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PubMed2025

CSGL: chemical synthesis graph learning for molecule representation.

MOTIVATION: Molecule representation learning (MRL) translates molecules into a real vector space, serving as input to downstream tasks in biology, chemistry, and computer science. This article introduces a chemical synthesis graph learning (CSGL) framework, which enhances MRL by considering both the atomic structures of molecules and their roles in chemical reactions through a hierarchical graph representation. Specifically, molecules are first modeled based on their molecular graphs, which capture atomic-level structural information. They are then further refined using a chemical synthesis graph, where nodes represent reactant and product molecule sets, and edges encode chemical transformations between reactants and products (e.g. changes in molecular structures). CSGL optimizes molecular embeddings of reactant and product nodes in a fashion that ensures the embeddings conform to a chemical balance constraint. RESULTS: Experimental results show that our method CSGL achieves strong performance on a variety of tasks, including product prediction, reaction classification, and molecular property prediction. AVAILABILITY AND IMPLEMENTATION: https://github.com/li-2023/CSGL.

Machine Learning↗

PubMed1993

Some variants of lethal neonatal short-limbed platyspondylic dysplasia: a radiological ultrasonographic, neuropathological and histopathological study of 22 cases.

Data on twenty-two infants with lethal neonatal short-limbed platyspondylic dysplasia are reported. Thanatophoric dysplasia (TD) is the most frequent diagnosis in this group. TD combined with a cloverleaf skull (CS), has been variably classified. TD type 1 with curved femora is rarely combined with CS; TD type 2 with straight femora is almost always associated with CS. Other varieties of TD, known as 'Torrance', 'San Diego' or 'Luton' types, are separate entities. Apart from the differences in radiography and osteochondrohistology, the temporal-lobe abnormalities seen in TD were absent in one of the cases of the 'Torrance' variety. There were also differences in the composition of the cartilage glycosaminoglycans between this case and TD. Nearly all of the cases of these different types mentioned in the literature, including those of this study group, have been sporadic and may result from new dominant mutations. Documentation and classification by full (postmortem) radiography and osteochondrohistology is essential for two reasons. It will be the foundation for the clinical geneticist to inform the parents about the risk of recurrence. It will also be the basis for a biochemical or molecular-biological classification in the near future.

Brain↗

PubMed1999

Cytogenetics and molecular genetics of childhood leukemia.

Childhood leukemia is the commonest form of childhood cancer and represents clonal proliferation of transformed hemopoietic cells as a result of genetic changes. Molecular characterization of these changes, in particular chromosomal translocations, has yielded a wealth of information on the mechanisms of leukemogenesis. These findings have also allowed the development of sensitive assays for the identification of underlying molecular defects, which is applicable to disease diagnosis and to monitor response to treatment. Genetic alterations in childhood leukemia are powerful prognostic indicators. TEL-AML1 fusion and hyperdiploidy >50 chromosomes are associated with a good prognosis in childhood acute lymphoblastic leukemia, whereas BCR-ABL fusion and MLL rearrangements are associated with a poor prognosis. Hence cytogenetic and molecular genetic classification of childhood leukemia will significantly improve the ability of clinicians to predict therapeutic response and prognosis, which paves the way for risk stratification based on clinical and genetic features. Finally, deciphering of genetic lesions in leukemia has allowed elucidation of the molecular basis of current treatment, as typified by the success of all-trans retinoic treatment in acute promyelocytic leukemia, and has identified targets for novel therapeutic approaches. It is envisaged that efforts in characterization of molecular defects in childhood leukemia will ultimately be translated into better clinical outcome for patients.

Biomarkers, Tumor↗

PubMed1985

Chloroplast biosystematics: chloroplast DNA as a molecular probe.

