Geographical Pattern and Environmental Correlates of Regional-Scale General Flowering in Peninsular Malaysia

In South-East Asian dipterocarp forests, many trees synchronize their reproduction at the community level, but irregularly, in a phenomenon known as general flowering (GF). Several proximate cues have been proposed as triggers for the synchronization of Southeast Asian GF, but the debate continues, as many studies have not considered geographical variation in climate and flora. We hypothesized that the spatial pattern of GF forests is explained by previously proposed climatic cues if there are common cues for GF among regions. During the study, GF episodes occurred every year, but the spatial occurrence varied considerably from just a few forests to the whole of Peninsular Malaysia. In 2001, 2002 and 2005, minor and major GF occurred widely throughout Peninsular Malaysia (GF2001, GF2002, and GF2005), and the geographical patterns of GF varied between the episodes. In the three regional-scale GF episodes, most major events occurred in regions where prolonged drought (PD) had been recorded prior, and significant associations between GF scores and PD were found in GF2001 and GF2002. However, the frequency of PD was higher than that of GF throughout the peninsula. In contrast, low temperature (LT) was observed during the study period only before GF2002 and GF2005, but there was no clear spatial relationship between GF and LT in the regional-scale episodes. There was also no evidence that last GF condition influenced the magnitude of GF. Thus, our results suggest that PD would be essential to trigger regional-scale GF in the peninsula, but also that PD does not fully explain the spatial and temporal patterns of GF. The coarse relationships between GF and the proposed climatic cues may be due to the geographical variation in proximate cues for GF, and the climatic and floristic geographical variations should be considered to understand the proximate factors of GF.     

The Pontin series of recombinant alien translocations in bread wheat: single translocations integrating combinations of Bdv2, Lr19 and Sr25 disease-resistance genes from Thinopyrum intermedium and Th. ponticum

Two bread wheat lines each with a translocation on chromosome 7DL from either Thinopyrum intermedium (TC5 and TC14) or Thinopyrum ponticum (T4m), were hybridized in a ph1b mutant background to enhance recombination between the two translocated chromosomal segments. The frequency of recombinants was high in lines derived from the larger and similar-sized translocations (TC5/T4m), but much lower when derived from different-sized translocations (TC14/T4m). Recombinant translocations contained combinations of resistance genes Bdv2, Lr19 and Sr25 conferring resistance to Barley yellow dwarf virus (BYDV), leaf rust and stem rust, respectively. Their genetic composition was identified using bioassays and molecular markers specific for the two progenitor Thinopyrum species. This set of 7DL Th. ponticum/intermedium recombinant translocations was termed the Pontin series. In addition to Thinopyrum markers, the size of the translocation was estimated with the aid of wheat markers mapped on each of the 7DL deletion bins. Bioassays for BYDV, leaf rust and stem rust were performed under greenhouse and field conditions. Once separated from ph1b background, the Pontin recombinant translocations were stable and showed normal inheritance in successive backcrosses. The reported Pontin translocations integrate important resistance genes in a single linkage block which will allow simultaneous selection of disease resistance. Combinations of Bdv2 + Lr19 or Lr19 + Sr25 in both long and short translocations, are available to date. The smaller Pontins, comprising only 20 % of the distal portion of 7DL, will be most attractive to breeders.     

Implementing vertex dynamics models of cell populations in biology within a consistent computational framework

The dynamic behaviour of epithelial cell sheets plays a central role during development, growth, disease and wound healing. These processes occur as a result of cell adhesion, migration, division, differentiation and death, and involve multiple processes acting at the cellular and molecular level. Computational models offer a useful means by which to investigate and test hypotheses about these processes, and have played a key role in the study of cell–cell interactions. However, the necessarily complex nature of such models means that it is difficult to make accurate comparison between different models, since it is often impossible to distinguish between differences in behaviour that are due to the underlying model assumptions, and those due to differences in the in silico implementation of the model. In this work, an approach is described for the implementation of vertex dynamics models, a discrete approach that represents each cell by a polygon (or polyhedron) whose vertices may move in response to forces. The implementation is undertaken in a consistent manner within a single open source computational framework, Chaste, which comprises fully tested, industrial-grade software that has been developed using an agile approach. This framework allows one to easily change assumptions regarding force generation and cell rearrangement processes within these models. The versatility and generality of this framework is illustrated using a number of biological examples. In each case we provide full details of all technical aspects of our model implementations, and in some cases provide extensions to make the models more generally applicable.     

