Initial assessment of reuse of sustainable wastes for fibreboard production : the case of waste paper and water hyacinth

In this early study, new cement-bonded bi-composite fibreboard (FB) was made from water hyacinth (WaHy) and waste paper (WP). Ordinary Portland cement (PdCe) used as a binder was mixed with other two additives: gypsum plasters (GyPl) and wood ash (WdAh), in defined proportions to form bonding matrices. The WP and WaHy were pre-treated and a linked process was developed for the mixing and consolidation steps. The FBs produced were based on different proportions of composites, binder, and additives mixed. The FBs produced were made from different proportions of composites, binders, and additives. Improved tensile strength was observed for bi-composite FB from WaHy mixed with WP. In general, FBs having densities in the range of 0.50–0.57 g cm−3 were compared favourably with the ASTM and ANSI standards (95%), thus making the FBs a potential alternative for building and construction purposes. More elaborate research with advanced analytical techniques is hereby suggested

Immunogenic Mycobacterium africanum Strains Associated with Ongoing Transmission in The Gambia

In West Africa, Mycobacterium tuberculosis strains co-circulate with M. africanum, and both pathogens cause pulmonary tuberculosis in humans. Given recent findings that M. tuberculosis T-cell epitopes are hyperconserved, we hypothesized that more immunogenic strains have increased capacity to spread within the human host population. We investigated the relationship between the composition of the mycobacterial population in The Gambia, as measured by spoligotype analysis, and the immunogenicity of these strains as measured by purified protein derivative-induced interferon-γ release in ELISPOT assays of peripheral blood mononuclear cells. We found a positive correlation between strains with superior spreading capacity and their relative immunogenicity. Although our observation is true for M. tuberculosis and M. africanum strains, the association was especially pronounced in 1 M. africanum sublineage, characterized by spoligotype shared international type 181, which is responsible for 20% of all tuberculosis cases in the region and therefore poses a major public health threat in The Gambia

Evolution of Mycobacterium tuberculosis complex lineages and their role in an emerging threat of multidrug resistant tuberculosis in Bamako, Mali

In recent years Bamako has been faced with an emerging threat from multidrug resistant TB (MDR-TB). Whole genome sequence analysis was performed on a subset of 76 isolates from a total of 208 isolates recovered from tuberculosis patients in Bamako, Mali between 2006 and 2012. Among the 76 patients, 61(80.3%) new cases and 15(19.7%) retreatment cases, 12 (16%) were infected by MDR-TB. The dominant lineage was the Euro-American lineage, Lineage 4. Within Lineage 4, the Cameroon genotype was the most prevalent genotype (n=20, 26%), followed by the Ghana genotype (n=16, 21%). A sub-clade of the Cameroon genotype, which emerged ~22 years ago was likely to be involved in community transmission. A sub-clade of the Ghana genotype that arose approximately 30 years ago was an important cause of MDR-TB in Bamako. The Ghana genotype isolates appeared more likely to be MDR than other genotypes after controlling for treatment history. We identifed a clade of four related Beijing isolates that included one MDR-TB isolate. It is a major concern to fnd the Cameroon and Ghana genotypes involved in community transmission and MDR-TB respectively. The presence of the Beijing genotype in Bamako remains worrying, given its high transmissibility and virulence

Evolutionary distances in the twilight zone -- a rational kernel approach

Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly. Alignment-free methods, on the other hand, are based on abstract string comparisons and avoid potential alignment problems. However, in general they are not biologically motivated and ignore our knowledge about the evolution of sequences. Thus, it is still a major open question how to define an evolutionary distance metric between divergent sequences that makes use of indel information and known substitution models without the need for a multiple alignment. Here we propose a new evolutionary distance metric to close this gap. It uses finite-state transducers to create a biologically motivated similarity score which models substitutions and indels, and does not depend on a multiple sequence alignment. The sequence similarity score is defined in analogy to pairwise alignments and additionally has the positive semi-definite property. We describe its derivation and show in simulation studies and real-world examples that it is more accurate in reconstructing phylogenies than competing methods. The result is a new and accurate way of determining evolutionary distances in and beyond the twilight zone of sequence alignments that is suitable for large datasets.Comment: to appear in PLoS ON

Evolution of virulent genotypes and an emerging threat of multidrug resistant tuberculosis in Bamako, Mali

