Extensive Variation Research Articles

Phenotypic Variability among Chilli Germplasms Using Shannon-Weiner Index (H')

The investigation was conducted during the rabi season (September 2019 to February 2020) of 2019 to 2020 at the research field of All India Co-ordinated Vegetable Crops, located at Bidhan Chandra Krishi Viswavidyalaya in Kalyani, Nadia, West Bengal, India. The aim of the study was to examine the characteristics of twenty-six chilli genotypes across twelve qualitative traits. The investigation unveiled a broad range of phenotypic variability using Randomized Block Design in three replications. Among the assessed traits, leaf density, leaf shape, fruit shape, plant habit, fruit curvature, and anther colour exhibited the most extensive variations among the genotypes. Conversely, the traits with the least diversity values, all falling below the overall mean, included fruit surface (0.28%), leaf colour (0.42%), stem pubescence (0.42%), stem colour (0.42%), anthocyanin colouration at nodes (0.48%), and leaf pubescence (0.48%). The Shannon-Weiner Diversity Index (H') ranged from 0.28 to 1.07. Of the traits evaluated, leaf density displayed the highest diversity index (1.07), followed by leaf shape (1.05), fruit shape (1.01), plant habit (0.86), fruit curvature (0.69), and anther colour (0.58). The obtained Shannon-Weiner Diversity Index, with an average value of 64.66%, confirmed the presence of significant diversity within the examined chilli genotypes. The results suggest that the indirect selection of chilli parent plants based on a range of morphological characteristics can offer advantages in the management of both biotic and abiotic stresses. The information holds significant value for effective pre-breeding, management, and utilization in crop improvement initiatives, in addition to augmenting the genetic potential of the crop.

Molecular characterization and phylogenetic analysis of porcine epidemic diarrhea virus in Xinjiang, China, from 2020 to 2022.

In recent years, the pig industry in Xinjiang, China, has been severely impacted by outbreaks of porcine epidemic diarrhea (PED), despite vaccination efforts. In this study, we investigated the genetic characteristics of currently prevalent porcine epidemic diarrhea virus (PEDV) strains in the region. We collected 548 samples from animals with suspected PED on large-scale pig farms in Xinjiang. Of these, 258 tested positive for PEDV by RT-PCR, yielding an overall positivity rate of 47.08%. S1 gene sequencing and phylogenetic analysis were conducted on 23 randomly selected RT-PCR-positive samples. Three endemic strains of PEDV (PEDV/CH/XU/2020, PEDV/CH/XK/2020, and PEDV/CH/XA/2020) were isolated, and their complete genome sequences were analyzed for evidence of genetic recombination. Sequence comparison of the S gene indicated significant variations in the S1 gene of the Xinjiang strains compared to the vaccine strains CV777, AJ1102, and LWL, with 90.2%-98.5% nucleotide sequence identity. Notably, both the N-terminal and C-terminal domains of the S protein showed significant variation. Genetic evolutionary analysis identified the GIIa subtype as the dominant genotype among the epidemic strains in Xinjiang. Recombination analysis revealed inter-subtype recombination events in the PEDV/CH/XK/2020 and XJ1904-34 strains. These findings highlight the extensive genetic variation in the predominant GIIa genotype of PEDV in Xinjiang, which does not match the genotype of the currently used vaccine strains. These data may guide further efforts toward the development of effective vaccines for the control of PED.

