The impact of boron seed priming on seedling establishment, growth, and grain biofortification of mungbean (Vigna radiata L.) in yermosols

Boron-deficiency in Yermosols is among the major constraints to mungbean productivity and grain biofortification in Pakistan. However, agronomic strategies such as boron (B) seed priming have potential to improve mungbean yield and grain biofortification. Moreover, deficiency to toxicity range for B is very narrow; therefore, it is pre-requisite to optimize its dose before field evaluation. A wire house experiment was planned out to reconnoiter the impact of seed priming with B on growth and quality of two cultivars of mungbean, i.e., ‘NM-2011’ and ‘NM-2016’. Four different B levels were used as seed priming, i.e., 0.01%, 0.05%, 0.1% and 1.0% B, (borax Na₂B₄O₇.10H₂O, 11.5% B) were tested, whereas hydropriming was regarded as control. Seed priming with 0.01% B significantly (p≤0.05) lowered time taken to start germination and time to reach 50% emergence, whereas improved mean emergence time, emergence index, final emergence percentage, number of leaves, dry and fresh weight of root, shoot, and total weight, root length, plant height, chlorophyll contents, number of pods and 100-grain weight, seeds per plant, grain yield per plant, B concentrations in stem and grain, grain protein, carbohydrate and fiber in both cultivars. Boron seed priming proved beneficial under a specific range; however, deficiency (hydropriming) and excess (above 0.01% B) of B were detrimental for mungbean growth and productivity. The cultivar ‘NM-2016’ had significantly (p≤0.05) higher yield due to prominent increase in yield related traits with 0.01% B priming as compared to ‘NM-2011’. In conclusion, B seed priming (0.01% B) seemed a feasible choice for improving mungbean growth, yield related traits and grain-B concentration of mungbean on Yermosols.

Tillage Systems Affecting Rice-Wheat Cropping System

Rice-wheat production is an essential component of cropping systems in the Indus-Ganga Plains (IGP) which play a pivotal role in food security of south Asia. These crops are being cultivated on an area of about 13.5 M ha of South Asia. In rice-wheat cropping system, the major reason for lower wheat grain yield is use of unwise tillage practices during wheat seedbed preparation, cultivation of late maturing rice varieties, water shortage, labor shortage, high cost of fertilizers and poor crop management practices. Resource-conserving technology improves the sustainability and productivity of wheat, which ultimately increase the farmer’s livelihood and reduce poverty. Tillage plays an important role in agricultural operation for soil manipulation to optimize the crop productivity. Different tillage systems are being practiced for wheat production in rice-wheat cropping systems including intensive tillage system, conventional and deep tillage, conservation tillage that consisting of minimum tillage, ridge tillage, and no-till or zero tillage system. Zero tillage gives more accessible and efficient planting system that ensures timely wheat cultivation, cut off the tillage operation, better crop residue management that ultimately minimize the cost of production and keeps environment clean. Operational costs for wheat sowing are 50-60% lower with zero tillage (ZT) sowing than with conventional sowing. The cost saving effect is the main reason for the spread of zero tillage technology in rice-wheat system. Current paper presented a review of different tillage systems and their effects on soil physical properties, plant available water, soil organic matter and nutrients, rice residues, wheat yield and farmer’s economics.

Lipoic Acid Combined with Melatonin Mitigates Oxidative Stress and Promotes Root Formation and Growth in Salt-Stressed Canola Seedlings (Brassica napus L.)

