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We present genome sequences for the caeciliansGeotrypetes seraphini(3.8Gb) andMicrocaecilia unicolor(4.7Gb), 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 the most abundant. We identify 1,150 orthogroups which 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 ZRS enhancer of Sonic Hedgehog which is also mutated in snakes.In vivodeletions 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.

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.

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.

The expression of long noncoding RNAs is highly enriched in the human nervous system. However, the function of neuronal lncRNAs in the cytoplasm and their potential translation remains poorly understood. Here we performed Poly-Ribo-Seq to understand the interaction of lncRNAs with the translation machinery and the functional consequences during neuronal differentiation of human SH-SY5Y cells. We discovered 237 cytoplasmic lncRNAs up-regulated during early neuronal differentiation, 58%–70% of which are associated with polysome translation complexes. Among these polysome-associated lncRNAs, we find 45 small ORFs to be actively translated, 17 specifically upon differentiation. Fifteen of 45 of the translated lncRNA-smORFs exhibit sequence conservation within Hominidea, suggesting they are under strong selective constraint in this clade. The profiling of publicly available data sets revealed that 8/45 of the translated lncRNAs are dynamically expressed during human brain development, and 22/45 are associated with cancers of the central nervous system. One translated lncRNA we discovered is LINC01116, which is induced upon differentiation and contains an 87 codon smORF exhibiting increased ribosome profiling signal upon differentiation. The resulting LINC01116 peptide localizes to neurites. Knockdown of LINC01116 results in a significant reduction of neurite length in differentiated cells, indicating it contributes to neuronal differentiation. Our findings indicate cytoplasmic lncRNAs interact with translation complexes, are a noncanonical source of novel peptides, and contribute to neuronal function and disease. Specifically, we demonstrate a novel functional role for LINC01116 during human neuronal differentiation.

Amelogenesis imperfecta (AI) describes a heterogeneous group of developmental enamel defects that typically have Mendelian inheritance. Exome sequencing of ten families with recessive hypomaturation AI revealed 4 novel and 1 known variants in the matrix metallopeptidase 20 (MMP20) gene that were predicted to be pathogenic. MMP20 encodes a protease that cleaves the developing extracellular enamel matrix and is necessary for normal enamel crystal growth during amelogenesis. New homozygous missense changes were shared between four families of Pakistani heritage (c.625G>C; p.(Glu209Gln)) and two of Omani origin (c.710C>A; p.(Ser237Tyr)). In two families of UK origin and one from Costa Rica, affected individuals were homozygous for the previously reported c.954-2A>T; p.(Ile319Phefs*19) variant. For each of these variants, microsatellite haplotypes appeared to exclude a recent founder effect, but elements of haplotype were conserved, suggesting more distant founding ancestors. New compound heterozygous changes were identified in one family of European heritage; c.809_811+12delinsCCAG; p.(?) and c.1122A>C; p.(Gln374His). This report further elucidates the mutation spectrum of MMP20 and the probable impact on protein function, confirms a consistent hypomaturation phenotype and shows that mutations in MMP20 are a common cause of autosomal recessive AI in some communities. This article is protected by copyright. All rights reserved.

We tested the hypothesis that a panel of placental mammal-specific miRNAs and their targets play important to establish receptivity to implantation and their dysregulated expression may be a feature in women with early pregnancy loss. Relative expression levels of miR-340-5p, −542-3p, and −671-5p all increased following treatment of Ishikawa cells with progesterone (10 μg/ml) for 24 hrs (p < 0.05). RNA sequencing of these P4-treated cells identified co-ordinate changes to 6,367 transcripts of which 1713 were predicted targets of miR-340-5p, 670 of miR-542-3p, and 618 of miR-671-5p. Quantitative proteomic analysis of Ishikawa cells transfected with mimic or inhibitor (48 hrs: n=3 biological replicates) for each of the P4-regulated miRNAs was carried out to identify targets of these miRNAs. Excluding off target effects, mir-340-5p mimic altered 1,369 proteins while inhibition changed expression of 376 proteins (p < 0.05) of which, 72 were common to both treatments. A total of 280 proteins were identified between predicted (mirDB) and confirmed (in vitro) targets. In total, 171 proteins predicted to be targets by mirDB were altered in vitro by treatment with miR-340-5p mimic or inhibitor and were also altered by treatment of endometrial epithelial cells with P4. In vitro targets of miR-542-3p identified 1,378 proteins altered by mimic while inhibition altered 975 a core of 200 proteins were changed by both. 100 protein targets were predicted and only 46 proteins were P4 regulated. miR-671-mimic altered 1,252 proteins with inhibition changing 492 proteins of which 97 were common to both, 95 were miDB predicted targets and 46 were also P4-regulated. All miRNAs were detected in endometrial biopsies taken from patients during the luteal phase of their cycle, irrespective of prior or future pregnancy outcomes Expression of mir-340-5p showed an overall increase in patients who had previously suffered a miscarriage and had a subsequent miscarriage, as compared to those who had infertility or previous miscarriage and subsequently went on to have a life birth outcome. The regulation of these miRNAs and their protein targets regulate the function of transport and secretion, and adhesion of the endometrial epithelia required for successful implantation in humans. Dysfunction of these miRNAs (and therefore the targets they regulate) may contribute to endometrial-derived recurrent pregnancy loss in women.

SummaryConflicting studies place a group of bilaterian invertebrates containing xenoturbellids and acoelomorphs, the Xenacoelomorpha, as either the primary emerging bilaterian phylum, or within Deuterostomia, sister to Ambulacraria. While 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. More recently, further studies have brought into question whether Deuterostomia should be considered monophyletic at all. Hidden paralogy presents a major challenge for reconstructing species phylogenies. Here we assess whether hidden paralogy has contributed to the conflict over the placement of Xenacoelomorpha. Our approach assesses previously published datasets, enriching for orthogroups whose gene trees support well resolved clans elsewhere in the animal tree of life. We find that the majority of constituent genes in previously published datasets violate incontestable clans, suggesting that hidden paralogy is rife at this depth. We demonstrate that enrichment for genes with orthologous signal alters the final topology that is inferred, whilst simultaneously improving fit of the model to the data. We discover increased, but ultimately not conclusive, support for the existence of Xenambulacraria in our orthology enriched set of genes. At a time when we are steadily progressing towards sequencing all of 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 modelled adequately.

The TIR domain-containing adapter inducing IFN-β (TRIF) protein is an innate immune system protein that mediates the MyD88-independent toll-like receptor response pathway in mice and humans. Previously, we identified positive selection at seven distinct residues in mouse TRIF (mTRIF), as compared with human and other mammalian orthologs, thus predicting protein functional shift in mTRIF. We reconstructed TRIF for the most recent common ancestor of mouse and human, and mutated this at the seven sites to their extant mouse/human states. We overexpressed these TRIF mutants in immortalized human and mouse cell lines and monitored TRIF-dependent cytokine production and gene expression induction. We show that optimal TRIF function in human and mouse is dependent on the identity of the positively selected sites. These data provide us with molecular data relating observed differences in response between mouse and human MyD88-independent signaling in the innate immune system with protein functional change.

