Human-specific gain of function in a developmental enhancer

Changes in gene regulation are thought to have contributed to the evolution of human development. However, in vivo evidence for uniquely human developmental regulatory function has remained elusive. In transgenic mice, a conserved noncoding sequence (HACNS1) that evolved extremely rapidly in humans acted as an enhancer of gene expression that has gained a strong limb expression domain relative to the orthologous elements from chimpanzee and rhesus macaque. This gain of function was consistent across two developmental stages in the mouse and included the presumptive anterior wrist and proximal thumb. In vivo analyses with synthetic enhancers, in which human-specific substitutions were introduced into the chimpanzee enhancer sequence or reverted in the human enhancer to the ancestral state, indicated that 13 substitutions clustered in an 81-base pair module otherwise highly constrained among terrestrial vertebrates were sufficient to confer the human-specific limb expression domain.     

SOM fractionation methods: Relevance to functional pools and to stabilization mechanisms

Soil organic matter (SOM) consists of various functional pools that are stabilized by specific mechanisms and have certain turnover rates. For the development of mechanistic models that predict changes in SOM storage, these pools have to be quantified and characterized. In the past, numerous fractionation schemes have been developed to separate and analyse such SOM fractions. In this review, the SOM fractions obtained with such operational fractionation procedures are described in terms of their pool sizes, chemical properties, and turnover rates. The main objective of this review is to evaluate these operationally defined fractions with respect to their suitability to describe functional SOM pools that could be used to parameterize SOM turnover models. Fractionation procedures include (1) physical separation of SOM into aggregate, particle size, and density fractions and fractions according to their magnetic susceptibility, and (2) various wet chemical procedures that fractionate SOM according to solubility, hydrolysability, and resistance to oxidation or by destruction of the mineral phase. Furthermore, combinations of fractionation methods are evaluated.The active SOM pool with turnover rates <10 years may best be represented by the soil microbial biomass and the light fraction (<1.6-2 g cm⁻³) obtained by density fractionation (if black carbon contents are considered). Most chemical and physical fractionations as well as combinations of methods yield SOM fractions that are not homogeneous in terms of turnover rates. It has proven to be particularly difficult to isolate functional fractions that represent the passive model pools in which the majority of soil SOM is stabilized. The available fractionation methods do not correspond to specific stabilization mechanisms and hence do not describe functional SOM pools. Another problem is that comprehensive data for turnover rates and data for whole soil profiles are only now becoming available, especially for new fractionation methods. Such information as well as the use of specific markers and compound-specific isotope analysis may be important for future differentiation and evaluation of functional SOM fractions.     

Growth and interactions of arbuscular mycorrhizal fungi in soils from limestone and acid rock habitats

Arbuscular mycorrhizal (AM) development in different soil types, and the influence of AM fungal hyphae on their original soil were investigated. Plantago lanceolata, which can grow in soils of a very wide pH range, was grown in two closely related limestone soils and an acid soil from rock habitats. Plants were colonised by the indigenous AM fungal community. The use of compartmented systems allowed us to compare soil with and without mycorrhizal hyphae. Root colonisation of P. lanceolata was markedly higher in the limestone soils (30-60%) than in the acid soil (5-20%), both in the original habitat and in the experimental study. Growth of extraradical AM fungal hyphae was detected in the limestone soils, but not in the acid soil, using the signature fatty acid 16:1ω5 as biomass indicator. Analysis of signature fatty acids demonstrated an increased microbial biomass in the presence of AM fungal hyphae as judged for example from an increased amount of NLFA 16:0 with 30 nmol g⁻¹ in one of the limestone soils. Bacterial activity, but not soil phosphatase activity, was increased by around 25% in the presence of mycorrhizal hyphae in the first harvest of limestone soils. AM fungal hyphae can thus stimulate microorganisms. However, no effect of AM hyphae was observed on the soil pH or organic matter content in the limestone soils and the available P was not depleted.     