Lipoic acid (LA) and melatonin (MT) are pleiotropic molecules participating in plant stress resistance by modulating cellular biochemical changes, ion homeostasis, and antioxidant enzyme activities. However, the combined role of these two molecules in counteracting the detrimental impacts of salinity stress is still unknown. In the present study, we determined the effects of exogenous LA (0.5 µM), MT (1 µM) and their combination (LA + MT) on growth performance and biomass accumulation, photosynthetic pigments, enzymatic and non-enzymatic antioxidant activities, and ions homeostatic in canola (Brassica napus L.) seedlings under salinity stress (0, 100 mM) for 40 days. The results indicate that exogenous application of LA + MT improved the phenotypic growth (by 25 to 45%), root thickness (by 68%), number of later lateral roots (by 52%), root viability (by 44%), and root length (by 50%) under salinity stress. Moreover, total soluble protein, chlorophyll pigments, the concentration of superoxide dismutase (SOD), catalase peroxidase (CAT), and ascorbic peroxidase (ASA) increased with the presence of salt concentration into the growth media and then decreased with the addition of LA + MT to saline solution. Leaf protein contents and the degradation of photosynthetic pigments were lower when LA + MT treatments were added into NaCl media. The proline and phenol contents decreased in the exogenous application of LA + MT treatments more than individual LA or MT treatments under the salinity stress. The incorporation of LA or MT or a combination of LA + MT to saline solution decreased salinity-induced malondialdehyde and electrolyte leakage. In conclusion, the alteration of metabolic pathways, redox modulation, and ions homeostasis in plant tissues by the combined LA and MT application are helpful towards the adaptation of Brassica napus L. seedlings in a saline environment. The results of this study provide, for the first time, conclusive evidence about the protective role of exogenous LA + MT in canola seedlings under salinity stress.

Soil applied boron (B) improves growth, yield and fiber quality traits of cotton grown on calcareous saline soil

Boron (B) is required during all growth stages of cotton crop, especially during boll formation. However, Typic Haplocambid soils of cotton growing belt in Pakistan are B-deficient, which results in low yield and economic returns. Foliar application of B improves cotton productivity; however, information is limited on the role of soil applied B in improving cotton growth and yield. The current study investigated the role of soil applied B in improving growth, yield and fiber quality of cotton crop. Five different B doses (i.e., 0.00, 2.60, 5.52, 7.78 and 10.04 mg kg^-1 of soil) and two cotton cultivars (i.e., CIM-600 and CIM-616) were included in the study. Soil applied B (2.60 mg kg^-1) significantly improved growth, yield, physiological parameters and fiber quality, while 10.04 mg kg^-1 application improved B distribution in roots, seeds, leaves and stalks. Significant improvement was noted in plant height (12%), leaf area (3%), number of bolls (48%), boll size (59%), boll weight (52%), seed cotton yield (52%), photosynthesis (50%), transpiration rate (10%), stomatal conductance (37%) and water use efficiency (44%) of CIM-600 with 2.60 mg kg^-1 compared to control treatment of CIM-616. Similarly, B accumulation in roots, seeds, leaves and stalk of CIM-600 was improved by 76, 41, 86 and 70%, respectively compared to control treatment. The application of 2.60 mg kg^-1 significantly improved ginning out turn (6%), staple length (3.5%), fiber fineness (17%) and fiber strength (5%) than no B application. The results indicated that cultivar CIM-600 had higher ginning out turn (1.5%), staple length (5.4%), fiber fineness (15.5%) and fiber strength (1.8%) than CIM-616. In crux, 2.60 mg kg^-1 soil B application improved growth, yield, physiological and fiber quality traits of cotton cultivar CIM-600. Therefore, cultivar CIM-600 and 2.60 mg kg^-1 soil B application is recommended for higher yield and productivity.

Abstract P4-08-10: MammaPrint identifies 46% of patients, age ≤50 years with oncotype RS 18-30, as low risk and safe to forgo chemotherapy

