BRAF and RET polymorphism association with thyroid cancer risk, a preliminary study from Khyber Pakhtunkhwa population

BACKGROUND

Thyroid cancer, originating in the neck's thyroid gland, encompasses various types. Genetic mutations, particularly in BRAF and RET genes are crucial in its development. This study investigates the association between BRAF (rs113488022) and RET (rs77709286) polymorphisms and thyroid cancer risk in the Khyber Pakhtunkhwa (KP) population.

METHODS

Blood samples from 100 thyroid cancer patients and 100 healthy controls were genotyped using ARMS-PCR followed by gel electrophoresis and statistical analysis.

RESULTS

Analysis revealed a significant association between the minor allele T of BRAF (rs113488022) and thyroid cancer risk (P = 0.0001). Both genotypes of BRAF (rs113488022) showed significant associations with thyroid cancer risk (AT; P = 0.0012 and TT; P = 0.045). Conversely, the minor allele G of RET (rs77709286) exhibited a non-significant association with thyroid cancer risk (P = 0.2614), and neither genotype showed significant associations (CG; P = 0.317, GG; P = 0.651). Demographic and clinical parameters analysis using SPSS showed a non-significant association between BRAF and RET variants and age group (P = 0.878 and P = 0.536), gender (P = 0.587 and P = 0.21), tumor size (P = 0.796 and P = 0.765), or tumor localization (P = 0.689 and P = 0.727).

CONCLUSION

In conclusion, this study emphasizes the significant association between BRAF polymorphism and thyroid cancer risk, while RET polymorphism showed a less pronounced impact. Further validation using larger and specific datasets is essential to establish conclusive results.

BRCA2 Polymorphisms and Breast Cancer Susceptibility: a Multi-Tools Bioinformatics Approach

BACKGROUND/AIMS

The main focus of this investigation is to identify deleterious single nucleotide polymorphisms (SNPs) located in the BRCA2 gene through in silico approach, thereby,providing an understanding of potential consequences regarding the susceptibility to breast cancer.

METHODS

The GenomAD database was used to identify SNPs. To determine the potential adverse consequences, our study employed various prediction tools, including SIFT, PolyPhen, PredictSNP, SNAP2, PhD-SNP, and ClinVar. The pathogenicity associated with the deleterious snSNPs was evaluated bu MutPred and Fathmm. Additionally, I-Mutant and MuPro were used to assess the stability, followed by conservation and protein-protein interaction analysis using robust computational tools. The 3D structure of BRCA2 protein was generated by SwissModel, followed by validation using PROCHECK and Errat.

RESULTS

The GenomAD database was used to identify a total of 7, 921 SNPs, including 1940 missense SNPs. A set of 69 SNPs predicted by consensus to be damaging across all platforms was identified. Mutpred and Fathmm identified 48 and 38 SNPs, respectively to be associated with cancer. While I- Mutant and MuPro assays suggested 22 SNPs to decrease protein stability. Additionally, these 22 SNPs reside within highly conserved regions of the BRCA2 protein. Domain analysis, utilizing InterPro, pinpointed 18 deleterious mutations within crucial DNA binding domains and one in the BRC repeat region.

CONCLUSION

This study establishes a foundation for future experimental validations and the creation of breast cancer-targeted treatment approaches.

Assessment of Babesia spp. prevalence in various domestic animals across Southern Punjab, Pakistan

Parasitic diseases, notably babesiosis, exert a substantial impact on the global cattle industry, posing challenges to commerce, economies, and human health. This study, conducted in Southern Punjab, Pakistan, aimed to assess the prevalence of Babesia spp. across various livestock species using microscopic and PCR methods. A total of 180 blood samples (60 from each district) were systematically collected from apparently healthy animals, with 36 samples obtained from each domestic animal species, including camel, cattle, buffalo, goat, and sheep, noting that 12 samples were collected from each district for each animal species. Overall prevalence was determined to be 32.8% (59/180), with varying rates among species: 25.0% in cattle, 41.66% in buffalo, 30.55% in goats, 33.3% in sheep, and 33.3% in camels. Microscopic examination revealed slightly varied infection rates among large and small domestic animals (22.2%), while PCR results indicated a 32.8% overall infection rate in both large and small domestic animals, with no statistical significance. District-wise analysis showed regional variations, with Muzaffargarh recording a prevalence rate of 23.33% through microscopic examination, while Lodhran and Bahawalpur recorded 21.67%. PCR results revealed higher rates (38.33%, 26.67%, and 33.33%, respectively), underlining the importance of employing PCR for accurate detection. Examining ruminant types, large ruminants exhibited a 32.4% infection rate, while small domestic animals showed 33.3%, with no significant difference (p=0.897). District-wise prevalence showcased significant variation, with Muzaffargarh demonstrating a 25% prevalence, Lodhran 22%, and Bahawalpur 22%, through microscopic examination. PCR results displayed 38.33%, 27%, and 33.3%, respectively, with no statistical significance. Detailed analysis of individual districts highlighted variations in infection rates among camels, cattle, buffalo, goats, and sheep. The binomial test indicated significant differences through microscopic analysis (P=0.011) but non-significant variations through PCR (P=0.065), emphasizing the precision of PCR. Regional variations in prevalence, notably with Punjab exhibiting the highest frequency (33.87%) and KPK the lowest (13.24%), suggest potential influences from varying veterinary practices and environmental factors. This study underscores the pivotal role of PCR alongside microscopy for accurate babesiosis diagnosis. These findings contribute to the broader understanding of babesiosis prevalence, emphasizing the necessity of advanced molecular techniques for informed control measures.

Human epidermal growth receptor polymorphisms (HER1-rs11543848 and HER2-rs1136201) exhibited significant association with breast cancer risk in Pashtun population of Khyber Pakhtunkhwa, Pakistan

Background and Aims

Breast cancer is the most common type of cancer in women. The genetic polymorphism in HER (HER1-rs11543848 and HER2-rs1136201) were found to be associated with breast cancer risk in different ethnicities worldwide with inconsistent results. The aim of this research study was to evaluate the association of HER1-rs11543848 and HER2-rs1136201 polymorphisms as a risk of breast cancer in Pashtun population of Khyber Pakhtunkhwa, Pakistan.

Methods

A total of 314 women including 164 breast cancer patients and 150 age and gender-matched healthy controls were enrolled from June 2021 to May 2022. All the samples were subjected to DNA extraction followed by Tetra-ARMS-PCR for genotyping and gel electrophoresis.

Results

Our results indicated that HER1-rs11543848 risk allele A (p = 0.0001) and heterozygous genotype GA (p = 0.0001) displayed highly significant association with breast cancer, while the homozygous mutant genotype AA indicated association but nonsignificant results (odds ratio [OR] = 2.637, 95% confidence interval [CI] = 1.2258-5.6756, p = 0.0833). Similarly, the HER2-rs1136201 risk allele G (p = 0.0023), the heterozygous genotype AG (p = 0.0530) and homozygous mutant genotype GG showed significant association (OR = 2.5946, 95% CI = 0.9876-6.8165, p = 0.0530) with breast cancer risk. Both the SNPs presented a higher but nonsignificant risk of breast cancer in postmenopausal women (OR = 2.242, p = 0.08 and OR = 2.009, p = 0.06). However, both the SNPs showed significant association (p < 0.005) with family history, metastasis, stage, luminal B, and TNBC.

Conclusion

In conclusion, HER1-rs11543848 and HER2-rs1136201 polymorphisms are significantly associated with the higher risk of breast cancer in Pashtun population of Khyber Pakhtunkhwa, Pakistan. These findings advocate for further exploration with larger datasets, offering promising avenues for personalized approaches in breast cancer research and potentially enhancing clinical practices for better risk assessment and targeted management strategies.

Transcriptome analysis and identification of the low potassium stress-responsive gene SiSnRK2.6 in foxtail millet (Setaria italica L.)

