Genetic and Morphometric Analysis of Cob Architecture and Biomass-Related Traits in the Intermated B73 × Mo17 Recombinant Inbred Lines of Maize

Expected future cellulosic ethanol production increases the demand for biomass in the US Corn Belt. With low nutritious value, low nitrogen content, and compact biomass, maize cobs can provide a significant amount of cellulosic materials. The value of maize cobs depends on cob architecture, chemical composition, and their relation to grain yield as primary trait. Eight traits including cob volume, fractional diameters, length, weight, tissue density, and grain yield have been analyzed in this quantitative trait locus (QTL) mapping experiment to evaluate their inheritance and inter-relations. One hundred eighty-four recombinant inbred lines of the intermated B73?×?Mo17 (IBM) Syn 4 population were evaluated from an experiment carried out at three locations and analyzed using genotypic information of 1,339 public SNP markers. QTL detection was performed using (1) comparison-wise thresholds with reselection of cofactors (α?=?0.001) and (2) empirical logarithm of odds score thresholds (P?=?0.05). Several QTL with small genetic effects (R ²?=?2.9–13.4 %) were found, suggesting a complex quantitative inheritance of all traits. Increased cob tissue density was found to add value to the residual without a commensurate negative impact on grain yield and therefore enables for simultaneous selection for cob biomass and grain yield.     

The Geometry of Locomotive Behavioral States in C. elegans

We develop a new hidden Markov model-based method to analyze C elegans locomotive behavior and use this method to quantitatively characterize behavioral states. In agreement with previous work, we find states corresponding to roaming, dwelling, and quiescence. However, we also find evidence for a continuum of intermediate states. We suggest that roaming, dwelling, and quiescence may best be thought of as extremes which, mixed in any proportion, define the locomotive repertoire of C elegans foraging and feeding behavior.     

Calcium and iron as key drivers of brown moss composition through differential effects on phosphorus availability

Brown moss-dominated rich fens are characterized by minerotrophic conditions, in which calcium (Ca) and iron (Fe) concentrations show large variations. We examined the relative importance of Ca and Fe in relation to the occurrence of three typical brown moss species: Scorpidium scorpioides, Scorpidium cossonii, and Hamatocaulis vernicosus. Peat chemistry was examined in 24 stands of brown moss-dominated rich fens: 12 in the Netherlands and 12 in central Sweden. Ca and Fe turned out to be important drivers of brown moss composition. Fens dominated by Scorpidium scorpioides or Scorpidium cossonii were characterized by high pore water Ca-concentrations and total soil Ca-contents, but low P-availability. In these Ca-rich, but Fe-poor fens, foliar N:P ratios of vascular vegetation exceeded 20?g?g^?1, indicating phosphorus (P)-limitation due to Ca-P precipitation or low P-sorption capacity due to low Fe-levels. In contrast, fens dominated by Hamatocaulis vernicosus were characterized by high pore water Fe-concentrations and total soil Fe-contents, but also relatively high P-availability. N:P ratios in these fens were below 13.5?g?g^?1, indicating potential nitrogen (N)-limitation. We conclude that the relative roles of Ca and Fe, as related to the geohydrological conditions present, strongly determine the brown moss composition in rich fens through their differential effects on plant P-availability.     

Defective Autophagy and mTORC1 Signaling in Myotubularin Null Mice

Autophagy is a vesicular trafficking pathway that regulates the degradation of aggregated proteins and damaged organelles. Initiation of autophagy requires several multiprotein signaling complexes, such as the ULK1 kinase complex and the Vps34 lipid kinase complex, which generates phosphatidylinositol 3-phosphate [PtdIns(3)P] on the forming autophagosomal membrane. Alterations in autophagy have been reported for various diseases, including myopathies. Here we show that skeletal muscle autophagy is compromised in mice deficient in the X-linked myotubular myopathy (XLMTM)-associated PtdIns(3)P phosphatase myotubularin (MTM1). Mtm1-deficient muscle displays several cellular abnormalities, including a profound increase in ubiquitin aggregates and abnormal mitochondria. Further, we show that Mtm1 deficiency is accompanied by activation of mTORC1 signaling, which persists even following starvation. In vivo pharmacological inhibition of mTOR is sufficient to normalize aberrant autophagy and improve muscle phenotypes in Mtm1 null mice. These results suggest that aberrant mTORC1 signaling and impaired autophagy are consequences of the loss of Mtm1 and may play a primary role in disease pathogenesis.     

