Sequencing Research Articles

Utilizing an automated, high-throughput platform to generate comprehensive clinical & molecular datasets to enable a real-world evidence approach for improving care of patients with gastrointestinal malignancies.

816 Background: More than 44,000 patients are seen at MD Anderson Cancer Center annually. However, using the diverse, mostly unstructured, data from these patient encounters has been challenging and required manual chart reviews. In 2018, MD Anderson and Palantir Technologies (Denver, CO) began developing a unified, cloud-based, graphical user interface clinical informatics platform to extract, structure, and integrate data from the different data sources that comprise the electronic health record (EHR). Here, we describe our experience using this novel platform to apply a real-world evidence (RWE) approach to study patients with gastrointestinal (GI) malignancies. Methods: Institutional Review Board approval for retrospective chart review of patients with GI malignancies was previously obtained. The Foundry platform was used to incorporate more than 150 datasets, including structured data elements like lab values, unstructured data as the full text of clinical notes, and natural language processing (NLP) derived datasets. The datasets include unique patient identifiers to allow the merging of demographic, clinical, molecular, and outcomes information. The platform allows processing of the note text through NLP to extract non-discrete data elements into a discrete form. In addition, it continuously updates new data on daily bases, allowing the inclusion of new patients' information in an automated fashion. Results: From 2,013,048 patients with date of diagnosis ranging from 1944 to 2024, we have created datasets for colorectal adenocarcinoma (CRC, >50,000 patients, >8,000 with molecular data), pancreatic adenocarcinoma (PDAC, >13,000 patients), and appendiceal adenocarcinoma (AA, >3,000 patients). More than 50 variables have been integrated, including demographic information, stage, grade, overall survival, and molecular information. Focused manual validation of the automated extraction across the cohorts consistently demonstrated an accuracy of over 94%. Work is underway to extract additional features including DFS and PFS, sites of metastasis, and to build out additional cohorts for biliary tract, upper GI, and neuroendocrine tumors. Initial discovery efforts have already led to multiple publications including discovery of molecular causes of racial and ethnic disparities in CRC, survival impact of KRAS and co-mutations in PDAC, and prognostic utility of serum tumor markers in AA. Conclusions: Utilizing an automated, highly dynamic platform allowed integration of comprehensive datasets for multiparameter oncology data in patients with GI malignancies. This resulted in dramatic acceleration of cohort identification, outcomes analysis, and enabled utilizing a data-driven approach to guide decision making in an effort to enhance and optimize outcomes.

A comprehensive molecular and clinical study of patients with young-onset CRC.

235 Background: Young-onset colorectal cancer (YO-CRC), defined as colorectal cancer diagnosed in individuals under 50 years of age, has emerged as a distinct clinical entity, often presenting at advanced stages. Despite the increasing incidence, molecular and clinical underpinnings of YO-CRC remain underexplored. This study aims to characterize the clinical and molecular features of YO-CRC and to evaluate their impact on OS. Methods: We retrospectively reviewed 110 patients diagnosed with YO-CRCfrom our institution’s molecular database. All patients underwent next-generation sequencing. Demographic, clinical, and molecular data, including age, gender, race, tumor location, cancer stage, and mutation status (KRAS, NRAS, BRAF, POLE, ERBB-2/HER2, microsatellite status), were collected by reviewing electronic medical records. For OS analysis, we focused on patients diagnosed with de novo Stage 4. Cox proportional hazards regression and Kaplan-Meier survival analysis were utilized to assess the association of these factors with OS, with statistical significance determined by a p-value threshold of <0.05. Results: Among 110 patients, N=44 (40%) presented with local disease (stage 1-3), while N=66 (60%) patients presented with de novo metastatic disease at the time of diagnosis. The median age at diagnosis was 44.5 years. The cohort consisted of 64% males and 36% females, with 84% of patients identified as White. Most tumors were left-sided (77%), including the distal colon/sigmoid (44%) and rectum (33%). KRAS and BRAF mutations were present 36% and 5.5%, respectively. ERBB-2/HER2 amplification and microsatellite instability were observed in 4.5% and 6.4% respectively. Tumor mutation burden (TMB) was <10 in 57% of patients, with 14% having TMB >20. CNV analysis revealed that 14% of patients had copy gains, 12% had concurrent gains/losses, and 31% had copy losses. Among the 66 Stage 4 patients, 44% had died by the time of analysis, with a median overall survival (OS) of 43.6 months (95% CI, 28.7 - not reached). KRAS mutation was found to be significantly associated with worse survival outcomes. Cox regression analysis reveals the prognostic significance of KRAS status, with a hazard ratio (HR) of 3.52 (95% CI: 1.59-7.76, P = 0.002 < 0.05), indicating a significantly higher risk of death for KRAS-mutant YO-CRC patients. Conclusions: KRAS mutations are a key prognostic factor in YO-CRC, highlighting the need for therapeutic need to improve outcomes in this high-risk group.

