Particle size influences decay rates of environmental DNA in aquatic systems

Environmental DNA (eDNA) analysis is a powerful tool for remote detection of target organisms. However, obtaining quantitative and longitudinal information from eDNA data is challenging, requiring a deep understanding of eDNA ecology. Notably, if the various size components of eDNA decay at different rates, and we can separate them within a sample, their changing proportions could be used to obtain longitudinal dynamics information on targets. To test this possibility, we conducted an aquatic mesocosm experiment in which we separated fish-derived eDNA components using sequential filtration to evaluate the decay rate and changing proportion of various eDNA particle sizes over time. We then fit four alternative mathematical decay models to the data, building towards a predictive framework to interpret eDNA data from various particle sizes. We found that medium-sized particles (1–10 μm) decayed more slowly than other size classes (i.e., <1 and > 10 μm), and thus made up an increasing proportion of eDNA particles over time. We also observed distinct eDNA particle size distribution (PSD) between our Common carp and Rainbow trout samples, suggesting that target-specific assays are required to determine starting eDNA PSDs. Additionally, we found evidence that different sizes of eDNA particles do not decay independently, with particle size conversion replenishing smaller particles over time. Nonetheless, a parsimonious mathematical model where particle sizes decay independently best explained the data. Given these results, we suggest a framework to discern target distance and abundance with eDNA data by applying sequential filtration, which theoretically has both metabarcoding and single-target applications.     

Purification, properties, and immunological characterization of GalT-3 (UDP-galactose: GM2 ganglioside, β1-3 galactosyltransferase) from embryonic chicken brain

A 1-3 galactosyltransferase (GalT-3; UDP-Gal; GM2 1-3galactosyltransferase) was purified over 5100-fold from 19-day-old embryonic chicken brain homogenate employing detergent solubilization, -lactalbumin Sepharose, Q-Sepharose, UDP-hexanolamine Sepharose, and GalNAc1-4Gal-Synsorb column chromatography. The purified enzyme was resolved into two bands on reducing gels with apparent molecular weights of 62 kDa and 65 kDa, respectively. GalT-3 activity was also localized in the same regions by activity gel analysis and sucrose-density gradient centrifugation of a detergent-solubilized extract of 19-day-old embryonic chicken brain. Purified GalT-3 exhibited apparentK _mS of 33 µm, 22 µm and 14.4mM with respect to the substrates GM2, UDP-galactose, and MnCl₂, respectively. Substrate specificity studies with the purified enzyme and a variety of glycosphingolipids, glycoproteins, and synthetic substrates revealed that the enzyme was highly specific only for the glycosphingolipid acceptors, GM2 and GgOse3Cer (asialo-GM2). Ovine-asialo-agalacto submaxillary mucin inhibited the transfer of galactose to GM2 but did not act as an acceptor in the range of concentrations tested. Polyclonal antibodies raised against purified GalT-3 inhibited GalT-3 activityin vitro and Western-immunoblot analysis of purified GalT-3 showed immunopositive bands at 62 and 65 kDa.Abbreviations CNS central nervous system - GM1 monosialotetraosylganglioside, Gal1-3GalNAc1-4(NeuAc2-3)Gal1-4Glc1-1Cer - GM2 monosialotriaosylganglioside, GalNAc1-4(NeuAc2-3)Gal1-4Glc1-1Cer - DSS detergent solubilized supernatant - ECB embryonic chicken brain - TBS Tris-buffered saline     

Domain exchanges between KNAT3 and KNAT1 suggest specificity of the kn1-like homeodomains requires sequences outside of the third helix and N-terminal arm of the homeodomain

Domain exchange constructs that traded regions surrounding the homeodomain were constructed for two kn1 -like genes, KNAT1 and KNAT3, and introduced into Arabidopsis thaliana under the control of the 35S CaMV promoter. The kn1-like homeodomain proteins all have the homeodomain located near the C-terminus of the protein, and also share a second conserved domain (the ELK domain) immediately N-terminal to the homeodomain. Progeny were scored for the appearance of the KNAT1 overexpression phenotype. A construct containing the KNAT3 N-terminus and the KNAT1 ELK- and homeodomain resulted in a KNAT1 overexpression phenotype, indicating that specificity mainly resides within the ELK- and homeodomain region. Further exchanges demonstrated that specificity probably does not arise from a single region within the ELK and/or homeodomain but rather requires sequences both N-terminal and C-terminal to residue 23 of the homeodomain. Further, in contrast to some animal homeodomains, KNAT1 does not utilize the residues of the N-terminal arm of the homeodomain for specificity.     

