bluuebunny/crossref_metadata_2025_split huggingface dataset:
Increased thermostability of an engineered flavin-containing monooxygenase to remediate trimethylamine in fish protein hydrolysates
Authors: Goris Marianne , Cea-Rama Isabel , Puntervoll Pål , Ree Rasmus , Almendral David , Sanz-Aparicio Julia , Ferrer Manuel , Bjerga Gro Elin Kjæreng 
Published: March 2023

AbstractProtein hydrolysates made from marine by-products are very nutritious, but frequently contain trimethylamine (TMA) which has an unattractive fish-like smell. Bacterial trimethylamine monooxygenases can oxidize TMA into the odorless trimethylamineN-oxide (TMAO) and have been shown to reduce TMA-levels in a salmon protein hydrolysate. To make theMethylophaga aminisulfidivoranstrimethylamine monooxygenase, mFMO, more suitable for industrial application, we engineered it using the Protein Repair One-Stop Shop (PROSS) algorithm. All seven mutant variants, containing 8-28 mutations, displayed increases in melting temperature between 4.7 °C and 9.0 °C. The crystal structure of the most thermostable variant, mFMO_20, revealed the presence of four new stabilizing interhelical salt bridges, each involving a mutated residue. Finally, mFMO_20 significantly outperformed native mFMO in its ability to reduce TMA levels in a salmon protein hydrolysate at industrially relevant temperatures.ImportanceMarine by-products are a high-quality source for peptide ingredients, but the unpleasant fishy odour caused by TMA limits their access to the food market. This problem can be mitigated by enzymatic conversion of TMA into the odourless TMAO. Enzymes isolated from nature must be adapted to industrial requirements, however, such as the ability to tolerate high temperatures. This study has demonstrated that mFMO can be engineered to become more thermostable. Moreover, unlike the native enzyme, the best thermostable variant efficiently oxidized TMA in a salmon protein hydrolysate at industrial temperatures. Our results present an important next step towards application of this novel and highly promising enzyme technology in marine biorefineries.
Structure-Activity Relationships, Tolerability and Efficacy of Microtubule-Active 1,2,4-Triazolo[1,5-a]pyrimidines as Potential Candidates to Treat Human African Trypanosomiasis
Authors: Monti Ludovica , Liu Lawrence J. , Varricchio Carmine , Lucero Bobby , Alle Thibault , Yang Wenqian , Bem-Shalom Ido , Gilson Michael , Brunden Kurt R. , Brancale Andrea , Caffrey Conor R. , Ballatore Carlo 
Published: March 2023

ABSTRACTTubulin and microtubules (MTs) are potential protein targets to treat parasitic infections and our previous studies have shown that the triazolopyrimidine (TPD) class of MT- active compounds hold promise as antitrypanosomal agents. MT-targeting TPDs include structurally related but functionally diverse congeners that interact with mammalian tubulin at either one or two distinct interfacial binding sites; namely, the seventh and vinca sites, which are found within or between α,β-tubulin heterodimers, respectively. Evaluation of the activity of 123 TPD congeners against culturedTrypanosoma bruceienabled a robust quantitative structure-activity relationship (QSAR) model and the prioritization of two congeners forin vivopharmacokinetics (PK), tolerability and efficacy studies. Treatment ofT. brucei-infected mice with tolerable doses of TPDs3and4significantly decreased blood parasitemia within 24 h. Further, two once-weekly doses of4at 10 mg/kg significantly extended the survival of infected mice relative to infected animals treated with vehicle. Further optimization of dosing and/or the dosing schedule of these CNS-active TPDs may provide alternative treatments for human African trypanosomiasis.
Control of neuronal excitation-inhibition balance by BMP-SMAD1 signaling
Authors: Okur Zeynep , Schlauri Nadia , Bitsikas Vassilis , Panopoulou Myrto , Ortiz Raul , Schwaiger Michaela , Karmakar Kajari , Schreiner Dietmar , Scheiffele Peter 
Published: March 2023

