bluuebunny/crossref_metadata_2025 huggingface dataset:
In defense of Apocynaceae: inference on evolution of pyrrolizidine alkaloids from evolution of an enzyme in their biosynthetic pathway, homospermidine synthase
Authors: Smith Chelsea R. , Kaltenegger Elisabeth , Teisher Jordan , Moore Abigail J. , Straub Shannon C. K. , Livshultz Tatyana
Published: April 2023

Premise

When enzymes encoded by paralogous genes produce identical specialized metabolites in distantly related plant lineages, it is strong evidence of parallel phenotypic evolution. Inference of phenotypic homology for metabolites produced by orthologous genes is not so straightforward, however, since orthologs may be recruited in parallel into novel pathways. Prior research on pyrrolizidine alkaloids (PAs), specialized metabolites of Apocynaceae, reconstructed evolution of homospermidine synthase (HSS), an enzyme of PA biosynthesis, and inferred a single origin of PAs because HSS enzymes of all known PA-producing Apocynaceae species are orthologous and descended from an ancestral enzyme with the predicted motif (VXXXD) of an optimized HSS.

Methods

We increased sampling, tested the effect of amino acid motif on HSS function, revisited motif evolution, and tested for selection to infer evolution of HSS function and its correlation with phenotype.

Key results

Some evidence supports a single origin of PAs: an IXXXD HSS, similar in function to VXXXD HSS, evolved in the shared ancestor of all PA-producing species; loss of optimized HSS occurred multiple times via pseudogenization and perhaps via evolution of an IXXXN motif. Other evidence indicates multiple origins: the VXXXD motif, highly correlated with the PA phenotype, evolved two or four times independently; the ancestral IXXXD gene was not under positive selection while some VXXXD genes were; substitutions at sites experiencing positive selection occurred on multiple branches in theHSS-like gene tree.

Conclusions

Complexity of the genotype-function-phenotype map confounds inference of PA homology fromHSSevolution in Apocynaceae.
Chromosome-level genome assembly provides insights into adaptive evolution of chromosome and important traits in the geckoGekko japonicus
Authors: Wang Yinwei , Yue Youxia , Li Chao , Chen Zhiyi , Cai Yao , Hu Chaochao , Qu Yanfu , Li Hong , Zhou Kaiya , Yan Jie , Li Peng
Published: April 2023

Gekko japonicuspossess excellent flexible climbing and detoxification ability under insectivorous habits, and its chromosomes and the genetic evolutionary mechanisms behind these traits are still unclarified. Here, we assembled a chromosome-level genome ofG. japonicuswith a total size of 2.53 Gb contained in 19 pairs of chromosomes. The evolutionary breakpoint regions (EBRs) are significantly enriched for some repetitive elements compared to the rest of genome and the genes located in the EBRs are enriched in defense response pathway.G. japonicusspecific gene families, expanded gene families and positively selected genes are mainly enriched in some pathways related to the immune, sensory and nervous systems. These results from comprehensive comparative genomics and evolutionary genomics analyses indicated that bitter taste receptor type 2 (T2Rs) expanded in different lineages by tandem gene duplication. The expansion and independent duplication events of T2Rs and positively selected branches were predominantly present in insectivorous species, suggests that T2Rs are associate with clearance of bitter toxins in gekkotans. Detoxification genes in detox and biosynthetic cytochrome P450 ofG. japonicashave frequent duplication and loss events, suggests that they undergo more birth and death processes compared to biosynthesis type genes. Pro, Cys, Gly and Ser are the most abundant amino acids in 66 epidermis formation corneous beta proteins (CBPs) ofG. japonicas, the abundance of Gly and Cys in CBPs implying significant effects on the flexibility and setae adhesiveness of gekkotans. Some thermosensitive thermoregulatory transient receptor potential channels under relaxed purifying selection or positive selection inG. japonicus, implying that one of the important factors improve the ability to adapt to climate change.
Dividing out quantification uncertainty allows efficient assessment of differential transcript expression with edgeR
Authors: Baldoni Pedro L. , Chen Yunshun , Hediyeh-zadeh Soroor , Liao Yang , Dong Xueyi , Ritchie Matthew E. , Shi Wei , Smyth Gordon K.
Published: April 2023

Differential expression analysis of RNA-seq is one of the most commonly performed bioinformatics analyses. Transcript-level quantifications are inherently more uncertain than gene-level read counts because of ambiguous assignment of sequence reads to transcripts. While sequence reads can usually be assigned unambiguously to a gene, reads are very often compatible with multiple transcripts for that gene, particularly for genes with many isoforms. Software tools designed for gene-level differential expression do not perform optimally on transcript counts because the read-to-transcript ambiguity (RTA) disrupts the mean-variance relationship normally observed for gene level RNA-seq data and interferes with the efficiency of the empirical Bayes dispersion estimation procedures. The pseudoaligners kallisto and Salmon provide bootstrap samples from which quantification uncertainty can be assessed. We show that the overdispersion arising from RTA can be elegantly estimated by fitting a quasi-Poisson model to the bootstrap counts for each transcript. The technical overdispersion arising from RTA can then be divided out of the transcript counts, leading to scaled counts that can be input for analysis by established gene-level software tools with full statistical efficiency. Comprehensive simulations and test data show that an edgeR analysis of the scaled counts is more powerful and efficient than previous differential transcript expression pipelines while providing correct control of the false discovery rate. Simulations explore a wide range of scenarios including the effects of paired vs single-end reads, different read lengths and different numbers of replicates.
Gelation of Uniform Interfacial Diffusant in Embedded 3D Printing
Authors: Shin Sungchul , Brunel Lucia G. , Cai Betty , Kilian David , Roth Julien G. , Seymour Alexis J. , Heilshorn Sarah C.
Published: April 2023

