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1.
Bone Rep ; 20: 101731, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38226334

RESUMO

X-linked hypophosphatemia (XLH) is a rare X-linked dominant inherited disorder caused by loss-of-function variants in the PHEX gene and characterized by renal phosphate wasting, hypophosphatemia, abnormal vitamin D metabolism, growth retardation and lower limb deformities. We describe a case of XLH-rickets in a 7-year-old girl with scaphocephaly, Chiari syndrome type I and syringomyelia, with a de novo non-canonical splice variant (c.1080-3C > G) in intron 9 of the PHEX gene, that has not been previously described.

2.
J Anat ; 244(1): 42-62, 2024 01.
Artigo em Inglês | MEDLINE | ID: mdl-37737476

RESUMO

Sturgeons belong to the family Acipenseridae, the most species-rich extant family of Acipenseriformes, a basal actinopterygian group of key importance in assessing the early radiations of the actinopterygians. At the same time, acipenseriforms display unique specializations in the morphology of the snout and jaws which make them a valuable model for studying evolutionary novelties. However, despite a long history of research, the homologies of the snout and the mandibular arch of acipenseriforms remain uncertain preventing further studies on the evolutionary origin of their unique snout and jaw structure, and in particular, of the upper jaw symphysis, the key apomorphy of the group and the preoral snout. In the present study, a detailed description of the upper jaw morphology and development in sturgeons is provided in order to address its composition in terms of the common actinopterygian archetype. Based on the obtained results, the upper jaw of acipenseriforms is assumed to have lost the autopalatine portion, which most likely is represented by the separate cartilages supporting the tentacles. Also, the conventional interpretation of the sturgeon's maxilla as dermopalatine is rejected on the grounds of this bone structure and development. Paedomorphosis is proposed to be the most likely mechanism explaining the evolutionary origin of the upper jaw symphysis and supposed modifications of the snout in sturgeons.


Assuntos
Arcada Osseodentária , Maxila , Animais , Maxila/anatomia & histologia , Arcada Osseodentária/anatomia & histologia , Evolução Biológica , Peixes/anatomia & histologia , Articulações , Cartilagem
3.
Life (Basel) ; 13(5)2023 May 17.
Artigo em Inglês | MEDLINE | ID: mdl-37240848

RESUMO

The Cercopithecini tribe includes terrestrial and arboreal clades whose relationships are controversial, with a high level of chromosome rearrangements. In order to provide new insights on the tribe's phylogeny, chromosome painting, using the complete set of human syntenic probes, was performed in Cercopithecus petaurista, a representative species of the Cercopithecini tribe. The results show C. petaurista with a highly rearranged karyotype characterized by the fission of human chromosomes 1, 2, 3, 5, 6, 8, 11, and 12. These results compared with the literature data permit us to confirm the monophyly of the Cercopithecini tribe (fissions of chromosomes 5 and 6), as previously proposed by chromosomal and molecular data. Furthermore, we support the monophyly of the strictly arboreal Cercopithecus clade, previously proposed by the molecular approach, identifying chromosomal synapomorphies (fissions of chromosomes 1, 2, 3, 11, 12). We also add additional markers that can be useful for deciphering arboreal Cercopithecini phylogeny. For example, the fission of chromosome 8 is synapomorphy linking C. petaurista, C. erythrogaster, and C. nictitans among the arboreal species. Finally, a telomeric sequence probe was mapped on C. petaurista, showing only classic telomeric signals and giving no support to a previous hypothesis regarding a link between interspersed telomeric sequences in high rearranged genomes.

4.
Bone ; 172: 116763, 2023 07.
Artigo em Inglês | MEDLINE | ID: mdl-37059315

RESUMO

X-linked hypophosphatemia is the most common cause of inherited rickets, due to inactivating variants of PHEX. More than 800 variants have been described to date and one which consists of a single base change in the 3' untranslated region (UTR) (c.*231A>G) is reported as prevalent in North America. Recently an exon 13-15 duplication has been found to occur in concert with the c.*231A>G variant, and thus it is unclear whether the pathogenicity is solely a function of the UTR variant. We present a family with XLH who harbors the exon 13-15 duplication but does not carry the 3'UTR variant, providing evidence that the duplication itself is the pathogenic variant when these two variants are found in cis.