Numeracy Education for Adult Learners: A Scan of the Field and Principles for Course and Materials Design

Additional research is needed to improve adult numeracy instruction, training for instructors, and our understanding of the feasibility and impact of innovations in these areas. The Adult Numeracy in the Digital Era (ANDE) project, funded by the Institute of Education Sciences (IES) at the U.S. Department of Education, seeks to develop and test an innovative, technology-enabled approach for improving adult numeracy and digital literacy instruction. We began this project guided by principles of user-centered design, specifically the principle of knowing the user’s wants and needs. We conducted a “field scan” of adult numeracy and digital literacy, by interviewing researchers, instructors, students; conducting classroom observations; and reviewing literature. We detail our key findings within two emergent themes: (1) extensive variability in learner backgrounds and readiness, instructors’ experiences, standards alignment, course structures, and classroom contexts; and (2) diversity of learner goals and the actions they and their instructors took as they worked together within the course and local policy contexts. We also identify three design principles to guide course development, suggesting that adult numeracy courses should be: aligned and relevant; interactive and participatory; and relationship-centered. These principles guided the design of our adult numeracy course, and we offer questions that current instructors can consider as they design their own adult numeracy lessons.

A Machine learning perspective on hardness prediction in multicomponent Al-Mg based lightweight alloys

Achieving the desired hardness in Al-Mg alloys through experimentation is challenging, costly, and time-consuming, given the extensive composition variations and diverse aging conditions. This research utilizes a range of machine learning (ML) techniques to expedite the advancement of high-performance Al-Mg alloys. The research focused on Al-Mg-X (where X represents elements like Cu, Zn, etc.) alloys, compiling data from literature sources that included composition of alloy, the conditions under which aging occurred (including both time and temperature factors), various physical properties, and the measurement of hardness. These datasets were employed to train seven different ML algorithms aimed at predicting Al alloys with enhanced hardnesses. The findings indicated that the CatBoost model proved effective in forecasting the hardness with excellent predictive performance, surpassing other machine learning approaches, as evidenced by various optimisation metrics.

The Genetic Homogeneity of Uganda’s East African Highland Bananas (Mutika/Lujugira) Does Not Match the Extensive Morphological Variation Identified in this Subgroup

The East African Highland banana (Mutika/Lujugira subgroup) is composed of triploid (AAA) cooking and beer banana varieties that are adapted to the high-altitude region of the Great Lakes region of East Africa. Banana production is affected by several biotic and abiotic factors. Breeding opportunities in bananas are limited due to female sterility and parthenocarpy. The genetic diversity of crops enables breeders to develop new germplasm. Molecular markers have been used widely to dissect crop plants’ genetic diversity. This study assessed the genetic variation in 27 varieties from the Mutika/Lujugira subgroup using random amplified polymorphic DNA (RAPD). No genetic variation was observed among the banana varieties, and the 18 ten-mer primers produced monomorphic banding profiles. The genetic homogeneity of this banana subgroup is not congruent with their extensive morphological variation. Domestication and the bottleneck effect are often cited as the cause of reduced diversity in crop plants. On the other hand, several mechanisms, including somatic mutations, transposable elements, polyploidy, genome plasticity, and epigenetic mechanisms, are known to increase plant phenotypic variability. Further in-depth research is needed to explain the puzzle between the genetic and morphological diversity in the Mutika/Lujugira subgroup.

Studying Venom Toxin Variation Using Accurate Masses from Liquid Chromatography–Mass Spectrometry Coupled with Bioinformatic Tools

This study provides a new methodology for the rapid analysis of numerous venom samples in an automated fashion. Here, we use LC-MS (Liquid Chromatography–Mass Spectrometry) for venom separation and toxin analysis at the accurate mass level combined with new in-house written bioinformatic scripts to obtain high-throughput results. This analytical methodology was validated using 31 venoms from all members of a monophyletic clade of Australian elapids: brown snakes (Pseudonaja spp.) and taipans (Oxyuranus spp.). In a previous study, we revealed extensive venom variation within this clade, but the data was manually processed and MS peaks were integrated into a time-consuming and labour-intensive approach. By comparing the manual approach to our new automated approach, we now present a faster and more efficient pipeline for analysing venom variation. Pooled venom separations with post-column toxin fractionations were performed for subsequent high-throughput venomics to obtain toxin IDs correlating to accurate masses for all fractionated toxins. This workflow adds another dimension to the field of venom analysis by providing opportunities to rapidly perform in-depth studies on venom variation. Our pipeline opens new possibilities for studying animal venoms as evolutionary model systems and investigating venom variation to aid in the development of better antivenoms.

