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PubMed1991

Resonant recognition model and protein topography. Model studies with myoglobin, hemoglobin and lysozyme.

This study describes the further extension of the resonant recognition model for the analysis and prediction of protein--protein and protein--DNA structure/function dependencies. The model is based on the significant correlation between spectra of numerical presentations of the amino acid or nucleotide sequences of proteins and their coded biological activity. According to this physico-mathematical method, it is possible to define amino acids in the sequence which are predicted to be the most critical for protein function. Using sperm whale myoglobin, human hemoglobin and hen egg white lysozyme as model protein examples, sets of predicted amino acids, or so-called 'hot spots', have been identified within the tertiary structure. It was found for each protein that the predicted 'hot spots', which are distributed along the primary sequence, are spatially grouped in a dome-like arrangement over the active site. The identified amino acids did not correspond to the amino acid residues which are involved in the chemical reaction site of these proteins. It is thus proposed that the resonant recognition model helps to identify amino acid residues which are important for the creation of the molecular structure around the catalytic active site and also the associated physical field conditions required for biorecognition, docking of the specific substrate and full biological activity.

Animals↗
PubMed2026

Follicular Lymphoma Transformation is Characterized by Cytokine-associated Remodeling of Stromal and Macrophage Compartments.

Across cancer, one of the most frequent examples of histologic transformation is the evolution of follicular lymphoma (FL) to an aggressive large cell lymphoma. Despite recent progress, understanding of the molecular and cellular underpinnings of transformation remains incomplete. Here, we dissect the interplay of tumor and microenvironment cell populations across transformation through a multimodal investigation of 95 FL and transformed FL (tFL) samples, including single-cell and bulk RNA-sequencing alongside spatial transcriptomics and proteomics, and validate findings across independent FL-tFL pairs. Upon transformation, fibroblasts and GPNMB+ macrophages increase while lymph-node organizing follicular dendritic and CCL21+ fibroblastic reticular cells were lost, resulting in an altered spatial distribution of cytokines that impacts T cell infiltration and macrophage differentiation and function. Secreted stromal and macrophage signals were further evident by non-invasive plasma proteomics. Taken together, our data reveal expansion of macrophages and fibroblasts as key features of transformation with potential diagnostic and therapeutic implications.

Journal Article↗
PubMed2026

The extracellular matrix in cancer-associated fibrosis: molecular mechanisms and clinical relevance.

The ECM is a dynamic component of the tumor microenvironment with a critical role in cancer progression, invasion, metastasis, immune exclusion, and response to therapy. Recent advances in proteomic analyses investigating the insoluble ECM fractions (termed "matrisome analysis"), along with single-cell RNA sequencing and spatial transcriptomics, have revealed cancer-specific patterns of ECM remodeling. These studies have identified a panel of recurrently upregulated ECM proteins, including annexin A1, fibrillin-1, fibronectin, periostin, and tenascin-C, actively contributing to tumor growth, invasion, angiogenesis, and immune exclusion. The expression of the cancer-associated ECM is largely driven by cancer-associated fibroblasts (CAFs), whose molecular diversity has been dissected through single-cell profiling and consolidated in emerging CAF atlases across cancers. By investigating the matrisome composition and CAF heterogeneity, these studies have unraveled the pivotal role of the stroma in shaping tumor biology. Based on these discoveries, ECM proteins and CAFs are now being explored as biomarkers and therapeutic targets. Future integration of multi-omics datasets with clinical outcomes will help to translate these insights into novel biomarkers for patient stratification and stroma-directed therapeutic interventions.

Humans↗
PubMed1998

Muscle and tendon morphogenesis in the avian hind limb.

The proper development of the musculoskeletal system in the tetrapod limb requires the coordinated development of muscle, tendon and cartilage. This paper examines the morphogenesis of muscle and tendon in the developing avian hind limb. Based on a developmental series of embryos labeled with myosin and tenascin antibodies in whole mount, an integrative description of the temporal sequence and spatial pattern of muscle and tendon morphogenesis and their relationship to cartilage throughout the chick hind limb is presented for the first time. Anatomically distinct muscles arise by the progressive segregation of muscle: differentiated myotubes first appear as a pair of dorsal and ventral muscle masses; these masses subdivide into dorsal and ventral thigh, shank and foot muscle masses; and finally these six masses segregate into individual muscles. From their initial appearance, most myotubes are precisely oriented and their pattern presages the pattern of future, individual muscles. Anatomically distinct tendons emerge from three tendon primordia associated with the major joints of the limb. Contrary to previous reports, comparison of muscle and tendon reveals that much of their morphogenesis is temporally and spatially closely associated. To test whether reciprocal muscle-tendon interactions are necessary for correct muscle-tendon patterning or whether morphogenesis of each of these tissues is autonomous, two sets of experiments were conducted: (1) tendon development was examined in muscleless limbs produced by coelomic grafting of early limb buds and (2) muscle development was analyzed in limbs where tendon had been surgically altered. These experiments demonstrate that in the avian hind limb the initial morphogenetic events, formation of tendon primordia and initial differentiation of myogenic precursors, occur autonomously with respect to one another. However, later morphogenetic events, such as subdivision of muscle masses and segregation of tendon primordia into individual tendons, do require to various degrees reciprocal interactions between muscle and tendon. The dependence of these later morphogenetic events on tissue interactions differs between different proximodistal regions of the limb.

