bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular signature and functional properties of human pluripotent stem cell-derived brain pericytes
Authors: Bosworth Allison , Griffin Casey , Chakhoyan Ararat , Sagare Abhay P. , Nelson Amy R. , Wang Yaoming , Kisler Kassandra , Montagne Axel , Clementel Veronica , TCW Julia , Rust Ruslan , Coba Marcelo , Zlokovic Berislav V.
Published: June 2023

Brain pericytes maintain blood-brain barrier (BBB), secrete neurotrophic factors and clear toxic proteins. Their loss in neurological disorders leads to BBB breakdown, neuronal dysfunction, and cognitive decline. Therefore, cell therapy to replace lost pericytes holds potential to restore impaired cerebrovascular and brain functions. Here, we show by a quantitative analysis of 8,344 proteins and 20,572 phosphopeptides that human iPSC-derived brain pericytes (iPSC-PC) share 96% of total proteins and 98% of protein phosphorylation sites with primary human brain pericytes. This includes cell adhesion and tight junction proteins, transcription factors, and different protein kinase families of the human kinome. In pericyte-deficient mice, iPSC-PC home to host brain capillaries to form hybrid human-mouse microvessels. They repair BBB leaks and protect against neuron loss, which we show requires PDGRFB and pleiotrophin. They also clear Alzheimer’s amyloid-β and tau neurotoxins via lipoprotein receptor. Thus, iPSC-PC may offer a valuable replacement therapy for pericyte-deficient neurological disorders.
The evolution and mutational robustness of chromatin accessibility inDrosophila
Authors: Khodursky Samuel , Zheng Eric B , Svetec Nicolas , Durkin Sylvia M , Benjamin Sigi , Gadau Alice , Wu Xia , Zhao Li
Published: June 2023

The evolution of regulatory regions in the genome plays a critical role in shaping the diversity of life. While this process is primarily sequence-dependent, the enormous complexity of biological systems has made it difficult to understand the factors underlying regulation and its evolution. Here, we apply deep neural networks as a tool to investigate the sequence determinants underlying chromatin accessibility in different tissues ofDrosophila. We train hybrid convolution-attention neural networks to accurately predict ATAC-seq peaks using only local DNA sequences as input. We show that a model trained in one species has nearly identical performance when tested in another species, implying that the sequence determinants of accessibility are highly conserved. Indeed, model performance remains excellent even in distantly-related species. By using our model to examine species-specific gains in chromatin accessibility, we find that their orthologous inaccessible regions in other species have surprisingly similar model outputs, suggesting that these regions may be ancestrally poised for evolution. We then usein silicosaturation mutagenesis to reveal evidence of selective constraint acting specifically on inaccessible chromatin regions. We further show that chromatin accessibility can be accurately predicted from short subsequences in each example. However,in silicoknock-out of these sequences does not qualitatively impair classification, implying that chromatin accessibility is mutationally robust. Subsequently, we demonstrate that chromatin accessibility is predicted to be robust to large-scale random mutation even in the absence of selection. We also performin silicoevolution experiments under the regime of strong selection and weak mutation (SSWM) and show that chromatin accessibility can be extremely malleable despite its mutational robustness. However, selection acting in different directions in a tissue-specific manner can substantially slow adaptation. Finally, we identify motifs predictive of chromatin accessibility and recover motifs corresponding to known chromatin accessibility activators and repressors. These results demonstrate the conservation of the sequence determinants of accessibility and the general robustness of chromatin accessibility, as well as the power of deep neural networks as tools to answer fundamental questions in regulatory genomics and evolution.
De NovoDesign of Peptide Binders to Conformationally Diverse Targets with Contrastive Language Modeling
Authors: Bhat Suhaas , Palepu Kalyan , Hong Lauren , Mao Joey , Ye Tianzheng , Iyer Rema , Zhao Lin , Chen Tianlai , Vincoff Sophia , Watson Rio , Wang Tian , Srijay Divya , Kavirayuni Venkata Srikar , Kholina Kseniia , Goel Shrey , Vure Pranay , Desphande Aniruddha J. , Soderling Scott H. , DeLisa Matthew P. , Chatterjee Pranam
Published: June 2023

Designing binders to target undruggable proteins presents a formidable challenge in drug discovery, requiring innovative approaches to overcome the lack of putative binding sites. Recently, generative models have been trained to design binding proteins via three-dimensional structures of target proteins, but as a result, struggle to design binders to disordered or conformationally unstable targets. In this work, we provide a generalizable algorithmic framework to design short, target-binding linear peptides, requiring only the amino acid sequence of the target protein. To do this, we propose a process to generate naturalistic peptide candidates through Gaussian perturbation of the peptidic latent space of the ESM-2 protein language model, and subsequently screen these novel linear sequences for target-selective interaction activity via a CLIP-based contrastive learning architecture. By integrating these generative and discriminative steps, we create aPeptidePrioritization viaCLIP(PepPrCLIP) pipeline and validate highly-ranked, target-specific peptides experimentally, both as inhibitory peptides and as fusions to E3 ubiquitin ligase domains, demonstrating functionally potent binding and degradation of conformationally diverse protein targetsin vitro. Overall, our design strategy provides a modular toolkit for designing short binding linear peptides to any target protein without the reliance on stable and ordered tertiary structure, enabling generation of programmable modulators to undruggable and disordered proteins such as transcription factors and fusion oncoproteins.
Bacillus subtilisYisK possesses oxaloacetate decarboxylase activity and exhibits Mbl-dependent localization
Authors: Guo Tingfeng , Sperber Anthony M. , Krieger Inna V. , Duan Yi , Chemelewski Veronica , Sacchettini James C. , Herman Jennifer K.
Published: June 2023

