Association between the BsmI Polymorphism in the Vitamin D Receptor Gene and Breast Cancer Risk: Results from a Pakistani Case-Control Study

Background

Vitamin D is postulated to decrease the risk of breast cancer by inhibiting cell proliferation via the vitamin D receptor (VDR). Two common single nucleotide polymorphisms (SNPs) in the VDR gene, rs1544410 (BsmI) and rs2228570 (FokI), are inconsistently associated with breast cancer risk in Caucasian populations, while data for Asians are scarce. Here, we investigated the possible contribution of these SNPs to breast cancer risk in Pakistani breast cancer patients and in controls participating in a hospital-based breast cancer case-control study (PAK-BCCC).

Methods

Genotyping of the BsmI and FokI SNPs was performed by PCR-based restriction fragment length polymorphism (RFLP) analysis of 463 genetically enriched female breast cancer cases with known BRCA1/2 status and in 1,012 controls from Pakistan. The association between SNP genotypes and breast cancer risk was investigated by logistic regression adjusted for potential breast cancer risk factors and stratified by BRCA1/2 status and family history. Odds ratios (ORs) and 95% confidence intervals (CIs) were reported.

Results

The b allele of the BsmI was associated with an increased breast cancer risk (per b allele OR 1.28, 95% CI 1.09–1.49, P = 0.003). Subgroup analysis revealed that this effect was restricted to BRCA1/2 non-carriers (per b allele OR 1.33, 95% CI 1.11–1.59, P = 0.002) and was stronger in those who reported a positive family history of breast and/or ovarian cancer (per b allele OR 1.64, 95% CI 1.20–2.22, P = 0.002). No association with breast cancer risk was detected for the FokI SNP.

Conclusions

The BsmI polymorphism in the VDR gene may be associated with an increased breast cancer risk in Pakistani women negative for BRCA1/2 germline mutations.     

The costs of migration: Injuries in migratory waterbirds along the west coast of India

The long distant, transcontinental migration of shorebirds entails many well identified costs in terms of time, energy, and direct mortality risk. Injuries from debris or from human structures and activities were observed as the major reasons for the direct mortality of shorebirds during migration worldwide. We recorded injured birds in major coastal wetlands of Kerala, for a period of 15 years from 2005 to 2019. The injured birds were observed in 9 different sites in various districts of Kerala. The highest instances of injuries were observed in Kadalundi-Vallikunnu Community Reserve, the major wintering and stop over site of migrant shorebirds in the west coast of India. During the study period, fifty-eight individuals of shorebirds belonging to four families were found to be injured. The highest proportion of injuries was recorded among the families Scolopacidae and Charadriidae comprising long distance migrant shorebird species and the lowest among Laridae and Ardeidae. We recommend that environmental authorities pay special attention to minimize anthropogenic debris along the flyways used by migratory birds thereby reducing the risk of injuries to some of these species. Proactive measures such as removal of discarded fishing gear or plastic debris from wintering areas as well as stopover areas could greatly reduce injuries in migratory birds arising from anthropogenic sources.     

The endangered forests of Bangladesh: why the process of implementation of the Convention on Biological Diversity is not working

Bangladesh has been a signatory to the Convention on Biological Diversity (CBD) although implementation of the convention has been poor. We independently assessed the extent to which the program of work (POW) of the CBD has been implemented in Bangladesh by carrying out workshops involving local communities, conservation organizations, universities, and government departments involved in forest conservation. Our analyses indicate that there is little or no understanding of the ecosystem approach that is central to the CBD; forestry practices remain primitive and largely ineffective; forest destruction continues at high rates; restoration of degraded forests are minimal; protected areas are small and ineffective; indigenous peoples’ rights are nominal and are outside any legislation; threats to species have been identified, but little is being done to reduce threats; there is no work on pollution and its mitigation; some work has been done to adapt to climate change; the institutional environment does not enable effective implementation of the ecosystem approach; laws and policies are ineffective; institutional capacity is poor; government will is limited or totally lacking; and knowledge base remains poor, although reporting has improved and various strategic plans have been formulated but never implemented. Thus, the implementation of CBD in Bangladesh requires systemic changes in policy at the institutional levels as well as complementary changes in attitudes and avenues of alternate income generation.     

