bluuebunny/crossref_metadata_2025 huggingface dataset:
Protein structure prediction in the era of AI: challenges and limitations when applying toin-silicoforce spectroscopy
Authors: Gomes Priscila S. F. C. , Gomes Diego E. B. , Bernardi Rafael C.
Published: July 2022

Mechanoactive proteins are essential for a myriad of physiological and pathological processes. Guided by the advances in single-molecule force spectroscopy (SMFS), we have reached a molecular-level understanding of how several mechanoactive proteins respond to mechanical forces. However, even SMFS has its limitations, including the lack of detailed structural information during force-loading experiments. That is where molecular dynamics (MD) methods shine, bringing atomistic details with femtosecond time-resolution. However, MD heavily relies on the availability of high-resolution structures, which is not available for most proteins. For instance, the Protein Data Bank currently has 192K structures deposited, against 231M protein sequences available on Uniprot. But many are betting that this gap might become much smaller soon. Over the past year, the AI-based AlphaFold created a buzz on the structural biology field by being able to, for the first time, predict near-native protein folds from their sequences. For some, AlphaFold is causing the merge of structural biology with bioinformatics. In this perspective, using anin silicoSMFS approach, we investigate how reliable AlphaFold structure predictions are to investigate mechanical properties of staph bacteria adhesins proteins. Our results show that AlphaFold produce extremally reliable protein folds, but in many cases is unable to predict high-resolution protein complexes accurately. Nonetheless, the results show that AlphaFold can revolutionize the investigation of these proteins, particularly by allowing high-throughput scanning of protein structures. Meanwhile, we show that the AlphaFold results need to be validated and should not be employed blindly, with the risk of obtaining an erroneous protein mechanism.
Riboflavin Depletion Promotes Longevity and Metabolic Hormesis in Caenorhabditis elegans
Authors: Yerevanian Armen , Murphy Luke , Emans Sinclair , Zhou Yifei , Ahsan Fasih , Baker Daniel , Li Sainan , Adedoja Adebanjo , Cedillo Lucydalila , Gnanatheepam Einstein , Dao Khoi , Jain Mohit , Georgakoudi Irene , Soukas Alexander
Published: July 2022

Riboflavin is an essential cofactor in many enzymatic processes and in the production of flavin adenine dinucleotide (FAD). Here we report that the partial depletion of riboflavin through knockdown of the C. elegans riboflavin transporter 1 (rft-1) promotes metabolic health by reducing intracellular flavin concentrations. Knockdown of rft-1 significantly increases lifespan in a manner dependent on FOXO/daf-16, AMP-activated protein kinase (AMPK)/aak-2, the mitochondrial unfolded protein response, and mTOR complex 2 (mTORC2). Riboflavin depletion promotes altered energetic and redox states and increases adiposity, independent of lifespan genetic dependencies. Riboflavin depleted animals also exhibit activation of caloric restriction reporters without a reduction in TORC1 signaling. Our findings indicate that riboflavin depletion activates an integrated, hormetic response that promotes lifespan and healthspan in C. elegans.
Predicting protease networks through human genetics
Authors: Iwamoto Kazunari , Eriksson Tore
Published: July 2022

By utilizing functional genetic variation within the participants of the UK Biobank project for a largescale PheWAS study we attempted to get a better understanding of how the set of human proteases and their endogenous inhibitors are involved in common diseases. Focusing on known human proteases, their inhibitors, and known substrates, we computed their ranked-biased similarity from phenome-wide association results. Putative regulatory networks were constructed from 250 high-scoring pairs of proteases and related genes. This analysis suggested thirteen network modules, five diagnosis-based and eight biomarker-based. Through genetic associations and published literature on module members, the modules could be classified into different disease modalities including cholesterol homeostasis and high blood pressure.
Senescent cell-derived extracellular vesicles inhibit cancer recurrence by coordinating immune surveillance
Authors: Ziglari Tahereh , Calistri Nicholas L. , Finan Jennifer M. , Derrick Daniel , Nakayasu Ernesto S. , Burnet Meagan C. , Kyle Jennifer E. , Hoare Matthew , Heiser Laura M. , Pucci Ferdinando
Published: July 2022

Extracellular vesicles (EVs) are key signaling mediators. To explore the role of senescent cell-derived extracellular vesicles (senEVs) in inflammatory responses to senescence, we developed an engraftment-based senescence model in wild-type mice and genetically blocked senEV release in vivo, without significantly affecting soluble mediators. Our results demonstrate that senEVs are both necessary and sufficient to trigger immune-mediated clearance of senescent cells, thereby suppressing tumor growth. In the absence of senEVs, the recruitment of MHC-II+ antigen-presenting cells to the senescence microenvironment was markedly impaired. Blocking senEV release redirected the primary target of senescent cell signaling from antigen-presenting cells to neutrophils.

Through comprehensive transcriptional and proteomic analyses, we identified six ligands specific to senEVs, highlighting their role in promoting antigen-presenting cell–T cell adhesion and synapse formation. Antigen-presenting cells activated CCR2+CD4+ TH17cells, which appeared to inhibit B cell activation. CD4 T cells were essential for preventing tumor recurrence, indicating that CCR2+ TH17cells function downstream of senEVs during senescence surveillance.

