Detached Maize Sheaths for Live-Cell Imaging of Infection by Fungal Foliar Maize Pathogens

We have optimized a protocol to inoculate maize leaf sheaths with hemibiotrophic and necrotrophic foliar pathogenic fungi. The method is modified from one originally applied to rice leaf sheaths and allows direct microscopic observation of fungal growth and development in living plant cells. Leaf sheaths collected from maize seedlings with two fully emerged leaf collars are inoculated with 20 µL drops of 5 x 105 spores/mL fungal spore suspensions and incubated in humidity chambers at 23 °C under continuous fluorescent light. After 24-72 h, excess tissue is removed with a razor blade to leave a single layer of epidermal cells, an optically clear sample that can be imaged directly without the necessity for chemical fixation or clearing. Plant and fungal cells remain alive for the duration of the experiment and interactions can be visualized in real-time. Sheaths can be stained or subjected to plasmolysis to study the developmental cytology and viability of host and pathogen cells during infection and colonization. Fungal strains transformed to express fluorescent proteins can be inoculated or co-inoculated on the sheaths for increased resolution and to facilitate the evaluation of competitive or synergistic interactions. Fungal strains expressing fluorescent fusion proteins can be used to track and quantify the production and targeting of these individual proteins in planta. Inoculated sheath tissues can be extracted to characterize nucleic acids, proteins, or metabolites. The use of these sheath assays has greatly advanced the detailed studies of the mechanisms of fungal pathogenicity in maize and also of fungal protein effectors and secondary metabolites contributing to pathogenicity.

Evidence of Recombination Suppression Blocks on the Y Chromosome of Date Palm (Phoenix dactylifera)

The genus Phoenix includes the fruit producing date palm tree among 14 species that are all dioecious. Females produce the fruit that are high in sugar content and used in multiple countries ranging from North Africa to South Asia, especially from the Phoenix dactylifera, Phoenix sylvestris, and Phoenix canariensis species. While females produce the fruit, understanding of the genetic basis of sex control only began recently. Through genus-wide sequencing of males and females we recently identified three genes that are conserved in all males and absent in all females of the genus and confirmed an XY sex chromosome system. While our previous study focused on conservation of male-specific sequences at the genus-level, it would be of interest to better understand the spread of male-specific sequences away from the core conserved male genes on the Y chromosome during speciation. To this end, we enumerated male-specific 16 bp sequences using three male/female pairs from the western subpopulation of date palm and documented the density of these sequences in contigs of a phased date palm genome assembly. Here we show that male specific sequences in the date palm Y chromosome have likely spread in defined events that appear as blocks of varying density with significant changes in density between them. Collinearity of genes in these blocks with oil palm shows high synteny with chromosome 10 between megabase 15 and 23 and reveals that large sections of the date palm Y chromosome have maintained the ancestral structure even as recombination has stopped between X and Y.

Novel subpopulations in date palm (Phoenix dactylifera) identified by population-wide organellar genome sequencing

Background

The date palm is one of the oldest cultivated fruit trees. The tree can withstand high temperatures and low water and the fruit can be stored dry offering nutrition across the year. The first region of cultivation is believed to be near modern day Iraq, however, where and if the date palm was domesticated is still a topic of debate. Recent studies of chloroplast and genomic DNA revealed two major subpopulations of cultivars centered in both the Eastern range of date palm cultivation including Arabian Peninsula, Iraq and parts of South Asia, and the Western range, including North Africa.

Results

To better understand the origins of date palm cultivation we sequenced and analyzed over 200 mitochondrial and chloroplast genomes from a geographically diverse set of date palms. Here we show that, based on mitochondrial and chloroplast genome-wide genotyping data, the most common cultivated date palms contain 4 haplotypes that appear associated with geographical region of cultivar origin.

Conclusions

These data suggest at least 3 and possibly 4 original maternal contributions to the current date palm population and doubles the original number. One new haplotype was found mainly in Tunisia, Algeria and Egypt and the second in Iraq, Iran and Oman. We propose that earliest date palm cultivation occurred independently in at least 3 distinct locations. This discovery will further inform understanding of the history and origins of cultivated date palm.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5834-7) contains supplementary material, which is available to authorized users.

