RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure.

RNA has the intrinsic property to base pair, forming complex structures fundamental to its diverse functions. Here, we develop PARIS, a method based on reversible psoralen crosslinking for global mapping of RNA duplexes with near base-pair resolution in living cells. PARIS analysis in three human and mouse cell types reveals frequent long-range structures, higher-order architectures, and RNA-RNA interactions in trans across the transcriptome. PARIS determines base-pairing interactions on an individual-molecule level, revealing pervasive alternative conformations. We used PARIS-determined helices to guide phylogenetic analysis of RNA structures and discovered conserved long-range and alternative structures. XIST, a long noncoding RNA (lncRNA) essential for X chromosome inactivation, folds into evolutionarily conserved RNA structural domains that span many kilobases. XIST A-repeat forms complex inter-repeat duplexes that nucleate higher-order assembly of the key epigenetic silencing protein SPEN. PARIS is a generally applicable and versatile method that provides novel insights into the RNA structurome and interactome. VIDEO ABSTRACT.

Protomelission is an early dasyclad alga and not a Cambrian bryozoan.

The animal phyla and their associated body plans originate from a singular burst of evolution occurring during the Cambrian period, over 500 million years ago1. The phylum Bryozoa, the colonial 'moss animals', have been the exception: convincing skeletons of this biomineralizing clade have been absent from Cambrian strata, in part because potential bryozoan fossils are difficult to distinguish from the modular skeletons of other animal and algal groups2,3. At present, the strongest candidate4 is the phosphatic microfossil Protomelission5. Here we describe exceptionally preserved non-mineralized anatomy in Protomelission-like macrofossils from the Xiaoshiba Lagerstätte6. Taken alongside the detailed skeletal construction and the potential taphonomic origin of 'zooid apertures', we consider that Protomelission is better interpreted as the earliest dasycladalean green alga-emphasizing the ecological role of benthic photosynthesizers in early Cambrian communities. Under this interpretation, Protomelission cannot inform the origins of the bryozoan body plan; despite a growing number of promising candidates7-9, there remain no unequivocal bryozoans of Cambrian age.

Control of stereogenic oxygen in a helically chiral oxonium ion.

The control of tetrahedral carbon stereocentres remains a focus of modern synthetic chemistry and is enabled by their configurational stability. By contrast, trisubstituted nitrogen1, phosphorus2 and sulfur compounds3 undergo pyramidal inversion, a fundamental and well-recognized stereochemical phenomenon that is widely exploited4. However, the stereochemistry of oxonium ions-compounds bearing three substituents on a positively charged oxygen atom-is poorly developed and there are few applications of oxonium ions in synthesis beyond their existence as reactive intermediates5,6. There are no examples of configurationally stable oxonium ions in which the oxygen atom is the sole stereogenic centre, probably owing to the low barrier to oxygen pyramidal inversion7 and the perception that all oxonium ions are highly reactive. Here we describe the design, synthesis and characterization of a helically chiral triaryloxonium ion in which inversion of the oxygen lone pair is prevented through geometric restriction to enable it to function as a determinant of configuration. A combined synthesis and quantum calculation approach delineates design principles that enable configurationally stable and room-temperature isolable salts to be generated. We show that the barrier to inversion is greater than 110 kJ mol-1 and outline processes for resolution. This constitutes, to our knowledge, the only example of a chiral non-racemic and configurationally stable molecule in which the oxygen atom is the sole stereogenic centre.

The human mitochondrial transcriptome.

The human mitochondrial genome comprises a distinct genetic system transcribed as precursor polycistronic transcripts that are subsequently cleaved to generate individual mRNAs, tRNAs, and rRNAs. Here, we provide a comprehensive analysis of the human mitochondrial transcriptome across multiple cell lines and tissues. Using directional deep sequencing and parallel analysis of RNA ends, we demonstrate wide variation in mitochondrial transcript abundance and precisely resolve transcript processing and maturation events. We identify previously undescribed transcripts, including small RNAs, and observe the enrichment of several nuclear RNAs in mitochondria. Using high-throughput in vivo DNaseI footprinting, we establish the global profile of DNA-binding protein occupancy across the mitochondrial genome at single-nucleotide resolution, revealing regulatory features at mitochondrial transcription initiation sites and functional insights into disease-associated variants. This integrated analysis of the mitochondrial transcriptome reveals unexpected complexity in the regulation, expression, and processing of mitochondrial RNA and provides a resource for future studies of mitochondrial function (accessed at http://mitochondria.matticklab.com).