Assuntos
Raquitismo Hipofosfatêmico Familiar , Doenças Genéticas Ligadas ao Cromossomo X , Hipofosfatemia , Humanos , Raquitismo Hipofosfatêmico Familiar/genética , Raquitismo Hipofosfatêmico Familiar/patologia , Endopeptidase Neutra Reguladora de Fosfato PHEX/genética , Éxons/genética , Regiões 3' não Traduzidas , Hipofosfatemia/genética , Mutação
5.
Genome Biol Evol ; 15(3)2023 03 03.
Artigo em Inglês | MEDLINE | ID: mdl-36790109

RESUMO

Kinetochores connect chromosomes to spindle microtubules to ensure their correct segregation during cell division. Kinetochores of human and yeasts are largely homologous, their ability to track depolymerizing microtubules, however, is carried out by the nonhomologous complexes Ska1-C and Dam1-C, respectively. We previously reported the unique anti-correlating phylogenetic profiles of Dam1-C and Ska-C found among a wide variety of eukaryotes. Based on these profiles and the limited presence of Dam1-C, we speculated that horizontal gene transfer could have played a role in the evolutionary history of Dam1-C. Here, we present an expanded analysis of Dam1-C evolution, using additional genome as well as transcriptome sequences and recently published 3D structures. This analysis revealed a wider and more complete presence of Dam1-C in Cryptista, Rhizaria, Ichthyosporea, CRuMs, and Colponemidia. The fungal Dam1-C cryo-EM structure supports earlier hypothesized intracomplex homologies, which enables the reconstruction of rooted and unrooted phylogenies. The rooted tree of concatenated Dam1-C subunits is statistically consistent with the species tree of eukaryotes, suggesting that Dam1-C is ancient, and that the present-day phylogenetic distribution is best explained by multiple, independent losses and no horizontal gene transfer was involved. Furthermore, we investigated the ancient origin of Dam1-C via profile-versus-profile searches. Homology among 8 out of the 10 Dam1-C subunits suggests that the complex largely evolved from a single multimerizing subunit that diversified into a hetero-octameric core via stepwise subunit duplication and subfunctionalization of the subunits before the origin of the last eukaryotic common ancestor.


Assuntos
Cinetocoros , Proteínas de Saccharomyces cerevisiae , Humanos , Proteínas Associadas aos Microtúbulos/genética , Filogenia , Microtúbulos , Divisão Celular , Proteínas de Ciclo Celular/genética , Proteínas de Saccharomyces cerevisiae/genética , Proteínas Cromossômicas não Histona/genética
6.
Brain Struct Funct ; 228(1): 47-61, 2023 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-35695934

RESUMO

The angular gyrus roughly corresponds to Brodmann's area 39, which is a multimodal association brain region located in the posterior apex of the human inferior parietal lobe, at its interface with the temporal and occipital lobes. It encompasses two cyto- and receptor architectonically distinct areas: caudal PGp and rostral PGa. The macaque brain does not present an angular gyrus in the strict sense, and the establishment of homologies was further hindered by the fact that Brodmann defined a single cytoarchitectonic area covering the entire guenon inferior parietal lobule in the monkey brain, i.e. area 7. Latter architectonic studies revealed the existence of 6 architectonically distinct areas within macaque area 7, further connectivity and functional imaging studies supported the hypothesis that the most posterior of these macaque areas, namely Opt and PG, may constitute the homologs of human areas PGp and PGa, respectively. The present review provides an overview of the cyto-, myelo and receptor architecture of human areas PGp and PGa, as well as of their counterparts in the macaque brain, and summarizes current knowledge on the connectivity of these brain areas. Finally, the present study elaborates on the rationale behind the definition of these homologies and their importance in translational studies.