Loss of redness (a*) as a tool to follow hemoglobin-mediated lipid oxidation in washed cod mince

Instrumental measurement of redness loss (decrease in a* value) was evaluated as a tool to follow hemoglobin (Hb)-mediated lipid oxidation in fish muscle. Two washed cod mince model systems were used (prepared at pH 6.5 and 5.5), both fortified with 15 micromol/kg of trout Hb and adjusted to pH 6.5 and 81% moisture. The rate of oxidation was varied through pH alterations (pH 6.1 and 6.9) and addition of an antioxidative cod muscle press juice. During ice storage, TBARS, painty odor, and a* values were followed. In all "oxidizing" samples, a* values correlated well with TBARS and painty odor development; r = -0.95 and -0.77, respectively. In press juice containing samples, the correlation was lower (0.55 for a vs TBARS) because there was a slight a* value decrease even in the absence of measurable lipid oxidation. a* values distinguished between "oxidizing" and stable samples within 1 day, before any lipid oxidation products could be chemically detected. It was confirmed in an aqueous phosphate buffer model system that the redness loss corresponded to a buildup of brownish met-Hb at the expense of oxy- and deoxy-Hb. The a* value data were best used as a lipid oxidation index by calculating the rate of decrease (k value) in the "initial phase" of the redness loss (before accumulation of lipid oxidation products) or in the "differentiation phase" (during the exponential raise in TBARS/painty odor). Calibration to lipid oxidation products must, however, be made for each specific sample type. Washing method, pH, Hb-type, etc., all affected both k values and absolute a* readings. Small yellowness (b*) increases also occurred along with a value losses, possibly the result of polymerized Schiff bases.     

A comparison of two methods for the isolation of free and occluded particulate organic matter

Various methods exist for the isolation of particulate organic matter (POM), one of the soil‐organic‐matter (SOM) fractions reacting most sensitive on land‐use or soil‐management changes. A combination of density separation and ultrasonic treatment allows to isolate two types of POM: (1) free POM and (2) POM occluded in soil aggregates. POM fractions are closely linked to their biochemical function for the formation and stabilization of aggregates, therefore methods using different aggregate sizes may result in different POM fractions isolated. We evaluated two physical fractionation procedures to reveal whether they yield different POM fractions with respect to amount and composition, using grassland and arable soils with sandy‐loam to sandy–clay‐loam texture and thus low macroaggregate stability. Method I used air‐dried aggregates of <2.0 mm size and a low‐energy sonication for aggregate disruption, method II used field‐moist aggregates <6.3 mm and a high‐energy–sonication procedure for aggregate disruption. POM fractions were analyzed by elemental analysis (C, N) and CPMAS ¹³C‐NMR spectroscopy. With both methods, about similar proportions of the SOM are isolated as free or occluded POM, respectively. The free‐ and occluded‐POM fractions obtained with method I are also rather similar in C and N concentration and composition as shown by ¹³C‐NMR spectroscopy. Method II isolates a free‐ and occluded‐POM fraction with significantly different C and N concentrations. NMR spectra revealed significant differences in the chemical composition of both fractions from method II, with the occluded POM having lower amounts of O‐alkyl C and higher amounts of aryl C and alkyl C than the free POM. Due to the use of larger, field‐moist aggregates with minimized sample pretreatment, two distinctly different POM fractions are isolated with method II, likely to be more closely linked to their biochemical function for the formation and stabilization of aggregates. High‐energy sonication as in method II also disrupts small microaggregates <63 µm and releases fine intraaggregate POM. This fraction seems to be a significant component of occluded POM, that allows a differentiation between free and occluded POM in sandy soils with significant microaggregation. It can be concluded, that microaggregation in arable soils with sandy texture is responsible for the storage of a more degraded occluded POM, that conversely supports the stabilization of fine microaggregates.     

In vivo bioinsecticidal activity toward Ceratitis capitata (fruit fly) and Callosobruchus maculatus (cowpea weevil) and in vitro bioinsecticidal activity toward different orders of insect pests of a trypsin inhibitor purified from tamarind tree (Tamarindus indica) seeds

