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PubMed1988

Local pathological findings in experimental dorsal root entry zone lesions performed by mechanical section, laser and radiofrequency. A comparative study.

Dorsal root entry zone lesions are nowadays accepted as a first choice of treatment to alleviate certain types of chronic pain though it is still controversial to decide proper procedure for lesioning. Based on this last argument in 15 mongrel dogs different types of lesions using mechanical microsection, radiofrequency and laser were done. Under general anaesthesia a C-3 to C-7 laminectomy was performed in all animals and after open the dura mater the posterior nerve rootlets and posterolateral sulcus were identified using magnification. In 5 dogs, a longitudinal 1 mm deep incision from C-4 to C-6 spinal cord segments coinciding with the sulcus was carried out with a microknife; in other 5, a sequence of thermocoagulations produced by a radiofrequency current lower than 35 mA was done at same places and level with intervals of 2 mm; and in the rest of animals, an alike incision in depth, location and level was realised by carbon dioxide laser. Four days and three months after lesioning 2 and 3 animals of each group were sacrificed and spinal cord specimens submitted for histological and ultrastructural studies. Low-power microscopic examination showed that all lesioning methods were able to produce a reasonable well delimited necrotic area involving the whole dorsal root entry zone structures, slightly more diffuse with the laser. Acute perilesional changes as well as chronic ones were nevertheless more evident in mechanical and radiofrequency lesions, over all regarding oedema, perivascular haemorrhage, intraluminal thrombosis and ischaemic alterations.

Animals↗
PubMed1993

Electrophysiological properties of neurons in the rat subiculum in vitro.

The present study determined the membrane and synaptic properties of neurons in the rat subiculum. Using the in vitro hippocampal slice preparation, intracellular recordings were obtained from 91 subicular neurons. Membrane properties and morphological characteristics were similar to those reported for hippocampal pyramidal neurons. Two categories of subicular neurons were distinguished based on their response to a depolarizing current pulse. One type of neuron showed bursting behavior and the second type was characterized as regular firing. Analysis of the charging functions during hyperpolarizing current pulses yielded a mean tau 0 and tau 1 for subicular neurons of about 13 ms and 0.60 ms, respectively. Using the model of an equivalent cylinder, the mean dendrite-to-soma conductance ratio (rho) was estimated at 6.0 and electrotonic length constant (L) at 0.7. There was no difference in these values between bursting and regular firing neurons. Tetrodotoxin-resistant potentials (presumed calcium hump/spike) were evoked from bursting subicular neurons at lower current intensities than CA1 pyramidal neurons. Calcium humps could only be evoked from about half the regular firing subicular neurons. Subicular cells showed an excitatory/inhibitory postsynaptic potential (EPSP/IPSP) sequence in response to electrical stimulation in different layers of the CA1 area. An EPSP could also be evoked from stimulation of the superficial or deep layers of the presubiculum and was attributed to activation of entorhinal fibers of passage. At high stimulation intensity, an antidromic spike was often evoked following stimulation in the presubicular area of CA1 alveus. The evoked EPSPs were blocked by addition of 6-cyano-7-nitroquinoxaline-2,3-dione (CNQX) to the bathing medium. In magnesium-free, CNQX bathing solution, a longer lasting depolarization was recorded; this response was blocked by application of a N-methyl-D-aspartate (NMDA) receptor antagonist (AP5). Iontophoretic application of glutamate or quisqualate (10 mM) along the soma-dendritic axis of subicular neurons leads to either a short-latency depolarization or a burst of action potentials. Application of 10 mM GABA near the recording site usually produced a hyperpolarization, which, at times, was mixed with a depolarization. Mixed hyperpolarizing/depolarizing responses were observed when GABA was applied to the basal or apical dendritic areas. There were no significant differences in the synaptic properties or responses to drug application between bursting and regular firing neurons.(ABSTRACT TRUNCATED AT 400 WORDS)

2-Amino-5-phosphonovalerate↗
PubMed2005

Structure-based functional identification of a novel heme-binding protein from Thermus thermophilus HB8.

