bluuebunny/crossref_metadata_2025 huggingface dataset:
Pain in Patients Living in Congregant Settings
Authors: Kalauokalani Donna , Budhwar Nitin
Published: May 2024

This chapter describes the challenges for assessing and treating pain in vulnerable populations who are in congregant settings, specifically in prison and in nursing homes. The unique circumstances surrounding incarceration and how those may mitigate considerations for assessment and selection of therapies are discussed. Understanding the relationship of prior trauma, adverse childhood experiences, co-occurring substance use disorder, and/or other mental health illness is explored. A stepwise, graduated approach is described to create an individualized treatment program. Compounding these challenges tied to long-term care settings are the unique medical risks of the older patient, including an increased susceptibility to acute injuries, a higher prevalence of chronic illness that may contribute to delayed recovery, and various forms and degrees of cognitive and physiologic decline. Systemic challenges such as staffing shortages, lack of standardized protocols, increasing cost of care, corporate priorities, and the interpretation and enforcement of rules and regulations add to the complexities one must navigate to provide optimal patient care.
Pain Related to Obesity
Authors: DeLateur Barbara
Published: May 2024

The most common definition of obesity is a body mass index (BMI) of 30 or greater, with subdivisions beyond that, and the term “morbid obesity” is applied to a BMI 40 or greater. Obesity has increased markedly, from 30.5% during the period of 1999–2000 to 41.9% during the period 2017–2020. Obesity increases the load on weight-bearing joints, especially the knee and hip. It also increases the load on the back, particularly when there is central adiposity. Visceral fat increases inflammation by sending out inflammatory cytokines. Obesity often leads to depression, which can lead to further obesity, especially by stress eating and inactivity. Obesity is often associated with sleep disorders, which lead to further obesity by decreasing the hormone leptin (fullness) and increasing ghrelin (the hunger hormone). Treatment strategies include getting good sleep; using canes and other load-bearing devices when needed; and weight-loss strategies based on the patient’s food and drink logs, examining content, frequency, and duration of eating. It is especially helpful to eliminate processed foods and eat whole, unprocessed foods such as fruits and vegetables, whole grains, legumes, and fish.
Pain and COVID-19
Authors: Han Andrew , Jolly Taranjeet S. , Cohen Steven P.
Published: May 2024

In late 2019 and early 2020, a global pandemic caused by severe acute respiratory syndrome coronavirus 2 occurred that as of April 2023 had cumulatively resulted in more than 760 million cases worldwide and nearly 7 million deaths. But although the mortality rate from the disease caused by the virus, COVID-19, has declined secondary to myriad preventative measures, vaccinations, and evolving viral strains, the impact continues to resound worldwide in terms of chronic pain, psychological morbidity, and reduced quality of life. Not only is COVID-19 more likely to affect vulnerable populations such as the elderly, underrepresented minorities, and impoverished people but also these individuals are more likely to suffer from both acute and chronic sequelae, including chronic pain. This chapter discusses epidemiology including in at-risk populations, acute and chronic pain sequelae, psychosocial sequelae that accompany active infection and its aftermath, and treatment.
Pain in Critically Ill Patients
Authors: Jaremko Kellie , Krish Brinda , Nikolic Katarina , Rayaz Hassan
Published: May 2024

This chapter discusses the unique vulnerabilities and risks for development of chronic pain in critically ill patients, as well as management for their acute post-traumatic, procedural, and postoperative pain. It describes pain prevalence, assessment, multicomponent treatment plans, and consequences to poorly controlled pain in the intensive care unit patient leading to chronicity, psychological distress, and poor long-term outcomes. It explores the specific vulnerabilities of these patients regarding communication barriers associated with sedation, delirium, and psychological distress. The chapter further addresses the known difficulties of assessing acute pain in critically ill patients and describes validated pain scales. Evidence-based and established national and international guidelines for sedation, delirium, and postoperative/post-traumatic analgesia optimization are reviewed. It expands on the use of opioids, multimodal analgesia, and regional anesthesia. The critical role of pain physicians is also highlighted, in addition to the importance of aggressive pain management in critically ill patients and the significant impact it has on patient outcomes.
Pain in Dental Settings and Facial Pain
Authors: Chavis Sydnee , Manrriquez Salvador L. , Reyes Marcela Romero
Published: May 2024

Dental pain is a significant contributor to decreased quality of life and disability throughout the life span. It usually derives from diseases of the teeth or oral tissues, but it can be caused by other local and systemic conditions. Dental pain is more prevalent and, often, more debilitating in vulnerable populations, such as people of minority groups, people of low socioeconomic status, people with special needs, and older adults. Dental pain is mostly preventable with routine oral health care. Other conditions, such as dry mouth, can put people at risk for caries and periodontal disease that can lead to dental pain and infection. Orofacial pain conditions of no-dental origin such as trigeminal neuralgia, and temporomandibular disorders can also affect greatly the quality of life of the sufferer. Awareness of the conditions and factors that lead to dental and orofacial pain as well as adequate access to dental and medical care and equitable treatment are imperative to address and manage pain among vulnerable people.
SBAs and EMQs for the MRCOG Part 2
Authors: Gnanasambanthan Sai , Datta Shree , Mahmood Tahir
Published: May 2024

