Sclerotium rot of sugarbeets in India

Sclerotium rot of sugar beets incited byP. rolfsii is described for the first time from India. The disease has been found widely prevalent around Pantnagar. Observations on the susceptibility of crops grown in the affected areas and the relative susceptibility of different sugarbeets varieties are presented. Ability of the pathogen to survive from one season to another under conditions at Pantnagat is indicated.Published with the approval of the Director as Paper No. 104, Journal Series, Experiment Station, UPAU Pantnagar.Ast. Prof. Plant Pathology.     

Engineering aspects of ensiling

Ensiling is a preservation method for moist forage crops, based on a lactic acid solid-state fermentation. Air is detrimental to silage because it enables the reactivation of detrimental aerobic microorganisms. The present review describes some of the major engineering and physical aspects of ensiling—silo types and the ensiling process—step by step. Issues considered include harvest and chopping, degree of consolidation, permeability to air ingress, sealing, additive application and unloading. Mathematical models that have been developed to simulate the ensiling process are mentioned. Experimentation methods are also described.     

Biological ensiling of sugarcane tops

The following lactic acid bacteria were isolated from sugarcane tops silage:Lactobacillus plantarum, Lactobacillus buchneri, Lactobacillus brevis, Lactobacillus delbrueckii, Pediococcus cerevisiae, Leuconostoc mesenteroides andStreptococcus lactis. The isolates were grown in a synthetic medium and the final pH, sugar uptake and the effect of adding CaCO₃ and L1, L2 and L3 factors was observed. The importance of the buffering capacity of the ensiled material for the silage process with a view to the occurrence of lactic acid bacteria is discussed.     

Biological ensiling of sugarcane tops

When a mixture of sugarcane tops, alfalfa (20%) and milled malt (0.5%) was ensiled, a pronounced decrease of pH was observed during the first week corresponding to a rapid production of laotic and acetic acids. After that pH and acid production detached. The number of microorganisms increased during the first days of silage. Then aerobes rapidly decreased and were the fewer after 50 days of silage. Anaerobes also decreased but not so substantially. Lactic aoid producers rose very quickly during the first 4–5 days to became more or less constant after that. Filamentous fungi were predominant at the beginning among the fungal population, but later on almost disappeared and yeasts were found instead. During the silage process the amount of total reducing hydrolyzate increased and readily utilizable sugars were found after the microbial activity had ceased.     

Biological ensiling of sugarcane tops

ThreeLactobacillus leichmannii ATCC 7830 growthpromoting factors have been isolated from sugarcane tops, alfalfa and malt. These substances proved to be active also with respect to the specific lactic bacteria isolated from sugarcane tops silage. The possible role of these factors in the selection and enhancement of the activity of lactic acid producing microorganisms in the silage process is discussed.     

Enzyme assisted ensiling of alfalfa with enzymes by solid substrate fermentation

A crude enzyme preparation, obtained by solid substrate fermentation (SSF) with a Gliocladium spp. and added at the 5% level to wilted or non-wilted alfalfa, improved the fermentation characteristics and stability of alfalfa silages as effectively as commercial preparations, Novo-Nordisk Celluclast 1.5 L and Viscozyme 120 L, applied at the 0.025% level. The effective dose of the crude enzyme costs about one-fourth of the cost of the commercial enzymes.     

Characterizing gene sets with FuncAssociate

SUMMARY: FuncAssociate is a web-based tool to help researchers use Gene Ontology attributes to characterize large sets of genes derived from experiment. Distinguishing features of FuncAssociate include the ability to handle ranked input lists, and a Monte Carlo simulation approach that is more appropriate to determine significance than other methods, such as Bonferroni or idák p-value correction. FuncAssociate currently supports 10 organisms (Vibrio cholerae, Shewanella oneidensis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Arabidopsis thaliana, Caenorhaebditis elegans, Drosophila melanogaster, Mus musculus, Rattus norvegicus and Homo sapiens). AVAILABILITY: FuncAssociate is freely accessible at http://llama.med.harvard.edu/Software.html. Source code (in Perl and C) is freely available to academic users 'as is'.     

Characterizing bacterial glycoproteins with LC-MS

Introduction: Though eukaryotic glycoproteins have been studied since their discovery in the 1930s, the first bacterial glycoprotein was not identified until the 1970s. As a result, their role in bacterial pathogenesis is still not well understood and they remain an understudied component of bacterial virulence. In recent years, mass spectrometry has emerged as a leading technology for the study of bacterial glycoproteins, largely due to its sensitivity and versatility.

Areas covered: Identification and comprehensive characterization of bacterial glycoproteins usually requires multiple complementary mass spectrometry approaches, including intact protein analysis, top-down analysis, and bottom-up methods used in combination with specialized liquid chromatography. This review provides an overview of liquid chromatography separation technologies, as well as current and emerging mass spectrometry approaches used specifically for bacterial glycoprotein identification and characterization.

