High-Throughput Sequencing And Analysis Of'chromosome 1 Of Eimerl4 Tenella

Eimeria tenella is one of seven Eimeria species that causes avian coccidiosis. It is also highly pathogenic and is one of the three most common species occurring in the field. High-throughput sequencing of the 1.05M.b chromosomes one of Eimeria tenella (Houghton strain) revealed genomic information which may be usehl in the discovery of genes such as those involved in drug resistance, cellular regulation and integration, and mechanisms of invasion. High-throughput and random chromosomal shotgun sequencing resulted in 61 unfinished contigs representing full shotgun state of chromosome one nucleotide sequences which are ready into the finishing phase. Out of these contigs, 57 of them were arranged into 11 scaffolds whereas 4 contigs remain unordered. All the contigs represent 86.9% or 9.29-fold coverage of chromosome one. The quality of the assembly is assured with 94.1% of consistent paired reads with only 5824.3 (0.5%) errors expected. In addition, contiguity of the assembly vastly improved with the integrated BAC-end sequences and HAPPY map markers. Consensus level assessment showed 99.2% of the unfinished chromosomal sequence has expected error rate less than 1 per 10,000 bases (PHRAP score > 40) and only 7.6% of them need further polishing. The GC content of chromosome one is 49.35% and long-ranged excursions from its mean are found prominently in three regions whereas chromosomal wide GC fluctuations ranged from 35% to 60% at a 12kb window length analysis. GC skews were found to be correlated with the repeats rich regions of the chromosome. Telomeric sequence at both ends of the chromosome is derived as 'ITTAGGG / CCCTAAA with undefined real length. A centromeric like region with approximately 1,453bp was found in chromosome one with 81.3% AT composition. Chromosome one is expected to bear at least 25.3% of repetitive elements with the most prominent tandem repeat, TGC, which are distributed throughout the chromosome. The longest minisatellite, mstl, is 3,624bp in length and occurs as a single stretch in the chromosome. Besides that, there are a few under-characterized interspersed repeats such as LINE and DNA transposons which were found in the chromosome and preliminary homology-based gene survey demonstrated the possibility of LTR elements in SCl1. Both the GC skews and distribution of repetitive elements divide the chromosome into 7 prominent regions. Alignments with non-redundant and EST databases during gene survey gave a coarse estimation of coding densities of chromosome one at 1 CDS per IOOObp which also corresponded to 12.6% as coding and 87.4% as non-coding. Careful inspection on the distribution revealed that the coding sequences are centrically arranged within the chromosome. GC composition (53.9%) is higher in coding sequences compared to non-coding sequences (48.6%). The number of genes embedded in chromosome one is unknown until further laboratory investigations are carried out. Some of the significant hits may reflect the presence of the genes in chromosome one such as previously characterized LPMC-61 antigen, elongation factor Tu, proteophosphoglycan, proteases, and AAA ATPase family proteins that are involved in the parasite's mobility, parasite-host interaction and possibly invasion. However, in silico gene prediction using a homology-based technique identified three full length genes, phosphatidylinositol-4-phosphate 5-kinase (PIPSK), glucose- 6-phosphate isomerase (PGI) and ma1ate:quinone oxidoreductase (MQO). These genes served as gene models and provided early information regarding the intron, exon and splicing sites. The average exon and intron sizes were predicted as 118.5bp and 535.3bp, respectively. The most commonly utilized splice pairs is AG ... GT. Chromosome one nucleotide sequences have been deposited in the data depository of the Interim Laboratory of National Institute for the Genomics and Molecular Biology, BIOVALLEY-UKM, Bangi, Malaysia

Ts1Cje mouse model for Down syndrome research

Intellectual disabilities, hypotonia and cranio-facial dysmorphism are the cardinal characteristics of Down syndrome (DS) individuals. To varying extent, DS individuals also exhibit other developmental problems such as heart defects, vision impairments, hearing loss, hypothyroidism, dental problems and gastrointestinal defects. They are also at a higher risk for certain disorders such as early onset neurodegeneration and childhood leukaemia. For many decades, scientists have been trying to elucidate how additional full or partial set of chromosome 21 may responsible for these developmental disabilities or disorders. To date, many investigations are based on molecular, cellular and behavioural analyses of mouse models exhibiting similar characteristics observed in DS individuals. Among various models, Ts1Cje, in particular, is suitable for dissecting the effect of additional genetic materials on learning and memory impairment as well as muscle weakness in DS. Ts1Cje has partial triplication of the mouse chromosome 16, which is syntenic to chromosome 21 in human. This talk will focus on the genetics of Ts1Cje mouse model for DS and discuss how much do we know about the model and the degree of resemblance between Ts1Cje and human DS individuals in term of neuropathology of Down syndrome

Expression profiling of genes involved in the development and function of skeletal muscles in Ts1Cje mouse model of down syndrome

