Multi‐gene phylogenetic analyses of New Zealand coralline algae: Corallinapetra Novaezelandiae gen. et sp. nov. and recognition of the Hapalidiales ord. nov.

Coralline red algae from the New Zealand region were investigated in a study focused on documenting regional diversity. We present a multi‐gene analysis using sequence data obtained for four genes (nSSU, psaA, psbA, rbcL) from 68 samples. The study revealed cryptic diversity at both genus and species levels, confirming and providing further evidence of problems with current taxonomic concepts in the Corallinophycidae. In addition, a new genus Corallinapetra novaezelandiae gen. et sp. nov. is erected for material from northern New Zealand. Corallinapetra is excluded from all currently recognized families and orders within the Corallinophycidae and thus represents a previously unrecognized lineage within this subclass. We discuss rank in the Corallinophycidae and propose the order Hapalidiales.     

Using dive behavior and active acoustics to assess prey use and partitioning by fin and humpback whales near Kodiak Island,Alaska

Near the Kodiak Archipelago, fin (Balaenoptera physalus) and humpback (Megaptera novaeangliae) whales frequently overlap spatially and temporally. The Gulf Apex Predator‐prey study (GAP) investigated the prey use and potential prey partitioning between these sympatric species by combining concurrent analysis of vertical whale distribution with acoustic assessment of pelagic prey. Acoustic backscatter was classified as consistent with either fish or zooplankton. Whale dive depths were determined through suction cup tags. Tagged humpback whales (n = 10) were most often associated with distribution of fish, except when zooplankton density was very high. Associations between the dive depths of tagged fin whales (n = 4) and the vertical distribution of either prey type were less conclusive. However, prey assessment methods did not adequately describe the distribution of copepods, a potentially significant resource for fin whales. Mean dive parameters showed no significant difference between species when compared across all surveys. However, fin whales spent a greater proportion of dive time in the foraging phase than humpbacks, suggesting a possible difference in foraging efficiency between the two. These results suggest that humpback and fin whales may target different prey, with the greatest potential for diet overlap occurring when the density of zooplankton is very high.     

Techno-economics of integrating bioethanol production from spent sulfite liquor for reduction of greenhouse gas emissions from sulfite pulping mills

Background

Flow sheet options for integrating ethanol production from spent sulfite liquor (SSL) into the acid-based sulfite pulping process at the Sappi Saiccor mill (Umkomaas, South Africa) were investigated, including options for generation of thermal and electrical energy from onsite bio-wastes, such as bark. Processes were simulated with Aspen Plus® for mass- and energy-balances, followed by an estimation of the economic viability and environmental impacts. Various concentration levels of the total dissolved solids in magnesium oxide-based SSL, which currently fuels a recovery boiler, prior to fermentation was considered, together with return of the fermentation residues (distillation bottoms) to the recovery boiler after ethanol separation. The generation of renewable thermal and electrical energy from onsite bio-wastes were also included in the energy balance of the combined pulping-ethanol process, in order to partially replace coal consumption. The bio-energy supplementations included the combustion of bark for heat and electricity generation and the bio-digestion of the calcium oxide SSL to produce methane as additional energy source.

Results

Ethanol production from SSL at the highest substrate concentration was the most economically feasible when coal was used for process energy. However this solution did not provide any savings in greenhouse gas (GHG) emissions for the concentration-fermentation-distillation process. Maximizing the use of renewable energy sources to partially replace coal consumption yielded a satisfactory economic performance, with a minimum ethanol selling price of 0.83 US$/l , and a drastic reduction in the overall greenhouse gas emissions for the entire facility.

Conclusion

High substrate concentrations and conventional distillation should be used when considering integrating ethanol production at sulfite pulping mills. Bio-wastes generated onsite should be utilized at their maximum potential for energy generation in order to maximize the GHG emissions reduction.

     

Further investigation of simian immunodeficiency virus Vif function in human cells