Specifically designed for the MRCOG exam part 2, SBAs and EMQs for MRCOG Part 2 offers practical questions mapped closely to the Royal College of Obstetrics and Gynaecology curriculum to help candidates prepare for the newly adapted exam. This book features 300 Single Best Answers multiple-choice questions and 300 extended multiple-choice questions with explanations and sources for further reading. The aim of this book is not to provide another revision text to consult, but rather to tackle the common and difficult areas faced by candidates undertaking the exam. Questions have been compiled by junior doctors who have recently passed the exam, together with consultants who have a special interest in postgraduate education and training. The structure and content of the book matches the format of the exam. A detailed explanation is provided along with each answer, as well as appropriate references where relevant.
Ghrelin alleviates intestinal ischemia–reperfusion injury by activating the GHSR‐1α/Sirt1/FOXO1 pathway
Authors: Liao Shi‐shi , Zhang Le‐le , Zhang Yi‐guo , Luo Jie , Kadier Tulanisa , Ding Ke , Chen Rong , Meng Qing‐tao
Published: May 2024

Ischemia–reperfusion (IR) injury is primarily characterized by the restoration of blood flow perfusion and oxygen supply to ischemic tissue and organs, but it paradoxically leads to tissue injury aggravation. IR injury is a challenging pathophysiological process that is difficult to avoid clinically and frequently occurs during organ transplantation, surgery, shock resuscitation, and other processes. The major causes of IR injury include increased levels of free radicals, calcium overload, oxidative stress, and excessive inflammatory response. Ghrelin is a newly discovered brain‐intestinal peptide with anti‐inflammatory and antiapoptotic effects that improve blood supply. The role and mechanism of ghrelin in intestinal ischemia–reperfusion (IIR) injury remain unclear. We hypothesized that ghrelin could attenuate IIR‐induced oxidative stress and apoptosis. To investigate this, we established IIR by using a non‐invasive arterial clip to clamp the root of the superior mesenteric artery (SMA) in mice. Ghrelin was injected intraperitoneally at a dose of 50 μg/kg 20 min before IIR surgery, and [D‐Lys3]‐GHRP‐6 was injected intraperitoneally at a dose of 12 nmol/kg 20 min before ghrelin injection. We mimicked the IIR process with hypoxia‐reoxygenation (HR) in Caco‐2 cells, which are similar to intestinal epithelial cells in structure and biochemistry. Our results showed that ghrelin inhibited IIR/HR‐induced oxidative stress and apoptosis by activating GHSR‐1α. Moreover, it was found that ghrelin activated the GHSR‐1α/Sirt1/FOXO1 signaling pathway. We further inhibited Sirt1 and found that Sirt1 was critical for ghrelin‐mediated mitigation of IIR/HR injury. Overall, our data suggest that pretreatment with ghrelin reduces oxidative stress and apoptosis to attenuate IIR/HR injury by binding with GHSR‐1α to further activate Sirt1.
Exploring Decisional Conflict Experienced by Individuals Considering Metoidioplasty and Phalloplasty Gender-affirming Surgery
Authors: Otto-Moudry Reade , Kinney Linda M. , Butcher Rebecca L. , Blasdel Gaines , Brown Lee K. , Elwyn Glyn , Myers Jeremy B. , Turco John H. , Nigriny John F. , Moses Rachel A.
Published: May 2024

Background:

Metoidioplasty and phalloplasty gender-affirming surgery (MaPGAS) is increasingly performed and requires patients to make complex decisions that may lead to decisional uncertainty. This study aimed to evaluate decisional conflict in individuals considering MaPGAS.

Methods:

We administered a cross-sectional survey to adult participants assigned female sex at birth and considering MaPGAS, recruited via social media platforms and community health centers. We collected data on demographics, medical and surgical history, MaPGAS type considered, and the Decisional Conflict Scale (DCS). DCS scores range from 0 to 100 (>37.5 indicates greater decisional conflict). Demographic characteristics and DCS scores were compared between subgroups, using descriptive and chi-square statistics. Participants commented on MaPGAS uncertainty, and their comments were evaluated and thematically analyzed.

Results:

Responses from 264 participants were analyzed: mean age 29 years; 64% (n = 168) trans men, 80% (n = 210) White, 78% (n = 206) nonrural, 45% (n = 120) privately insured, 56% (n = 148) had 4 or more years of college, 23% (n = 84) considering metoidioplasty, 24% (n = 87) considering phalloplasty, and 26% (n = 93) considering metoidioplasty and phalloplasty. DCS total scores were significantly higher (39.8; P < 0.001) among those considering both MaPGAS options, as were mean ratings on the Uncertainty subscale [64.1 (SD 25.5; P < 0.001)]. Concerns surrounding complications were the top factor contributing to uncertainty and decisional conflict.

Conclusions:

In a cross-sectional national sample of individuals seeking MaPGAS, decisional uncertainty was the highest for those considering both MaPGAS options compared with metoidioplasty or phalloplasty alone. This suggests this cohort would benefit from focused decision support.
Limbal stem cell therapy
Authors: Bonnet Clemence , Gonzalez Sheyla , Deng Sophie X.
Published: May 2024

Purpose of review

To highlight the progress and future direction of limbal stem cell (LSC) therapies for the treatment of limbal stem cell deficiency (LSCD).