YisK is an uncharacterized protein inBacillus subtilispreviously shown to interact genetically with the elongasome protein Mbl. YisK overexpression leads to cell widening and lysis, phenotypes that are dependent onmbland suppressed bymblmutations. In the present work we characterize YisK’s localization, structure, and enzymatic activity. We show that YisK localizes in a punctate and/or punctate-helical pattern that depends on Mbl, and that YisK interacts directly with another elongasome protein, FtsE. YisK belongs to the fumarylacetoacetate hydrolase (FAH) superfamily and crystal structures revealed close structural similarity to two oxaloacetate (OAA) decarboxylases: human mitochondrial FAHD1 andCorynebacterium glutamicumCg1458. We demonstrate that YisK can also catalyze the decarboxylation of OAA (Km= 134 µM, Kcat= 31 min-1). A catalytic dead variant (YisK E148A, E150A) retains wild-type localization and still widens cells following overexpression, indicating these activities are not dependent on YisK catalysis. Conversely, a non-localizing variant (YisK E30A) retains wild-type enzymatic activity in vitro, but no longer widens cells following overexpression. Together these results suggest YisK may be subject to spatial regulation that depends on the cell envelope synthesis machinery.

IMPORTANCE

The elongasome is a protein complex that guides lengthwise growth in some bacteria. We previously showed that inB. subtilis, overexpression of an uncharacterized enzyme (YisK), perturbed function of the actin-like elongasome protein Mbl. Here we show that YisK exhibits Mbl-dependent localization and interacts directly with another component of the elongasome, FtsE. Through biochemical and structural characterization, we demonstrate that like it’s mitochondrial homolog FAHD1, YisK can catalyze the decarboxylation of the oxaloacetate to pyruvate and CO2. YisK is the first example of an enzyme implicated in central carbon metabolism with subcellular localization that depends on Mbl.
Make like a tree and leave: How will tree species loss and climate change alter future temperate broadleaved forests?
Authors: West Bede , Jones Davey L. , Robinson Emma L. , Keith Aidan M. , Kallow Simon , Marrs Robert H. , Smart Simon M.
Published: June 2023

Forest creation has the potential to reduce biodiversity loss and mitigate climate change but, tree disease emergence may counteract this. Further, given decadal timescales required for forest establishment, climate change is increasingly likely to act as a filter on plant community assembly. In the temperate lowlands succession takes 30 to 50 years for non-forest land to establish woodland plant assemblages, while the timescales required for new forest to sequester carbon suggest unassisted succession will be too slow for net zero 2050 targets. However, if plantations can establish faster than succession it would be beneficial to recommend planting native species as soon as possible. We explore scenarios of broadleaved woodland development across Wales, UK, as a case study area. We use a suite of empirical species niche models for British plants to estimate the potential species composition of forests with, and without, projected climate change. Additionally, we examine how tree canopy composition alters ifFraxinus excelsioris widely impacted by ash-dieback (Hymenoscyphus fraxineus). The results suggest soil total carbon and nitrogen could achieve baseline broadleaved forest values in less than 30 years. However only timber and woody flora species groups showed diversity surpassing baseline broadleaved forest diversity, with nectar plants and ancient woodland indicator species failing to reach baseline equivalents within 30 years; although complete congruence is unlikely given baseline forests could be hundreds of years old. WhereFraxinus excelsiorwas removed from the species pool we predicted that a scrub phase will persist or, if present,Acer pseudoplatanuswill become the canopy dominant. The heavier shade cast this species is likely to result in differences in species composition of the understory and ground flora diversity is likely to decrease. Reliance on unassisted succession will also depend critically on (a) dispersal from local source populations and (b) on establishment filters that could be severe in landscapes with high management intensity history. These findings indicate that leaving the UK’s fragmented habitats to relying on already degraded successional processes could lead to poor afforestation outcomes.

Highlights

Afforestation can mitigate global change but tree disease makes outcomes uncertain

Afforestation methods establishment timescales and time for benefits to occur

We model afforestation and predict how soils and plants change with climate

Ash loss from die-back is replaced by low low-canopy woodland / scrub over 30 years

Afforestation achieves baseline forest values for some variables within 30 years
Antiviral Type III CRISPR signalling via conjugation of ATP and AdoMet
Authors: Chi Haotian , Hoikkala Ville , Grüschow Sabine , Graham Shirley , Shirran Sally , White Malcolm F
Published: June 2023