Our findings suggest that senEVs complement the activity of secreted inflammatory mediators by recruiting and activating distinct immune cell subsets, thereby enhancing the efficient clearance of senescent cells. These conclusions may have implications not only for tumor recurrence but also for understanding senescence during de novo carcinogenesis. Consequently, this work could inform the development of novel cancer early detection strategies based on the biology of cellular senescence.
A review of socioeconomic inequalities in HIV infections among women in Low and Middle-income countries
Authors: Adegbosin Adeoluwa P , Adegbosin Adeyinka E
Published: July 2022

Background

Evidence shows that HIV is more prevalent among women in low and middle-income countries, this disparity is partly due to biological and socioeconomic factors. In this study we synthesised evidence on the relationship between socioeconomic factors and HIV prevalence among women.

Method

We searched PubMed, Cochrane, Scopus, and Embase, for articles published between 2010 and 2020 that investigated the relationship between socioeconomic factors and HIV prevalence among women in low and middle-income countries. We analysed and reported our findings based on the PRISMA guidelines.

Findings

A total of 14 studies were included in the final analysis. Six studies explored the effect of disparity in level of education on the prevalence of HIV among women. The effect of income disparity was explored in eight studies, while two studies each explored the effects of occupation and employment status. Overall, evidence shows that women with low socioeconomic status were more at risk of HIV infection.

Interpretation

Targeted Interventions aimed at improving the socioeconomic status of women in low and middle-income countries will play a significant role in reducing the prevalence of HIV infection in these settings.
A Measurement Invariance Analysis of Selected Opioid Overdose Knowledge Scale (OOKS) Items among Bystanders and First Responders
Authors: Swartz James A. , Lin Qiao , Kim Yerim
Published: July 2022

The Opioid Overdose Knowledge Scale (OOKS) is widely used as an adjunct to opioid education and naloxone distribution (OEND) for assessing pre- and post-training knowledge. However, the extent to which the OOKS performs comparably for bystander and first responder groups has not been well determined. We used exploratory structural equation modeling (ESEM) to assess the measurement invariance of an OOKS item subset when used as an OEND training pre-test. We used secondary analysis of pre-test data collected from 446 first responders and 1,349 bystanders (N=1,795) attending OEND trainings conducted by two county public health departments. Twenty-four items were selected by practitioner/trainer consensus from the original 45-item OOKS instrument with an additional 2 removed owing to low response variation. We used exploratory factor analysis (EFA) followed by ESEM to identify a factor structure, which we assessed for configural, metric, and scalar measurement invariance by participant group using the 22 dichotomous items (correct/incorrect) as factor indicators. EFA identified a 3-factor model consisting of items dealing with: basic overdose risk information, signs of an overdose, and rescue procedures/advanced overdose risk information.Model fit by ESEM estimation versus confirmatory factor analysis showed the ESEM model afforded a better fit. Measurement invariance analyses indicated the 3-factor model fit the data across all levels of invariance per standard fit statistic metrics. The reduced set of 22 OOKS items appears to offer comparable measurement of pre-training knowledge on opioid overdose risks, signs of an overdose, and rescue procedures for both bystanders and first responders.
Using the sanitation safety planning tool to improve the occupational health and safety of de-sludging operators in Uganda: a protocol for a controlled before and after study
Authors: Ssekamatte Tonny , Nalugya Aisha , Fuhrimann Samuel , Mugambe Richard K. , Kansiime Winnifred K. , Tigaiza Arnold , Nakalembe Doreen , Moodley Nishai , Nuwagaba Fred , Kimbugwe Ceaser , Mselle Jane Sembuche , Tamale Bridget Nagawa , Halage Abdullah Ali , Isunju John Bosco
Published: July 2022

Background

De-sludging operators play a critical role in ensuring access to safe sanitation services. De-sludging activities, however, increase the operators’ risk of exposure to physical, chemical, ergonomic, psychological, and biological hazards, which eventually affect their health-related quality of life (HRQoL). Despite immense exposure to occupational hazards, only a few evidence-based interventions have been implemented to improve the occupational health and safety (OHS) of de-sludging operators.

Objective

The proposed study intends to utilise the sanitation safety planning (SSP) tool to improve the OHS of de-sludging operators in Uganda. The study aims to generate evidence of the prevalence of exposure to occupational hazards and the associated health outcomes, knowledge, attitude and uptake of OHS measures, as well as the HRQoL of de-sludging operators. The facilitators and barriers to the promotion of OHS shall also be explored.

Methods

A mixed-methods study will be conducted among 356 desludging operators in the Greater Kampala Metropolitan Area. A structured questionnaire pre-loaded on the KoboCollect mobile data collection application will be used to obtain information on socio-demographic characteristics, history of work-related accidents and diseases, uptake of safety measures, and health-related quality of life. A total of 10 focus group discussions (FGDs) will be conducted among desludging operators, to understand how they cope with associated occupational hazards. In addition, 25 in-depth interviews (IDIs) will be conducted among purposively selected employers to understand the barriers and facilitators of provision and implementation of safety measures among desludging operators. Quantitative data will be analyzed using STATA version 15 while qualitative data will be transcribed verbatim and the analysis aided by the NVIVO software.