Recent findings

Direct LSC transplantation have demonstrated good long-term outcomes. Cultivated limbal epithelial transplantation (CLET) has been an alternative to treat severe to total LSCD aiming to improve the safety and efficacy of the LSC transplant. A prospective early-stage uncontrolled clinical trial shows the feasibility and safety of CLET manufactured under xenobiotic free conditions. Other cell sources for repopulating of the corneal epithelium such as mesenchymal stem cells (MSCs) and induced pluripotent stem cells are being investigated. The first clinical trials of using MSCs showed short-term results, but long-term efficacy seems to be disappointing. A better understanding of the niche function and regulation of LSC survival and proliferation will lead to the development of medical therapies to rejuvenate the residual LSCs found in a majority of eyes with LSCD in vivo. Prior efforts have been largely focused on improving LSC transplantation. Additional effort should be placed on improving the accuracy of diagnosis and staging of LSCD, and implementing standardized outcome measures which enable comparison of efficacy of different LSCD treatments for different severity of LSCD. The choice of LSCD treatment will be customized based on the severity of LSCD in the future.

New approaches for managing different stages of LSCD are being developed. This concise review summarizes the progresses in LSC therapies for LSCD, underlying mechanisms, limitations, and future areas of development.
Recognizing unique characteristics to create equitable, culturally competent teams
Authors: Stern Robert , Kester Kelly , Engel Jill
Published: May 2024

A new approach to selecting members for an interdisciplinary medical mission trip
Different Frequency and Clinical Role for MTAP Loss in Pleural and Peritoneal Mesothelioma
Authors: Davidson Ben , Holth Arild , Hummel Charlotte , Flatmark Kjersti , Torgunrud Annette
Published: May 2024

The objective of this study was to analyze the expression and prognostic role of methylthioadenosine phosphorylase (MTAP) in mesothelioma. MTAP protein expression by immunohistochemistry was analyzed in 113 mesotheliomas (60 pleural and 53 peritoneal), consisting of 36 effusions and 77 surgical specimens. MTAP expression was fully lost in 38 tumors and partially lost in 8 tumors. Loss of expression was significantly more common in effusions compared with biopsies/surgical resection specimens (20/36 vs. 26/77; P=0.017), and in pleural compared with peritoneal mesotheliomas (35/60 vs. 11/53; P<0.001). MTAP performed less robustly than BAP1 in comparative analysis of 57 tumors previously analyzed for expression of the latter protein (46 vs. 25 cases with loss of expression). In survival analysis for 69 patients with partial clinical data, male gender was significantly associated with shorter overall survival (OS; P=0.042), whereas loss of MTAP was associated with a trend for shorter OS (P=0.058), with no prognostic role for patient age (P=0.379) or anatomic site (P=0.381). The association between loss of MTAP and poor OS became significant when survival analysis was limited to patients with pleural mesothelioma (P=0.018). In conclusion, loss of MTAP expression is more frequent in pleural compared with peritoneal mesothelioma and has limited diagnostic relevance at the latter anatomic site. More frequent loss in effusion specimens suggests a role for this marker in effusion cytology. MTAP loss in pleural mesothelioma is associated with poor survival.
Large and Extensive Multilocular Peritoneal Inclusion Cysts Lack Genomic Alterations and Follow an Indolent Clinical Course Despite Rare Recurrences
Authors: Devins Kyle M. , Baranov Esther , Hung Yin P. , Dickson Brendan C. , Oliva Esther , Deshpande Vikram
Published: May 2024

Peritoneal inclusion cysts (PICs) are unilocular or multilocular cystic lesions lined by bland mesothelial cells. While most are small and localized, rare examples may be large or multifocal with diffuse peritoneal involvement, causing clinical and even pathologic concern for malignancy. We examined 20 PIC, including 8 large solitary and 12 multifocal lesions. Solitary PIC were found in 7 female and 1 male patients ranging from 19 to 55 (median: 37) years. Expanded collagenous (n=2) or edematous (n=1) areas were occasionally seen in the septae, and 1 had microscopic foci of myxoid stroma. Four had hobnail cells, and 1 had minor areas of papillary mesothelial hyperplasia. Multifocal PICs occurred in 9 female and 3 male patients ranging from 26 to 80 (median: 53) years. Three showed extensive associated fibrosis with entrapment of preexisting adipose tissue, 2 had areas resembling granulation tissue, and 3 had scattered foci of myxoid stroma. Hobnail cells were present in 9, papillary mesothelial hyperplasia in 2, entrapped single cells in 1, and 2 had areas resembling adenomatoid tumors. Two of the multifocal PICs had limited local recurrences at 18 and 21 months. No patients died of disease. Clonal alterations were not identified in any of the tested PICs (mutational and fusion analysis in 5, chromosomal microarray in 1). Despite limited local recurrences, we demonstrate that even large and multifocal PICs may lack identifiable genomic alterations and are associated with benign outcomes.
Decoding huge phage diversity: a taxonomic classification of Lak megaphages
Authors: Cook Ryan , Crisci Marco A. , Pye Hannah V. , Telatin Andrea , Adriaenssens Evelien M. , Santini Joanne M.
Published: May 2024

