The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation.

Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomics resources is more urgent than ever due to the increasing threats to this group. Amphibians are one of the most imperiled taxonomic groups, with approximately 41% of species threatened with extinction due to habitat loss, changes in land use patterns, disease, climate change, and their synergistic effects. Amphibian genomics resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, antipredator strategies, and resilience and adaptive responses. They also serve as critical models for understanding widespread genomic characteristics, including evolutionary genome expansions and contractions given they have the largest range in genome sizes of any animal taxon and multiple mechanisms of genetic sex determination. Despite these features, genome sequencing of amphibians has significantly lagged behind that of other vertebrates, primarily due to the challenges of assembling their large, repeat-rich genomes and the relative lack of societal support. The advent of long-read sequencing technologies, along with computational techniques that enhance scaffolding capabilities and streamline computational workload is now enabling the ability to overcome some of these challenges. To promote and accelerate the production and use of amphibian genomics research through international coordination and collaboration, we launched the Amphibian Genomics Consortium (AGC) in early 2023. This burgeoning community already has more than 282 members from 41 countries (6 in Africa, 131 in the Americas, 27 in Asia, 29 in Australasia, and 89 in Europe). The AGC aims to leverage the diverse capabilities of its members to advance genomic resources for amphibians and bridge the implementation gap between biologists, bioinformaticians, and conservation practitioners. Here we evaluate the state of the field of amphibian genomics, highlight previous studies, present challenges to overcome, and outline how the AGC can enable amphibian genomics research to "leap" to the next level.

Amyloid precursor protein induces reactive astrogliosis.

AIM: Astrocytes respond to stressors by acquiring a reactive state characterized by changes in their morphology and function. Molecules underlying reactive astrogliosis, however, remain largely unknown. Given that several studies observed increase in the Amyloid Precursor Protein (APP) in reactive astrocytes, we here test whether APP plays a role in reactive astrogliosis. METHODS: We investigated whether APP instigates reactive astroglios by examining in vitro and in vivo the morphology and function of naive and APP-deficient astrocytes in response to APP and well-established stressors. RESULTS: Overexpression of APP in cultured astrocytes led to remodeling of the intermediate filament network, enhancement of cytokine production, and activation of cellular programs centered around the interferon (IFN) pathway, all signs of reactive astrogliosis. Conversely, APP deletion abrogated remodeling of the intermediate filament network and blunted expression of IFN-stimulated gene products in response to lipopolysaccharide. Following traumatic brain injury (TBI), mouse reactive astrocytes also exhibited an association between APP and IFN, while APP deletion curbed the increase in glial fibrillary acidic protein observed canonically in astrocytes in response to TBI. CONCLUSIONS: The APP thus represents a candidate molecular inducer and regulator of reactive astrogliosis. This finding has implications for understanding pathophysiology of neurodegenerative and other diseases of the nervous system characterized by reactive astrogliosis and opens potential new therapeutic avenues targeting APP and its pathways to modulate reactive astrogliosis.

Understanding conceptus-maternal interactions: what tools do we need to develop?

Communication between the maternal endometrium and developing embryo/conceptus is critical to support successful pregnancy to term. Studying the peri-implantation period of pregnancy is critical as this is when most pregnancy loss occurs in cattle. Our current understanding of these interactions is limited, due to the lack of appropriate in vitro models to assess these interactions. The endometrium is a complex and heterogeneous tissue that is regulated in a transcriptional and translational manner throughout the oestrous cycle. While there are in vitro models to study endometrial function, they are static and 2D in nature or explant models and are limited in how well they recapitulate the in vivo endometrium. Recent developments in organoid systems, microfluidic approaches, extracellular matrix biology, and in silico approaches provide a new opportunity to develop in vitro systems that better model the in vivo scenario. This will allow us to investigate in a more high-throughput manner the fundamental molecular interactions that are required for successful pregnancy in cattle.

Adenosine Deaminase Acting on RNA (ADAR) Enzymes: A Journey from Weird to Wondrous.

