Comparison of the Effect of Cognitive Rehabilitation and Neurofeedback on Sustained Attention Among Elementary School Students with Specific Learning Disorder: A Preliminary Randomized Controlled Clinical Trial

Specific learning disorder (SLD) can occur along with the problems of attention performance and be complicated by them. Recent studies have reported the positive effects of cognitive rehabilitation (CR) and neurofeedback (NFB) on sustained attention (SA) in SLD. Nevertheless, it has not yet been determinedwhat kind of treatment may be the most appropriate option for this disorder in terms of the different functions of cognitive status, especially SA. This preliminary study aimed to compare CR and NFB effects on SA among elementary school students with SLD using a randomized controlled clinical trial (RCT). Fifty- three eligible students with a DSM-5 SLD diagnosis, aged 7–10, were randomly allocated in NFB (n?=?18), CR (n?=?18), and control groups (n?=?17). All the participants were evaluated for SA by performing the continuous performance test (CPT) on the studied groups at the time of their inclusion in the study and 7 weeks after it. The intervention groups took part in 20 sessions of CR and 20 sessions of NFB. Conversely, the untreated group were evaluated without any intervention.15 boys and 30 girls in 3 groups completed the study (n?=?15 per group). The mean and standard deviation of participants’ age were (8.66?±?1.48) years, (8.40?±?1.73) years and (8.53?±?1.63) years in CR, NFB and untreated groups, respectively. The results showed significant differences between the groups based on the variables of the CPT test (p?<?0.05). Also, the significant effects of the variables represented the higher scores of the CR compared to the NFB group (p?<?0.001). This study provides einitial evidence that CR is more effective than NFB on SA improvement among students with SLD.     

Comparison of proteomes between wheat-rye translocations and their recurrent parents

2BS.2RL wheat-rye translocations have presented phenotypes of improved agronomic performance, such as Hessian fly resistance. The main objective of this work was to use two-dimensional electrophoresis to identify the proteomic differences between 2BS.2RL wheat-rye translocations and their recurrent parents. The investigation of seeds revealed line-specific protein spots, such as α-amylase inhibitor 0.19. More diverse expression patterns were observed in leaves than in seeds. Protein spots found specifically in 2BS.2RL, but not in non-2RL translocations were identified as β-glucosidase and vacuolar ATP synthase subunit B2, demonstrating the effects of translocated rye chromatin 2RL on common wheat genetic background. When the leaf protein spots were compared in the control and Hessian fly-infested near-isogenic line (NIL) (2BS.2RL), many down-regulated proteins and specific proteins, such as β-glucosidase, were detected in the latter.     

<Emphasis Type="Italic">Scopulibacillus cellulosilyticus</Emphasis> sp. nov., a cellulose-degrading bacterium isolated from tea

A Gram-stain positive, aerobic, non-motile, endospore-forming and rod-shaped strain (THG-NT9^T) was isolated from a green tea sample. Growth occurred at 20–45 °C (optimum 28–35 °C), at pH 6.0–8.0 (optimum 7.0) and at 0–2.0% NaCl (optimum 0%). Based on 16S rRNA gene sequence analysis, the near phylogenetic neighbours of strain THG-NT9^T were identified as Scopulibacillus daqui DSM 28236^T (98.6%), Scopulibacillus darangshiensis DSM 19377^T (97.4%), Pullulanibacillus pueri CGMCC 1.12777^T (96.7%) and Pullulanibacillus camelliae CGMCC 1.15371^T (96.3%). The DNA G?+?C content of strain THG-NT9^T was determined to be 47.5 mol %. DNA–DNA hybridization values between strain THG-NT9^T and S. daqui DSM 28236^T, S. darangshiensis DSM 19377^T, P. pueri CGMCC 1.12777^T, P. camelliae CGMCC 1.15371^T and Pullulanibacillus naganoensis DSM 10191^T were 41.3?±?0.1 (39.4?±?0.4% reciprocal analysis), 39.1?±?0.1 (37.3?±?0.1%), 21.4?±?0.7 (20.1?±?0.3%), 20.7?±?0.1 (20.1?±?0.4%) and 12.1?±?0.2% (8.3?±?0.2%). The polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and three unidentified lipids. The quinone was identified as MK-7. The major fatty acids were C_18:3 ω7c, iso-C_15:0, iso-C_16:0, iso-C_17:0 and anteiso-C_17:0. The cell wall type was determined to be A1γ peptidoglycan with meso-diaminopimelic acid as the diagnostic diamino acid plus alanine and glutamic acid and glucose as the cell wall sugar. On the basis of the phylogenetic analysis, chemotaxonomic data, physiological characteristics, and DNA–DNA hybridization data, strain THG-NT9^T represents a novel species of the genus Scopulibacillus, for which the name Scopulibacillus cellulosilyticus sp. nov. is proposed. The type strain is THG-NT9^T (=?KCTC 33918^T?=?CGMCC 1.16305^T).     