A proteinaceous inhibitor with high activity against trypsin-like serine proteinases was purified from seeds of the tamarind tree (Tamarindus indica) by gel filtration on Shephacryl S-200 followed by a reverse-phase HPLC Vidac C18 TP. The inhibitor, called the tamarind trypsin inhibitor (TTI), showed a Mr of 21.42 kDa by mass spectrometry analysis. TTI was a noncompetitive inhibitor with a Ki value of 1.7 x 10(-9) M. In vitro bioinsecticidal activity against insect digestive enzymes from different orders showed that TTI had remarkable activity against enzymes from coleopteran, Anthonomus grandis (29.6%), Zabrotes subfasciatus (51.6%), Callosobruchus maculatus (86.7%), Rhyzopertha dominica(88.2%), and lepidopteron, Plodia interpuncptella (26.7%), Alabama argillacea (53.8%), and Spodoptera frugiperda (75.5%). Also, digestive enzymes from Diptera, Ceratitis capitata (fruit fly), were inhibited (52.9%). In vivo bioinsecticidal assays toward C. capitata and C. maculatus larvae were developed. The concentration of TTI (w/w) in the artificial seed necessary to cause 50% mortality (LD50) of larvae was 3.6%, and that to reduce mass larvae by 50.0% (ED50) was 3.2%. Furthermore, the mass C. capitata larvae were affected at 53.2% and produced approximately 34% mortality at a level of 4.0% (w/w) of TTI incorporated in artificial diets.     

Isoflavonoids isolated from Cuban propolis

Chemical investigation of a red-type Cuban propolis sample has led to the isolation of 11 isoflavonoids (2 isoflavones, 3 isoflavans, and 6 pterocarpans), together with gallic acid, isoliquiritigenin, and (-)-liquiritigenin. Structural determination, including the absolute stereochemistry, was accomplished by spectroscopic analysis, particularly CD and 2D NMR techniques. The fragmentation behavior of pterocarpans was studied by electrospray ionization (ESI) tandem mass spectrometry (MS/MS) using an ion-trap analyzer, and a generalized fragmentation pathway, useful in the identification and structural characterization of pterocarpans, is proposed. Isoflavonoids are reported for the first time from propolis samples.     

Consistency and solubility changes in herring (Clupea harengus) light muscle homogenates as a function of pH

Fish muscle proteins can be isolated from a variety of low-value raw materials by solubilization in either acid or base. If the consistency of the resulting solution is sufficiently low, it is possible to recover most of the solubilized proteins and remove most of the lipids by centrifugation. Lipid removal should greatly stabilize the isolated proteins. In a previous investigation into the use of herring for production of these protein isolates, it was observed that this species had particularly high consistency values when the proteins were solubilized. This study was undertaken to determine the consistencies obtained with herring light muscle tissue over the pH range covered by the two processes, from about pH 2.7 to 10.8. Protein solubility was compared to consistency of the resultant solutions. Maximum consistencies of the homogenates, approximately 220 and approximately 175 mPa.s, were obtained at pH values of approximately 3.5 and 10.5, respectively. Consistency began to increase approximately when solubilization began. Storage of homogenates at pH 2.7 decreased the consistency over a 10 min time period. The magnitude of the consistency peaks at both acid and alkaline pH values increased when using ice-stored as well as frozen-stored herring, especially in the acid range. Protein solubility at pH <4 and pH >/=10.8 slightly decreased after post-mortem storage of the herring muscle. It is suggested that the observed changes in consistency result from the expansion and solvation of protein aggregates which eventually dissociate into smaller units, perhaps even monomers.     

Direct HPLC analysis of quercetin and trans-resveratrol in red wine,grape, and winemaking byproducts

A simple and fast reversed-phase HPLC method using diode array detection was developed and validated for the simultaneous determination of trans-resveratrol and quercetin in Sicilian red wine from the Nero d'Avola red grape variety. Investigation was also extended to the quantitative determination of resveratrol and quercetin in grape skins and winemaking byproducts obtained from the same cultivar. Samples were eluted using a C18 narrow-bore column under isocratic conditions in less than 20 min. Quantification of trans-resveratrol and quercetin in red wine was performed without any sample pretreatment, whereas the determination of these phenolic compounds in grape skins and wine pomage required a solvent extraction procedure. Linearity was demonstrated over the 0.39-12.5 and 0.45-57.6 microg/mL range for trans-resveratrol and quercetin, respectively. Detection limits in real samples were in the low ppm level (0.07 mg/L for trans-resveratrol and 0.12 mg/L for quercetin). The HPLC-UV/DAD method was applied for the routine analyses of red wine and grape skin and winemaking byproduct extracts to evaluate their trans-resveratrol and quercetin content. In particular, a very high content of quercetin was found in wine pomace, suggesting the use of this wine byproduct as a potential source of this health-promoting phenolic compound.