bluuebunny/crossref_metadata_2025_split huggingface dataset:
Higher multiplication rates ofPlasmodium falciparumin isolates from hospital cases compared with community infections
Authors: Stewart Lindsay B. , Escolar Elena Lantero , Philpott James , Claessens Antoine , Amambua-Ngwa Alfred , Conway David J. 
Published: May 2024

AbstractBackgroundParasite multiplication rates vary amongPlasmodium falciparumisolates from patients with malaria, suggesting differences in virulence potential, although direct comparisons between hospital-based clinical cases and community infections are needed.MethodsCryopreserved blood samples from malaria cases presenting to a district hospital in The Gambia and infections detected in local communities were introduced to continuous culture under the same conditions. Thirty-four isolates (23 hospital-based and 11 community-based) were successfully established and then tested under exponential growth conditions over six days to derive estimatedP. falciparummultiplication rates per cycle based on a 48-hour typical cycle length.ResultsA range of parasite multiplication rates in culture was seen across isolates, from 1.5-fold to 5.0-fold per cycle. Multiplication rates were significantly higher in the hospital-based isolates than the community-based isolates. There was a significantly positive correlation between parasitaemia in peripheral blood and multiplication rates in culture. There was no significant difference in multiplication rates between isolates with single or multiple parasite genotypes.ConclusionsThese findings are consistent with a hypothesis that intrinsic natural variation in parasite multiplication rate may affect levels of parasitaemia achieved during infection, and that this affects likelihood of hospital presentation. Results do not support a hypothesis that parasites modify their multiplication rates in response to competing parasites with different genotypes.SummaryRelevant to understanding parasite virulence, this study finds higherPlasmodium falciparummultiplication rates in cultured isolates from malaria cases presenting to hospital than in isolates from local community infections, and positive correlation with parasitaemia in peripheral blood of individuals.
Decoding scalp health and microbiome dysbiosis in dandruff
Authors: Rasheedkhan Regina Viduthalai , Chopra Tarun , Weihao Kwok , Cheruvalli Sreelakshmi , Sabrina Ang , Fatimah Binte Jamal Mohamed Hashmath , Ramasamy Kesava Priyan , Sarah Kay , Yan Chong Yik , Kaliyamoorthi Eganathan , Williams Rohan , Xianghui Liu , Krishna Vedula , Bourokba Nasrine , Jhingan Anjali , Thng Tien Guan Steven , Da Cruz Olivier , Riu Sylvie , De Dormael Romain , Abed Kahina , Touriguine Olivia , Jourdain Roland , Cupferman Sylvie , Aguilar Luc , Rice Scott A. 
Published: May 2024

AbstractA balanced scalp microbiome is crucial for scalp health, yet the mechanisms governing this balance and the etiology of dysbiosis in scalp disorders remain elusive. We conducted a detailed investigation of the scalp and hair follicles, in healthy individuals and those with dandruff/seborrheic dermatitis (D/SD). It was demonstrated that the microbiome inhabiting hair follicles serves as a reservoir for the scalp microbiome, thereby integrating the scalp, follicle, and the hair into one functional unit. Using in vitro models, we further elucidated mechanisms governing the assembly and interactions of the follicular microbiome under healthy and D/SD conditions. We show that propionic acid, produced byC. acnes, plays a pivotal role in maintaining microbiome balance, with implications for scalp health, which was validated through a clinical study.
Imaging flow cytometry enables label-free cell sorting of morphological variants from unculturable bacterial populations
Authors: Vocelle Daniel , Thompson Lindsey , Bernard Matthew P. , Wale Nina 
Published: May 2024