While the human body has many different examples of perfusable structures with complex geometries, biofabrication methods to replicate this complexity are still lacking. Specifically, the fabrication of self-supporting, branched networks with multiple channel diameters is particularly challenging. Here, we present the Gelation of Uniform Interfacial Diffusant in Embedded 3D Printing (GUIDE-3DP) approach for constructing perfusable networks of interconnected channels with precise control over branching geometries and vessel sizes. To achieve user-specified channel dimensions, this technique leverages the predictable diffusion of crosslinking reaction-initiators released from sacrificial inks printed within a hydrogel precursor. We demonstrate the versatility of GUIDE-3DP to be adapted for use with diverse physiochemical crosslinking mechanisms by designing seven printable material systems. Importantly, GUIDE-3DP allows for the independent tunability of both the inner and outer diameters of the printed channels and the ability to fabricate seamless junctions at branch points. This 3D bioprinting platform is uniquely suited for fabricating lumenized structures with complex shapes characteristic of multiple hollow vessels throughout the body. As an exemplary application, we demonstrate the fabrication of vasculature-like networks lined with endothelial cells. GUIDE-3DP represents an important advance toward the fabrication of self-supporting, physiologically relevant networks with intricate and perfusable geometries.
Importance of Leaf Age in Grapevines Under Salt Stress
Authors: Lupo Yaniv , Prashanth Kakarla , Lazarovitch Naftali , Fait Aaron , Rachmilevitch Shimon
Published: April 2023

The combined effects of salt stress and leaf age on photosynthesis and stomatal conductance are not fully understood. Salt stress develops at different rates in various plant organs and tissues, leading to osmotic and ionic stresses. We studied the development of salt stress (30 mM NaCl) in two grapevine rootstocks by examining the gas exchange, photochemistry, and salt accumulation of leaves at different ages. Our results indicate that leaf age strongly affected photosynthesis but had a minor effect on stomatal conductance in both control and salinity conditions. Surprisingly, salt stress lowered stomatal conductance but had little effect on photosynthesis, opposite to the leaf age effects. Reduction in photosystem II efficiency explained the age-associated decline in photosynthesis, suggesting that the light-dependent phase of photosynthesis is the first process affected by leaf aging. We also found that the sodium exclusion capacity decreased as leaves matured and was age and variety dependent, indicating the importance of leaf age when sampling for salt tolerance studies. Therefore, we suggest that sampling only young leaves is missing critical information in the evaluation of salt-tolerant traits in grapevines.
Mechanism of ADP-inhibited ATP hydrolysis in single proton-pumping FoF1-ATP synthase trapped in solution
Authors: Pérez Iván , Heitkamp Thomas , Börsch Michael
Published: April 2023

FoF1-ATP synthases in mitochondria, in chloroplasts and in most bacteria are the proton-driven membrane enzymes supplying the cells with ATP made from ADP and phosphate. To monitor and prevent the reverse chemical reaction of fast wasteful ATP hydrolysis by the enzymes, different control mechanisms exist including mechanical or redox-based blockade of catalysis and ADP inhibition. In general product inhibition is expected to slow down the mean catalytic turnover. However, biochemical assays are ensemble measurements and cannot discriminate between a mechanism affecting all enzymes equally or individually. For example, all enzymes could work slower at a decreasing substrate/product ratio, or more and more individual enzymes are blocked completely. Here, we examined how increasing amounts of ADP affected ATP hydrolysis of singleEscherichia coliFoF1-ATP synthases in liposomes. We observed individual catalytic turnover of the enzymes one after another by monitoring the internal subunit rotation using single-molecule Förster resonance energy transfer (smFRET). Observation times of single FRET-labeled FoF1-ATP synthase in solution were increased up to seconds using a confocal Anti-Brownian electrokinetic trap (ABEL trap). By counting active versus inhibited enzymes we revealed that ADP inhibition did not decrease the catalytic turnover of all FoF1-ATP synthases equally. Instead, increasing ADP in the ADP/ATP mixture reduced the number of the remaining active enzymes which were operating at similar catalytic rates for varying substrate/product ratios.
Machine Learning exploratory technic detected that men might be up to eight times more affected by the control effect and three times more affected by the placebo effect than women
Authors: Nahon Roberto Lohn , Lazzoli José Kawazoe , Verli Marcio Vinícius de Abreu , Gonçalves Luis Carlos Oliveira , Magalhães Neto Aníbal Monteiro de
Published: April 2023

Background

The Placebo effect has been historically described since the beginning of Medicine. When the most skeptical researchers say they do not believe in Noetic Science but use a placebo in their research, they generate an apparent contradiction. The present study aimed to understand the noetic influence on high-level athletes, using a sportomics strategy, statistical exploratory techniques of machine learning and holistic analysis.

Methods

The study included 14 volunteer volleyball athletes. Each volunteer was submitted to four running tests of 3,000 meters, on a 400-meter track, with one test each subsequent day. On the first day, the athletes performed the first test of 3,000, aiming to adapt to the trial (ADAPT 1), and on the second day, the same adaptation (ADAPT 2). On the third and fourth days, the placebos were introduced, and on the third day, the athletes received the information that that would be just a placebo, which was called (CONTROL). On the fourth day, when the identical placebo was given, the athletes received the information that it would be a new cutting-edge nutritional supplement being studied (PLACEBO).