SummaryThroughout life, neuronal networks in the mammalian neocortex maintain a balance of excitation and inhibition which is essential for neuronal computation. Deviations from a balanced state have been linked to neurodevelopmental disorders and severe disruptions result in epilepsy. To maintain balance, neuronal microcircuits composed of excitatory and inhibitory neurons sense alterations in neural activity and adjust neuronal connectivity and function. Here, we identified a signaling pathway in the adult mouse neocortex that is activated in response to elevated neuronal network activity. Over-activation of excitatory neurons is signaled to the network through the elevation of BMP2, a growth factor well-known for its role as morphogen in embryonic development. BMP2 acts on parvalbumin-expressing (PV) interneurons through the transcription factor SMAD1, which controls an array of glutamatergic synapse proteins and components of peri-neuronal nets. PV interneuron-specific disruption of BMP2-SMAD1 signaling is accompanied by a loss of PV cell glutamatergic innervation, underdeveloped peri-neuronal nets, and decreased excitability. Ultimately, this impairment of PV interneuron functional recruitment disrupts cortical excitation – inhibition balance with mice exhibiting spontaneous epileptic seizures. Our findings suggest that developmental morphogen signaling is re-purposed to stabilize cortical networks in the adult mammalian brain.
A transcriptome-based phylogeny of Scarabaeoidea confirms the sister group relationship of dung beetles and phytophagous pleurostict scarabs (Coleoptera)
Authors: Dietz Lars , Seidel Matthias , Eberle Jonas , Misof Bernhard , Pacheco Thaynara L. , Podsiadlowski Lars , Ranasinghe Sasanka , Gunter Nicole L. , Niehuis Oliver , Mayer Christoph , Ahrens Dirk 
Published: March 2023

AbstractScarab beetles (Scarabaeidae) are a diverse and ecologically important group of angiosperm-associated insects. As conventionally understood, scarab beetles comprise two major lineages: dung beetles and the phytophagous Pleurosticti. However, previous phylogenetic analyses have not been able to convincingly answer the question whether or not the two lineages form a monophyletic group. Here we report our results from phylogenetic analyses of more than 4,000 genes mined from transcriptomes of more than 50 species of Scarabaeidae and other Scarabaeoidea. Our results provide convincing support for the monophyly of Scarabaeidae, confirming the debated sister group relationship of dung beetles and phytophagous pleurostict scarabs. Supermatrix-based maximum likelihood and multispecies coalescent phylogenetic analyses strongly imply the subfamily Melolonthinae as currently understood being paraphyletic. We consequently suggest various changes in the systematics of Melolonthinae: Sericinae Kirby, 1837 stat. rest. and sensu n. to include the tribes Sericini, Ablaberini and Diphucephalini, and Sericoidinae Erichson, 1847 stat. rest. and sensu n. to include the tribes Automoliini, Heteronychini, Liparetrini, Maechidiini, Scitalini, Sericoidini, and Phyllotocini. Both subfamilies appear to consistently form a monophyletic sister group to all remaining subfamilies so far included within pleurostict scarabs except Orphninae. Our results represent a major step towards understanding the diversification history of one of the largest angiosperm-associated radiations of beetles.
Establishment and characterization of a newPseudomonas aeruginosainfection model using 2D airway organoids and dual RNA sequencing
Authors: Pleguezuelos-Manzano Cayetano , Beenker Wouter A. G. , van Son Gijs J.F. , Begthel Harry , Amatngalim Gimano D. , Beekman Jeffrey M. , Clevers Hans , den Hertog Jeroen 
Published: March 2023

AbstractPseudomonas aeruginosais a Gram-negative bacterium that is notorious for infections in the airway of cystic fibrosis (CF) subjects. Often, these infections become chronic, leading to higher morbidity and mortality rates. Bacterial quorum sensing (QS) coordinates the expression of virulence factors and the formation of biofilms at a population level. QS has become the focus of attention for development of alternatives to antimicrobials targetingP. aeruginosainfections. However, a better understanding of the bacteria-host interaction, and the role of QS in infection, is required. In this study, we set up a newP. aeruginosainfection model, using 2D airway organoids derived from healthy and CF individuals. Using dual RNA-sequencing, we dissected their interaction, focusing on the role of QS. As expected,P. aeruginosainduced epithelial inflammation. However, QS signaling did not affect the epithelial airway cells. The epithelium influenced several infection-related processes ofP. aeruginosa, including metabolic changes, induction of type 3 and type 6 secretion systems (T3SS and T6SS), and increased expression of antibiotic resistance genes, includingmexXYefflux pump and several porins. Interestingly, the epithelium influenced the regulation by QS of the type 2 (T2SS) and T6SS. Finally, we compared our model within vivo P. aeruginosatranscriptomic datasets, from samples directly isolated from the airways of CF subjects. This shows that our model recapitulates important aspects ofin vivoinfection, like enhanced denitrification, betaine/choline metabolism, increased antibiotic resistance, as well as an overall decrease of motility-related genes. This relevant infection model is interesting for future investigations, helping to reduce the burden ofP. aeruginosainfections in CF.
Hsc70-4 mediates internalization of environmental dsRNA at the surface ofDrosophilaS2 cells
Authors: Fletcher Sabrina Johanna , Tomé-Poderti Lorena , Mongelli Vanesa , Frangeul Lionel , Blanc Hervé , Verdier Yann , Vinh Joelle , Saleh Maria-Carla 
Published: March 2023

