Graph clustering of Piper nigrum L. (black pepper)

A profound degree of morphological variation exists among the cultivars of Piper nigrum cultivated in Kerala State, South India. Fifty one cultivars of this crop species from the State were subjected to graph clustering by the ‘Graph Theory’ model, based on 27 morphological characters, both qualitative and quantitative, aimed at clustering them into groups with an appreciable degree of intracluster discreteness and intercluster distance. The result was presented in a ‘Skyline Plot’. Ten C-clusters were formed at the c-value of 0.46 corresponding to a fairly high moat value. The number of members from different clusters ranged from 3–8. Distribution of various characters among the clusters formed, shows a considerable degree of intracluster similarity (connectedness) and intercluster distance (isolation). The present graph clustering is significant as it provides reliable clues for selecting parental cultivars with fair degree of genetic difference, from clusters exhibiting appreciable isolation, for future intervarietal hybridization programmes in the crop. This revised version was published online in July 2006 with corrections to the Cover Date.     

Occurrence of vesicular-arbuscular mycorrhizae with Amaranthaceae in soils of the Indian semi-arid region

Summary Some members of the family Amaranthaceae, which has mostly been reported as non-mycorrhizal, were examined for a symbiotic association with mycorrhizae in the semiarid and arid zones. Ten species belonging to five genera, Achyranthes, Aerva, Alternanthera, Amaranthus, and Celosia were examined, using 1.0-cm long root standards. Intercellular hyphae, vesicles and arbuscules were observed in the root cortex. The number of different types of spores in the rhizosphere soil of different plants ranged from one to three. The spores isolated represented nine species belonging to four genera, Glomus, Gigaspora, Sclerocystis, and Scutellospora. No correlation could be established between spore counts and either soil pH or soil moisture.     

Multiresidue determination of pesticides in malt beverages by capillary gas chromatography with mass spectrometry and selected ion monitoring

A method was developed to determine pesticides in malt beverages using solid phase extraction on a polymeric cartridge and sample cleanup with a MgSO4-topped aminopropyl cartridge, followed by capillary gas chromatography with electron impact mass spectrometry in the selected ion monitoring mode [GC-MS(SIM)]. Three GC injections were required to analyze and identify organophosphate, organohalogen, and organonitrogen pesticides. The pesticides were identified by the retention times of peaks of the target ion and qualifier-to-target ion ratios. GC detection limits for most of the pesticides were 5-10 ng/mL, and linearity was determined from 50 to 5000 ng/mL. Fortification studies were performed at 10 ng/mL for three malt beverages that differ in properties such as alcohol content, solids, and appearance. The recoveries from the three malt beverages were greater than 70% for 85 of the 142 pesticides (including isomers) studied. The data showed that the different malt beverage matrixes had no significant effect on the recoveries. This method was then applied to the screening and analysis of malt beverages for pesticides, resulting in the detection of the insectide carbaryl and the fungicide dimethomorph in real samples. The study indicates that pesticide levels in malt beverages are significantly lower than the tolerance levels set by the United States Environmental Protection Agency for malt beverage starting ingredients. The use of the extraction/cleanup procedure and analysis by GC-MS(SIM) proved effective in screening malt beverages for a wide variety of pesticides.     

Multiresidue pesticide analysis in wines by solid-phase extraction and capillary gas chromatography-mass spectrometric detection with selective ion monitoring

A method was developed to determine pesticides in wines. The pesticides were extracted from the wine using solid-phase extraction on a polymeric cartridge, and the coextractives were removed with an aminopropyl-MgSO(4) cartridge. Analysis was performed using capillary gas chromatography with electron impact mass spectrometric detection in selective ion monitoring mode (GC-MSD/SIM). Three injections are required to analyze all 153 organohalogen, organonitrogen, organophosphate, and organosulfur pesticides and residues. Pesticides were confirmed by retention times of the target ions and three qualifier-to-target ion ratios. Detection limits for most of the pesticides were less than 0.005 mg/L, and quantitation was determined from approximately 0.01 to 5 mg/L. Spike recoveries were performed by fortifying red and white wines at 0.01 and 0.10 mg/L. At the 0.01 ppm level, the spike recoveries were greater than 70% for 116 and 124 pesticides (out of 153) in red and white wines, respectively, whereas at the higher spike concentration of 0.10 mg/L, the recoveries were greater than 70% for 123 and 128 pesticides in red and white wines, respectively. The recoveries of less than 70% were most likely from pesticide polarity or lability, resulting in the inefficient adsorption of the pesticide to the polymeric sorbent, ineffective elution of the pesticide from the sorbent, or thermal degradation of the pesticide under GC-MSD conditions.     

Modelling runoff and soil erosion in logged forests: Scope and application of some existing models

Predictive erosion models are useful tools for evaluating the impact of land-use practices on soil and water properties, and as often used by environmental protection authorities, for setting guidelines and standards for regulation purposes. This study examines the application of three erosion models of varying complexity and design for predicting runoff and soil erosion from logged forest compartments in south eastern Australia. These are: the Universal Soil Loss Equation (USLE), the Water Erosion Prediction Project (WEPP), and TOPOG, a physically based hydrologic modelling package. Data on rates of soil loss and redistribution collected during a series of large-scale rainfall simulator experiments were used as model input parameters and validation. The models were evaluated in terms of general ease of use, input data requirements and accuracy of process understanding and prediction. Results suggest that in this application the USLE overestimated soil loss, and have the limitation that it does not predict sediment yield or sediment redistribution for specific storm events. When used at the hillslope scale, WEPP and TOPOG have predicted runoff and soil loss reasonably well, particularly on disturbed surfaces such as skid trails. On less disturbed surfaces such as the general harvesting area, both models performed less accurately, generally under-predicting soil loss and sediment yield, notably on sites with low observed values. The complexity and data requirements of WEPP and TOPOG limit their usability as a general-purpose, erosion hazard predicting tool. In terms of process understanding, none of the existing models accurately depict the nature and extent of sediment redistribution quantified in the rainfall simulator experiments. In order to advance the application and accuracy of modelling tools in forestry environments, this redistribution process should be considered integral to the refinement and redevelopment of future models.     

