0321 has promising application value for controlling tobacco root rot diseases, and it could provide a new biocontrol agent against root rot caused by F. oxysporum in other plant species.
Distinct microbiome profiles in convergent wisdom tooth impactions
Authors: Campbell Paul M , Toedtling Verena , Humphreys Gavin J , Knight Christopher G , Devlin Hugh , McBain Andrew J
Published: March 2023

Aims

Long-term retention of impacted third molars (wisdom teeth) is associated with plaque stagnation and the development of caries on the adjacent surface of the neighboring second molar. While caries and tooth loss are common outcomes of impaction, there is currently insufficient evidence to support the pre-emptive removal of asymptomatic wisdom teeth. Emerging evidence suggests that convergently growing impactions are associated with caries. We have therefore investigated the composition of dental plaque on the distal surface of the mandibular second molar at various impaction angles.

Methods and Results

We have compared the microbiome of these surfaces at four impaction angulations using short-read sequencing of the bacterial 16S rRNA gene: two convergent (horizontal and mesial) and two divergent (distal and vertical) angulations, and in cases where the wisdom tooth is missing. Horizontal angulations exhibited lower microbial diversity than mesial impactions. Amplicon Sequence Variants (ASVs) associated with Veillonella were significantly more abundant at impactions with angulations toward the midline. Using machine learning, a random forest classifier trained to distinguish microbiome profiles was used to predict the native angulations for a subset of samples, with samples from the two convergent impactions estimated with the greatest accuracy.

Conclusions

Differences in microbial diversity were apparent between caries-associated convergent (horizontal and mesial) impacted wisdom teeth, as well as greater abundances of Veillonella ASVs at horizontal impactions.
Screening of potential phosphate solubilizing bacteria inoculants should consider the contrast in phosphorus bio-solubilization rate along with plant growth promotion and phosphorus use efficiency
Authors: Elhaissoufi Wissal , Ibnyasser Ammar , Haddine Meryem , Zeroual Youssef , Ghani Rachid , Barakat Abdellatif , Rchiad Zineb , Ghoulam Cherki , Bargaz Adnane
Published: March 2023

Aims

Although phosphate solubilizing bacteria (PSB) have been globally reported to improve soil phosphorus (P) availability and plant growth, technical gaps such as the lack of an ideal screening approach, is yet to be addressed. The potential of non-halo-forming PSB remains underestimated because of the currently adopted screening protocols that exclusively consider halo-forming and PSB with high phosphorus solubilization (PS) capacities. Yet, caution should be taken to properly assess PSB with contrasting PS rates regardless of the presence or absence of the solubilization halo.

Methods and Results

This study sought to examine the PS rate and plant growth promotion ability of 12 PSB categorized as high PSB (H-PSB), medium PSB (M-PSB), and low PSB (L-PSB) based on their PS rates of rock phosphate (RP). The non-halo-forming PSB Arthrobacter pascens was categorized as H-PSB, which might have been eliminated during the classical screening process. In addition, induction of organic acids and phosphatase activity in rhizosphere soils by H-, M-, and L-PSB was proportional to increased wheat P content by 143.22, 154.21, and 77.76 mg P g−1 compared to uninoculated plants (18.1 mg P g−1).

Conclusions

Isolates considered as M- and L-PSB could positively influence wheat above-ground physiology and root traits as high as H-PSB. In addition, non-halo-forming PSB revealed significant PS rates along with positive effects on plant growth as high as halo-forming PSB.
Brazilian red propolis in combination with β-lactams exerts an efficient antibacterial action over methicillin-resistantStaphylococcus aureus(MRSA) strains
Authors: Ripari Nicolas , Pereira Ana Flávia Marques , Júnior Ary Fernandes , Rall Vera Lúcia Mores , Aldana-Mejía Jennyfer A , Bastos Jairo Kenupp , Sforcin José Maurício
Published: March 2023

Aims

The antibacterial activity of red propolis extract (RPE) and brown propolis extracts (BPE) and the synergistic effect of RPE with cefoxitin (CEFO), imipenem (IMI), and ertapenem (ERTA) was evaluated in vitro against methicillin-resistant Staphylococcus aureus (MRSA) strains.

