Y chromosomal noncoding RNAs regulate autosomal gene expression via piRNAs in mouse testis

Background

Deciphering the functions of Y chromosome in mammals has been slow owing to the presence of repeats. Some of these repeats transcribe coding RNAs, the roles of which have been studied. Functions of the noncoding transcripts from Y chromosomal repeats however, remain unclear. While a majority of the genes expressed during spermatogenesis are autosomal, mice with different deletions of the long arm of the Y chromosome (Yq) were previously also shown to be characterized by subfertility, sterility and sperm abnormalities, suggesting the presence of effectors of spermatogenesis at this location. Here we report a set of novel noncoding RNAs from mouse Yq and explore their connection to some of the autosomal genes expressed in testis.

Results

We describe a set of novel mouse male-specific Y long arm (MSYq)-derived long noncoding (lnc) transcripts, named Pirmy and Pirmy-like RNAs. Pirmy shows a large number of splice variants in testis. We also identified Pirmy-like RNAs present in multiple copies at different loci on mouse Y chromosome. Further, we identified eight differentially expressed autosome-encoded sperm proteins in a mutant mouse strain, XY^RIIIqdel (2/3 Yq-deleted). Pirmy and Pirmy-like RNAs have homology to 5′/3′UTRs of these deregulated autosomal genes. Several lines of experiments show that these short homologous stretches correspond to piRNAs. Thus, Pirmy and Pirmy-like RNAs act as templates for several piRNAs. In vitro functional assays reveal putative roles for these piRNAs in regulating autosomal genes.

Conclusions

Our study elucidates a set of autosomal genes that are potentially regulated by MSYq-derived piRNAs in mouse testis. Sperm phenotypes from the Yq-deleted mice seem to be similar to that reported in inter-specific male-sterile hybrids. Taken together, this study provides novel insights into possible role of MSYq-derived ncRNAs in male sterility and speciation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-021-01125-x.

Medical thoracoscopic cryoevacuation: A novel technique to manage retained hemothorax

Hemothorax is an important complication of blunt trauma chest. The presentation may be delayed, especially in elderly patients with multiple rib fractures. Delayed presentation can be associated with retained hemothorax where a simple chest drain is often insufficient to evacuate the pleural cavity. Video-assisted thoracoscopy surgery is often used to manage such patients in a minimally invasive manner. Here, we demonstrate a novel application of flexi-rigid thoracoscopy with CryoProbe^® for evacuation of retained hemothorax in an elderly woman through a subcentimeter incision.

Bronchoscopic lung cryobiopsy: An Indian association for bronchology position statement

BACKGROUND

Bronchoscopic lung cryobiopsy (BLC) is a novel technique for obtaining lung tissue for the diagnosis of diffuse parenchymal lung diseases. The procedure is performed using several different variations of technique, resulting in an inconsistent diagnostic yield and a variable risk of complications. There is an unmet need for standardization of the technical aspects of BLC.

METHODOLOGY

This is a position statement framed by a group comprising experts from the fields of pulmonary medicine, thoracic surgery, pathology, and radiology under the aegis of the Indian Association for Bronchology. Sixteen questions on various technical aspects of BLC were framed. A literature search was conducted using PubMed and EMBASE databases. The expert group discussed the available evidence relevant to each question through e-mail and a face-to-face meeting, and arrived at a consensus.

RESULTS

The experts agreed that patients should be carefully selected for BLC after weighing the risks and benefits of the procedure. Where appropriate, consideration should be given to perform alternate procedures such as conventional transbronchial biopsy or subject the patient directly to a surgical lung biopsy. The procedure is best performed after placement of an artificial airway under sedation/general anesthesia. Fluoroscopic guidance and occlusion balloon should be utilized for positioning the cryoprobe to reduce the risk of pneumothorax and bleeding, respectively. At least four tissue specimens (with at least two of adequate size, i.e., ≥5 mm) should be obtained during the procedure from different lobes or different segments of a lobe. The histopathological findings of BLC should be interpreted by an experienced pulmonary pathologist. The final diagnosis should be made after a multidisciplinary discussion. Finally, there is a need for structured training for performing BLC.

