Shared Motifs Research Articles

THI1 Gene Evolutionary Trends: A Comprehensive Plant-Focused Assessment via Data Mining and Large-Scale Analysis.

Molecular evolution analysis typically involves identifying selection pressure and reconstructing evolutionary trends. This process usually requires access to specific data related to a target gene or gene family within a particular group of organisms. While recent advancements in high-throughput sequencing techniques have resulted in the rapid accumulation of extensive genomics and transcriptomics data and the creation of new databases in public repositories, extracting valuable insights from such vast datasets remains a significant challenge for researchers. Here, we elucidated the evolutionary history of THI1, a gene responsible for encoding thiamine thiazole synthase. The thiazole ring is a precursor for vitamin B1 and a crucial cofactor in primary metabolic pathways. A thorough search of complete genomes available within public repositories reveals 702 THI1 homologs of Archaea and Eukarya. Throughout its diversification, the plant lineage has preserved the THI1 gene by incorporating the N-terminus and targeting the chloroplasts. Likewise, evolutionary pressures and lifestyle appear to be associated with retention of TPP-riboswitch sites and consequent dual post-transcriptional regulation of the de novo biosynthesis pathway in basal groups. Multicopy retention of THI1 is not a typical plant pattern, even after successive genome duplications. Examining cis-regulatory sites in plants uncovers two shared motifs across all plant lineages. A data mining of 484 transcriptome datasets supports the THI1 homolog expression under a light/dark cycle response and a tissue-specific pattern. Finally, the work presented brings a new look at public repositories as an opportunity to explore evolutionary trends to THI1.

Production and characterization of a panel of anti-mouse placenta-specific protein 1 (plac1) monoclonal antibodies

Placenta-Specific Protein 1 (PLAC1) is essential for normal placental and embryonic development. It is widely expressed in various types of cancer cells. We produced a panel of anti-mouse plac1 monoclonal antibodies (mAbs) with different applications. Two recombinant proteins were produced containing either the extracellular domain (ED) plus tetanus toxin P2, P30, pan-DR epitope (PADRE), and KDEL3 (main plac1) or ED plus KDEL3 (control plac1). Recombinant proteins were used for immunization and screening. Positive clones were selected by ELISA and flow cytometry. Purified mAbs were tested by ELISA, WB, flow cytometry, immunohistochemistry (IHC), and immunofluorescent (IF). A combination of bioinformatics tools was used to predict the target epitope(s) of the mAbs. Eight anti-mouse plac1 mAbs (all IgG1/κ1) were generated, all reacting with high affinity in ELISA. Seven clones recognized plac1 in both reduced and non-reduced Western blots, while one only recognized the non-reduced form. Cross-inhibition ELISA revealed that all mAbs recognized overlapping epitopes with a shared motif except for 5C9. Four clones reacted with the native antigen in flow cytometry, but none were functional in IF or IHC staining. The produced multifunctional mAbs can be used to investigate different aspects of PLAC1 biology in reproduction and cancer.

Irish and Palestinian Mythopoetic Cultural Resistance in the Verse of Yeats, Heaney, and Darwish

This academic inquiry delves into the exploration of mythological resilience and poetic resistance in the literary works of W. B. Yeats, Mahmoud Darwish, and Seamus Heaney amidst the contexts of Irish and Palestinian national resistance movements. Through a detailed analysis of major poetic works such as Yeats’s “Deirdre,” Darwish’s “The Phases of Anat,” and Heaney’s “Bog Queen,” the study investigates the ways in which these poets employ mythology, symbolism, and language as mechanisms of opposition against colonialism, oppression, and cultural obliteration. By embracing a comparative approach in literary studies and integrating postcolonial frameworks, the research endeavors to shed light on shared motifs, thematic concerns, and mythopoeic techniques utilized by these writers. Through their examination of mythic narratives, cultural manifestations, patriotism, and the active function of literature as a tool for resistance, this scholarly work addresses notable gaps in existing academic discourse and presents a sophisticated comprehension of how literary creations influence collective awareness and contribute to movements of cultural and national liberation.