Primate lentivirus Vif proteins function by suppressing the antiviral activity of the cell-encoded apolipoprotein B mRNA-editing enzyme-catalytic polypeptide-like (APOBEC) proteins APOBEC3G and APOBEC3F. It has been hypothesized that species-specific susceptibilities of APOBEC proteins to Vif proteins may help govern the transmission of primate lentiviruses to new host species. Consistent with this view and with previous results, we report that the Vif proteins of several diverse simian immunodeficiency viruses (SIVs) that are not known to infect humans are not effective inhibitors of human APOBEC3G or APOBEC3F when assessed in transient-transfection experiments. Unexpectedly, this lack of SIV Vif function did not prevent the replication of two vif-deficient SIVs (SIVtan and SIVmnd1; isolated from tantalus monkeys and mandrills, respectively) in a human T-cell line, HUT78, that expresses both APOBEC 3G and APOBEC3F, a finding which demonstrates that some SIVs are partially resistant to the antiretroviral effects of these enzymes irrespective of Vif function. Additional virus replication studies also revealed that the Vif protein of SIVtan is, in fact, active in human T cells, as it substantially enhanced the replication of its cognate virus and human immunodeficiency virus type 1. In sum, we now consider it improbable that species-specific restrictions to SIV Vif function can explain the lack of human infection with certain SIVs. Instead, our data reveal that the species-specific modulation of Vif function is more complex than previously envisioned and that additional (as-yet-unidentified) viral or host factors may be involved in regulating this dynamic interaction between host and pathogen.     

Genetic diversity of Typha latifolia (Typhaceae) and the impact of pollutants examined with tandem-repetitive DNA probes

Genetic diversity at variable-number-tandem-repeat (VNTR) loci was examined in the common cattail, Typha latifolia (Typhaceae), using three synthetic DNA probes composed of tandemly repeated “core” sequences (GACA, GATA, and GCAC). The principal objectives of this investigation were to determine whether: (1) the previously reported almost complete lack of polymorphism at allozyme loci in this species was indicative of a reduced amount of genetic diversity at VNTR loci as well; (2) VNTR markers were informative about possible clonal propagation; and (3) significant differences in genetic structure of sampling sites were associated with differences in environmental levels of pollutants at those sites. Previously, widespread sampling across the eastern United States, surveying across ten allozyme loci, has detected only two genotypes, involving a difference at a single locus, among 104 populations. In this study, the amount of genetic diversity detected at VNTR loci: (1) among ramets (N = 40; 40 genotypes detected) collected at ∼8-km intervals along a 320-km transect; (2) among ramets (N = 220; 117 genotypes detected) from five study sites separated by 50–3000 m; and (3) even among ramets within each study site [N = 44 per site; from 13 to 34 genotypes detected per site (270 m²)] exceeds that previously found in those more geographically widespread allozyme surveys. Among the 260 ramets analyzed here, the mean number of bands scored per individual was 48.61 (SD = 2.80). Mean genetic similarity among ramets collected along the 320-km transect was 0.91, which was within the range of mean genetic similarity within the five study sites (range: 0.89–0.95). Among the five study sites, 61% of the samples analyzed appeared to be clonal ramets, with up to 12 clones detected for 44 ramets sampled within a site. Clones grew intermingled and ranged up to 39 m in extent. Permutation tests of genetic similarity revealed significant genetic differentiation between each of the five study sites. Consistent with the previous allozyme studies, T. latifolia was characterized by extremely low genetic variation relative to levels of polymorphism detected at VNTR loci in other plant species. Estimated heterozygosity among ramets along the 320-km transect ranged from 0.11 to 0.13, while that within the five study sites ranged from 0.05 to 0.12. Estimates of F_st (0.32–0.41) also indicated considerable genetic subdivision among these stands. Significantly higher genetic diversity was detected at the two study sites that chemistry and toxicity data indicate to be the most severely impacted by pollutants. Although this correlation does not establish cause and effect, the results of this study indicate that the analysis of genetic diversity at VNTR loci may be a useful tool for monitoring anthropogenic-induced changes in the genetic structure of natural populations of plants.     

The universal design, operation and maintenance guidelines for farm constructed wetlands (FCW) in temperate climates

This paper comprises the scientific justification for the Farm Constructed Wetland (FCW) Design Manual for Northern Ireland and Scotland. Moreover, this document addresses an international audience interested in applying wetland systems in the wider agricultural context. Farm constructed wetlands combine farm wastewater (predominantly farmyard runoff) treatment with landscape and biodiversity enhancements, and are a specific application and class of integrated constructed wetlands (ICW), which have wider applications in the treatment of other wastewater types such as domestic sewage. The aim of this review paper is to propose guidelines highlighting the rationale for FCW, including key water quality management and regulatory issues, important physical and biochemical wetland treatment processes, assessment techniques for characterizing potential FCW sites and discharge options to water bodies. The paper discusses universal design, construction, planting, maintenance and operation issues relevant specifically for FCW in a temperate climate, but highlights also catchment-specific requirements to protect the environment.     

