Expanding the genetic and phenotypic landscape of replication factor C complex-related disorders: RFC4 deficiency is linked to a multisystemic disorder.

The precise regulation of DNA replication is vital for cellular division and genomic integrity. Central to this process is the replication factor C (RFC) complex, encompassing five subunits, which loads proliferating cell nuclear antigen onto DNA to facilitate the recruitment of replication and repair proteins and enhance DNA polymerase processivity. While RFC1's role in cerebellar ataxia, neuropathy, and vestibular areflexia syndrome (CANVAS) is known, the contributions of RFC2-5 subunits on human Mendelian disorders is largely unexplored. Our research links bi-allelic variants in RFC4, encoding a core RFC complex subunit, to an undiagnosed disorder characterized by incoordination and muscle weakness, hearing impairment, and decreased body weight. We discovered across nine affected individuals rare, conserved, predicted pathogenic variants in RFC4, all likely to disrupt the C-terminal domain indispensable for RFC complex formation. Analysis of a previously determined cryo-EM structure of RFC bound to proliferating cell nuclear antigen suggested that the variants disrupt interactions within RFC4 and/or destabilize the RFC complex. Cellular studies using RFC4-deficient HeLa cells and primary fibroblasts demonstrated decreased RFC4 protein, compromised stability of the other RFC complex subunits, and perturbed RFC complex formation. Additionally, functional studies of the RFC4 variants affirmed diminished RFC complex formation, and cell cycle studies suggested perturbation of DNA replication and cell cycle progression. Our integrated approach of combining in silico, structural, cellular, and functional analyses establishes compelling evidence that bi-allelic loss-of-function RFC4 variants contribute to the pathogenesis of this multisystemic disorder. These insights broaden our understanding of the RFC complex and its role in human health and disease.

Concanavalin A Delivers a Photoactive Protein to the Bacterial Wall.

Modular supramolecular complexes, where different proteins are assembled to gather targeting capability and photofunctional properties within the same structures, are of special interest for bacterial photodynamic inactivation, given their inherent biocompatibility and flexibility. We have recently proposed one such structure, exploiting the tetrameric bacterial protein streptavidin as the main building block, to target S. aureus protein A. To expand the palette of targets, we have linked biotinylated Concanavalin A, a sugar-binding protein, to a methylene blue-labelled streptavidin. By applying a combination of spectroscopy and microscopy, we demonstrate the binding of Concanavalin A to the walls of Gram-positive S. aureus and Gram-negative E. coli. Photoinactivation is observed for both bacterial strains in the low micromolar range, although the moderate affinity for the molecular targets and the low singlet oxygen yields limit the overall efficiency. Finally, we apply a maximum entropy method to the analysis of autocorrelation traces, which proves particularly useful when interpreting signals measured for diffusing systems heterogeneous in size, such as fluorescent species bound to bacteria.

Prevalence of Toxoplasma gondii Antibodies and Risk Factors in Two Sympatric Invasive Carnivores (Procyon lotor and Nyctereutes procyonoides) from Zgorzelec County, Poland.

The intracellular protozoan Toxoplasma gondii is distributed worldwide and infects many species of warm-blooded animals. Most mammals, including humans, can serve as intermediate hosts. This pathogen, with its zoonotic potential, causes toxoplasmosis, a condition that can range from subclinical to fatal in humans. It is therefore important to assess the occurrence of the pathogen, even if only indirectly through the detection of antibodies. Epidemiological data on the seroprevalence in wild animals, including invasive species, are rare in Poland. Therefore, we tested 197 wild raccoons (Procyon lotor) and 89 raccoon dogs (Nyctereutes procyonoides) from Zgorzelec County, southwestern Poland, for the presence of antibodies. Samples were collected between January 2019 and December 2020 and analysed using a commercial indirect modified agglutination test (MAT, cut-off 1:25). The statistical analysis revealed significant differences in seroprevalence between the two predatory species. Of the 197 surveyed raccoons, 96 (48.73%; 95% confidence interval (CI): 41.73-55.73%) tested positive, while 25 of the 89 raccoon dogs (28.09%; 95% CI: 18.70-37.48%) were positive. Regarding risk factors, body weight and sex influenced the presence of T. gondii antibodies in both the species, with a higher likelihood of seropositivity among heavier animals and females, respectively. For raccoon dogs, juveniles were more likely to be seropositive than adults at a given weight. Our results suggest that T. gondii infection is widespread in the regional raccoon and raccoon dog populations, indicating a high level of parasite circulation in the environment.