High-throughput sequencing for uncultivated viruses has accelerated the understanding of global viral diversity and uncovered viral genomes substantially larger than any that have so far been cultured. Notably, the Lak phages are an enigmatic group of viruses that present some of the largest known phage genomes identified in human and animal microbiomes, and are dissimilar to any cultivated viruses. Despite the wealth of viral diversity that exists within sequencing datasets, uncultivated viruses have rarely been used for taxonomic classification. We investigated the evolutionary relationships of 23 Lak phages and propose a taxonomy for their classification. Predicted protein analysis revealed the Lak phages formed a deeply branching monophyletic clade within the class Caudoviricetes which contained no other phage genomes. One of the interesting features of this clade is that all current members are characterised by an alternative genetic code. We propose the Lak phages belong to a new order, the ‘Grandevirales’. Protein and nucleotide-based analyses support the creation of two families, three sub-families, and four genera within the order ‘Grandevirales’. We anticipate that the proposed taxonomy of Lak megaphages will simplify the future classification of related viral genomes as they are uncovered. Continued efforts to classify divergent viruses are crucial to aid common analyses of viral genomes and metagenomes.
Bioenergetics of human spermatozoa in patients with testicular germ cell tumour
Authors: Simonik Ondrej , Bryndova Barbora , Sur Vishma Pratap , Ded Lukas , Cockova Zuzana , Benda Ales , Qasemi Maryam , Pecina Petr , Pecinova Alena , Spevakova Daniela , Hradec Tomas , Skrobanek Pavel , Ezrova Zuzana , Kratka Zuzana , Kren Radomir , Jeseta Michal , Boublikova Ludmila , Zamecnik Libor , Büchler Tomas , Neuzil Jiri , Postlerova Pavla , Komrskova Katerina
Published: May 2024

In testicular germ cell tumour (TGCT) patients, sperm cryopreservation prior to anti-cancer treatment represents the main fertility preservation approach. However, it is associated with low sperm recovery rate after thawing. Since sperm is a high-energy demanding cell, which is supplied by glycolysis and oxidative phosphorylation (OXPHOS), mitochondrial dysfunctionality can directly result in sperm anomalies. In this study, we investigated the bioenergetic pattern of cryopreserved sperm of TGCT patients in comparison with normozoospermic samples using two state-of-the-art methods; the Extracellular Flux Analyzer (XF Analyzer) and Two-Photon Fluorescence Lifetime imaging (2P-FLIM), in order to assess the contributions of OXPHOS and glycolysis to energy provision. A novel protocol for combined measurement of OXPHOS (Oxygen Consumption Rate – OCR) and glycolysis (Extracellular Acidification Rate – ECAR) using the XF Analyzer was developed together with a unique customized AI-based approach for semiautomated processing of 2P-FLIM images. Our study delivers optimized Low-HEPES modified Human Tubal Fluid media (mHTF) for sperm handling during pre-analytical and analytical phases to maintain sperm physiological parameters and optimal OCR, equivalent of OXPHOS. The negative effect of cryopreservation was signified by deterioration of both bioenergetic pathways represented by modified OCR and ECAR curves and the derived parameters. This was true for normozoospermic as well as TGCT samples, which showed even a stronger damage within the respiratory chain compared to the level of glycolytic activity impairment. The impact of cryopreservation and pathology are supported by 2P-FLIM analysis showing a significant decrease in bound NADH in contrast to unbound NAD(P)H which reflects decreased metabolic activity in samples from TGCT patients. Our study provides novel insight into the impact of TGCT on sperm bioenergetics and delivers a verified protocol to be used for assessment of human sperm metabolic activity, which can be a valuable tool for further research and clinical andrology.

Abstract Figure
Genealogical asymmetry under the IM model and a two-taxon test for gene flow
Authors: Mackintosh Alexander , Setter Derek
Published: May 2024

Methods for detecting gene flow between populations often rely on asymmetry in the average length of particular genealogical branches, with the ABBA-BABA test being a well known example. Currently, asymmetry-based methods cannot be applied to a pair of populations and such analyses are instead performed using model-based methods. Here we investigate genealogical asymmetry under a two-population isolation-migration model. We focus on genealogies where the first coalescence event is between lineages sampled from different populations, as the external branches of these genealogies have equal expected length as long as there is no post-divergence gene flow. We show that unidirectional gene flow breaks this symmetry and results in the recipient population having longer external branches. We derive expectations for the probability of this genealogical asymmetry under the isolation-migration model and propose a simple statistic (Am) to detect it from genome sequence data.Amprovides a two-taxon test for gene flow that only requires a single unphased diploid genome from each population, with no outgroup information. We use analytic expectations and coalescent simulations to explore how recombination, unequal effective population sizes and bidirectional gene flow influenceAmand find that the statistic provides unambiguous evidence for gene flow under a continent-island history. We estimateAmfor genome sequence data fromHeliconiusbutterflies andOdocoileusdeer, generating results consistent with previous model-based analyses. Our work highlights a signal of gene flow overlooked to date and provides a method that complements existing approaches for investigating the demographic history of recently diverged populations.
Operating principles of interconnected feedback loops underlying cell fate decisions
Authors: Hegade Abhiram , Rashid Mubasher
Published: May 2024

Interconnected feedback loops are prevalent across biological mechanisms including cell fate transitions enabled by epigenetic mechanisms driving phenotypic plasticity of carcinoma cells. However, the operating principles of these networks remain largely unexplored. Here, we identify numerous coupled feedback loops driving phenotypic transition in cancers and CD4+ T cell lineage decisions. These networks have three generic structures, serial type (ST), hub type (HT), and cyclic, which we discover to be the hallmarks of lower- and higher-order dynamics. While networks having ST or cyclic topology exhibit multiple alternative states, those having HT topology enable at most two states. We also show that topologically distinct networks with equal node or loop count exhibit different steady-state distributions, highlighting the crucial influence of network structure on emergent dynamics. Irrespective of the topology, networks with autoregulated genes exhibit multiple states thereby “liberating” network dynamics from absolute topological control. Finally, we identify precise gene interaction targets to restrict the multistable network dynamics to a unique state. Our results thus reveal design principles of coupled feedback loops in enabling multiple alternative states while also identifying perturbations to restrict it. These findings can serve as crucial inputs to comprehend multi-fate decisions of cells and phenotypic plasticity in carcinomas.
Responses of chlorophyll fluorescence to CO2elimination as an indicator of Crassulacean acid metabolism photosynthesis
Authors: Bekki Sae , Suetsugu Kenji , Kobayashi Koichi
Published: May 2024