Methods and results

MRSA ATCC 33591, community-associated (CA-MRSA) USA300, and four clinical isolates were used. A broth microdilution assay was performed to obtain inhibitory and bactericidal concentrations of BPE, RPE, CEFO, IMI, and ERTA. RPE in combination with CEFO, IMI, and ERTA was evaluated on the formation or eradication of biofilm. The bacterial relative membrane conductivity of the strains was assessed after RPE and combinations exposition. Surface/binding computational analyzes between RPE compounds and penicillin binding protein 2a (PBP2a) were performed. BPE samples had no activity against MRSA (MICs 3.2–5 g l−1; MBCs 10–15 g l−1), so the subsequent assays were carried out only with RPE and antimicrobials. RPE exerted a bacteriostatic action (MICs 0.0156–0.125 g l−1; MBCs 0.5–2 g l−1) but the combinations with IMI and ERTA showed the highest inhibition, as observed in the time-kill curve. However, the FICI index showed synergism (≥0.5) only to RPE + IMI. This combination was the most effective in inhibiting the biofilm and showed the highest values of membrane conductivity. Computational predictions indicated that RPE constituents may interact with PBP2a.

Conclusion

RPE and RPE + IMI exerted an antibacterial and antibiofilm activity on MRSA strains probably due to membrane/wall damage and interactions with PBP2a.
De novogenomic analysis ofEnterobacter asburiaeEBRJ12, a plant growth-promoting rhizobacteria isolated from the rhizosphere ofPhaseolus vulgarisL
Authors: Saikia Juthika , Kotoky Rhitu , Debnath Rajal , Kumar Niraj , Gogoi Priyanka , Yadav Archana , Saikia Ratul
Published: March 2023

Aim

Environmental stresses such as water deficit induced stress are one of the major limiting factors in crop production. However, some plant growth-promoting rhizobacteria (PGPR) can promote plant growth in such adverse condition. Therefore, the objective was to isolate rhizospheric bacteria from Phaseolus vulgaris L. growing in a drought-affected soil and to analyze its plant growth promoting (PGP) efficacy to black gram (Vigna mungo L.) and Bhut jolokia (Capsicum chinense Jacq.). Whole-genome sequencing of the potential bacteria was targeted to analyze the genetic potential of the isolate as a plant growth-promoting agent.

Methods and results

The isolate Enterobacter asburiae EBRJ12 was selected based on its PGP efficacy, which significantly improved plant growth and development. The genomic analysis revealed the presence of one circular chromosome of size 4.8 Mb containing 16 genes for osmotic stress regulation including osmotically inducible protein osmY, outer membrane protein A precursor ompA, aquaporin Z, and an operon for osmoprotectant ABC transporter yehZYXW. Moreover, the genome has a complete genetic cluster for biosynthesis of siderophore Enterobactin and siderophore Aerobactin.

The PGP effects were verified with black gram and Bhut jolokia in pot experiments. The isolate significantly increased the shoot length by 35.0% and root length by 58.0% of black gram, while 41.0% and 57.0% of elevation in shoot and root length were observed in Bhut jolokia compared to non-inoculated plants.

Conclusions

The EBRJ12 has PGP features that could improve the growth in host plants, and the genomic characterization revealed the presence of genetic potential for plant growth promotion.
Antifungal and antiaflatoxigenic mechanism activity of freeze-dried culture filtrate ofStreptomyces philanthiRL-1-178 on the two aflatoxigenic fungi and identification of its active component
Authors: Boukaew Sawai , Zhang Zhiwei , Prasertsan Poonsuk , Igarashi Yasuhiro
Published: March 2023

Aims

The study reports the antifungal and antiaflatoxigenic mechanism activity of freeze-dried culture filtrate of Streptomyces philanthi RL-1-178 (DCF RL-1-178) against two aflatoxigenic strains (Aspergillus parasiticus and A. flavus) and identification of its active component.