Nutrient supplementation changes chemical composition of soil organic matter density fractions in desert steppe soil in northern China

The influence of reactive nitrogen (N) and phosphorus (P) supplementation on ecosystem dynamics of soil organic matter (SOM) shows extensive variations. The underlying mechanisms of regulation of the chemical composition and dynamics of different SOM density fractions (DFs) in aggregates in a desert steppe by N and P supplementation are unclear. Here, the chemical composition and organic carbon (C) and N dynamics of various SOM DFs under N and P addition were assessed. Surface soil samples taken at 0–10 cm depth were obtained from 4-year (2017–2021) experiments under four conditions, namely N treatment, P treatment, combined N and P treatment (NP), and no nutrient supplementation (CK), in a desert steppe located in northern China. Nutrient supplementation significantly increased (P < 0.05) SOM content by 8.89–35.4%; however, the total N content remained constant. N addition mainly increased SOM content in the macroaggregates (>0.25 mm), while P enhanced SOM in microaggregates (0.25–0.053 mm) and silt-clay (<0.053 mm). The fine particulate organic matter (fPOM) proportion was increased significantly (P < 0.05) by 18.4% and 16.4% in macro- and microaggregates under N addition, respectively; P addition mainly enhanced mineral-associated SOM (mSOM) proportion in aggregates. N supplementation remarkably enhanced (P < 0.05) fPOM’s organic C content by 27.3% and 32.0%, and N content by 40.9% and 145.7% in macro- and microaggregates, respectively. Single N and P addition promoted the enrichment of labile and resistant organic components in light fraction (LF), respectively. N promoted the enrichment of stable organic components in the mSOM of microaggregates. Nutrient inputs drive mSOM formation through the interaction of carboxyl-C and mineral surface. Based on a stronger δ13C and δ15N signal, N addition enhanced SOM decomposition in aggregates. Nutrient supplementation promoted SOM accumulation through the formation of more stable old C in POM and silt-clay. Our findings suggest that SOM accumulation in desert steppe probably increases following nutrient addition, but the mechanism is different through which N or P enrichment affects soil dynamics and chemical composition of SOM DFs in desert steppe.

Comparative analysis and classification of highly divergent mouse rDNA units based on their intergenic spacer (IGS) variability.

Ribosomal DNA (rDNA) repeat units are organized into tandem clusters in eukaryotic cells. In mice, these clusters are located on at least eight chromosomes and show extensive variation in the number of repeats between mouse genomes. To analyze intra- and inter-genomic variation of mouse rDNA repeats, we selectively isolated 25 individual rDNA units using Transformation-Associated Recombination (TAR) cloning. Long-read sequencing and subsequent comparative sequence analysis revealed that each full-length unit comprises an intergenic spacer (IGS) and a ∼13.4 kb long transcribed region encoding the three rRNAs, but with substantial variability in rDNA unit size, ranging from ∼35to ∼46 kb. Within the transcribed regions of rDNA units, we found 209 variants, 70 of which are in external transcribed spacers (ETSs); but the rDNA size differences are driven primarily by IGS size heterogeneity, due to indels containing repetitive elements and some functional signals such as enhancers. Further evolutionary analysis categorized rDNA units into distinct clusters with characteristic IGS lengths; numbers of enhancers; and presence/absence of two common SNPs in promoter regions, one of which is located within promoter (p)RNA and may influence pRNA folding stability. These characteristic features of IGSs also correlated significantly with 5'ETS variant patterns described previously and associated with differential expression of rDNA units. Our results suggest that variant rDNA units are differentially regulated and open a route to investigate the role of rDNA variation on nucleolar formation and possible associations with pathology.