Assuntos
Macaca , Lobo Parietal , Animais , Humanos , Vias Neurais , Lobo Parietal/diagnóstico por imagem , Lobo Occipital , Sistema Límbico , Mapeamento Encefálico
7.
Endocr J ; 68(9): 1135-1141, 2021 Sep 28.
Artigo em Inglês | MEDLINE | ID: mdl-33907069

RESUMO

X-linked hypophosphatemic rickets (XLH) is primarily characterized by renal phosphate wasting with hypophosphatemia, short stature, and bone deformity of the leg. Here we present a male case of XLH with relatively mild bone deformity caused by a mosaic mutation of the phosphate-regulating gene with homologies to endopeptidases on the X chromosome (PHEX). Polymerase chain reaction (PCR) direct sequencing revealed a novel in-frame deletion, NM-000444.6:c.671-685del p.Gln224-Ser228del, at exon 6 in PHEX as a mosaic pattern. This mutation was not found in any database and may result in a significant change in higher-order protein structure and function. TA cloning of the PCR product and clone sequencing estimated the mutation allele frequency at 21%. Literature review of the previously reported three cases with novel mosaic mutations in PHEX, together with the present case, suggests that the rates of the mutation allele correlate with phenotype severity to some extent. We initially treated him with nutritional vitamin D supplements and phosphate salts. However, to avoid the development of secondary/tertiary hyperparathyroidism, we had switched nutritional to active vitamin D supplementation with reduced phosphorus salts. The present report contributes to understanding the relationship between the mosaic rate, in addition to the mutation locus, of the PHEX gene, and clinical features of XLH.


Assuntos
Osso e Ossos/anormalidades , Raquitismo Hipofosfatêmico Familiar/genética , Doenças Genéticas Ligadas ao Cromossomo X/genética , Endopeptidase Neutra Reguladora de Fosfato PHEX/genética , Povo Asiático/genética , Osso e Ossos/diagnóstico por imagem , Raquitismo Hipofosfatêmico Familiar/sangue , Raquitismo Hipofosfatêmico Familiar/terapia , Humanos , Japão , Masculino , Pessoa de Meia-Idade , Mosaicismo , Hormônio Paratireóideo/sangue , Fenótipo , Fosfatos/uso terapêutico , Radiografia , Deleção de Sequência/genética , Vitamina D/sangue , Vitamina D/uso terapêutico
8.
J Anat ; 239(2): 405-423, 2021 08.
Artigo em Inglês | MEDLINE | ID: mdl-33721329

RESUMO

Rodents are the most diverse order of extant mammals, and caviomorph rodents, or New World hystricognaths, have a remarkable morphological disparity and a long fossil record that begins in the Eocene. Chinchilloidea is a poorly understood clade within Caviomorpha, from an evolutionary and phylogenetic perspective. It includes the extant families Chinchillidae and Dinomyidae, the extinct Neoepiblemidae and Cephalomyidae, and several extinct chinchilloids without a clear phylogenetic position, like Eoincamys, Borikenomys, Chambiramys, Ucayalimys, Incamys, Saremmys, Garridomys and Scotamys. The family Chinchillidae includes the extant Chinchilla and Lagidium, grouped in Chinchillinae, and the only living Lagostominae, Lagostomus maximus. Among extinct chinchillids, Eoviscaccia (early Oligocene-early Miocene of Argentina, Bolivia and Chile), Prolagostomus (early-middle Miocene of Argentina, Bolivia and Chile) and Pliolagostomus (early-middle Miocene of Argentina) are the only genera originally described as members of the family. Based on the study of specimens with unworn or little-worn cheek teeth, belonging to extinct and extant taxa, we propose homologies of the cheek teeth structures and perform a combined molecular and morphological phylogenetic analysis including extinct and extant taxa of all families of Chinchilloidea and all genera of Chinchillidae. Our phylogenetic analysis recovered three major lineages in the evolutionary history of Chinchilloidea. The first major lineage is composed of the extant taxa Chinchilla, Lagidium and Lagostomus, and the extinct genera Eoviscaccia, Prolagostomus, Pliolagostomus, Garridomys, Incamys, Loncolicu and Saremmys. Cephalomyid (Banderomys, Cephalomys, Litodontomys, Soriamys) and neoepiblemid (Neoepiblema, Perimys, Phoberomys, Scotamys) genera are part of the second major lineage, while dinomyids such as Dinomys, Drytomomys, Scleromys, 'Scleromys' and Tetrastylus constitute the third major lineage within Chinchilloidea. The phylogenetic position of some taxa previously considered as incertae sedis chinchilloids or without a clear suprageneric group (i.e. Incamys, Saremmys, Garridomys and Loncolicu) show that they belong to pan-Chinchillidae and conform the stem Chinchillidae along with Eoviscaccia. The euhypsodont crown Chinchillidae includes the living subfamilies Chinchillinae and Lagostominae. Dinomyidae and Eoincamys pascuali are recovered as the sisters of a major clade composed by 'Cephalomyidae'+Neopiblemidae and pan-Chinchillidae, and Chambiramys sylvaticus occupies a basal position to the same clade. Four major radiation events are identified in the evolutionary history of Chinchilloidea. The analysis of new morphological characters linked with molecular evidence as well as the addition of taxa of uncertain or unstable phylogenetic position or not considered in previous studies allowed us resolve part of the relationships within Chinchilloidea, particularly that of Chinchillidae, supporting preceding morphological hypotheses.