Methods and Results

Significant inhibition in ergosterol biosynthesis by the DCF RL-1-178 appeared on the plasma membrane. Moreover, the DCF RL-1-178 showed dose-dependent inhibition of methylglyoxal (MG) (an aflatoxin inducer) biosynthesis and exhibited a novel antiaflatoxigenic action mechanism. Significant impairments in enzymatic [superoxide dismutase (SOD) and catalase (CAT)] and nonenzymatic [oxidized and reduced glutathione (GSH) and ratio of oxidized and reduced glutathione (GSSG)] anti-oxidative defense molecules were observed in the two aflatoxigenic cells. The active component of the DCF RL-1-178 was identified as natamycin. The natamycin exhibited against A. parasiticus and A. flavus with the minimum inhibitory concentration (MIC) values of 0.5 and 1.0 µg ml−1, respectively, while the minimum fungicidal concentration values were the same (4.0 µg ml−1).

Conclusions

The DCF RL-1-178 containing natamycin exhibited the following effects: (1) inhibition of cellular ergosterol biosynthesis on plasma membrane, (2) reduction in MG (aflatoxin inducer) confirmed novel antiaflatoxigenic mechanism of action, and (3) caused remarkable debasement in antioxidant defense enzymes (SOD and CAT) and nonenzymatic defense molecules (GSH and GSSG) revealing biochemical mechanism of action.
Development and Validation of Stability-Indicating Impurity Profiling Method for Azelastine Hydrochloride and Fluticasone Propionate in Nasal Spray Product Using HPLC with a UV/PDA Detector
Authors: Musmade Bhaskar , Korhale Rasika , Sable Mangal , Lokhande Surbhi , Padmanabhan Sriram , Bhope Shrinivas
Published: March 2023

Background

Azelastine HCl (AZ) and fluticasone propionate (FL) nasal spray drug product is commonly used in the treatment of allergic rhinitis worldwide. To date, the impurity profiling of this product has not been reported.

Objective

The present study aimed to develop and validate a novel RP-HPLC stability-indicating analytical method for the estimation of impurities from AZ and FL nasal spray drug product.

Methods

A mixture of octane sulfonic acid sodium salt and trifluroacetic acid is used as a mobile phase A. Acetonitrile is used as a mobile phase B. Good separation was achieved on Baker bond phenyl hexyl, 250 × 4.6, 5 µm column at 1 mL/min flow rate in gradient elution mode. The chromatograms were monitored at 239 nm.

Results

The LOD and LOQ were found to be 0.006 and 0.019 µg/mL for AZ and 0.010 and 0.030 µg/mL for FL, respectively. The correlation coefficient for all the known impurities and principal analytes was 0.999 from LOQ level to 150% of standard concentration. The recovery for all the known impurities was found to be between 90 and 110%. In the stress study, 15% degradation was observed in basic conditions and 8.7% in acidic conditions. No significant degradation was observed in thermal and oxidative conditions.

Conclusion

An impurity profiling method for AZ and FL combination nasal spray product was successfully developed, validated, and demonstrated to be accurate, precise, specific, robust, and stability-indicating. The method can be routinely used for impurity testing of commercial batches in QC laboratories in the pharmaceutical industry.

Highlights

No impurity study has been reported for this combination product until now.
Development of Method for Evaluation of Edible Bird’s Nest Content in Ready-to-Eat Beverages
Authors: Poon Peggy Miu-Yee , Sze Eric Tung-Po
Published: March 2023

Background

Edible bird’s nest (EBN) is one of the most valuable tonic Chinese foods, made from glutinous salivary secretion with highly concentrated mucin glycoprotein. For ease of consumption, manufacturers have marketed different ready-to-eat EBN products, in which the EBN content varies. This is the first study to analyze the EBN content in ready-to-eat beverages.

Objective

To determine the EBN content in ready-to-eat beverages by its active ingredient, N-acetylneuraminic acid (sialic acid).

Method

Sialic acid in ready-to-eat beverages and raw EBN was extracted in sodium hydrogen sulfate solution, followed by derivatization using o-phenylenediamine dihydrochloride and determination using high-performance liquid chromatography (HPLC). Method precision, recovery of extraction, degradation of sialic acid due to cooking, and measurement uncertainty were evaluated.