Distribution of myosin and the glial fibrillary acidic protein (GFA Protein) in rat spinal cord and in the human frontal cortex as revealed by immunofluorescence microscopy

Summary The glial fibrillary acidic (GFA) protein and myosin were localized in rat spinal cord and human frontal cortex using specific antibodies against GFA protein from human spinal cord and highly purified smooth myosin from chicken gizzard by means of an indirect immunofluorescence microscopical approach. A strong GFA protein and myosin immunoreactivity was found in astrocytes of the white and grey matter and in the external glial limitans membrane. The very fine branches of astrocytic processes stained with antiGFA protein, but not with anti-myosin. Similar results were obtained with the human frontal cortex, where myosin antibodies failed to reveal the very fine branches of protoplasmic astrocytes.As a whole, staining with the GFA protein antiserum was more crisp than with the myosin antibody.Thanks are due to Professor J.R. Wolff, Max-Planck Institute for Biophysical Chemistry, Göttingen, for stimulating discussions, to Ursula König, Christa Mahlmeister and Renate Steffens for skilful technical assistance, and to Heidi Waluk for the photographic workSupported by grants from Deutsche Forschungsgemeinschaft (Br 634/1, Dr 91/1, Un 34/4, Ste 105/19)Dedicated to Prof. Dr. med. H. Leonhardt on the occasion of his 60. birthday     

Transparent Golgi Impregnations: A Way to Examine Both Details of Cellular Processes and Components of the Nerve Cell Body

A method is described by which the precipitate that normally fills impregnated cells in Golgi preparations is confined to a thin and transparent scattering of fine particles that defines the somata and cellular processes. The coating is stable enough to withstand counterstaining and thus makes possible direct evaluation of structural features not only of cellular processes but also of cytoplasmic components.     

L-carnitine delays the killing of cultured hepatocytes by 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine

The role of fatty acid metabolism in chemical-dependent cell injury is poorly understood. Addition of L-carnitine to the incubation medium of cultured hepatocytes delayed cell killing initiated by 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP). Protection by L-carnitine was stereospecific and observed as late as 1 h following addition of MPTP. D-Carnitine, but not iodoacetate, reversed the L-carnitine effect. Monoamine oxidase A and B activities, MPTP/N-methyl-4-phenyl-pyridinium levels, and MPTP-dependent loss of mitochondrial membrane potential measured by release of [3H]triphenylmethylphosphonium were not altered by addition of L-carnitine. Significant changes in MPTP-induced depletion of total cellular ATP did not occur with excess L-carnitine. Although the mechanism of cytoprotection exerted by L-carnitine remains unresolved, the data suggest that L-carnitine does not significantly alter: (i) mitochondrial-dependent bioactivation of MPTP; (ii) MPTP-dependent loss of mitochondrial membrane potential; or (iii) MPTP-mediated depletion of total cellular ATP content. We conclude that alterations of fatty acid metabolism may contribute to the toxic consequences of exposure to MPTP. Moreover, the lack of L-carnitine-mediated cytoprotection of monolayers incubated with 4-phenylpyridine or potassium cyanide suggests: (i) a link between fatty acid metabolism and mitochondrial membrane-mediated, bioactivation-dependent cell killing; and (ii) that inhibition of NADH dehydrogenase may not totally explain the mechanism of MPTP cytotoxicity.     