Background: The PROMIS trial (NCT01617954) previously showed that an OncotypeDx (ODx) Intermediate Recurrence Score (RS 18-30) led to uncertainty in prescribing chemotherapy (CT), especially in the middle of the intermediate range from RS 21-26 where an equal number of patients were recommended to receive and forego CT (Tsai, JAMA Oncology 2018). Forty-seven percent (3183/6711) of randomized TAILORx patients were classified as RS 18-25 and are well represented in PROMIS. These patients with RS 18-25 may still lack definitive CT recommendation following TAILORx, reflexing to age and menopausal status to make a decision. Here, we re-evaluate PROMIS using the subgroup analyses adopted by TAILORx. Methods: MammaPrint (MP) risk of recurrence was determined for ODx intermediate patients by standard diagnostic testing (Agendia, Irvine, CA). Clinical risk was assessed using the MINDACT, modified Adjuvant Online! algorithm (Cardoso, NEJM 2016). The MP high and low risk classification, and patient and tumor characteristics were re-evaluated and subdivided by RS 18-25 vs. RS 26-30. Results: The 840 eligible patients in PROMIS were classified as 61.3% (515/840) clinically low risk and 37.0% (311/840) clinically high risk (including 84 lymph node positive patients). Half (342/684) of all patients with an RS 18-25 and 20.5% (32/156) patients with RS 26-30 were MP low risk. There was no significant difference in the distribution of MP risk in women age ≤50 yrs vs. >50 years (Yates chi-square P=0.62); MP classified 46.4% (84/181) patients age ≤50 yrs and 44.0% (290/659) patients age >50 yrs as low risk. In the clinically-low risk subset of 515 patients, there was also no significant difference in the distribution of MP risk by age (Yates chi-square P=0.89); MP classified 48.3% (56/116) patients age ≤50 yrs and 49.6% (198/399) patients age >50 yrs as low risk. Conclusions: In light of TAILORx and uncertain CT benefit in women ≤50 yrs, MammaPrint provides a definitive high or low risk answer and identifies 46% of these women who may safely forego CT based on MINDACT data. An analysis of young patients in the MINDACT trial showed that MP low risk patients age <45 yrs and 45-55 yrs had very good 5-yr DMFS of 95-98%, in both clinically low and high risk groups (Alders, SABCS 2017).

MammaPrint Risk by RS and AgeMammaPrint RiskRS 18-25  RS 26-30  GrandClassification≤50 yrs>50 yrsAll Ages≤50 yrs>50 yrsAll AgesTotalHigh Risk7426834223101124466Low Risk8026234242832374All15453068427129156840

Citation Format: Soliman H, Lo S, Qamar R, Budway R, Levine E, Whitworth P, Mavromatis B, Zon R, Untch S, Treece T, Blumencranz L, Audeh W, Tsai M, PROMIS Investigators Group. MammaPrint identifies 46% of patients, age ≤50 years with oncotype RS 18-30, as low risk and safe to forgo chemotherapy [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-08-10.

Low Seroprevalence of Torque Teno Virus in HCV positive patients and phylogenetic analysis from Pakistani isolates

The torque teno virus (TTV) has a heterogeneous genome and its role in hepatitis C (HCV) infection is still controversial, therefore the purpose of the present study was to determine if there is any association between Hepatitis C and TTV co-infection and to determine the phylogenetic relationship between existing types in the Pakistani population. A total of 500 individuals (250 HCV positive patients and 250 healthy controls) were selected. DNA was extracted from serum samples and polymerase chain reaction (PCR) of the open reading frame 1 (ORF1) region of TTV was performed. Out of 500 samples 9 HCV positive index cases (3.6%) and 8 healthy samples (3.2%) were found to be positive for TTV. A comparison was made between TTV sequences reported from all over the world with the ones obtained in the present study by sequencing of TTV positive samples followed by phylogenetic analysis using maximum parsimony (MP) method. Our results indicated that the virus was undergoing divergent evolution as very high sequence diversity was found in the ORF1 gene. The study also shows that association between HCV and TTV was not found. Because the virus was found to be affecting both healthy individuals and HCV infected population with almost same frequency. Therefore a thorough screening of TTV virus at the population level is required in order to draw a comprehensive inference.

Abstract P3-12-10: Feasibility of four cycles of docetaxel and cyclophosphamide every 14 days as an adjuvant regimen for breast cancer: A Wisconsin oncology network study

Background: Dose-dense therapies have had a major impact on reducing toxicity and improving outcomes in breast cancer. A combination of docetaxel plus cyclophosphamide (TC) every 3 weeks has emerged as a common chemotherapy regimen used for treatment of node-negative or lower-risk node-positive breast cancer. We tested whether it is feasible to deliver TC on a dose-dense schedule.

Patients and Methods: We enrolled women with early stage breast cancer on a single-arm phase II study of adjuvant dose-dense TC (ddTC) through a regional oncology network (WON). All women completed primary surgery; subsequent therapy with TC was deemed appropriate by the treating physician. Planned treatment was docetaxel 75 mg/m2 plus cyclophosphamide 600 mg/m2 every 2 weeks for 4 cycles with subcutaneous pegfilgrastim 6 mg administered 24-48 hours after the administration of each chemotherapy cycle. The primary endpoint was feasibility of administering therapy within 10 weeks. A Simon Optimal 2-Stage design was employed for the study design.