A comprehensive study of clinical and molecular features in patients with metastatic colorectal cancer with and without liver mets.

242 Background: Colorectal cancer (CRC) most frequently metastasizes to the liver, and patients (pts) with liver metastasis (mets) at the time of metastatic diagnosis tend to have poorer outcomes compared to pts with non-liver mets. However, the reason for this discrepancy is not well-defined. We thus aimed to identify any distinct molecular or clinical characteristics that could contribute to the poor outcomes associated with liver mets of CRC. Methods: Pts diagnosed with metastatic CRC from 2014-2022 were identified using the institutional molecular database of CRC. Demographic, clinical, and molecular data were collected by reviewing electronic medical records. Time to next treatment was defined as the time between 1st and 2nd line treatment. We utilized Fisher’s exact tests for categorical variables and both Kaplan-Meier analysis and multivariate Cox proportional hazards models to analyze survival data, with a p-value threshold of <0.05 for statistical significance. Results: We identified a total of 217 pts, including pts with liver mets (N=146) and non-liver mets (N=71) at time of diagnosis. Pts with non-liver mets were more likely to have rectal primary than those pts with liver mets (40% vs. 15%, p=0.0001), indicating a distinct pattern of recurrence. Common driver mutations such as KRAS, BRAF, and TP53 were observed at equal frequencies in the liver and non-liver cohorts. In pts without liver mets, age had a significant effect on OS (p < 0.05, HR 1.1). Pts without liver mets with colon primary had worse OS compared to rectum primary (HR= 0.48, 95% CI: 0.24–0.96, p = 0.038). For pts without liver mets, KRAS was not a predictor of outcomes, while BRAF was associated with poorer OS (p<0.001, HR 7.09, 95%CI: 2.31-21.8). Contrarily, for pts with liver mets, KRAS mutation was significantly associated with worse survival (mOS 40.4 vs 61.7 mos, HR 2.04, 95% CI: 1.26-3.30, p=0.004). BRAF mutations were also associated with worse OS for this cohort (p=0.039 and HR 2.86, 95%CI: 1.06-7.77). Median time to the next treatment was significantly shorter in pts with liver mets (13.6 mos) than in pts with non-liver mets (22.6 mos) (HR 1.82, 95% CI 1.28-2.59; p<0.001). OS was longer for pts with non-liver mets compared to those with liver mets (mOS 52.9 mos vs 46.7 mos) though it did not reach statistical significance, likely due to the small sample size. Conclusions: Liver metastasis of CRC is associated with systemic therapy resistance with a shorter time on treatment, indicating treatment resistance associated with liver mets is not limited to immunotherapy. Given similar molecular characteristics in pts with and without liver mets, treatment resistance may be related to the inherent tumor microenvironment of the liver. In this study, pts with distinct molecular features had poorer outcomes, highlighting the importance of developing targeted therapeutics in this population.

Unravelling a new focus of spotted fever rickettsioses as causative agents of acute undifferentiated febrile illness in Odisha, a state in eastern coastal India.