Surgical resolution of an avulsion fracture of the peroneus tertius origin in a giraffe (Giraffa camelopardalis reticulata)

A 4-mo-old, 185-kg male giraffe (Giraffa camelopardalis reticulata) was presented due to stifle effusion and lameness of 3-wk duration. Radiographs revealed a fracture of the extensor fossa of the lateral trochlear ridge of the femur at the origin of the peroneus tertius. Under anesthesia, dysfunction of the reciprocal apparatus was documented by flexing the stifle while the tarsus remained extended. An avulsion fracture of the origin of the peroneus tertius and extensor digitorum longus muscle was diagnosed. An exploratory arthroscopy of the femorotibial joint was followed by arthrotomy to excise the large bone fragment from its soft tissue attachments. Because of the fractious temperament of the animal, postoperative care was restricted to stall rest for 3 mo, and no postoperative complications arose. Only a mild residual lameness remained by 6 mo after surgery.     

Crystallographic R factor refinement by molecular dynamics

Molecular dynamics was used to refine macromolecular structures by incorporating the difference between the observed crystallographic structure factor amplitude and that calculated from an assumed atomic model into the total energy of the system. The method has a radius of convergence that is larger than that of conventional restrained least-squares refinement. Test cases showed that the need for manual corrections during refinement of macromolecular crystal structures is reduced. In crambin, the dynamics calculation moved residues that were misplaced by more than 3 angstroms into the correct positions without human intervention.     

Cancer proliferation gene discovery through functional genomics

Retroviral short hairpin RNA (shRNA)-mediated genetic screens in mammalian cells are powerful tools for discovering loss-of-function phenotypes. We describe a highly parallel multiplex methodology for screening large pools of shRNAs using half-hairpin barcodes for microarray deconvolution. We carried out dropout screens for shRNAs that affect cell proliferation and viability in cancer cells and normal cells. We identified many shRNAs to be antiproliferative that target core cellular processes, such as the cell cycle and protein translation, in all cells examined. Moreover, we identified genes that are selectively required for proliferation and survival in different cell lines. Our platform enables rapid and cost-effective genome-wide screens to identify cancer proliferation and survival genes for target discovery. Such efforts are complementary to the Cancer Genome Atlas and provide an alternative functional view of cancer cells.     

Radiographic Calibration for Analysis of Bone Mineral Density of the Equine Third Metacarpal Bone

Digital radiography represents the primary diagnostic tool the veterinarian uses to diagnose skeletal injuries in the horse. Advances in digital radiography have provided the veterinarian with opportunities to make simple radiographic assessments from calibrated digital radiographs such as dimensional analyses; however, more complex variables such as radiographic opacity have yet to be standardized. Therefore, we investigated the quantification of bone mineral density (BMD) via computed radiographic absorptiometry at various radiographic exposure intensities (kV), times (sec), and milliamps (mA) in the third metacarpal in the horse. By developing a brightness/darkness index (BDI), the grayscale of radiographs, calibrated with an aluminum (Al) marker of various known thicknesses and uniform densities, can be compared to the average BMD of a region of interest at various radiographic exposures. Al BDI was a significant predictor of bone BDI (r² = 0.960, P < .001) and BMD (r² = 0.971, P < .001). This method of calibration can be used for quantitative noninvasive bone mineral analysis and allows direct comparison of radiographs taken under different exposure settings.     

An acellular aortic matrix of buffalo origin crosslinked with 1‐ethyl‐3‐3‐dimethylaminopropylcarbodiimide hydrochloride for the repair of inguinal hernia in horses

An acellular aortic matrix (AAM) crosslinked with 1‐ethyl‐3‐3‐dimethylaminopropylcarbodiimide hydrochloride (EDC) was evaluated for the repair of inguinal hernias in 5 horses. The aorta from buffalo was acellularised using 1% sodium dodecyl sulfate (SDS) and 0.25% trypsin. The AAM was crosslinked with 1% EDC. Under anaesthesia, inguinal hernias were repaired with EDC‐crosslinked AAM graft using an inlay graft technique. Blood samples collected on Days 0, 15 and 30 post implantation, were used for SDS polyacrylamide gel electrophoresis (PAGE) analysis to assess the animals' serum protein concentration, and gelatin zymography for the identification of matrix metalloproteinases. All animals that underwent hernia repair demonstrated successful healing without clinical signs of wound dehiscence, infection or recurrence during a 6‐month follow‐up period. SDS‐PAGE analysis of serum protein concentrations revealed that, this was increased at Day 15 and had decreased again at Day 30. Gelatin zymography of serum of implanted horses expressed a band of 92 kDa, corresponding to MMP‐9 activity. The relative amount of the 92 kDa band was higher at Day 15 as compared to Days 0 and 30. It may be concluded that EDC‐crosslinked AAM of buffalo origin can be used safely in horses for the repair of inguinal hernia with adequate strength and minimal foreign body reaction.