Assuntos
Evolução Biológica , Chinchila/anatomia & histologia , Filogenia , Dente/anatomia & histologia , Animais , Chinchila/genética
9.
Biol Rev Camb Philos Soc ; 96(3): 943-960, 2021 06.
Artigo em Inglês | MEDLINE | ID: mdl-33432779

RESUMO

The ovule and its developmental successor, the seed, together represent a highly characteristic feature of seed plants that has strongly enhanced the reproductive and dispersal potential of this diverse group of taxa. Ovules encompass multiple tissues that perform various roles within a highly constrained space, requiring a complex cascade of genes that generate localized cell proliferation and programmed cell death during different developmental stages. Many heritable morphological differences among lineages reflect relative displacement of these tissues, but others, such as the second (outer) integuments of angiosperms and Gnetales, represent novel and apparently profound and independent innovations. Recent studies, mostly on model taxa, have considerably enhanced our understanding of gene expression in the ovule. However, understanding its evolutionary history requires a comparative and phylogenetic approach that is problematic when comparing extant angiosperms not only with phylogenetically distant extant gymnosperms but also with taxa known only from fossils. This paper reviews ovule characters across a phylogenetically broad range of seed plants in a dynamic developmental context. It discusses both well-established and recent theories of ovule and seed evolution and highlights potential gaps in comparative data that will usefully enhance our understanding of evolutionary transitions and developmental mechanisms.


Assuntos
Magnoliopsida , Óvulo Vegetal , Fósseis , Magnoliopsida/genética , Óvulo Vegetal/genética , Filogenia , Sementes/genética
10.
Arthropod Struct Dev ; 60: 100999, 2021 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-33120186

RESUMO

The main synapomorphy for Aculeata is the sting apparatus, which allows the female to envenom potential prey or hosts. The sting is the modified ovipositor which is not used for laying eggs anymore. Here, we explore the morphology of the sting apparatus within the families of Chrysidoidea. 27 skeletal structures were recognized, including three (dp1vf, dorsal projection of first valvifer; ppa, projection of posterior area of the second valvifer; vl9, ventral lap of tergite 9) that have not been observed previously, and 13 pairs of muscles, including four (superior dorsal T9-2vf (M5); inferior dorsal T9-2vf (M6); postero-lateral T9-2vf/mbr (M9); anterolateral 2vf/bl-2vv/fu (M11)) that have not been observed previously. Very conserved morphological patterns were observed; character support in the sting apparatus was found at the subfamily level, and within three families at the genus level. In addition, we describe the variation within the sting apparatus structures and musculature, propose evolutionary hypotheses about the function and evolution of the structures, and summarize phylogenetic conclusions for Chrysidoidea.


Assuntos
Vespas/anatomia & histologia , Animais , Feminino , Mordeduras e Picadas de Insetos , Oviposição , Filogenia
11.
Biotechniques ; 68(1): 45-47, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31825241

RESUMO

We searched for viral protein sequences that could be important for tissue tropism. To achieve this goal, human pathogenic viruses were classified according to the tissue they infect (e.g., pulmonary), irrespective of whether they were enveloped or non-enveloped RNA or DNA viruses. Next, we developed an amino acid sequence alignment program and identified the conserved amino acid motif, VAIVLGG, in alphaviruses. The VAIVLGG sequence is located on the structural capsid protein of the chikungunya virus, a mosquito-borne arthrogenic member of the alphaviruses. Capsid protein translocation onto the host cell membrane is a required step for virion budding. Our identified VAIVLGG consensus sequence might potentially be used for developing a pan-vaccine effective against alphaviruses.


