Disentangling clustering configuration intricacies for divergently selected chicken breeds.

Divergently selected chicken breeds are of great interest not only from an economic point of view, but also in terms of sustaining diversity of the global poultry gene pool. In this regard, it is essential to evaluate the classification (clustering) of varied chicken breeds using methods and models based on phenotypic and genotypic breed differences. It is also important to implement new mathematical indicators and approaches. Accordingly, we set the objectives to test and improve clustering algorithms and models to discriminate between various chicken breeds. A representative portion of the global chicken gene pool including 39 different breeds was examined in terms of an integral performance index, i.e., specific egg mass yield relative to body weight of females. The generated dataset was evaluated within the traditional, phenotypic and genotypic classification/clustering models using the k-means method, inflection points clustering, and admixture analysis. The latter embraced SNP genotype datasets including a specific one focused on the performance-associated NCAPG-LCORL locus. The k-means and inflection points analyses showed certain discrepancies between the tested models/submodels and flaws in the produced cluster configurations. On the other hand, 11 core breeds were identified that were shared between the examined models and demonstrated more adequate clustering and admixture patterns. These findings will lay the foundation for future research to improve methods for clustering as well as genome- and phenome-wide association/mediation analyses.

Optical density of mandible in orthodontic patients.

OBJECTIVE: Introduction: The given article is concerned with peculiarities of the change in the bone mineral density of the jaw bones in the dynamics of bone structure growth in the locomotor apparatus of orthodontic patients. The aim of the paper is to carry out a comparative analysis of the mineral density of the bone tissue of the lower jaw (mandible) and the mineral density of the second cervical vertebra (C2) in patients with malocclusion. PATIENTS AND METHODS: Materials and methods: 37 computer tomograms of orthodontic patients were studied, which were divided into three age groups according to the periods of the formation of the dentoalveolar system. Measurement of bone density of (second cervical vertebra) C2 was performed in the sagittal projection along the middle of the height of the vertebra. In the mandible, measurements were made on axial sections in the vestibular and oral direction in the region of the alveolar process between the central incisors, between the canine and the first premolar at the mid-root level, in the region of the first molars below the bifurcation level, in the retromolar region and the region of the articular process. RESULTS: Results: The greatest similarity in densitometric parameters of bone density is established between the second cervical vertebrae and the density of the joint head. The most dense site on the lower jaw is the alveolar process between the central incisors, which increases with age from 1274.71 ± 34.7 in group I to 1400.6 ± 75, 56 in the III group, these indicators are almost 2-2.5 times higher than the density of C2. CONCLUSION: Conclusions: Mandible presents irregular density of bone based on optic denstitometry in different areas. Maximal indices of bone density are established in the area of alveolar processes where the jaw is exposed to maximal occlusal loading.

Optical density of upper jaw in patients with malocclusion.

INTRODUCTION: The growth and formation of facial skeleton is in interrelation with growth of cervical spine. Computer tomography plays an important role to examine and investigate the density of bony tissue resulting from total increase of osteopenic diseases and diseases of periodontal tissue. The aim of the paper is to compare indices of mineral density of bony tissue of the upper jaw and mineral density of the second cervical vertebra in patients with malocclusion. MATERIALS AND METHODS: 37 orthodontic patients were involved in the investigation. They were divided into three age groups depending on the period of formation of dentofacial system. Density measurement of bone of the second cervical vertebra was done and also density measurement of upper jaw in the area of alveolar process between central incisors, canines and the first premolar on the level of the middle of roots, in the area of the first molars under the level of bifurcation and in cusp was performed. RESULTS: Optical density of bone of the second cervical vertebra with age increases from 501±61,06 to 587,6±48,81. The densest area on the upper jaw is alveolar process between central incisors, which increases with age from 1045,14±59,81 to 1318±69,28. The least indices of optical density were determined in area of the cusp of the upper jaw: the first group presented 174,21±38,94, and the third one included 338,87±26,91. CONCLUSIONS: Densitometry of bony tissue with computer tomography is diagnostically informative and available method for investigation and it can be used for diagnostics of bony tissue condition and for evaluation of orthodontic treatment.

Functional condition of masseters muscles of patients with class ?? subdivision.

