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At least 91 records · Page 5Linked to original sources
PubMed1994

Hippocampal-entorhinal relationships: electrophysiological analysis of the ventral hippocampal projections to the ventral entorhinal cortex.

The hippocampal output to the ventral entorhinal area was studied in the guinea-pig by field potential analysis. Perforant path volleys, synaptically elicited by stimulation of dorsal psalterium fibers, were used to obtain activation of the lamellar circuit of the dorsal hippocampal formation and the subsequent activation, through intrahippocampal longitudinal connections, of pyramidal neurons in the ventral hippocampus. The latter activation was obtained by low-frequency (0.1-2.0/s) repetitive dorsal psalterium stimulation. A response occurred in the ventral entorhinal area only following low-frequency (0.1-2.0/s) repetitive stimulation. The ventral entorhinal response occurred both in the medial and lateral divisions of the ventral entorhinal area. It consisted of a negative wave with associated unit firing in all cellular layers of the medial and lateral ventral entorhinal area. The latency of the entorhinal response increased moving from the deep to the superficial layers. These findings suggest the generation of excitatory synaptic effects in temporal sequence in the deep and then in the superficial layers of the entorhinal cortex. The ventral entorhinal response showed longer latency and a higher threshold than the ventral hippocampal response, and was eliminated by interruption of the caudally directed ventral hippocampal projections. These data suggest that the ventral entorhinal response was mediated by projections from the ventral hippocampus. The results show that the ventral hippocampal output evokes excitatory synaptic effects in all cellular layers of the medial and the lateral ventral entorhinal area. The massive involvement of the entorhinal area, together with the widespread distribution of the entorhinal projections, support the idea that the entorhinal cortex represents a crucial link between the hippocampus and the other brain regions.

Animals↗
PubMed2026

In vitro reconstitution of chromatin replication recapitulates symmetric histone recycling.

Symmetric histone recycling is vital for maintaining epigenetic inheritance upon eukaryotic DNA replication. Recent genome-wide studies have uncovered key determinants of this process, but how these factors collectively support parental histone transfer remains incompletely understood. Here, we successfully reconstitute histone recycling with 24 purified proteins and analyze the products digested by Micrococcal nuclease with Repli-pore-seq, the newly developed pipeline combining nanopore sequencing and deep-learning-based classification. As a result, we identify histones symmetrically recycled as tetrasomes or hexasomes on nucleosome-favorable sequences. We also observe the discordance of the recycled position between lagging and leading strands on the GC-rich DNA sequences. Moreover, removal of Pol δ, Pol32, Dpb3/4, Ctf4, Csm3/Tof1, or Mrc1 disrupts the balance of histone recycling between the two daughter strands, whereas removal of Ctf4, Csm3/Tof1, or Mrc1 additionally alters the positions at which histones were recycled. Furthermore, addition of the lagging-strand maturation factors Fen1 and Cdc9 enhances histone recycling to the lagging strand. These findings provide critical insights into the molecular players and mechanisms underlying symmetric histone recycling.

Histones↗
PubMed1997

Comparison of the gene expression of aspartate beta-D-semialdehyde dehydrogenase at elevated hydrostatic pressure in deep-sea bacteria.

Aspartate beta-D-semialdehyde dehydrogenase genes (asd) were cloned and sequenced from a deep-sea-adapted strictly barophilic bacterium, Shewanella sp. strain DB6705, and a moderately barophilic bacterium, Shewanella sp. strain DSS12. The determined asd sequences of these two strains were very similar, and the identity of the deduced amino acids sequences was 96.2%. The 5'-ends of the asd mRNA from both strains were localized at corresponding sites by primer extension analysis, and two transcriptional starting points, which differed by only 1 base, were detected. In strain DB6705, a pressure-regulated transcript was mainly observed, whereas in strain DSS12, a pressure-tolerant transcript was observed together with the pressure-regulated transcript. Western-blotting analysis showed that the ASD protein was expressed under higher pressure conditions in DB6705, and under all pressure conditions tested in DSS12, as reflected in the primer extension results. Our findings suggest that asd expression controlled by pressure is one of the important mechanisms involved in the adaptation of microorganisms to the deep-sea environment.

Adaptation, Physiological↗
PubMed1991

African populations and the evolution of human mitochondrial DNA.