Animals↗
PubMed1999

Conformational difference between nuclear and cytoplasmic actin as detected by a monoclonal antibody.

Using a reconstituted complex of profilin and skeletal muscle actin as an antigen, we generated a monoclonal mouse antibody against actin, termed 2G2. As revealed by immunoblots of proteolytic actin fragments and by pepscan analysis, the antibody recognises a nonsequential epitope on actin which is located within three different regions of the sequence, consisting of aa131-139, aa155-169, and aa176-187. In the actin model derived from X-ray diffraction, these sequences lie spatially close together in the region of the nucleotide-binding cleft, but do not form a coherent patch. In immunoblots, 2G2 reacts with all SDS-denatured actin isoforms and with actins of many vertebrates. In contrast, its immunofluorescence reactivity is highly selective and fixation-dependent. In fibroblasts and myogenic cells, fixed and extracted by formaldehyde/detergent, stress fibres or myofibrils, respectively, remained unstained. Likewise, after microinjection into living cells, 2G2 did not bind to such microfilament bundles. Extraction of myosin and tropomyosin did not alter this pattern indicating that the lack in reactivity is probably not due to epitope-masking by actin-binding proteins. More likely, the reason for the lack of reactivity with filamentous actin is that its epitope is not accessible in F-actin. However, the antibody revealed a distinct pattern of nuclear dots in differentiated myogenic cells but not in myoblasts, and of fibrillar structures in nuclei of Xenopus oocytes. In contrast, after methanol treatment, a 2G2-specific staining of stress fibres and myofibrils was observed, but no nuclear dot staining. We conclude that 2G2, in addition to binding to SDS- and methanol-denatured actin, recognises a specific conformation of native actin which is present in the nucleus and specified by compaction of the antibody-reactive region into a coherent patch. This conformation is apparently present in differentiated myogenic cells and oocytes, but not in cytoplasmic actin filament bundles.

Actins↗
PubMed1994

Robust physics-based analysis of thermal and visual imagery.

Extensions to an existing physics-based approach for intersensory perception in which thermal and visual imagery of outdoor scenes is analyzed simultaneously for object recognition are discussed. The existing approach uses a model that is based on the principle of the conservation of energy at the surface of the imaged object. The model permits the computation of physically meaningful features that may be used for object classification. Two significant extensions are discussed. First, the model is used to analyze a temporal sequence of spatially registered thermal and visual imagery. Second, the energy-exchange model is used to formulate a linear-regression task in which the physical properties of the imaged object are the unknown parameters that are estimated. A statistically robust scheme is presented for this task. The robust technique minimizes sensitivity to outliers caused by segmentation errors and misregistration, which are endemic to multisensor fusion. Thus reliable physics-based features are made available by this approach.

Hot Temperature↗
PubMed2026

Microplastics and nanoplastics-related genes signature predicts prognosis in pancreatic ductal adenocarcinoma and functional validation of interleukin 1 alpha.