Expected outcomes

The study will generate evidence of the occupational health and safety of desludging operators and the effectiveness of the SSP tool. These findings will be critical in informing the design and implementation of occupational health and safety programmes among desludging operators.
A multimodal neuroimaging study of brain abnormalities and clinical correlates in post treatment Lyme disease
Authors: Marvel Cherie L. , Alm Kylie H. , Bhattacharya Deeya , Rebman Alison W. , Bakker Arnold , Morgan Owen P. , Creighton Jason A. , Kozero Erica A. , Venkatesan Arun , Nadkarni Prianca A. , Aucott John N.
Published: July 2022

Lyme disease is the most common vector-borne infectious disease in the United States. Post-treatment Lyme disease (PTLD) is a condition affecting 10-20% of patients in which symptoms persist despite antibiotic treatment. Cognitive complaints are common among those with PTLD, suggesting that brain changes are associated with the course of the illness. However, there has been a paucity of evidence to explain the cognitive difficulties expressed by patients with PTLD.

This study administered a working memory task to a carefully screened group of 12 patients with well-characterized PTLD and 18 healthy controls while undergoing functional MRI (fMRI). A subset of 12 controls and all 12 PTLD participants also received diffusion tensor imaging (DTI) to measure white matter integrity. Clinical variables were also assessed and correlated with these multimodal MRI findings.

On the working memory task, the patients with PTLD responded more slowly, but no less accurately, than did controls. FMRI activations were observed in expected regions by the controls, and to a lesser extent, by the PTLD participants. The PTLD group also hypoactivated several regions relevant to the task. Conversely, novel regions were activated by the PTLD group that were not observed in controls, suggesting a compensatory mechanism. Notably, three activations were located in white matter of the frontal lobe. DTI measures applied to these three regions of interest revealed that higher axial diffusivity correlated with fewer cognitive and neurological symptoms. Whole-brain DTI analyses revealed several frontal lobe regions in which higher axial diffusivity in the patients with PTLD correlated with longer duration of illness. Together, these results show that the brain is altered by PTLD, involving changes to white matter within the frontal lobe. Higher axial diffusivity may reflect white matter repair and healing over time, rather than pathology, and cognition appears to be dynamically affected throughout this repair process.
The impact of residency training in family medicine on hospital admissions due to Ambulatory-care Sensitive Conditions in Rio de Janeiro
Authors: Jantsch Adelson Guaraci , Burström Bo , Nilsson Gunnar , de Leon Antônio Ponce
Published: July 2022

BACKGROUND

Lack of skilled human resources in primary care remains a major concern for policymakers in low- and middle-income countries. There is little evidence supporting the impact of residency training in family medicine in the quality of care, and it perpetuates misconceptions among policymakers that the provision of primary care can be easily done by any physician without special training.

METHODS

This article compares the risk of patients being hospitalized due to Ambulatory care sensitive conditions and the odds of having follow-up visits in primary care after hospital discharge, according to the type of their medical provider: (1) Generalists (reference), (2) Family physicians; and, (3) patients with no consultations prior to the event. Multilevel multivariate binomial regression models estimated the relative risks of a patient being hospitalized in a given month and the relative risks for the occurrence of a follow-up visit in primary care in a retrospective cohort of 636.640 patients between January 2013 and July 2018 in Rio de Janeiro.

FINDINGS

For all 14 conditions, there was a higher risk of hospitalization when patients had no consultation in primary care prior to the event. Except for Ear, Nose and Throat infections, patients seen by family physicians had a lower risk of being hospitalized, compared to patients seen by Generalists. Follow-up visits were more likely to happen among patients treated by family physicians for almost every condition analyzed.

CONCLUSION

With two years of training in family medicine, Family physicians can reduce the risk of their patients being hospitalized and increase the likelihood of those patients having a follow-up consultation in primary care. Investments in residency training in family medicine should be made to fix the shortage of skilled physicians in primary care, reduce hospitalizations and improve quality and continuity of care.
Dating the photosynthetic organelle evolution in Archaeplastida,Paulinellaand secondary-plastid bearing lineages
Authors: Pietluch Filip , Mackiewicz Paweł , Sidorczuk Katarzyna , Gagat Przemysław
Published: July 2022