Spotted fever group Rickettsia (SFGR) infections remain largely under-investigated as causative agents of acute undifferentiated febrile illness (AUFI) in resource-limited settings. Few studies are available on the prevalence of SFGR infections in India, especially in eastern India. In a cross-sectional study conducted in 192 hospitalized adult and paediatric patients with AUFI, the frequency of SFGR using sequential PCR targeting genes encoding citrate synthase (gltA), 17 kDa lipoprotein precursor antigen (17kDa), outer membrane proteins A and B (omp A & omp B) was 6.2% (12/192) including 7.4% (8/108) in adults and 4.7% (4/84) in paediatric patients with AUFI. Phylogenetic analysis of SFGR based on the concatenated sequences of omp A-gltA-17kDa-omp B showed that the patients' isolates obtained in the study clustered with Rickettsia conorii str. Malish 7 (AE006914.1). The SFGR cases described here, to the best of our knowledge, are the first human cases diagnosed in Odisha, eastern coastal India that were laboratory-confirmed by molecular detection and sequencing. The findings of this study will be beneficial for designing systematic future studies covering more geographical locations for continued surveillance of SFGR human infections along with vector surveillance.

The childhood cancer data initiative: enabling data sharing to drive research advances and transform pediatric cancer diagnosis and treatment.

With growing emphasis on data-driven research in pediatric oncology, particularly in the context of advances in molecular characterization and precision medicine, there is an urgent need for comprehensive data-sharing initiatives. This review explores how the Childhood Cancer Data Initiative (CCDI) addresses this critical need. CCDI plays a key role in enhancing pediatric cancer research by improving data integration, sharing, and collaboration. Its Molecular Characterization Initiative advances the field by leveraging detailed molecular data to inform clinical trials and therapeutic strategies. For small patient populations, such as those with rhabdomyosarcoma, CCDI's efforts in integrating data across institutions are vital for advancing risk-based treatment strategies to achieve meaningful clinical outcomes. CCDI's advancements in data sharing have profound implications for both clinical practice and research. By enabling precise diagnoses, tailoring treatments based on individual genetic profiles, and addressing the challenges associated with small patient populations, CCDI is driving transformative changes in pediatric oncology. Continued support and expansion of such initiatives are crucial to fully realizing their potential in improving outcomes for children with cancer.

Variation in weed seed DNA detectability among arable carabids with different trophic specialization

While most ground beetles (Coleoptera: Carabidae) include seeds in their diet, preferences for seed feeding vary among carabid species and range from facultative diet supplementation to obligate seed feeding. DNA-based diet analyses have been used to study their regulatory effect on soil seedbanks. It is unknown whether specialized granivores digest seed species they are adapted to (‘essential seeds’) faster, and whether this affects food web construction based on molecular data. We hypothesized that specialized granivores digest their essential seed faster than other seeds, and at faster rates than generalist granivores or carnivores. Further, we assumed that generalist granivores digest different seeds equally fast, while carnivorous carabids digest seeds slower than granivores. In feeding experiments, three carabid species—Amara similata (specialized granivore), Harpalus affinis (generalist granivore), and Poecilus cupreus (generalist carnivore)—were fed either a broadly accepted seed or the specialist's essential seed. Gut content samples were collected 0, 6, 12, 24, 48, and 72 h after feeding and screened with plant-primers to trace seed DNA. Time until 50% detection probability in the specialists was shorter for its essential than the broadly accepted seed and shorter than in the generalist granivore, which digested both seed species equally fast. The carnivore was reluctant to feed on the seed species offered, and detection probabilities did not significantly decrease with digestion time. Our findings suggest that the strength of specialized granivores’ feeding interactions and their role in weed seed regulation might be underestimated when assessed with DNA-based diet analysis, due to their more efficient seed digestion.

Tgfbr1 regulates lateral plate mesoderm and endoderm reorganization during the trunk to tail transition.