Characterization and stress-responsive regulation of CmPHT1 genes involved in phosphate uptake and transport in Melon (Cucumis melo L.)

BackgroundPhosphorus (P) deficiency, a major nutrient stress, greatly hinders plant growth. Phosphate (Pi) uptake in plant roots relies on PHT1 family transporters. However, melon (Cucumis melo L.) lacks comprehensive identification and characterization of PHT1 genes, particularly their response patterns under diverse stresses.ResultsThis study identified and analyzed seven putative CmPHT1 genes on chromosomes 3, 4, 5, 6, and 7 using the melon genome. Phylogenetic analysis revealed shared motifs, domain compositions, and evolutionary relationships among genes with close histories. Exon number varied from 1 to 3. Collinearity analysis suggested segmental and tandem duplications as the primary mechanisms for CmPHT1 gene family expansion. CmPHT1;4 and CmPHT1;5 emerged as a tandemly duplicated pair. Analysis of cis-elements in CmPHT1 promoters identified 14 functional categories, including putative PHR1-binding sites (P1BS) in CmPHT1;4, CmPHT1;6, and CmPHT1;7. We identified that three WRKY transcription factors regulated CmPHT1;5 expression by binding to its W-box element. Notably, CmPHT1 promoters harbored cis-elements responsive to hormones and abiotic factors. Different stresses regulated CmPHT1 expression differently, suggesting that the adjusted expression patterns might contribute to plant adaptation.ConclusionsThis study unveils the characteristics, evolutionary diversity, and stress responsiveness of CmPHT1 genes in melon. These findings lay the foundation for in-depth investigations into their functional mechanisms in Cucurbitaceae crops.

1228 Comprehensive T-cell Profiling in Chordomas: Single-cell RNA-Seq and TCR Profiling Analysis Uncover Antitumor and Exhaustion Phenotypes for Targeted Immunotherapies

INTRODUCTION: Chordomas, a rare type of tumor, originate from residual notochord tissue. These tumors present important challenges due to the limited treatment options. Investigating the intricacies of T-cell composition and function in chordoma immunity holds the potential to advance immunotherapy strategies for these patients. METHODS: We generated a comprehensive single-cell atlas of T cells of chordomas, incorporating paired single-cell transcriptomic samples from the tumor and blood of five patients and single-cell TCR sequencing data to assess T-cell clonality. Additionally, we analyzed T cells in 33 chordomas (22 newly diagnosed and 11 recurrent tumors) using multiplex immunofluorescence. RESULTS: Our results demonstrate that CD8+ T-cell antitumoral immunity originates in the periphery, marked by clonal expansion of cytotoxic and memory T cells in the blood. However, this immunity experiences progressive exhaustion upon tumor infiltration. Notably, a large percentage of CD8+ T-cells from the tumors and blood shared their TCRs with exhausted CD8+ T-cells known for tumor specificity, confirming the origin of a peripheral antitumor response. We identified specific antigen peptide sequences through TCR analysis that were enriched in exhausted T cell receptors' binding sites that uncovered shared motifs within the reactive tumor-infiltrating compartment. Moreover, we observed that CTLA-expressing central memory and Tregs made up most of the CD4 T-cell tumoral landscape. Interestingly, multiplex immunofluorescence showed a higher abundance of CD3+ T cells in newly diagnosed chordomas compared to recurrent cases. CONCLUSIONS: This study sheds light on the composition and function of T cells in chordomas, revealing the origin and exhaustion of CD8+ T-cell antitumor immunity. These findings contribute to our understanding of chordoma immunity to guide the development of targeted immunotherapies for both newly diagnosed and recurrent cases.

