Multiple cis elements and GATA factors regulate a cuticle collagen gene in Caenorhabditis elegans.

The cuticle of the nematode Caenorhabditis elegans is a specialized extracellular matrix whose major component is collagen. Cuticle collagens are encoded by a large multigene family consisting of more than 150 members. Cuticle collagen genes are expressed in epidermis (hypodermis) and may be stage-specific or cyclically expressed. We identified cuticle collagen genes as transcriptional targets of the DBL-1 TGF-ß-related signaling pathway. These studies prompted us to investigate the cis-regulatory sequences required for transcription of one of the target genes, col-41. We generated reporter constructs that reproduce stage- and tissue-specific expression of fluorescent markers. We identify four conserved sequence elements that are required for transcription of reporters. Finally, we provide evidence that col-41 expression is controlled by a sequence element containing two GATA sites and by the epidermal GATA transcription factors ELT-1 and ELT-3.

Characteristic wavelength optimization for partial least squares regression using improved flower pollination algorithm.

Wavelength selection is crucial to the success of near-infrared (NIR) spectroscopy analysis as it considerably improves the generalization of the multivariate model and reduces model complexity. This study proposes a new wavelength selection method, interval flower pollination algorithm (iFPA), for spectral variable selection in the partial least squares regression (PLSR) model. The proposed iFPA consists of three phases. First, the flower pollination algorithm is applied to search for informative spectral variables, followed by variable elimination. Subsequently, the iFPA performs a local search to determine the best continuous interval spectral variables. The interpretability of the selected variables is assessed on three public NIR datasets (corn, diesel and soil datasets). Performance comparison with other competing wavelength selection methods shows that the iFPA used in conjunction with the PLSR model gives better prediction performance, with the root mean square error of prediction values of 0.0096-0.0727, 0.0015-3.9717 and 1.3388-29.1144 are obtained for various responses in corn, diesel and soil datasets, respectively.

New approach for sugarcane disease recognition through visible and near-infrared spectroscopy and a modified wavelength selection method using machine learning models.

The proliferation of pathogenic fungi in sugarcane crops poses a significant threat to agricultural productivity and economic sustainability. Early identification and management of sugarcane diseases are therefore crucial to mitigate the adverse impacts of these pathogens. In this study, visible and near-infrared spectroscopy (380-1400 nm) combined with a novel wavelength selection method, referred to as modified flower pollination algorithm (MFPA), was utilized for sugarcane disease recognition. The selected wavelengths were incorporated into machine learning models, including Naïve Bayes, random forest, and support vector machine (SVM). The developed simplified SVM model, which utilized the MFPA wavelength selection method yielded the best performances, achieving a precision value of 0.9753, a sensitivity value of 0.9259, a specificity value of 0.9524, and an accuracy of 0.9487. These results outperformed those obtained by other wavelength selection approaches, including the selectivity ratio, variable importance in projection, and the baseline method of the flower pollination algorithm.

C. elegans ADAMTS ADT-2 regulates body size by modulating TGFß signaling and cuticle collagen organization.

Organismal growth and body size are influenced by both genetic and environmental factors. We have utilized the strong molecular genetic techniques available in the nematode Caenorhabditis elegans to identify genetic determinants of body size. In C. elegans, DBL-1, a member of the conserved family of secreted growth factors known as the Transforming Growth Factor ß superfamily, is known to play a major role in growth control. The mechanisms by which other determinants of body size function, however, is less well understood. To identify additional genes involved in body size regulation, a genetic screen for small mutants was previously performed. One of the genes identified in that screen was sma-21. We now demonstrate that sma-21 encodes ADT-2, a member of the ADAMTS (a disintegrin and metalloprotease with thrombospondin motifs) family of secreted metalloproteases. ADAMTS proteins are believed to remodel the extracellular matrix and may modulate the activity of extracellular signals. Genetic interactions suggest that ADT-2 acts in parallel with or in multiple size regulatory pathways. We demonstrate that ADT-2 is required for normal levels of expression of a DBL-1-responsive transcriptional reporter. We further demonstrate that adt-2 regulatory sequences drive expression in glial-like and vulval cells, and that ADT-2 activity is required for normal cuticle collagen fibril organization. We therefore propose that ADT-2 regulates body size both by modulating TGFß signaling activity and by maintaining normal cuticle structure.

A HS-PRP-Type Hybrid Conjugate Gradient Method with Sufficient Descent Property.

In this paper, based on the HS method and a modified version of the PRP method, a hybrid conjugate gradient (CG) method is proposed for solving large-scale unconstrained optimization problems. The CG parameter generated by the method is always nonnegative. Moreover, the search direction possesses the sufficient descent property independent of line search. Utilizing the standard Wolfe-Powell line search rule to yield the stepsize, the global convergence of the proposed method is shown under the common assumptions. Finally, numerical results show that the proposed method is promising compared with two existing methods.