Integrative analysis of DNA replication origins and ORC-/MCM-binding sites in human cells reveals a lack of overlap.

Based on experimentally determined average inter-origin distances of ~100 kb, DNA replication initiates from ~50,000 origins on human chromosomes in each cell cycle. The origins are believed to be specified by binding of factors like the origin recognition complex (ORC) or CTCF or other features like G-quadruplexes. We have performed an integrative analysis of 113 genome-wide human origin profiles (from five different techniques) and five ORC-binding profiles to critically evaluate whether the most reproducible origins are specified by these features. Out of ~7.5 million union origins identified by all datasets, only 0.27% (20,250 shared origins) were reproducibly obtained in at least 20 independent SNS-seq datasets and contained in initiation zones identified by each of three other techniques, suggesting extensive variability in origin usage and identification. Also, 21% of the shared origins overlap with transcriptional promoters, posing a conundrum. Although the shared origins overlap more than union origins with constitutive CTCF-binding sites, G-quadruplex sites, and activating histone marks, these overlaps are comparable or less than that of known transcription start sites, so that these features could be enriched in origins because of the overlap of origins with epigenetically open, promoter-like sequences. Only 6.4% of the 20,250 shared origins were within 1 kb from any of the ~13,000 reproducible ORC-binding sites in human cancer cells, and only 4.5% were within 1 kb of the ~11,000 union MCM2-7-binding sites in contrast to the nearly 100% overlap in the two comparisons in the yeast, Saccharomyces cerevisiae. Thus, in human cancer cell lines, replication origins appear to be specified by highly variable stochastic events dependent on the high epigenetic accessibility around promoters, without extensive overlap between the most reproducible origins and currently known ORC- or MCM-binding sites.

Integrative analysis of DNA replication origins and ORC-/MCM-binding sites in human cells reveals a lack of overlap

Based on experimentally determined average inter-origin distances of ~100 kb, DNA replication initiates from ~50,000 origins on human chromosomes in each cell cycle. The origins are believed to be specified by binding of factors like the origin recognition complex (ORC) or CTCF or other features like G-quadruplexes. We have performed an integrative analysis of 113 genome-wide human origin profiles (from five different techniques) and five ORC-binding profiles to critically evaluate whether the most reproducible origins are specified by these features. Out of ~7.5 million union origins identified by all datasets, only 0.27% (20,250 shared origins) were reproducibly obtained in at least 20 independent SNS-seq datasets and contained in initiation zones identified by each of three other techniques, suggesting extensive variability in origin usage and identification. Also, 21% of the shared origins overlap with transcriptional promoters, posing a conundrum. Although the shared origins overlap more than union origins with constitutive CTCF-binding sites, G-quadruplex sites, and activating histone marks, these overlaps are comparable or less than that of known transcription start sites, so that these features could be enriched in origins because of the overlap of origins with epigenetically open, promoter-like sequences. Only 6.4% of the 20,250 shared origins were within 1 kb from any of the ~13,000 reproducible ORC-binding sites in human cancer cells, and only 4.5% were within 1 kb of the ~11,000 union MCM2-7-binding sites in contrast to the nearly 100% overlap in the two comparisons in the yeast, Saccharomyces cerevisiae. Thus, in human cancer cell lines, replication origins appear to be specified by highly variable stochastic events dependent on the high epigenetic accessibility around promoters, without extensive overlap between the most reproducible origins and currently known ORC- or MCM-binding sites.

High-resolution KIR and HLA genotyping in three Chinese ethnic minorities reveals distinct origins.