Prevalence of Toxoplasma gondii in Wild American Mink (Neogale vison): The First Serological Study in Germany and Poland.

Toxoplasma gondii is an obligate intracellular protozoan that causes toxoplasmosis in warm-blooded animals. Although most infections in humans and animals are subclinical, an infection can nevertheless be fatal. One of the important characteristics in the epidemiology of this parasite is waterborne transmission. The American mink (Neogale vison), a mammal closely adapted to freshwater ecosystems, is a potential sentinel for T. gondii. We analysed meat juice from the heart of 194 wild minks collected between 2019 and 2022 in five study areas from Germany and Poland and tested for the presence of antibodies against T. gondii. The analysis was performed using a commercial enzyme-linked immunosorbent assay test (ELISA). Antibodies were detected in 45.36% (88/194, 95% confidence interval (CI): 38.39-52.41%) of the analysed animals. While the prevalence values ranged from 37.50% to 49.30%, there was no significant difference in seroprevalence between the study areas. Juveniles were less likely to carry T. gondii antibodies than adults (odds ratio: 0.216), whereas there was no significant difference in prevalence between the sexes (odds ratio: 0.933). The results of our study show that contact with T. gondii is widespread in minks, and the parasite is common in inland freshwater ecosystems in Germany and Poland. This indicates that watercourses play an important role in the spread of T. gondii oocysts.

Providing AI expertise as an infrastructure in academia.

Artificial intelligence (AI) is proliferating and developing faster than any domain scientist can adapt. To support the scientific enterprise in the Helmholtz association, a network of AI specialists has been set up to disseminate AI expertise as an infrastructure among domain scientists. As this effort exposes an evolutionary step in science organization in Germany, this article aspires to describe our setup, goals, and motivations. We comment on past experiences, current developments, and future ideas as we bring our expertise as an infrastructure closer to scientists across our organization. We hope that this offers a brief yet insightful view of our activities as well as inspiration for other science organizations.

Bi-allelic SNAPC4 variants dysregulate global alternative splicing and lead to neuroregression and progressive spastic paraparesis.

The vast majority of human genes encode multiple isoforms through alternative splicing, and the temporal and spatial regulation of those isoforms is critical for organismal development and function. The spliceosome, which regulates and executes splicing reactions, is primarily composed of small nuclear ribonucleoproteins (snRNPs) that consist of small nuclear RNAs (snRNAs) and protein subunits. snRNA gene transcription is initiated by the snRNA-activating protein complex (SNAPc). Here, we report ten individuals, from eight families, with bi-allelic, deleterious SNAPC4 variants. SNAPC4 encoded one of the five SNAPc subunits that is critical for DNA binding. Most affected individuals presented with delayed motor development and developmental regression after the first year of life, followed by progressive spasticity that led to gait alterations, paraparesis, and oromotor dysfunction. Most individuals had cerebral, cerebellar, or basal ganglia volume loss by brain MRI. In the available cells from affected individuals, SNAPC4 abundance was decreased compared to unaffected controls, suggesting that the bi-allelic variants affect SNAPC4 accumulation. The depletion of SNAPC4 levels in HeLa cell lines via genomic editing led to decreased snRNA expression and global dysregulation of alternative splicing. Analysis of available fibroblasts from affected individuals showed decreased snRNA expression and global dysregulation of alternative splicing compared to unaffected cells. Altogether, these data suggest that these bi-allelic SNAPC4 variants result in loss of function and underlie the neuroregression and progressive spasticity in these affected individuals.

