Spatio‐temporal water dynamics in mature Banksia menziesii trees during drought

Southwest Australian Banksia woodlands are highly diverse plant communities that are threatened by drought‐ or temperature‐induced mortality due to the region's changing climate. We examined water relations in dominant Banksia menziesii R. Br. trees using magnetic leaf patch clamp pressure (ZIM‐) probes that allow continuous, real‐time monitoring of leaf water status. Multiple ZIM‐probes across the crown were complemented by traditional ecophysiological measurements. During summer, early stomatal downregulation of transpiration prevented midday balancing pressures from exceeding 2.5 MPa. Diurnal patterns of ZIM‐probe and pressure chamber readings agreed reasonably well, however, ZIM‐probes recorded short‐term dynamics, which are impossible to capture using a pressure chamber. Simultaneous recordings of three ZIM‐probes evenly spaced along leaf laminas revealed intrafoliar turgor gradients, which, however, did not develop in a strictly basi‐ or acropetal fashion and varied with cardinal direction. Drought stress manifested as increasing daily signal amplitude (low leaf water status) and occasionally as rising baseline at night (delayed rehydration). These symptoms occurred more often locally than across the entire crown. Microclimate effects on leaf water status were strongest in crown regions experiencing peak morning radiation (East and North). Extreme spring temperatures preceded the sudden death of B. menziesii trees, suggesting a temperature‐ or humidity‐related tipping point causing rapid hydraulic failure as evidenced by collapsing ZIM‐probe readings from an affected tree. In a warmer and drier future, increased frequency of B. menziesii mortality will result in significantly altered community structure and ecosystem function.     

Role of fimbriae as antigens and intestinal colonization factors of Salmonella serovars

The ascomycete Pulvinula constellatio was found to form competing ectomycorrhizal relationships with plants that had been inoculated with Tuber spp. and other edible ectomycorrhizal fungi. In order to be able to distinguish P. constellatio mycorrhizae from those of the Tuber spp., we determined the morphological and bio-molecular characteristics of P. constellatio. The complete sequence of the ITS regions was determined, in order to select specific primers. The ITS region was also studied using restriction fragment length polymorphism analyses with several restriction enzymes that allowed an unambiguous identification of the species.     

Profile and Treatment Outcomes of Tuberculosis in the Elderly in Southeastern Nigeria, 2011–2012

Background

The demographic transition and increasing life expectancy in Africa has lead to a rising elderly population. In Nigeria, little is known about the profile of and treatment outcomes of tuberculosis (TB) in the elderly.

Methods

Retrospective cohort study of adult TB patients treated between January 2011 and December 2012 in two large health facilities in Nigeria. The demographic, clinical and treatment outcomes of patients aged 60 and older were compared with those aged 15 to 59 years.

Results

Elderly (≥60 years) TB patients accounted for 12.7% of all (1668) adult TB enrolled. Elderly patients had a higher proportion of men compared to non-elderly (64.2% vs 56.8%; p = 0.043); but a lower proportion of smear-positive TB at baseline (40.7% vs 65.8%; p<0.001). A higher proportion of elderly patients failed to smear convert after the intensive phase of treatment (23.7% vs 19.8%; p = 0.06), and overall elderly patients had lower treatment success rates (68.9% vs 77.1%; p = 0.009). Unsuccessful outcomes were mainly due to higher default and deaths in the elderly. The risk factors for unsuccessful outcomes in the elderly were: extrapulmonary TB case (adjusted odds ratio (aOR) 10.9; 95% confidence interval (CI) 1.1–108), and HIV co-infection (aOR 3.6; CI 1.1–11.7).

Conclusions

Treatment outcomes of elderly TB patients were inferior to non-elderly adults with higher death and default rates being implicated. With the rising elderly population, specific strategies are needed to quickly address TB management in the elderly in resource-limited settings.     