Results

Men might be up to eight times more affected by the control effect and three times more by the placebo effect than women. Regarding performance, there was an antagonistic behavior concerning gender for the control effect and an agonistic effect for the placebo effect, but with less impact on women. Men also showed a faster adaptation to the test.

Conclusion

Noetic science, always considered but never assumed by researchers, is confirmed when the present study reveals that men are more affected by the control effect and the placebo effect than women, with antagonistic behavior concerning gender for the control effect and an agonist effect for the placebo effect, but with less impact on women about performance.
A minimally-invasive method for ancient DNA sampling of Prehistoric bone and antler tools and hunting weapons
Authors: Tejero José-Miguel , Cheronet Olivia , Gelabert Pere , Zagorc Brina , Alvarez Esteban , Averbouh Aline , Bar-Oz Guy , Belfer-Cohen Anna , Bosch Marjolein D. , Brück Florian , Cueto Marián , Dockner Martin , Fullola Josep Maria , Gárate Diego , Giannakoulis Michael , González Cynthia , Jakeli Nino , Mangado Xavier , Meshveliani Tengiz , Neruda Petr , Nigst Philip , Šimková Petra G. , Tapia Jesús , de la Torre Marta Sánchez , Schwab Catherine , Weber Gerhard , Pinhasi Ron
Published: April 2023

Internal and external bony tissues from diverse mammalian taxa are one of the primary animal raw materials exploited for technical and symbolic purposes by Eurasian Upper Palaeolithic hunter-gatherers. Identifying the source species used for osseous raw material is critical to gain insights into these populations’ behaviour, technology, and subsistence. The study of osseous tools has advanced in the last few years by combining archaeological and biomolecular methods. Ancient genomics opens many new analytical opportunities. Ancient DNA (aDNA) can provide a wealth of information about the animal sources of these objects. Unfortunately, aDNA analyses often involve destructive sampling. Here, we develop and apply a minimally-invasive aDNA sampling method for an assemblage of 42 prehistoric hunting weapons and tools from various Eurasian archaeological sites. We evaluated the impact of our approach on the specimens visually, microscopically and through Micro-CT scans. The surface impacts are marginal, ranging from 0.3-0.4 mm. Using a custom-made DNA capture kit for 54 mammalian species, we obtained sufficient aDNA to identify the taxa of 33% of the objects. For one of the tools, we recovered enough endogenous aDNA to infer the genetic affinities of the individual. Our results also demonstrate that ancient antler, one of the primary raw materials used during a large part of prehistory, is a reliable source of aDNA. Our minimally-invasive aDNA sampling method is therefore effective while preserving osseous objects for potential further analyses: morphometric, technical, genetic, radiometric and more.
Transcriptomic analyses reveal regional signatures in lung allograft recipients
Authors: Agudelo-Romero Patricia , Ling Kak-Ming , Lavender Melanie A. , Wrobel Jeremy P. , Musk Michael , Stick Stephen M , Kicic Anthony
Published: April 2023

Background

Long term outcomes of allograft recipients are compromised by the development of chronic lung allograft dysfunction (CLAD) promoting bronchiolitis obliterans syndrome (BOS). We established baseline transcriptomic profiles of both the large and small airway epithelial cells (referred as LAEC and SAEC, respectively) to identify regional differences irrespective of initiating disease.

Methods

We obtained matched primary LAEC and SAEC from lung allograft recipients (n=4, 42.5 ± 4.2 years) and established primary cultures. Bulk RNA sequencing was performed to determine differentially expressed genes.

Results

We observed differences in the transcriptional program between LAEC and SAEC Transcription factors (TF) were ranked within the top ten differentially regulated genes. The most abundant TF families included C2H2-ZF, homeobox and bHLH. Upstream regulator analyses identified homeobox genes being significantly in LAEC. Protein-protein interaction network analysis emphasised the role of TFs (ISL1, MSX1, HOXA1, GATA6, ZNF423) in airway modulation. Additionally, functional enrichment analysis revealed the activation of chemotaxis, metalloendipeptidase/metallopeptidase activity and pro-inflammatory signatures (IL17 signalling and RAGE), in LAEC, while SAEC were characterised by elevated expression of surfactant metabolism related genes. Moreover, alveolar and club cells-related genes were expressed in SAEC, suggesting a lower airway-specific signature.

Conclusion

Our analysis shows robust transcriptional differences between LAEC and SAEC. We suggest a potential role for homeobox TF family as well as the activation of the immune system in the biology of LAEC. Conversely, we observed an alveoli-like transcriptional signature in SAEC, including gas-exchange signals and surfactant metabolism; pathways involved in lung homeostasis.
Astrocytic Slc4a4 regulates blood-brain barrier integrity in healthy and stroke brains via a NO-CCL2-CCR2 pathway
Authors: Ye Qi , Jo Juyeon , Wang Chih-Yen , Oh Heavin , Choy Tiffany J. , Kim Kyoungin , D’Alessandro Angelo , Reshetnyak Yana K. , Jung Sung Yun , Chen Zheng , Marrelli Sean P. , Lee Hyun Kyoung
Published: April 2023

