Altered telomeres in tumors with ATRX and DAXX mutations

The proteins encoded by ATRX and DAXX participate in chromatin remodeling at telomeres and other genomic sites. Because inactivating mutations of these genes are common in human pancreatic neuroendocrine tumors (PanNETs), we examined the telomere status of these tumors. We found that 61% of PanNETs displayed abnormal telomeres that are characteristic of a telomerase-independent telomere maintenance mechanism termed ALT (alternative lengthening of telomeres). All of the PanNETs exhibiting these abnormal telomeres had ATRX or DAXX mutations or loss of nuclear ATRX or DAXX protein. ATRX mutations also correlate with abnormal telomeres in tumors of the central nervous system. These data suggest that an alternative telomere maintenance function may operate in human tumors with alterations in the ATRX or DAXX genes.     

Mutations in CIC and FUBP1 contribute to human oligodendroglioma

Oligodendrogliomas are the second most common malignant brain tumor in adults and exhibit characteristic losses of chromosomes 1p and 19q. To identify the molecular genetic basis for this alteration, we performed exomic sequencing of seven tumors. Among other changes, we found that the CIC gene (homolog of the Drosophila gene capicua) on chromosome 19q was somatically mutated in six cases and that the FUBP1 gene [encoding far-upstream element (FUSE) binding protein] on chromosome 1p was somatically mutated in two tumors. Examination of 27 additional oligodendrogliomas revealed 12 and 3 more tumors with mutations of CIC and FUBP1, respectively, 58% of which were predicted to result in truncations of the encoded proteins. These results suggest a critical role for these genes in the biology and pathology of oligodendrocytes.     

A description of the growth and moulting of feathers in commercial broilers

ABSTRACT

1. Changes in feather length and weight and daily losses of down, contour feathers, remiges and retrices were studied in two commercial broiler strains to determine feather growth and moult in broilers up to 112 d of age.

2. Ten pens of 20 chicks for each sex x strain were fed adequate amounts of dietary protein in a four-phase feeding programme. Ten birds were sampled per genotype at 14, 28, 42, 56, 70, 84, 98 and 112 d. Feather loss was determined for individual birds caged within a nylon net.

3. All feathers were dry-plucked from each of seven tracts, with representative feathers from the capital-cervical, dorsopelvic and interscapular, pectoral and femoral tracts being randomly selected. Three rectrices of the dorsocaudal tract and three primaries and secondaries of the humeral-alar tract of the right wing were evaluated.

4. The length of the selected feathers was measured, and the feathers from each tract and from the whole bird were weighed.

5. A wide range of rates of maturing (0.0250–0.0907/d) and mature weights (9.62–52.9 g) were evident between sampled tracts.

6. Feather weight failed to predict some moults which were detected by the measurement of feather losses. From the weight data, moulting was evident only in the humeral-alar and dorsocaudal tracts, whereas, when daily losses were measured, contour feathers accounted for over 0.7 proportion of feather losses. Logistic equations adequately described the cumulative losses of down, contour feathers and remiges.

7. Feather loss needs to be considered when feather growth is determined from feather weight at different ages.

8. The rate of maturing (B) of feathers was numerically higher in Ross males and females than in the Cobb strain. In females, B was higher than in males (0.0483 vs. 0335/d) but the mature weight was lower (162 vs. 230 g).     

Threshold change in forest understory vegetation as a result of selective fuelwood extraction in Nairobi, Kenya

We examined whether heavy fuelwood collection can cause threshold change in understory forest community and evaluated how selective wood extraction might lead to delayed forest recovery in an urban forest of Nairobi, Kenya. Piecewise regression which represents strongest support for threshold change provided the best fit for the relationships between understory floristic composition (i.e. DCA axis 1) and human disturbance gradients (i.e. canopy cover, and distance from the slum), where threshold changes were detected at c.a. 350 m from the slum and c.a. 30% canopy cover. Only one tree species significantly indicated communities beyond the threshold while an aggressive invasive alien plant (IAP) Lantana camara was strongly represented. Total species diversity along the two human disturbance gradients peaked before the threshold was reached, suggesting that decline in species diversity along the prevailing disturbance gradient might be able to forecast threshold change. Tree species richness in the understory rapidly declined as the threshold was surpassed while other growth forms (i.e. shrubs, herbs and climbers) were relatively unaffected. The effect of selective tree cutting was indirectly impacting the forest understory as species richness pattern of preferred and non-preferred species paralleled that of trees and shrubs, respectively. Thickets of L. camara can negatively affect indigenous flora and its establishment was favored under selective fuelwood extraction removing certain tree species while leaving the IAP untouched. Shading can readily eliminate the IAP, but weak tree regeneration beyond the threshold suggested forest recovery might be delayed for longer than expected because of the interaction between selective fuelwood use and the IAP.     