The proposal that all mitochondrial DNA (mtDNA) types in contemporary humans stem from a common ancestor present in an African population some 200,000 years ago has attracted much attention. To study this proposal further, two hypervariable segments of mtDNA were sequenced from 189 people of diverse geographic origin, including 121 native Africans. Geographic specificity was observed in that identical mtDNA types are shared within but not between populations. A tree relating these mtDNA sequences to one another and to a chimpanzee sequence has many deep branches leading exclusively to African mtDNAs. An African origin for human mtDNA is supported by two statistical tests. With the use of the chimpanzee and human sequences to calibrate the rate of mtDNA evolution, the age of the common human mtDNA ancestor is placed between 166,000 and 249,000 years. These results thus support and extend the African origin hypothesis of human mtDNA evolution.

Africa↗
PubMed1997

Re: Congruence and phylogenetic reanalysis of perching bird cytochrome b sequences.

In a study of the phylogenetic relationships among perching bird mtDNA sequences, Edwards et al. (1991; Proc. R. Soc. London Ser B. 243: 99-107) sequenced part of the mitochondrial cytochrome b gene from 13 perching birds (Passeriformes) and a woodpecker outgroup. However, recently the validity of part of the sequence of the hermit thrush (Catharus guttatus) in that study has been questioned. To determine the effect of inclusion of this apparently chimeric sequence on the conclusions of the original analysis, we reanalyzed these sequences using a different published hermit thrush sequence. In addition, we applied tests of congruence to examine the possibility that the aberrant phylogenetic behavior of chimeric mtDNA sequences might be detected. The reanalysis confirms the ability of slow evolving first and second codon positions of cytochrome b sequences to resolve deep branches in the avian tree. The fact that the new data set does not reject the DNA hybridization tree of these species probably indicates poor ability of the cytochrome b sequences to discriminate among alternative trees, rather than consistency among data sets. Statistical testing of trees based on individual amplified segments of mtDNA indicates that congruence tests may be one useful way of identifying chimeric mtDNA sequences when they have not been detected in the laboratory or during standard phylogenetic analysis.

Animals↗
PubMed1993

Sequence of the ompH gene from the deep-sea bacterium Photobacterium SS9.

In contrast to studies of many other extremophiles, the molecular characterization of the barophilic or high-pressure-adapted bacteria of the deep ocean is virtually nonexistent. One exception is the discovery that the moderate barophile Photobacterium SS9 preferentially synthesizes a 37-kDa outer membrane protein, designated OmpH, in response to elevated hydrostatic pressure. We report here on the molecular characterization of the ompH gene. The deduced amino acid sequence of mature OmpH is similar to a number of porin proteins, including significant similarity to porin protein P2 from Haemophilus influenzae. It appears likely that OmpH is a unique porin whose synthesis is responsive to changes in the pressure regime of the deep-sea bacterium.

Adaptation, Physiological↗
PubMed2025

DeepES: deep learning-based enzyme screening to identify orphan enzyme genes.

MOTIVATION: Progress in sequencing technology has led to determination of large numbers of protein sequences, and large enzyme databases are now available. Although many computational tools for enzyme annotation were developed, sequence information is unavailable for many enzymes, known as orphan enzymes. These orphan enzymes hinder sequence similarity-based functional annotation, leading gaps in understanding the association between sequences and enzymatic reactions. RESULTS: Therefore, we developed DeepES, a deep learning-based tool for enzyme screening to identify orphan enzyme genes, focusing on biosynthetic gene clusters and reaction class. DeepES uses protein sequences as inputs and evaluates whether the input genes contain biosynthetic gene clusters of interest by integrating the outputs of the binary classifier for each reaction class. The validation results suggested that DeepES can capture functional similarity between protein sequences, and it can be implemented to explore orphan enzyme genes. By applying DeepES to 4744 metagenome-assembled genomes, we identified candidate genes for 236 orphan enzymes, including those involved in short-chain fatty acid production as a characteristic pathway in human gut bacteria. AVAILABILITY AND IMPLEMENTATION: DeepES is available at https://github.com/yamada-lab/DeepES. Model weights and the candidate genes are available at Zenodo (https://doi.org/10.5281/zenodo.11123900).