CRISPR systems are widespread in the prokaryotic world, providing adaptive immunity against mobile genetic elements (MGE)1, 2. Type III CRISPR systems, with the signature genecas10, use CRISPR RNA (crRNA) to detect non-self RNA, activating the enzymatic Cas10 subunit to defend the cell against MGE either directly, via the integral HD nuclease domain3–5or indirectly, via synthesis of cyclic oligonucleotide (cOA) second messengers to activate diverse ancillary effectors6–9. A subset of type III CRISPR systems encode an uncharacterised CorA-family membrane protein and an associated NrN family phosphodiesterase predicted to function in antiviral defence. Here, we demonstrate that the CorA associated type III-B (Cmr) CRISPR system fromBacteroides fragilisprovides immunity against MGE when expressed inE. coli. However,B. fragilisCmr does not synthesise cOA species on activation, instead generating a previously undescribed sigalling molecule, SAM-AMP (3’-adenylyl-AdoMet) by conjugating ATP to S-adenosyl methionine via a phosphodiester bond. Once synthesised, SAM-AMP binds to the CorA effector, presumably leading to cell death by disruption of the membrane integrity. SAM-AMP is degraded by CRISPR associated phosphodiesterases or a SAM-AMP lyase, providing an “off switch” analogous to cOA specific ring nucleases10. SAM-AMP thus represents a new class of second messenger for antiviral signalling, which may function in different roles in diverse cellular contexts.
The RgaS-RgaR two-component system promotesClostridioides difficilesporulation through a small RNA and the Agr1 system
Authors: Edwards Adrianne N. , McBride Shonna M.
Published: June 2023

The ability to form a dormant spore is essential for the survival of the anaerobic, gastrointestinal pathogenClostridioides difficileoutside of the mammalian gastrointestinal tract. The initiation of sporulation is governed by the master regulator of sporulation, Spo0A, which is activated by phosphorylation. Multiple sporulation factors control Spo0A phosphorylation; however, this regulatory pathway is not well defined inC. difficile. We discovered that RgaS and RgaR, a conserved orphan histidine kinase and orphan response regulator, function together as a cognate two-component regulatory system to directly activate transcription of several genes. One of these targets,agrB1D1, encodes gene products that synthesize and export a small quorum- sensing peptide, AgrD1, which positively influences expression of early sporulation genes. Another target, a small regulatory RNA now known as SrsR, impacts later stages of sporulation through an unknown regulatory mechanism(s). Unlike Agr systems in many organisms, AgrD1 does not activate the RgaS-RgaR two-component system, and thus, is not responsible for autoregulating its own production. Altogether, we demonstrate thatC. difficileutilizes a conserved two-component system that is uncoupled from quorum-sensing to promote sporulation through two distinct regulatory pathways.

AUTHOR SUMMARY

The formation of an inactive spore by the anaerobic gastrointestinal pathogen,Clostridioides difficile, is required for its survival outside of the mammalian host. The sporulation process is induced by the regulator, Spo0A; yet, how Spo0A is activated inC. difficileremains unknown. To address this question, we investigated potential activators of Spo0A. Here, we demonstrate that the sensor RgaS activates sporulation, but not by direct activation of Spo0A. Instead, RgaS activates the response regulator, RgaR, which in turn activates transcription of several genes. We found two direct RgaS- RgaR targets independently promote sporulation:agrB1D1, encoding a quorum-sensing peptide, AgrD1, andsrsR, encoding a small regulatory RNA. Unlike most other characterized Agr systems, the AgrD1 peptide does not affect RgaS-RgaR activity, indicating that AgrD1 does not activate its own production through RgaS-RgaR. Altogether, the RgaS-RgaR regulon functions at multiple points within the sporulation pathway to tightly controlC. difficilespore formation.
Association of Domains of Sedentary Behavior with Cardiovascular Disease Events in The Multi-Ethnic Study of Atherosclerosis
Authors: Mayo Nicole L. , Lopez Daniel A. , Block Robert C. , Shi Hangchuan , Bertoni Alain G. , Diaz Keith M. , Ding Jingzhong , Post Wendy S. , Liu Yongmei , Li Dongmei
Published: June 2023

Structured Abstract

Background

Sedentary behavior is associated with an increased risk for adverse health outcomes, including cardiovascular disease (CVD), independent of physical activity status. Little is known about this relationship in an ethnically diverse population. The objective of our study is to assess the effects of leisure time and occupational sedentary behavior on multiple cardiovascular outcomes in a multi-ethnic cohort.

Methods

The Multi-Ethnic Study of Atherosclerosis (MESA) includes 2619 Caucasian, 1495 Hispanic, 1891 Black, and 804 Chinese-American adults aged 45-84 years and free of clinical CVD at enrollment, Sedentary behavior was self-reported at baseline. Participants were followed for an average of 13.6 years, and 14 types of cardiovascular outcomes were ascertained. Hazards of each cardiovascular outcome were modeled with adjustment for potential confounders, including physical activity.

Results

Every one hour per day increase in leisure time sedentary behavior predicts a 6% increase in the adjusted hazards for CVD death (P< 0.05). Every one hour increase in occupational sedentary time predicts a 21% and 20% decrease in the hazard for PVD and other revascularization, respectively (P< 0.05).

Conclusions

Leisure time sedentary behavior was associated with increased hazards for CVD death, but occupational sedentary time appears to be protective of peripheral vascular disease and other revascularization.