Introduction: Down syndrome (DS) is caused by trisomy of human chromosome 21 (HSA21). Motor dysfunction due to hypotonia has limited labour productivity and have significant effects on socio-economic status in DS individuals. Ts1Cje, a mouse model of DS that exhibits muscle weakness was employed, to investigate the expression profile of selected trisomic and disomic genes involved in skeletal muscle structure and function. Methods: Quadriceps and triceps were harvested from the Ts1Cje (C57BL/6) postnatal day 60-70 mice and corresponding wild-type littermates. Total RNA extracted from these tissues was subjected for quantitative expression profiling of three trisomic genes (Itsn1, Synj1 and Rcan1) involved in neurotransmission and six disomic genes (Lamc1, Leprel1, Myl6b, Msn, Pgm5 and Tmod1) essential for maintenance of muscle structure and function. Real-time quantitative PCR method was used for the profiling. Results: Differential gene expression in DS is reflected by 1.5-fold or more increase in the level of expression as predicted by the gene dosage imbalance hypothesis. The analysis showed no significant changes in the expression level of trisomic genes (Itsn1, Synj1 and Rcan1). On contrary, disomic genes, Leprel1 and Pgm5, were upregulated for more than 1.5-fold in DS quadriceps whereas Lamc1, Myl6b and Pgm5 were upregulated for more than 1.5 fold in DS triceps as compared to the wild-type group. Conclusions: Our findings suggest that the dysregulation of Lamc1, Leprel1, Myl6b and Pgm5 genes is associated to muscle weakness seen in Ts1Cje and may play a role in molecular pathogenesis of muscle weakness in DS

Challenges and future perspectives for 3D cerebral organoids as a model for complex brain disorders

The human brain is made up of billions of neurons and glial cells which are interconnected and organized into specific patterns of neural circuitry, and hence is arguably the most sophisticated organ in human, both structurally and functionally. Studying the underlying mechanisms responsible for neurological or neurodegenerative disorders and the developmental basis of complex brain diseases such as autism, schizophrenia, bipolar disorder, Alzheimer’s and Parkinson’s disease has proven challenging due to practical and ethical limitations on experiments with human material and the limitations of existing biological/animal models. Recently, cerebral organoids have been proposed as a promising and revolutionary model for understanding complex brain disorders and preclinical drug screening

The efficiency of cell sorting and harvesting methods for in vitro expansion of human umbilical cord blood derived CD34+ hematopoietic stem cells

Introduction: During the last three decades hematopoietic stem cell transplantation (HSCT) has become a well-established treatment for many hematologic malignancies. The most important limitation for HSC transplantation is the low number of hematopoietic stem cells (HSC) that can lead to delayed engraftment or graft failures. Numerous attempts have been made to improve in vitro HSC expansion via optimization of various methods such as isolation techniques, supplementing with growth factors, utilizing stromal cells as feeder layer and other culture conditions. Objective: This project is aimed to decipher the efficiency of an isolation technique and retrieval of culture expanded HSC from feeder layer using two different harvesting methods. Materials and Methods: Hematopoietic stem cells from human umbilical cord blood were isolated via MACS mediated CD34+ double sorting. Then, the cells were cultured onto MSC feeder layer for 3 and 5 days. Culture expanded cells were harvested using two different harvesting method namely cell aspiration and trypsinization methods. Hematopoietic stem cell expansion index were calculated based on harvesting methods for each time point. Results: The numbers of HSC isolated from human umbilical cord blood were 1.64 x 106 and 1.20 x106 cells at single and double sortings respectively. Although the number of sorted cells diminished at the second sorting yet the yield of CD34+ purity has increased from 43.73% at single sorting to 81.40% at double sorting. Employing the trypsinization method, the HSC harvested from feeder layer showed a significant increase in expansion index (EI) as compared to the cell aspiration harvesting method (p≤ 0.05). However, the purity of CD34+ HSC was found higher when the cells were harvested using aspiration method (82.43%) as compared to the trypsinization method (74.13%). Conclusion: A pure population of CD34+ HSC can be retrieved when the cells were double sorted using MACS and expanded in culture after being harvested using cell aspiration method

Association of maternal and cord plasma total, free and bioavailable 25-hyrodroxyvitamin D with neonatal anthropometric measurements at birth: a preliminary study in a private hospital

Introduction: 25-hydroxyvitamin D (25OHD) is the principal biomarker of vitamin D status. In circulation, 25OHD is primarily bound to vitamin D binding protein (VDBP), leaving a small proportion bound to albumin and as free form. Previous studies have suggested that free 25OHD is better correlated with health outcomes. However, in pregnancy where VDBP level is extremely elevated, the correlations between free 25OHD with health outcomes are far from conclusive. Here we show the associations of maternal and cord total, free and bioavailable 25OHD con-currently with neonatal anthropometric measurements in healthy pregnant mothers-neonates pairs. Method: Total 25OHD level was measured by using chemiluminescent immunoassay. Free and bioavailable 25OHD were calculated using published mathematical models. Results: The results showed that birth weight and head circumference were negatively associated with maternal total 25OHD but not significantly associated with free and bioavailable 25OHD. There were no significant associations between cord total, free and bioavailable 25OHD with any of the neonatal anthropometric measurements. Conclusion: The outcomes of this study should encourage further research in a larger sample size. Notably, future research could lead to the establishment of causative relationships and plausible mechanisms between maternal and cord 25OHD with neonatal anthropometric measurements