First detection and low prevalence of Pearsonema spp. in wild raccoons (Procyon lotor) from Central Europe.

The urinary bladder and lower urinary tract of domestic and wild carnivores can be parasitised by filamentous nematodes from the genus Pearsonema (syn. Capillaria). Infestations are often asymptomatic, but severe courses in dogs and cats have been described. Hosts are infested through the ingestion of earthworms (Lumbricidae) which act as intermediate hosts. Epidemiological studies of Pearsonema in raccoons (Procyon lotor) in North America are scarce and previous studies of urinary bladder parasites of European raccoons did not provide evidence of infestation. We examined urine sediment or rinse water from urinary bladders of 499 wild raccoons from Luxembourg, Poland and five study sites in Germany. Pearsonema eggs were found in the urine sediment of 31 (6.2%) raccoons. Infested animals were found in all study areas with prevalence values ranging from 3.7% to 8.7%. No significant difference in prevalence was found either between animals in urban and rural areas or between sexes and age classes. Based on their morphology, the eggs were likely to be P. plica. Considering their increasing density in Central Europe, raccoons may play a previously overlooked role in environmental contamination with Personema eggs.

Molecular analysis of blood-associated pathogens in European wildcats (Felis silvestris silvestris) from Germany.

European wildcats (Felis silvestris silvestris) have not been investigated in large numbers for blood-associated pathogens in Germany, because wildcats, being a protected species, may not be hunted, and the collection of samples is therefore difficult. Thus, spleen tissue and whole blood from 96 wildcats from Germany found as roadkill or dead from other causes in the years 1998-2020 were examined for the prevalence of blood associated pathogens using molecular genetic tools. PCR was used to screen for haemotrophic Mycoplasma spp., Hepatozoon spp., Cytauxzoon spp., Bartonella spp., Filarioidea, Anaplasmataceae, and Rickettsiales, and positive samples were subsequently sequenced. Phylogenetic analyses were performed for Mycoplasma spp. and Hepatozoon spp. by calculating phylogenetic trees and DNA haplotype networks. The following pathogens were found: Candidatus Mycoplasma haematominutum (7/96), Mycoplasma ovis (1/96), Hepatozoon silvestris (34/96), Hepatozoon felis (6/96), Cytauxzoon europaeus (45/96), and Bartonella spp. (3/96). This study elucidates the prevalence of blood-associated pathogens in wildcats from Germany.

Recommendations on compiling test datasets for evaluating artificial intelligence solutions in pathology.

Artificial intelligence (AI) solutions that automatically extract information from digital histology images have shown great promise for improving pathological diagnosis. Prior to routine use, it is important to evaluate their predictive performance and obtain regulatory approval. This assessment requires appropriate test datasets. However, compiling such datasets is challenging and specific recommendations are missing. A committee of various stakeholders, including commercial AI developers, pathologists, and researchers, discussed key aspects and conducted extensive literature reviews on test datasets in pathology. Here, we summarize the results and derive general recommendations on compiling test datasets. We address several questions: Which and how many images are needed? How to deal with low-prevalence subsets? How can potential bias be detected? How should datasets be reported? What are the regulatory requirements in different countries? The recommendations are intended to help AI developers demonstrate the utility of their products and to help pathologists and regulatory agencies verify reported performance measures. Further research is needed to formulate criteria for sufficiently representative test datasets so that AI solutions can operate with less user intervention and better support diagnostic workflows in the future.

Newly identified disorder of copper metabolism caused by variants in CTR1, a high-affinity copper transporter.

