Ancient hybridization and repetitive element proliferation in the evolutionary history of the monocot genus Amomum (Zingiberaceae)

Genome size variation is a crucial aspect of plant evolution, influenced by a complex interplay of factors. Repetitive elements, which are fundamental components of genomic architecture, often play a role in genome expansion by selectively amplifying specific repeat motifs. This study focuses on Amomum, a genus in the ginger family (Zingiberaceae), known for its 4.4-fold variation in genome size. Using a robust methodology involving PhyloNet reconstruction, RepeatExplorer clustering, and repeat similarity-based phylogenetic network construction, we investigated the repeatome composition, analyzed repeat dynamics, and identified potential hybridization events within the genus. Our analysis confirmed the presence of four major infrageneric clades (A-D) within Amomum, with clades A-C exclusively comprising diploid species (2n = 48) and clade D encompassing both diploid and tetraploid species (2n = 48 and 96). We observed an increase in the repeat content within the genus, ranging from 84% to 89%, compared to outgroup species with 75% of the repeatome. The SIRE lineage of the Ty1-Copia repeat superfamily was prevalent in most analyzed ingroup genomes. We identified significant difference in repeatome structure between the basal Amomum clades (A, B, C) and the most diverged clade D. Our investigation revealed evidence of ancient hybridization events within Amomum, coinciding with a substantial proliferation of multiple repeat groups. This finding supports the hypothesis that ancient hybridization is a driving force in the genomic evolution of Amomum. Furthermore, we contextualize our findings within the broader context of genome size variations and repeatome dynamics observed across major monocot lineages. This study enhances our understanding of evolutionary processes within monocots by highlighting the crucial roles of repetitive elements in shaping genome size and suggesting the mechanisms that drive these changes.

CMV infection is a risk factor for hemorrhagic cystitis after hematopoietic stem cell transplantation

Hemorrhagic cystitis (HC) is a common complication after transplantation. The purpose of this study was to examine the incidence and risk factors for HC after hematopoietic stem cell transplantation (HSCT). The records of patients who underwent allogenic HSCT from January 2012 to December 2018 at our institution were retrospectively reviewed. Cox proportional regression and Kaplan-Meier analyses were performed to determine independent risk factors for HC. The statistical analysis was performed in May 2020. A total of 173 patients underwent HSCT, and 53 (30.6%) developed grade 2 or 3 HC cystitis at a median of 37 days (range - 5 to 98 days) after transplantation. Thirty-two patients developed moderate (grade 2) cystitis and 21 severe (grade 3) cystitis. Of the 173 patients, 61 developed acute graft-versus-host disease (GVHD) (median onset day 24) and 79 experienced cytomegalovirus (CMV) reactivation (median onset day 35). The relative risk (RR) of developing a CMV infection for patients with acute GVHD was 2.77 times that of patients without acute GVHD (P < 0.001). CMV infection was the only independent variable significantly associated with HC in both univariate and multivariate analyses. The estimated hazard ratio (HR) of CMV infection for the development of HC was 5.57 (95% confidence interval [CI]: 2.52 to 12.33, P < 0.001). CMV infection is an independent risk factor for the development of HC after HSCT, and acute GVHD is a risk factor for CMV reactivation. Decreasing the frequency of GVHD after HSCT may result in a lower frequency of HC.

Study of Left Ventricular Mass in Normal Nepalese Population

Background: A prospective study was conducted to find distribution of the left ventricular mass in normal adult Nepalese population in order to establish the upper reference limit. Materials and Methods: A total of 100 consecutive male and 100 female participants of age 18 years and above visiting for cardiac checkup were enrolled prospectively in this study.  Participants with hypertension, diabetes, obesity and significant cardiovascular disease were excluded. Results: Mean age of study population was 43 years. Mean left ventricular mass in total, male and female population was 127.45±29 gm, 136.48±30.64gm and 118.43±24.24 gm respectively.  Mean left ventricular mass index (LVMI) in total, male and female population was 74.52±15.78 gm/m2, 80.04±16.5 gm/m2 and 69.17±13.05 gm/m2 respectively. Left ventricular mass and left ventricular mass index increased with age, Body Mass Index, Systolic and Diastolic Blood Pressure, and were statistically significant (p-value <0.05). Conclusion: Normal left ventricular mass in Nepalese Population was found to be lesser in female compared to male.  Left ventricular mass increased with increasing Age and Body Mass Index.

Childhood Invasive Bacterial Disease in Kathmandu, Nepal (2005-2013)

BACKGROUND

Invasive bacterial disease (IBD; including pneumonia, meningitis, sepsis) is a major cause of morbidity and mortality in children in low-income countries.