ConspectusThe adenosine deaminase acting on RNA (ADAR) enzymes that catalyze the conversion of adenosine to inosine in double-stranded (ds)RNA are evolutionarily conserved and are essential for many biological functions including nervous system function, hematopoiesis, and innate immunity. Initially it was assumed that the wide-ranging biological roles of ADARs are due to inosine in mRNA being read as guanosine by the translational machinery, allowing incomplete RNA editing in a target codon to generate two different proteins from the same primary transcript. In humans, there are approximately seventy-six positions that undergo site-specific editing in tissues at greater than 20% efficiency that result in recoding. Many of these transcripts are expressed in the central nervous system (CNS) and edited by ADAR2. Exploiting mouse genetic models revealed that transgenic mice lacking the gene encoding Adar2 die within 3 weeks of birth. Therefore, the role of ADAR2 in generating protein diversity in the nervous system is clear, but why is ADAR RNA editing activity essential in other biological processes, particularly editing mainly involving ADAR1? ADAR1 edits human transcripts having embedded Alu element inverted repeats (AluIRs), but the link from this activity to innate immunity activation was elusive. Mice lacking the gene encoding Adar1 are embryonically lethal, and a major breakthrough was the discovery that the role of Adar1 in innate immunity is due to its ability to edit such repetitive element inverted repeats which have the ability to form dsRNA in transcripts. The presence of inosine prevents activation of the dsRNA sensor melanoma differentiation-associated protein 5 (Mda5). Thus, inosine helps the cell discriminate self from non-self RNA, acting like a barcode on mRNA. As innate immunity is key to many different biological processes, the basis for this widespread biological role of the ADAR1 enzyme became evident.Our group has been studying ADARs from the outset of research on these enzymes. In this Account, we give a historical perspective, moving from the initial purification of ADAR1 and ADAR2 and cloning of their encoding genes up to the current research focus in the field and what questions still remain to be addressed. We discuss the characterizations of the proteins, their localizations, posttranslational modifications, and dimerization, and how all of these affect their biological activities. Another aspect we explore is the use of mouse and Drosophila genetic models to study ADAR functions and how these were crucial in determining the biological functions of the ADAR proteins. Finally, we describe the severe consequences of rare mutations found in the human genes encoding ADAR1 and ADAR2.

Effect of synbiotics on weight loss and metabolic health in adults with overweight and obesity: A randomized controlled trial.

OBJECTIVE: The study aimed to investigate the effect of synbiotics on body composition and metabolic health in individuals with excessive body weight. METHODS: The 12-week randomized, double-blind, placebo-controlled clinical trial had individuals aged 30 to 60 years with BMI of 25 to 34.9 kg/m2 . In total, 172 participants were randomly allocated to either synbiotic V5 or V7 groups or the placebo group. The primary outcome was change in BMI and body fat percentage. Secondary outcomes were changes in weight, other metabolic health and inflammatory markers, gastrointestinal quality of life, and eating behaviors. RESULTS: The V5 and V7 groups had a significant reduction in BMI (p < 0.0001) from baseline to the end of the study, as opposed to the nonsignificant change in the placebo group (p = 0.0711). This reduction in the V5 and V7 groups was statistically significant when compared individually with the change in the placebo group (p < 0.0001). This corresponded well with the decrease in body weight with V5 and V7 (p < 0.0001). In addition, compared with placebo, the increase in high-density lipoprotein was statistically significant in the V5 (p < 0.0001) and V7 groups (p = 0.0205). A similar trend was observed in the high-sensitivity C-reactive protein levels, with a statistically significant decrease in the V5 (p < 0.0001) and V7 (0.0005) groups. CONCLUSIONS: The study demonstrates that synbiotic V5 and V7 were effective in reducing body weight in individuals with lifestyle modification.

Caecilian Genomes Reveal the Molecular Basis of Adaptation and Convergent Evolution of Limblessness in Snakes and Caecilians.

