Multilocus DNA profiling using the probe 33.6 in the Tamil Nadu population of South India

Using the multilocus minisatellite probe 33.6 in combination with the HinfI restriction enzyme, the extent of genetic variation detected by DNA fingerprinting was estimated in 102 unrelated individuals of the Dravidian Hindu population of Tamil Nadu, South India. In this first study of its kind on an anthropologically defined Indian population, DNA fragments of size >2.5 kb could be reliably scored. Results indicate that the Tamilian Hindus show an average number of bands per individual somewhat smaller (15.69 for fragments of size >2.5 kb) than that in other Caucasian populations. For comparable molecular weight of fragment sizes, the Tamilian Hindus show a lower level of band sharing probabilities between unrelated individuals compared with other Caucasians. Nevertheless, the probe 33.6 offers a high level of individualization of DNA fingerprints for unrelated individuals in Tamil Nadu. Computations on expected band sharing frequencies between various biological relatives and expected DNA fingerprint identity indicate that this multilocus minisatellite probe can be efficiently used in resolving forensic identification and parentage testing cases in this South Indian population in spite of its high level of inbreeding. Am. J. Hum. Biol. 10:87–93, 1998. © 1998 Wiley-Liss, Inc.     

Evaluation of Hybridization Capture Versus Amplicon‐Based Methods for Whole‐Exome Sequencing

Next‐generation sequencing has aided characterization of genomic variation. While whole‐genome sequencing may capture all possible mutations, whole‐exome sequencing remains cost‐effective and captures most phenotype‐altering mutations. Initial strategies for exome enrichment utilized a hybridization‐based capture approach. Recently, amplicon‐based methods were designed to simplify preparation and utilize smaller DNA inputs. We evaluated two hybridization capture‐based and two amplicon‐based whole‐exome sequencing approaches, utilizing both Illumina and Ion Torrent sequencers, comparing on‐target alignment, uniformity, and variant calling. While the amplicon methods had higher on‐target rates, the hybridization capture‐based approaches demonstrated better uniformity. All methods identified many of the same single‐nucleotide variants, but each amplicon‐based method missed variants detected by the other three methods and reported additional variants discordant with all three other technologies. Many of these potential false positives or negatives appear to result from limited coverage, low variant frequency, vicinity to read starts/ends, or the need for platform‐specific variant calling algorithms. All methods demonstrated effective copy‐number variant calling when evaluated against a single‐nucleotide polymorphism array. This study illustrates some differences between whole‐exome sequencing approaches, highlights the need for selecting appropriate variant calling based on capture method, and will aid laboratories in selecting their preferred approach.     

Bioactive nano‐fibrous scaffold for vascularized craniofacial bone regeneration

There has been a growing demand for bone grafts for correction of bone defects in complicated fractures or tumours in the craniofacial region. Soft flexible membrane like material that could be inserted into defect by less invasive approaches; promote osteoconductivity and act as a barrier to soft tissue in growth while promoting bone formation is an attractive option for this region. Electrospinning has recently emerged as one of the most promising techniques for fabrication of extracellular matrix such as nano‐fibrous scaffolds that can serve as a template for bone formation. To overcome the limitation of cell penetration of electrospun scaffolds and improve on its osteoconductive nature, in this study, we fabricated a novel electrospun composite scaffold of polyvinyl alcohol (PVA)‐poly (ε) caprolactone (PCL)‐Hydroxyapatite based bioceramic (HAB), namely, PVA‐PCL‐HAB. The scaffold prepared by dual electrospinning of PVA and PCL with HAB overcomes reduced cell attachment associated with hydrophobic PCL by combination with a hydrophilic PVA and the HAB can contribute to enhance osteoconductivity. We characterized the physicochemical and biocompatibility properties of the new scaffold material. Our results indicate PVA‐PCL‐HAB scaffolds support attachment and growth of stromal stem cells; [human bone marrow skeletal (mesenchymal) stem cells and dental pulp stem cells]. In addition, the scaffold supported in vitro osteogenic differentiation and in vivo vascularized bone formation. Thus, PVA‐PCL‐HAB scaffold is a suitable potential material for therapeutic bone regeneration in dentistry and orthopaedics.     

Silencing NOTCH signaling causes growth arrest in both breast cancer stem cells and breast cancer cells

Background:

Breast cancer stem cells (BCSCs) are characterized by high aldehyde dehydrogenase (ALDH) enzyme activity and are refractory to current treatment modalities, show a higher risk for metastasis, and influence the epithelial to mesenchymal transition (EMT), leading to a shorter time to recurrence and death. In this study, we focused on examination of the mechanism of action of a small herbal molecule, psoralidin (Pso) that has been shown to effectively suppress the growth of BSCSs and breast cancer cells (BCCs), in breast cancer (BC) models.

Methods:

ALDH⁻ and ALDH⁺ BCCs were isolated from MDA-MB-231 cells, and the anticancer effects of Pso were measured using cell viability, apoptosis, colony formation, invasion, migration, mammosphere formation, immunofluorescence, and western blot analysis.

Results:

Psoralidin significantly downregulated NOTCH1 signaling, and this downregulation resulted in growth inhibition and induction of apoptosis in both ALDH⁻ and ALDH⁺ cells. Molecularly, Pso inhibited NOTCH1 signaling, which facilitated inhibition of EMT markers (β-catenin and vimentin) and upregulated E-cadherin expression, resulting in reduced migration and invasion of both ALDH⁻ and ALDH⁺ cells.

