Evaluation of Diffusion-Tensor Imaging-Based Global Search and Tractography for Tumor Surgery Close to the Language System

Pre-operative planning and intra-operative guidance in neurosurgery require detailed information about the location of functional areas and their anatomo-functional connectivity. In particular, regarding the language system, post-operative deficits such as aphasia can be avoided. By combining functional magnetic resonance imaging and diffusion tensor imaging, the connectivity between functional areas can be reconstructed by tractography techniques that need to cope with limitations such as limited resolution and low anisotropic diffusion close to functional areas. Tumors pose particular challenges because of edema, displacement effects on brain tissue and infiltration of white matter. Under these conditions, standard fiber tracking methods reconstruct pathways of insufficient quality. Therefore, robust global or probabilistic approaches are required. In this study, two commonly used standard fiber tracking algorithms, streamline propagation and tensor deflection, were compared with a previously published global search, Gibbs tracking and a connection-oriented probabilistic tractography approach. All methods were applied to reconstruct neuronal pathways of the language system of patients undergoing brain tumor surgery, and control subjects. Connections between Broca and Wernicke areas via the arcuate fasciculus (AF) and the inferior fronto-occipital fasciculus (IFOF) were validated by a clinical expert to ensure anatomical feasibility, and compared using distance- and diffusion-based similarity metrics to evaluate their agreement on pathway locations. For both patients and controls, a strong agreement between all methods was observed regarding the location of the AF. In case of the IFOF however, standard fiber tracking and Gibbs tracking predominantly identified the inferior longitudinal fasciculus that plays a secondary role in semantic language processing. In contrast, global search resolved connections in almost every case via the IFOF which could be confirmed by probabilistic fiber tracking. The results show that regarding the language system, our global search is superior to clinically applied conventional fiber tracking strategies with results similar to time-consuming global or probabilistic approaches.     

Eye Movement Patterns in Natural Reading: A Comparison of Monolingual and Bilingual Reading of a Novel

Introduction and Method

This paper presents a corpus of sentence level eye movement parameters for unbalanced bilingual first language (L1) and second-language (L2) reading and monolingual reading of a complete novel (56 000 words). We present important sentence-level basic eye movement parameters of both bilingual and monolingual natural reading extracted from this large data corpus.

Results and Conclusion

Bilingual L2 reading patterns show longer sentence reading times (20%), more fixations (21%), shorter saccades (12%) and less word skipping (4.6%), than L1 reading patterns. Regression rates are the same for L1 and L2 reading. These results could indicate, analogous to a previous simulation with the E-Z reader model in the literature, that it is primarily the speeding up of lexical access that drives both L1 and L2 reading development. Bilingual L1 reading does not differ in any major way from monolingual reading. This contrasts with predictions made by the weaker links account, which predicts a bilingual disadvantage in language processing caused by divided exposure between languages.     

Deterioration in Motor Function Over Time in Older Adults With Type 2 Diabetes is Associated with Accelerated Cognitive Decline

Objective: Type 2 diabetes (T2D) is associated with motor impairments and a higher dementia risk. The relationships of motor decline with cognitive decline in T2D older adults has rarely been studied. Using data from the Israel Diabetes and Cognitive Decline study (N = 892), we examined associations of decline in motor function with cognitive decline over a 54-month period.Methods: Motor function measures were strength (handgrip) and gait speed (time to walk 3 m). Participants completed a neuropsychologic battery of 13 tests transformed into z-scores, summarized into 4 cognitive domains: episodic memory, attention/working memory, executive functions, and language/semantic categorization. The average of the 4 domains’ z-scores defined global cognition. Motor and cognitive functions were assessed in 18-months intervals. A random coefficients model delineated longitudinal relationships of cognitive decline with baseline and change from baseline in motor function, adjusting for sociodemographic, cardiovascular, and T2D-related covariates.Results: Slower baseline gait speed levels were significantly associated with more rapid decline in global cognition (P = .004), language/semantic categorization (P = .006) and episodic memory (P = .029). Greater decline over time in gait speed was associated with an accelerated rate of decline in global cognition (P = .050), attention/working memory (P = .047) and language/semantic categorization (P<.001). Baseline strength levels were not associated with cognitive decline but the rate of declining strength was associated with an accelerated decline in executive functions (P = .025) and language/semantic categorization (P = .006).Conclusion: In T2D older adults, the rate of decline in motor function, beyond baseline levels, was associated with accelerated cognitive decline, suggesting that cognitive and motor decline share common neuropathologic mechanisms in T2D.     

