Recursive Feature Elimination-based Biomarker Identification for Open Neural Tube Defects

Background: Open spina bifida (myelomeningocele) is the result of the failure of spinal cord closing completely and is the second most common and severe birth defect. Open neural tube defects are multifactorial, and the exact molecular mechanism of the pathogenesis is not clear due to disease complexity for which prenatal treatment options remain limited worldwide. Artificial intelligence techniques like machine learning tools have been increasingly used in precision diagnosis.Objective: The primary objective of this study is to identify key genes for open neural tube defects using a machine learning approach that provides additional information about myelomeningocele in order to obtain a more accurate diagnosis.Materials and Methods: Our study reports differential gene expression analysis from multiple datasets ({"type":"entrez-geo","attrs":{"text":"GSE4182","term_id":"4182"}}GSE4182 and {"type":"entrez-geo","attrs":{"text":"GSE101141","term_id":"101141"}}GSE101141) of amniotic fluid samples with open neural tube defects. The sample outliers in the datasets were detected using principal component analysis (PCA). We report a combination of the differential gene expression analysis with recursive feature elimination (RFE), a machine learning approach to get 4 key genes for open neural tube defects. The features selected were validated using five binary classifiers for diseased and healthy samples: Logistic Regression (LR), Decision tree classifier (DT), Support Vector Machine (SVM), Random Forest classifier (RF), and K-nearest neighbour (KNN) with 5-fold cross-validation.Results: Growth Associated Protein 43 (GAP43), Glial fibrillary acidic protein (GFAP), Repetin (RPTN), and CD44 are the important genes identified in the study. These genes are known to be involved in axon growth, astrocyte differentiation in the central nervous system, post-traumatic brain repair, neuroinflammation, and inflammation-linked neuronal injuries. These key genes represent a promising tool for further studies in the diagnosis and early detection of open neural tube defects.Conclusion: These key biomarkers help in the diagnosis and early detection of open neural tube defects, thus evaluating the progress and seriousness in diseases condition. This study strengthens previous literature sources of confirming these biomarkers linked with open NTD’s. Thus, among other prenatal treatment options present until now, these biomarkers help in the early detection of open neural tube defects, which provides success in both treatment and prevention of these defects in the advanced stage.     

Presence of interleukin 10 (IL-10) in the ascites of patients with ovarian and other intra-abdominal cancers.

Typically, ovarian cancer remains restricted to the peritoneal cavity. Because of this unique localization, the study of ovarian cancer is particularly suitable for immune analysis and for the development of immunotherapy. Here we report that peritoneal fluid from patients with ovarian or other intra-abdominal cancers contained significantly elevated levels of interleukin 10 (IL-10) (542 +/- 77 pg/ml, N = 35), compared with peritoneal fluid from patients with benign gynecological conditions (34.2 +/- 7.5 pg/ml, N = 63) (P < 0.001). Peritoneal fluid IL-10 levels did not correlate with histology, tumor stage, grade, or prognosis. IL-10 levels were also elevated in the serum of patients with intra-abdominal cancer (1353 +/- 906, N = 8). Established ovarian cancer cell lines (N = 5) did not produce any detectable IL-10. Investigation of the cell surface phenotype of the cells in the peritoneal cavity indicated the presence of significant amounts of activated immune cells. The presence of cytokines such as IL-10 in the peritoneal cavity of ovarian cancer bearing patients could be important in the growth and development of cancer, more specifically, in relation to host immune responsiveness.     

Discovery and evaluation of nNav1.5 sodium channel blockers with potent cell invasion inhibitory activity in breast cancer cells

Voltage-gated sodium channels (VGSC) are a well-established drug target for anti-epileptic, anti-arrhythmic and pain medications due to their presence and the important roles that they play in excitable cells. Recently, their presence has been recognized in non-excitable cells such as cancer cells and their overexpression has been shown to be associated with metastatic behavior in a variety of human cancers. The neonatal isoform of the VGSC subtype, Na_v1.5 (nNa_v1.5) is overexpressed in the highly aggressive human breast cancer cell line, MDA-MB-231. The activity of nNa_v1.5 is known to promote the breast cancer cell invasion in vitro and metastasis in vivo, and its expression in primary mammary tumors has been associated with metastasis and patient death. Metastasis development is responsible for the high mortality of breast cancer and currently there is no treatment available to specifically prevent or inhibit breast cancer metastasis. In the present study, a 3D-QSAR model is used to assist the development of low micromolar small molecule VGSC blockers. Using this model, we have designed, synthesized and evaluated five small molecule compounds as blockers of nNa_v1.5-dependent inward currents in whole-cell patch-clamp experiments in MDA-MB-231 cells. The most active compound identified from these studies blocked sodium currents by 34.9?±?6.6% at 1?μM. This compound also inhibited the invasion of MDA-MB-231 cells by 30.3?±?4.5% at 1?μM concentration without affecting the cell viability. The potent small molecule compounds presented here have the potential to be developed as drugs for breast cancer metastasis treatment.     