KEY MESSAGE

The transcriptome is beneficial for dissecting the mechanism of millet in response to low potassium stress and SiSnRK2.6 was identified as a potential target for improving low potassium stress tolerance. Foxtail millet (Setaria italica L.), which originated in China, has high nutrient utilization character. Nevertheless, the molecular mechanism of its tolerance to low potassium stress is largely unclear. In this research, the low potassium tolerant variety "Yugu28" was screened out by low potassium stress treatment, and the transcriptome of "Yugu28" under low potassium stress was comprehensively analyzed. A total of 4254 differentially expressed genes (DEGs) were identified, including 1618 up-regulated and 2636 down-regulated genes, respectively. In addition, there were 302 transcription factor (TF) genes in the DEGs and MYB TFs accounted for the highest proportion, which was 14.9%. After functional analysis of all DEGs, a total of 7 genes involved in potassium transport and potassium ion channels and 50 genes corresponding to hormones were screened. The expression levels of randomly selected 17 DEGs were verified by qRT-PCR and the results coincided well with the RNA-seq analysis, indicating the reliability of our transcriptome data. Moreover, one of the ABA signaling pathway genes, SiSnRK2.6, was identified and selected for further functional verification. Compared with the wild type, transgenic rice with ecotopic expression of SiSnRK2.6 showed remarkably increased root length and root number, indicating that overexpression of SiSnRK2.6 can enhance the resistance of transgenic plants to low potassium stress.

Assessment of HER1 (rs11543848) and HER2 (rs1136201) polymorphism and their association with colorectal cancer susceptibility in Khyber Pakhtunkhwa, Pakistan

BACKGROUND

Colorectal cancer (CRC) is a widespread malignancy characterized by uncontrolled growth in the colon or rectum and remains a leading cause of cancer-related mortality globally. Various genes polymorphisms have been linked with the risk of CRC, but our study aimed to investigate the association between HER1 (rs11543848) and HER2 (rs1136201) polymorphisms with the risk of CRC in the Khyber Pakhtunkhwa (KPK) population of Pakistan. The association of the selected polymorphisms (rs11543848 and rs1136201) with CRC risk has been investigated in various ethnic groups, but their impact remains unexplored in Pakistan, particularly within the KPK population, highlighting the need of the study in this region.

METHODS

In this study 120 CRC patients and 120 healthy controls were enrolled. The DNA was extracted from the blood by salting-out method and genotyping was done using ARMS-PCR.

RESULTS

Our investigations provided convincing evidence of a strong association between HER1 (rs11543848) and the risk of CRC. Both the genotypes heterozygous GA (OR = 2.07, CI = 1.18 to 3.64, P = 0.01) and homozygous AA (OR = 6.22, CI = 2.56 to 15.08, P = 0.0001) showed higher risk and significant association with the CRC risk. Similarly, heterozygous genotype AG of HER2 (rs1136201) was significantly associated (OR = 3.16, 95% CI = 1.78 to 5.58, P = 0.0001) while mutant genotype GG showed higher risk but non-significant association (OR = 3.23, 95% CI = 0.84 to 12.43, P = 0.08) with CRC patients. HER1 (rs11543848) demonstrated a significant association (P = 0.003) with the age at diagnosis in CRC patients, while HER2 (rs1136201) showed a non-significant association (P = 0.434). Both the SNPs were non-significantly associated with gender (P = 0.793 and 0.117), metastasis (P = 0.582 and 0.129), location of the tumor (P = 0.555 and 0.993), tumor grade (P = 0.290 and 0.920), tumor size (P = 0.535 and 0.289) and stages of cancer (P = 0.892 and 0.352).

CONCLUSION

In conclusion, both the polymorphisms rs11543848 and rs1136201 displayed susceptibility with CRC in the KPK population. However, further investigations are recommended while using whole exome sequencing on a larger sample size for more precise results.

Arsenic level in groundwater and biological samples in Khanewal, Pakistan

Groundwater is the most valuable natural source in our earth's planet, being contaminated in various regions worldwide. Despite considerable research, there are scarce data regarding arsenic (As) levels in groundwater and its build-up in biological samples in Pakistan. The current investigation analyzed As contamination in four tehsils of District Khanewal (Kabirwala tehsil, Jahaniyan tehsil, Mian Channu tehsil, and Khanewal tehsil). For that, 123 groundwater samples, 19 animal milk samples, 20 human nails, and 20 human hair samples were collected from the study area. Arsenic concentration in groundwater was up to 51.8 µg/L with an average value of 7.2 µg/L. About 28 water samples (23%) had As contents > WHO limit and 38 samples (31%) > DEP-NJ limit. Low levels of As were detected in biological samples. Average As levels were 23 µg/L in the milk samples and 298 µg/kg in human hair. Arsenic contents were not detected in nail samples, except in one sample from Kabirwala tehsil. The maximum values of hazard quotient and cancer risk in District Khanewal were 4.9 and 0.0022, respectively. It is anticipated that long-term use of As-containing water may led to poisoning of humans in the study area, especially in Kabirwala. Therefore, it is necessary to monitor As contamination in the groundwater of Kabirwala tehsil to reduce the potential health hazards.

Significant association of BRCA1 (rs1799950), BRCA2 (rs144848) and TP53 (rs1042522) polymorphism with breast cancer risk in Pashtun population of Khyber Pakhtunkhwa, Pakistan

BACKGROUND

Single nucleotide polymorphism (SNPs) in BRCA1, BRCA2 and TP53 has been widely associated with breast cancer risk in different ethnicities with inconsistent results. There is no such study conducted so far in the Pashtun population of Khyber Pakhtunkhwa, Pakistan. Therefore, this study was conducted to check BRCA1 (rs1799950), BRCA2 (rs144848) and TP53 (rs1042522) polymorphism with breast cancer risk in Pashtun population of Khyber Pakhtunkhwa, Pakistan.

METHODS

This study, consisting 140 breast cancer patients and 80 gender and age matched healthy controls were subjected to confirm BRCA1, BRCA2 and TP53 polymorphism. Clinicopathological data and blood samples were taken from all the participants. DNA was extracted and SNPs were confirmed using T-ARMS-PCR protocol.

RESULTS

Our data indicated that BRCA1, BRCA2, and TP53 selected SNPs risk allele and risk allele containing genotypes displayed significant association (p < 0.05) with breast cancer risk in the Pashtun population of Khyber Pakhtunkhwa, Pakistan.

CONCLUSION

All the three selected SNPs of BRCA1, BRCA2 and TP53 showed significant association with breast cancer risk in the Pashtun population of Khyber Pakhtunkhwa, Pakistan. However, more investigation will be required on large data sets to confirm the selected SNPs and other SNPs in the selected and other related genes with the risk of breast cancer.

Natural variation in Tiller Number 1 affects its interaction with TIF1 to regulate tillering in rice

Tiller number per plant-a cardinal component of ideal plant architecture-affects grain yield potential. Thus, alleles positively affecting tillering must be mined to promote genetic improvement. Here, we report a Tiller Number 1 (TN1) protein harbouring a bromo-adjacent homology domain and RNA recognition motifs, identified through genome-wide association study of tiller numbers. Natural variation in TN1 affects its interaction with TIF1 (TN1 interaction factor 1) to affect DWARF14 expression and negatively regulate tiller number in rice. Further analysis of variations in TN1 among indica genotypes according to geographical distribution revealed that low-tillering varieties with TN1-hap^L are concentrated in Southeast Asia and East Asia, whereas high-tillering varieties with TN1-hap^H are concentrated in South Asia. Taken together, these results indicate that TN1 is a tillering regulatory factor whose alleles present apparent preferential utilization across geographical regions. Our findings advance the molecular understanding of tiller development.

