bluuebunny/crossref_metadata_2025 huggingface dataset:
Computed Tomography and Magnetic Resonance Imaging Signs of Chronic Liver Rejection: A Case-Control Study
Authors: Asmundo Luigi , Rizzetto Francesco , Sgrazzutti Cristiano , Carbonaro Luca A. , Mazzarelli Chiara , Centonze Leonardo , Rutanni Davide , De Carlis Luciano , Vanzulli Angelo
Published: July 2023

Objective

In liver transplantation, chronic rejection is still poorly studied. This study aimed to investigate the role of imaging in its recognition.

Methods

This study is a retrospective observational case-control series. Patients with histologic diagnosis of chronic liver transplant rejection were selected; the last imaging examination (computed tomography or magnetic resonance imaging) before the diagnosis was evaluated. At least 3 controls were selected for each case; radiological signs indicative of altered liver function were analyzed. χ2 Test with Yates correction was used to compare the rates of radiologic signs in the case and control groups, also considering whether patients suffered chronic rejection within or after 12 months. Statistical significance was set at P < 0.050.

Results

A total of 118 patients were included in the study (27 in the case group and 91 in the control group). Periportal edema was appreciable in 19 of 27 cases (70%) and in 6 of 91 controls (4%) (P < 0.001); ascites and hepatomegaly were present in 14 of 27 cases (52%) and 12 of 27 cases (44%), respectively, and in 1 of 91 controls (1%) (P < 0.001); splenomegaly was present in 13 of 27 cases (48%) and in 8 of 91 controls (10%) (P < 0.001); and biliary tract dilatation was present in 13 of 27 cases (48%) and in 11 of 91 patients controls (5%) (P < 0.001). In the controls, periportal edema was significantly less frequent beyond 12 months after transplant (1% vs 11%; P = 0.020); the other signs after 12 months were not significant.

Conclusions

The identification of periportal edema, biliary dilatation, ascites, and hepatosplenomegaly can serve as potential warning signs of ongoing chronic liver rejection. It is especially important to investigate periportal edema if it is present 1 year or more after orthotopic liver transplantation.
Mutant SPART causes defects in mitochondrial protein import and bioenergetics reversed by Coenzyme Q
Authors: Diquigiovanni Chiara , Rizzardi Nicola , Kampmeier Antje , Liparulo Irene , Bianco Francesca , De Nicolo Bianca , Cataldi-Stagetti Erica , Cuna Elisabetta , Severi Giulia , Seri Marco , Bertrand Miriam , Haack Tobias B. , Marina Adela Della , Braun Frederik , Fato Romana , Kuechler Alma , Bergamini Christian , Bonora Elena
Published: July 2023

Pathogenic variants in
SPART
cause Troyer syndrome, characterized by lower extremity spasticity and weakness, short stature and cognitive impairment, and a severe mitochondrial impairment. Herein, we report the identification of a role of Spartin in nuclear-encoded mitochondrial proteins.
SPART
biallelic missense variants were detected in a 5-year-old boy with short stature, developmental delay and muscle weakness with impaired walking distance. Patient-derived fibroblasts showed an altered mitochondrial network, decreased mitochondrial respiration, increased mitochondrial reactive oxygen species and altered Ca
2+
versus control cells. We investigated the mitochondrial import of nuclear-encoded proteins in these fibroblasts and in another cell model carrying a
SPART
loss-of-function mutation. In both cell models the mitochondrial import was impaired, leading to a significant decrease in different proteins, including two key enzymes involved in CoQ10 (CoQ) synthesis, COQ7 and COQ9, with a severe reduction in CoQ content, versus control cells. CoQ supplementation restored cellular ATP levels to the same extent shown by the re-expression of wild-type SPART, suggesting CoQ treatment as a promising therapeutic approach for patients carrying mutations in
SPART
.
Modelling the Effect of Allopregnanolone on the Resolution of Spike-Wave Discharges
Authors: Ahmed Maliha , Campbell Sue Ann
Published: July 2023

Objective

Childhood absence epilepsy (CAE) is a paediatric generalized epilepsy disorder with a confounding feature of resolving in adolescence in a majority of cases. In this study, we modelled how the small-scale (synapse-level) effect of progesterone metabolite allopregnanolone induces a large-scale (network-level) effect on a thalamocortical circuit associated with this disorder. In particular, our goal was to understand the role of sex steroid hormones in the spontaneous remission of CAE.

Methods

The conductance-based computational model consisted of single-compartment cortical pyramidal, cortical interneurons, thalamic reticular and thalamocortical relay neurons, each described by a set of ordinary differential equations. Excitatory and inhibitory synapses were mediated by AMPA, GABAa and GABAb receptors. The model was implemented using the NetPyne modelling tool and the NEURON simulator.

Results

The action of allopregnanolone on individual GABAa-receptor mediated synapses has an ameliorating effect on spike-wave discharges (SWDs) associated with absence seizures. This effect is region-specific and most significant in the thalamus, particularly the synapses between thalamic reticular neurons.