The classification of plants has traditionally been dependent upon the comparative analysis of morphological and biochemical data. In this paper the use of molecular probe analysis of chloroplast DNA (ctDNA) is used to expand the data base used in taxonomic studies. Chloroplast DNA size, homogeneity, the global arrangement of ctDNA structure, gene content, gene cluster array and gene sequence determination are discussed as useful criteria in the analysis of phylogenetic relationships.

Base Sequence↗

PubMed1996

The STATIS method: characterization of conformational states of flexible molecules from molecular dynamics simulations in solution.

STATIS, a data analysis method used when data can be expressed as matrices, seems particularly well suited to characterize the internal molecular motions and conformational states extracted from MD trajectories. We first outline this method and the "adapted STATIS" method. Applications are presented for 18-crown-6 (simulated for 2 nsec in acetonitrile solution) and for the (L30)2Cu+ catenate (stimulated for 150 psec in chloroform). STATIS should be valuable for the classification of molecular conformations and simplified visualization of MD trajectories.

Acetonitriles↗

PubMed2006

Chromosomal distribution and organization of three cervid satellite DNAs in Chinese water deer (Hydropotes inermis).

The species-specific profile and centromeric heterochromatin localization of satellite DNA in mammalian genomes imply that satellite DNA may play an important role in mammalian karyotype evolution and speciation. A satellite III DNA family, CCsatIII was thought to be specific to roe deer (Capreolus capreolus). In this study, however, this satellite DNA family was found also to exist in Chinese water deer (Hydropotes inermis) by PCR-Southern screening. A satellite III DNA element of this species was then generated from PCR-cloning by amplifying this satellite element using primer sequences from the roe deer satellite III clone (CCsatIII). The newly generated satellite III DNA along with previously obtained satellite I and II DNA clones were used as probes for FISH studies to investigate the genomic distribution and organization of these three satellite DNA families in centromeric heterochromatin regions of Chinese water deer chromosomes. Satellite I and II DNA were observed in the pericentric/centric regions of all chromosomes, whereas satellite III was distributed on 38 out of 70 chromosomes. The distribution and orientation of satellite DNAs I, II and III in the centromeric heterochromatin regions of the genome were further classified into four different types. The existence of a Capreolus-like satellite III in Chinese water deer implies that satellite III is not specific to the genus Capreolus (Buntjer et al., 1998) and supports the molecular phylogeny classification of Randi et al. (1998) which suggests that Chinese water deer and roe deer are closely related.

Animals↗

PubMed2004

Molecular phylogenetic evidence for the geographic origin and classification of Canary Island Lotus (Fabaceae: Loteae).

Molecular phylogenetic analyses of Macaronesian Lotus and related genera were conducted to assess their biogeographic history and taxonomy. Macaronesian Lotus, which are typically classified within one of two subgenera, Lotus subgenus Pedrosia or L. subg. Rhyncholotus, are diagnosed by the presence of a forked or toothed style and differences in corolla morphology. Maximum parsimony and Bayesian analyses of internal transcribed spacer sequences identify a well-supported northwest African-Cape Verde Island clade that includes all members of Lotus subgenus Pedrosia+L. subg. Rhyncholotus. There is modest support for two independently nested clades containing the Canary Island species and two non-Canarian species, Lotus assakensis from Africa and Lotus azoricus endemic to the Azores. Biogeographic reconstruction based on a parsimony topology unequivocally identifies an African origin for the Canary Island group with subsequent back dispersal to the African continent and a single dispersal event to the Azores. A phylogeographic assessment of colonization and diversification patterns suggests that geographic isolation via interisland colonization of ecologically similar habitats is the primary mode of species diversification in Canary Island Lotus.

Africa↗

PubMed2003

Phylogenetic significance of morphological characters in the taxonomy of Pestalotiopsis species.

