bluuebunny/crossref_metadata_2025 huggingface dataset:
Conspicuous shell shape plasticity across lake-stream habitats in a freshwater mussel (Pyganodon grandis)
Authors: Keogh Sean M. , Minerich Ben J. , Ohlman Lindsay M. , Pletta Madeline E. , Scheunemann Anna E. , Schroeder Zoe K. , Secrist Zebulin A. , Franzen Alex J. , Sietman Bernard E. , Simons Andrew M.
Published: November 2023

2.

Hydrodynamic forces and their absence appears to exert differential selection pressure between lake and stream populations, creating a tight fit between organismal phenotypes and their environments. Ecophenotypic variants may be the result from isolated genetic evolution or phenotypic plasticity, where a widespread genotype can produce multiple phenotypes dependent on the environment. Freshwater mussels possess a wide degree of morphological variation that frequently covaries with the environment, making them a good system to understand the mechanisms of ecophenotypic variation across hydrological conditions. We designed a two-year experiment where individuals from the samePyganodon grandismaternal brood (half-full siblings) were reared at a controlled site and four natural sites involving one lake and three streams. At the end of the experiment, shell shape was quantified for recaptured (N=70), wild (N=206), and zoo-reared (N=305) mussels. Analysis of covariance found significant differences in shell shape between rearing sites, particularly between stream and lake habitats, but no shape differences were detected across the three stream sites. At two of the four sites, shell shape of recaptured individuals matched the morphology of wild populations. Genomic sequencing and parentage analysis identified 27 different fathers among recaptured individuals. Yet, no genetic differences were present between stream and lake habitats and there was no effect of parentage on shell shape. Taken together, phenotypic plasticity, over genetic differentiation, is identified as the primary mechanism of shell shape ecophenotypy. Plasticity may be a key adaptation for freshwater mussels and possibly provide a buffer against their imperilment in degraded habitats.

1.

Summary statement

Streamlined and obese freshwater mussel shell shapes in stream-lake environments are developed from the same maternal brood and may reflect adaptations to the presence and absence of streamflow.
Mining the neuroimaging literature
Authors: Dockès Jérôme , Oudyk Kendra , Torabi Mohammad , de la Vega Alejandro I , Poline Jean-Baptiste
Published: November 2023

Automated analysis of the biomedical literature (literature-mining) offers a rich source of insights. However, such analysis requires collecting a large number of articles and extracting and processing their content. This task is often prohibitively difficult and time-consuming. Here, we provide tools to easily collect, process and annotate the biomedical literature. In particular,pubgetis an efficient and reliable command-line tool for downloading articles in bulk from PubMed Central, extracting their contents and meta-data into convenient formats, and extracting and analyzing information such as stereotactic brain coordinates.Labelbuddyis a lightweight local application for annotating text, which facilitates the extraction of complex information or the creation of ground-truth labels to validate automated information extraction methods. Further, we describe repositories where researchers can share their analysis code and their manual annotations in a format that facilitates re-use. These resources can help streamline text-mining and meta-science projects and make text-mining of the biomedical literature more accessible, effective, and reproducible. We describe a typical workflow based on these tools and illustrate it with several example projects.
Behavioral Syndromes in Paper Wasps: links between social and non-social personality inPolistes fuscatus
Authors: Jomaa Fatima W. , Laub Emily C. , Tibbetts Elizabeth A.
Published: November 2023

Although much work has focused on non-social personality traits such as activity, exploration, and neophobia, there is a growing appreciation that social personality traits play an important role in group dynamics, disease transmission, and fitness, and that social personality traits may be linked to non-social personality traits. These relationships are important because behavioral syndromes, defined here as correlated behavioral phenotypes, can constrain evolutionary responses. However, the strength and direction of relationships between social and non-social personality traits remain unclear. In this project, we examine social and non-social personality traits, and the relationships between them, in the paper waspPolistes fuscatus. With a novel assay we identify five personality traits, two non-social (exploration and activity) and three social (aggression, affiliation, and antennation) personality traits. We also find that social and non-social personality traits are phenotypically linked. We find a positive correlation between aggression and activity (rs =0.33) and a negative correlation between affiliation and activity (rs =- 0.35). We also find a positive correlation between exploration and activity. Our work is an important step in understanding how phenotypic linkage between social and non-social behaviors may influence behavioral evolution. As a burgeoning model system for the study of genetic and neurobiological mechanisms of social behavior,Polistes fuscatushas potential to add to this work through exploring the causes and consequences of individual behavioral variation.
Charting the transcriptomic landscape of primary and metastatic cancers in relation to their origin and target normal tissues
Authors: Sanghvi Neel , Calvo-Alcañiz Camilo , Rajagopal Padma S. , Scalera Stefano , Canu Valeria , Sinha Sanju , Schischlik Fiorella , Wang Kun , Madan Sanna , Shulman Eldad , Papanicolau-Sengos Antonios , Blandino Giovanni , Ruppin Eytan , Nair Nishanth Ulhas
Published: November 2023