Analysis of NCL Proteins from an Evolutionary Standpoint

The Neuronal Ceroid Lipofuscinoses (NCLs) are the most common group of neurodegenerative disorders of childhood. While mutations in eight different genes have been shown to be responsible for these clinically distinct types of NCL, the NCLs share many clinical and pathological similarities. We have conducted an exhaustive Basic Local Alignment Search Tool (BLAST) analysis of the human protein sequences for each of the eight known NCL proteins- CLN1, CLN2, CLN3, CLN5, CLN6, CLN7, CLN8 and CLN10. The number of homologous species per CLN-protein identified by BLAST searches varies depending on the parameters set for the BLAST search. For example, a lower threshold is able to pull up more homologous sequences whereas a higher threshold decreases this number. Nevertheless, the clade confines are consistent despite this variation in BLAST searching parameters. Further phylogenetic analyses on the appearance of NCL proteins through evolution reveals a different time line for the appearance of the CLN-proteins. Moreover, divergence of each protein shows a different pattern, providing important clues on the evolving role of these proteins. We present and review in-depth bioinformatic analysis of the NCL proteins and classify the CLN-proteins into families based on their structures and evolutionary relationships, respectively. Based on these analyses, we have grouped the CLN-proteins into common clades indicating a common evolving pathway within the evolutionary tree of life. CLN2 is grouped in Eubacteria, CLN1 and CLN10 in Viridiplantae, CLN3 in Fungi/ Metazoa, CLN7 in Bilateria and CLN5, CLN6 and CLN8 in Euteleostomi.     

Adoptive transfer of PR1 cytotoxic T lymphocytes associated with reduced leukemia burden in a mouse acute myeloid leukemia xenograft model

Background aimsTumor antigen-specific cytotoxic T lymphocytes (CTL) have been used in the treatment of human cancer, including leukemia. Several studies have established PR1 peptide, an HLA-A2.1-restricted peptide derived from proteinase 3 (P3), as a human leukemia-associated antigen. PR1-specific CTL elicited in vitro from healthy donors have been shown to lyse P3-expressing AML cells from patients. We investigated whether PR1-CTL can be adoptively transferred into NOD/SCID mice to eliminate human leukemia cells.MethodsPR1-CTL were generated in bulk culture from peripheral blood mononuclear cells (PBMC) stimulated with autologous dendritic cells. Human acute myeloid leukemia (AML) patient samples were injected and engrafted in murine bone marrow at 2 weeks post-transfer.ResultsFollowing adoptive transfer, bone marrow aspirate from mice that received AML alone had 72–88% blasts in a hypercellular marrow, whereas mice that received AML plus PR1-CTL co-infusion had normal hematopoietic elements and only 3–18% blasts in a hypocellular marrow. The PR1-CTL persisted in the bone marrow and liver and maintained a CD45RA^? CD28⁺ effector phenotype.ConclusionsWe found that adoptive transfer of PR1-CTL generated in vitro is associated with reduced AML cells in NOD/SCID mice. PR1-CTL can migrate to the sites of disease and maintain their capacity to kill the AML cells. The surface phenotype of PR1-CTL was consistent with their trafficking pattern in both vascular and end-organ tissues.     