Identification of a canonical SCFSLF complex involved in S-RNase-based self-incompatibility of Pyrus (Rosaceae)

S-RNase-based self-incompatibility (SI) is an intraspecific reproductive barrier to prevent self-fertilization found in many species of the Solanaceae, Plantaginaceae and Rosaceae. In this system, S-RNase and SLF/SFB (S-locus F-box) genes have been shown to control the pistil and pollen SI specificity, respectively. Recent studies have shown that the SLF functions as a substrate receptor of a SCF (Skp1/Cullin1/F-box)-type E3 ubiquitin ligase complex to target S-RNases in Solanaceae and Plantaginaceae, but its role in Rosaceae remains largely undefined. Here we report the identification of two pollen-specific SLF-interacting Skp1-like (SSK) proteins, PbSSK1 and PbSSK2, in Pyrus bretschneideri from the tribe Pyreae of Rosaceae. Both yeast two-hybrid and pull-down assays demonstrated that they could connect PbSLFs to PbCUL1 to form a putative canonical SCF^SLF (SSK/CUL1/SLF) complex in Pyrus. Furthermore, pull-down assays showed that the SSK proteins could bind SLF and CUL1 in a cross-species manner between Pyrus and Petunia. Additionally, phylogenetic analysis revealed that the SSK-like proteins from Solanaceae, Plantaginaceae and Rosaceae form a monoclade group, hinting their shared evolutionary origin. Taken together, with the recent identification of a canonical SCF^SFB complex in Prunus of the tribe Amygdaleae of Rosaceae, our results show that a conserved canonical SCF^SLF/SFB complex is present in Solanaceae, Plantaginaceae and Rosaceae, implying that S-RNase-based self-incompatibility shares a similar molecular and biochemical mechanism.     

Predictions of methane emission levels and categories based on milk fatty acid profiles from dairy cows

Milk fatty acid (MFA) have already been used to model methane (CH₄) emissions from dairy cows. However, the data sets used to develop these models covered limited variation in dietary conditions, reducing the robustness of the predictions. In this study, a data set containing 140 observations from nine experiments (41 Holstein cows) was used to develop models predicting CH₄ expressed as g/day, g/kg dry matter intake (DMI) and g/kg milk. The data set was divided into a training (n=112) and a test data set (n=28) for model development and validation, respectively. A generalized linear mixed model was fitted to the data using the marginal R²_(m) and the Akaike information criterion to evaluate the models. The coefficient of determination of validation (R²_(v)) for different models developed ranged between 0.18 and 0.41. Form the intake-related parameters, only inclusion of total DMI improved the prediction (R²_(v)=0.58). In addition, in an attempt to further explore the relationships between MFA and CH₄ emissions, the data set was split into three categories according to CH₄ emissions: LOW (lowest 25% CH₄ emissions); HIGH (highest 25% CH₄ emissions); and MEDIUM (50% remaining observations). An ANOVA revealed that concentrations of several MFA differed for observations in HIGH compared with observations in LOW. Furthermore, the Gini coefficient was used to describe the MFA distribution for groups of MFA in each CH₄ emission category. The relative distribution of the MFA, particularly of the odd- and branched-chain fatty acids and mono-unsaturated fatty acids of observations in category HIGH differed from those in the other categories. Finally, in an attempt to validate the potential of MFA to identify cases of high or low emissions, the observations were re-classified into HIGH, MEDIUM and LOW according to the proportion of each individual MFA. The proportion of observations correctly classified were recorded. This was done for each individual MFA and for the calculated Gini coefficients, finding that a maximum of 67% of observations were correctly classified as HIGH CH₄ (trans-12 C18:1) and a maximum of 58% of observations correctly classified as LOW CH₄ (cis-9 C17:1). Gini coefficients did not improve this classification. These results suggest that MFA are not yet reliable predictors of specific amounts of CH₄ emitted by a cow, while holding a modest potential to differentiate cases of high or low emissions.     

Updates on industrial production of amino acids using <Emphasis Type="Italic">Corynebacterium glutamicum</Emphasis>

l-Amino acids find various applications in biotechnology. l-Glutamic acid and its salts are used as flavor enhancers. Other l-amino acids are used as food or feed additives, in parenteral nutrition or as building blocks for the chemical and pharmaceutical industries. l-amino acids are synthesized from precursors of central carbon metabolism. Based on the knowledge of the biochemical pathways microbial fermentation processes of food, feed and pharma amino acids have been developed. Production strains of Corynebacterium glutamicum, which has been used safely for more than 50 years in food biotechnology, and Escherichia coli are constantly improved using metabolic engineering approaches. Research towards new processes is ongoing. Fermentative production of l-amino acids in the million-ton-scale has shaped modern biotechnology and its markets continue to grow steadily. This review focusses on recent achievements in strain development for amino acid production including the use of CRISPRi/dCas9, genome-reduced strains, biosensors and synthetic pathways to enable utilization of alternative carbon sources.     