The high-affinity copper transporter CTR1 is encoded by CTR1 (SLC31A1), a gene locus for which no detailed genotype-phenotype correlations have previously been reported. We describe identical twin male infants homozygous for a novel missense variant NM_001859.4:c.284 G > A (p.Arg95His) in CTR1 with a distinctive autosomal recessive syndrome of infantile seizures and neurodegeneration, consistent with profound central nervous system copper deficiency. We used clinical, biochemical and molecular methods to delineate the first recognized examples of human CTR1 deficiency. These included clinical phenotyping, brain imaging, assays for copper, cytochrome c oxidase (CCO), and mitochondrial respiration, western blotting, cell transfection experiments, confocal and electron microscopy, protein structure modeling and fetal brain and cerebral organoid CTR1 transcriptome analyses. Comparison with two other critical mediators of cellular copper homeostasis, ATP7A and ATP7B, genes associated with Menkes disease and Wilson disease, respectively, revealed that expression of CTR1 was highest. Transcriptome analyses identified excitatory neurons and radial glia as brain cell types particularly enriched for copper transporter transcripts. We also assessed the effects of Copper Histidinate in the patients' cultured cells and in the patients, under a formal clinical protocol. Treatment normalized CCO activity and enhanced mitochondrial respiration in vitro, and was associated with modest clinical improvements. In combination with present and prior studies, these infants' clinical, biochemical and molecular phenotypes establish the impact of this novel variant on copper metabolism and cellular homeostasis and illuminate a crucial role for CTR1 in human brain development. CTR1 deficiency represents a newly defined inherited disorder of brain copper metabolism.

Interactions of cranial helminths in the European polecat (Mustela putorius): Implications for host body condition.

Multiple helminth species commonly co-occur within mammals and their interactions may negatively affect the survival and breeding success of their hosts. However, it has been difficult to prove competition or mutualism between co-infesting helminths in field studies of wild mammals. The sinus cavities of European polecats (Mustela putorius) can be parasitised by the trematode Troglotrema acutum and the nematode Skrjabingylus nasicola and both helminths can co-occur within hosts. While both parasites can damage the host's bone structure and cause severe pathologies, their impact on host body condition is unclear. It is also unknown whether both parasites interact and how this might affect cranial damage and host body condition. We examined 515 fresh polecat skulls for the presence of both helminths and measured the hosts' amount of kidney perirenal fat as a measure of body condition. Our results demonstrated that, in addition to a host-intrinsic fixed factor (sex) and random factors accounting for spatial and temporal stochasticity, the helminths influenced each other's presence. Infestation with T. acutum increased the probability of catching S. nasicola with increasing age of the host, while males already infested with S. nasicola were more likely to become infested with T. acutum than females infested with the nematode. While we speculate that both effects resulted from parasite-induced behavioural alterations (increased foot consumption), it is not clear why, in the latter case, this effect would be stronger in males than females. We showed that the abundances of both parasites had significant positive effect on the likely presence of skull damage and a significant negative effect on the predicted presence of kidney fat. Given the evolutionary arms race that both host-parasite systems have undergone, it appears unlikely that either helminth played a significant factor in the population decline of the polecat in Europe.

Modulation of free energy landscapes as a strategy for the design of antimicrobial peptides.

Computational design of antimicrobial peptides (AMPs) is a promising area of research for developing novel agents against drug-resistant bacteria. AMPs are present naturally in many organisms, from bacteria to humans, a time-tested mechanism that makes them attractive as effective antibiotics. Depending on the environment, AMPs can exhibit α-helical or ß-sheet conformations, a mix of both, or lack secondary structure; they can be linear or cyclic. Prediction of their structures is challenging but critical for rational design. Promising AMP leads can be developed using essentially two approaches: traditional modeling of the physicochemical mechanisms that determine peptide behavior in aqueous and membrane environments and knowledge-based, e.g., machine learning (ML) techniques, that exploit ever-growing AMP databases. Here, we explore the conformational landscapes of two recently ML-designed AMPs, characterize the dependence of these landscapes on the medium conditions, and identify features in peptide and membrane landscapes that mediate protein-membrane association. For both peptides, we observe greater conformational diversity in an aqueous solvent than in a less polar solvent, and one peptide is seen to alter its conformation more dramatically than the other upon the change of solvent. Our results support the view that structural rearrangement in response to environmental changes is central to the mechanism of membrane-structure disruption by linear peptides. We expect that the design of AMPs by ML will benefit from the incorporation of peptide conformational substates as quantified here with molecular simulations.