Condensed Abstract

Sedentary behavior has been consistently associated with an increased risk for adverse health outcomes, including cardiovascular disease (CVD), independent of physical activity status. The Multi-Ethnic Study of Atherosclerosis (MESA) consists of a racially and ethnically diverse cohort of adults age 45-84, free from CVD at baseline. Greater levels of leisure time sedentary behavior predicted increased hazards for PVD and CVD death after an average follow up of 13.6 years whereas occupational sedentary behaviors predicted reduced PVD. These results underscore the importance of reducing time spent sitting in addition to advocating for meeting physical activity targets across ethnicities.
LPCAT2 Regulates CD14 Expression During Macrophage Inflammatory Response to E. coli O111:B4
Authors: Poloamina Victory Ibigo , Abate Wondwossen , Fejer Gyorgy , Jackson Simon K
Published: June 2023

LPCAT2 is a lipid-modifying enzyme that co-localises in lipid rafts with TLR4 and regulates macrophage inflammatory response; however, its effect on TLR4 co-receptor–CD14 is unknown. RAW264.7 cells, a common murine macrophage experimental model, were used to study the effect of LPCAT2 on CD14 expression. The expression of LPCAT2 in RAW264.7 cells was silenced using RNA interference and treated with 100ng/ml of various lipopolysaccharide chemotypes. We found that CD14 expression induced by smooth lipopolysaccharide was significantly decreased (p < 0.05) in RAW264.7 macrophages with LPCAT2 silenced. This study suggests that LPCAT2 regulates CD14 gene and protein expression. This implies that LPCAT2 can regulate CD14-dependent cellular activities.
Decline of DNA damage response along with myogenic differentiation
Authors: Sutcu Haser Hasan , Rassinoux Phoebe , Donnio Lise-Marie , Neuillet Damien , Vianna François , Gabillot Olivier , Mari Pierre-Olivier , Baldeyron Céline , Giglia-Mari Giuseppina
Published: June 2023

DNA integrity is incessantly confronted to endogenous and exogenous agents inducing DNA lesions, which are harmful for cellular homeostasis. Luckily all organisms are equipped with a network of DNA damage response (DDR) mechanisms that will repair DNA lesions and restore the proper cellular activities. Despite DNA repair mechanisms have been revealed in vitro and in replicating cells, still little is known on how DNA lesions are repaired and consequently how cellular homeostasis is maintained in post-mitotic cells. Muscle fibers are highly specialised post-mitotic cells organized in syncytia and, they are vulnerable to age-related degeneration and atrophy following radiotherapy treatment. We have here studied in detail the DNA repair capacity of muscle fibers nuclei and compared it with the one measured in proliferative myoblasts. We focused on the DNA repair mechanisms that correct ionizing radiation (IR)-induced lesions, namely the base excision repair (BER), the non-homologous end joining (NHEJ) and the homologous recombination (HR). We found that in the most differentiated myogenic cells, myotubes, all of these DNA repair mechanisms present weakened kinetics of recruitment of DNA repair proteins to IR-damaged DNA. For BER and HR, this decline can be linked to reduced steady state levels of key proteins involved in these processes, probably since nuclei within muscle fibers no longer replicate their DNA.

SIGNIFICANCE

Although skeletal muscle tissue has been considered as resistant to injury caused by ionizing radiations (IR), in the long term, muscle surrounding irradiated regions of the body following radiotherapy has physiological consequences such as atrophy and muscle wasting. To prevent and/or counteract the harmful effects of IR in muscle fibers, it is essential, to evaluate the DNA repair capacity of post-mitotic myonuclei. By using fluorescently tagged DNA repair proteins expressed in myoblasts and myotubes, we were able to assess the kinetics of the DNA damage response in these cells and determine that DNA damage response is weakened during the process of myofibrillogenesis.
Dual-specific autophosphorylation of kinase IKK2 enables phosphorylation of substrate IκBα through a phosphoenzyme intermediate
Authors: Borar Prateeka , Biswas Tapan , Chaudhuri Ankur , Pallavi Rao T , Raychaudhuri Swasti , Huxford Tom , Chakrabarti Saikat , Ghosh Gourisankar , Polley Smarajit
Published: June 2023

Rapid and high-fidelity phosphorylation of two serines (S32 and S36) of IκBα by a prototype Ser/Thr kinase IKK2 is critical for fruitful canonical NF-κB activation. Here, we report that IKK2 is a dual specificity Ser/Thr kinase that autophosphorylates itself at tyrosine residues in addition to its activation loop serines. Mutation of one such tyrosine, Y169, located in proximity to the active site, to phenylalanine, renders IKK2 inactive for phosphorylation of S32 of IκBα. Surprisingly, auto-phosphorylated IKK2 relayed phosphate group(s) to IκBα without ATP when ADP is present. We also observed that mutation of K44, an ATP-binding lysine conserved in all protein kinases, to methionine renders IKK2 inactive towards specific phosphorylation of S32 or S36 of IκBα, but not non-specific substrates. These observations highlight an unusual evolution of IKK2, in which autophosphorylation of tyrosine(s) in the activation loop and the invariant ATP-binding K44 residue define its signal-responsive substrate specificity ensuring the fidelity of NF-κB activation.
Acyl-CoA thioesterase-2 facilitates β-oxidation in glycolytic skeletal muscle in a lipid supply dependent manner
Authors: Bekeova Carmen , Han Ji In , Xu Heli , Kerr Evan , Blackburne Brittney , Lynch Shannon C. , Mesaros Clementina , Murgia Marta , Vadigepalli Rajanikanth , Beld Joris , Leonardi Roberta , Snyder Nathaniel W. , Seifert Erin L.
Published: June 2023