Metastasis is a leading cause of cancer-related deaths, yet understanding how metastatic tumors adapt from their origin to target tissues is challenging. To address this, we assessed whether primary and metastatic tumors resemble their tissue of origin or target tissue in terms of gene expression. We analyzed gene expression profiles from various cancer types, including single-cell and bulk RNA-seq data, in both paired and unpaired primary and metastatic patient cohorts. We quantified the transcriptomic distances between tumor samples and their normal tissues, revealing that primary tumors are more similar to their tissue of origin, while metastases shift towards the target tissue. Pathway-level analysis highlighted critical transcriptomic changes during metastasis. Notably, primary cancers exhibited higher activity in cancer hallmarks, includingActivating Invasion and Metastasis, compared to metastatic cancers. This comprehensive landscape analysis provides insight into how cancer tumors adapt to their metastatic environments, providing a transcriptome-wide view of the processes involved.
Latitudinal trends in genetic diversity and distinctiveness ofQuercus roburrear edge forest remnants call for new conservation priorities
Authors: Avanzi Camilla , Bagnoli Francesca , Romiti Edoardo , Spanu Ilaria , Tsuda Yoshiaki , Vajana Elia , Vendramin Giovanni Giuseppe , Piotti Andrea
Published: November 2023

Knowledge of the spatial distribution of intraspecific genetic variation is essential for planning conservation actions, designing networks of protected areas, and informing possible assisted migration strategies. Although the Italian peninsula harbours unique genetic variation as a legacy of Quaternary migrations, only sporadic genetic information is available for forest tree species.

Here, we present the first geographically comprehensive genetic characterisation ofQuercus robur, an iconic broadleaved species of European floodplain forests, in an area which acted as a primary glacial refugium for the species. 745 individuals from 25 populations were sampled and genotyped with 16 microsatellite markers. Their genetic structure was assessed through various metrics of diversity and distinctiveness, as well as by Bayesian clustering and multivariate methods. The demographic history of inferred gene pools was evaluated through Approximate Bayesian Computation analysis.

Genetic distinctiveness showed a decline with increasing latitude, while allelic richness reached its peak in central Italy. A south-to-north trend in the complexity of the genetic structure was observed, with peninsular Italy being characterised by intermingled gene pools in contrast to the relative homogeneity exhibited by northern populations. Demographic inference indicated that the southern gene pool has been genetically isolated since the penultimate interglacial, whereas populations from central Italy persisted locally in a mosaic of small refugia during the last glaciation.

Our results brought out the complexity of the genetic structure of forest trees’ populations in southern Europe. At least threeQ. roburrefugia contributed to the genetic layout of extant populations after the last glacial period, but refugial areas were probably even more numerous in central Italy. Such a detailed characterization sheds new light on the priorities to be established for the conservation of highly fragmentedQ. roburpopulations in an area rich in diversified genetic lineages.
Developmental differences in canonical cortical networks: insights from microstructure-informed tractography
Authors: Genc Sila , Schiavi Simona , Chamberland Maxime , Tax Chantal , Raven Erika , Daducci Alessandro , Jones Derek K
Published: November 2023

There is a growing interest in incorporating white matter fibre-specific microstructural properties into structural connectomes to obtain a more quantitative assessment of brain connectivity. In a developmental sample aged 8-18 years, we studied age-related patterns of microstructure-informed network properties locally and globally. First, we computed the diffusion-weighted signal fraction associated with each tractography-reconstructed streamline. Then, we generated microstructure-informed connectomes from diffusion MRI data using the convex optimization modelling for microstructure-informed tractography (COMMIT) approach. Finally, we estimated network characteristics in eight functionally defined networks (visual, somatomotor, dorsal attention, ventral attention, limbic, frontoparietal, default mode and subcortical networks). Our findings reveal that throughout child and adolescent development, global efficiency increases in the visual, somatomotor, and default mode networks, and mean strength increases in the somatomotor and visual networks. Nodes belonging to the dorsal and ventral visual pathways demonstrate the largest age-dependence in local efficiency, supporting previous evidence of protracted maturation of dorsal and ventral visual pathways. Our results provide compelling evidence that there is a prolonged development of visual association cortices.
Left Ventricular Reverse Remodeling After Revascularization and Its Predictive Role for Survival
Authors: Wang Shaoping , Borah Bijan J. , Cheng Shujuan , Li Shiying , Liu Yanci , Gu Xiaoyan , Li Jinhua , Lyu Yi , Liu Jinghua
Published: November 2023

Aims

For patients with ischemic heart failure who underwent revascularization, ejection fraction (EF) improvement is a major predictor of survival benefit. However, the association between left ventricular (LV) remodeling and outcomes has not been well-established. The aim of the study is to investigate the extent of LV remodeling after revascularization and its predictive role for long-term survival.

