A tabu search algorithm for post-processing multiple sequence alignment

Tabu search is a meta-heuristic approach that is proven to be useful in solving combinatorial optimization problems. We implement the adaptive memory features of tabu search to refine a multiple sequence alignment. Adaptive memory helps the search process to avoid local optima and explores the solution space economically and effectively without getting trapped into cycles. The algorithm is further enhanced by introducing extended tabu search features such as intensification and diversification. The neighborhoods of a solution are generated stochastically and a consistency-based objective function is employed to measure its quality. The algorithm is tested with the datasets from BAliBASE benchmarking database. We have observed through experiments that tabu search is able to improve the quality of multiple alignments generated by other software such as ClustalW and T-Coffee. The source code of our algorithm is available at http://www.bii.a-star.edu.sg/~tariq/tabu/.     

Genomewide significant linkage to stuttering on chromosome 12

Stuttering is a common and sometimes severe communication disorder, of unknown primary etiology, that exists in populations worldwide. Many types of evidence suggest a genetic contribution to stuttering; however, the complex inheritance of this disorder has hindered identification of these factors. We have employed highly inbred families to increase the power of linkage analysis of this disorder. Forty-four Pakistani families with documented or probable consanguinity, from the city of Lahore and surrounding areas, were included. Each family contained multiple cases of stuttering, which were diagnosed using the Stuttering Severity Instrument. Using the Marshfield Weber 9 marker panel, we performed a genomewide linkage scan focused on affected individuals and their parents. The analysis included 199 genotyped individuals, 144 affected and 55 unaffected. The Pedigree Relationship Statistical Test (PREST) was used to identify pedigrees that required additional specification of inbreeding. Initial nonparametric analysis gave evidence of linkage on chromosomes 1, 5, 7, and 12. Additional genotyping was performed on chromosome 12 to a 5-cM level of resolution, and 16 additional individuals were then included, bringing the number of families to 46. Analysis of the enlarged data set provided consistent evidence of linkage on chromosome 12: the S(homoz) scoring function gave a nonparametric LOD score of 4.61, and a LOD score of 3.51 was obtained using the S(all) scoring function. These results suggest that a locus on chromosome 12q may contain a gene with a large effect in this sample.     

New natural cholinesterase inhibiting and calcium channel blocking quinoline alkaloids

During this study, one new coumarin; 7-O-beta-D-glucopyranoside-2H-1-benzopyran-2-one (1) and three quinoline alkaloids; 3-hydroxy, 2, 2, 6-trimethyl-3, 4, 5, 6-tetrahydro-2H-pyrano[3,2-c] quinoline 5-one (2), ribalinine (3) and methyl isoplatydesmine (4) were isolated from the aerial parts of Skimmia laureola and their structures established by spectroscopic studies. Compounds 2-4 were found to be linear mixed type inhibitors of acetylcholinesterase (K(i) = 110.0, 30.0 and 30.0 microM, respectively). Compounds 2 and 3 were also found to be linear mixed type inhibitors of butyrylcholinesterase, while compound 4 was a noncompetitive inhibitor of the enzyme (K(i) = 90.0, 70.0 and 19.0 microM, respectively). The inhibition of acetyl- and butyryl-cholinesterase enzymes persists as the most promising therapeutic strategy for activating the impaired cholinergic functions in Alzheimer's disease and related dementias. Compound 4 also showed dose-dependent spasmolytic activity in the isolated rabbit jejunum intestinal preparation by relaxing the spontaneous (EC50 = 0.1 mg/mL) and K(+)-induced contractions (EC50 = 0.4 mg/mL), suggesting that the spasmolytic effect of compound 4 is mediated through the blockade of voltage-dependent Ca2+ channels.     

A framework genetic map of Muscadinia rotundifolia

This study presents a framework linkage map based on microsatellite markers for Muscadinia rotundifolia (1n?=?20). The mapping population consisted of 206 progeny generated from a cross of two M. rotundifolia varieties, 'Fry' and 'Trayshed'. A total of 884 primers were tested for their ability to amplify markers: 686 amplified and 312 simple sequence repeat (SSR) primer pairs generated 322 polymorphic markers for either one or both parents. The map for the female parent 'Fry' consisted of 212 markers and covered 879?cM on 18 chromosomes. The average distance between the markers was 4.1?cM and chromosome 6 was not represented due to a lack of polymorphic markers. The map for the male parent 'Trayshed' consisted of 191 markers and covered 841?cM on 19 chromosomes. The consensus map consisted of 314 markers on 19 chromosomes with a total distance of 1,088?cM, which represented 66?% of the distance covered by the Vitis vinifera reference linkage map. Marker density varied greatly among chromosomes from 5 to 35 mapped markers. Relatively good synteny was observed across 19 chromosomes based on markers in common with the V. vinifera reference map. Extreme segregation distortion was observed for chromosome 8 and 14 on the female parent map, and 4 on the male parent map. The lack of mapping coverage for the 20th M. rotundifolia chromosome is discussed in relation to possible evolutionary events that led to the reduction in chromosome number from 21 to 19 in the ancestral genome.     