Conflict, violence, and warfare among early farmers in Northwestern Europe.

Bioarchaeological evidence of interpersonal violence and early warfare presents important insights into conflict in past societies. This evidence is critical for understanding the motivations for violence and its effects on opposing and competing individuals and groups across time and space. Selecting the Neolithic of northwestern Europe as an area for study, the present paper examines the variation and societal context for the violence recorded in the human skeletal remains from this region as one of the most important elements of human welfare. Compiling data from various sources, it becomes apparent that violence was endemic in Neolithic Europe, sometimes reaching levels of intergroup hostilities that ended in the utter destruction of entire communities. While the precise comparative quantification of healed and unhealed trauma remains a fundamental problem, patterns emerge that see conflict likely fostered by increasing competition between settled and growing communities, e.g., for access to arable land for food production. The further development of contextual information is paramount in order to address hypotheses on the motivations, origins, and evolution of violence as based on the study of human remains, the most direct indicator for actual small- and large-scale violence.

Unraveling complex causal processes that affect sustainability requires more integration between empirical and modeling approaches.

Scientists seek to understand the causal processes that generate sustainability problems and determine effective solutions. Yet, causal inquiry in nature-society systems is hampered by conceptual and methodological challenges that arise from nature-society interdependencies and the complex dynamics they create. Here, we demonstrate how sustainability scientists can address these challenges and make more robust causal claims through better integration between empirical analyses and process- or agent-based modeling. To illustrate how these different epistemological traditions can be integrated, we present four studies of air pollution regulation, natural resource management, and the spread of COVID-19. The studies show how integration can improve empirical estimates of causal effects, inform future research designs and data collection, enhance understanding of the complex dynamics that underlie observed temporal patterns, and elucidate causal mechanisms and the contexts in which they operate. These advances in causal understanding can help sustainability scientists develop better theories of phenomena where social and ecological processes are dynamically intertwined and prior causal knowledge and data are limited. The improved causal understanding also enhances governance by helping scientists and practitioners choose among potential interventions, decide when and how the timing of an intervention matters, and anticipate unexpected outcomes. Methodological integration, however, requires skills and efforts of all involved to learn how members of the respective other tradition think and analyze nature-society systems.

A fine balance of hydrophobic-electrostatic communication pathways in a pH-switching protein.

Allostery is the phenomenon of coupling between distal binding sites in a protein. Such coupling is at the crux of protein function and regulation in a myriad of scenarios, yet determining the molecular mechanisms of coupling networks in proteins remains a major challenge. Here, we report mechanisms governing pH-dependent myristoyl switching in monomeric hisactophilin, whereby the myristoyl moves between a sequestered state, i.e., buried within the core of the protein, to an accessible state, in which the myristoyl has increased accessibility for membrane binding. Measurements of the pH and temperature dependence of amide chemical shifts reveal protein local structural stability and conformational heterogeneity that accompany switching. An analysis of these measurements using a thermodynamic cycle framework shows that myristoyl-proton coupling at the single-residue level exists in a fine balance and extends throughout the protein. Strikingly, small changes in the stereochemistry or size of core and surface hydrophobic residues by point mutations readily break, restore, or tune myristoyl switch energetics. Synthesizing the experimental results with those of molecular dynamics simulations illuminates atomistic details of coupling throughout the protein, featuring a large network of hydrophobic interactions that work in concert with key electrostatic interactions. The simulations were critical for discerning which of the many ionizable residues in hisactophilin are important for switching and identifying the contributions of nonnative interactions in switching. The strategy of using temperature-dependent NMR presented here offers a powerful, widely applicable way to elucidate the molecular mechanisms of allostery in proteins at high resolution.