Polymorphism of killer-cell immunoglobulin-like receptors (KIRs) and their HLA class I ligands impacts the effector activity of cytotoxic NK cell and T cell subsets. Therefore, understanding the extent and implications of KIR and HLA class I genetic polymorphism across various populations is important for immunological and medical research. In this study, we conducted a high-resolution investigation of KIR and HLA class I diversity in three distinct Chinese ethnic minority populations. We studied the She, Yugur, and Tajik, and compared them with the Zhejiang Han population (Zhe), which represents the majority Southern Han ethnicity. Our findings revealed that the Tajik population exhibited the most diverse KIR copy number, allele, and haplotype diversity among the four populations. This diversity aligns with their proposed ancestral origin, closely resembling that of Iranian populations, with a relatively higher presence of KIR-B genes, alleles, and haplotypes compared with the other Chinese populations. The Yugur population displayed KIR distributions similar to those of the Tibetans and Southeast Asians, whereas the She population resembled the Zhe and other East Asians, as confirmed by genetic distance analysis of KIR. Additionally, we identified 12.9% of individuals across the three minority populations as having KIR haplotypes characterized by specific gene block insertions or deletions. Genetic analysis based on HLA alleles yielded consistent results, even though there were extensive variations in HLA alleles. The observed variations in KIR interactions, such as higher numbers of 2DL1-C2 interactions in Tajik and Yugur populations and of 2DL3-C1 interactions in the She population, are likely shaped by demographic and evolutionary mechanisms specific to their local environments. Overall, our findings offer valuable insights into the distribution of KIR and HLA diversity among three distinct Chinese ethnic minority populations, which can inform future clinical and population studies.

Design and comparative analysis of alternative mooring systems for offshore floating photovoltaics arrays in ultra-shallow water with significant tidal range

Large-scale floating photovoltaics (FPV) are garnering increased attention as a sustainable solution for renewable energy production and efficient utilization of ocean spaces. These FPV arrays are predominantly deployed in shallow water environments, which present significant challenges in mooring system design due to substantial tidal fluctuations. In such settings, mooring systems may become slack and lose functionality at low tide or risk damage from excessive stiffness at high tide. The primary aim of this study is to develop a mooring system tailored to FPV arrays, capable of withstanding extensive tidal variations without causing damage to the floating modules due to high mooring line tension. Employing HydroD, a hydrodynamic analysis tool based on potential flow theory, alongside OrcaFlex, a time-domain coupled analysis tool predicated on the lumped mass method, we conducted a comparative assessment of six distinct mooring configurations. These configurations, varying in mooring line materials and components, were evaluated from static, dynamic, and fatigue analysis standpoints across a range of tidal levels. The results indicate that taut mooring systems integrated with buoys or clumps consistently exhibit superior performance in all test scenarios. Accordingly, these systems are highly recommended for securing FPV arrays in shallow water environments characterized by severe tidal variations, offering optimal stability and resilience.

Cellular Immunity of Drosophila willistoni Reveals Novel Complexity in Insect Anti-Parasitoid Defense.

Coevolution of hosts and their parasites has shaped heterogeneity of effector hemocyte types, providing immune defense reactions with variable effectiveness. In this work, we characterize hemocytes of Drosophila willistoni, a species that has evolved a cellular immune system with extensive variation and a high degree of plasticity. Monoclonal antibodies were raised and used in indirect immunofluorescence experiments to characterize hemocyte subpopulations, follow their functional features and differentiation. Pagocytosis and parasitization assays were used to determine the functional characteristics of hemocyte types. Samples were visualized using confocal and epifluorescence microscopy. We identified a new multinucleated giant hemocyte (MGH) type, which differentiates in the course of the cellular immune response to parasitoids. These cells differentiate in the circulation through nuclear division and cell fusion, and can also be derived from the central hematopoietic organ, the lymph gland. They have a binary function as they take up bacteria by phagocytosis and are involved in the encapsulation and elimination of the parasitoid. Here, we show that, in response to large foreign particles, such as parasitoids, MGHs differentiate, have a binary function and contribute to a highly effective cellular immune response, similar to the foreign body giant cells of vertebrates.

Nonbinary 2D Distribution Tool Maps Autonomic Nerve Fiber Clustering in Lumbosacral Ventral Roots of Rhesus Macaques.

