Distinct Patterns of Genetic Variations in Potential Functional Elements in Long Noncoding RNAs

Non‐protein‐coding RNAs have increasingly been shown to be an important class of regulatory RNAs having significant roles in regulation of gene expression. The long noncoding RNA (lncRNA) gene family presently constitutes a large number of noncoding RNA (ncRNA) loci almost equaling the number of protein‐coding genes. Nevertheless, the biological roles and mechanisms of the majority of lncRNAs are poorly understood, with exceptions of a very few well‐studied candidates. The availability of genome‐scale variation datasets, and increasing number of variant loci from genome‐wide association studies falling in lncRNA loci have motivated us to understand the patterns of genomic variations in lncRNA loci, their potential functional correlates, and selection in populations. In the present study, we have performed a comprehensive analysis of genomic variations in lncRNA loci. We analyzed for patterns and distributions of genomic variations with respect to potential functional domains in lncRNAs. The analysis reveals a distinct distribution of variations in subclasses of long ncRNAs and in potential functional domains of lncRNAs. We further examined signals of selections and allele frequencies of these prioritized set of lncRNAs. To the best of our knowledge, this is the first and comprehensive large‐scale analysis of genetic variations in long ncRNAs.     

Optimization of immunohistochemical detection of collagen type II in osteochondral sections by comparing decalcification and antigen retrieval agent combinations

Bone containing tissues such as osteochondral joint are resistant to routine tissue processing, therefore require decalcification. This technique causes removal of mineral salts, but in the process may macerate the organic tissue, hence the need for tissue fixation. Such severe processing demands careful antigen retrieval to necessitate optimal staining. The aim of our study was to compare five different antigen retrieval protocols (heat retrieval and protein digestion) following decalcification of rabbit knee joints using two different techniques (20% formic acid and 10% ethylenediamine-tetra acetic acid: EDTA). Osteochondral sections were compared based on time required for decalcification, ease of sectioning, morphological integrity using HE staining and antigen preservation (Collagen type II) using immunohistochemistry. The two decalcification solutions did not impair the tissue morphology and ease of sectioning. Joints processed with formic acid decalcified four times faster than EDTA. Among the five antigen retrieval approaches, maximal collagen II uptake with minimal nonspecific staining was found with protein digestion (pronase and hyaluronidase) in both formic acid and EDTA sections. For osteo-chondral sections, we recommend using 10% EDTA for decalcification and pronase plus hyaluronidase for antigen retrieval if maintaining tissue morphology is crucial, whereas if time is of the essence, 20% FA with pronase plus hyaluronidase is the faster option while still preserving structural integrity. Clin. Anat. 33:343–349, 2020. © 2019 Wiley Periodicals, Inc.     

Recruitment of complement factor H-like protein 1 promotes intracellular invasion by group A streptococci

Numerous microbial pathogens exploit complement regulatory proteins such as factor H (FH) and factor H-like protein 1 (FHL-1) for immune evasion. Fba is an FHL-1 and FH binding protein expressed on the surface of the human pathogenic bacterium, Streptococcus pyogenes, a common agent of pharyngeal, skin, and soft-tissue infections. In the present study, we demonstrate that Fba and FHL-1 work in concert to promote invasion of epithelial cells by S. pyogenes. Fba fragments were expressed as recombinant proteins and assayed for binding of FHL-1 and FH by Western blotting, enzyme-linked immunosorbent assay, and surface plasmon resonance. A binding site for FHL-1 and FH was localized to the N-terminal half of Fba, a region predicted to contain a coiled-coil domain. Deletion of this coiled-coil domain greatly reduced FHL-1 and FH binding. PepSpot analyses identified a 16-amino-acid segment of Fba which overlaps the coiled-coil domain that binds both FHL-1 and FH. To localize the Fba binding site in FHL-1 and FH, surface plasmon resonance was used to assess the interactions between the streptococcal protein and a series of recombinant FH deletion constructs. The Fba binding site was localized to short consensus repeat 7 (SCR 7), a domain common to FHL-1 and FH. SCR 7 contains a heparin binding site, and heparin was found to inhibit FHL-1 binding to Fba. FHL-1 promoted entry of Fba(+) group A streptococci into epithelial cells in a dose-dependent manner but did not affect invasion by an isogenic fba mutant. To our knowledge, this is the first report of a bacterial pathogen exploiting a soluble complement regulatory protein for entry into host cells.     