Variations in OsSPL10 confer drought tolerance by directly regulating OsNAC2 expression and ROS production in rice

Drought is a major factor restricting the production of rice (Oryza sativa L.). The identification of natural variants for drought stress-related genes is an important step toward developing genetically improved rice varieties. Here, we characterized a member of the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) family, OsSPL10, as a transcription factor involved in the regulation of drought tolerance in rice. OsSPL10 appears to play a vital role in drought tolerance by controlling reactive oxygen species (ROS) production and stomatal movements. Haplotype and allele frequency analyses of OsSPL10 indicated that most upland rice and improved lowland rice varieties harbor the OsSPL10^Hap1 allele, whereas the OsSPL10^Hap2 allele was mainly present in lowland and landrace rice varieties. Importantly, we demonstrated that the varieties with the OsSPL10^Hap1 allele showed low expression levels of OsSPL10 and its downstream gene, OsNAC2, which decreases the expression of OsAP37 and increases the expression of OsCOX11, thus preventing ROS accumulation and programmed cell death (PCD). Furthermore, the knockdown or knockout of OsSPL10 induced fast stomatal closure and prevented water loss, thereby improving drought tolerance in rice. Based on these observations, we propose that OsSPL10 confers drought tolerance by regulating OsNAC2 expression and that OsSPL10^Hap1 could be a valuable haplotype for the genetic improvement of drought tolerance in rice.

Estrogen receptor alpha (ESR1) gene polymorphism (rs2234693 and rs2046210) with breast cancer risk in pashtun population of Khyber Pakhtunkhwa

BACKGROUND

Breast cancer susceptibility is greatly influenced by single nucleotide polymorphisms (SNPs) both in penetrance and non-penetrance genes. The Estrogen Receptor Alfa (ESR1- rs2234693 and rs2046210) have been reported as risk factor of breast cancer in different ethnic groups with inconsistent results. In this study the association of ESR1 (rs2234693 and rs2046210) with breast cancer risk was investigated in patients of Khyber Pakhtunkhwa.

METHODS

A total of 312 females including 162 breast cancer patients and 150 healthy controls were enrolled in this study. The polymorphism was confirmed using T-ARMS-PCR.

RESULTS

Our results revealed that ESR1-rs2234693 risk allele (C) (P = 0.21, OR = 1.27, CI = 0.87 to 1.87) and containing genotypes CC (P = 0.68, OR = 1.24, CI = 0.42 to 3.68) and TC (P = 0.23, OR = 1.32, CI = 0.83 to 2.13) were not associated with the risk of breast cancer. In case of rs2046210, the risk allele A (P < 0.0001, OR = 2.42, CI = 1.74 to 3.38) and corresponding genotypes GA (P = 0.0001, OR = 2.55, CI = 1.62 to 4.03) and AA (P = 0.02, OR = 2.20, CI = 1.12 to 4.34) were significantly associated with higher risk of breast cancer. Moreover, ESR1-rs2234693 was significantly (P < 0.05) associated with family history, stages, PR status, ER status and luminal B. The ESR1-rs2046210 showed significant (P ≤ 0.05) association with menstrual status, tumor grade and TNBC. Both the SNPs showed non-significant (P > 0.05) association with nulliparity, nodal status, HER2 status, metastasis, HER2 enriched subtype and luminal A.

CONCLUSION

It is concluded that ESR1-rs2234693 is not associated with breast cancer, while rs2046210 is significantly associated with the risk of breast cancer in Khyber Pakhtunkhwa population. Further, to confirm the exact situation of ESR1 polymorphism, ESR1 existing and other SNPs need to be investigated in diverse data sets.

Natural variation of RGN1a regulates grain number per panicle in japonica rice

The grain number per panicle (GNP) is an important yield component. Identifying naturally favorable variations in GNP will benefit high-yield rice breeding. Here, we performed a genome-wide association study using a mini-core collection of 266 cultivated rice accessions with deep sequencing data and investigated the phenotype for three years. Three genes, i.e., TOTOU1 (TUT1), Grain height date 7 (Ghd7), and Days to heading 7/Grain height date 7.1/Pseudo-Response Regulator37 (DTH7/Ghd7.1/OsPRR37), which regulate GNP, were found in the quantitative trait loci (QTL) identified in this study. A stable QTL, qGNP1.3, which showed a strong correlation with variations in GNP, was repeatedly detected. After functional and transgenic phenotype analysis, we identified a novel gene, regulator of grain number 1a (RGN1a), which codes for protein kinase, controlling GNP in rice. The RGN1a mutation caused 37.2%, 27.8%, 51.2%, and 25.5% decreases in grain number, primary branch number per panicle, secondary branch number per panicle, and panicle length, respectively. Furthermore, breeding utilization analysis revealed that the additive effects of the dominant allelic variants of RGN1a and DTH7 played a significant role in increasing the grain number per panicle in japonica rice. Our findings enrich the gene pool and provide an effective strategy for the genetic improvement of grain numbers.

Genetic resilience in chickens against bacterial, viral and protozoal pathogens

The genome contributes to the uniqueness of an individual breed, and enables distinctive characteristics to be passed from one generation to the next. The allelic heterogeneity of a certain breed results in a different response to a pathogen with different genomic expression. Disease resistance in chicken is a polygenic trait that involves different genes that confer resistance against pathogens. Such resistance also involves major histocompatibility (MHC) molecules, immunoglobulins, cytokines, interleukins, T and B cells, and CD4+ and CD8+ T lymphocytes, which are involved in host protection. The MHC is associated with antigen presentation, antibody production, and cytokine stimulation, which highlight its role in disease resistance. The natural resistance-associated macrophage protein 1 (Nramp-1), interferon (IFN), myxovirus-resistance gene, myeloid differentiation primary response 88 (MyD88), receptor-interacting serine/threonine kinase 2 (RIP2), and heterophile cells are involved in disease resistance and susceptibility of chicken. Studies related to disease resistance genetics, epigenetics, and quantitative trait loci would enable the identification of resistance markers and the development of disease resistance breeds. Microbial infections are responsible for significant outbreaks and have blighted the poultry industry. Breeding disease-resistant chicken strains may be helpful in tackling pathogens and increasing the current understanding on host genetics in the fight against communicable diseases. Advanced technologies, such as the CRISPR/Cas9 system, whole genome sequencing, RNA sequencing, and high-density single nucleotide polymorphism (SNP) genotyping, aid the development of resistant breeds, which would significantly decrease the use of antibiotics and vaccination in poultry. In this review, we aimed to reveal the recent genetic basis of infection and genomic modification that increase resistance against different pathogens in chickens.

Era of Molecular Diagnostics Techniques before and after the COVID-19 Pandemic

Despite the growth of molecular diagnosis from the era of Hippocrates, the emergence of COVID-19 is still remarkable. The previously used molecular techniques were not rapid enough to screen a vast population at home, in offices, and in hospitals. Additionally, these techniques were only available in advanced clinical laboratories.The pandemic outbreak enhanced the urgency of researchers and research and development companies to invent more rapid, robust, and portable devices and instruments to screen a vast community in a cost-effective and short time. There has been noteworthy progress in molecular diagnosing tools before and after the pandemic. This review focuses on the advancements in molecular diagnostic techniques before and after the emergence of COVID-19 and how the pandemic accelerated the implantation of molecular diagnostic techniques in most clinical laboratories towardbecoming routine tests.