Significance

The remedying effect of allopregnanolone on SWDs may possibly be true only for individuals that are predisposed to remission due to intrinsic connectivity differences or differences in tonic inhibition. These results are a useful first-step and prescribe directions for further investigation into the role of ALLO together with these differences to distinguish between models for CAE-remitting and non-remitting individuals.
Integrative spatial analysis reveals a multi-layered organization of glioblastoma
Authors: Greenwald Alissa C. , Darnell Noam Galili , Hoefflin Rouven , Simkin Dor , Gonzalez-Castro L. Nicolas , Mount Christopher , Hirsch Dana , Nomura Masashi , Talpir Tom , Kedmi Merav , Goliand Inna , Medici Gioele , Li Baoguo , Keren-Shaul Hadas , Weller Michael , Addadi Yoseph , Neidert Marian C. , Suvá Mario L. , Tirosh Itay
Published: July 2023

Glioma contains malignant cells in diverse states. Hypoxic regions are associated with a unique histology of pseudopalisading cells, while other regions appear to have limited histological organization, reflecting the diffuse nature of glioma cells. Here, we combine spatial transcriptomics with spatial proteomics and novel computational approaches to define glioma cellular states at high granularity and uncover their organization. We find three prominent modes of cellular organization. First, cells in any given state tend to be spatially clustered, such that tumors are composed of small local environments that are each typically enriched with one major cellular state. Second, specific pairs of states preferentially reside in proximity across multiple scales. Despite the unique composition of each tumor, this pairing of states remains largely consistent across tumors. Third, the pairwise interactions that we detect collectively define a global architecture composed of five layers. Hypoxia appears to drive this 5-layered organization, as it is both associated with unique states of surrounding cells and with a long-range organization that extends from the hypoxic core to the infiltrative edge of the tumor. Accordingly, tumor regions distant from any hypoxic foci and tumors that lack hypoxia such as IDH-mutant glioma are less organized. In summary, we provide a conceptual framework for the organization of gliomas at the resolution of cellular states and highlight the role of hypoxia as a long-range tissue organizer.
Multimodal imaging for validation and optimization of ion channel-based chemogenetics in nonhuman primates
Authors: Hori Yuki , Nagai Yuji , Hori Yukiko , Oyama Kei , Mimura Koki , Hirabayashi Toshiyuki , Inoue Ken-ichi , Fujinaga Masayuki , Zhang Ming-Rong , Takada Masahiko , Higuchi Makoto , Minamimoto Takafumi
Published: July 2023

Chemogenetic tools provide an opportunity to manipulate neuronal activity and behavior selectively and repeatedly in nonhuman primates (NHPs) with minimal invasiveness. Designer Receptors Exclusively Activated by Designer Drugs are one example that is based on mutated muscarinic acetylcholine receptors. Another channel-based chemogenetic system available for neuronal modulation in NHPs uses Pharmacologically Selective Actuator Modules (PSAMs), which are selectively activated by Pharmacologically Selective Effector Molecules (PSEMs). To facilitate the use of the PSAM/PSEM system, the selection and dosage of PSEMs should be validated and optimized for NHPs. To this end, we used a multimodal imaging approach. We virally expressed excitatory PSAM (PSAM4-5HT3) in the striatum and the primary motor cortex of two macaque monkeys, and visualized its location through positron emission tomography (PET) with the reporter ligand [18F]ASEM. Chemogenetic excitability of neurons triggered by two PSEMs (uPSEM817 and uPSEM792) was evaluated using [18F]fluorodeoxyglucose-PET imaging, with uPSEM817 being more efficient than uPSEM792. Pharmacological magnetic resonance imaging showed that increased brain activity in the PSAM4-expressing region began approximately 13 min after uPSEM817 administration and continued for at least 60 min. Our multimodal imaging data provide valuable information regarding the manipulation of neuronal activity using the PSAM/PSEM system in NHPs, facilitating future applications.

Significance statement

Like other chemogenetic tools, the ion channel-based system called Pharmacologically Selective Actuator Module/Pharmacologically Selective Effector Molecule (PSAM/PSEM) allows remote manipulation of neuronal activity and behavior in living animals. Nevertheless, its application in non-human primates (NHPs) is still limited. Here, we used multi-tracer positron emission tomography (PET) imaging and pharmacological magnetic resonance imaging (MRI) to visualize an excitatory chemogenetic ion channel (PSAM4-5HT3) and validate its chemometric function in macaque monkeys. Our results provide the optimal agonist, dose, and timing for chemogenetic neuronal manipulation, facilitating the use of the PSAM/PSEM system and expanding the flexibility and reliability of circuit manipulation in NHPs in a variety of situations.
Deviance detection in subthalamic neural population responses to natural stimuli in bats
Authors: Wetekam Johannes , Hechavarría Julio , López-Jury Luciana , González-Palomares Eugenia , Kössl Manfred
Published: July 2023

Deviance detection describes an increase of neural response strength caused by a stimulus with a low probability of occurrence. This ubiquitous phenomenon has been reported for multiple species, from subthalamic areas to auditory cortex. While cortical deviance detection has been well characterised by a range of studies covering neural activity at population level (mismatch negativity, MMN) as well as at cellular level (stimulus-specific adaptation, SSA), subcortical deviance detection has been studied mainly on cellular level in the form of SSA. Here, we aim to bridge this gap by using noninvasively recorded auditory brainstem responses (ABRs) to investigate deviance detection at population level in the lower stations of the auditory system of a hearing specialist: the batCarollia perspicillata. Our present approach uses behaviourally relevant vocalisation stimuli that are closer to the animals’ natural soundscape than artificial stimuli used in previous studies that focussed on subcortical areas. We show that deviance detection in ABRs is significantly stronger for echolocation pulses than for social communication calls or artificial sounds, indicating that subthalamic deviance detection depends on the behavioural meaning of a stimulus. Additionally, complex physical sound features like frequency- and amplitude-modulation affected the strength of deviance detection in the ABR. In summary, our results suggest that at population level, the bat brain can detect different types of deviants already in the brainstem. This shows that subthalamic brain structures exhibit more advanced forms of deviance detection than previously known.
Mass2SMILES: deep learning based fast prediction of structures and functional groups directly from high-resolution MS/MS spectra
Authors: Elser David , Huber Florian , Gaquerel Emmanuel
Published: July 2023