Uptake of l-Phenylalanine in Synchronous Chlorella fusca. Characterization of the Uptake System

Phenylalanine uptake in Chlorella fusca was measured, using the membrane filter technique. The cells were synchronized, and harvested at specific points of the life cycle. Experiments with autospores showed that the uptake followed saturation kinetics, with a K_m= 5 μM. V_max, was 0.1 nmol/min × 10⁷ cells. The optimum temperature for the uptake was 40°C, and the activation energy was 1700 J/mol. The uptake showed a high specificity towards l -phenylalanine; presence of the unlabelled stereoisomer did not inhibit the uptake. Uptake of l -phenylalanine was inhibited in the presence of other analogues or other amino acids, but only if they were present in concentrations considerably higher than that of L-phenylalanine. Variations in the ratio of Na4⁺ to K⁺ in the external solution during uptake experiments did not have any influence upon the uptake rate of l -phenylalanine. The cells were able to take up the amino acid against a concentration gradient. At pool maximum the ratio between internal and external amino acid concentration was 1000/1. 2,4-Dinitro-phenol inhibited the uptake completely. Exchange between internal and external l -phenylalanine could not be demonstrated. The K_m value did not change during the life cycle of the cells. The uptake rate reached a maximum at the end of the light period, and fell to a minimum just before sporulation started. It is concluded that Chlorella fusca cells have a highly specific, active uptake system for l -phenylalanine. The system is constitutive, independent on the K or Na concentration, and the mechanism of uptake does not change during the life cycle of the cells.     

The bovine papillomavirus E5 oncogene can cooperate with ras: identification of p21 amino acids critical for transformation by c-rasH but not v-rasH.

We have previously used a series of insertion-deletion mutants of the mutationally activated v-rasH gene to identify several regions of the encoded protein that are dispensable for cellular transformation (B. M. Willumsen, A. G. Papageorge, H.-F. Kung, E. Bekesi, T. Robins, M. Johnsen, W. C. Vass, and D. R. Lowy, Mol. Cell. Biol. 6:2646-2654, 1986). To determine if some of these amino acids are more important for the biological activity of c-rasH, we have now tested many of the same insertion-deletion mutants in the c-rasH form for their ability to transform NIH 3T3 cells. Since the transforming activity of c-rasH is low, we have used cotransfection with the bovine papillomavirus (BPV) genome to develop a more sensitive transformation assay for c-rasH mutants. The increased sensitivity of the assay, which is seen both in focal transformation and in anchorage-independent growth, is mediated by cooperation between the BPV E5 gene and ras. E5-dependent cooperation was seen for v-rasH as well as for c-rasH, which suggests that the major effect of E5 was to increase the susceptibility of the cell to transformation to a given level of ras activity. The cooperation assay was used to test the potential importance, in c-rasH, of codons 93 to 108, 123 to 130, and 166 to 183, which were nonessential for v-rasH transformation. Relative to the respective transforming activity of wild-type c-rasH and v-rasH, mutants with lesions in codons 102 and 103 were significantly less active in their c-rasH forms than in their v-rasH forms. We conclude that a region including amino acids 102 and 103 encodes a function that is more critical to c-rasH than to v-rasH. Guanine nucleotide exchange is one function that is compatible with such a phenotype.     

Phylogeny and taxonomy of the Prenolepis genus‐group of ants (Hymenoptera: Formicidae)

Abstract. We investigated the phylogeny and taxonomy of the Prenolepis genus‐group, a clade of ants we define within the subfamily Formicinae comprising the genera Euprenolepis, Nylanderia, gen. rev. , Paraparatrechina, gen. rev. & stat. nov. , Paratrechina, Prenolepis and Pseudolasius. We inferred a phylogeny of the Prenolepis genus‐group using DNA sequence data from five genes (CAD, EF1αF1, EF1αF2, wingless and COI) sampled from 50 taxa. Based on the results of this phylogeny the taxonomy of the Prenolepis genus‐group was re‐examined. Paratrechina (broad sense) species segregated into three distinct, robust clades. Paratrechina longicornis represents a distinct lineage, a result consistent with morphological evidence; because this is the type species for the genus, Paratrechina is redefined as a monotypic genus. Two formerly synonymized subgenera, Nylanderia and Paraparatrechina, are raised to generic status in order to provide names for the other two clades. The majority of taxa formerly placed in Paratrechina, 133 species and subspecies, are transferred to Nylanderia, and 28 species and subspecies are transferred to Paraparatrechina. In addition, two species are transferred from Pseudolasius to Paraparatrechina and one species of Pseudolasius is transferred to Nylanderia. A morphological diagnosis for the worker caste of all six genera is provided, with a discussion of the morphological characters used to define each genus. Two genera, Prenolepis and Pseudolasius, were not recovered as monophyletic by the molecular data, and the implications of this result are discussed. A worker‐based key to the genera of the Prenolepis genus‐group is provided.     