CONCLUSION

This position statement is an attempt to provide practical recommendations for the performance of BLC in DPLDs.

The safety and efficacy of different methods for obtaining transbronchial lung cryobiopsy in diffuse lung diseases

INTRODUCTION

Most data on transbronchial lung cryobiopsy (TBLC) are from single centers, with little evidence on the outcome of different methods for performing TBLC.

OBJECTIVE

To report the diagnostic yield and safety of TBLC with different procedural techniques.

MATERIALS AND METHODS

Retrospective multicenter study of subjects who underwent TBLC for the diagnosis of diffuse parenchymal lung diseases (DPLDs). The procedure was performed using various methods: flexible or rigid bronchoscopy, with or without the use of fluoroscopy or occlusion balloon.

RESULTS

In total, 128 subjects (59% women) with a mean age of 48.9 years were included. The overall diagnostic yield of TBLC was 78.1%, with a definite diagnosis on multidisciplinary discussion made in 57 (44.5%) subjects. On a multivariate analysis, the diagnostic yield was associated with the number of biopsies taken {ajdusted odds ratio [AOR] [95% confidence interval (CI)], 2.17 [1.29-3.67]}. The incidence of pneumothorax was lower in subjects who underwent TBLC with fluoroscopic guidance (5.9% vs 20.9%), [AOR (95% CI), 0.26 (0.07-0.94)]. Moderate-to-severe bleeding occurred less frequently when an occlusion balloon was used [1.8% vs 35.7%; AOR (95% CI), 0.02 (0.001-0.18)], after adjusting for age, use of fluoroscopy, number of biopsies obtained and number of lobes sampled. Four deaths occurred; 2 because of acute exacerbation of idiopathic pulmonary fibrosis.

CONCLUSIONS

Transbronchial lung cryobiopsy was found to offer a reasonable yield in the diagnosis of DPLDs. The incidence of pneumothorax and moderate-to-severe bleeding was lower with the use of fluoroscopy and an occlusion balloon, respectively.

A multicenter study on the utility and safety of EBUS-TBNA and EUS-B-FNA in children

BACKGROUND AND AIM

Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) and endoscopic ultrasound with an echobronchoscope-guided fine needle aspiration (EUS-B-FNA) are useful modalities in the evaluation of mediastinal lymphadenopathy in adults; however, there is sparse data in children. The aim of this multicenter study is to describe the efficacy and safety of EBUS-TBNA and EUS-B-FNA in children with mediastinal lymphadenopathy of undefined etiology.

METHODS

Retrospective analysis of consecutive pediatric (<18 years) subjects who underwent EBUS-TBNA or EUS-B-FNA for the evaluation of mediastinal lymphadenopathy. The demographic characteristics, indications, procedural details, pathological, cytological and microbiological diagnosis, diagnostic yield, and complications are presented.

RESULTS

Of the 3,424 EBUS/EUS-B-FNA procedures, 67 (1.9%) were performed in the pediatric (3-17 years) population. Of these, 19 (28.4%) were performed in children ≤12 years of age. Overall, EBUS-TBNA and EUS-B-FNA were performed in 53 and 12 subjects, respectively. In two subjects, no significant lymph node was seen on EBUS. The procedure was performed under moderate sedation in spontaneously breathing subjects in 54 (80.6%) instances. An adequate sample was obtained in 60 (92.3%) subjects while a diagnostic sample was obtained in 37 (56.9%) of the 65 subjects. The diagnostic yield was not significantly different (P = 0.59) between EBUS-TBNA (58.5%) and EUS-B-FNA (50%). The sensitivity of EBUS-TBNA/EUS-B-FNA was 79.1% and led to a change in diagnosis in 28 (41.8%) subjects. Complications, all minor were encountered in six (8.9%) subjects.