Photosynthetic eukaryotes have shaped the Earth’s biosphere by producing O2and converting light into organic compounds in specialized organelles called plastids. Plastids evolved from free-living cyanobacteria engulfed by heterotrophic unicellular eukaryotes in processes called cyanobacterial endosymbioses. Two independent such processes have been reported so far. The first gave rise to primary plastids and three Archaeplastida lineages: glaucophytes, red algae and green algae with land plants, whereas the second resulted in chromatophores in the rhizarian amoebaPaulinella. Importantly, archaeplastidans donated their plastids to many protist groups, thereby further spreading photosynthesis across the tree of life. To reveal the complex plastid evolution, we performed comprehensive phylogenetic and multi-clock analyses based on new fossil calibration points and the greatest number yet of plastid-encoded proteins from 108 taxa, representing a large diversity of photosynthetic organisms. Our results indicate that primary plastids evolved prior to 2.1 - 1.8 Bya, i.e. before glaucophytes diverged from the other archaeplastidans. Like the primary plastids before,Paulinellachromatophores evolved in low salinity habitats and possibly before 292 - 266 Mya. Red and green algae were engulfed by cryptophyte and chlorarachniophyte ancestors between 1.7 - 1.4 Bya, and 1.1 - 1.0 Bya, respectively; the former subsequently triggered plastid transfers to other eukaryotes. The diversification rate of the photosynthetic organisms increased with temperature and CO2but decreased with O2and volcanic activity. We also studied the impact of various molecular clocks and calibration sets on the age estimation and clearly indicate that the clocks are the source of greater differences.

Significance Statement

Cyanobacteria and eukaryote endosymbioses created a multitude of photosynthetic organelles called plastids that feed most life on our planet. For decades scientists have been trying to untangle the puzzle of plastid evolution, i.e. when and how plastids were acquired and spread throughout the eukaryotic tree of life. To answer these questions we applied phylogenetic and multi-clock methods combined with new fossil calibration points on large data sets. Our results push back in the Earth’s history most key events concerning plastid evolution compared to previous reports. Additionally, we discovered a significant impact of climatic and atmospheric parameters on the diversification rate of plastid lineages. The estimated divergence times enabled us to reinterpret taxonomic classification of controversial fossils.
Gene Regulatory Network Reconfiguration in Direct Lineage Reprogramming
Authors: Kamimoto Kenji , Adil Mohd Tayyab , Jindal Kunal , Hoffmann Christy M. , Kong Wenjun , Yang Xue , Morris Samantha A.
Published: July 2022

In direct lineage reprogramming, transcription factor (TF) overexpression reconfigures Gene Regulatory Networks (GRNs) to convert cell identities between fully differentiated cell types. We previously developed CellOracle, a computational pipeline that integrates single-cell transcriptome and epigenome profiles to infer GRNs. CellOracle leverages these inferred GRNs to simulate gene expression changes in response to TF perturbation, enabling network re-configuration during reprogramming to be interrogated in silico. Here, we integrate CellOracle analysis with lineage tracing of fibroblast to induced endoderm progenitor (iEP) conversion, a prototypical direct lineage reprogramming paradigm. By linking early network state to reprogramming success or failure, we reveal distinct network configurations underlying different reprogramming outcomes. Using these network analyses and in silico simulation of TF perturbation, we identify new factors to coax cells into successfully converting cell identity, uncovering a central role for the AP-1 subunit Fos with the Hippo signaling effector, Yap1. Together, these results demonstrate the efficacy of CellOracle to infer and interpret cell-type-specific GRN configurations at high resolution, providing new mechanistic insights into the regulation and reprogramming of cell identity.
Convergent gene expression highlights shared vocal motor microcircuitry in songbirds and humans
Authors: Gedman Gregory L , Biegler Matthew T. , Haase Bettina , Wirthlin Morgan E. , Fedrigo Olivier , Pfenning Andreas R. , Jarvis Erich D.
Published: July 2022

Vocal learning is a skilled motor behavior observed in several mammalian and avian species and is critical for human speech. While convergent gene expression patterns have highlighted similar primary motor and striatal pathways for vocal imitation in songbirds and humans, the extent of molecular and circuit convergence remains unresolved. Here we profiled the four principal song nuclei of the zebra finch (HVC, LMAN, RA, Area X) and their surrounding brain regions using RNA-Seq and compared them with specialized markers we identified for human speech brain regions. Expanding previous work, both songbird RA and HVC exhibited convergent specialized gene expression of ∼350 genes with human laryngeal sensorimotor cortex. The songbird HVCRAintratelencephalic (IT) neurons were the predominant cell type that was convergent with human, specifically layer 2/3 IT neurons, while the songbird RA extratelencephalic (ET) projection neurons exhibited convergent expression with human layer 5 ET projection neurons. The molecular specializations of both songbird LMAN and human Broca’s area were more unique to each species. These findings demonstrate the extent of convergent molecular specializations in distantly related species for vocal imitation and emphasize important evolutionary constraints for this complex trait.