INTRODUCTION: Main functional characteristics of masticator muscles in patients with class ?? malocclusions is activity dominance of m. temporalis in comparison with m. ?asseter. We have not found datum about functional status of the masticators in patients with class II subdivision. THE AIM: The purpose of our study was to investigate the functional characteristics of m. ?asseter, m. temporalis in adult patients with class II subdivision malocclusion. MATERIALS AND METHODS: There have been carried out the surface electromyographic study of m. masseter, m. temporalis in 17 adult patients with class II subdivision. It was realized quantitative analysis of 271 electromyogram, it was determined the average bioelectric activity, index activity, symmetry and torsion index. RESULTS: It was observed predominance of the bioelectrical activity of m. temporales on m. masseter for all persons with class II subdivision. Bioelectrical activity for m. masseter was bigger on side of distal ratio and for m. temporales on side of neutral ratio. In class ?? subdivision right, the mandible was deviated to the left side and in class ?? subdivision left is deviated to the right side. Thus, rotational moment generated during compression of the jaws, causes deviation of the lower jaw to the side, with a neutral molar ratio. During voluntary chewing bioelectrical activity of m. masseter and m. temporalis was higher in the right side. CONCLUSION: In accordance with the functional condition of the masticatory muscles of class II subdivision is characterized with functional features of distal occlusion.

Symmetry of elements of temporomandibular joint (TMJ).

OBJECTIVE: Introduction: Dysfunction of temporomandibular joint is present in 70-75% of orthodontic patients. Evaluation of TMJ and detailed characteristics of its elements with additional methods of examination in children and adults is necessary for clinical definition of proposed disturbances of the structure and functions of the joint. The aim of the investigation is to study morphological symmetry of TMJ in patients with dentofacial abnormalities and with dentofacial abnormalities complicated by secondary edentulism. PATIENTS AND METHODS: Materials and Methods: 57 patients were involved in the examination. Based on gender principle patients' distribution was almost equal: there were 30 women and 27 men. Cone-beam computerized tomography (CBCT) Galileos (SIRONA DENTAL, Germany) was used to all patients. RESULTS: Results: It was done analysis of parameters (height and length) of right and left heads (condyles) of temporomandibular joint in both groups. Asymmetry of parameters of heads' length in saggital area in patients of the second group was defined. It was proved statistically (left 10,38±0,76, right 8,16±0,78). CONCLUSION: Conclusions: Increase of asymmetry of length of heads of TMJ in saggital area with age was determined. It can be explained by complication of dentofacial abnormalities and the presence of secondary edentulism. Depending on bite type length of condyle, especially at prognathism (in saggital) area peculiar clinical problems with TMJ can be present due to asymmetry of condyles. The size of joint gaps of TMJ due to the presence of dentofacial abnormalities with age demonstrates compensatory ability and saves its.

Engulfment adapter PTB domain containing 1 interacts with and affects processing of the amyloid-ß precursor protein.

Previous studies identified engulfment adapter phosphotyrosine binding (PTB) domain containing 1 (GULP1) as an NPXY-motif interactor of low-density lipoprotein receptor-related protein 1 (LRP1) and suggested a potential relevance in Alzheimer's disease (AD). Since AD associated proteins amyloid-ß A4 precursor protein (APP) and LRP1 were shown to interact with the PTB domain of Fe65 and several other adapters via their intracellular NPXY-motifs, we examined a possible interaction of GULP1 PTB domain with the YENPTY-motif of APP. Here we demonstrate that GULP1 is present in human hippocampal and neocortical neurons. Confocal live cell imaging revealed that coexpressed and endogenous GULP1 colocalizes with APP in the Golgi and endoplasmic reticulum. Analysis of the interacting domains by co-immunoprecipitation of point and deletion mutants revealed that the interaction depends on the PTB domain of GULP1 and the YENPTY-motif of APP. Coexpression of GULP1 affected APP cell surface localization and suppressed generation of Aß40/42 and sAPPα. Taken together, these data identify GULP1 as a novel neuronal APP interacting protein that alters trafficking and processing of APP.

The effects of amyloid precursor protein on postsynaptic composition and activity.

