Characterization of T-DNA insertion sites in Arabidopsis thaliana and the implications for saturation mutagenesis

A key component of a sound functional genomics infrastructure is the availability of a knockout mutant for every gene in the genome. A fruitful approach to systematically knockingout genes in the plant Arabidopsis thaliana has been the use of transferred-DNA (T-DNA) from Agrobacterium tumefaciens as an insertional mutagen. One of the assumptions underlying the use of T-DNA as a mutagen is that the insertion of these DNA elements into the Arabidopsis genome occurs at randomly selected locations. We have directly investigated the distribution of T-DNA insertions sites in populations of transformed Arabidopsis using two different approaches. To begin with, we utilized a polymerase chain reaction (PCR) procedure to systematically catalog the precise locations of all the T-DNA elements inserted within a 65 kb segment of chromosome IV. Of the 47 T-DNA insertions identified, 30% were found within the coding regions of genes. We also documented the insertion of T-DNA elements within the centromeric region of chromosome IV. In addition to these targeted T-DNA screens, we also mapped the genomic locations of 583 randomly chosen T-DNA elements by sequencing the genomic DNA flanking the insertion sites from individual T-DNA-transformed lines. 35% of these randomly chosen T-DNA insertions were located within the coding regions of genes. For comparison, coding sequences account for 44% of the Arabidopsis genome. Our results demonstrate that there is a small bias towards recovering T-DNA insertions within intergenic regions. However, this bias does not limit the utility of T-DNA as an effective insertional mutagen for use in reverse-genetic strategies.     

Excess biglycan causes eyelid malformation by perturbing muscle development and TGF-alpha signaling

Tissue morphogenesis during development is regulated by growth factors and cytokines, and is characterized by constant remodeling of extracellular matrix (ECM) in response to signaling molecules, for example, growth factors, cytokines, and so forth. Proteoglycans that bind growth factors are potential regulators of tissue morphogenesis during embryonic development. In this study, we showed that transgenic mice overexpressing biglycan under the keratocan promoter exhibited exposure keratitis and premature eye opening from noninfectious eyelid ulceration due to perturbation of eyelid muscle formation and the failure of meibomian gland formation. In addition, in vitro analysis revealed that biglycan binds to TGF-alpha, thus interrupting EGFR signaling pathways essential for mesenchymal cell migration induced by eyelid epithelium. The defects of TGF-alpha signaling by excess biglycan were further augmented by the interruption of the autocrine or paracrine loop of the EGFR signaling pathway of HB-EGF expression elicited by TGF-alpha. These results are consistent with the notion that under physiological conditions, biglycan secreted by mesenchymal cells serves as a regulatory molecule for the formation of a TGF-alpha gradient serving as a morphogen of eyelid morphogenesis.     

Metmyoglobin promotes arachidonic acid peroxidation at acid pH

The ability of metmyoglobin and other heme proteins to promote peroxidation of arachidonic acid under acidic conditions was investigated. Incubation of metmyoglobin with arachidonic acid resulted in a pH-dependent increase in lipid peroxidation as measured by the formation of thiobarbituric acid reactive products and oxygen consumption. Increased peroxidation was observed at pH levels below 6.0, reaching a plateau between pH 5.5 and 5.0. At comparable heme concentrations, metmyoglobin was more efficient than oxymyoglobin, methemoglobin, or ferricytochrome c in promoting arachidonic acid peroxidation. Metmyoglobin also promoted peroxidation of 1-palmityl-2-arachidonyl phosphatidylcholine and methylarachidonate but at significantly lower rates than arachidonic acid. Addition of fatty acid-free albumin inhibited arachidonic acid peroxidation in a molar ratio of 6 to 1 (arachidonic acid:albumin). Both ionic and non-ionic detergents inhibited metmyoglobin-dependent arachidonic acid peroxidation under acidic conditions. The anti-oxidants butylated hydroxytoluene and nordihydroguaiaretic acid and low molecular weight compounds with reduced sulfhydryl groups inhibited the reaction. However, mannitol, benzoic acid, and deferoxamine were without significant effect. Visible absorption spectra of metmyoglobin following reaction with arachidonic acid showed minimal changes consistent with a low level of degradation of the heme protein during the reaction. These observations support the hypothesis that metmyoglobin and other heme proteins can promote significant peroxidation of unsaturated fatty acids under conditions of mildly acidic pH such as may occur at sites of inflammation and during myocardial ischemia and reperfusion. This may be the result of enhanced aggregation of the fatty acid and/or interaction of the fatty acid with heme under acidic conditions.     

Corneal crystallins and the development of cellular transparency

Past studies have established that the cornea like the lens abundantly expresses a few water-soluble enzyme/proteins in a taxon specific fashion. Based on these similarities it has been proposed that the lens and the cornea form a structural unit, the 'refracton', that has co-evolved through gene sharing to maximize light transmission and refraction to the retina. Thus far, the analogy between corneal crystallins and lens crystallins has been limited to similarities in the abundant expression, with few reports concerning their structural function. This review covers recent studies that establish a clear relationship between expression of corneal crystallins and light scattering from corneal stromal cells, i.e. keratocytes, that support a structural role for corneal crystallins in the development of transparency similar to that of lens crystallins that would be consistent with the 'refracton' hypothesis.     