Widespread formation of double-stranded RNAs in testis.

The testis transcriptome is highly complex and includes RNAs that potentially hybridize to form double-stranded RNA (dsRNA). We isolated dsRNA using the monoclonal J2 antibody and deep-sequenced the enriched samples from testes of juvenile Dicer1 knockout mice, age-matched controls, and adult animals. Comparison of our data set with recently published data from mouse liver revealed that the dsRNA transcriptome in testis is markedly different from liver: In testis, dsRNA-forming transcripts derive from mRNAs including promoters and immediate downstream regions, whereas in somatic cells they originate more often from introns and intergenic transcription. The genes that generate dsRNA are significantly expressed in isolated male germ cells with particular enrichment in pachytene spermatocytes. dsRNA formation is lower on the sex (X and Y) chromosomes. The dsRNA transcriptome is significantly less complex in juvenile mice as compared to adult controls and, possibly as a consequence, the knockout of Dicer1 has only a minor effect on the total number of transcript peaks associated with dsRNA. The comparison between dsRNA-associated genes in testis and liver with a reported set of genes that produce endogenous siRNAs reveals a significant overlap in testis but not in liver. Testis dsRNAs also significantly associate with natural antisense genes-again, this feature is not observed in liver. These findings point to a testis-specific mechanism involving natural antisense transcripts and the formation of dsRNAs that feed into the RNA interference pathway, possibly to mitigate the mutagenic impacts of recombination and transposon mobilization.

HIVepsilon-seq-scalable characterization of intact persistent proviral HIV reservoirs in women.

IMPORTANCE: The lack of a reliable method to accurately detect when replication-competent HIV has been cleared is a major challenge in developing a cure. This study introduces a new approach called the HIVepsilon-seq (HIVε-seq) assay, which uses long-read sequencing technology and bioinformatics to scrutinize the HIV genome at the nucleotide level, distinguishing between defective and intact HIV. This study included 30 participants on antiretroviral therapy, including 17 women, and was able to discriminate between defective and genetically intact viruses at the single DNA strand level. The HIVε-seq assay is an improvement over previous methods, as it requires minimal sample, less specialized lab equipment, and offers a shorter turnaround time. The HIVε-seq assay offers a promising new tool for researchers to measure the intact HIV reservoir, advancing efforts towards finding a cure for this devastating disease.

Toward a coordinated understanding of hydro-biogeochemical root functions in tropical forests for application in vegetation models.

Tropical forest root characteristics and resource acquisition strategies are underrepresented in vegetation and global models, hampering the prediction of forest-climate feedbacks for these carbon-rich ecosystems. Lowland tropical forests often have globally unique combinations of high taxonomic and functional biodiversity, rainfall seasonality, and strongly weathered infertile soils, giving rise to distinct patterns in root traits and functions compared with higher latitude ecosystems. We provide a roadmap for integrating recent advances in our understanding of tropical forest belowground function into vegetation models, focusing on water and nutrient acquisition. We offer comparisons of recent advances in empirical and model understanding of root characteristics that represent important functional processes in tropical forests. We focus on: (1) fine-root strategies for soil resource exploration, (2) coupling and trade-offs in fine-root water vs nutrient acquisition, and (3) aboveground-belowground linkages in plant resource acquisition and use. We suggest avenues for representing these extremely diverse plant communities in computationally manageable and ecologically meaningful groups in models for linked aboveground-belowground hydro-nutrient functions. Tropical forests are undergoing warming, shifting rainfall regimes, and exacerbation of soil nutrient scarcity caused by elevated atmospheric CO2. The accurate model representation of tropical forest functions is crucial for understanding the interactions of this biome with the climate.