The amyloid precursor protein (APP) is cleaved to produce the Alzheimer disease-associated peptide Abeta, but the normal functions of uncleaved APP in the brain are unknown. We found that APP was present in the postsynaptic density of central excitatory synapses and coimmunoprecipitated with N-methyl-d-aspartate receptors (NMDARs). The presence of APP in the postsynaptic density was supported by the observation that NMDARs regulated trafficking and processing of APP; overexpression of the NR1 subunit increased surface levels of APP, whereas activation of NMDARs decreased surface APP and promoted production of Abeta. We transfected APP or APP RNA interference into primary neurons and used electrophysiological techniques to explore the effects of APP on postsynaptic function. Reduction of APP decreased (and overexpression of APP increased) NMDAR whole cell current density and peak amplitude of spontaneous miniature excitatory postsynaptic currents. The increase in NMDAR current by APP was due to specific recruitment of additional NR2B-containing receptors. Consistent with these findings, immunohistochemical experiments demonstrated that APP increased the surface levels and decreased internalization of NR2B subunits. These results demonstrate a novel physiological role of postsynaptic APP in enhancing NMDAR function.

The LDL receptor-related protein can form homo-dimers in neuronal cells.

The ability of the low density lipoprotein receptor-related protein (LRP) to form homo-dimers was studied in mouse neuroblastoma and human neuroglioma cells as well as in primary cortical cultures from adult mouse brain. Homo-dimerization of LRP light chain (LC) was shown by several methods including co-immunoprecipitation, fluorescence lifetime imaging microscopy, and bimolecular fluorescence complementation assay. The requirement of intact NPXY motifs of LRP LC for homo-dimerization was ruled out by co-immunoprecipitation assay.

Two postprocessing techniques for the elimination of background autofluorescence for fluorescence lifetime imaging microscopy.

The analysis of fluorescence lifetime imaging microscopy (FLIM) data under complex biological conditions can be challenging. Particularly, the presence of short-lived autofluorescent aggregates can confound lifetime measurements in fluorescence energy transfer (FRET) experiments, where it can become confused with the signal from exogenous fluorophores. Here we report two techniques that can be used to discriminate the contribution of autofluorescence from exogenous fluorphores in FLIM. We apply the techniques to transgenic mice that natively express yellow fluorescence protein (YFP) in a subset of cortical neurons and to histological slices of aged human brain tissue, where we study the misfolding of intracellular tau protein in the form of neurofibrillary tangles.

Fyn modulation of Dab1 effects on amyloid precursor protein and ApoE receptor 2 processing.

Dab1 is an intracellular adaptor protein that interacts with amyloid precursor protein (APP) and apoE receptor 2 (apoEr2), increases their levels on the cell surface, and increases their cleavage by alpha-secretases. To investigate the mechanism underlying these alterations in processing and trafficking of APP and apoEr2, we examined the effect of Fyn, an Src family-tyrosine kinase known to interact with and phosphorylate Dab1. Co-immunoprecipitation, co-immunostaining, and fluorescence lifetime imaging demonstrated an association between Fyn and APP. Fyn induced phosphorylation of APP at Tyr-757 of the (757)YENPTY(762) motif and increased cell surface expression of APP. Overexpression of Fyn alone did not alter levels of sAPPalpha or cytoplasmic C-terminal fragments, although it significantly decreased production of Abeta. However, in the presence of Dab1, Fyn significantly increased sAPPalpha and C-terminal fragments. Fyn-induced APP phosphorylation and cell surface levels of APP were potentiated in the presence of Dab1. Fyn also induced phosphorylation of apoEr2 and increased its cell surface levels and, in the presence of Dab1, affected processing of its C-terminal fragment. In vivo studies showed that sAPPalpha was decreased in the Fyn knock-out, supporting a role for Fyn in APP processing. These data demonstrate that Fyn, due in part to its effects on Dab1, regulates the phosphorylation, trafficking, and processing of APP and apoEr2.

Mac-1 promotes FcgammaRIIA-dependent cell spreading and migration on immune complexes.

The integrin Mac-1 plays a critical role in Fc receptor (FcR)-mediated antibody-dependent cellular cytotoxicity (ADCC). However, the mechanism by which Mac-1 facilitates the functions of FcgammaRIIA, a major FcR expressed on human leukocytes, is not fully understood. We report here that Mac-1 sustains cell adhesion, enhances cell spreading, and accelerates cell migration on preformed immune complexes (ICs) by directly interacting with FcgammaRIIA but not with the IC substrate. Coupling Mac-1 to FcgammaRIIA allows FcgammaRIIA to reside in the leading front of actin polymerization at the filopodial extension and thus could potentially enhance FcgammaRIIA-mediated cell spreading and migration. The direct interaction between Mac-1 and FcgammaRIIA is demonstrated by co-immunoprecipitation, by cell surface co-localization, and by solid-phase binding assays using recombinant alpha(M)I-domain and soluble FcgammaRIIA. Further mutational analysis identifies the E(253)-R(261) sequence within the alpha(M)I-domain as part of the FcgammaRIIA binding interface within Mac-1. Altogether, these results demonstrate that FcgammaRIIA recognizes Mac-1 via the alpha(M)I-domain but not the lectin domain, a distinct feature from other FcRs, and that Mac-1 binding confers FcgammaRIIA with the ability to prolong cell adhesion as well as to spread and migrate on the ICs, leading to effective cell killing by ADCC.