Correction to: A comparative genomic analysis of putative pathogenicity genes in the host-specific sibling species Colletotrichum graminicola and Colletotrichum sublineola

Following the publication of this article [1], the authors informed us of the following error.

Vector Transmission Alone Fails to Explain the Potato Yellow Vein Virus Epidemic among Potato Crops in Colombia

The potato yellow vein disease, caused by the potato yellow vein virus (PYVV), is a limiting potato disease in northern South America. The virus can be transmitted either by the greenhouse whitefly (GWF), Trialeurodes vaporariorum (Westwood) (Hemiptera: Aleyrodidae), or through vegetative propagules, such as infected tubers. Recently, GWF populations have been spotlighted as one of the main drivers of PYVV re-emergence, and consequently, PYVV management has been predominantly directed toward vector control, which is heavily based on insecticide use. However, the drivers of the PYVV outbreaks as well as the contribution of GWF populations on the spread of PYVV among potato crops are still not completely understood. This study aims to assess the role of the GWF as a driver of the PYVV epidemic in the potato-producing areas in Colombia, one of the countries more severely affected by the PYVV epidemic, and whose geography allows the study of the spatial association between the vector and the disease epidemic across a wide altitude range. The geographical clusters where the PYVV epidemic is concentrated, as well as those of farms affected by the GWF were identified using a novel spatial epidemiology approach. The influence of altitude range on the association between PYVV and T. vaporarioum was also assessed. We found a relatively poor spatial association between PYVV epidemic and the presence of the GWF, especially at altitudes above 3,000 m above mean sea level. Furthermore, GWF populations could only explain a small fraction of the extent of the PYVV epidemic in Colombia. Movement of infected seed tubers might be the main mechanism of dispersion, and could be a key driver for the PYVV infection among potato crops. Agricultural policies focused on improving quality of seed tubers and their appropriate distribution could be the most efficient control intervention against PYVV dispersion.

A comparative genomic analysis of putative pathogenicity genes in the host-specific sibling species Colletotrichum graminicola and Colletotrichum sublineola

Background

Colletotrichum graminicola and C. sublineola cause anthracnose leaf and stalk diseases of maize and sorghum, respectively. In spite of their close evolutionary relationship, the two species are completely host-specific. Host specificity is often attributed to pathogen virulence factors, including specialized secondary metabolites (SSM), and small-secreted protein (SSP) effectors. Genes relevant to these categories were manually annotated in two co-occurring, contemporaneous strains of C. graminicola and C. sublineola. A comparative genomic and phylogenetic analysis was performed to address the evolutionary relationships among these and other divergent gene families in the two strains.

Results

Inoculation of maize with C. sublineola, or of sorghum with C. graminicola, resulted in rapid plant cell death at, or just after, the point of penetration. The two fungal genomes were very similar. More than 50% of the assemblies could be directly aligned, and more than 80% of the gene models were syntenous. More than 90% of the predicted proteins had orthologs in both species. Genes lacking orthologs in the other species (non-conserved genes) included many predicted to encode SSM-associated proteins and SSPs. Other common groups of non-conserved proteins included transporters, transcription factors, and CAZymes. Only 32 SSP genes appeared to be specific to C. graminicola, and 21 to C. sublineola. None of the SSM-associated genes were lineage-specific. Two different strains of C. graminicola, and three strains of C. sublineola, differed in no more than 1% percent of gene sequences from one another.

Conclusions

Efficient non-host recognition of C. sublineola by maize, and of C. graminicola by sorghum, was observed in epidermal cells as a rapid deployment of visible resistance responses and plant cell death. Numerous non-conserved SSP and SSM-associated predicted proteins that could play a role in this non-host recognition were identified. Additional categories of genes that were also highly divergent suggested an important role for co-evolutionary adaptation to specific host environmental factors, in addition to aspects of initial recognition, in host specificity. This work provides a foundation for future functional studies aimed at clarifying the roles of these proteins, and the possibility of manipulating them to improve management of these two economically important diseases.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3457-9) contains supplementary material, which is available to authorized users.