CONCLUSIONS

EBUS-TBNA and EUS-B-FNA are safe techniques with a good diagnostic yield in the evaluation of children with mediastinal lymphadenopathy. Pediatr Pulmonol. 2016;51:1031-1039. © 2016 Wiley Periodicals, Inc.

Whistle lower-better late than never

16 years old boy with childhood history of chronic respiratory symptoms requiring several admissions presented with recent worsening of symptoms. Chest x-ray showed left lower lobe collapse and flexible bronchoscopy revealed stenosis of left main bronchus. Foreign body was seen beyond the stenosis, which was removed after dilatation of narrowed bronchus under general anesthesia using rigid bronchoscopy. Patient's father gave a history of aspiration of whistle 14 years ago, which had then been removed. Patient is now free of symptoms after removal of foreign body.

Evaluation of lactate dehydrogenase enzyme activity in saliva and serum of oral submucous fibrosis patients

BACKGROUND

Of all oral precancerous conditions, Oral Submucous Fibrosis is of greater concern because of its disabling nature and relative greater chances of malignant transformation. This malignant transformation involves glycolytic pathways that can alter lactate dehydrogenase levels. Therefore the aim of this study was to estimate the LDH levels in saliva and serum of subjects with OSMF and to compare them with healthy controls and to correlate the relationship between pathogenesis of OSMF and the LDH enzyme.

METHODS

Sixty Subjects were recruited for this study and divided into two groups, 30 subjects with OSMF (Group A) and 30 healthy controls (Group B). Venous blood and unstimulated whole saliva measuring 1 ml was collected from each of these evaluated for LDH levels using the standard kit method. The data obtained were subjected to statistical analysis using the SPSS software version 17.

RESULTS

The average salivary LDH value for Group A was 606.83 ± 60.09 U/l and for Group B was 80.73 ± 20.06 U/l. salivary LDH was greater in group A than Group B and this was statistically significant. On comparing the serum and salivary LDH in Group A with the clinical staging of OSMF, the results were not statistically significant. Similarly no statistically significant relationship was found on comparing the serum and salivary LDH in Group A (OSMF subjects) with duration of habit.

CONCLUSION

This study provides additional rationale for the role of salivary LDH in the early diagnosis and prognosis of oral submucous fibrosis.

Surgical correction of excessive gingival display in class I vertical maxillary excess: Mucosal strip technique

There are several conditions that results in excessive gingival display. In case of class I vertical maxillary excess the reason for this excessive display is the hypermobile lip. Though orthodontic treatment is the choice of treatment, surgical repositioning along with the orthodontics gives more predictable and stable results. This case report discusses cosmetic surgical management of case with class I vertical maxillary excess with excessive gingival display. The technique involves removal of strip of mucosal tissue from the labial vestibule thereby limiting the retraction of elevator muscles.

Giant cell fibroma: A clinicopathological study

OBJECTIVE

Giant cell fibromas (GCF) of the oral cavity are found predominantly in Caucasians and rarely in other races. This retrospective study was done to evaluate the clinicopathological features of GCFs in a sample of Indian population.

MATERIALS AND METHODS

21 oral GCF cases were investigated from the year 1995 to 2010. Clinical data and microscopic features were reviewed and analyzed.

RESULTS

The mean age of patients at the time of diagnosis was 39years. Oral GCF occurred in patients between 6 and 67 years of age. The lesions were 4-17 mm in greatest dimension. GCF frequently has the provisional diagnosis of fibroma or papilloma. All tumors were treated by total surgical excision and no recurrence was reported. The consistent and diagnostic feature was the presence of large stellate giant cells, usually with one or two nuclei. Multinucleated giant cells were seen occasionally. These giant cells were most numerous in the connective tissue beneath the epithelium.

CONCLUSION

Though there are distinct histopathologic features for GCF, its clinical presentation and prognosis are similar to the conventional fibroma/fibroepithelial polyp.