Cold-adaptive evolution at the reproductive stage in Geng/japonica subspecies reveals the role of OsMAPK3 and OsLEA9

Cold stress at the reproductive stage severely affects the production and geographic distribution of rice. The Geng/japonica subpopulation gradually developed stronger cold adaptation than the Xian/indica subpopulation during the long-term domestication of cultivated rice. However, the evolutionary path and natural alleles underlying the cold adaptability of intra-Geng subspecies remain largely unknown. Here, we identified MITOGEN-ACTIVATED PROTEIN KINASE 3 (OsMAPK3) and LATE EMBRYOGENESIS ABUNDANT PROTEIN 9 (OsLEA9) as two important regulators for the cold adaptation of Geng subspecies from a combination of transcriptome analysis and genome-wide association study. Transgenic validation showed that OsMAPK3 and OsLEA9 confer cold tolerance at the reproductive stage. Selection and evolution analysis suggested that the Geng version of OsMAPK3 (OsMAPK3^Geng ) directly evolved from Chinese Oryza rufipogon III and was largely retained in high-latitude and high-altitude regions with low temperatures during domestication. Later, the functional nucleotide polymorphism (FNP-776) in the Kunmingxiaobaigu and Lijiangxiaoheigu version of the OsLEA9 (OsLEA9^KL ) promoter originated from novel variation of intra-Geng was selected and predominantly retained in temperate Geng to improve the adaptation of Geng together with OsMAPK3^Geng to colder climatic conditions in high-latitude areas. Breeding potential analysis suggested that pyramiding of OsMAPK3^Geng and OsLEA9^KL enhanced the cold tolerance of Geng and promotes the expansion of cultivated rice to colder regions. This study not only highlights the evolutionary path taken by the cold-adaptive differentiation of intra-Geng, but also provides new genetic resources for rice molecular breeding in low-temperature areas.

RGN1 controls grain number and shapes panicle architecture in rice

Yield in rice is determined mainly by panicle architecture. Using map-based cloning, we identified an R2R3 MYB transcription factor REGULATOR OF GRAIN NUMBER1 (RGN1) affecting grain number and panicle architecture. Mutation of RGN1 caused an absence of lateral grains on secondary branches. We demonstrated that RGN1 controls lateral grain formation by regulation of LONELY GUY (LOG) expression, thus controlling grain number and shaping panicle architecture. A novel favourable allele, RGN1^C , derived from the Or-I group in wild rice affected panicle architecture by means longer panicles. Identification of RGN1 provides a theoretical basis for understanding the molecular mechanism of lateral grain formation in rice; RGN1 will be an important gene resource for molecular breeding for higher yield.

Elucidating antiviral activity of Curcuma longa against H9 N2 influenza virus using embryonated chicken egg model

Curcumin is a potent antimicrobial herb used traditionally as a spice in culinary. This study was designed to evaluate the antiviral effects of curcuma longa extract against H₉ influenza virus. A total of 60 embryonated eggs were equally divided into 5 groups with 12 eggs in each group. Group 1 (G1) served as uninfected negative control. Whereas Group 2 (G2) was kept as positive control infected with known virus @ 0.2 ml with 10^-9.3 EID₅₀. Group 3 (G3) was offered Curcuma longa @ 0.2 mg/0.2 ml and H₉N₂ virus (@ 0.2 ml with 10^-9.3 EID₅₀. Similarly, Group 4 (G4) was inoculated with extract of Curcuma longa @ 0.2 mg/0.2 ml per egg, whereas Group 5 (G5) was given Ribazole @ 0.2 ml/ egg. The crude extract and virus were administered on the 15^th day of incubation and were checked after every 24 hours up to 96th hour post inoculation by random selection of 3 eggs. Death and survival rate were noted in all groups. Gross and histopathological lesions were also observed. Results revealed that Curcuma longa extract had significantly (p<0.05) reduced the mortality rate of embryos infected with H₉N₂ virus. In G3, increased lymphocytes and mild fatty changes were seen in liver. Whereas, mature RBCs, plasma cells and some lymphoblast's were observed in Spleen. Similarly, the bursa follicles were with lymphocytic aggregation. The G4 (Curcuma longa) and G5 (Ribazole) were with maximum embryo survival after 48 and 72 h post inoculation. This study revealed potential antiviral activity of Curcuma longa against H9N2 influenza viruses and can be opted as alternative to antibiotics and antiviral drugs to minimize the antimicrobial resistance in human and animal population.

Genetic architecture to cause dynamic change in tiller and panicle numbers revealed by genome-wide association study and transcriptome profile in rice

Panicle number (PN) is one of the three yield components in rice. As one of the most unstable traits, the dynamic change in tiller number (DCTN) may determine the final PN. However, the genetic basis of DCTN and its relationship with PN remain unclear. Here, 377 deeply re-sequenced rice accessions were used to perform genome-wide association studies (GWAS) for tiller/PN. It was found that the DCTN pattern rather than maximum tiller number or effective tiller ratio is the determinant factor of high PN. The DCTN pattern that affords more panicles exhibits a period of stable tillering peak between 30 and 45 days after transplant (called DT30 and DT45, respectively), which was believed as an ideal pattern contributing to the steady transition from tiller development to panicle development (ST-TtP). Consistently, quantitative trait loci (QTL) expressed near DT30-DT45 were especially critical to the rice DCTN and in supporting the ST-TtP. The spatio-temporal expression analysis showed that the expression pattern of keeping relatively high expression in root at 24:00 (R24-P2) from about DT30 to DT45 is a typical expression pattern of cloned tiller genes, and the candidate genes with R24-P2 can facilitate the prediction of PN. Moreover, gene OsSAUR27 was identified by an integrated approach combining GWAS, bi-parental QTL mapping and transcription. These findings related to the genetic basis underlying the DCTN will provide the genetic theory in making appropriate decisions on field management, and in developing new varieties with high PN and ideal dynamic plant architecture.

Prevalence of dengue virus serotypes in the 2017 outbreak in Peshawar, KP, Pakistan

Background

Dengue is a viral disease, transmitted by infected Aedes aegypti and Aedes albopictus female mosquitoes. Worldwide, 96 million infections were estimated in 2010. The dengue virus comprises four distinct serotypes (DENV‐1, DENV‐2, DENV‐3, and DENV‐4) which belong to the genus Flavivirus. Determining the serotypes during dengue outbreaks is crucial for its effective management in terms of diagnostics improvement and polyvalent vaccine development. The aim of the present study is to determine the prevalence rate of dengue virus serotypes in the samples collected from patients during the 2017 outbreak in Khyber Pakhtunkhwa, Pakistan.

Methods

A total of 800 ELISA‐positive samples were collected, of which 513 (290 males, 223 females) samples were confirmed positive by PCR.

Results

Out of 513, 25 were found serotype 1 (5%), 196 were serotype 2 (38%), 192 were serotype 3 (37%), 56 were serotype 4 (11%), and 44 (8%) were found to have mix serotypes.

Conclusion

We can conclude that serotypes 2 and 3 of dengue virus were the predominated serotypes of dengue virus in the 2017 outbreak in Peshawar, capital city of Khyber Pakhtunkhwa, Pakistan.

Genetic basis and identification of candidate genes for salt tolerance in rice by GWAS

Soil salinity is a major factor affecting rice growth and productivity worldwide especially at seedling stage. Many genes for salt tolerance have been identified and applied to rice breeding, but the actual mechanism of salt tolerance remains unclear. In this study, seedlings of 664 cultivated rice varieties from the 3000 Rice Genome Project (3K-RG) were cultivated by hydroponic culture with 0.9% salt solution for trait identification. A genome-wide association study (GWAS) of salt tolerance was performed using different models of analysis. Twenty-one QTLs were identified and two candidate genes named OsSTL1 (Oryza sativa salt tolerance level 1) and OsSTL2 (Oryza sativa salt tolerance level 2) were confirmed using sequence analysis. Haplotype and sequence analysis revealed that gene OsSTL1 was a homolog of salt tolerance gene SRP1 (Stress associated RNA-binding protein 1) in Arabidopsis. The hap1 of OsSTL1 was identified as the superior haplotype and a non-synonymous SNP was most likely to be the functional site. We also determined that the level of salt tolerance was improved by combining haplotypes of different genes. Our study provides a foundation for molecular breeding and functional analysis of salt tolerance in rice seedlings.