Modern mass spectrometry-based metabolomics generates vast amounts of mass spectral data as part of the chemical inventory of biospecimens. Annotation of the resulting MS/MS spectra remains a challenging task that mostly relies on database interrogations,in silicoprediction and interpretation of diagnostic fragmentation schemes and/or expert knowledge-based manual interpretations. A key limitation is additionally that these approaches typically leave a vast proportion of the (bio)chemical space unannotated. Here we report a deep neural network method to predict chemical structures solely from high-resolution MS/MS spectra. This novel approach initially relies on the encoding of SMILES strings from chemical structures using a continuous chemical descriptor space that had been previously implemented for molecule design. The deep neural network was trained on 83,358 natural product-derived MS/MS spectra of the GNPS library and of the NIST HRMS database with addition of the calculated neutral losses for those spectra. After this training and parameter optimization phase, the deep neural network approach was then used to predict structures from MS/MS spectra not included in the training data-set. Our current version, implemented in the Python programming language, accurately predicted 7 structures from 744 validation structures and the following 14 structures had aTanimotosimilarity score above 0.9 when compared to the true structure. It was also able to correctly identify two structures from the CASMI 2022 international contest. On average theTanimotosimilarity is of 0.40 for data of the CASMI 2022 international contest and of 0.39 for the validation data-set. Finally, our deep neural network is also able to predict the number of 60 functional groups as well as the molecular formula of chemical structures and adduct type for the analyzed MS/MS spectra. Importantly, this deep neural network approach is extremely fast, in comparison to currently available methods, making it suitable to predict on regular computers structures for all substances within large metabolomics datasets.
On-Pathway Oligomer of Human Islet Amyloid Polypeptide Induced and Stabilized by Mechanical Rotation During MAS NMR
Authors: McCalpin Samuel D , Dickwella Widanage Malitha C , Fu Riqiang , Ramamoorthy Ayyalusamy
Published: July 2023

Intermediates along the fibrillation pathway are generally considered to be the toxic species responsible for the pathologies of amyloid diseases. However, structural studies of these species have been hampered by heterogeneity and poor stability in standard aqueous conditions. Here, we report a novel methodology for producing stable, on-pathway oligomers of the human Type-2 Diabetes-associated islet amyloid polypeptide (hIAPP, or amylin) using the mechanical forces associated with magic angle spinning (MAS). The species were a heterogeneous mixture of globular and short rod-like species with significant beta-sheet content and the capability of seeding hIAPP fibrillation. We used MAS NMR to demonstrate that the nature of the species was sensitive to sample conditions including peptide concentration, ionic strength, and buffer. The methodology should be suitable for studies of other aggregating systems.
Increasing Chemotherapeutic Efficacy Using pH Modulating and Doxorubicin Releasing Injectable Chitosan-Polyethylene Glycol Hydrogels
Authors: Ahmed Zahra , LoGiudice Kevin , Mays Gavin , Schorr Angelina , Rowey Rachel , Yang Haisong , Trivedi Shruti , Srivastava Vikas
Published: July 2023

Modulation of pH is crucial to maintaining the chemical homeostasis of biological environments. The irregular metabolic pathways exhibited by cancer cells result in the production of acidic byproducts that are excreted and accumulate in the extracellular tumor microenvironment, reducing its pH. As a consequence of the lower pH in tumors, cancer cells increase the expression of metastatic phenotypes and chemotherapeutic resistance. A significant limitation in current cancer therapies is the inability to locally deliver the chemotherapy, leading to significant damage to healthy cells in systemic administration. To overcome these challenges, we present an injectable chitosan-polyethylene glycol hydrogel that is dual-loaded with doxorubicin and sodium bicarbonate providing alkaline buffering of extracellular acidity and simultaneous chemotherapeutic delivery to increase chemotherapeutic efficacy. We conducted in vitro studies of weak base chemotherapeutic and alkaline buffer release from the hydrogel. The release of doxorubicin from hydrogels increased in a low pH environment and was dependent on the encapsulated sodium bicarbonate concentration. We investigated the influence of pH on doxorubicin efficacy and viability of MCF-7 and MDA-MB-231 breast cancer cell lines. The results show a 2 to 3 fold increase in IC50values from neutral pH to low pH, showing decreased cancer cell viability at neutral pH as compared to acidic pH. The IC50results were shown to correlate with a decrease in intracellular uptake of doxorubicin at low pH. The proposed hydrogels were confirmed to be non-toxic to healthy MCF-10A mammary epithelial cells. Rheological studies were performed to verify that the dual loaded hydrogels were injectable. The mechanical and release properties of the hydrogels were maintained after extended storage. The chemotherapeutic activity of doxorubicin was evaluated in the presence of the proposed pH regulating hydrogels. The findings suggest a promising non-toxic, biodegradable hydrogel buffer delivery system that can achieve two simultaneous important goals of local acidosis neutralization and chemotherapeutic release.
National seroprevalence and risk factors of bluetongue virus in domestic ruminants in Peru
Authors: Navarro-Mamani Dennis A. , Jurado Pucllas Jessica , Vargas-Calla Ana , Ponce Dextre Kevin , Zarate Quispe Yari , Murga-Moreno César A. , Ibelice Perez C , Ruben Villacaqui A , Miguel Ara G , Incil Edith , Pedro Ortiz O , Gerónimo Hermelinda Rivera
Published: July 2023