Results

The mean concentrations of raw EBN in different origins and colors ranged from 5.77 to 10.92%. Ten different brands of traditional ready-to-eat EBN beverages from the market were analyzed, in which estimated concentrations of EBN were diversified, ranging from 0.014 ± 0.010 to 0.66 ± 0.069% (w/w) (95% confidence level). The concentration of sialic acid was found to range from 11.4 to 527 mg/kg.

Conclusions

Based on the results, sialic acid content can provide a better estimation of the EBN content in traditional ready-to-eat beverages. Neither the selling price nor dried matter could be used as an indicator of the quality of the ready-to-eat EBN beverage among the samples obtained.

Highlights

Sialic acid can be used as an indicator to estimate EBN content, where the sialic acid and EBN content in ready-to-eat beverages from the market were found to vary significantly.
Design of a low-density SNP panel for intramuscular fat content and fatty acid composition of backfat in free-range Iberian pigs
Authors: Palma-Granados Patricia , García-Casco Juan María , Caraballo Carmen , Vázquez-Ortego Pedro , Gómez-Carballar Fernando , Sánchez-Esquiliche Fernando , Óvilo Cristina , Muñoz María
Published: March 2023

Intramuscular fat (IMF) content and fatty acids (FA) profile determine important sensory and technological characteristics of the meat, being interesting traits to be included in breeding programs for Iberian pig. In a previous study, we analyzed the longissimus dorsi transcriptome of Iberian pigs with divergent breeding values for IMF identifying 63 and 12 functional candidate genes and long non-coding RNA being differentially expressed. The first objective of this work was to use the RNA-seq data generated in that study in order to design a low-density panel with 50 single-nucleotide polymorphisms (SNP). The second aim was to evaluate the effects of this SNP panel on IMF content and backfat FA profile in a closed commercial population of Iberian pigs. The IMF content and backfat FA composition were determined in 940 Iberian pigs. A total of 837 SNPs were identified in the selection of genes and lncRNA. Out of the 50 selected SNP, 11 were monomorphic in the population and 2 failed in their genotyping. Association analyses were carried out for the 37 SNP segregating in the population (minor allele frequency, MAF > 0.05). Regarding IMF content, a significant additive effect (q-value < 0.05) was observed for ADIPOQ:g.124646194T > G SNP, in which the G allele was linked to an increase of 7.59% (additive effect expressed as a percentage of the mean of the trait). For the backfat FA composition, we observed 24 SNP with significant associations. The strongest effects were detected for the ELOVL6:g.112186423A > G and FASN_rs331694510G > A SNP. The A allele of both SNPs were associated to a lower percentage of palmitic (C16:0) and palmitoleic (C16:1) acids and an increase in oleic acid (C18:1). In addition, the AMPD3:g.49043886C > G SNP had significant effects on C16:0, stearic (C18:0), C18:1 and on the sum of saturated and monounsaturated fatty acids. Finally, significant effects of the EGR2:66286345G > T SNP on C18:0 and C18:1 and other minor FA were observed. Our findings reveal ADIPOQ:g.124646194T > G, ELOVL6:g.112186423A > G, and FASN_rs331694510G > A may be useful in breeding programs for Iberian pigs including FA profile and IMF content as selection goals, provided that their potential effects on other traits of interest are controlled.
Novel regulatory mechanisms underlying angiogenesis during wound healing revealed by fluorescence-based live-imaging in zebrafish
Authors: Yuge Shinya , Ishii Tomohiro , Noishiki Chikage , Fukuhara Shigetomo
Published: March 2023