Cognitive assessment and health education in children from two different cultures

This paper presents research aimed at investigating high level comprehension and problem solving processes in children in two different countries, India and Colombia. To this end, we use a series of health-related cognitive tasks as assessment tools. In one study, we also examine children's performance on these cognitive tasks, in relation to their nutritional status and parasitic load. The ages of the children tested ranged from 2 through 14 years. The tasks were designed to assess comprehension of sequences, organization of concepts, understanding of health routines (hygiene practices) and evaluation of hypothesis and evidence. The results show that children approach the different tasks with a baggage of beliefs and local knowledge of the world which determines their reasoning process, their comprehension and their problems solving. The results are discussed in terms of cognitive assessment approaches, as applied to classroom instruction. Given that children construct their understanding of reality based on what they already know and that education does not take this into account, we recommend that assessment tools should be devised that can tap prior knowledge and understanding, such that this can be analyzed and understood in relation to knowledge taught in the classroom. Current educational assessment fails in such an endeavor.

Reasoning about childhood nutritional deficiencies by mothers in rural India: a cognitive analysis

This study examines reasoning about the cause and treatment of three types of childhood protein energy malnutrition (PEM) by 108 mothers in rural South India. The mothers were interviewed and their explanations of the childhood nutritional problems were verbally recorded, transcribed and then analyzed using cognitive methods of analysis. The results indicated that knowledge and practices associated with traditional systems of Indian medicine prevalent in rural areas greatly influenced the mothers' reasoning. Their explanations were shown to have story-like structures, with sequences of events linked by strong causal explanations. Mothers with higher levels of formal education showed greater verbal use of concepts related to biomedical theories of nutritional disorders. However, their interpretations of these concepts were still based on the traditional theory. The study revealed both positive and negative aspects of traditional knowledge and beliefs for adequate child nutrition and health. The development of improved instructional strategies for nutrition and health education in relation to knowledge organization is discussed in the context of rural India.

Proximity and ligand-induced movement of interdomain residues in myosin subfragment 1 containing trapped MgADP and MgPPi probed by multifunctional cross-linking

The conformations of myosin subfragment 1 containing trapped MgADP or MgPPi have been studied by investigating the spatial disposition of the remainder of the subfragment 1 structure to the covalently bridged ATPase-related thiols SH1 and SH2. This has been done by synthesizing a trifunctional photoactivatable reagent 4,4'-bis(N-maleimido)benzophenone and reacting it with subfragment 1 in the presence of these ligands. Modification of subfragment 1 by this reagent mimics closely the changes in the ATPase properties as noted previously for modification with p-phenylenedimaleimide. In addition, noncovalent trapping of nucleotide also results, presumably by the bridging of the SH1 and SH2 thiols. On photolysis, cross-linking from the reagent bridging the thiols to other regions in subfragment 1 can be observed, but the extent and course of the photoinduced cross-linking depend on the nature of the trapped ligand. For subfragment 1 with trapped MgADP, a high efficiency cross-linking occurs between the 21-kDa segment and the 50-kDa segment. With MgPPi as the trapped ligand, low efficiency cross-linking occurs between the bridged thiols and either the 27-kDa N-terminal or the 50-kDa segments of the heavy chain. These results indicate that without the adenosine moiety, the binding of MgPPi to subfragment 1 leaves the protein in a flexible state so that residues in both the 27-kDa and the 50-kDa segment can move within the cross-linking span of the activated benzophenone triplet. The trapping of MgADP apparently results in a more rigid state for the subfragment 1 in which residues in the 50-kDa segment are spatially close to the bridged thiols, thus enabling photocross-linking to proceed with higher efficiency.