Results: Of 42 women enrolled, 41 were evaluable by prespecified criteria. Median age was 54 (28-73). Most subjects had node negative (73%) or hormone receptor positive (71%) tumors. Of the 41 subjects, 37 (90.2%) completed therapy within 10 weeks and 34 (83%) completed therapy at 8 weeks without dose modification. Rates of grade 2 neuropathy were similar to that reported previously (15%) and there were no cases of grade 3 or higher neuropathy. The rate of neutropenic fever was low (2.5%). Rash and plantar/palmar erythrodythesia were common and reached grade 3 in four subjects (9.8%).

Conclusion: Dose-dense TC is feasible with tolerability profiles similar to standard TC and a low likelihood of neutropenic fever. This study supports further clinical development of this 8-week adjuvant chemotherapy regimen.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P3-12-10.

Genetic associations of psoriasis in a Pakistani population

BACKGROUND

Genetic predisposition to psoriasis, an inflammatory skin disease affecting 0·2-4% of the world population, is well established. Thus far, 41 psoriasis susceptibility loci reach genome-wide significance (P ≤ 5 × 10(-8) ). Identification of genetic susceptibility loci in diverse populations will help understand the underlying biology of psoriasis susceptibility.

OBJECTIVES

The primary objective of this study was to examine psoriasis susceptibility associations previously reported in Chinese and caucasian populations in a Pakistani cohort.

METHODS

Blood samples and phenotype data were collected from psoriasis cases and controls in Islamabad, Pakistan. DNA was isolated and genotypes of selected susceptibility markers were determined. The data were analysed using χ(2) tests or logistic regression for psoriasis association.

RESULTS

HLA-Cw6 showed the strongest association [odds ratio (OR) 2·43, P = 2·3 × 10(-12) ]. HLA-Cw1 showed marginally significant association (OR 1·66, P = 0·049), suggesting that the HLA-Cw1-B46 risk haplotype may be present in the Pakistani population. Three other loci (IL4/IL13, NOS2, TRAF3IP2) showed nominally significant association (P < 0·05).

CONCLUSIONS

HLA-Cw6 is strongly associated with psoriasis susceptibility in the Pakistani population, as has been found in every other population studied. In addition, HLA-Cw1 showed marginal association, reflecting the relative geographical proximity and thus likely genetic relatedness to other populations in which the HLA-Cw1-B46 haplotype is known to be associated. A larger cohort and a denser marker set will be required for further analysis of psoriasis associations in the South Asian population.

Virulence factors profile of drug-resistant Escherichia coli isolates from urinary tract infections in Punjab, Pakistan

Escherichia coli is considered to be the main causative agent of urinary tract infections (UTIs). The primary objective of this study was to investigate the spectrum of five virulence factors among drug-resistant clinical E. coli isolates associated with pyelonephritis and cystitis. A total of 101 samples were positive for E. coli (42 from pyelonephritis cases and 59 from cystitis cases) out of 457 urine samples of patients. Among toxins, haemolysin and secreted autotransporter toxin are found more frequently in isolates causing pyelonephritis (p < 0.020) than cystitis (p < 0.083). The frequent occurrence of P-pili, S-fimbria and protein involved in intestinal colonisation was noted among E. coli isolates associated with pyelonephritis. Overall, the study suggests that clinical isolates associated with pyelonephritis are more virulent than those associated with cystitis and diversified association with various antimicrobial resistance phenotypes was noted.

SABRE-B: an evaluation of paclitaxel and bevacizumab with or without sunitinib as first-line treatment of metastatic breast cancer

BACKGROUND

The vascular endothelial growth factor (VEGF) pathway can be targeted through VEGF neutralization or VEGF receptor (VEGFR) blockade using tyrosine kinase inhibition. Because laboratory models suggest that combining these approaches might be synergistic, we sought to evaluate the feasibility and efficacy of combining sunitinib with paclitaxel + bevacizumab (PB).

METHODS

Patients with human epidermal growth factor receptor 2 (HER2)-negative, metastatic breast cancer receiving first-line chemotherapy were randomized to PB or PB with sunitinib (PBS), with planned escalation of the sunitinib dose.

