Effects of Added Vegetation on Sand Bar Stability and Stream Hydrodynamics

Vegetation was added to a fully developed sandy point bar in the meander of a constructed stream. Significant changes in the flow structure and bed topography were observed. As expected, the addition of vegetative resistance decreased the depth-averaged streamwise velocity over the bar and increased it in the open region. In addition, the secondary circulation increased in strength but became confined to the deepest section of the channel. Over the point bar, the secondary flow was entirely outward, i.e., toward the outer bank. The changes in flow led to changes in bar shape. Although the region of the bar closest to the inner bank accumulated sediment, erosion of the bar and the removal of plants by scouring were observed at the interface between the planted bar and the open channel.     

Short communication: Genomic prediction using imputed whole-genome sequence variants in Brown Swiss Cattle

The accuracy of genomic prediction determines response to selection. It has been hypothesized that accuracy of genomic breeding values can be increased by a higher density of variants. We used imputed whole-genome sequence data and various single nucleotide polymorphism (SNP) selection criteria to estimate genomic breeding values in Brown Swiss cattle. The extreme scenarios were 50K SNP chip data and whole-genome sequence data with intermediate scenarios using linkage disequilibrium-pruned whole-genome sequence variants, only variants predicted to be missense, or the top 50K variants from genome-wide association studies. We estimated genomic breeding values for 3 traits (somatic cell score, nonreturn rate in heifers, and stature) and found differences in accuracy levels between traits. However, among different SNP sets, accuracy was very similar. In our analyses, sequence data led to a marginal increase in accuracy for 1 trait and was lower than 50K for the other traits. We concluded that the inclusion of imputed whole-genome sequence data does not lead to increased accuracy of genomic prediction with the methods.     

Elimination of experimentally induced bovine intramammary infection assessed by multiplex real-time PCR and bacterial culture

Diagnosis of bovine intramammary infection (IMI) has traditionally been based on bacterial culture, but currently IMI can also be detected with DNA based methods, such as multiplex real-time PCR. The aim of this study was to describe the elimination of bacteria in experimentally induced IMI on the quarter level, using conventional bacterial culture (BC) and multiplex real-time PCR. Two coagulase-negative staphylococcal species, Staphylococcus epidermidis and Staphylococcus simulans, were experimentally inoculated into 14 healthy quarters of 8 dairy cows during 4 consecutive study periods. Intramammary infections were followed with 20 milk samplings per each quarter. Milk somatic cell count was monitored to evaluate the inflammation process in the quarters. Four quarters cured spontaneously during the study period according to the culture. The PCR detected staphylococcal DNA from these quarters for several days after they were defined as cured in BC. Agreement between BC and PCR results varied from substantial to almost perfect agreement for the first 36 h postchallenge, decreasing to moderate levels toward the end of the sampling period. Based on this study, we recommend collecting possible follow-up samples to assess the bacteriological cure from IMI not until 2 to 3 wk after the onset of mastitis or after the quarter milk somatic cell count has normalized when PCR is used.     

Towards a home-grown approach to strategic environmental assessment: adapting practice and participation in Kenya

Abstract

Kenya is among the first countries in sub-Saharan Africa to formally require the assessment of public policies, plans and programs. National strategic environmental assessment (SEA) guidelines were finalized in 2012 to adapt and enhance SEA practice in the Kenyan context. The purpose of this research was to examine recent Kenyan SEA, with a particular emphasis on public participation, by developing and applying an analysis framework that both incorporates commonly accepted SEA principles and approaches and is cognizant of the national context in shaping SEA practice. Results reveal that a number of SEA practices are consistent with the framework in the nine cases considered, such as containing standard SEA components and developing monitoring plans. A requirement that each SEA must include educating the public about SEA is an innovative local adaptation. Results also show a number of practices that are still emerging, such as initiating SEA early and disseminating results to the participants. We conclude that SEA is still developing in Kenya, but processes for conducting it are slowly adapting to the Kenyan context.     

Fatty Acid Profile of Sunshine Bass: I. Profile Change is Affected by Initial Composition and Differs Among Tissues

Fatty acid (FA) composition of fillet tissue can be tailored by transitioning fish from alternative lipid-based, low long-chain polyunsaturated fatty acid (LC-PUFA) grow-out feeds to high LC-PUFA "finishing" feeds. To address whether grow-out feed composition influences the responsiveness of fillet tissue to finishing, sunshine bass (SB, Morone chrysops x M. saxatilis) were reared to a submarketable size on grow-out feeds containing fish oil (FO) or a 50:50 blend of FO and coconut (CO), grapeseed (GO), linseed (LO), or poultry (PO) oil. For the final 8 weeks of the trial, fish were either maintained on assigned grow-out feeds or finished with the 100% FO feed. Production performance was unaffected by dietary lipid source, but fillet FA profile generally conformed to nutritional history. Regardless of grow-out regimen, finishing had a significant restorative effect on fillet FA composition; however, complete restoration of control levels of 20:5n-3, 22:6n-3, total LC-PUFA and n-3:n-6 FA ratio was achieved only among fish fed the CO-based grow-out feed. Saturated fatty acids (SFA) appear to be preferential catabolic substrates, whereas medium-chain and long-chain PUFA are selectively deposited in tissues. Provision of SFA in grow-out feeds appears to optimize selective FA metabolism and restoration of beneficial fillet FA profile during finishing.     