There has been considerable disagreement regarding the relationships among Pestalotiopsis species and their delimitations. A molecular phylogenetic analysis was conducted on 32 species of Pestalotiopsis in order to evaluate the utility of morphological characters currently used in their taxonomy. Phylogenetic relationships were inferred from nucleotide sequences in the ITS regions and 5.8S gene of the rDNA under four optimality criteria: maximum parsimony, weighted parsimony, maximum likelihood, and neighbor joining. Phylogenies estimated from all analyses yielded trees of essentially similar topology and revealed 3 major groups that correspond with morphology-based classification systems. Molecular data indicated that the genus contains two distinct lineages based on pigmentation of median cells and four distinct groupings based on morphology of apical appendages. The analyses did not support reliability of other phenotypic characters of this genus, such as spore dimensions. Characters with particular phylogenetic significance are discussed in relation to the taxonomy of Pestalotiopsis.

Ascomycota↗

PubMed2004

Molecular phylogeny of the nasuta subgroup of Drosophila based on 12S rRNA, 16S rRNA and CoI mitochondrial genes, RAPD and ISSR polymorphisms.

The nasuta subgroup is a cluster of morphologically almost similar forms with a wide range of geographic distribution. During the last three decades nature of inter-relationship among the members has been investigated at different levels of organization. The phylogenetic relationships of the members of the nasuta subgroup of the immigrans species group of Drosophila was made by employing Random Amplified Polymorphic DNA (RAPD), Inter Simple Sequence Repeats-PCR (ISSR-PCR) polymorphisms, mitochondrial 12S rRNA, 16S rRNA and Cytochrome C Oxidase subunit I (CoI) gene sequences. The phylogenetic tree generated by RAPD analysis is in nearly complete congruence with the classification based on morphophenotypic characters. The 12S and 16S rRNA genes were highly conserved across the nasuta subgroup and revealed only 3 and 4 variable sites respectively, of which only one site was informative. The CoI gene, on the other hand, revealed 57 variable sites of which 25 sites were informative. All the three species of orbital sheen complex were included in a major cluster in the phylogenetic trees derived from mitochondrial gene sequence data consistent with the morphophenotypic classification. The CoI analysis placed two species of frontal sheen complex, D. n. nasuta and D. n. albomicans in two different clades and this is inconsistent with morphological classification. The molecular clock suggested that divergence between the kohkoa complex and the albomicans complex occurred approximately 2.2 MYA, indicating recent evolution of the nasuta subgroup. The higher transition bias in the mitochondrial genes reported in the present study also suggested recent evolution of the nasuta subgroup.

Animals↗

PubMed2003

Absorption classification of oral drugs based on molecular surface properties.

The aim of this study was to investigate whether easily calculated and comprehended molecular surface properties can predict drug solubility and permeability with sufficient accuracy to allow theoretical absorption classification of drug molecules. For this purpose, structurally diverse, orally administered model drugs were selected from the World Health Organization (WHO)'s list of essential drugs. The solubility and permeability of the drugs were determined using well-established in vitro methods in highly accurate experimental settings. Descriptors for molecular surface area were generated from low-energy conformations obtained by conformational analysis using molecular mechanics calculations. Correlations between the calculated molecular surface area descriptors, on one hand, and solubility and permeability, on the other, were established with multivariate data analysis (partial least squares projection to latent structures (PLS)) using training and test sets. The obtained models were challenged with external test sets. Both solubility and permeability of the druglike molecules could be predicted with high accuracy from the calculated molecular surface properties alone. The established correlations were used to perform a theoretical biopharmaceutical classification of the WHO-listed drugs into six classes, resulting in a correct prediction for 87% of the essential drugs. An external test set consisting of Food and Drug Administration (FDA) standard compounds for biopharmaceutical classification was predicted with 77% accuracy. We conclude that PLS models of easily comprehended molecular surface properties can be used to rapidly provide absorption profiles of druglike molecules early on in drug discovery.

Administration, Oral↗

PubMed2004

Progress in epidermolysis bullosa: genetic classification and clinical implications.