RESULTS

Forty-six patients were randomized to PB or PBS with sunitinib dosed at 25 mg p.o. daily. Patients receiving PBS encountered substantial toxicity that precluded adequate treatment. The percentage of patients with grade ≥3 adverse events was greater in the PBS arm than the PB arm (83% versus 57%), and sunitinib dosing was modified in 78% of patients, most often due to neutropenia, febrile neutropenia, and fatigue. In addition, 44% of patients had sunitinib dose reduction to 12.5 mg, and 39% required discontinuation. Patients receiving PBS had more bevacizumab treatment interruptions and discontinuations because of toxicity. Median treatment duration was longer in the PB arm compared with the PBS arm (14.1 versus 11.1 weeks), reflecting early treatment discontinuation of PBS. Because of poor tolerability of the addition of sunitinib to PB, the planned sunitinib dose escalation was halted and the study accrual was terminated.

CONCLUSION

Adding sunitinib to standard doses of bevacizumab plus paclitaxel for metastatic breast cancer is not feasible. Different strategies will be required to evaluate whether there is additional clinical benefit to combining VEGF/VEGFR-targeted agents.

A Novel Familial BBS12 Mutation Associated with a Mild Phenotype: Implications for Clinical and Molecular Diagnostic Strategies

Bardet-Biedl syndrome (BBS) is an autosomal recessively inherited ciliopathy mainly characterized by rod-cone dystrophy, postaxial polydactyly, obesity, renal tract anomalies, and hypogonadism. To date, 14 BBS genes, BBS1 to BBS14, have been identified, accounting for over 75% of mutations in BBS families. In this study, we present a consanguineous family from Pakistan with postaxial polydactyly and late-onset retinal dysfunction. Adult affected individuals did not show any renal or genital anomalies, obesity, mental retardation or learning difficulties and did thus not fulfill the proposed clinical diagnostic criteria for BBS. We mapped the disease in this family to the BBS12 locus on chromosome 4q27 and identified the novel homozygous p.S701X nonsense mutation in BBS12 in all three affected individuals of this family. We conclude that BBS12 mutations might cause a very mild phenotype, which is clinically not diagnosed by the current diagnostic criteria for BBS. Consequently, we suggest the use of less strict diagnostic criteria in familial BBS families with mild phenotypic expression.

Pilot study of sequential vinorelbine and cisplatin followed by docetaxel for selected IIIB and stage IV non-small cell lung cancer

Vinorelbine, cisplatin and docetaxel are known to be efficacious in non-small cell lung cancer (NSCLC). This limited institution pilot study evaluated the novel strategy of sequencing active first line agents prior to progression. The primary objective of this study was to assess the toxicity profile in anticipation of a larger cooperative group standard phase II study. Patients with selected stage IIIB and IV NSCLC, Southwest Oncology Group (SWOG) performance status (PS) of 1 or less and measurable or evaluable disease were eligible. Treatment was cisplatin 100 mg/m(2) day 1 and 29, vinorelbine 25 mg/m(2) weekly for 8 weeks, followed by docetaxel 100 mg/m(2) every 21 days for four cycles if no progression. If grade IV neutropenia developed, G-CSF 5 mcg/kg/day was used in subsequent cycles. Of 18 eligible patients, 17 patients had stage IV disease with a median age of 66 years (range 48-80). Eight patients had a SWOG PS of 1, 10 had a PS of zero. Six of eighteen patients received all 8 weeks of vinorelbine/cisplatin and six of eight patients who went on to receive docetaxel received all four planned cycles; only two patients overall received all planned therapy. One grade III/IV event each of cardiotoxicity (myocardial infarction), renal toxicity (acute renal failure), anemia and thrombocytopenia occurred with vinorelbine and cisplatin, and 2 Grade IV hypersensitivity reactions, manifested by severe back pain with docetaxel occurred. Three deaths occurred during the study, all during treatment with vinorelbine and cisplatin: one due to neutropenic sepsis; one from a pulmonary embolism; and one secondary to severe hypoglycemia in a diabetic patient. Of the 16 patients evaluable for response after vinorelbine/cisplatin, there were two complete responses (12.5%) and three partial responses (19%) for an overall response rate of 31% (95% CI 8-58). One additional patient who received docetaxel experienced a partial response. Two patients remain alive (21+ and 18+ months, respectively). The 1-year survival was 44%.