Las características de las raíces de los bosques tropicales y las estrategias de adquisición de recursos están subrepresentadas en modelos de vegetación, lo que dificulta la predicción del efecto de cambio de clima para estos ecosistemas ricos en carbono. Los bosques tropicales a menudo tienen combinaciones únicas a nivel mundial de alta biodiversidad taxonómica y funcional, estacionalidad de precipitación, y suelos infértiles, dando lugar a patrones distintos en los rasgos y funciones de las raíces en comparación con los ecosistemas de latitudes más altas. Integramos los avances recientes en nuestra comprensión de la función subterránea de los bosques tropicales en modelos de vegetación, centrándonos en la adquisición de agua y nutrientes. Ofrecemos comparaciones de avances recientes en la comprensión empírica y de modelos de las características de las raíces que representan procesos funcionales importantes en los bosques tropicales. Nos centramos en: (1) estrategias de raíces finas para adquisición de recursos del suelo, (2) acoplamiento y compensaciones entre adquisición del agua y de nutrientes, y (3) vínculos entre funciones sobre tierra y debajo del superficie en bosques tropicales. Sugerimos vías para representar estas comunidades de plantas extremadamente diversas en grupos computacionalmente manejables y ecológicamente significativos en modelos. Los bosques tropicales se están calentando, tienen cambios en los regímenes de lluvias, y tienen una exacerbación de la escasez de nutrientes del suelo causada por el elevado CO2 atmosférico. La representación precisa de las funciones de los bosques tropicales en modelos es crucial para comprender las interacciones de este bioma con el clima.

Comparative immune profiling of pancreatic ductal adenocarcinoma progression among South African patients.

BACKGROUND: Pancreatic Ductal Adenocarcinoma (PDAC) is an aggressive cancer characterized by an immunosuppressive microenvironment. Patients from specific ethnicities and population groups have poorer prognoses than others. Therefore, a better understanding of the immune landscape in such groups is necessary for disease elucidation, predicting patient outcomes and therapeutic targeting. This study investigated the expression of circulating key immune cell markers in South African PDAC patients of African ancestry. METHODS: Blood samples were obtained from a total of 6 healthy volunteers (HC), 6 Chronic Pancreatitis (CP) and 34 PDAC patients consisting of 22 resectable (RPC), 8 locally advanced (LAPC) and 4 metastatic (MPC). Real-time Quantitative Polymerase Chain reactions (RT-qPCR), Metabolomics, Enzyme-Linked Immunosorbent Assay (ELISA), Reactive Oxygen Species (ROS), and Immunophenotyping assays were conducted. Statistical analysis was conducted in R (v 4.3.2). Additional analysis of single-cell RNA data from 20 patients (16 PDAC and 4 controls) was conducted to interrogate the distribution of T-cell and Natural Killer cell populations. RESULTS: Granulocyte and neutrophil levels were significantly elevated while lymphocytes decreased with PDAC severity. The total percentages of CD3 T-cell subpopulations (helper and double negative T-cells) decreased when compared to HC. Although both NK (p = 0.014) and NKT (p < 0.001) cell levels increased as the disease progressed, their subsets: NK CD56dimCD16- (p = 0.024) and NKTs CD56+ (p = 0.008) cell levels reduced significantly. Of note is the negative association of NK CD56dimCD16- (p < 0.001) cell levels with survival time. The gene expression analyses showed no statistically significant correlation when comparing the PDAC groups with the controls. The inflammatory status of PDAC was assessed by ROS levels of serum which were elevated in CP (p = 0.025), (RPC (p = 0.003) and LAPC (p = 0.008)) while no significant change was observed in MPC, compared to the HC group. ROS was shown to be positively correlated with GlycA (R = 0.45, p = 0.0096). Single-cell analyses showed a significant difference in the ratio of NKT cells per total cell counts in LAPC (p < 0.001) and MPC (p < 0.001) groups compared with HC, confirming observations in our sample group. CONCLUSION: The expression of these immune cell markers observed in this pilot study provides insight into their potential roles in tumour progression in the patient group and suggests their potential utility in the development of immunotherapeutic strategies.

