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PubMed2006

A protein evolution model with independent sites that reproduces site-specific amino acid distributions from the Protein Data Bank.

BACKGROUND: Since thermodynamic stability is a global property of proteins that has to be conserved during evolution, the selective pressure at a given site of a protein sequence depends on the amino acids present at other sites. However, models of molecular evolution that aim at reconstructing the evolutionary history of macromolecules become computationally intractable if such correlations between sites are explicitly taken into account. RESULTS: We introduce an evolutionary model with sites evolving independently under a global constraint on the conservation of structural stability. This model consists of a selection process, which depends on two hydrophobicity parameters that can be computed from protein sequences without any fit, and a mutation process for which we consider various models. It reproduces quantitatively the results of Structurally Constrained Neutral (SCN) simulations of protein evolution in which the stability of the native state is explicitly computed and conserved. We then compare the predicted site-specific amino acid distributions with those sampled from the Protein Data Bank (PDB). The parameters of the mutation model, whose number varies between zero and five, are fitted from the data. The mean correlation coefficient between predicted and observed site-specific amino acid distributions is larger than = 0.70 for a mutation model with no free parameters and no genetic code. In contrast, considering only the mutation process with no selection yields a mean correlation coefficient of = 0.56 with three fitted parameters. The mutation model that best fits the data takes into account increased mutation rate at CpG dinucleotides, yielding = 0.90 with five parameters. CONCLUSION: The effective selection process that we propose reproduces well amino acid distributions as observed in the protein sequences in the PDB. Its simplicity makes it very promising for likelihood calculations in phylogenetic studies. Interestingly, in this approach the mutation process influences the effective selection process, i.e. selection and mutation must be entangled in order to obtain effectively independent sites. This interdependence between mutation and selection reflects the deep influence that mutation has on the evolutionary process: The bias in the mutation influences the thermodynamic properties of the evolving proteins, in agreement with comparative studies of bacterial proteomes, and it also influences the rate of accepted mutations.

Algorithms↗

PubMed1998

Ligand size is a major determinant of specificity in periplasmic oxyanion-binding proteins: the 1.2 A resolution crystal structure of Azotobacter vinelandii ModA.

BACKGROUND: . Periplasmic receptors constitute a diverse class of binding proteins that differ widely in size, sequence and ligand specificity. Nevertheless, almost all of them display a common beta/alpha folding motif and have similar tertiary structures consisting of two globular domains. The ligand is bound at the bottom of a deep cleft, which lies at the interface between these two domains. The oxyanion-binding proteins are notable in that they can discriminate between very similar ligands. RESULTS: . Azotobacter vinelandii is unusual in that it possesses two periplasmic molybdate-binding proteins. The crystal structure of one of these with bound ligand has been determined at 1.2 A resolution. It superficially resembles the structure of sulphate-binding protein (SBP) from Salmonella typhimurium and uses a similar constellation of hydrogen-bonding interactions to bind its ligand. However, the detailed interactions are distinct from those of SBP and the more closely related molybdate-binding protein of Escherichia coli. CONCLUSIONS: . Despite differences in the residues involved in binding, the volumes of the binding pockets in the A. vinelandii and E. coli molybdate-binding proteins are similar and are significantly larger than that of SBP. We conclude that the discrimination between molybdate and sulphate shown by these binding proteins is largely dependent upon small differences in the sizes of these two oxyanions.

Amino Acid Sequence↗

PubMed1984

Treatment of Class II deep bite by orthodontic and surgical means.