Background: Bamako, Mali, has a well-structured hierarchyfor tuberculosis (TB) case management. However, in recent yearsBamako has been faced with an emerging threat from multidrugresistant TB (MDR-TB). Here we present insights into the genomicepidemiology of TB and the evolutionary mechanisms driving theemergence of MDR-TB in Bamako.Methods & Materials:Isolates recovered from tuberculosispatients from local reference centers and the University Teach-ing Hospital at Point G, in Bamako, Mali between 2006 and 2012(n = 208), were tested for antimicrobial susceptibility at the MRCUnit The Gambia. A subset of 76 isolates were analysed using wholegenome sequencing. A time dated phylogenetic tree was recon-structed using BEAST. Lineage and resistance conferring mutationswere inferred using PhyResSe.Results:Patients included 21 females and 55 males agedbetween 3 to 78 years, among whom 12(16%) were infectedby MDR-TB. Most patients 61(80%) were new cases and among15 retreatment cases 9(60%) were MDR-TB. The phylogeny wasreconstructed from 8508 variant core genome sites. The dom-inant lineage was the Euro-American super lineage, lineage 4.Within lineage 4, the Cameroon genotype was the most preva-lent genotype (n = 20, 26%) followed by the Ghana genotype (n = 16,21%). Cameroon genotype isolates diverged from a common recentancestor∼161 years ago to form three clusters, one of whichemerged∼22 years ago and is likely to be involved in on-goingtransmission. Seven Ghana genotype isolates were MDR-TB repre-senting over half all MDR-TB in this dataset (7/12). Ghana genotypeisolates were more likely to cause MDR-TB than other genotypesafter controlling for treatment status (OR = 5.6, p-value = 0.043).The MDR-TB Ghana genotype isolates formed a clade that divergedapproximately 30 years ago, in which thekatGSer315Thr mutationwas conserved. Other Euro-American genotypes included the sixLAM, two H37Rv-like and one Uganda. Four patients were infectedwith closely related Beijing strains and five patients were infectedwith non-MDRMycobacterium africanum2

A grammar-based distance metric enables fast and accurate clustering of large sets of 16S sequences

Background: We propose a sequence clustering algorithm and compare the partition quality and execution time of the proposed algorithm with those of a popular existing algorithm. The proposed clustering algorithm uses a grammar-based distance metric to determine partitioning for a set of biological sequences. The algorithm performs clustering in which new sequences are compared with cluster-representative sequences to determine membership. If comparison fails to identify a suitable cluster, a new cluster is created. Results: The performance of the proposed algorithm is validated via comparison to the popular DNA/RNA sequence clustering approach, CD-HIT-EST, and to the recently developed algorithm, UCLUST, using two different sets of 16S rDNA sequences from 2,255 genera. The proposed algorithm maintains a comparable CPU execution time with that of CD-HIT-EST which is much slower than UCLUST, and has successfully generated clusters with higher statistical accuracy than both CD-HIT-EST and UCLUST. The validation results are especially striking for large datasets. Conclusions: We introduce a fast and accurate clustering algorithm that relies on a grammar-based sequence distance. Its statistical clustering quality is validated by clustering large datasets containing 16S rDNA sequences

A Novel Role for GADD45\u3ci\u3eβ\u3c/i\u3e as a Mediator of \u3ci\u3eMMP-13\u3c/i\u3e Gene Expression during Chondrocyte Terminal Differentiation

The growth arrest and DNA damage-inducible 45β (GADD45β) gene product has been implicated in the stress response, cell cycle arrest, and apoptosis. Here we demonstrated the unexpected expression of GADD45β in the embryonic growth plate and uncovered its novel role as an essential mediator of matrix metalloproteinase-13 (MMP-13) expression during terminal chondrocyte differentiation. We identified GADD45β as a prominent early response gene induced by bone morphogenetic protein-2 (BMP-2) through a Smad1/Runx2-dependent pathway. Because this pathway is involved in skeletal development, we examined mouse embryonic growth plates, and we observed expression of Gadd45β mRNA coincident with Runx2 protein in prehypertrophic chondrocytes, whereas GADD45β protein was localized prominently in the nucleus in late stage hypertrophic chondrocytes where Mmp-13 mRNA was expressed. In Gadd45β−/− mouse embryos, defective mineralization and decreased bone growth accompanied deficient Mmp-13 and Col10a1 gene expression in the hypertrophic zone. Transduction of small interferin

Reprogrammed Transcriptome in Rhesus-Bovine Interspecies Somatic Cell Nuclear Transfer Embryos

Global activation of the embryonic genome (EGA), one of the most critical steps in early mammalian embryo development, is recognized as the time when interspecies somatic cell nuclear transfer (iSCNT) embryos fail to thrive.In this study, we analyzed the EGA-related transcriptome of rhesus-bovine iSCNT 8- to 16-cell embryos and dissected the reprogramming process in terms of embryonic gene activation, somatic gene silencing, and maternal RNA degradation. Compared with fibroblast donor cells, two thousand and seven genes were activated in iSCNT embryos, one quarter of them reaching expression levels comparable to those found in in vitro fertilized (IVF) rhesus embryos. This suggested that EGA in iSCNT embryos had partially recapitulated rhesus embryonic development. Eight hundred and sixty somatic genes were not silenced properly and continued to be expressed in iSCNT embryos, which indicated incomplete nuclear reprogramming. We compared maternal RNA degradation in bovine oocytes between bovine-bovine SCNT and iSCNT embryos. While maternal RNA degradation occurred in both SCNT and iSCNT embryos, we saw more limited overall degradation of maternal RNA in iSCNT embryos than in SCNT embryos. Several important maternal RNAs, like GPF9, were not properly processed in SCNT embryos.Our data suggested that iSCNT embryos are capable of triggering EGA, while a portion of somatic cell-associated genes maintain their expression. Maternal RNA degradation seems to be impaired in iSCNT embryos. Further understanding of the biological roles of these genes, networks, and pathways revealed by iSCNT may expand our knowledge about cell reprogramming, pluripotency, and differentiation