One-Sentence Summary

Our data provide hundreds of candidate genes to study the molecular basis and evolution of song and speech across species.
Polyunsaturated fatty acids alter the formation of lipid droplets and eicosanoid production in Leishmania promatigotes
Authors: de Sousa Andrade Yasmin Monara Ferreira , de Castro Monara Viera , de Souza Tavares Victor , Oliveira Souza Rayane da Silva , Helena Faccioli Lúcia , Lima Jonilson Berlink , Sorgi Carlos Arterio , de Matos Borges Valéria , Araújo-Santos Théo
Published: July 2022

Leishmania parasites contain lipid droplets (LD, or lipid bodies) and the molecular machinery responsible for synthesizing prostaglandins (PGs) and other bioactive lipids. We studied the effects of polyunsaturated fatty acids (PUFA) on LD biogenesis and eicosanoid production in distinct Leishmania species associated with different clinical forms of leishmaniasis. We also compared structural models of human-like cyclooxygenase-2 (GP63) and prostaglandin F synthase (PGFS) proteins of Leishmania, and we evaluated their enzymatic production in logarithmic and stationary growth phases of procyclic L. amazonensis, L. braziliensis and L. infantum. PUFAs modulate the formation of LDs in L. braziliensis and L. infantum. Leishmania species with equivalent clinical manifestations and tissue tropism had same protein mutations in GP63 and PGFS. No differences in GP63 production were observed among L. amazonensis, L. braziliensis and L. infantum, however increased PGFS production was detected during the parasite differentiation. Stimulation with arachidonic acid resulted in highly elevated production of hydroxyeicosatetraenoic acids compared to prostaglandins quantified by LC-MS/MS. The present findings open new perspectives on the role of eicosanoid metabolism in Leishmania and could contribute to the development of novel antiparasitic drugs.
Selection for increased post-infection survival ameliorates mating induced immune suppression in Drosophila melanogaster females
Authors: Basu Aabeer , Singh Aparajita , Ruchitha B G , Prasad Nagaraj Guru
Published: July 2022

Sexual activity (mating) negatively affects immune function in various insect species, in both sexes. In the experiments reported in this manuscript, we tested if hosts adapted to regular pathogen challenges are less susceptible to mating induced immune suppression, using experimentally evolved Drosophila melanogaster populations selected for increased post-infection survival when infected with a Gram-positive bacterium, Enterococcus faecalis. Mating increased susceptibility of females to bacterial pathogens, but in a pathogen specific manner. Mating-induced increase in susceptibility was also affected by host evolutionary history, with females from selected populations exhibiting similar post-infection survival irrespective of mating status, while females from control populations became more susceptible to bacterial infections after mating. Post-infection survival of males, irrespective of their evolutionary history, was not affected by their mating status. We therefore conclude that hosts evolved to better survive bacterial infections are also better at resisting mating-induced increase in susceptibility to infections in Drosophila melanogaster.
Optimization of information transmission through a noisy biochemical pathway explains the choice of reaction rates
Authors: Mahajan Anush , Ghosh Bhaswar
Published: July 2022

Living organisms are required to sense the environment accurately in order to ensure appropriate responses. The cells utilize specific signaling pathways to estimate the signal. The accuracy of estimating the input signal is severely limited by noise stemming from inherent stochasticity of the chemical reactions involved in signaling pathways. Cells employ multiple strategies to improve the accuracy by tuning the reaction rates, for instance amplifying the response, reducing the noise etc.. However, the pathway also consumes energy through incorporating ATP in phosphorylating key signaling proteins involved in the reaction pathways. In many instances, improvements in accuracy elicit extra energetic cost. For example, higher deactivation rate suppresses the basal pathway activity effectively amplifying the dynamic range of the response which leads to improvement in accuracy. However, higher deactivation rate also enhances the energy dissipation rate. Here, we employed a theoretical approach based on non-equilibrium thermodynamics of information to explore the role of accuracy and energetic cost in the performance of a MAPK signaling system. Our study shows that the accuracy-energy trade-off can explain the optimality of the reaction rates of the reaction pathways rather than accuracy alone. Our analysis elucidates the important role of the interplay between accuracy and related energetic cost in evolutionary shaping of the parameter space of signaling pathways.
Insight into diatoms diversity at two European coastal sites (LTER-MC in the Mediterranean Sea and SOMLIT-Astan in the Western English Channel) using a DNA Metabarcoding approach
Authors: Caracciolo Mariarita , Berney Cédric , Alric Benjamin , Piredda Roberta , Zingone Adriana , Sarno Diana , Percopo Isabella , Romac Sarah , Gall Florence Le , Rigaut-Jalabert Fabienne , Baudoux Anne-Claire , Simon Nathalie , Henry Nicolas
Published: July 2022