Bluetongue virus (BTV) is a global infection primarily transmitted among domestic and wild ruminant populations throughCulicoidesspp. midges. Infection is highly prevalent across temperate and tropical regions; however, significant changes in the global distribution of BTV have been observed in recent years. We aimed to evaluate the national BTV seroprevalence and its risk factors among domestic ruminants (cattle, sheep and goats) in Peru. Ruminant sera (cattle= 3 452, sheep= 2 786 and goats=1 568) were collected using a random, two-stage clustering method and analyzed by c-ELISA. The national BTV seroprevalence was 12.7% (95% CI: 11.00-14.63%) and the seropositivity rate for each species was 19.29% (95% CI: 16.0%–31.1%) in cattle, 8.4 (95% CI: 6.6%–10.5%) in sheep, and 9.2% (95% CI: 5.6%–14.8%) in goats. Bivariate and multiple logistic regression analysis were used to evaluate risk factors for BTV seropositivity and to estimate Odds Ratios (OR) with 95% CI. We found that age, altitude, and maximum temperature were identified as crucial factors influencing the prevalence of BTV seroprevalence in cattle, sheep and goats. Older animals, particularly cattle and goats between 6 and 24 months and above 24 months, exhibited a significantly higher likelihood of BTV infection. Additionally, higher altitudes above 3000 masl played a protective role, reducing the risk of BTV transmission. Furthermore, increased maximum temperatures, especially exceeding 30 °C, were associated with a greater prevalence of BTV. This study lays the groundwork for identifying BTV serotypes andCulicoidesspp. in different regions, including altitudes above 3000 masl, to enhance BTV surveillance in Peru.
Unsuspected consequences of synonymous and missense variants inOCA2can be detected in blood cell RNA samples of patients with albinism
Authors: Michaud Vincent , Sequeira Angèle , Mercier Elina , Lasseaux Eulalie , Plaisant Claudio , Hadj-Rabia Smail , Whalen Sandra , Bonneau Dominique , Dieux-Coeslier Anne , Morice-Picard Fanny , Coursimault Juliette , Arveiler Benoît , Javerzat Sophie
Published: July 2023

Oculocutaneous albinism type 2 (OCA2) is the second most frequent form of albinism and represents about 30% of OCA worldwide. As with all types of OCA, patients present with hypopigmentation of hair and skin as well as severe visual abnormalities. We focused on a subgroup of 29 patients for whom genetic diagnosis was pending because at least one of their identified variants in or around exon 10 ofOCA2is of uncertain significance (VUS). By minigene assay, we investigated the effect of these VUS on exon 10 skipping and showed that not only intronic but also some synonymous variants can result in enhanced exon skipping. We further found that excessive skipping of exon 10 could be detected directly on blood samples of patients and of their one parent with the causal variant, avoiding invasive skin biopsies. Moreover, we show that variants which result in lack of detectableOCA2mRNA can be identified from blood samples as well, as shown for the most commonOCA2pathogenic missense variant c.1327G>A/p.(Val443Ile). In conclusion, blood cell RNA analysis allows testing the potential effect of anyOCA2VUS on transcription products. This should help to elucidate yet unsolved OCA2 patients and improve genetic counseling.

SIGNIFICANCE

Our study allows us to reconsider variants of unknown significance ofOCA2as pathogenic as they induce exon 10 skipping. We show that mis-splicing as well as other types of transcripts imbalance can be detected directly from blood cell samples, avoiding invasive biopsies. We recommend systematic collection of a blood RNA sample from patients with inconclusive genetic diagnosis and suspected OCA2 (e.g., only one pathogenic variant inOCA2; 1 VUS; 2 VUS intrans).
Assessing GPT-3.5 and GPT-4 in Generating International Classification of Diseases Billing Codes
Authors: Soroush Ali , Glicksberg Benjamin S. , Zimlichman Eyal , Barash Yiftach , Freeman Robert , Charney Alexander W. , Nadkarni Girish N , Klang Eyal
Published: July 2023

Background

Large Language Models (LLMs) like GPT-3.5 and GPT-4 are increasingly entering the healthcare domain as a proposed means to assist with administrative tasks. To ensure safe and effective use with billing coding tasks, it is crucial to assess these models’ ability to generate the correct International Classification of Diseases (ICD) codes from text descriptions.

Objectives

We aimed to evaluate GPT-3.5 and GPT-4’s capability to generate correct ICD billing codes, using the ICD-9-CM (2014) and ICD-10-CM and PCS (2023) systems.

Methods

We randomly selected 100 unique codes from each of the most recent versions of the ICD-9-CM, ICD-10-CM, and ICD-10-PCS billing code sets published by the Centers for Medicare and Medicaid Services. Using the ChatGPT interface (GPT-3.5 and GPT-4), we prompted for the ICD codes that corresponding to each provided code description. Outputs were compared with the actual billing codes across several performance measures. Errors were qualitatively and quantitatively assessed for any underlying patterns.