Methods

Patients with reduced EF (≤40%), who underwent either coronary artery bypass grafting or percutaneous coronary intervention, and had echocardiography reassessment 3 months after revascularization were enrolled in a real-world cohort study (No. ChiCTR2100044378). Patients were categorized into 4 groups according to whether LV end-systolic dimension (LVESD) reduction was ≤7% or >7%, and absolute EF improvement ≤5% or >5%

Results

A total of 923 patients were identified. The percentage of LVESD reduction was 4.5±18.4%. The median follow-up time was 3.4 years, during which 123 patients died. Patients with greater percentage of LVESD reduction had lower risk of all-cause death (hazard ratio [HR] per 1% decrement in LVESD, 0.98; 95% CI, 0.97-0.99;P<.001). A reduction in LVESD of 7.2% was the optimal cutoff value to predict survival. Compared to patients with LVESD reduced and EF improved, 2.11-fold (95% CI, 1.04-4.29), 3.56-fold (95% CI, 1.60-7.91), and 7.54-fold (95% CI, 4.20-13.53) higher mortality were found in LVESD unreduced but EF improved, LVESD reduced but EF unimproved, and LVESD unreduced and EF unimproved group, respectively.

Conclusions

After revascularization among patients with ischemic HF, a reduction in LVESD of 7% signifies clinically relevant revers remodeling. Combination of EF improvement and LVESD reduction might be more clinically precise approach of risk stratification in this population.

Clinical Trial Registration

The name of the registry: Coronary Revascularization in Patients with Ischemic Heart Failure and Prevention of Sudden Cardiac Death.

Registration number: ChiCTR2100044378 (http://www.chictr.org.cn).
Association between triglyceride glucose index and heart failure with preserved ejection fraction in patients with coronary heart disease — a RCSCD-TCM study in China
Authors: Li Zhu , Fan Xiang , Liu Yijia , Yu Lu , He Yuanyuan , Li Lin , Gao Shan , Chen Wei , Yang Rongrong , Yu Chunquan
Published: November 2023

Background

The triglyceride glucose (TyG) index serves as a surrogate indicator of insulin resistance. However, there is limited evidence on the association between the TyG index and heart failure with preserved ejection fraction (HFpEF) in patients with coronary heart disease (CHD).

Methods

The 62,794 CHD patients were included used to analyze the relationship between the TyG index and heart failure (HF) in CHD patients. Of these, 8,606 patients who underwent echocardiography were included to identify different types of HF, including HF with reduced ejection fraction (HFrEF), HF with intermediate-range ejection fraction (HFmrEF), and HFpEF. Logistic regression was used to analyze the relationship between the TyG index and HFpEF in CHD patients. The relationship between the TyG index and HFpEF according to sex, age, blood lipids and blood pressure states were also assessed.

Results

A baseline analysis of CHD patients divided into four groups according to the tertile level of the TyG index showed that there were significant differences in related parameters between the groups. In the multi-adjusted modles, the TyG index was significantly associated with the risk of HFpEF (OR: 1.56; 95% CI: 1.08–1.23). In addition, the TyG index of CHD patients was significantly associated with HFpEF in elderly (> 60 years old) patients (OR:1.19; 95% CI: 1.10-1.48), hypertension (OR:1.17; 95% CI: 1.10-1.25) and dyslipidemia (OR:1.16; 95% CI: 1.08-1.23). The association between the TyG index and HFpEF was not affected by sex. And the association between the TyG index of female and HFpEF was (OR:1.21; 95% CI: 1.10-1.34), which was higher than that of male (OR:1.11; 95% CI: 1.02-1.21).

Conclusions

This study demonstrated a significant association of the TyG index and HFpEF in CHD patients. In this study, the results show that the TyG index was independently associated with HFpEF in hypertension, dyslipidemia, and elder patients (> 60 years old). In addition, the association between the TyG index and HFpEF in CHD patients was higher in female.

Graphical abstract
Desiccated cyanobacteria serve as efficient plasmid DNA carrier in space flight
Authors: Kakouridis Anne , Diamond Spencer , Eng Thomas , Mills Heath J. , Holzhaus Olivia Gámez , Summers Michael L. , Garcia-Pichel Ferran , Mukhopadhyay Aindrila
Published: November 2023

Effective transport of biological systems as cargo during space travel is a critical requirement to use synthetic biology and biomanufacturing in outer space. Bioproduction using microbes will drive the extent to which many human needs can be met in environments with limited resources. Vast repositories of biological parts and strains are available to meet this need, but their on-site availability requires effective transport. Here, we explore an approach that allows DNA plasmids, a ubiquitous synthetic biology part, to be safely transported to the International Space Station and back to the Kennedy Space center, without low-temperature or cryogenic stowage. Our approach relied on the cyanobacteriumNostoc punctiformePC73102, that is naturally tolerant to prolonged desiccation. DesiccatedN. punctiformewas able to carry the non-native pSCR119 plasmid as intracellular cargo safely to space and back. Upon return to the laboratory, the extracted plasmid showed no DNA damage or additional mutations and could be used as intended to transform the model Synbio hostEscherichia colito bestow Kanamycin resistance. This proof-of-concept study provides the foundation for a ruggedized transport host for DNA to environments where there is a need to reduce equipment and infrastructure for biological parts stowage and storage.
The molecular groundplan of male reproduction is partially preserved in parthenogenetic stick insects
Authors: Forni Giobbe , Mantovani Barbara , Mikheyev Alexander S. , Luchetti Andrea
Published: November 2023