We present genome sequences for the caecilians Geotrypetes seraphini (3.8 Gb) and Microcaecilia unicolor (4.7 Gb), representatives of a limbless, mostly soil-dwelling amphibian clade with reduced eyes, and unique putatively chemosensory tentacles. More than 69% of both genomes are composed of repeats, with retrotransposons being the most abundant. We identify 1,150 orthogroups that are unique to caecilians and enriched for functions in olfaction and detection of chemical signals. There are 379 orthogroups with signatures of positive selection on caecilian lineages with roles in organ development and morphogenesis, sensory perception, and immunity amongst others. We discover that caecilian genomes are missing the zone of polarizing activity regulatorysequence (ZRS) enhancer of Sonic Hedgehog which is also mutated in snakes. In vivo deletions have shown ZRS is required for limb development in mice, thus, revealing a shared molecular target implicated in the independent evolution of limblessness in snakes and caecilians.

A burst of genomic innovation at the origin of placental mammals mediated embryo implantation.

The origin of embryo implantation in mammals ~148 million years ago was a dramatic shift in reproductive strategy, yet the molecular changes that established mammal implantation are largely unknown. Although progesterone receptor signalling predates the origin of mammals and is highly conserved in, and critical for, successful mammal pregnancy, it alone cannot explain the origin and subsequent diversity of implantation strategies throughout the placental mammal radiation. MiRNAs are known to be flexible and dynamic regulators with a well-established role in the pathophysiology of mammal placenta. We propose that a dynamic core microRNA (miRNA) network originated early in placental mammal evolution, responds to conserved mammal pregnancy cues (e.g. progesterone), and facilitates species-specific responses. Here we identify 13 miRNA gene families that arose at the origin of placental mammals and were subsequently retained in all descendent lineages. The expression of these miRNAs in response to early pregnancy molecules is regulated in a species-specific manner in endometrial epithelia of species with extreme implantation strategies (i.e. bovine and human). Furthermore, this set of miRNAs preferentially target proteins under positive selective pressure on the ancestral eutherian lineage. Discovery of this core embryo implantation toolkit and specifically adapted proteins helps explain the origin and evolution of implantation in mammals.

MicroRNAs emerging coordinate with placental mammals alter pathways in endometrial epithelia important for endometrial function.

We tested the hypothesis that conserved placental mammal-specific microRNAs and their targets facilitate endometrial receptivity to implantation. Expression of miR-340-5p, -542-3p, and -671-5p was regulated by exposure of endometrial epithelial cells to progesterone (10 µg/ml) for 24 h coordinate with 1,713 of their predicted targets. Proteomic analysis of cells transfected with miRNA mimic/inhibitor (48 h: n = 3) revealed 1,745 proteins altered by miR-340-5p (mimic; 1,369, inhibitor; 376) of which 171 were predicted targets and P4-regulated. MiR-542-3p altered 2,353 (mimic; 1,378, inhibitor; 975) 100 which were mirDB predicted, including 46 P4-regulated. MiR-671-5p altered 1,744 proteins (mimic; 1,252, inhibitor; 492) 95 of which were predicted targets and 46 P4-regulated. All miRNAs were detected in luteal phase endometrial biopsies, irrespective of pregnancy outcomes. miR-340-5p expression increased in biopsies from individuals suffering previous and subsequent miscarriage compared to those with subsequent live birth. Dysfunction of these miRNAs and their targets contribute to endometrial-derived recurrent pregnancy loss.

The impact of COVID-19 on select considerations in patients of reproductive age: Brief talking points for pharmacists.

The coronavirus disease 2019 (COVID-19) pandemic has elicited many health concerns, including the impact of the infection and vaccine on reproductive health. Although robust evidence demonstrates the safety of all available COVID-19 vaccines, misinformation and disinformation related to the vaccine continue to circulate. As accessible and essential health care workers, it is crucial that pharmacists are informed of the evidence related to effects of the COVID-19 infection and vaccinations on reproductive health care. Menstrual cycle changes have been noted owing to COVID-19 infection, pandemic stress, and COVID-19 vaccination. COVID-19 infection and vaccination have not been shown to influence female fertility, pregnancy rates, and lactation. The use of exogenous estrogen may further contribute to an increased risk of thromboembolism with COVID-19 infection, and differences in the risk of cerebral venous sinus thrombosis appear to exist between the types of vaccines. The benefits of COVID-19 vaccination outweigh any risks. Shared decision-making is necessary when discussing vaccination with patients. Pharmacists play a vital role in dispelling misinformation and disinformation related to the impact of COVID-19 illness and vaccination on reproductive health care.

