Past hybridization between Quercus macrocarpa and Quercus gambelii

Introgression between two allopatric species,Quercus macrocarpa andQ. gambelii, has been observed in two separate locations: northeastern New Mexico and the Black Hills of western South Dakota and adjacent Wyoming. The probability that this introgression is the result of long-range pollination appears remote. Presumably these two species hybridized during a period of past sympatric association. Further indication of past sympatry in the Black Hills is the presence of a common species of obligate parasite, i.e., wasp(Cynips insulensis) onQ. gambelii in the Rocky Mountains and onQ. macrocarpa of the Black Hills. The hybrid oaks in New Mexico probably reflect a westward migration ofQ. macrocarpa during pluvial periods of the Pleistocene.Quercus gambelii most likely reached the Black Hills during the warmer postglacial hypsithermal era. The hybridization reported here may reflect secondary sympatry, i.e., sympatric occurrence after the species, or their ancestors, became geographically separated.     

Genome-Wide Analysis of Simple Sequence Repeats in Marine Animals—a Comparative Approach

Tandem simple sequence repeats (SSRs) are one of the most popular molecular markers in genetic analysis owing to their ubiquitous occurrence,high reproducibility, multiallelic nature, and codominant mode. High mutability makes SSRs play a role in genome evolution and correspondingly show different patterns. Comparative analysis of genomic SSRs in different taxonomic groups usually focuses on land species, while marine animals have been neglected. This study examined the abundance of genomic SSRs with repeated unit lengths of 1–6 bp in 30 marine animals including nine taxonomic groups and further compared with the land species. More than thousands of SSRs were discovered in every organism which provided a huge resource for the development of molecular markers. Thirty marine animals showed profound differences in SSR characteristics, but some group-specific trends were also found. Both similarities and differences of repeat patterns were discovered between the land and marine species. Two taxon-specific SSR types were discovered: the pentanucleotides motif AGAGG in Euteleostei and the hexanucleotide repeats of ATGTAC in Porifera and Echinodermata. Gene ontology (GO) enrichment analysis of two representative species (Amphimedon queenslandica for Porifera and Strongylocentrotus purpuratus for Echinodermata) revealed functional preference of the ATGTAC motif associated genes, and this might hint at evolutionary significance.     

Characteristics of migration in the population of Yevpatoria (Crimea)

Indicators characterizing population migration were calculated according to the marriage records of Yevpatoria (Crimea) of 1960/1961, 1985, and 1994/1995. The marital migration coefficient m in those years was 0.80, 0.75, and 0.66, the endogamy index was 0.04, 0.08, and 0.15, and the rate of marriage contingency by birthplace was 0.15, 0.16, and 0.19, respectively. The highest values of the positive mating assortative index were recorded for people from the Caucasus, Central, Central Black Earth Oblast, and Northwest regions of Russia in 1960/1961 and for migrants from Moldavia, the republics of Central Asia and Caucasus, Western Siberia, and Ukraine in 1985. In 1994/1995, natives of Yevpatoria were also included in this group. The average distance of migration by year was 909, 1280, and 1314 km, and the marital distance was 960, 1397, and 1171 km. The “radius” of the Yevpatoria population, in accordance with the Maleco model in the years under study, was 98, 134, and 137 km. The distance isolation indicator b was decreasing and amounted to 0.00049, 0.00043, and 0.00038. In the migration flow in all of the periods, the majority of immigrants came from different regions of Ukraine outside Crimea (27–31%), followed by natives of various places in Crimea (21–24%), Central (3.6–8.5%), and Central Black Earth (1.8–6.1%) regions of Russia, and the South Caucasus (4.0–5.7%). The proportion of Russians and Jews decreased in the migration flow, while the proportion of Ukrainians and representatives of non-Slavic nationalities increased.     

Diversity of Prokaryotic Community at a Shallow Marine Hydrothermal Site Elucidated by Illumina Sequencing Technology

