Transforming growth factor β2 is negatively regulated by endogenous retinoic acid during early heart morphogenesis

Vitamin A‐deficient (VAD) quail embryos lack the vitamin A‐active form, retinoic acid (RA) and are characterized by a phenotype that includes a grossly abnormal cardiovascular system that can be rescued by RA. Here we report that the transforming growth factor, TGFβ2 is involved in RA‐regulated cardiovascular development. In VAD embryos TGFβ2 mRNA and protein expression are greatly elevated. The expression of TGFβ receptor II is also elevated in VAD embryos but is normalized by treatment with TGFβ2‐specific antisense oligonucleotides (AS). Administration of this AS or an antibody specific for TGFβ2 to VAD embryos normalizes posterior heart development and vascularization, while the administration of exogenous active TGFβ2 protein to normal quail embryos mimics the excessive TGFβ2 status of VAD embryos and induces VAD cardiovascular phenotype. In VAD embryos pSmad2/3 and pErk1 are not activated, while pErk2 and pcRaf are elevated and pSmad1/5/8 is diminished. We conclude that in the early avian embryo TGFβ2 has a major role in the retinoic acid‐regulated posterior heart morphogenesis for which it does not use Smad2/3 pathways, but may use other signaling pathways. Importantly, we conclude that retinoic acid is a critical negative physiological regulator of the magnitude of TGFβ2 signals during vertebrate heart formation.     

HLA Class-II Associated HIV Polymorphisms Predict Escape from CD4+ T Cell Responses

Antiretroviral therapy, antibody and CD8⁺ T cell-mediated responses targeting human immunodeficiency virus-1 (HIV-1) exert selection pressure on the virus necessitating escape; however, the ability of CD4⁺ T cells to exert selective pressure remains unclear. Using a computational approach on HIV gag/pol/nef sequences and HLA-II allelic data, we identified 29 HLA-II associated HIV sequence polymorphisms or adaptations (HLA-AP) in an African cohort of chronically HIV-infected individuals. Epitopes encompassing the predicted adaptation (AE) or its non-adapted (NAE) version were evaluated for immunogenicity. Using a CD8-depleted IFN-γ ELISpot assay, we determined that the magnitude of CD4⁺ T cell responses to the predicted epitopes in controllers was higher compared to non-controllers (p<0.0001). However, regardless of the group, the magnitude of responses to AE was lower as compared to NAE (p<0.0001). CD4⁺ T cell responses in patients with acute HIV infection (AHI) demonstrated poor immunogenicity towards AE as compared to NAE encoded by their transmitted founder virus. Longitudinal data in AHI off antiretroviral therapy demonstrated sequence changes that were biologically confirmed to represent CD4⁺ escape mutations. These data demonstrate an innovative application of HLA-associated polymorphisms to identify biologically relevant CD4⁺ epitopes and suggests CD4⁺ T cells are active participants in driving HIV evolution.     

Receptor binding of NBD-labeled fluorescent estrogens and progestins in whole cells and cell-free preparations

We have studied the interactions of four fluorescent steroid conjugates with either the estrogen or progesterone receptor, both in whole cells and cell-free receptor preparations. The fluorophore, nitrobenzoxadiazole (NBD), was conjugated with a synthetic progestin, with a steroidal estrogen, a non-steroidal estrogen, and with an antiestrogen. With all compounds, receptor-specific binding could be detected by fluorescence measurements following extraction from the protein into an organic solvent. In the native state, however, the NBD-ligand-receptor complex is essentially non-emissive, although these ligands fluoresce strongly when associated with non-specific binders such as albumin. The binding site concentrations and relative affinities determined by fluorescence (after extraction) correspond well with those determined by [3H]estradiol or [3H]R5020 binding to their respective receptors. In T47D breast cancer cells, the NBD-progestin showed receptor-mediated uptake and nuclear localization. These compounds have provided valuable information about the interactions of low and medium affinity ligands with their receptors; however, the successful use of fluorescent ligands for detecting steroid receptors under native-bound conditions, by "imaging" modalities (fluorescence microscopy and flow cytometry) will require the development of fluorophores that are emissive while receptor bound or assay protocols that enable the environment of ligands associated with the receptor to be controlled.     