Endocytic receptor LRP together with tPA and PAI-1 coordinates Mac-1-dependent macrophage migration.

Migration of activated macrophages is essential for resolution of acute inflammation and the initiation of adaptive immunity. Here, we show that efficient macrophage migration in inflammatory environment depends on Mac-1 recognition of a binary complex consisting of fibrin within the provisional matrix and the protease tPA (tissue-type plasminogen activator). Subsequent neutralization of tPA by its inhibitor PAI-1 enhances binding of the integrin-protease-inhibitor complex to the endocytic receptor LRP (lipoprotein receptor-related protein), triggering a switch from cell adhesion to cell detachment. Genetic inactivation of Mac-1, tPA, PAI-1 or LRP but not the protease uPA abrogates macrophage migration. The defective macrophage migration in PAI-1-deficient mice can be restored by wild-type but not by a mutant PAI-1 that does not interact with LRP. In vitro analysis shows that tPA promotes Mac-1-mediated adhesion, whereas PAI-1 and LRP facilitate its transition to cell retraction. Our results emphasize the importance of ordered transitions both temporally and spatially between individual steps of cell migration, and support a model where efficient migration of inflammatory macrophages depends on cooperation of three physiologically prominent systems (integrins, coagulation and fibrinolysis, and endocytosis).

Proteases and lipoprotein receptors in Alzheimer's disease.

Alzheimer's disease (AD) is the leading cause of senile dementia, and is a complex disorder. The pathological hallmarks of AD were discovered by Dr. Alois Alzheimer in 1907, and include deposits of amyloid or senile plaques and neurofibrillar tangles. Plaques are composed of a peptide, termed the Abeta peptide, that is derived by proteolytic processing of the amyloid precursor protein (APP), while neurofibrillar tangles result from a hyperphosphorylation of the tau protein. Mechanisms associated with the formation of plaques and neurofibrillar tangles and their respective contributions to the disease process have been intensely investigated. Proteolytic processing of APP that results in the generation of the Abeta peptide is now well understood and is influenced by several proteins. Recent evidence suggests that the Abeta levels are carefully regulated, and several proteases play an important role in removing the Abeta peptide. Finally, it is becoming apparent that several members of the LDL receptor family play important roles in the brain, and may modulate the course of AD.

The low density lipoprotein receptor-related protein modulates protease activity in the brain by mediating the cellular internalization of both neuroserpin and neuroserpin-tissue-type plasminogen activator complexes.

Proteases contribute to a variety of processes in the brain; consequently, their activity is carefully regulated by protease inhibitors, such as neuroserpin. This inhibitor is thought to be secreted by axons at synaptic regions where it controls tissue-type plasminogen activator (tPA) activity. Mechanisms regulating neuroserpin are not known, and the current studies were undertaken to define the cellular pathways involved in neuroserpin catabolism. We found that both active neuroserpin and neuroserpin.tPA complexes were internalized by mouse cortical cultures and embryonic fibroblasts in a process mediated by the low density lipoprotein receptor-related protein (LRP). Surprisingly, despite the fact that active neuroserpin is internalized by LRP, this form of the molecule does not directly bind to LRP on its own, indicating the requirement of a cofactor for neuroserpin internalization. Our studies ruled out the possibility that endogenously produced plasminogen activators (i.e. tPA and urokinase-type plasminogen activator) are responsible for the LRP-mediated internalization of active neuroserpin, but could not rule out the possibility that another cell-associated proteases capable of binding active neuroserpin functions in this capacity. In summary, neuroserpin levels appear to be carefully regulated by LRP and an unidentified cofactor, and this pathway may be critical for maintaining the balance between proteases and inhibitors.