After the loss of a trait, theory predicts that the molecular machinery underlying its phenotypic expression should decay. Yet, empirical evidence is contrasting. Here, we test the hypotheses that (1) the molecular ground plan of a lost trait could persist due to pleiotropic effects on other traits and (2) that gene co-expression network architecture could constrain individual gene expression. Our testing ground has been theBacillusstick insect species complex, which contains close relatives that are either bisexual or parthenogenetic. After the identification of genes expressed in male reproductive tissues in a bisexual species, we investigated their gene co-expression network structure in two parthenogenetic species. We found that gene co-expression within the male gonads was preserved in parthenogens. Furthermore, parthenogens did not show relaxed selection on genes upregulated in male gonads in the bisexual species. As these genes were mostly expressed in female gonads, this preservation could be driven by pleiotropic interactions and an ongoing role in female reproduction. Connectivity within the network also played a key role, with highly connected - and more pleiotropic - genes within male gonad also having a gonad-biased expression in parthenogens. Our findings provide novel insight into the mechanisms which could underlie the production of rare males in parthenogenetic lineages; more generally, they provide an example of the cryptic persistence of a lost trait molecular ground plan, driven by gene pleiotropy on other traits and within their co-expression network.

Significance

Loss of traits commonly occurs in diverse lineages of organisms. Here we investigate what happens to genes and regulatory networks associated with these traits, using parthenogenetic insect species as a model. We investigated the fate of genes and gene regulatory networks associated with male gonads in a bisexual species in closely related parthenogens. Rather than showing signs of disuse and decay, they have been partially preserved in parthenogens. More highly pleiotropic genes in male gonads were more likely to have a gonad-biased expression profile in parthenogens. These results highlight the role of pleiotropy in the cryptic persistence of a trait molecular ground plan, despite its phenotypical absence.
Col4a2-eGFPmouse model reveals the molecular and functional dynamics of basement membrane remodelling in hair follicle morphogenesis
Authors: Wuergezhen Duligengaowa , Gindroz Eleonore , Morita Ritsuko , Hashimoto Kei , Abe Takaya , Kiyonari Hiroshi , Fujiwara Hironobu
Published: November 2023

The precisely controlled remodelling of the basement membrane (BM) is considered vital for morphogenesis. However, the molecular and tissue-level dynamics of the BM during morphogenesis and their functional significance remain largely unknown, especially in mammals, due to limited visualization tools. We developed knock-in mouse lines in which the endogenous collagen IV gene (Col4a2) was fused with a fluorescent tag. Through live imaging of developing hair follicles, we revealed a spatial gradient in the turnover rate of COL4A2 that is closely coupled with the BM expansion rate. The proliferation of epithelial progenitors coincided with the increased expansion of their underlying BM. Epithelial progenitors displaced with directionally expanding BM, but did not actively migrate on stable BM. The addition of a matrix metalloproteinase inhibitor delayed the turnover of COL4A2, restrained the expansion of the BM, and induced a directional shift in the division angle of epithelial progenitors, altering the hair follicle morphology. Our findings revealed spatially distinct BM dynamics within the continuous epithelial BM and affirmed their significance in orchestrating the proliferation, movement and fate of progenitor cells, as well as the macro-level shape of organs during development.
Multi-omics analyses of early-onset familial Alzheimer’s disease and Sanfilippo syndrome zebrafish models reveal commonalities in disease mechanisms
Authors: Barthelson Karissa , Protzman Rachael A , Snel Marten F , Hemsley Kim , Lardelli Michael
Published: November 2023

Sanfilippo syndrome (mucopolysaccharidosis type III, MPSIII) causes childhood dementia, while Alzheimer’s disease is the most common type of adult-onset dementia. There is no cure for either of these diseases, and therapeutic options are extremely limited. Increasing evidence suggests commonalities in the pathogenesis of these diseases. However, a direct molecular-level comparison of these diseases has never been performed. Here, we exploited the power of zebrafish reproduction (large families of siblings from single mating events raised together in consistent environments) to conduct sensitive, internally controlled, comparative transcriptome and proteome analyses of zebrafish models of early-onset familial Alzheimer’s disease (EOfAD,psen1Q96_K97del/+) and MPSIIIB (nagluA603fs/A603fs) within single families. We examined larval zebrafish (7 days post fertilisation), representing early disease stages. We also examined the brains of 6-month-old zebrafish, which are approximately equivalent to young adults in humans. We identified substantially more differentially expressed genes and pathways in MPS III zebrafish than in EOfAD-like zebrafish. This is consistent with MPS III being a rapidly progressing and earlier onset form of dementia. Similar changes in expression were detected between the two disease models in gene sets representing extracellular matrix receptor interactions in larvae, and the ribosome and lysosome pathways in 6-month-old adult brains. Cell type-specific changes were detected in MPSIIIB brains at 6 months of age, likely reflecting significant disturbances of oligodendrocyte, neural stem cell, and inflammatory cell functions and/or numbers. Our ‘omics analyses have illuminated similar disease pathways between EOfAD and MPS III indicating where efforts to find mutually effective therapeutic strategies can be targeted.
Protection conferred by intraperitoneal Group AStreptococcusimmunization relies on macrophages and IFN-γ but not on concurrent adaptive immune responses
Authors: Emami Shiva , Westerlund Elsa , Converso Thiago Rojas , Johansson-Lindbom Bengt , Persson Jenny J
Published: November 2023