The TT1485 gene from Thermus thermophilus HB8 encodes a hypothetical protein of unknown function with about 20 sequence homologs of bacterial or archaeal origin. Together they form a family of uncharacterized proteins, the cluster of orthologous group COG3253. Using a combination of amino acid sequence analysis, three-dimensional structural studies and biochemical assays, we identified TT1485 as a novel heme-binding protein. The crystal structure reveals that this protein is a pentamer and each monomer exhibits a beta-barrel fold. TT1485 is structurally similar to muconolactone isomerase, but this provided no functional clues. Amino acid sequence analysis revealed remote homology to a heme enzyme, chlorite dismutase. Strikingly, amino acid residues that are highly conserved in the homologous hypothetical proteins and chlorite dismutase cluster around a deep cavity on the surface of each monomer. Molecular modeling shows that the cavity can accommodate a heme group with a strictly conserved His as a heme ligand. TT1485 reconstituted with iron protoporphyrin IX chloride gave a low chlorite dismutase activity, indicating that TT1485 catalyzes a reaction other than chlorite degradation. The presence of a possible Fe-His-Asp triad in the heme proximal site suggests that TT1485 functions as a novel heme peroxidase to detoxify hydrogen peroxide within the cell.

Amino Acid Sequence↗
PubMed2026

Research on the ecology of the carnivorous sponge-associated iridovirus (CaSpA-IV) reveals its presence in the Cnidaria.

UNLABELLED: Carnivorous sponge-associated iridovirus (CaSpA-IV) is a recently described virus identified in two deep-sea cladorhizid sponge species from the Gulf of Maine and Baffin Bay. To assess its ecological distribution and potential transmission pathways, we molecularly screened for CaSpA-IV in 32 calanoid copepod samples collected across Newfoundland and Labrador coastal and shelf waters, along with 24 mucus swab and tissue samples collected from six individual deep-sea Paragorgia arborea coral colonies, and three seawater samples from the Gulf of Maine. Two P. arborea tissue specimens from different colonies were sequence-confirmed as CaSpA-IV-positive, making this the first detection of an iridovirus in this host. All copepod and seawater samples tested negative. However, calanoid copepods cannot be definitively ruled out as a transmission vector due to limited sampling. These findings demonstrate that CaSpA-IV may infect two invertebrate phyla in geographically distant benthic habitats. Future work should focus on whole-genome sequencing of diverse CaSpA-IVs and targeted sampling of other potential vectors/hosts to elucidate transmission routes and the ecological impact of this virus. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at https://doi.org/10.1007/s44370-026-00057-w.

Cladorhizidae↗
PubMed1994

Vimentin-positive rosary-bead-like formations in the rabbit superior colliculus during postnatal development.

Strings of vimentin-positive rosary-bead-like formations in the rabbit superior colliculus were studied. The size and distance between beads varied from one string to another, and within a given string. The formations were similar in number and distribution in the two superior colliculi. Successions of beads were found mainly in the medial and deep layers, and represented not more than 1% of the radial glial fibers. The strings were in continuity at deep levels with segments of varicose fibers of radial glia, which in turn were continuous with fibers of normal appearance. These observations suggest a temporal sequence of evolution, starting with the normal radial glial fiber, which acquires swellings that in turn give rise to discrete beads; in subsequent stages, the beads become smaller and more widely separated. In the newborn rabbit, these formations are seen mainly in laterobasal regions of the superior colliculus, and spread throughout the colliculus by the end of week one of postnatal life, becoming more numerous in medial regions. We suggest that these formations represent a mechanism of removal of at least part of the radial glial fibers, and discuss the possible relation between these formations and the transformation of radial glia into astrocytes.

Aging↗
PubMed1987

Transduction proteins of olfactory receptor cells: identification of guanine nucleotide binding proteins and protein kinase C.

