Application of Bacillus species in the control of root rot diseases of crop plants

Bio control potential of three Bacillus spp viz., Bacillus subtilis, B. thuringiensis and B. cereus, against soil borne root-infecting fungi on cowpea and mash bean plants were tested both in vitro and in vivo. All three species showed efficiency and produced nodules on mash bean and cow pea plants. In vitro dual culture plate method showed significant inhibition of Fusarium spp. by all these three species of Bacillus with the appearance of a prominent zone of inhibition while a maximum zone of inhibition of Fusarium spp. was observed by B. thuringiensis, whereas in case of Macrophomina phaseolina and Rhizoctonia solani, the highest zone of inhibition was observed by B. subtilis. Bacillus spp. used as seed dressing and soil drenching showed a significant increase in shoot length, shoot weight, root length and root weight in cow pea and mash bean plants. Maximum shoot length was observed in cow pea plants where Bacillus spp. were drenched in soil, whereas maximum root length and root weight in cow pea was observed when B. thuringiensis used as seed dressing. Seed dressing and soil drenching with species of Bacillus viz., B. subtilis, B. thuringiensis and B. cereus, were found to be an effective method for the control of soil borne root-infecting fungi like M. phaseolina, R. solani and Fusarium spp., on cow pea and mash bean plants.     

Virulence and Molecular Diversity of Venturia inaequalis in Commercial Apple Growing Regions in Kashmir

Seventy‐one isolates of Venturia inaequalis collected from commercial apple growing areas of Kashmir were characterized on international differential apple hosts and analyzed by Random Amplified Polymorphic Microsatellites (RAMS), PCR–RFLP and sequencing of rDNA for elucidation of variability. Virulence analysis on a differential set categorized them into four pathogenic races, viz. (0), (1), (2) and (1,2) in the first time comprehensive molecular analysis of this in India and especially from Jammu and Kashmir, a north‐western Himalayan state of India. Race groups (0), (1), (2) and (1,2) contained isolates from diverse areas without specificity to any geographical zone or region. Cluster analysis of the RAMS and PCR–RFLP revealed a high genotypic diversity within V. inaequalis isolates. Three major clusters were obtained and the isolates could not be categorized on the basis of either their geographical distribution or the cultivar from which they were isolated. amova analysis of pathogen populations at regional or race level revealed high diversity within the populations. Pairwise F_ST comparisons between the populations revealed less genetic differentiation, thereby indicating existence of frequent gene flow in Kashmir. The 24 rDNA sequences of V. inaequalis showed high haplotype diversity of 0.938 and 0.40 nucleotide diversity. Again clustering at regional or race level detected greater part of variability within groups than among groups, thereby indicating high diversity in V. inaequalis populations in Kashmir valley.     

Evaluation of Genome Sequencing Quality in Selected Plant Species Using Expressed Sequence Tags

Background

With the completion of genome sequencing projects for more than 30 plant species, large volumes of genome sequences have been produced and stored in online databases. Advancements in sequencing technologies have reduced the cost and time of whole genome sequencing enabling more and more plants to be subjected to genome sequencing. Despite this, genome sequence qualities of multiple plants have not been evaluated.

Methodology/Principal Finding

Integrity and accuracy were calculated to evaluate the genome sequence quality of 32 plants. The integrity of a genome sequence is presented by the ratio of chromosome size and genome size (or between scaffold size and genome size), which ranged from 55.31% to nearly 100%. The accuracy of genome sequence was presented by the ratio between matched EST and selected ESTs where 52.93% ∼ 98.28% and 89.02% ∼ 98.85% of the randomly selected clean ESTs could be mapped to chromosome and scaffold sequences, respectively. According to the integrity, accuracy and other analysis of each plant species, thirteen plant species were divided into four levels. Arabidopsis thaliana, Oryza sativa and Zea mays had the highest quality, followed by Brachypodium distachyon, Populus trichocarpa, Vitis vinifera and Glycine max, Sorghum bicolor, Solanum lycopersicum and Fragaria vesca, and Lotus japonicus, Medicago truncatula and Malus × domestica in that order. Assembling the scaffold sequences into chromosome sequences should be the primary task for the remaining nineteen species. Low GC content and repeat DNA influences genome sequence assembly.

Conclusion

The quality of plant genome sequences was found to be lower than envisaged and thus the rapid development of genome sequencing projects as well as research on bioinformatics tools and the algorithms of genome sequence assembly should provide increased processing and correction of genome sequences that have already been published.     

Structure reveals function of the dual variable domain immunoglobulin (DVD-Ig™) molecule

Several bispecific antibody-based formats have been developed over the past 25 years in an effort to produce a new generation of immunotherapeutics that target two or more disease mechanisms simultaneously. One such format, the dual-variable domain immunoglobulin (DVD-Ig™), combines the target binding domains of two monoclonal antibodies via flexible naturally occurring linkers, which yields a tetravalent IgG - like molecule. We report the structure of an interleukin (IL)12-IL18 DVD-Ig™ Fab (DFab) fragment with IL18 bound to the inner variable domain (VD) that reveals the remarkable flexibility of the DVD-Ig™ molecule and how the DVD-Ig™ format can function to bind four antigens simultaneously. An understanding of how the inner variable domain retains function is of critical importance for designing DVD-Ig™ molecules, and for better understanding of the flexibility of immunoglobulin variable domains and linkers, which may aid in the design of improved bi- and multi-specific biologics in general.     