Crassulacean acid metabolism (CAM) is found in a wide variety of vascular plant species, mainly those inhabiting water-limited environments. Identifying and characterizing diverse CAM species enhances our understanding of the physiological, ecological, and evolutionary significance of CAM photosynthesis. In this study, we examined the effect of CO2elimination on chlorophyll fluorescence-based photosynthetic parameters in two constitutive CAMKalanchoespecies and six orchids. In CAM-performingKalanchoespecies, the effective quantum yield of photosystem II showed no change in response to CO2elimination during the daytime but decreased with CO2elimination at dusk. We applied this method to reveal the photosynthetic mode of epiphytic orchids and found thatGastrochilus japonicus,Oberonia japonica, andBulbophyllum inconspicuum, but notBulbophyllum drymoglossum, are constitutive CAM. AlthoughB. drymoglossumhad relatively high malate content in leaves, they did not depend on it to perform photosynthesis even under water deficient or high light conditions. Anatomical comparisons revealed a notable difference in the leaf structure betweenB. drymoglossumandB. inconspicuum;B. drymoglossumleaves possess the large water storage tissue internally, unlikeB. inconspicuumleaves, which develop pseudobulbs. Our data propose a novel approach to identify and characterize CAM plants without labor-intensive experimental procedures.

Highlight

Responses of chlorophyll fluorescence-based photosynthetic parameters to CO2elimination differ between Crassulacean acid metabolism (CAM) and C3metabolism, proposing a novel approach to identify and characterize CAM plants.
Using an agent based model to inform sampling design for animal social network analysis
Authors: Kaur Prabhleen , Ciuti Simone , Salter-Townshend Michael , Farine Damien
Published: May 2024

Producing accurate and reliable inference from animal social network analysis depends on the sampling strategy during data collection. An increasing number of studies now use large-scale deployment of GPS tags to collect data on social behaviour. However, these can rarely capture whole populations or sample at very high frequencies. To date, little guidance exists when makingpriordecisions about how to maximise sampling effort to ensure that the data collected can be used to construct reliable social networks. We use a simulation-based approach to generate a functional understanding of how the accuracy of various network metrics is affected by decisions along three fundamental axes of sampling effort: coverage, frequency and duration. Researchers often face trade-offs between these three sampling axes, for example due to resource limitations, and thus we identify which axes need to be prioritised as well as the effectiveness of different deployment and analytical strategies. We found that the sampling level across the three axes has different consequences depending on the social network metrics that are estimated. For example, global metrics are more sensitive than local metrics to the proportion of the population tracked, and that among local metrics some are more sensitive to sampling duration than others. Our research demonstrates the importance of establishing an optimal sampling configuration for drawing relevant and robust inferences, and presents a range of practical advice for designing GPS based sampling strategies in accordance with the research objectives.
Mapping and Engineering Antibody-Antigen Interaction Landscapes for Systematic Affinity Enhancement
Authors: Chun Changju , Sohn Byeong-Kwon , Jo Ji Hye , Lee Jiyu , Yu Booyoung , Baek Minkyung , Yoon Tae-Young
Published: May 2024

Antibodies, crucial in adaptive immunity, recognize antigens through specific interactions facilitated by Complementarity Determining Regions (CDRs), diversified via Variable-Diversity-Joining (VDJ) recombination. Traditional antibody development, limited by the scope of animal models and phage display libraries, captures a fraction of the potential antibody-antigen interactions. This underscores a gap in understanding antibody specificity and the relationship between antibody sequence and binding affinity. Here we introduce an approach using the Single-Protein Interaction Detection (SPID) platform, repurposed to systematically map local landscapes of antibody-antigen interactions with unprecedented depth and speed, aiming to rival the precision of methods like Surface Plasmon Resonance (SPR) and Bio-Layer Interferometry (BLI) while significantly boosting throughput. By editing CDR sequences and measuring effects on dissociation constants, we elucidated pathways for optimizing antibody affinity, enhancing predictive models for interactions. Our findings demonstrate the capability of the SPID platform to characterize thousands of variants weekly, offering a deeper insight into antibody-antigen interactions and advancing antibody development with finely-tuned affinities.
Association between mosaic loss of chromosome Y and pulmonary fibrosis susceptibility and severity
Authors: Wang Dapeng , Hadad Niran , Moss Samuel , Lopez-Jimenez Elena , Johnson Simon R. , Maher Toby M , Molyneaux Philip L , Zhao Yajie , Perry John R. B. , Wolters Paul J. , Kropski Jonathan A. , Jenkins R Gisli , Banovich Nicholas E. , Stewart Iain
Published: May 2024

Background

Pulmonary fibrosis (PF) is a rare lung disease with diverse pathogenesis and multiple interconnected underlying biological mechanisms. Mosaic loss of chromosome Y (mLOY) is one of the most common forms of acquired chromosome abnormality in men, which has been reported to be associated with increased risk of various chronic progressive diseases including fibrotic diseases. However, the exact role of mLOY in the development of PF remains elusive and to be elucidated.