Alternative trans-splicing of Caenorhabditis elegans sma-9/schnurri generates a short transcript that provides tissue-specific function in BMP signaling.

BACKGROUND: Transcription cofactors related to Drosophila Schnurri facilitate the transcriptional programs regulated by BMP signaling in C. elegans, Drosophila, Xenopus, and mouse. In different systems, Schnurri homologs have been shown to act as either agonists or antagonists of Smad function, and as either positive or negative regulators of transcription. How Schnurri proteins achieve this diversity of activities is not clear. The C. elegans sma-9/schnurri locus undergoes alternative splicing, including an unusual trans-splicing event that could generate two non-overlapping shorter transcripts. RESULTS: We demonstrate here that the shorter transcripts are expressed in vivo. Furthermore, we find that one of the short transcripts plays a tissue-specific role in sma-9 function, contributing to the patterning of male-specific sensory rays, but not to the regulation of body size. Based on previous results, we suggest that this transcript encodes a C-terminal SMA-9 isoform that may provide transcriptional activation activity, while full length isoforms may mediate transcriptional repression and/or activation in a context-dependent manner. CONCLUSION: The alternative trans-splicing of sma-9 may contribute to the diversity of functions necessary to mediate tissue-specific outputs of BMP signaling.

The effect of calcineurin activator, extracted from Chinese herbal medicine, on memory and immunity in mice.

Calcineurin (CN) is a highly abundant phosphatase in the brain and it is the only Ca(2+)- and calmodulin-dependent protein serine/threonine phosphatase. There is considerable evidence to suggest that CN plays an essential role in activity-dependent modulation of synaptic efficacy. It has been shown recently that inhibitors of CN, such as CsA or FK506, impair memory formation in day-old chicks. In our present study, extract of Fructus cannabis (EFC) with activation of CN, extracted from Chinese traditional medicine, was used to determine the effects on memory and immunity. In the step-down-type passive avoidance test, the plant extract (0.2 g/kg) significantly improved amnesia induced by chemical drugs in mice, and greatly enhanced the ability of cell-mediated type hypersensitivity and nonspecific immune responses in normal mice. The present study provided pharmacological evidence for Chinese herbal medicine screening from molecular model.

Transcriptional repressor and activator activities of SMA-9 contribute differentially to BMP-related signaling outputs.

In the nematode Caenorhabditis elegans, the BMP-related growth factor DBL-1 regulates body size and male tail morphogenesis via a conserved receptor/Smad signaling pathway. Smads are transcription factors, but rely on transcription cofactors for appropriate regulation of target genes in response to TGF-beta- and BMP-related signals. In the DBL-1 pathway, sma-9 encodes multiple zinc finger transcription factors homologous to Drosophila Schnurri, which functions in Dpp/BMP signaling. We have studied the molecular functions of SMA-9 as a model for transcription cofactor-dependent regulation of gene expression. Using SMA-9 fusions to known transcriptional activators and repressors, we demonstrate that SMA-9 acts primarily as a transcriptional repressor in body size regulation in vivo. In contrast, both activator and repressor functions contribute to male tail patterning. We further show that different SMA-9 regions have intrinsic repressor and activator activities using a yeast transcription assay. We use microarray analysis to identify transcriptional target genes in body size regulation. Consistent with the importance of repression in mediating body size regulation, we find more repressed genes than activated genes in this pool. Finally, we identify five transcriptional targets with body size and/or male tail patterning phenotypes, including transcription factors related to Runx and fos and signaling molecules related to hedgehog and patched. Our results thus suggest that SMA-9 products function differentially as transcriptional repressors and activators in DBL-1/BMP pathway regulated body size and male tail morphogenesis.

Extract from Fructus cannabis activating calcineurin improved learning and memory in mice with chemical drug-induced dysmnesia.

AIM: To investigate the effects of extract from Fructus cannabis (EFC) that can activate calcineurin on learning and memory impairment induced by chemical drugs in mice. METHODS: Bovine brain calcineurin and calmodulin were isolated from frozen tissues. The activity of calcineurin was assayed using p-nitrophenyl phosphate (PNPP) as the substrate. Step-down type passive avoidance test and water maze were used together to determine the effects of EFC on learning and memory dysfunction. RESULTS: EFC activated calcineurin activity at a concentration range of 0.01-100 g/L. The maximal value of EFC on calcineurin activity (35 %+/-5 %) appeared at a concentration of 10 g/L. The chemical drugs such as scopolamine, sodium nitrite, and 45 % ethanol, and sodium pentobarbital induced learning and memory dysfunction. EFC administration (0.2, 0.4, and 0.8 g/kg, igx7 d) prolonged the latency and decreased the number of errors in the step-down test. EFC, given for 7 d, enhanced the spatial resolution of amnesic mice in water maze test. EFC overcome amnesia of three stages of memory process at the dose of 0.2 g/kg. CONCLUSION: EFC with an activation role of calcineurin can improve the impaired learning and memory induced by chemical drugs in mice.