Acyl-Coenzyme A (acyl-CoA) thioesters are compartmentalized intermediates that participate in in multiple metabolic reactions within the mitochondrial matrix. The limited availability of free CoA (CoASH) in the matrix raises the question of how the local acyl-CoA concentration is regulated to prevent trapping of CoASH from overload of any specific substrate. Acyl-CoA thioesterase-2 (ACOT2) hydrolyzes long-chain acyl-CoAs to their constituent fatty acids and CoASH, and is the only mitochondrial matrix ACOT refractory to inhibition by CoASH. Thus, we reasoned that ACOT2 may constitutively regulate matrix acyl-CoA levels.Acot2deletion in murine skeletal muscle (SM) resulted in acyl-CoA build-up when lipid supply and energy demands were modest. When energy demand and pyruvate availability were elevated, lack of ACOT2 activity promoted glucose oxidation. This preference for glucose over fatty acid oxidation was recapitulated in C2C12 myotubes with acute depletion ofAcot2, and overt inhibition of β-oxidation was demonstrated in isolated mitochondria fromAcot2-depleted glycolytic SM. In mice fed a high fat diet, ACOT2 enabled the accretion of acyl-CoAs and ceramide derivatives in glycolytic SM, and this was associated with worse glucose homeostasis compared to when ACOT2 was absent. These observations suggest that ACOT2 supports CoASH availability to facilitate β-oxidation in glycolytic SM when lipid supply is modest. However, when lipid supply is high, ACOT2 enables acyl-CoA and lipid accumulation, CoASH sequestration, and poor glucose homeostasis. Thus, ACOT2 regulates matrix acyl-CoA concentration in glycolytic muscle, and its impact depends on lipid supply.
Establishment of a novel non-integrated human pluripotent stem cell-based gastruloid model
Authors: Yuan Gege , Wang Jiachen , Liu Zhaode , Chen Mengqi , Zhu Pinmou , Zhang Hao , Hu Zhibin , Cui Yiqiang , Yuan Yan , Sha Jiahao
Published: June 2023

Embryo loss and pregnancy disorders are prevalent worldwide, with both conditions critically associated with dysfunctioning gastrulation processes. Gastrulation and post-gastrulation organogenesis are crucial stages of embryonic development that establish the blueprint for body part formation. These processes involve the sequential generation of three germ layer cells and primordial germ cells, as well as the assembly of the precursor tissues for body parts. However, due to ethical limitations associated with studying human embryogenesis, a more detailed understanding of gastrulation and post-gastrulation organogenesis remains elusive. To ensure that the knowledge obtained from gastruloids is biologically meaningful and clinically relevant, it is critical to create high-fidelity human embryo models that closely mimic embryogenesisin vivo. Here, we developed a two-stage derivation gastruloidsin vitrobased on human pluripotent stem cells. Morphological tracking mimicks the developmental processes of models from Carnegie Stage 4 (CS4) to early CS7. Our gastruloids exhibit key structures characteristic of human embryos, including amniotic cavity, embryonic disc, primitive streak, primary yolk sac, secondary yolk sac, and blood islets. Comparison of our cell lineage development maps showed that gastruloids closely resembled human natural CS7 gastrula. Our gastruloids exhibited transcriptional characteristics that mimicked the molecular pathways observed in natural embryos development. Importantly, we found that in our model, extraembryonic mesoderm originates from the yolk sac and primordial germ cells originate from the posterior epiblast of the embryonic disc. Moreover, we found that thalidomide affects the differentiation of three germ layer cells, resulting in the arrest of human gastruloid development. In conclusion, by establishing a human gastruloid, we were able to gain valuable insights into the mechanisms responsible for human gastrulation and shed light on the causes of early embryo loss and pregnancy disorders.
Synergistic effects of PARP inhibitors by Schlafen 11 and BRCA2-deficiency through accumulation of single-strand DNA gaps behind a fork
Authors: Onji Hiroshi , Tate Sota , Sakaue Tomohisa , Onishi Nobuyuki , Matsumoto Takashi , Sugiyama Takashi , Higashiyama Shigeki , Murai Junko
Published: June 2023

Poly (ADP-ribose) polymerase (PARP) inhibitors (PARPis) induce synthetic lethality in breast cancer gene (BRCA)-deficient tumors. Besides the original model proposed by accumulation of double-strand DNA breaks due to the impaired homologous recombination, accumulation of single-strand DNA (ssDNA) gaps due to impaired BRCA-mediated Okazaki fragment processing has emerged as an alternative mechanism of synthetic lethality. Accordingly, PARPis induce ssDNA gaps behind a replication fork in BRCA-deficient cells. Schlafen 11 (SLFN11), a member of the SLFN family, binds replication protein A (RPA)-coated ssDNA gaps and sensitizes cancer cells to DNA-damaging anticancer agents. These facts motivated us to examine the combinational effects of SLFN11 and BRCA-deficiency on PARPis sensitivity. Here, we show that SLFN11 and BRCA2-deficiency synergistically increased sensitivity to PARPis (talazoparib, niraparib, olaparib, and veliparib) at specific concentrations, where SLFN11 alone showed marginal effects. Using chromatin-bound proteins and alkaline BrdU comet assays in human cancer cells, we revealed that ssDNA gaps induced by PARPis were increased by SLFN11 or BRCA2-deficiency and that the combination of the two had the greatest effect. SLFN11 was recruited to and colocalized with chromatin-bound RPA2 under PARPis. SLFN11 recruited around a fork under DNA damage blocked replication, whereas SLFN11 recruited behind a fork under PARPis did not. Chromatin recruitment of SLFN11 and RPA2 was attenuated by the MRE11 inhibitor mirin. Hence, our studies showed that BRCA2-deficiency increased ssDNA gaps behind a fork under PARPis treatment, where SLFN11 bound and further increased the gaps. Our findings provide a mechanistic understanding of favorable responses to PARPis in SLFN11-proficient and BRCA-deficient tumors.