Conventional orthodontic correction of the Class II deep-bite deformity with a decreased lower anterior facial height tendency can be mechanically difficult, inefficient and, in many instances, impossible. Orthodontic treatment alone of either adults or adolescents with such deformities frequently can neither increase lower anterior facial height sufficiently to achieve ideal facial proportions nor achieve long-term occlusal stability. Despite the need for surgical intervention to achieve satisfactory occlusal and esthetic results, many patients with such deformities are still being treated in clinical practice by traditional orthodontic procedures, with less than ideal esthetic and/or occlusal results. The challenge to achieve efficient and stable treatment of this deformity has been met by the use of various surgical techniques in combination with orthodontic treatment. This combined surgical-orthodontic approach can provide increased treatment efficiency, long-term stability, and optimal esthetic results. The proper sequencing and correct selection of orthodontic mechanotherapy are essential to ensure the desired results. This article purposes to detail basic problems involved in diagnosis and treatment planning for the combined surgical-orthodontic approach to patients exhibiting Class II deep bite and decreased lower facial height. Orthodontic and surgical treatment objectives are explained, and representative case reports are presented and discussed to illustrate this method of treatment. Extraction patterns, control of the transverse dimension, arch wire selection, auxiliary wires, elastics, and extraoral appliance use are described. Surgically, the dentofacial disharmony associated with this deformity may defy treatment by surgical advancement of the mandible only. Genioplasty, Le Fort I osteotomy, symphyseal osteotomy, anterior or total mandibular subapical osteotomy, body osteotomy, submental lipectomy, and rhinoplasty are adjunctive procedures that are described and may be used in concert with mandibular advancement surgery.

Adult↗

PubMed1994

Polynesian mitochondrial DNAs reveal three deep maternal lineage clusters.

The 4000-year-old human population expansion into Remote Oceania has been studied from a variety of genetic perspectives. Here, we report the discovery that Polynesians, traditionally considered to be a single cohesive linguistic and cultural unit, exhibit at least three distinct mitochondrial DNA (mtDNA) groups that probably shared a common maternal ancestor more than 85,000 years ago. The major lineage groups were first identified by PCR amplification of the mitochondrial region V deletion marker, known to be present at high frequency in Polynesian populations. Sequence analysis of mtDNA hypervariable control regions reveals a surprising number of lineages in Polynesia. We also note high sequence divergence between lineage groups deleted and not deleted in region V. Major group I lineages are common in Remote Oceania and include about 95% of the Native Hawaiian, 90% of the Samoan, and 100% of the Tongan donors in our sample. They contain the region V deletion and generally share three control region transition substitutions. This group also contains non-Polynesian individuals, such as Indonesians, Native Americans, Micronesians, Malaysians, Japanese, and Chinese. The group I Polynesians differ by 4.4% in sequence identity from major lineage group II Polynesians, who do not have the region V deletion and who share among themselves four distinct single-base substitutions. Group II individuals are seen at low frequency (< 10%) in Hawaii, Samoa, and the Cook Islands and may represent the predominant maternal lineage group of Papuan Melanesia. Major lineage group III, not found in Hawaii, tentatively links Samoa to Indonesia. Our observation of deep maternal genetic branches in Polynesia today confirms the notion that during the colonization of the Pacific, mainland Asian immigrants mixed with Melanesian peoples already inhabiting Near Oceania and carried a complex assortment of maternal genotypes derived from two distinct geographic sources to isolated island archipelagoes.

Base Sequence↗

PubMed2005

Composition of pH-sensitive triad in C-lobe of human serum transferrin. Comparison to sequences of ovotransferrin and lactoferrin provides insight into functional differences in iron release.