Astrocytes play vital roles in blood-brain barrier (BBB) maintenance, yet how they support BBB integrity under normal or pathological conditions remains poorly defined. Recent evidence suggests pH homeostasis is a new cellular mechanism important for BBB integrity. In the current study, we investigated the function of an astrocyte-specific pH regulator, Slc4a4, in BBB maintenance and repair. We show that astrocytic Slc4a4 is required for normal astrocyte morphological complexity and BBB function. Multi-omics analyses identified increased astrocytic secretion of CCL2 coupled with dysregulated arginine-NO metabolism after Slc4a4 deletion. Using a model of ischemic stroke, we found that loss of Slc4a4 exacerbates BBB disruption and reactive gliosis, which were both rescued by pharmacological or genetic inhibition of the NO-CCL2 pathwayin vivo.Together, our study identifies the astrocytic Slc4a4-NO-CCL2 axis as a pivotal mechanism controlling BBB integrity and repair, while providing insights for a novel therapeutic approach against BBB-related CNS disorders.
Short-term auditory priming in freely-moving mice
Authors: Sivroni Shir , Sloin Hadas , Stark Eran
Published: April 2023

Priming, a change in the mental processing of a stimulus as a result of prior encounter with a related stimulus, has been observed repeatedly and studied extensively. Yet currently there is no behavioral model of short-term priming in lab animals, limiting the study of the neurobiological basis of priming. Here, we describe an auditory discrimination paradigm for studying response priming in freely-moving mice. We find a priming effect in success rate in all mice tested on the task. In contrast to humans, we do not find a priming effect in response times. Compared to non-primed discrimination trials, the addition of incongruent prime stimuli reduces success rate more than congruent prime stimuli, suggesting a cognitive mechanism based on differential interference. The results establish the short-term priming phenomenon in rodents, and the paradigm opens the door to studying the cellular-network basis of priming.
Disruption of the rice4-DEOXYOROBANCHOL HYDROXYLASEunravels specific functions of canonical strigolactones
Authors: Chen Guan-Ting Erica , Wang Jian You , Votta Cristina , Braguy Justine , Jamil Muhammad , Kirschner Gwendolyn K , Fiorilli Valentina , Berqdar Lamis , Balakrishna Aparna , Blilou Ikram , Lanfranco Luisa , Al-Babili Salim
Published: April 2023

Strigolactones (SLs) regulate many developmental processes, including shoot-branching/tillering, and mediate rhizospheric interactions. SLs are structurally diverse, divided into a canonical and a non-canonical sub-family. To better understand the biological function of particular SLs, we generated CRISPR/Cas9 mutants disrupted inOsMAX1-1400orOsMAX1-1900, which encode cytochrome P450 enzymes (CYP711A clade) contributing to SL diversity. The disruption ofOsMAX1-1900did neither affect the SL pattern nor plant architecture, indicating a functional redundancy. In contrast, disruption of OsMAX1-1400 activity, a 4-deoxyorobanchol hydroxylase, led to a complete lack of orobanchol and an accumulation of its precursor 4-deoxyorobanchol (4DO), both of which are a canonical SLs common in different plant species, accompanied by higher levels of the non-canonical methyl 4-oxo-carlactonoate (4-oxo-MeCLA).Os1400mutants showed also shorter plant height, panicle and panicle base length, but did not exhibit a tillering phenotype. Hormone quantification and transcriptome analysis revealed elevated auxin levels and changes in the expression of auxin-related, as well as of SL biosynthetic genes. Interestingly, theOs900/1400double mutant lacking both orobanchol and 4DO did not show the observedOs1400architectural phenotypes, indicating that they are a result of 4DO accumulation. A comparison of the mycorrhization and Striga seed germinating activity ofOs900, Os900/1400, andOs1400loss-of-function mutants demonstrates that the germination activity positively correlates with 4DO content while disruptingOsMAX1-1400negatively impact mycorrhizal symbiosis. Taken together, our paper deciphers the biological function of canonical SLs in rice and depicts their particular contributions to establishing architecture and rhizospheric communications.
Sweet and sour synergy: exploring the antibacterial and antibiofilm activity of acetic acid and vinegar combined with medical-grade honeys
Authors: Harrison Freya , Blower Anisa , de Wolf Chris , Connelly Erin
Published: April 2023

Oxymel, a combination of honey and vinegar, has been used as a remedy for wounds and infections from antiquity to the present day. While honey is now clinically used to treat infected wounds, this use of a complex, raw natural product (NP) mixture is unusual in modern western medicine. Research into the antimicrobial activity of NPs more usually focusses on finding a single active compound. The acetic acid in vinegar is known to have antibacterial activity at low concentrations and is in clinical use to treat burn wound infections. Here, we investigated the potential for synergistic activity of different compounds present in a complex ingredient used in historical medicine (vinegar) and in an ingredient mixture (oxymel). We conducted a systematic review to investigate published evidence for antimicrobial effects of vinegars against human pathogenic bacteria and fungi. No published studies explicitly compared the activity of vinegar with that of a comparable concentration of acetic acid. We then characterised selected vinegars by high-performance liquid chromatography (HPLC) and assessed the antibacterial and antibiofilm activity of the vinegars and acetic acid, alone and in combination with medical-grade honeys, againstP. aeruginosaandS. aureus. We found that some vinegars have antibacterial activity that exceeds that predicted by their acetic acid content alone, but that this depends on the bacterial species being investigated and the growth conditions (media type, planktonic vs. biofilm). Pomegranate vinegars may be particularly interesting candidates for further study. We also conclude that there is potential for acetic acid, and some vinegars, to show synergistic antibiofilm activity with manuka honey.