Angiogenesis is a dynamic morphogenetic process that refers to the growth of new blood vessels from the pre-existing vessels and is critical for tissue repair during wound healing. In adult normal tissues, quiescent endothelial cells and pericytes maintain vascular integrity, whereas angiogenesis is immediately induced upon tissue injury, thereby forming neovascular networks to maintain homeostasis. However, impaired angiogenesis results in development of chronic and non-healing wounds in various diseases such as diabetes and peripheral artery diseases. Zebrafish are a vertebrate model organism widely used for studying many medical and life science fields. Indeed, the molecular and cellular mechanisms underlying regulation of wound angiogenesis have recently been studied by performing fluorescence-based live-imaging of adult zebrafish. In this review, we describe how endothelial cells and pericytes establish neovascular networks during wound angiogenesis and also introduce a novel role of blood flow-driven intraluminal pressure in regulating angiogenesis during wound healing.
Effect of nitrogen management in cultivation on the stability and microbial community of post-harvest Monoraphidium sp. algae biomass
Authors: Wahlen Bradley D , Wendt Lynn M , St. Germain Chelsea C , Traynor Sarah M , Barboza Caitlin , Dempster Thomas , Gerken Henri , McGowen John , You Yaqi
Published: March 2023

Long-term storage is necessary to mitigate for seasonal variation in algae productivity, to preserve biomass quality and to guarantee a constant biomass supply to a conversion facility. While ensiling has shown promise as a solution, biomass attributes for successful storage are poorly understood. Storage studies of Monoraphidium sp. biomass indicate a strong correlation between nitrogen management in algae cultivation and stability of post-harvest algae biomass. Algae cultivated with periodic nitrogen addition were stored poorly (>20% loss, dry basis) compared to biomass from nitrogen depleted cultivation (8% loss, dry basis). A follow-up study compared the post-harvest stability of Monoraphidium biomass cultivated in nitrogen-deplete or nitrogen-replete conditions. Replete biomass experienced the largest degradation (24%, dry basis), while deplete biomass experienced the least (10%, dry basis). Dry matter loss experienced among blends of each correlated positively with nitrogen-replete biomass content. The composition of the post-storage algae microbial community was also affected by cultivation conditions, with Clostridia species being more prevalent in stored biomass obtained from nitrogen-replete cultivations. Nitrogen management has long been known to influence algae biomass productivity and biochemical composition; here, we demonstrate that it also strongly influences the stability of post-harvest algae biomass in anaerobic storage.
Analyzing CRISPR screens in non-conventional microbes
Authors: Trivedi Varun , Ramesh Adithya , Wheeldon Ian
Published: March 2023

The multifaceted nature of CRISPR screens has propelled advancements in the field of functional genomics. Pooled CRISPR screens involve creating programmed genetic perturbations across multiple genomic sites in a pool of host cells subjected to a challenge, empowering researchers to identify genetic causes of desirable phenotypes. These genome-wide screens have been widely used in mammalian cells to discover biological mechanisms of diseases and drive the development of targeted drugs and therapeutics. Their use in non-model organisms, especially in microbes to improve bioprocessing-relevant phenotypes, has been limited. Further compounding this issue is the lack of bioinformatic algorithms for analyzing microbial screening data with high accuracy. Here, we describe the general approach and underlying principles for conducting pooled CRISPR knockout screens in non-conventional yeasts and performing downstream analysis of the screening data, while also reviewing state-of-the-art algorithms for identification of CRISPR screening outcomes. Application of pooled CRISPR screens to non-model yeasts holds considerable potential to uncover novel metabolic engineering targets and improve industrial bioproduction.

One-Sentence Summary

This mini-review describes experimental and computational approaches for functional genomic screening using CRISPR technologies in non-conventional microbes.
Overcoming the challenges to implementation of artificial intelligence in pathology
Authors: Reis-Filho Jorge S , Kather Jakob Nikolas
Published: March 2023

Pathologists worldwide are facing remarkable challenges with increasing workloads and lack of time to provide consistently high-quality patient care. The application of artificial intelligence (AI) to digital whole-slide images has the potential of democratizing the access to expert pathology and affordable biomarkers by supporting pathologists in the provision of timely and accurate diagnosis as well as supporting oncologists by directly extracting prognostic and predictive biomarkers from tissue slides. The long-awaited adoption of AI in pathology, however, has not materialized, and the transformation of pathology is happening at a much slower pace than that observed in other fields (eg, radiology). Here, we provide a critical summary of the developments in digital and computational pathology in the last 10 years, outline key hurdles and ways to overcome them, and provide a perspective for AI-supported precision oncology in the future.
Intussusception of the appendix in a young adult: an important differential diagnosis of abdominal pain in cystic fibrosis patients?
Authors: Venkatasami Meena , Cobby Ellen
Published: March 2023