Structural and gene expression analyses of uptake hydrogenases and other proteins involved in nitrogenase protection in Frankia

The actinorhizal bacterium Frankia expresses nitrogenase and can therefore convert molecular nitrogen into ammonia and the by-product hydrogen. However, nitrogenase is inhibited by oxygen. Consequently, Frankia and its actinorhizal hosts have developed various mechanisms for excluding oxygen from their nitrogen-containing compartments. These include the expression of oxygen-scavenging uptake hydrogenases, the formation of hopanoid-rich vesicles, enclosed by multi-layered hopanoid structures, the lignification of hyphal cell walls, and the production of haemoglobins in the symbiotic nodule. In this work, we analysed the expression and structure of the so-called uptake hydrogenase (Hup), which catalyses the in vivo dissociation of hydrogen to recycle the energy locked up in this ‘waste’ product. Two uptake hydrogenase syntons have been identified in Frankia: synton 1 is expressed under free-living conditions while synton 2 is expressed during symbiosis. We used qPCR to determine synton 1 hup gene expression in two Frankia strains under aerobic and anaerobic conditions. We also predicted the 3D structures of the Hup protein subunits based on multiple sequence alignments and remote homology modelling. Finally, we performed BLAST searches of genome and protein databases to identify genes that may contribute to the protection of nitrogenase against oxygen in the two Frankia strains. Our results show that in Frankia strain ACN14a, the expression patterns of the large (HupL1) and small (HupS1) uptake hydrogenase subunits depend on the abundance of oxygen in the external environment. Structural models of the membrane-bound hydrogenase subunits of ACN14a showed that both subunits resemble the structures of known [NiFe] hydrogenases (Volbeda et al. 1995), but contain fewer cysteine residues than the uptake hydrogenase of the Frankia DC12 and Eu1c strains. Moreover, we show that all of the investigated Frankia strains have two squalene hopane cyclase genes (shc1 and shc2). The only exceptions were CcI3 and the symbiont of Datisca glomerata, which possess shc1 but not shc2. Four truncated haemoglobin genes were identified in Frankia ACN14a and Eu1f, three in CcI3, two in EANpec1 and one in the Datisca glomerata symbiont (Dg).     

Effect of background colour on growth and adhesion strength of Ulva sporelings

This study examined the effects of a range of black, grey and white substrata on the growth and attachment strength of Ulva sporelings on glass and polydimethylsiloxane (Silastic®-T2) surfaces. The rate of development of sporelings was strongly influenced by the colour of the substratum on which they grew. On black backgrounds, sporelings grew slowly and germination was delayed. Laboratory screening methods for antifouling and fouling-release coatings that rely on the growth of Ulva sporelings can be compromised if samples are of different colours. Hydrodynamic removal of sporelings from coatings may also be affected by substratum colour, since smaller plants generate lower hydrodynamic forces making them more difficult to remove.     