Data Summary

Raw quantitative data and R code for analyses are provided in the supplementary data (Document S1).
Identification of a novel MCR-1 variant displaying low level of co-resistance to β-lactam antibiotics that uncovers a potential novel antimicrobial peptide
Authors: Liang Lujie , Zhong Lan-Lan , Wang Lin , Zhou Dianrong , Li Yaxin , Li Jiachen , Chen Yong , Liang Wanfei , Wei Wenjing , Zhang Chenchen , Zhao Hui , Lyu Lingxuan , Stoesser Nicole , Doi Yohei , Paterson David L , Bai Fang , Feng Siyuan , Tian Guo-Bao
Published: April 2023

The emerging and global spread of a novel plasmid-mediated colistin resistance gene,mcr-1, threatens human health. It is accepted that MCR-1 affects bacterial fitness, and this fitness cost correlates with bacterial membrane lipid A perturbation. However, the detailed molecular mechanism remains unclear. Here, we screened out a novel MCR-1 variant, named M6, with a two-point mutation that rendered a low level of co-resistance to β-lactam antibiotics. Compared to wild-type (WT) MCR-1, this variant caused severe lipid A perturbation resulting in peptidoglycan layer remodelling and thus resulted in phenotypic co-resistance to β-lactams. Moreover, we found that a lipid A loading cavity is localized at the linker domain of MCR-1 and governs colistin resistance and bacterial membrane permeability, and the mutated pocket of M6 facilitates the binding affinity of lipid A. More importantly, synthetic peptides derived from M6 achieved broad-spectrum antimicrobial activity. These findings provide insights into a potential vulnerability that could be exploited in future antimicrobial drug design.
Targeting the TCA cycle can ameliorate widespread axonal energy deficiency in neuroinflammatory lesions
Authors: Tai Yi-Heng , Engels Daniel , Locatelli Giuseppe , Emmanouilidis Ioanna , Fecher Caroline , Theodorou Delphine , Müller Stephan A. , Licht-Mayer Simon , Kreutzfeldt Mario , Wagner Ingrid , Prudente de Mello Natalia , Gkotzamani Sofia-Natsouko , Trovo Laura , Kendirli Arek , Aljovic Almir , Breckwoldt Michael O. , Naumann Ronald , Bareyre Florence M. , Perocchi Fabiana , Mahad Don , Merkler Doron , Lichtenthaler Stefan F. , Kerschensteiner Martin , Misgeld Thomas
Published: April 2023

Inflammation in the central nervous system (CNS) can impair the function of neuronal mitochondria and contributes to axon degeneration in the common neuroinflammatory disease multiple sclerosis (MS). Here we combine cell type-specific mitochondrial proteomics within vivobiosensor imaging to dissect how inflammation alters the molecular composition and functional capacity of neuronal mitochondria. We show that neuroinflammatory lesions in the mouse spinal cord cause widespread and persisting axonal ATP deficiency, which precedes mitochondrial oxidation and calcium overload. This axonal energy deficiency is associated with impaired electron transport chain function, but also an upstream imbalance of tricarboxylic acid (TCA) cycle enzymes, with several, including key rate-limiting, enzymes being depleted in neuronal mitochondria in experimental models and in MS lesions. Notably, viral overexpression of individual TCA enzymes can ameliorate the axonal energy deficits in neuroinflammatory lesions, suggesting that TCA cycle dysfunction in MS may be amendable to therapy.
Multi-resolution deep learning characterizes tertiary lymphoid structures in solid tumors
Authors: van Rijthoven Mart , Obahor Simon , Pagliarulo Fabio , Broek Maries van den , Schraml Peter , Moch Holger , Laak Jeroen van der , Ciompi Francesco , Silina Karina
Published: April 2023

Tertiary lymphoid structures (TLSs) are dense accumulations of lym-phocytes in inflamed peripheral tissues, including cancer, and are associated with improved survival and response to immunotherapy in various solid tumors. Histological TLS quantification has been pro-posed as a novel predictive and prognostic biomarker, but lack of standardized methods of TLS characterization hampers assessment of TLS densities across different patients, diseases, and clinical centers. We introduce a novel approach based on HookNet-TLS, a multi-resolution deep learning model, for automated and unbiased TLS quantification and identification of germinal centers in routine hema-toxylin and eosin stained digital pathology slides. We developed a HookNet-TLS model using n=1019 manually annotated TCGA slides from clear cell renal cell carcinoma, muscle-invasive blad-der cancer, and lung squamous cell carcinoma. We show that HookNet-TLS automates TLS quantification with a human-level performance and demonstrates prognostic associations similar to visual assessment. We made HookNet-TLS publicly available to aid the adoption of objective TLS assessment in routine pathology.
Keystone pathobionts associated with colorectal cancer promote oncogenic reprograming
Authors: Jones Josh , Shi Qiaojuan , Nath Rahul R. , Brito Ilana L.
Published: April 2023