Results

GPT-4 and GPT-3.5 demonstrated varied performance across each ICD system. In ICD-9-CM, GPT-4 and GPT-3.5 achieved an exact match rate of 22% and 10%, respectively. 13% (GPT-4) and 10% (GPT-3.5) of generated ICD-10-CM codes were exact matches. Notably, both models struggled considerably with the procedurally focused ICD-10-PCS, with neither GPT-4 or GPT-3.5 producing any exactly matched codes. A substantial number of incorrect codes had semantic similarity with the actual codes for ICD-9-CM (GPT-4: 60.3%, GPT-3.5: 51.1%) and ICD-10-CM (GPT-4: 70.1%, GPT-3.5: 61.1%), in contrast to ICD-10-PCS (GPT-4: 30.0%, GPT-3.5: 16.0%).

Conclusion

Our evaluation of GPT-3.5 and GPT-4’s proficiency in generating ICD billing codes from ICD-9-CM, ICD-10-CM and ICD-10-PCS code descriptions reveals an inadequate level of performance. While the models appear to exhibit a general conceptual understanding of the codes and their descriptions, they have a propensity for hallucinating key details, suggesting underlying technological limitations of the base LLMs. This suggests a need for more rigorous LLM augmentation strategies and validation prior to their implementation in healthcare contexts, particularly in tasks such as ICD coding which require significant digit-level precision.
Prognostic value of advanced lung cancer inflammation index (ALI) combined with geriatric nutritional risk index (GNRI) in patients with chronic heart failure
Authors: Shi Tao , Wang Yan , Peng Yunzhu , Wang Meifen , Zhou Yanji , Gu Wenyi , Li Yanyan , Zou Jie , Zhu Na , Chen Lixing
Published: July 2023

Background

This study was undertaken to explore the predictive value of the advanced lung cancer inflammation index (ALI) combined with the geriatric nutritional risk index (GNRI) for all‐cause mortality in patients with CHF.

Methods and Results

We enrolled 1123 patients with HF admitted to our cardiology department from January 2017 to October 2021. Patients were divided into Group 1 (ALI<24.60 and GNRI<94.41), Group 2 (ALI<24.60 and GNRI≥94.41), Group 3 (ALI≥24.60 and GNRI<94.41) and Group 4 (ALI≥24.60 and GNRI≥94.41), according to the median ALI and GNRI. From the analysis of the relationship between the ALI and GNRI, we concluded that there was a mild positive linear correlation (r= 0.348, p< 0.001) and no interaction (p=0.140) between the ALI and GNRI. Kaplan‒Meier analysis showed that the cumulative incidence of all‐cause mortality in patients with CHF was highest in Group 1 (log‐rank χ2126.244, p<0.001). Multivariate Cox proportional hazards analysis revealed that ALI and GNRI were independent predictors of all‐cause mortality in CHF patients (ALI: HR 0.313, 95% CI 0.228‐0.430, p <0.001; GNRI: HR 0.966, 95% CI 0.953‐0.979, p <0.001). The area under the curve (AUC) for ALI combined with GNRI was 0.711 (p<0.001), according to the time‐dependent ROC curve.

Conclusion

ALI and GNRI were independent predictors of all‐cause mortality in CHF patients. Patients with CHF had the highest risk of all‐cause mortality when the ALI was <24.60 and the GNRI was <94.41. ALI combined with the GNRI has good predictive value for the prognosis of CHF patients.
From colonial clusters to colonial sheaths: analysis ofMicrocystismorphospecies in mesocosm by imaging flow cytometry
Authors: Zhumakhanova Adina , Mirasbekov Yersultan , Malashenkov Dmitry V. , Davidson Thomas A. , Levi Eti Ester , Jeppesen Erik , Barteneva Natasha S.
Published: July 2023

The alarming increase in the frequency of blooms ofMicrocystisin freshwater lakes and reservoirs occurs worldwide, with major implications for their ecosystem functioning and water quality. We applied FlowCAM-based imaging flow cytometry together with PCR and sequencing to get a comprehensive picture of the seasonal development ofMicrocystiscommunity in a long-term running lake mesocosm experiment. The IFC analysis with manual taxonomic classification confirmed early findings with a machine learning algorithm that someMicrocystismorphospecies completely disappeared and re-appeared along the mesocosm experiment timeline. This observation supports the hypothesis of the main transition pathways of colonialMicrocystis. For the first time, colonial mucilaginous envelopes or sheaths were reported as separate entities, and not as a part ofMicrocystiscolonies. The colonial sheaths may contain a few single Microcystis cells and reach significant numbers (thousands) during a cyanobacterial bloom. We also found that non-identifiable colonial small clusters ofMicrocystiscells are an important stage in the complex mosaic of aMicrocystisbloom and are associated with the development of colonial forms. Our findings were validated by the principal component analysis coupled with the constructed associative matrices. We hypothesize that colonial sheaths may be crucial atMicrocystisspp. dispersal and represent one of the stages of colonies development.
Modeling the seasonal variation of windborne transmission of porcine reproductive and respiratory syndrome virus between swine farms
Authors: Lim Seunghyun , Perez Andres M. , Kanankege Kaushi S. T.
Published: July 2023

