Cotton leafroll dwarf disease: An enigmatic viral disease in cotton

Taxonomy: Cotton leafroll dwarf virus (CLRDV) is a member of the genus Polerovirus, family Solemoviridae. Geographical Distribution: CLRDV is present in most cotton-producing regions worldwide, prominently in North and South America. Physical Properties : The virion is a nonenveloped icosahedron with T = 3 icosahedral lattice symmetry that has a diameter of 26–34 nm and comprises 180 molecules of the capsid protein. The CsCl buoyant density of the virion is 1.39–1.42 g/cm³ and S_20w is 115–127S. Genome: CLRDV shares genomic features with other poleroviruses; its genome consists of monopartite, single-stranded, positive-sense RNA, is approximately 5.7–5.8 kb in length, and is composed of seven open reading frames (ORFs) with an intergenic region between ORF2 and ORF3a. Transmission: CLRDV is transmitted efficiently by the cotton aphid (Aphis gossypii Glover) in a circulative and nonpropagative manner. Host: CLRDV has a limited host range. Cotton is the primary host, and it has also been detected in different weeds in and around commercial cotton fields in Georgia, USA. Symptoms: Cotton plants infected early in the growth stage exhibit reddening or bronzing of foliage, maroon stems and petioles, and drooping. Plants infected in later growth stages exhibit intense green foliage with leaf rugosity, moderate to severe stunting, shortened internodes, and increased boll shedding/abortion, resulting in poor boll retention. These symptoms are variable and are probably influenced by the time of infection, plant growth stage, varieties, soil health, and geographical location. CLRDV is also often detected in symptomless plants. Control: Vector management with the application of chemical insecticides is ineffective. Some host plant varieties grown in South America are resistant, but all varieties grown in the United States are susceptible. Integrated disease management strategies, including weed management and removal of volunteer stalks, could reduce the abundance of virus inoculum in the field.     

Genes, diet and serum lipid concentrations: lessons from ethnically diverse populations and their relevance to coronary heart disease in Asia

PURPOSE OF REVIEW: The burden of coronary heart disease (CHD) in Asia has risen in tandem with socio-economic development and urbanization. Although all ethnic groups have been affected, some appear to be at particularly high risk. The basis of these ethnic differences remains poorly understood. RECENT FINDINGS: Differing levels of risk factors for CHD have been observed between ethnic groups. Previous studies, however, may be confounded by a large ethnic variation in socio-economic status and place of residence. Few studies have taken dietary factors into account. Recent studies involving Chinese, Malays and Asian Indians living in Singapore suggest that neither dietary nor genetic factors, taken in isolation, sufficiently explain ethnic differences in serum lipid profiles. Several genetic variants in key candidate genes (apolipoprotein E, APOE, cholesteryl ester transfer protein, CETP and hepatic lipase, LIPC) have recently been found to modulate the association between dietary factors and serum lipid concentrations in these ethnic groups and in other populations. SUMMARY: To fully evaluate the differences in CHD risk between ethnic groups, environmental exposures, including dietary factors need to be carefully evaluated, and gene-environment interactions that may give rise to these differences need to be taken into account. These are critical steps in the development of targeted strategies to contain the epidemic of coronary heart disease in Asia. An understanding of the basis of these differences may also provide insights into the pathogenesis of disease that one cannot get through the examination of more homogenous populations.     

Thermoadaptation trait revealed by the genome sequence of thermophilic Geobacillus kaustophilus

We present herein the first complete genome sequence of a thermophilic Bacillus-related species, Geobacillus kaustophilus HTA426, which is composed of a 3.54 Mb chromosome and a 47.9 kb plasmid, along with a comparative analysis with five other mesophilic bacillar genomes. Upon orthologous grouping of the six bacillar sequenced genomes, it was found that 1257 common orthologous groups composed of 1308 genes (37%) are shared by all the bacilli, whereas 839 genes (24%) in the G.kaustophilus genome were found to be unique to that species. We were able to find the first prokaryotic sperm protamine P1 homolog, polyamine synthase, polyamine ABC transporter and RNA methylase in the 839 unique genes; these may contribute to thermophily by stabilizing the nucleic acids. Contrasting results were obtained from the principal component analysis (PCA) of the amino acid composition and synonymous codon usage for highlighting the thermophilic signature of the G.kaustophilus genome. Only in the PCA of the amino acid composition were the Bacillus-related species located near, but were distinguishable from, the borderline distinguishing thermophiles from mesophiles on the second principal axis. Further analysis revealed some asymmetric amino acid substitutions between the thermophiles and the mesophiles, which are possibly associated with the thermoadaptation of the organism.     