Postmodernism in Lord Of The Lost’s Judas: The apocryphal The Gospel of Judas, William Shakespeare’s Romeo and Juliet, and the role of the stars

Lord Of The Lost’s Judas (2021) is a thematic concept album exploring different aspects of the Judas reception without a straightforward narrative or interpretation, but covering varying viewpoints on betrayal and salvation. It hereby pushes the boundaries of heavy metal as a genre by combining different texts. The band explicitly points out their first source of inspiration, the apocryphal The Gospel of Judas (~100–80 ad), and adds that the album also features the literary theme of impossible (here: brotherly) love. I argue that the album references a specific text implementing this theme, namely William Shakespeare’s Romeo and Juliet (1597), most prominently implied by ‘star-crossed’. These two texts are as different as they could be, contrasting, e.g. religious enlightenment and entertainment. Still, they have one thing in common: they both rely heavily on Christian astrology. By investigating how the album makes use of this shared motif to create its own version of star-induced fate, I show how both texts overlap and intermingle on the album. The result is a kaleidoscope that is a prime example of postmodernism. By refusing a fixed depiction of Christian imagery and even adding another text, Judas demonstrates that art does not have to be linear or limiting, and opens heavy metal to new, postmodern ways.

PRDM16 co-operates with LHX2 to shape the human brain.

PRDM16 is a dynamic transcriptional regulator of various stem cell niches, including adipocytic, hematopoietic, cardiac progenitors, and neural stem cells. PRDM16 has been suggested to contribute to 1p36 deletion syndrome, one of the most prevalent subtelomeric microdeletion syndromes. We report a patient with a de novo nonsense mutation in the PRDM16 coding sequence, accompanied by lissencephaly and microcephaly features. Human stem cells were genetically modified to mimic this mutation, generating cortical organoids that exhibited altered cell cycle dynamics. RNA sequencing of cortical organoids at day 32 unveiled changes in cell adhesion and WNT-signaling pathways. ChIP-seq of PRDM16 identified binding sites in postmortem human fetal cortex, indicating the conservation of PRDM16 binding to developmental genes in mice and humans, potentially at enhancer sites. A shared motif between PRDM16 and LHX2 was identified and further examined through comparison with LHX2 ChIP-seq data from mice. These results suggested a collaborative partnership between PRDM16 and LHX2 in regulating a common set of genes and pathways in cortical radial glia cells, possibly via their synergistic involvement in cortical development.

Yoshihiro Tatsumi’s Influence on Adrian Tomine’s Short-Story Cycle Killing and Dying

ABSTRACT Adrian Tomine’s Killing and Dying (2015) is one of the most celebrated graphic novels of the twenty-first century—although that genre designation is misleading inasmuch as the book is actually a short-story cycle composed of six seemingly autonomous short stories linked together by shared topics and motifs. This essay examines how Tomine achieves overall narrative unity despite the individual stories’ heterogeneous settings, plots, and characters. In particular, this analysis examines how Tomine employs the theme of “striving and failing” to link the texts: each entry is united by a character’s need to connect, to be seen, to be understood. Protagonists suffer from worries and fears they are unable to articulate, their anxieties rarely fully framed on the page. Additionally, this reading of Killing and Dying explores how Tomine sublimates the influence of 1960s manga artist Yoshihiro Tatsumi (1935–2015), whose work Tomine helped bring to English-speaking audiences after decades of neglect, in organizing the cycle.

JS07.4.A REGIONAL B-CELL MEDIATED IMMUNOSUPPRESSION IDENTIFIED THROUGH SPATIAL AND SINGLE-CELL TRANSCRIPTOMIC ANALYSIS OF CHORDOMA

