Biclustering extends the traditional clustering techniques by attempting to find (all) subgroups of genes with similar expression patterns under to-be-identified subsets of experimental conditions when applied to gene expression data. Still the real power of this clustering strategy is yet to be fully realized due to the lack of effective and efficient algorithms for reliably solving the general biclustering problem. We report a QUalitative BIClustering algorithm (QUBIC) that can solve the biclustering problem in a more general form, compared to existing algorithms, through employing a combination of qualitative (or semi-quantitative) measures of gene expression data and a combinatorial optimization technique. One key unique feature of the QUBIC algorithm is that it can identify all statistically significant biclusters including biclusters with the so-called ‘scaling patterns’, a problem considered to be rather challenging; another key unique feature is that the algorithm solves such general biclustering problems very efficiently, capable of solving biclustering problems with tens of thousands of genes under up to thousands of conditions in a few minutes of the CPU time on a desktop computer. We have demonstrated a considerably improved biclustering performance by our algorithm compared to the existing algorithms on various benchmark sets and data sets of our own. QUBIC was written in ANSI C and tested using GCC (version 4.1.2) on Linux. Its source code is available at: http://csbl.bmb.uga.edu/∼maqin/bicluster. A server version of QUBIC is also available upon request.

Extremely thermophilic bacteria of the genus Caldicellulosiruptor utilize carbohydrate components of plant cell walls, including cellulose and hemicellulose, facilitated by a diverse set of glycoside hydrolases (GHs). From a biofuel perspective, this capability is crucial for deconstruction of plant biomass into fermentable sugars. While all species from the genus grow on xylan and acidpretreated switchgrass, growth on crystalline cellulose is variable. The basis for this variability was examined using microbiological, genomic, and proteomic analyses of eight globally diverse Caldicellulosiruptor species. The open Caldicellulosiruptor pangenome (4,009 open reading frames [ORFs]) encodes 106 GHs, representing 43 GH families, but only 26 GHs from 17 families are included in the core (noncellulosic) genome (1,543 ORFs). Differentiating the strongly cellulolytic Caldicellulosiruptor species from the others is a specific genomic locus that encodes multidomain cellulases from GH families 9 and 48, which are associated with cellulose-binding modules. This locus also encodes a novel adhesin associated with type IV pili, which was identified in the exoproteome bound to crystalline cellulose. Taking into account the core genomes, pangenomes, and individual genomes, the ancestral Caldicellulosiruptor was likely cellulolytic and evolved, in some cases, into species that lost the ability to degrade crystalline cellulose while maintaining the capacity to hydrolyze amorphous cellulose and hemicellulose. Interest in cellulosic biofuels (29) has sparked efforts to isolate microorganisms capable of both hydrolysis and fermentation of plant biomass, a process referred to as consolidated bioprocessing (CBP) (49, 50). Since plant biomass deconstruction could be accelerated at elevated temperatures, thermophilic microorganisms have been considered catalysts for CBP (8). Of particular note in this regard are members of the extremely thermophilic genus Caldicellulosiruptor that inhabit globally diverse, terrestrial hot springs (12,27,56,57,61,69,80,98) and thermally heated mud flats (31). Caldicellulosiruptor species are Gram-positive bacteria and typically associate with plant debris; consequently, all isolates characterized to date hydrolyze certain complex carbohydrates characteristic of plant cell walls (8, 97). As such, members of the genus Caldicellulosiruptor are excellent genetic reservoirs of enzymes for plant biomass degradation and, pending the development of functional genetics systems, are potential metabolic hosts for CBP (9).Currently, there are two main paradigms described for microbial degradation of crystalline cellulose: cellulosomal (3) and noncellulosomal (48, 54). Enzymatically, both systems require the concerted efforts of cellobiohydrolases, endocellulases, and ␤-glucosidases (49). Crystalline cellulose deconstruction via cell membrane-bound cellulosomes was first described in the thermophile Clostridium thermocellum and has since been described in other mesophilic Firmicutes, such as Clostridium cellulolyticum,...

Aflatoxin B 1 (AFB 1 ) is one of the most harmful mycotoxins in animal production and food industry. A safe, effective and environmentally sound detoxification method is needed for controlling this toxin. In this study, 65 samples were screened from various sources with vast microbial populations using a newly developed medium containing coumarin as the sole carbon source. Twenty five single-colony bacterial isolates showing AFB 1 reduction activity in a liquid culture medium were selected from the screen. Isolate 35-3, obtained from tapir feces and identified to be Stenotrophomonas maltophilia, reduced AFB 1 by 82.5% after incubation in the liquid medium at 37 °C for 72 h. The culture supernatant of isolate 35-3 was able to degrade AFB 1 effectively, whereas the viable cells and cell extracts were far less effective. Factors influencing AFB 1 degradation by the culture supernatant were investigated. Activity was reduced to 60.8% and 63.5% at 20 °C and 30 °C, respectively, from 78.7% at 37 °C. The highest degradation rate was 84.8% at pH 8 and the lowest was only 14.3% at pH 4.