Substructure of skeletal myosin subfragment 1. Preferential destabilization of a domain by methanol and its effect on catalytic activity

Evidence is presented that in increasing concentrations of methanol the structure of the subfragment 1 is perturbed in such a way that the Mr = 50,000 central portion of the associated heavy chain is preferentially unfolded. This unfolding is accompanied by the loss in ATPase function where the rate of inactivation can be correlated with the loss in the amount of the Mr = 50,000 fragment generated under standard tryptic digestion conditions. The residual protein appears to be a soluble aggregate of a complex of the Mr = 27,000, 21,000, and light chain with no intact Mr = 50,000 fragment. Tryptic digestions in the presence of MgATP are restricted to the usual linker regions and the Mr = 50,000 fragment is completely protected from attack. Binding of actin to subfragment 1 also results in the protection of the Mr = 50,000 segment and of the Mr = 50,000/21,000 junction from tryptic attack. The data suggest that, in terms of methanolic perturbation, the subfragment 1 appears to be comprised of two domains with differential stability. One domain appears to be the central Mr = 50,000 segment of the heavy chain which is preferentially unfolded by methanol and requires the presence of MgATP or of actin for stabilization. The other domain is more stable and appears to consist of the interacting Mr = 27,000, 21,000, and light chain. The results also suggest that the integrity of the Mr = 50,000 segment is essential for the ATPase function of the protein.

Isolation of heavy chain isoenzymes of myosin subfragment 1 by high performance ion exchange chromatography

The procedure of high performance ion-exchange chromatography has been used to fractionate subfragment 1 of myosin (SF1) into its isoenzymic forms. In contrast to conventional ion-exchange procedures which yield two fractions corresponding to SF1(A1) and SF1(A2), the high performance liquid chromatography (HPLC) procedure resolves SF1 into four discrete fractions. The first pair that is eluted appears to be A1-containing isoenzymes while the latter pair corresponds to the A2 forms based on their polypeptide compositions by gel electrophoresis in the presence of sodium dodecyl sulfate. By gel electrophoresis under nondenaturing conditions it is not possible to differentiate between the two fractions corresponding to each isoenzyme. Although very minor differences between the fractions can be seen by the presence of extraneous peptides, these are present in far below stoichiometric amounts and, therefore, make it very unlikely that the superior fractionation by the HPLC procedure is based on their presence. An examination of the heavy chain heterogeneity in each of these fractions by peptide mapping revealed that the extra separation was based on this factor. Thus the HPLC procedure is capable of providing separation of SF1 into heavy chain-based isozymes as well as the light chain forms. ATPase measurements of these fractions reveal only minor differences in the Ca2+- and EDTA-activated ATPase.

The free heavy chain of vertebrate skeletal myosin subfragment 1 shows full enzymatic activity

Vertebrate skeletal fast-twitch muscle myosin subfragment 1 is comprised of a heavy polypeptide chain of 95,000 daltons and one alkali light chain of either 21,000 daltons (A1) or 16,500 daltons (A2). In the present study, the heavy chain of subfragment 1 has been separated from the alkali light chain under nondenaturing conditions resembling those in vivo. The heavy chain exhibits the same ATPase activity as myosin subfragment 1, indicating that the heavy chain alone contains the catalytic site for ATP hydrolysis and that the alkali light chains are nonessential for activity. The free heavy chain associates readily at 4 degrees C or 37 degrees C with free A1 or A2 to form the subfragment 1 isozymes SF1(A1) or SF1(A2) respectively. Actin activates the MgATPase activity of the heavy chain in the same manner as occurs with the native isozyme, indicating that the heavy chain possesses the actin binding domain.

Subunit interactions of skeletal muscle myosin and myosin subfragment 1. Formation and properties of thermal hybrids