Abstract BACKGROUND Chordomas, rare indolent neoplasms, mainly occur in the skull base or lower spine. Therapies, including surgery and radiotherapy, often fail to impede local recurrence. Though checkpoint inhibition therapy shows promise, recent immunotherapy trials failed to reach endpoints. Here, we aim to investigate the immunological landscape of chordomas using spatial and single-cell transcriptomics, and TCR/BCR profiling, elucidating cellular interplay and the intricate mechanisms governing the immunosuppressive tumor microenvironment. MATERIAL AND METHODS We generated a comprehensive single-cell atlas of the chordoma neoplastic landscape and its associated microenvironment, incorporating paired single-cell transcriptomic samples from blood and tumor cells of six patients, as well as single-cell BCR and TCR sequencing data. Utilizing scGEN, we integrated pre-annotated gene expression datasets and identified both established and novel antigen binding patterns by employing TCR Bidirectional Encoder Representations from Transformers (BERT). Moreover, we conducted GeoMx Digital Spatial Profiler (DSP) analysis by selecting regions of interest (ROIs) that encompass critical immunological and malignant niches. We also curated and quantified cell distributions in immunohistochemical staining for a total of 107 chordomas. RESULTS Utilizing pseudo-temporal mapping, we delineated the trajectories of CD8 and CD4 T cells in chordomas, spanning from blood to tumor stroma and encompassing naïve, memory, cytotoxic, and T cell exhaustion profiles. Through an integrated TCR profiling methodology, we observed extratumoral clonal expansion of cytotoxic and memory T cells in the blood, whereas the majority of intratumoral T cells with shared motifs exhibited terminal exhaustion. Leveraging TCR-BERT, we identified binding patterns exclusively enriched in exhausted T cell receptors' binding sites and uncovered shared motifs within the reactive tumor-infiltrating compartment, implying the existence of potential reservoirs for anti-tumor immunity. Investigating the cell-cell interactions driving intratumoral exhaustion, we identified M2 tumor-associated macrophages and a plasma cell phenotype-like subset upregulating TGFB and IL10 expression, referred to as regulatory B cells (Bregs). Spatial profiling substantiated the proximity of regulatory B cells and exhausted T cells within immunosuppressive niches, suggesting an underexplored mechanism contributing to tumor-derived T cell exhaustion. CONCLUSION Regulatory B-cells have been identified in the TME of various solid tumors, including colorectal, breast, cervical, and ovarian carcinomas. Our study emphasizes the role of regulatory B cells in the chordoma immune environment, providing crucial insights into novel immunosuppressive mechanisms and pathways leading to T cell exhaustion in chordoma.

Mining for a new class of fungal natural products: the evolution, diversity, and distribution of isocyanide synthase biosynthetic gene clusters.

The products of non-canonical isocyanide synthase (ICS) biosynthetic gene clusters (BGCs) mediate pathogenesis, microbial competition, and metal-homeostasis through metal-associated chemistry. We sought to enable research into this class of compounds by characterizing the biosynthetic potential and evolutionary history of these BGCs across the Fungal Kingdom. We amalgamated a pipeline of tools to predict BGCs based on shared promoter motifs and located 3800 ICS BGCs in 3300 genomes, making ICS BGCs the fifth largest class of specialized metabolites compared to canonical classes found by antiSMASH. ICS BGCs are not evenly distributed across fungi, with evidence of gene-family expansions in several Ascomycete families. We show that the ICS dit1/2 gene cluster family (GCF), which was prior only studied in yeast, is present in ∼30% of all Ascomycetes. The dit variety ICS exhibits greater similarity to bacterial ICS than other fungal ICS, suggesting a potential convergence of the ICS backbone domain. The evolutionary origins of the dit GCF in Ascomycota are ancient and these genes are diversifying in some lineages. Our results create a roadmap for future research into ICS BGCs. We developed a website (https://isocyanides.fungi.wisc.edu/) that facilitates the exploration and downloading of all identified fungal ICS BGCs and GCFs.

Z-flipon variants reveal the many roles of Z-DNA and Z-RNA in health and disease.

Identifying roles for Z-DNA remains challenging given their dynamic nature. Here, we perform genome-wide interrogation with the DNABERT transformer algorithm trained on experimentally identified Z-DNA forming sequences (Z-flipons). The algorithm yields large performance enhancements (F1 = 0.83) over existing approaches and implements computational mutagenesis to assess the effects of base substitution on Z-DNA formation. We show Z-flipons are enriched in promoters and telomeres, overlapping quantitative trait loci for RNA expression, RNA editing, splicing, and disease-associated variants. We cross-validate across a number of orthogonal databases and define BZ junction motifs. Surprisingly, many effects we delineate are likely mediated through Z-RNA formation. A shared Z-RNA motif is identified in SCARF2, SMAD1, and CACNA1 transcripts, whereas other motifs are present in noncoding RNAs. We provide evidence for a Z-RNA fold that promotes adaptive immunity through alternative splicing of KRAB domain zinc finger proteins. An analysis of OMIM and presumptive gnomAD loss-of-function datasets reveals an overlap of Z-flipons with disease-causing variants in 8.6% and 2.9% of Mendelian disease genes, respectively, greatly extending the range of phenotypes mapped to Z-flipons.