BACKGROUND: Microplastics and nanoplastics (MNPs), as emerging environmental pollutants, have garnered significant attention from the global scientific community due to their potential threats to human health, particularly their association with the occurrence and development of cancer. The goal of our study is to create a predictive marker for pancreatic ductal adenocarcinoma (PAAD) based on MNPs-related genes, with the purposes of predicting survival outcomes and assessing the tumor immune microenvironment. METHODS: Using multi-cohort data from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), and International Cancer Genome Consortium (ICGC), we assessed the association between MNPs and PAAD prognosis through the Xiantao Academic (https://www.xiantao.love/). The development of a prognostic signature was followed by an assessment of its significance through the Kaplan-Meier method, time-dependent receiver operating characteristic (ROC), and decision curve analysis (DCA). The validity of the risk model was confirmed through the ICGC and GSE71729 cohorts. The model was then assessed for levels of tumor immune infiltration. To explore MNPs-related genes expression characteristics within immune cells in PAAD, we performed single-cell RNA sequencing and spatial transcriptomics analysis through the Sparkle Platform (https://grswsci.top/). Finally, in vitro experiments were conducted to investigate the biological function of interleukin 1 alpha (IL1A). RESULTS: A four-gene signature comprising XDH, IL1A, KIF20A, and ASPM, based on MNPs, was developed to stratify PAAD patients into two distinct risk groups. The high-risk group showed a significantly poorer prognosis. A similar trend was verified in the external cohorts ICGC and GSE71729. The signature risk score affected immune cell infiltration in the PAAD microenvironment. The infiltration of B cells, CD8+ T cells, cytotoxic cells, immature dendritic cells (iDCs), mast cells, plasmacytoid dendritic cell (pDC), T cells, Tem cells, T follicular helper (TFH) cells, and T helper 17 (Th17) cells had a positive correlation with the low-risk group. In contrast, high-risk patients tended to have increased number of T helper (Th2) cells and higher expression of SIGLEC15, CD274, IGSF8. Knockdown of IL1A in PAAD cells inhibited their tumor proliferation ability in vitro. CONCLUSIONS: Using MNPs-related genes, we built a prognostic model for PAAD, revealing that patients with high-risk scores are likely to have a worse prognosis. This model is designed to develop personalized treatment strategies tailored to the specific needs of each patient, thereby improving clinical outcomes for PAAD patients. Furthermore, IL1A could be a promising therapeutic candidate for PAAD.

Microplastics↗
PubMed1999

Molecular surface sequence analysis of several E. coli enzymes and implications for existence of casein kinase-2 bacterial predecessor.

Casein kinase-2 (CK2) is known as pleiotropic eukaryotic protein kinase that phosphorylates significant number of cellular proteins. Not all functions of the protein were registered up to the present time. However, it is known that this Ser/Thr-specific kinase is involved in the cell cycle progression and is essentially required for the eukaryotic cell viability. Fully automated molecular surface analysis procedure for identification of functionally significant surface residues and sequences on the base of protein spatial structure was elaborated. Using the elaborated procedure, several E. coli enzymes spatial structures and sequences were investigated. It was found that most of the casein kinase 2 potential sites found in sequences of enzymes are accessible for modification. Four of the 5 structures studied have CK2 consensus sites that may definitely influence the activity of the enzyme upon phosphorylation. Some of the potential "CK2-sites" has amino acid contents characteristic for physiological substrates of casein kinase 2 in eukaryotes. The main point of the elaborated method and the structural evidence for existence of a putative casein kinase E. coli predecessor or a protein with similar kinase activity are discussed. Physiological, biochemical, structural and evolutionary aspects of the existence of the putative predecessor are considered.

Adenylate Kinase↗
PubMed2026

Targeting USP22 reprograms the tumor microenvironment and sensitizes KRAS/p53-driven lung cancer to anti-PD-1 immunotherapy.

RATIONALE: Ubiquitin-specific peptidase 22 (USP22), a deubiquitinase and component of the "Death-from-Cancer" 11-gene signature, is overexpressed in multiple malignancies and linked to recurrence, therapy resistance, and poor prognosis. Its role in KRAS/p53-driven lung cancer and the response to immune checkpoint inhibitors (ICIs) remains poorly defined. Here, we investigated USP22 as a potential therapeutic target in KRAS/p53-driven lung cancer. METHODS: A conditional Usp22 knockout (Usp22-KO) was generated in the KRASG12D; p53-/- (KP) mouse model. Cancer progression was monitored by micro-computed tomography (micro-CT). Multiplex immunofluorescence (mIF), RNA sequencing, and spatial transcriptomics profiled cancer and tumor microenvironment (TME) changes. Responses to anti-PD-1/PD-L1 therapies were compared between KP and Usp22-KO KP (KPU-) lung cancers. RESULTS: USP22 was highly expressed in early-stage KRAS/p53-driven mouse lung cancers and strongly correlated with proliferation marker Ki67. Usp22 deletion suppressed cancer growth, prolonged survival, and promoted cancer differentiation. Spatial transcriptomics and mIF revealed reduced CD206+ M2 macrophages, myeloid-derived suppressor cells (MDSCs), TGF-β1, and angiogenesis, along with increased functional CD8+ T cells. Mechanistically, USP22 regulated gene expression and protein stability, reducing c-Myc, PD-L1, TGF-β1, and SPARC upon Usp22 loss. Compared with KP cancer, KPU- and SPARC-knockdown KP cancers showed reduced macrophage chemotaxis and impaired basal- and TGF-β1-induced M2 polarization of RAW264.7 cells, suggesting that TGF-β1 and SPARC downregulation partially contributes to decreased M2 macrophage infiltration in KPU- cancers. Notably, Usp22 loss enhanced the efficacy of anti-PD-L1 and anti-PD-1 therapies in orthotopic and subcutaneous KP lung cancer models, respectively. USP22 and SPARC expression were also strongly correlated in human lung cancers. CONCLUSIONS: USP22 promotes progression and immune evasion in KRAS/p53-driven lung cancer. Targeting USP22 reprograms the TME, suppresses oncogenic signaling, and sensitizes tumors to ICI, establishing USP22 as a promising therapeutic target.