Aspiration cytology diagnosis of a primary amyloid tumor of thoracic vertebra: a case report

Isolated primary amyloid tumor of bone is rare; however, preoperative diagnosis can be rewarding because the prognosis is excellent. There are no clinical or roentgenographic criteria that can establish this diagnosis. There are few previous reports of fine-needle aspiration (FNA) where diagnosis of amyloidoma was made retrospectively. They describe the presence of extracellular hyaline material along with plasma cells and lymphocytes. A 35-year-old female was referred to the FNA clinic with swelling in the right upper chest wall. Radiologic findings revealed a destructive lytic lesion involving the bodies of D1 and D2 vertebrae with extension into surrounding soft tissue. Repeated FNA smears were hypocellular but had abundant homogeneous flocculent material, which stained positive with Congo red. A few plasma cells and foreign-body giant cells were also seen. We conclude that preoperative FNA cytology diagnosis of amyloid tumor is possible. Hypocellular smears with flocculent material, plasma cells, and foreign-body giant cells in absence of granulation tissue should suggest the diagnosis.     

Retino-hypothalamic-pineal hypothesis in the pathophysiology of primary headaches

Primary headaches include migraine, tension, cluster headaches, paroxysmal hemicrania and miscellaneous headaches unassociated with structural lesions. A putative role of the retino-hypothalamic-pineal (RHP) axis in the pathophysiology of primary headaches is reviewed in terms of (1) retinal dysfunction, (2) hypothalamic dysfunction and human circadian desynchrony, (3) pineal melatonin dysfunction and (4) rostral limbic dysfunction mediating the human stress response. Unified RHP hypothesis is proposed, suggesting that an acute, periodic or chronic, circadian desynchrony and dysfunction of the whole or part of the RHP axis is implicated in the pathophysiology of primary headaches. Supportive evidence for the RHP hypothesis, including recent PET studies showing changes in dorsal pons, hypothalamus and rostral limbic structures, is presented.     

Spectral evaluation of aging effects on blood pressure and heart rate variations in healthy subjects

The background to heart rate variability (HRV) and blood pressure variability (BPV), and their determinants and physiological correlates, remain obscure. The impact of age must be taken into account if HRV and BPV are used for predictive purposes in clinical settings. Healthy subjects show wide inter-individual variation in their heart rate behaviour and the factors affecting heart rate dynamics are not well known. This paper has undertaken to evaluate heart rate variability (HRV) and baroreflex sensitivity (BRS) in a random sample of subjects without evidence of heart disease, and to estimate the relation of HRV and BPV behaviour to age. The aim of this study was to analyse the effects of ageing on HRV and BPV for simultaneous recordings of electrocardiograph (ECG) and blood pressure (BP) signals at rest in healthy subjects. We studied eight young (21-34 years old) and eight elderly (68-85 years old) rigorously screened subjects from the Fantasia Database to make the reproducibility and comparability of the results more extensive. Time- and frequency-domain analysis of HRV and BPV was performed on 5-minute ectopic-free recordings. BRS on the heart was estimated by frequency-domain analysis of spontaneous variability of systolic blood pressure (SBP) and RR interval. It has been observed that compared to young the elderly subjects have (i) diminished HRV; (ii) a shift in the power spectral density and median frequency to low frequency side for HRV and to higher frequency side for BPV; and (iii) increased low-frequency alpha index and decreased high-frequency alpha index of BRS with overall alpha index augmented. The results convey that normal ageing in the absence of disease is associated with lesser parasympathetic regulation of heart rate. Thus it is concluded that the age is an important factor to be considered for prognosis and diagnosis by HRV and BPV. For reliable clinical applications, more research needs to be done on a broad spectrum of subjects. In addition, these observations will prove to be useful for dynamic modelling of cardiovascular regulation for testing the authentication of new techniques for analysis purposes.     