Buffering an Acidic Stream in New Hampshire with a Silicate Mineral

Ground and pelletized Wollastonite (Wo; CaSiO₃) was added to a 50‐m reach of an anthropogenically acidified stream within the Hubbard Brook Experimental Forest, New Hampshire, to evaluate its buffering and restoration potential. The Wo was highly effective in raising the pH, acid‐neutralizing capacity (ANC), dissolved inorganic carbon (DIC), and Ca²⁺ concentrations of the stream water, but during the short duration of the experiment had no discernable effect on the stream biota. After initial, spike‐like fluctuations in pH and concentrations of ANC, DIC, and Ca²⁺, the relatively slow dissolution rates of the Wo dampened extreme concentrations and contributed to relatively long‐lasting (4 months) amelioration of streamwater acidity. Changes in concentrations of Ca²⁺, dissolved Si, ANC, and DIC were inversely related to streamflow. After several high, stream‐discharge events, concentrations quickly and consistently returned to pre‐event conditions.     

The digestive gland of the Southern Dumpling Squid (Euprymna tasmanica): structure and function

The cephalopod digestive gland plays an important role in the efficient assimilation of nutrients and therefore the fast growth of the animal. The histological and enzymatic structure of Euprymna tasmanica was studied and used in this experiment to determine the dynamics of the gland in response to feeding. The major roles of the digestive gland were secretion of digestive enzymes in spherical inclusions (boules) and excretion of metabolic wastes in brown body vacuoles. High levels of trypsin, chymotrypsin and α-amylase, low levels of α-glucosidase and negligible carboxypeptidase activity were produced by the gland. There was no evidence of secretion of digestive enzymes in other organs of the digestive tract. Within 60 min of a feeding event, the gland produced increasing numbers of boules to replace those lost from the stomach during the feeding event. Initially, small boules were seen in the digestive cells, they increased in size until they are released into the lumen of the gland where they are transported to the stomach. There was no evidence of an increase in activity of digestive enzymes following a feeding event, despite structural changes in the gland. However, there was large variation among individuals in the level of digestive enzyme activity. A negative correlation between boule and brown body vacuole density suggested that the large variation in enzyme activity may be due to the digestive gland alternating between enzyme production and excretion.     

Are European starlings breeding in the Azores archipelago genetically distinct from birds breeding in mainland Europe?

The European starling (Sturnus vulgaris) has recently been found to eat eggs of the endangered roseate tern (Sterna dougallii) in the Azores. Azorean starlings are considered an endemic subspecies (S. vulgaris granti), so we investigated how much genetic divergence has accumulated between the Azores and other European populations in order to assess whether lethal control measures might be possible, as previous experiments have found that taste aversion is not likely to be successful. For this purpose, we sequenced a region of the protein-coding mitochondrial gene ND2 for samples from six different populations. Of the 1,026 base pairs sequenced, 19 (1.7%) were variable and formed 15 different haplotypes. The Azores had high and significant genetic differentiation from all the other populations studied. Haplotype diversity was high in the mainland populations studied, ranging from 0.767 to 0.900, but there was no variation among the Azores samples, which were collected from a geographically broad region. Given the lack of genetic variability in the Azores birds and their abundance throughout the archipelago, lethal control on a local basis and as part of an integrated control plan can be seen as a reasonable measure to protect tern colonies.     

Decline of FoxP3+ Regulatory CD4 T Cells in Peripheral Blood of Children Heavily Exposed to Malaria

FoxP3+ regulatory CD4 T cells (T_regs) help to maintain the delicate balance between pathogen-specific immunity and immune-mediated pathology. Prior studies suggest that T_regs are induced by P. falciparum both in vivo and in vitro; however, the factors influencing T_reg homeostasis during acute and chronic infections, and their role in malaria immunopathogenesis, remain unclear. We assessed the frequency and phenotype of T_regs in well-characterized cohorts of children residing in a region of high malaria endemicity in Uganda. We found that both the frequency and absolute numbers of FoxP3+ T_regs in peripheral blood declined markedly with increasing prior malaria incidence. Longitudinal measurements confirmed that this decline occurred only among highly malaria-exposed children. The decline of T_regs from peripheral blood was accompanied by reduced in vitro induction of T_regs by parasite antigen and decreased expression of TNFR2 on T_regs among children who had intense prior exposure to malaria. While T_reg frequencies were not associated with protection from malaria, there was a trend toward reduced risk of symptomatic malaria once infected with P. falciparum among children with lower T_reg frequencies. These data demonstrate that chronic malaria exposure results in altered T_reg homeostasis, which may impact the development of antimalarial immunity in naturally exposed populations.