Assuntos
Alphavirus/química , Motivos de Aminoácidos , Alinhamento de Sequência/métodos , Proteínas Virais/química , Alphavirus/patogenicidade , Sequência de Aminoácidos , Vírus Chikungunya/química , Sequência Conservada , Humanos
12.
Annu Rev Vis Sci ; 4: 381-402, 2018 09 15.
Artigo em Inglês | MEDLINE | ID: mdl-30059648

RESUMO

Inferior temporal cortex (IT) is a key part of the ventral visual pathway implicated in object, face, and scene perception. But how does IT work? Here, I describe an organizational scheme that marries form and function and provides a framework for future research. The scheme consists of a series of stages arranged along the posterior-anterior axis of IT, defined by anatomical connections and functional responses. Each stage comprises a complement of subregions that have a systematic spatial relationship. The organization of each stage is governed by an eccentricity template, and corresponding eccentricity representations across stages are interconnected. Foveal representations take on a role in high-acuity object vision (including face recognition); intermediate representations compute other aspects of object vision such as behavioral valence (using color and surface cues); and peripheral representations encode information about scenes. This multistage, parallel-processing model invokes an innately determined organization refined by visual experience that is consistent with principles of cortical development. The model is also consistent with principles of evolution, which suggest that visual cortex expanded through replication of retinotopic areas. Finally, the model predicts that the most extensively studied network within IT-the face patches-is not unique but rather one manifestation of a canonical set of operations that reveal general principles of how IT works.


Assuntos
Lobo Temporal/fisiologia , Córtex Visual/fisiologia , Vias Visuais/fisiologia , Percepção Visual/fisiologia , Animais , Percepção de Cores/fisiologia , Reconhecimento Facial/fisiologia , Humanos , Modelos Neurológicos
13.
Comp Cytogenet ; 12(2): 171-199, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29896323

RESUMO

The development of avian cytogenetics is significantly behind that of mammals. In fact, since the advent of cytogenetic techniques, fewer than 1500 karyotypes have been established. The Barbary partridge Alectoris barbara Bonnaterre, 1790 is a bird of economic interest but its genome has not been studied so far. This species is endemic to North Africa and globally declining. The Chukar partridge Alectoris chukar Gray, 1830 is an introduced species which shares the same habitat area as the Barbary partridge and so there could be introgressive hybridisation. A cytogenetic study has been initiated in order to contribute to the Barbary partridge and the Chukar partridge genome analyses. The GTG, RBG and RHG-banded karyotypes of these species have been described. Primary fibroblast cell lines obtained from embryos were harvested after simple and double thymidine synchronisation. The first eight autosomal pairs and Z sex chromosome have been described at high resolution and compared to those of the domestic fowl Gallus domesticus Linnaeus, 1758. The diploid number was established as 2n = 78 for both partridges, as well as for most species belonging to the Galliformes order, underlying the stability of chromosome number in avian karyotypes. Wide homologies were observed for macrochromosomes and gonosome except for chromosome 4, 7, 8 and Z which present differences in morphology and/or banding pattern. Neocentromere occurrence was suggested for both partridges chromosome 4 with an assumed paracentric inversion in the Chukar partridge chromosome 4. Terminal inversion in the long arm of the Barbary partridge chromosome Z was also found. These rearrangements confirm that the avian karyotypes structure is conserved interchromosomally, but not at the intrachromosomal scale.