The origin of placentation in mammals required a symphony of events from protein innovation to the evolution of regulatory networks that could support successful pregnancy from implantation to full gestation. There is variation across mammals in terms of the types of implantation, degree of invasiveness of the trophoblast into the maternal endometrium, and the type of placenta formed. However, there are some signalling networks, e.g. progesterone receptor signalling, that are shared across the clade. We wished to determine what regulates the diverse molecular interactions and morphologies that underpin successful pregnancy in eutheria. Whilst the relationship between miRNAs and pathophysiology of placenta is well established, their role in early implantation and diversity of implantation strategies is not well understood. We identify a cohort of miRNAs that arose coincident with the emergence of placental mammals (mir-127, -185, -188, -28, -324, -331, -340, -378, -423, -433, -505, -542, and -671). We identify 115 genes under positive selection on the stem eutherian lineage and 88 of these are predicted to be regulated by the 13 stem lineage miRNAs. Using two species of mammal that demonstrate the extremes of implantation strategies (invasive and superficial in humans and bovine respectively), we assessed the response of the endometrial epithelium in terms of expression of these miRNAs to early pregnancy molecules. We show that the 13 stem lineage miRNAs are regulated in a species-specific manner. We propose these species-specific regulatory networks contribute to the diversity of pregnancy morphologies observed in eutheria.

Ribosomes have long been thought of as homogeneous macromolecular machines, but recent evidence suggests they are heterogeneous and could be specialised to regulate translation. Here, we have characterised ribosomal protein heterogeneity across 4 tissues of Drosophila melanogaster. We find that testes and ovaries contain the most heterogeneous ribosome populations, which occurs through a combination of paralog-enrichment and paralog-switching. We have solved structures of ribosomes purified from in vivo tissues by cryo-EM, revealing differences in precise ribosomal arrangement for testis and ovary 80S ribosomes. Differences in the amino acid composition of paralog pairs and their localisation on the ribosome exterior indicate paralog-switching could alter the ribosome surface, enabling different proteins to regulate translation. One testis-specific paralog-switching pair is also found in humans, suggesting this is a conserved site of ribosome heterogeneity. Overall, this work allows us to propose that mRNA translation might be regulated in the gonads through ribosome heterogeneity, providing a potential means of ribosome specialisation.

Drought stress, caused by lack of precipitation or irrigation, is one of the most challenging problems in crop production in the US and worldwide. Drought alone affects 45% of the world’s agricultural land, further, 19.5% of irrigated agricultural lands are considered saline. A combination of two or more abiotic stresses, such as drought and salinity results in more yield loss than a single stress. Drought along with salinization is expected to cause up to 50% of arable land loss worldwide. Development of drought and/or salt stress tolerant cultivars represents one of the most practical solutions. Genetic variation in abiotic stress tolerance exists within Upland cotton (Gossypium hirsutum L.); however, most if not all Upland cultivars have been developed under normal well-watered and non-saline conditions. Pima, Sea-Island or Egyptian cotton (G. barbadense L.), carries some level of tolerance to abioitc stresses due to their origin near sea-coasts, and this tolerance can be transferred to Upland cotton by interspecific introgression. Although drought and salt stress tolerances are presumed to be interconnected, the genetic basis is not fully understood due to complexity of the stress resistance and difficulties in phenotyping. The objective of this review was to summarize the progress in screening methodology, resistance germplasm sources, inheritance, biochemical and molecular aspects, transgenic approaches, and quantitative trait loci (QTL) for drought and salt stress tolerance in cotton. In the last 10–15 years, significant progress has been made in understanding the genetic basis of drought and salt tolerance through QTL mapping using molecular markers on biparental and multi-parental populations and natural populations. Numerous drought or salt responsive genes have been identified, some of which include those commonly associated with drought or salt tolerance in other plants and are used in transgenic approaches for enhancement of abiotic stress tolerance. However, none of these genes have been utilized in commercial cotton breeding programs, and no abiotic stress tolerance QTL has been used in cotton breeding through marker-assisted selection (MAS). More and larger permanent intra-specific and interspecific mapping populations using diverse and multiple parents should be developed. These populations are necessary for repeated phenotyping for abiotic stress tolerance and for high resolution mapping of QTL using genome-wide SNP markers and for MAS to transfer tolerance genes to high-yielding cultivars. Further, quick, reliable and high throughput screening methods applicable for large scale populations need to be developed to improve the reliability and scale of phenotyping of the cotton germplasm in these populations for drought and salt stress tolerance.

LncRNAs are less conserved, yet more tissue and developmental-stage specific than mRNAs and are particularly enriched in the nervous system ofDrosophila melanogaster, mouse and human. The function of cytoplasmic lncRNAs and their potential translation remains poorly understood. Here we performed Poly-Ribo-Seq to understand the interaction of lncRNAs with the translation machinery and the functional consequences during neuronal differentiation of SH-SH5Y cells. We discovered 237 cytoplasmic lncRNAs upregulated during early neuronal differentiation, most of which are associated with polysome complexes. The majority are cytoplasmically enriched and are intergenic or anti-sense. In addition, we find 45 small ORFs in lncRNAs to be actively translated, 17 specifically upon differentiation. 11 of these smORFs exhibit high sequence conservation acrossHominidaesuggesting they are under strong selective constraint with putative function in this clade. We discover LINC01116 is induced upon differentiation and contains an 87 codon smORF, which we detect as translated, with increased ribosome profiling signal upon differentiation. The LINC01116 peptide exhibits a cytoplasmic distribution and is detected in neurites. Knockdown of LINC01116 results in significant reduction of neurite length in differentiated cells indicating it contributes to neuronal differentiation. Our findings indicate lncRNAs are a source of non-canonical peptides and contribute to neuronal function.