Comparative geno-plasticity analysis of Mycoplasma bovis HB0801 (Chinese isolate)

Mycoplasma bovis pneumonia in cattle has been epidemic in China since 2008. To investigate M. bovis pathogenesis, we completed genome sequencing of strain HB0801 isolated from a lesioned bovine lung from Hubei, China. The genomic plasticity was determined by comparing HB0801 with M. bovis strain ATCC? 25523?/PG45 from cow mastitis milk, Chinese strain Hubei-1 from lesioned lung tissue, and 16 other Mycoplasmas species. Compared to PG45, the genome size of HB0801 was reduced by 11.7 kb. Furthermore, a large chromosome inversion (580 kb) was confirmed in all Chinese isolates including HB0801, HB1007, a strain from cow mastitis milk, and Hubei-1. In addition, the variable surface lipoproteins (vsp) gene cluster existed in HB0801, but contained less than half of the genes, and had poor identity to that in PG45, but they had conserved structures. Further inter-strain comparisons revealed other mechanisms of gene acquisition and loss in HB0801 that primarily involved insertion sequence (IS) elements, integrative conjugative element, restriction and modification systems, and some lipoproteins and transmembrane proteins. Subsequently, PG45 and HB0801 virulence in cattle was compared. Results indicated that both strains were pathogenic to cattle. The scores of gross pathological assessment for the control group, and the PG45- and HB0801-infected groups were 3, 13 and 9, respectively. Meanwhile the scores of lung lesion for these three groups were 36, 70, and 69, respectively. In addition, immunohistochemistry detection demonstrated that both strains were similarly distributed in lungs and lymph nodes. Although PG45 showed slightly higher virulence in calves than HB0801, there was no statistical difference between the strains (P>0.05). Compared to Hubei-1, a total of 122 SNP loci were disclosed in HB0801. In conclusion, although genomic plasticity was thought to be an evolutionary advantage, it did not apparently affect virulence of M. bovis strains in cattle.     

Mesenchymal stem cells conditioned with glucose depletion augments their ability to repair-infarcted myocardium

Mesenchymal stem cells (MSCs) are an attractive candidate for autologous cell therapy, but their ability to repair damaged myocardium is severely compromised with advanced age. Development of viable autologous cell therapy for treatment of heart failure in the elderly requires the need to address MSC ageing. In this study, MSCs from young (2 months) and aged (24 months) C57BL/6 mice were characterized for gene expression of IGF‐1, FGF‐2, VEGF, SIRT‐1, AKT, p16^INK4a, p21 and p53 along with measurements of population doubling (PD), superoxide dismutase (SOD) activity and apoptosis. Aged MSCs displayed senescent features compared with cells isolated from young animals and therefore were pre‐conditioned with glucose depletion to enhance age affected function. Pre‐conditioning of aged MSCs led to an increase in expression of IGF‐1, AKT and SIRT‐1 concomitant with enhanced viability, proliferation and delayed senescence. To determine the myocardial repair capability of pre‐conditioned aged MSCs, myocardial infarction (MI) was induced in 24 months old C57BL/6 wild type mice and GFP expressing untreated and pre‐conditioned aged MSCs were transplanted. Hearts transplanted with pre‐conditioned aged MSCs showed increased expression of paracrine factors, such as IGF‐1, FGF‐2, VEGF and SDF‐1α. This was associated with significantly improved cardiac performance as measured by dp/dt_max, dp/dt_min, LVEDP and LVDP, declined left ventricle (LV) fibrosis and apoptosis as measured by Masson's Trichrome and TUNEL assays, respectively, after 30 days of transplantation. In conclusion, pre‐conditioning of aged MSCs with glucose depletion can enhance proliferation, delay senescence and restore the ability of aged cells to repair senescent infarcted myocardium.     

Molecular evidence for a single genetic clone of invasive Arundo donax in the United States

Arundo donax (giant reed) is an aggressive invasive weed of riparian habitats throughout the southern half of the United States from California to Maryland. Native to Asia, the species is believed to have been initially introduced into North America from the Mediterranean region although subsequent introductions were from multiple regions. To provide insight into the potential for biological control of A. donax, genetic variation in plants sampled from a wide geographical area in the United States was analyzed using Sequence Related Amplification Polymorphism (SRAP) and transposable element (TE)-based molecular markers. Invasive individuals from 15 states as well as four populations in southern France were genetically fingerprinted using 10 SRAP and 12 TE-based primer combinations. With the exception of simple mutations detected in four plants, A. donax exhibited a single multilocus DNA fingerprint indicating a single genetic clone. The genetic uniformity of invasive A. donax suggests that classical biological control of the species could be successful. A lack of genetic diversity in the invaded range simplifies identification of native source populations to search for natural enemies that could be used as biocontrol agents.