Fibroblast biology in three-dimensional collagen matrices

Research on fibroblast biology in three-dimensional collagen matrices offers new opportunities to understand the reciprocal and adaptive interactions that occur between cells and surrounding matrix in a tissue-like environment. Such interactions are integral to the regulation of connective tissue morphogenesis and dynamics that characterizes tissue homeostasis and wound repair. During fibroblast-collagen matrix remodeling, mechanical signals from the remodeled matrix feed back to modulate cell behavior in an iterative process. As mechanical loading (tension) within the matrix increases, the mechanisms used by cells to remodel the matrix change. Fibroblasts in matrices that are under tension or relaxed respond differently to growth factor stimulation, and switching between mechanically loaded and unloaded conditions influences whether cells acquire proliferative/biosynthetic active or quiescent/resting phenotypes.     

FastMG: a simple,fast, and accurate maximum likelihood procedure to estimate amino acid replacement rate matrices from large data sets

Background

Amino acid replacement rate matrices are a crucial component of many protein analysis systems such as sequence similarity search, sequence alignment, and phylogenetic inference. Ideally, the rate matrix reflects the mutational behavior of the actual data under study; however, estimating amino acid replacement rate matrices requires large protein alignments and is computationally expensive and complex. As a compromise, sub-optimal pre-calculated generic matrices are typically used for protein-based phylogeny. Sequence availability has now grown to a point where problem-specific rate matrices can often be calculated if the computational cost can be controlled.

Results

The most time consuming step in estimating rate matrices by maximum likelihood is building maximum likelihood phylogenetic trees from protein alignments. We propose a new procedure, called FastMG, to overcome this obstacle. The key innovation is the alignment-splitting algorithm that splits alignments with many sequences into non-overlapping sub-alignments prior to estimating amino acid replacement rates. Experiments with different large data sets showed that the FastMG procedure was an order of magnitude faster than without splitting. Importantly, there was no apparent loss in matrix quality if an appropriate splitting procedure is used.

Conclusions

FastMG is a simple, fast and accurate procedure to estimate amino acid replacement rate matrices from large data sets. It enables researchers to study the evolutionary relationships for specific groups of proteins or taxa with optimized, data-specific amino acid replacement rate matrices. The programs, data sets, and the new mammalian mitochondrial protein rate matrix are available at http://fastmg.codeplex.com.     

Cell migration in 3D matrix

The ability of cells to migrate within the extracellular matrix and to remodel it depends as much on the physical and biochemical characteristics of a particular matrix as on cellular properties. Analyzing the different modes of migration of cells in matrices, and how cells switch between these modes, is vital for understanding a variety of physiological and pathological processes. Recent work provides new insights, but also raises some debates about the mechanisms and regulation of cell migration in three-dimensional matrices.     