Amelogenesis imperfecta (AI) describes a heterogeneous group of developmental enamel defects that typically have Mendelian inheritance. Exome sequencing of ten families with recessive hypomaturation AI revealed 4 novel and 1 known variants in the matrix metallopeptidase 20 (MMP20) gene that were predicted to be pathogenic. MMP20 encodes a protease that cleaves the developing extracellular enamel matrix and is necessary for normal enamel crystal growth during amelogenesis. New homozygous missense changes were shared between four families of Pakistani heritage (c.625G>C; p.(E209Q)) and two of Omani origin (c.710C>A; p.(S237Y)). In two families of UK origin and one from Costa Rica, affected individuals were homozygous for the previously reported c.954-2A>T; p.(I319Ffs*19) variant. For each of these variants, microsatellite haplotypes appeared to exclude a recent founder effect, but elements of haplotype were conserved, suggesting more distant founding ancestors. New compound heterozygous changes were identified in one family of European heritage; c.809_811+12delACGgtaagattattainsCCAG; p.(?) and c.1122A>C; p.(Q374H). All four new variants are within the zinc dependant peptidase domain. This report further elucidates the mutation spectrum of MMP20 and the probable impact on protein function, confirms a consistent hypomaturation phenotype and shows that mutations in MMP20 are a common cause of autosomal recessive AI in some communities.Data AvailabilityThe data that support the findings of this study are openly available in ClinVar at https://www.ncbi.nlm.nih.gov/clinvar/, accession numbers: SCV001338799 - SCV001338802 and in the AI Leiden Open Variation Database (LOVD) at http://dna2.leeds.ac.uk/LOVD/ with reference numbers: 0000000313 – 0000000317.

During the pre-implantation period of pregnancy in eutherian mammals, changes to the uterine endometrium are required (both at the transcriptional and protein level) to facilitate the endometrium becoming receptive to an implanting embryo. We know that the developing conceptus (embryo and extraembryonic membranes) produces proteins during this developmental stage. We hypothesised that this common process in early pregnancy in eutheria may be facilitated by highly conserved conceptus-derived proteins such as macrophage capping protein CAPG. More specifically, we propose that CAPG may share functionality in modifying the transcriptome of the endometrial epithelial cells to facilitate receptivity to implantation in species with different implantation strategies, such as human and bovine. A recombinant bovine form of CAPG (91% sequence identity between bovine and human) was produced and bovine endometrial epithelial (bEECs) and stromal (bESCs) cells and human endometrial epithelial cells (hEECs) were cultured for 24 h with or without rbCAPG. RNA sequencing and quantitative real-time PCR analysis was used to assess the transcriptional response to rbCAPG (Control, vehicle, CAPG 10, 100, 1000 ng/ml: n=3 biological replicates per treatment per species). Treatment of bEECs with CAPG resulted in changes to 1052 transcripts (629 increased and 423 decreased) compared to vehicle controls, including those previously only identified as regulated by interferon-tau, the pregnancy recognition signal in cattle. Treatment of hEECs with bovine CAPG increased expression of transcripts previously known to interact with CAPG in different systems (CAPZB, CAPZA2, ADD1andADK) compared with vehicle controls (P

Amelogenesis imperfecta (AI) is a heterogeneous group of genetic diseases characterised by dental enamel malformation. Pathogenic variants in at least 33 genes cause syndromic or non‐syndromic AI. Recently variants in RELT, encoding an orphan receptor in the tumour necrosis factor (TNF) superfamily, were found to cause recessive AI, as part of a syndrome encompassing small stature and severe childhood infections. Here we describe four additional families with autosomal recessive hypomineralised AI due to previously unreported homozygous mutations in RELT. Three families carried a homozygous missense variant in the fourth exon (c.164C>T, p.(T55I)) and a fourth family carried a homozygous missense variant in the 11th exon (c.1264C>T, p.(R422W)). We found no evidence of additional syndromic symptoms in affected individuals. Analyses of tooth microstructure with computerised tomography and scanning electron microscopy suggest a role for RELT in ameloblasts' coordination and interaction with the enamel matrix. Microsatellite genotyping in families segregating the T55I variant reveals a shared founder haplotype. These findings extend the RELT pathogenic variant spectrum, reveal a founder mutation in the UK Pakistani population and provide detailed analysis of human teeth affected by this hypomineralised phenotype, but do not support a possible syndromic presentation in all those with RELT‐variant associated AI.

The evolution and structure of prokaryotic genomes are largely shaped by horizontal gene transfer. This process is so prevalent that DNA can be seen as a public good—a resource that is shared across individuals, populations, and species. The consequence is a network of DNA sharing across prokaryotic life, whose extent is becoming apparent with increased availability of genomic data. Within prokaryotic species, gene gain (via horizontal gene transfer) and gene loss results in pangenomes, the complete set of genes that make up a species. Pangenomes include core genes present in all genomes, and accessory genes whose presence varies across strains. In this chapter, we discuss how we can understand pangenomes from a network perspective under the view of DNA as a public good, how pangenomes are maintained in terms of drift and selection, and how they may differ between prokaryotic groups. We argue that niche adaptation has a major impact on pangenome structure. We also discuss interactions between accessory genes within genomes, and introduce the concepts of ‘keystone genes’, whose loss leads to concurrent loss of other genes, and ‘event horizon genes’, whose acquisition may lead to adaptation to novel niches and towards a separate, irreversible evolutionary path.

Of the vast amount of literary correspondence that has survived from the Romantic period, a significant proportion of it is between authors and publishers. These letters are fascinating and multifaceted documents, highlighting the ways in which authors negotiate the artistic and commercial imperatives of their work with the figure who was responsible for facilitating the production and sale of the text. This essay examines a selection of correspondence between Romantic writers and their publishers in order to explore the ways in which these letters function simultaneously as business and personal correspondence. Looking at letters from authors of different levels of fame, social position, class, and gender (including Mary Wollstonecraft, William Wordsworth, Percy Shelley, Byron, and Jane Austen) and publishers of varying degrees of influence (including Joseph Johnson, Charles Ollier, John Murray) the essay will investigate how Romantic writers communicated with their publishers—the people who, in the words of Leslie Chard, acted as ‘banker, postal clerk and packager, literary agent and editor, social chairman, and psychiatrist’.

Advance care planning (ACP) does not readily occur in medical settings and often gets missed. Older Latinos need ACP information to encourage advance directive (AD) completion indicating preferences for end-of-life (EOL) care. Objective: To explore the experiences with counseling using motivational interviewing (MI) techniques and social workers to encourage ACP communication among older Latinos with advance chronic diseases. This study describes stages of readiness to plan for EOL care. Design: We conducted a qualitative study with older Latinos who participated in a community-based intervention in Southern New Mexico. Methods: Participants in the intervention were selected because they received ACP education plus counseling involving MI to address resistance to ACP. Motivational interviewing counseling involved the following: (1) engaging in structured dialogue about ACP, (2) using and completing AD documentation, (3) encouraging ACP communication with providers and families, and (4) applying AD information into actionable behavior. We utilized a constant comparative method and thematic analysis to explore the meaning of older Latinos’ experiences with MI counseling and stages of change. Results: Participants (n = 32) were mostly women (74.3%), half born in the United States and half from Mexico in the United States on average for 31.75 (standard deviation 16.22) years. Many had less than sixth grade education (31.3%) or had not completed high school (21.9%). Key themes indicate the following stages of change: (1) precontemplation, (2) contemplation, (3) preparation, (4) ACP action, and (5) maintenance. Conclusion: This study contributes to the literature by identifying areas for adaption to enhance understanding and increase information to ultimately achieve the completion of ACP among Latinos.