During the trunk to tail transition the mammalian embryo builds the outlets for the intestinal and urogenital tracts, lays down the primordia for the hindlimb and external genitalia, and switches from the epiblast/primitive streak (PS) to the tail bud as the driver of axial extension. Genetic and molecular data indicate that Tgfbr1 is a key regulator of the trunk to tail transition. Tgfbr1 has been shown to control the switch of the neuromesodermal competent cells from the epiblast to the chordoneural hinge to generate the tail bud. We now show that in mouse embryos Tgfbr1 signaling also controls the remodeling of the lateral plate mesoderm (LPM) and of the embryonic endoderm associated with the trunk to tail transition. In the absence of Tgfbr1, the two LPM layers do not converge at the end of the trunk, extending instead as separate layers until the caudal embryonic extremity, and failing to activate markers of primordia for the hindlimb and external genitalia. The vascular remodeling involving the dorsal aorta and the umbilical artery leading to the connection between embryonic and extraembryonic circulation was also affected in the Tgfbr1 mutant embryos. Similar alterations in the LPM and vascular system were also observed in Isl1 null mutants, indicating that this factor acts in the regulatory cascade downstream of Tgfbr1 in LPM-derived tissues. In addition, in the absence of Tgfbr1 the embryonic endoderm fails to expand to form the endodermal cloaca and to extend posteriorly to generate the tail gut. We present evidence suggesting that the remodeling activity of Tgfbr1 in the LPM and endoderm results from the control of the posterior PS fate after its regression during the trunk to tail transition. Our data, together with previously reported observations, place Tgfbr1 at the top of the regulatory processes controlling the trunk to tail transition.

Hepatosplenic T-cell lymphoma in children and adolescents.

Hepatosplenic T-cell lymphoma (HSTCL) is an aggressive mature T-cell lymphoma characterized by significant hepatosplenomegaly, bone marrow involvement, and minimal or no lymphadenopathy. Primarily affecting young adults, it is exceptionally rare in children and adolescents. This makes diagnosis and treatment particularly challenging for pathologists and pediatric oncologists. Diagnosis typically relies on bone marrow, spleen, or liver biopsy, with histopathological features including small/medium lymphoid cells with irregular nuclear contours that obstruct the sinuses or sinusoids of the spleen or liver. Immunophenotyping usually reveals CD2/3/7 positivity and CD4/8 negativity, with γδ T-cell receptor rearrangements in most cases. Some genetic distinctions described in pediatric and adolescent patients include chromosome 7 and 8 abnormalities and mutations involving SETD2 and STAT5B. Given the lack of standardized approaches, childhood and adolescent patients with HSTCL are often treated with adult protocols, such as intensive cytotoxic chemotherapy regimens followed by allogeneic hematopoietic stem cell transplantation (HSCT). Despite these highly intensive treatments, prognosis for HSTCL remains poor in children and adolescents, with an estimated five-year overall survival of <15%. HSTCL's rarity in children and adolescents limits accurate epidemiologic estimates, clinical experience, data collection, treatment advances, and surveillance recommendations. Data on relapsed/refractory disease is even more limited. This review summarizes known clinical and histopathologic features as well as outcomes specific to children and adolescents with HSTCL, highlighting potential distinctions from adults. We will also discuss future strategies to acquire additional biologic and molecular data, streamline diagnosis, and advance treatment approaches to ultimately improve outcomes for young patients with this deadly disease.

First Report of Neoscytalidium dimidiatum Causing Fruit Rot on Fig in China.