Animals↗
PubMed1988

[Circahoral rhythms of the skin biopotentials outside of digestion and their relationship to the periodic motility of the gastrointestinal tract].

Circahoral rhythms of the skin surface potentials recorded simultaneously with periodic motor activity of stomach in 4 dogs and 7 healthy subjects revealed the rhythms to be an electrophysiological equivalent of the latter in dogs. A "migration" of the group potentials in a certain spatial-temporal sequence was observed among the leads. It corresponded to the cycles of periodic motor activity of the stomach in dogs. The circahoral rhythms are a major topic for research in humans, too.

Adult↗
PubMed1984

Models for positional signalling, the threefold subdivision of segments and the pigmentation pattern of molluscs.

Models of biological pattern formation are discussed. The regulatory features expected from the models are compared to those observed experimentally. It will be shown that: (i) Stable gradients appropriate to supply positional information can be produced by local autocatalysis and long-range inhibition. (ii) Spatially ordered sequences of differentiated cell states can emerge if these cell states mutually activate each other on long range but exclude each other locally. Segmentation results from the repetition of three such cell states, S, A and P (and not of only two, as is usually assumed). With a repetition of three states, each segment has a defined polarity. The confrontation of P cells and S cells lead to the formation of a segment border (...P/SAP/SAP/S...) while the A-P confrontation is a prerequisite for appendage formation. Mutations of Drosophila affecting larval segmentation are discussed in terms of this model. (iii) The two models for the generation of sequences of structures in space (positional information including interpretation versus mutual activation) lead to different predictions with respect to intercalary regeneration. This allows a distinction between the two models on the basis of experiments. (iv) The pigmentation patterns of certain molluscs emerge from a coupled oscillation of cells (that is, a lateral inhibition in time, instead of space). The oblique lines result from a chain of triggering events.

Animals↗
PubMedDate not supplied

[Participation of the hippocampus in delayed spatial choice and discrimination of time intervals in rhesus macaques].

Participation of the hippocampus in morpho-functional systems of delayed spatial choice and differentiation of trace reflexes to time was shown in 2 macaco rhesus by the method of phase-correlational analysis. Application of 0.05 per cent solution of amysyl into the hippocampus disturbed the behaviour of monkeys, probably, as a result of desintegration of entire morpho-functional system regulating spatial-temporal sequence of nervous processes of delayed behavioural act.

Animals↗
PubMed1996

[Genetic control of limb development].

Vertebrate limbs are an amazing example of successful adaptation to various environmental conditions. In higher vertebrates, forelimbs help to fly, swim, walk, dig, grasp or play the Passacaille, yet their basic structure (the sequence and spatial arrangement of bony elements) is always the same. This implies the existence of a unique developmental strategy for building a limb (a limb plan) that imposes early on a basic scheme, on the top of which subsequent species-specific customizations will occur. The description of such a universal limb plan, hence the idea that the genetic and developmental processes that generate this plan are very ancient, has been controversial for about a century. It is worth asking whether recent discoveries of important genes involved in these processes can bring novel arguments to the debate.

Animals↗
PubMed1997

[Control of limb morphogenesis by the Hox genes].

Vertebrate limbs are an amazing example of successful adaptation to various environmental conditions. In higher vertebrates, forelimbs help to fly, swim, walk, dig or grasp, yet their basic structure (the sequence and spatial arrangement of bony elements) is always the same. This implies the existence of a unique developmental strategy for building a limb (a limb plan) that imposes early on a basic scheme, on the top of which subsequent species-specific customizations will occur. The description of such a universal limb plan, hence the idea that the genetic and developmental processes that generate this plan are very ancient, has been controversial for about a century. It is worth asking whether recent discoveries of important genes involved in these processes can bring novel arguments to the debate.

Animals↗
PubMed1998

Regulation of alternative processing of the sarco/endoplasmic reticulum Ca2+ ATPase (SERCA2) gene transcripts during muscle differentiation.