Fusobacterium nucleatum(Fn) and enterotoxigenicBacteroides fragilis(ETBF) are two pathobionts consistently enriched in the gut microbiomes of patients with colorectal cancer (CRC) compared to healthy counterparts and frequently observed for their direct association within tumors. Although several molecular mechanisms have been identified that directly link these organisms to features of CRC in specific cell types, their specific effects on the epithelium and local immune compartment are not well-understood. To fill this gap, we leveraged single-cell RNA sequencing (scRNA-seq) on wildtype mice and mouse model of CRC. We find that Fn and ETBF exacerbate cancer-like transcriptional phenotypes in transit-amplifying and mature enterocytes in a mouse model of CRC. We also observed increased T cells in the pathobiont-exposed mice, but these pathobiont-specific differences observed in wildtype mice were abrogated in the mouse model of CRC. Although there are similarities in the responses provoked by each organism, we find pathobiont-specific effects in Myc-signaling and fatty acid metabolism. These findings support a role for Fn and ETBF in potentiating tumorigenesis via the induction of a cancer stem cell-like transit-amplifying and enterocyte population and the disruption of CTL cytotoxic function.
Directed evolution of piperazic acid incorporation by a nonribosomal peptide synthetase
Authors: Stephan Philipp , Langley Chloe , Winkler Daniela , Basquin Jérôme , Caputi Lorenzo , O’Connor Sarah E. , Kries Hajo
Published: April 2023

Engineering of biosynthetic enzymes is increasingly employed to synthesize structural analogues of antibiotics. Of special interest are non-ribosomal peptide synthetases (NRPSs) responsible for production of important antimicrobial peptides. Here, directed evolution of an adenylation domain of a Pro-specific NRPS module completely switched substrate specificity to the non-standard amino acid piperazic acid (Piz) bearing a labile N-N bond. This success was achieved by LC-MS/MS based screening of small, rationally designed mutant libraries and can presumably be replicated with a larger number of substrates and NRPS modules. The evolved NRPS produces a Piz-derived gramicidin S analog. Thus, we give new impetus to the too-early dismissed idea that widely accessible low-throughput methods can switch the specificity of NRPSs in a biosynthetically useful fashion.
Cell-free expressed membraneless organelles sequester RNA in synthetic cells
Authors: Robinson Abbey O , Lee Jessica , Cameron Anders , Keating Christine D , Adamala Katarzyna P.
Published: April 2023

Compartments within living cells create specialized microenvironments, allowing for multiple reactions to be carried out simultaneously and efficiently. While some organelles are bound by a lipid bilayer, others are formed by liquid-liquid phase separation, such as P-granules and nucleoli. Synthetic minimal cells have been widely used to study many natural processes, including organelle formation. Here we describe a synthetic cell expressing RGG-GFP-RGG, a phase-separating protein derived from LAF-1 RGG domains, to form artificial membraneless organelles that can sequester RNA and reduce protein expression. We create complex microenvironments within synthetic cell cytoplasm and introduce a tool to modulate protein expression in synthetic cells. Engineering of compartments within synthetic cells furthers understanding of evolution and function of natural organelles, as well as it facilitates the creation of more complex and multifaceted synthetic life-like systems.
Noninvasive estimation of mean pulmonary artery pressure by CMR in under 2 minutes scan time
Authors: Abdula Goran , Ramos Joao G , Marlevi David , Fyrdahl Alexander , Engblom Henrik , Sörensson Peder , Giese Daniel , Jin Ning , Sigfridsson Andreas , Ugander Martin
Published: April 2023

Background

Non-invasive estimation of mean pulmonary artery pressure (mPAP) by cardiovascular magnetic resonance (CMR) four-dimensional (4D) flow analysis has shown excellent agreement with invasive right heart catheterization. However, clinical application is limited by relatively long scan times.

Objectives

The aim of this study was to evaluate the accuracy and time reduction of compressed sensing (CS) accelerated acquisition for mPAP estimation.

Methods

Patients (n=51) referred for clinical CMR at 1.5T or 3T underwent imaging with both a prototype CS□accelerated and a non-CS-accelerated flow sequence acquiring time-resolved multiple 2D slice phase contrast three-directional velocity-encoded images covering the pulmonary artery. Prototype software was used for blinded analysis of pulmonary artery (PA) vortex duration to estimate mPAP as previously validated.

Results

CS-accelerated and non-CS-accelerated acquisition showed increased mPAP in 22/51 (43%) and 24/51 (47%) patients, respectively. Mean bias for estimating mPAP between the two methods was 0.1±1.9 mmHg and the intraclass correlation coefficient was 0.97 [95% confidence interval 0.94-0.98]. Effective scan time was lower for the CS-accelerated acquisition (1 min 55 sec ± 27 sec vs 9 min 6 sec ± 2 min 20 sec, p<0.001, 79% reduction).

Conclusions

CS-accelerated CMR acquisition enables preserved accuracy for estimating mPAP compared to a non-CS-accelerated sequence, allowing for an average scan time of less than 2 minutes. CS-acceleration thereby increases the clinical utility of CMR 4D flow analysis to estimate mPAP.
At the head and heart of oxytocin’s stress-regulatory neural and cardiac effects: a chronic administration RCT in children with autism
Authors: Alaerts Kaat , Daniels Nicky , Moerkerke Matthijs , Evenepoel Margaux , Tang Tiffany , Van der Donck Stephanie , Chubar Viktoria , Claes Stephan , Steyaert Jean , Boets Bart , Prinsen Jellina
Published: April 2023

Intranasal administration of oxytocin is increasingly explored as a new approach to facilitate social development and reduce disability associated with a diagnosis of autism spectrum disorder (ASD). In light of the growing number of trials, it is crucial to gain deeper insights into the neuroplastic changes that are induced from multiple-dose, chronic use of oxytocin, over a course of weeks. To date however, oxytocin’s chronic neuromodulatory impact in the pediatric brain remains unknown.