ALDH3A1 Plays a Functional Role in Maintenance of Corneal Epithelial Homeostasis

Aldehyde dehydrogenase 1A1 (ALDH1A1) and ALDH3A1 are corneal crystallins. They protect inner ocular tissues from ultraviolet radiation (UVR)-induced oxidative damage through catalytic and non-catalytic mechanisms. Additionally, ALDH3A1 has been postulated to play a regulatory role in the corneal epithelium based on several studies that report an inverse association between ALDH3A1 expression and corneal cell proliferation. The underlying molecular mechanisms and the physiological significance of such association remain poorly understood. In the current study, we established Tet-On human corneal epithelial cell (hTCEpi) lines, which express tetracycline-inducible wild-type (wt) or catalytically-inactive (mu) ALDH3A1. Utilizing this cellular model system, we confirmed that human ALDH3A1 decreases corneal cell proliferation; importantly, this effect appears to be partially mediated by its enzymatic activity. Mechanistically, wt-ALDH3A1, but not mu-ALDH3A1, promotes sequestering of tumor suppressor p53 in the nucleus. In the mouse cornea, however, augmented cell proliferation is noted only in Aldh1a1^-/-/3a1^-/- double knockout (DKO) mice, indicating in vivo the anti-proliferation effect of ALDH3A1 can be rescued by the presence of ALDH1A1. Interestingly, the hyper-proliferative epithelium of the DKO corneas display nearly complete loss of p53 expression, implying that p53 may be involved in ALDH3A1/1A1-mediated effect. In hTCEpi cells grown in high calcium concentration, mRNA levels of a panel of corneal differentiation markers were altered by ALDH3A1 expression and modulated by its enzyme activity. In conclusion, we show for the first time that: (i) ALDH3A1 decreases corneal epithelial proliferation through both non-enzymatic and enzymatic properties; (ii) ALDH1A1 contributes to the regulation of corneal cellular proliferation in vivo; and (iii) ALDH3A1 modulates corneal epithelial differentiation. Collectively, our studies indicate a functional role of ALDH3A1 in the maintenance of corneal epithelial homeostasis by simultaneously modulating proliferation and differentiation through both enzymatic and non-enzymatic mechanisms.     

The effect of a taurine-containing drink on performance in 10 endurance-athletes

Summary To determine the effect of a taurine-enriched drink Red Bull on performance, 10 endurance-athletes performed three trials. After 60 min. cycling at approximately 70% VO₂ max, the subjects pedalled to exhaustion on a cycle ergometer. During each exercise, the subjects received 500 ml of a test-drink after 30 min. submaximal cycling: Red Bull without taurine, without glucuronolacton (U1), Red Bull without taurine, without glucuronolacton, without caffeine (U2) and Red Bull original drink containing taurine, glucuronolacton and caffeine (U3).The heart rate level was significantly lower in U3 (p = 0,0031) 15 min. after application. The plasma catecholamines increased slightly from begin of exercise to 15 min. after application of the drinks in all trials but remained on a significantly lower level in U3 (epinephrine (p = 0,0011) and norepinephrine (p = 0,0003). Endurance time was significantly longer with Red Bull original in U3 (p = 0,015). The results of this study show a positive effect of a taurine-containing drink on hormonal responses which leads to a higher performance.     

The herpetofauna of Timor-Leste: a first report

Fieldwork conducted throughout Timor-Leste in September 2004 and July 2009 resulted in a collection or recording of 263 herpetological specimens (100 amphibians, 163 reptiles), comprising at least seven species of frogs and toads, 20 species of lizards, seven species of snakes, two species of turtles, and one species of crocodile. Among the amphibians, the most frequently encountered species were toads (Duttaphrynus melanostictus), rice paddy frogs (genus Fejervarya), and rhacophorid treefrogs (Polypedates cf. leucomystax). All three variants of rice paddy frogs encountered represent undescribed species similar to Fejervarya verruculosa from neighboring Wetar Island. Records of Fejervarya cancrivora and Fejervarya limnocharis for Timor Island are apparently errors based on misidentification. We obtained voucher specimens for a total of 147 lizards and voucher photographs only for four specimens of Varanus timorensis. Aside from geckos frequently associated with human habitations (e.g., Gehyra mutilata, Gekko gecko, Hemidactylus frenatus, Hemidactylus platyurus), we discovered an as yet undescribed species of bent-toed gecko, genus Cyrtodactylus, in the Same valley. Our specimens of Hemidactylus platyurus are the first record of this species from Timor-Leste. Commonly encountered skinks included four-fingered skinks (genus Carlia), wedge skinks (genus Sphenomorphus), and night skinks (genus Eremiascincus). Notable among the 15 snakes collected was the frequency of pitvipers (Cryptelytrops insularis), which amounted to over 25% of all snakes. Our specimen of the wolfsnake Lycodon subcinctus is the first record of this species for Timor-Leste. Based on these findings, it appears that the biodiversity of amphibians and reptiles in this remote corner of Wallacea is much greater than previously thought, particularly with respect to scincid lizards. The detail we provide in the species accounts is designed to allow the use of this report as a preliminary field guide to the amphibians and reptiles of Timor-Leste. However, survey work is ongoing.     

Using Vaccinia's innate ability to introduce DNA into mammalian cells for production of recombinant proteins

Production of recombinant protein in mammalian cells is time-consuming, labor-intensive and costly. While seeking to overcome these limitations, we discovered that Vaccinia virus has the innate ability to transfer exogenous plasmid DNA into mammalian cells during the infection process. Parameters influencing the efficiency of this event were characterized and a quick, simple and inexpensive way to produce eukaryotic proteins was established.