A novel model to characterize structure and function of BRCA1

BRCA1 plays a central role in DNA repair. Although N‐terminal RING and C‐terminal BRCT domains are studied well, the functions of the central region of BRCA1 are poorly characterized. Here, we report a structural and functional analysis of BRCA1 alleles and functional human BRCA1 in chicken B‐lymphocyte cell line DT40. The combination of “homologous recombineering” and “RT‐cassette” enables modifications of chicken BRCA1 gene in Escherichia coli. Mutant BRCA1 knock‐in DT40 cell lines were generated using BRCA1 mutation constructs by homologous recombination with a targeting efficiency of up to 100%. Our study demonstrated that deletion of motifs 2–9 BRCA1^{Δ/Δ181‐1415} (Caenorhabditis elegans BRCA1 mimic) or deletion of motif 1 BRCA1^{Δ/Δ126‐136} decreased cell viability following cisplatin treatment. Furthermore, deletion of motifs 5 and 6 BRCA1^{Δ/Δ525‐881} within DNA‐binding region, even the conserved 7‐amino acid deletion BRCA1^{Δ/Δ872‐878} within motif 6, caused a decreased cell viability upon cisplatin treatment. Surprisingly, human BRCA1 is functional in DT40 cells as indicated by DNA damage‐induced Rad 51 foci formation in human BRCA1 knock‐in DT40 cells. These results demonstrate that those conserved motifs within the central region are essential for DNA repair functions of BRCA1. These findings provide a valuable tool for the development of new therapeutic modalities of breast cancer linked to BRCA1.     

Length‐weight relationships of three gobiid species (Perciformes: Gobiidae) along the Iranian intertidal coast of the Persian Gulf and Makran Sea

Length weight relationships (LWRs) were estimated for three gobiid species, Bathygobius meggitti(Hora & Mukerji, 1936), Acentrogobius dayi Koumans, 1941 and Cryptocentroides arabicus(Gmelin, 1789) (Perciformes: Gobiidae) collected from 13 localities of the Iranian intertidal coast of the Persian Gulf and Makran Sea in seven times from November 2015 to September 2017 using a hand net with mesh size 1.30 mm. The b values showed significant differences between males and females of all species except the C. arabicus. Bailey's t test revealed that b value significantly deviated from the expected cube value of 3 in three species.     

Reassessment of the status of Lymantria albescens and Lymantria postalba (Lepidoptera: Erebidae: Lymantriinae) as distinct ‘Asian gypsy moth’ species,using both mitochondrial and nuclear sequence data

For regulatory purposes, the name ‘Asian gypsy moth’ refers to a group of closely related Asian Lymantria species and subspecies whose female moths display flight capability, a trait believed to confer enhanced invasiveness relative to the European gypsy moth, Lymantria dispar dispar, whose females are flightless. Lymantria albescens and Lymantria postalba are Asian gypsy moths occurring in the southern Ryukyu Islands and in the northern Ryukyu and adjacent Kyushu and Shikoku Islands of Japan, respectively. Although once considered subspecies of L. dispar, their status as distinct species, relative to the latter, is now well established. While postalba was subsequently considered a subspecies of L. albescens, largely on the basis of differences in forewing ground colour in males, both taxa were later given distinct species status by Pogue & Schaefer (2007) following their revision of the genus Lymantria. Here, we re-examined the validity of this revised status through the sequencing of a large portion of the mitochondrial genome (c. 60%) and multiple nuclear marker genes [elongation factor 1-alpha (Ef-1α), wingless (Wgl), internal transcribed spacer 2 (ITS-2), ribosomal protein S5 (RpS5)] in representative specimens of both taxa and other Lymantria species, including L. monacha, L. xylina, L. mathura and members of the L. dispar + L. umbrosa clade. A comparison of the number of substitutions in these genomic regions among the taxa we considered showed lower or equivalent variation between L. albescens and L. postalba compared with subspecies of L. dispar, for mitochondrial and nuclear sequences, respectively. This finding was reflected in the maximum likelihood trees generated independently for mitochondrial and nuclear data, where L. albescens and L. postalba formed, in both analyses, a short-branch sister clade basal to the L. dispar + L. umbrosa clade. We further sequenced three markers [cytochrome c oxydase 1 (COI), EF-1α, Wgl] in multiple L. albescens–L. postalba specimens collected along a south-to-north transect across the Ryukyu Arc and observed no clear distinction among the sampled specimens as a function of taxonomic designation. We conclude that L. albescens and L. postalba form a single species, with postalba representing a darker-winged morph along an apparent south-to-north wing colour cline. Accordingly, L. postalba is relegated to synonymy under L. albescens ( syn.n. ).     