Effect of seaweed liquid fertilizer on yield and quality of Capsicum annum L.

In the present study, intensive investigation was made on the effect of seaweed liquid fertilizer (SLF) of Codium decorticatum on the seed germination yield biochemical and pigment characteristic of Capsium annum under laboratory conditions and in pots. Different concentrations such as 10%, 20%, 30%, 40% and 50% of SLF were prepared using distilled water. The seeds were soaked in 10 h for each SLF concentration then placed in separate Petri plates. Similarly, water soaked seeds were used as controls. Application of a lower concentration (20%) of SLF Showed maximum seed germination, fresh weight, dry weight, root and shoot length, number of branches, leaf area, number of pods and content of total chlorophyll, chl a, and chl b, protein, carbohydrate and lipids were observed. Therefore, the results of the present study suggested that the SLF of C. decortianum could serve as an alternative bio-fertilizer as is eco-friendly, cost-effective, deliver substantial economic and environmental benefits to farmer.     

Lysine Succinylation of VBS Contributes to Sclerotia Development and Aflatoxin Biosynthesis in Aspergillus flavus

Aspergillus flavus is a common saprophytic and pathogenic fungus, and its secondary metabolic pathways are one of the most highly characterized owing to its aflatoxin (AF) metabolite affecting global economic crops and human health. Different natural environments can cause significant variations in AF synthesis. Succinylation was recently identified as one of the most critical regulatory post-translational modifications affecting metabolic pathways. It is primarily reported in human cells and bacteria with few studies on fungi. Proteomic quantification of lysine succinylation (Ksuc) exploring its potential involvement in secondary metabolism regulation (including AF production) has not been performed under natural conditions in A. flavus. In this study, a quantification method was performed based on tandem mass tag labeling and antibody-based affinity enrichment of succinylated peptides via high accuracy nano-liquid chromatography with tandem mass spectrometry to explore the succinylation mechanism affecting the pathogenicity of naturally isolated A. flavus strains with varying toxin production. Altogether, 1240 Ksuc sites in 768 proteins were identified with 1103 sites in 685 proteins quantified. Comparing succinylated protein levels between high and low AF-producing A. flavus strains, bioinformatics analysis indicated that most succinylated proteins located in the AF biosynthetic pathway were downregulated, which directly affected AF synthesis. Versicolorin B synthase is a key catalytic enzyme for heterochrome B synthesis during AF synthesis. Site-directed mutagenesis and biochemical studies revealed that versicolorin B synthase succinylation is an important regulatory mechanism affecting sclerotia development and AF biosynthesis in A. flavus. In summary, our quantitative study of the lysine succinylome in high/low AF-producing strains revealed the role of Ksuc in regulating AF biosynthesis. We revealed novel insights into the metabolism of AF biosynthesis using naturally isolated A. flavus strains and identified a rich source of metabolism-related enzymes regulated by succinylation.     

White matter connectivity in children with autism spectrum disorders: a tract-based spatial statistics study

Background

Autism spectrum disorders (ASD) are associated with widespread alterations in white matter (WM) integrity. However, while a growing body of studies is shedding light on microstructural WM alterations in high-functioning adolescents and adults with ASD, literature is still lacking in information about whole brain structural connectivity in children and low-functioning patients with ASD. This research aims to investigate WM connectivity in ASD children with and without mental retardation compared to typically developing controls (TD).

Methods

Diffusion tensor imaging (DTI) was performed in 22 young children with ASD (mean age: 5.54 years) and 10 controls (mean age: 5.25 years). Data were analysed both using the tract-based spatial statistics (TBSS) and the tractography. Correlations were investigated between the WM microstructure in the identified altered regions and the productive language level.

Results

The TBSS analysis revealed widespread increase of fractional anisotropy (FA) in major WM pathways. The tractographic approach showed an increased fiber length and FA in the cingulum and in the corpus callosum and an increased mean diffusivity in the indirect segments of the right arcuate and the left cingulum. Mean diffusivity was also correlated with expressive language functioning in the left indirect segments of the arcuate fasciculus.