Molecular mapping of a new temperature-sensitive gene <Emphasis Type="Italic">LrZH22</Emphasis> for leaf rust resistance in Chinese wheat cultivar Zhoumai 22

Leaf rust, caused by Puccinia triticina, is one of the most widespread diseases in common wheat globally. The Chinese wheat cultivar Zhoumai 22 is highly resistant to leaf rust at the seedling and adult stages. Seedlings of Zhoumai 22 and 36 lines with known leaf rust resistance genes were inoculated with 13 P. triticina races for gene postulation. The leaf rust response of Zhoumai 22 was different from those of the single gene lines. With the objective of identifying and mapping, the new gene(s) for resistance to leaf rust, F₁, F₂ plants and F_2:3 lines from the cross Zhoumai 22/Chinese Spring were inoculated with Chinese P. triticina race FHDQ at the seedling stage. A single dominant gene, tentatively designated LrZH22, conferred resistance. To identify other possible genes in Zhoumai 22, ten P. triticina races avirulent on Zhoumai 22 were used to inoculate 24 F_2:3 lines. The same gene conferred resistance to all ten avirulent races. A total of 1300 simple sequence repeat (SSR) markers and 36 EST markers on 2BS were used to test the parents, and resistant and susceptible bulks. Resistance gene LrZH22 was mapped in the chromosome bin 2BS1-0.53-0.75 and closely linked to six SSR markers (barc183, barc55, gwm148, gwm410, gwm374 and wmc474) and two EST markers (BF202681 and BE499478) on chromosome arm 2BS. The two closest flanking SSR loci were Xbarc55 and Xgwm374 with genetic distances of 2.4 and 4.8 cM from LrZH22, respectively. Six designated genes (Lr13, Lr16, Lr23, Lr35, Lr48 and Lr73) are located on chromosome arm 2BS. In seedling tests, LrZH22 was temperature sensitive, conferring resistance at high temperatures. The reaction pattern of Zhoumai 22 was different from that of RL 4031 (Lr13), RL 6005 (Lr16) and RL 6012 (Lr23), Lr35 and Lr48 are adult-plant resistance genes, and Lr73 is not sensitive to the temperature. Therefore, LrZH22 is likely to be a new leaf rust resistance gene or allele.     

Genetic and environmental influences on root development in cuttings of selected <Emphasis Type="Italic">Salix</Emphasis> and <Emphasis Type="Italic">Populus</Emphasis> clones – a greenhouse experiment

Aims

This study investigated how genetic determination of adventitious root development compared in experimental hybrid and parental Salix and Populus clones, and how soil bulk density influenced root development.

Methods

Cuttings of 11 Salix clones and 10 Populus clones were grown in pots with water, a low bulk density soil and a high bulk density soil for 4 (water) or 10 weeks (soils). Parameters relating to root development were measured.

Results

Root initiation, total root length (RL), and dry mass (DM), as well as root: shoot relationships in Salix clones exceeded that of Populus clones in all media. For Salix clones RL and DM were highest in S. matsudana?×?pentandra and for Populus clones RL and DM were generally higher in hybrid clones having P. trichocarpa parentage. Mean RL and DM for all clones were generally greater in the low bulk density soil than in the high bulk density soil. There were a greater proportion of thinner roots in the low bulk density soil than in the high bulk density soil.

Conclusions

There were significant differences in root initiation, RL, and DM among clones within each genus. Increasing soil bulk density significantly reduced root development in both Salix and Populus clones. Evaluating cutting root development in pot trials could be a useful clone selection tool in willow and poplar breeding.

     

Reassessment of the evolution of wheat chromosomes 4A, 5A,and 7B

Key message

Comparison of genome sequences of wild emmer wheat and Aegilops tauschii suggests a novel scenario of the evolution of rearranged wheat chromosomes 4A, 5A, and 7B.