The transferrins (TF) are a family of bilobal glycoproteins that tightly bind ferric iron. Each of the homologous N- and C-lobes contains a single iron-binding site situated in a deep cleft. Human serum transferrin (hTF) serves as the iron transport protein in the blood; circulating transferrin binds to receptors on the cell surface, and the complex is internalized by endocytosis. Within the cell, a reduction in pH leads to iron release from hTF in a receptor-dependent process resulting in a large conformational change in each lobe. In the hTF N-lobe, two critical lysines facilitate this pH-dependent conformational change allowing entry of a chelator to capture the iron. In the C-lobe, the lysine pair is replaced by a triad of residues: Lys534, Arg632, and Asp634. Previous studies show that mutation of any of these triad residues to alanine results in significant retardation of iron release at both pH 7.4 and pH 5.6. In the present work, the role of the three residues is probed further by conversion to the residues observed at the equivalent positions in ovotransferrin (Q-K-L) and human lactoferrin (K-N-N) as well as a triad with an interchanged lysine and arginine (K534R/R632K). As expected, all of the constructs bind iron and associate with the receptor with nearly the same K(D) as the wild-type monoferric hTF control. However, interesting differences in the effect of the substitutions on the iron release rate in the presence and absence of the receptor at pH 5.6 are observed. Additionally, titration with KCl indicates that position 632 must have a positively charged residue to elicit a robust rate acceleration as a function of increasing salt. On the basis of these observations, a model for iron release from the hTF C-lobe is proposed. These studies provide insight into the importance of charge and geometry of the amino acids at these positions as a partial explanation for differences in behavior of individual TF family members, human serum transferrin, ovotransferrin, and lactoferrin. The studies collectively highlight important features common to both the N- and C-lobes of TF and the critical role of the receptor in iron release.

Amino Acid Sequence↗

PubMed2026

An Integrative Morphological and Genomic Analysis With a Refined Fluorescence In Situ Hybridization (FISH) Threshold and Novel Kinase Fusions in a Large Asian Cohort of Spitzoid Neoplasms.

Differentiating atypical Spitz tumors (ASTs) from true Spitz melanomas (SMs) and conventional melanomas with spitzoid features (MSFs) remains a formidable diagnostic challenge. Because current molecular epidemiological data are overwhelmingly derived from Caucasian cohorts, the genomic landscape of Asian populations remains largely unexplored. To elucidate the molecular progression landscape and refine the diagnostic criteria, we performed a comprehensive multimodal analysis-integrating histomorphology, immunohistochemistry, multiprobe fluorescence in situ hybridization (FISH), and targeted RNA/DNA-based next-generation sequencing (NGS)-on a cohort of 140 spitzoid neoplasms. This cohort, comprising 126 ASTs, 8 SMs, and 6 MSFs, represents the largest Asian cohort to date. Malignant phenotype strongly correlated with lesional asymmetry, deep atypical mitoses, a sheet-like growth pattern, diffuse preferentially expressed antigen of melanoma positivity, and significant loss of p16 expression (64.3% in SM/MSF vs 9.5% in ASTs; P < .0001). Building upon the established melanoma FISH criteria, we optimized a prognostic threshold of ≥2 FISH abnormalities specifically tailored for spitzoid neoplasms. We demonstrated that isolated single chromosomal aberrations (particularly MYB loss) are relatively stable events that are frequent in indolent ASTs, whereas our refined ≥2 threshold yielded 100% sensitivity and 92.5% specificity for predicting regional lymph node metastasis/local recurrence. Molecularly, NGS identified mutually exclusive initiating driver alterations (comprising kinase fusions and HRAS mutations) in 89.9% of true Spitz neoplasms, a remarkably high prevalence suggesting a distinct genetic background in Asian populations. We also characterized 5 entirely novel kinase fusions (ZNF24::ROS1, PCBP1::ROS1, NUMA1::RET, CBWD1::ALK, and TPR::NTRK1). Furthermore, NGS definitively segregated true Spitz neoplasms from morphological mimics (MSF), which lacked fusions and were driven by canonical genomic alterations of the conventional melanoma pathway. Integrating these genomic landscapes validated a stepwise progression model. Although isolated kinase fusions drove indolent ASTs, malignant SM invariably harbored concurrent pathogenic secondary alterations, demonstrating a profound reliance on CDKN2A/B, TP53, and CDK4 aberrations. Ultimately, we propose an integrated diagnostic algorithm combining morphological evaluation, the refined FISH threshold, and comprehensive NGS profiling, providing a precise, evidence-based framework for pathway classification and clinical management of spitzoid neoplasms.

fluorescence in situ hybridization↗

PubMed2026

[Applications and Challenges of Deep Learning in Human Genome Research].