CONCLUSION

This sequence, as defined, was tolerated marginally well in patients with advanced NSCLC. Granulocytopenia was the major toxicity requiring dose adjustments throughout the sequence. Based on response rates and tolerability that were somewhat comparable to other regimens in this disease setting, a modified version of this program, adjusted to decrease the incidence of grade III and IV toxicity, was selected as one arm of a recent randomized phase II trial in the Southwest Oncology Group (SWOG), S9806, evaluating sequential therapy in advanced NSCLC.

Y-chromosomal STR haplotypes in Pakistani populations

16 Y-specific STR loci have been analysed in 711 males from 12 populations in Pakistan. Individual loci showed between 4 and 10 alleles, and diversities ranged from 0.07 to 0.77. A total of 527 different haplotypes were found and the haplotype diversity ranged from 0.92 to 0.99 for the different populations. 446 haplotypes occurred in single individuals, and only 19 haplotypes were present in more than three males, but two striking examples of haplotype sharing were found, one involving 13 individuals, and the other 17. The 13 individuals were all Parsis, and 16 of the 17 were Brahuis, providing evidence for population substructuring.

Y-chromosome lineages trace diffusion of people and languages in southwestern Asia

The origins and dispersal of farming and pastoral nomadism in southwestern Asia are complex, and there is controversy about whether they were associated with cultural transmission or demic diffusion. In addition, the spread of these technological innovations has been associated with the dispersal of Dravidian and Indo-Iranian languages in southwestern Asia. Here we present genetic evidence for the occurrence of two major population movements, supporting a model of demic diffusion of early farmers from southwestern Iran-and of pastoral nomads from western and central Asia-into India, associated with Dravidian and Indo-European-language dispersals, respectively.

P53 mutations, polymorphisms, and haplotypes in Pakistani ethnic groups and breast cancer patients

Inactivation of the p53 gene has been found to be associated with the pathogenesis of several neoplasias. Three biallelic polymorphisms in the p53 gene have been linked to predisposition to the development of various malignancies. These include a 16-bp duplication in intron 3 and BstU I and Msp I restriction fragment length polymorphisms (RFLPs) in exon 4 and intron 6, respectively. The prevalence of these polymorphisms was studied in breast cancer patients and nine major ethnic groups of Pakistan. Differences in allele frequencies for all three polymorphisms were observed among the various ethnic groups and breast cancer patients. The absence of the 16-bp duplication was common among the northern ethnic groups, being highest in the Hazara (0.90). The Msp I A1 allele frequency in the southern Makrani population was significantly higher in comparison with the other ethnic groups. In the cancer patients, the absence of the 16-bp duplication in combination with the BstU I Pro and absence of Msp I restriction site were the most frequent. In these patients, ten substitution mutations were found in the p53 gene, seven of which have been reported previously for breast cancer. The remaining three mutations have been found in other malignancies, but not in carcinoma of the breast.

A polymorphic L1 retroposon insertion in the centromere of the human Y chromosome

We have identified a novel polymorphic L1 retroposon insertion, designated LY1, in the centromeric alphoid array of the human Y chromosome. The element belongs to the transpositionally active Ta subset and its presence is compatible with normal centromere function. It was found at highest frequency in China, where it accounts for 23% of the Han sample, and was present at low frequencies in the surrounding areas, but was not found at all outside Asia. Chromosomes carrying LY1 show considerable microsatellite diversity, suggesting an ancient origin for the lineage at approximately 10 000 years ago (with wide confidence limits), but only limited subsequent migration.

Identification and characterisation of novel human Y-chromosomal microsatellites from sequence database information

1.33 Mb of sequence from the human Y chromosome was searched for tri- to hexanucleotide microsatellites. Twenty loci containing a stretch of eight or more repeat units with complete repeat sequence homo-geneity were found, 18 of which were novel. Six loci (one tri-, four tetra- and one pentanucleotide) were assembled into a single multiplex reaction and their degree of polymorphism was investigated in a sample of 278 males from Pakistan. Diversities of the individual loci ranged from 0.064 to 0.727 in Pakistan, while the haplotype diversity was 0.971. One population, the Hazara, showed particularly low diversity, with predominantly two haplotypes. As the sequence builds up in the databases, direct methods such as this will replace more biased and technically demanding indirect methods for the isolation of microsatellites.