Abstract

Past research suggested that wheat chromosome 4A was subjected to a reciprocal translocation T(4AL;5AL)1 that occurred in the diploid progenitor of the wheat A subgenome and to three major rearrangements that occurred in polyploid wheat: pericentric inversion Inv(4AS;4AL)1, paracentric inversion Inv(4AL;4AL)1, and reciprocal translocation T(4AL;7BS)1. Gene collinearity along the pseudomolecules of tetraploid wild emmer wheat (Triticum turgidum ssp. dicoccoides, subgenomes AABB) and diploid Aegilops tauschii (genomes DD) was employed to confirm these rearrangements and to analyze the breakpoints. The exchange of distal regions of chromosome arms 4AS and 4AL due to pericentric inversion Inv(4AS;4AL)1 was detected, and breakpoints were validated with an optical Bionano genome map. Both breakpoints contained satellite DNA. The breakpoints of reciprocal translocation T(4AL;7BS)1 were also found. However, the breakpoints that generated paracentric inversion Inv(4AL;4AL)1 appeared to be collocated with the 4AL breakpoints that had produced Inv(4AS;4AL)1 and T(4AL;7BS)1. Inv(4AS;4AL)1, Inv(4AL;4AL)1, and T(4AL;7BS)1 either originated sequentially, and Inv(4AL;4AL)1 was produced by recurrent chromosome breaks at the same breakpoints that generated Inv(4AS;4AL)1 and T(4AL;7BS)1, or Inv(4AS;4AL)1, Inv(4AL;4AL)1, and T(4AL;7BS)1 originated simultaneously. We prefer the latter hypothesis since it makes fewer assumptions about the sequence of events that produced these chromosome rearrangements.

     

Matrix compositions and the development of breast acini and ducts in 3D cultures

Breast epithelial cells develop into polarized and highly organized acinar and ductal structures in response to stromal cues, including extracellular matrix composition and density, which can in part be reproduced in 3D culture conditions. Here, we present the effects of various 3D in vitro stroma compositions (termed “matrices” or “substrates”) on the ability of heterotypic cultures of epithelial and mesenchymal stem cells to organize into acinar and tubular structures. Normal murine mammary gland (NMuMG) cells were cultured, either alone or in combination (30:70) with mouse mesenchymal stem cells (D1), in 3D matrices generated by agarose, collagen, and Matrigel® alone or by a combination thereof. After 3–5 d in culture, cell distribution, organization, and the presence of acinus-like and tubule-like structures were determined. The number of acinar structures was significantly higher in cultures grown in combination matrices of agarose with Matrigel® or collagen I when compared with cultures grown in Matrigel® or collagen I alone (p?p?相似文献   

Genetic analyses of cell death in maize (Zea mays, Poaceae) leaves reveal a distinct pathway operating in the camouflage1 mutant

Controlled cell death is vital for many physiological processes in plants, such as xylem development, the hypersensitive response (HR), and senescence; however, the pathways governing cell death are incompletely understood. Studies of mutants that display a cell-death phenotype have greatly contributed to our knowledge of how this process is regulated. The maize camouflage1 (cf1) mutant displays the novel phenotype of cell-specific death of bundle sheath (BS) cells in discrete yellow leaf tissues. To investigate the BS cell death in cf1 mutants, we characterized potential underlying factors. Hydrogen peroxide (H(2)O(2)) is known to be involved in many cell-death events in plants, including the HR. However, in vivo staining found no accumulation of H(2)O(2) in cf1 mutant leaves. Additionally, genetic analyses determined that functional chloroplasts are required for cf1 BS cell death. These results demonstrate that cf1 BS cell death occurs via a distinct pathway from that seen in a functionally related maize mutant or in the HR, suggesting that cell death in maize leaves can be caused by multiple mechanisms.     

Fibronectin polymerization regulates the composition and stability of extracellular matrix fibrils and cell-matrix adhesions

Remodeling of extracellular matrices occurs during development, wound healing, and in a variety of pathological processes including atherosclerosis, ischemic injury, and angiogenesis. Thus, identifying factors that control the balance between matrix deposition and degradation during tissue remodeling is essential for understanding mechanisms that regulate a variety of normal and pathological processes. Using fibronectin-null cells, we found that fibronectin polymerization into the extracellular matrix is required for the deposition of collagen-I and thrombospondin-1 and that the maintenance of extracellular matrix fibronectin fibrils requires the continual polymerization of a fibronectin matrix. Further, integrin ligation alone is not sufficient to maintain extracellular matrix fibronectin in the absence of fibronectin deposition. Our data also demonstrate that the retention of thrombospondin-1 and collagen I into fibrillar structures within the extracellular matrix depends on an intact fibronectin matrix. An intact fibronectin matrix is also critical for maintaining the composition of cell-matrix adhesion sites; in the absence of fibronectin and fibronectin polymerization, neither alpha5beta1 integrin nor tensin localize to fibrillar cell-matrix adhesion sites. These data indicate that fibronectin polymerization is a critical regulator of extracellular matrix organization and stability. The ability of fibronectin polymerization to act as a switch that controls the organization and composition of the extracellular matrix and cell-matrix adhesion sites provides cells with a means of precisely controlling cell-extracellular matrix signaling events that regulate many aspects of cell behavior including cell proliferation, migration, and differentiation.     