Older Latinos with serious medical conditions such as cancer and other chronic diseases lack information about advance care planning (ACP). ACP Intervention (ACP-I Plan) was designed for informational and communication needs of older Latinos to improve communication and advance directives (ADs).To determine the feasibility of implementing ACP-I Plan among seriously ill, older Latinos (≥50 years) in Southern New Mexico with one or more chronic diseases (e.g., cancer, heart disease, renal/liver failure, stroke, hypertension, diabetes, chronic obstructive pulmonary disease, and HIV/AIDS).We conducted a prospective, pretest/post-test, two-group, randomized, community-based pilot trial by using mixed data collection methods.Older Latino/Hispanic participants were recruited from community-based settings in Southern New Mexico.All participants received ACP education, whereas the intervention group added: (1) emotional support addressing psychological distress; and (2) systems navigation for resource access, all of which included interactive ACP treatment decisional support and involved motivational interview (MI) methods. Purposive sampling was guided by a sociocultural framework to recruit Latino participants from community-based settings in Southern New Mexico. Feasibility of sample recruitment, implementation, and retention was assessed by examining the following: recruitment strategies, trial enrollment, retention rates, duration of MI counseling, type of visit (home vs. telephone), and satisfaction with the program.We contacted 104 patients, enrolled 74 randomized to usual care 39 (UC) and treatment 35 (TX) groups. Six dropped out before the post-test survey, three from TX before the post-test survey because of sickness (n = 1) or could not be located (n = 2), and the same happened for UC. Completion rates were 91.4% UC and 92.3% TX groups. All participants were Latino/Hispanic, born in the United States (48%) or Mexico (51.4%) on average in the United States for 25 years; majority were female, 76.5%; 48.6% preferred Spanish; and 31.4% had less than sixth-grade education. Qualitative data indicate satisfaction with the ACP-I Plan intervention.Based on enrollment and intervention completion rates, time to completion tests, and feedback from qualitative post-study, follow-up interviews, the ACP-I Plan was demonstrated to be feasible and perceived as extremely helpful.

Several studies have suggested that activation of signal transducer and activator of transcription 3 (STAT3) is associated with initiation, progression and metastasis of numerous types of malignancy. However, the role of the Janus kinase-interleukin 6-STAT3 signaling pathway in the pathogenesis and recurrence of meningiomas is unknown. The present study evaluated STAT3 activation by western blotting and immunohistochemistry and assessed its association with Ki-67 labeling in 13 cases of meningioma in which frozen tissue and ≥5.5-year follow-up information were available, and in formalin-fixed meningioma tissues from 14 cases with an 8.4-year follow-up. The results of the western blot analysis indicated that STAT3 phosphorylation was markedly higher in grade II meningiomas compared with that in grade I, with mean densitometric values of 8.6 and 1.7 following normalization to actin, respectively. High STAT3 phosphorylation/activation was identified in 2 of 3 recurrent World Health Organization (WHO) grade I meningiomas and 0 of 3 non-recurrent meningiomas. Strong STAT3 phosphorylation/activation signal was also found in 2 of 4 recurrent grade II meningiomas and 1 of 3 non-recurrent cases. According to the immunohistochemistry results, phospho-STAT3 was not increased in WHO grade II tumors compared with that in grade I tumors, and was not significantly different between recurrent and non-recurrent cases. Ki-67 labeling was significantly increased in grade II vs. grade I tumors, and was also significantly increased in recurrent compared with non-recurrent grade I meningiomas. The results of the current study suggest that, while detection of phosphorylated/activated STAT3 may be useful in isolated cases, identifying activation may be of little value in predicting recurrence.

Background Strigolactones (SLs) are an important class of carotenoid-derived signalling molecule in plants, which function both as exogenous signals in the rhizosphere and as endogenous plant hormones. In flowering plants, SLs are synthesized by a core pathway of four enzymes and are perceived by the DWARF14 (D14) receptor, leading to degradation of SMAX1-LIKE7 (SMXL7) target proteins in a manner dependent on the SCFMAX2 ubiquitin ligase. The evolutionary history of SLs is poorly understood, and it is not clear whether SL synthesis and signalling are present in all land plant lineages, nor when these traits evolved. Results We have utilized recently-generated genomic and transcriptomic sequences from across the land plant clade to resolve the origin of each known component of SL synthesis and signalling. We show that all enzymes in the core SL synthesis pathway originated at or before the base of land plants, consistent with the previously observed distribution of SLs themselves in land plant lineages. We also show that the late-acting enzyme LATERAL BRANCHING OXIDOREDUCTASE (LBO) may be considerably more ancient than previously thought. We perform a detailed phylogenetic analysis of SMXL proteins and show that specific SL target proteins only arose in flowering plants. We also assess diversity and protein structure in the SMXL family, identifying several previously unknown clades. Conclusions Overall, our results suggest that SL synthesis is much more ancient than canonical SL signalling, consistent with the idea that SLs first evolved as rhizosphere signals and were only recruited much later as hormonal signals. Electronic supplementary material The online version of this article (10.1186/s12915-019-0689-6) contains supplementary material, which is available to authorized users.

Gene fusion occurs when two or more individual genes with independent open reading frames becoming juxtaposed under the same open reading frame creating a new fused gene. A small number of gene fusions described in detail have been associated with novel functions, for example, the hominid-specific PIPSL gene, TNFSF12, and the TWE-PRIL gene family. We use Sequence Similarity Networks and species level comparisons of great ape genomes to identify 45 new genes that have emerged by transcriptional readthrough, that is, transcription-derived gene fusion. For 35 of these putative gene fusions, we have been able to assess available RNAseq data to determine whether there are reads that map to each breakpoint. A total of 29 of the putative gene fusions had annotated transcripts (9/29 of which are human-specific). We carried out RT-qPCR in a range of human tissues (placenta, lung, liver, brain, and testes) and found that 23 of the putative gene fusion events were expressed in at least one tissue. Examining the available ribosome foot-printing data, we find evidence for translation of three of the fused genes in human. Finally, we find enrichment for transcription-derived gene fusions in regions of known segmental duplication in human. Together, our results implicate chromosomal structural variation brought about by segmental duplication with the emergence of novel transcripts and translated protein products., The authors would like to thank the following funding agencies: Irish Research Council (IRC) to AMMC (RS/2012/466), Pierse Trust fund, and Orla Benson scholarships to A.M.M.C. 250 Great Minds University of Leeds Fellowship to M.J.O'.C.,IRC to R.J.M. (GOIPG/2014/306), and the Irish Centre for High End Computing (ICHEC) for computational resources. TMB is supported by BFU2017-86471-P (MINECO/FEDER, UE), U01 MH106874 grant, Howard Hughes International Early Career, Obra Social “La Caixa” and Secretaria d'Universitats i Recerca and CERCA Programme del Departament d'Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 880).