14.
Eur J Protistol ; 61(Pt A): 137-179, 2017 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-29073503

RESUMO

Uniquely in eukaryotes, euglenoid pellicles comprise longitudinal proteinaceous, epiplasmic strips underlain by microtubules. Contradictory interpretations of pellicle microtubule duplication and segregation assumed opposite microtubule polarity from kinetoplastid Euglenozoa and conservative microtubule segregation. Distigma shows new pellicle microtubules nucleating posteriorly as in trypanosomatids, unifying euglenoid and kinetoplastid pellicle morphogenesis, but strip-growth is unpolarised. Epiplasmic insertion and cutting make new strip junctions between alternating wide and narrow daughter strips that grow intussusceptively. Nanotubules, overlooked epiplasm-associated components, define strip edges. At strip heel/toe junctions all euglenoids have a morphogenetic centre microtubule mt2/3 pair. Arguably, proteolysis, epiplasmic growth, and toe-nanotubule-associated epiplasmic scission initiate daughter strips, separating old mts2/3; new mt2/3/bridge-B assembly, sub-heel scission, nanotubule-bridge-A assembly complete duplication. Only mt2/3 pair fully enters the canal, one master microtubule also the reservoir, other pellicle microtubules terminating near canal rims. A related cytokinesis model involving ciliary attachment zone duplication explains near-universally even spirocute strip number. I consider Serpenomonas and Entosiphon alternating heteromorphic strips developmental stages of 'strip transformation'; explain intergroup diversity of strip morphology and dorsoventral strip differentiation causally by specific pellicle-complex components; propose centrin-based mechanisms for strip shaping and euglenoid movement; unify pellicle cytokinetic microtubule segregation across Euglenozoa; and discuss origin and diversification of pellicle complexes.


Assuntos
Euglenozoários/fisiologia , Euglenozoários/ultraestrutura , Morfogênese , Evolução Biológica , Euglenozoários/crescimento & desenvolvimento , Microtúbulos/fisiologia , Microtúbulos/ultraestrutura
15.
J Struct Biol ; 200(1): 45-53, 2017 10.
Artigo em Inglês | MEDLINE | ID: mdl-28890162

RESUMO

For the past 50years there has been considerable debate over the sub-structure of the fully differentiated (oxidised) trichocyte keratin intermediate filament. Depending on the staining and preparative procedures employed, IF observed in transverse section in the transmission electron microscope have varied in appearance between that of a "ring" and a "ring-core" structure, corresponding to the so-called (8+0) and (7+1) protofilament arrangements. In a new analysis of the fine structure of the 1nm equatorial region of the X-ray diffraction pattern of quill we show that the observed pattern is consistent with the (8+0) model and we are also able to assign values to the various parameters. In contrast, we show that the observed X-ray pattern is inconsistent with a (7+1) arrangement. Furthermore, in the (7+1) model steric hindrance would be encountered between the core protofilament and those constituting the ring. The appearance of a central "core" in transverse TEM sections, previously attributed to a central protofilament, is explained in terms of portions of the apolar, disulfide-bonded head and/or tail domains of the trichocyte keratin IF molecules, including the conserved H subdomains, lying along the axis of the IF, thereby decreasing the efficacy of the reducing agents used prior to staining. The H1 subdomain, previously shown to be important in the assembly of epidermal IF molecules at the two- to four-molecule level, is likely to have a similar role for the trichocyte keratins and may form part of a central scaffold on which the molecules assemble into fully functional IF.


Assuntos
Queratinas Específicas do Cabelo/ultraestrutura , Sequência de Aminoácidos , Animais , Sequência Conservada , Queratinas Específicas do Cabelo/química , Microscopia Eletrônica de Transmissão e Varredura , Oxirredução , Porcos-Espinhos , Estrutura Quaternária de Proteína
16.
BMC Bioinformatics ; 17(1): 328, 2016 Aug 30.
Artigo em Inglês | MEDLINE | ID: mdl-27578239