Divergence estimates and early evolutionary history of Figitidae (Hymenoptera: Cynipoidea)

We examine the phylogenetic relationships of Figitidae and discuss host use within this group in light of our own and previously published divergence time data. Our results suggest Figitidae, as currently defined, is not monophyletic. Furthermore, Mikeiinae and Pycnostigminae are sister‐groups, nested adjacent to Thrasorinae, Plectocynipinae and Euceroptrinae. The recovery of Pycnostigminae as sister‐group to Mikeiinae suggests two major patterns of evolution: (i) early Figitidae lineages demonstrate a Gondawanan origin (Plectocynipinae: Neotropical; Mikeiinae and Thrasorinae: Australia; Pycnostigminae: Africa); and (ii) based on host records for Mikeiinae, Thrasorinae and Plectocynipinae, Pycnostigminae are predicted to be parasitic on gall‐inducing Hymenoptera. The phylogenetic position of Parnips (Parnipinae) was unstable, and various analyses were conducted to determine the impact of this uncertainty on both the recovery of other clades and inferred divergence times; when Parnips was excluded from the total evidence analysis, Cynipidae was found to be sister‐group to [Euceroptrinae + (Plectocynipinae (Thrasorinae + (Mikeiinae + Pycnostigminae)))], with low support. Divergence dating analyses using BEAST indicate the stem‐group node of Figitidae to be c. 126 Ma; the dipteran parasitoids (Eucoilinae and Figitinae), were estimated to have a median age of 80 and 88 Ma, respectively; the neuropteran parasitoids (Anacharitinae), were estimated to have a median age of 97 Ma; sternorrhynchan hyperparasitoids (Charipinae), were estimated to have a median age of 110 Ma; the Hymenoptera‐parasitic subfamilies (Euceroptinae, Plectocynipinae, Trasorinae, Mikeiinae, Pycnostigminae, and Parnipinae), ranged in median ages from 48 to 108 Ma. Rapid radiation of Eucoilinae subclades appears chronologically synchronized with the origin of their hosts, Schizophora (Diptera). Overall, the exclusion of Parnips from the BEAST analysis did not result in significant changes to divergence estimates. Finally, though sparsely represented in the analysis, our data suggest Cynipidae have a median age of 54 Ma, which is somewhat older than the age of Quercus spp (30–50 Ma), their most common host.     

Recovery techniques for waterlogged archaeological sediments: a comparison of different treatment methods for samples from Neolithic lake shore settlements

This paper presents the first comparable overview of different recovery techniques used for waterlogged Neolithic sediments in the surroundings of the Alps in the last decades. Such an investigation became necessary because it was not known which parts of plants and types of remains were absent or completely underrepresented due to inappropriate recovery techniques in Slovenian archaeobotany up to 2006. During the 2007 excavation of the approximately 5,200 years old Neolithic pile dwelling site of Stare gmajne, Ljubljansko barje, Slovenia, we compared three methods for the investigation of botanical macroremains: method 1 (M1) included rough wet-sieving and subsequent drying of the fractions; method 2 (M2) rough wet sieving and keeping the fractions wet; and method 3 (M3) washing over and keeping the fractions wet. M3 with gentle washing, systematic subsampling, examination, and sorting of macroremains while wet, as well as using 0.355 mm as the smallest sieve mesh size gave the best results. When using the cruder M2 or M1 methods, waterlogged uncarbonized seeds of taxa such as Linum usitatissimum, Papaver somniferum and Brassica rapa, waterlogged chaff of Cerealia and pericarps of Maloideae and Quercus sp., which are all fragile, were underrepresented or even completely absent and therefore the plant spectra were strongly biased. On the contrary, taxa with lignified seed/fruit walls like Cornus mas, Corylus avellana or Rubus sp. were overrepresented when using the M2 and particularly the M1 method. The application of the M3, instead of the M1 method which has been traditionally used in Slovenian archaeobotany, helped us to identify uncarbonized remains of Linum usitatissimum and various species of Triticum for the first time in a waterlogged Neolithic site in Slovenia. Our study should contribute to a standardization of methods, which is desperately needed in archaeobotany. The study clearly shows that the plant spectra can be strongly biased if inappropriate handling techniques are used. The conclusions hold for all kinds of waterlogged sediments of different periods.