In vitro propagation of temperate Australian terrestrial orchids: revisiting asymbiotic compared with symbiotic germination

Using a common temperate herbaceous terrestrial orchid from Australia (Caladenia latifolia) this study investigated 19 asymbiotic media variations comprising four commonly used basal media [half‐strength Murashige and Skoog (½MS), Knudson C (KC), Pa5, and Vacin and Went (VW), with combinations of the plant growth regulators 6‐benzylaminopurine (BA) and α‐naphthalene acetic acid (NAA) or coconut water (CW) and compared their performance with germination on a standard symbiotic germination medium, oatmeal agar (OMA). Percentage germination of seeds every 2 weeks for a total of 8 weeks (five replicates per treatment), time to germination, and growth and development phases in seedlings were recorded. ½MS with 5% (v/v) fresh CW delivered 93% germination, with seedling vigour and development indistinguishable from OMA (95% germination). The same protocol was applied to a further ten species (including the endangered Caladenia huegelii), demonstrating high asymbiotic germination performance (60–93%) across a wide phylogenetic range of terrestrial orchid species. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 176 , 556–566.     

Contribution of the Community Health Volunteers in the Control of Buruli Ulcer in Bénin

Background

Buruli ulcer (BU) is a neglected tropical disease caused by Mycobacterium ulcerans. Usually BU begins as a painless nodule, plaque or edema, ultimately developing into an ulcer. The high number of patients presenting with ulcers in an advanced stage is striking. Such late presentation will complicate treatment and have long-term disabilities as a consequence. The disease is mainly endemic in West Africa. The primary strategy for control of this disease is early detection using community village volunteers.

Methodology/Principal Findings

In this retrospective, observational study, information regarding Buruli ulcer patients that reported to one of the four BU centers in Bénin between January 2008 and December 2010 was collected using the WHO/BU01 forms. Information used from these forms included general characteristics of the patient, the results of diagnostic tests, the presence of functional limitations at start of treatment, lesion size, patient delay and the referral system. The role of the different referral systems on the stage of disease at presentation in the hospital was analyzed by a logistic regression analysis. About a quarter of the patients (26.5%) were referred to the hospital by the community health volunteers. In our data set, patients referred to the hospital by community health volunteers appeared to be in an earlier stage of disease than patients referred by other methods, but after adjustment by the regression analysis for the health center, this effect could no longer be seen. The Polymerase Chain Reaction (PCR) for IS2404 positivity rate among patients referred by the community health volunteers was not systematically lower than in patients referred by other systems.

Conclusions/Significance

This study clarifies the role played by community health volunteers in Bénin, and shows that they play an important role in the control of BU.     

Trichloroethene Reductive Dehalogenase from Dehalococcoides ethenogenes: Sequence of tceA and Substrate Range Characterization

The anaerobic bacterium Dehalococcoides ethenogenes is the only known organism that can completely dechlorinate tetrachloroethene or trichloroethene (TCE) to ethene via dehalorespiration. One of two corrinoid-containing enzymes responsible for this pathway, TCE reductive dehalogenase (TCE-RDase) catalyzes the dechlorination of TCE to ethene. TCE-RDase dehalogenated 1,2-dichloroethane and 1,2-dibromoethane to ethene at rates of 7.5 and 30 μmol/min/mg, respectively, similar to the rates for TCE, cis-dichloroethene (DCE), and 1,1-DCE. A variety of other haloalkanes and haloalkenes containing three to five carbon atoms were dehalogenated at lower rates. The gene encoding TCE-RDase, tceA, was cloned and sequenced via an inverse PCR approach. Sequence comparisons of tceA to proteins in the public databases revealed weak sequence similarity confined to the C-terminal region, which contains the eight-iron ferredoxin cluster binding motif, (CXXCXXCXXXCP)₂. Direct N-terminal sequencing of the mature enzyme indicated that the first 42 amino acids constitute a signal sequence containing the twin-arginine motif, RRXFXK, associated with the Sec-independent membrane translocation system. This information coupled with membrane localization studies indicated that TCE-RDase is located on the exterior of the cytoplasmic membrane. Like the case for the two other RDases that have been cloned and sequenced, a small open reading frame, tceB, is proposed to be involved with membrane association of TCE-RDase and is predicted to be cotranscribed with tceA.     

High resolution assembly and characterization of genomes of Canadian isolates of Salmonella Enteritidis

Background

There is a need to characterize genomes of the foodborne pathogen, Salmonella enterica serovar Enteritidis (SE) and identify genetic information that could be ultimately deployed for differentiating strains of the organism, a need that is yet to be addressed mainly because of the high degree of clonality of the organism. In an effort to achieve the first characterization of the genomes of SE of Canadian origin, we carried out massively parallel sequencing of the nucleotide sequence of 11 SE isolates obtained from poultry production environments (n = 9), a clam and a chicken, assembled finished genomes and investigated diversity of the SE genome.