We have analyzed guanine nucleotide binding proteins (G-proteins) in the olfactory epithelium of Rana catesbeiana using subunit-specific antisera. The olfactory epithelium contained the alpha subunits of three G-proteins, migrating on polyacrylamide gels in SDS with apparent molecular weights of 45,000, 42,000, and 40,000, corresponding to Gs, Gi, and Go, respectively. A single beta subunit with an apparent molecular weight of 36,000 was detected. An antiserum against the alpha subunit of retinal transducin failed to detect immunoreactive proteins in olfactory cilia detached from the epithelium. The olfactory cilia appeared to be enriched in immunoreactive Gs alpha relative to Gi alpha and Go alpha when compared to membranes prepared from the olfactory epithelium after detachment of the cilia. alpha subunits of G-proteins were not detected in cilia detached from the nonchemosensory respiratory epithelium of the palate. Immunohistochemical studies using an antiserum against the beta subunit of G-proteins revealed intense staining of the ciliary surface of the olfactory epithelium and of the axon bundles in the lamina propria. In contrast, an antiserum against a common sequence of the alpha subunits preferentially stained the cell membranes of the olfactory receptor cells and the acinar cells of Bowman's glands and the deep submucosal glands. Prolonged incubation periods with these antisera tended to obliterate these differences in staining patterns, giving rise to staining by both antisera of the ciliary surface, the olfactory receptor cell membranes, the axon bundles, and the acinar cells of the glands. In addition to G-proteins, we have identified protein kinase C in olfactory cilia via a protein kinase C specific antiserum and via phorbol ester binding.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1996

S-allele diversity in a natural population of Physalis crassifolia (Solanaceae) (ground cherry) assessed by RT-PCR.

Allelic diversity at the self-incompatibility (S-) locus in the ground cherry, Physalis crassifolia (Solanaceae), was surveyed in a natural population occurring in Deep Canyon, CA, using a molecular assay to determine the genotype of individual plants. A total of 28 different S-alleles were identified and sequenced from a sample of 22 plants. All plants examined were heterozygous, as expected under gametophytic self-incompatibility (GSI). The estimated number of alleles in this population is 43-44, comparable to allelic diversity reported for other species, as determined by the standard diallel crossing method. Allele frequencies in the sample deviated from the expectation of equal frequency under GSI; it is suggested that this deviation may result from sampling of related individuals. Molecular analysis of genotypes within single pollen donor families indicates that, for all alleles examined, segregation is consistent with predictions for single-locus GSI. The implications of a reliable and efficient molecular assay for determining the S-genotype of plants are discussed.

Alleles↗
PubMed2024

Molecular basis for antibody recognition of multiple drug-peptide/MHC complexes.

The HapImmuneTM platform exploits covalent inhibitors as haptens for creating major histocompatibility complex (MHC)-presented tumor-specific neoantigens by design, combining targeted therapies with immunotherapy for the treatment of drug-resistant cancers. A HapImmune antibody, R023, recognizes multiple sotorasib-conjugated KRAS(G12C) peptides presented by different human leukocyte antigens (HLAs). This high specificity to sotorasib, coupled with broad HLA-binding capability, enables such antibodies, when reformatted as T cell engagers, to potently and selectively kill sotorasib-resistant KRAS(G12C) cancer cells expressing different HLAs upon sotorasib treatment. The loosening of HLA restriction could increase the patient population that can benefit from this therapeutic approach. To understand the molecular basis for its unconventional binding capability, we used single-particle cryogenic electron microscopy to determine the structures of R023 bound to multiple sotorasib-peptide conjugates presented by different HLAs. R023 forms a pocket for sotorasib between the VH and VL domains, binds HLAs in an unconventional, angled way, with VL making most contacts with them, and makes few contacts with the peptide moieties. This binding mode enables the antibody to accommodate different hapten-peptide conjugates and to adjust its conformation to different HLAs presenting hapten-peptides. Deep mutational scanning validated the structures and revealed distinct levels of mutation tolerance by sotorasib- and HLA-binding residues. Together, our structural information and sequence landscape analysis reveal key features for achieving MHC-restricted recognition of multiple hapten-peptide antigens, which will inform the development of next-generation therapeutic antibodies.