AbstractThe siRNA pathway is the primary antiviral defense mechanism in invertebrates and plants. The systemic nature of this defense mechanism is one of its more fascinating characteristics and the recognition and transport of double-stranded RNA (dsRNA) of viral origin is required for the systemic activity of the siRNA pathway. Indeed, cellular internalization of dsRNA from the environment is a widespread phenomenon among insects. Here we aimed to identify cell surface proteins that bind to extracellular dsRNA and mediate its internalization. To this end, we developed a novel co-immunoprecipitation protocol that we followed with proteomics analysis. Among the hits from our screens was Hsc70-4, a constitutively expressed member of the heat shock protein family that has been implicated in clathrin-mediated endocytosis. We found that silencing Hsc70-4 impaired dsRNA internalization. Surprisingly, despite lacking a predicted transmembrane domain, Hsc70-4 localizes to the cell membrane and this localization was preserved when Hsc70-4 was expressed in mammalian cells, suggesting a conserved role at the cell surface. Furthermore, Hsc70-4 shows a previously undescribed dsRNA-specific binding capacity. Our results show that Hsc70-4 is a key element of the dsRNA internalization process and its detailed study may facilitate the development of RNA interference (RNAi)-based technologies for pest and vector borne disease control.ImportanceTo protect plants from pathogens or pests, the technology of “Host-induced gene silencing” has emerged as a powerful alternative to chemical treatments. This is an RNAi-based technology where small RNAs made in the plant silence the genes of the pests or pathogens that attack the plant. The small RNAs are generally derived from dsRNA expressed in transgenic plants. Alternatively, dsRNA can be sprayed onto the plant surface, where it can be taken up into the plant or ingested by pests. We have identified a cell surface protein that mediates the early steps of extracellular dsRNA internalization in insect cells. This could facilitate the development of new strategies for pest management.
Susceptibility of Cu(I) transport ATPases to sodium dodecyl sulfate. Relevance of the composition of the micellar phase
Authors: Recoulat Angelini Alvaro A. , Melian Noelia A. , González-Flecha F. Luis 
Published: March 2023

AbstractSodium dodecylsulfate (SDS) is a well-known protein denaturing agent. A less known property of this detergent is that it can activate or inactivate some enzymes at sub-denaturing concentrations. In this work we explore the effect of SDS at sub-denaturing concentrations on the ATPase activity of a hyper-thermophilic and a mesophilic Cu(I) ATPase reconstituted in mixed micelles of phospholipids and a non-denaturing detergent. We first develop an iterative procedure to evaluate the partition of SDS between the aqueous and the micellar phases. This procedure allows to determine the composition of micelles prepared with variable amphiphiles content. When incubating the enzymes with SDS in the presence of different amounts of phospholipids, it can be observed that higher SDS concentrations are required to obtain the same degree of inactivation when the initial concentration of phospholipids is increased. Notably, we found that, if represented as a function of the mole fraction of SDS in the micelle, the degree of inactivation obtained at different amounts of amphiphiles converges to a single inactivation curve. To interpret this result, we propose a simple model involving active and inactive enzyme molecules in equilibrium. This model allowed us to determine the Gibbs free energy change for the inactivation process and its derivative respect to the mole fraction of SDS in the micellar phase, this last being a measure of the susceptibility of the enzyme to SDS. Our results showed that the inactivation free energy changes are similar for both proteins, and indicate that the equilibrium is highly shifted towards the active form in both enzymes. Conversely, susceptibility to SDS is significantly lower for the hyperthermophilic ATPase, suggesting an inverse relation between thermophilicity and susceptibility to SDS.
Histone modifications regulate pioneer transcription factor binding and cooperativity
Authors: Sinha Kalyan , Bilokapic Silvija , Du Yongming , Malik Deepshikha , Halic Mario 
Published: March 2023