Group AStreptococcus(GAS;Streptococcus pyogenes) is an important bacterial pathogen estimated to cause over 700 million superficial infections and around 500.000 deaths due to invasive disease or severe post-infection sequelae in the world yearly. In spite of this major impact on society, there is currently no vaccine available against this bacterium. GAS strains can be separated into >200 distinctemm(M)-types, and protective immunity against GAS is believed to in part be dependent on type-specific antibodies. Here, we analyze the nature of protective immunity generated against GAS in a model of intraperitoneal immunization in mice. We demonstrate that multiple immunizations are required for the ability to survive a subsequent lethal challenge, and although significant levels of GAS-specific antibodies are produced, these are redundant for protection. Instead, our data show that the immunization-dependent protection in this model is induced in the absence of B and T cells, is accompanied by an altered cytokine profile upon subsequent infection and requires macrophages and the macrophage-activating cytokine IFN-γ. To our knowledge these findings are the first to suggest that GAS has the ability to induce forms of trained innate immunity. Taken together, the current study reveals a novel mechanism of the innate immune system in response to GAS infections that potentially could be leveraged for future development of effective vaccines.

Author summary

The bacterium Group A Streptococcus (GAS) causes many hundred million infections and around 500.000 deaths in the world every year. GAS can give rise to a wide spectrum of diseases ranging from mild strep throat to life-threatening necrotizing fasciitis (often referred to as “flesh-eating disease”). There is currently no vaccine available for this pathogen, much due to our incomplete knowledge of how the immune system reacts to different GAS infections, what immune responses are in fact required for long-term protection and how these are generated. Here we show that protective immunity arising after immunization through the intraperitoneal (ip) cavity requires multiple injections using heat killed GAS. Surprisingly, although typical adaptive immune responses are activated and generate production of GAS-specific antibodies these are redundant for protection, which instead hinges on macrophages and the cytokine IFN-γ. Our findings suggest that ip GAS immunizations trigger what is known as ‘trained immunity’, where innate immune cells become imprinted to respond with increased efficiency towards subsequent infection. Overall, these observations highlight a previously unknown ability of GAS to induce non-canonical forms of protective immunity, discoveries that may significantly contribute to our thinking about how the immune system reacts to such infections and broaden the scope for future vaccine strategies.
S RNA Intergenic Deletions Drive Viral Interference during Arenavirus Infections
Authors: Hackbart Matthew , López Carolina B.
Published: November 2023

Arenaviruses, a family of negative-sense RNA viruses spread by rodents, are a leading cause of severe hemorrhagic fever in humans. Due to a paucity of antivirals and vaccines for arenaviruses, there is a need to identify new mechanisms for interfering with arenavirus replication. In several negative-sense RNA viruses, natural viral interference results from the production of non-standard viral genomes (nsVGs) that activate the innate immune system and/or compete for essential viral products. Although it is well established that arenaviruses produce strong interfering activities, it is unknown if they produce interfering nsVGs. Here we show that arenaviruses produce deletions within the intergenic region of their Small (S) RNA genome, which prevents the production of viral mRNA and protein. These deletions are more abundant when arenaviruses are grown in high-interfering conditions and are associated with inhibited viral replication. Overall, we found that arenaviruses produce internal deletions within the S RNA intergenic region that are produced by arenaviruses and can block viral replication. These natural arenavirus interfering molecules provide a new target for the generation of antivirals as well as an alternative strategy for producing attenuated arenaviruses for vaccines.

AUTHOR SUMMARY

Arenaviruses are hemorrhagic fever-causing pathogens that infect millions of people a year. There are currently no approved antivirals that target arenaviruses and understanding natural mechanisms that inhibit arenavirus replication is crucial for the development of effective therapeutics. Here, we identify multiple deletions within arenavirus genomes that are associated with the inhibition of viral replication. We show that these deletions prevent viral protein production through the removal of the intergenic region of the viral genome. These deletions were found in all arenaviruses tested in this study representing a novel mechanism for development of new antivirals and vaccines that broadly target the arenavirus family.
Opportunity nest egg: insights on the nutritional ecology, life history and captive management of three species of kiwi (Apteryxspp.) chick from Operation Nest Egg zoo hand-rearing records
Authors: Gray L.J. , Mitchell B.A. , Milner-Bradford I.L. , Keller L. , Bell G. , McGuire K.J. , Travers C.
Published: November 2023

Zoo data collected by keepers while looking after endangered species are increasingly recognised as important scientific resources. As chicks, New Zealand’s threatened kiwi (Apteryxspp.) are subject to the protective conservation programme Operation Nest Egg (ONE), during which growth, developmental and life history data are recorded. We have conducted comparative analyses on hand rearing records from 306 chicks, from Coromandel, Eastern and Western populations of Brown kiwi (A. mantelli), and rowi (A. rowi) and Haast tokoeka (A. australis“Haast”). We analysed chick responses to an old dietvs. a new kiwi diet, introduced in 2017. Both diets are fixed nutrient ratio mixtures. The old diet was high-protein, low-energy, while the new diet is high-fat, high-energy, with better micronutrient levels. We found Coromandel chicks, who originate from the environmentally variable Kūaotunu Peninsula, grow the most efficiently overall on either diet, indicating they may be nutritional generalists. Western and Eastern chicks’ growth efficiency was intermediate, while the South Island species grew the least efficiently on either diet.