Improving Orthologous Signal and Model Fit in Datasets Addressing the Root of the Animal Phylogeny.

There is conflicting evidence as to whether Porifera (sponges) or Ctenophora (comb jellies) comprise the root of the animal phylogeny. Support for either a Porifera-sister or Ctenophore-sister tree has been extensively examined in the context of model selection, taxon sampling, and outgroup selection. The influence of dataset construction is comparatively understudied. We re-examine five animal phylogeny datasets that have supported either root hypothesis using an approach designed to enrich orthologous signal in phylogenomic datasets. We find that many component orthogroups in animal datasets fail to recover major lineages as monophyletic with the exception of Ctenophora, regardless of the supported root. Enriching these datasets to retain orthogroups recovering ≥3 major lineages reduces dataset size by up to 50% while retaining underlying phylogenetic information and taxon sampling. Site-heterogeneous phylogenomic analysis of these enriched datasets recovers both Porifera-sister and Ctenophora-sister positions, even with additional constraints on outgroup sampling. Two datasets which previously supported Ctenophora-sister support Porifera-sister upon enrichment. All enriched datasets display improved model fitness under posterior predictive analysis. While not conclusively rooting animals at either Porifera or Ctenophora, we do see an increase in signal for Porifera-sister and a decrease in signal for Ctenophore-sister when data are filtered for orthologous signal. Our results indicate that dataset size and construction as well as model fit influence animal root inference.

The Health of Women (HOW) Study®: a web-based survey of breast cancer risk factors, diagnosis, and treatment.

PURPOSE: Although improvements in breast cancer detection and treatment have significantly increased survival, important questions related to breast cancer risk, prognosis, and survivorship remain. This brief report describes the Health of Women (HOW) Study® methodology and characterizes the participants who completed the My Health Overview and My Breast Cancer modules. METHODS: The HOW Study® was a collection of cross-sectional, web-based modules designed to survey a large number of participants with and without breast cancer. RESULTS: A total of 42,540 participants completed the My Health Overview module, of whom 13,285 (31.2%) reported a history of breast cancer. The majority of participants were white (94.3%), female (99.5%), married (74.1%), college educated (73.2%), post-menopausal (91.1%), parous (68.8%), and reported breastfeeding their children (56.0%). A total of 11,670 participants reported a history of breast cancer in the My Breast Cancer module. The majority of survivors reported on their primary breast cancer and were diagnosed over the age of 40 years (83.5%), had either Stage I or Stage II breast cancer (63.1%), and were treated with surgery (98.8%), radiation (64.8%), and/or chemotherapy (62.3%). CONCLUSIONS: The HOW Study® provides an innovative framework for collecting large amounts of epidemiological data in an efficient and minimally invasive way. Data are publicly available to researchers upon request. IMPLICATIONS FOR CANCER SURVIVORS: The HOW Study® can be leveraged to answer important questions about survivorship, and researchers are encouraged to utilize this new data source.

High-throughput detection of a large set of viruses and viroids of pome and stone fruit trees by multiplex PCR-based amplicon sequencing.

A comprehensive diagnostic method of known plant viruses and viroids is necessary to provide an accurate phytosanitary status of fruit trees. However, most widely used detection methods have a small limit on either the number of targeted viruses/viroids or the number of samples to be evaluated at a time, hampering the ability to rapidly scale up the test capacity. Here we report that by combining the power of high multiplexing PCR (499 primer pairs) of small amplicons (120-135bp), targeting 27 viruses and 7 viroids of fruit trees, followed by a single high-throughput sequencing (HTS) run, we accurately diagnosed the viruses and viroids on as many as 123 pome and stone fruit tree samples. We compared the accuracy, sensitivity, and reproducibility of this approach and contrast it with other detection methods including HTS of total RNA (RNA-Seq) and individual RT-qPCR for every fruit tree virus or viroid under the study. We argue that this robust and high-throughput cost-effective diagnostic tool will enhance the viral/viroid knowledge of fruit trees while increasing the capacity for large scale diagnostics. This approach can also be adopted for the detection of multiple viruses and viroids in other crops.

The mechanical regulation of RNA binding protein hnRNPC in the failing heart.