Neuromodulation of the peripheral nervous system (PNS) by electrical stimulation may augment autonomic function after injury or in neurodegenerative disorders. Nerve fiber size, myelination, and distance between individual fibers and the stimulation electrode may influence response thresholds to electrical stimulation. However, information on the spatial distribution of nerve fibers within the PNS is sparse. We developed a new two-dimensional (2D) morphological mapping tool to assess spatial heterogeneity and clustering of nerve fibers. The L6-S3 ventral roots (VRs) in rhesus macaques were used as a model system to map preganglionic parasympathetic, γ-motor, and α-motor fibers. Random and ground truth distributions of nerve fiber centroids were determined for each VR by light microscopy. The proposed tool allows for nonbinary determinations of fiber heterogeneity by defining the minimum distance between nerve fibers for cluster inclusion and comparisons with random fiber distributions for each VR. There was extensive variability in the relative composition of nerve fiber types and degree of 2D fiber heterogeneity between different L6-S3 VR levels within and across different animals. There was a positive correlation between the proportion of autonomic fibers and the degree of nerve fiber clustering. Nerve fiber cluster heterogeneity between VRs may contribute to varied functional outcomes from neuromodulation.

Extensive variation and strain-specificity in dengue virus susceptibility among African Aedes aegypti populations.

African populations of the mosquito Aedes aegypti are usually considered less susceptible to infection by human-pathogenic flaviviruses than globally invasive populations found outside Africa. Although this contrast has been well documented for Zika virus (ZIKV), it is unclear to what extent it is true for dengue virus (DENV), the most prevalent flavivirus of humans. Addressing this question is complicated by substantial genetic diversity among DENV strains, most notably in the form of four genetic types (DENV1 to DENV4), that can lead to genetically specific interactions with mosquito populations. Here, we carried out a survey of DENV susceptibility using a panel of seven field-derived Ae. aegypti colonies from across the African range of the species and a colony from Guadeloupe, French West Indies as non-African reference. We found considerable variation in the ability of African Ae. aegypti populations to acquire and replicate a panel of six DENV strains spanning the four DENV types. Although African Ae. aegypti populations were generally less susceptible than the reference non-African population from Guadeloupe, in several instances some African populations were equally or more susceptible than the Guadeloupe population. Moreover, the relative level of susceptibility between African mosquito populations depended on the DENV strain, indicating genetically specific interactions. We conclude that unlike ZIKV susceptibility, there is no clear-cut dichotomy in DENV susceptibility between African and non-African Ae. aegypti. DENV susceptibility of African Ae. aegypti populations is highly heterogeneous and largely governed by the specific pairing of mosquito population and DENV strain.

Duplicated Copy Number Variant of the Maize 9-Lipoxygenase ZmLOX5 Improves 9,10-KODA-Mediated Resistance to Fall Armyworms.

Extensive genome structure variations, such as copy number variations (CNVs) and presence/absence variations, are the basis for the remarkable genetic diversity of maize; however, the effect of CNVs on maize herbivory defense remains largely underexplored. Here, we report that the naturally occurring duplication of the maize 9-lipoxygenase gene ZmLOX5 leads to increased resistance of maize to herbivory by fall armyworms (FAWs). Previously, we showed that ZmLOX5-derived oxylipins are required for defense against chewing insect herbivores and identified several inbred lines, including Yu796, that contained duplicated CNVs of ZmLOX5, referred to as Yu796-2×LOX5. To test whether introgression of the Yu796-2×LOX5 locus into a herbivore-susceptible B73 background that contains a single ZmLOX5 gene is a feasible approach to increase resistance, we generated a series of near-isogenic lines that contained either two, one, or zero copies of the Yu796-2×LOX5 locus in the B73 background via six backcrosses (BC6). Droplet digital PCR (ddPCR) confirmed the successful introgression of the Yu796-2×LOX5 locus in B73. The resulting B73-2×LOX5 inbred line displayed increased resistance against FAW, associated with increased expression of ZmLOX5, increased wound-induced production of its primary oxylipin product, the α-ketol, 9-hydroxy-10-oxo-12(Z),15(Z)-octadecadienoic acid (9,10-KODA), and the downstream defense hormones regulated by this molecule, 12-oxo-phytodienoic acid (12-OPDA) and abscisic acid (ABA). Surprisingly, wound-induced JA-Ile production was not increased in B73-2×LOX5, resulting from the increased JA catabolism. Furthermore, B73-2×LOX5 displayed reduced water loss in response to drought stress, likely due to increased ABA and 12-OPDA content. Taken together, this study revealed that the duplicated CNV of ZmLOX5 quantitively contributes to maize antiherbivore defense and presents proof-of-concept evidence that the introgression of naturally occurring duplicated CNVs of a defensive gene into productive but susceptible crop varieties is a feasible breeding approach for enhancing plant resistance to herbivory and tolerance to abiotic stress.