To investigate the prokaryotic community structure and composition in an active hydrothermal site, named Black Point, off Panarea Island (Eolian Islands, Italy), we examined sediment and fluid samples, differing in temperature, by a massive parallel sequencing (Illumina) technique targeting the V3 region of the 16S rRNA gene. The used technique enabled us to detect a greater prokaryotic diversity than that until now observed and to reveal also microorganisms occurring at very low abundance (≤0.01 %). Most of sequences were assigned to Bacteria while Archaea were a minor component of the microbial community in both low- and high-temperature samples. Proteobacteria (mainly consisting of Alpha-, Gamma-, and Epsilonproteobacteria) dominated among all samples followed by Actinobacteria and Bacteroidetes. Analyzed DNA obtained from samples taken at different temperatures indicated the presence of members of different dominant genera. The main differences were observed between sediment samples where Rhodovulum and Thiohalospira prevailed at high temperature, while Thalassomonas and Sulfurimonas at low temperature. Chlorobium, Acinetobacter, Sulfurimonas, and Brevundimonas were abundant in both low- and high-temperature fluid samples. Euryarchaeota dominated the archaeal community in all samples. Classes of Euryarchaeota embracing hyperthermophilic members (Thermococci and Thermoplasmata) and of Crenarchaeota (Thermoprotei) were more abundant in high-temperature samples. A great number of sequences referred to Bacteria and Archaea still remained unaffiliated, indicating that Black Point site represents a rich source of so-far uncharted prokaryotic diversity.     

Co-pigmentation and the color change with age in petals ofFuchsia hybrida

Pure or genuine malvin was isolated fromFuchsia petals for the first time and characterized as the malvin anhydro-base. The conditions for the co-pigmentation were examinedin vitro with regard to anthocyanin, co-pigment and pH, and the co-pigmentation occurred as the result of interaction between anthocyanin and co-pigment without any participation of metallic elements. The blue-violet color of youngFuchsia petals appeared at pH 4.8 in the 1∶0.6 molar ratio of anthocyanin to co-pigments. The color change from blue-violet in young petals to purple-red in old ones was caused by co-pigmentation and the pH change from 4.8 to 4.2. The decrease of pH in the old petals was due to the increase of organic acids such as aspartic, malic and tartaric acids.     

Diversity,dynamic and ecology of freshwater snails related to environmental factors in urban and suburban streams in Douala–Cameroon (Central Africa)

Urban land use has increased dramatically over the past few decades, resulting in high variability in nutrients loading which is likely to alter the biological component of urban streams. Freshwater snails and environmental variables that might structure their diversity and distribution were studied from September 2012 to September 2013 in three contiguous watersheds in Douala. Twelve stations were monitored monthly, two of these are located in a suburban forest area, and the rest situated in urbanized and industrialized zones. Snails were collected using a long-handled net (30 × 30 cm side, 400-µm mesh). Meanwhile, measurements of the environmental variables were taken. Ten species were recorded which are as follows: Melanoides tuberculata (Thiaridae); Gabbiella africana (Bythiniidae); Physa acuta, Aplexa sp. (Physidae); Lymnaea natalensis, Lymnaea stagnalis, Lymnaea columella (Lymnaeidae); Biomphalaria pfeifferi, Bulinus forskalii (Planorbidae) and one undetermined taxon of Bythiniidae. All these snails were identified at nine of the ten urban stations; no species being found in suburban stations. These urban streams have very poor health status with highly polluted waters. Among the species found P. acuta (76.95 %), L. natalensis (19.46 %) and M. tuberculata (2.79 %) were the most abundant. Multiple stepwise regression analysis, Spearman correlation test and redundancy analysis showed that snail occurrences and abundances were probably influenced by water temperature, conductivity, suspended solids, alkalinity, nitrites, nitrates, ammonium, phosphates, oxydability, biochemical oxygen demand, rainfall, encumbrance rate of the riverbed and water width. Moreover, snail dynamics showed a seasonal pattern with peak population abundances and recruitment of young generations during rainy season. This malacological survey spotlighted the impacts of anthropogenic activities on snail’s diversity and distribution, with the proliferation of the invasive pulmonate P. acuta in Douala urban streams.     

Characterization of camel nanobodies specific for superfolder GFP fusion proteins

Superfolder green fluorescent protein (sfGFP) is a fusion tag which plays a dual role in monitoring and purifying the recombinant fusion proteins using specific binders. Nanobodies are the smallest intact antigen binding fragments derived from heavy chain-only antibodies (HCAbs) occurring in camelids. They are produced as recombinant proteins in E. coli and have different biotechnological applications, including the detection and purification of their specific antigens. To produce anti-sfGFP specific nanobodies, an adult one-humped camel was successfully immunized and immune response was evaluated by ELISA, which showed an active participation of HCAbs in this response. A relatively large nanobody “immune” library of 5 × 10⁸ individual transformants, with 87.5 % positivity, was prepared from the blood of the immunized camel. Phage display biopanning on this nanobody library resulted in the isolation of seven anti-sfGFP specific nanobodies, referred to as NbsfGFP01, 02, 03, 04, 06, 07 and 08. These nanobodies were able to recognize sfGFP tag as free or in fusion with growth hormone in ELISA and immuno-blotting. Furthermore, they showed important apparent affinities in the detection and capture of sfGFP by ELISA, and they targeted three different epitopes on the surface of their antigen. The interesting characteristics of these molecular binders make them valuable tools for more in-depth structural and functional studies related to sfGFP fusion proteins.     