Rowi chicks developed the fastest overall on either diet, while Haast tokoeka chicks developed the most slowly, especially on the new diet. Rowi chicks therefore had to eat large volumes of either diet over a short time to maintain their rapid development, while Haast chicks were required to eat large volumes, especially of the new diet, over a protracted developmental period. This situation may have led South Island chicks to over-consume one or another diet component, with likely health consequences. Neither diet was obviously superior for chick wellbeing overall, though the new diet better supported chicks that needed hand feeding. This work demonstrates different genetic populations of kiwi differ in their physiological responses to nutrition. As ONE is ongoing, tailored diets for chicks from each genetic group should be developed, and we present methods to achieve this. In our life history trait analyses, we found chick starting size (hatch mass) did not significantly influence growth efficiency across kiwi genetic group, nor did chick sex. We identified that chicks malpositioned as embryos were more likely to require extended periods of hand feeding, and that Eastern males produce more malpositioned embryos than other populations. Our study shows that effective zoo records can be used to improve captive care, to stimulate future research to refine species management practices, and to explore fundamental questions of life history evolution in wild and captive populations.
Riparian forests shape trophic interactions in detrital stream food webs
Authors: Oester Rebecca , Altermatt Florian , Bruder Andreas
Published: November 2023

Freshwater and terrestrial biodiversity is linked through resource flows. For example, subsidies from the riparian vegetation form the base of food webs in small streams. Despite the key role of detritivores in these food webs, consequences of altered resource availability and riparian vegetation type on their trophic strategies are largely unknown. Therefore, we experimentally tested direct and indirect effects of riparian vegetation type on trophic interactions and dietary imbalances of detritivores. We used stoichiometric and isotopic differences between consumers and resources as functional measures of trophic link strength. Our results show that the lack – compared to the presence – of riparian forests directly affected both stoichiometric and isotopic differences in detrital food webs, yet with diverging patterns between resources and consumers, ultimately leading to aquatic-terrestrial decoupling. Consequently, our findings demonstrate that riparian forests are essential for aquatic food webs by influencing both organisms and interactions networks.
Utilization of a Clark electrode device as a respirometer for small insects: a convincing test on ants allowing to detect discontinuous respiration
Authors: Kervella Maïly , Cansell Céline , Criscuolo François , Bouillaud Frederic
Published: November 2023

Respirometry provides a direct measure of an organism’s respiration, which is a significant component of its metabolic rate. Amongst ants, variations in lifespan between different social castes (such as workers and queens) can be substantial, varying according to the species. As metabolic rate is higher in short-living species, we aimed to establish how metabolic rate and longevity may have coevolved within ant’s casts. As a first methodological step, we validate here the use of a Clark electrode initially design for measuring mitochondrial respiration control pathways, for flow-through oxygen consumption in ant, by comparison with stop flow oxygen consumption and carbon dioxide production utilizing the indirect calorimetry methodology. The global aim is to provide a reliable methodology to conduct accurate comparisons of metabolic rates within and among ant species. As expected, using Clarck electrode entails high time resolution and revealed that queens and workers exhibited discontinuous respiration, with episodes of apnea up to 20 minutes.
Phosphatidic Acid Dependent Recruitment of Microtubule Motors to Spherical Supported Lipid Bilayers forIn-vitroMotility Assays
Authors: Kumar Pankaj , Sanghavi Paulomi , Chaudhury Dwiteeya , Mallik Roop
Published: November 2023

A variety of membrane-bound vesicles are transported by the kinesin and dynein motor proteins respectively towards plus and minus ends of microtubules inside cells. How specific lipids, particularly rare lipids, bind and activate motors on the vesicle membrane and the biological consequences thereof are poorly understood. Here we preparesphericalsupported lipid bilayers (SLBs) consisting of a latex bead enclosed within a membrane that contains phosphatidic acid (PA). When incubated with motor-protein enriched fractions fromDictyosteliumor from Rat brain, PA-coated SLBs exhibit robust motion alongin-vitropolymerized microtubules. We quantify the activity of SLB-bound motors by measuring their force generation against an Optical trap on polarity-labelled microtubules. Such experiments reveal that PA recruits dynein-dynactin fromDictyostelium, but kinesin-1 from rat brain fractions to drive SLB motion. Kinesin-1 is able to dominate over dynein when dynactin, an activator of dynein, is deficient on SLBs. We demonstrate how inhibiting only kinesin can block both kinesin and dynein activity on a cargo, thus providing an explanation for the long-standing “paradox of co-dependence” in the field of intracellular transport. We also find that as the size of a motor-driven SLB increases, the SLB is able to reverse direction more easily along a microtubule. This observation provides clues as to how micron-sized cargoes are efficiently able to navigate the crowded cytoskeletal space inside cells.
Origin, age, and metabolisms of dominant anammox bacteria in the global oxygen deficient zones
Authors: Zhao Rui , Zhang Irene H. , Jayakumar Amal , Ward Bess B. , Babbin Andrew R.
Published: November 2023