Genetic basis and identification of candidate genes for salt tolerance in rice by GWAS

Soil salinity is a major factor affecting rice growth and productivity worldwide especially at seedling stage. Many genes for salt tolerance have been identified and applied to rice breeding, but the actual mechanism of salt tolerance remains unclear. In this study, seedlings of 664 cultivated rice varieties from the 3000 Rice Genome Project (3K-RG) were cultivated by hydroponic culture with 0.9% salt solution for trait identification. A genome-wide association study (GWAS) of salt tolerance was performed using different models of analysis. Twenty-one QTLs were identified and two candidate genes named OsSTL1 (Oryza sativa salt tolerance level 1) and OsSTL2 (Oryza sativa salt tolerance level 2) were confirmed using sequence analysis. Haplotype and sequence analysis revealed that gene OsSTL1 was a homolog of salt tolerance gene SRP1 (Stress associated RNA-binding protein 1) in Arabidopsis. The hap1 of OsSTL1 was identified as the superior haplotype and a non-synonymous SNP was most likely to be the functional site. We also determined that the level of salt tolerance was improved by combining haplotypes of different genes. Our study provides a foundation for molecular breeding and functional analysis of salt tolerance in rice seedlings.

Interleukin-6 polymorphisms in HCC patients chronically infected with HCV

Hepatocellular carcinoma is a primary liver malignancy in which the risk of development is always multifunctional. Interleukin-6 is a proinflammatory and multifunctional cytokine, which plays an important role in the immune response, haematopoiesis and defence against viral infection. We aimed to evaluate the frequency of Interleukin-6 mutations (rs2069837 and rs17147230) associated with genetic risk of hepatocellular carcinoma in Khyber Pakthunkhwa population. A total of 72 hepatocellular carcinoma cases and 38 controls were included in this study. The genomic DNA was extracted from the peripheral blood cells and Interleukin-6 genotyping was performed using T-ARMS-PCR technique. Our results show a significant increase risk of developing hepatocellular carcinoma with the mutation within Interleukin-6 gene with heterozygous G allele (rs2069837) (OR = 10.667, 95%CI = 3.923–29.001, p = < 0.0001) and heterozygous T allele (rs17147230) (OR = 75.385, 95%CI = 9.797–580.065, p = < 0.0001). However, under recessive gene model the results were insignificant in case of Interleukin-6 rs2069837 (OR = 0.605, 95%CI = 0.217–1.689, p = 0.337), while significant in case of Interleukin-6 rs17147230 (OR = 0.298, 95%CI = 0.121–0.734, p = 0.0085). In conclusion, Interleukin-6 mutation is associated with hepatocellular carcinoma susceptibility. More related studies with other associated interleukins and their whole gene sequencing will be required.

Prevalence of Hepatitis C virus genotypes in nine selected European countries: A systematic review

BACKGROUND

Hepatitis C virus (HCV) infection is a global health problem especially for its increasing level of mortality. Detailed knowledge of HCV genotypes prevalence has clinical relevance since the efficacy of therapies is impacted by genotypes and subtypes distribution. Moreover, HCV exhibits a great genetic variability regionally. To date, there are no published studies assessing HCV genotypes distribution in specific countries of the Mediterranean basin. The aim of this study was to review data published from 2000 to 2017 with the purpose to estimate genotypes distribution of HCV infection in nine European countries all located in the Mediterranean basin.

METHODS

A systematic research of peer-reviewed journals indexed in PubMed, Scopus, and EMBASE databases selected if containing data regarding distribution of HCV genotypes in nine selected European countries (Albania, Bosnia, Croatia, France, Greece, Italy, Montenegro, Slovenia, and Spain) was performed.

RESULTS

Genotype 1 is the most common (61.0%), ranging from 80.0% in Croatia to 46.0% in Greece, followed by genotype 3 (20.0%), varying from 38.0% in Slovenia to 7.0% and 8.0%, respectively, in Italy and in Albania and by genotype 4 (10.0%) that shows an increase of 1.1% with respect to data obtained till 2014 probably due to the increasing migrants arrivals to Southern Europe. G2, the fourth most frequent genotype (8.5%), particularly common in Italy (27.0%) and Albania (18.0%) might be probably introduced in Southern Italy as a result of Albanian campaign during Second World War and more and more increased by the migration flows from Albania to Italy in the 90s.

CONCLUSION

Epidemiology of HCV infection shows a high variability across the European countries that border the Mediterranean Sea. HCV genotyping is a relevant tool to monitor the dynamic process influenced by both evolving transmission trends and new migration flows on HCV scenario.

Prevalence of Hepatitis C virus genotypes in nine selected European countries: A systematic review

BACKGROUND

Hepatitis C virus (HCV) infection is a global health problem especially for its increasing level of mortality. Detailed knowledge of HCV genotypes prevalence has clinical relevance since the efficacy of therapies is impacted by genotypes and subtypes distribution. Moreover, HCV exhibits a great genetic variability regionally. To date, there are no published studies assessing HCV genotypes distribution in specific countries of the Mediterranean basin. The aim of this study was to review data published from 2000 to 2017 with the purpose to estimate genotypes distribution of HCV infection in nine European countries all located in the Mediterranean basin.

METHODS

A systematic research of peer-reviewed journals indexed in PubMed, Scopus, and EMBASE databases selected if containing data regarding distribution of HCV genotypes in nine selected European countries (Albania, Bosnia, Croatia, France, Greece, Italy, Montenegro, Slovenia, and Spain) was performed.

RESULTS

Genotype 1 is the most common (61.0%), ranging from 80.0% in Croatia to 46.0% in Greece, followed by genotype 3 (20.0%), varying from 38.0% in Slovenia to 7.0% and 8.0%, respectively, in Italy and in Albania and by genotype 4 (10.0%) that shows an increase of 1.1% with respect to data obtained till 2014 probably due to the increasing migrants arrivals to Southern Europe. G2, the fourth most frequent genotype (8.5%), particularly common in Italy (27.0%) and Albania (18.0%) might be probably introduced in Southern Italy as a result of Albanian campaign during Second World War and more and more increased by the migration flows from Albania to Italy in the 90s.

CONCLUSION

Epidemiology of HCV infection shows a high variability across the European countries that border the Mediterranean Sea. HCV genotyping is a relevant tool to monitor the dynamic process influenced by both evolving transmission trends and new migration flows on HCV scenario.

Identifying natural genotypes of grain number per panicle in rice (Oryza sativa L.) by association mapping

INTRODUCTION

As one of the main yield components, grain number per panicle (GNP) played critical role in the rice yield improvement. The identification of natural advantageous variations under different situations will promote the sustainable genetic improvement in rice yield.

OBJECTIVES

This study was designed to identify natural genotypes in a rice mini-core collection, to examine the genotypic effects across the indica and japonica genetic background in different environments, and excavating the superior genotypes that had drove the modern genetic improvement.

METHODS

The association mapping of GNP was carried out using a mini-core collection including 154 indica and 119 japonica accessions in seven different environments. Genotypic effects of each genotype for each QTL were calculated and genotype frequency distortion between the commercial rice cultivars and landraces was screened by χ²-test.

RESULTS

In total, 74 QTLs containing stable and sensitive QTLs in various environments were detected. Within them, 20 positive and 24 negative genotypes in indica, and 24 positive and 16 negative genotypes in japonica were identified. When checking the accumulation of positive genotypes identified in indica across cultivars in each of the two subspecies, it indicated that increased number of positive genotypes identified in indica results in the substantially increased GNP in both indica and japonica across all of the environments, while this trend was not obvious for the positive genotypes identified in japonica especially in short day environments. Moreover, the positive and negative genotype frequency distortion between the landraces and commercial rice cultivars indicated that both positive selection of positive genotypes and negative selection of negative genotypes had driven the genetic improvement on GNP.

CONCLUSION

Our findings suggested that the accumulation of positive genotypes and purifying negative genotypes played equivalently important roles in the improvement of rice yield, but the efficient use for some QTLs or genotypes depends on the comprehensive evaluation of their effect under diverse genetic backgrounds and environments.

Determining the Actual Prevalence of Hepatitis B in Khyber Pakhtunkhwa-Pakistan: A Meta-Analysis

Background:

Hepatitis B is considered the most dangerous among the five types of Hepatitis, as it is clinically asymptomatic. It can silently damage the liver over many years without being diagnosed. Hepatitis B is one of the top risks of liver complications in Khyber Pakhtunkhwa (KP), a province of Pakistan, with an average prevalence rate of 2.70%.