Breast cancer associated mutations reported among Malaysian Malay, Chinese and Indian patients

Breast cancer among women has reached an alarming stage compared to 20 years ago. It was found that single nucleotide polymorphisms (SNPs) play an important role in the development of breast cancer. SNPs may suppress or activate the functional genes, which then leads to an increased survival of cells due to the suppression of tumour suppressor genes or increased activity in detrimental proteins, resulting in cancers. Recently, breast cancer research is given significant attention due to the increasing number of breast cancer patients in Malaysia each year. However, breast cancer researches in Malaysia are mainly focused on well known breast cancer genes such as BRCA1 and BRCA2. There is less emphasis on the other breast cancer contributing genes. This paper was aimed to review the research findings on mutations associated with breast cancer in Malaysian Malay, Malaysian Chinese and Malaysian Indian as it has never been cumulatively reported and to ascertain the common mutations found in these three major Malaysia ethnicity

MicroRNA-based therapy and breast cancer: a comprehensive review of novel therapeutic strategies from diagnosis to treatment

MicroRNAs (miRNA) are 21–23 nucleotide molecules not translated into proteins that bind and target the 3′ untranslated regions of mRNA. These characteristics make them a possible tool for inhibiting protein translation. Different cellular pathways involved in cancer development, such as cellular proliferation, apoptosis, and migration, are regulated by miRNAs. The objective of this review is to discuss various miRNAs involved in breast cancer in detail as well as different therapeutic strategies from the clinic to industry. A comprehensive discussion is provided on various miRNAs involved in breast cancer development, progression, and metastasis as well as the roles, targets, and related therapeutic strategies of different miRNAs associated with breast cancer. miRNAs known to be clinically useful for the diagnosis and prognosis of breast cancer are also discussed. Different strategies and challenges, including nucleic acid-based (miRNA mimics, antagomiRs, and miRNA sponges) and drug-based (drug resistance, drugs/miRNA interaction, nanodelivery, and sensing systems) approaches to suppress specific oncogenes and/or activate target tumor suppressors are discussed. In contrast to other articles written on the same topic, this review focuses on the therapeutic and clinical value of miRNAs as well as their corresponding targets in order to explore how these strategies can overcome breast cancer, which is the second most frequent type of cancer worldwide. This review focuses on promising and validated miRNAs involved in breast cancer. In particular, two miRNAs, miR-21 and miR-34, are discussed as the most promising targets for RNA-based therapy in non-invasive and invasive breast cancer, respectively. Finally, relevant and commercialized therapeutic strategies are highlighted

Spatiotemporal expression profiling and molecular characterisation of miR-344b and miR-344c in the developing mouse brain

MicroRNAs are small non-coding RNAs of about 22 nucleotides that regulate gene expression through inhibition or repression processes during post-transcriptional or translational stages. Studies have shown that miRNAs play a crucial role in spatiotemporal regulation of the brain development. A recent study had shown that miR-344 is expressed in a developing mouse brain. In this study, we focused to characterise the spatiotemporal expression of miR-344b and miR-344c during the development of mouse brain. Out in situ hybridisation studies have shown that both miR-344b and miR-344c were strongly expressed in the germinal layer during the early stages of mouse brain development. Postnatally, expression of miR-344b was not detectable in P1 and adult brains. In contrast, miR-344c was expressed globally in P1 brain and was expressed exclusively in the olfactory bulb and granular cell layer of the cerebellum in the adult mouse brain. A subsequent stemloop RT-qPCR analysis showed that expression of the miR-344b and miR-344c was increased from E11.5 and peaked at E15.5. Postnatally, expression level of the miR-344b was reduced while miR-344c continued to express until adulthood. We further investigated the expression of miR-344b and miR-344c in adult mouse multiple organs and the pancreas showed the highest expression for both miRNAs. Subsequent bioinformatics analysis predicted that miR-344b and miR-344c were found to target a total of 1540 and 863 downstream target genes respectively. Genes associated with transcription regulation and nervous system development were subjected to further screening. We found that Olig2 and Otx2 were predicted as the potential downstream target gene for miR-344b and miR-344c respectively. However, luciferase protein suppression assay showed that the expression of Olig2 and Otx2 were not suppressed by overexpression of miR-344b and miR-344c. In conclusion, miR-344b and miR-344c were expressed in the developing mouse brain and may play a role during early mouse brain development although not directly targeting Olig2 and Otx2

Little man inside us

The concept of ‘homunculus’ (“little man” in Greek) was mentioned in psychology and brain anatomy in 19th century, specifically in brain mapping to different body parts. The brain is connected by many sensory and motor neurones. Hence, our brain sees two different homunculi in us - the sensory and the motor homunculus. Contrary to how we perceive ourselves, our brain could actually ‘see’ us as Gollum in Lord of the Rings