Lumbar Bone Stress Injuries and Nonunited Defects in Elite Australian Cricket Players.

OBJECTIVE: To describe the presentation and management of lumbar bone stress injuries (LBSI), recurrent LBSI, and lumbar nonunited defects in elite Australian male and female cricket players. DESIGN: Retrospective case series. SETTING: Professional domestic and international cricket teams over 13 seasons. PARTICIPANTS: Elite Australian cricket players. INDEPENDENT VARIABLES: Symptomatic LBSI requiring time off cricket and lumbar nonunited defects, both confirmed by imaging. MAIN OUTCOME MEASURES: Incidence, presentation, history, healing, and management. RESULTS: 211 LBSI were identified at an average incidence of 5.4 per 100 players per season. LBSI were most common in male pace bowlers younger than 20 years of age (58.1 per 100 players per season), however, were also observed in older players, females, and non-pace bowlers. Recurrent LBSI accounted for 33% (27%-40%) of all LBSI. Median days to return to match availability was 182 (128-251) days for all LBSI, with a shorter time frame observed for new and less severe injuries, and male spin bowlers. Healing was demonstrated in 87% (81%-91%) of all LBSI cases. 29 nonunited defects were identified and predisposed subsequent pain, LBSI, and spondylolisthesis. CONCLUSIONS: LBSI are experienced by approximately 5.4 in every 100 elite Australian cricket players per season, with a high time cost of approximately 4 to 8 months. Nonunited defects also have a high time cost with associated subsequent lumbar spine issues. The findings of this study reinforce the importance of early detection and conservative management of LBSI, particularly for younger male pace bowlers and players with recurrent LBSI, which may be supported by MRI.

Automatic Self Recriminations: Development and Validation of a Measure of Self-Condemnatory Internal Dialogue.

This article introduces a measure of self-condemnatory internal dialogue as an element of the relationship with the self: The Automatic Self-Recrimination Scale (ASRS). Using the construct validation approach to test construction, we describe the initial development of items and report on findings from a clinical and nonclinical sample showing the ASRS is best understood as a multidimensional measure of self-critical internal dialogue composed of one higher-order factor and four lower-order facets: Not Mattering, Self as Failure, Undeserving Self, and Loathsomeness. The overall scale and four subscales demonstrated acceptable internal consistency and test-retest reliability. Moreover, there was evidence of good convergent and incremental validity of the ASRS subscales with measures of perfectionism, self-criticism, and dysfunctional attitudes. Overall, the ASRS appears to be a reliable and valid measure of an automatic self-recriminatory internal dialogue.

The equivalence of psychodynamic therapy and cognitive behavioral therapy for depressive disorders in adults: A meta-analytic review.

BACKGROUND: Meta-analyses on the relative efficacy of psychodynamic psychotherapy (PDT) and cognitive behavioral therapy (CBT) for depressive disorders are limited by heterogeneity in diagnostic samples and comparators and a lack of equivalence testing. OBJECTIVE: We addressed this through a meta-analytic test of the equivalence of manualized PDT and CBT in treating adults with depressive disorders as determined by diagnostic interviews. Sensitivity analyses evaluated the impact of pretreatment differences, mixed diagnostic samples, author allegiance, study quality, year of publication and outliers on findings. METHOD: A comprehensive literature search across multiple databases using reliable screening methods identified nine randomized controlled trials directly comparing manualized PDT and CBT for diagnosed depressive disorders in adults. Following pre-registration, we employed random effect models for our meta-analyses and two one-sided test procedures for equivalence testing. RESULTS: Independent raters determined that all studies were of adequate quality. Immediately posttreatment, depressive symptoms were statistically equivalent across PDT and CBT (k = 9; g = -0.11, 90% confidence interval [90% CI]: -0.24 to 0.02, pequivalence = .048, pNHST = .212, I2 = 32.7). At follow-up, the longest time point within a year, depressive symptoms were neither statistically equivalent nor statistically different (k = 6; g = -0.16, 90% CI: -0.31 to -0.02, pequivalence = .184, pNHST = .126, I2 = 0.00). CONCLUSION: The efficacy of manualized PDT is equal to manualized CBT immediately at posttreatment for depressive disorders in the adult general population. Nevertheless, insufficient data exists to reach a conclusion regarding equivalence at follow-up.