African and Levantine origins of Pakistani YAP+ Y chromosomes

We surveyed 9 Pakistani subpopulations for variation on the nonrecombining portion of the Y chromosome. The polymorphic systems examined were the Y-chromosome Alu insertion polymorphism (YAP) at DYS287, 5 single nucleotide polymorphisms, and the tetranucleotide microsatellite DYS19. Y chromosomes carrying the YAP element (YAP+) were found in populations from southwestern Pakistan at frequencies ranging from 2% to 8%, whereas northeastern populations appeared to lack YAP+ chromosomes. In contrast to other South Asian populations, several Pakistani subpopulations had a high frequency of the DYS19*B allele, the most frequent allele in West Asian, North African, and European populations. The combination of alleles at all polymorphic sites gave rise to 9 YAP-DYS19 combination haplotypes in Pakistani populations, including YAP+ haplotypes 4-A, 4-B, 5-C, and 5-E. We hypothesize that the geographic distributions of YAP+ haplotypes 4 and 5 trace separate migratory routes to Pakistan: YAP+ haplotype 5 may have entered Pakistan from the Arabian Peninsula by means of migrations across the Gulf of Oman, whereas males possessing YAP+ haplotype 4 may have traveled over land from the Middle East. These inferences are consistent with ethnohistorical data suggesting that Pakistan's ethnic groups have been influenced by migrations from both African and Levantine source populations.

Network analyses of Y-chromosomal types in Europe, northern Africa, and western Asia reveal specific patterns of geographic distribution

In a study of 908 males from Europe, northern Africa, and western Asia, the variation of four Y-linked dinucleotide microsatellites was analyzed within three "frames" that are defined by mutations that are nonrecurrent, or nearly so. The rapid generation and extinction of new dinucleotide length variants causes the haplotypes within each lineage to diverge from one another. We constructed networks of "adjacent" haplotypes within each frame, by assuming changes of a single dinucleotide unit. Two small and six large networks were obtained, the latter including 94.9% of the sampled Y chromosomes. We show that the phenetic relationships among haplotypes, represented as a network, result largely from common descent and subsequent molecular radiation. The grouping of haplotypes of the same network thus fits an evolutionarily relevant criterion. Notably, this method allows the total diversity within a sample to be partitioned. Networks can be considered optimal markers for population studies, because reliable frequency estimates can be obtained in small samples. We present synthetic maps describing the incidence of different Y-chromosomal lineages in the extant human populations of the surveyed areas. Dinucleotide diversity also was used to infer time intervals for the coalescence of each network.

Differential structuring of human populations for homologous X and Y microsatellite loci

The global pattern of variation at the homologous microsatellite loci DYS413 (Yq11) and DXS8174 and DXS8175 (Xp22) was analyzed by examination of 30 world populations from four continents, accounting for more than 1,100 chromosomes per locus. The data showed discordant patterns of among- and within-population gene diversity for the Y-linked and the X-linked microsatellites. For the Y-linked polymorphism, all groups of populations displayed high FST values (the correlation between random haplotypes within subpopulations, relative to haplotypes of the total population) and showed a general trend for the haplotypes to cluster in a population-specific way. This was especially true for sub-Saharan African populations. The data also indicated that a large fraction of the variation among populations was due to the accumulation of new variants associated with the radiation process. Europeans exhibited the highest level of within-population haplotype diversity, whereas sub-Saharan Africans showed the lowest. In contrast, data for the two X-linked polymorphisms were concordant in showing lower FST values, as compared with those for DYS413, but higher within-population variances, for African versus non-African populations. Whereas the results for the X-linked loci agreed with a model of greater antiquity for the African populations, those for DYS413 showed a confounding pattern that is apparently at odds with such a model. Possible factors involved in this differential structuring for homologous X and Y microsatellite polymorphisms are discussed.

pH dependence of the kinetic mechanism of the adenosine 3',5'-monophosphate dependent protein kinase catalytic subunit in the direction of magnesium adenosine 5'-diphosphate phosphorylation