Genome-Wide Analysis of DREB Family Genes and Characterization of Cold Stress Responses in the Woody Plant Prunus nana.

Dehydration response element binding factor (DREB) is a family of plant-specific transcription factors, whose members participate in the regulation of plant responses to various abiotic stresses. Prunus nana, also known as the wild almond, is a member of the Rosaceae family that is rare and found to grow in the wild in China. These wild almond trees are found in hilly regions in northern Xinjiang, and exhibit greater drought and cold stress resistance than cultivated almond varieties. However, the response of P. nana DREBs (PnaDREBs) under low temperature stress is still unclear. In this study, 46 DREB genes were identified in the wild almond genome, with this number being slightly lower than that in the sweet almond (Prunus dulcis cultivar 'Nonpareil'). These DREB genes in wild almond were separated into two classes. All PnaDREB genes were located on six chromosomes. PnaDREB proteins that were classified in the same groups contained specific shared motifs, and promoter analyses revealed that PnaDREB genes harbored a range of stress-responsive elements associated with drought, low-temperature stress, light responsivity, and hormone-responsive cis-regulatory elements within their promoter regions. MicroRNA target site prediction analyses also suggested that 79 miRNAs may regulate the expression of 40 of these PnaDREB genes, with PnaDREB2. To examine if these identified PnaDREB genes responded to low temperature stress, 15 of these genes were selected including seven homologous to Arabidopsis C-repeat binding factor (CBFs), and their expression was assessed following incubation for 2 h at 25 °C, 5 °C, 0 °C, -5 °C, or -10 °C. In summary, this analysis provides an overview of the P. nana PnaDREB gene family and provides a foundation for further studies of the ability of different PnaDREB genes to regulate cold stress responses in almond plants.

Cultural Connections Between China and Foreign Civilizations Through the Kucha Donor Images in the Kizil Caves

Kucha was a small country once existed in the western border of China. Its famous Kizil Caves represents the importance of Buddhism to this country. This research focuses on the Kucha donor images found in some of the Kizil Caves, mainly two group of donors from cave No. 199 and No. 205. The dates, traits of clothing and “tipping toe” standing posture, and identity of these donors are argued and discussed, and they are compared to Sogdian, Bactrian, Persian, and Roman artworks that share similar clothing style or standing posture. Historical evidence is then presented throughout the paper to prove that the similar clothing style and standing posture between Kucha donors and foreign figures reflect cultural connections across the Eurasian continent, on the Silk Road. The paper also explains how the “tipping toe” standing posture is a shared artistic motif but is interpreted and used differently across cultures, thus leading to the author attempting to answer the question: why these Kucha donors were drawn in the Kizil Buddhist Caves. The research mainly uses articles and books written by professional scholars, with the support of some primary texts as historical evidence. Additional archaeological discoveries and art history visual analysis are applied to aid the conclusion of this paper.

Autoimmunity-associated T cell receptors recognize HLA-B*27-bound peptides.

Human leucocyte antigen B*27 (HLA-B*27) is strongly associated with inflammatory diseases of the spine and pelvis (for example, ankylosing spondylitis (AS)) and the eye (that is, acute anterior uveitis (AAU))1. How HLA-B*27 facilitates disease remains unknown, but one possible mechanism could involve presentation of pathogenic peptides to CD8+ T cells. Here we isolated orphan T cell receptors (TCRs) expressing a disease-associated publicβ-chain variable region-complementary-determining region 3β (BV9-CDR3β) motif2-4 from blood and synovial fluid T cells from individuals with AS and fromthe eye in individuals withAAU. These TCRs showed consistent α-chain variable region (AV21) chain pairing and were clonally expanded in the joint and eye. We used HLA-B*27:05 yeast display peptide libraries to identify shared self-peptides and microbial peptides that activated the AS- and AAU-derived TCRs. Structural analysis revealed that TCR cross-reactivity for peptide-MHC was rooted in a shared binding motif present in both self-antigens and microbial antigens that engages the BV9-CDR3β TCRs. These findings support the hypothesis that microbial antigens and self-antigens could play a pathogenic role in HLA-B*27-associated disease.