Diatoms are among the most successful marine eukaryotic phytoplankton groups. Their diversity has been investigated in the world’s oceans through expeditions and observations carried out from the equator to the poles. Traditionally, diatom species have been distinguished based on morphological characters of their frustules, but high-throughput sequencing offers new, high-resolution data that can be used to re-examine spatial and/or temporal patterns of diversity. Here we investigated diatoms’ genetic diversity using metabarcoding (18S V4 rRNA gene) obtained along the years 2011 to 2013 at two coastal time series stations (SOMLIT-Astan and LTER-MareChiara) installed respectively off Roscoff in the Western English Channel and in the Gulf of Naples in the Mediterranean Sea. Diatom species pools detected were different, which fitted with previous observations and with our expectations, since these stations are installed in two contrasted pelagic habitats (permanently-mixed versus stratified in summer). However, this analysis also shows a pool of common ASVs among which some are persistent and dominant in both sites. The observed synchronous variations in relative read abundances of shared ASVs assigned to Chaetoceros socialis, C. tenuissimus, Cyclotella, Mediolabrus comicus and Leptocylindrus aporus at the two geographically distant sites could indicate that internal controls of growth rate and sexual reproduction, rather that external environmental parameters are at work.
The Fatty Acid Binding Protein Family Represents a Novel Target in Multiple Myeloma
Authors: Farrell Mariah , Fairfield Heather , Karam Michelle , D’Amico Anastasia , Murphy Connor S. , Falank Carolyne , Pistofidis Romanos Sklavenitis , Cao Amanda , Marinac Catherine R. , Dragon Julie A. , McGuinness Lauren , Gartner Carlos , Di Iorio Reagan , Jachimowicz Edward , DeMambro Victoria , Vary Calvin , Reagan Michaela R.
Published: July 2022

Background

Multiple myeloma is an incurable plasma cell malignancy with only a 53% 5-year survival rate, highlighting a critical need for new multiple myeloma vulnerabilities and therapeutic avenues. Herein, we explored a novel multiple myeloma target: the fatty acid binding protein (FABP) family.

Methods

Myeloma cells treated with FABP inhibitors (BMS3094013 and SBFI-26) were examined in vivo and in vitro for cell cycle, proliferation, apoptosis, mitochondrial membrane potential, cellular metabolism (oxygen consumption rates and fatty acid oxidation), and DNA methylation. Myeloma cell responses to BMS309403 and/or SBFI-26 were assessed with RNA-sequencing and proteomic analysis, and confirmed with western blotting and qRT-PCR. Myeloma cell dependency on FABPs was assessed using DepMap. Finally, MM patient datasets (CoMMpass and GEO) were mined for FABP expression correlations with clinical outcomes.

Results

Myeloma cells treated with FABPi or with FABP5 knockout (generated via CRISPR/Cas9 editing) exhibited diminished proliferation in vitro. FABPi had potent anti- tumor effects both in vitro and in vivo in two pre-clinical MM mouse models where increased mouse survival was observed. FABPi negatively impacted mitochondrial respiration and reduced expression of MYC and other key signaling pathways in MM cells. Clinical data demonstrated worse overall and progression-free survival in patients with high FABP5.

Conclusions

This study establishes the FABP family as a therapeutically actionable dependency in multiple myeloma with a multitude of actions and cellular roles that result in the support of myeloma progression.

Statement of translational relevance

Multiple myeloma (MM) is an incurable disease of the plasma cell and MM patients require better treatments as soon as possible. The fatty acid binding protein (FABP) family plays a number of roles in cells, including supporting fatty acid oxidation, lipid shuttling and signal transduction. Here, we demonstrate with CoMMpass and other clinical data that FABPs represent a biomarker for aggressive disease in MM, and are a novel, targetable protein family expressed by myeloma cells. Pharmacologically inhibiting FABPs kills tumor cells and induces cell cycle arrest in vitro and in pre-clinical models. Mechanisms of action are multitudinous, as we discovered with RNA-sequencing, proteomic analysis, and phenotyping assays. Cell metabolism, cell signaling, cell stress, and epigenetic signatures were altered in MM cells when FABPs were inhibited. In summary, targeting FABP5 holds great therapeutic potential for killing diseased cells, with few negative off-target effects on healthy cells.
Loosenin-like proteins fromPhanerochaete carnosaimpact both cellulose and chitin fiber networks
Authors: Monschein Mareike , Ioannou Eleni , Amin Leamon AKM AL , Varis Jutta J. , Wagner Edward R. , Mikkonen Kirsi S. , Cosgrove Daniel J. , Master Emma R.
Published: July 2022

Microbial expansin-related proteins are ubiquitous across bacterial and fungal organisms, and reportedly play a role in the modification and deconstruction of cell wall polysaccharides including lignocellulose. So far, very few microbial expansin related proteins, including loosenins and loosenin-like (LOOL) proteins, have been functionally characterized. Herein, four LOOLs encoded byPhanerochaete carnosaand belonging to different subfamilies (i.e., PcaLOOL7 and PcaLOOL9 from subfamily A; PcaLOOL2 and PcaLOOL12 from subfamily B) were recombinantly produced and the purified proteins were characterized using diverse cellulose and chitin substrates. Whereas all of the purified PcaLOOLs weakened cellulose filter paper and cellulose nanofibril networks (CNF), none significantly boosted cellulase activity on the selected cellulose substrates (Avicel and Whatman paper). Binding of PcaLOOLs to alpha-chitin was higher than to cellulose (Avicel), and highest at pH 5.0. Notably, whereas PcaLOOL9 reduced the yield strain of chitin nanofibrils (ChNF) in a protein-dose dependent manner, the reverse pattern was observed for PcaLOOL7 despite belonging to the same LOOL subfamily. The current study reveals the potential of microbial expansin-related proteins to impact both cellulose and chitin networks, and provides further evidence pointing to a non-lytic mode of action.
Optimization and comparison of two methods for spike train estimation in an unfused tetanic contraction of low threshold motor units
Authors: Rohlén Robin , Antfolk Christian , Grönlund Christer
Published: July 2022