Cystic fibrosis (CF) is commonly associated with gastrointestinal manifestations from infancy to adulthood. Distal intestinal obstruction syndrome (DIOS) affects 20% of CF patients, where intussusception can be a rare complication. A 20-year-old CF male was diagnosed with a 3-day history of right iliac fossa pain and diarrhoea. Clinical examination revealed a tender palpable mass in the right iliac fossa and raised serum inflammatory markers. Contrast computerized-tomography of the abdomen-pelvis suggested intussusception of the appendix and further confirmed on histological analyses. The patient underwent an open appendicectomy where the intussusception had self-resolved. The literature review indicated a scarcity of data with 10 cases reported of intussusception in adult CF patients. Our case was in line with previous research of transient intussusception. This rare case highlights an importance to carry a higher index of suspicion for gastrointestinal manifestations in CF patients where differential diagnoses of DIOS and intussusception should be considered in the acute presentation.
Break-induced replication is the primary recombination pathway in plant somatic hybrid mitochondria: a model for mitochondrial horizontal gene transfer
Authors: Gandini Carolina L , Garcia Laura E , Abbona Cinthia C , Ceriotti Luis F , Kushnir Sergei , Geelen Danny , Sanchez-Puerta M Virginia
Published: March 2023

Somatic hybrids between distant species offer a remarkable model to study genomic recombination events after mitochondrial fusion. Recently, we described highly chimeric mitogenomes in two somatic hybrids between the Solanaceae Nicotiana tabacum and Hyoscyamus niger resulting from interparental homologous recombination. To better examine the recombination map in somatic hybrid mitochondria, we developed a more sensitive bioinformatic strategy to detect recombination activity based on high-throughput sequencing without assembling the hybrid mitogenome. We generated a new intergeneric somatic hybrid between N. tabacum and Physochlaina orientalis, and re-analyzed the somatic hybrids that we previously generated. We inferred 213 homologous recombination events across repeats of 2.1 kb on average. Most of them (~80%) were asymmetrical, consistent with the break-induced replication pathway. Only rare (2.74%) non-homologous events were detected. Interestingly, independent events frequently occurred in the same regions within and across somatic hybrids, suggesting the existence of recombination hotspots in plant mitogenomes. Break-induced replication is the main pathway of interparental recombination in somatic hybrid mitochondria. Findings of this study are relevant to mitogenome editing assays and to mechanistic aspects of DNA integration following mitochondrial DNA horizontal transfer events.
X-ray emission from Ae/Be Herbig stars due to disc–stellar magnetosphere interaction
Authors: Ryspaeva Elizaveta , Kholtygin Alexander , Lyutikov Maxim
Published: March 2023

We reanalyse archival X-ray data of 16 Ae/Be Herbig stars obtained by the XMM–Newton and Chandra satellites. Stellar X-ray spectra in the energy range 0.2–8 keV were fitted with the use of APEC and MEKAL hot plasma emission models, and with models with an additional power-law component. We find that for Herbig stars, the dependence of the unabsorbed X-ray luminosity on stellar mass and radius, LX ∝ RαMβ with α ≈ 3 and β ≈ 2, is similar to that for T Tauri stars. The independently determined accretion rates, rotation periods, and the surface magnetic fields follow a tight correlation predicted by the standard magnetospheric accretion theory. We suggest that X-ray emission from Herbig stars is powered by magnetic reconnection events in the tenuous corona at the disc–magnetosphere boundary.
Direct analysis of the broad-line SN 2019ein: connection with the core-normal SN 2011fe
Authors: Yarbrough Zach , Baron E , DerKacy James M , Washington I , Hoeflich P , Burrow Anthony
Published: March 2023