Conclusions

Our study confirmed the presence of several structural connectivity abnormalities in young ASD children. In particular, the TBSS profile of increased FA that characterized the ASD patients extends to children a finding previously detected in ASD toddlers only. The WM integrity abnormalities detected may be relevant to the pathophysiology of ASD, since the structures involved participate in some core atypical characteristics of the disorder.

     

Energetic metabolism during acute stretch-related atrial fibrillation

Background and methods Perturbations in energetic metabolism and impaired atrial contractility may play an important role in the pathogenesis of atrial fibrillation (AF). Besides, atrial stretch is commonly associated with AF. However, the atrial energetics of stretch-related AF are poorly understood. Here, we measured indicators of energy metabolism during acute stretch-related AF. PCr, adenine nucleotides, and derivatives concentrations as well as the activity of the F₀F₁-ATPase and Na,K-ATPase were obtained after 1 h of stretch and/or AF in isolated rabbit hearts and compared to control hearts without stretch and AF. Results After 1 h of stretch-related AF, the total adenine nucleotides’ pool was significantly lower (42.2 ± 2.6 vs. 63.7 ± 8.3 μmol/g protein in control group, P < 0.05) and the PCr/ATP ratio significantly higher (2.3 ± 0.3 vs. 1.1 ± 0.1 in control group P < 0.05), because of ATP, ADP, and AMP decrease and PCr increase. The sum of high-energy phosphate compounds did not change. There were no significant differences in F₀F₁-ATPase nor Na,K-ATPase activity between the groups. Conclusions Results show that in this experimental model, acute stretch-related AF induces specific modifications of atrial myocytes energetics that may play a pivotal role in the perpetuation of the arrhythmia.     

Metabolic flux analyses of Pseudomonas aeruginosa cystic fibrosis isolates

Pseudomonas aeruginosa is a metabolically versatile wide-ranging opportunistic pathogen. In humans P. aeruginosa causes infections of the skin, urinary tract, blood, and the lungs of Cystic Fibrosis patients. In addition, P. aeruginosa's broad environmental distribution, relatedness to biotechnologically useful species, and ability to form biofilms have made it the focus of considerable interest. We used ¹³C metabolic flux analysis (MFA) and flux balance analysis to understand energy and redox production and consumption and to explore the metabolic phenotypes of one reference strain and five strains isolated from the lungs of cystic fibrosis patients. Our results highlight the importance of the oxidative pentose phosphate and Entner-Doudoroff pathways in P. aeruginosa growth. Among clinical strains we report two divergent metabolic strategies and identify changes between genetically related strains that have emerged during a chronic infection of the same patient. MFA revealed that the magnitude of fluxes through the glyoxylate cycle correlates with growth rates.     

Hybrid metabolic flux analysis and recombinant protein prediction in <Emphasis Type="Italic">Pichia pastoris</Emphasis> X-33 cultures expressing a single-chain antibody fragment

Despite the growing importance of the Pichia pastoris expression system as industrial workhorse, the literature is almost absent in systematic studies on how culture medium composition affects central carbon fluxes and heterologous protein expression. In this study we investigate how 26 variations of the BSM+PTM1 medium impact central carbon fluxes and protein expression in a P. pastoris X-33 strain expressing a single-chain antibody fragment. To achieve this goal, we adopted a hybrid metabolic flux analysis (MFA) methodology, which is a modification of standard MFA to predict the rate of synthesis of recombinant proteins. Hybrid MFA combines the traditional parametric estimation of central carbon fluxes with non-parametric statistical modeling of product-related quantitative or qualitative measurements as a function of central carbon fluxes. It was observed that protein yield variability was 53.6 % (relative standard deviation) among the different experiments. Protein yield is much more sensitive to medium composition than biomass growth, which is mainly determined by the carbon source availability and main salts. Hybrid MFA was able to describe accurately the protein yield with normalized RMSE of 6.3 % over 5 independent experiments. The metabolic state that promotes high protein yields is characterized by high overall metabolic rates through main central carbon pathways concomitantly with a relative shift of carbon flux from biosynthetic towards energy generating pathways.     

Hybrid dynamic/static method for large-scale simulation of metabolism

Background  

Many computer studies have employed either dynamic simulation or metabolic flux analysis (MFA) to predict the behaviour of biochemical pathways. Dynamic simulation determines the time evolution of pathway properties in response to environmental changes, whereas MFA provides only a snapshot of pathway properties within a particular set of environmental conditions. However, owing to the large amount of kinetic data required for dynamic simulation, MFA, which requires less information, has been used to manipulate large-scale pathways to determine metabolic outcomes.     