The impact of acidification on diatoms and chemistry of Dutch moorland pools

Summary Moorland pools are shallow oligotrophic soft water lakes on poorly buffered sandy soils. Diatom assemblages of samples from 16 pools taken in 1920 and 1978 were compared by analysis of pH-spectra, diversity, dissimilarity and multivariate statistical techniques.The pH-spectra of pools in the southern (S) and central (C) part of the country indicate a fall in pH from 4.5–6.0 in the old samples to 3.7–4.6 in the recent ones. The pH-spectra of the northern pools (N) do not indicate a significant shift from the original pH (ca 4.5).The number of species in the count and the diversity (indices of Simpson and Shannon) decreased significantly in S+C, and that goes also for the dissimilarity index of Dyer. No changes were found in N.The first component (PC 1) of the principal component analysis explains 61% of total variance. PC 1 is correlated with log [SO₄] (r=0.83, p<0.001) and even better (r=0.95, p<0.001) with the relative sulphate concentration,i.e. the ratio of sulphate to all major anions (sulphate, chloride, bicarbonate). All old samples have low scores on PC 1, recent samples have low scores on the second (PC 2) and third (PC 3) principal component. Old samples have high scores on PC 2 and PC 3, explaining 9 and 6% of total variance, respectively.The orginal variation, caused by regional factors, is replaced by a SO₄ ^2– controlled variation. PC 1 is nearly completely determined by the relative abundance ofEunotia exigua. This species, which is known to be very resistant to pollution by sulphur, aluminium and heavy metals, increased largely from 1920 to 1978.In spite of the rather homogeneous distribution of wet sulphate deposition in the Netherlands, substantial differences in SO₄ ^2– content in the pools are observed, being lowest in N (0.13–0.48 meq.l^–1) and highest in S+C (0.38–1.65 meq.l^–1). Sulphate is positively correlated with calcium, aluminum and magnesium but negatively with factors that characterize humic acid waters (e.g. permanganate-consumption, iron and the ratio of univalent to divalent cations). Sulphate concentration depends on the intensity of sulphate reduction, accumulation by dry deposition in surrounding forests of Scots pine, drought and atmospheric deposition.     

Pigment architecture of the human telencephalic cortex

Summary Cortical lamination and parcellation of the retrosplenial region in the human brain is evaluated with the aid of frontal serial sections stained for nerve cells (15 m), myelin sheaths (100 m), and lipofuscin granules (800 m).For the most part, the retrosplenial region is buried in the depth of the sulcus corporis callosi covering the posterior parts of the cingulate gyrus. It lies between the supracallosal derivatives of the allocortex (fascia dentata, cornu ammonis, subiculum) and the mature parietal isocortex.The region can be subdivided into five areas. The transitory periallocortical Area ectosplenialis is followed by a richly differentiated proisocortical core displaying extremely externopyramidal, externoteniate, and astriate to unitostriate characteristics. The parvocellular core is averagely poor in pigment (Typus clarus) and rich in myelinated fibres (Typus dives). Minor structural differences allow for its subdivision into a lateral, an intermediate, and a medial retrosplenial field. The accompanying Area parasplenialis is adjacent to the equoteniate parietal isocortex. It is only weakly externopyramidal, externoteniate, and propebistriate. The already homotypical field shows an average pigmentation and myelin content. These structural features permit its classification as a belt area of the retrosplenial core.Supported by grants from the Deutsche Forschungsgemeinschaft     

Bacteriological activity in unfiltered calf sera collected for tissue culture use

Summary Bacteriological tests were made on 24 lots of unfiltered calf serum collected for subsequent use as a component of tissue culture media. The examination included the isolation and identification of bacteria, assay of phages, and demonstration of endotoxin material. Only Gram-positive bacteria were isolated and 96% of the sera were contaminated with bacteria. The prevalent strains of bacteria found wereBacillus species and streptococci and 63% of the sera coagulatedLimulus amebocyte lysate. More than 90% of the lots contained phages demonstrable with the C-3000 strain ofEscherichia coli. Only one lot of the serum was found to be free from bacteria, phages, and endotoxin by the tests used.