AbstractPioneer transcription factors have the ability to access DNA in compacted chromatin. Multiple transcription factors can bind together to a regulatory element in a cooperative way and cooperation between pioneer transcription factors Oct4 and Sox2 is important for pluripotency and reprogramming. However, the molecular mechanisms by which pioneer transcription factors function and cooperate remain unclear. Here we present cryo-EM structures of human Oct4 bound to a nucleosome containing human Lin28B and nMatn1 DNA sequences, which bear multiple binding sites for Oct4. Our structural and biochemistry data reveal that Oct4 binding induces changes to the nucleosome structure, repositions the nucleosomal DNA and facilitates cooperative binding of additional Oct4 and of Sox2 to their internal binding sites. The flexible activation domain of Oct4 contacts the histone H4 N-terminal tail, altering its conformation and thus promoting chromatin decompaction. Moreover, the DNA binding domain of Oct4 engages with histone H3 N-terminal tail, and posttranslational modifications at H3K27 modulate DNA positioning and affect transcription factor cooperativity. Thus, our data show that the epigenetic landscape can regulate Oct4 activity to ensure proper cell reprogramming.
Protection of catalytic cofactors by polypeptides as a driver for the emergence of primordial enzymes
Authors: Gutierrez-Rus Luis I. , Gamiz-Arco Gloria , Gavira J.A. , Gaucher Eric A. , Risso Valeria A. , Sanchez-Ruiz Jose M. 
Published: March 2023

AbstractEnzymes catalyze the chemical reactions of life. For nearly half of known enzymes, catalysis requires the binding of small molecules known as cofactors. Polypeptide-cofactor complexes likely formed at a primordial stage and became starting points for the evolution of many efficient enzymes. Yet, evolution has no foresight so the driver for the primordial complex formation is unknown. Here, we use a resurrected ancestral TIM-barrel protein to identify one potential driver. Heme binding at a flexible region of the ancestral structure yields a peroxidation catalyst with enhanced efficiency when compared to free heme. This enhancement, however, does not arise from protein-mediated promotion of catalysis. Rather, it reflects protection of bound heme from common degradation processes and a resulting longer life time and higher effective concentration for the catalyst. Protection of catalytic cofactors by polypeptides emerges as a general mechanism to enhance catalysis and may have plausibly benefited primordial polypeptide-cofactor associations.
One Health Assessment of an Urban Temporary Settlement Reveals Gut Microbiome Serving as Antimicrobial Resistance Gene Reservoir
Authors: Napit Rajindra , Gurung Anupama , Poudel Ajit , Manadhar Prajwol , Chaudhary Ashok B. , Sharma Ajay Narayan , Raut Samita , Pradhan Saman Man , Joshi Jyotsna , Poyet Mathilde , Groussin Mathieu , Rajbhandari Rajesh M. , Karmacharya Dibesh B. 
Published: March 2023