Deep Learning↗
PubMed1981

The total number, time or origin and kinetics of proliferation of neurons comprising the deep cerebellar nuclei in the rhesus monkey.

The genesis of the neurons that form the cerebellar nuclei was studied by autoradiographic methods in 30 postnatal rhesus monkeys which were exposed to 3H-thymidine at various embryonic (E) and postnatal (P) ages. As a basis for this quantitative analysis, five 2-3 month old monkeys were used for cell counting and estimation of the total number of neurons in each of the cerebellar nuclei. The results show that the cerebellar nuclei on each side contain 131,000 neurons. There are 68,000 neurons in the dentate nucleus, 25,000 neurons in the posterior interposed nucleus, and 19,000 neurons in both the anterior interposed the fastigial nuclei. All of the neurons comprising the deep nuclei are generated during the first half of the 165 days gestation period in this species. Although neurogenesis lasts from E30 through E70, approximately 81% of the neuron population is generated during a one week period between E36 and E40, with the peak of proliferation occurring at E36. Before E45 both large (maximum diameter greater than 35 micrometers) and small (maximum diameter 35 micrometers or less) neurons are produced simultaneously; after this period only small neurons are generated. Although no clearcut spatio-temporal gradients of neurogenesis could be discerned along any of the cardinal axes, each cerebellar nucleus has a somewhat distinctive developmental history in terms of the onset and cessation of neurogenesis and the tempo of cell proliferation. Thus, genesis of neurons destined for the dentate nucleus begins earlier and ends later than proliferation of the neurons that ultimately comprise the fastigial nucleus. Generation of the neurons destined for the anterior and posterior interposed nuclei follows an intermediate time course. The present data on neurogenetic sequences in the deep nuclei could not be correlated with the zonal pattern of reciprocal axonal connections that link the deep nuclei and overlying cerebellar cortex.

Aging↗
PubMed1993

N-terminal amino acid sequences of 440 kDa hemoglobins of the deep-sea tube worms, Lamellibrachia sp.1, Lamellibrachia sp.2 and slender vestimentifera gen. sp.1 evolutionary relationship with annelid hemoglobins.

The deep-sea tube worm Lamellibrachia, belonging to the phylum Vestimentifera, contains two types of extracellular hemoglobins, a 3,000 kDa hemoglobin and a 440 kDa hemoglobin. The latter hemoglobin is composed of four heme-containing chains with molecular masses of 16-18 kDa. We have collected Lamellibrachia sp.1, Lamellibrachia sp.2 and Slender vestimentifera gen. sp.1 from the deep-sea cold-seep or hydrothermal areas at a depth of 1100-1400 m. The four constituent chains of the 440 kDa hemoglobin were isolated from each of the three tube worms by reverse-phase chromatography, and the N-terminal amino acid sequences of 16-44 residues were determined by automated protein sequencer. The amino acid sequences of the homologous chains showed high homology (76-85%), suggesting that they are closely related. The sequences also showed 45-49% homology with annelid hemoglobins. A phylogenetic tree constructed from hemoglobin sequences showed that the tube worm Lamellibrachia, the polychaete Tylorrhynchus and the oligochaete Lumbricus diverged from a common ancestor at almost the same time, about 450 million years before present.

Amino Acid Sequence↗
PubMed1988

Sequential development of connections between striate and extrastriate visual cortical areas in the rat.

In these experiments we have asked whether the projection from the rat's primary visual cortex, area 17, to the extrastriate visual cortical area 18a is formed in a sequence and whether that sequence resembles the pattern of inside-out cortical neurogenesis. For this purpose fluorescent retrograde tracers were injected into area 18a at different postnatal ages (P1, P5, adult). Animals survived until 3-4 weeks of age, after migration is complete and neurons have arrived at their final laminar location. In the ipsilateral cortex, P1 injections retrogradely labeled cells in layers 5 and 6 of area 17. Labeling after P5 injections extended into more superficial layers and included the bottom of layer 2/3 and layers 4-6. After P5, more labeled cells were found at the top of layer 2/3, producing the adult laminar pattern, where the projection originates predominantly from layer 2/3. A similar sequence of laminar labeling was observed in the transcallosal connection of area 18a. This sequence of labeling, deep layers before superficial, resembles the pattern in which cortical neurons are born and indicates that axons arrive at their cortical targets in the order the cells were generated.