Humans↗
PubMed2006

Functional diversification of B MADS-box homeotic regulators of flower development: Adaptive evolution in protein-protein interaction domains after major gene duplication events.

B-class MADS-box genes have been shown to be the key regulators of petal and stamen specification in several eudicot model species such as Arabidopsis thaliana, Antirrhinum majus, and Petunia hybrida. Orthologs of these genes have been found across angiosperms and gymnosperms, and it is thought that the basic regulatory function of B proteins is conserved in seed plant lineages. The evolution of B genes is characterized by numerous duplications that might represent key elements fostering the functional diversification of duplicates with a deep impact on their role in the evolution of the floral developmental program. To evaluate this, we performed a rigorous statistical analysis with B gene sequences. Using maximum likelihood and Bayesian methods, we estimated molecular substitution rates and determined the selective regimes operating at each residue of B proteins. We implemented tests that rely on phylogenetic hypotheses and codon substitution models to detect significant differences in substitution rates (DSRs) and sites under positive adaptive selection (PS) in specific lineages before and after duplication events. With these methods, we identified several protein residues fixed by PS shortly after the origin of PISTILLATA-like and APETALA3-like lineages in angiosperms and shortly after the origin of the euAP3-like lineage in core eudicots, the 2 main B gene duplications. The residues inferred to have been fixed by positive selection lie mostly within the K domain of the protein, which is key to promote heterodimerization. Additionally, we used a likelihood method that accommodates DSRs among lineages to estimate duplication dates for AP3-PI and euAP3-TM6, calibrating with data from the fossil record. The dates obtained are consistent with angiosperm origins and diversification of core eudicots. Our results strongly suggest that novel multimer formation with other MADS proteins could have been crucial for the functional divergence of B MADS-box genes. We thus propose a mechanism of functional diversification and persistence of gene duplicates by the appearance of novel multimerization capabilities after duplications. Multimer formation in different combinations of regulatory proteins can be a mechanistic basis for the origin of novel regulatory functions and a gene regulatory mechanism for the appearance of morphological innovations.

Amino Acid Sequence↗
PubMed2006

Macroscopic and molecular symmetries of unconventional nematic phases.

The effects of the molecular symmetry on macroscopic properties of conventional and unconventional nematic phases are investigated theoretically. These effects concern: (1) the form of the molecular orientation fluctuations, (2) the thermodynamic behavior and the list of stable ordered phases, (3) the effective symmetry of the molecules in the ordered phases. The order-parameter consists of tensors forming the main harmonics of the fluctuation distribution. In conventional models (valid for uniaxial molecules) a single tensor is sufficient while unconventional models (valid for less symmetric molecules) need several tensors with the same rank. We analyze the qualitative differences arising when the number of equivalent tensors varies. We show how to work out complete models in the general case, and to calculate the sequences of stable phases and the corresponding effective molecular symmetries. This yields, for each molecular group and each tensor rank, a complete classification and a deep insight into the structure of thermotropic nematics. This work generalizes the approach we have applied to polar nematics recently observed in polyester compounds and to unconventional uniaxial and biaxial phases of bent-core materials.

Journal Article↗
PubMed2004

Comparative genomics of rice and Arabidopsis. Analysis of 727 cytochrome P450 genes and pseudogenes from a monocot and a dicot.