Aims:

We aimed to carefully review the previously published data on prevalence of Hepatitis B Virus (HBV) in KP-Pakistan and use the statistical approach to obtain more precise estimate of the prevalence of HBV in KP-Pakistan. This study on one hand will provide a more reliable and consolidated estimate (pooled estimate) of HBV in the stated region, on the other hand, it enabled us to judge the heterogeneity among the estimates found from these studies. The study is intended to provide more authentic prevalence record and help government/ non-government organizations and health professionals, which plan to initiate HBV prevention programs in KP-Pakistan.

Methods:

A meta-analysis was performed based on studies found in literature search from electronic databases and bibliography on the prevalence of HBV in KP-Pakistan from 2007 to 2017. Abstracts and results of twenty papers were thoroughly studied and the data were extracted. The findings from these studies were distributed in two groups (general and population at high risk) constituting 15 and 5 studies respectively.

Results:

The combined prevalence by considering random model for the general population of KP-Pakistan was observed to be 2.71%, while population at high risk was reasonably high i.e. 5.64%. By comparing this prevalence rate to the highest global prevalence of HBV in the adult population of Western Pacific Region (6.2%), significant (p-value= 0.000) heterogeneity was observed among the estimates in each group. However, the funnel plot provides a symmetric look, eliminating the effect of publication bias. We can say that HBV has an alarming prevalence rate in KP-Pakistan. However, HBV is thrice more prevalent in male population of KP-Pakistan than the female population.

Conclusion:

The above results lead that HBV infection has reached an alarming state in KP-Pakistan, though projects like Prime Minister’s Program for Prevention & Control of Hepatitis which are contributing in improving the health of the people of KP by trying to prevent and control the incidence of HBV. More massive vaccination and awareness programs should be initiated to prevent the spread of HBV on urgent basis. Provision of diagnostics and treatment facilities against HBV in healthcare units of KP-Pakistan should be assured.

The Protein Elicitor PevD1 Enhances Resistance to Pathogens and Promotes Growth in Arabidopsis

The protein elicitor PevD1, isolated from Verticillium dahlia, could enhance resistance to TMV in tobacco and Verticillium wilt in cotton. Here, the pevd1 gene was over-expressed in wild type (WT) Arabidopsis, and its biological functions were investigated. Our results showed that the transgenic lines were more resistant to Botrytis cinerea and Pseudomonas syringae pv. tomato DC3000 than the WT line was. In transgenic plants, both the germination time and bolting time required were significantly shorter and fresh weights and plant heights were significantly higher than those in the WT line. A transcriptomics study using digital gene expression profiling (DGE) was performed in transgenic and WT Arabidopsis. One hundred and thirty-six differentially expressed genes were identified. In transgenic Arabidopsis, three critical regulators of JA biosynthesis were up-regulated and JA levels were slightly increased. Three important repressors of the ABA-responsive pathway were up-regulated, indicating that ABA signal transduction may be suppressed. One CML and two WRKY TFs involved in Ca²⁺-responsive pathways were up-regulated, indicating that this pathway may have been triggered. In conclusion, we show that PevD1 is involved in regulating several plant endogenous signal transduction pathways and regulatory networks to enhance resistance and promote growth and development in Arabidopsis.

Anaphylaxis: incidence, presentation, causes and outcome in patients in a tertiary-care hospital in Karachi, Pakistan

BACKGROUND

Anaphylaxis is a potentially fatal condition requiring immediate resuscitation. Data regarding the epidemiology of anaphylaxis are limited and inconsistent. A reason for the variability was unavailability of a universally acceptable case definition till 2005. We reviewed cases using this new definition

AIM

To review the incidence, clinical presentation, cause and outcome of anaphylaxis at a tertiary-care centre in a low-income country.

DESIGN

Retrospective, case series

METHODS

Chart review of all patients discharged from Aga Khan University Hospital between January 1988 and December 2012 (24 years) with anaphylaxis definition as per second National Institute of Allergy and Infection disease/Food Allergy and Anaphylaxis Network Symposium

RESULTS

Total of 129 cases were found with mean age of 41.6 years (SD 18.8). Majority of patients had cutaneous features (76.7%), followed by respiratory (68.9%), cardiac (64.3%) and gastrointestinal (20.9%) symptoms, respectively. About 22.4% of patients had positive history for allergens out of which 31% (n = 9) were exposed to the same allergens. The common causes identified for anaphylaxis were drugs (60.5%), food (16.3%) and intravenous contrast (10.9%), respectively. Only 22.5% of cases received epinephrine as a part of their initial management. In four patients (3.1%) the cause of death was attributed to anaphylaxis.

CONCLUSION

Anaphylaxis is a rare but life-threatening condition. Though cutaneous features are most common, their absence does not exclude the diagnosis. Drugs were the most common cause and epinephrine was not commonly used as first-line agent for its management.

Pregnancy-associated plasma protein-A levels in individuals with and without coronary artery disease

OBJECTIVE

To compare pregnancy-associated plasma protein-A (PAPP-A) levels in individuals with and without coronary artery disease (CAD).

STUDY DESIGN

Cross-sectional comparative study.

PLACE AND DURATION OF STUDY

Department of Chemical Pathology and Endocrinology, Armed Forces Institute of Pathology (AFIP), Rawalpindi, in collaboration with Armed Forces Institute of Cardiology (AFIC), from September 2008 to March 2010.

METHODOLOGY

One hundred and twenty five (125) individuals both male and female were included in the study. Blood for PAPP-A and lipid profile was collected, just before angiography. On the basis of angiography, the individuals were divided into those with and without CAD. PAPP-A was analyzed by using Diagnostic System Laboratories (DSL) Enzyme Linked Immunosorbent Assay (ELISA) kit and reading was taken by ELISA reader. Lipid profile was determined on automated analyzers Selectra-2 and Vitros 5.1.

RESULTS

Amongst the 125 individuals, 41 individuals were without CAD whereas 84 individuals were having CAD. Mean PAPP-A levels were 0.74 ± 0.35 mIU/L in those without CAD whereas mean PAPP-A levels in those with CAD were 1.35 ± 0.57 mIU/L. The difference between the two groups was statistically significant (p < 0.001). A PAPP-A cut off level of 0.85 mIU/L had a sensitivity and specificity of 78% and 70% respectively for diagnosing atherosclerotic CAD.

CONCLUSION

PAPP-A is a potentially relevant marker of the presence and extent of coronary atherosclerosis as its levels are elevated in CAD as compared to individuals without CAD.

Creating synergies for health systems strengthening through partnerships in Pakistan--a case study of the national eye health programme

Blindness and visual impairment are major causes of noncomrnunicable diseases in Pakistan. Two national population-based blindness surveys conducted in 1988 and 2002-04 demonstrated a reduction in prevalence of blindness from 1.78% to 0.9% with a significant drop in cataract blindness as a result of accelerated nationwide interventions and eye care integration in primary health care. In addition, between 2006 and 2008, 88 facilities were upgraded as a result of the national eye health programme. These measures resulted in a 279% increase in eye outpatient attendances and a 375% increase in eye surgeries performed. Investment in human resources development and policy change contributed significantly to the sustainability of the programme. Key challenges facing the programme include aligning national eye health strategies with health system strengthening informed through health systems research. This paper attempts to document this extraordinary success.