Animals↗
PubMed1997

Mechanisms underlying memory impairment in schizophrenia.

BACKGROUND: The purpose of this experiment was to investigate mechanisms underlying commonly-observed verbal memory impairments in schizophrenia, and especially the hypothesized encoding deficit. METHODS: A verbal memory task was administered to 38 patients with schizophrenia and 38 normal controls. Three functions involved in long-term memory-encoding, early phase of storage, retrieval-were investigated. First, non-organizable lists were compared to semantically-organizable lists in a free recall task, in order to vary encoding conditions. Superficial encoding (measured by a 'sequence' index) and deep encoding (measured by a categorization index) were assessed. Secondly, early storage was investigated by varying the delay between learning and recall. Lastly, cues were provided for organizable lists (semantic cues) and non-organizable lists (recognition sheet), in order to vary retrieval conditions. RESULTS: An analysis of variance revealed an interaction between type of list (organizable, non-organizable) and group, showing that patients used organization less than controls. A further analysis showed that deep encoding was impaired. Also, although the propensity to use superficial encoding was unimpaired, its efficiency was less. The analysis of variance revealed no interaction with delay or with either type of cue. A correlation was found between deep processing and memory performance in both groups. CONCLUSIONS: A major deficit in encoding appeared in the patient group, with a lesser use of deep encoding and a lesser efficiency of superficial encoding. On the other hand, the early phase of storage and the retrieval function seemed unaffected. Overall memory performance appeared to be related to the depth of encoding.

Adult↗
PubMed1994

Kv3.3b: a novel Shaw type potassium channel expressed in terminally differentiated cerebellar Purkinje cells and deep cerebellar nuclei.

A two-step hybridization/subtraction procedure was employed to isolate markers for the later stages of Purkinje cell differentiation. From this screen, a novel Shaw potassium channel cDNA (Kv3.3b) was identified that is developmentally regulated. Expression of this channel is highly enriched in the brain, particularly in the cerebellum, where its expression is confined to Purkinje cells and deep cerebellar nuclei. Sequence analysis revealed that it is an alternatively spliced form of the mouse Kv3.3 gene, and that the previously reported Kv3.3 mRNA (Ghanshani et al., 1992) is not expressed in cerebellum. Expression of the Kv3.3b mRNA begins in cerebellar Purkinje cells between postnatal day 8 (P8) and P10 and continues through adulthood, coinciding with elaboration of the mature Purkinje cell dendritic arbor. The timing of expression of Kv3.3b mRNA is maintained in mixed, dissociated primary cerebellar cell culture. These results suggest that the Kv3.3b K+ channel function is restricted to terminally differentiated Purkinje cells, and that analysis of the mechanisms governing its expression in vivo and in vitro can reveal molecular mechanisms governing Purkinje cell differentiation.

Amino Acid Sequence↗
PubMed2026

A deep intronic IFT172 variant causing pseudoexon inclusion identified by whole-genome sequencing in nephronophthisis.

Nephronophthisis is an autosomal recessive ciliopathy and a major genetic cause of end-stage kidney disease in children and young adults. Although next-generation sequencing panels have improved diagnostic yield, some patients remain genetically unresolved, partly due to deep intronic variants that disrupt pre-mRNA splicing and are not captured by exon-focused approaches. We report a 13-year-old boy who presented with advanced kidney dysfunction, small renal cysts, and kidney histopathology consistent with nephronophthisis. Targeted gene panel sequencing failed to identify causative pathogenic variants beyond a missense variant of uncertain significance. Whole-genome sequencing subsequently revealed compound heterozygous variants in IFT172 (NM_015662.3): a missense variant (c.4696C > T, p.Arg1566Cys) and a deep intronic variant (c.4915-94A > G). In silico analysis predicted activation of cryptic splice sites leading to inclusion of an 86-bp pseudoexon, which was confirmed by a minigene splicing assay. These findings established a molecular diagnosis of IFT172-related nephronophthisis. To our knowledge, this is the first report demonstrating pseudoexon inclusion in IFT172, thereby expanding its mutational spectrum. Our case underscores the importance of evaluating deep intronic regions using whole-genome sequencing and functional validation in genetically unresolved nephronophthisis.