A Colletotrichum graminicola mutant deficient in the establishment of biotrophy reveals early transcriptional events in the maize anthracnose disease interaction

BACKGROUND

Colletotrichum graminicola is a hemibiotrophic fungal pathogen that causes maize anthracnose disease. It progresses through three recognizable phases of pathogenic development in planta: melanized appressoria on the host surface prior to penetration; biotrophy, characterized by intracellular colonization of living host cells; and necrotrophy, characterized by host cell death and symptom development. A "Mixed Effects" Generalized Linear Model (GLM) was developed and applied to an existing Illumina transcriptome dataset, substantially increasing the statistical power of the analysis of C. graminicola gene expression during infection and colonization. Additionally, the in planta transcriptome of the wild-type was compared with that of a mutant strain impaired in the establishment of biotrophy, allowing detailed dissection of events occurring specifically during penetration, and during early versus late biotrophy.

RESULTS

More than 2000 fungal genes were differentially transcribed during appressorial maturation, penetration, and colonization. Secreted proteins, secondary metabolism genes, and membrane receptors were over-represented among the differentially expressed genes, suggesting that the fungus engages in an intimate and dynamic conversation with the host, beginning prior to penetration. This communication process probably involves reception of plant signals triggering subsequent developmental progress in the fungus, as well as production of signals that induce responses in the host. Later phases of biotrophy were more similar to necrotrophy, with increased production of secreted proteases, inducers of plant cell death, hydrolases, and membrane bound transporters for the uptake and egress of potential toxins, signals, and nutrients.

CONCLUSIONS

This approach revealed, in unprecedented detail, fungal genes specifically expressed during critical phases of host penetration and biotrophic establishment. Many encoded secreted proteins, secondary metabolism enzymes, and receptors that may play roles in host-pathogen communication necessary to promote susceptibility, and thus may provide targets for chemical or biological controls to manage this important disease. The differentially expressed genes could be used as 'landmarks' to more accurately identify developmental progress in compatible versus incompatible interactions involving genetic variants of both host and pathogen.

A first genetic map of date palm (Phoenix dactylifera) reveals long-range genome structure conservation in the palms

Background

The date palm is one of the oldest cultivated fruit trees. It is critical in many ways to cultures in arid lands by providing highly nutritious fruit while surviving extreme heat and environmental conditions. Despite its importance from antiquity, few genetic resources are available for improving the productivity and development of the dioecious date palm. To date there has been no genetic map and no sex chromosome has been identified.

Results

Here we present the first genetic map for date palm and identify the putative date palm sex chromosome. We placed ~4000 markers on the map using nearly 1200 framework markers spanning a total of 1293 cM. We have integrated the genetic map, derived from the Khalas cultivar, with the draft genome and placed up to 19% of the draft genome sequence scaffolds onto linkage groups for the first time. This analysis revealed approximately ~1.9 cM/Mb on the map. Comparison of the date palm linkage groups revealed significant long-range synteny to oil palm. Analysis of the date palm sex-determination region suggests it is telomeric on linkage group 12 and recombination is not suppressed in the full chromosome.

Conclusions

Based on a modified gentoyping-by-sequencing approach we have overcome challenges due to lack of genetic resources and provide the first genetic map for date palm. Combined with the recent draft genome sequence of the same cultivar, this resource offers a critical new tool for date palm biotechnology, palm comparative genomics and a better understanding of sex chromosome development in the palms.

Evidence for a diffusible factor that induces susceptibility in the Colletotrichum-maize disease interaction

Colletotrichum graminicola, the causal agent of maize anthracnose, is a hemibiotrophic fungus that initially infects living host cells via primary hyphae surrounded by a membrane. A nonpathogenic mutant disrupted in a gene encoding a component of the signal peptidase complex, and believed to be deficient in protein processing and secretion, regained pathogenicity when it was inoculated onto maize leaf sheaths close to the wild-type fungus. Evidence is presented suggesting that the wild-type produces a diffusible factor(s) that induces the localized susceptibility of host cells at the borders of expanding colonies, causing them to become receptive to biotrophic invasion. The induced susceptibility effect is limited to a distance of approximately eight cells from the edge of the wild-type colony, is dosage dependent and is specific to C. graminicola.

Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses

Colletotrichum species are fungal pathogens that devastate crop plants worldwide. Host infection involves the differentiation of specialized cell types that are associated with penetration, growth inside living host cells (biotrophy) and tissue destruction (necrotrophy). We report here genome and transcriptome analyses of Colletotrichum higginsianum infecting Arabidopsis thaliana and Colletotrichum graminicola infecting maize. Comparative genomics showed that both fungi have large sets of pathogenicity-related genes, but families of genes encoding secreted effectors, pectin-degrading enzymes, secondary metabolism enzymes, transporters and peptidases are expanded in C. higginsianum. Genome-wide expression profiling revealed that these genes are transcribed in successive waves that are linked to pathogenic transitions: effectors and secondary metabolism enzymes are induced before penetration and during biotrophy, whereas most hydrolases and transporters are upregulated later, at the switch to necrotrophy. Our findings show that preinvasion perception of plant-derived signals substantially reprograms fungal gene expression and indicate previously unknown functions for particular fungal cell types.

[Comparative analysis of growth and sexual maturation in girls of Santa Rosa (La Pampa) and La Plata (Buenos Aires), Argentina]

The aim of this study was to analyze growth in relation to menarche in girls from two Argentinean urban populations. We performed a comparative-descriptive cross sectional study in 2474 schoolchildren between 8.0 and 16.9 years old from Santa Rosa (SR) and La Plata (LP) cities. We registered the presence of menarche and anthropometrics variables of body weight, total and sitting heights, arm circumference, triceps and subscapular skinfolds. Body mass index, subscapular/triceps index and muscle and fat arm areas were calculated. The study group was divided into 4 groups according to the city and menarche. The socio-environmental structured survey indicated significant differences between cities with these variables: tenure status, building materials and services, health care coverage, cash assistance, educational level and parents' occupation, therefore establishing a higher welfare in youngsters of SR. Menarche at a mean age of 12.7 years old was more prevalent in SR (40.6%) than in LP (33.7%) (c2 = 12.9; p < 0.01). The ANOVA indicated significant differences between cities in total and sitting heights and muscle area (p < 0.01), body weight and arm circumference (p < 0.05) which were generally held in the post hoc comparison by age in pre-menarche and post-menarche groups. The presence of a small body size at the expense of lowering in: total height, muscle area and leg length in LP youngsters, associated with a lower prevalence of menarche in this city, it would represents the adaptive cost of a lower welfare environment.

Fish fauna as an indicator of environmental quality in an urbanised region of the Amazon estuary

This study describes the biological importance of Guajará Bay (Belém, Pará, Brazil) for fish fauna and presents a diagnosis of water quality in the main channel and creeks, using the icthyofauna as an ecological indicator. A total of 567 individuals from 40 species were identified. About 58% of these use Guajará Bay as a nursery ground, 49 and 81% use the bay as a breeding and feeding ground, respectively. There were no significant differences between environments as measured by the diversity index; however, fish relative abundance (catch per unit of effort) was greater in the creeks than in the main channel. A significant difference was detected in the fish fauna inhabiting the main channel compared with the creeks. In the main channel, icthyofauna significantly differed during December relative to other months.

Reduced ratio of protective versus proinflammatory cytokine responses to commensal bacteria in HLA-B27 transgenic rats

Germ-free HLA-B27 transgenic (TG) rats do not develop colitis, but colonization with specific pathogen-free (SPF) bacteria induces colitis accompanied by immune activation. To study host-dependent immune responses to commensal caecal bacteria we investigated cytokine profiles in mesenteric lymph node (MLN) cells from HLA-B27 TG versus nontransgenic (non-TG) littermates after in vitro stimulation with caecal bacterial lysates (CBL). Supernatants from CBL-stimulated unseparated T- or B- cell-depleted MLN cells from HLA-B27 TG and non-TG littermates were analysed for IFN-gamma, IL-12, TNF, IL-10 and TGF-beta production. Our results show that unfractionated TG MLN cells stimulated with CBL produced more IFN-gamma, IL-12 and TNF than did non-TG MLN cells. In contrast, CBL-stimulated non-TG MLN cells produced more IL-10 and TGF-beta. T cell depletion abolished IFN-gamma and decreased IL-12 production, but did not affect IL-10 and TGF-beta production. Conversely, neither IL-10 nor TGF-beta was produced in cultures of B cell-depleted MLN. In addition, CD4(+) T cells enriched from MLN of HLA-B27 TG but not from non-TG rats produced IFN-gamma when cocultured with CBL-pulsed antigen presenting cells from non-TG rats. Interestingly, IL-10 and TGF-beta, but not IFN-gamma, IL-12 and TNF were produced by MLN cells from germ-free TG rats. These results indicate that the colitis that develops in SPF HLA-B27 TG rats is accompanied by activation of IFN-gamma-producing CD4(+) T cells that respond to commensal bacteria. However, B cell cytokine production in response to components of commensal intestinal microorganisms occurs in the absence of intestinal inflammation.