Prooxidant property of green tea polyphenols epicatechin and epigallocatechin-3-gallate: implications for anticancer properties

It is believed that anticancer and apoptosis inducing properties of green tea are mediated by it's polyphenolic constituents particularly catechins. A number of reports have shown that green tea polyphenol (-)-epigallocatechin-3-gallate (EGCG) is among the most effective chemopreventive and apoptosis-inducing agents present in the beverage. Plant polyphenols are naturally occurring antioxidants but they also exhibit prooxidant properties. Over the last several years we have shown that various classes of plant polyphenols including flavonoids, curcuminoids and tannins are capable of catalyzing oxidative DNA cleavage particularly in the presence of transition metal ions such as copper and iron. With a view to understand the chemical basis of various pharmacological properties of green tea, in this paper we have compared the prooxidant properties of green tea polyphenols--EGCG and EC ((-)-epicatechin). The rate of oxidative DNA degradation as well as hydroxyl radical and superoxide anion formation was found to be greater in the case of EGCG as compared with EC. It was also shown that copper mediated oxidation of EC and EGCG possibly leads to the formation of polymerized polyphenols. Further, it was indicated that copper oxidized catechins were more efficient prooxidants as compared with their unoxidized forms. These results correlate with the observation by others that EGCG is the most effective apoptosis inducing polyphenol present in green tea. They are also in support of our hypothesis that prooxidant action of plant polyphenols may be an important mechanism of their anticancer properties. A model for binding of Cu(II) to EC has been presented where the formation of quinone and a quinone methide has been proposed.

The biflavonoid, amentoflavone degrades DNA in the presence of copper ions

Previous reports from this laboratory have shown that flavonoids including apigenin are capable of inducing oxidative DNA cleavage in the presence of copper ions. In the present report, we have examined the ability of amentoflavone, a biflavonoid which is a dimer of apigenin, to catalyze the degradation of DNA. Amentoflavone was found to degrade calf thymus DNA in the presence of Cu(II) at a rate almost twice that of apigenin. Amentoflavone was also shown to reduce Cu(II) to Cu(I) and to generate hydroxyl radicals in the presence of copper ions. In the presence of Cu(II), the absorption spectrum of amentoflavone undergoes a shift and a quenching effect indicating that the biflavonoid is capable of binding to copper ions. Amentoflavone and apigenin were isolated from Cycas rumphii and Trifolium alexandrinum, respectively. The results are discussed in relation to the putative chemopreventive mechanism of amentoflavone.

Serotonin-Cu(II)-mediated DNA cleavage: mechanism of copper binding by serotonin

It has been proposed that considerable DNA damage may be caused by endogenous metabolites produced during the body's normal metabolic processes. 5-hydroxytryptamine (serotonin) is an important neurotransmitter in brain and spinal cord. We have previously shown that serotonin induces oxidative cleavage of DNA strands in the presence of copper ions. In the present paper we have examined the mechanism of copper binding by serotonin using absorption spectroscopy, Cu(II)-mediated lipid peroxidation and by determining the oxidation of the serotonin molecule. Addition of increasing concentrations of Cu(II) to serotonin leads to a progressive enhancement in the absorption band and is accompanied by a shift towards a lower wavelength indicative of the formation of an oxidised species of serotonin. Studies with the structurally related molecules tryptophan and melatonin showed that only serotonin is able to reduce Cu(II) to Cu(I). Similarly, only serotonin was found to be able to abolish the copper-mediated peroxidation of mitochondria. These results suggested the involvement of the phenolic group in copper binding. Further, it was also shown that the binding of copper to serotonin leads to the formation of a quinone in the absence of molecular oxygen. Based on these results, a model has been proposed in which serotonin reduces two molar equivalents of Cu(II) to Cu(I) through a reaction involving two electron oxidation of the phenolic ring to a quinone methide.

Potential antifilarial activity of the leaves and seeds extracts of Psoralea corylifolia on cattle filarial parasite Setaria cervi

The effect of aqueous and alcohol extracts of the leaves and seeds of Psoralea corylifolia, on the spontaneous movements of both the whole worm and the nerve muscle preparation of Setaria cervi and on the survival of microfilariae in vitro was studied. Alcohol extracts of both leaves and seeds caused the inhibition of spontaneous movements of the whole worm and the nerve muscle preparation of S. cervi, characterised by initial, short lasting small increase in tone of contractions followed by paralysis. The initial stimulatory effect was not observed by alcohol extract of leaves on nerve muscle preparation. The concentrations required to inhibit the movements of whole worm and nerve muscle preparations for alcohol extracts of leaves and seeds were 160, 30, and 150, 20 microg/ml, respectively suggesting a cuticular permeability barrier. Alcohol extracts of both leaves and seeds caused death of microfilariae in vitro, LC(50) and LC(90) being 15 and 25 ng/ml for alcohol extract of leaves and 12 and 18 ng/ml for alcohol extract of seeds, respectively.

Bleeding from the lung surface: a unique complication of off-pump CABG operation

A patient, with post myocardial infarction (MI) thrombolysis, underwent emergency off-pump coronary artery bypass graft. Her post-operative course was complicated by excessive bleeding. At re-exploration, the bleeding was caused by a graze on the lung surface by the needle used during the insertion of the deep pericardial retraction suture.

Oxidative DNA damage by capsaicin and dihydrocapsaicin in the presence of Cu(II)

Capsaicin is the pungent phenolic principle of the Capsicum species, and has shown a wide range of pharmacological properties, including antigenotoxic, antimutagenic, and anticarcinogenic effects. Other studies have, however, shown it to be a tumor promoter and potential mutagen, and a carcinogen, resulting in capsaicin being termed a 'double edged sword'. In the present study, we show that capsaicin is capable of causing strand scission in calf thymus and plasmid DNA in the presence of Cu(II) and that this breakage is mediated by reactive oxygen species, especially the hydroxyl radical. Our results further show that capsaicin can directly generate hydroxyl radicals in the presence of Cu(II). To explore the chemical basis of the DNA breakage reaction by capsaicin, we have compared these properties of capsaicin with its saturated structural analog dihydrocapsaicin (DHC). The rate of DNA degradation, as well as hydroxyl radical formation, was found to be greater in the case of capsaicin. Both capsaicin and DHC are able to reduce Cu(II) to Cu(I), which was shown to be an essential intermediate in the DNA cleavage reaction. Stoichiometric analysis indicated that whereas 1 mol of capsaicin reduced 3 mol of Cu(II), 1 mol of DHC reduced only 2 mol of Cu(II). This explains the greater activity of capsaicin and also leads to a model for copper binding to the capsaicins.

Prooxidant and antioxidant activities of bilirubin and its metabolic precursor biliverdin: a structure-activity study

Bilirubin, which is derived from its metabolic precursor biliverdin, is the end product of heme catabolism. It has been proposed as a physiological antioxidant present in human extracellular fluids. We have earlier shown that bilirubin in the presence of the transition metal ion Cu(II) causes strand cleavage in DNA through generation of reactive oxygen species, particularly the hydroxyl radical. Thus bilirubin possesses both antioxidant and prooxidant properties. In order to understand the chemical basis of various biological properties of bilirubin, we have studied the structure-activity relationship between bilirubin and its precursor biliverdin. The latter has also been reported to possess both antioxidant and toxic properties. In the present studies bilirubin was found to be more effective in the DNA cleavage reaction and a more efficient reducer of Cu(II). The rate of formation of hydrogen peroxide and hydroxyl radicals by the compounds also showed a similar pattern. The relative antioxidant activity was also examined by studying the effect of these compounds on DNA cleavage by a hydroxyl radical generating system and their quenching effect on hydroxyl radicals. The results indicate that bilirubin is more active both as an antioxidant as well as an oxidative DNA cleaving agent. A model for binding of copper to bilirubin has been proposed where two copper ions are bound to two molecules of bilirubin through their terminal pyrrole nitrogens. In order to account for the enhanced copper reducing capacity of bilirubin we have further proposed that an additional copper binding site is provided for in the case of bilirubin due to the absence of a double bond between pyrrole rings II and III. Further it would appear that the structural features of the bilirubin molecule which are important for its prooxidant action are also the ones that render it a more effective antioxidant.