Here, we present a double-blind, randomized, placebo-controlled pharmaco-neuroimaging trial examining the neural effects of a four-week intranasal oxytocin administration regime (12 IU, twice daily) in pre-pubertal school-aged children with ASD (8-12 years, 45 boys, 12 girls). Resting-state fMRI scanning and simultaneous, in-scanner heart rate measurements were assessed before, immediately after and four weeks after the nasal spray administration period.

Four weeks of chronic oxytocin administration in children with ASD induced significant reductions in intrinsic functional connectivity between amygdala and orbitofrontal cortex, particularly at the four-week follow-up session, thereby replicating prior observations of neuromodulatory changes in the adult brain. Notably, the observed reductions in amygdala-orbitofrontal connectivity were associated with improved autonomic stress-regulation, indexed by increased high-frequency heart rate variability. Further, oxytocin’s neural and cardiac autonomic effects were significantly modulated by epigenetic modifications of the oxytocin receptor gene, indicating that oxytocin-induced stress-regulatory effects were more pronounced in children with reduced epigenetic methylation, and thus higher oxytocin receptor expression. Finally, whole-brain exploratory functional connectivity analyses also revealed an overall oxytocin-induced enhancing effect on amygdala coupling to regions of the salience network (insula, anterior cingulate cortex), likely reflective of oxytocin’s (social) salience effects.

Together, these observations provide initial insights into the stress-regulatory neural and cardiac effects induced by chronic oxytocin administration in children with ASD, and point toward important epigenetic modulators that may explain inter-individual variations in oxytocin-induced responses.
PRADclass: Multi-pronged Gleason grade-informed computational strategy identifies consensus biomarker features of prostate adenocarcinoma that predict aggressive cancer
Authors: Balraj Alex Stanley , Muthamilselvan Sangeetha , Raja Rachanaa , Palaniappan Ashok
Published: April 2023

Background

Prostate adenocarcinoma (PRAD) is the most common cancer in men worldwide, yet gaps in our knowledge persist with respect to molecular bases of PRAD progression and aggression. It is largely an indolent cancer, asymptomatic at early stage, and slow-growing in most cases, but aggressive prostate cancers cause significant morbidity and mortality within five years. Automated methods to type the aggressiveness of PRAD are necessary and urgent for informed treatment management.

Methods

Based on TCGA transcriptomic data pertaining to PRAD and the associated clinical metadata, we used the grading guidelines of the International Society of Urological Pathology (ISUP), and converted the clinical information of a cancer sample to its Gleason grade. To model the distinction between aggressive prostate cancers (Gleason grade IV or V) and indolent prostate cancers (Gleason grade I or II), we performed: (i) Gleason-grade wise linear modeling, followed by five contrasts against controls and ten contrasts between grades; and (ii) Gleason-grade wise network modeling using weighted gene correlation network analysis (WGCNA). Consensus between the grade-salient genes from the statistical modeling and the trait-specific key genes from network modeling were used as features for learning a ternary classification: benign, indolent or aggressive malignancy.

Results

The statistical modeling yielded 77 Gleason grade-salient genes, viz. ten genes in grade-1, two genes in grade-II, one gene in grade-III, 34 genes in grade-IV, and 30 genes in grade-V. Using the WGCNA method, we reconstructed grade-specific networks, and defined trait-specific key genes in grade-wise significant modules. Consensus analysis yielded two genes in Grade 1 (SLC43A1, PHGR1), 26 genes in Grade 4 (LOC100128675, PPP1R3C, NECAB1, UBXN10, SERPINA5, CLU, RASL12, DGKG, FHL1, NCAM1), and seven genes in Grade 5 (CBX2, DPYS, FAM72B, SHCBP1, TMEM132A, TPX2, UBE2C). PRADclass, a RandomForest model trained on these 35 consensus biomarkers, yielded 100% cross-validation accuracy on the ternary classification problem.

Conclusions

Consensus of orthogonal computational strategies has yielded Gleason grade-specific biomarkers that are useful in pre-screening (cancer vs normal) as well as typing the aggressiveness of cancer. PRADclass has been deployed at:https://apalania.shinyapps.io/pradclass/for scientific and non-commercial use.
Plant Arbovirus Mobilizes a Vector Salivary Protein to Initiate Plant Infection
Authors: Zhao Jing , Yang Jie , Meng Xiangyi , Fang Rongxiang , Huo Yan , Zhang Lili
Published: April 2023

Plant arboviruses rely heavily on insects’ feeding activities for successful transmission. Insect salivary proteins have been suggested to be essential for successful viral infection, but their exact mechanisms are largely unknown. In this study, we reveal that salivary factors fromLaodelphax striatellusare necessary for infection ofRice stripe virus(RSV) in plants. A salivary carbonic anhydrase (LssaCA) is identified as an essential factor in promoting RSV infection. LssaCA interacts with a rice thaumatin-like protein (OsTLP) that has endo-β-1,3-glucanase activity and can degrade callose in plants. RSV infection induces callose deposition, which can be reversed by LssaCA. Furthermore, LssaCA directly binds to the RSV nucleocapsid protein (NP) in salivary glands, and the LssaCA-RSV NP complex still binds OsTLP and further increases its glucanase activity. This study provides new insights into the tripartite virus-insect vector-plant interaction, which is relevant to many agriculturally important plant arboviruses whose transmission is facilitated by insect salivary proteins.
A Rab6 to Rab11 transition is required for dense-core granule and exosome biogenesis inDrosophilasecondary cells
Authors: Wells Adam , Mendes Cláudia C. , Castellanos Felix , Mountain Phoebe , Wright Tia , Wainwright S. Mark , Stefana M. Irina , Harris Adrian L. , Goberdhan Deborah C. I. , Wilson Clive
Published: April 2023