Conclusion:

Together, our results suggest that inhibition of NOTCH1 by Pso resulted in growth arrest and inhibition of EMT in BCSCs and BCCs. Psoralidin appears to be a novel agent that targets both BCSCs and BCCs.     

2-chloroadenosine attenuates kainic acid-induced toxicity within the rat straitum: relationship to release of glutamate and Ca2+ influx.

1. The mechanism by which 2-chloroadenosine (2-chloroado) exerts a neuroprotective action against the excitotoxic effect of kainic acid (KA) when injected into the rat striatum was investigated. 2. Histological examination two weeks after a single injection of KA (2.2 nmol) into rat striatum revealed widespread neuronal damage. Co-injection of 2-chloroado (6-25 nmol) with the neurotoxin afforded dose-dependent neuroprotection. This effect was reversed by administration of an equimolar concentration of the adenosine receptor antagonist theophylline. 3. Both K+ (30 mM) and KA (1 mM) enhanced the release of endogenous glutamate from guinea-pig purified cerebrocortical synaptosomes in a predominantly (approximately 70%) Ca2+-dependent manner. 2-Chloroado (10 nM-1 microM) inhibited the release of glutamate evoked by both KA and K+. These effects were partially reversed by the selective A1-adenosine receptor antagonist 8-cyclopentyltheophylline (CPT) (1 microM). 4. Crude rat cortical synaptosomes were loaded with the fluorescent calcium indicator quin-2 and Ca2+ influx monitored following two successive depolarising stimuli (30 mM K+; 'S1' and 'S2'). 2-Chloroado (10 nM-1 microM) produced a dose-dependent reduction in the S2:S1 ratio when added before the S2 period of stimulation. This effect was reversed by 1 microM theophylline. However, KA (1 mM) failed to enhance Ca2+ influx in the same preparation. 5. These results suggest that the anti-excitotoxic action of 2-chloroado is mediated primarily through a specific presynaptic receptor mechanism involving reduction of transmitter glutamate release, possibly occurring through an inhibition of Ca2+ influx.     

p19ARF is a critical mediator of both cellular senescence and an innate immune response associated with MYC inactivation in mouse model of acute leukemia

MYC-induced T-ALL exhibit oncogene addiction. Addiction to MYC is a consequence of both cell-autonomous mechanisms, such as proliferative arrest, cellular senescence, and apoptosis, as well as non-cell autonomous mechanisms, such as shutdown of angiogenesis, and recruitment of immune effectors. Here, we show, using transgenic mouse models of MYC-induced T-ALL, that the loss of either p19ARF or p53 abrogates the ability of MYC inactivation to induce sustained tumor regression. Loss of p53 or p19ARF, influenced the ability of MYC inactivation to elicit the shutdown of angiogenesis; however the loss of p19ARF, but not p53, impeded cellular senescence, as measured by SA-beta-galactosidase staining, increased expression of p16INK4A, and specific histone modifications. Moreover, comparative gene expression analysis suggested that a multitude of genes involved in the innate immune response were expressed in p19ARF wild-type, but not null, tumors upon MYC inactivation. Indeed, the loss of p19ARF, but not p53, impeded the in situ recruitment of macrophages to the tumor microenvironment. Finally, p19ARF null-associated gene signature prognosticated relapse-free survival in human patients with ALL. Therefore, p19ARF appears to be important to regulating cellular senescence and innate immune response that may contribute to the therapeutic response of ALL.     

Tumor-induced interleukin 10 suppresses the ability of splenic dendritic cells to stimulate CD4 and CD8 T-cell responses

Dendritic cell (DC) maturation and function are influenced by the surrounding cytokine milieu. We demonstrate tumor-associated suppression of DCs in stimulating allogeneic and tumor-specific CTL and type 1 (IFN-gamma-producing) responses in both CD4- and CD8-positive T cells. DCs from MB49-bearing female mice fail to stimulate proliferative and IFN-gamma-producing responses in allogeneic mixed lymphocyte cultures. MB49 also inhibited DC function in stimulating type 1 responses against our tumor-specific antigen, the male antigen, HY. DCs from MB49-bearing male mice were unable to restimulate effective HY-specific CTLs or IFN-gamma. Tumor-induced interleukin (IL) 10 was found to be specifically responsible for DC dysfunction in response to antigenic driven maturation. This was demonstrated by restoration of DC function in splenic DCs from MB49-bearing female IL-10 knockout mice (HY disparity), whereas not in MB49-bearing male IL-10 knockout mice (no HY disparity). Finally, any tumor-induced systemic inhibitory effect on bone marrow precursors could be overcome by generation of bone marrow-derived DCs ex vivo. These bone marrow-derived DCs derived from MB49-bearing B6 mice were capable of inducing control levels of proliferation in allogeneic mixed lymphocyte reactions and a type 1 (IFN-gamma) cytokine profile. The BM-DCs were also capable of restimulating HY-specific CTL and IFN-gamma production. These studies reveal the tumor-associated in vivo effects of IL-10 inhibition on DC function in eliciting a type 1 immune response in both allogeneic and tumor-specific responses.