Exploration of antifilarial potential and possible mechanism of action of the root extracts of Saxifraga stracheyion on cattle filarial parasite Setaria cervi

The effect of aqueous and alcohol extracts of the roots of Saxifraga stracheyi Engl. On the spontaneous movements of both the whole worm and the nerve muscle preparation of Setaria cervi and on the survival of microfilariae in vitro was studied. Both extracts caused the inhibition of spontaneous movements of the whole worm and the nerve-muscle preparation of S. cervi, characterized by an increase in the amplitude and a decrease in the rate of contractions, while the tone of the contractions remained visibly unaffected. The concentration required to inhibit the movements of the whole worm preparation was 140 microg/ml for the aqueous and 250 microg/ml for the alcohol extract. The concentration of S. stracheyi extracts required to produce an equivalent effect on the nerve-muscle preparation was 30 microg/ml for aqueous, and 20 microg/ml for the alcohol extract, suggesting a cuticular permeability barrier.

Reactivities of flavonoids with different hydroxyl substituents for the cleavage of DNA in the presence of Cu(II)

DNA strand scission reactions of flavonoids in the presence of Cu(II) have been extended by using flavonoids with a variety of patterns of hydroxyl substitution. In particular we have examined for the first time a flavonoid (7,8-dihydroxyflavone) that lacks the possibility of forming a complex involving the oxygen at position 4. By comparing the reactivities of several flavonoids, including data from the literature, we draw generalizations for the correlation of structure and activity and present evidence for at least three different modes of action of flavonoids as genotoxic agents.

Pro-oxidant, anti-oxidant and cleavage activities on DNA of curcumin and its derivatives demethoxycurcumin and bisdemethoxycurcumin

Curcumin, a naturally occurring phytochemical responsible for the colour of turmeric shows a wide range of pharmacological properties including antioxidant, anti-inflammatory and anti-cancer effects. We have earlier shown that curcumin in the presence of Cu(II) causes strand cleavage in DNA through generation of reactive oxygen species, particularly the hydroxyl radical. Thus, curcumin shows both antioxidant as well as pro-oxidant effects. In order to understand the chemical basis of various biological properties of curcumin, we have studied the structure-activity relationship between curcumin and its two naturally occurring derivatives namely demethoxycurcumin (dmC) and bisdemethoxycurcumin (bdmC). Curcumin was found to be the most effective in the DNA cleavage reaction and a reducer of Cu(II) followed by dmC and bdmC. The rate of formation of hydroxyl radicals by the three curcuminoids also showed a similar pattern. The relative antioxidant activity was examined by studying the effect of these curcuminoids on cleavage of plasmid DNA by Fe(II)-EDTA system (hydroxyl radicals) and the generation of singlet oxygen by riboflavin. The results indicate that curcumin is considerably more active both as an antioxidant as well as an oxidative DNA cleaving agent. The DNA cleavage activity is the consequence of binding of Cu(II) to various sites on the curcumin molecule. Based on the present results, we propose three binding sites for Cu(II). Two of the sites are provided by the phenolic and methoxy groups on the two benzene rings and the third site is due to the presence of 1,3-diketone system between the rings. Furthermore, both the antioxidant as well as pro-oxidant effects of curcuminoids are determined by the same structural moieties.

Antifilarial activity of Mallotus philippensis Lam. on Setaria cervie (Nematoda: Filarioidea) in vitro

The effect of aqueous and alcoholic extracts of the leaves of Mallotus philippensis (Lam.) Muell. Arg. was studied on the spontaneous movements of the whole worm and nerve-muscle (n.m.) preparation of Setaria cervi and on the survival of microfilariae in vitro. Both the extracts caused inhibition of spontaneous motility of whole worm and the n.m. preparation of S. Cervi characterized by initial stimulation followed by depression in amplitude. The tone and rate of contractions remained visibly unaffected. Aqueous extract at higher concentration showed immediate reduction in tone. The concentration required to inhibit the movements of n.m. preparation was 1/5th for aqueous and 1/11th for alcoholic extract compared to that for the whole worm, suggesting a cuticular permeability barrier. The stimulatory response of acetylcholine was blocked by aqueous extract on whole worm movements. On the microfilariae the LC50 and LC90 were 18 and 20 ng/ml for aqueous and 12 and 15 ng/ml for alcoholic extracts respectively.

Potential antifilarial activity of roots of Asparagus adscendens Roxb, against Setaria cervi in vitro

Effect of aqueous and alcoholic extracts of the roots of A. adscendens was studied on the spontaneous movements of whole worm and nerve muscle (n.m.) preparation of S. cervi and on the survival of microfilariae in vitro. Aqueous as well alcoholic extracts caused inhibition of spontaneous motility of whole worm and n.m. preparation of S. cervi characterized by initial, short lasting small increase in amplitude and tone of contractions followed by paralysis. The initial stimulatory effect was not observed by aqueous extract on n.m. preparation. The concentration required to inhibit the movements of n.m. preparation was 1/4th for aqueous and 1/3rd for alcoholic extract suggesting a cuticular permeability barrier. The effect of acetylcholine on n.m. preparation was concentration related being more with a concentration of 5 micrograms/ml as compared to 1 microgram/ml. Both alcoholic as well as aqueous extracts caused death of microfilariae in vitro, LC50 and LC90 being 8 and 16 ng/ml for aqueous, 3 and 12 ng/ml for alcoholic extracts respectively.

In vitro antifilarial activity of Sencio nudicaulis Buch. Ham. Effect on Setaria cervi (Nematoda Filarioidea)

The effect on aqueous and alcoholic extracts of the leaves of Sencio nudicaulis Buch. Ham. was studied on the spontaneous movements of the whole worm and nerve-muscle preparation of Setaria cervi and on the survival of micro-filariae in vitro. Aqueous as well as alcoholic extracts caused inhibition of spontaneous motility of the whole worm and nerve-muscle preparation of S. cervi characterized by decreased amplitude, rate and tone of contractions. The concentration required to inhibit the movements of n.m. preparation was 1/3rd for aqueous and 1/20th for alcoholic extract suggesting a cuticular permeability barrier. The effect of S nudicaulis extracts was different than that produced by calcium channel blocker nifedipine on the whole worm and n.m. preparation. While nifedipine blocks the stimulant effect of Ach the extracts of S. nudicaulis fails to do so. While the response bears similarity with DEC which also does not block Ach response. Both aqueous and alcoholic extracts exhibited microfilaricidal action in vitro LC50 and LC90 being 10 and 15 ng/ml for aqueous extract, 5 and 12 ng/ml for alcoholic extract.

Experience with frontonasal dysplasia of varying severity

Nine cases of frontonasal dysplasia were seen during an 8-year period. Seven were managed in the authors' institution, and the two adult relatives were referred to adult units. The age and sex distribution, the types of defects, and the family pedigree of an affected family are described. Management criteria were formulated according to the severity and other associated abnormalities.

The distribution of immunoreactive interferon-gamma-containing cells in normal human tissues

An immunohistochemical technique has been used to study the distribution of lymphocytes expressing interferon-gamma in normal adult tissues. The greatest concentrations of these cells were seen in mucosal sites exposed to a resident microflora. It is proposed that such organisms, by eliciting immune responses, provide the stimulus for the production of 'physiological' interferon-gamma. This in turn may act to preserve the 'tone' or readiness of the immune system.

The distribution of immunoreactive interferon-alpha in formalin-fixed paraffin-embedded normal human foetal and infant tissues

Human foetal and infant tissues were studied to test the hypothesis that microbes have a role in switching on interferon-alpha (IFN-alpha) synthesis. Foetal tissues were essentially 'germ free', while the infants had been exposed to a normal microbial environment in life. IFN-alpha was first seen at 9 weeks gestation in macrophages in the liver and thereafter was seen in macrophages in most other organs. When infant lungs were compared with foetal lungs, a statistically significant increase in the number of macrophages and the percentage of these cells expressing IFN-alpha was noted in the infant lungs. No such change was observed in spleen, liver and thymus following birth. These findings suggest that there is a basal production of IFN-alpha by macrophages that is not dependent on microbial products, but that such products can enhance synthesis of this cytokine.