In recent years, the advent of high-throughput omics technologies has fueled an explosive growth in human genomic data. Uncovering the latent functions within this vast data has become a significant challenge in functional genomics research. While traditional statistical methods have proved successful for analyzing smaller-scale datasets in the past, they exhibit clear limitations in analytical efficiency and integrating multi-dimensional data, struggling to meet the escalating demands of contemporary genomic analysis. The introduction of deep learning (DL) technologies offers a novel paradigm for this field. This review systematically examines the advances in applying deep learning to human genomics research. Studies demonstrate that when ample labeled data is available, discriminative DL computational methods-such as Convolutional Neural Networks (CNNs) and Long Short-Term Memory networks (LSTMs)-achieve high accuracy and efficiency in genomic variant discovery tasks. Furthermore, generative DL methods, particularly Large Language Models (LLMs) leveraging self-supervised pre-training strategies, effectively integrate complex genomic information and exhibit superior performance in functional genomic sequence annotation and gene regulation studies. This review also explores the application of LLMs in multi-omics data integration and prediction. Looking ahead, the continued accumulation of long-read sequencing and high-dimensional data is expected to enable DL technologies to integrate increasingly complex and heterogeneous genomic information, playing an increasingly crucial role in human genomics research.

Deep Learning↗

PubMed2006

Phylogenetic relationships within the order Halobacteriales inferred from 16S rRNA gene sequences.

Phylogenetic relationships within the halophilic archaea were inferred from comparisons of the 16S rRNA gene sequences from 61 strains, representing 18 genera with validly published names within the order Halobacteriales. Trees produced using distance-matrix (least-squares and neighbour-joining) methods affirm with strong bootstrap support that the members of the order Halobacteriales are a monophyletic group. Ten genera were supported as monophyletic groups [Haloarcula, Halobiforma, Halococcus, Haloferax, Halorubrum, Halosimplex (multiple sequences from a single strain), Natrialba, Natrinema, Natronococcus and Natronorubrum] and eight genera were represented by a single strain (Halobacterium, Halobaculum, Halogeometricum, Halomicrobium, Halorhabdus, Halosimplex, Natronobacterium and Natronomonas). The genus Haloterrigena was always paraphyletic, and the phylogenetic placement of and sister groups to Halobacterium and Natronomonas could not be resolved. Both treeing methods failed to resolve the deep branching patterns within the order Halobacteriales and the relationships between the major clades. Additional representation from the currently monospecific genera and/or the use of other macromolecules may be required to resolve the relationships within the order Halobacteriales.

Base Sequence↗

PubMed1989

Primary structure of a dimeric haemoglobin from the deep-sea cold-seep clam Calyptogena soyoae.

The heterodont clam Calyptogena soyoae, living in the cold-seep area of the upper bathyal depth of Sagami Bay, Japan, has two homodimeric haemoglobins (Hb I and Hb II) in erythrocytes. The complete amino acid sequence of 136 residues of C. soyoae Hb II was determined. The sequence showed low homology with any other globins (at most 20% identity) and lacked the N-terminal extension of seven to nine amino acid residues characteristic of all the molluscan haemoglobins sequenced hitherto. Although the subunit assembly of molluscan haemoglobin is known to be 'back-to-front' relative to vertebrate haemoglobin, C. soyoae Hb II is unlikely to undergo such a subunit assembly because it lacks homology in the sequence involving subunit interaction. These structural features suggest that C. soyoae haemoglobin may have accomplished a unique molecular evolution. The distal (E7) histidine residue of C. soyoae Hb II is unusually replaced by glutamine. However, the oxyhaemoglobin is stable enough to act as an O2 carrier, since the autoxidation rate at near physiological temperature (3 degrees C) is about 3 times lower than that of human haemoglobin at 37 degrees C. H.p.l.c. patterns of peptides (Figs. 5-7), amino acid compositions of intact protein and peptides (Table 1) and amino acid sequences of intact protein and peptides (Tables 2 and 3) have been deposited as Supplementary Publication SUP 50150 (11 pages) at the British Library Document Supply Centre, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies may be obtained on the terms indicated in Biochem. J. (1989) 257, 5.