First record of Troglotrema acutum (Trematoda, Troglotrematidae) in European polecats Mustela putorius from Luxembourg.

We report the first record of the trematode Troglotrema acutum in skulls of European polecats (Mustela putorius) from Luxembourg. Thirty-one road-killed polecats from the northern and eastern parts of the country were examined. We found the trematode in three polecats from the administrative districts of Clervaux and Vianden in the northeast of the country. The parasites were detected in the frontal sinuses of one juvenile male as well as one adult of each sex. The animals were infected with six, nine and 13 adult trematodes, respectively, and we recovered 24 trematode eggs from one polecat. While the two adult hosts showed the lesions and deformations of the skull that are typical of T. acutum infections in polecats, the skull of the juvenile was not deformed. The prevalence of 9.7% reported here was lower than the values reported from Central European studies. Our findings indicate that the distribution range of T. acutum in western Central Europe extends to the Ardennes low mountain range.

A point mutation in the nuclease domain of MLH3 eliminates repeat expansions in a mouse stem cell model of the Fragile X-related disorders.

The Fragile X-related disorders (FXDs) are Repeat Expansion Diseases, genetic disorders that result from the expansion of a disease-specific microsatellite. In those Repeat Expansion Disease models where it has been examined, expansion is dependent on functional mismatch repair (MMR) factors, including MutLγ, a heterodimer of MLH1/MLH3, one of the three MutL complexes found in mammals and a minor player in MMR. In contrast, MutLα, a much more abundant MutL complex that is the major contributor to MMR, is either not required for expansion or plays a limited role in expansion in many model systems. How MutLγ acts to generate expansions is unclear given its normal role in protecting against microsatellite instability and while MLH3 does have an associated endonuclease activity, whether that contributes to repeat expansion is uncertain. We show here, using a gene-editing approach, that a point mutation that eliminates the endonuclease activity of MLH3 eliminates expansions in an FXD mouse embryonic stem cell model. This restricts the number of possible models for repeat expansion and supports the idea that MutLγ may be a useful druggable target to reduce somatic expansion in those disorders where it contributes to disease pathology.

Detection of Cryptosporidium spp. Infection in Wild Raccoons (Procyon lotor) from Luxembourg Using an ELISA Approach.

BACKGROUND: Cryptosporidium spp. are protozoan parasites that cause enteric infection in a wide range of mammals, including humans. The raccoon (Procyon lotor) is an invasive species in many parts of the world and studies have shown that they can be infected with Cryptosporidium spp. both outside and in their original distribution area. The aim of the present study was to determine the presence of Cryptosporidium spp. antigens in the faeces of raccoons in Luxembourg. METHODS: Using an enzyme-linked immunosorbent assay (ELISA), we tested 81 faeces samples, collected between 2014 and 2018, for the presence of Cryptosporidium spp. coproantigens. Samples with an optical density equal to or greater than 0.15% were considered positive. RESULTS: Antigens were detected in 12.35% (10/81; 95% CI 6.68-21.26) of the tested samples. There was no significant difference in the prevalence of Cryptosporidium spp. infection between the sexes and age categories. Cryptosporidium spp.-positive raccoons were found in 7 of the 12 Luxembourg administrative districts (Clervaux, Diekirch, Echternach, Mersch, Remich, Vianden and Wiltz). CONCLUSION: The results show that Cryptosporidium infections are not uncommon in Luxembourg raccoons and suggest possible transmission of Cryptosporidium by raccoons.

First detection and molecular identification of Anaplasma phagocytophilum in an introduced population of Reeve's muntjac (Muntiacus reevesi) in United Kingdom.