Modeling windborne transmission of aerosolized pathogens is challenging. We adapted an atmospheric dispersion model named Hybrid Single-Particle Lagrangian Integrated Trajectory model (HYSPLIT) to simulate windborne dispersion of porcine reproductive and respiratory syndrome virus (PRRSv) between swine farms and incorporated the findings into an outbreak investigation. The risk was estimated semi-quantitatively based on the cumulative daily deposition of windborne particles, and the distance to closest emitting farm with an ongoing outbreak. Five years of data (2014 : 2018) were used to study seasonal differences of deposition thresholds of the airborne particles containing PRRSv and to evaluate model in relation to risk prediction and barn air filtration. When considered the 14-day cumulative deposition, in Winter, above threshold particle depositions would reach up to 30 km from emitting farms with 84% of them being within 10km. Long-distance pathogen transmission was highest in Winter and Fall, lower in Spring, and least in Summer. The model successfully replicated the observed seasonality of PRRSv where Fall and Winter posing a higher risk for outbreaks. Reaching the humidity and temperature thresholds tolerated by the virus in Spring and Summer reduced the survival and infectivity of aerosols beyond 10 -20 km. Within in the data limitations of voluntary participation, when assumed wind as the sole route of PRRSv transmission, the predictive performance of the model was fair with >0.64 AUC. Barn air filtration was associated with fewer outbreaks, particularly when exposed to high levels of viral particles. The study confirms the usefulness of HYSPLIT models as a tool when determining seasonal effects, distances, and inform near real-time risk of windborne PRRSv transmission that can be useful in future outbreak investigations and implementing timely control measures.
Preserved striatal innervation and motor function despite severe loss of nigral dopamine neurons following mitochondrial dysfunction induced by mtDNA mutations
Authors: Paß Thomas , Ricke Konrad M. , Hofmann Pierre , Chowdhury Roy , Nie Yu , Chinnery Patrick , Endepols Heike , Neumaier Bernd , Carvalho André , Rigoux Lionel , Steculorum Sophie , Prudent Julien , Riemer Trine , Aswendt Markus , Brachvogel Bent , Wiesner Rudolf J.
Published: July 2023

Degeneration of dopamine neurons in the substantia nigra and their striatal axon terminals causes cardinal motor symptoms of Parkinson’s disease (PD). In idiopathic cases, high levels of mitochondrial DNA (mtDNA) mutations associated with mitochondrial dysfunction are a central feature of these vulnerable neurons. Here we present a mouse model expressing the K320E-variant of the mitochondrial helicase Twinkle in dopamine neurons, leading to accelerated mtDNA ageing. K320E-TwinkleDaNmice showed normal motor function at 20 months of age, although already ∼70% of nigral dopamine neurons had perished. The remaining neuron population still preserved ∼75% of axon terminals in the dorsal striatum, which enabled normal dopamine release. Transcriptome analysis and viral tracing confirmed compensatory axonal sprouting of surviving nigral dopamine neurons. We conclude that a small population of substantia nigra neurons can adapt to mtDNA mutations and maintain motor control in mice, holding chances for new treatment strategies in PD patients.
Towards establishing a 24-hour, microplate-based, transcriptomics assay for rainbow trout embryos
Authors: Basu Niladri , Marshall Aylish , Marchand Hugo , Boulanger Emily , Mittal Krittika , Head Jessica
Published: July 2023

There is interest in the development of early-life stage (ELS) tests with fish embryo models that are high-throughput and can generate transcriptomics point of departure (tPOD) values. The objective of this study was to establish a method in rainbow trout (Oncorhynchus mykiss) hatchlings that could satisfy both of these interests. We based our pilot method on recent efforts by U.S. EPA researchers to establish a larval fathead minnow high throughput transcriptomics assay. Here, 1-2 day post hatch trout were assayed in 24-well plates in which they were exposed for 24 hours to 12 different concentrations of test chemicals, including a negative control (DMSO, culture water). Test concentrations were anchored with a chemical’s LC50 data from the US EPA ECOTOX database and EnviroTox database, and from this, concentrations were spaced on a half-log basis that spanned 6-7 orders of magnitude. In pilot study 1 we tested 3,4-dichloroaniline, CuSO4(0.34 mg/L), and ethinylestradiol. In pilot study 2 we tested 3,4-dichloroaniline (58.5 mg/L), CuSO4(0.34 and 0.41 mg/L), ethinylestradiol (>10 µg/L), permethrin (>10 µg/L), malathion (0.61 mg/L), 6PPD quinone (5.6 µg/L), acetaldehyde (41.2 mg/L), 4-fluoroaniline (242.7 mg/L), glyphosate (∼150 mg/L), ethanol (>1 g/L), thiamethoxam (>300 mg/L), and allyl alcohol (>30 mg/L). In both pilot studies derived LC50 values are provided in parentheses. Repeated studies of CuSO4yielded consistent LC50 values (0.34, 0.34, 0.41 mg/L). The correlation between LC50s from the current study for rainbow trout embryos versus those from the literature on adult rainbow trout for 7 chemicals was r2= 0.91. Work is underway to optimize transcriptomics assays from these samples using EcoToxChips and UPXome, with the ultimate goal to be able to derive transcriptomics points of departure. Taken together these results provide a foundation towards establishing a novel testing platform for chemical and environmental risk assessment that is much quicker (24 hrs), ethical (non-protected life stages), resource efficient (e.g., microplate-based, small volumes of chemicals), and more informative (molecular clues into MOA) than traditional bioassay approaches.
Genetic approaches reveal a healthy population and an unexpectedly recent origin for an isolated desert spring fish
Authors: Sidlauskas Brian L. , Mathur Samarth , Aydoğan Hakan , Monzyk Fred R. , Black Andrew N.
Published: July 2023