Data mining methods have been used to identify 356 Cyt P450 genes and 99 related pseudogenes in the rice (Oryza sativa) genome using sequence information available from both the indica and japonica strains. Because neither of these genomes is completely available, some genes have been identified in only one strain, and 28 genes remain incomplete. Comparison of these rice genes with the 246 P450 genes and 26 pseudogenes in the Arabidopsis genome has indicated that most of the known plant P450 families existed before the monocot-dicot divergence that occurred approximately 200 million years ago. Comparative analysis of P450s in the Pinus expressed sequence tag collections has identified P450 families that predated the separation of gymnosperms and flowering plants. Complete mapping of all available plant P450s onto the Deep Green consensus plant phylogeny highlights certain lineage-specific families maintained (CYP80 in Ranunculales) and lineage-specific families lost (CYP92 in Arabidopsis) in the course of evolution.

Arabidopsis↗
PubMed1993

Symptomatic type II protein C deficiency caused by a missense mutation (Gly 381-->Ser) in the substrate-binding pocket.

A patient with recurrent deep vein thrombosis and heterozygous type II deficiency, characterized by reduced protein C activity in both amidolytic and clotting functional assays, was investigated by direct sequencing of PCR fragments derived from the coding portion of the protein C gene. AG (8856) to A transition was noted in the patient which was not present in healthy controls. This mutation is predicted to cause the substitution of Ser for Gly 381, an evolutionari'y conserved residue in the substrate binding pocket of serine-proteases (Gly 216, chymotrypsin numbering). A computer model of the structure of the serine-protease domain indicates that the properties of the altered protein C molecule can be explained on the basis of steric hindrance between the substituted serine and the substrate arginine side chains.

Adult↗
PubMed2004

Osedax: bone-eating marine worms with dwarf males.

We describe a new genus, Osedax, and two new species of annelids with females that consume the bones of dead whales via ramifying roots. Molecular and morphological evidence revealed that Osedax belongs to the Siboglinidae, which includes pogonophoran and vestimentiferan worms from deep-sea vents, seeps, and anoxic basins. Osedax has skewed sex ratios with numerous dwarf (paedomorphic) males that live in the tubes of females. DNA sequences reveal that the two Osedax species diverged about 42 million years ago and currently maintain large populations ranging from 10(5) to 10(6) adult females.

Animals↗
PubMed2005

MRI for diagnosis and monitoring of patients with eosinophilic fasciitis.

OBJECTIVE: The objective of this study was to describe MRI findings in patients with eosinophilic fasciitis (EF) and to correlate clinical and laboratory findings with the MRI findings. MATERIALS AND METHODS: Six patients with histologically proven EF underwent MRI at the time of diagnosis and after therapy (15 MRI examinations). Unenhanced T1-weighted, T2-weighted, and STIR sequences were performed using a 1.5-T MRI system. In addition, all patients were imaged with contrast-enhanced T1-weighted sequences. MRI findings, clinical findings, and laboratory parameters were retrospectively reviewed. RESULTS: At the time the six patients presented, all eight MRI examinations revealed symmetric thickening and hyperintensity of the superficial muscle fasciae of the thigh, calves, or arms on unenhanced T1-weighted, T2-weighted, or STIR sequences, with strong enhancement after administration of IV contrast agent. In seven of the eight MRI examinations, similar signal changes were also present in the deep muscle fasciae. After treatment, the fascial abnormalities found on MRI disappeared on six of eight MRI examinations performed in five patients-a rate that correlated well with the clinical findings. In one patient with EF involvement of the thigh, the MRI abnormalities showed partial remission, which also correlated well with the clinical findings. CONCLUSION: In EF, MRI reveals characteristic findings including thickening, signal abnormalities, and contrast enhancement of the superficial and, to a lesser extent, deep muscle fasciae. MRI is useful for establishing the diagnosis, guiding the choice of biopsy site, and assessing treatment response.

Adult↗
PubMed1990

Influence of tolazoline on caudal epidural administration of xylazine in cattle.