Effects of intrinsically disordered regions in gp120 underlying HIV neutralization phenotypes

HIV envelope protein gp120 is considered a primary molecular determinant of viral neutralization phenotype due to its critical role in viral entry and immune evasion. The intrinsically disordered regions (IDRs) in gp120 are responsible for their extensive sequence variations and significant structural rearrangements. Despite HIV neutralization phenotype and sequence/structural information of gp120 have been experimentally characterized, there remains a gap in our understanding of the correlation between the viral phenotype and IDRs in gp120. Here, we combined machine learning (ML) techniques and molecular dynamics (MD) simulations to gain data-driven and molecule-mechanism insights into relationships between viral sequence, structure, and phenotypes from the perspective of IDRs in gp120. ML models, trained only on the length and disorder score of IDRs, achieved equivalent performance to the best baseline model using amino acid sequences to discriminate HIV neutralization phenotype, indicating that the lengths or disorder of specific IDRs are strongly related to HIV neutralization phenotypes. Comparative MD analysis reveals that gp120 with extreme neutralization phenotypes in multiple conformational states, especially some IDRs, exhibit significantly distinct structural dynamics, conformational flexibility, and thermodynamic distributions. Taken together, our study provided insights into the role of IDRs in gp120 responding to HIV neutralization phenotypes, which will advance the understanding of molecular mechanisms underlying viral function associated with HIV neutralization phenotype and help develop antiviral vaccines or drugs.

Abstract 893: Studying the impact of CNVs on expression at single-cell resolution in HGSOC using autoencoders

Abstract High-grade serous ovarian cancer (HGSOC) is one of the most lethal gynecological malignancies. Lack of common targetable oncogenic mutations has complicated the development of directed therapies to combat emerging resistance. This malignancy is mainly characterized by the mutation of gene TP53, which promotes genome instability for the emergence of extensive copy number variations (CNVs). However its impact on gene expression at the single-cell level is not well understood. In this study, we aim to investigate the effect of CNVs on transcriptomic signatures by taking advantage of variational autoencoders (VAE) ability for dimensionality reduction, unsupervised learning and feature extraction. The use of VAEs is becoming more popular for the analysis of scRNAseq data, and scVI is one of the most versatile VAE applications performing wide variety of tasks. Here, we used single-cell RNA sequencing (scRNA-seq) data from 90 longitudinal samples of 64 HGSOC patients and inferred CNVs in each cell using inferCNV, an established computational pipeline. Then, we modified scVI algorithm to allow the VAE to reconstruct CNVs from a latent space originated from gene expression profiles and viceversa. Our models were capable of reconstructing CNV profiles accurately from expression data and also remove batch effect. From these models we could observe how, after the integration of genomic information, the latent clusters produced from the transcriptomic space were influenced by the amplifications or deletions of certain genomic regions. Moreover, some of these clusters were characterized by the alteration of important oncogenes in HGSOC, such as KRAS and CCNE1, and allowed us to focus on the transcriptomic consequences of their amplifications. With the results from the approach presented here, we gained a more comprehensive picture of the impact of genomic alterations on HGSOC. As future work, we plan to validate of this results on external cohorts and link the identified signatures to clinically relevant features such as prognosis or chemotherapy response. Citation Format: Matias Marin Falco, Teemu Närhi, Erdogan Pekcan Erkan, Johanna Hynninen, Anna Vähärautio. Studying the impact of CNVs on expression at single-cell resolution in HGSOC using autoencoders [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 893.