Adaptive immune defects and delayed rejection of allogeneic tumor cells in beige mice

The effect of the beige (bg) mutation on adaptive allogeneic tumor rejection was examined by monitoring tumor cell survival in vivo using [131I]iododeoxyuridine-prelabeled cells. Accelerated elimination of allogeneic tumor cells normally begins 8 days after ip injection and is due to active immune responses. Two independent mutations to beige on two different inbred backgrounds (C57BL/6J bgJ and DBA/2JCo bg8J) were tested, and bg/bg mice showed a 1-day delay in immune elimination of allogeneic cells. This delayed rejection was not due to a defect in clearing label from dead cells, nor to an inability to effect antibody-induced killing in vivo. Both humoral and cell-mediated responses against the allogeneic tumor cells were significantly lower in bg/bg than in +/bg mice.     

Copper and Zinc Nutritional Issues for Agricultural Animal Production

Livestock have presented unique requirements and toxicity issues depending on the species for the various concentrations of Cu and Zn and their interactions with other nutrients especially Fe, Se, Mo, and S. Soil concentrations of these elements and their availability to crops influence the health of the crop and the amount found in vegetative tissues and seeds. Hence, many livestock issues are a result of the soils in the area where production is occurring (Loneragan et al. 1981). While water can provide minerals to animals, the amount consumed and availability are highly variable. Many discoveries about Cu were a result of low Cu concentrations and its availability due to interactions with other nutrients in the soils. Anemia, bone disorders, cardiovascular abnormalities, defective wool and hair, and infertility are signs/symptoms of Cu deficiency. Toxicity due to excess Cu is more likely to occur in sheep than other farm species. Swine are tolerant of high concentrations of dietary Cu, and it is often used as a growth stimulant in production. There are many species and physiological stages where the animal’s Cu requirement is not known. Grazing animals can exhibit Zn deficiency when soils and forages contain limited concentrations of Zn. Pastures have been observed to be Zn-deficient in many parts of the world. However, non-ruminant animals usually receive adequate Zn when fed corn and soybean meal diets if there is not excessive Ca and Fe in their diets, but this is not true for rapidly growing young animals. Characteristics of a Zn deficiency include loss of appetite, reduced growth and reproduction, and impaired health of bone and skin tissues.

     

Autophosphorylation of the alpha subunit of phosphorylase kinase from rabbit skeletal muscle

The autophosphorylation of the alpha subunit of phosphorylase kinase occurs simultaneously at multiple sites during incorporation of the first mol of phosphate. The predominant and initial autophosphorylation site on this subunit is different than the major site phosphorylated by cAMP-dependent protein kinase, which also phosphorylates multiple sites, as evidenced by two-dimensional phosphopeptide maps. All of the sites on the alpha subunit phosphorylated by cAMP-dependent protein kinase comigrate on peptide maps with autophosphorylation phosphopeptides; however, several phosphopeptides observed after autophosphorylation are not evident following phosphorylation by cAMP-dependent protein kinase. The phosphopeptide maps of the alpha subunit are the same whether autophosphorylation is carried out at pH 6.8 or 8.2 or whether MnATP is used instead of MgATP; there is only a slight difference in the maps brought about by EGTA-insensitive autophosphorylation. The autophosphorylation is shown to be an intrinsic activity of the phosphorylase kinase molecule; this conclusion is based on the observed copurification of the autophosphorylation activity with activities toward phosphorylase b and kappa-casein and the unaltered influence of various effectors on these activities throughout different sequential adsorption chromatography purification steps. Additional support to that already in the literature that the initial autophosphorylation events are predominantly intramolecular is gained by showing that previously autophosphorylated enzyme has little ability to catalyze the phosphorylation of nonphosphorylated enzyme.     

Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence

Background

The Drosophila melanogaster genome was the first metazoan genome to have been sequenced by the whole-genome shotgun (WGS) method. Two issues relating to this achievement were widely debated in the genomics community: how correct is the sequence with respect to base-pair (bp) accuracy and frequency of assembly errors? And, how difficult is it to bring a WGS sequence to the accepted standard for finished sequence? We are now in a position to answer these questions.

Results

Our finishing process was designed to close gaps, improve sequence quality and validate the assembly. Sequence traces derived from the WGS and draft sequencing of individual bacterial artificial chromosomes (BACs) were assembled into BAC-sized segments. These segments were brought to high quality, and then joined to constitute the sequence of each chromosome arm. Overall assembly was verified by comparison to a physical map of fingerprinted BAC clones. In the current version of the 116.9 Mb euchromatic genome, called Release 3, the six euchromatic chromosome arms are represented by 13 scaffolds with a total of 37 sequence gaps. We compared Release 3 to Release 2; in autosomal regions of unique sequence, the error rate of Release 2 was one in 20,000 bp.

Conclusions

The WGS strategy can efficiently produce a high-quality sequence of a metazoan genome while generating the reagents required for sequence finishing. However, the initial method of repeat assembly was flawed. The sequence we report here, Release 3, is a reliable resource for molecular genetic experimentation and computational analysis.     

Analog of vertebrate anionic sites in blood-brain interface of larval Drosophila

The blood-brain barrier ensures brain function in vertebrates and in some invertebrates by maintaining ionic integrity of the extraneuronal bathing fluid. Recent studies have demonstrated that anionic sites on the luminal surface of vascular endothelial cells collaborate with tight junctions to effect this barrier in vertebrates. We characterize these two analogous barrier factors for the first time on Drosophila larva by an electron-dense tracer and cationic gold labeling. Ionic lanthanum entered into but not through the extracellular channels between perineurial cells. Tracer is ultimately excluded from neurons in the ventral ganglion mainly by an extensive series of (pleated sheet) septate junctions between perineurial cells. Continuous junctions, a variant of the septate junction, were not as efficient as the pleated sheet variety in blocking tracer. An anionic domain now is demonstrated in Drosophila central nervous system through the use of cationic colloidal gold in LR White embedment. Anionic domains are specifically stationed in the neural lamella and not noted in the other cell levels of the blood-brain interface. It is proposed that in the central nervous system of the Drosophila larva the array of septate junctions between perineurial cells is the physical barrier, while the anionic domains in neural lamella are a charge-selective barrier for cations. All of these results are discussed relative to analogous characteristics of the vertebrate blood-brain barrier.     

Plants versus animals: do they deal with stress in different ways?

Both plants and animals respond to stress by using adaptationsthat help them evade, tolerate, or recover from stress. In asynthetic paper A. D. Bradshaw (1972) noted that basic biologicaldifferences between plants and animals will have diverse evolutionaryconsequences, including those influencing how they deal withstress. For instance, Bradshaw argued that animals, becausethey have relatively well-developed sensory and locomotor capacities,can often use behavior and movement to evade or ameliorate environmentalstresses. In contrast, he predicted that plants will have toemphasize increased physiological tolerance or phenotypic plasticity,and also that plants should suffer stronger selection and showmore marked differentiation along environmental gradients. Herewe briefly review the importance of behavior in mitigating stress,the behavioral capacities of animals and plants, and examplesof plant responses that are functionally similar to behaviorsof animals. Next, we try to test some of Bradshaw's predictions.Unfortunately, critical data often proved non-comparable: plantand animal biologists often study different stressors (e.g.,water versus heat) and measure different traits (photosynthesisversus locomotion). Nevertheless, we were able to test someof Bradshaw's predictions and some related ones of our own.As Bradshaw predicted, the phenology of plants is more responsiveto climate shifts than is that of animals and the micro-distributionsof non-mobile, intertidal invertebrates ("plant" equivalents)are more sensitive to temperature than are those of mobile invertebrates.However, mortality selection is actually weaker for plants thanfor animals. We hope that our review not only redraws attentionto some fascinating issues Bradshaw raised, but also encouragesadditional tests of his predictions. Such tests should be informative.