Natural dispersal mechanisms and dispersal potential of the invasive ascidian Didemnum vexillum

Over the past decade, several species of non-indigenous ascidians have had adverse effects on a range of coastal ecosystems, and associated industries like aquaculture. One such species, the colonial ascidian Didemnum vexillum, poses a threat to the highly-valued New Zealand green-lipped mussel industry, and there is interest in whether and to what extent its spread can be managed at a regional scale (<100 km). An important component in the decision-making process for managing human-mediated pathways of spread is an understanding of D. vexillum’s natural dispersal potential. Here we use a weight-of-evidence approach, combining laboratory and field studies, to assess the role of natural dispersal mechanisms in the spread of D. vexillum. Under laboratory conditions, >70 % of D. vexillum larvae remained viable and were able to settle and undergo metamorphosis successfully following an artificial delay of 2 h. Larval viability decreased with increasing delay duration, although 10 % of larvae remained viable following a 36 h delay. A field-based study documented larval dispersal from two discrete source populations, with recruitment consistently detected on settlement plates at 250 m from source populations at one experimental site. Exponential decay models used to predict maximum larval dispersal distances at this site indicated that dispersal greater than 250 m is theoretically possible (>1 km in some situations). That being so, we recognise that the successful establishment and persistence of populations will depend on a wide range of processes not taken into account here. Our findings are supported by surveillance of D. vexillum spread in the wider study region; there are a number of instances where the species established on artificial structures that were several kilometres from known source populations, at a time when intensive regional-scale management of anthropogenic vectors was underway. Collectively, our findings indicate that D. vexillum has the ability to spread further by natural dispersal than previously assumed; probably hundreds of metres to kilometres depending on the local hydrological conditions, which has important implications for the ongoing management of this pest species world-wide.     

Nymphal development and lerp construction of Glycaspis sp. (Hemiptera: Psylloidea) on Eucalyptus sideroxylon (Myrtaceae) in central-west New South Wales,Australia

The ability to form lerps is common in Australian Psylloidea. Various species of Glycaspis Taylor (Aphalaridae) form conical lerps on different species of Eucalyptus. Lerps, being a rich sugar source, are preferentially fed by bell miners (Aves: Meliphagidae). In this paper we report the process of lerp construction by a purported new species of Glycaspis living on Eucalyptus sideroxylon. This taxon constructs lerps with anal sugary exudates first building the ribs of the lerps and later filling the space between the polymerized ribs with horizontal tractions of the same sugary substance. Developmental events in this taxon do not follow Dyar's rule strictly. Oviposition induces a non-lethal hypersensitive response in the host leaf. Population trends assessed in 2011–2012 and 2012–2013 showed distinct variations, which have been related to environmental factors. In the 2012–2013 sampling, oviposition occurred preferentially proximally to leaf cracks (possibly induced by intense frost events); we infer that this could be a strategy of this taxon to establish an ‘easier’ access to moisture. Sensillar designs vary between the nymphal instars and adults. The trichoid sensilla and sensillar cavities on the antennae perform mechanosensory and olfactory functions. The mouthpart complex includes a relatively long stylet bundle.     

UDP-glucuronic acid decarboxylases of Bacteroides fragilis and their prevalence in bacteria

Xylose is rarely described as a component of bacterial glycans. UDP-xylose is the nucleotide-activated form necessary for incorporation of xylose into glycans and is synthesized by the decarboxylation of UDP-glucuronic acid (UDP-GlcA). Enzymes with UDP-GlcA decarboxylase activity include those that lead to the formation of UDP-xylose as the end product (Uxs type) and those synthesizing UDP-xylose as an intermediate (ArnA and RsU4kpxs types). In this report, we identify and confirm the activities of two Uxs-type UDP-GlcA decarboxylases of Bacteroides fragilis, designated BfUxs1 and BfUxs2. Bfuxs1 is located in a conserved region of the B. fragilis genome, whereas Bfuxs2 is in the heterogeneous capsular polysaccharide F (PSF) biosynthesis locus. Deletion of either gene separately does not result in the loss of a detectable phenotype, but deletion of both genes abrogates PSF synthesis, strongly suggesting that they are functional paralogs and that the B. fragilis NCTC 9343 PSF repeat unit contains xylose. UDP-GlcA decarboxylases are often annotated incorrectly as NAD-dependent epimerases/dehydratases; therefore, their prevalence in bacteria is underappreciated. Using available structural and mutational data, we devised a sequence pattern to detect bacterial genes encoding UDP-GlcA decarboxylase activity. We identified 826 predicted UDP-GlcA decarboxylase enzymes in diverse bacterial species, with the ArnA and RsU4kpxs types confined largely to proteobacterial species. These data suggest that xylose, or a monosaccharide requiring a UDP-xylose intermediate, is more prevalent in bacterial glycans than previously appreciated. Genes encoding BfUxs1-like enzymes are highly conserved in Bacteroides species, indicating that these abundant intestinal microbes may synthesize a conserved xylose-containing glycan.     