Uprooted Phylogenetic Networks

The need for structures capable of accommodating complex evolutionary signals such as those found in, for example, wheat has fueled research into phylogenetic networks. Such structures generalize the standard model of a phylogenetic tree by also allowing for cycles and have been introduced in rooted and unrooted form. In contrast to phylogenetic trees or their unrooted versions, rooted phylogenetic networks are notoriously difficult to understand. To help alleviate this, recent work on them has also centered on their “uprooted” versions. By focusing on such graphs and the combinatorial concept of a split system which underpins an unrooted phylogenetic network, we show that not only can a so-called (uprooted) 1-nested network N be obtained from the Buneman graph (sometimes also called a median network) associated with the split system \(\Sigma (N)\) induced on the set of leaves of N but also that that graph is, in a well-defined sense, optimal. Along the way, we establish the 1-nested analogue of the fundamental “splits equivalence theorem” for phylogenetic trees and characterize maximal circular split systems.     

Microencapsulation by spray drying of nitrogen-fixing bacteria associated with lupin nodules

Plant growth promoting bacteria and nitrogen-fixing bacteria (NFB) used for crop inoculation have important biotechnological potential as a sustainable fertilization tool. However, the main limitation of this technology is the low inoculum survival rate under field conditions. Microencapsulation of bacterial cells in polymer matrices provides a controlled release and greater protection against environmental conditions. In this context, the aim of this study was to isolate and characterize putative NFB associated with lupin nodules and to evaluate their microencapsulation by spray drying. For this purpose, 21 putative NFB were isolated from lupin nodules and characterized (16S rRNA genes). Microencapsulation of bacterial cells by spray drying was studied using a mixture of sodium alginate:maltodextrin at different ratios (0:15, 1:14, 2:13) and concentrations (15 and 30 % solids) as the wall material. The microcapsules were observed under scanning electron microscopy to verify their suitable morphology. Results showed the association between lupin nodules of diverse known NFB and nodule-forming bacteria belonging to Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria and Bacteroidetes. In microencapsulation assays, the 1:14 ratio of sodium alginate:maltodextrin (15 % solids) showed the highest cell survival rate (79 %), with a microcapsule yield of 27 % and spherical microcapsules of 5–50 µm in diameter. In conclusion, diverse putative NFB genera and nodule-forming bacteria are associated with the nodules of lupine plants grown in soils in southern Chile, and their microencapsulation by spray drying using sodium alginate:maltodextrin represents a scalable process to generate a biofertilizer as an alternative to traditional nitrogen fertilization.     

Material flow analysis of feedstock for enhancing its conversion efficiency during continuous photo‐hydrogen production

The practical application of photofermentative hydrogen production process has been generally limited by the low feedstock conversion efficiency. In this work, material flow analysis (MFA) was applied into continuous photohydrogen to investigate the material flow of feedstock. Maximum feedstock utilization for hydrogen production (31.87%) was obtained at an hydraulic retention time of 60 h and influent acetate concentration of 40 mmol l^?1, corresponding to maximum hydrogen yield of 1.89 mol H₂ mol^?1 acetate. MFA showed that due to the poor flocculation, photofermentative bacteria (PFB) cannot be efficiently separated from supernatant and rushed out with effluent continuously. To replenish the biomass washout, most of feedstock was continuously utilized for cell growth rather than hydrogen production, which caused low feedstock conversion efficiency. The results showed that poor flocculation of PFB resulting in low biomass retention capacity of photobioreactor was the origin of low feedstock conversion efficiency. Therefore, enhancing flocculation of PFB and using high biomass retaining operation modes are essential to further develop photofermentative hydrogen production process.     