Amino Acid Sequence↗

PubMed2005

The Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza.

Rice (Oryza sativa L.) is the most important food crop in the world and a model system for plant biology. With the completion of a finished genome sequence we must now functionally characterize the rice genome by a variety of methods, including comparative genomic analysis between cereal species and within the genus Oryza. Oryza contains two cultivated and 22 wild species that represent 10 distinct genome types. The wild species contain an essentially untapped reservoir of agriculturally important genes that must be harnessed if we are to maintain a safe and secure food supply for the 21st century. As a first step to functionally characterize the rice genome from a comparative standpoint, we report the construction and analysis of a comprehensive set of 12 BAC libraries that represent the 10 genome types of Oryza. To estimate the number of clones required to generate 10 genome equivalent BAC libraries we determined the genome sizes of nine of the 12 species using flow cytometry. Each library represents a minimum of 10 genome equivalents, has an average insert size range between 123 and 161 kb, an average organellar content of 0.4%-4.1% and nonrecombinant content between 0% and 5%. Genome coverage was estimated mathematically and empirically by hybridization and extensive contig and BAC end sequence analysis. A preliminary analysis of BAC end sequences of clones from these libraries indicated that LTR retrotransposons are the predominant class of repeat elements in Oryza and a roughly linear relationship of these elements with genome size was observed.

Base Sequence↗

PubMed2001

Distribution and identification of red yeasts in deep-sea environments around the northwest Pacific Ocean.

We isolated 99 yeast strains, including 40 red yeasts, from benthic animals and sediments collected from the deep-sea floor in various areas in the northwest Pacific Ocean. Comparing the yeast isolates from animals and sediments collected from shallow locations, the proportion of red yeasts differed considerably, comprising 81.5% and 10.6% of the isolates from animals and sediments, respectively. All of the red yeast isolates belonged to the genera Rhodotorula and Sporobolomyces. On the basis of morphological and physiological characteristics, the isolates were identified as R. aurantiaca, R. glutinis, R. minuta and R. mucilaginosa of the genus Rhodotorula, and S. salmonicolor and S. shibatanus of the genus Sporobolomyces. Only R. glutinis and R. mucilaginosa were isolated from sediments. All of the others were isolated from animal sources. Phylogenetic analyses based on internal transcribed spacer (ITS) regions and 5.8S rRNA gene sequences allowed us to establish the precise taxonomic placement of each of the isolates and thereby investigate the intraspecific relationships among the isolates. Twenty-two strains identified as members of R. glutinis, which showed a wide distribution in the deep-sea, and five isolates identified as R. minuta, which were isolated only from benthic animals, showed substantial heterogeneity within the species. The isolates phenotypically identified as Sporobolomyces species and R. mucilaginosa phylogenetically occupied the placements corresponding to these species. Some strains assigned to known species on the basis of phenotypic features should be regarded as new species as suggested by the results of molecular analysis.

Ascomycota↗

PubMed1993

Localization of NaPi-1, a Na-Pi cotransporter, in rabbit kidney proximal tubules. I. mRNA localization by reverse transcription/polymerase chain reaction.

We have recently isolated from a rabbit cortex cDNA library a cDNA clone (NaPi-1), which, after in vitro transcription (cRNA) and injection into Xenopus laevis oocytes, expresses Na-dependent Pi uptake [Werner A, et al. (1991) Proc Natl Acad Sci USA 88:9608-9612]. The aim of the present work was to study the nephron location of the NaPi-1-related mRNA(s) by combining nephron microdissection procedures, reverse transcription (RT) and amplification of the resultant cDNA by the polymerase chain reaction (PCR). RT-PCR using NaPi-1-specific primers (different combinations) and either total kidney cortex RNA or microdissected proximal tubule segments resulted in two PCR products, both of approximately the expected length (but differing by about 30 base pairs). Restriction-enzyme analysis and nucleotide sequencing confirmed that both PCR products are related to NaPi-1 and that the "longer" PCR product has an insert of 26 base pairs containing an AluI restriction site. Nephron microdissection documents expression of NaPi-1-related mRNA(s) in superficial and deep proximal tubules (S1, S2 and S3 segments) and their absence in glomeruli, thin descending limb and thick ascending limbs of Henle's loop, distal convoluted tubules and cortical and inner medullary collecting ducts. These experiments suggest a "microheterogeneity" of NaPi-1-related mRNA(s) (which is not detected in Northern blot analysis) and proximal tubular expression of NaPi-1.