METHODS

We analyzed data from a surveillance study of suspected community-acquired IBD in children <15 years of age in Kathmandu, Nepal, from 2005 to 2013 before introduction of pneumococcal conjugate vaccines (PCV). We detailed the serotype-specific distribution of invasive pneumococcal disease (IPD) and incorporated antigen and PCR testing of cerebrospinal fluid (CSF) from children with meningitis.

RESULTS

Enhanced surveillance of IBD was undertaken during 2005-2006 and 2010-2013. During enhanced surveillance, a total of 7956 children were recruited of whom 7754 had blood or CSF culture results available for analysis, and 342 (4%) had a pathogen isolated. From 2007 to 2009, all 376 positive culture results were available, with 259 pathogens isolated (and 117 contaminants). Salmonella enterica serovar Typhi was the most prevalent pathogen isolated (167 cases, 28% of pathogens), followed by Streptococcus pneumoniae (98 cases, 16% pathogens). Approximately, 73% and 78% of pneumococcal serotypes were contained in 10-valent and 13-valent PCV, respectively. Most cases of invasive pneumococcal disease (IPD) were among children ≥5 years of age from 2008 onward. Antigen and PCR testing of CSF for pneumococci, Haemophilus influenzae type b and meningococci increased the number of these pathogens identified from 33 (culture) to 68 (culture/antigen/PCR testing).

CONCLUSIONS

S. enterica serovar Typhi and S. pneumoniae accounted for 44% of pathogens isolated. Most pneumococcal isolates were of serotypes contained in PCVs. Antigen and PCR testing of CSF improves sensitivity for IBD pathogens.

Bone Marrow Mesenchymal Stem Cells-Derived Exosomal miR-425-5p Inhibits Acute Myeloid Leukemia Cell Proliferation, Apoptosis, Invasion and Migration by Targeting WTAP

Introduction

Acute myeloid leukemia (AML) is a predominant blood malignancy with high mortality and severe morbidity. AML is affected by microRNAs (miRNAs) loaded in exosomes derived from bone marrow mesenchymal stem cells (BM-MSCs). MiR-425-5p has been reported to participate in different cancer models. However, the function of BM-MSCs-derived exosomal miR-425-5p in AML is unclear.

Methods

The expression of miR-425-5p was measured by qRT-PCR in clinical AML samples. The immunophenotype of BM-MSCs was analyzed using antibodies against CD44, CD90, and CD105. The exosome was isolated from BM-MSCs. The effect of BM-MSCs-derived exosomal miR-425-5p on AML was analyzed by CCK-8 assay, Edu assay, transwell assay, flow cytometry in AML cells. qRT-PCR, luciferase reporter gene assay and Western blot analysis were also conducted in AML cells.

Results

The expression levels of miR-425-5p were decreased in CD34 + CD38-AML cells from primary AML patients compared to that from the bone marrow of healthy cases, and were reduced in exosomes from AML patients compared that from healthy cases. Similarly, miR-425-5p was also down-regulated in AML cell lines compared with BM-MSCs. MiR-425-5p was able to express in exosomes from BM-MSCs. CCK-8, Edu, transwell assay and flow cytometry analysis revealed that BM-MSCs-derived exosomal miR-425-5p significantly inhibited cell viability, Edu positive cells, invasion and migration, and induced apoptosis of AML cells. Meanwhile, the expression levels of cleaved PARP and cleaved caspase3 were increased by BM-MSCs-derived exosomal miR-425-5p in cells. MiR-425-5p inhibited the expression of Wilms tumor 1-associated protein (WTAP). Moreover, overexpression of WTAP could reverse the miR-425-5p-induced inhibition effect on AML cell proliferation, apoptosis, migration and invasion.

Conclusion

BM-MSCs-derived exosomal miR-425-5p inhibits proliferation, invasion and migration of AML cells and induced apoptosis of AML cells by targeting WTAP. Therapeutically, BM-MSCs-derived exosomal miR-425-5p may serve as a potential target for AML therapy.

MicroRNA‑93 knockdown inhibits acute myeloid leukemia cell growth via inactivating the PI3K/AKT pathway by upregulating DAB2

Acute myeloid leukemia (AML) is associated with a poor prognosis in elderly adults and currently lacks optimal treatment strategies. MicroRNAs (miRNAs or miRs) have increasingly been reported to be associated with AML progression; however, the mechanisms of action of miR-93 in AML with the involvement of disabled 2 (DAB2) are currently unknown. In the present study, miR-93 expression was assessed in patients with AML and in AML cell lines. The association between miR-93 expression and the pathological characteristics of patients with AML was analyzed. AML cells were then transfected to knockdown or overexpress miR-93 in order to elucidate its function in AML progression. The target gene of miR-93 was assessed using a dual-luciferase reporter gene assay. The expression levels of miR-93, DAB2 and phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT) pathway-related proteins were measured and in vivo experiments were conducted to confirm the results. It was observed that miR-93 was highly expressed in patients with AML and in AML cells. The knockdown of miR-93 in HL-60 cells inhibited AML cell proliferation and resistance to apoptosis, while the overexpression of miR-93 in THP-1 cells led to contrasting results. Moreover, miR-93 targeted DAB2 to inactivate the PI3K/AKT pathway, and the overexpression of DAB2 reversed the effects of miR-93 on THP-1 cell growth. Tumor volume, tumor weight, and the positive expression of Ki67, survivin and p53 were increased in THP-1 cells overexpressing miR-93. On the whole, the present study demonstrates that miR-93 is highly expressed in AML cells, and that the suppression of miR-93 inhibits AML cell growth by targeting DAB2 and inhibiting the PI3K/AKT pathway.