Genomic imprinting is an epigenetic phenomenon where autosomal genes display uniparental expression depending on whether they are maternally or paternally inherited. Genomic imprinting can arise from parental conflicts over resource allocation to the offspring, which could drive imprinted loci to evolve by positive selection. We investigate whether positive selection is associated with genomic imprinting in the inbreeding species Arabidopsis thaliana. Our analysis of 140 genes regulated by genomic imprinting in the A. thaliana seed endosperm demonstrates they are evolving more rapidly than expected. To investigate whether positive selection drives this evolutionary acceleration, we identified orthologs of each imprinted gene across 34 plant species and elucidated their evolutionary trajectories. Increased positive selection was sought by comparing its incidence among imprinted genes with nonimprinted controls. Strikingly, we find a statistically significant enrichment of imprinted paternally expressed genes (iPEGs) evolving under positive selection, 50.6% of the total, but no such enrichment for positive selection among imprinted maternally expressed genes (iMEGs). This suggests that maternally- and paternally expressed imprinted genes are subject to different selective pressures. Almost all positively selected amino acids were fixed across 80 sequenced A. thaliana accessions, suggestive of selective sweeps in the A. thaliana lineage. The imprinted genes under positive selection are involved in processes important for seed development including auxin biosynthesis and epigenetic regulation. Our findings support a genomic imprinting model for plants where positive selection can affect paternally expressed genes due to continued conflict with maternal sporophyte tissues, even when parental conflict is reduced in predominantly inbreeding species.

Candida glabrata currently accounts for 25 % of all fungal cases in UK hospitals, second only to C. albicans. This number is expected to rise given the intrinsic anti-fungal resistance of this species and the difficulty in treating it. In an effort to identify novel-anti fungal targets in C. glabrata, we used comparative genomics within Saccharomycotina yeast to predict which genes are under positive selection in this species specifically. Such genes are predicted to have influenced the adaptation of C. glabrata from a free-living microbe to a human pathogen, potentially due to functional shift(s) of the proteins they encode. Our analysis predicts that histone acetylation pathways are under positive selection in C. glabrata. Thereforewe hypothesised that we could use histone deacetylase inhibitors (HDACi) to interfere with histone acetylation levels and impact C. glabrata virulence. By treating C. glabrata withbroad spectrum HDACis we show it has a reduced capacity to form biofilms, it is less well adapted to high salt conditions typically found within a human host, and most importantly, it reverts to a more anti-fungal sensitive state. RNAseq analysis indicates that HDACi treatment interferes with the C. glabrata transcriptional response to anti-fungal treatment, rendering it incapable of combating against these drugs. Furthermore, using an in vivo worm model of candidiasis, we show that HDACi treatment in conjunction with the anti-fungal fluconazole, can increase the survival rate of individuals with C. glabrata infections. Taken together our data suggest that the health threat posed by C. glabrata might be addressed by repurposing HDACi to treat this infection.

Candidiasis is one of the most prevalent mycoses worldwide, and there are few successful treatments for this disease. In the UK, Candida glabrataaccounts for 25 % of Candida infections, and due to the increasing incidence of multidrug resistance, C. glabrata poses an eminent threat to public health, exacerbated by the limited range of antifungal therapies. Our aim is to elucidate the molecular mechanisms underlying the emergence of pathogenicity in the C. glabrata lineage, to identify novel therapeutical targets. Using comparative phylogenomics, we putatively identified 19 genes under positive selection in the C. glabrata lineage. Each of these genes influences chromatin structure by regulating histone post-translational modifications (PTMs). To assess the contribution of these genes to virulence, we monitored the phenotypic consequences of individually removing each gene in clinically-relevant assays. To date, we have focused on 3 genes, cg-SPP1 (regulates histone H3 methylation), cg-HAT1 (histone H4 acetyltransferase) and cg-AHC1 (subunit of Ada histone acetyltransferase complex). Preliminary data show that the individual deletion of these genes increases biofilm formation and fluconazole resistance in C. glabrata. Furthermore, acetyltransferase knockout strains show hypervirulence in an in vivo Galleria melonella infection model, and phenotypic differences in abiotic stress assays. RNA-sequencing was performed on the type-strain, cg-hat1Δ, and cg-ahc1Δ, in the presence and absence of fluconazole to determine the molecular bases for these phenotypes, revealing commonality between differentially expressed genes in both mutants. Together, our data suggest that histone PTMs play a significant, and overlapping, role in dictating virulence in C. glabrata, and detail the global transcriptomic response to fluconazole.

Poison frogs secrete alkaloid toxins in their skin as defence mechanisms against predators. Numerous studies have shown that the origin of alkaloid toxins in the skin is through ‘sequestration from diet’, i.e. uptake and storage of toxins or their chemical precursors, mostly from consumed arthropods. There exists the intriguing possibility that the gut microbiome of these frogs may play a role in this process. We address this question by looking at the organism together with its associated microbial communities, an effective symbiotic relationship between host and microbiome that could have allowed phenotypic adaptation of the host to a toxic diet. We sequenced the Bacterial and Archaeal 16S rRNA regions of the gut microbiome of 7 Poison frog species and 9 outgroup frog species caught in the rainforest of Eastern Peru. Frog species were selected based on sharing similar microhabitats and comparable individual sizes. A comparative analysis of the microbiome composition across all our samples allowed us to identify a core group of abundant symbiotic microbes unique to poison frogs in spite of intrinsic variation within species. We speculate this group could be associated to their ability to sequester toxins and we carried further metagenomic sequencing to allow us to determine possible functions that may be involved in toxin processing in these frogs.

Cetaceans are a clade of highly specialized aquatic mammals that include the largest animals that have ever lived. The largest whales can have ∼1,000× more cells than a human, with long lifespans, leaving them theoretically susceptible to cancer. However, large-bodied and long-lived animals do not suffer higher risks of cancer mortality than humans—an observation known as Peto’s Paradox. To investigate the genomic bases of gigantism and other cetacean adaptations, we generated a de novo genome assembly for the humpback whale (Megaptera novaeangliae) and incorporated the genomes of ten cetacean species in a comparative analysis. We found further evidence that rorquals (family Balaenopteridae) radiated during the Miocene or earlier, and inferred that perturbations in abundance and/or the interocean connectivity of North Atlantic humpback whale populations likely occurred throughout the Pleistocene. Our comparative genomic results suggest that the evolution of cetacean gigantism was accompanied by strong selection on pathways that are directly linked to cancer. Large segmental duplications in whale genomes contained genes controlling the apoptotic pathway, and genes inferred to be under accelerated evolution and positive selection in cetaceans were enriched for biological processes such as cell cycle checkpoint, cell signaling, and proliferation. We also inferred positive selection on genes controlling the mammalian appendicular and cranial skeletal elements in the cetacean lineage, which are relevant to extensive anatomical changes during cetacean evolution. Genomic analyses shed light on the molecular mechanisms underlying cetacean traits, including gigantism, and will contribute to the development of future targets for human cancer therapies.