Expert commentary: Bacterial glycoproteins may have significant clinical utility as a result of their unique structures and exposure on the surface of the cells. Better understanding of these glycoconjugates is an essential first step towards that goal. These often unique structures, and by extension the key enzymes involved in their synthesis, represent promising targets for novel antimicrobials, while unique carbohydrate structures may be used as antigens in vaccines or as biomarkers.     

Characterizing the Metabolism of Dehalococcoides with a Constraint-Based Model

Dehalococcoides strains respire a wide variety of chloro-organic compounds and are important for the bioremediation of toxic, persistent, carcinogenic, and ubiquitous ground water pollutants. In order to better understand metabolism and optimize their application, we have developed a pan-genome-scale metabolic network and constraint-based metabolic model of Dehalococcoides. The pan-genome was constructed from publicly available complete genome sequences of Dehalococcoides sp. strain CBDB1, strain 195, strain BAV1, and strain VS. We found that Dehalococcoides pan-genome consisted of 1118 core genes (shared by all), 457 dispensable genes (shared by some), and 486 unique genes (found in only one genome). The model included 549 metabolic genes that encoded 356 proteins catalyzing 497 gene-associated model reactions. Of these 497 reactions, 477 were associated with core metabolic genes, 18 with dispensable genes, and 2 with unique genes. This study, in addition to analyzing the metabolism of an environmentally important phylogenetic group on a pan-genome scale, provides valuable insights into Dehalococcoides metabolic limitations, low growth yields, and energy conservation. The model also provides a framework to anchor and compare disparate experimental data, as well as to give insights on the physiological impact of “incomplete” pathways, such as the TCA-cycle, CO₂ fixation, and cobalamin biosynthesis pathways. The model, referred to as iAI549, highlights the specialized and highly conserved nature of Dehalococcoides metabolism, and suggests that evolution of Dehalococcoides species is driven by the electron acceptor availability.     

Characterizing differences in precipitation regimes of extreme wet and dry years: implications for climate change experiments

Climate change is intensifying the hydrologic cycle and is expected to increase the frequency of extreme wet and dry years. Beyond precipitation amount, extreme wet and dry years may differ in other ways, such as the number of precipitation events, event size, and the time between events. We assessed 1614 long‐term (100 year) precipitation records from around the world to identify key attributes of precipitation regimes, besides amount, that distinguish statistically extreme wet from extreme dry years. In general, in regions where mean annual precipitation (MAP) exceeded 1000 mm, precipitation amounts in extreme wet and dry years differed from average years by ~40% and 30%, respectively. The magnitude of these deviations increased to >60% for dry years and to >150% for wet years in arid regions (MAP<500 mm). Extreme wet years were primarily distinguished from average and extreme dry years by the presence of multiple extreme (large) daily precipitation events (events >99th percentile of all events); these occurred twice as often in extreme wet years compared to average years. In contrast, these large precipitation events were rare in extreme dry years. Less important for distinguishing extreme wet from dry years were mean event size and frequency, or the number of dry days between events. However, extreme dry years were distinguished from average years by an increase in the number of dry days between events. These precipitation regime attributes consistently differed between extreme wet and dry years across 12 major terrestrial ecoregions from around the world, from deserts to the tropics. Thus, we recommend that climate change experiments and model simulations incorporate these differences in key precipitation regime attributes, as well as amount into treatments. This will allow experiments to more realistically simulate extreme precipitation years and more accurately assess the ecological consequences.     

The nutritive value of concentrate feedstuffs for ruminant animals: Part I: In situ ruminal degradability of dry matter and organic matter

The aim of the study was to generate a database of ruminal degradability of dry matter (DM), and organic matter (OM) of different sources of concentrate ingredients (classified as protein, energy or protein+energy feeds) commonly offered to ruminants in European countries. The ruminal disappearance of DM and OM was measured using the in situ nylon bag technique, where the test feedstuffs were subject to ruminal incubation in four Friesian steers offered grass silage and concentrate. Disappearance of DM and OM from the test feeds from the rumen was measured at 0, 2, 4, 8, 14, 24 and 48 h. The exponential model of Ørskov and McDonald (1979) was used to calculate degradation kinetics. Test protein feeds were sunflower meal (SUN), rapeseed meal (RAP), soyabean meal (SBM) and cottonseed meal (CSM). Test energy feeds were palm kernel meal (PK), pollard (PO), barley (BA) and beet pulp (BP). Test protein+energy feeds were maize distillers grains (MDG), maize gluten feed (MGF), copra meal (CO) and malt combings (MC).

The effective degradability (degradability of feed, whilst considering rate of flow of feed from rumen to small intestine) of DM (EDDM) and OM (EDOM) in the protein feed SBM, where outflow rate k=0.02, was not influenced (P>0.05) by the sample of feed used. For the feeds classified as protein+energy feeds, the EDDM in MGF and MC were not affected (P>0.05) by the sample of feed for k=0.02. For the remainder of the concentrate feedstuffs used in this study, the sample of feed used had a pronounced effect on in situ degradability values. These data have shown that for the majority of feeds examined in this study, the different sources of any one feed are not equal in nutritive value and it is necessary to screen feeds for nutritive value before using them in ration formulation systems.     