A Regulatory Loop Involving Notch and Wnt Signaling Maintains Leukemia Stem Cells in T-Cell Acute Lymphoblastic Leukemia

Leukemia-initiating cells play critical role in relapse, resistance to therapies and metastases but the mechanism remains largely elusive. We report that β-catenin is over-expressed in almost all T-ALL patients and flow sorted β-catenin^high fractions are highly resistant to therapy, leading to liver metastases in nude mice as well as dysregulated lncRNAs. Pharmacological inhibition through XAV-939 as well as si-RNA mediated inhibition of β-catenin is initially effective in re-sensitization to therapy, however, prolonged inhibition shifts dependency from β-catenin to Notch signaling, with particularly high levels of receptors Notch 1 and Notch 2. The results are verifiable in a cohort of T-ALL patients comprising of responders vs. those who have progressed, with β-catenin, Notch 1 and Notch 2 elevated in progressed patients. Further, in patients-derived cells, silencing of Notch 1 or Notch 2 does not counter resistance to β-catenin inhibition, rather pharmacological pan-Notch inhibition is needed to overcome resistance and its effect on in vitro tumor sphere formations as well as in vivo liver metastases. Thus, wnt and Notch signaling are part of a regulatory loop mutually compensating for each other in T-ALL, while ensuring the maintenance of stem cell phenotype.

HDAC8 promotes daunorubicin resistance of human acute myeloid leukemia cells via regulation of IL-6 and IL-8

The chemoresistance is one of the major challenges for acute myeloid leukemia (AML) treatment. We found that the expression of histone deacetylase 8 (HDAC8) was increased in daunorubicin (DNR) resistant AML cells, while targeted inhibition of HDAC8 by its specific siRNA or inhibitor can restore sensitivity of DNR treatment . Further, targeted inhibition of HDAC8 can suppress expression of interleukin 6 (IL-6) and IL-8. While recombinant IL-6 (rIL-6) and rIL-8 can reverse si-HDAC8-resored DNR sensitivity of AML cells. Mechanistical study revealed that HDAC8 increased the expression of p65, one of key components of NF-κB complex, to promote the expression of IL-6 and IL-8. It might be due to that HDAC8 can directly bind with the promoter of p65 to increase its transcription and expression. Collectively, our data suggested that HDAC8 promotes DNR resistance of human AML cells via regulation of IL-6 and IL-8.

CircRNA circ_0000190 inhibits the progression of multiple myeloma through modulating miR-767-5p/MAPK4 pathway

Background

Multiple myeloma (MM) accounts for 10% of all hematological malignancies. Dysregulation of microRNAs (miRNAs) or long non-coding RNAs (lncRNAs) has important impacts on progression of MM. Circular RNAs (circRNAs) are correlated with malignancy in the modulation of tumor progression. This study aims to investigate the effect of circ_0000190 on regulating the progression of MM.

Method

Microscopic examination via single molecule fluorescent in situ hybridization indicates the location of circ_0000190. qRT-PCR and Western blot were used to evaluate the expression of RNAs and proteins. Potential target of circ_0000190 was searched as miRNA, and examined by luciferase reporter assay. A computational screen was also conducted to search the potential target of miRNA. In vitro cell viability, proliferation, apoptosis assays and flow cytometric were performed to assess the effects of circ_0000190 and its target on MM. Mice model of human MM was established with subcutaneous xenograft tumor, qRT-PCR and western blot were performed to detect the underlying mechanisms of circ_0000190 on MM.

Results

Circ_0000190 was located in the cytoplasm, and down-regulated in both bone marrow tissue and peripheral blood, while the target of circ_0000190, miR-767-5p, was up-regulated, suggesting a negative correlation between them. The binding ability between circ_0000190 and miR-767-5p was confirmed by luciferase reporter assay. Moreover, circ_0000190 inhibited cell viability, proliferation and induced apoptosis of MM thus inhibiting cell progression, which is partially through the negative regulation of miR-767-5p. Mitogen-activated protein kinase 4 (MAPK4) is a direct target of miR-767-5p. In addition, over-expression of miR-767-5p promoted cell progression by directly targeting and regulating MAPK4. The MM model mice with administration of circ_0000190 suppressed tumor growth and progression.