Fig (Ficus carica L.) holds economic significance in Atushi, Xinjiang, but as fig cultivation expands, disease prevalence has risen. In July 2024, approximately 22% of harvested fig (cv. Xinjiang Zaohuang) from 20 commercial orchards (covering 40 hectares) in Atushi (39°39'37.65" N, 76°14'3.62" E) showed varying degrees of fruit rot symptoms. The initial symptoms were characterized by the appearance of small, brown lesions on the fruit surface. These lesions rapidly progressed into water-soaked spots, which expanded quickly. As the disease advanced, the affected areas became covered with dense, white, fluffy mycelia, accompanied by prominent black sporulation. In later stages, the infected tissues softened further, ultimately resulting in the complete decay of the fruit. Twenty diseased fig were collected from the sampling site. Tissue samples (5×5×5 mm) were cut at the diseased-healthy junction, surface-sterilized in 0.5% NaClO for 1 minute, rinsed twice in sterile distilled water, air-dried, and transferred aseptically onto potato dextrose agar (PDA), and incubated at 25°C for 5 days with a 12-hour photoperiod. Fifteen isolates were obtained from the infected tissues, with two representative isolates (WH 12 and WH 23) selected for further study due to morphological similarity. The fungal colonies initially appeared as white mycelium, later turning olive green to grayish-black. Colony growth was rapid (32 mm/day). Arthrospores were colorless to light brown, short columnar, aseptate, with a truncated base, 0 to 1 septate, averaging 11.9±2.3×3.6±0.8 μm (n = 50), and sometimes formed arthric chains. Chlamydospores were dark brown, round or oval, 0 to 1 septate, averaging 7.26±1.7×5.05±1.0 μm (n = 50). Genomic DNA was extracted from the two isolates. The internal transcribed spacer (ITS), translation elongation factor 1-alpha (TEF1-α), and beta-tubulin (TUB2) genes were amplified using primers ITS1/ITS4 (White et al. 1990), EF1-728F/EF1-986R (Carbone & Kohn. 1999), and BT2a/BT2b (Glass & Donaldson. 1995), respectively, and sequences were deposited in GenBank (ITS: PQ555020, PQ555021; TUB2: PQ557519, PQ557521; TEF1-α: PQ557520, PQ557522). BLAST analysis revealed 99-100% similarity to Neoscytalidium dimidiatum Arp2-D (ITS: MK813852; TUB2: MK816354; TEF1-α: MK816355). Phylogenetic analysis using IQ-Tree and MrBayes3.2.7 based on concatenated ITS-TEF1-TUB sequences showed WH 12 and WH 23 clustering with N. dimidiatum Arp2-D (99% bootstrap). Morphological and molecular data identified the isolates as N. dimidiatum (Penz.) Crous & Slippers (Crous et al. 2006). Pathogenicity tests were conducted on 20 healthy fig (cv. Xinjiang Zaohuang) by inoculating each fruit with 10 µl of a WH 12 conidial suspension (1 × 10⁶ conidia/ml) using sterile needles. The Control were treated with 10 µl of sterile distilled water. All fruits were placed in sterile plastic containers and incubated at 25 ± 1°C, 90% relative humidity, and a 12-hour light cycle. This experiment was performed twice. On the 1st day post-inoculation, brown lesions began to develop on the fruit. By the 4th day post-inoculation, the entire fruit was completely decayed and covered with white mycelia and black spores, while the control fruit showed no symptoms. The fungus was successfully reisolated from the inoculated fruits and identified as N. dimidiatum following the methods described above, fulfilling Koch's postulates. N. dimidiatum has been reported to have a wide range of hosts in China, such as Jacaranda mimosifolia, Hylocereus megalanthus, Hylocereus undatus, and Styphnolobium japonicum (Li et al. 2024; Zeng et al. 2024; Lan et al. 2022; Luo et al. 2024). To our knowledge, this study is the first report of N. dimidiatum as the causal agent of fruit rot in fig in China. Our findings have expanded the host range of N. dimidiatum in China and provide a theoretical basis for the diagnosis and treatment of the disease.

Developing Adverse Outcome Pathways to support radioecological risk assessment: Challenges and insights.

Environmental pollution associated with long term effects, especially in the case of ionizing radiation, poses significant risks to wildlife, necessitating a more nuanced approach to Ecological Risk Assessment (ERA). In radioecology, current methods, as outlined by the International Commission on Radiological Protection (ICRP), focus primarily on exposure and individual/population-level effects, often both suffering a lack of ecological realism due to the nature of data used, and, sidelining a big amount of critical non-individual effects such as sub-individual one like genotoxicity. This review aims to address these gaps by suggesting the integration of New Approach Methods (NAMs) and the Adverse Outcome Pathway (AOP) framework in the field of radioecology. NAMs encompass innovative techniques, such as in silico and in vitro methodologies, that can provide predictive insights without relying solely on traditional animal testing. The AOP framework, developed by the Organization for Economic Cooperation and Development (OECD), structures effects data into a sequence of causally linked events, enabling a clearer understanding of how molecular changes lead to adverse ecological outcomes. In the first section of the review, we explore the challenges of applying AOPs within radioecology, including the complexities of modelling realistic exposure scenarios, the temporal dynamics of effects, and the impacts of multiple stressors. The second section highlights the potential and the application of some NAMs within an AOP framework to contribute improving risk assessment methodologies (in species realism issue and the use of sub-individual data). This part also offers other potential solutions to increase the number of data to be used in ERA as well as their ecological realism, through the use of AOP framework with relevant biological scales and ecological endpoints still uninvestigated in such way. In conclusion, leveraging NAMs and AOPs is much valuable for bridging molecular data and ecological implications, thereby advancing regulatory practices in radioecology and ensuring more comprehensive protection of ecosystems from radiological hazards.