Eight adult female cattle (6 Holstein, 1 Jersey, 1 Brown Swiss) were used to determine the antagonistic effects of tolazoline, and alpha 2-adrenoceptor antagonist, on xylazine-induced (via caudal epidural administration) depression of CNS, respiratory, and cardiovascular activity and rumen motility. A 2% solution of xylazine HCl was injected into the epidural space at the first coccygeal interspace, using a dosage of 0.05 mg/kg of body weight, diluted to a 5-ml volume with sterile water, and administered at a rate of approximately 1 ml/30 s. Eight minutes after xylazine injection, either tolazoline (0.3 mg/kg) or saline solution (4 ml) was administered IV. All 8 cattle were treated, using both regimens in a random sequence; at least 1 week elapsed between treatments. Epidurally administered xylazine induced caudal analgesia (S3 to coccyx), as evaluated by no response to superficial and deep muscular pinprick, and induced sedation, cardiopulmonary depression, and inhibition of rumen motility, but all cattle remained standing. Tolazoline effectively reversed xylazine-induced rumen hypomotility, and partially antagonized xylazine-induced cardiopulmonary depression without affecting sedation and desirable local (S3 to coccyx) analgesic effects.

Animals↗
PubMed1995

Bone histomorphometry in the pathophysiological evaluation of primary and secondary osteoporosis and various treatment modalities.

In normal individuals, peak bone mass is reached at 25-35 years of age and thereafter a decrease with age occurs in both sexes. An acceleration in the bone loss is observed in normal women at menopause. Because of either a low peak bone mass or a more pronounced bone loss with age or during menopause, some individuals reach the fracture threshold for bone mass and suffer spontaneous fractures. To understand the mechanism behind age related bone loss, one must recognize that bone in adults is continually renewed through internal reorganization by which bone is turned over by localized osteoclastic resorption followed by osteoblastic formation (remodelling). A total reconstruction of the resorptive and formative phase can be performed by histomorphometric methods applied on iliac crest bone biopsies and thereby give a detailed description of resorptive and formative events. By the remodelling process bone may be gained or lost by 3 mechanisms: 1. Reversible bone loss depending on the magnitude of the remodelling space, which is the amount of bone resorbed and not yet reformed during the remodelling sequence. 2. Irreversible thinning of the trabeculae due to a negative balance at the remodelling site. 3. Irreversible loss of whole trabecular elements caused by deep resorption lacunae perforating the trabecular plates. Although the bone mass is significantly reduced by 20-30% in postmenopausal osteoporotic patients with vertebral fractures compared with normal controls a substantial overlap exists. Our study and several other studies have shown that beside the slight reduction in trabecular bone volume significant differences in microstructure exist between osteoporotic patients and normal controls. These changes in structure are probably a consequence of trabecular plate perforations. Although osteoporotic patients in term of remodelling (bone turnover) are a very heterogeneous group, with patients having a low, normal and even increased bone turnover, no signs in the ongoing remodelling process was found in our study that could explain why these patients had developed osteopenia and changes in the trabecular structure. The bone balance was in the patients slightly negative but no different from the balance found in normal controls. The cause of osteoporosis may therefore be factors occurring earlier in life, maybe long before the manifestation of the disease. Bone mass at any age is the result of two variables--the amount of bone achieved during growth and the subsequent rate of bone loss. Peak bone mass at maturity may be of great importance in determining the risk of developing symptomatic osteoporosis.(ABSTRACT TRUNCATED AT 400 WORDS)

Adult↗
PubMedDate not supplied

Noninvasive diagnosis of pulmonary embolism.