Epidermolysis bullosa (EB), a heterogenous group of genodermatoses, is characterized by fragility and blistering of the skin associated with extracutaneous manifestations. Based on clinical severity, constellation of the phenotypic manifestations, and the level of tissue separation within the cutaneous basement membrane zone (BMZ), EB has been divided into distinct subcategories. Traditionally, these include the simplex, junctional, and dystrophic forms of EB, and recently attention has been drawn to hemidesmosomal variants demonstrating tissue separation at the level of the hemidesmosomes. Specific mutations in ten distinct genes expressed within the cutaneous BMZ have been delineated in >500 families with different variants of EB. The types of mutations, their positions along the affected genes, and their consequences at the mRNA and protein levels provide explanation for the phenotypic variability and genetic heterogeneity of this group of genodermatoses. Elucidation of mutations in different forms of EB has direct translational applications for improved diagnosis and molecularly based classification with prognostic implications as well as for genetic counseling and DNA-based prenatal testing in families with EB.

Basement Membrane↗

PubMed1993

The respiratory burst oxidase and the molecular genetics of chronic granulomatous disease.

The phagocyte respiratory burst oxidase plays a central role in the inflammatory response. This membrane-bound enzyme complex is comprised of both integral membrane and cytosolic proteins and catalyzes the formation of large quantities of superoxide in response to inflammatory stimuli. While superoxide and its oxidant derivatives normally serve a microbicidal function, excessive or inappropriate release of these products contribute to inflammatory tissue injury. Chronic granulomatous disease (CGD) is a group of inherited disorders characterized by an absent neutrophil respiratory burst, which leads to recurrent and often life-threatening infections in affected patients. The analysis of the specific cellular defects in CGD has been instrumental in the identification and characterization of individual oxidase components. Four distinct genetic subgroups are presently recognized, each involving a different protein essential for respiratory burst oxidase function. This article summarizes recent advances in the characterization of the protein components and cellular biochemistry of the respiratory burst oxidase and reviews the classification and molecular genetics of CGD. The application of these findings to new approaches to the diagnosis and treatment of CGD are also reviewed.

Cytochrome b Group↗

PubMed2005

Classification of wheat low-molecular-weight glutenin subunit genes and its chromosome assignment by developing LMW-GS group-specific primers.

On the basis of sequence analysis, 69 known low-molecular-weight glutenin subunit (LMW-GS) genes were experimentally classified into nine groups by the deduced amino acid sequence of the highly conserved N-terminal domain. To clarify the chromosomal locations of these groups, 11 specific primer sets were designed to carry out polymerase chain reactions (PCR) with the genomic DNA of group 1 ditelosomic lines of Chinese Spring, among which nine primer sets proved to be LMW-GS group-specific. Each group of LMW-GS genes was specifically assigned on a single chromosome arm and hence to a specific locus. Therefore, these results provided the possibility to predict the chromosome location of a new LMW-GS gene based on its deduced N-terminal sequence. The validity of the classification was confirmed by the amplifications in 27 diploid wheat and Aegilops accessions. The length polymorphisms of LMW-GS genes of groups 1 and 2, and groups 3 and 4.1 were detected in diploid A-genome and S-genome accessions, respectively. The diploid wheat and Aegilops species could be used as valuable resources of novel allele variations of LMW-GS gene in the improvement of wheat quality. The nine LMW-GS group-specific primer sets could be utilized to select specific allele variations of LMW-GS genes in the marker-assisted breeding.

Breeding↗

PubMed2002

Molecular and ultrastructural confirmation of classification of ATCC 35122 as a strain of Pirellula staleyi.