Improving ECG classification accuracy using an ensemble of neural network modules

This paper illustrates the use of a combined neural network model based on Stacked Generalization method for classification of electrocardiogram (ECG) beats. In conventional Stacked Generalization method, the combiner learns to map the base classifiers' outputs to the target data. We claim adding the input pattern to the base classifiers' outputs helps the combiner to obtain knowledge about the input space and as the result, performs better on the same task. Experimental results support our claim that the additional knowledge according to the input space, improves the performance of the proposed method which is called Modified Stacked Generalization. In particular, for classification of 14966 ECG beats that were not previously seen during training phase, the Modified Stacked Generalization method reduced the error rate for 12.41% in comparison with the best of ten popular classifier fusion methods including Max, Min, Average, Product, Majority Voting, Borda Count, Decision Templates, Weighted Averaging based on Particle Swarm Optimization and Stacked Generalization.     

Type 2 IDI performs better than type 1 for improving lycopene production in metabolically engineered E. coli strains

In this study a comparison was made between type 1 and type 2 isopentenyl diphosphate isomerases (IDI) in improving lycopene production in Escherichia coli. The corresponding genes of Bacillus licheniformis and the host (i _Bl and i _Ec , respectively) were expressed in lycopene producing E. coli strains by pTlyci_Bl and pTlyci_Ec plasmids, under the control of tac promoter. The results showed that the overexpression of i _Ec improved the lycopene production from 33 ± 1 in E. coli Tlyc to 68 ± 3 mg/gDCW in E. coli Tlyci_Ec. In contrast, the expression of i _Bl increased the lycopene production more efficiently up to 80 ± 9 mg/gDCW in E. coli Tlyci_Bl. The introduction of a heterologous mevalonate pathway to elevate the IPP abundance resulted in a lycopene production up to 132 ± 5 mg/gDCW with i _Ec in E. coli Tlyci_Ec-mev and 181 ± 9 mg/gDCW with i _Bl in E. coli Tlyci_Bl-mev, that is, 4 and 5.6 times respectively. When fructose, mannose, arabinose, and acetate were each used as an auxiliary substrate with glycerol, lycopene production was inhibited by different extents. Among auxiliary substrates tested, only citrate was an improving one for lycopene production in all strains with a maximum of 198 ± 3 mg/gDCW in E. coli Tlyci_Bl-mev. It may be concluded that the type 2 IDI performs better than the type 1 in metabolic engineering attempts for isoprenoid production in E. coli. In addition, the metabolic engineering of citrate pathway seems a promising approach to have more isoprenoid accumulation in E. coli.     

Heterologous virus-induced gene silencing as a promising approach in plant functional genomics

VIGS (virus induced gene silencing) is considered as a powerful genomics tool for characterizing the function of genes in a few closely related plant species. The investigations have been carried out mainly in order to test if a pre-existing VIGS vector can serve as an efficient tool for gene silencing in a diverse array of plant species. Another route of investigation has been the constructing of new viral vectors to act in their hosts. Our approach was the creation of a heterologous system in which silencing of endogenous genes was achieved by sequences isolated from evolutionary remote species. In this study, we showed that a TRV-based vector cloned with sequences from a gymnosperm, Taxus baccata L. silenced the endogenous phytoene desaturase in an angiosperm, N. benthamiana. Our results showed that inserts of between 390 and 724 bp isolated from a conserved fragment of the Taxus PDS led to silencing of its homolog in tobacco. The real time analysis indicated that the expression of PDS was reduced 2.1- to 4.0-fold in pTRV-TbPDS infected plants compared with buffer treated plants. Once the best insert is identified and the conditions are optimized for heterologous silencing by pTRV-TbPDS in tobacco, then we can test if TRV can serve as an efficient silencing vector in Taxus. This strategy could also be used to silence a diverse array of genes from a wide range of species which have no VIGS protocol. The results also showed that plants silenced heterologously by the VIGS system a minimally affected with respect to plant growth which may be ideal for studying the genes that their complete loss of function may lead to decrease of plant growth or plant death.     