Multilocus interactions restrict gene introgression in interspecific populations of polyploid Gossypium (cotton)

Abstract.— Experimental advanced-generation backcross populations contain individuals with genomic compositions similar to those resulting from interspecific hybridization in nature. By applying a detailed restriction fragment length polymorphism (RFLP) map to 3662 BC₃F₂ plants derived from 24 different BC₁ individuals of a cross between Gossypium hirsutum and G. barbadense , large and widespread deficiencies of donor ( G. barbadense ) chromatin were found, and seven independent chromosomal regions were entirely absent. This skewed chromatin transmission is best accounted for by multilocus epistatic interactions affecting chromatin transmission. The observed frequencies of two-locus genotypes were significantly different from Mendelian expectations about 26 times more often than could be explained by chance ( P ≤ 0.01). For identical pairs of loci, different two-locus genotypes occurred in excess in different BC₃ families, implying the existence of higher-order interlocus interactions beyond the resolution of these data. Some G. barbadense markers occurred more frequently than expected by chance, indicating that genomic interactions do not always favor host chromatin. A preponderance of interspecific allelic interactions involved one locus each in the two different subgenomes of (allotetraploid) Gossypium , thus supporting several other lines of evidence suggesting that intersubgenomic interactions contribute to unique features that distinguish tetraploid cotton from its diploid ancestors.     

Two genes encoding fruit body lectins of Pleurotus cornucopiae: sequence similarity with the lectin of a nematode-trapping fungus

Our previous studies on the fruit body lectin of Pleurotus cornucopiae revealed the existence of three isolectins, composed of two homodimers and one heterodimer of 16- and 15-kDa subunits. In this study, two genes encoding the lectins were cloned and characterized. Both genes encoded 144 amino acids and only 5 amino acids were different within the coding region, but the nucleotide sequences of the 5'-upstream and 3'-downstream regions differed extensively. Southern hybridization with gene-specific probes showed that one gene encoded the 16-kDa and the other encoded the 15-kDa subunit. Functional lectins were synthesized in Escherichia coli under the direction of these genes. On SDS-PAGE, the recombinant lectins showed the same banding patterns as the native lectins. In amino acid sequence, these lectins showed extensive similarity with the lectin from a nematode-trapping ascomycete fungus, Arthrobotrys oligospora, suggesting that the lectins might also function in capturing nematodes.     

Strain-Specific Differences in Surface Antigens of Symbiotic Algae

Intracellular symbiotic dinoflagellates (zooxanthellae) isolated from different invertebrate hosts are morphologically similar but could be differentiated by the fluorescent-antibody technique.     

SARS-CoV-2 lineage B.6 was the major contributor to early pandemic transmission in Malaysia

Malaysia had 10,219 confirmed cases of COVID-19 as of September 20, 2020. About 33% were associated with a Tablighi Jamaat religious mass gathering held in Kuala Lumpur between February 27 and March 3, 2020, which drove community transmission during Malaysia’s second wave. We analysed genome sequences of SARS-CoV-2 from Malaysia to better understand the molecular epidemiology and spread. We obtained 58 SARS-CoV-2 whole genome sequences from patients in Kuala Lumpur and performed phylogenetic analyses on these and a further 57 Malaysian sequences available in the GISAID database. Nine different SARS-CoV-2 lineages (A, B, B.1, B.1.1, B.1.1.1, B.1.36, B.2, B.3 and B.6) were detected in Malaysia. The B.6 lineage was first reported a week after the Tablighi mass gathering and became predominant (65.2%) despite being relatively rare (1.4%) globally. Direct epidemiological links between lineage B.6 viruses and the mass gathering were identified. Increases in reported total cases, Tablighi-associated cases, and community-acquired B.6 lineage strains were temporally linked. Non-B.6 lineages were mainly travel-associated and showed limited onward transmission. There were also temporally correlated increases in B.6 sequences in other Southeast Asian countries, India and Australia, linked to participants returning from this event. Over 95% of global B.6 sequences originated from Asia Pacific. We also report a nsp3-C6310A substitution found in 47.3% of global B.6 sequences which was associated with reduced sensitivity using a commercial diagnostic real-time PCR assay. Lineage B.6 became the predominant cause of community transmission in Malaysia after likely introduction during a religious mass gathering. This event also contributed to spikes of lineage B.6 in other countries in the Asia-Pacific. Mass gatherings can be significant causes of local and global spread of COVID-19. Shared genomic surveillance can be used to identify SARS-CoV-2 transmission chains to aid prevention and control, and to monitor diagnostic molecular assays.Clinical Trial Registration: COVID-19 paper.