Biodegradability continuum and biodegradation kinetics of natural organic matter described by the beta distribution

We followed a long-term (up to 503 days) microbial mineralization of dissolved organic carbon (DOC) from lake water in a bioassay and described the kinetics of biodegradation with a new model based on a reactivity continuum approach. The biodegradability of DOC was expressed as the probability of biodegradation, which was assumed to follow a beta distribution. We compared the performance of our beta model to five earlier models: the simplest first order kinetic model, two G models, the power model and the gamma model. The simplest first order kinetic model described the decreasing microbial mineralization of DOC poorly (r ² = 0.73), but the other models explained the observed kinetics of biodegradation well (r ² > 0.95). When we assessed the extrapolation power of models beyond the length of the bioassay by reducing the amount of data, the predictive power of the G models was poor. Instead, the beta model predicted the biodegradation kinetics consistently and correctly based on even only three observations in time. The beta model provided also long-term predictions (up to 5,000 years) along the observed long-term mineralization trajectory of organic carbon in sediments. Additionally, the beta model formulated the biodegradability continuum of DOC, which was skewed towards low biodegradability. During the bioassay, the skew towards low biodegradability increased as the most biodegradable parts of DOC were consumed. The beta model describes the biodegradability continuum quantitatively and can predict biodegradation in a realistic manner, thus, improving our understanding about the biodegradability and the role of natural organic matter in the environment.     

A thymosin beta15-like peptide promotes intersegmental myotome extension in the chicken embryo

Beta-thymosins constitute a group of small actin-sequestering peptides. These highly conserved peptides are involved in cytoskeleton dynamics and can influence different cell properties such as motility, substrate adhesion, shape and chemotaxis. As a marker for tumour metastasis, the mammalian thymosin beta15 is believed to have an important diagnostic relevance in cancer prognosis, although little is known about its physiological function. In order to study the role of thymosin beta15 ^avian in embryogenesis, we cloned the chicken and quail orthologues of thymosin beta15 and used the chicken as a model for vertebrate development. Avian thymosin beta15, the first known non-mammalian thymosin beta15-like gene, encodes a peptide that possesses a cysteine at position one after the methionine which is a significant difference compared to its mammalian counterparts. Thymosin beta15 ^avian expression starts at an early stage of development. The expression pattern changes rapidly with development and differs from that of the related thymosin beta4 gene. The most prominent expression domain is seen in developing muscles of limbs and trunk. Gain-of-function experiments revealed that thymosin beta15^avian has a function in normal myotome development. Ectopic over-expression of thymosin beta15 ^avian leads to premature elongation of myotome cells trespassing segment borders. We conclude that thymosin beta15 ^avian has a still undescribed function in promoting myocyte elongation.     

Distribution of detritivores in tropical forest streams of peninsular Malaysia: role of temperature,canopy cover and altitude variability

The diversity and abundance of macroinvertebrate shredders were investigated in 52 forested streams (local scale) from nine catchments (regional scale) covering a large area of peninsular Malaysia. A total of 10,642 individuals of aquatic macroinvertebrates were collected, of which 18.22 % were shredders. Biodiversity of shredders was described by alpha (α_average ), beta (β) and gamma diversity (γ) measures. We found high diversity and abundance of shredders in all catchments, represented by 1,939 individuals (range 6–115 and average per site of 37.29?±?3.48 SE) from 31 taxa with 2–13 taxa per site (α_average?=?6.98?±?0.33 SE) and 10–15 taxa per catchment (γ?=?13.33?±?0.55 SE). At the local scale, water temperature, stream width, depth and altitude were correlated significantly with diversity (Adj-R ²?=?0.205). Meanwhile, dissolved oxygen, stream velocity, water temperature, stream width and altitude were correlated to shredder abundance (Adj-R ²?=?0.242). At regional scale, however, water temperature was correlated negatively with β and γ diversity (r ²?=?0.161 and 0.237, respectively) as well as abundance of shredders (r ²?=?0.235). Canopy cover was correlated positively with β diversity (r ²?=?0.378) and abundance (r ²?=?0.266), meanwhile altitude was correlated positively with β (quadratic: r ²?=?0.175), γ diversity (quadratic: r ²?=?0.848) as well as abundance (quadratic: r ²?=?0.299). The present study is considered as the first report describing the biodiversity and abundance of shredders in forested headwater streams across a large spatial scale in peninsular Malaysia. We concluded that water temperature has a negative effect while altitude showed a positive relationship with diversity and abundance of shredders. However, it was difficult to detect an influence of canopy cover on shredder diversity.     