AbstractBacterial populations often display remarkable morphological heterogeneity. Flow cytometric cell sorting (often called FACS) is an important tool for understanding this diversity. FACs allows researchers to obtain pure samples of each morphological variant (or morphotype) that is present within a mixed population of cells and thus permits each morphotype to be phenotyped. In FACS, cells are first labeled with fluorescent markers such as antibodies or transgenic constructs, and then separated out based on their possession of these labels. However, since the development of fluorescent labels requiresa prioriknowledge of bacterial biology, it is often impossible to apply FACS to understudied and/or unculturable bacteria. This challenge has limited our capacity to investigate the biology of bacterial size and shape in all but a small, largely culturable subset of bacterial taxa. Here, we present an innovative strategy that permits label-free cell sorting of bacterial morphotypes, using an unculturable, pleiomorphic pathogen (Pasteuria ramosa) as a model bacterium. We show that imaging flow cytometry (IFC) can be used to systematically identify light-scattering and autofluorescence “signatures” of bacterial morphotypes, on which basis cell sorting can be conducted. Critically, our IFC-enabled cell sorting strategy yields samples of sufficient purity (>90%) for common downstream analyses e.g., “-omics” analyses. Our work represents an innovative application of IFC and provides an economical, widely applicable solution to a central problem in the study of bacterial diversity.ImportanceBacteria come in many different shapes and sizes. Why this morphological variation exists is a longstanding question in microbiology, but it remains difficult to answer. To phenotype different morphological variants (morphotypes) within a bacterial population, we need to separate them from one another. This is normally achieved using flow cytometric cell-sorting, whereby morphotypes are labelled with fluorescent antibodies and separated on the basis of their differential fluorescence. Unfortunately, it is difficult to develop fluorescent-labels specific to unculturable or poorly studied bacteria because of the limited availability of appropriate molecular tools. Here, we demonstrate that imaging flow cytometry can be used to design and validate label-free cell sorting strategies. Recently, there has been a resurgence of interest in bacterial morphological diversity and a call to expand its study across the tree of life. Our work will help microbiologists to answer this call.
Rationally Designed Pooled CRISPRi-Seq Uncovers an Inhibitor of Bacterial Peptidyl-tRNA Hydrolase
Authors: Rahman A. S. M. Zisanur , Syroegin Egor A. , Novomisky Nechcoff Julieta , Devarajan Archit , Polikanov Yury S. , Cardona Silvia T. 
Published: May 2024

AbstractPooled knockdown libraries of essential genes are useful tools for elucidating the mechanisms of action of antibacterial compounds, a pivotal step in antibiotic discovery. However, achieving genomic coverage of antibacterial targets poses a challenge due to the uneven proliferation of knockdown mutants during pooled growth, leading to the unintended loss of important targets. To overcome this issue, we describe the construction of CIMPLE (CRISPRi-mediatedpooled library ofessential genes), a rationally designed pooled knockdown library built in a model antibiotic-resistant bacteria,Burkholderia cenocepacia.By analyzing growth parameters of clonal knockdown populations of an arrayed CRISPRi library, we predicted strain depletion levels during pooled growth and adjusted mutant relative abundance, approaching genomic coverage of antibacterial targets during antibiotic exposure. We first benchmarked CIMPLE by chemical-genetic profiling of known antibacterials, then applied it to an uncharacterized bacterial growth inhibitor from a new class. CRISPRi-Seq with CIMPLE, followed by biochemical validation, revealed that the novel compound targets the peptidyl-tRNA hydrolase (Pth). Overall, CIMPLE leverages the advantages of arrayed and pooled CRISPRi libraries to uncover unexplored targets for antibiotic action.SummaryBacterial mutant libraries in which antibiotic targets are downregulated are useful tools to functionally characterize novel antimicrobials. These libraries are used for chemical-genetic profiling as target-compound interactions can be inferred by differential fitness of mutants during pooled growth. Mutants that are functionally related to the antimicrobial mode of action are usually depleted from the pool upon exposure to the drug. Although powerful, this method can fail when the unequal proliferation of mutant strains before exposure causes mutants to fall below the detection level in the library pool. To address this issue, we constructed an arrayed essential gene mutant library (EGML) in the antibiotic-resistant bacteriumBurkholderia cenocepaciausing CRISPR interference (CRISPRi) and analyzed the growth parameters of individual mutant strains. We then modelled depletion levels during pooled growth and used the model to rationally design an optimized CRISPR interference-mediated pooled library of essential genes (CIMPLE). By adjusting the initial inoculum of the knockdown mutants, we achieved coverage of the bacterial essential genome with mutant sensitization. We exposed CIMPLE to a recently discovered antimicrobial of a novel class and discovered it inhibits the peptidyl-tRNA hydrolase, an essential bacterial enzyme. In summary, we demonstrate the utility of CIMPLE and CRISPRi-Seq to uncover the mechanism of action of novel antimicrobial compounds.Graphical abstract
Systematic large-scale application of ClinGen InSiGHTAPC-specific ACMG/AMP variant classification criteria substantially alleviates the burden of variants of uncertain significance in ClinVar and LOVD databases
Authors: Yin Xiaoyu , Richardson Marcy , Laner Andreas , Shi Xuemei , Ognedal Elisabet , Vasta Valeria , Hansen Thomas v. O. , Pineda Marta , Ritter Deborah , den Dunnen Johan T. , Hassanin Emadeldin , Lyman Lin Wencong , Borras Ester , Krahn Karl , Nordling Margareta , Martins Alexandra , Mahmood Khalid , Nadeau Emily A.W. , Beshay Victoria , Tops Carli , Genuardi Maurizio , Pesaran Tina , Frayling Ian M. , Capellá Gabriel , Latchford Andrew , Tavtigian Sean V. , Maj Carlo , Plon Sharon E. , Greenblatt Marc S. , Macrae Finlay A. , Spier Isabel , Aretz Stefan 
Published: May 2024