Animals↗

PubMed2026

Genomic Footprints of Historical Introgression Between Ancient Lineages of Wild Oryza AA-Genome Species With Widely Separated Contemporary Distributions.

Phylogenetic incongruence is increasingly recognized as pervasive, yet the extent to which reticulate evolution occurs between groups separated by substantial geographical distances and deep phylogenetic divergence remains poorly characterized. In the Oryza AA-genome group-a model for plant speciation and domestication-the traditional bifurcation model posits that Australian Oryza meridionalis and African Oryza longistaminata occupy basal branches, distinct from the more recently diversified monophyletic clade comprising Asian and other African lineages, including major cultivars. However, recent evidence from endogenous viral sequences has hinted at unexpected genetic relatedness between African O. longistaminata and Asian Oryza sativa, which are geographically and phylogenetically distant. Here, we conducted a genome-wide survey across 11 Oryza species to systematically identify genomic regions exhibiting phylogenetic incongruence. Widespread phylogenetic discordance was observed, notably involving genomic segments in which O. longistaminata showed phylogenetic proximity to Asian species, contradicting their established deep divergence. To distinguish between introgression and incomplete lineage sorting, we performed four-taxon ABBA-BABA tests, which provided statistical support for introgression. Furthermore, divergence time estimates for these incongruent regions were younger than the species divergence times, suggesting historical introgression between the ancestors of lineages that are currently separated by vast geographical distances. Systematic assessments indicated that potential analytical artifacts, such as compositional bias and substitution saturation, were unlikely to explain the observations. These convergent lines of evidence suggest that ancient introgression had occurred between currently geographically separated and evolutionarily divergent Oryza lineages, leaving detectable footprints across their modern genomes.

Oryza↗

PubMed1990

Global field power and topographic similarity.

Multichannel recordings are commonly presented as topographic maps series displaying the change of the potential distribution over time. When reviewing a sequence of potential maps it becomes obvious that there are epochs with only little activity (few field lines; small extrema values) while at other times the fields display high peaks and deep troughs with steep gradients. The measure of global field power (GFP) corresponds to the spatial standard deviation, and it quantifies the amount of activity at each time point in the field considering the data from all recording electrodes simultaneously resulting in a reference-independent descriptor of the potential field. Global field power is plotted as a function of time, and the occurrence times of GFP maxima are used to determine the latencies of evoked potential components. The topographical change occurring in subsequent potential field distributions may also be quantified by computing an index of global dissimilarity. Global field power and global dissimilarity show a complementary behavior over time: in general, high GFP is associated with similar fields while during periods between GFP peaks the topographic patterns of successive field distributions change rapidly accompanied by high dissimilarity values. The topographic changes, however, are best recognized by a segmentation procedure that considers field structure independent of GFP and global dissimilarity. The principles and practical applications of GFP computation, component latency determination and global dissimilarity of potential field distributions as well as a topographical time segmentation procedure will be illustrated with multichannel data evoked by visual stimuli.

Brain↗

PubMed2000

Cloning, expression, and characterization of DNA polymerase I from the hyperthermophilic archaea Thermococcus fumicolans.