The Tryptophan Fluorescence of Tetracarbidium conophorum Agglutinin II and a Solution-Based Assay for the Binding of a Biantennary Glycopeptide

The plant lectin Tetracarbidium conophorum agglutinin II binds to glycoproteins and glycopeptides in a structurally specific manner [Animashaun et al., (1994) Glycoconjugate J. 11, 299–303]. We have characterized the steady-state and time-resolved fluorescence of the tryptophan residues of this lectin. The fluorescence (λ_ex = 295 nm, λ_em = 350 nm) decay is complex and can be described by four decay times with the following values: τ₁ = 7.4nsec, α₁ = 0.22; τ₂ = 2.9 nsec, α₂ = 0.25; τ₃ = l.0 nsec, α₃ = 0.34; τ₄ = 0.2 nsec, α₄ = 0.18. The addition of a biantennary glycopeptide $\begin{array}{*{20}c} {Gal\beta (1 \to 4)GlcNAc\beta (1 \to 2)Man\alpha (1 \to 6)\neg } \\ {Man\beta (1 \to 4)GlcNAC\beta (1 \to 4)GlcAc\beta (1 \to )\begin{array}{*{20}c} {Glu - Nh_2 } \\ | \\ {Asn} \\ | \\ {COOH} \\ \end{array} } \\ {Gal\beta (1 \to 4)GlcNAc\beta (1 \to 2)Man\alpha (1 \to 3)} \\ \end{array} $ to the lectin results in a quench and an 8 nm blue shift of the emission spectrum. The effect is saturable, and is described by an association constant of 1.8×10⁵ M^?1. The tryptophan fluorescence of Tetracarbidium conophorum agglutinin II may therefore be utilized to characterize thermodynamically the binding interactions between this lectin and complex glycoprotein.     

Preparation and use of α-maltosyl fluoride as a substrate by beta amylase

The preparation of pure (amorphous) α-maltosyl fluoride is described. A modification of the procedure of Brauns was used to obtain analytically pure, crystalline hepta-O-acetyl-α-maltosyl fluoride, the structure of which was assigned by¹⁹F-and¹H-n.m.r. spectroscopy. α-Maltosyl fluoride was obtained by deacetylating the heptaacetate. It behaved as a single compound on thin-layer and paper chromatography, and was essentially completely hydrolyzed to maltose and hydrogen fluoride by 0.01M sulfuric acid in 10 min at 100°. Crystalline beta amylase, likewise, catalyzed essentially complete hydrolysis of α-maltosyl fluoride to give maltose and hydrogen fluoride. The rates of hydrolysis catalyzed by beta amylase preparations from sweet potatoes and soybeans acting on a range of concentrations of the substrate produced linear curves for the relationship, 1/v vs 1/S; reaction constants for crystalline, sweet-potato enzyme were K_m 3.6 mM and V_max ~ 2 μ mol/min/mg. The finding that α-maltosyl fluoride is hydrolyzed 30–60 times faster than maltotriose demonstrates for the first time that beta amylase is capable of effecting hydrolysis at an appreciable rate of a substrate having only two d-glucose residues.     

Solvent Water for Electrolytes in the Muscle Fiber of the Giant Barnacle

Seven experiments are described which permit estimation of the "solvent water" or the "osmotically active water" of the dissected fiber from the giant barnacle, Balanus nubilus. Each of the first four experiments includes the measurement of a free ion activity in the myoplasm by means of a Na⁺, K⁺, or Cl^- ion-specific microelectrode. The fifth experiment makes use of a membrane potential vs. [K]_o curve. The last two experiments measured fiber water and fiber volume as bath osmolarity was changed. The seven independent estimations of solvent water ranged from 0.64 to 0.72 of fiber water with a mean of 0.68. Since the extracellular space of single fibers was about 7% of fiber water, it was concluded that 25% of analyzable water was not acting as solvent for the osmotically active solutes in the myoplasm.     