Foskett Spring in Oregon’s desert harbors a historically threatened population of Western Speckled Dace (Rhinichthys klamathensis). Though recently delisted, the dace’s recruitment depends upon regular removal of encroaching vegetation. Previous studies assumed that Foskett Dace separated from others in the Warner Valley about 10,000 years ago, thereby framing an enigma about the population’s surprising ability to persist for so long in a tiny habitat easily overrun by plants. To investigate the phenomenon of persistence and the effectiveness of interventions to augment population size, we assessed genetic diversity among daces inhabiting Foskett Spring, a refuge at Dace Spring, and three nearby streams. Analysis revealed a robust effective population size (Ne) of nearly 5,000 within Foskett Spring, though Nein the Dace Spring refuge is just 10% of that value. Heterozygosity is slightly lower than expected based on random mating at all five sites, indicating mild inbreeding, but not at a level of concern. These results confirm the genetic health of Foskett Dace. Unexpectedly, genetic differentiation reveals closer similarity between Foskett Dace and a newly discovered population from Nevada’s Coleman Creek than between Foskett Dace and dace elsewhere in Oregon. Demographic modeling inferred Coleman Creek as the ancestral source of Foskett Dace just 600 years ago, much more recently than previously suspected and coincident with the arrival of large herbivores whose grazing may have maintained open water suitable for reproduction. These results solve the enigma of persistence by greatly shortening the duration over which Foskett Dace have inhabited their isolated spring.
Human complement Factor H and Properdin act as soluble pattern recognition receptors and differentially modulate SARS-CoV-2 Infection
Authors: Beirag Nazar , Varghese Praveen M , Kumar Chandan , Idicula-Thomas Susan , Neto Martin Mayora , Khan Haseeb A. , Sim Robert B. , Madan Taruna , Temperton Nigel , Kishore Uday
Published: July 2023

Severe cases of SARS-CoV-2 infection are characterised by an imbalanced immune response, excessive inflammation, and the development of acute respiratory distress syndrome, which can lead to multiorgan failure and death. Several studies have demonstrated dysregulated complement activity as an indicator of immunopathogenesis in the SARS-CoV-2 infection. Notably, the complement alternative pathway has been implicated in driving the excessive inflammation during severe SARS-CoV-2 infection. Reduced levels of factor H (FH), a down-regulator of the alternative pathway, and increased levels of properdin (Factor P/FP), the only known up-regulator of the alternative pathway, have been observed in individuals with severe COVID-19 infection. The present study investigated the complement activation-independent, and a more direct role of FH and FP against SARS-CoV-2 infection. Using direct ELISA, the interactions of FH and FP with the SARS-CoV-2 spike (S) and receptor binding domain (RBD) were assessed. Using S protein expressing lentiviral pseudotypes, the cell binding and luciferase-based virus entry assays were employed to assess the potential modulatory effects of FH, FP, and recombinant thrombospondin repeats 4 and 5 (TSR4+5) on SARS-CoV-2 cell entry. We also evaluated the immunomodulatory functions of FH and FP in the cytokine response triggered by SARS-CoV-2 pseudotypes via RT-qPCR. SARS-CoV-2 S and RBD proteins were found to bind both FH and FP. Treatment of A549 cells expressing human ACE2 and TMPRSS2 with FP or TSR4+5 resulted in increased cell entry and binding of SARS-CoV-2 pseudotypes. In silico studies revealed that FP increases affinity between SARS-CoV-2 and host ACE2. The impact of FP on viral cell entry and binding was reversed by anti-FP antibody treatment in A549-hACE2+TMPRSS2 cells. However, FH treatment reduced the cell entry and binding of SARS-CoV-2 lentiviral pseudotypes. Furthermore, the A549-hACE2+TMPRSS2 cells challenged with SARS-CoV-2 spike, envelope, nucleoprotein, and membrane protein expressing alphaviral pseudotypes pre-treated with FP or TSR4+5, exhibited upregulation of the transcripts of pro-inflammatory cytokines, such as IL-1β, IL-8, IL-6, TNF-α, IFN-α and RANTES (as well as NF-κB). Conversely, FH pre-treatment downregulated the expression of these pro-inflammatory cytokines. Treatment of A549-hACE2+TMPRSS2 cells with FP increased S protein-mediated NF-κB activation, while FH treatment reduced it. These findings suggest that FH may act as an inhibitor of SARS-CoV-2 cell entry and binding, thereby attenuating the infection-associated inflammatory response in a complement activation-independent manner. FP may contribute to viral cell entry, binding, and exacerbating the immune response. That may result in potentially influencing the severity of the infection.
Molossus molossus bats encompass at least two distinct genera of totivirus-like
Authors: Silva Couto Roseane da , Foro Ramos Endrya do Socorro , Abreu Wandercleyson Uchôa , Ribeiro Rodrigues Luis Reginaldo , Marinho Luis Fernando , Santos Morais Vanessa dos , Villanova Fabiola , Pandey Ramendra Pati , Deng Xutao , Delwart Eric , da Costa Antonio Charlys , Leal Elcio
Published: July 2023