The effects of Propionibacterium acidipropionici and Lactobacillus plantarum, applied at ensiling, on the fermentation and aerobic stability of low dry matter corn and sorghum silages

The aim of this work was to study the effects of applying a strain of Propionibacterium acidipropionici, with or without Lactobacillus plantarum, on the fermentation and aerobic stability characteristics of low dry matter (DM) corn (Zea mays L.) and sorghum (Sorghum bicolor L.) silages. Corn at the dent stage and sorghum at the flowering stage were harvested. Treatments comprised control (no additives), P. acidipropionici, L. plantarum and a combination of P. acidipropionici and L. plantarum. Fresh forages were sampled prior to ensiling. Bacterial inoculants were applied to the fresh forage at 1.0×10⁶ colony-forming units per gram. After treatment, the chopped fresh materials were ensiled in 1.5-l anaerobic glass jars equipped with a lid that enabled gas release only. Three jars per treatment were sampled on days 2, 4, 8, 16 and 60 after ensiling, for chemical and microbiological analysis. At the end of the ensiling period, 60 days, the silages were subjected to an aerobic stability test. The L. plantarum inoculated silages had significantly higher levels of lactic acid than the controls, P. acidipropionici and combination of P. acidipropionici and L. plantarum inoculated silages (P<0.05). The P. acidipropionici did not increase propionic and acetic acid levels of the silages. After the aerobic exposure test, the L. plantarum and combination of P. acidipropionici and L. plantarum had produced more CO₂ than the controls and the silages inoculated with P. acidipropionici (P<0.05). All silages had high levels of CO₂ and high numbers of yeasts and molds in the experiment. Therefore, all silages were deteriorated under aerobic conditions. The P. acidipropionici and combination of P. acidipropionici and L. plantarum were not able to improve the aerobic stability of fast-fermenting silages, because they could not work well in this acidic environment. The results showed that P. acidipropionici and combination of P. acidipropionici and L. plantarum did not improve the aerobic stability of low DM corn and sorghum silages, which are prone to aerobic deterioration.     

Characterizing heterogeneous properties of cerebral aneurysms with unknown stress-free geometry: a precursor to in vivo identification

Knowledge of elastic properties of cerebral aneurysms is crucial for understanding the biomechanical behavior of the lesion. However, characterizing tissue properties using in vivo motion data presents a tremendous challenge. Aside from the limitation of data accuracy, a pressing issue is that the in vivo motion does not expose the stress-free geometry. This is compounded by the nonlinearity, anisotropy, and heterogeneity of the tissue behavior. This article introduces a method for identifying the heterogeneous properties of aneurysm wall tissue under unknown stress-free configuration. In the proposed approach, an accessible configuration is taken as the reference; the unknown stress-free configuration is represented locally by a metric tensor describing the prestrain from the stress-free configuration to the reference configuration. Material parameters are identified together with the metric tensor pointwisely. The paradigm is tested numerically using a forward-inverse analysis loop. An image-derived sac is considered. The aneurysm tissue is modeled as an eightply laminate whose constitutive behavior is described by an anisotropic hyperelastic strain-energy function containing four material parameters. The parameters are assumed to vary continuously in two assigned patterns to represent two types of material heterogeneity. Nine configurations between the diastolic and systolic pressures are generated by forward quasi-static finite element analyses. These configurations are fed to the inverse analysis to delineate the material parameters and the metric tensor. The recovered and the assigned distributions are in good agreement. A forward verification is conducted by comparing the displacement solutions obtained from the recovered and the assigned material parameters at a different pressure. The nodal displacements are found in excellent agreement.     

Characterizing bacterial assemblages in sediments and aerosols at a dry lake bed in Australia using high-throughput sequencing

Dust storms are responsible for the transport of a large quantity of bacteria from arid regions. A severe drought in the first decade of the new millennium in Australia increased the incidence of dust transport further. The major aims of this study were to characterize the bacterial communities in aerosols and their associated source sediments using high-throughput sequencing (HTS) and to investigate the possibility of using HTS to link dust to its source, which has not been previously performed in this way. Four field campaigns were conducted at the recently evaporated saline playa Lake Gnarpurt in the Australian state of Victoria between 2008 and 2010 (3 in the austral summer, 1 in winter) to collect aerosol and sediment samples. Aerosol samples were collected on filters up to 150 m above the lake bed using a tethered helium-filled balloon. DNA was extracted from all samples using commercial kits, and the bacterial communities were examined using 454 HTS on the 16S rRNA gene. Over 200,000 sequences from 29 samples were analysed. In both sediment and aerosol samples, Salinimicrobium was the most abundant taxon; however, there was great variation and diversity across all samples. Analysis of similarities of the bacterial communities indicated that there was a significant overlap between the sediment samples and the aerosols collected above that location, showing that the bacteria in the air was derived from a subset of dust from a nearby source. The challenge remains to use bacterial profiling to link an aerosol sample to a distant source.