Screening for organic phosphorus compounds in aquatic sediments by liquid chromatography coupled to ICP-AES and ESI-MS/MS

The structures of organic phosphorous (P) compounds in aquatic sediments are to a large extent unknown although these compounds are considered to play an important role in regulating lake trophic status. To enhance identification of these compounds, a liquid chromatography (LC) method for their separation was developed. The stationary phase was porous graphitic carbon (PGC), and the mobile phases used in the gradient elution were compatible with both inductive coupled plasma atomic emission spectroscopy (ICP-AES) and electrospray ionization tandem mass spectrometry (ESI-MS/MS). With LC-ICP-AES, eight different P containing peaks could be observed in the P chromatogram indicating that at least eight different P compounds were separated. With the setup of an information dependent acquisition (IDA) with ESI-MS/MS, the mass over charge ( m/ z) of compounds containing a phosphate group (H 2PO 3 (-), m/ z 97) could be measured and further fragmentation experiments gave additional information on the structure of almost 40 separated P compounds, several were verified to be nucleotides. ICP-AES was very suitable in the development of the LC method and allowed screening and quantification of P compounds. The presented LC-ESI-MS/MS technique was able to identify several sediment organic P compounds.     

Regioisomeric structure determination of alpha- and gamma-linolenoyldilinoleoylglycerol in blackcurrant seed oil by silver ion high-performance liquid chromatography and mass spectrometry

Gamma-linolenic acid (Gla) and oils containing Gla have evident positive effects on a variety of disorders, and therefore, the structure of triacylglycerols (TAGs) containing Gla is of special interest. The regioisomeric structures of TAGs 18:3(n-3)/18:2/18:2 (Ala/L/L) and 18:3(n-6)/18:2/18:2 (Gla/L/L) in blackcurrant seed oil were determined by Ag-HPLC/APCI-MS and Ag-HPLC/ESI-MS/MS techniques. In the latter, silver ion adducts were prepared by adding silver nitrate to the postcolumn flow. A new Ag-HPLC solvent system containing nonchlorinated solvents for the separation of Gla- and Ala-containing TAGs is introduced. Ag-HPLC separation of Ala/L/L and Gla/L/L was sufficient and regioisomers sn-LnLL + sn-LLLn and sn-LLnL (Ln, linolenic acid) could be differentiated well with the MS methods used. No discrimination was made between the sn-1 and sn-3 positions. The results show that the methods used are suitable to discriminate and determine the regioisomeric structure of TAGs. The regioisomeric structure of TAG with the fatty acid combination Gla/L/L in blackcurrant seed oil was considered to be practically random (32.7-37.8% of sn-LGlaL). In the fatty acid combination Ala/L/L, the regioisomeric structure is nonrandom (7.3-12.1% of sn-LAlaL) with Ala preferentially in a primary position. It can be concluded that the positional distribution of Ala and Gla is different in Ln/L/L TAGs of blackcurrant seed oil.     

Near-infrared spectroscopy for cocrystal screening. A comparative study with Raman spectroscopy

Near-infrared (NIR) spectroscopy is a well-established technique for solid-state analysis, providing fast, noninvasive measurements. The use of NIR spectroscopy for polymorph screening and the associated advantages have recently been demonstrated. The objective of this work was to evaluate the analytical potential of NIR spectroscopy for cocrystal screening using Raman spectroscopy as a comparative method. Indomethacin was used as the parent molecule, while saccharin and l-aspartic acid were chosen as guest molecules. Molar ratios of 1:1 for each system were subjected to two types of preparative methods. In the case of saccharin, liquid-assisted cogrinding as well as cocrystallization from solution resulted in a stable 1:1 cocrystalline phase termed IND-SAC cocrystal. For l-aspartic acid, the solution-based method resulted in a polymorphic transition of indomethacin into the metastable alpha form retained in a physical mixture with the guest molecule, while liquid-assisted cogrinding did not induce any changes in the crystal lattice. The good chemical peak selectivity of Raman spectroscopy allowed a straightforward interpretation of sample data by analyzing peak positions and comparing to those of pure references. In addition, Raman spectroscopy provided additional information on the crystal structure of the IND-SAC cocrystal. The broad spectral line shapes of NIR spectra make visual interpretation of the spectra difficult, and consequently, multivariate modeling by principal component analysis (PCA) was applied. Successful use of NIR/PCA was possible only through the inclusion of a set of reference mixtures of parent and guest molecules representing possible solid-state outcomes from the cocrystal screening. The practical hurdle related to the need for reference mixtures seems to restrict the applicability of NIR spectroscopy in cocrystal screening.