Methods

We adopted three complementary approaches to explore the role of mLOY in the pathogenesis of PF. We used copy number on chromosome Y to estimate mLOY comparing patients in PROFILE and gnomAD cohorts and between cases and control patients from the GE100KGP cohort. Correlation of mLOY with demographic and clinical variables was tested using patients from PROFILE cohort. Lung single-cell transcriptomic data were analysed to assess the cell types implicated in mLOY. We performed Mendelian randomisation to examine the causal relationship between mLOY, IPF, and telomere length.

Results

The genetic analysis suggests that mLOY is found in PF from both case cohorts but when compared with an age matched population the effect is minimal (P = 0.0032). mLOY is related to age (P = 0.00021) and shorter telomere length (P = 0.0081) rather than PF severity or progression. Single-cell analysis indicates that mLOY appears to be found primarily in immune cells and appears to be related to presence and severity of fibrosis. Mendelian randomisation demonstrates that mLOY is not on the causal pathway for IPF, but partial evidence supports that telomere shortening is on the causal pathway for mLOY.

Conclusion

Our study confirms the existence of mLOY in PF patients and suggests that mLOY is not a major driver of IPF. The combined evidence suggests a triangulation model where telomere shortening leads to both IPF and mLOY.
A discrete character evolution model for phylogenetic comparative biology with Γ-distributed rate heterogeneity among branches of the tree
Authors: Revell Liam J. , Harmon Luke J.
Published: May 2024

Phylogenetic comparative methods are now widely used to measure trait evolution on the tree of life. Often these methods involve fitting an explicit model of character evolution to trait data and then comparing the explanatory power of this model to alternative scenarios. In this article, we present a new model for discrete trait evolution in which the rate of character change in the tree varies from edge (i.e., “branch”) to edge of the phylogeny according to a discretized Γ distribution. When the edge-wise rates of evolution are, in fact, Γ-distributed, we show via simulation that this model can be used to reliably estimate the shape parameter (α) of the distribution of rate variation among edges. We also describe how our model can be employed in ancestral state reconstruction, and demonstrate via simulation how doing so will tend to increase the accuracy of our estimated states when the generating edge rates are Γ-distributed. We discuss how marginal edge rates are estimated under the model, and apply our method to a real dataset of digit number in squamate reptiles, modified from Brandley et al. (2008).
JUNB O-GlcNAcylation-mediated promoter accessibility of metabolic genes modulates distinct epithelial lineage in pulmonary fibrosis
Authors: Bammert Marie-Therese , Ansari Meshal , Haag Leoni , Ahmad Zuhdi , Schröder Victoria , Birch Joseph , Santacruz Diana , Rust Werner , Viollet Coralie , Strobel Benjamin , Dick Alec , Gantner Florian , Schlüter Holger , Ramirez Fidel , Lizé Muriel , Thomas Matthew J. , Le Huy Q.
Published: May 2024

Idiopathic pulmonary fibrosis (IPF) is a lethal disease with substantial unmet medical needs. While aberrant epithelial remodelling is a key factor in IPF progression, the molecular mechanisms behind this process remain elusive. Using a patient-derived 3D distal airway epithelial organoid model, we successfully recapitulate important IPF features, including the emergence of aberrant KRT5+/COL1A1+ basal cells and a metabolic shift towards increased O-linked β-N-acetylglucosamine (O-GlcNAc) levels. Consistent with this, single-cell analysis of accessible chromatin reveals an increased chromatin accessibility in these aberrant basal cells, particularly at JUNB motif-enriched promoter regions of metabolic genes. O-GlcNAcylation shapes JUNB function and promotes a pro-fibrotic response to chronic injury, leading to aberrant epithelial remodelling. Site-specific deletion of O-GlcNAcylation on JUNB attenuates the metaplastic differentiation of basal cells, thereby aiding in the restoration of the alveolar lineage. Together, these data establish a novel link between metabolic dysregulation, mediated by the O-GlcNAc-JUNB axis, and bronchiolization in IPF, offering new therapeutic strategies to treat this fatal disease.
UsingCupriavidus necatorH16 to provide a roadmap for increasing electroporation efficiency in non-model bacteria
Authors: Vajente Matteo , Clerici Riccardo , Ballerstedt Hendrik , Blank Lars M. , Schmidt Sandy
Published: May 2024

Bacteria are a treasure trove of metabolic reactions, but most industrial biotechnology applications rely on a limited set of established host organisms. In contrast, adopting non-model bacteria for the production of various chemicals of interest is often hampered by their limited genetic amenability coupled with their low transformation efficiency. In this study, we propose a series of steps that can be taken to increase electroporation efficiency in non-model bacteria. As a test strain, we useCupriavidus necatorH16, a lithoautotrophic bacterium that has been engineered to produce a wide range of products from CO2and hydrogen. However, its low electroporation efficiency hinders the high-throughput genetic modifications required to developC. necatorinto an industrially relevant host organism. First, we propose a species-independent technique based on natively methylated DNA and Golden Gate assembly to increase one-pot cloning and electroporation efficiency by 70-fold. Second, bioinformatic tools were used to predict defense systems and develop a restriction avoidance strategy that was used to introduce suicide plasmids by electroporation to obtain a domesticated strain. The results are discussed in the context of metabolic engineering of non-model bacteria.