Results

The median genome size was 4,678,683 bp. A total of 4,833 chromosomal genes defined the pan genome of our field SE isolates consisting of 4,600 genes present in all the genomes, i.e., core genome, and 233 genes absent in at least one genome (accessory genome). Genome diversity was demonstrable by the presence of 1,360 loci showing single nucleotide polymorphism (SNP) in the core genome which was used to portray the genetic distances by means of a phylogenetic tree for the SE isolates. The accessory genome consisted mostly of previously identified SE prophage sequences as well as two, apparently full- sized, novel prophages namely a 28 kb sequence provisionally designated as SE-OLF-10058 (3) prophage and a 43 kb sequence provisionally designated as SE-OLF-10012 prophage.

Conclusions

The number of SNPs identified in the relatively large core genome of SE is a reflection of substantial diversity that could be exploited for strain differentiation as shown by the development of an informative phylogenetic tree. Prophage sequences can also be exploited for SE strain differentiation and lineage tracking. This work has laid the ground work for further studies to develop a readily adoptable laboratory test for the subtyping of SE.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-713) contains supplementary material, which is available to authorized users.     

Evidence of unique genotypes of beak and feather disease virus in southern Africa

Psittacine beak and feather disease (PBFD), caused by Beak and feather disease virus (BFDV), is the most significant infectious disease in psittacines. PBFD is thought to have originated in Australia but is now found worldwide; in Africa, it threatens the survival of the indigenous endangered Cape parrot and the vulnerable black-cheeked lovebird. We investigated the genetic diversity of putative BFDVs from southern Africa. Feathers and heparinized blood samples were collected from 27 birds representing 9 psittacine species, all showing clinical signs of PBFD. DNA extracted from these samples was used for PCR amplification of the putative BFDV coat protein (CP) gene. The nucleotide sequences of the CP genes of 19 unique BFDV isolates were determined and compared with the 24 previously described sequences of BFDV isolates from Australasia and America. Phylogenetic analysis revealed eight BFDV lineages, with the southern African isolates representing at least three distinctly unique genotypes; 10 complete genome sequences were determined, representing at least one of every distinct lineage. The nucleotide diversity of the southern African isolates was calculated to be 6.4% and is comparable to that found in Australia and New Zealand. BFDVs in southern Africa have, however, diverged substantially from viruses found in other parts of the world, as the average distance between the southern African isolates and BFDV isolates from Australia ranged from 8.3 to 10.8%. In addition to point mutations, recombination was found to contribute substantially to the level of genetic variation among BFDVs, with evidence of recombination in all but one of the genomes analyzed.     

Seed Coat Dormancy in Two Species of Grevillea(Proteaceae)

The role played by the seed coat in seed dormancy of Grevillealinearifolia(Cav.) Druce and G. wilsonii(A. Cunn.) was testedby a series of manipulations in which the seed coat was dissectedand removed, dissected and returned to the decoated seed, ordissected, removed and given a heat shock, and returned to thedecoated seed. Germination of intact seeds of both species wasalso examined after exposure to heat shock, smoke, or heat shockand smoke combined. Water permeability of the seed coat wasinvestigated by examining imbibition. For intact seeds, virtuallyno germination occurred under any treatment (G. wilsonii), orgermination was increased by exposure to either heat or smoke(G. linearifolia). Removal of the seed coat led to germinationof all decoated seeds for G. linearifolia, or a proportion ofdecoated seeds for G. wilsonii. Inclusion of smoked water inthe incubation medium led to a higher proportion of decoatedseeds germinating for G. wilsonii. Returning the seed coat,either with or without heat shock to the seed coat, did notsignificantly affect germination in either species. Seed coatswere permeable to water in both species. For the two Grevilleaspecies, there were different dormancy mechanisms that werecontrolled by the seed coat (G. linearifolia) or by both theseed coat and embryo (G. wilsonii). Copyright 2000 Annals ofBotany Company Grevillea linearifolia, Grevillea wilsonii, dormancy, seed coat dormancy, seed coat permeability, smoke, heat shock, germination