The Totiviridae family of viruses has a unique genome consisting of double-stranded RNA with two open reading frames that encode the capsid protein (Cap) and the RNA-dependent RNA polymerase (RdRp). Most virions in this family are isometric in shape, approximately 40 nm in diameter, and lack envelope. There are five genera within this family, including Totivirus,Victorivirus, Giardiavirus, Leishmaniavirus, andTrichomonasvirus. WhileTotivirusandVictorivirusprimarily infect fungi,Giardiavirus, Leishmaniavirus, andTrichomonasvirusinfect diverse hosts, including protists, insects, and vertebrates. Recently, new totivirus-like species have been discovered in fish and plant hosts, and through metagenomic analysis, a novel totivirus-like virus (named Tianjin totivirus) has been isolated from bat guano. Interestingly, Tianjin totivirus causes cytopathic effects in insect cells but cannot grow in mammalian cells, suggesting that it infects insects consumed by insectivorous bats. In this study, we used next-generation sequencing and identified totivirus-like viruses in liver tissue fromMolossus molossusbats () in the Amazon region of Brazil. Comparative phylogenetic analysis based on the RNA-dependent RNA polymerase region revealed that the viruses identified in Molossus bats belong to two distinct phylogenetic clades, possibly comprising different genera within the Totiviridae family. Notably, the mean similarity between Tianjin totivirus and the totiviruses identified in Molossus bats is less than 18%. These findings suggest that the diversity of totiviruses in bats is more extensive than previously recognized and highlight the potential for bats to serve as reservoirs for novel toti-like viruses.
Direct optical measurement of intra-molecular distances down to the Ångström scale
Authors: Sahl Steffen J. , Matthias Jessica , Inamdar Kaushik , Khan Taukeer A. , Weber Michael , Becker Stefan , Griesinger Christian , Broichhagen Johannes , Hell Stefan W.
Published: July 2023

Optical investigations of nanometer distances between proteins, their subunits, or other biomolecules have been the exclusive prerogative of Förster Resonance Energy Transfer (FRET) microscopy for decades. Here we show that MINFLUX fluorescence nanoscopy measures intra-molecular distances down to 1 nm – and in planar projections down to 1 Angström – directly, linearly, and with Angström precision. Our method is validated by quantifying well-characterized 1-to-10 nm distances in polypeptides and proteins. Moreover, we visualize the orientations of immunoglobulin subunits and reveal specific configurations of a histidine kinase domain dimer. Our results open the door for examining proximities and interactions of macromolecules under physiological conditions.
Molecular Mechanism of a FRET Biosensor for the Cardiac Ryanodine Receptor Pathologically Leaky State
Authors: Svensson Bengt , Nitu Florentin R. , Rebbeck Robyn T. , McGurran Lindsey M. , Oda Tetsuro , Thomas David D. , Bers Donald M. , Cornea Razvan L.
Published: July 2023

Ca2+leak from cardiomyocyte sarcoplasmic reticulum (SR) via hyperactive resting cardiac ryanodine receptor channels (RyR2) is pro-arrhythmic. An exogenous peptide, (DPc10) detects leaky RyR2 in cardiomyocytes. Conversely, calmodulin (CaM) inhibits RyR2 leak. These observations have led to designing a FRET biosensor for drug discovery targeting RyR2. Here we used FRET to understand the molecular mechanism driving the DPc10-CaM interdependence when binding RyR2 in SR vesicles. We used donor-FKBP12.6 (D-FKBP) to resolve RyR2 binding of acceptor-CaM (A-CaM). In low nanomolar Ca2+, DPc10 decreased both FRETmax(under saturating [A-CaM]) and the CaM/RyR2 binding affinity. In micromolar Ca2+, DPc10 decreased FRETmaxwithout affecting CaM/RyR2 binding affinity. This correlates with analysis of fluorescence-lifetime-detected FRET indicating that DPc10 lowers occupancy of the RyR2 CaM-binding sites in nanomolar (not micromolar) Ca2+and lengthens D-FKBP/A-CaM distances independent of [Ca2+]. To observe DPc10/RyR2 binding, we used acceptor-DPc10 (A-DPc10). CaM weakens A-DPc10/RyR2 binding, this effect being larger in micromolar vs. nanomolar Ca2+. Moreover, A-DPc10/RyR2 binding is cooperative in CaM- and FKBP-dependent manner, suggesting that both endogenous modulators promote concerted structural changes between RyR2 protomers for channel regulation. Aided by analysis of cryo-EM structures, these insights inform further development of the DPc10-CaM paradigm for therapeutic discovery targeting RyR2.
DataPLAN: a web-based data management plan generator for the plant sciences
Authors: Zhou Xiao-Ran , Beier Sebastian , Brilhaus Dominik , Rodrigues Cristina Martins , Mühlhaus Timo , von Suchodoletz Dirk , Twyman Richard M. , Usadel Björn , Kranz Angela
Published: July 2023

Research Data Management (RDM) is a system for the effective handling of research data that enables scientists to structure their research questions and ensure best practices throughout the data lifecycle, from acquisition, computation and annotation to data publication and re-use. Data management plans (DMPs) are documents that formally set out the RDM of a project and are required by many funding bodies. DMPs help to organize and structure RDM strategies, thus promoting data findability, accessibility, interoperability and reusability (FAIR). Although DMPs incorporate methods and standards that can be reused by different research projects, the standardization of DMP content is not as evident as the standardization of RDM practices and data/metadata. To address this issue in the plant sciences, we developed DataPLAN – a tool that combines a questionnaire with pre-written standardized responses. We wrapped the questionnaire in a serverless single-page web application that can then generate standardized responses from DMP templates. The current templates cater to plant research grant proposals for Horizon 2020, Horizon Europe and the German Research Foundation (Deutsche Forschungsgemeinschaft, DFG). In the future the range of templates will be extended to accommodate other funding schemes, thereby enabling more users to generate their own templates. The DataPLAN web application is open-source and does not require an internet connection. By utilizing DataPLAN, the workload associated with creating, updating, and adhering to DMPs is significantly reduced.