Toward Ecologically Relevant Genetics of Interactions Between Host Plants and Plant Growth‐Promoting Bacteria

AbstractThe social movement to reduce reliance on pesticides and synthesized fertilizers and the growing global demand for sustainable food supplies require the development of eco‐friendly and sustainable agricultural practices. In line, plant growth‐promoting bacteria (PGPB) can participate in creating innovative agroecological systems. While the effectiveness of PGPB is highly influenced by abiotic conditions and microbe–microbe interactions, beneficial plant–PGPB interactions can also highly depend on both host and PGPB genotype. Here, the state of the art on the extent of natural genetic variation of plant–PGPB interactions and the underlying genetic architecture, in particular in Arabidopsis thaliana is reviewed. Extensive natural plant genetic variation in response to PGPB is associated with a polygenic architecture and genetic pathways rarely mentioned as being involved in the response to PGPB. To date, natural genetic variation within PGPB is little explored, which may in turn allow the identification of new genetic pathways underlying benefits to plants. Accordingly, several avenues to better understand the genomic and molecular landscape of plant–PGPB interactions are introduced. Finally, the need for establishing thorough functional studies of candidate genes underlying Quantitative Trait Loci and estimating the extent of genotype‐by‐genotype‐by‐environment interactions within the context of realistic (agro‐)ecological conditions is advocated.

Reflexive Morphology in the Kikongo Language Cluster: Variation and Diachrony

This paper provides a comparative and diachronic account of reflexive morphology in the Kikongo language cluster, a genealogically closely related group of 40+ West Coastal Bantu languages. This study is based on data from 34 grammatical descriptions from 1659 to 2017 and fieldwork data collected in 2012 and 2015. Previous studies have shown that Kikongo languages, despite being closely related to each other, demonstrate extensive phonological and morphological variation. This is also the case for reflexive morphology. First, six different reflexive prefixes are attested in the database. These are, in alphabetical order, di- (with cognate li-), ké-, ki-, ku-, lu- and a vocalic morpheme variably written as i-, ii- or yi-. Second, while most Kikongo languages have one reflexive prefix, some descriptions report the use of two or more different prefix forms in a single language. Languages with multiple reflexive prefixes fall into two groups: one group has different prefixes in free alternation, while the overall verbal construction is claimed to determine which prefix is used in the other group. Following an overview of the formal variation, I discuss the possible origins of the various reflexive prefixes. One hypothesis assumes that the vocalic prefix is inherited from Proto-Kikongo, the most recent common ancestor of the Kikongo languages. A second hypothesis relates the origin of some reflexive prefixes to object indexes of various noun classes, in particular, noun classes 5, 7 and 11. A third hypothesis suggests that in some Kikongo languages, the vocalic reflexive prefix became fused with other pre-stem verbal morphology and developed into ku- and ki-. A fourth hypothesis proposes the development of the reflexive prefix ké- from an auxiliary. These four hypotheses are not mutually exclusive, and I discuss how multiple diachronic scenarios are necessary to account for the full range of variation of reflexive morphology in the Kikongo language cluster. It is proposed that the distribution of di-/li- and ki- is contact-induced through borrowing, both between different Kikongo languages and between Kikongo and non-Kikongo languages. I tentatively reconstruct the vocalic reflexive prefix *i- to Proto-Kikongo.