Genetic landscape of human platelet antigen variants in the Indian population analysed from 1029 whole genomes

Genetic variants in human platelet antigens (HPAs) considered allo- or auto antigens are associated with various disorders, including neonatal alloimmune thrombocytopenia, platelet transfusion refractoriness and post-transfusion purpura. Although global differences in genotype frequencies were observed, the distributions of HPA variants in the Indian population are largely unknown. This study aims to explore the landscape of HPA variants in India to provide a basis for risk assessment and management of related complications. Population-specific frequencies of genetic variants associated with the 35 classes of HPAs (HPA-1 to HPA-35) were estimated by systematically analysing genomic variations of 1029 healthy Indian individuals as well as from global population genome datasets. Allele frequencies of the most clinically relevant HPA systems in the Indian population were found as follows, HPA-1a – 0.884, HPA-1b – 0.117, HPA-2a – 0.941, HPA-2b – 0.059, HPA-3a – 0.653, HPA-3b – 0.347, HPA-4a – 0.999, HPA-4b – 0.0010, HPA-5a – 0.923, HPA-5b – 0.077, HPA-6a – 0.998, HPA-6b – 0.002, HPA-15a – 0.582 and HPA-15b – 0.418. This study provides the first comprehensive analysis of HPA allele and genotype frequencies using large scale representative whole genome sequencing data of the Indian population.     

Fractures of the shaft of humerus

Humeral shaft fractures account for 1–3% of all fractures. Non-surgical management with functional bracing is arguably the standard of care for most humeral shaft fractures.It results in high union rates and in general the outcome is excellent. Surgical management is indicated in some cases, such as open fractures, polytrauma, those with associated vascular injury, pathological fractures, floating elbow injuries and fractures that have failed non-surgical management. Options for surgical fixation include open reduction and internal fixation with plate osteosynthesis, antegrade or retrograde intramedullary nailing and external fixation. Both plate osteosynthesis and intramedullary nailing yield similar results, with a slightly higher rate of complications and re-operations with nailing. A high incidence of radial nerve injury has been associated with humeral shaft fractures and should be actively sought. The management of nerve injuries is still a matter of debate, however; initial expectant treatment with delayed exploration if needed seems to yield similar results to early exploration. Proper patient selection is key to achieving good outcomes with both surgical and non-surgical management of these injuries.     

Regulation of prepubertal dynorphin secretion in the medial basal hypothalamus of the female rat

The onset of puberty is the result of an increase in secretion of hypothalamic gonadotrophin‐releasing hormone (GnRH). This action is a result of not only the development of stimulatory inputs to its release, but also the gradual decrease in inhibitory inputs that restrain release of the peptide prior to pubertal onset. Dynorphin (DYN) is one of the inhibitory inputs produced in the medial basal hypothalamus (MBH); however, little is known about what substance(s) control its prepubertal synthesis and release. Because neurokinin B (NKB) increases in the hypothalamus as puberty approaches, we considered it a candidate for such a role. An initial study investigated the acute effects of an NKB agonist, senktide, on the secretion of DYN from MBH tissues incubated in vitro. In other experiments, central injections of senktide were administered to animals for 4 days then MBHs were collected for assessment of DYN synthesis or for the in vitro secretion of both DYN and GnRH. Because insulin‐like growth factor (IGF)‐1 has been shown to play an important role at puberty, additional animals received central injections of this peptide for 4 days to assess NKB and DYN synthesis or the in vitro secretion of NKB. The results obtained show that senktide administration up‐regulates the NKB receptor protein, at the same time as suppressing the DYN and its receptor. Senktide consistently suppressed DYN and elevated GnRH secretion in the same tissue incubates from both the acute and chronic studies. IGF‐1 administration caused an increase in NKB protein, at the same time as decreasing DYN protein. Furthermore, the central administration of IGF‐1 caused an increase in NKB release, an action blocked by the IGF‐1 receptor blocker, JB‐1. These results indicate that the IGF‐1/NKB pathway contributes to suppressing the DYN inhibitory tone on prepubertal GnRH secretion and thus facilitates the puberty‐related increase in the release of GnRH to accelerate the onset of puberty.