AbstractAntimicrobial resistance (AMR) is an emerging and growing global health challenge that could result in 10.2 million deaths annually by 2050. The unrestricted and haphazard use of antibiotics is contributing to the rapid emergence and spread of AMR, and the problem is exacerbated by release of untreated waste water from high-risk sources like hospitals into rivers. Bacteria often develop resistance through horizontal gene transfer mechanism and gut flora can act as a source for new Antimicrobial Resistance Genes (ARG). Upcoming methods like metagenomics can identify the resistance profile (AMR) of gut microbiome, and detect bacterial infections that otherwise go unnoticed. Our study focused on understanding the presence of AMR mutations and gene transfer dynamics in human, animal and environmental samples collected in one of the temporary settlements of Kathmandu (Nepal) using One Health approach. Current AMR reporting based on clinical cases is limited and does not provide information on specific pathogen and associated AMR genes-our study is an effort to contribute information to fulfill this gap.Twenty-one samples were collected from a temporary settlement in Thapathali (Kathmandu), which included fecal samples from birds (n=3) and humans (n=14), and environmental samples (n=4). Microbiological assessment was carried out based on 16S sequence metagenomic analysis using MiSeq (Illumina, USA). Taxonomic classification on obtained 16S sequences were determined by using Metaphlan 2 and Qiime 2 bioinformatics tools. ShortBRED was used to classify ARG and virulence factors, and WAFFLE was used for horizontal gene transfer event prediction. The network analysis was carried out using Gephi v0.9 and the ResistoXplorer web tool to identify ARG in the collected samples.Prevotella spp. was the dominant gut microbiome in humans. We detected diverse phages and viruses, including Stx-2 converting phages. 72 virulence factors and 53 ARG subtypes were detected, with poultry samples having the highest number of subtypes. The cluster and network analysis showed a strong association between gut microbiome and ARG, which was also supported by Horizontal Gene Transfer (HGT) analysis. One-Health interface showed ARG dynamics and revealed gut microbiomes of humans and animals serving as a reservoir for the circulating ARG.
Integrated reporting, audit quality: presence of environmental auditing in an international context
Authors: Hichri Abir 
Published: March 2023

PurposeThis paper aims to investigate the effect of audit quality and environmental auditing on integrated reporting and the effect of environmental auditing on audit quality.Design/methodology/approachData was collected from a sample of 300 international companies during the period 2010–2019. The author collected the data from the Thomson Reuters Eikon database, sustainability reports and annual reports. A multiple regression analysis was performed to test the hypotheses.FindingsThe finding of this study confirms a positive and significant relationship between audit quality and integrated reporting. It is also found that environmental auditing has a positive and significant effect on integrated reporting. Thus, this study found a positive and significant relationship between environmental auditing and audit quality.Practical implicationsThe findings in this paper identify strategies for improving integrated reporting as a crucial element in the processing of financial and nonfinancial information, to help managers and investors and shareholders take a long-term perspective. Therefore, the results encourage companies to invest in economic, environmental and social aspects. This enables accounting professionals, stock exchange authorities and users of environmental and social information to be aware of the factors associated with environmental reporting, to improve the efficiency of those producing the audit service.Originality/valueThe originality of this study lies in its consideration of a particular aspect of auditing, namely, environmental auditing. However, despite the large body of research on auditing and integrated reporting, to the best of the author’s knowledge, this is the first study to examine the relationship between environmental auditing and integrated reporting. Furthermore, in this research, the author has emphasized the importance of the role played by environmental auditing on audit quality. This design has been neglected in previous studies. Finally, the choice of the field of investigation for the reliability of the data used and the generalization of the results obtained, enables us to make important contributions to the user of the information.
Vacation vengeance: an interpretive phenomenological analysis of revenge travel in India
Authors: Singh Snigdha , Srivastava Pallavi 
Published: March 2023

PurposeAfter each of the COVID-19-induced lockdowns, an unprecedented surge in leisure travel was observed, resulting in tourists flocking to places of tourist interest. This phenomenon was termed revenge travel in popular literature. The purpose of this study is to explore the phenomenon of revenge travel in detail through an academic lens. It examines the psychological and emotional motivations for revenge travel while studying the differences in travel behaviour pre- and post-pandemic.Design/methodology/approachThe study applies an interpretive phenomenological approach to explore post-pandemic travel behaviour. Data were collected via personal in-depth semi-structured interviews. Thematic analysis of the transcripts was conducted to arrive at discussion themes.FindingsDrawing on the established theories, the findings of the study indicate that lockdown fatigue coupled with mortality salience induced individuals towards leisure travel. This in turn led to mood alleviation and compensation for the deprivation undergone.Practical implicationsThe study reveals important insights into post-pandemic preferences of travel destinations (off-beat locations near urban clusters), accommodation options (more travellers choosing home stays and stand-alone properties) and vacation itineraries (a gradual shift towards slow tourism with more focus on immersive experiences). Further, there are indications that hotels may develop “workcations” and “staycations” as a new line of offering.Originality/valueThe study adds to the small body of knowledge on revenge travel. It adopts a phenomenological approach, thereby capturing the “lived experiences” of the participants and providing an in-depth look into the psychological and emotional motivations of revenge travel that have not been explored previously. The study provides insights into the travellers' psychology post a period of withdrawal and restraint.