Conclusion

Our results revealed that the ability of circ_0000190 to protect against MM was inherited through repression of miR-767-5p, and miR-767-5p might be a tumor drive through targeting MAPK4. Therefore, a novel role of circ_0000190 on regulating the progression of MM was found, and the clinical application of circRNAs might represent a strategy in MM.

Electronic supplementary material

The online version of this article (10.1186/s13046-019-1071-9) contains supplementary material, which is available to authorized users.

Effect of Maternal Socio-demographic Factors and Child Feeding Practice on Wasting Among Under Five Years Children in Slum Area of Rupandehi District in Nepal

INTRODUCTION

Childhood wasting although well studied elsewhere, it has not been well understood about in slum area of Nepal. This study aimed to assess effect of socio-demographic factors and child feeding practice in the determination of wasting among the children under five years of age in slum area of Nepal.

METHODS

A community based cross-sectional study was performed among 150 children under five years of age from the slum area of Nepal between 1st January and 28th February 2013 using simple random sampling techniques. Multivariate analyses were performed to determine factors associated with wasting controlling the potential confounders.

RESULTS

In a total of 150 under five years children, the prevalence of wasting was 56 (37.33%). The current study demonstrated that children of mothers from dalit Adjusted Odds Ratio (OR) 11.5; 95% CI: 03.1 - 41.3), aadibasi/janajati (AOR 4.6; 95% CI: 1.2 - 17.0), illiterate mothers (AOR 3.6; 95% CI: 1.1 - 13.6), laborer mothers (AOR 2.1; 95% CI: 1.1-9.4), child age group 25-36 months (AOR 2.8; 95% CI: 1.5-5.3), multiple child birth order (AOR 10.0; 95% CI: 2.5-25.0), children who were not fed colostrums (AOR 15.0; 95% CI: 1.25-10.0) were more likely to develop wasting compared to their counterparts.

CONCLUSIONS

As incremental childhood wasting is associated with maternal socio-demographic factors and child feeding practice, health promotion strategies should focus maternal socio-demographic factors, age of children and early initiation of breast feeding for the improved child nutrition in slum area of Nepal.

Spontaneous Expulsion of Ingested Foreign Bodies: Case Series and Review of Literature

Foreign body ingestion is a commonly seen event in emergencies, usually in children, psychiatric patients, chronic alcoholics, drug abusers and the elderly patients with poor fitting dentures as well as the mentally challenged individuals. While ingestion of foreign bodies into Gastrointestinal Tract (GIT) may be accidental (especially in children), or experimental (anal insertion by adults), it may be purely intentional as in smugglers of illicit drugs, jewels and other valuables so as to evade detection by the security. About, 90% of ingested foreign bodies pass through the gastrointestinal tract without complications, 1020% necessitate endoscopic removal, while only 1% of them will finally need surgical intervention. In clinical practice we often face the dilemma of choosing the appropriate treatment modality. We present five cases treated in the emergency ward of B P Koirala Institute of Health Sciences, Dharan, Nepal, emphasizing in a "waiting and close observation" policy. Among these cases, all expelled the foreign body spontaneously in their stool without any complications.Birat Journal of Health Sciences 2016 1(1): 78-82

MICROBIAL QUALITY OF MILK AVAILABLE IN KATHMANDU VALLEY

With an objective to find microbial quality of the market milk available in Kathmandu valley, this studywas conducted in the Microbiology Laboratory, Himalayan College of Agriculture Science and Technology(HICAST). Different milk brands were collected from different outlets in the valley and analyzed formicrobial quality. The samples were cultured using the standard microbiological techniques. Almost all thesamples showed the presence of bacterial growth including coliform bacteria. The bacterial isolates were of7 different genera. E. coli was the most frequently isolated organism (92%) followed by coagulase negativeStaphylococci (CONS) (24%). Other organisms isolated were Bacillus species, Staphylococcus aureus,Streptococcus species, Salmonella species, Shigella species. The culture results were similar to directmicroscopic count results and showed that bacterial contamination in some of the samples was too numerousto be counted. Thus, it was concluded that the market milk available in Kathmandu is contaminated withvarious types of microorganisms and does not meet the required standard. The dairy industries shouldwork seriously to maintain the standards of their products.* Integrated Bioscientific Research Group (BIOINT), Kupondol, Lalitpur, Nepal.** Himalayan College of Agriculture Science and Technology (HICAST), Gatthaghar, Bhaktapur, Nepal.Address for correspondence : Charu ArjyalIntegrated Bioscientific Research Group (BIOINT), Kupondol, Lalitpur, Nepal.Email: charuarjyal@hotmail.comKey Words: Microbiology, Contamination, Milk, Quality, Coliform.