RESUMO

BACKGROUND: Sequence matching is extremely important for applications throughout biology, particularly for discovering information such as functional and evolutionary relationships, and also for discriminating between unimportant and disease mutants. At present the functions of a large fraction of genes are unknown; improvements in sequence matching will improve gene annotations. Universal amino acid substitution matrices such as Blosum62 are used to measure sequence similarities and to identify distant homologues, regardless of the structure class. However, such single matrices do not take into account important structural information evident within the different topologies of proteins and treats substitutions within all protein folds identically. Others have suggested that the use of structural information can lead to significant improvements in sequence matching but this has not yet been very effective. Here we develop novel substitution matrices that include not only general sequence information but also have a topology specific component that is unique for each CATH topology. This novel feature of using a combination of sequence and structure information for each protein topology significantly improves the sequence matching scores for the sequence pairs tested. We have used a novel multi-structure alignment method for each homology level of CATH in order to extract topological information. RESULTS: We obtain statistically significant improved sequence matching scores for 73 % of the alpha helical test cases. On average, 61 % of the test cases showed improvements in homology detection when structure information was incorporated into the substitution matrices. On average z-scores for homology detection are improved by more than 54 % for all cases, and some individual cases have z-scores more than twice those obtained using generic matrices. Our topology specific similarity matrices also outperform other traditional similarity matrices and single matrix based structure methods. When default amino acid substitution matrix in the Psi-blast algorithm is replaced by our structure-based matrices, the structure matching is significantly improved over conventional Psi-blast. It also outperforms results obtained for the corresponding HMM profiles generated for each topology. CONCLUSIONS: We show that by incorporating topology-specific structure information in addition to sequence information into specific amino acid substitution matrices, the sequence matching scores and homology detection are significantly improved. Our topology specific similarity matrices outperform other traditional similarity matrices, single matrix based structure methods, also show improvement over conventional Psi-blast and HMM profile based methods in sequence matching. The results support the discriminatory ability of the new amino acid similarity matrices to distinguish between distant homologs and structurally dissimilar pairs.


Assuntos
Análise de Sequência de Proteína/métodos , Homologia Estrutural de Proteína , Algoritmos , Substituição de Aminoácidos , Estrutura Secundária de Proteína
17.
J Comp Neurol ; 524(2): 408-28, 2016 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-26234725

RESUMO

In the weakly electric gymnotiform fish, Apteronotus leptorhynchus, the dorsolateral pallium (DL) receives diencephalic inputs representing electrosensory input utilized for communication and navigation. Cell counts reveal that, similar to thalamocortical projections, many more cells are present in DL than in the diencephalic nucleus that provides it with sensory input. DL is implicated in learning and memory and considered homologous to medial and/or dorsal pallium. The gymnotiform DL has an apparently simple architecture with a random distribution of simple multipolar neurons. We used multiple neurotracer injections in order to study the microcircuitry of DL. Surprisingly, we demonstrated that the intrinsic connectivity of DL is highly organized. It consists of orthogonal laminar and vertical excitatory synaptic connections. The laminar synaptic connections are symmetric sparse, random, and drop off exponentially with distance; they parcellate DL into narrow (60 µm) overlapping cryptic layers. At distances greater than 100 µm, the laminar connections generate a strongly connected directed graph architecture within DL. The vertical connectivity suggests that DL is also organized into cryptic columns; these connections are highly asymmetric, with superficial DL cells preferentially projecting towards deeper cells. Our experimental analyses suggest that the overlapping cryptic columns have a width of 100 µm, in agreement with the minimal distance for strong connectivity. The architecture of DL and the expansive representation of its input, taken together with the strong expression of N-methyl-D-aspartate (NMDA) receptors by its cells, are consistent with theoretical ideas concerning the cortical computations of pattern separation and memory storage via bump attractors.


Assuntos
Peixe Elétrico/anatomia & histologia , Vias Neurais/fisiologia , Telencéfalo/citologia , Telencéfalo/fisiologia , Animais , Contagem de Células , Feminino , Corantes Fluorescentes/metabolismo , Técnicas In Vitro , Masculino , Microscopia Confocal , Neurônios/fisiologia , Técnicas Estereotáxicas
18.
J Neural Transm (Vienna) ; 122(11): 1509-14, 2015 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-26133164

RESUMO

Biochemical studies had previously demonstrated examples of heteromerization between opioid and chemokine receptors. Based on the triplet puzzle theory, it has been discovered that opioid receptors are structurally more closely related to chemokine receptors than to other class A G-protein-coupled receptors. Their similarity is established in terms of the number of triplet homologies Asn-Leu-Ala, Thr-Leu-Pro, and Tyr-Ala-Phe in the amino acid code of extensive numbers of members of these two receptor groups. Such widespread similarities probably mean that many opioid and chemokine receptor subtypes utilize some of these mutual triplets to form heteromers. The findings underline that heteromerization among these two receptor groups can represent a major general mechanism for significant interactions between opioid peptides and chemokines in pain and neuroinflammation within the neural-glial networks of the CNS including immune cells.