Background

Human movement is generated by activating motor units (MUs), i.e., the smallest structures that can be voluntarily controlled. Recent findings have shown imaging of voluntarily activated MUs using ultrafast ultrasound based on displacement velocity images and a decomposition algorithm. Given this, estimates of trains of twitches (unfused tetanic signals) evoked by the neural discharges (spikes) of spinal motor neurons are provided. Based on these signals, a band-pass filter method (BPM) has been used to estimate its spike train. In addition, an improved spike estimation method consisting of a continuous Haar wavelet transform method (HWM) has been suggested. However, the parameters of the two methods have not been optimized, and their performance has not been compared rigorously.

Method

HWM and BPM were optimized using simulations. Their performance was evaluated based on simulations and two experimental datasets with 21 unfused tetanic contractions considering their rate of agreement, spike offset, and spike offset variability with respect to the simulated or experimental spikes.

Results

A range of parameter sets that resulted in the highest possible agreement with simulated spikes was provided. Both methods highly agreed with simulated and experimental spikes, but HWM was a better spike estimation method than BPM because it had a higher agreement, less bias, and less variation (p< 0.001).

Conclusions

The optimized HWM will be an important contributor to further developing the identification and analysis of MUs using imaging, providing indirect access to the neural drive of the spinal cord to the muscle by the unfused tetanic signals.
Impacts of maternal microbiota and microbial metabolites on fetal intestine, brain and placenta
Authors: Husso Aleksi , Pessa-Morikawa Tiina , Koistinen Ville Mikael , Kärkkäinen Olli , Lahti Leo , Iivanainen Antti , Hanhineva Kati , Niku Mikael
Published: July 2022

The maternal microbiota modulates fetal development, but the mechanisms of these earliest host-microbe interactions are unclear. We compared full-term fetuses from germ-free (GF) and normally colonized mouse dams by gene expression profiling and non-targeted metabolomics. The developing immune system was strongly dependent on the maternal microbial status. In the fetal intestine, critical components mediating host-microbe interactions were differentially expressed. In fetal brain and placenta, interferon and inflammatory signaling were downregulated in germ-free fetuses. Neural system development and function, translation and RNA metabolism, and regulation of energy metabolism were significantly affected at the gene expression level. These impacts were strongly associated with microbial metabolite concentrations in the fetal tissues, suggesting that they are largely, although perhaps not exclusively mediated by maternal microbial metabolites absorbed through placenta. Several aryl sulfates were among the compounds strongly associated with gene expression differences. The germ-free fetus may suffer from depletion of queuine, a bacterial hypermodified nucleobase essential for eukaryotic tRNA stability and function.
Voltage to Calcium Transformation Enhances Direction Selectivity in Drosophila T4 neurons
Authors: Mishra Abhishek , Borst Alexander , Haag Juergen
Published: July 2022

A critical step in neural information processing is the transformation of membrane voltage into calcium signals leading to transmitter release. However, the effect of voltage to calcium transformation on neural responses to different sensory stimuli is not well understood. Here, we use in vivo two-photon imaging of genetically encoded voltage and calcium indicators, Arclight and GCaMP6f respectively, to measure responses in Drosophila direction-selective T4 neurons.

Comparison between Arclight and GCaMP6f signals revealed calcium signals to have a significantly higher direction selectivity compared to voltage signals. Using these recordings we build a model which transforms T4 voltage responses to calcium responses. The model reproduces experimentally measured calcium responses across different visual stimuli using different temporal filtering steps and a stationary non-linearity. These findings provide a mechanistic underpinning of the voltage-to-calcium transformation and show how this processing step, in addition to synaptic mechanisms on the dendrites of T4 cells, enhances direction selectivity in the output signal of T4 neurons.
ProSelfLC: Progressive Self Label Correction Towards A Low-Temperature Entropy State
Authors: Wang Xinshao , Hua Yang , Kodirov Elyor , Mukherjee Sankha Subhra , Clifton David A. , Robertson Neil M.
Published: July 2022

To train robust deep neural networks (DNNs), we systematically study several target modification approaches, which include output regularisation, self and non-self label correction (LC). Three key issues are discovered: (1) Self LC is the most appealing as it exploits its own knowledge and requires no extra models. However, how to automatically decide the trust degree of a learner as training goes is not well answered in the literature. (2) Some methods penalise while the others reward low-entropy predictions, prompting us to ask which one is better. (3) Using the standard training setting, a trained network is of low confidence when severe noise exists, making it hard to leverage its high-entropy self knowledge.