Anammox bacteria inhabiting oxygen deficient zones (ODZs) are a major functional group mediating fixed nitrogen loss and thus exerting a critical control on the nitrogen budget in the global ocean. However, the diversity, origin, and broad metabolisms of ODZ anammox bacteria remain unknown. Here we report two novel metagenome-assembled genomes ofScalindua, which represent most, if not all, of the anammox bacteria in the global ODZs. Beyond the core anammox metabolism, both organisms contain cyanase and the more dominant one encodes a urease, indicating ODZ anammox bacteria can utilize cyanate and urea in addition to ammonium. The first ODZScalindualikely derived from the benthos ∼200 million years ago. Compared to benthic strains of the same clade, ODZScalinduauniquely encode genes for urea utilization but lost genes related to growth arrest, flagellum synthesis, and chemotaxis, presumably for adaptation to the anoxic water column.
SARS-CoV-2 infection leads to sustained testicular injury and functional impairments in K18 hACE2 mice
Authors: Giannakopoulos Stefanos , Ward Monika A , Bakse Jackson , Pak Jin , Nerurkar Vivek R , Tallquist Michelle D , Verma Saguna
Published: November 2023

Compromised male reproductive health is one of the symptoms of long COVID with a decrease in male fertility markers including testosterone levels and sperm count for months in recovering patients. However, the long-term impact of SARS-CoV-2 infection on testicular injury and underlying mechanisms remains unknown. We previously demonstrated a disrupted tissue architecture with no evidence of virus replication in the testis during the acute stage of the disease in K18-hACE2 mice. Here, we systematically delineate the consequences of SARS-CoV-2 infection on the testis injury and function both during the acute stage of the disease and up to 4 weeks after infection in survivor K18-hACE2 mice. The gross morphological defects included sloughing of healthy spermatids and spermatocytes into the lumen, lack of lumen, and increase in apoptotic cells that sustained for at least 2 weeks after infection. Testis injury correlated with systemic and testicular inflammation, and infiltration of immune cells in the interstitial space and seminiferous tubules. Transcriptomic analysis identified dysregulation of key pathways of testicular immune homeostasis, spermatogenesis, and cell death at the symptomatic and short-term recovery stages. Further, a significant reduction in testosterone levels was associated with transient reduction in sperm count and mouse fertility. Most of the testicular impairments except testosterone levels were resolved within 4 weeks, which is almost one spermatogenesis cycle in mice. These findings provide much-needed mechanistic insights beyond our current understanding of testicular pathogenesis, suggesting that recovering COVID-19 patients should be closely monitored to rescue the pathophysiological effects on male reproductive health.
Habitual and supplemented prebiotic diets and their links to inflammatory serum markers and hypothalamic microstructure in young, overweight adults: a pre-registered study
Authors: Töws Emmy , Medawar Evelyn , Thieleking Ronja , Beyer Frauke , Stumvoll Michael , Villringer Arno , Witte A. Veronica
Published: November 2023

Background

Prebiotic dietary fiber and related metabolites have been suggested to attenuate low-grade systemic and central inflammation through improving gut-brain axis signaling. We here aimed to test whether habitual or short-term high-dose fiber intake is linked to inflammatory markers in blood and to indicators of central hypothalamic inflammation.

Methods

In total, 59 adults (19 women, aged 28.3 years ± 6.6 SD, mean body mass index, BMI, 27.3 ± 1.5 SD) were included into analyses. Participants completed a food frequency questionnaire, underwent diffusion-weighted magnetic resonance imaging (MRI) at 3 Tesla for provision of mean diffusivity (MD) as a marker of brain tissue inflammation and donated fasting blood. Measurements took place at up to 4 timepoints, i.e. before and after 14 days of supplementary fiber and placebo intake, respectively. High-sensitive C-reactive protein (CRP), tumor-necrosis factor alpha (TNF-α) and interleukin-6 (IL6) were assessed in serum. The study was preregistered athttps://osf.io/uzbav.

Results

Habitual and interventional high-fiber diet was not significantly associated with neither inflammatory markers (|ßintervention|> 0.1, p > 0.32) nor with hypothalamic MD (|ßintervention| = 1.8, p = 0.07) according to linear mixed effects modeling. Male sex and higher body fat mass related to higher CRP. Further, higher BMI was borderline related to lower hypothalamic MD.

Conclusions

In this sample of overweight adults, dietary fiber intake was not related to inflammatory blood markers or hypothalamic microstructure. Instead, sex and body composition were of higher importance for prediction of interindividual differences in markers of (neuro)inflammation.