A comparison of the effect of two types of brief psychodynamic group therapy on perfectionism-related attitudes, self-relatedness, and self-esteem.

Objective: This randomized controlled trial investigated the efficacy of dynamic relational group therapy (DRT) relative to group psychodynamic supportive therapy (PST) in improving perfectionism-related attitudes and components of the perfectionistic self-relationship. Method: Based on a comprehensive conceptualization of perfectionism, 80 community-recruited, highly perfectionistic individuals were randomly allocated to 12 sessions of group DRT (n = 41; 5 groups) or group PST (n = 39; 5 groups). Patients completed measures of dysfunctional attitudes, self-criticism, self-esteem, and self-reassurance at pre-, mid-, and post-treatment, and six months post-treatment. Results: Multigroup latent growth curve modeling revealed significant (p < .05) decreases in dysfunctional attitudes, concern over mistakes, two types of self-criticism, and self-esteem problems, along with a significant increase in self-reassurance, from pre-treatment to six-month follow-up in both DRT and PST. Moderate-to-large between-group differences favoring DRT over PST were found for dysfunctional attitudes and self-reassurance. A majority of patients in both conditions maintained reliable improvement at six-month follow-up in dysfunctional attitudes, concern over mistakes, and self-criticism focused on inadequacy. Conclusion: Findings provide evidence for the use of psychodynamic group therapy approaches in treating perfectionism-related attitudes and self-relational elements of perfectionism, and support the relative efficacy of DRT for dysfunctional attitudes and self-reassurance.

Hydraulic variability of tropical forests is largely independent of water availability.

Tropical rainforest woody plants have been thought to have uniformly low resistance to hydraulic failure and to function near the edge of their hydraulic safety margin (HSM), making these ecosystems vulnerable to drought; however, this may not be the case. Using data collected at 30 tropical forest sites for three key traits associated with drought tolerance, we show that site-level hydraulic diversity of leaf turgor loss point, resistance to embolism (P50 ), and HSMs is high across tropical forests and largely independent of water availability. Species with high HSMs (>1 MPa) and low P50 values (< -2 MPa) are common across the wet and dry tropics. This high site-level hydraulic diversity, largely decoupled from water stress, could influence which species are favoured and become dominant under a drying climate. High hydraulic diversity could also make these ecosystems more resilient to variable rainfall regimes.

Catalytic Enantioselective 6π Photocyclization of Acrylanilides.

Controlling absolute stereochemistry in catalytic photochemical reactions is generally challenging owing to high rates of background reactivity. Successful strategies broadly rely on selective excitation of the reaction substrate when associated with a chiral catalyst. Recent studies have demonstrated that chiral Lewis acid complexes can enable selective energy transfer from a photosensitizer to facilitate enantioselective triplet state reactions. Here, we apply this approach to the enantioselective catalysis of a 6π photocyclization through the design of an iridium photosensitizer optimized to undergo energy transfer to a reaction substrate only in the presence of a chiral Lewis acid complex. Among a group of iridium(III) sensitizers, enantioselectivity and yield closely correlate with photocatalyst triplet energy within a narrow window enabled by a modest reduction in substrate triplet energy upon binding a scandium/ligand complex. These results demonstrate that photocatalyst tuning offers a means to suppress background reactivity and improve enantioselectivity in photochemical reactions.

Molecular barcoding of native RNAs using nanopore sequencing and deep learning.