Prediction and Motif Analysis of 2’-O-methylation Using a Hybrid Deep Learning Model from RNA Primary Sequence and Nanopore Signals

Background: 2’-O-Methylation (2’-O-Me) is a post-transcriptional RNA modification that occurs in the ribose sugar moiety of all four nucleotides and is abundant in both coding and non-coding RNAs. Accurate prediction of each subtype of 2’-O-Me (Am, Cm, Gm, Um) helps understand their role in RNA metabolism and function. Objective: This study aims to build models that can predict each subtype of 2’-O-Me from RNA sequence and nanopore signals and exploit the model interpretability for sequence motif mining. Methods: We first propose a novel deep learning model DeepNm to better capture the sequence features of each subtype with a multi-scale framework. Based on DeepNm, we continue to propose HybridNm, which combines sequences and nanopore signals through a dual-path framework. The nanopore signalderived features are first passed through a convolutional layer and then merged with sequence features extracted from different scales for final classification. Results: A 5-fold cross-validation process on Nm-seq data shows that DeepNm outperforms two stateof- the-art 2’-O-Me predictors. After incorporating nanopore signal-derived features, HybridNm further achieved significant improvements. Through model interpretation, we identified not only subtypespecific motifs but also revealed shared motifs between subtypes. In addition, Cm, Gm, and Um shared motifs with the well-studied m6A RNA methylation, suggesting a potential interplay among different RNA modifications and the complex nature of epitranscriptome regulation. Conclusion: The proposed frameworks can be useful tools to predict 2’-O-Me subtypes accurately and reveal specific sequence patterns.

Exploration of shared features of B cell receptor and T cell receptor repertoires reveals distinct clonotype clusters.

Although B cells and T cells are integral players of the adaptive immune system and act in co-dependent ways to orchestrate immune responses, existing methods to study the immune repertoire have largely focused on separate analyses of B cell receptor (BCR) and T cell receptor (TCR) repertoires. Based on our hypothesis that the shared history of immune exposures and the shared cellular machinery for recombination result in similarities between BCR and TCR repertoires in an individual, we examine any commonalities and interrelationships between BCR and TCR repertoires. We find that the BCR and TCR repertoires have covarying clonal architecture and diversity, and that the pattern of correlations appears to be altered in immune-mediated diseases. Furthermore, hierarchical clustering of public B and T cell clonotypes in both health and disease based on correlation of clonal proportion revealed distinct clusters of B and T cell clonotypes that exhibit increased sequence similarity, share motifs, and have distinct amino acid characteristics. Our findings point to common principles governing memory formation, recombination, and clonal expansion to antigens in B and T cells within an individual. A significant proportion of public BCR and TCR repertoire can be clustered into nonoverlapping and correlated clusters, suggesting a novel way of grouping B and T cell clonotypes.

Super-enhancers conserved within placental mammals maintain stem cell pluripotency

Despite pluripotent stem cells sharing key transcription factors, their maintenance involves distinct genetic inputs. Emerging evidence suggests that super-enhancers (SEs) can function as master regulatory hubs to control cell identity and pluripotency in humans and mice. However, whether pluripotency-associated SEs share an evolutionary origin in mammals remains elusive. Here, we performed comprehensive comparative epigenomic and transcription factor binding analyses among pigs, humans, and mice to identify pluripotency-associated SEs. Like typical enhancers, SEs displayed rapid evolution in mammals. We showed that BRD4 is an essential and conserved activator for mammalian pluripotency-associated SEs. Comparative motif enrichment analysis revealed 30 shared transcription factor binding motifs among the three species. The majority of transcriptional factors that bind to identified motifs are known regulators associated with pluripotency. Further, we discovered three pluripotency-associated SEs (SE-SOX2, SE-PIM1, and SE-FGFR1) that displayed remarkable conservation in placental mammals and were sufficient to drive reporter gene expression in a pluripotency-dependent manner. Disruption of these conserved SEs through the CRISPR-Cas9 approach severely impaired stem cell pluripotency. Our study provides insights into the understanding of conserved regulatory mechanisms underlying the maintenance of pluripotency as well as species-specific modulation of the pluripotency-associated regulatory networks in mammals.