A freshwater isolate from Campus Lake, Baton Rouge, LA, USA, strain ATCC 35122 (= ICPB 4362 = Schmidt CLPM White = Tekniepe BT2 white), which had been proposed as a putative reference strain for 'Planctomyces staleyi' (later reclassified as Pirellula staleyi), has been re-examined to establish its relationship to the type strain of Pirellula staleyi, ATCC 27377T. 165 rRNA sequencing confirms its very close relationship to ATCC 27377T and its membership of the order Planctomycetales. Ultrastructural characteristics are also consistent with its membership of the planctomycetes and of the genus Pirellula. These characteristics include polar crateriform structures and the occurrence of the unique internal, single-membrane-bounded compartment enclosing the nucleoid and ribosome-like particles, the pirellulosome, and a polar cap region. Cells of strain ATCC 35122 often displayed pointed, hump-like protrusions opposite each other on the cell, constituting prosthecae, and these were also found to be present on cells of strain ATCC 27377T. The original identification of ATCC 35122 as a strain of Pirellula staleyi is confirmed on both molecular and phenotypic grounds.

Bacteria↗

PubMedDate not supplied

Tissue microarrays for high-throughput molecular pathology.

Modern research technologies, including DNA, protein, and antibody microarrays identify a steadily growing number of clues that are useful in molecular disease classification, drug development, and the prediction of response to treatment. Subsequent validation of the clinical importance of such candidate genes or proteins requires large-scale analysis of human tissues. To date, this analysis constitutes an important bottleneck in the process of discovery because tissue analysis by the conventional slide-by-slide strategy is slow and expensive. To overcome these limitations, tissue microarray (TMA) technology has been developed. TMA allows for the simultaneous analysis of up to 1,000 tissue samples in a single experiment, using all types of in-situ analyses including immunohistochemistry (IHC), fluorescence in situ hybridization (FISH), and RNA in situ hybridization (RNA-ISH). TMA technology has the potential to greatly facilitate the translation of basic research into clinical practice. Potential applications include the establishment of associations between molecular changes and clinical endpoints, testing of potential therapeutic targets using tissue samples from specific cancer patients, standardization of molecular detection of targets, and rapid translation of results from cell lines and animal models to human cancer. Because of its beneficial economic aspects and ability to differentiate ethnic differences in tumor biology, TMA applications may become particularly important in developing countries.

Developing Countries↗

PubMed2005

Molecular pathogenesis and a consequent classification of multiple myeloma.

There appear to be two pathways involved in the pathogenesis of premalignant non-immunoglobulin M (IgM) monoclonal gammopathy of undetermined significance (MGUS) and multiple myeloma (MM). Nearly half of tumors are nonhyperdiploid, and mostly have one of five recurrent IgH translocations: 16% 11q13 (CCN D1), 3% 6p21 (CCN D3), 5% 16q23 (MAF), 2% 20q12 (MAFB), and 15% 4p16 (FGFR3 and MMSET). The remaining hyperdiploid tumors have multiple trisomies involving chromosomes 3, 5, 7, 9, 11, 15, 19, and 21, and infrequently one of these five translocations. Although cyclin D1 is not expressed by healthy lymphoid cells, it is bi-allelically dysregulated in a majority of hyperdiploid tumors. Virtually all MM and MGUS tumors have dysregulated and/or increased expression of cyclin D1, D2, or D3, providing an apparent early, unifying event in pathogenesis. The patterns of translocations and cyclin D expression (TC) define a novel classification that includes eight groups: 11q; 6p; MAF; 4p; D1 (34%); D1+D2 (6%); D2 (17%); and none (2%). The hyperdiploid D1 group is virtually absent in extramedullary MM and MM cell lines, suggesting a particularly strong dependence on interaction with the bone marrow microenvironment. Despite shared progression events (RAS mutations, MYC dysregulation, p53 mutations, and additional disruption of the retinoblastoma pathway), the phenotypes of MGUS and MM tumors in the eight TC groups is determined mainly by early oncogenic events. Similar to acute lymphocytic leukemia, MM seems to include several diseases (groups) that have differences in early or initiating events, global gene expression patterns, bone marrow dependence, clinical features, prognosis, and response to therapy.

Biopsy, Needle↗

PubMed2004

New satellite DNA in Lacerta s. str. lizards (Sauria: Lacertidae): evolutionary pathways and phylogenetic impact.