In the present study, we investigated blood samples of 196 invasive Reeve's muntjac (Muntiacus reevesi) and 91 native roe deer (Capreolus capreolus) originating from the same area in Thetford Forest in Eastern England for the occurrence of blood pathogens such as Anaplasmatacae, Rickettsiales and Piroplasmida (Babesia spp., Theileria spp.) by using PCR. Babesia spp., Rickettsia spp. and Theileria spp. were not detected. Only two male (1%) Reeve's muntjacs and six (6.6%) roe deer were positive for Anaplasma phagocytophilum with 100% identity among their sequences. However, it is not clear whether Reeve's muntjac is less susceptible to infection, less susceptible to infestation by I. ricinus, or an infection in Reeve's muntjac is more lethal and therefore less positive animals are taken during hunting events.

Geographic Distribution of Raccoon Roundworm, Baylisascaris procyonis, Germany and Luxembourg.

Infestation with Baylisascaris procyonis, a gastrointestinal nematode of the raccoon, can cause fatal disease in humans. We found that the parasite is widespread in central Germany and can pose a public health risk. The spread of B. procyonis roundworms into nematode-free raccoon populations needs to be monitored.

Nanosecond-Timescale Dynamics and Conformational Heterogeneity in Human GCK Regulation and Disease.

Human glucokinase (GCK) is the prototypic example of an emerging class of proteins with allosteric-like behavior that originates from intrinsic polypeptide dynamics. High-resolution NMR investigations of GCK have elucidated millisecond-timescale dynamics underlying allostery. In contrast, faster motions have remained underexplored, hindering the development of a comprehensive model of cooperativity. Here, we map nanosecond-timescale dynamics and structural heterogeneity in GCK using a combination of unnatural amino acid incorporation, time-resolved fluorescence, and 19F nuclear magnetic resonance spectroscopy. We find that a probe inserted within the enzyme's intrinsically disordered loop samples multiple conformations in the unliganded state. Glucose binding and disease-associated mutations that suppress cooperativity alter the number and/or relative population of these states. Together, the nanosecond kinetics characterized here and the millisecond motions known to be essential for cooperativity provide a dynamical framework with which we address the origins of cooperativity and the mechanism of activated, hyperinsulinemia-associated, noncooperative variants.

HLA and autoantibodies define scleroderma subtypes and risk in African and European Americans and suggest a role for molecular mimicry.

Systemic sclerosis (SSc) is a clinically heterogeneous autoimmune disease characterized by mutually exclusive autoantibodies directed against distinct nuclear antigens. We examined HLA associations in SSc and its autoantibody subsets in a large, newly recruited African American (AA) cohort and among European Americans (EA). In the AA population, the African ancestry-predominant HLA-DRB1*08:04 and HLA-DRB1*11:02 alleles were associated with overall SSc risk, and the HLA-DRB1*08:04 allele was strongly associated with the severe antifibrillarin (AFA) antibody subset of SSc (odds ratio = 7.4). These African ancestry-predominant alleles may help explain the increased frequency and severity of SSc among the AA population. In the EA population, the HLA-DPB1*13:01 and HLA-DRB1*07:01 alleles were more strongly associated with antitopoisomerase (ATA) and anticentromere antibody-positive subsets of SSc, respectively, than with overall SSc risk, emphasizing the importance of HLA in defining autoantibody subtypes. The association of the HLA-DPB1*13:01 allele with the ATA+ subset of SSc in both AA and EA patients demonstrated a transancestry effect. A direct correlation between SSc prevalence and HLA-DPB1*13:01 allele frequency in multiple populations was observed (r = 0.98, P = 3 × 10-6). Conditional analysis in the autoantibody subsets of SSc revealed several associated amino acid residues, mostly in the peptide-binding groove of the class II HLA molecules. Using HLA α/ß allelic heterodimers, we bioinformatically predicted immunodominant peptides of topoisomerase 1, fibrillarin, and centromere protein A and discovered that they are homologous to viral protein sequences from the Mimiviridae and Phycodnaviridae families. Taken together, these data suggest a possible link between HLA alleles, autoantibodies, and environmental triggers in the pathogenesis of SSc.