Summary Kinesin-1 transports numerous cellular cargoes along microtubules. The kinesin-1 light chain (KLC) mediates cargo binding and regulates kinesin-1 motility. To investigate the molecular basis for kinesin-1 recruitment and activation by cargoes, we solved the crystal structure of the KLC2 tetratricopeptide repeat (TPR) domain bound to the cargo JIP3. This, combined with biophysical and molecular evolutionary analyses, reveals a kinesin-1 cargo binding site, located on KLC TPR1, which is conserved in homologs from sponges to humans. In the complex, JIP3 crosslinks two KLC2 TPR domains via their TPR1s. We show that TPR1 forms a dimer interface that mimics JIP3 binding in all crystal structures of the unbound KLC TPR domain. We propose that cargo-induced dimerization of the KLC TPR domains via TPR1 is a general mechanism for activating kinesin-1. We relate this to activation by tryptophan-acidic cargoes, explaining how different cargoes activate kinesin-1 through related molecular mechanisms., Highlights • Crystal structure of the kinesin-1 KLC2 TPR domain bound to the cargo JIP3 • JIP3 binding site is located on KLC TPR1 and is conserved from sponges to humans • Molecular mechanism by which ARF6 regulates kinesin-1 recruitment by JIP3/4 revealed • A unified framework explaining how unrelated cargoes activate kinesin-1, Cockburn et al. present the structure of the cargo binding TPR domain of kinesin light chain bound to the cargo molecule JIP3. From this they propose a mechanism by which multiple, unrelated cellular cargo molecules can “hotwire” the kinesin-1 molecule into motility.

The mitogen activated protein kinase (MAPK) p38MAPK has been implicated in regulation of cell proliferation and apoptosis. However, expression, activation and regulation has not been studied in meningiomas, to our knowledge. p38MAPK is regulated, in part, by dual specificity phosphatases (DUSP) that inactivate signaling by dephosphorylation. DUSP10 is also a likely participant in regulating meningioma proliferation. Five fetal and an adult human leptomeninges and 37 meningioma cultures (MC) were evaluated for DUSP10 as well as phosphorylation of its substrates p38MAPK and p44/42MAPK by western blot and DUSP10 expression by polymerase chain reaction. Platelet derived growth factor-BB (PDGF-BB), transforming growth factor B1 (TGFB1) and cerebrospinal fluid effects on DUSP10 and signaling were also studied in vitro. DUSP10 and phospho-p38MAPK and phospho-p44/42MAPK were detected in all six leptomeninges. DUSP10 was detected in 13 of 17 World Health Organization grade I, 11 of 14 grade II and four of six grade III meningiomas. Phospho-p38MAPK was detected in nine of 17 grade I, two of six grade II, and four of six grade III meningiomas. In the majority of meningiomas DUSP10 expression correlated inversely with phosphorylation of p38MAPK. PDGF-BB increased DUSP10 in MC2 and MC4 and weakly in MC3. TGFB1 increased phosphorylation of p38MAPK and caspase 3 activation. Thus p38MAPK and DUSP10 likely participate in the pathogenesis of meningiomas.

Gastrointestinal nematodes are a serious cause of morbidity and mortality in grazing ruminants. The major ovine defence mechanism is acquired immunity, with protective immunity developing over time in response to infection. Nematode resistance varies both within and between breeds and is moderately heritable. A detailed understanding of the genes and mechanisms involved in protective immunity, and the factors that regulate this response, is required to aid both future breeding strategies and the development of effective and sustainable nematode control methods. The aim of this study was to compare the abomasal lymph node transcriptome of resistant and susceptible lambs in order to determine biological processes differentially expressed between resistant and susceptible individuals. Scottish Blackface lambs, with divergent phenotypes for resistance, were challenged with 30,000 Teladorsagia circumcincta larvae (L3), and abomasal lymph nodes recovered at 7 and 14 days post-infection (dpi). High-throughput sequencing of cDNA from the abomasal lymph node was used to quantitatively sample the transcriptome with an average of 32 million reads per sample. A total of 194 and 144 genes were differentially expressed between resistant and susceptible lambs at 7 and 14 dpi respectively. Differentially expressed networks and biological processes were identified using Ingenuity Pathway Analysis. Genes involved in the inflammatory response, attraction of T lymphocytes and binding of leukocytes were more highly expressed in resistant animals at 7 dpi and in susceptible animals at 14 dpi indicating that resistant animals respond to infection earlier than susceptible animals. Twenty-four Single Nucleotide Polymorphisms (SNP) within 11 differentially expressed genes, were tested for association with gastrointestinal nematode resistance in the Scottish Blackface lambs. Four SNP, in 2 genes (SLC30A2 and ALB), were suggestively associated with faecal egg count. In conclusion, a large number of genes were differentially expressed in the abomasal lymph node of resistant and susceptible lambs responding to gastrointestinal nematode challenge. Resistant Scottish Blackface lambs appear to generate an earlier immune response to T. circumcincta. In susceptible lambs this response appears to be delayed. SNP in 2 differentially expressed genes were suggestively associated with faecal egg count indicating that differentially expressed genes may be considered candidate loci for mediating nematode resistance.

Eukaryotic cells, with complex features such as membrane-bound nuclei, evolved from prokaryotic cells that lack these components. A newly identified prokaryotic group reveals intermediate steps in eukaryotic-cell evolution. See Article p.353 Although the origin of eukaryotic cells from prokaryotic ancestors remains an enigma, it has become clear that the root of eukaryotes lies among a group of prokaryotes known as archaea. The recent identification of newly described archaea belonging to the Asgard superphylum, including Lokiarchaeota and Thorarchaeota, revealed a group of prokaryotes containing many proteins and genetic sequences that are otherwise found only in eukaryotes. Thijs Ettema and colleagues extend the search for eukaryotic roots by describing further additions to the Asgard superphylum: the Odinarchaeota and Heimdallarchaeota. The new Asgard genomes encode homologues of several components of eukaryotic membrane-trafficking machineries, suggesting that the archaeal ancestor of eukaryotes was well equipped to evolve the complex cellular features that are characteristic of eukaryotic cells.