Nanopore sequencing enables direct measurement of RNA molecules without conversion to cDNA, thus opening the gates to a new era for RNA biology. However, the lack of molecular barcoding of direct RNA nanopore sequencing data sets severely affects the applicability of this technology to biological samples, where RNA availability is often limited. Here, we provide the first experimental protocol and associated algorithm to barcode and demultiplex direct RNA nanopore sequencing data sets. Specifically, we present a novel and robust approach to accurately classify raw nanopore signal data by transforming current intensities into images or arrays of pixels, followed by classification using a deep learning algorithm. We demonstrate the power of this strategy by developing the first experimental protocol for barcoding and demultiplexing direct RNA sequencing libraries. Our method, DeePlexiCon, can classify 93% of reads with 95.1% accuracy or 60% of reads with 99.9% accuracy. The availability of an efficient and simple multiplexing strategy for native RNA sequencing will improve the cost-effectiveness of this technology, as well as facilitate the analysis of lower-input biological samples. Overall, our work exemplifies the power, simplicity, and robustness of signal-to-image conversion for nanopore data analysis using deep learning.

The Cambrian cirratuliform Iotuba denotes an early annelid radiation.

The principal animal lineages (phyla) diverged in the Cambrian, but most diversity at lower taxonomic ranks arose more gradually over the subsequent 500 Myr. Annelid worms seem to exemplify this pattern, based on molecular analyses and the fossil record: Cambrian Burgess Shale-type deposits host a single, early-diverging crown-group annelid alongside a morphologically and taxonomically conservative stem group; the polychaete sub-classes diverge in the Ordovician; and many orders and families are first documented in Carboniferous Lagerstätten. Fifteen new fossils of the 'phoronid' Iotuba (=Eophoronis) chengjiangensis from the early Cambrian Chengjiang Lagerstätte challenge this picture. A chaetal cephalic cage surrounds a retractile head with branchial plates, affiliating Iotuba with the derived polychaete families 'Flabelligeridae' and Acrocirridae. Unless this similarity represents profound convergent evolution, this relationship would pull back the origin of the nested crown groups of Cirratuliformia, Sedentaria and Pleistoannelida by tens of millions of years-indicating a dramatic unseen origin of modern annelid diversity in the heat of the Cambrian 'explosion'.

Proteomic analysis identifies dysregulated proteins and associated molecular pathways in a cohort of gallbladder cancer patients of African ancestry.

BACKGROUND: Gallbladder cancer (GBC) is a lethal cancer with a poor prognosis. The lack of specific and sensitive biomarkers results in delayed diagnosis with most patients presenting at late stages of the disease. Furthermore, there is little known about the molecular mechanisms associated with GBC, especially in patients of African ancestry. This study aimed to determine dysregulated proteins in South African GBC patients to identify potential mechanisms of the disease progression and plausible biomarkers. METHODS: Tissues (27 GBC, 13 Gallstone disease, and 5 normal tissues) and blood plasma (54 GBC and 73 Benign biliary pathology) were obtained from consenting patients. Protein extraction was performed on all tissues and liquid chromatography-mass spectrometry was used for proteomic profiling. A project-specific spectral library was built using the Pulsar search algorithm. Principal component and Spearman's rank correlation analyses were performed using PAST (V4.07b). Pathway and Network analyses were conducted using REACTOME (v3.7) and stringAPP (v1.7.0), respectively. RESULTS: In the tissue sample group, there were 62 and 194 dysregulated proteins in GBC compared to normal and gallstone groups, respectively. In the plasma group, there were 33 altered proteins in GBC compared to the benign biliary pathology group. We found 9 proteins (APOA1, APOA2, RET4, TTR, HEMO, HBB, HBA, PIGR, and APOE) to be commonly dysregulated in both tissue and plasma. Furthermore, a subset analysis demonstrated that 2 proteins, S100A8 and S100A9, were downregulated in GBC patients with GD history compared to those without. Pathway analysis showed that the dysregulated proteins in GBC patients were enriched in pathways involved in smooth muscle contraction, metabolism, ECM organization, and integrin cell surface interactions. CONCLUSION: The identified dysregulated proteins help in understanding GBC molecular mechanisms in our patient group. Furthermore, the alteration of specific proteins in both tissue and plasma samples suggests their potential utility as biomarkers of GBC in this sample cohort.