In order to determine the acid-base chemical mechanism of the adenosine 3',5'-monophosphate dependent protein kinase catalytic subunit, the pH dependence of the kinetic mechanism in the direction of MgADP phosphorylation has been determined using initial velocity studies in the presence and absence of dead-end inhibitors. The kinetic mechanism in the direction of MgADP phosphorylation is random, with changes in the preference of substrate binding as a function of pH. At pH 7.2 and below, the kinetic mechanism is ordered with phosphorylated peptide binding prior to MgADP. At pH 7.6, the opposite pathway with MgADP binding prior to phosphorylated peptide is preferred. The pH independence of V/Et is consistent with a mechanism in which reactants only bind to the correctly protonated form of the enzyme. The V/KMgADP value decreases, as the pH increases, giving a pK of about 7 which is likely that of a general acid, the same group that serves as a general base in the opposite reaction direction [Yoon, M.-Y., & Cook, P.F. (1987) Biochemistry 26, 4118]. The pKiPSP decreases at low pH giving a pK of about 6.5, probably reflecting the phosphate group of the peptide.

A method for counting active sites of cyclic AMP-dependent protein kinase

A method has been developed for counting active sites of cyclic-AMP-dependent protein kinase. Known concentrations of a synthetic peptide similar to a fragment of the endogenous inhibitor of the kinase were included in otherwise routine assay mixes containing several different volumes of enzyme stock solution. The concentration of active sites of the catalytic subunit of the cyclic AMP-dependent protein kinase in the stock solution was then determined by fitting observed velocities to an equation that accounts for the presence of a tight-binding inhibitor. The method yielded estimates of catalytic subunit concentration comparable with those derived from more traditional measures of catalytic subunit concentration. Both purified and heterogeneous samples were assayed, since active-sites counting assumes only a mutually specific, high-affinity interaction between enzyme and inhibitor and does not require that samples be pure. In principle, the method can be adapted to other protein kinases for which a specific, tight-binding, reversible inhibitor is available.

Kinetic mechanism of the adenosine 3',5'-monophosphate dependent protein kinase catalytic subunit in the direction of magnesium adenosine 5'-diphosphate phosphorylation

In order to define the overall kinetic mechanism of adenosine 3',5'-monophosphate dependent protein kinase catalytic subunit and also to elaborate the kinetic mechanism in the direction of peptide phosphorylation, we have determined its kinetic mechanism in the direction of MgADP phosphorylation. Studies of initial velocity as a function of uncomplexed Mg2+ (Mgf) in the absence and presence of dead-end inhibitors were used to define the kinetic mechanism. Data are consistent with the overall kinetic mechanism in the direction of MgADP phosphorylation being random with both the pathways allowed, i.e., the pathway in which MgADP binds to the enzyme prior to phosphorylated peptide and the pathway in which phosphorylated peptide binds to enzyme prior to MgADP. In addition, depending on the concentration of Mgf, one or the other pathway predominates. At low (0.5 mM) Mgf, the mechanism is steady-state ordered with the pathway in which phosphorylated peptide binds first being preferred; at high (10 mM) Mgf, the kinetic mechanism is equilibrium ordered, and the pathway in which MgADP binds first is preferred. This change in mechanism to equilibrium ordered at higher concentration of Mgf is due to an increase in affinity of the enzyme for MgADP and a decrease in affinity for the phosphorylated peptide. The Haldane relationship gives a Keq of 2 +/- 1 x 10(3) at pH 7.2, in agreement with the values obtained from 31P NMR (1.6 +/- 0.8 x 10(3)) and direct determination of reactant concentrations at equilibrium (3.5 +/- 0.6 x 10(3)).

Clinical profile of 100 cases of liver abscess

One hundred patients with liver abscess were studied for clinical features and complications. They were diagnosed by radiography, ultrasonography, serology and by needle aspiration. A variety of interesting clinical, haematological and ultrasonographic findings were observed. Literature on liver abscess was reviewed and results compared.

Serodiagnosis of amoebic liver abscess by IHA method

Serological test based on IHA (Indirect Haemagglutination Method) was performed in 100 cases of hepatic abscess. The test was 100% sensitive and 94% specific. The cut off point of antibody titer between normal population and patients with invasive amoebiasis was 1:128. Antibody titer in amoebic liver abscess was 1:5242 +/- 2795. A significant (P less than 0.001) correlation was found between total leucocyte count and antibody titer.