Community-based participatory research can help reduce health disparities among underserved populations. The New Mexico State University - Fred Hutchinson Cancer Research Center Partnership for the Advancement of Cancer Research (NMSU – Fred Hutch PACR) aims to reduce cancer health disparities in part through the establishment of community-academic partnerships. The Outreach Core of the PACR has supported a small grants program since 2015 to award funds to competitive community-academic partnership teams addressing regional cancer or health disparities issues through health education. Each year, the Outreach Core staff presents a grant-writing workshop to assist community groups in the development of competitive proposals and to identify academic partners at NMSU. Participants at the grant-writing workshop submit proposals, which are then reviewed by two NMSU faculty researchers. All participants, including the awardees, receive the reviewers’ feedback on their proposal. Over the past four cycles, the grant-writing workshop has trained 60 community members. The top two proposals are funded each year. To date, eight different proposals have been funded, six at $7500 each and two at $5,000 each. All of the funded projects undergo an IRB review at NMSU before the start of the research project. The NMSU academic partners are involved with the community groups through the design, submission of Human Subjects protocol to the IRB, and through data analysis and reporting. Examples of small grant proposals will be presented, including a discussion of how their partnerships worked. This interaction between the community groups and research academics increases the relevance of academic research by assisting the community groups in evaluating their novel educational interventions through robust research projects. Furthermore, these small grant partnerships may serve to provide pilot data for more extensive efforts funded by other agencies. Citation Format: Karoline Sondgeroth, Rebecca Palacios, Graciela A Unguez, Mary O'Connell, Helena B Loest, Kaitlin Englund. Community-academic partners working in a small grants program [abstract]. In: Proceedings of the Twelfth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2019 Sep 20-23; San Francisco, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(6 Suppl_2):Abstract nr B047.

Background We have previously shown that SLE BMSC have decreased proliferation, increased ROS, increased DNA damage and repair (DDR), a senescence associated secretory phenotype, and increased senescence-associated β-galactosidase. We have also shown SLE BMSC produce increased amounts of interferon beta (IFNβ), have increased mRNA for several genes induced by IFNβ, and have a pro-inflammatory feedback loop mediated by a MAVS. To better understand the phenotype of SLE BMSC we conducted mRNA sequencing. Methods Patients fulfilling SLE classification criteria and age and sex matched healthy controls were recruited under an Institutional Review Board approved protocol. Bone marrow aspirates and peripheral blood samples were obtained. BMSC were isolated and grown in tissue culture. Early passage BMSC were harvested and mRNA samples were sent for RNAseq. Serum samples were assayed for IFNβ by ELISA. Results On the basis of top differentially expressed genes between SLE and healthy controls, SLE patients with high levels of serum IFNβ clustered together while SLE patients with low levels of IFNβ clustered with healthy controls. Those genes differentially expressed in SLE patients generally belonged to known IFN pathways, and showed a strong overlap with the set of genes differentially expressed in IFNβ high subjects, per se. Moreover, gene expression changes induced by treating healthy BMSC with exogenous IFNβ were remarkably similar to gene expression differences in SLE IFNβ high vs low BMSC. Conclusions BMSCs from SLE patients are heterogeneous. A subgroup of SLE BMSC is distinguished from other SLE BMSC and from controls by increased levels of mRNAs induced by type I interferons. This subgroup of SLE patients had increased levels of IFNβ in vivo.

Background We have previously shown that SLE BMSCs have a pro-inflammatory mediated by a MAVS and IFNβ feedback loop. Compared to healthy controls, SLE BMSCs produced increased amounts of IFNβ and had increased mRNA for several genes induced relatively specifically by IFNβ. They also had decreased proliferation, increased ROS, increased DNA damage and repair (DDR), a senescence associated secretory phenotype, and increased senescence-associated β-galactosidase. To better understand the phenotype of SLE BMSCs we conducted RNA sequencing. Methods Patients fulfilling SLE classification criteria and age and sex matched healthy controls were recruited under an Institutional Review Board approved protocol (6 pairs). Bone marrow aspirates and peripheral blood samples were obtained. BMSCs were isolated with low density Ficoll/Hypaque and grown in tissue culture. Purity of BMSC cultures were verified by flow cytometry. Early passage BMSC were harvested and mRNA samples were sent for RNAseq through the University of Rochester Genomics Core. Serum samples with assayed for IFNβ using an ELISA from PBL. Results Hierarchical clustering of normalized RNAseq profiles found SLE patients with high levels of serum IFNβ (>13 units per XXX) grouped together while SLE patients with low levels of IFNβ grouped together with healthy controls. Principal component analysis found the majority of the variance could be explained by PC1 (32.3%) and PC2 (25.5%). While PC1 did not separate SLE or SLE IFNβ high from the other samples, PC2 clearly differentiated SLE IFNβ high samples from SLE IFNβlow and control samples. SLE IFNβ low and control sample overlapped in both PC1 and PC2. The top upregulated genes in PC2 were RSAD2, MX1, IFIT1, IFIT2, OAS1, CMPK2, OASL, IFIT3, ISG15, IDO1, IFI6, MX2, HERC5, and IFIH1 … all type I interferon-induced genes. Conclusions BMSCs from SLE patients are heterogeneous. A subgroup of SLE BMSC are distinguished from other SLE BMSC and from controls by increased levels of mRNAs induced by type I interferons. Moreover, SLE BMSC with increased levels of mRNA for type I interferon-induced genes when grown in vitro are derived from patients with increased levels of IFNβ in vivo. Acknowledgements This work was supported in part by a grant from the Lupus Research Alliance.

Background Age-associated B cells (ABCs) are associated with autoantibody production in lupus-like mice. This population is expanded upon exposure to self-antigen and interferon-γ. ABCs in mice are identified as CD11c+, CD21− and T-bet+. However, the characterization of these cells and factors promoting their generation in human SLE is unclear. The purpose of this study was to define ABCs in human SLE patients and their association with interferon (IFN) status. Methods Peripheral blood leukocytes were purified by density gradient centrifugation from 26 lupus patients with a range of disease activity (n=10 with flaring disease, n=16 controlled disease) and 6 normal healthy donors. Surface and T-bet intracellular antibody staining was analyzed in a blinded fashion by flow cytometry. A putative population of ABCs was defined as CD3− CD19+ CD11c+ CD21− cells. Samples were divided into groups regardless of disease status based upon percentage of B cells with putative ABC phenotype. B cell subset analysis was completed on the groups expressing minimal (≤2%), intermediate (2%–7%), or high (≥8%) levels of ABCs. In addition, the B cell subset distribution (switched memory, unswitched memory, total naive, and CD27- IgD- double negative) and phenotypic markers (CXCR3, T-bet, CD24, IgD, and CD27) of putative ABCs were assessed. IFN-α, IFN-β, and IFN-λ levels were quantitated by ELISA from sera drawn at the same time. Results Five samples were identified as having high putative ABC levels (range 8.4%–20.5% of B cells, mean 14.9%). These CD11c+CD21− CD19+CD3− cells were predominantly CD24− CD27− IgD−. Across all 32 samples, the percentage of putative ABCs positively correlated with percentage of T-bet+ B cells (r=0.819, p=5.4 × 10−9), IgD- CD27- (double negative) B cells (r=0.59, p=0.0003), and CD24- double negative cells (r=0.74, p=8.72 × 10−7) with a high degree of statistical significance. Paired serum samples had a range of type I and type IIII interferon levels (mean +SEM for all samples): 6.2±2.1 pg/m (IFN-α), 4.0±0.6 pg/ml (IFN-β), and 44.1±9.6 pg/ml (IFN-λ1). Analysis including correlation between B cell subsets, interferon status, clinical features and disease activity is in progress. Conclusions An expanded putative ABC population (CD11c+ CD21− CD19+ CD3−) was identified in a subset of human peripheral blood samples. This subset is positively correlated with IgD−CD27−CD24− B cells (DN2 cells), whose expansion has been described previously in lupus patients.