Structure of dynein-dynactin on microtubules shows tandem adaptor binding.

Cytoplasmic dynein is a microtubule motor that is activated by its cofactor dynactin and a coiled-coil cargo adaptor1-3. Up to two dynein dimers can be recruited per dynactin, and interactions between them affect their combined motile behaviour4-6. Different coiled-coil adaptors are linked to different cargos7,8, and some share motifs known to contact sites on dynein and dynactin4,9-13. There is limited structural information on how the resulting complex interacts with microtubules and how adaptors are recruited. Here we develop a cryo-electron microscopy processing pipeline to solve the high-resolution structure of dynein-dynactin and the adaptor BICDR1 bound to microtubules. This reveals the asymmetric interactions between neighbouring dynein motor domains and how they relate to motile behaviour. We found that two adaptors occupy the complex. Both adaptors make similar interactions with the dyneins but diverge in their contacts with each other and dynactin. Our structure has implications for the stability and stoichiometry of motor recruitment by cargos.

Cryo-EM structure of anchorless RML prion reveals variations in shared motifs between distinct strains

Little is known about the structural basis of prion strains. Here we provide a high (3.0 Å) resolution cryo-electron microscopy-based structure of infectious brain-derived fibrils of the mouse anchorless RML scrapie strain which, like the recently determined hamster 263K strain, has a parallel in-register β-sheet-based core. Several structural motifs are shared between these ex vivo prion strains, including an amino-proximal steric zipper and three β-arches. However, detailed comparisons reveal variations in these shared structural topologies and other features. Unlike 263K and wildtype RML prions, the anchorless RML prions lack glycophosphatidylinositol anchors and are severely deficient in N-linked glycans. Nonetheless, the similarity of our anchorless RML structure to one reported for wildtype RML prion fibrils in an accompanying paper indicates that these post-translational modifications do not substantially alter the amyloid core conformation. This work demonstrates both common and divergent structural features of prion strains at the near-atomic level.

Genome Wide Identification and Expression Profiling Indicate Expansion of Family I84 Protease Inhibitor via Gene Tandem Duplication and Divergence in Razor Clam Sinonovacula constricta.

Family I84 protease inhibitors represent a novel family in the MEROPS peptidase database and are likely unique for molluscan host defense. Two Family I84 members, scSI-1 and scSI-2, were reported from the razor clam Sinonovacula constricta in a previous research. In the present study, 12 additional genes, named scSI-3 to scSI-14, were identified via genome wide sequence analyses. Among them, 10 genes were predicted to have a signal sequence, but one (scSI-7) was not. Besides, one sequence (scSI-14) was likely to encode a prematurely terminated peptide. The predicted mature peptides shared characteristics including 12 conserved cysteine residues, isoelectric points of 4.98 to 6.11, and molecular weights of 7.1 to 9.3 kDa with previously reported family members. Four motifs were characterized in 13 predicted mature peptides (with exception of scSI-14), which shared two to four conserved cysteine residues, are possibly to form two functional domain comprised 6 cysteine residues, respectively. At genomic level, all the 14 razor clam Family I84 genes were organized into 3 exons and 2 introns; 13 of them clustered in 3 regions of 100 kb on 3 separate chromosomes, suggesting tandem duplications of related genes. The promoter region of all the 14 genes was predicted to share some transcription factor binding sites, in particular those responsive to pathological and physiological stimuli, but no shared motifs were identified. Analyses also revealed differences in expression patterns among the genes. One gene in a tandem duplicated gene pairs usually showed a higher expression level than the other whereas non-tandem duplicated genes exhibited a higher degree of correlation in expression level. In addition, 8 of the 14 genes demonstrated higher level of expression in Vibrio tolerant clams than in non-tolerant clams following challenges with Vibrio parahaemolyticus. These results generated important information about the evolution of Family I84 protease inhibitors in S. constricta.