Zearalenone degradation by two Pseudomonas strains from soil

This study describes the screening of soil bacteria for their capability to degrade zearalenone (ZEN), employing an enrichment technique in which ZEN is used as the sole carbon source. Two isolates that were able to degrade ZEN belonged to the genus Pseudomonas according to biochemical characterization and 16S rRNA gene sequence and were named as Pseudomonas alcaliphila TH-C1 and Pseudomonas plecoglossicida TH-L1, respectively. The results showed that the degradation rates of P. alcaliphila TH-C1 and P. plecoglossicida TH-L1 for ZEN (2 μg/ml) were 68?±?0.85 % and 57?±?0.73 %, when incubated for 72 h at 30 °C in a rotary shaker (160 rpm) and detected by high-performance liquid chromatograms (HPLC). These results suggest that the two Pseudomonas strains are new bacterial resource for degrading ZEN and can provide a new approach for the detoxification of ZEN.     

High CO2 detrimentally affects tissue regeneration of Red Sea corals

Ocean acidification (OA) from rising atmospheric carbon dioxide (CO₂) is threatening the future of coral reef ecosystems. Mounting experimental evidence suggests that OA negatively impacts fundamental life functions of scleractinian corals, including growth and sexual reproduction. Although regeneration is regarded as a chief life function in scleractinian corals and essential to maintain the colony’s integrity, the effect of OA on regeneration processes has not yet been investigated. To evaluate the effects of OA on regeneration, the common Indo-Pacific corals Porites sp., Favia favus, Acropora eurystoma, and Stylophora pistillata were inflicted with lesions (314–350 mm², depending on species) and incubated in different pCO₂: (1) ambient seawater (400 µatm, pH 8.1), (2) intermediate (1,800 µatm, pH 7.6), and (3) high (4,000 µatm, pH 7.3) for extended periods of time (60–120 d). While all coral species after 60 d had significantly higher tissue regeneration in ambient conditions as compared to the intermediate and high treatments, reduction in regeneration rate was more pronounced in the slow-growing massive Porites sp. and F. favus than the relatively fast-growing, branching S. pistillata and A. eurystoma. This coincided with reduced tissue biomass of Porites sp., F. favus, and A. eurystoma in higher pCO₂, but not in S. pistillata. Porites sp., F. favus, and S. pistillata also experienced a decrease in Symbiodinium density in higher pCO₂, while in A. eurystoma there was no change. We hypothesize that a lowered regenerative capacity under elevated pCO₂ may be related to resource trade-offs, energy cost of acid/base regulation, and/or decrease in total energy budget. This is the first study to demonstrate that elevated pCO₂ could have a compounding influence on coral regeneration following injury, potentially affecting the capacity of reef corals to recover following physical disturbance.     

Calcium-independent uncoupling activity of palmitic acid in liver mitochondria is regulated by the ion fluxes causing the interconversion of Δψ and ΔpH across the inner membrane

The effect of ion fluxes across the inner membrane on calcium-independent uncoupling activity of palmitic acid was investigated in experiments on rat liver mitochondria energized by the oxidation of succinate. The following compounds were used as the inductors of ion fluxes: the K⁺/H⁺ antiporter nigericin causing transformation of ΔpH into electrical potential difference (Δψ) across the inner membrane; tetraphenylphosphonium (TPP⁺) that freely crosses phospholipid membranes; protonophore carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone (FCCP) that induces a flow of H⁺ from the intermembrane space into the matrix and reduces Δψ and ΔpH. It was found that nigericin at a concentration of 20 nM, which causes an increase in maximal Δψ, partially inhibits the ability of palmitic acid to reduce Δψ and stimulates mitochondrial respiration. A specific inhibitor of the ATP/ADP antiporter (carboxyatractylate) and a substrate of the aspartate/glutamate antiporter (glutamate) increase Δψ and partially inhibit mitochondrial respiration in the presence of palmitic acid. Under these conditions, 10 μM cyclosporin A also inhibits respiration but has no effect on Δψ. The specific uncoupling activity of palmitic acid (V _U) and its specific components that characterize participation of the ATP/ADP antiporter (V _Catr), aspartate/glutamate antiporter (V _Glu), and cyclosporin-A-sensitive system (V _CsA) in the palmitic acid-induced uncoupling were estimated. It was shown that nigericin substantially reduces V _U, V _Catr and V _Glu but increases V _CsA. TPP⁺ at a concentration of 20 μM increases V _U and V _Glu, does not affect V _Catr and reduces V _CsA. FCCP at concentrations of 20 and 40 nM reduces Δψ by not more than 17% but does not affect V _U, V _Catr, V _Glu and V _CsA. The results suggest that the calcium-independent uncoupling effect of palmitic acid in liver mitochondria is caused by the return of protons to the matrix with participation of ADP/ATP and aspartate/glutamate antiporters and owing to activation of cyclosporin A-sensitive electron transport along the respiratory chain without affecting Δψ. The induced ion fluxes across the inner mitochondrial membrane can be considered as a factor of the calcium-independent regulation of uncoupling activity of palmitic acid in liver mitochondria with participation of the ADP/ATP and aspartate/glutamate antiporters and of the cyclosporin A-sensitive electron transport system.     