Can stumps tell what people want: Pattern and preference of informal wood extraction in an urban forest of Nairobi, Kenya

Detailed patterns and preferences of informal wood extraction were investigated in an urban forest used by slum inhabitants of Nairobi, Kenya, as such information determines the sustainability of resource use. Instead of asking the people what they had secretly cut, a survey was conducted of the stumps and trees left in the forest to (i) evaluate how accessibility and patrolling affected spatial patterns of resource use, and to (ii) estimate a broad spectrum of species and species-specific size preferences. Both probability and size of cutting increased with better accessibility (represented by distance from the slum), and stump size exceeded that of living stem size around 1.7 km from the slum, which suggested magnified impact of tree cutting near the slum. Patrolling (represented by distance from ranger stations) had little effect in reducing the probability of cutting but was effective in reducing cut size. With the use of random effect models, a broad species preference spectrum (including less abundant and non-preferred species) was estimated, which indicated trends in vegetation change. Smaller stems were preferred for most species presumably used for domestic fuelwood, but major exploitation of large Brachylaena huillensis stems traded in the woodcarving industry was also revealed. Such detailed information on informal wood use can help forest managers to understand threats to the forests as well as the needs of local communities. This is a first step to redefining ‘acceptable’ resource use by the local community for their increased role and responsibility in sustainable forest management, especially when conventional controls of informal activities (i.e. exclusion and penalty) are not functioning well.     

Signature-tagged mutagenesis of Vibrio vulnificus

Vibrio vulnificus is the causative agent of primary septicemia, wound infection and gastroenteritis in immunocompromised people. In this study, signature-tagged mutagenesis (STM) was applied to identify the virulence genes of V. vulnificus. Using STM, 6,480 mutants in total were constructed and divided into 81 sets (INPUT pools); each mutant in a set was assigned a different tag. Each INPUT pool was intraperitoneally injected into iron-overloaded mice, and in vivo surviving mutants were collected from blood samples from the heart (OUTPUT pools). From the genomic DNA of mixed INPUT or OUTPUT pools, digoxigenin-labeled DNA probes against the tagged region were prepared and used for dot hybridization. Thirty tentatively attenuated mutants, which were hybridized clearly with INPUT probes but barely with OUTPUT probes, were negatively selected. Lethal doses of 11 of the 30 mutants were reduced to more than 1/100; of these, the lethal doses of 2 were reduced to as low as 1/100,000. Transposon-inserted genes in the 11 attenuated mutants were those for IMP dehydrogenase, UDP-N-acetylglucosamine-2-epimerase, aspartokinase, phosphoribosylformylglycinamidine cyclo-ligase, malate Na (+) symporter and hypothetical protein. When mice were immunized with an attenuated mutant strain into which IMP dehydrogenase had been inserted with a transposon, they were protected against V. vulnificus infection. In this study, we demonstrated that the STM method can be used to search for the virulence genes of V. vulnificus.     

Manufacture of Biquara (Haemulon Plumierii - Lacepède, 1801) Fishburger with Addition of Wheat Bran

Biquara is one of the main fish species caught in the northeast coast of Brazil but presents low commercial value. Therefore, the elaboration of biquara-based products with the addition of plant bran as a source of dietary fiber should be studied as a way to add value to biquara. The objective of the present study was to evaluate the physicochemical, microbiological, and sensory aspects of fishburgers made with biquara fillet with the addition of wheat bran (WB) (0, 1, 2, and 3%). The increase in WB decreased moisture and increased protein levels, ash, fiber, carbohydrates, and energy value. In addition, the inclusion of WB increased the cooking shrinkage and decreased hardness and cohesiveness of the samples. The fishburgers with the greatest WB levels presented a reddish-yellow hue. The microbial counts of the products were below the maximum limit allowed by the Brazilian legislation. The overall acceptance of the fishburgers improved with the addition of 0 to 2% WB. Therefore, the biquara fillets have a potential for the elaboration of fishburgers with the addition of 2% WB, once the products presented suitable physicochemical composition, sensory acceptance, and hygienic sanitary control according to the current national legislation.     

Cetacean Toll-like receptor 4 and myeloid differentiation factor 2, and possible cetacean-specific responses against Gram-negative bacteria

Toll-like receptor 4 (TLR4) and myeloid differentiation factor 2 (MD-2) are essential for recognizing the lipopolysaccharides (LPS) of Gram-negative bacteria. We determined the sequences of cDNAs encoding TLR4 and MD-2 from cetaceans and generated three-dimensional (3D) models for a better understanding of their modes of interaction and LPS recognition. The 3D reconstructions showed that cetacean TLR4 and MD-2 formed a horseshoe-like structure comprised of parallel β-strands and a β-cup structure consisting of two anti-parallel β-sheets, respectively. The (TLR4-MD-2)₂ duplex-heterodimer was shown to form a symmetrical structure. Comparison with the interfaces of the complexes in other mammals revealed that cetacean TLR4s have some amino acid residue substitutions involved in duplex-heterodimer formation and in species variation for LPS recognition. These substitutions in the changed amino acid residues may alter the interaction among TLR4, MD-2, and LPS and modify the TLR4/MD-2 immunological responses.