To resolve the issue (1), taking two well-accepted propositions–deep neural networks learn meaningful patterns before fitting noise and minimum entropy regularisation principle–we propose a novel end-to-end method named ProSelfLC, which is designed according to learning time and entropy. Specifically, given a data point, we progressively increase trust in its predicted label distribution versus its annotated one if a model has been trained for enough time and the prediction is of low entropy (high confidence). For the issue (2), according to ProSelfLC, we empirically prove that it is better to redefine a meaningful low-entropy status and optimise the learner toward it. This serves as a defence of entropy minimisation. To address the issue (3), we decrease the entropy of self knowledge using a low temperature before exploiting it to correct labels, so that the revised labels redefine a low-entropy target state.

We demonstrate the effectiveness of ProSelfLC through extensive experiments in both clean and noisy settings, and on both image and protein datasets. Furthermore, our source code is available athttps://github.com/XinshaoAmosWang/ProSelfLC-AT.
Competing constraints shape the non-equilibrium limits of cellular decision making
Authors: Lammers Nicholas C. , Flamholz Avi I. , Garcia Hernan G.
Published: July 2022

Gene regulation is central to cellular function. Yet, despite decades of work, we lack quantitative models that can predict how transcriptional control emerges from molecular interactions at the gene locus. Thermodynamic models of transcription, which assume that gene circuits operate at equilibrium, have previously been employed with considerable success in the context of bacterial systems. However, the presence of ATP-dependent processes within the eukaryotic transcriptional cycle suggests that equilibrium models may be insufficient to capture how eukaryotic gene circuits sense and respond to input transcription factor concentrations. Here, we employ simple kinetic models of transcription to investigate how energy dissipation within the transcriptional cycle impacts the rate at which genes transmit information and drive cellular decisions. We find that biologically plausible levels of energy input can lead to significant gains in how rapidly gene loci transmit information, but discover that the regulatory mechanisms underlying these gains change depending on the level of interference from non-cognate activator binding. When interference is low, information is maximized by harnessing energy to push the sensitivity of the transcriptional response to input transcription factors beyond its equilibrium limits. Conversely, when interference is high, conditions favor genes that harness energy to increase transcriptional specificity by proofreading activator identity. Our analysis further reveals that equilibrium gene regulatory mechanisms break down as transcriptional interference increases, suggesting that energy dissipation may be indispensable in systems where non-cognate factor interference is sufficiently large.
EasyGuide plasmids support in vivo assembly of gRNAs for CRISPR/Cas9 applications in Saccharomyces cerevisiae
Authors: Jacobus Ana P. , Barreto Joneclei A. , de Bem Lucas S. , Menegon Yasmine A. , Fier Ícaro , Bueno João G.R. , dos Santos Leandro V. , Gross Jeferson
Published: July 2022

Most CRISPR/Cas9 applications in yeast rely on a plasmid-based expression of Cas9 and its guide RNA (gRNA) containing a 20-nucleotides (nts) spacer tailored to each genomic target. The lengthy assembly of this customized gRNA requires at least 3–5 days for its pre-cloning in Escherichia coli, purification, validation, and co-transformation with Cas9 into a yeast strain. Here, we constructed a series of 12 EasyGuide plasmids to simplify CRISPR/Cas9 applications in Saccharomyces cerevisiae. The new vectors provide templates for generating PCR fragments that can assemble up to six functional gRNAs directly into yeasts via homologous recombination between the 20-nts spacers. By dispensing pre-cloning in E. coli, yeast in vivo gRNA assembly significantly reduces the CRISPR/Cas9 experimental workload. A highly efficient yeast genome editing procedure, involving PCR amplification of gRNAs and donors, followed by their transformation into a Cas9-expressing strain, can be easily accomplished in a single day.
pH Effect on Ligand Binding to an Enzyme Active Site
Authors: Singh Kushal , Muttathukattil Aswathy N. , Singh Prashant Chandra , Reddy Govardhan
Published: July 2022

Understanding the mechanism of ligands binding to their protein targets and the influence of various factors governing the binding thermodynamics is essential for rational drug design. The solution pH is one of the critical factors that can influence ligand binding to a protein cavity, especially in enzymes whose function is sensitive to the pH. Using computer simulations, we studied the pH effect on the binding of a guanidinium ion (Gdm+) to the active site of hen-egg white lysozyme (HEWL). HEWL serves as a model system for enzymes with two acidic residues in the active site and ligands with Gdm+ moieties, which can bind to the active sites of such enzymes and are present in several approved drugs treating various disorders. The computed free energy surface (FES) shows that Gdm+ binds to the HEWL active site using two dominant binding pathways populating multiple intermediates. We show that the residues close to the active site that can anchor the ligand could play a critical role in ligand binding. Using a Markov state model, we quantified the lifetimes and kinetic pathways connecting the different states in the FES. The protonation and deprotonation of the acidic residues in the active site in response to the pH change strongly influence the Gdm+ binding. There is a sharp jump in the ligand-binding rate constant when the pH approaches the largest pKa of the acidic residue present in the active site. The simulations reveal that, at most, three Gdm+ can bind at the active site, with the Gdm+ bound in the cavity of the active site acting as a scaffold for the other two Gdm+ ions binding. This result implies the possibility of designing single large molecules containing multiple Gdm+ moieties that can have high binding affinities to inhibit the function of enzymes with two acidic residues in their active site.