Discovering new long non-coding RNAs (lncRNAs) has been a fundamental step in lncRNA-related research. Nowadays, many machine learning-based tools have been developed for lncRNA identification. However, many methods predict lncRNAs using sequence-derived features alone, which tend to display unstable performances on different species. Moreover, the majority of tools cannot be re-trained or tailored by users and neither can the features be customized or integrated to meet researchers' requirements. In this study, features extracted from sequence-intrinsic composition, secondary structure and physicochemical property are comprehensively reviewed and evaluated. An integrated platform named LncFinder is also developed to enhance the performance and promote the research of lncRNA identification. LncFinder includes a novel lncRNA predictor using the heterologous features we designed. Experimental results show that our method outperforms several state-of-the-art tools on multiple species with more robust and satisfactory results. Researchers can additionally employ LncFinder to extract various classic features, build classifier with numerous machine learning algorithms and evaluate classifier performance effectively and efficiently. LncFinder can reveal the properties of lncRNA and mRNA from various perspectives and further inspire lncRNA-protein interaction prediction and lncRNA evolution analysis. It is anticipated that LncFinder can significantly facilitate lncRNA-related research, especially for the poorly explored species. LncFinder is released as R package (https://CRAN.R-project.org/package=LncFinder). A web server (http://bmbl.sdstate.edu/lncfinder/) is also developed to maximize its availability.

Abstract. Multi-year droughts in Mediterranean climates may shift the water balance, that is, the partitioning rule of precipitation across runoff, evapotranspiration, and sub-surface storage. Mechanisms causing these shifts remain largely unknown and are not well represented in hydrologic models. Focusing on measurements from the headwaters of California's Feather River, we found that also in these mixed rain–snow Mediterranean basins a lower fraction of precipitation was partitioned to runoff during multi-year droughts compared to non-drought years. This shift in the precipitation–runoff relationship was larger in the surface-runoff-dominated than subsurface-flow-dominated headwaters (−39 % vs. −18 % decline of runoff, respectively, for a representative precipitation amount). The predictive skill of the Precipitation Runoff Modeling System (PRMS) hydrologic model in these basins decreased during droughts, with evapotranspiration (ET) being the only water-balance component besides runoff for which the drop in predictive skill during drought vs. non-drought years was statistically significant. In particular, the model underestimated the response time required by ET to adjust to interannual climate variability, which we define as climate elasticity of ET. Differences between simulated and data-driven estimates of ET were well correlated with accompanying data-driven estimates of changes in sub-surface storage (ΔS, r=0.78). This correlation points to shifts in precipitation–runoff relationships being evidence of a hysteretic response of the water budget to climate elasticity of ET during and after multi-year droughts. This hysteresis is caused by carryover storage offsetting precipitation deficit during the initial drought period, followed by vegetation mortality when storage is depleted and subsequent post-drought vegetation expansion. Our results point to a general improvement in hydrologic predictions across drought and recovery cycles by including the climate elasticity of ET and better accounting for actual subsurface water storage in not only soil, but also deeper regolith that stores water accessible to roots. This can be done by explicitly parametrizing carryover storage and feedback mechanisms capturing vegetation response to atmospheric demand for moisture.

Light significantly inhibits hypocotyl cell elongation, and dark-grown seedlings exhibit elongated, etiolated hypocotyls. Microtubule regulatory proteins function as positive or negative regulators that mediate hypocotyl cell elongation by altering microtubule organization. However, it remains unclear how plants coordinate these regulators to promote hypocotyl growth in darkness and inhibit growth in the light. Here, we demonstrate that WAVE-DAMPENED 2-LIKE3 (WDL3), a microtubule regulatory protein of the WVD2/WDL family from Arabidopsis thaliana, functions in hypocotyl cell elongation and is regulated by a ubiquitin-26S proteasome-dependent pathway in response to light. WDL3 RNA interference Arabidopsis seedlings grown in the light had much longer hypocotyls than controls. Moreover, WDL3 overexpression resulted in overall shortening of hypocotyl cells and stabilization of cortical microtubules in the light. Cortical microtubule reorganization occurred slowly in cells from WDL3 RNA interference transgenic lines but was accelerated in cells from WDL3-overexpressing seedlings subjected to light treatment. More importantly, WDL3 protein was abundant in the light but was degraded through the 26S proteasome pathway in the dark. Overexpression of WDL3 inhibited etiolated hypocotyl growth in regulatory particle nonATPase subunit-1a mutant (rpn1a-4) plants but not in wild-type seedlings. Therefore, a ubiquitin-26S proteasome-dependent mechanism regulates the levels of WDL3 in response to light to modulate hypocotyl cell elongation.

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