Adh 1 first intron polymorphisms in Argentinean populations of Ceratitis capitata

DNA size polymorphisms were utilized in a study of 24 natural populations of Ceratitis capitata Wiedemann (Diptera: Tephritidae) from Argentina. The first intron of alcohol dehydrogenase 1 gene (Adh₁) was amplified using exon priming intron crossing‐polymerase chain reaction. Three size variants were detected among the 307 samples analyzed. To better differentiate the size variants, further digestion of PCR products with the EcoRI restriction enzyme was carried out. Complete nucleotide sequences of the three‐allele variants were obtained and single changes, insertions, deletions, and EcoRI recognition sites were located. Population allele frequencies were analyzed and a global mean heterozygosity (He) of 0.33 was obtained. In most populations, observed allelic frequencies conformed to Hardy–Weinberg expectations. Significant differences between provinces and sampling sites within these provinces, and among some populations were found. The average number of insects exchanged among populations (Nm) was estimated and high values were observed between Argentina and populations from two African countries (Morocco and Kenya), Australia, and Hawaii (Kauai). Pest introduction sources and dispersion patterns in Argentina are discussed based on these results as well as on available bibliographical data.     

The anchorless adhesin Eap (extracellular adherence protein) from Staphylococcus aureus selectively recognizes extracellular matrix aggregates but binds promiscuously to monomeric matrix macromolecules.

Besides a number of cell wall-anchored adhesins, the majority of Staphylococcus aureus strains produce anchorless, cell wall-associated proteins, such as Eap (extracellular adherence protein). Eap contains four to six tandem repeat (EAP)-domains. Eap mediates diverse biological functions, including adherence and immunomodulation, thus contributing to S. aureus pathogenesis. Eap binding to host macromolecules is unusually promiscuous and includes matrix or matricellular proteins as well as plasma proteins. The structural basis of this promiscuity is poorly understood. Here, we show that in spite of the preferential location of the binding epitopes within triple helical regions in some collagens there is a striking specificity of Eap binding to different collagen types. Collagen I, but not collagen II, is a binding substrate in monomolecular form. However, collagen I is virtually unrecognized by Eap when incorporated into banded fibrils. By contrast, microfibrils containing collagen VI as well as basement membrane-associated networks containing collagen IV, or aggregates containing fibronectin bound Eap as effectively as the monomeric proteins. Therefore, Eap-binding to extracellular matrix ligands is promiscuous at the molecular level but not indiscriminate with respect to supramolecular structures containing the same macromolecules. In addition, Eap bound to banded fibrils after their partial disintegration by matrix-degrading proteinases, including matrix metalloproteinase 1. Therefore, adherence to matrix suprastructures by S. aureus can be supported by inflammatory reactions.     

Anticancer potential of rhamnocitrin 4′-β-d-galactopyranoside against N-diethylnitrosamine-induced hepatocellular carcinoma in rats

The hepatoprotective activity of flavonoid rhamnocitrin 4′-β-d-galactopyranoside (RGP) obtained from leaves of Astragalus hamosus L. against N-diethylnitrosamine (DENA)-induced hepatic cancer in Wistar albino rats was evaluated. Hepatic cancer in rats was induced by single-dose intraperitoneal administration of DENA (200 mg/kg). Induction of hepatic cancer was confirmed after 7 days of DENA administration by measurement of elevated level of serum α-feto protein (AFP). Administration of DENA in a single dose lofted the levels of serum biochemical parameters like alanine aminotransferase, aspartate aminotransferase, alkaline phosphatase, total bilirubin, total protein and AFP. Antioxidant enzymes like superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx), glutathione-S-transferase (GST) and lipid per oxidation (LPO) were annealed significantly by administration of RGP in a dose-dependant manner. The histopathological examination of rat liver section was found to reinforce the biochemical observations significantly. It was observed that a substantial and dose-dependent reversal of DENA-diminished activity of antioxidant enzymes like SOD, CAT, GPx, GST and the reduced DENA-elevated level of LPO with a marked change. Any elevation in the levels of serum markers along with suppression of free radical formation by scavenging the hydroxyl radicals is significantly prevented by RGP. It also modulates the levels of LPO and perceptibly increases the endogenous antioxidant enzymes level in DENA-induced hepatocellular carcinogenesis. The findings suggest that RGP prevents hepatocellular carcinoma by suppressing the marked increase in the levels of serum marker enzymes, and suppresses the free radical by scavenging hydroxyl radicals.