Telomeres do not shorten with age in longest-lived bats., Understanding aging is a grand challenge in biology. Exceptionally long-lived animals have mechanisms that underpin extreme longevity. Telomeres are protective nucleotide repeats on chromosome tips that shorten with cell division, potentially limiting life span. Bats are the longest-lived mammals for their size, but it is unknown whether their telomeres shorten. Using >60 years of cumulative mark-recapture field data, we show that telomeres shorten with age in Rhinolophus ferrumequinum and Miniopterus schreibersii, but not in the bat genus with greatest longevity, Myotis. As in humans, telomerase is not expressed in Myotis myotis blood or fibroblasts. Selection tests on telomere maintenance genes show that ATM and SETX, which repair and prevent DNA damage, potentially mediate telomere dynamics in Myotis bats. Twenty-one telomere maintenance genes are differentially expressed in Myotis, of which 14 are enriched for DNA repair, and 5 for alternative telomere-lengthening mechanisms. We demonstrate how telomeres, telomerase, and DNA repair genes have contributed to the evolution of exceptional longevity in Myotis bats, advancing our understanding of healthy aging.

Bone morphogenetic proteins (BMP) 4 and 7 have important roles in neuronal differentiation and cortical development in the murine brain. However BMP4 and BMP7 expression and functions in the developing human brain are unknown. In this study, frozen tissue human fetal leptomeninges, formalin-fixed tissue and primary fetal leptomeningeal cell cultures were studied. By western blot, BMP4, BMP7 and BMPRIa were demonstrated in 15, 17 20, 23 week (wk) human leptomeninges. BMP receptor II was detected at 15 and 17 wks. Immunohistochemically, BMP4 immunoreactivity was also found in 20 to 39 wk human leptomeninges. BMP4 significantly reduced basal DNA synthesis at 22 wks. BMP7 100 and 300 ng/ml stimulated basal DNA synthesis in the 15, 17 and 22 wk leptomeninges. BMP4 and BMP7 increased phosphorylation of SMAD-1, 5, 8 in most cells and had no effect on phosphorylation of p-38MAPK, or p44/42MAPK. BMP4 and BMP7 produced a decrease in VEGF RNA expression in 2 of 4 leptomeninges. BMP4 and BMP7 increased VEGFR1 RNA in 2 or 3 of 4 leptomeningeal cultures respectively. BMP4 produced a decrease in VEGFR2 RNA in 2 of 4 and BMP7 in 3 of 4 while BMP7 reduced VEGFR2 protein in the leptomeninges. The findings show, for the first time, BMP4, BMP7 and receptors are expressed and active in the human fetal leptomeninges. They suggest these BMPs influence vascular development in this tissue by regulating VEGF and its receptors.

There are numerous phylogenetic reconstruction methods and models available—but which should you use and why? Important considerations in phylogenetic analyses include data quality, structure, signal, alignment length and sampling. If poorly modelled, variation in rates of change across proteins and across lineages can lead to incorrect phylogeny reconstruction which can then lead to downstream misinterpretation of the underlying data. The risk of choosing and applying an inappropriate model can be reduced with some critical yet straightforward steps outlined in this paper. We use the question of the position of the root of placental mammals as our working example to illustrate the topological impact of model misspecification. Using this case study we focus on using models in a Bayesian framework and we outline the steps involved in identifying and assessing better fitting models for specific datasets.

Autocrine platelet derived growth factor-BB (PDGF-BB) and cerebrospinal fluid, which also contains PDGF, stimulate proliferation of leptomeningeal and meningioma cells, in part, by activation of the Raf-1-MEK-1-MAPK pathway. The negative regulators of this activation are not known. However, PDGF receptors and p44/42 MAPK are regulated, in part, by mitogen activated kinase phosphatase 3 (MKP-3) and Src homology carboxyl terminus protein (SHP-2). Six fetal and one adult human leptomeninges specimens and 22 meningiomas were evaluated for MKP-3, SHP-2, and phospho-SHP-2 as well as activation/phosphorylation of MEK1/2, p44/42 MAPK, Akt and signal transducer and activator of transcription 3 (STAT3) by western blot and MKP3 expression by polymerase chain reaction. PDGF-BB and cerebrospinal fluid effects on these phosphatases and signaling were also studied in vitro. MKP-3 and phospho-p44/42 MAPK were detected in all or six of seven leptomeninges, respectively. MKP-3 was detected in six of eight World Health Organization grade I and II meningiomas. Three of four grade I and five of five grade II with no or low MKP-3 had high levels of phospho-p44/42MAPK. MKP3 was not detected in four of six grade III meningiomas. These had high levels of phospho-p44/42MAPK. SHP2 was found in all leptomeninges and meningiomas while phospho-SHP-2 was found in 11 to 33% of grade I–III meningiomas. Reduced MKP-3 may facilitate PDGF-BB autocrine and paracrine mitogenic effects in a subpopulation of higher grade meningiomas by increasing phospho-p44/42 MAPK.

It has been proposed that positive selection may be associated with protein functional change. For example, human and macaque have different outcomes to HIV infection and it has been shown that residues under positive selection in the macaque TRIM5α receptor locate to the region known to influence species-specific response to HIV. In general, however, the relationship between sequence and function has proven difficult to fully elucidate, and it is the role of large-scale studies to help bridge this gap in our understanding by revealing major patterns in the data that correlate genotype with function or phenotype. In this study, we investigate the level of species-specific positive selection in innate immune genes from human and mouse. In total, we analyzed 456 innate immune genes using codon-based models of evolution, comparing human, mouse, and 19 other vertebrate species to identify putative species-specific positive selection. Then we used population genomic data from the recently completed Neanderthal genome project, the 1000 human genomes project, and the 17 laboratory mouse genomes project to determine whether the residues that were putatively positively selected are fixed or variable in these populations. We find evidence of species-specific positive selection on both the human and the mouse branches and we show that the classes of genes under positive selection cluster by function and by interaction. Data from this study provide us with targets to test the relationship between positive selection and protein function and ultimately to test the relationship between positive selection and discordant phenotypes.