Exopeptidase activity in eggs of Trichostrongylus colubriformis (Nematoda)

Summary

A supernatant from eggs of the ruminant nematode Trichostrongylus colubriformis contained an enzyme that was similar to leucine aminopeptidase (LAP), based on hydrolysis of the substrate L-leucine β-naphthylamide to β-naphthylamine. A Michaelis-Menten constant (K _m) of 0.155 mM was obtained. Rate of hydrolysis of 16 substrates revealed that L-phenylalanine and L-tyrosine β-naphthylamides were hydrolyzed most readily while seven additional substrates were hydrolyzed at lesser rates. The optimum pH for enzymatic activity was 6.75–7.5. Enzymatic activity was lost by heating the egg supernatant to 60°C for 5 min or freezing at 0°C for 28 days. Addition of millimolar concentrations of the chlorides of zinc, manganese and magnesium to the egg supernatant had no stimulatory effect on enzyme activity while 10 and 100 mM concentrations significantly reduced activity. Ethylenediamine tetraacetic acid at 10^?4 M had no effect on enzymatic activity. Activity was inhibited by 10^?4 M 1,10-phenanthroline, but the inhibition was reversed by zinc chloride at 10^?3 M. Di-isopropylphosphofluoridate at 10^?3 M reduced enzymatic activity moderately. Enzyme activity in egg supernatant increased 2.2-fold from 21 days to 60–90 days of a primary infection in the host while a 3.3-fold increase was found in primary versus secondary infections.     

Birds to watch: a Red Data List for East Africa

Bennun, L.A., Njoroge, P. & Pomeroy, D. 2000. Birds to watch: a Red Data List for East Africa. Ostrich 71 (1 & 2): 310–314.

The value of Red Data books and lists is well established; there has been much recent work on improving the criteria for listing species of conservation concern. So far these have been applied mainly at the global level. Regional lists can be useful, however, in improving the resolution of conservation priorities and setting an agenda for research, monitoring and conservation, especially where data are collected by amateur naturalists. A Red Data list for East African birds has been drawn up following an eight-month process that involved wide consultation within the region, defined as Uganda, Rwanda, Tanzania, Kenya and Burundi. The criteria for listing were based on those defined by IUCN, and summarised in a single, simple table that could be used for screening large numbers of species. A criterion based on geographic range eliminated from consideration vagrant species or those on the extreme edge of their range. A separate Near Threatened category (Lower Risk but very close to Vulnerable) proved useful. An additional category of Regional Responsibility captured species that are entirely or mainly confiied to East Africa, or to three habitats where the region has special responsibility: coastal forests, Albertine Rift forests, and papyrus swamps. A total of 107 species (about 8% of the regional avifauna) were listed as regionally threatened. This includes four Critical, 18 Endangered and 85 Vulnerable species, proportions very close to those expected from the theoretical probabilities of extinction in each case. One hundred and four species were listed as Near-threatened and 153 as Regional Responsibility, 87 of which are not under threat. Placing a species in a particular category of threat, for explicit reasons, poses an hypothesis about its status that can be tested with additional data. This process is now under way with the compilation of a more detailed, annotated list.     