AbstractBackgroundPathogenic constitutionalAPCvariants underlie familial adenomatous polyposis, the most common hereditary gastrointestinal polyposis syndrome. To improve variant classification and resolve the interpretative challenges of variants of uncertain significance (VUS), APC-specific ACMG/AMP variant classification criteria were developed by the ClinGen-InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (VCEP).MethodsA streamlined algorithm using theAPC-specific criteria was developed and applied to assess allAPCvariants in ClinVar and the InSiGHT international referenceAPCLOVD variant database.ResultsA total of 10,228 uniqueAPCvariants were analysed. Among the ClinVar and LOVD variants with an initial classification of (Likely) Benign or (Likely) Pathogenic, 94% and 96% remained in their original categories, respectively. In contrast, 41% ClinVar and 61% LOVD VUS were reclassified into clinically actionable classes, the vast majority as (Likely) Benign. The total number of VUS was reduced by 37%. In 21 out of 36 (58%) promisingAPCvariants that remained VUS despite evidence for pathogenicity, a data mining-driven work-up allowed their reclassification as (Likely) Pathogenic.ConclusionsThe application ofAPC-specific criteria substantially reduced the number of VUS in ClinVar and LOVD. The study also demonstrated the feasibility of a systematic approach to variant classification in large datasets, which might serve as a generalisable model for other gene-/disease-specific variant interpretation initiatives. It also allowed for the prioritization of VUS that will benefit from in-depth evidence collection. This subset ofAPCvariants was approved by the VCEP and made publicly available through ClinVar and LOVD for widespread clinical use.
Facultative endosymbiosis between cellulolytic protists and methanogenic archaea in the gut of the Formosan termiteCoptotermes formosanus
Authors: Kaneko Masayuki , Omori Tatsuki , Igai Katsura , Mabuchi Takako , Sakai-Tazawa Miho , Nishihara Arisa , Kihara Kumiko , Yoshimura Tsuyoshi , Ohkuma Moriya , Hongoh Yuichi 
Published: May 2024

ABSTRACTAnaerobic protists frequently harbour methanogenic archaea, which apparently contribute to the hosts’ fermentative metabolism by consuming excess H2. However, the ecological properties of endosymbiotic methanogens remain elusive in many cases. Here we investigated the ecology and genome of the endosymbiotic methanogen of theCononymphaprotists in the hindgut of the termiteCoptotermes formosanus. Microscopic and 16S rRNA amplicon sequencing analyses revealed that a single species, designated here ‘CandidatusMethanobrevibacter cononymphae’, is associated with bothCononympha leidyiandCononympha koidzumiiand that its infection rate inCononymphacells varied from 0.0 to 99.8% among termite colonies. Fine-scale network analysis indicated that multiple 16S rRNA sequence variants coexisted within a single host cell and that identical variants were present in bothCononymphaspecies and also on the gut wall. Thus, ‘Ca.Methanobrevibacter cononymphae’ is a facultative endosymbiont, transmitted vertically with frequent exchanges with the gut environment. Indeed, transmission electron microscopy showed escape or uptake of methanogens from/by aCononymphacell. The genome of ‘Ca.Methanobrevibacter cononymphae’ showed features consistent with its facultative lifestyle: i.e., the genome size (2.7 Mbp) comparable to those of free-living relatives; the pseudogenization of the formate dehydrogenase genefdhA, unnecessary within the non-formate-producing host cell; the dependence on abundant acetate in the host cell as an essential carbon source; and the presence of a catalase gene, required for colonization on the microoxic gut wall. Our study revealed a versatile endosymbiosis between the methanogen and protists, which may be a strategy responding to changing conditions in the termite gut.
The avian and human influenza A virus receptors sialic acid (SA)-α2,3 and SA-α2,6 are widely expressed in the bovine mammary gland
Authors: Kristensen Charlotte , Jensen Henrik E. , Trebbien Ramona , Webby Richard J. , Larsen Lars E. 
Published: May 2024