A new tandemly repeated (satellite) DNA family namely Agi160, from Lacerta agilis and Lacerta strigata (Lacerta sensu stricto (s. str.), Linnaeus 1758) have been cloned and sequenced. Agi160 is found in the above two species, as well as two other representatives of the same genus, L. viridis and L. media. DNA hybridization did not reveal it in Darevskia, Podarcis, Zootoca, Eremias, Ophisops, and Gallotia - the other genera of the family Lacertidae. The results suggest that Agi160 is a Lacerta s. str. specific family of tandem DNA repeats. However, a comparison between sequences of Agi160 and CLsat repeat units revealed 60 bp regions 62-74% identical. The latter is a satellite DNA family typical for Darevskia (syn. "L. saxicola complex") (Grechko et al., Molecular-genetic classification and phylogenetic relatedness of some species of Lacertidae lizards by taxonoprint data. Mol Biol 32:172-183, 1988.). Both Agi160 and CLsat tandem repeats share several common features (e.g., the same AT content and distribution of multiple short A-T runs, internal structure of repeated units, the presence of conservative regions). These data are indicative of their common origin and a possibly strong selective pressure upon conserving both satellites. A comparative analysis of structure, organization, and abundance of these two families of satDNA reveals evolutionary pathways that led to their formation and divergence. The data are consistent with the hypotheses of the concerted evolution of satellite DNA families. The possibility of use of Agi160 as a phylogenetic tool, defining relationships within Lacerta s. str., as well as within the whole family of Lacertidae is discussed.

Animals↗

PubMed1997

Pathogenetic and clinical implications of Bcl-6 and Bcl-2 gene configuration in nodal diffuse large B-cell lymphomas.

Bcl-6 (LAZ-3) and Bcl-2 gene rearrangements have been respectively reported in 20-35 per cent and 10-25 per cent of diffuse large B-cell lymphomas (DLBCLs). Although these genetic lesions have been associated with different clinical outcomes (i.e., more favourable in Bcl-6 rearranged cases and poorer in Bcl-2 rearranged cases), their prognostic significance is still controversial. In the present study, we have investigated by Southern blot analysis the Bcl-6 and Bcl-2 gene configuration in a series of 80 lymph nodes involved by well-characterized DLBCLs, histologically defined according to the REAL and the updated Kiel classifications. The molecular findings have been correlated with the clinical features at presentation and with response to therapy. The majority of cases (57/80 = 71.2 per cent) had a centroblastic morphology. Bcl-6 rearrangements were detected in 23/80 cases (28.8 per cent), and were similarly associated with centroblastic (18/57 = 31.6 per cent) or immunoblastic (3/11 = 27.3 per cent) histotypes. In contrast, Bcl-2 was found to be rearranged in only three cases of centroblastic lymphoma (3.8 per cent). No significant differences were found between Bcl-6 rearranged and germline cases, as far as the clinical features at presentation are concerned. Forty-one patients, in whom the lymph node biopsy was performed at diagnosis, could be evaluated for response to treatment and clinical outcome. Most of these cases (30/41 = 73.2 per cent) were nodal DLBCL, without extranodal site involvement. Analysis of the clinical outcome showed no statistically significant differences between Bcl-6 rearranged and Bcl-6 germline cases (actuarial overall survival 50 per cent vs. 48 per cent, event-free survival 45 per cent vs. 46 per cent, at 4 years). These findings confirm that Bcl-6 rearrangements are the most frequent genetic lesion in DLBCL. The incidence of Bcl-2 involvement in our series is significantly lower than the figures reported in other studies, mainly from North American countries, probably reflecting heterogeneous patient selection and/or epidemiological variability. Finally, our results suggest that no relevant clinical differences are observed between Bcl-6 rearranged and Bcl-6 germline cases, when nodal DLBCLs are considered.

Adolescent↗