Type Ia supernovae (SNe Ia) are important cosmological probes and contributors to galactic nucleosynthesis, particularly of the iron group elements. To improve both their reliability as cosmological probes and to understand galactic chemical evolution, it is vital to understand the binary progenitor system and explosion mechanism. The classification of SNe Ia into Branch groups has led to some understanding of the similarities and differences among the varieties of observed SNe Ia. Branch groups are defined by the pseudo-equivalent widths of the two prominent Si ii lines, leading to four distinct groups: core-normal (CN), shallow-silicon, cool, and broad-line (BL). However, partly due to small sample size, little work has been done on the BL group. We perform direct spectral analysis on the pre-maximum spectra of the BL SN 2019ein, comparing and contrasting to the CN SN 2011fe. Both SN 2019ein and SN 2011fe were first observed spectroscopically within 2 d of discovery, allowing us to follow the spectroscopic evolution of both SNe in detail. We find that the optical depths of the primary features of both the CN and BL SNe are very similar, except that there is a Doppler shift between them. We further examine the BL group and show that for nine objects with pre-maximum spectra in the range (−6)–(−2) d with respect to B-maximum all the emission peaks of the Si ii λ6355 line of BL are blueshifted pre-maximum, suggesting a possible classification criterion.
Scattering of light in thin magnetized envelopes – II
Authors: Silant’ev N A , Alekseeva G A , Ananjevskaja Yu K
Published: March 2023

We consider optically thin spherical stellar envelopes with dipole magnetic field. The source of magnetic dipole field is assumed point like and emits the non-polarized monochromatic radiation. This paper carry on the previous paper of authors, where the general theory is presented and the circular polarization of scattered radiation is calculated for small values of magnetic fields corresponding to parameter x ≪ 1 (x = ωB/ω ≃ 0.933 × 10−8λ(μm)B(G)). The Stokes parameters of scattered radiation mutually transform into each other due to interference. Here we obtained the explicit formulas describing the transformation of all Stokes parameters for any value of parameter x. The qualitative discussion of these formulas is presented. These formulas show that for x ∼ 1 the transformation leads to large variations of all Stokes parameters. The linear and circular polarizations acquire oscillating dependence on the propagation path. For x ≫ 1 the single scattered radiation has very small circular polarization of the order ∼1/x ≪ 1 and large linear polarization. In this case the transformation gives rise to additional value of observed circular polarization, which is proportional to initial single scattered value. The observed linear polarization acquires small inclination angle relative to the plane ‘line of sight–direction of magnetic dipole’ due to existence of small circular polarization. The Stokes parameters of single scattered radiation from all envelope without taking into account the interference effects are given for x ≫ 1.
Evolutionary Trajectories are Contingent on Mitonuclear Interactions
Authors: Biot-Pelletier Damien , Bettinazzi Stefano , Gagnon-Arsenault Isabelle , Dubé Alexandre K , Bédard Camille , Nguyen Tuc H M , Fiumera Heather L , Breton Sophie , Landry Christian R
Published: March 2023

Critical mitochondrial functions, including cellular respiration, rely on frequently interacting components expressed from both the mitochondrial and nuclear genomes. The fitness of eukaryotic organisms depends on a tight collaboration between both genomes. In the face of an elevated rate of evolution in mtDNA, current models predict that the maintenance of mitonuclear compatibility relies on compensatory evolution of the nuclear genome. Mitonuclear interactions would therefore exert an influence on evolutionary trajectories. One prediction from this model is that the same nuclear genome evolving with different mitochondrial haplotypes would follow distinct molecular paths toward higher fitness. To test this prediction, we submitted 1,344 populations derived from 7 mitonuclear genotypes of Saccharomyces cerevisiae to >300 generations of experimental evolution in conditions that either select for a mitochondrial function or do not strictly require respiration for survival. Performing high-throughput phenotyping and whole-genome sequencing on independently evolved individuals, we identified numerous examples of gene-level evolutionary convergence among populations with the same mitonuclear background. Phenotypic and genotypic data on strains derived from this evolution experiment identify the nuclear genome and the environment as the main determinants of evolutionary divergence, but also show a modulating role for the mitochondrial genome exerted both directly and via interactions with the two other components. We finally recapitulated a subset of prominent loss-of-function alleles in the ancestral backgrounds and confirmed a generalized pattern of mitonuclear-specific and highly epistatic fitness effects. Together, these results demonstrate how mitonuclear interactions can dictate evolutionary divergence of populations with identical starting nuclear genotypes.