Forming Sustainable Communities under Increasing Environmental Constraint and Decreasing Population

Additional file 6: Fig. S5. Contact angle measurement of E. coli knockout strains (A) JM109 (control), (B) △yghW, and (C) △yibT. Three biological replicates were performed

MFAI: A Scalable Bayesian Matrix Factorization Approach to Leveraging Auxiliary Information

In various practical situations, matrix factorization methods suffer from poor data quality, such as high data sparsity and low signal-to-noise ratio (SNR). Here, we consider a matrix factorization problem by using auxiliary information, which is massively available in real-world applications, to overcome the challenges caused by poor data quality. Unlike existing methods that mainly rely on simple linear models to combine auxiliary information with the main data matrix, we propose to integrate gradient boosted trees in the probabilistic matrix factorization framework to effectively leverage auxiliary information (MFAI). Thus, MFAI naturally inherits several salient features of gradient boosted trees, such as the capability of flexibly modeling nonlinear relationships and robustness to irrelevant features and missing values in auxiliary information. The parameters in MFAI can be automatically determined under the empirical Bayes framework, making it adaptive to the utilization of auxiliary information and immune to overfitting. Moreover, MFAI is computationally efficient and scalable to large datasets by exploiting variational inference. We demonstrate the advantages of MFAI through comprehensive numerical results from simulation studies and real data analyses. Our approach is implemented in the R package mfair available at https://github.com/YangLabHKUST/mfair. Supplementary materials for this article are available online.</p

Table_1_Uncovering the biogeographic pattern of the widespread nematode-trapping fungi Arthrobotrys oligospora: watershed is the key.XLSX

Studies of biogeographic patterns of fungi have long been behind those of plants and animals. The presence of worldwide species, the lack of systematic sampling design and adequate sampling effort, and the lack of research units are responsible for this status. This study investigates the biogeographical patterns of Arthrobotrys oligospora, the most widespread globally distributed nematode-trapping fungi (NTF), by stratified collecting and analyzing 2,250 samples from 228 sites in Yunnan Province, China. The A. oligospora was isolated, and 149 strains were subjected to ITS, TUB, TEF and RPB2 gene sequencing and multi-gene association phylogeographic analysis. The results show that at population level A. oligospora is randomly distributed throughout Yunnan Province and has no biogeographical distribution pattern. At the genetic level, the phylogenetic tree of A. oligospora diverges into five major evolutionary clades, with a low degree of gene flow between the five clades. However, the correlation between the phylogenetic diversity of A. oligospora and geographical factors was low. There was no clear pattern in the phylogenetic clades distribution of A. oligospora either without dividing the study unit or when the grid was used as the study unit. When watersheds were used as the study unit, 67.4%, 63.3%, 65.9%, 83.3%, and 66.7% of clade 1–5 strains were distributed in the Jinsha river, Red river, Peal river, Lancang river, and Nujiang-Irawaddy river watersheds, respectively. The clades distribution of A. oligospora was highly consistent with the watersheds distribution. Training predictions of the clades distributions using randomly generated polygons were also less accurate than watersheds. These results suggest that watersheds are key to discovering the biogeographic distribution patterns of A. oligospora. The A. oligospora populations are blocked by mountains in the watershed, and gene flow barriers have occurred, which may have resulted in the formation of multiple cryptic species. Watersheds are also ideal for understanding such speciation processes, explaining factors affecting biodiversity distribution and coupling studies of plant and animal and microbial diversity.</p

Table_2_Uncovering the biogeographic pattern of the widespread nematode-trapping fungi Arthrobotrys oligospora: watershed is the key.XLSX

Studies of biogeographic patterns of fungi have long been behind those of plants and animals. The presence of worldwide species, the lack of systematic sampling design and adequate sampling effort, and the lack of research units are responsible for this status. This study investigates the biogeographical patterns of Arthrobotrys oligospora, the most widespread globally distributed nematode-trapping fungi (NTF), by stratified collecting and analyzing 2,250 samples from 228 sites in Yunnan Province, China. The A. oligospora was isolated, and 149 strains were subjected to ITS, TUB, TEF and RPB2 gene sequencing and multi-gene association phylogeographic analysis. The results show that at population level A. oligospora is randomly distributed throughout Yunnan Province and has no biogeographical distribution pattern. At the genetic level, the phylogenetic tree of A. oligospora diverges into five major evolutionary clades, with a low degree of gene flow between the five clades. However, the correlation between the phylogenetic diversity of A. oligospora and geographical factors was low. There was no clear pattern in the phylogenetic clades distribution of A. oligospora either without dividing the study unit or when the grid was used as the study unit. When watersheds were used as the study unit, 67.4%, 63.3%, 65.9%, 83.3%, and 66.7% of clade 1–5 strains were distributed in the Jinsha river, Red river, Peal river, Lancang river, and Nujiang-Irawaddy river watersheds, respectively. The clades distribution of A. oligospora was highly consistent with the watersheds distribution. Training predictions of the clades distributions using randomly generated polygons were also less accurate than watersheds. These results suggest that watersheds are key to discovering the biogeographic distribution patterns of A. oligospora. The A. oligospora populations are blocked by mountains in the watershed, and gene flow barriers have occurred, which may have resulted in the formation of multiple cryptic species. Watersheds are also ideal for understanding such speciation processes, explaining factors affecting biodiversity distribution and coupling studies of plant and animal and microbial diversity.</p

MOESM3 of Significantly improved solvent tolerance of Escherichia coli by global transcription machinery engineering

Additional file 3: Figure S3. Recombinant expression of pepB, gapA, sdhB and yfgM in E. coli JM109 and their corresponding knockout strains

MOESM1 of Significantly improved solvent tolerance of Escherichia coli by global transcription machinery engineering

Additional file 1: Figure S1. 2D-PAGE of total proteins of E. coli JM109/pHACM-rpoD WT without solvent

MOESM4 of DNA microarray of global transcription factor mutant reveals membrane-related proteins involved in n-butanol tolerance in Escherichia coli

Additional file 4: Fig. S3. Transcription profile analysis of genes exhibiting significantly different expression levels in σ70 mutant B8 and WT. Hierarchical clustering using differentially expressed genes (probe sets) (p < 0.05; FC ≥ 2). Abscissa represents samples of B8 and WT, the ordinate represents different genes. Three biological replicates were performed

Efficient synthesis of benzothiazole derivatives by reaction of bis(2-aminophenyl) disulfides with aldehydes mediated by NaSH under microwave irradiation

<p>2-Substituted benzothiazoles were synthesized through condensation of bis(2-aminophenyl) disulfides with arylaldehydes catalyzed by inexpensive NaSH in PEG-300 and assisted by low energy microwave irradiation(25 W). Various 2-substitutedbenzothiazoles were obtained in moderate to high yields after simple post-reaction processing including adding distilled water, filtrating, and drying. Moreover, it was found that the S-S bond of the disulfide was reduced by NaSH and also by the intermediate benzothiazoline.</p