Application of a virulent bacteriophage cocktail leads to reduction of Salmonella enterica serovar Enteritidis counts in processed meat products

Salmonella enterica serotype Enteritidis (SE) is a major cause of food-borne disease outbreaks worldwide. We evaluated the effectiveness of five lytic bacteriophages applied as a cocktail to reduce the counts of SE in two types of processed meat products: cooked (turkey ham (TB) and chicken sausage (CS)) and cured sausage (Italian salami (IS) and barbecue sausage (BS)). Groups of 25 samples each were contaminated with SE, treated with a phage cocktail using a multiplicity of infection of 10⁵ and then incubated for ten days at 18°C and 4°C. A significant reduction in bacteria was obtained on days 3, 6 and 10 in all matrices incubated at 18°C (from 0.48 to 2.12?log Colony Forming Units (CFU)?g^?1) and at 4°C (from 0.23 to 2.06?log CFU?g^?1), with the exception of BS at day 3 at 4°C, and IS at both incubation temperatures throughout the trial. The viral titre remained stable in all matrices analysed except in BS. These results show the effectiveness of this bacteriophage cocktail against S. enterica serovar Enteritidis in some processed meat products such as CS, BS and TB.     

Complementary roles of initiation factor 1 and ribosome recycling factor in 70S ribosome splitting

We demonstrate that ribosomes containing a messenger RNA (mRNA) with a strong Shine-Dalgarno sequence are rapidly split into subunits by initiation factors 1 (IF1) and 3 (IF3), but slowly split by ribosome recycling factor (RRF) and elongation factor G (EF-G). Post-termination-like (PTL) ribosomes containing mRNA and a P-site-bound deacylated transfer RNA (tRNA) are split very rapidly by RRF and EF-G, but extremely slowly by IF1 and IF3. Vacant ribosomes are split by RRF/EF-G much more slowly than PTL ribosomes and by IF1/IF3 much more slowly than mRNA-containing ribosomes. These observations reveal complementary splitting of different ribosomal complexes by IF1/IF3 and RRF/EF-G, and suggest the existence of two major pathways for ribosome splitting into subunits in the living cell. We show that the identity of the deacylated tRNA in the PTL ribosome strongly affects the rate by which it is split by RRF/EF-G and that IF3 is involved in the mechanism of ribosome splitting by IF1/IF3 but not by RRF/EF-G. With support from our experimental data, we discuss the principally different mechanisms of ribosome splitting by IF1/IF3 and by RRF/EF-G.     

Identification and polymorphism of pectinase genes <Emphasis Type="Italic">PGU</Emphasis> in the <Emphasis Type="Italic">Saccharomyces bayanus</Emphasis> complex

Pectinase (endo-polygalacturonase) is the key enzyme splitting plant pectin. The corresponding single gene PGU1 is documented for the yeast S. cerevisiae. On the basis of phylogenetic analysis of the PGU nucleotide sequence available in the GenBank, a family of divergent PGU genes is found in the species complex S. bayanus: S. bayanus var. uvarum, S. eubayanus, and hybrid taxon S. pastorianus. The PGU genes have different chromosome localization.     

Formation of Intercellular Collagen Matrix by Cultured Liver Epithelial Cells and Loss of its Ability in Hepatocarcinogenesis in vitro

Epithelial cells of normal rat liver origin (strain RL34) synthesized the α1 peptide of type I collagen. In nononcogenic cultures (RL34 and RL34EC) and a marginally oncogenic culture (RL34HII), the peptide was continuously secreted from the proliferating cells. Part of the soluble peptide was incorporated into the intercellular matrix of contact-inhibited cells after confluency, while the remainder was degraded. The intercellular matrix contained characteristic collagen fibrils which were argyrophilic and revealed a 64 nm axial periodicity. Epithelial cells of an oncogenic culture (RL34HT) secreted procollagen into the medium continuously throughout their proliferative phases and were unable to accumulate collagen fibrils in the intercellular matrix. The depletion of collagen accumulation in the hepatocarcinoma cell culture was ascribed to lack of the binding of native collagen molecules to the cell membrane and the persistence of high proteolytic activity on the cell surface.