Ethnobotanical assessment of plant resources of Banda Daud Shah,District Karak,Pakistan

Background

The Indigenous knowledge of plants is scientifically and culturally very significant. This paper elucidates the empirical findings of an ethnobotanical survey of Banda Daud Shah, District Karak, Pakistan.

Methods

Data collection was carried out from October 2011 to September 2012. Total twelve survey trips were made, three in each season. About 100 respondents were interviewed; most of them were aged people between 60–70 years. Interviews were conducted using structured questionnaire composed of variety of questions regarding ethnomedicinal uses of plants of the study area. Direct matrix ranking (DMR), informant citations and market survey of multipurpose plants were also carried out.

Results

The local community was using 58 plant species belonging to 52 genera and 34 families for different purposes. A total of 25 plant species were herbs followed by 18 shrubs. Leaf (45%) was the most commonly used plant part followed by the whole plants (23%). In total, 40 plant species were medicinally used to treat variety of diseases, of which highest number of species being used for gastro-intestinal problems (19 spp.), expectorant (3 spp.) and antipyretic (3 spp.). Beside medicinal values, 25 species were used for fuel and 18 for fodder purposes. Informant consensus showed that gastrointestinal and respiratory infections were ranked highest (F_IC?=?0.75) among all ailments. According to DMR output, Dalbergia sisso ranked first due to high multipurpose uses among all species and was found most threatened with higher market value.

Conclusion

The investigated area is rural in nature and the inhabitants are highly dependent on the native plants for their health care needs and other requirements like fuel wood and fodder due to financial constraints and unavailability of resources. Medicinal plants for high ranked diseases may be phtyochemicaly and pharmacologically investigated to prove their efficacy. The local medicinal flora is facing overexploitation, overgrazing and improper way of collection. Proper conservation strategies such as controlled grazing, reforestation and rangeland management among many others may be adopted to promote the sustainable use of medicinal plants.

     

Use of Whole Genome Sequencing to Determine the Microevolution of Mycobacterium tuberculosis during an Outbreak

Rationale

Current tools available to study the molecular epidemiology of tuberculosis do not provide information about the directionality and sequence of transmission for tuberculosis cases occurring over a short period of time, such as during an outbreak. Recently, whole genome sequencing has been used to study molecular epidemiology of Mycobacterium tuberculosis over short time periods.

Objective

To describe the microevolution of M. tuberculosis during an outbreak caused by one drug-susceptible strain.

Method and Measurements

We included 9 patients with tuberculosis diagnosed during a period of 22 months, from a population-based study of the molecular epidemiology in San Francisco. Whole genome sequencing was performed using Illumina’s sequencing by synthesis technology. A custom program written in Python was used to determine single nucleotide polymorphisms which were confirmed by PCR product Sanger sequencing.

Main results

We obtained an average of 95.7% (94.1–96.9%) coverage for each isolate and an average fold read depth of 73 (1 to 250). We found 7 single nucleotide polymorphisms among the 9 isolates. The single nucleotide polymorphisms data confirmed all except one known epidemiological link. The outbreak strain resulted in 5 bacterial variants originating from the index case A1 with 0–2 mutations per transmission event that resulted in a secondary case.

Conclusions

Whole genome sequencing analysis from a recent outbreak of tuberculosis enabled us to identify microevolutionary events observable during transmission, to determine 0–2 single nucleotide polymorphisms per transmission event that resulted in a secondary case, and to identify new epidemiologic links in the chain of transmission.     

Fetal DNA Methylation Associates with Early Spontaneous Preterm Birth and Gestational Age

Spontaneous preterm birth (PTB, <37 weeks gestation) is a major public health concern, and children born preterm have a higher risk of morbidity and mortality throughout their lives. Recent studies suggest that fetal DNA methylation of several genes varies across a range of gestational ages (GA), but it is not yet clear if fetal epigenetic changes associate with PTB. The objective of this study is to interrogate methylation patterns across the genome in fetal leukocyte DNA from African Americans with early PTB (24^1/7–34^0/7 weeks; N = 22) or term births (39^0/7–40^6/7weeks; N = 28) and to evaluate the association of each CpG site with PTB and GA. DNA methylation was assessed across the genome with the HumanMethylation450 BeadChip. For each individual sample and CpG site, the proportion of DNA methylation was estimated. The associations between methylation and PTB or GA were evaluated by fitting a separate linear model for each CpG site, adjusting for relevant covariates. Overall, 29 CpG sites associated with PTB (FDR<.05; 5.7×10⁻¹⁰<p<2.9×10⁻⁶) independent of GA. Also, 9637 sites associated with GA (FDR<.05; 9.5×10⁻¹⁶<p<1.0×10⁻³), with 61.8% decreasing in methylation with shorter GA. GA-associated CpG sites were depleted in the CpG islands of their respective genes (p<2.2×10⁻¹⁶). Gene set enrichment analysis (GSEA) supported enrichment of GA-associated CpG sites in genes that play a role in embryonic development as well as the extracellular matrix. Additionally, this study replicated the association of several CpG sites associated with gestational age in other studies (CRHBP, PIK3CD and AVP). Dramatic differences in fetal DNA methylation are evident in fetuses born preterm versus at term, and the patterns established at birth may provide insight into the long-term consequences associated with PTB.