In silico analysis of SNPs and miRNAs of KCTD13, CSDE1, SLC6A1 genes associated with autism spectrum disorder

BackgroundSingle nucleotide polymorphism (SNP) is called changes in a single base sequence in DNA between individuals. Micro-RNAs (miRNAs) are short, non-coding RNA molecules that control gene expression after transcription. Today, SNPs and miRNAs are associated with many diseases, and one of them is autism spectrum disorder (ASD). ASD is a neurodevelopmental condition identified by symptoms that reduce the quality of life such as stereotypical movements, lack of social interaction and communication skills, cognitive and language disorders. The objective of this study is to utilize in silico tools to predict the possible damaging impacts of SNPs (missense) in ASD-related KCTD13, CSDE1, and SLC6A1 genes that cause amino acid substitution on protein function, stability, structure, and miRNA target binding sites.MethodsThe SNPs and protein amino acid sequences were obtained from the NCBI dbSNP and UniProt databases. This data served as input for predictions, which were carried out using different computational tools like SIFT, PolyPhen-2, SNPs&GO, PROVEAN, MutationAssessor, PhD-SNP, PANTHER, SNAP-2, Meta-SNP, I-Mutant 2.0, MUpro, and Project HOPE. For miRNA analysis, the miRSNP and PolymiRTS tools were utilized. GeneMANIA and STRING were also employed to explore gene–gene and protein–protein interactions.ResultsA total of 16 variants in these three genes were estimated to be potentially harmful via in silico analysis. As a result of the miRSNP and PolymiRTS analyses, it was found that 407 miRNAs could affect the regulation of target genes through the identified SNP variations. Furthermore, the predictive impact of those SNPs on protein stabilization was examined and three-dimensional protein models were created.ConclusionThis study revealed the potential effects of genetic variations on three genes associated with ASD. The findings suggest that computational analysis of miRNA and SNPs on these ASD-related genes could provide valuable insights into the genetic mechanisms underlying ASD. In addition, it is suggested to investigate through experimental research whether the findings can be utilized as potential biomarkers for diagnosing and treating autism.

Fish Evo‐Devo: Moving Toward Species‐Specific and Knowledge‐Based Interactome

ABSTRACTA knowledge‐based interactome maps interactions among proteins and molecules within a cell using experimental data, computational predictions, and literature mining. These interactomes are vital for understanding cellular functions, pathways, and the evolutionary conservation of protein interactions. They reveal how interactions regulate growth, differentiation, and development. Transitioning to functionally validated interactomes is crucial in evolutionary developmental biology (Evo‐Devo), especially for non‐model species, to uncover unique regulatory networks, evolutionary novelties, and reliable gene interaction models. This enhances our understanding of complex trait evolution across species. The European Evo‐Devo 2024 conference in Helsinki hosted the first fish‐specific Evo‐Devo symposium, highlighting the growing interest in fish models. Advances in genome annotation, genome editing, imaging, and molecular screening are expanding fish Evo‐Devo research. High‐throughput molecular data have enabled the deduction of gene regulatory networks. The next steps involve creating species‐specific interactomes, validating them functionally, and integrating additional molecular data to deepen the understanding of complex regulatory interactions in fish Evo‐Devo. This short review aims to address the logical steps for this transition, as well as the necessities and limitations of this journey.

Development of a qPCR assay to identify and differentiate insect-associated strains of the Serratia marcescens complex.