AbstractAn outbreak of H5N1 highly pathogenic influenza A virus (HPIAV) has been detected in dairy cows in the United States. Influenza A virus (IAV) is a negative-sense, single-stranded, RNA virus that has not previously been associated with widespread infection in cattle. As such, cattle are an extremely under-studied domestic IAV host species. IAV receptors on host cells are sialic acids (SAs) that are bound to galactose in either an α2,3 or α2,6 linkage. Human IAVs preferentially bind SA-α2,6 (human receptor), whereas avian IAVs have a preference for α2,3 (avian receptor). The avian receptor can further be divided into two receptors: IAVs isolated from chickens generally bind more tightly to SA-α2,3-Gal-β1,4 (chicken receptor), whereas IAVs isolated from duck to SA-α2,3-Gal-β1,3 (duck receptor). We found all receptors were expressed, to a different degree, in the mammary gland, respiratory tract, and cerebrum of beef and/or dairy cattle. The duck and human IAV receptors were widely expressed in the bovine mammary gland, whereas the chicken receptor dominated the respiratory tract. In general, only a low expression of IAV receptors was observed in the neurons of the cerebrum. These results provide a mechanistic rationale for the high levels of H5N1 virus reported in infected bovine milk and show cattle have the potential to act as a mixing vessel for novel IAV generation.Graphical abstractCreated withBiorender.com
CUAD biotechnology offers 0.5 USD per hectare for aphid control: innovative platform for low-cost plant protection
Authors: Oberemok Volodymyr V. , Puzanova Yelizaveta V. , Gal’chinsky Nikita V. 
Published: May 2024

Abstract20 years ago it was difficult to imagine the use of nucleic acids in plant protection as insecticides, but today it is a reality. At the very beginning, new technologies often work inefficiently and are expensive; in the process of their development, qualitative changes occur that make new technologies accessible and work flawlessly. Invented in 2008, oligonucleotide insecticides based on CUAD (contact unmodified antisense DNA) platform have been improved and today possess characteristics that amaze the imagination: low carbon footprint, high safety for non-target organisms, rapid biodegradability in ecosystems, avoidance of target-site resistance. This next generation class of insecticides creates opportunities to develop insecticides which are well-tailored for a particular population of insect pest. CUAD biotechnology combines the achievements of molecular genetics, bioinformatics, andin vitronucleic acid synthesis providing a simple and flexible platform for plant protection. Aphids, as one of the key pests of important agricultural crops that shape food security, can be controlled by oligonucleotide insecticides at affordable price already today, ensuring effective control with minimal risks for the environment. In this article, low-dose concentration (0.1 ng/µL; 20 mg per hectare in 200 L of water solution) of 11-nt long oligonucleotide insecticide Schip-11 shows effectiveness on aphidSchizolachnus pineticausing 76.06 ± 7.68 mortality rate on the 12th day (p<0.05). At a consumption rate of 200 L per hectare, the price of the required amount of oligonucleotide insecticide will be about 0.5 USD/ha using liquid-phase DNA synthesis and makes oligonucleotide insecticides very competitive on the market. Also we show that non-canonical base pairing G:T (T:G) between target pre-rRNA and olinscide is well tolerated in aphids. Thus, non-canonical base-pairing should be taken into consideration during design of olinscides not to harm non-target organisms.
Isolation, cloning and expression analysis of two pyruvate orthophosphate dikinase genes ofChlamydomonas reinhardtii
Authors: Demirel Fadime , Cebrailoglu Nicat , Mammadova Faxriyya , Tangut Taha , Aksoy Munevver , Mammadova Gulshan , Hasanova Gulnara , Mamedov Tarlan 
Published: May 2024