Humans↗
PubMed2024

SIMS: A deep-learning label transfer tool for single-cell RNA sequencing analysis.

Cell atlases serve as vital references for automating cell labeling in new samples, yet existing classification algorithms struggle with accuracy. Here we introduce SIMS (scalable, interpretable machine learning for single cell), a low-code data-efficient pipeline for single-cell RNA classification. We benchmark SIMS against datasets from different tissues and species. We demonstrate SIMS's efficacy in classifying cells in the brain, achieving high accuracy even with small training sets (<3,500 cells) and across different samples. SIMS accurately predicts neuronal subtypes in the developing brain, shedding light on genetic changes during neuronal differentiation and postmitotic fate refinement. Finally, we apply SIMS to single-cell RNA datasets of cortical organoids to predict cell identities and uncover genetic variations between cell lines. SIMS identifies cell-line differences and misannotated cell lineages in human cortical organoids derived from different pluripotent stem cell lines. Altogether, we show that SIMS is a versatile and robust tool for cell-type classification from single-cell datasets.

Single-Cell Analysis↗
PubMed2025

Refining sequence-to-activity models by increasing model resolution.

Decoding the cis-regulatory syntax that controls gene expression is essential for improving our understanding of cell differentiation and disease. To identify regulatory motifs and their regulatory syntax, deep learning based sequence-to-activity (S2A) models learn transcription factor binding motifs and their combinations from DNA sequence by modeling measured chromatin accessibility. Previously, we developed AI-TAC, a S2A model that predicts chromatin accessibility across various immune cell types in multi-task fashion, effectively decoding the regulatory syntax underlying immune cell differentiation. While ATAC-seq is commonly used to measure regional accessibility, it also provides high-resolution profiles, the distribution of Tn5 insertion sites, that offer additional insights into the precise location and strength of TF binding sites. Here we demonstrate that modeling ATAC-seq profiles alongside accessibility consistently improves predictions of differential chromatin accessibility across cell types. Moreover, we also find that multi-task learning across related immune cell types consistently outperforms single-task models. To understand what additional information bpAITAC learns from ATAC-seq profiles, we systematically compare sequence attributions from models trained with and without ATAC-seq profiles. We identify novel motifs with strong effect sizes that emerge only when profile data is included. Our findings suggest that modeling ATAC-seq at base-pair resolution enables the model to learn a more nuanced and sensitive representation of the cis-regulatory syntax driving immune cell-specific chromatin landscapes.

ATAC-seq↗
PubMed1996

Phylogeny of oral asaccharolytic Eubacterium species determined by 16S ribosomal DNA sequence comparison and proposal of Eubacterium infirmum sp. nov. and Eubacterium tardum sp. nov.

16S rRNA gene sequences of Eubacterium brachy, Eubacterium nodatum, Eubacterium saphenum, Eubacterium timidum, and two previously unnamed taxa were determined. The results of a phylogenetic analysis indicated that all of the strains sequenced belonged to a deep branch of the low-G+C-content gram-positive group. The levels of 16S ribosomal DNA sequence similarity between species were low, suggesting that a number of genera may be represented in this group. The representatives of the two unnamed taxa, which were isolated from patients with periodontitis, were clearly distinct from the previously described species, and, therefore, the following two new species are proposed: Eubacterium infirmum (type strain, NCTC 12940) and Eubacterium tardum (type strain, NCTC 12941).

Base Sequence↗
PubMed1998

Distribution of the pressure-regulated operons in deep-sea bacteria.

DNA regions corresponding to portions of two different pressure-regulated operons previously identified in two deep-sea barophilic bacteria were separately PCR amplified from a variety of deep-sea microorganisms and sequenced. With the two sets of primers employed, amplification was particularly successful from the more barophilic bacteria examined. 16S rRNA sequence analysis revealed that these bacteria are all phylogenetically related and belong in a sub-branch of the genus Shewanella containing only the deep-sea Shewanella barophilic bacteria. We define this sub-branch as the 'Shewanella barophile branch' containing at least two different species. Our results suggest that the DNA sequences of the pressure-regulated operons can be regarded as marker sequences to identify the Shewanella barophilic strains.

Amino Acid Sequence↗