Significance

This study reveals how SLFN11 enhances the antitumor effects of PARP inhibitors in BRCA2-deficient cancer cells and highlights the importance of analyzing SLFN11 expression in addition to BRCA analysis in clinical practice.
FISHtoFigure: An easy-to-use tool for rapid, multi-target partitioning and analysis of sub-cellular mRNA transcripts in smFISH data
Authors: Bentley-Abbot Calum , Heslop Rhiannon , Pirillo Chiara , Sinton Matthew C. , Chandrasegaran Praveena , McConnell Gail , Roberts Ed , Hutchinson Edward , MacLeod Annette
Published: June 2023

Single molecule fluorescencein situhybridisation (smFISH) has become a valuable tool to investigate the mRNA expression of single cells. However, it requires a considerable amount of bioinformatic expertise to use currently available open-source analytical software packages to extract and analyse quantitative data about transcript expression. Here, we present FISHtoFigure, a new software tool developed specifically for the analysis of mRNA abundance and co-expression in QuPath-quantified, multi-labelled smFISH data. FISHtoFigure facilitates the automated spatial analysis of transcripts of interest, allowing users to analyse populations of cells positive for specific combinations of mRNA targets without the need for bioinformatics expertise. As a proof of concept and to demonstrate the capabilities of this new research tool, we have validated FISHtoFigure in multiple biological systems. We used FISHtoFigure to identify an upregulation of T-cells in the spleens of mice infected with influenza A virus, before analysing more complex data showing crosstalk between microglia and regulatory B-cells in the brains of mice infected withTrypanosoma brucei brucei. These analyses demonstrate the ease of analysing cell expression profiles using FISHtoFigure and the value of this new tool in the field of smFISH data analysis.
Female smallholder farmers’ preferences for digital and conventional credit attributes: evidence from Madagascar
Authors: Wahbi Annkathrin , Sarfo Yaw , Musshoff Oliver
Published: June 2023

Purpose

Digital credit is spreading rapidly across Sub-Saharan Africa and holds potential for financial inclusion and female financial autonomy. Women in developing economies have long been targeted by microfinance institutions due to the women’s reliability and positive spillover effects. Yet, adoption rates for digital financial innovations remain moderate among rural women in Sub-Saharan Africa. The authors explore whether female preferences for digital and conventional credit differ from males.

Design/methodology/approach

The authors conduct a Discrete Choice Experiment with 420 smallholder farmers in central Madagascar, one of the region's poorest countries, to assess preferences for selected digital and conventional credit attributes.

Findings

Results of the mixed logit model and the comparison of the willingness-to-pay via Poe-test suggest high general demand for both credit forms. The demand of female respondents is higher than that of males, suggesting that they might be underserved. This holds for both credit forms. However, differences in willingness to pay for the credit attributes are mostly not statistically significant, indicating that designing gender-specific services may not be advisable.

Originality/value

This article is believed to be the first to assess and compare gendered willingness to pay for digital and conventional credit. The study’s findings give valuable insights to decision-makers in development politics as well as the fintech industry.
Using accounting theory to develop a theoretical model for credit card rewards programme transactions
Authors: Brink Sophia , Steenkamp Gretha
Published: June 2023

Purpose

After the effective date of International Financial Reporting Standard (IFRS) 15, the accounting treatment of credit card rewards programmes (CCRPs) is no longer explicitly prescribed. Uncertainty regarding what constitutes faithful representation, and the inconsistent accounting practices observed, has created a need for guidance on the appropriate accounting treatment of CCRP transactions. Accounting theory has the potential to provide the foundation for this guidance. As a result, the objective of this study was to develop a theoretical model for the accounting treatment of CCRP transactions using accounting theory.

Design/methodology/approach

This non-empirical qualitative conceptual study utilised document analysis, focussing specifically on accounting theory, to construct an accounting treatment model.

Findings

Applying the relevant accounting theory (International Accounting Standards Board's (IASB's) Conceptual Framework), a theoretical model for the accounting treatment of CCRP transactions was developed, which emphasises the importance of understanding the economic phenomenon (the CCRP transaction) and determining how management views the transaction (in isolation as marketing or as an integral part of the credit card transaction).

Originality/value

Addressing the problem of accounting for CCRP transactions with reference to accounting theory (which is the main element of scholarly activity in accounting) distinguishes this study from previous research on the topic. The CCRP accounting treatment theoretical model could assist CCRP management in faithfully accounting for a CCRP transaction and reduce uncertainty and inconsistency in practice. Moreover, this study identified the procedures to be employed when using accounting theory to determine the appropriate accounting treatment of business transactions. These procedures could be employed by accountants when faced with other transactions not covered by specific accounting standards.
Current earnings, persistence and schooling returns
Authors: Andini Corrado , Santos José Eusébio
Published: June 2023

Purpose

The aim is to study the impact of schooling on between-groups wage inequality beyond the lens of the standard approach in the literature.