TABLE OF CONTENT
Protamine 2 Deficiency Results In Septin 12 Abnormalities
Authors: Sanovec Ondrej , Frolikova Michaela , Kraus Veronika , Vondrakova Jana , Qasemi Maryam , Spevakova Daniela , Simonik Ondrej , Moritz Lindsay , Caswell Drew Lewis , Liska Frantisek , Ded Lukas , Cerny Jiri , Avidor-Reiss Tomer , Hammoud Saher Sue , Schorle Hubert , Postlerova Pavla , Steger Klaus , Komrskova Katerina
Published: May 2024

There is a well-established link between abnormal sperm chromatin states and poor motility, however, how these two processes are interdependent is unknown. Here, we identified a possible mechanistic insight by showing that Protamine 2, a nuclear DNA packaging protein in sperm, directly interacts with cytoskeletal protein Septin 12, which is associated with sperm motility. Septin 12 has several isoforms, and we show, that in thePrm2-/-sperm, the short one (Mw 36 kDa) is mislocalized, while two long isoforms (Mw 40 and 41 kDa) are unexpectedly lost inPrm2-/-sperm chromatin-bound protein fractions. Septin 12 co-immunoprecipitated with Protamine 2 in the testicular cell lysate of WT mice and with Lamin B1/B2/B3 in co-transfected HEK cells despite we did not observe changes in Lamin B2/B3 protein or SUN4 expression inPrm2-/-testes. Furthermore, thePrm2-/-sperm have on average a smaller sperm nucleus and aberrant acrosome biogenesis. In humans, patients with low sperm motility (asthenozoospermia) have imbalanced histone– protamine 1/2 ratio and modified levels of cytoskeletal proteins. We detected retained Septin 12 isoforms (Mw 40 and 41 kDa) in the sperm membrane, chromatin-bound and tubulin/mitochondria protein fractions, which was not true for healthy normozoospermic men. In conclusion, our findings expand the current knowledge regarding the connection between Protamine 2 and Septin 12 expression and localization, resulting in low sperm motility and morphological abnormalities.
The Latent Aging of Cells
Authors: Niimi Peter , Gould Victoria , Thrush-Evensen Kyra , Levine Morgan E.
Published: May 2024

As epigenetic clocks have evolved from powerful estimators of chronological aging to predictors of mortality and disease risk, it begs the question of what role DNA methylation plays in the aging process. We hypothesize that while it has the potential to serve as an informative biomarker, DNA methylation could also be a key to understanding the biology entangled between aging, (de)differentiation, and epigenetic reprogramming. Here we use an unsupervised approach to analyze time associated DNA methylation from bothin vivoandin vitrosamples to measure an underlying signal that ties these phenomena together. We identify a methylation pattern shared across all three, as well as a signal that tracks aging in tissues but appears refractory to reprogramming, suggesting that aging and reprogramming may not be fully mirrored processes.
Branched chain α-ketoacids aerobically activate HIF1α signaling in vascular cells
Authors: Xiao Wusheng , Shrimali Nishith , Oldham William M. , Clish Clary B. , He Huamei , Wong Samantha J. , Wertheim Bradley M. , Arons Elena , Haigis Marcia C. , Leopold Jane A. , Loscalzo Joseph
Published: May 2024

Hypoxia-inducible factor 1α (HIF1α) is a master regulator of numerous biological processes under low oxygen tensions. Yet, the mechanisms and biological consequences of aerobic HIF1α activation by intrinsic factors, particularly in primary cells remain elusive. Here, we show that HIF1α signaling is activated in several human primary vascular cells under ambient oxygen tensions, and in vascular smooth muscle cells (VSMCs) of normal human lung tissue, which contributed to a relative resistance to further enhancement of glycolytic activity in hypoxia. Mechanistically, aerobic HIFα activation is mediated by paracrine secretion of three branched chain α-ketoacids (BCKAs), which suppress prolyl hydroxylase domain-containing protein 2 (PHD2) activityviadirect inhibition andvialactate dehydrogenase A (LDHA)-mediated generation of L-2-hydroxyglutarate (L2HG). Metabolic dysfunction induced by BCKAs was observed in the lungs of rats with pulmonary arterial hypertension (PAH) and in pulmonary artery smooth muscle cells (PASMCs) from idiopathic PAH patients. BCKA supplementation stimulated glycolytic activity and promoted a phenotypic switch to the synthetic phenotype in PASMCs of normal and PAH subjects. In summary, we identify BCKAs as novel signaling metabolites that activate HIF1α signaling in normoxia and that the BCKA-HIF1α pathway modulates VSMC function and may be relevant to pulmonary vascular pathobiology.
CENP-C-Mis12 complex establishes a regulatory loop through Aurora B for chromosome segregation
Authors: Kong Weixia , Hara Masatoshi , Tokunaga Yurika , Okumura Kazuhiro , Hirano Yasuhiro , Miao Jiahang , Takenoshita Yusuke , Hashimoto Masakazu , Sasaki Hiroshi , Fujimori Toshihiko , Wakabayashi Yuichi , Fukagawa Tatsuo
Published: May 2024