Fluctuations, exchange processes, and water diffusion in aqueous protein systems: A study of bovine serum albumin by diverse NMR techniques

Experimental frequency, concentration, and temperature dependences of the deuteron relaxation times T₁ and T₂ of D₂O solutions of bovine serum albumin are reported and theoretically described in a closed form without formal parameters. Crucial processes of the theoretical concept are material exchange, translational diffusion of water molecules on the rugged surfaces of proteins, and tumbling of the macromolecules. It is also concluded that, apart from averaging of the relaxation rates in the diverse deuteron phases, material exchange contributes to transverse relaxation by exchange modulation of the Larmor frequency. The rate limiting factor of macromolecular tumbling is determined by the free water content. In a certain analogy to the classical free-volume theory, a “free-water-volume theory” is presented. There are two characteristic water mass fractions indicating the saturation of the hydration shells (C_s ≈ 0.3) and the onset of protein tumbling (C₀ ≈ 0.6). The existence of the translational degrees of freedom of water molecules in the hydration shells has been verified by direct measurement of the diffusion coefficient using an NMR field-gradient technique. The concentration and temperature dependences show phenomena indicating a percolation transition of clusters of free water. The threshold water content was found to be C_c^w ≈ 0.43.     

The role of <Emphasis Type="Italic">Viviparus contectus</Emphasis> (Millet) (Mollusca,Viviparidae) in the sedimentation of suspension and transformation of organic matter in the Tnya River (Ukraine)

As active filterers and sedimentators, mollusks Viviparus contectus (Millet) clear water from suspensions in the Tnya River. The sedimentation ability of mollusks is assessed on the basis of experimental studies at three stations using the funneling technique. Mollusks at the age of 3 and 5 years are used. The rate of sedimentation of V. contectus is 7.3 to 13.7 mg/(spec. day) in July 2014. The efficiency of suspended sedimentation is higher in younger individuals. The rate of sedimentation is determined by the total body weight of mollusks; the ratio between these parameters is described by the exponential function. V. contectus contributes to the decrease in the content of organic matter in the water with a rate of 0.055 to 0.069 mg of O₂/(dm³ spec. h), as well as to the enrichment of the near-bottom water layer with organic matter.     

Re-expression of igf-ii is important for Beta cell regeneration in adult mice

Background

The key factors which support re-expansion of beta cell numbers after injury are largely unknown. Insulin-like growth factor II (IGF-II) plays a critical role in supporting cell division and differentiation during ontogeny but its role in the adult is not known. In this study we investigated the effect of IGF-II on beta cell regeneration.

Methodology/Principal Findings

We employed an in vivo model of ‘switchable’ c-Myc-induced beta cell ablation, pIns-c-MycER^TAM, in which 90% of beta cells are lost following 11 days of c-Myc (Myc) activation in vivo. Importantly, such ablation is normally followed by beta cell regeneration once Myc is deactivated, enabling functional studies of beta cell regeneration in vivo. IGF-II was shown to be re-expressed in the adult pancreas of pIns-c-MycER^TAM/IGF-II^+/+ (MIG) mice, following beta cell injury. As expected in the presence of IGF-II beta cell mass and numbers recover rapidly after ablation. In contrast, in pIns-c-MycER^TAM/IGF-II^+/− (MIGKO) mice, which express no IGF-II, recovery of beta cell mass and numbers were delayed and impaired. Despite failure of beta cell number increase, MIGKO mice recovered from hyperglycaemia, although this was delayed.

Conclusions/Significance

Our results demonstrate that beta cell regeneration in adult mice depends on re-expression of IGF-II, and supports the utility of using such ablation-recovery models for identifying other potential factors critical for underpinning successful beta cell regeneration in vivo. The potential therapeutic benefits of manipulating the IGF-II signaling systems merit further exploration.     

Water permeability of chlorella cell membranes by nuclear magnetic resonance: measured diffusion coefficients and relaxation times

Measurement by two nuclear magnetic resonance (NMR) techniques of the mean residence time τ_a of water molecules inside Chlorella vulgaris (Beijerinck) var. “viridis” (Chodot) is reported. The first is the Conlon and Outhred (1972 Biochim Biophys Acta 288: 354-361) technique in which extracellular water is doped with paramagnetic Mn²⁺ ions. Some complications in application of this technique are identified as being caused by the affinity of Chlorella cell walls for Mn²⁺ ions which shortens the NMR relaxation times of intra- and extracellular water. The second is based upon observations of effects of diffusion on the spin echo of intra- and extracellular water. Echo attenuation of intracellular water is distinguished from that of extracellular water by the extent to which diffusive motion is restricted. Intracellular water, being restricted to the cell volume, suffers less echo attenuation. From the dependence of echo amplitude upon gradient strength at several values of echo time, the mean residence time of intracellular water can be determined. From the mean residence time of intracellular water, the diffusional water permeability coefficient of the Chlorella membrane is calculated to be 2.1 ± 0.4 × 10⁻³ cm sec⁻¹.     