Cardiac pathologies are characterized by intense remodeling of the extracellular matrix (ECM) that eventually leads to heart failure. Cardiomyocytes respond to the ensuing biomechanical stress by reexpressing fetal contractile proteins via transcriptional and posttranscriptional processes, such as alternative splicing (AS). Here, we demonstrate that the heterogeneous nuclear ribonucleoprotein C (hnRNPC) is up-regulated and relocates to the sarcomeric Z-disc upon ECM pathological remodeling. We show that this is an active site of localized translation, where the ribonucleoprotein associates with the translation machinery. Alterations in hnRNPC expression, phosphorylation, and localization can be mechanically determined and affect the AS of mRNAs involved in mechanotransduction and cardiovascular diseases, including Hippo pathway effector Yes-associated protein 1. We propose that cardiac ECM remodeling serves as a switch in RNA metabolism by affecting an associated regulatory protein of the spliceosome apparatus. These findings offer new insights on the mechanism of mRNA homeostatic mechanoregulation in pathological conditions.

Birth Control Use and Access Including Pharmacist-Prescribed Contraception Services during COVID-19.

The COVID-19 pandemic influenced health care with effects on contraception access emerging. The study objectives were to analyze pandemic impacts on birth control (BC) use and access; and evaluate perceptions of pharmacist-prescribed BC. A 50-item survey was distributed by 31 Michigan community pharmacies to women aged 18-45 over a three-month period. The survey link was also posted on two websites. 147 surveys were analyzed. Respondents were 29 ± 7.9 years old, primarily white (77%) and straight (81%). Fifty-eight percent of respondents used prescription BC, mostly to prevent pregnancy (84%) with oral pills (76%) being the most common formulation. Some BC users (25%) were worried about BC access and 27% had difficulty taking BC regularly. Half of the respondents (50%) would likely use pharmacist-prescribed BC if available, with advantages being more convenient than visiting a doctor's office (71%) and easier access (69%). The major concern about pharmacist-prescribed BC was women not receiving PAP smears and screenings (61%). Respondents reported high confidence (72%) in pharmacist-prescribed BC and believe it would help prevent unintended pregnancies (69%). Some respondents experienced altered BC use and access. Half of the respondents supported pharmacist-prescribed BC. Pharmacist-prescribed BC could help solve pandemic-related access problems.

Filtering artifactual signal increases support for Xenacoelomorpha and Ambulacraria sister relationship in the animal tree of life.

Conflicting studies place a group of bilaterian invertebrates containing xenoturbellids and acoelomorphs, the Xenacoelomorpha, as either the primary emerging bilaterian phylum1,2,3,4,5,6 or within Deuterostomia, sister to Ambulacraria.7,8,9,10,11 Although their placement as sister to the rest of Bilateria supports relatively simple morphology in the ancestral bilaterian, their alternative placement within Deuterostomia suggests a morphologically complex ancestral bilaterian along with extensive loss of major phenotypic traits in the Xenacoelomorpha. Recent studies have questioned whether Deuterostomia should be considered monophyletic at all.10,12,13 Hidden paralogy and poor phylogenetic signal present a major challenge for reconstructing species phylogenies.14,15,16,17,18 Here, we assess whether these issues have contributed to the conflict over the placement of Xenacoelomorpha. We reanalyzed published datasets, enriching for orthogroups whose gene trees support well-resolved clans elsewhere in the animal tree.16 We find that most genes in previously published datasets violate incontestable clans, suggesting that hidden paralogy and low phylogenetic signal affect the ability to reconstruct branching patterns at deep nodes in the animal tree. We demonstrate that removing orthogroups that cannot recapitulate incontestable relationships alters the final topology that is inferred, while simultaneously improving the fit of the model to the data. We discover increased, but ultimately not conclusive, support for the existence of Xenambulacraria in our set of filtered orthogroups. At a time when we are progressing toward sequencing all life on the planet, we argue that long-standing contentious issues in the tree of life will be resolved using smaller amounts of better quality data that can be modeled adequately.19.

ADAR2 enzymes: efficient site-specific RNA editors with gene therapy aspirations.