The formation of hybrid myosin and subfragment 1 species by incubation of these proteins with free alkali light chains at physiological ionic and temperature conditions is described. Exchange of bound alkali light chain on myosin by free alkali light chains under these conditions is readily demonstrated from the subunit composition of the isolated myosin. Therefore, the light chain exchange previously described for the one-headed subfragment 1 [Sivaramakrishnan, M., & Burke, M (1981) J. Biol. Chem. 256, 2607--2610] also occurs in the two-headed myosin molecule. It is found than the isozyme to hybrid transformation is dependent on both the temperature and the ionic strength of the incubation mixture but is relatively independent of pH in the range 6.5--8.0. A comparison of the SF1(A1) leads to SF1(A2)h system with the SF1(A2) leads to SF1(A1)h system indicates that more hybrid is formed in the latter case. With the assumption that hybrid formation reflects the degree of reversible dissociation exhibited by the isozyme, under the particular experimental condition employed, the data signify that the subunit interactions in the two isozymes are not identical and that the heavy chain--A1 interactions are significantly more stable that the heavy chain--A2 ones. An examination of the ATPase properties of the thermal hybrids in the presence and absence of actin indicates close similarities to their corresponding "native" isozymic counterparts.

Subunit interactions in myosin subfragment 1. Subunit scrambling is independent of catalytic center involvement

Evidence is presented that, under conditions of 4.7 M NH4Cl and 10 mM Mg-ATP where no subunit dissociation can be detected by transport methods, a dynamic equilibrium exists in subfragment 1 between the associated and dissociated subunits. This is readily discerned by the formation of hybrid subfragment 1 species when a subfragment 1 isozyme is incubated with excess free light chains of the alternate isozyme. A similar process occurs with p-N,N'-phenylenedimaleimide (pPDM)-modified subfragment 1 containing [14C]Mg-ADP, but in this case, although extensive amounts of hybrid are formed, no loss of the trapped nucleotide is observed. Subunit scrambling without loss of the trapped nucleotide is apparent from incubating pPDM-SF1(A2)-[14C]Mg-ADP with unmodified SF1(A1) under similar conditions since the mixture subsequently contains SF1(A1), SF1(A2)h, pPDM-SF1(A1)h-[14C]Mg-ADP and pPDM-SF1(A2)-[14C]Mg-ADP. These data show that the nucleotide trapped in the presumptive active site does not escape during the dissociation-reassociation cycle, and suggest that the ATPase site resides solely on the heavy chain.

Studies on the interaction of myosin subfragment 1 and immobilized nucleotide. Evidence for different binding domains operating under different solvent conditions

The binding interaction between myosin subfragment 1 isozymes with immobilized nucleotide, where they show differential behavior, has been examined. By employing subfragment 1 hybrids formed by crosses between heavy and alkali light chains, it is possible to demonstrate that the differential behavior is modulated by the alkali light chain component of the protein and not by differences in the heavy chain subunits in these isozymes resulting from the proteolytic treatment used in their formation. The fact that the free alkali light chains show weak differential binding under these conditions suggests that the binding in the case of the subfragment 1 isozymes may occur at a site distinct from the ATPase site. This was substantiated by examining the behavior of subfragment 1 containing [14C] MgADP noncovalently trapped in the ATPase site by the bifunctional reagent N, N-p-phenylenedimaleimide, on agarose-ATP. The data suggest that different ATP binding domains may be operating in myosin depending on the ionic conditions being employed.

Studies on the subunit interactions of skeletal muscle myosin subfragment 1. Evidence for subunit exchange between isozymes under physiological ionic strength and temperature

Evidence is presented that under physiological conditions of ionic strength and temperature, where myosin Subfragment 1 is hydrolyzing MgATP, the interaction between its subunits is extremely labile. Incubation of [3H]N-ethylmaleimide-SF1(A1) with N-ethylmaleimide-SF1(A2) in the presence of 10 mM MgATP at 37 degrees C resulted in the exchange of subunits between these isozymes. This is readily discernible from the subunit composition and distribution of the 3H label after separation of the isozymes by ion exchange chromatography. Moreover, incubation of unmodified SF1(A1) or SF1(A2) with the free Alkali light chains A2 and A1, respectively, under the same conditions led to the formation of significant amounts of the hybrid species. These findings suggest that in vivo the Alkali light chain-heavy chain interaction of Subfragment 1 is in a state of dynamic equilibrium between associated and dissociated states.