Design/methodology/approach

Simple econometric theory is used to make the main point of the paper. Supporting empirical evidence is also presented.

Findings

Disregarding the persistence of current earnings implies a bias in the estimation of the wage return to schooling both at labour-market entry and in the rest of the working life.

Research limitations/implications

The use of current earnings as a dependent variable in wage-schooling models may be problematic and requires specific handling.

Social implications

The impact of schooling on the between-groups dimension of wage inequality may be different than previously thought.

Originality/value

The paper is the first to show that, when current earnings are used as a dependent variable, the identification of a wage-schooling model with the standard (time-invariant external instrument-variable) approach may lead to misleading conclusions.
Factors affecting financial decisions of university students: evidence from Pakistan
Authors: Khurshid Muzammil , Zahid R.M. Ammar , Nisa Meher Un
Published: June 2023

Purpose

This study examined the factors affecting university students' financial decisions in Pakistan.

Design/methodology/approach

Structural equation models were used to analyze data from 300 university students using a questionnaire. Students' financial decisions were used as the dependent variable, while financial literacy, money ethics, money attitude, time preference, financial experience, and financial specialization agents were the independent variables.

Findings

Resultantly, power, personal financial literacy, achievement, financial behavior, avoidance, reward for efforts, financial experience, financial attitude, financial socialization agents, and time preference influence the students' financial decisions.

Practical implications

The findings are useful for financial and educational institutions and policymakers who design academic courses.

Originality/value

This study measured the effects of several critical contextual areas regarding financial literacy and students' decisions in Pakistani universities.
Purification of antibacterial attacins induced in Hyalophora cecropia pupae immunized with Enterobacter cloacae C7‐501 using ion‐exchange chromatography, hydrophobic interaction chromatography, and Rotofor® isoelectric focusing
Authors: Ko Kisung , Kim Kibum , Kim Yerin , Norelli John L. , Brown Susan K. , Aldwinckle Herb S.
Published: June 2023

Hyalophora cecropia pupae were infected by Enterobacter cloacae C7‐501 to induce antibacterial attacins for purification. The induction of attacins in immunized pupae was confirmed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS‐PAGE). Ion‐exchange chromatography (IEC), hydrophobic interaction chromatography (HIC), and Rotofor® isoelectric focusing (ISEF) were applied to isolate attacins from the hemolymph. IEC separated attacins from most hemolymph proteins, but the fractions containing attacins also had other proteins of 20 and 64 kDa in length. In IEC, attacin was eluted with ~0.2 M NaCl. The best conditions for IEC were pH 9, flow rate of 2 mL/min, with step elution (0.025, 0.05, 0.075, 0.1, 0.2, 0.4 and 1.0 M NaCl). In HIC, most other proteins were eluted with the ammonium persulfate treatment. HIC isolated attacin proteins under hydrophobic conditions, at ~50% EtOH. However, the fraction with attacins also contained other proteins. The Rotofor® ISEF produced fractions containing attacins at isoelectric points ranging between 5.7 and 8.3. However, non‐specific proteins were detected in the fraction samples, and the recovery of attacins was low. The purification efficiency of ISEF was lower than IEC and HIC. In this study, the expression of attacins was induced in H. cecropia pupae infected with E. cloacae C7‐501, and attacins could be purified by IEC and ISEF. Overall, IEC provided better separation of attacins from the hemolymph of H. cecropia pupae immunized with E. cloacae bacteria than HIC and Rotofor® ISEF.
Utilizing retrograde autologous priming for blood conservation in cardiac surgery
Authors: Mekhail Andrew , Clayton Nicholas , Rhadakrishnan Kamaraj , Blakey Amber , Galvin Sean
Published: June 2023

Background

The use of crystalloid priming for extracorporeal circuit in adult cardiac surgery causes inevitable haemodilution. The haemodilution can be reduced by using methods such as retrograde autologous priming (RAP) with the patient's blood. This study compares the RAP technique with standard priming with regards to safety and the impact on haemodilution.

Methods

This was a retrospective cohort study between a control group (n = 100) consisting of consecutive patients undergoing first time isolated coronary artery bypass surgery (CABG) with crystalloid priming solution in the circuit, and the RAP group (n = 100) consisting of patients undergoing isolated first time CABG with the RAP method. All demographics, procedure and perfusion data were gathered from the local surgical and perfusion database.

Results

Despite starting with comparable mean pre‐operative haemoglobin (Hb) levels (control 127 mg/dL versus RAP 129 mg/dL), the RAP group had significantly higher mean post‐op Hb level (109 mg/dL versus 92 mg/dL, P < 0.01). Crystalloid use was also significantly lower in RAP group (3.15 L versus 4.17 L P < 0.02). Freedom from red blood cell transfusion (86% versus 76% P = 0.038) and freedom from blood products (78% versus 66%, P = 0.032) was also significantly better in the RAP group.