Contribution to the study on the reparative effect of exogenous DNA in the irradiated meristem ofVicia faba

The present report is focused on the study of participation of exogenous DNA in the process of postirradiation reparation of meristematic cells ofVicia faba primary roots. It is aimed at comparison of the positive reparative effect of isologous DNA with postirradiation action of heterologous DNA in its native, thermally denatured and DNAase-degraded forms, or DNA degraded by ultrasound, and with the effect of other biologically important macromolecules (RNA, histone, heparin, and dextran sulphate). For this purpose, the roots ofVicia faba irradiated by 150 r exposure were cultivated in solutions containing the above substances for an appropriate time interval. In squash slides both mitotic activity of the investigated cell population and frequency of postmetaphase chromosomal aberrations induced by radiation were evaluated. It was shown that a stimulation of cell division and reparation of chromosome damages were supported exclusively by isologous DNA. On the contrary, exogenously applied heterologous DNA increased postirradiation frequency of aberrations; maintenance of native structure of applied DNA was an essential condition for the above effect. Other macromolecules investigated on the course of postirradiation reparation ofVicia faba meristematic cells were without effect.     

Influence of bovine lactoferrin on the growth of selected probiotic bacteria under aerobic conditions

Bovine lactoferrin (bLf) is a natural glycoprotein, and it shows broad-spectrum antimicrobial activity. However, reports on the influences of bLf on probiotic bacteria have been mixed. We examined the effects of apo-bLf (between 0.25 and 128 mg/mL) on both aerobic and anaerobic cultures of probiotics. We found that bLf had similar effects on the growth of probiotics under aerobic or anaerobic conditions, and that it actively and significantly (at concentrations of >0.25 mg/mL) retarded the growth rate of Bifidobacterium bifidum (ATCC 29521), B. longum (ATCC 15707), B. lactis (BCRC 17394), B. infantis (ATCC 15697), Lactobacillus reuteri (ATCC 23272), L. rhamnosus (ATCC 53103), and L. coryniformis (ATCC 25602) in a dose-dependent manner. Otherwise, minimal inhibitory concentrations (MICs) were 128 or >128 mg/mL against B. bifidum, B. longum, B. lactis, L. reuteri, and L. rhamnosus (ATCC 53103). With regard to MICs, bLf showed at least four-fold lower inhibitory effect on probiotics than on pathogens. Intriguingly, bLf (>0.25 mg/mL) significantly enhanced the growth of Rhamnosus (ATCC 7469) and L. acidophilus (BCRC 14065) by approximately 40–200 %, during their late periods of growth. Supernatants produced from aerobic but not anaerobic cultures of L. acidophilus reduced the growth of Escherichia coli by about 20 %. Thus, bLf displayed a dose-dependent inhibitory effect on the growth of most probiotic strains under either aerobic or anaerobic conditions. An antibacterial supernatant prepared from the aerobic cultures may have significant practical use.     

Sayl andghayl: The ecology of water allocation in Yemen

In this article, comparison is made between the two major types of water allocation systems in Yemen: seasonal flood (sayl)and highland spring flow (ghayl).Constraints in the nature of water as a flowing resource are defined for each system. The major distinctions between the two types of systems are variability in water flow (which influences the determination of access rights), techniques of water control, measurement of water turns, the need for supervision of irrigation activities, and the potential for economic expansion of the production system. It is argued that tribal political organization is an adaptive response to highland spring flow allocation in Yemen, but undergoes stress in coastal flood systems where competition for the same water source extends across tribal boundaries in upstream-downstream conflict.