Secretory cells in glands and the nervous system frequently package and store proteins destined for regulated secretion in dense-core granules (DCGs), which disperse when released from the cell surface. Despite the relevance of this dynamic process to diseases such as diabetes and human neurodegenerative disorders, our mechanistic understanding is relatively limited, because of the lack of good cell models to follow the nanoscale events involved. Here, we employ the prostate-like secondary cells (SCs) of theDrosophilamale accessory gland to dissect the cell biology and genetics of DCG biogenesis. These cells contain unusually enlarged DCGs, which are assembled in compartments that also form secreted nanovesicles called exosomes. We demonstrate that known conserved regulators of DCG biogenesis, including the small G-protein Arf1 and the coatomer complex AP-1, play key roles in making SC DCGs. Using real-time imaging, we find that the aggregation events driving DCG biogenesis are accompanied by a change in the membrane associated small Rab GTPases which are major regulators of membrane and protein trafficking in the secretory and endosomal systems. Indeed, a transition fromtrans-Golgi Rab6 to recycling endosomal protein Rab11, which requires conserved DCG regulators like AP-1, is essential for DCG and exosome biogenesis. Our data allow us to develop a model for DCG biogenesis that brings together several previously disparate observations concerning this process and highlights the importance of communication between the secretory and endosomal systems in controlling regulated secretion.

Author summary

Cells communicate with each other by releasing signalling molecules that bind receptors on target cells and alter their behaviour. Before their release, these signals are typically stored in condensed structures called dense-core granules (DCGs). DCGs are found in many animal species and their dysregulation is linked to several major human diseases, such as diabetes and neurodegenerative disorders. However, the mechanisms controlling DCG formation and secretion are only partly understood. Here we study this process in fruit flies using a secretory cell, which contains unusually large DCGs. We show that known regulators of DCG formation in mammals also control DCG production in these fly cells and identify new DCG assembly steps by following the process in living cells. Furthermore, we show that the cell’s secretory and recycling endosomal compartments must interact to induce the rapid condensation of proteins into a DCG, and that known regulators of DCG formation are needed for this crucial event to take place. Our work provides a platform from which to work out the molecular mechanisms that enable this critical secretory-endosomal interaction and probe its roles in diseases of secretion.
Exchange rate pass-through to inflation in South Africa: is there non-linearity?
Authors: Gereziher Hayelom Yrgaw , Nuru Naser Yenus
Published: April 2023

Purpose

This paper aims to examine the asymmetric effects of exchange rate shocks on inflation for a small open economy, namely South Africa, over the period 1970Q1–2020Q1.

Design/methodology/approach

A threshold vector autoregressive model that allows parameters to switch according to whether a threshold variable crosses an estimated threshold is employed to address the objective of this paper. The threshold value is determined endogenously using the Hansen (1996) test. Generalized impulse responses introduced by Koop et al. (1996) are used to study the effects of exchange rate shocks on inflation depending on their size, sign and timing to the inflation cycle. The authors also employed a Cholesky decomposition identification scheme to identify exchange rate shocks in the non-linear model.

Findings

The results show that there is a non-linearity effect of the exchange rate shock on inflation. In particular, the effects of 1 or 2 standard deviations of positive (appreciation) or negative (depreciation) exchange rate shock on inflation are small in the long run but a bit larger in the high inflation regime than the low inflation regime.

Originality/value

This paper contributes to the literature on the non-linear effects of exchange rate pass-through (ERPT) to inflation for Sub-Saharan African economies in general and the South African economy in particular by incorporating the size and timing of the exchange rate shocks to the inflation cycle.
Knowledge-oriented leadership and workers' performance: do individual knowledge management engagement and empowerment matter?
Authors: Malik Mehwish , Abbas Muhammad , Imam Hassan
Published: April 2023

Purpose

Drawing upon social cognitive theory (SCT), the authors aimed to examine the relationship between supervisors' knowledge-oriented leadership (KOL) style and knowledge workers' performance. The authors further investigated the conditional indirect effects of KOL on workers' performance through knowledge management (KM) engagement at different levels of workers' empowerment.

Design/methodology/approach

The authors used a time-lagged field survey and collected data from 212 knowledge workers and their 72 supervisors working in 15 knowledge-intensive firms across Pakistan.

Findings

The results showed that supervisors' KOL positively affected knowledge workers' performance both directly and through KM engagement. Similarly, the effect of KM engagement on workers' performance was stronger for those who experienced higher levels of empowerment. Finally, the indirect effects of KOL on workers' performance through KM engagement were stronger for higher levels of empowerment.

Originality/value

The study provided theoretical implications, specifically in a non-Western work context where KOL is relatively less explored. Additionally, the authors examined the concept of empowerment, using SCT, as a boundary condition, providing evidence for empowerment as a contingency factor that fosters employees' performance.