Significance Statement

Prebiotic dietary fiber has been discussed to lower systemic and central inflammation. While previous studies investigated the effects of fiber on inflammatory blood markers, the knowledge of the effect of fiber on neuroinflammation is limited. Thus, in this pre-registered randomized controlled trial analysis we examined the relationship between dietary fiber intake and inflammatory markers in blood and hypothalamus. 3T MRI and blood markers were assessed before and after high-fiber intake and placebo in 59 adults. In our overweight study sample of 19-42 years old adults, fiber intake had no significant impact on inflammatory markers. The current null findings can inform future nutrition neuroimaging trials and add to the discussion about how diet may affect brain structure and function.
Alzheimer’s Disease cerebrospinal fluid Biomarkers and kidney function in normal and cognitively impaired older adults
Authors: Hajjar Ihab , Neal Reem , Yang Zhiyi , Lah James J.
Published: November 2023

Importance

Recent Alzheimer’s disease (AD) clinical trials have used Cerebrospinal fluid (CSF) biomarker levels for screening and enrollment. Preliminary evidence suggests Alzheimer’s Disease (AD) risk may be related to impaired renal function but the association of variation in levels of commonly used AD biomarkers with kidney function are unknown.

Objective

To investigate the association between estimated glomerular filtration rate (eGFR), CSF levels of AD biomarkers: amyloid beta1–42 (Aβ42), Tau or phosphorylated Tau181 (pTau).

Design, Setting, and Participants

We conducted an analysis using data from participants enrolled in two research protocols at the Goizueta Alzheimer’s Disease Research Center that had simultaneous measurements of serum creatinine at the time of their Cerebrospinal fluid (CSF) collection (N=973). The participants had a mean age of 66.52 years, 23.33% were African American, and 63% were women, with 42.46% having mild cognitive impairment (MCI). The estimated glomerular filtration rate (eGFR) was obtained from chronic kidney disease Epidemiology Collaboration. All participants had similar CSF collection procedures. Aβ42, Tau or pTau were measured on the Luminex ALZBIO platform. General linear models and individual data were used to assess relationships between biomarkers and eGFR.

Results

Lower eGFR was associated with lower Aβ42/Tau ratio (slope= 0.033 units, p<0.0001) and Aβ42 (slope=0.75, p=0.002) and higher Tau (slope= -0.39, p<0.0001) and pTau (slope= -0.13, p=0.0002). Although these associations remained significant after adjusting for cognitive status, we observed interactions between MCI and eGFR. This interaction revealed that the impact of eGFR on AD biomarker levels was more robust in individuals with cognitive impairment (interaction MCI*GFR p-values were 0.005 for Ab42, 0.04 for tau and pTau, and 0.05 for the ratio).

Conclusion

We found a significant association between eGFR with CSF AD-biomarkers that may differ by cognitive status. This suggests that kidney function should be considered both in the context of interpreting AD biomarkers as well as exploring potential systemic factors that may increase risk of AD. Future longitudinal studies need to further explore the impact of kidney function on the pathogenesis of AD and related Biomarkers.

KEY POINTS

Question

Are Cerebrospinal Fluid (CSF)AD-biomarker measurements impacted by kidney function?

Findings

In this analysis of data from 973 individuals who had both cerebrospinal fluid (CSF) AD-biomarkers (Aβ42, Tau, and pTau181) and kidney function measurements, there were significant associations between estimated glomerular filtration rate (eGFR) and measures of CSF AD-biomarkers. These associations were more pronounced in those with cognitive impairment.

Meaning

Kidney function may have a significant impact on AD-biomarker measurements in the CSF, especially in those in the early symptomatic stages of AD.
Prognostic implications of intraventricular conduction disorders for sudden cardiac death in coronary artery disease
Authors: Lahti Roope , Rankinen Jani , Järvensivu-Koivunen Minna , Tynkkynen Juho , Eskola Markku , Nikus Kjell , Hernesniemi Jussi
Published: November 2023

Backround and aims

Prolonged QRS duration (≥ 110 ms) and coronary artery disease are risk factors for sudden cardiac death (SCD). We explored the SCD risk associated with intraventricular conduction disorders – a prolonged QRS duration of 110–119 ms, right bundle branch block (RBBB), left bundle branch block (LBBB), and a nonspecific intraventricular conduction delay (NIVCD) – in patients with acute coronary syndrome (ACS).

Methods

This is a retrospective study of 9,700 consecutive, invasively treated ACS patients with ECGs available for analysis (2007–2018). SCD definition was based on an in-depth review of written medical records and death certificates describing the circumstances leading to the events. Endpoint data were available until December 31, 2021 (no losses to follow-up). The risk associated with conduction disorders was analyzed by calculating subdistribution hazard estimates (deaths due to other causes being considered competing events).

Results

The median follow-up time was 6.8 years (IQR 4.0–10.2), during which 3,420 (35.3%) patients died. SCDs were overrepresented as a cause of death among patients with NIVCD (16.4%) or with a prolonged QRS duration (15.3%) when compared to patients with LBBB (5.3%), RBBB (7.1%), or with a normal QRS duration (10.5%). In an analysis adjusted for age, sex, and cardiac comorbities, NIVCD and a prolonged QRS were significant predictors of SCD (HR 3.00, 2.06– 4.35, P < 0.001; and HR 1.80, 1.37–2.35, P < 0.001, respectively). After adjusting the analysis with left ventricular ejection fraction, NIVCD and a prolonged QRS duration remained as significant risk factors for SCD. LBBB and RBBB did not predict SCD.

Conclusion

The incidence of SCD is significantly higher in patients with NIVCD and a prolonged QRS duration. Approximately 23% of all SCDs occur among these patients.