The DNA polymerase I gene of a newly described deep-sea hydrothermal vent Archaea species, Thermococcus fumicolans, from IFREMERS's collection of hyperthermophiles has been cloned in Escherichia coli. As in Thermococcus litoralis, the gene is split by two intervening sequences (IVS) encoding inteins inserted in sites A and C of family B DNA polymerases. The entire DNA polymerase gene, containing both inteins, was expressed at 30 degrees C in E. coli strain BL21(DE3)pLysS using the pARHS2 expression vector. The native polypeptide precursor of 170kDa was obtained, and intein splicing as well as ligation of the three exteins was observed in vitro after heat exposure. The recombinant enzyme was purified and some of its activities were characterized: polymerization, thermostability, exonuclease activities, and fidelity.

Cloning, Molecular↗

PubMed2003

A patient in whom only hepatitis B virus (HBV) was thought to have been contracted, by kissing, from a same-sex partner coinfected with HBV and human immunodeficiency virus-1.

A 31-year-old homosexual man was admitted to our hospital in August 2001 with liver dysfunction. His diagnosis was acute hepatitis B. He had had a steady partner coinfected with hepatitis B virus (HBV) and human immunodeficiency virus-1 (HIV) from August 2000 to July 2001. Because he knew that the partner was infected with HIV, the sexual relationship had included only deep kissing, with no oral-genital or anal-genital sex. The serum HBV DNA level of the partner was relatively high compared with the serum HIV RNA level. Direct sequencing of the full HBV DNA genome from serum showed that the entire base sequences of the viruses from both patients were of genotype A and identical. HBV infectivity was shown to be stronger than that of HIV in our patient, in whom only HBV was transmitted from a partner coinfected with HBV and HIV. This case highlights the importance of HBV as a sexually transmitted disease.

Acute Disease↗

PubMed2006

Degradability of dimethyl terephthalate by Variovorax paradoxus T4 and Sphingomonas yanoikuyae DOS01 isolated from deep-ocean sediments.

Two strains of bacteria were isolated from deep-ocean sediments of the South China Sea using enrichment culturing technique and they were identified as Sphingomonas yanoikuyae DOS01 (AY878409) and Variovorax paradoxus T4 (AY878410) based on 16S rRNA gene sequences. S. yanoikuyae DOS01 was only capable of transforming dimethyl terephthalate (DMTP) to monomethyl terephthalate (MMTP) without further degradation while V. paradoxus T4 exhibited ability in mineralizing DMTP as the sole source of carbon and energy. The biochemical pathway of DMTP degradation was through MMTP and terephthalic acid (TA) as major detectable degradation intermediates in the culture media by both microorganisms. V. paradoxus T4 utilized DMTP and MMTP via hydrolysis of diester and monoester in the initial steps in degradation as confirmed by total organic carbon analysis of the culture medium and esterase activity assay of the lysed cells and fraction. The specific hydrolysis activity of esterase induced by DMTP or MMTP showed that greater hydrolysis of p-nitrophenyl acetate by esterase induced by DMTP-grown cells than that induced by MMTP. Results of this research suggest that the cleavage of the two identical carboxylic ester groups of phthalate diester are carried out by highly specific esterases of the same bacteria in the environment.

Carbon↗

PubMed2025

Single-cell analysis of dup15q syndrome reveals developmental and postnatal molecular changes in autism.

Duplication 15q (dup15q) syndrome is a leading genetic cause of autism spectrum disorder, offering a key model for studying autism-related mechanisms. Using single-cell and single-nucleus RNA sequencing of cortical organoids from dup15q patient-derived iPSCs and post-mortem brain samples, we identify increased glycolysis, disrupted layer-specific marker expression, and aberrant morphology in deep-layer neurons during fetal-stage organoid development. In adolescent-adult postmortem brains, upper-layer neurons exhibit heightened transcriptional burden related to synaptic signaling, a pattern shared with idiopathic autism. Using spatial transcriptomics, we confirm these cell-type-specific disruptions in brain tissue. By gene co-expression network analysis, we reveal disease-associated modules that are well preserved between postmortem and organoid samples, suggesting metabolic dysregulation that may lead to altered neuron projection, synaptic dysfunction, and neuron hyperexcitability in dup15q syndrome.

Humans↗