The Serratia marcescens complex contains important opportunistic pathogens of humans and vertebrate animals, as well as insects and other invertebrates. To date, the methods used for the identification of species within the genus Serratia, including PCR assays, have poor discriminatory power and may require further molecular typing or genomic sequence analysis to determine clinical relevance. We developed a duplex TaqMan probe-based quantitative real-time PCR (qPCR) assay targeting the chiP gene, which is involved in chitin degradation and transport, and the ureD gene, which is involved in urease production. This allowed us to simultaneously identify all members of the S. marcescens complex (chiP positive) and differentiate those most likely to act as insect pathogens (chiP and ureD positive). We applied our assay to identify potentially entomopathogenic members of the S. marcescens complex in the context of a conservation program for the critically endangered insect Dryococelus australis and found it to be a useful aid for rapid and accurate detection of infection with S. marcescens complex strains in insects and determination of their clinical relevance. By targeting 2 genes likely to be virulence factors, this assay may also be of use for research investigating the pathogenesis of entomopathogenic Serratia spp.

On the phylogenetic position of Rhinolophus sakejiensis (Chiroptera: Rhinolophidae)

Abstract The Sakeji horseshoe bat Rhinolophus sakejiensis is an endemic to south-central Africa. Until recently, it remained known only from the type series of three specimens collected in Nchila Wildlife Reserve, north-western Zambia. The phylogenetic position of R. sakejiensis was evaluated based on morphologic traits and it was suggested that it represents a part of the ‘clivosus-complex’ within the Rhinolophus ferrumequinum clade of the genus. In this study, we provide an insight into the phylogenetic position of R. sakejiensis employing molecular data, using a newly discovered specimen that originates from the identical area as the type series. We assessed the genetic relationships of R. sakejiensis using the mitochondrial cytochrome b gene. This analysis revealed this species to be phylogenetically distinct from morphologically similar congeners of the capensis, fumigatus, and ferrumequinum species groups. In fact, it does not belong to any recognised species group but rather represents a distinct evolutionary lineage – along with another African relic bat, Rhinolophus horaceki. The divergence time of R. sakejiensis from R. horaceki, its closest relative, was estimated to have occurred in the Middle Miocene, roughly at 15.3 Ma, a period of dynamic environmental changes that may have led to widely separated occurrences of various relic bat lineages.

"Energetics of the outer retina II: Calculation of a spatio-temporal energy budget in retinal pigment epithelium and photoreceptor cells based on quantification of cellular processes".

The outer retina (OR) is highly energy demanding. Impaired energy metabolism combined with high demands are expected to cause energy insufficiencies that make the OR susceptible to complex blinding diseases such as age-related macular degeneration (AMD). Here, anatomical, physiological and quantitative molecular data were used to calculate the ATP expenditure of the main energy-consuming processes in three cell types of the OR for the night and two different periods during the day. The predicted energy demands in a rod dominated (perifovea) area are 1.69 x 1013 ATP/s/mm2 tissue in the night and 6.53 x 1012 ATP/s/mm2 tissue during the day with indoor light conditions. For a cone-dominated foveal area the predicted energy demands are 6.41 x 1012 ATP/s/mm2 tissue in the night and 6.75 x 1012 ATP/s/mm2 tissue with indoor light conditions during daytime. We propose the likely need for diurnal/circadian shifts in energy demands to efficiently stagger all energy consuming processes. Our data provide insights into vulnerabilities in the aging OR and suggest that diurnal constraints may be important when considering therapeutic interventions to optimize metabolism.

Semirational Protein Engineering of a Decarboxylative Aldolase for the Regiodivergent and Stereodivergent Synthesis of Cyclic Imino Acids

AbstractAldolases are powerful C−C bond‐forming enzymes for asymmetric organic synthesis because of their supreme stereoselectivity, compatibility with diverse electrophiles and nucleophiles, and promising scalability. Stereodivergent engineering of aldolases to tune the selectivity for the synthesis of stereoisomers of chiral molecules is highly desirable but has rarely been reported. Herein we report the semirational engineering of the decarboxylative aldolase UstD with a focused rational iterative site‐specific mutagenesis (FRISM) strategy to perform a C−C bond‐forming reaction with dione electrophiles. The variant obtained from a small mutant library showed divergent regioselectivity and diastereoselectivity compared to the wild‐type enzyme, resulting in the production of 30 cyclic imino acids with stereocenters at the α and γ positions. Molecular dynamics simulation and kinetic data revealed the basis of selectivity.