Relationships between methane emission of Holstein Friesian dairy cows and fatty acids,volatile metabolites and non-volatile metabolites in milk

This study investigated the relationships between methane (CH₄) emission and fatty acids, volatile metabolites (V) and non-volatile metabolites (NV) in milk of dairy cows. Data from an experiment with 32 multiparous dairy cows and four diets were used. All diets had a roughage : concentrate ratio of 80 : 20 based on dry matter (DM). Roughage consisted of either 1000 g/kg DM grass silage (GS), 1000 g/kg DM maize silage (MS), or a mixture of both silages (667 g/kg DM GS and 333 g/kg DM MS; 333 g/kg DM GS and 677 g/kg DM MS). Methane emission was measured in climate respiration chambers and expressed as production (g/day), yield (g/kg dry matter intake; DMI) and intensity (g/kg fat- and protein-corrected milk; FPCM). Milk was sampled during the same days and analysed for fatty acids by gas chromatography, for V by gas chromatography–mass spectrometry, and for NV by nuclear magnetic resonance. Several models were obtained using a stepwise selection of (1) milk fatty acids (MFA), V or NV alone, and (2) the combination of MFA, V and NV, based on the minimum Akaike’s information criterion statistic. Dry matter intake was 16.8±1.23 kg/day, FPCM yield was 25.0±3.14 kg/day, CH₄ production was 406±37.0 g/day, CH₄ yield was 24.1±1.87 g/kg DMI and CH₄ intensity was 16.4±1.91 g/kg FPCM. The observed CH₄ emissions were compared with the CH₄ emissions predicted by the obtained models, based on concordance correlation coefficient (CCC) analysis. The best models with MFA alone predicted CH₄ production, yield and intensity with a CCC of 0.80, 0.71 and 0.69, respectively. The best models combining the three types of metabolites included MFA and NV for CH₄ production and CH₄ yield, whereas for CH₄ intensity MFA, NV and V were all included. These models predicted CH₄ production, yield and intensity better with a higher CCC of 0.92, 0.78 and 0.93, respectively, and with increased accuracy (C_b) and precision (r). The results indicate that MFA alone have moderate to good potential to estimate CH₄ emission, and furthermore that including V (CH₄ intensity only) and NV increases the CH₄ emission prediction potential. This holds particularly for the prediction model for CH₄ intensity.     

Biosynthesis of l-Sorbose and l-Psicose Based on C—C Bond Formation Catalyzed by Aldolases in an Engineered Corynebacterium glutamicum Strain

The property of loose stereochemical control at aldol products from aldolases helped to synthesize multiple polyhydroxylated compounds with nonnatural stereoconfiguration. In this study, we discovered for the first time that some fructose 1,6-diphosphate aldolases (FruA) and tagatose 1,6-diphosphate (TagA) aldolases lost their strict stereoselectivity when using l-glyceraldehyde and synthesized not only l-sorbose but also a high proportion of l-psicose. Among the aldolases tested, TagA from Bacillus licheniformis (BGatY) showed the highest enzyme activity with l-glyceraldehyde. Subsequently, a “one-pot” reaction based on BGatY and fructose-1-phosphatase (YqaB) generated 378 mg/liter l-psicose and 199 mg/liter l-sorbose from dihydroxyacetone-phosphate (DHAP) and l-glyceraldehyde. Because of the high cost and instability of DHAP, a microbial fermentation strategy was used further to produce l-sorbose/l-psicose from glucose and l-glyceraldehyde, in which DHAP was obtained from glucose through the glycolytic pathway, and some recombination pathways based on FruA or TagA and YqaB were constructed in Escherichia coli and Corynebacterium glutamicum strains. After evaluation of different host cells and combinations of FruA or TagA with YqaB and optimization of gene expression, recombinant C. glutamicum strain WT(pXFTY) was selected and produced 2.53 g/liter total ketoses, with a yield of 0.50 g/g l-glyceraldehyde. Moreover, deletion of gene cgl0331, encoding the Zn-dependent alcohol dehydrogenase in C. glutamicum, was confirmed for the first time to significantly decrease conversion of l-glyceraldehyde to glycerol and to increase yield of target products. Finally, fed-batch culture of strain SY14(pXFTY) produced 3.5 g/liter l-sorbose and 2.3 g/liter l-psicose, with a yield of 0.61 g/g l-glyceraldehyde. This microbial fermentation strategy also could be applied to efficiently synthesize other l-sugars.