Assuntos
Receptores de Quimiocinas/metabolismo , Receptores Opioides/metabolismo , Sequência de Aminoácidos , Humanos , Modelos Moleculares , Receptores de Quimiocinas/genética , Receptores Opioides/genética
19.
Neuroimage ; 116: 10-29, 2015 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-25970649

RESUMO

Based on its diverse and wide-spread patterns of connectivity, primate posteromedial cortex (PMC) is well positioned to support roles in several aspects of sensory-, cognitive- and motor-related processing. Previous work in both humans and non-human primates (NHPs) using resting-state functional MRI (rs-fMRI) suggests that a subregion of PMC, the medial parieto-occipital cortex (mPOC), by virtue of its intrinsic functional connectivity (FC) with visual cortex, may only play a role in higher-order visual processing. Recent neuroanatomical tracer studies in NHPs, however, demonstrate that mPOC also has prominent cortico-cortical connections with several frontoparietal structures involved in movement planning and control, a finding consistent with increasing observations of reach- and grasp-related activity in the mPOC of both NHPs and humans. To reconcile these observations, here we used rs-fMRI data collected from both awake humans and anesthetized macaque monkeys to more closely examine and compare parcellations of mPOC across species and explore the FC patterns associated with these subdivisions. Seed-based and voxel-wise hierarchical cluster analyses revealed four broad spatially separated functional boundaries that correspond with graded differences in whole-brain FC patterns in each species. The patterns of FC observed are consistent with mPOC forming a critical hub of networks involved in action planning and control, spatial navigation, and working memory. In addition, our comparison between species indicates that while there are several similarities, there may be some species-specific differences in functional neural organization. These findings and the associated theoretical implications are discussed.


Assuntos
Lobo Occipital/anatomia & histologia , Lobo Occipital/fisiologia , Lobo Parietal/anatomia & histologia , Lobo Parietal/fisiologia , Adulto , Animais , Mapeamento Encefálico/métodos , Análise por Conglomerados , Feminino , Humanos , Macaca fascicularis , Macaca mulatta , Imageamento por Ressonância Magnética/métodos , Masculino , Rede Nervosa/anatomia & histologia , Rede Nervosa/fisiologia , Especificidade da Espécie , Adulto Jovem
20.
Am J Bot ; 101(12): 2136-47, 2014 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-25480710

RESUMO

UNLABELLED: • PREMISE OF THE STUDY: Two ovulate conifer cones, one of which is attached terminally to a short leafy shoot, reveal the presence of a new species of Hughmillerites in the Early Cretaceous Apple Bay flora of Vancouver Island, British Columbia, Canada. This ancient conifer expands the diversity of Cupressaceae in the Mesozoic and reveals details about the evolution of Subfamily: Cunninghamioideae.• METHODS: Specimens were studied from anatomical sections prepared using the cellulose acetate peel technique.• KEY RESULTS: Vegetative shoots have helically arranged leaves that are Cunninghamia-like. Seed cones have many helically arranged bract/scale complexes in which the bract is larger than the ovuliferous scale. Each ovuliferous scale has three free tips that separate from the bract immediately distal to an inverted seed. Several ovuliferous scales show interseminal ridges between seeds.• CONCLUSIONS: This study documents a new extinct species of cunninghamioid conifers, Hughmillerites vancouverensis, expanding the record of the genus from the Late Jurassic to the Early Cretaceous. This new extinct species emphasizes the important role that conifers from subfamily Cunninghamioideae played in the initial evolutionary radiation of Cupressaceae. In light of recent findings in conifer regulatory genetics, we use H. vancouverensis to hypothesize that variations of expression in certain gene homologues played an important role in the evolution of the cupressaceous ovuliferous scale.


Assuntos
Evolução Biológica , Cupressaceae/genética , Fósseis , Óvulo Vegetal , Filogenia , Componentes Aéreos da Planta/anatomia & histologia , Sementes , Colúmbia Britânica , Cupressaceae/anatomia & histologia , Folhas de Planta , Reprodução
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