A stable biologically motivated learning mechanism for visual feature extraction to handle facial categorization

The brain mechanism of extracting visual features for recognizing various objects has consistently been a controversial issue in computational models of object recognition. To extract visual features, we introduce a new, biologically motivated model for facial categorization, which is an extension of the Hubel and Wiesel simple-to-complex cell hierarchy. To address the synaptic stability versus plasticity dilemma, we apply the Adaptive Resonance Theory (ART) for extracting informative intermediate level visual features during the learning process, which also makes this model stable against the destruction of previously learned information while learning new information. Such a mechanism has been suggested to be embedded within known laminar microcircuits of the cerebral cortex. To reveal the strength of the proposed visual feature learning mechanism, we show that when we use this mechanism in the training process of a well-known biologically motivated object recognition model (the HMAX model), it performs better than the HMAX model in face/non-face classification tasks. Furthermore, we demonstrate that our proposed mechanism is capable of following similar trends in performance as humans in a psychophysical experiment using a face versus non-face rapid categorization task.     

RNA Catalyst as a Reporter for Screening Drugs against RNA Editing in Trypanosomes

Substantial progress has been made in determining the mechanism of mitochondrial RNA editing in trypanosomes. Similarly, considerable progress has been made in identifying the components of the editosome complex that catalyze RNA editing. However, it is still not clear how those proteins work together. Chemical compounds obtained from a high-throughput screen against the editosome may block or affect one or more steps in the editing cycle. Therefore, the identification of new chemical compounds will generate valuable molecular probes for dissecting the editosome function and assembly. In previous studies, in vitro editing assays were carried out using radio-labeled RNA. These assays are time consuming, inefficient and unsuitable for high-throughput purposes. Here, a homogenous fluorescence-based “mix and measure” hammerhead ribozyme in vitro reporter assay to monitor RNA editing, is presented. Only as a consequence of RNA editing of the hammerhead ribozyme a fluorescence resonance energy transfer (FRET) oligoribonucleotide substrate undergoes cleavage. This in turn results in separation of the fluorophore from the quencher thereby producing a signal. In contrast, when the editosome function is inhibited, the fluorescence signal will be quenched. This is a highly sensitive and simple assay that should be generally applicable to monitor in vitro RNA editing or high throughput screening of chemicals that can inhibit the editosome function.     

Efficiency Enhancement of Ultra-thin CIGS Solar Cells Using Bandgap Grading and Embedding Au Plasmonic Nanoparticles

The objective of this study is to enhance the efficiency of copper indium gallium selenide (CIGS) solar cells. To accomplish that, composition grading of absorber layer was carried out by using SILVACO’s technology aided computer design (TCAD) ATLAS program. Results showed a meaningful improvement of output parameters including open-circuit voltage (V_oc), short-circuit current (I_sc), fill factor (FF), and power conversion efficiency (η). For further performance improvement of the cell, Au plasmonic scattering nanoparticles were loaded on the top of the ZnO window layer. Plasmonic nanoparticles can restrict, absorb, navigate, or scatter the incident light. By using the spherical Au nanoparticles, a very good increase in the light absorption in the cell over the reference planar CIGS solar cell was observed. The highest η = 19.01% was achieved for the designed ultra-thin bandgap-graded CIGS solar cell decorated by Au nanoparticles.

     

“Plastic” and “static” behavior of vessel-anatomical features in Oriental beech (Fagus orientalis Lipsky) in view of xylem hydraulic conductivity

Key message

Xylem anatomical traits can be categorized into two groups: plastic properties which show a high inter-annual variability, and static characteristics which vary in a more conservative range.

Abstract

Water conduction in broad-leaved trees depends mainly on the size, number, and arrangement of vessels, which vary from year to year in response to varying exogenous factors, thus contributing to a safe and/or efficient water transport. However, the nature of such compensation is not clear; in particular, it is not obvious which traits act independently and which ones coincidentally. To better understand these inter-relations, tree-ring width (TRW), vessel-related anatomical traits, and the theoretical hydraulic conductivity were measured or modeled in the last 50 growth rings of mature Oriental beech trees growing at different altitudes in northern Iran. The study trees followed similar strategies compensating the effects of external factors by modifying their vessel-anatomical features. TRW and the number of vessels per unit of area were highly but negatively correlated and both were affected by exogenous factors. However, a decrease in vessel frequency (VF) is not a mirror effect of wider tree rings, but trees actively control the number of vessels produced. Principal component analysis revealed that the features VF, TRW and relative total conductivity were more plastic, whereas average vessel-lumen area, tree-ring porosity, and relative specific conductivity behaved more static. Moreover, we suggest that in theoretical approaches, total hydraulic conductivity rather than the specific hydraulic conductivity is a better indicator of a tree’s hydraulic behavior in a given growing season.