The Ca2+ transport ATPases of the sarcoplasmic or endoplasmic reticulum (SERCA) mediate the uptake of Ca2+ into intracellular stores. These Ca2+ pumps are encoded by three different genes. Alternative processing of the SERCA2 messenger generates two different protein isoforms. These two isoforms differ in their C-terminal part and this divergence is responsible for the functional difference between SERCA2a and SERCA2b. The aim of this study was to characterise the cis-active elements and the trans-acting factors required for the generation of the muscle-specific messenger during myogenic differentiation. A competition model between muscle-type splicing and non-muscle polyadenylation was excluded as inactivation of the non-muscle polyadenylation site did not induce muscle-type splicing in non-muscle or in undifferentiated muscle cells. We therefore propose that the expression of the SERCA2a isoform is due to the regulation of the muscle-specific splice process during myogenic differentiation. We characterised the spatial and sequence requirements essential for tissue-specific transcript processing. It was demonstrated that the processing signals in the transcript, i.e. both donor splice sites and the polyadenylation site located in the muscle-specific intron, have to be weak. An exception to this rule is the 3' acceptor splice site that has to be strong in order to get muscle-specific splicing. We also found an inverse relationship between intron length and splice efficiency as shortening the terminal intron resulted in muscle-specific splicing in non-muscle and in undifferentiated muscle cells. Finally, it was demonstrated that sequences around the muscle-specific acceptor region as well as in the muscle-specific exon are required to prevent muscle-specific splicing in undifferentiated muscle cells. Especially a region upstream of the 3' acceptor contains important sequence information required for the inhibition of muscle-specific splicing. It was demonstrated that the trans-acting factors regulating the alternative SERCA2 splicing are muscle specific. First, myogenin, a transcription factor that plays a key role in muscle differentiation, induced muscle-specific SERCA2 splicing in a fibroblast cell line. Second, changes in general splice and polyadenylation efficiency, as observed during B-cell maturation, did not affect SERCA2 splicing. Finally, expression and overexpression studies did not support the hypothesis that changes in the level of the alternative splice factor ASF or other arginine and serine rich proteins are involved in the regulation of muscle-specific splicing. We conclude that muscle-specific SERCA2a expression is a tightly regulated process dependent on the inhibition of the muscle-specific splice process at the 3' end of the primary transcript. During differentiation this inhibition is overcome by the downregulation of an inhibitory factor and/or the expression of a positive trans-acting factor.

Animals↗
PubMed1988

A pattern formation mechanism to control spatial organization in the embryo of Drosophila melanogaster.

It is known that cells are already committed to a particular segment at the cellular blastoderm stage during embryogenesis of Drosophila melanogaster. Recently, several segmentation genes have been observed to be expressed in a sequence of banded spatial patterns in the syncytial blastoderm, prior to the formation of the cellular blastoderm. It is demonstrated in this paper that a two component reaction-diffusion (RD) system with net production functions which are antisymmetric with respect to the uniform steady-state values, is capable of producing a sequence of seven spatial patterns in the syncytial blastoderm. The sequence of patterns obtained exhibit a strong preference for banded or striped patterns. The first pattern is a simple anteroposterior gradient while the second is a gradient in the dorsoventral direction. The next five patterns are a sequence of banded patterns which exhibit frequency doubling, i.e. the number of bands in each pattern tend to be double the number in the previous pattern. The predicted pattern sequence is comparable to that observed in the expression of some segmentation genes. It is suggested that a pattern formation mechanism based on such an RD system may exist in the embryo where it produces a sequence of prepatterns to regulate the expression of various segmentation genes leading ultimately to a segmented embryo. There is sufficient spatial information in the sequence of banded prepatterns for the segments to be unique.

Animals↗
PubMed1992

Perceptual and academic patterns of learning-disabled/gifted students.

This research explored ways gifted children with learning disabilities perceive and recall auditory and visual input and apply this information to reading, mathematics, and spelling. 24 learning-disabled/gifted children and a matched control group of normally achieving gifted students were tested for oral reading, word recognition and analysis, listening comprehension, and spelling. In mathematics, they were tested for numeration, mental and written computation, word problems, and numerical reasoning. To explore perception and memory skills, students were administered formal tests of visual and auditory memory as well as auditory discrimination of sounds. Their responses to reading and to mathematical computations were further considered for evidence of problems in visual discrimination, visual sequencing, and visual spatial areas. Analyses indicated that these learning-disabled/gifted students were significantly weaker than controls in their decoding skills, in spelling, and in most areas of mathematics. They were also significantly weaker in auditory discrimination and memory, and in visual discrimination, sequencing, and spatial abilities. Conclusions are that these underlying perceptual and memory deficits may be related to students' academic problems.

Achievement↗