Effect of the flow field on the rheological behavior of aqueous cetyltrimethylammonium p-toluenesulfonate solutions

It is well-known that solutions of cetyltrimethylammonium p-toluenesulfonate in water exhibit a pronounced shear-thickening phenomenon in a specific concentration range (0.1-0.8%) when they are subjected to simple-shear flows, as a consequence of flow-induced self-assembly of wormlike micelles. This work shows that a strong elongational flow field (opposed-jets flow), applied to the same solutions, does not lead to extension thickening because the extensional flow prevents or destroys micellar association. In flow through a porous medium, a substantial increase in apparent viscosity is observed beyond a critical apparent shear rate, which surpasses increases observed in simple-shear flows. This is explained as the result of a synergistic effect of shear and relatively weak elongation on the solution microstructure.

Cluster of Mycobacterium chelonae keratitis cases following laser in-situ keratomileusis

PURPOSE

To describe a cluster of Mycobacterium chelonae keratitis cases involving patients who underwent laser in-situ keratomileusis (LASIK) at a single refractive surgery center.

DESIGN

Descriptive case series of four patients and cohort study to identify disease associations.

METHODS

Examination schedules, diagnostic tests, and therapy were based on best medical judgment. Isolates from three patients were compared by pulsed-field gel electrophoresis. Epidemiologic studies were performed to identify the source of infection.

RESULTS

Seven of eight eyes developed M. chelonae keratitis following bilateral simultaneous LASIK. Each patient was thought to have diffuse lamellar keratitis initially, but all seven eyes were noted to have opacities suggestive of infectious keratitis by 13 to 21 days after surgery. All eyes had undergone hyperopic LASIK over four days in April 2001 by one surgeon in a community-based refractive surgery center. A cohort study of all patients undergoing LASIK at the same center in April 2001 revealed that M. chelonae keratitis occurred only in persons undergoing correction of hyperopia (seven of 14 eyes vs. none of 217 eyes undergoing myopic LASIK, P <.001). The only difference identified between procedures was use of masks created from a soft contact lens in hyperopic LASIK. Three isolates (three patients) were indistinguishable by pulsed-field gel electrophoresis. Eyes were treated with a combination of antimicrobial agents, including topical azithromycin in three patients, with resolution of infection in all eyes over 6 to 14 weeks. The source of infection was not identified on environmental cultures.

CONCLUSION

Postoperative nontuberculous mycobacterial keratitis can occur in an epidemic fashion following LASIK. Topical amikacin, azithromycin, clarithromycin, ciprofloxacin, or a combination of these agents, appears to be effective treatment for these infections.

Norfloxacin monodose use in patients with cholera in Salta Argentina

The use of monodose (800 mg) per os of Norfloxacin was evaluated in 32 patients with cholera at Salvador Mazza's Hospital, Salta, Argentina. It was considered the celerity in negativization of stool culture (100% of cases: 12 hours post administration), it efficiency along time (24/24 controlled patients were negative at 10th day) and MIC of isolated strains (100% of strains were sensitive: range 0.008 to 0.016 micrograms/ml). It was included oral administration of sorbitol 70% in peanut oil in order to study patients at 10th day's control. This method could be an alternative one in the study of asymptomatic carrier. Norfloxacin monodose shows good performance in early negativization of stool culture and it was also effective along the whole observation period, suggesting it could prevent carriage.

Cutaneous leishmaniasis in Guatemala: isoenzyme characterization of isolates from humans

Leishmania organisms cultivated from cutaneous lesions of humans in Guatemala were characterized by cellulose acetate electrophoresis. Six isolates had electrophoretic enzyme patterns identical to World Health Organization reference strains of Leishmania braziliensis braziliensis, and 5 had patterns identical to reference strains of Leishmania mexicana mexicana.