Conclusions

This study demonstrates that retrograde autologous priming is a safe and effective method for priming the cardiopulmonary bypass circuit in adult cardiac surgery, with significantly beneficial effects on transfusion rates and intra operative fluid requirements. Given these results the RAP method should be considered as a routine step in priming an extracorporeal circuit for adult cardiac operations.
Biomarkers at 6 weeks' gestation in the prediction of early miscarriage in pregnancy following assisted reproductive technology
Authors: Guo Jun , Feng Qiaoli , Chaemsaithong Piya , Appiah Kubi , Sahota Daljit S. , Leung Bo Wah , Chung Jacqueline P. , Li Tin Chiu , Poon Liona C.
Published: June 2023

Introduction

Miscarriage is a major concern in early pregnancy among women having conceived with assisted reproductive treatments. This study aimed to examine potential miscarriage‐related biophysical and biochemical markers at 6 weeks' gestation among women with confirmed clinical pregnancy following in vitro fertilization (IVF)/embryo transfer (ET) and evaluate the performance of a model combining maternal factors, biophysical and biochemical markers at 6 weeks' gestation in the prediction of first trimester miscarriage among singleton pregnancies following IVF/ET.

Material and methods

A prospective cohort study was conducted in a teaching hospital between December 2017 and January 2020 including women who conceived through IVF/ET. Maternal mean arterial pressure, ultrasound markers including mean gestational sac diameter, fetal heart activity, crown rump length and mean uterine artery pulsatility index (mUTPI) and biochemical biomarkers including maternal serum soluble fms‐like tyrosine kinase‐1 (sFlt‐1), placental growth factor (PlGF), kisspeptin and glycodelin‐A were measured at 6 weeks' gestation. Logistic regression analysis was carried out to determine significant predictors of miscarriage prior to 13 weeks' gestation and performance of screening was estimated by receiver‐operating characteristics curve analysis.

Results

Among 169 included pregnancies, 145 (85.8%) pregnancies progressed to beyond 13 weeks' gestation and had live births whereas 24 (14.2%) pregnancies resulted in a miscarriage during the first trimester. In the miscarriage group, compared to the live birth group, maternal age, body mass index, and mean arterial pressure were significantly increased; mean gestational sac diameter, crown rump length, mUTPI, serum sFlt‐1, glycodelin‐A, and the rate of positive fetal heart activity were significantly decreased, while no significant differences were detected in PlGF and kisspeptin. Significant prediction for miscarriage before 13 weeks' gestation was provided by maternal age, fetal heart activity, mUTPI, and serum glycodelin‐A. The combination of maternal age, ultrasound (fetal heart activity and mUTPI), and biochemical (glycodelin‐A) markers achieved the highest area under the curve (AUC: 0.918, 95% CI 0.866–0.955), with estimated detection rates of 54.2% and 70.8% for miscarriage before 13 weeks' gestation, at fixed false positive rates of 5% and 10%, respectively.

Conclusions

A combination of maternal age, fetal heart activity, mUTPI, and serum glycodelin‐A at 6 weeks' gestation could effectively identify IVF/ET pregnancies at risk of first trimester miscarriage.
Psilocybin: The most effective moral bio‐enhancer?
Authors: Rakić Vojin
Published: June 2023

This paper addresses the possible effects of psychedelic drugs, notably psilocybin, on moral bio‐enhancement (MBE). It will be argued that non‐psychedelic substances, such as oxytocin, serotonin/serotonin reuptake inhibitors, or vasopressin, have indirect effects on M(B)E, whereas psilocybin has direct effects. Additionally, morality and happiness have been shown to operate in a circularly supportive relationship. It will be argued that psilocybin also has more direct effects on the augmentation of human happiness than non‐psychedelic substances. Hence, psilocybin multiplies its effects on morality and on moral enhancement (as well as on happiness) if compared with non‐psychedelic substances. Still, caution is advised if psilocybin is being used, and the correct dosage should be prescribed by an appropriate physician. Furthermore, the use of psilocybin has additional effects on moral enhancement and happiness if combined with meditation, preferably under the guidance of an experienced meditation specialist.
Pleistocene river diversions caused by large landslides in the western Pyrenees (Oria River drainage basin, N Spain)
Authors: Iribar V. , Ábalos B.
Published: June 2023

River‐blocking landslides exert a deep impact on mountain range landscapes and the organization of catchments. A blocked river diverted to another watershed modifies both original and transferred drainage networks both up‐ and downstream. Using western Pyrenees examples, a geological and geomorphic framework with diagnostic criteria to detect river diversion by landslides is presented, including the identification of elbows of diversion, eroded divides, beheaded underfit rivers, diverted overfit rivers, reversed river segments and the landslides at fault. Some landslides caused the formation of lakes that overflowed upstream at catchment divide segments with elevations lower than those of blocking landslide tops. Unravelling the presence of fan deltas at distinct sites/elevations of palaeolake shores contributed as well to identification of river damming and later diversion episodes. Reconstruction of the sedimentary organization of river palaeovalleys and of their associated fluvial terraces and palaeoriver channels (some currently submerged by the Cantabrian Sea), along with the reconstruction of river profiles, analysis of bedrock and morphology of watershed divides, identify seven river diversions caused by landslides and 14 additional slides that variably constrained river basin dynamics in the area studied. The diverting slides have current areas between 0.06 and 12.3 km2 (thus including giant examples), thicknesses up to 300 m and translational–rotational rupture surfaces usually with low dip angles (3.5–12.3°). A combination of relative dating methods and published absolute ages suggests that diversion events occurred during the Quaternary. This study shows that river diversion by landslides can be significant in mountainous areas of moderate relief.