Visual apparent motion and some preferred paths in the rotation group SO(3)

The sequential presentation of two distinct stimulus objects to the visual system will, under certain conditions, induce an apparentmotion effect, called beta motion, in which the first object appears to smoothly transform into the second. This study is concerned with the kinds of paths selected by the visual system in effecting beta motion in which the metric structure of the object is preserved throughout. Two schemes are advanced according to which the visual system might operate. The first concentrates upon the manifold M in which the object appears to transform and the second upon the group G of transformations of M onto itself in which the particular transformation describing this motion lie. Under the identification of M with the 2-sphere S ², each scheme specifies the action-minimizing curves in the rotation group SO(3) for a particular “natural” Riemannian metric. An experiment is described in which a determination is made of the actual paths taken by an object under-going various rigid-motion beta motions. The results obtained indicate that the visual system behaves more in accordance with the second scheme than with the first. A generalization of this result is briefly discussed.     

Method for overcoming the antiethylene effects of ag

A technique is described for eliminating the antiethylene effects of the Ag⁺ ion in the intact pea plant (Pisum sativum). The technique is based on the ability of the ethylene mimic, acetylene, to negate the antiethylene effect of Ag⁺, presumably through salt formation, and subsequently to induce the ethylene response.     

Identification of cyclic guanosine monophosphate-binding proteins in Drosophila by direct photoaffinity labeling

A procedure for direct photoaffinity labeling with [³²P]cGMP has been used to identify cGMP-binding proteins in Drosophila. This method provides better sensitivity and resolution than previously described direct methods, because the proteins can be visualized by autoradiography following sodium dodecyl sulfate-gel electrophoresis. Labeling is observed with cGMP concentrations as low as 4 × 10^?8m and is specific for cGMP. The sensitivity of the technique is sufficient to permit detection of cGMP-binding proteins in crude extracts. With this technique a single cytoplasmic cGMP-binding protein of subunit M_r 108,000 has been identified in Drosophila embryos and cultured cells.     

Preparative solvent partition chromatography of butyrylated cyclic AMP analogues

A simple and effective separation of cyclic adenosine-3′,5′-monophosphate (cAMP) and its butyryl-substituted analogues using partition chromatography on columns of Sephadex gel in isopropanol/0.5 m ammonium acetate (4:1) is described. The technique is suitable for preparative separations as demonstrated by revised uv spectral data obtained on butyrylated cAMP's purified by this technique. In addition, it has analytical utility in that it allows complete separation of N⁶-monobutyryl cAMP from O^2′-monobutyryl cAMP, thereby permitting simultaneous and independent assessment of the rate of acyl substituent hydrolysis from the disubstituted derivative (N⁶,O^2′-dibutyryl cAMP), and this is demonstrated under several conditions.     

Occurrence and Genetic Diversity of Uncultured Legionella spp. in Drinking Water Treated at Temperatures below 15°C

Representatives of the genus Legionella were detected by use of a real-time PCR method in all water samples collected directly after treatment from 16 surface water (SW) supplies prior to postdisinfection and from 81 groundwater (GW) supplies. Legionella concentrations ranged from 1.1 × 10³ to 7.8 × 10⁵ cells liter⁻¹ and were significantly higher in SW treated with multiple barriers at 4°C than in GW treated at 9 to 12°C with aeration and filtration but without chemical disinfection. No Legionellae (<50 CFU liter⁻¹) were detected in treated water by the culture method. Legionella was also observed in untreated SW and in untreated aerobic and anaerobic GW. Filtration processes in SW and GW treatment had little effect or increased the Legionella concentration, but ozonation in SW treatment caused about 1-log-unit reduction. A phylogenetic analysis of 16S rRNA gene sequences of 202 clones, obtained from a selection of samples, showed a high similarity (>91%) with Legionella sequences in the GenBank database. A total of 40 (33%) of the 16S rRNA gene sequences obtained from treated water were identified as described Legionella species and types, including L. bozemanii, L. worsleiensis, Legionella-like amoebal pathogen types, L. quateirensis, L. waltersii, and L. pneumophila. 16S rRNA gene sequences with a similarity of below 97% from described species were positioned all over the phylogenetic tree of Legionella. Hence, a large diversity of yet-uncultured Legionellae are common members of the microbial communities in SW and GW treated at water temperatures of below 15°C.     