BACKGROUND AND OBJECTIVE: Pulmonary embolism (PE), with an incidence of 23 per 100,000 patients per year, is a frequent clinical problem, responsible for 200,000 deaths each year in the United States. Pulmonary angiography, the gold standard for diagnosing PE, is invasive, costly and not universally available. Moreover, PE is confirmed in only approximately 30% of patients in whom it is suspected, rendering noninvasive screening tests necessary. Several strategies have been recently proposed to reduce the need for pulmonary angiography in the diagnostic workup of pulmonary embolism. The objective of this article is to analyze the individual performance of the new diagnostic instruments and their combination in rational diagnostic strategies. METHODS: The author has been working in this field and has contributed original papers on diagnosis of pulmonary embolism and cost-effectiveness of noninvasive diagnostic tests. In addition, the material examined in this article includes articles published in the journals covered by the Science Citation Index and Medline. RESULTS: Several strategies have been recently proposed to reduce the need for pulmonary angiography in the diagnostic workup of pulmonary embolism. The PIOPED study has established the value of ventilation-perfusion lung scan, a normal perfusion lung scan virtually ruling out PE, whereas a high probability lung scan is considered diagnostic in face of reasonable clinical suspicion. All other lung scan results are nondiagnostic. However, clinical evaluation, although insufficiently accurate to yield a definitive diagnosis, is probably reliable enough to be used for estimating pretest probability of PE. The combination of a low clinical probability of PE and a so-called low probability lung scan yields a very low posttest probability of PE, thus foregoing the need for pulmonary angiography. Other useful instrument in patients with nondiagnostic scans is plasma D-dimer (DD) measurement (ELISA assay), which when under a cutoff value of 500 micrograms/L potentially exclude PE, due to high sensitivity (97%). Conversely, venous compression ultrasonography of the lower limbs (US) is highly specific (98%) for deep vein thrombosis (DVT), and disclosing a DVT warrants anticoagulant treatment without resorting to angiography. The potential role of echocardiography is also discussed. The rational sequence of noninvasive tests is currently under discussion. Performing D-dimer and US before lung scan may be the most cost-effective strategy, pulmonary angiography being performed only in case of an inconclusive noninvasive workup. INTERPRETATION AND CONCLUSIONS: Even though PE remains a difficult diagnostic challenge, the availability of novel noninvasive tests (plasma D-dimer and ultrasonography of the lower limbs) and the rehabilitation of clinical assessment allow a more rational and sparse prescription of pulmonary angiography. More work needs to be done to assess test performances and refine diagnostic strategies in distinct patient subgroups, particularly those hospitalized. Screening patients with plasma D-dimer and ultrasonography of the lower limbs may be the most cost-effective strategy, at least in outpatients.

Algorithms↗
PubMed2026

Deep subsurface organic-rich shale supports abundant, diverse, and novel fungi.

As Earth's principal reservoir of organic carbon and microbial biomass, the deep subsurface hosts microorganisms capable of mobilizing this once-sequestered carbon. Contrary to standard assumptions of eukaryotic scarcity, this study documents abundant fungal communities, ranging from 4.2 × 103 to 6.8 × 103 fungal cells ml-1, across a methane-producing organic-rich shale 247-556 meters below the surface. Although fungal:bacterial cell ratios ranged from 1:7028 to 1:713, application of biomass conversion factors developed for oceanic systems yielded a median fungal:bacterial biomass ratio of 1:4.7. 16S ribosomal ribonucleic acid (rRNA) gene amplicons revealed bacterial and archaeal communities mirroring those found in well-characterized extremophilic, carbon-degrading environments, while sequencing of 18S rRNA gene and internal transcribed spacer rRNA spacer amplicons collectively identified a eukaryotic hotspot with 689 fungal operational taxonomic units across six phyla. The dominant fungal classes, Agaricomycetes and Dothideomycetes, are well-established degraders of recalcitrant carbon compounds at the surface, suggesting they may similarly contribute to organic matter degradation and ecosystem maintenance in the subsurface. Cultivation and isolation efforts yielded 205 fungal strains, including 13 candidate novel taxa, underscoring the deep subsurface as an underexplored eukaryotic habitat. Stable carbon isotopes indicate methane is predominantly generated via microbial conversion of the fossil carbon, while water isotopes suggest in situ geochemical conditions have been relatively stable since the Late Pleistocene, with subglacial recharge as a plausible mechanism for microbial introduction. Collectively, these findings suggest that fungi are underrecognized contributors to organic matter transformation and functional diversity in the deep biosphere, revealing a critical gap in our understanding of deep subsurface ecosystem processes.

Fungi↗