Blood-based epigenome-wide association study and prediction of alcohol consumption

Alcohol consumption is an important risk factor for multiple diseases. It is typically assessed via self-report, which is open to measurement error through recall bias. Instead, molecular data such as blood-based DNA methylation (DNAm) could be used to derive a more objective measure of alcohol consumption by incorporating information from cytosine-phosphate-guanine (CpG) sites known to be linked to the trait. Here, we explore the epigenetic architecture of self-reported weekly units of alcohol consumption in the Generation Scotland study. We first create a blood-based epigenetic score (EpiScore) of alcohol consumption using elastic net penalized linear regression. We explore the effect of pre-filtering for CpG features ahead of elastic net, as well as differential patterns by sex and by units consumed in the last week relative to an average week. The final EpiScore was trained on 16,717 individuals and tested in four external cohorts: the Lothian Birth Cohorts (LBC) of 1921 and 1936, the Sister Study, and the Avon Longitudinal Study of Parents and Children (total N across studies > 10,000). The maximum Pearson correlation between the EpiScore and self-reported alcohol consumption within cohort ranged from 0.41 to 0.53. In LBC1936, higher EpiScore levels had significant associations with poorer global brain imaging metrics, whereas self-reported alcohol consumption did not. Finally, we identified two novel CpG loci via a Bayesian penalized regression epigenome-wide association study of alcohol consumption. Together, these findings show how DNAm can objectively characterize patterns of alcohol consumption that associate with brain health, unlike self-reported estimates.

Myiasis by Cordylobia anthropophaga and C. rodhaini (Diptera: Calliphoridae) in Polish travelers to Africa with new molecular data.

Myiasis is a parasitic infestation of soft vertebrate tissues by larval stages of Diptera. We briefly described the lesion-causing genus Cordylobia Grünberg (Diptera: Calliphoridae). Three Polish travelers to Uganda, Gambia, and Senegal returned with furuncular myiasis. To identify the third-instar larvae removed from their skin, we examined the morphological features of the 3 specimens and sequenced a 5' barcoding fragment of the cytochrome c oxidase subunit I gene (COI-5P). One larva was identified as C. rodhaini Gedoelst, and 2 larvae were identified as C. anthropophaga (Blanchard). We were the first to submit the COI-5P of C. rodhaini to GenBank and the Barcode of Life Database. This is the first record of the importation of C. anthropophaga and the second record of the importation of C. rodhaini to Poland.

A new species Cyathus hiloensis (Nidulariaceae, Basidiomycota) in the Hawaiian Archipelago

ABSTRACT This study focuses on expanding knowledge of Cyathus species in the Hawaiian archipelago through the description of a newly discovered species from Hilo, the largest town in Hawaii County. Based on morphological and molecular data, Cyathus hiloensis is proposed as new taxon within the pallidum group. A comprehensive description of its distinguishing features is provided, along with a detailed comparison to closely related taxa.

Connecting electronic health records to a biomedical knowledge graph to link clinical phenotypes and molecular endotypes in atopic dermatitis

Precision medicine is defined by the U.S. Food & Drug Administration as “an innovative approach to tailoring disease prevention and treatment that considers differences in people’s genes, environments, and lifestyles”. To succeed in providing personalized medicine to patients, it will be necessary to integrate medical, biological and molecular data in order to identify all complex disease subtypes and understand their pathobiological mechanism. Since biomedical knowledge graphs (BKGs) are limited to the integration of prior knowledge data and do not integrate real-world data (RWD) that would allow for the incorporation of patient level information, we propose a first step towards using RWD, BKGs and graph machine learning (ML) to enable a fully integrated precision medicine strategy. In this study, we established a link between RWD and a BKG. Our methodology introduced a novel patient representation using graph ML applied to the BKG. This approach facilitated the interpretation and extension of ML findings, particularly in disease subtype identification with molecular data contained in the BKG. We applied our innovative methodology to deepen our understanding of atopic dermatitis, a condition with a complex underlying pathophysiological mechanism. Through our analysis, we identified seven subgroups of patients each characterized by clinical and genomic characteristics.