The adenosine deaminase acting on RNA (ADAR) enzymes are essential for neuronal function and innate immune control. ADAR1 RNA editing prevents aberrant activation of antiviral dsRNA sensors through editing of long, double-stranded RNAs (dsRNAs). In this review, we focus on the ADAR2 proteins involved in the efficient, highly site-specific RNA editing to recode open reading frames first discovered in the GRIA2 transcript encoding the key GLUA2 subunit of AMPA receptors; ADAR1 proteins also edit many of these sites. We summarize the history of ADAR2 protein research and give an up-to-date review of ADAR2 structural studies, human ADARBI (ADAR2) mutants causing severe infant seizures, and mouse disease models. Structural studies on ADARs and their RNA substrates facilitate current efforts to develop ADAR RNA editing gene therapy to edit disease-causing single nucleotide polymorphisms (SNPs). Artificial ADAR guide RNAs are being developed to retarget ADAR RNA editing to new target transcripts in order to correct SNP mutations in them at the RNA level. Site-specific RNA editing has been expanded to recode hundreds of sites in CNS transcripts in Drosophila and cephalopods. In Drosophila and C. elegans, ADAR RNA editing also suppresses responses to self dsRNA.

Preventive health therapy and behavior outcomes from a brown bag medication review for older adults.

BACKGROUND: Morbidity and mortality associated with preventable diseases can be reduced with the use of preventive health services. We evaluated the uptake and retention of preventive health behaviors and management of accidental medication poisonings in older adults after a health prevention educational component was combined with a brown bag medication review. METHODS: This study used a cohort design and was conducted in six urban senior centers and three independent senior living communities in Detroit, Michigan. Participants included 85 older adults (>60 years old) taking five or more medications with 63 participants returning follow up materials. Pharmacy personnel conducted brown bag medication reviews that were combined with a preventive health education component. Information was collected on medications, vaccinations, supplement use, and accidental medication poisoning management. Participants were given written recommendations on prescription medications and preventive health therapies to improve health and medication use. An investigator developed program satisfaction survey was administered immediately after the review. An investigator-developed follow-up preventive health implementation survey was conducted at least 3 months later to assess recommendation implementation. RESULTS: Participants' mean age was 75.9 ± 8.5 years. Fifty-six older adults had 124 recommendations in preventive health in total (1-5/participant). Eleven participants had no recommendations. Sixty-three participants (74%) returned follow-up preventive health surveys. Twenty-three percent of recommendations were already implemented with 34% planned to be done in the future. Poisoning management knowledge increased for 13 participants, reporting they would call the poison control center. The program was well received, with participants reporting high satisfaction scores (4.8 ± 0.7 out of 5). CONCLUSIONS: Brown bag medication reviews can be an effective method to promote the uptake of preventive health behaviors among older adults, but additional accidental medication poisoning management education is still needed.

Behavioral Research in Cancer Prevention and Control: Emerging Challenges and Opportunities.

It is estimated that behaviors such as poor diet, alcohol consumption, tobacco use, sedentary behavior, and excessive ultraviolet exposure account for nearly one-half of all cancer morbidity and mortality. Accordingly, the behavioral, social, and communication sciences have been important contributors to cancer prevention and control research, with methodological advances and implementation science helping to produce optimally effective interventions. To sustain these contributions, it is vital to adapt to the contemporary context. Efforts must consider ancillary effects of the 2019 coronavirus disease pandemic, profound changes in the information environment and public understanding of and trust in science, renewed attention to structural racism and social determinants of health, and the rapidly increasing population of cancer survivors. Within this context, it is essential to accelerate reductions in tobacco use across all population subgroups; consider new models of energy balance (diet, physical activity, sedentary behavior); increase awareness of alcohol as a risk factor for cancer; and identify better communication practices in the context of cancer-related decisions such as screening and genetic testing. Successful integration of behavioral research and cancer prevention depends on working globally and seamlessly across disciplines, taking a multilevel approach where possible. Methodological and analytic approaches should be emphasized in research training programs and should use new and underused data sources and technologies. As the leadership core of the National Cancer Institute's Behavioral Research Program, we reflect on these challenges and opportunities and consider implications for the next phase of behavioral research in cancer prevention and control.