Cryptosporidium Oocyst Detection in Water Samples: Floatation Technique Enhanced with Immunofluorescence Is as Effective as Immunomagnetic Separation Method

Cryptosporidium can cause gastrointestinal diseases worldwide, consequently posing public health problems and economic burden. Effective techniques for detecting contaminated oocysts in water are important to prevent and control the contamination. Immunomagnetic separation (IMS) method has been widely employed recently due to its efficiency, but, it is costly. Sucrose floatation technique is generally used for separating organisms by using their different specific gravity. It is effective and cheap but time consuming as well as requiring highly skilled personnel. Water turbidity and parasite load in water sample are additional factors affecting to the recovery rate of those 2 methods. We compared the efficiency of IMS and sucrose floatation methods to recover the spiked Cryptosporidium oocysts in various turbidity water samples. Cryptosporidium oocysts concentration at 1, 10¹, 10², and 10³ per 10 µl were spiked into 3 sets of 10 ml-water turbidity (5, 50, and 500 NTU). The recovery rate of the 2 methods was not different. Oocyst load at the concentration < 10² per 10 ml yielded unreliable results. Water turbidity at 500 NTU decreased the recovery rate of both techniques. The combination of sucrose floatation and immunofluorescense assay techniques (SF-FA) showed higher recovery rate than IMS and immunofluorescense assay (IMS-FA). We used this SF-FA to detect Cryptosporidium and Giardia from the river water samples and found 9 and 19 out of 30 (30% and 63.3%) positive, respectively. Our results favored sucrose floatation technique enhanced with immunofluorescense assay for detecting contaminated protozoa in water samples in general laboratories and in the real practical setting.     

A method for the assay of chymotrypsin in crude biological materials

A method suitable for assaying chymotrypsin in crude biological materials such as feces has been described. The procedure employs a water soluble peptide, N-benzoyl-l-tyrosyl-para-aminobenzoate (Na), which is hydrolyzed by chymotrypsin (K_m = 2.9 × 10^?3M) to yield the TCA-soluble diazotizable aromatic amine.     

Yeasts of the White Sea intertidal zone and description of Glaciozyma litorale sp. nov.

The intertidal yeast communities inhabiting various environments in the territories of the White Sea Biological Station “Kartesh” (WSBS ZIN RAS) and the N.A. Pertsov White Sea Biological Station (WSBS MSU) were studied. A total of 31 yeast species were isolated using a conventional plating technique and identified using molecular methods. The yeast community of the White Sea intertidal zone consists of members that are typical for marine substrates, ubiquist species that are common in water and in low-temperature terrestrial environments, and a group of species that was isolated from marine substrates for the first time. The most diverse yeast communities formed on the surface of marine algae and in silt. Metschnikowia zobellii, which is a typical inhabitant of northern seas, was the most abundant yeast on algae from both biological stations. A new basidiomycetous yeast species, which was described in this work as Glaciozyma litorale sp. nov., dominated in the silt samples. The type strain of this new species is K94b^T (=KBP 4246^T = VKPM Y-3850^T = PYCC 6252^T = CBS 12957^T = DSM 28204^T); MycoBank registration number is MB 805475.     

Isolation of covalently closed circular DNA of high molecular weight from bacteria.

A simple method is described in detail for the efficient isolation of high molecular weight covalently closed circular DNA (ccc-DNA) from Agrobacterium. Although this method was developed for isolating ccc-DNA of molecular weights greater than 10⁸ daltons in Agrobacterium, the technique also proves to be useful in isolating ccc-DNA of varying sizes from a variety of other bacteria. The technique involves the shearing and alkali denaturation of the chromosomal DNA, followed by the preferential removal of the single-stranded DNA by phenol extraction. The DNA which remains is largely ccc-DNA. The DNA is then concentrated, and the ccc-DNA is separated from the chromosomal DNA by centrifugation in a cesium chloride-ethidium bromide density gradient. By this technique, ccc-DNA of varying sizes has also been isolated from species of Escherichia, Rhizobium, Citrobacter, and Lactobacillus.     

Radioenzymatic estimation of S-adenosylmethionine in rat brain regions and subcellular fractions

A rapid, sensitive, and specific method for the analysis of S-adenosyl-l-methionine (SAMe) in tissues is described. The assay is based on the measurement of the conversion of SAMe and [³H]dopamine to 3-[³H]methoxytyramine in the presence of catechol-O-methyltransferase (COMT). The linearity of the quantitative measurement is greatly improved by including an internal standard of [¹⁴C]SAMe in each test. Using the described technique, nanogram quantities of SAMe can be measured in tissue. SAMe is distributed relatively evenly throughout the anatomical regions of the brain. Studies of its subcellular distribution indicate that while SAMe is located primarily in the soluble fraction, a considerable amount is also associated with the synaptosomal fraction.