Greater phosphorus uptake in forested headwater streams modified by clearfell forestry

Clearfell, burn and sow (CBS) forestry can potentially alter stream environments by increasing available light and the input of woody debris. However, little is known about how CBS forestry affects in-stream processes such as nutrient uptake. We evaluate whether short-term (2–7 years) environmental changes (e.g. light availability and woody debris) associated with CBS forestry lead to differences in nutrient uptake metrics. To do this, we measured in-stream uptake of soluble reactive phosphorus (SRP) and ammonium (NH₄) in three old growth (OG) and four CBS-affected headwater stream reaches. The abundance of fine woody debris and light availability were significantly greater in CBS-affected than in OG reaches. Uptake velocities varied from 0.0880 to 0.951 mm min^?1 for NH₄ and from 0.0383 to 1.06 mm min^?1 for SRP across all sites. The mean uptake of SRP, but not NH₄, was significantly greater (i.e. higher uptake velocities and lower uptake lengths) in CBS-affected than in OG reaches. These results suggest that CBS forestry altered the stream environment enabling greater SRP uptake relative to OG reaches. Our findings highlight the tight linkage between headwater streams and their surrounding terrestrial environment, which has direct implications for catchment-scale biogeochemical processes.     

Functional,structural and phylogenetic analysis of domains underlying the Al sensitivity of the aluminum‐activated malate/anion transporter,TaALMT1

Triticum aestivum aluminum‐activated malate transporter (TaALMT1) is the founding member of a unique gene family of anion transporters (ALMTs) that mediate the efflux of organic acids. A small sub‐group of root‐localized ALMTs, including TaALMT1, is physiologically associated with in planta aluminum (Al) resistance. TaALMT1 exhibits significant enhancement of transport activity in response to extracellular Al. In this study, we integrated structure–function analyses of structurally altered TaALMT1 proteins expressed in Xenopus oocytes with phylogenic analyses of the ALMT family. Our aim is to re‐examine the role of protein domains in terms of their potential involvement in the Al‐dependent enhancement (i.e. Al‐responsiveness) of TaALMT1 transport activity, as well as the roles of all its 43 negatively charged amino acid residues. Our results indicate that the N‐domain, which is predicted to form the conductive pathway, mediates ion transport even in the absence of the C‐domain. However, segments in both domains are involved in Al³⁺ sensing. We identified two regions, one at the N‐terminus and a hydrophobic region at the C‐terminus, that jointly contribute to the Al‐response phenotype. Interestingly, the characteristic motif at the N‐terminus appears to be specific for Al‐responsive ALMTs. Our study highlights the need to include a comprehensive phylogenetic analysis when drawing inferences from structure–function analyses, as a significant proportion of the functional changes observed for TaALMT1 are most likely the result of alterations in the overall structural integrity of ALMT family proteins rather than modifications of specific sites involved in Al³⁺ sensing.     

Impacts of inundation and drought on eukaryote biodiversity in semi‐arid floodplain soils

Floodplain ecosystems are characterized by alternating wet and dry phases and periodic inundation defines their ecological character. Climate change, river regulation and the construction of levees have substantially altered natural flooding and drying regimes worldwide with uncertain effects on key biotic groups. In southern Australia, we hypothesized that soil eukaryotic communities in climate change affected areas of a semi‐arid floodplain would transition towards comprising mainly dry‐soil specialist species with increasing drought severity. Here, we used 18S rRNA amplicon pyrosequencing to measure the eukaryote community composition in soils that had been depleted of water to varying degrees to confirm that reproducible transitional changes occur in eukaryotic biodiversity on this floodplain. Interflood community structures (3 years post‐flood) were dominated by persistent rather than either aquatic or dry‐specialist organisms. Only 2% of taxa were unique to dry locations by 8 years post‐flood, and 10% were restricted to wet locations (inundated a year to 2 weeks post‐flood). Almost half (48%) of the total soil biota were detected in both these environments. The discovery of a large suite of organisms able to survive nearly a decade of drought, and up to a year submerged supports the concept of inherent resilience of Australian semi‐arid floodplain soil communities under increasing pressure from climatic induced changes in water availability.