Caspase-1-processed cytokines IL-1beta and IL-18 promote IL-17 production by gammadelta and CD4 T cells that mediate autoimmunity

IL-1β plays a critical role in promoting IL-17 production by γδ and CD4 T cells. However, IL-1-targeted drugs, although effective against autoinflammatory diseases, are less effective against autoimmune diseases. Conversely, gain-of-function mutations in the NLRP3 inflammasome complex are associated with enhanced IL-1β and IL-18 production and Th17 responses. In this study, we examined the role of caspase-1-processed cytokines in IL-17 production and in induction of experimental autoimmune encephalomyelitis (EAE). Killed Mycobacterium tuberculosis, the immunostimulatory component in CFA used for inducing EAE, stimulated IL-1β and IL-18 production by dendritic cells through activation of the inflammasome complex and caspase-1. Dendritic cells stimulated with M. tuberculosis and myelin oligodendrocyte glycoprotein promoted IL-17 production by T cells and induced EAE following transfer to naive mice, and this was suppressed by a caspase-1 inhibitor and reversed by administration of IL-1β or IL-18. Direct injection of the caspase-1 inhibitor suppressed IL-17 production by CD4 T cells and γδ T cells in vivo and attenuated the clinical signs of EAE. γδ T cells expressed high levels of IL-18R and the combination of IL-18 and IL-23, as with IL-1β and IL-23, stimulated IL-17 production by γδ T cells, but also from CD4 T cells, in the absence of TCR engagement. Our findings demonstrate that caspase-1-processed cytokines IL-1β and IL-18 not only promote autoimmunity by stimulating innate IL-17 production by T cells but also reveal redundancy in the functions of IL-1β and IL-18, suggesting that caspase-1 or the inflammasome may be an important drug target for autoimmune diseases.     

Role for MyD88, TLR2 and TLR9 but not TLR1, TLR4 or TLR6 in experimental autoimmune encephalomyelitis

The potential roles of TLRs in the cause and pathogenesis of autoimmune CNS inflammation remain contentious. In this study, we examined the effects of targeted deletions of TLR1, TLR2, TLR4, TLR6, TLR9, and MyD88 on the induction of myelin oligodendrocyte glycoprotein 35-55 (MOG(35-55)) peptide/CFA/pertussis toxin-induced autoimmune encephalomyelitis. Although C57BL/6.Tlr1(-/-), C57BL/6.Tlr4(-/-) and C57BL/6.Tlr6(-/-) mice showed normal susceptibility to disease, signs were alleviated in female C57BL/6.Tlr2(-/-) and C57BL/6.Tlr9(-/-) mice and C57BL/6.Tlr2/9(-/-) mice of both sexes. C57BL/6.Myd88(-/-) mice were completely protected. Lower clinical scores were associated with reduced leukocyte infiltrates. These results were confirmed by passive adoptive transfer of disease into female C57BL/6.Tlr2(-/-) and C57BL/6.Tlr9(-/-) mice, where protection in the absence of TLR2 was associated with fewer infiltrating CD4(+) cells in the CNS, reduced prevalence of detectable circulating IL-6, and increased proportions of central (CD62L(+)) CD4(+)CD25(+)Foxp3(+) regulatory T cells. These results provide a potential molecular mechanism for the observed effects of TLR signaling on the severity of autoimmune CNS inflammation.