Establishing the correct kinetochore-microtubule attachment is crucial for faithful chromosome segregation. The kinetochore has various regulatory mechanisms for establishing correct bipolar attachment. However, how the regulations are coupled is not fully understood. Here, we demonstrate a regulatory loop between the kinetochore protein CENP-C and Aurora B kinase, which is critical for the error correction of kinetochore-microtubule attachment. This regulatory loop is mediated through the binding of CENP-C to the outer kinetochore Mis12 complex (Mis12C). Although the Mis12C binding region of CENP-C is dispensable for mouse development and proliferation in human RPE-1 cells, those cells lacking this region display increased mitotic defects. The CENP-C-Mis12C interaction facilitates the centromeric recruitment of Aurora B and the mitotic error correction in human cells. Given that Aurora B reinforces the CENP-C-Mis12C interaction, our findings reveal a positive regulatory loop between Aurora B recruitment and the CENP-C-Mis12C interaction, which ensures chromosome bi-orientation for accurate chromosome segregation.
Fabrication, evolution, and mutual conversion of D-fucose-activatable and -repressible acetyltransferase upon mutations
Authors: Yanai Yuki , Tsukada Miyu , Kimura Yuki , Umeno Daisuke
Published: May 2024

The fusion of different proteins can result in the linkage-dependent emergence of molecular switches. In cases where allosteric regulation is designed between the input and output modules of fusion proteins, it is hard to predict whether on-switching or off-switching will occur. However, binding-induced folding, a non-allosteric molecular switch mechanism, has the potential to quickly establish a mutually regulatory relationship between the two fused proteins, in the way whether on-switching or off-switching will occur would be predictable. We inserted chloramphenicol acetyltransferase (CAT) fromE. coliinto a loop of a D-fucose-responsive mutant of transcription factor AraC, using linker libraries with various lengths. We found that on-switches tend to emerge when two proteins are fused with a small pitch gap at the junction, while fusion designs with a large pitch gap result in the frequent emergence of off-switches. Both types of switches rapidly evolved their switching efficiency upon mutations, establishing the D-fucose-on and -off regulation of CAT activity without disrupting the D-fucose-inducible logic of AraC function. To our surprise, both one-input/two-output split gates thus obtained could be easily inter-converted upon mutations. Through mutations, proteins not only frequently acquire properties as binding-induced folders, but also rapidly establish and evolve a mutual regulatory relationship with unrelated fusion partners, as well as transform their regulatory logic.
AAV Capsid Screening for Translational Pig Research Using a Mouse Xenograft Liver Model
Authors: Willimann Melanie , Tiyaboonchai Amita , Adachi Kei , Li Bin , Waldburger Lea , Nakai Hiroyuki , Grompe Markus , Thöny Beat
Published: May 2024

In gene therapy, delivery vectors are a key component for successful gene delivery and safety, based on which adeno-associated viruses (AAVs) gained popularity in particular for the liver, but also for other organs. Traditionally, rodents have been used as animal models to develop and optimize treatments, but species and organ specific tropism of AAV desire large animal models more closely related to humans for preclinical in-depth studies. Relevant AAV variants with the potential for clinical translation in liver gene therapy were previously evolvedin vivoin a xenogeneic mouse model transplanted with human hepatocytes. Here, we selected and evaluated efficient AAV capsids using chimeric mice with a >90% xenografted pig hepatocytes. The pig is a valuable preclinical model for therapy studies due to its anatomic and immunological similarities to humans. Using a DNA-barcoded recombinant AAV library containing 47 different capsids and subsequent Illumina sequencing of barcodes in the AAV vector genome DNA and transcripts in the porcine hepatocytes, we found the AAVLK03 and AAVrh20 capsid to be the most efficient delivery vectors regarding transgene expression in porcine hepatocytes. In attempting to validate these findings with primary porcine hepatocytes, we observed capsid-specific differences in cell entry and transgene expression efficiency where the AAV2, AAVAnc80, and AAVDJ capsids showed superior efficiency to AAVLK03 and AAVrh20. This work highlights intricacies ofin vitrotesting with primary hepatocytes and the requirements for suitable pre-clinical animal models but suggests the chimeric mouse to be a valuable model to predict AAV capsids to transduce porcine hepatocytes efficiently.
Bright New Resources for Syphilis Research: Genetically Encoded Fluorescent Tags forTreponema pallidumand Sf1Ep Cells
Authors: Grillová Linda , Romeis Emily , Lieberman Nicole A. P. , Tantalo Lauren C. , Xu Linda H. , Molini Barbara , Trejos Aldo T. , Lacey George , Goulding David , Thomson Nicholas R. , Greninger Alexander L. , Giacani Lorenzo
Published: May 2024

The recently discovered methodologies to cultivate and genetically manipulateTreponema pallidumsubsp.pallidum(T. pallidum) have significantly helped syphilis research, allowing thein vitroevaluation of antibiotic efficacy, performance of controlled studies to assess differential treponemal gene expression, and generation of loss-of-function mutants to evaluate the contribution of specific genetic loci toT. pallidumvirulence. Building on this progress, we engineered theT. pallidumSS14 strain to express a red-shifted Green Fluorescent Protein (GFP) and Sf1Ep cells to express mCherry and blue fluorescent protein (BFP) for enhanced visualization. These new resources improve microscopy- and cell sorting-based applications forT. pallidum, better capturing the physical interaction between the host and pathogen, among other possibilities. Continued efforts to develop and share new tools and resources are required to help our overall knowledge ofT. pallidumbiology and syphilis pathogenesis reach that of other bacterial pathogens, including spirochetes.

Graphical abstract

By employing genetic engineering,T. pallidumwas modified to express GFP, and Sf1Ep cells to express mCherry on the cytoplasmic membrane and BFP in the nucleus. These new resources for syphilis research will facilitate experimental designs to better define the complex interplay betweenT. pallidumand the host during infection.