AbstractThe green algaeC. reinhardtiiserves as a useful model for studying photosynthetic cells and has been extensively utilized for investigating various physiological processes. Currently, limited information is available regarding the molecular mechanisms controlling oil accumulation in microalgae. C4 photosynthesis metabolic pathways are essential for high rates of CO2fixation in plants. High rates of photosynthesis are crucial for the biomass accumulation of algae. Surprisingly, C4 pathway enzymes and their regulatory factors have not been studied at the molecular level in any green algae, except for our efforts, which focused on the molecular characterization of phosphoenolpyruvate carboxylase (PEPC) genes (Ppc) inC. reinhardtii(Mamedov et al., 2005; Moellering et al., 2007) and phosphoenolpyruvate carboxykinase (Cebarailoglu, 2017). In this study, we isolated and cloned two pyruvate orthophosphate dikinase (PPDK) genes from the green microalgaC. reinhardtiifor the first time and performed expression analysis under different conditions. We demonstrate that bothppdkgenes encode functional PPDK enzymes inC. reinhardtiiand that both genes are responsive to changes in carbon dioxide or ammonium concentration during growth. Phylogenetic analysis suggests thatC. reinhardtiiPPDK2 is evolutionarily closer to PPDKs from plants rather than to protozoan and bacterial enzymes. Furthermore, alignment data indicate that the global structure and key amino acid residues involved in catalysis and substrate binding are well conserved in both PPDK enzymes in plants,C. reinhardtii, bacteria, and protozoa.
Systematic analysis of the target recognition and repression by the Pumilio proteins
Authors: Farberov Svetlana , Ulitsky Igor 
Published: May 2024

AbstractRNA binding proteins orchestrate the post-transcriptional fate of RNA molecules, but the principles of their action remain poorly understood. Pumilio (PUM) proteins bind 3’UTRs of mRNAs and lead to mRNA decay. To comprehensively map the determinants of recognition of sequences by PUM proteins in cells and to study the binding outcomes, we developed a massively parallel RNA assay that profiled thousands of PUM binding sites in cells undergoing various perturbations or RNA immunoprecipitation. By studying fragments from theNORADlong noncoding RNA, we find two features that antagonize repression by PUM proteins – G/C rich sequences, particularly those upstream of the PUM recognition element, and binding of FAM120A, which limits the repression elicited by PUM binding sites. We also find that arrays of PUM sites separated by 8–12 bases offer particularly strong repression and use them to develop a particularly sensitive reporter for PUM repression. In contrast, PUM sites separated by shorter linkers, such as some of those found inNORAD, exhibit strong activity interdependence, likely mediated by competition between PUM binding and formation of strong secondary structures. Overall, our findings expand our understanding of the determinants of PUM protein activity in human cells.HighlightsA massively parallel assay reports on the binding and activity of Pumilio proteins in human cellsG/C rich sequence context inhibits repression by Pumilio proteinsFAM120a binds sequences with Pumilio sites and antagonizes repression by Pumilio proteinsArrays of Pumilio binding sites are most effective at distances of 8–12 nt.Strong inter-dependency in the tandem Pumilio binding sites in NORAD.
Glutamate (E299) is a key residue in the evolutionarily divergence of the SAM-dependent methyltransferases DnrK and RdmB in anthracycline biosynthesis
Authors: Sang Moli , Yang Qingyu , Guo Jiawei , Feng Peiyuan , Ma Wencheng , Li Shengying , Zhang Wei 
Published: May 2024

AbstractA novel sub-class ofS-adenosyl-L-methionine (SAM)-dependent methyltransferases catalyze atypical chemical transformations in the biosynthesis of anthracyclines, which include antineoplastic compounds. Intriguingly, the closely related methyltransferases DnrK and RdmB have markedly divergent functions. We investigated their catalytic activities and discovered a previously unknown 10-hydroxylation activity for DnrK and 4-O-methylation activity for RdmB. Isotope-labeling demonstrated that the 10-hydroxy group introduced by DnrK is derived from water molecules while RdmB utilizes O2. A single residue, E299, was the key modulator in the differing catalytic functions of DnrK and RdmB, especially the decarboxylative oxidation activity. Furthermore, the multifunctionality of DnrK was demonstrated to be SAM-tunable and concerted, whereas RdmB activity was cofactor-dependent and stepwise. Our findings expand the versatility and importance of methyltransferases and should aid studies to enrich the structural diversity and bioactivities of anthracyclines.